Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 142 of 168
Found at i:41870797 original size:24 final size:23
Alignment explanation
Indices: 41870755--41870820 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 23
41870745 TCAAAATGAC
*
41870755 TAAATTGTTTAATTTTTATAATTT
1 TAAATT-TTTAATTTTTATAATTA
*
41870779 TATATTTTTAATGTTTTATAATTA
1 TAAATTTTTAAT-TTTTATAATTA
*
41870803 TAAATTTTTGAATATTTA
1 TAAATTTTT-AATTTTTA
41870821 GAATAATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.17
24 27 0.75
25 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.61
Consensus pattern (23 bp):
TAAATTTTTAATTTTTATAATTA
Found at i:41871565 original size:10 final size:11
Alignment explanation
Indices: 41871553--41871582 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41871543 CTATTGCTTC
41871553 TTTCTTTTTCT
1 TTTCTTTTTCT
*
41871564 TTTTTTTTTCT
1 TTTCTTTTTCT
41871575 TTTCTTTT
1 TTTCTTTT
41871583 GCATTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:41876119 original size:3 final size:3
Alignment explanation
Indices: 41876111--41876135 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41876101 GATTGCCGAT
41876111 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
41876136 TTGTGGGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41877317 original size:35 final size:36
Alignment explanation
Indices: 41877278--41877355 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
41877268 TTAAAAATCC
*
41877278 AATAAAAGAAATCCAATATGTT-AATTA-AAAAATAA
1 AATAAAAGAAATCCAATAT-TTGAAATACAAAAATAA
* ** *
41877313 AATAAAAGGAATTGAATATTTGAAATACAAGAATAA
1 AATAAAAGAAATCCAATATTTGAAATACAAAAATAA
41877349 AATAAAA
1 AATAAAA
41877356 TTATATGTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 2 0.06
35 20 0.56
36 14 0.39
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (36 bp):
AATAAAAGAAATCCAATATTTGAAATACAAAAATAA
Found at i:41877554 original size:23 final size:24
Alignment explanation
Indices: 41877509--41877555 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41877499 ACAAGTTGGA
* *
41877509 TTAAAAAAAAACTTAGATATCAAG
1 TTAAAAAAAAAATTAAATATCAAG
41877533 TTAAAAAAAAAATTAAAT-TCAAG
1 TTAAAAAAAAAATTAAATATCAAG
41877556 CACCAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (24 bp):
TTAAAAAAAAAATTAAATATCAAG
Found at i:41878836 original size:18 final size:18
Alignment explanation
Indices: 41878810--41878848 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41878800 TTTAAAAAAA
*
41878810 TTATATTTAAAGTGAGTT
1 TTATATTTAAAGTAAGTT
* *
41878828 TTATTTTTAAATTAAGTT
1 TTATATTTAAAGTAAGTT
41878846 TTA
1 TTA
41878849 AATATGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (18 bp):
TTATATTTAAAGTAAGTT
Found at i:41883451 original size:11 final size:13
Alignment explanation
Indices: 41883435--41883468 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
41883425 AATTTTACGG
41883435 AAAAATTTCG-T-
1 AAAAATTTCGTTC
41883446 AAAAATTTCGTTC
1 AAAAATTTCGTTC
41883459 AAAAATTTCG
1 AAAAATTTCG
41883469 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:41886698 original size:11 final size:11
Alignment explanation
Indices: 41886682--41886719 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
41886672 TATTTTTTAA
41886682 TTTTAAAATAT
1 TTTTAAAATAT
*
41886693 TTTTAAAATAC
1 TTTTAAAATAT
41886704 TTTTAAAATACT
1 TTTTAAAATA-T
41886716 TTTT
1 TTTT
41886720 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:41890132 original size:46 final size:46
Alignment explanation
Indices: 41890074--41890212 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 46
41890064 CATGGCAAAG
* **
41890074 TGTGGAACGTAGGTATGGTATTTTGGTGAAGAAAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
41890120 TGTGAAACGTAGGTATGATATTTCAGT-AACGAAAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTGAA-GAAAACCATACTGAGT
* *
41890166 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATATTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
41890212 T
1 T
41890213 ATAGCATTGT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
45 2 0.02
46 80 0.95
47 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (46 bp):
TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:41890534 original size:2 final size:2
Alignment explanation
Indices: 41890527--41890579 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
41890517 TAGATTGACG
41890527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41890569 TA TA TA TA TA T
1 TA TA TA TA TA T
41890580 GTTTGGAGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41892190 original size:31 final size:31
Alignment explanation
Indices: 41892155--41892221 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
41892145 TTCATCATAG
41892155 AGTAAATTACACCCAAGGTCACTCAAATATT
1 AGTAAATTACACCCAAGGTCACTCAAATATT
** *
41892186 AGTAAATTATGCCCAAGGTCACTCAACTATT
1 AGTAAATTACACCCAAGGTCACTCAAATATT
41892217 AGTAA
1 AGTAA
41892222 GTTTATACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (31 bp):
AGTAAATTACACCCAAGGTCACTCAAATATT
Found at i:41900879 original size:21 final size:19
Alignment explanation
Indices: 41900854--41900893 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
41900844 CCGGCCCGAT
41900854 TTTTAATAAACACAAAAAATA
1 TTTTAA-AAACA-AAAAAATA
*
41900875 TTTTAAAAATAAAAAAATA
1 TTTTAAAAACAAAAAAATA
41900894 AAAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
TTTTAAAAACAAAAAAATA
Found at i:41911016 original size:2 final size:2
Alignment explanation
Indices: 41911009--41911045 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
41910999 ATTGACCTTT
*
41911009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41911046 TAGTGTAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41914974 original size:153 final size:153
Alignment explanation
Indices: 41914816--41915660 Score: 1148
Period size: 153 Copynumber: 5.5 Consensus size: 153
41914806 CCTTTTTCAA
** * *
41914816 TAAATAAATTT-AAAAAACCCTTATTTCGAACATTTGTTCGTATTTTTTTCCCGGATTTTATTAT
1 TAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTAC
*
41914880 TTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGA
65 TTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGA
*
41914945 AATGTATTAATTTAGTGTTTTTTT
130 AATGTATTAATTTAGTGTGTTTTT
* * * *
41914969 TAAATAAATTTAAAAAAATCATTATTTTGGGCCTTTGTTCGTA-TTTTTCCCGGATTTTATTACT
1 TAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACT
*
41915033 TTCAATAAAAAATATATTATTTTCTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGA
66 TTCAAT-AAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGA
*
41915098 AATGTATTAATTTACTGTGTTTTT
130 AATGTATTAATTTAGTGTGTTTTT
* * * * *
41915122 TAAATAAATTAAAAAAAATCCTTATTTCGGCCCTTTGTTCATATTTTTTTCCCCAGAGTTTATTA
1 TAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTA-TTTTTT-CCCGGATTTTATTA
* * *
41915187 CTTT-TA-AAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATATTT
64 CTTTCAATAAAAATATATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTT
* *
41915249 GAAATTTATTTATTTAGTGTGTTTTT
128 GAAATGTATTAATTTAGTGTGTTTTT
** *
41915275 TAAATAAATTTAAAAAAAACCCCTTATTTCCACACTTTGTTCGTATTTTTTCCCGGATTTTATTA
1 TAAATAAATTT-AAAAAAA-CCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTA
*
41915340 CTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
64 CTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
**
41915405 AAATGTATTAATTTTCTGTGTTTTT
129 AAATGTATTAATTTAGTGTGTTTTT
* * * * *
41915430 AAAATAAATTTAAAAAAACCCTTAATTTCGGCCCTTTGTTCATATTTTTCCCCAGAGTTTATTA-
1 TAAATAAATTTAAAAAAACCCTT-ATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTAC
* * * *
41915494 TTTTAA-AAAAATATACTATTTT-ATAATATTATTATTTTACATTATTGTTAGTACATTATGTTT
65 TTTCAATAAAAATATATTATTTTCGT-ATTTTATTATTTTACATTATT-TTAGTACATTATGTTT
*
41915557 GAAATGTATTCATTTAGTGTGTTTTT
128 GAAATGTATTAATTTAGTGTGTTTTT
* * * *
41915583 TAAATAAATTAAAAAAAAACTCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCTGAATTTTATTA
1 TAAATAAATT-TAAAAAAACCCTTATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTA
41915648 CTTTCAATAAAAA
64 CTTTCAATAAAAA
41915661 AACACACACT
Statistics
Matches: 609, Mismatches: 65, Indels: 33
0.86 0.09 0.05
Matches are distributed among these distances:
151 1 0.00
152 62 0.10
153 305 0.50
154 105 0.17
155 114 0.19
156 22 0.04
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.51
Consensus pattern (153 bp):
TAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACT
TTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAA
ATGTATTAATTTAGTGTGTTTTT
Found at i:41915415 original size:308 final size:305
Alignment explanation
Indices: 41914816--41915660 Score: 1247
Period size: 308 Copynumber: 2.7 Consensus size: 305
41914806 CCTTTTTCAA
* ** * * * *
41914816 TAAATAAATTTAAAAAACCCTTATTTCGAACATTTGTTCGTATTTTTTT-CCCGGATTTTATTAT
1 TAAATAAATTAAAAAAACCCTTATTTCGGCCCTTTGTTCATATTTTTTTCCCCAGAGTTTATTAT
* *
41914880 TTTCAATAAAAATATATTATTTTCGT-ATTTTATTATTTTAAATTATTTTAGTACATTATGTTTG
66 TTT-AA-AAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
* * * *
41914944 AAATGTATTAATTTAGTGTTTTTTTTAAATAAATTT-AAAAAAATCATTATTTTGGGCCTTTGTT
128 AAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAACCCTTA-TTTCGGCCTTTGTT
41915008 CGTA-TTTTTCCCGGATTTTATTACTTTCAATAAAAAATATATTATTTTCTTATTTTATTATTTT
192 CGTATTTTTTCCCGGATTTTATTACTTTCAAT-AAAAATATATTATTTTCTTATTTTATTATTTT
41915072 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTT
256 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTT
*
41915122 TAAATAAATTAAAAAAAATCCTTATTTCGGCCCTTTGTTCATATTTTTTTCCCCAGAGTTTATTA
1 TAAATAAATT-AAAAAAACCCTTATTTCGGCCCTTTGTTCATATTTTTTTCCCCAGAGTTTATTA
*
41915187 CTTTT-AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATATTTGA
65 -TTTTAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGA
* * **
41915251 AATTTATTTATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAACCCCTTATTTCCACACTTTGTT
129 AATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAA-CCCTTATTTCGGC-CTTTGTT
