Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 119 of 290
Found at i:40515318 original size:8 final size:8
Alignment explanation
Indices: 40515305--40515329 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40515295 CTAAAGTGTC
40515305 AAAATGTG
1 AAAATGTG
40515313 AAAATGTG
1 AAAATGTG
40515321 AAAATGTG
1 AAAATGTG
40515329 A
1 A
40515330 GGGCTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AAAATGTG
Found at i:40517584 original size:69 final size:70
Alignment explanation
Indices: 40517458--40517605 Score: 280
Period size: 69 Copynumber: 2.1 Consensus size: 70
40517448 GAAGATGCGT
*
40517458 TTTTAACATATCCCTCCCTTCTTCATTTTTTTTTCCTTTTTAGTCTCTAAAACAGGAGGCTCTCC
1 TTTTATCATATCCCTCCCTTCTTCATTTTTTTTTCCTTTTTAGTCTCTAAAACAGGAGGCTCTCC
40517523 CCCTA
66 CCCTA
40517528 TTTTATCATATCCCTCCCTTCTTCA-TTTTTTTTCCTTTTTAGTCTCTAAAACAGGAGGCTCTCC
1 TTTTATCATATCCCTCCCTTCTTCATTTTTTTTTCCTTTTTAGTCTCTAAAACAGGAGGCTCTCC
40517592 CCCTA
66 CCCTA
40517597 TTTTATCAT
1 TTTTATCAT
40517606 CTCTCCTGAC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 53 0.69
70 24 0.31
ACGTcount: A:0.18, C:0.29, G:0.07, T:0.46
Consensus pattern (70 bp):
TTTTATCATATCCCTCCCTTCTTCATTTTTTTTTCCTTTTTAGTCTCTAAAACAGGAGGCTCTCC
CCCTA
Found at i:40523028 original size:13 final size:13
Alignment explanation
Indices: 40523010--40523059 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
40523000 AAAAGTTTGT
40523010 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
*
40523023 AAAAAGAAAACAA
1 AAAAAGAAAAGAA
40523036 ACAAAA-AAAA-AA
1 A-AAAAGAAAAGAA
*
40523048 CGAAAAGAAAAG
1 -AAAAAGAAAAG
40523060 TAGAGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 6 0.19
13 21 0.68
14 4 0.13
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:40523800 original size:17 final size:18
Alignment explanation
Indices: 40523769--40523802 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40523759 AAAAATAAAC
*
40523769 TTTTAAATTTCTTTTTAT
1 TTTTAAAGTTCTTTTTAT
40523787 TTTTAAAGTT-TTTTTA
1 TTTTAAAGTTCTTTTTA
40523803 AAATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTAAAGTTCTTTTTAT
Found at i:40525167 original size:21 final size:22
Alignment explanation
Indices: 40525126--40525184 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
40525116 AATTTTTTAA
*
40525126 ATTTTAAAAAATTATAGAATTT
1 ATTTTAAAAAATTATAAAATTT
*
40525148 ATTTTGAAAAATTA-AAAA-TT
1 ATTTTAAAAAATTATAAAATTT
*
40525168 A--TTATAAAATTATAAAA
1 ATTTTAAAAAATTATAAAA
40525185 AAATATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.28
19 4 0.12
20 3 0.09
21 3 0.09
22 13 0.41
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
ATTTTAAAAAATTATAAAATTT
Found at i:40529551 original size:38 final size:38
Alignment explanation
Indices: 40529494--40529630 Score: 177
Period size: 38 Copynumber: 3.6 Consensus size: 38
40529484 TGTAATAGAA
* ** *
40529494 CAATTCAACACTAGTAGTAGACATGTATAACAAGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
* *
40529532 CAATTCAGCACTAACAGTAGAAATGTTTAAC-AGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
* * *
40529569 CAATTTATCATTAACAGTAGACATGTTTAACATGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
*
40529607 CAATTCATCATTAACAGTAGACAT
1 CAATTCATCACTAACAGTAGACAT
40529631 ACTTATCATG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 33 0.38
38 54 0.62
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (38 bp):
CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
Found at i:40529641 original size:38 final size:38
Alignment explanation
Indices: 40529509--40529630 Score: 183
Period size: 38 Copynumber: 3.2 Consensus size: 38
40529499 CAACACTAGT
* * * *
40529509 AGTAGACATGTATAACAAGTACTCAATTCAGCACTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
* *
40529547 AGTAGAAATGTTTAACA-GTACTCAATTTATCATTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
40529584 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
40529622 AGTAGACAT
1 AGTAGACAT
40529631 ACTTATCATG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
37 33 0.43
38 43 0.57
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (38 bp):
AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
Found at i:40531059 original size:20 final size:21
Alignment explanation
Indices: 40531005--40531059 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
40530995 TTTGCCTAAG
* * *
40531005 ATGTGAATTGGATTGAATTGA
1 ATGTAAATTGTATTAAATTGA
40531026 ATGTAAATTGTATTAAATTG-
1 ATGTAAATTGTATTAAATTGA
40531046 ATGTTAAATT-TATT
1 ATG-TAAATTGTATT
40531060 CGTATAGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (21 bp):
ATGTAAATTGTATTAAATTGA
Found at i:40531400 original size:24 final size:25
Alignment explanation
Indices: 40531362--40531414 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
40531352 CAACTCGAAA
* * *
40531362 GAGCATTCCGTTA-TTAGCTTTCAT
1 GAGCATCCCGATATTTAGCTCTCAT
*
40531386 GAGCATCCCGATATTTGGCTCTCAT
1 GAGCATCCCGATATTTAGCTCTCAT
40531411 GAGC
1 GAGC
40531415 TTCCTGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCATCCCGATATTTAGCTCTCAT
Found at i:40531575 original size:27 final size:25
Alignment explanation
Indices: 40531541--40531602 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
40531531 TGGCTCTTTG
*
40531541 GAGCTTCCCAATTAAAGGCTCTTTCA
1 GAGCTTCCCAATTAAAGGCTC-TCCA
** *
40531567 TGAGCTTCCTGATTAATGGCTCTCCA
1 -GAGCTTCCCAATTAAAGGCTCTCCA
40531593 GAGCTTCCCA
1 GAGCTTCCCA
40531603 GTATTGGCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 8 0.28
26 3 0.10
27 18 0.62
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCAATTAAAGGCTCTCCA
Found at i:40531693 original size:25 final size:25
Alignment explanation
Indices: 40531664--40531726 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
40531654 ATGGCTTTCT
*
40531664 AGAGCTTCCCGTTGCATGGCTC-ACA
1 AGAGCTTCCCGTTACATGGCTCGA-A
* *
40531689 TGAGCTTCCCGTTATATGGCTCGAA
1 AGAGCTTCCCGTTACATGGCTCGAA
40531714 AGAGCTTCCCGTT
1 AGAGCTTCCCGTT
40531727 TATGTACTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (25 bp):
AGAGCTTCCCGTTACATGGCTCGAA
Found at i:40531736 original size:25 final size:25
Alignment explanation
Indices: 40531664--40531743 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
40531654 ATGGCTTTCT
** *
40531664 AGAGCTTCCCGTTGCATGGCTC-ACA
1 AGAGCTTCCCGTTATATGACTCGA-A
* *
40531689 TGAGCTTCCCGTTATATGGCTCGAA
1 AGAGCTTCCCGTTATATGACTCGAA
*
40531714 AGAGCTTCCCGTT-TATGTACTCGTA
1 AGAGCTTCCCGTTATATG-ACTCGAA
40531739 AGAGC
1 AGAGC
40531744 ATTATTGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.09
25 42 0.89
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (25 bp):
AGAGCTTCCCGTTATATGACTCGAA
Found at i:40534620 original size:23 final size:23
Alignment explanation
Indices: 40534593--40534640 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
40534583 TCAAAATTCT
40534593 TTAAAAATAA-AAAAAAATATAAA
1 TTAAAAA-AACAAAAAAATATAAA
*
40534616 TTAAAAAAACTAAAAAATTATAAA
1 TTAAAAAAAC-AAAAAAATATAAA
40534640 T
1 T
40534641 ATATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 7 0.32
24 13 0.59
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (23 bp):
TTAAAAAAACAAAAAAATATAAA
Found at i:40535730 original size:22 final size:21
Alignment explanation
Indices: 40535704--40535745 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40535694 AAATTTTATG
40535704 ATTTTTAAAGTTTTTTTAATAT
1 ATTTTTAAAG-TTTTTTAATAT
**
40535726 ATTTTTTTAGTTTTTTAATA
1 ATTTTTAAAGTTTTTTAATA
40535746 CCTCACATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTTAAAGTTTTTTAATAT
Found at i:40541561 original size:32 final size:32
Alignment explanation
Indices: 40541509--40541647 Score: 230
Period size: 32 Copynumber: 4.4 Consensus size: 32
40541499 AAAATACCAA
40541509 ATATAAAAAA-T--ATCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
40541538 ATATAAAAAAGTAGATCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
* *
40541570 ATATAAAAAAGTTGATCATACATTAGTTTTGC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
*
40541602 ATATAAAAAAGTAGAGCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