41915316 CGTATTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATTTT-TGTATTTTATTATTTT
192 CGTATTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATTTTCT-TATTTTATTATTTT
*
41915380 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTTCTGTGTTTTT
256 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTT
*
41915430 AAAATAAATTTAAAAAAACCCTTAATTTCGGCCCTTTGTTCATA--TTTTTCCCCAGAGTTTATT
1 TAAATAAA-TTAAAAAAACCCTT-ATTTCGGCCCTTTGTTCATATTTTTTTCCCCAGAGTTTATT
* *
41915493 ATTTTAAAAAAATATACTATTTTATAATATTATTATTTTACATTATTGTTAGTACATTATGTTTG
64 ATTTTAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATT-TTAGTACATTATGTTTG
* * *
41915558 AAATGTATTCATTTAGTGTGTTTTTTAAATAAATTAAAAAAAAACTCTTATTTCGGCCCTTTGTT
128 AAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAACCCTTATTTCGG-CCTTTGTT
* *
41915623 CGTATTTTTTTCCTGAATTTTATTACTTTCAATAAAAA
192 CGTA-TTTTTTCCCGGATTTTATTACTTTCAATAAAAA
41915661 AACACACACT
Statistics
Matches: 491, Mismatches: 33, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
305 1 0.00
306 99 0.20
307 125 0.25
308 213 0.43
309 53 0.11
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.51
Consensus pattern (305 bp):
TAAATAAATTAAAAAAACCCTTATTTCGGCCCTTTGTTCATATTTTTTTCCCCAGAGTTTATTAT
TTTAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
TGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAACCCTTATTTCGGCCTTTGTTCGTA
TTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATTTTCTTATTTTATTATTTTACATT
ATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTT
Found at i:41915935 original size:18 final size:19
Alignment explanation
Indices: 41915909--41915946 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
41915899 TTTTTTTATA
41915909 TATTATTTTGGTATT-TTT
1 TATTATTTTGGTATTATTT
* *
41915927 TATTTTTTTTGTATTATTT
1 TATTATTTTGGTATTATTT
41915946 T
1 T
41915947 TTGTAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (19 bp):
TATTATTTTGGTATTATTT
Found at i:41916780 original size:9 final size:9
Alignment explanation
Indices: 41916763--41916799 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41916753 TAAGTTTTCG
41916763 AATTCGAAT
1 AATTCGAAT
*
41916772 AACTCGAAT
1 AATTCGAAT
41916781 AATTCGAAT
1 AATTCGAAT
41916790 AATTCGAAT
1 AATTCGAAT
41916799 A
1 A
41916800 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41924769 original size:2 final size:2
Alignment explanation
Indices: 41924762--41924800 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
41924752 GATATTTGAA
**
41924762 AT AT AT AT AT GC 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 A
41924801 ACAAATGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:41925843 original size:20 final size:20
Alignment explanation
Indices: 41925818--41925857 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41925808 TTTAATTACC
* *
41925818 CCCTCTCTCTTTCTCTTTCT
1 CCCTCTCCCTCTCTCTTTCT
41925838 CCCTCTCCCTCTCTCTTTCT
1 CCCTCTCCCTCTCTCTTTCT
41925858 TTCTCTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (20 bp):
CCCTCTCCCTCTCTCTTTCT
Found at i:41928392 original size:23 final size:23
Alignment explanation
Indices: 41928344--41928392 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
41928334 TTATATTTTT
* *
41928344 TTAATAAATATGATAAAATATTA
1 TTAATAAATATGATAAAAAATAA
*
41928367 TTAATATAATAT-TTAAAAAATAA
1 TTAATA-AATATGATAAAAAATAA
41928390 TTA
1 TTA
41928393 TAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TTAATAAATATGATAAAAAATAA
Found at i:41928737 original size:15 final size:16
Alignment explanation
Indices: 41928717--41928756 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
41928707 ATTTTTTAGT
41928717 AATAACATTAATT-AA
1 AATAACATTAATTAAA
41928732 AATAACA-T-ATTAAA
1 AATAACATTAATTAAA
*
41928746 AATTACATTAA
1 AATAACATTAA
41928757 ATACAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
13 3 0.14
14 9 0.43
15 8 0.38
16 1 0.05
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAACATTAATTAAA
Found at i:41942028 original size:12 final size:12
Alignment explanation
Indices: 41942013--41942056 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
41942003 ACTAATGTAG
41942013 TTAATAATATTA
1 TTAATAATATTA
41942025 TTAATAATATTA
1 TTAATAATATTA
* * *
41942037 ATAATTAGATTA
1 TTAATAATATTA
41942049 -TAATAATA
1 TTAATAATA
41942057 AAACAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 6 0.22
12 21 0.78
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
TTAATAATATTA
Found at i:41951291 original size:12 final size:12
Alignment explanation
Indices: 41951276--41951302 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41951266 TTTTAAATTG
41951276 TTTTTAAACCCT
1 TTTTTAAACCCT
41951288 TTTTTAAACCCT
1 TTTTTAAACCCT
41951300 TTT
1 TTT
41951303 ATCTCGATAA
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:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTTAAACCCT
Found at i:41955650 original size:30 final size:30
Alignment explanation
Indices: 41955616--41955688 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
41955606 AATTTTGAAC
* * *
41955616 TATCTAATACATGAATGATCTCAAGAAACT
1 TATCTAATACATGAATGATCCCAACAAACG
* *
41955646 TATCTAATAGATGAATGATCCCAACAAGCG
1 TATCTAATACATGAATGATCCCAACAAACG
*
41955676 CATCTAATACATG
1 TATCTAATACATG
41955689 GTGGGTAGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (30 bp):
TATCTAATACATGAATGATCCCAACAAACG
Found at i:41959523 original size:8 final size:8
Alignment explanation
Indices: 41959513--41959552 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
41959503 AAAAAGCAAG
*
41959513 AAAATAAG
1 AAAATAAA
41959521 AAAAT-AA
1 AAAATAAA
41959528 AAAATAAA
1 AAAATAAA
41959536 AAAATAAA
1 AAAATAAA
41959544 AAAATAAA
1 AAAATAAA
41959552 A
1 A
41959553 CCAAGTCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:41959533 original size:15 final size:15
Alignment explanation
Indices: 41959513--41959552 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
41959503 AAAAAGCAAG
*
41959513 AAAATAAGAAAATAA
1 AAAATAAAAAAATAA
41959528 AAAATAAAAAAATAAA
1 AAAATAAAAAAAT-AA
41959544 AAAATAAAA
1 AAAATAAAA
41959553 CCAAGTCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAATAAAAAAATAA
Found at i:41962721 original size:3 final size:3
Alignment explanation
Indices: 41962713--41962747 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
41962703 ATTAATTGGG
41962713 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
41962748 CAGCACCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41965770 original size:19 final size:19
Alignment explanation
Indices: 41965746--41965871 Score: 207
Period size: 19 Copynumber: 6.5 Consensus size: 19
41965736 AATTTTTGAG
41965746 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
41965765 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
41965784 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41965803 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
41965824 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
41965843 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41965862 GATATGCAAT
1 GATATGCAAT
41965872 GATAACACTC
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
19 80 0.81
21 19 0.19
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41965813 original size:59 final size:59
Alignment explanation
Indices: 41965747--41965866 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
41965737 ATTTTTGAGG
*
41965747 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
* *
41965806 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATATAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
41965865 AT
1 AT
41965867 GCAATGATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (59 bp):
ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
Found at i:41974876 original size:12 final size:11
Alignment explanation
Indices: 41974854--41974899 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
41974844 AGTTCAGATT
41974854 CAAAAAAAAAA
1 CAAAAAAAAAA
41974865 CAAAAAACAAAA
1 CAAAAAA-AAAA
41974877 CAAAAAATAAAA
1 CAAAAAA-AAAA
41974889 -AAAAAGAAAAA
1 CAAAAA-AAAAA
41974900 TGGAGAGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 16 0.50
12 16 0.50
ACGTcount: A:0.87, C:0.09, G:0.02, T:0.02
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:41976440 original size:133 final size:133
Alignment explanation
Indices: 41976201--41976806 Score: 884
Period size: 133 Copynumber: 4.6 Consensus size: 133
41976191 GAGCATGTTA
*
41976201 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCTGATCGAAGATGGCGGATTTTACCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAGATGGCGGATTTTACCTC
*
41976266 CCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTAGGCAGCAGTGGAATAGA
66 CCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAGCAGTGGAATAGA
41976331 TT-
131 TTG
* *
41976333 AGAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
1 A-AGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAGATGGCGGATTTTACCT
* * *
41976398 CCCTGTGGTTATAGTGGAATACATTGAAGCCAATAATTCTACTTCTCTGGGCAGCAGTGGAATTG
65 CCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAGCAGTGGAATAG
*
41976463 ATTA
130 ATTG
*
41976467 AAGATAGCAGATCTTGCCTTCTTGCATTGACAGTGAAGCAGATCGAAGATGGCGGATTTTACCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAGATGGCGGATTTTACCTC
*
41976532 CCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGA
66 CCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAGCAGTGGAATAGA
41976597 TTG
131 TTG
** ** * * *
41976600 AAGATTTCAGATCTTATCTCCCTAAGCA--G-TAGTGGAGCAGATCGAAGATGGCGGATTTTACC
1 AAGATAGCAGATCTTGCCTTCCT--GCATTGACAGTGAAGCAGATCGAAGATGGCGGATTTTACC
*
41976662 TCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAACAGTGGAATA
64 TCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAGCAGTGGAATA
41976727 GATTG
129 GATTG
** ** * * * *
41976732 AAGATTTCAGATCTTATCTCCCTAAGCA--G-TAGTGGAGCAGATTGAAGATGGCGGATTTTACC