40541634 ATATAAAAAAGTAG
1 ATATAAAAAAGTAG
40541648 TATAGTTATA
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
29 10 0.10
30 1 0.01
32 91 0.89
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (32 bp):
ATATAAAAAAGTAGATCATACATTAGTTTTAC
Found at i:40545092 original size:5 final size:5
Alignment explanation
Indices: 40545082--40545138 Score: 96
Period size: 5 Copynumber: 11.4 Consensus size: 5
40545072 AGCTACAATC
* *
40545082 ATTAG ATTAG ATTAG ATTAG ACTAG ATTAG ATTAG ATTAG AATAG ATTAG
1 ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG
40545132 ATTAG AT
1 ATTAG AT
40545139 GTTTATCTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (5 bp):
ATTAG
Found at i:40549770 original size:21 final size:21
Alignment explanation
Indices: 40549745--40549785 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40549735 AATATATTTG
* *
40549745 ACATATAATTTTTATTTTTAA
1 ACATATAATGTTTAATTTTAA
40549766 ACATATAATGTTTAATTTTA
1 ACATATAATGTTTAATTTTA
40549786 GATAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (21 bp):
ACATATAATGTTTAATTTTAA
Found at i:40554452 original size:8 final size:9
Alignment explanation
Indices: 40554431--40554455 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40554421 GTTGATGGTA
40554431 AAAAATTTT
1 AAAAATTTT
40554440 AAAAATTTT
1 AAAAATTTT
40554449 AAAAATT
1 AAAAATT
40554456 AATTGACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAAATTTT
Found at i:40554723 original size:15 final size:15
Alignment explanation
Indices: 40554660--40554709 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
40554650 TAACATTGAA
* *
40554660 TTTTAGAATTATTTT
1 TTTTAAAATTATATT
*
40554675 TTTTAAAATTTTATT
1 TTTTAAAATTATATT
40554690 TTTTAAAATTATATT
1 TTTTAAAATTATATT
40554705 TTTTA
1 TTTTA
40554710 TTTTTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTAAAATTATATT
Found at i:40555339 original size:17 final size:18
Alignment explanation
Indices: 40555309--40555342 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40555299 TCAAAAATGG
*
40555309 TAAAAATTATTAAAAATA
1 TAAAAATTAATAAAAATA
40555327 TAAAAA-TAATAAAAAT
1 TAAAAATTAATAAAAAT
40555343 GAACCCCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATTAATAAAAATA
Found at i:40566764 original size:14 final size:14
Alignment explanation
Indices: 40566745--40566774 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40566735 AAGATATTCT
40566745 TTTTCTAAATAAAG
1 TTTTCTAAATAAAG
*
40566759 TTTTCTAAATGAAG
1 TTTTCTAAATAAAG
40566773 TT
1 TT
40566775 GAACCAGAAT
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:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAG
Found at i:40566813 original size:14 final size:16
Alignment explanation
Indices: 40566794--40566830 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
40566784 TCGATATCCT
40566794 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
40566808 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
40566824 TTT-CATC
1 TTTGCATC
40566831 ACATCGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Found at i:40566830 original size:15 final size:15
Alignment explanation
Indices: 40566794--40566843 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
40566784 TCGATATCCT
40566794 TTTGCAT-TCATGCA
1 TTTGCATCTCATGCA
40566808 TTTGCATCTCATAGCA
1 TTTGCATCTCAT-GCA
* *
40566824 TTT-CATCACAT-CG
1 TTTGCATCTCATGCA
40566837 TTTGCAT
1 TTTGCAT
40566844 TCAAAGTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 10 0.32
15 11 0.35
16 6 0.19
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (15 bp):
TTTGCATCTCATGCA
Found at i:40572112 original size:26 final size:26
Alignment explanation
Indices: 40572083--40572190 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
40572073 TGGTACAAAT
*
40572083 TGATAATGGGTAAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
40572109 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
40572135 CGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