1 AAGATAGCAGATCTTGCCTTCCT--GCATTGACAGTGAAGCAGATCGAAGATGGCGGATTTTACC
41976794 TCCCTGTGGTTAT
64 TCCCTGTGGTTAT
41976807 TGTAATAGCC
Statistics
Matches: 444, Mismatches: 26, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
132 174 0.39
133 266 0.60
134 1 0.00
135 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (133 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAGATGGCGGATTTTACCTC
CCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAGCAGTGGAATAGA
TTG
Found at i:41976797 original size:44 final size:44
Alignment explanation
Indices: 41976594--41976798 Score: 117
Period size: 44 Copynumber: 4.7 Consensus size: 44
41976584 GCAGTGGAAT
** * *
41976594 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 AGATTGAAGATGGCAGATTTTACCTCCCTAAGCAGTAGTGGAGC
* * ** * *
41976638 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA-TAGTGGAGT
1 AGATTGAAGATGGCAGATTTTACCTCCCT-AAG-CAGTAGTGGAGC
* *** * * * * ** ** **
41976683 ACATTGAAGCCAGTA-ATTCTACTTCTCTGGGCAACAGTGGAAT
1 AGATTGAAGATGGCAGATTTTACCTCCCTAAGCAGTAGTGGAGC
** * *
41976726 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 AGATTGAAGATGGCAGATTTTACCTCCCTAAGCAGTAGTGGAGC
*
41976770 AGATTGAAGATGGCGGATTTTACCTCCCT
1 AGATTGAAGATGGCAGATTTTACCTCCCT
41976799 GTGGTTATTG
Statistics
Matches: 111, Mismatches: 46, Indels: 8
0.67 0.28 0.05
Matches are distributed among these distances:
42 1 0.01
43 18 0.16
44 74 0.67
45 17 0.15
46 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (44 bp):
AGATTGAAGATGGCAGATTTTACCTCCCTAAGCAGTAGTGGAGC
Found at i:41977933 original size:44 final size:44
Alignment explanation
Indices: 41977885--41978079 Score: 132
Period size: 44 Copynumber: 4.4 Consensus size: 44
41977875 CCTGAGCAAC
* *
41977885 AGTGGAATAGATTGAATATTTCAGATCTTATCTCCCTAATCAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
** * * * * **
41977929 AGTGGAGCAGATTGAAGATTGCGGATTTTACCTCCCT--GTGGTT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG-T
* * * * * *
41977972 ACAGTGGAGTACATTGAAGCTAGT-A-AT-TCTA-CTTCCCTAGGCAAT
1 --AGTGGAATAGATTGAAGAT-TTCAGATCT-TATC-TCCCTAAGCAGT
41978017 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
* *
41978061 AGTGGACTAGATCGAAGAT
1 AGTGGAATAGATTGAAGAT
41978080 GGTGGAAATT
Statistics
Matches: 112, Mismatches: 27, Indels: 24
0.69 0.17 0.15
Matches are distributed among these distances:
42 2 0.02
43 20 0.18
44 70 0.62
45 19 0.17
46 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (44 bp):
AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
Found at i:41978079 original size:132 final size:132
Alignment explanation
Indices: 41977837--41978079 Score: 382
Period size: 132 Copynumber: 1.8 Consensus size: 132
41977827 GGGTGTTACA
* * *
41977837 GTTATAGTGGAGTACATTGAAGCCAATAATTCTATTTCCCTGAGCAACAGTGGAATAGATTGAAT
1 GTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCAACAGTGGAATAGATTGAAG
* *
41977902 ATTTCAGATCTTATCTCCCTAATCAGTAGTGGAGCAGATTGAAGATTGCGGATTTTACCTCCCTG
66 ATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTGCGGATTTTACCTCCCTG
41977967 TG
131 TG
* * *
41977969 GTTACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCT-AGGCAATAGTGGAATAGATTGAA
1 GTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGA-GCAACAGTGGAATAGATTGAA
41978033 GATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA-CTAGATCGAAGAT
65 GATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGC-AGATCGAAGAT
41978080 GGTGGAAATT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
131 2 0.02
132 99 0.98
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (132 bp):
GTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCAACAGTGGAATAGATTGAAG
ATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTGCGGATTTTACCTCCCTG
TG
Found at i:41978097 original size:10 final size:10
Alignment explanation
Indices: 41978082--41978111 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
41978072 TCGAAGATGG
41978082 TGGAAATTTT
1 TGGAAATTTT
41978092 TGGAAATTTT
1 TGGAAATTTT
41978102 TGGAAATTTT
1 TGGAAATTTT
41978112 ACCTCTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (10 bp):
TGGAAATTTT
Found at i:41978919 original size:8 final size:8
Alignment explanation
Indices: 41978906--41978941 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
41978896 AACGAAACAG
41978906 AGAAGGAA
1 AGAAGGAA
41978914 AGAAGGAA
1 AGAAGGAA
*
41978922 AGAAGAAA
1 AGAAGGAA
*
41978930 AGAAAGAA
1 AGAAGGAA
41978938 AGAA
1 AGAA
41978942 AAGGGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (8 bp):
AGAAGGAA
Found at i:41978931 original size:16 final size:16
Alignment explanation
Indices: 41978851--41978941 Score: 58
Period size: 16 Copynumber: 5.4 Consensus size: 16
41978841 TATGTAAAAA
41978851 AAAGAA-AAAAGAAAG
1 AAAGAAGAAAAGAAAG
* * *
41978866 AAACAAAAACAAAAAAG
1 AAAGAAGAA-AAGAAAG
*
41978883 AAACAGAGAGCAAAACGAAAC
1 -AA-AGA-AG-AAAA-GAAAG
* * *
41978904 AGAGAAGGAAAGAAGG
1 AAAGAAGAAAAGAAAG
41978920 AAAGAAGAAAAGAAAG
1 AAAGAAGAAAAGAAAG
41978936 AAAGAA
1 AAAGAA
41978942 AAGGGAAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
15 5 0.09
16 24 0.43
17 9 0.16
18 4 0.07
19 5 0.09
20 4 0.07
21 5 0.09
ACGTcount: A:0.71, C:0.07, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAG
Found at i:41981717 original size:97 final size:98
Alignment explanation
Indices: 41981538--41981731 Score: 320
Period size: 97 Copynumber: 2.0 Consensus size: 98
41981528 TTAAAATAAT
* *
41981538 AAAGGAAATATTCCGAATTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCT
1 AAAGGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
*
41981603 TAAATCTTGGATAAGTGGATGTTCTTTTAAAGA
66 TAAATCTTGGATAAGTGGATGTTATTTTAAAGA
* *
41981636 AAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCC-AACGTATTGGGTGTGATTTCT
1 AAAGGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
41981700 TAAATAC-TGGATAAGTGGATGTTATTTTAAAG
66 TAAAT-CTTGGATAAGTGGATGTTATTTTAAAG
41981732 TTTTATTGTA
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
97 50 0.56
98 40 0.44
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (98 bp):
AAAGGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
TAAATCTTGGATAAGTGGATGTTATTTTAAAGA
Found at i:41991709 original size:3 final size:3
Alignment explanation
Indices: 41991701--41991728 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41991691 CATATATTTA
41991701 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41991729 TTAATTGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42007302 original size:44 final size:44
Alignment explanation
Indices: 42007204--42008204 Score: 643
Period size: 44 Copynumber: 21.9 Consensus size: 44
42007194 CACCGTGACG
* ** *
42007204 AATCTTATCTCCCTGAAGTTGAAGTGGAAAAGATTAAAG-TCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACA
* * * * *
42007248 AAT-TTCATCTCCTTAAAGTTGCAGTGGAGTATATTGAAGATATA
1 AATCTT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * * * **
42007292 AGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CA
* ** ** * *
42007337 AATCTTATTTCCCTGAAGTTGCAGAAGAATAGATAAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT------T-GAAGATACA
* * * *
42007388 AATCTTATCTCCCTGAAGTGGCAGTGGAGTAGTTTGAATATACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* *
42007432 AATTTTATCTCCCAGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CA
* * * * *
42007477 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * **
42007521 AATCTTATCTCCCTTAAGTTGTAGTGGAAAAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CA
* * * * *
42007566 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* ** *
42007610 AATCTTATCTCCCTGAAGTTGCAGTGCAAAAGATTGAAGATAGAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CA
* * * * * * * * *
42007655 AATTTTATCTCTCTAAAGTTGTAGTAGAGCATATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * * * *
42007699 AATTTTATCTCCCTGAAGTTGCAGTAGAGAAGGTTGAAGATGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * * ** *
42007743 AATCTTATTTCCCTAAAGTTGTAGTGGAATAGATTAAAGCTACAAGTCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-----A-T-ACA
* * ** * *
42007794 AATCCTATGC-CCCTGAAG-TGATAGTGGAAAATATTAAAG-TCACA
1 AATCTTAT-CTCCCTGAAGTTG-CAGTGGAGCAGATTGAAGAT-ACA
* *
42007838 AAT-TTCATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
1 AATCTT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * * *
42007882 AATCTTAT-TCCCTCAAGTTGCAGTGGAACAGATTAAAGCTACAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC-A
* * * ** *
42007926 GTTGCAAGTCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCAAAGCTA-A
1 -----AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* *
42007975 AAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAAATTGAAGCTACAAGTTACA
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-----A--TACA
* * *
42008027 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * *
42008071 AATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * *
42008115 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT-AAAACTACAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TAC-----A
* *
42008164 CGAATCTTATCTCCCTAAAGTAGCAGTGGAGCAGATTGAAG
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
42008205 CGACAAACCC
Statistics
Matches: 747, Mismatches: 157, Indels: 98
0.75 0.16 0.10
Matches are distributed among these distances:
43 36 0.05
44 392 0.52
45 141 0.19
49 5 0.01
50 9 0.01
51 155 0.21
52 9 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
Found at i:42007529 original size:89 final size:89
Alignment explanation
Indices: 42007204--42008204 Score: 739
Period size: 89 Copynumber: 10.9 Consensus size: 89
42007194 CACCGTGACG
* ** * * *
42007204 AATCTTATCTCCCTGAAGTTGAAGTGGAAAAGATTAAAG-TCACAAAT-TTCATCTCCTTAAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT-ATAAATCTT-ATCTCCCTGAAGT
* * *
42007267 TGCAGTGGAGTATATTGAAGATA-TA
64 TGCAGTGGAGCAGATTGAAGATAGCA
* * * * * *