40572161 TGACAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40572187 TGAT
1 TGAT
40572191 GGGCATTTCA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40578395 original size:204 final size:204
Alignment explanation
Indices: 40578029--40578477 Score: 702
Period size: 204 Copynumber: 2.2 Consensus size: 204
40578019 TGATTTGGCT
*
40578029 TGATTTGATATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGACAGAGAG
1 TGATTTGGTATCTC--TATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGACAGAGAG
*
40578094 CAGATACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAAGATCCAAGATAATTTGGCAT
64 CAGATACATAGCAGATCTCACCTTCAGATAATTTCACTGAAGCAAGATCCAAGATAATTTGGCAT
* * *
40578159 CTTTGTGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAG
129 CCTTGTGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTAAAG
40578224 CAAATCTAAGA
194 CAAATCTAAGA
*
40578235 TGATTTGGTATCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGA-TGAAGAGC
1 TGATTTGGTATCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGACAG-AGAGC
** *
40578299 AGATACATAGCAGATCTCACCTTCAGATAATTTCACTGAAGCAAGATCCAAGATGGTTTGGTATC
65 AGATACATAGCAGATCTCACCTTCAGATAATTTCACTGAAGCAAGATCCAAGATAATTTGGCATC
* * **
40578364 CTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGTTTTTGCGTGCTTACGCTAAAGC
130 CTTGTGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTAAAGC
40578429 AAATCTAAGA
195 AAATCTAAGA
* * *
40578439 TGATTTGGCATCTTTGTATTGTTAGAGAACAAATCGAAG
1 TGATTTGGTATC--TCTATTGTCAGAGAACAAATCGAAG
40578478 AAGCAGATTT
Statistics
Matches: 224, Mismatches: 16, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
203 1 0.00
204 187 0.83
206 36 0.16
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (204 bp):
TGATTTGGTATCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGACAGAGAGCA
GATACATAGCAGATCTCACCTTCAGATAATTTCACTGAAGCAAGATCCAAGATAATTTGGCATCC
TTGTGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTAAAGCA
AATCTAAGA
Found at i:40580157 original size:20 final size:19
Alignment explanation
Indices: 40580112--40580162 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
40580102 TTTAATATGA
*
40580112 ATATATGTAC-TATATTTT
1 ATATATTTACTTATATTTT
40580130 ATATTATTTACTTATATTTT
1 ATA-TATTTACTTATATTTT
40580150 AT-TATATTACTTA
1 ATATAT-TTACTTA
40580163 ATATCTTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 13 0.45
20 10 0.34
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (19 bp):
ATATATTTACTTATATTTT
Found at i:40580299 original size:16 final size:15
Alignment explanation
Indices: 40580280--40580348 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 15
40580270 ATTAACCATA
40580280 TATTATTTCATATTAT
1 TATTATTT-ATATTAT
40580296 TATTA-TT-TATTAT
1 TATTATTTATATTAT
*
40580309 ATATT-TTTAAATTAT
1 -TATTATTTATATTAT
*
40580324 TATTATTT-TA-CAT
1 TATTATTTATATTAT
40580337 TATTATTTATAT
1 TATTATTTATAT
40580349 ATTTTTACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
13 16 0.36
14 13 0.30
15 10 0.23
16 5 0.11
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTATTTATATTAT
Found at i:40580323 original size:38 final size:38
Alignment explanation
Indices: 40580281--40580389 Score: 91
Period size: 38 Copynumber: 2.9 Consensus size: 38
40580271 TTAACCATAT
*
40580281 ATTATT-TCATATTATTATTATT-TATTATATATTTTTAA
1 ATTATTATCATATTA-CATTATTAT-TTATATATTTTTAA
* * *
40580319 ATTATTATTATTTTACATTATTATTTATATATTTTTAC
1 ATTATTATCATATTACATTATTATTTATATATTTTTAA
* * *
40580357 TTGTATTAT-ATCTT-TATTAATTATTTATATATT
1 AT-TATTATCATATTACATT-ATTATTTATATATT
40580390 ATACATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
37 3 0.05
38 44 0.73
39 13 0.22
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (38 bp):
ATTATTATCATATTACATTATTATTTATATATTTTTAA
Found at i:40580341 original size:57 final size:59
Alignment explanation
Indices: 40580280--40580395 Score: 143
Period size: 57 Copynumber: 2.0 Consensus size: 59
40580270 ATTAACCATA
*
40580280 TATTATTTCATATTATTATTA-TT-TATTATATATTT-TTAAATTA-TTAT-TATTTTACAT
1 TATTATTT-ATA-TATTATTACTTGTATTATATATTTATT-AATTATTTATATATTATACAT
* *
40580337 TATTATTTATATATTTTTACTTGTATTATATCTTTATTAATTATTTATATATTATACAT
1 TATTATTTATATATTATTACTTGTATTATATATTTATTAATTATTTATATATTATACAT
40580396 ATATACTTNN
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
55 7 0.14
56 5 0.10
57 24 0.47
58 6 0.12
59 9 0.18
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (59 bp):
TATTATTTATATATTATTACTTGTATTATATATTTATTAATTATTTATATATTATACAT
Found at i:40580367 original size:19 final size:18
Alignment explanation
Indices: 40580300--40580389 Score: 69
Period size: 19 Copynumber: 4.8 Consensus size: 18
40580290 TATTATTATT
40580300 ATTTATTATATATTTTTA
1 ATTTATTATATATTTTTA
*
40580318 AATTATTAT-TA-TTTTA
1 ATTTATTATATATTTTTA
40580334 CATTATTATTTATATATTTTTA
1 -A-T-TTA-TTATATATTTTTA
* *
40580356 CTTGTATTATATCTTTATTA
1 ATT-TATTATATATTT-TTA
40580376 A-TTATTTATATATT
1 ATTTA-TTATATATT
40580390 ATACATATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
16 5 0.09
17 3 0.05
18 10 0.18
19 22 0.39
20 10 0.18
21 2 0.04
22 5 0.09
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
ATTTATTATATATTTTTA
Found at i:40581753 original size:18 final size:20
Alignment explanation
Indices: 40581718--40581771 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
40581708 ATTTTCTATT
*
40581718 TTTTAATATATATTTTTTAAAA
1 TTTTAATAT-T-TTTTTGAAAA
*
40581740 TTTTAA-ATTTTTTTGTAAA
1 TTTTAATATTTTTTTGAAAA
40581759 TTTTAATATTTTT
1 TTTTAATATTTTT
40581772 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 14 0.48
20 7 0.24
21 2 0.07
22 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTAATATTTTTTTGAAAA
Found at i:40584284 original size:60 final size:59
Alignment explanation
Indices: 40584207--40584346 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 59
40584197 TTTAGTGTTA
40584207 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCT-TAC-AGTAAC-AGAGTAT
1 ACTGGGCC-TAGCCCATATCAATATTAATCTGGGCCATAG-CCCTATACAAGT--CGAGA-TAT
* *
40584268 ACTGGGCCTAGCCCATATCAATATTAATCTGGGTCGTAGCCCTATACAAGTCGAGATAT
1 ACTGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCTATACAAGTCGAGATAT
* *
40584327 ATTGGGCCTTGCCCATATCA
1 ACTGGGCCTAGCCCATATCA
40584347 GCACAGTTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
59 26 0.36
60 35 0.49
61 11 0.15
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (59 bp):
ACTGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCTATACAAGTCGAGATAT
Found at i:40586824 original size:20 final size:20
Alignment explanation
Indices: 40586792--40586830 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40586782 TTTCAACTAC
*
40586792 AATAATATATATATTTTCCT
1 AATAATATATATAATTTCCT
40586812 AATAATA-ATTATAATTTCC
1 AATAATATA-TATAATTTCC
40586831 ATAAATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATATATATAATTTCCT
Found at i:40586841 original size:23 final size:24
Alignment explanation
Indices: 40586791--40586842 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
40586781 ATTTCAACTA
40586791 CAATAATATATATATTTTCCTAAT
1 CAATAATATATATATTTTCCTAAT
40586815 -AATAAT-TATA-A-TTTCCATAAAT
1 CAATAATATATATATTTTCC-T-AAT
40586837 CAATAA
1 CAATAA
40586843 AAATAGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 5 0.20
21 2 0.08
22 7 0.28
23 11 0.44
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (24 bp):
CAATAATATATATATTTTCCTAAT
Found at i:40588560 original size:13 final size:13
Alignment explanation
Indices: 40588542--40588585 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
40588532 TCCATGTCAT
40588542 CACCATCCACCGC
1 CACCATCCACCGC
*
40588555 CACCATCCACCAC
1 CACCATCCACCGC
**
40588568 CGTC-TCCACCGC
1 CACCATCCACCGC
40588580 CACCAT
1 CACCAT
40588586 AACAAACAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.23, C:0.59, G:0.07, T:0.11
Consensus pattern (13 bp):
CACCATCCACCGC
Found at i:40590573 original size:19 final size:19
Alignment explanation
Indices: 40590545--40590587 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
40590535 TTGTTTGAAA
40590545 AAAT-ATTTGCTTGTACAT
1 AAATAATTTGCTTGTACAT