42007292 AGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGATAGTGAATCTTATTTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-TAAATCTTATCTCCCTGAAGTT
** ** ** *
42007357 GCAGAAGAATAGATAAAAGCTACAAGTTACA
65 GCAGTGGAGCAGATTGAAG--A-TAG---CA
* * * * ** * * *
42007388 AATCTTATCTCCCTGAAGTGGCAGTGGAGTAGTTTGAATATACAAATTTTATCTCCCAGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTG
42007453 CAGTGGAGCAGATTGAAGATAGCA
66 CAGTGGAGCAGATTGAAGATAGCA
* * *
42007477 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCTTATCTCCCTTAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTG
* **
42007542 TAGTGGAAAAGATTGAAGATAGCA
66 CAGTGGAGCAGATTGAAGATAGCA
* *
42007566 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTG
* ** *
42007631 CAGTGCAAAAGATTGAAGATAGAA
66 CAGTGGAGCAGATTGAAGATAGCA
* * * * * * *
42007655 AATTTTATCTCTCTAAAGTTGTAGTAGAGCATATTAAAGCTATAAATTTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTG
* * *
42007720 CAGTAGAGAAGGTTGAAGAT-GCA
66 CAGTGGAGCAGATTGAAGATAGCA
* * * ** *
42007743 AATCTTATTTCCCTAAAGTTGTAGTGGAATAGATTAAAGCTACAAGTCACAAATCCTATGC-CCC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT---A-T---AAATCTTAT-CTCCC
* ** * *
42007807 TGAAG-TGATAGTGGAAAATATTAAAG-TCA-CA
58 TGAAGTTG-CAGTGGAGCAGATTGAAGAT-AGCA
* * * *
42007838 AAT-TTCATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTAT-TCCCTCAAGTT
1 AATCTT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTT
* * *
42007901 GCAGTGGAACAGATTAAAGCTACAAGTTGCA
65 GCAGTGGAGCAGATTGAAG-----A-TAGCA
* * * * *
42007932 AGTCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCAAAGCTA-AAAGTCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAA-TCTTATCTCCCTGAAGTT
* * *
42007996 GCAGTGAAGCAAATTGAAGCTACAAGTTACA
65 GCAGTGGAGCAGATTGAAG--A-TAG---CA
* * * * * *
42008027 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCTCTCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTG
*
42008092 CAGTGGAGCAGATTGAAGCTA-CA
66 CAGTGGAGCAGATTGAAGATAGCA
* * *
42008115 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAACTACAAGTTACGAATCTTATCTCCCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT---A--TA--AATCTTATCTCCCT
* *
42008180 AAAGTAGCAGTGGAGCAGATTGAAG
59 GAAGTTGCAGTGGAGCAGATTGAAG
42008205 CGACAAACCC
Statistics
Matches: 736, Mismatches: 131, Indels: 85
0.77 0.14 0.09
Matches are distributed among these distances:
87 22 0.03
88 118 0.16
89 265 0.36
90 2 0.00
91 3 0.00
92 9 0.01
93 5 0.01
94 48 0.07
95 225 0.31
96 39 0.05
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (89 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAGATTGAAGATAGCA
Found at i:42008236 original size:139 final size:139
Alignment explanation
Indices: 42007937--42008229 Score: 369
Period size: 139 Copynumber: 2.1 Consensus size: 139
42007927 TTGCAAGTCT
* * * * **
42007937 TATCTCTCTGAAGTTGCAGTAGAGTAGATCAAAGCTAAAAGTCTTATCTCCCTGAAGTTGCAGTG
1 TATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGCTAAAAGTCTTATCTCCCTGAAGTTGCAGTG
* * * * *
42008002 AAGCAAATTGAAGCTACAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGC
66 AAGCAAATTAAAACTACAAGTTACAAGTCTTATCTCCCTAAAGTAGCAGTGGAGCAGATTGAAGC
* * *
42008067 TACAAATCT
131 GACAAACCC
* *
42008076 TATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTACAAA-TCTTATTTCCCTGAAGTTGCAGT
1 TATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGCTA-AAAGTCTTATCTCCCTGAAGTTGCAGT
*
42008140 GGAA-CAGATTAAAACTACAAGTTACGAA-TCTTATCTCCCTAAAGTAGCAGTGGAGCAGATTGA
65 -GAAGCAAATTAAAACTACAAGTTAC-AAGTCTTATCTCCCTAAAGTAGCAGTGGAGCAGATTGA
42008203 AGCGACAAACCC
128 AGCGACAAACCC
42008215 TATAC-CTCTAAAGTT
1 TAT-CTCTCTAAAGTT
42008230 GTAGTGGGTT
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
139 125 0.93
140 9 0.07
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (139 bp):
TATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGCTAAAAGTCTTATCTCCCTGAAGTTGCAGTG
AAGCAAATTAAAACTACAAGTTACAAGTCTTATCTCCCTAAAGTAGCAGTGGAGCAGATTGAAGC
GACAAACCC
Found at i:42008848 original size:6 final size:6
Alignment explanation
Indices: 42008837--42008864 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42008827 GATACATGTA
42008837 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
42008865 GAAAGAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:42009711 original size:27 final size:27
Alignment explanation
Indices: 42009673--42009729 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
42009663 ATCTTTCTTC
42009673 AAACCAAAACAAAAAGAAAAGAAAAAG
1 AAACCAAAACAAAAAGAAAAGAAAAAG
42009700 AAACCAAAACAAAAAGAAAAGAAAAAG
1 AAACCAAAACAAAAAGAAAAGAAAAAG
42009727 AAA
1 AAA
42009730 TAAGGAAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (27 bp):
AAACCAAAACAAAAAGAAAAGAAAAAG
Found at i:42013054 original size:16 final size:15
Alignment explanation
Indices: 42013028--42013060 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
42013018 TTCATTTATT
42013028 TTATTTTATTATCTA
1 TTATTTTATTATCTA
42013043 TTATTATTATTATCTA
1 TTATT-TTATTATCTA
42013059 TT
1 TT
42013061 TATGTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTATTATCTA
Found at i:42021003 original size:24 final size:24
Alignment explanation
Indices: 42020971--42021018 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42020961 CGTCAAAAGA
42020971 ATTAACCACGTAACTATATGATAC
1 ATTAACCACGTAACTATATGATAC
42020995 ATTAACCACGTAACTATATGATAC
1 ATTAACCACGTAACTATATGATAC
42021019 CATCTCTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (24 bp):
ATTAACCACGTAACTATATGATAC
Found at i:42022383 original size:62 final size:62
Alignment explanation
Indices: 42022307--42022430 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
42022297 CCGACTTACC
42022307 AAAGTTTGTTAAGTTATGTTTTGGTATTGAATTGAGCATGTACCTAAGTTGGGTTGTTTTGG
1 AAAGTTTGTTAAGTTATGTTTTGGTATTGAATTGAGCATGTACCTAAGTTGGGTTGTTTTGG
42022369 AAAGTTTGTTAAGTTATGTTTTGGTATTGAATTGAGCATGTACCTAAGTTGGGTTGTTTTGG
1 AAAGTTTGTTAAGTTATGTTTTGGTATTGAATTGAGCATGTACCTAAGTTGGGTTGTTTTGG
42022431 TATTAAGCTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.23, C:0.05, G:0.27, T:0.45
Consensus pattern (62 bp):
AAAGTTTGTTAAGTTATGTTTTGGTATTGAATTGAGCATGTACCTAAGTTGGGTTGTTTTGG
Found at i:42024175 original size:2 final size:2
Alignment explanation
Indices: 42024168--42024199 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42024158 GGCATGTTAA
42024168 AT AT 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 AT AT
42024200 TTGTAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42025311 original size:21 final size:21
Alignment explanation
Indices: 42025285--42025418 Score: 164
Period size: 21 Copynumber: 6.5 Consensus size: 21
42025275 TTAGCACTTT
* *
42025285 CGAGCTTCCGTTCAGCTCTCA
1 CGAGCTTCTGTTCAGCTCTTA
* *
42025306 CGAGCTTCTGTTAAACTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
* * *
42025327 TGAGTTTCTGTTTAGCTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
*
42025348 CGAGTTTCTGTTCAGCTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
*
42025369 CAAGCTTCTGTTCAGCTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
*
42025390 CAAGCTTCTGTTCAGCT-TT-
1 CGAGCTTCTGTTCAGCTCTTA
42025409 CGAGCTTCTG
1 CGAGCTTCTG
42025419 ATTGGCGTAT
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
19 9 0.09
20 2 0.02
21 89 0.89
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (21 bp):
CGAGCTTCTGTTCAGCTCTTA
Found at i:42025696 original size:10 final size:8
Alignment explanation
Indices: 42025681--42025707 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
42025671 TGATGGCACA
42025681 TGATATAT
1 TGATATAT
42025689 TGATATAT
1 TGATATAT
42025697 TGATATAT
1 TGATATAT
42025705 TGA
1 TGA
42025708 AATGGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (8 bp):
TGATATAT
Found at i:42027601 original size:22 final size:22
Alignment explanation
Indices: 42027574--42027620 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
42027564 TCTCCAATTA
42027574 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
*
42027596 TTAGCACATTCGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
42027618 TTA
1 TTA
42027621 ATAATGCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:42032865 original size:20 final size:20
Alignment explanation
Indices: 42032809--42032875 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
42032799 CATCAACACA
42032809 AGATCAAGAATGGAAAACATG
1 AGATCAAGAA-GGAAAACATG
* * * **
42032830 ATATAAAGCATTAAAACATG
1 AGATCAAGAAGGAAAACATG
* *
42032850 AGATCAAGTAGGAAAAGAT-
1 AGATCAAGAAGGAAAACATG
42032869 AGATCAA
1 AGATCAA
42032876 AGTTAAGAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
19 7 0.20
20 21 0.60
21 7 0.20
ACGTcount: A:0.54, C:0.09, G:0.19, T:0.18
Consensus pattern (20 bp):
AGATCAAGAAGGAAAACATG
Found at i:42033780 original size:44 final size:44
Alignment explanation
Indices: 42033721--42033812 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
42033711 AGAATTATGC
42033721 ACTAAAGTTAGTAAATTATAACTCTCTTTTGGAGAGTTATCACT
1 ACTAAAGTTAGTAAATTATAACTCTCTTTTGGAGAGTTATCACT
42033765 ACTAAAGTTAGTAAATTATAACTCTCTTTTGGAGAGTTATCACT
1 ACTAAAGTTAGTAAATTATAACTCTCTTTTGGAGAGTTATCACT
42033809 ACTA
1 ACTA
42033813 CTTTAGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (44 bp):
ACTAAAGTTAGTAAATTATAACTCTCTTTTGGAGAGTTATCACT
Found at i:42033816 original size:23 final size:23
Alignment explanation
Indices: 42033746--42033816 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
42033736 TTATAACTCT
42033746 CTTTTGGAGAGTTATCACTACTAA
1 CTTTTGGAGAGTTATCACTACT-A
** * * * *
42033770 AGTTAGTA-AATTATAACT-CT-
1 CTTTTGGAGAGTTATCACTACTA
42033790 CTTTTGGAGAGTTATCACTACTA
1 CTTTTGGAGAGTTATCACTACTA
42033813 CTTT
1 CTTT
42033817 AGTTTTCTGA
Statistics
Matches: 32, Mismatches: 12, Indels: 7
0.63 0.24 0.14
Matches are distributed among these distances:
20 4 0.12
21 8 0.25
22 4 0.12
23 12 0.38
24 4 0.12
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (23 bp):
CTTTTGGAGAGTTATCACTACTA
Found at i:42036533 original size:3 final size:3