40590563 AAATAATTTGCTTGTACAT
1 AAATAATTTGCTTGTACAT
40590582 AAATAA
1 AAATAA
40590588 ATAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (19 bp):
AAATAATTTGCTTGTACAT
Found at i:40590587 original size:4 final size:4
Alignment explanation
Indices: 40590580--40590613 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
40590570 TTGCTTGTAC
*
40590580 ATAA ATAA ATAA ATAAA ATGA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA A
40590614 GGCTCAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:40592093 original size:125 final size:125
Alignment explanation
Indices: 40591871--40592116 Score: 429
Period size: 125 Copynumber: 2.0 Consensus size: 125
40591861 ACTCATGGGT
*
40591871 TTTTAAACATGAATCCTAACTCAAAATAATGGTAGAAATAGGTAAATTGAGTTACGGGGACTTCA
1 TTTTAAACATGAATCCTAACTCAAAATAATGGTAGAAATAGGTAAATCGAGTTACGGGGACTTCA
* * *
40591936 AAAATGAAAAGAACATTAAAAACGTGGCTAGGATGCATTTACTATGGAGCTTGGAAAAAA
66 AAAATGAAAAGAACATTAAAAACGGGGCTAGGATGCACTTACTATAGAGCTTGGAAAAAA
*
40591996 TTTTAAACATGAATCCTAGCTCAAAATAATGGTAGAAATAGGTAAATCGAGTTACGGGGACTTCA
1 TTTTAAACATGAATCCTAACTCAAAATAATGGTAGAAATAGGTAAATCGAGTTACGGGGACTTCA
* *
40592061 AAAATGTAAAGAACATTAAAAACGGGGCTAGGATGTACTTACTATAGAGCTTGGAA
66 AAAATGAAAAGAACATTAAAAACGGGGCTAGGATGCACTTACTATAGAGCTTGGAA
40592117 GCTTGACCCA
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 114 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.26
Consensus pattern (125 bp):
TTTTAAACATGAATCCTAACTCAAAATAATGGTAGAAATAGGTAAATCGAGTTACGGGGACTTCA
AAAATGAAAAGAACATTAAAAACGGGGCTAGGATGCACTTACTATAGAGCTTGGAAAAAA
Found at i:40594335 original size:13 final size:13
Alignment explanation
Indices: 40594317--40594341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40594307 GAAGCACGAT
40594317 TCACATGGGCGTG
1 TCACATGGGCGTG
40594330 TCACATGGGCGT
1 TCACATGGGCGT
40594342 ATCCCTGCCG
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (13 bp):
TCACATGGGCGTG
Found at i:40598533 original size:19 final size:20
Alignment explanation
Indices: 40598490--40598535 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40598480 ATTGGGCCTT
40598490 GCCCATATCAACACAGTTGG
1 GCCCATATCAACACAGTTGG
* *
40598510 GCCCATTTCAATACAGTT-G
1 GCCCATATCAACACAGTTGG
40598529 GCCCATA
1 GCCCATA
40598536 ACAAATCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
GCCCATATCAACACAGTTGG
Found at i:40600998 original size:3 final size:3
Alignment explanation
Indices: 40600930--40600978 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
40600920 ATTCAATACC
40600930 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
40600978 A
1 A
40600979 CAACAACAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40601693 original size:22 final size:21
Alignment explanation
Indices: 40601668--40601708 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
40601658 TCCCCTGTTC
*
40601668 TTCTCTGTTTCGTTTTCTTTGT
1 TTCTCTGTTTC-ATTTCTTTGT
*
40601690 TTCTCTTTTTCATTTCTTT
1 TTCTCTGTTTCATTTCTTT
40601709 TATTTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.71
Consensus pattern (21 bp):
TTCTCTGTTTCATTTCTTTGT
Found at i:40601805 original size:22 final size:23
Alignment explanation
Indices: 40601762--40601814 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
40601752 AACTATTATA
* *
40601762 ATATTTATTATTTATACATGTGT
1 ATATTTATTATATACACATGTGT
40601785 ATATTTATTA-ATACACATGTGT
1 ATATTTATTATATACACATGTGT
40601807 -TAATTTAT
1 AT-ATTTAT
40601815 CACCTCACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.59
23 10 0.37
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.53
Consensus pattern (23 bp):
ATATTTATTATATACACATGTGT
Found at i:40605830 original size:14 final size:14
Alignment explanation
Indices: 40605811--40605857 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
40605801 CCTGAACCTA
40605811 TTTTTAGGCA-AAAT
1 TTTTTAGG-AGAAAT
40605825 TTTTTAGGATGAAAT
1 TTTTTAGGA-GAAAT
40605840 TTTTTAGGATGAAAT
1 TTTTTAGGA-GAAAT
40605855 TTT
1 TTT
40605858 AATAGCCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.03
14 8 0.26
15 22 0.71
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (14 bp):
TTTTTAGGAGAAAT
Found at i:40605839 original size:15 final size:15
Alignment explanation
Indices: 40605821--40605857 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
40605811 TTTTTAGGCA
40605821 AAATTTTTTAGGATG
1 AAATTTTTTAGGATG
40605836 AAATTTTTTAGGATG
1 AAATTTTTTAGGATG
40605851 AAATTTT
1 AAATTTT
40605858 AATAGCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (15 bp):
AAATTTTTTAGGATG
Found at i:40616290 original size:16 final size:16
Alignment explanation
Indices: 40616269--40616313 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
40616259 AAGCGGGATG
40616269 AGAAAATTATTTAATT
1 AGAAAATTATTTAATT
*
40616285 AGAAAATTAATTAATT
1 AGAAAATTATTTAATT
40616301 --AAAATTAATTTAA
1 AGAAAATT-ATTTAA
40616314 CAAATAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 6 0.23
15 5 0.19
16 15 0.58
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (16 bp):
AGAAAATTATTTAATT
Found at i:40617520 original size:18 final size:18
Alignment explanation
Indices: 40617497--40617535 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
40617487 TTTGGCCTTC
40617497 TTTCCCTCGAGCAGAGGT
1 TTTCCCTCGAGCAGAGGT
40617515 TTTCCCTCGAGCAGAGGT
1 TTTCCCTCGAGCAGAGGT
40617533 TTT
1 TTT
40617536 TATGAGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (18 bp):
TTTCCCTCGAGCAGAGGT
Found at i:40619961 original size:22 final size:20
Alignment explanation
Indices: 40619920--40619961 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40619910 CTTGTACTTA
*
40619920 AGTACATTTTGTTGCATTTT
1 AGTACATTTTATTGCATTTT
40619940 AGTACATTTTAATTAGCATTTT
1 AGTACATTTT-ATT-GCATTTT
40619962 TAATATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (20 bp):
AGTACATTTTATTGCATTTT
Found at i:40623492 original size:22 final size:23
Alignment explanation
Indices: 40623467--40623512 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
40623457 CAACCAATCC
*
40623467 AATTCA-ACATATTTTTAAGATA
1 AATTCATACATATTTATAAGATA
*
40623489 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
40623512 A
1 A
40623513 CGTCATCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:40623518 original size:23 final size:23
Alignment explanation
Indices: 40623474--40623518 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40623464 TCCAATTCAA
* *
40623474 CATATTTTTAAGATAAATTCATG
1 CATATTTATAAGATAAAGTCATG
*
40623497 CATATTTATAAGATAACGTCAT
1 CATATTTATAAGATAAAGTCAT
40623519 CACATACCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (23 bp):
CATATTTATAAGATAAAGTCATG
Found at i:40628945 original size:46 final size:46
Alignment explanation
Indices: 40628878--40629052 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
40628868 TGTAACCCGC
*
40628878 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
40628924 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * * *
40628974 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
40629017 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
40629053 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 2 0.02
46 61 0.58
47 27 0.25
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:40628998 original size:93 final size:93
Alignment explanation
Indices: 40628885--40629056 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
40628875 CGCCCATAAG
* * *
40628885 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40628950 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
*
40628978 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40629043 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
40629057 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:40637517 original size:17 final size:17
Alignment explanation
Indices: 40637495--40637530 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
40637485 ATAACTGAGG
*
40637495 ATTAAACAGGCAAATGA
1 ATTAAACAGGCAAACGA
40637512 ATTAAACAGGCAAACGA
1 ATTAAACAGGCAAACGA
40637529 AT
1 AT
40637531 AATGGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.17