Alignment explanation
Indices: 42036527--42036581 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
42036517 TCTGTTCCAC
42036527 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42036575 TAT TAT T
1 TAT TAT T
42036582 TTTGCATGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42038092 original size:28 final size:28
Alignment explanation
Indices: 42038060--42038115 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
42038050 TCTATTGGCT
*
42038060 GTTCTTATGAACAAAGTTGACTGCAAAA
1 GTTCTTATGAACAAAGTTAACTGCAAAA
42038088 GTTCTTATGAACAAAGTTAACTGCAAAA
1 GTTCTTATGAACAAAGTTAACTGCAAAA
42038116 AGTTATCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (28 bp):
GTTCTTATGAACAAAGTTAACTGCAAAA
Found at i:42040285 original size:21 final size:20
Alignment explanation
Indices: 42040261--42040307 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
42040251 AAATTAAATT
42040261 TTAAAATTTGAAATATAAAAA
1 TTAAAATTTGAAA-ATAAAAA
*
42040282 TTAAAAATTTTAAAATAAAAA
1 TT-AAAATTTGAAAATAAAAA
42040303 -TAAAA
1 TTAAAA
42040308 AAAGGAGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 9 0.38
22 10 0.42
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAAATTTGAAAATAAAAA
Found at i:42040308 original size:21 final size:22
Alignment explanation
Indices: 42040263--42040309 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
42040253 ATTAAATTTT
*
42040263 AAAATTTGAAATATAAAAATTA
1 AAAATTTGAAATATAAAAATAA
*
42040285 AAAATTTTAAA-ATAAAAATAA
1 AAAATTTGAAATATAAAAATAA
42040306 AAAA
1 AAAA
42040310 AGGAGGGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAATTTGAAATATAAAAATAA
Found at i:42043524 original size:41 final size:41
Alignment explanation
Indices: 42043469--42043558 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
42043459 GATGCAGTTG
* *
42043469 TATTTGTTGCCTATTACCTCAACTGATATTT-TGATGAGTCA
1 TATTTATTGCCTATTACCTCAACCGAT-TTTGTGATGAGTCA
* * **
42043510 TATTTATTGTCTATTATCTCAACCGATTTTGTGATGAGTTG
1 TATTTATTGCCTATTACCTCAACCGATTTTGTGATGAGTCA
42043551 TATTTATT
1 TATTTATT
42043559 ACATCTTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 3 0.07
41 39 0.93
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.49
Consensus pattern (41 bp):
TATTTATTGCCTATTACCTCAACCGATTTTGTGATGAGTCA
Found at i:42054234 original size:32 final size:32
Alignment explanation
Indices: 42054174--42054236 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
42054164 ATTAATCAGT
* **
42054174 ATGAGTTATCAAATTAAATTAATTAATTTATC
1 ATGAGTTATCAAATTAAAGTAACCAATTTATC
* *
42054206 ATGAGTTATTAAATTTAAGTAACCAATTTAT
1 ATGAGTTATCAAATTAAAGTAACCAATTTAT
42054237 AAATGTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAACCAATTTATC
Found at i:42054401 original size:16 final size:16
Alignment explanation
Indices: 42054380--42054422 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
42054370 GTGAAATTTA
42054380 AATATTTTATTAAAAT
1 AATATTTTATTAAAAT
*
42054396 AATATTTTAATTAATAT
1 AATATTTT-ATTAAAAT
*
42054413 CAT-TTTTATT
1 AATATTTTATT
42054423 TAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
AATATTTTATTAAAAT
Found at i:42054728 original size:24 final size:21
Alignment explanation
Indices: 42054679--42054734 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 21
42054669 GGTGCGAATC
42054679 AATTTTTTATATTAAAAAATAT
1 AATTTTTTAT-TTAAAAAATAT
42054701 --TTTTTTATTTAAATAAAATATT
1 AATTTTTTATTT-AA-AAAATA-T
42054723 AATTTTTTATTT
1 AATTTTTTATTT
42054735 TTATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.07
20 10 0.34
21 6 0.21
22 1 0.03
24 10 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTTTTATTTAAAAAATAT
Found at i:42054744 original size:26 final size:26
Alignment explanation
Indices: 42054683--42054748 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
42054673 CGAATCAATT
*
42054683 TTTTATATTAAAAA-A-TATTTTTTTA
1 TTTT-TATTAAAAATATTAATTTTTTA
* *
42054708 -TTTAAAT-AAAATATTAATTTTTTA
1 TTTTTATTAAAAATATTAATTTTTTA
42054732 TTTTTATTAAAAATATT
1 TTTTTATTAAAAATATT
42054749 TAAATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
22 4 0.12
23 3 0.09
24 12 0.38
25 5 0.16
26 8 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTTATTAAAAATATTAATTTTTTA
Found at i:42055060 original size:13 final size:12
Alignment explanation
Indices: 42055042--42055107 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 12
42055032 CCCATCCACC
42055042 AAAAGAGAGAAAG
1 AAAAGA-AGAAAG
42055055 AAAAGAGAGAAAGG
1 AAAAGA-AGAAA-G
*
42055069 AGAAGAA-AAA-
1 AAAAGAAGAAAG
42055079 AAAAGAAG-AAG
1 AAAAGAAGAAAG
42055090 AAGAAGAAAGAAAG
1 AA-AAG-AAGAAAG
42055104 AAAA
1 AAAA
42055108 AGGTAATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
10 8 0.18
11 2 0.04
12 6 0.13
13 18 0.40
14 11 0.24
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAG
Found at i:42055071 original size:22 final size:23
Alignment explanation
Indices: 42055049--42055102 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
42055039 ACCAAAAGAG
*
42055049 AGAAAGAAAAGAG-AGAAAGGAGA
1 AGAAAGAAAAAAGAAG-AAGGAGA
*
42055072 AGAAA-AAAAAAGAAGAAGAAGA
1 AGAAAGAAAAAAGAAGAAGGAGA
42055094 AGAAAGAAA
1 AGAAAGAAA
42055103 GAAAAAGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (23 bp):
AGAAAGAAAAAAGAAGAAGGAGA
Found at i:42055350 original size:60 final size:60
Alignment explanation
Indices: 42055271--42055389 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
42055261 TTGCTTTTTA
* * *
42055271 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
42055331 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
42055390 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
Found at i:42055979 original size:21 final size:21
Alignment explanation
Indices: 42055942--42055981 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42055932 TGACAAATAC
*
42055942 TTTTATTAAAATTATTTAAAA
1 TTTTATTAAAATAATTTAAAA
42055963 TTTTAATTAAAA-AATTTAA
1 TTTT-ATTAAAATAATTTAA
42055982 CACCCACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATTAAAATAATTTAAAA
Found at i:42062102 original size:13 final size:13
Alignment explanation
Indices: 42062084--42062108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42062074 TAATTTAATA
42062084 TTATTTTGTGTGT
1 TTATTTTGTGTGT
42062097 TTATTTTGTGTG
1 TTATTTTGTGTG
42062109 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:42063291 original size:21 final size:19
Alignment explanation
Indices: 42063226--42063319 Score: 152
Period size: 19 Copynumber: 4.8 Consensus size: 19
42063216 AATTTTTGAG
42063226 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
42063245 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
42063264 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
42063283 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
42063304 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
42063320 AGATATGATT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 51 0.73
21 19 0.27
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:42063301 original size:40 final size:38
Alignment explanation
Indices: 42063226--42063326 Score: 152
Period size: 40 Copynumber: 2.7 Consensus size: 38
42063216 AATTTTTGAG
42063226 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
*
42063264 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
*
42063304 GATATGTAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
42063327 ATTTTGTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
36 5 0.08
38 21 0.36
39 1 0.02
40 32 0.54
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:42063338 original size:23 final size:22
Alignment explanation
Indices: 42063258--42063342 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
42063248 ATGCAATCCT
*
42063258 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
42063279 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
42063298 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
42063320 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
42063343 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 13 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:42063352 original size:22 final size:23
Alignment explanation
Indices: 42063308--42063352 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42063298 AGATATGATA
*
42063308 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
42063331 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
42063353 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:42064533 original size:19 final size:20
Alignment explanation
Indices: 42064492--42064533 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
42064482 ATTTCTATGC
* *
42064492 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
42064512 CATTGT-ATATTTAATATAG
1 CATTGTAATATTTAATATAG
42064531 CAT
1 CAT
42064534 CACATCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:42065438 original size:12 final size:12
Alignment explanation
Indices: 42065421--42065453 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42065411 TGAAGTTCGA
42065421 ATATGTATATAT
1 ATATGTATATAT
*
42065433 ATATGTATATCT
1 ATATGTATATAT
42065445 AT-TGTATAT
1 ATATGTATAT
42065454 TTGATGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:42065538 original size:114 final size:114
Alignment explanation
Indices: 42065312--42065521 Score: 402
Period size: 114 Copynumber: 1.8 Consensus size: 114
42065302 TATATATACA
42065312 TATATATATATGTATATCTATTGTATATTTGATCAGCTATAATTAAAAGTATATGAATTGAAATT
1 TATATATATATGTATATCTATTGTATATTTGATCAGCTATAATTAAAAGTATATGAATTGAAATT
42065377 AGTTAAGTATGAATGTTATATATATACACATAAATGAAGTTCGAATATG
66 AGTTAAGTATGAATGTTATATATATACACATAAATGAAGTTCGAATATG
*
42065426 TATATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATGAATTGAAATT
1 TATATATATATGTATATCTATTGTATATTTGATCAGCTATAATTAAAAGTATATGAATTGAAATT
*
42065491 AGTTAAGTATGAATGTTATATATATGCACAT
66 AGTTAAGTATGAATGTTATATATATACACAT
42065522 GTGTGAGGTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 94 1.00
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.41
Consensus pattern (114 bp):
TATATATATATGTATATCTATTGTATATTTGATCAGCTATAATTAAAAGTATATGAATTGAAATT
AGTTAAGTATGAATGTTATATATATACACATAAATGAAGTTCGAATATG
Found at i:42065913 original size:41 final size:41
Alignment explanation
Indices: 42065859--42066008 Score: 230
Period size: 41 Copynumber: 3.7 Consensus size: 41
42065849 TTTCGGACTT
42065859 TAAGTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
1 TAAGTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
42065900 TAAGTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
1 TAAGTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
** * * *
42065941 TAAACCTAGCAGACTAAGTGTCGGTGATCTGAATCAGGCTA
1 TAAGTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
*
42065982 TAAG-CTTAGCAGGCTAAATGCCGGTGA
1 TAAGTC-TAGCAGGCTAAGTGCCGGTGA
42066009 ATATGTTAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 98 0.99
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (41 bp):
TAAGTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
Found at i:42072235 original size:29 final size:30
Alignment explanation
Indices: 42072176--42072233 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
42072166 TCCGAGCCTT
*
42072176 GGGGCACAAATGTAATTATGTAAAAGTTTA
1 GGGGCACAAATGTAATTATGAAAAAGTTTA
*
42072206 GGGGCA-AAATTGTAATTTTGAAAAAGTT
1 GGGGCACAAA-TGTAATTATGAAAAAGTT
42072234 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCACAAATGTAATTATGAAAAAGTTTA
Found at i:42072464 original size:13 final size:13
Alignment explanation
Indices: 42072446--42072476 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42072436 TTCCAGCAAC
42072446 TATGAATTTATTT
1 TATGAATTTATTT
42072459 TATGAATTTATTT
1 TATGAATTTATTT
*
42072472 GATGA
1 TATGA
42072477 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:42072646 original size:50 final size:50
Alignment explanation
Indices: 42072571--42072863 Score: 487
Period size: 50 Copynumber: 5.8 Consensus size: 50
42072561 ATTTGGGTAA
42072571 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
42072621 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
42072671 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
42072721 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
42072771 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
42072821 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42072864 TGTTATTATC
Statistics
Matches: 226, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 192 0.85
51 34 0.15
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:42075874 original size:23 final size:23
Alignment explanation
Indices: 42075848--42075901 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
42075838 TAATGGCAAA
*
42075848 AAATATATATAACTT-TTTTATAT
1 AAATATA-ATAAATTATTTTATAT
*
42075871 AAATA-AATAAATTATTTTTTAT
1 AAATATAATAAATTATTTTATAT
42075893 AACATATAA
1 AA-ATATAA
42075902 CATCGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.23
22 10 0.38
23 8 0.31
24 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATAATAAATTATTTTATAT
Found at i:42079692 original size:22 final size:24
Alignment explanation
Indices: 42079654--42079698 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
42079644 AATGCAATAT
42079654 TGTTGAAAAATCAAATAA-AAAAG
1 TGTTGAAAAATCAAATAACAAAAG
42079677 TGTTG-AAAA-CACAATAACAAAA
1 TGTTGAAAAATCA-AATAACAAAA
42079699 AAACATAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.10
22 9 0.45
23 9 0.45
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (24 bp):
TGTTGAAAAATCAAATAACAAAAG
Found at i:42081290 original size:19 final size:19
Alignment explanation
Indices: 42081259--42081301 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
42081249 ACTTATTTTT
42081259 TTAAAATTTTATAAAATATA
1 TTAAAATTTTATAAAA-ATA
42081279 TTAAAA-TTTATAAAAATA
1 TTAAAATTTTATAAAAATA
42081297 TTAAA
1 TTAAA
42081302 TAAAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAATTTTATAAAAATA
Found at i:42082031 original size:21 final size:21
Alignment explanation
Indices: 42081986--42082036 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
42081976 GTTTTGAACT
* * *
42081986 TTTTGAATAATATTTTTATACA
1 TTTT-AATAATATTTCTACAAA
42082008 TTTTAATAATATTTCTACAAA
1 TTTTAATAATATTTCTACAAA
42082029 TTTATAAT
1 TTT-TAAT
42082037 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTAATAATATTTCTACAAA
Found at i:42082057 original size:18 final size:19
Alignment explanation
Indices: 42082026--42082064 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
42082016 ATATTTCTAC
42082026 AAATTTATAATTTTTTAAA
1 AAATTTATAATTTTTTAAA
42082045 AAATTTA-AATTTTTTAAA
1 AAATTTATAATTTTTTAAA
42082063 AA
1 AA
42082065 TGTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTATAATTTTTTAAA
Found at i:42092081 original size:35 final size:34
Alignment explanation
Indices: 42092027--42092096 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
42092017 ATATATGTAA
* *
42092027 ATATATATGTGTATATGTATATAAATTGTAAAAT
1 ATATAAATGTGTATATGTATATAAATTATAAAAT
*
42092061 ATATAAATGATGTATGTGTATATAAATTATAAAAT
1 ATATAAATG-TGTATATGTATATAAATTATAAAAT
42092096 A
1 A
42092097 AAAAAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 8 0.25
35 24 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.41
Consensus pattern (34 bp):
ATATAAATGTGTATATGTATATAAATTATAAAAT
Found at i:42093022 original size:44 final size:44
Alignment explanation
Indices: 42092857--42093058 Score: 128
Period size: 44 Copynumber: 4.5 Consensus size: 44
42092847 TTCTGCAACG
* * * *
42092857 CACTGCAACTTCAG-GGGATGAGGTTAGTGGT-TTTAGTCTGCTC
1 CACTGCAACTTCAGAGAGAT-AGGTTGGTGGTATTTAATCCGCTC
* * *
42092900 CACTGCAACTTCAGGGAGATAAGACTTGTCATGGTAAATTTAATCCGAC-C
1 CACTGCAACTTCAGAGAGAT-AG-GTTG--GTGGT--ATTTAATCCG-CTC
* *
42092950 TACTGCAACTCCAGAG-GTATAAGGTTGGTGGT-TTTAATCCGCTC
1 CACTGCAACTTCAGAGAG-AT-AGGTTGGTGGTATTTAATCCGCTC
* * ** *
42092994 CACTGCAACTTCAGAGAGATAGGATTGGT-TTCTTTTGTCTGCTC
1 CACTGCAACTTCAGAGAGATAGG-TTGGTGGTATTTAATCCGCTC
*
42093038 CACTGCAACTTCGGAGAGATA
1 CACTGCAACTTCAGAGAGATA
42093059 AGACTGGATG
Statistics
Matches: 127, Mismatches: 19, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
43 19 0.15
44 66 0.52
45 3 0.02
47 8 0.06
49 4 0.03
50 26 0.20
51 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (44 bp):
CACTGCAACTTCAGAGAGATAGGTTGGTGGTATTTAATCCGCTC
Found at i:42093197 original size:50 final size:50
Alignment explanation
Indices: 42093143--42093877 Score: 591
Period size: 50 Copynumber: 14.7 Consensus size: 50
42093133 TACAATTTCG
* * * *
42093143 GGGAAATAAGATTCGCCGTCGTAGCTTCAATCTTTTCCACTACACCG-CAA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTC-A
* *
42093193 GGGAAGTAAGATTCGCCGTTGTGGCTTCAGTCTTTTCCACTGCACCGCCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
* * * * * ** * * ** *
42093243 AGGAAGTCAGATTCACCGTTGTGACTTAAATCTTTTTAATTACAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
* * * *
42093293 GGGAAGCAAGATTCGCTGTTGTTGCTTCAATCTGTTCCACTGCACCG-CTA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTC-A
* * ** * **
42093343 GGCAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
** ** * * * *
42093392 GAGGAAACAAGATTCATCATCGTAGCTTCAATCTGTTCCACTGCACCGTCA
1 G-GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
* ** * **
42093443 GGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
* * * *
42093493 GGGAAGCAAGATTCGCCGTTGTAGTTTCAATCTGTTCCACTGCACCG-CA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
** * ** *
42093542 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
** * * * * *
42093592 GGGAAACAAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
* * ** * **
42093642 AGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
* * * * * *
42093691 GGTGAAGCAAAATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
1 GG-GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
* * * ** * ** *
42093742 GGGAAGTAAGATTTGCCTTTATGGCTTCAATCTTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
* * * * *
42093792 GGGAAGCAAGATTTGCCATTGTAGCTTCAATCTGTTCCACTGCACCG-CTA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTC-A
*
42093842 GGGAAGTAAGATTCGCCGTTGTGGATTCAATCTTTT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTT
42093878 TAATTGTAAC
Statistics
Matches: 513, Mismatches: 163, Indels: 18
0.74 0.23 0.03
Matches are distributed among these distances:
49 44 0.09
50 464 0.90
51 5 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCCACTGCACCGTCA
Found at i:42093314 original size:100 final size:100
Alignment explanation
Indices: 42093193--42093883 Score: 997
Period size: 100 Copynumber: 6.9 Consensus size: 100
42093183 TACACCGCAA
* * * * * * *
42093193 GGGAAGTAAGATTCGCCGTTGTGGCTTCAGTCTTTTCCACTGCACCGCCAAGGAAGTCAGATTCA
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
* * *
42093258 CCGTTGTGACTTAAATCTTTTTAATTACAATGTCG
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
* * * *
42093293 GGGAAGCAAGATTCGCTGTTGTTGCTTCAATCTGTTCCACTGCACCGCTAGGCAAGTAAGATTCG
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
*
42093358 TCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
* * ** * * *
42093393 AGGAAACAAGATTCATCATCGTAGCTTCAATCTGTTCCACTGCACCGTCAGGGAAGTAAGATTCG
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
* * *
42093458 TCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
*
42093493 GGGAAGCAAGATTCGCCGTTGTAGTTTCAATCTGTTCCACTGCACCG-CAGGGAAGTAAGATTCG
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
42093557 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
* * * * *
42093592 GGGAAACAAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCACCGCCAAGGAAGTAAGATTCG
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
*
42093657 TCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
* * * *
42093692 GTGAAGCAAAATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTTG
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
* *
42093757 CCTTTATGGCTTCAATCTTTTTAATTGCAATGTCG
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
* * *
42093792 GGGAAGCAAGATTTGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGTAAGATTCG
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
*
42093857 CCGTTGTGGATTCAATCTTTTTAATTG
66 CCGTTGTGGCTTCAATCTTTTTAATTG
42093884 TAACCTCAAG
Statistics
Matches: 525, Mismatches: 65, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
99 91 0.17
100 434 0.83
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (100 bp):
GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
Found at i:42093674 original size:299 final size:299
Alignment explanation
Indices: 42093192--42093883 Score: 1030
Period size: 299 Copynumber: 2.3 Consensus size: 299
42093182 CTACACCGCA
* * * * * *
42093192 AGGGAAGTAAGATTCGCCGTTGTGGCTTCAGTCTTTTCCACTGCACCGCCAAGGAAGTCAGATTC
1 AGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG-CAGGGAAGTAAGATTC
* * * * * * * * *
42093257 ACCGTTGTGACTTAAATCTTTTTAATTACAATGTCGGGGAAGCAAGATTCGCTGTTGTTGCTTCA
65 GCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATTCACCGTCGTAGCTTCA
* *
42093322 ATCTGTTCCACTGCACCGCTAGGCAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCA
130 ATCTATTCCACTGCACCGCAAGGCAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCA
* *
42093387 ATGTCGAG-GAAACAAGATTCAT-CATCGTAGCTTCAATCTGTTCCACTGCACCGTCAGGGAAGT
195 ATGTCG-GTGAAACAAAATTC-TCCATCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* *
42093450 AAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTGCAATGTC
258 AAGATTCGCCGTTATGGCTTCAATCTTTTAAATTGCAATGTC
*
42093492 AGGGAAGCAAGATTCGCCGTTGTAGTTTCAATCTGTTCCACTGCACCGCAGGGAAGTAAGATTCG
1 AGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCAGGGAAGTAAGATTCG
42093557 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATTCACCGTCGTAGCTTCAA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATTCACCGTCGTAGCTTCAA
42093622 TCTATTCCACTGCACCGCCAAGG-AAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCA
131 TCTATTCCACTGCACCG-CAAGGCAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCA
* * *
42093686 ATGTCGGTGAAGCAAAATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAA
195 ATGTCGGTGAAACAAAATTCTCCATCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAA
* * *
42093751 GATTTGCCTTTATGGCTTCAATCTTTTTAATTGCAATGTC
260 GATTCGCCGTTATGGCTTCAATCTTTTAAATTGCAATGTC
* * *
42093791 GGGGAAGCAAGATTTGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGTAAGATTC
1 AGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC-AGGGAAGTAAGATTC
*
42093856 GCCGTTGTGGATTCAATCTTTTTAATTG
65 GCCGTTGTGGCTTCAATCTTTTTAATTG
42093884 TAACCTCAAG
Statistics
Matches: 355, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
298 2 0.01
299 264 0.74
300 89 0.25
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (299 bp):
AGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCAGGGAAGTAAGATTCG
CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATTCACCGTCGTAGCTTCAA
TCTATTCCACTGCACCGCAAGGCAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCAA
TGTCGGTGAAACAAAATTCTCCATCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAG
ATTCGCCGTTATGGCTTCAATCTTTTAAATTGCAATGTC
Found at i:42095153 original size:6 final size:6
Alignment explanation
Indices: 42095142--42095226 Score: 74
Period size: 6 Copynumber: 14.8 Consensus size: 6
42095132 TGGCCTCTCC
** *
42095142 TTTTCT TTTTCT TTTTC- TTTTCT TCCTCT TCTT-T TTTTCT TCTTT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT
*
42095188 TTTTCT TTTTC- -TTTCT TTTTCT TTTT-T TCTCTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTC
42095227 CTTCCCTTGG
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.06
5 14 0.22
6 42 0.65
7 5 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:42095155 original size:11 final size:11
Alignment explanation
Indices: 42095141--42095212 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
42095131 TTGGCCTCTC
42095141 CTTTTCTTTTT
1 CTTTTCTTTTT
42095152 CTTTT-TCTTTT
1 CTTTTCT-TTTT
*
42095163 CTTCCTCTTCTTT
1 CTT-TTCTT-TTT
42095176 -TTTTCTTCTTT
1 CTTTTCTT-TTT
*
42095187 TTTTTCTTTTT
1 CTTTTCTTTTT
42095198 C-TTTCTTTTT
1 CTTTTCTTTTT
42095208 CTTTT
1 CTTTT
42095213 TTTCTCTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
10 11 0.21
11 26 0.50
12 11 0.21
13 4 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:42095173 original size:26 final size:25
Alignment explanation
Indices: 42095139--42095226 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
42095129 CCTTGGCCTC
*
42095139 TCCTTTTCTTTTTCTTTTTCTTTTCT
1 TCCTCTTCTTTTTCTTTTTCTTTT-T
*
42095165 TCCTCTTCTTTTT-TTCTTCTTTTT
1 TCCTCTTCTTTTTCTTTTTCTTTTT
* *
42095189 T-TTCTTTTTCTTTCTTTTTCTTTTT
1 TCCTCTTCTT-TTTCTTTTTCTTTTT
*
42095214 TTCTC-TCTTTTTC
1 TCCTCTTCTTTTTC
42095227 CTTCCCTTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
23 6 0.12
24 9 0.17
25 23 0.44
26 14 0.27
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (25 bp):
TCCTCTTCTTTTTCTTTTTCTTTTT
Found at i:42095175 original size:20 final size:20
Alignment explanation
Indices: 42095150--42095201 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
42095140 CCTTTTCTTT
42095150 TTCTTTTTCTTTTCTTCCTC
1 TTCTTTTTCTTTTCTTCCTC
** *
42095170 TTCTTTTT-TTCTTCTTTTTT
1 TTCTTTTTCTT-TTCTTCCTC
42095190 TTCTTTTTCTTT
1 TTCTTTTTCTTT
42095202 CTTTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTCTTTTTCTTTTCTTCCTC
Found at i:42095189 original size:10 final size:10
Alignment explanation
Indices: 42095168--42095230 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
42095158 CTTTTCTTCC
42095168 TCTTCTTTTTT
1 TCTTC-TTTTT
42095179 TCTTCTTTTT
1 TCTTCTTTTT
42095189 T-TTC-TTTT
1 TCTTCTTTTT
42095197 TCTT-TCTTTT
1 TCTTCT-TTTT
42095207 TC-T-TTTTT
1 TCTTCTTTTT
42095215 TCTCTCTTTTT
1 TCT-TCTTTTT
*
42095226 CCTTC
1 TCTTC
42095231 CCTTGGAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
8 11 0.24
9 7 0.16
10 15 0.33
11 12 0.27
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TCTTCTTTTT
Found at i:42095213 original size:35 final size:35
Alignment explanation
Indices: 42095154--42095226 Score: 71
Period size: 33 Copynumber: 2.1 Consensus size: 35
42095144 TTCTTTTTCT
*
42095154 TTTTCTTTTCTTC-CTCTTCTTTTTTTCTTCTTT-T
1 TTTTC-TTTCTTCTCTCTTCTTCTTTTCTTCTTTCT
* * * *
42095188 TTTTCTTT-TTCTTTCTTTTTCTTTTTTTCTCTCT
1 TTTTCTTTCTTCTCTCTTCTTCTTTTCTTCTTTCT
42095222 TTTTC
1 TTTTC
42095227 CTTCCCTTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
32 3 0.09
33 18 0.56
34 11 0.34
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (35 bp):
TTTTCTTTCTTCTCTCTTCTTCTTTTCTTCTTTCT
Found at i:42095217 original size:36 final size:40
Alignment explanation
Indices: 42095147--42095225 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 40
42095137 TCTCCTTTTC
42095147 TTTTTCTTTTTCTTTTCTTCCTCTTCTTTTTTTCT-TCTTT
1 TTTTTCTTTTTCTTTTCTT-CTCTTCTTTTTTTCTCTCTTT
42095187 TTTTTCTTTTTC-TTTCTT-T-TTCTTTTTTTCTCTCTTT
1 TTTTTCTTTTTCTTTTCTTCTCTTCTTTTTTTCTCTCTTT
42095224 TT
1 TT
42095226 CCTTCCCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
36 12 0.32
37 8 0.21
39 6 0.16
40 12 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (40 bp):
TTTTTCTTTTTCTTTTCTTCTCTTCTTTTTTTCTCTCTTT
Found at i:42099487 original size:18 final size:18
Alignment explanation
Indices: 42099464--42099505 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42099454 GACAACAATG
42099464 ATATATGTAAATATATAT
1 ATATATGTAAATATATAT
* *
42099482 ATATATGTATATGTATAT
1 ATATATGTAAATATATAT
*
42099500 GTATAT
1 ATATAT
42099506 AAATTGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (18 bp):
ATATATGTAAATATATAT
Found at i:42099498 original size:12 final size:12
Alignment explanation
Indices: 42099465--42099505 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
42099455 ACAACAATGA
* *
42099465 TATATGTAAATA
1 TATATGTATATG
*
42099477 TATATATATATG
1 TATATGTATATG
42099489 TATATGTATATG
1 TATATGTATATG
42099501 TATAT
1 TATAT
42099506 AAATTGTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (12 bp):
TATATGTATATG
Found at i:42099900 original size:3 final size:3
Alignment explanation
Indices: 42099892--42099945 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
42099882 AAAAGTATAC
42099892 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42099940 ATA ATA
1 ATA ATA
42099946 TTAGTGAACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42100599 original size:2 final size:2
Alignment explanation
Indices: 42100592--42100633 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
42100582 GTTTTATGTC
42100592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42100634 CATGATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42102100 original size:9 final size:9
Alignment explanation
Indices: 42102086--42102129 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
42102076 TTGCAAAAAG
42102086 GACGATGAC
1 GACGATGAC
42102095 GACGATGAC
1 GACGATGAC
42102104 GACGATGAC
1 GACGATGAC
*
42102113 GACGACGAC
1 GACGATGAC
*
42102122 GATGATGA
1 GACGATGA
42102130 TGTTTCTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.34, T:0.11
Consensus pattern (9 bp):
GACGATGAC
Found at i:42102940 original size:25 final size:25
Alignment explanation
Indices: 42102906--42102953 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
42102896 TTAAGATTTG
42102906 ATTGTTTGTAATTAAATTCAAATTA
1 ATTGTTTGTAATTAAATTCAAATTA
42102931 ATTGTTTGTAATTAAATTCAAAT
1 ATTGTTTGTAATTAAATTCAAAT
42102954 AAGTAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
ATTGTTTGTAATTAAATTCAAATTA
Found at i:42103045 original size:16 final size:16
Alignment explanation
Indices: 42103024--42103057 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42103014 ATATAAATTC
42103024 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
42103040 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
42103056 AA
1 AA
42103058 CTTTTAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:42106753 original size:3 final size:3
Alignment explanation
Indices: 42106747--42106772 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42106737 CCTGACTGTC
42106747 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
42106773 ACAAGCTCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:42110023 original size:62 final size:63
Alignment explanation
Indices: 42109938--42110062 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 63
42109928 GGAGAGAGTG
* * *
42109938 CAAATTAATTTATTAGGAAACATTCAATGAGTATATTTTGTTAAACC-TTTGAGAGTTTTGAT
1 CAAATTAATTTACTAAGAAACATTCAATGAGCATATTTTGTTAAACCTTTTGAGAGTTTTGAT
* * *
42110000 CAAATTAATTTACTAAGTAACATTCAGTGAGCGTATTTTGTTAAACCTTTTGAGAGTTTTGAT
1 CAAATTAATTTACTAAGAAACATTCAATGAGCATATTTTGTTAAACCTTTTGAGAGTTTTGAT
42110063 TGTGCTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 41 0.73
63 15 0.27
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (63 bp):
CAAATTAATTTACTAAGAAACATTCAATGAGCATATTTTGTTAAACCTTTTGAGAGTTTTGAT
Found at i:42116149 original size:21 final size:21
Alignment explanation
Indices: 42116081--42116150 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
42116071 TTTCAAGTTT
*
42116081 TTTATAGTATTATACATTATA
1 TTTATAGTATTATATATTATA
* *
42116102 --AAGTAG-ATTATATATTATT
1 TTTA-TAGTATTATATATTATA
42116121 TTTATAGTATTATATATTATGA
1 TTTATAGTATTATATATTAT-A
42116143 TTT-TAGTA
1 TTTATAGTA
42116151 AATTCATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 12 0.31
20 6 0.15
21 18 0.46
22 3 0.08
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTATAGTATTATATATTATA
Found at i:42116192 original size:17 final size:18
Alignment explanation
Indices: 42116167--42116212 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
42116157 TATAAGAACA
*
42116167 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
42116184 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
42116202 ATTAAATTATA
1 ATTAAATTATA
42116213 TTTAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:42116431 original size:17 final size:18
Alignment explanation
Indices: 42116406--42116451 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
42116396 GATAAGAATA
*
42116406 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
42116423 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
42116441 ATTAAATTATA
1 ATTAAATTATA
42116452 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:42116480 original size:119 final size:119
Alignment explanation
Indices: 42116115--42116550 Score: 766
Period size: 119 Copynumber: 3.7 Consensus size: 119
42116105 TAGATTATAT
* *
42116115 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAACAATTATATTAAGA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAGATAAGAATAATTATATTAAGA
42116179 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAG
66 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAG
* * * *
42116233 ATTATATTTTATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTGAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAGATAAGAATAATT-ATATTAAG
*
42116298 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAG
65 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAG
42116353 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAGATAAGAATAATTATATTAAGA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAGATAAGAATAATTATATTAAGA
*
42116418 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAAAAATTATTATTTTAG
66 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAG
* *
42116472 ATTCTATTTTATAGTATTATATATTATGATTTTAGTAAATTCAGATAAAAATAATTATATTAAGA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAGATAAGAATAATTATATTAAGA
42116537 ATTTTATTAAATTA
66 ATTTTATTAAATTA
42116551 GACTTCTCTC
Statistics
Matches: 303, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
118 5 0.02
119 184 0.61
120 114 0.38
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.52
Consensus pattern (119 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAGATAAGAATAATTATATTAAGA
ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAG
Found at i:42122713 original size:120 final size:120
Alignment explanation
Indices: 42122498--42122721 Score: 414
Period size: 120 Copynumber: 1.9 Consensus size: 120
42122488 NNNNNNNNNN
42122498 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGTAATTTTATTAAATTATA
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG-AATTTTATTAAATTATA
*
42122563 TATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATACTATT
65 TATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATACTATT
42122619 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAA-AAGTTTTATTAAATTATA
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA-TTTTATTAAATTATA
42122683 TATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
65 TATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
42122722 ATATGATTAA
Statistics
Matches: 101, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
119 2 0.02
120 53 0.52
121 46 0.46
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (120 bp):
ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
ATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATACTATT
Found at i:42122945 original size:45 final size:44
Alignment explanation
Indices: 42122860--42122947 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
42122850 ACAACATCAT
*
42122860 TCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTCCAA
1 TCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTCCAA
*
42122904 TCCATTCAACCAAACA-ATTGAATTACTATTAC-GCCTCTATTCCA
1 TCCATTCAACCAAACACA-AGAA-TACTATTACAG-CTCTATTCCA
42122948 TTACAGCGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
43 1 0.03
44 20 0.51
45 18 0.46
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.30
Consensus pattern (44 bp):
TCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTCCAA
Found at i:42127913 original size:16 final size:16
Alignment explanation
Indices: 42127894--42127927 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42127884 TGAATATTTA
42127894 ATCATCTACATATTAT
1 ATCATCTACATATTAT
* *
42127910 ATCATTTACTTATTAT
1 ATCATCTACATATTAT
42127926 AT
1 AT
42127928 TTATATTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCATCTACATATTAT
Found at i:42129035 original size:7 final size:7
Alignment explanation
Indices: 42129023--42129056 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
42129013 TTCAACATTC
42129023 CACAATT
1 CACAATT
42129030 CACAATT
1 CACAATT
42129037 CACAATT
1 CACAATT
42129044 CACAATT
1 CACAATT
*
42129051 AACAAT
1 CACAAT
42129057 ACTATTGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (7 bp):
CACAATT
Found at i:42130837 original size:23 final size:21
Alignment explanation
Indices: 42130811--42130852 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
42130801 TAATTAAATT
42130811 TGTAGATTATTTTCAAAAAAAAA
1 TGTAG-TT-TTTTCAAAAAAAAA
*
42130834 TGTAGTTTTTTTAAAAAAA
1 TGTAGTTTTTTCAAAAAAA
42130853 TTTGAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (21 bp):
TGTAGTTTTTTCAAAAAAAAA
Found at i:42141424 original size:13 final size:13
Alignment explanation
Indices: 42141408--42141432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42141398 ATTATTTACA
42141408 AAAATTAAATAAT
1 AAAATTAAATAAT
42141421 AAAATTAAATAA
1 AAAATTAAATAA
42141433 ATTAAAATTT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAATAAT
Found at i:42146035 original size:83 final size:84
Alignment explanation
Indices: 42145942--42146106 Score: 287
Period size: 83 Copynumber: 2.0 Consensus size: 84
42145932 AAATAAGAAA
* *
42145942 ATTTGATTACATAGAAAGTCTTAAAAGGATCATTACTTGACTT-ATTTTATTTACGTTTTGACTT
1 ATTTGATTACATAGAAAGTCTTAAAAAGATCATTACTTGACTTAATTTTATTTACATTTTGACTT
42146006 TAATAAAGAGTTTCAAGAT
66 TAATAAAGAGTTTCAAGAT
*
42146025 ATTTGATTACATAGAAAGTCTTAAAAAGATCATTACTTGACTTAATTTTCTTTACATTTTGACTT
1 ATTTGATTACATAGAAAGTCTTAAAAAGATCATTACTTGACTTAATTTTATTTACATTTTGACTT
*
42146090 TAATAAAGTGTTTCAAG
66 TAATAAAGAGTTTCAAG
42146107 GTATATAATC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
83 42 0.55
84 35 0.45
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (84 bp):
ATTTGATTACATAGAAAGTCTTAAAAAGATCATTACTTGACTTAATTTTATTTACATTTTGACTT
TAATAAAGAGTTTCAAGAT
Found at i:42149958 original size:15 final size:17
Alignment explanation
Indices: 42149927--42149959 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
42149917 TACAAATTTC
42149927 AGCACATAATAATAATA
1 AGCACATAATAATAATA
42149944 AGCACA-AAT-ATAATA
1 AGCACATAATAATAATA
42149959 A
1 A
42149960 TTTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (17 bp):
AGCACATAATAATAATA
Found at i:42150541 original size:21 final size:23
Alignment explanation
Indices: 42150515--42150562 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
42150505 ATTAAAATAG
42150515 AAAAAAATCA-TAAA-AA-TTATA
1 AAAAAAAT-AGTAAAGAATTTATA
42150536 AAAAAAATAGTAAAGAATTTATA
1 AAAAAAATAGTAAAGAATTTATA
42150559 AAAA
1 AAAA
42150563 TTGTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 2 0.08
23 9 0.38
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (23 bp):
AAAAAAATAGTAAAGAATTTATA
Found at i:42154585 original size:15 final size:15
Alignment explanation
Indices: 42154562--42154603 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
42154552 AAGATTTAAT
42154562 TAAAATTAAAAAATA
1 TAAAATTAAAAAATA
* *
42154577 TATAATTAAAATATA
1 TAAAATTAAAAAATA
42154592 TAAAATTAAAAA
1 TAAAATTAAAAA
42154604 GAATGGCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAATTAAAAAATA
Found at i:42161059 original size:3 final size:3
Alignment explanation
Indices: 42161051--42161089 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
42161041 CTTCATTACT
42161051 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
42161090 AAAGCTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.