Consensus pattern (17 bp):
ATTAAACAGGCAAACGA
Found at i:40641785 original size:21 final size:20
Alignment explanation
Indices: 40641747--40641785 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40641737 TCATGCTCTC
* *
40641747 TTTTTTTTTTCTTTTTAAAT
1 TTTTTTTTTTCATGTTAAAT
40641767 TTTTTTATTTTCATGTTAA
1 TTTTTT-TTTTCATGTTAA
40641786 TGAAAGCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTTTTTTCATGTTAAAT
Found at i:40643138 original size:47 final size:47
Alignment explanation
Indices: 40643069--40643162 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
40643059 ATTTGCATTG
40643069 GGAAAGAGTTTCATTAAAAGTTGCTCAAGTGGAAGGACCTGAGATTT
1 GGAAAGAGTTTCATTAAAAGTTGCTCAAGTGGAAGGACCTGAGATTT
*
40643116 GGAAAGAGTTTCATTAAAAGTTGCTCAAGTGGAAGTACCTGAGATTT
1 GGAAAGAGTTTCATTAAAAGTTGCTCAAGTGGAAGGACCTGAGATTT
40643163 CGTTATGCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.29
Consensus pattern (47 bp):
GGAAAGAGTTTCATTAAAAGTTGCTCAAGTGGAAGGACCTGAGATTT
Found at i:40651335 original size:87 final size:87
Alignment explanation
Indices: 40651234--40651497 Score: 447
Period size: 87 Copynumber: 3.0 Consensus size: 87
40651224 GGCTATGGAC
40651234 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTCACTAAGTGTTTAA
1 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTCACTAAGTGTTTAA
40651299 ACTATGTTTCAATACTTGAGCA
66 ACTATGTTTCAATACTTGAGCA
40651321 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTCACTAAGTGTTTAA
1 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTCACTAAGTGTTTAA
40651386 ACTATGTTTCAATACTTGAGCA
66 ACTATGTTTCAATACTTGAGCA
* * * * * * *
40651408 CTCTTACTTTCCGTCAATGTTAGGTTCTGACTTAGCTTCAAAATTTTCTTTAACTAAATGCTTGA
1 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTCACTAAGTGTTTAA
* *
40651473 ACTATGTTTCAGTACTTGAGAA
66 ACTATGTTTCAATACTTGAGCA
40651495 CTC
1 CTC
40651498 CAAAAGATTA
Statistics
Matches: 168, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 168 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (87 bp):
CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTCACTAAGTGTTTAA
ACTATGTTTCAATACTTGAGCA
Found at i:40658556 original size:20 final size:20
Alignment explanation
Indices: 40658531--40658572 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
40658521 TTCGATCAAT
*
40658531 CCATCAAATAAGATCCCAAC
1 CCATCAAATAAGATCCAAAC
40658551 CCATCAAATAAGATCCAAAC
1 CCATCAAATAAGATCCAAAC
40658571 CC
1 CC
40658573 TAACAGCGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.36, G:0.05, T:0.14
Consensus pattern (20 bp):
CCATCAAATAAGATCCAAAC
Found at i:40659966 original size:9 final size:9
Alignment explanation
Indices: 40659956--40659988 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
40659946 CATGTGAATT
*
40659956 AATAAAATT
1 AATAAAATA
40659965 AATAAAATA
1 AATAAAATA
40659974 AAT-AAATA
1 AATAAAATA
40659982 AATAAAA
1 AATAAAA
40659989 ATTCATGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATAAAATA
Found at i:40662879 original size:21 final size:21
Alignment explanation
Indices: 40662854--40662896 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
40662844 ATCCATTTAA
*
40662854 TGGTTCAAGTTTTGCTATCAC
1 TGGTTCAAGTTTTGCAATCAC
40662875 TGGTTCAAGTTTTGCAATCAC
1 TGGTTCAAGTTTTGCAATCAC
40662896 T
1 T
40662897 ACTTCGCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (21 bp):
TGGTTCAAGTTTTGCAATCAC
Found at i:40667646 original size:8 final size:9
Alignment explanation
Indices: 40667623--40667649 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40667613 TTAATATAAT
40667623 TTAAAAATA
1 TTAAAAATA
40667632 TTAAAAATA
1 TTAAAAATA
40667641 TTAAAAATA
1 TTAAAAATA
40667650 ACAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAATA
Found at i:40668253 original size:31 final size:33
Alignment explanation
Indices: 40668186--40668259 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 33
40668176 TATAGTTATC
* ** *
40668186 TTAAATTTAAATAATACATATTTTATGATAATTT
1 TTAAATTT-AATAATACATATTTAAAAATAAATT
40668220 TTAAATTTAATAA-A-ATATTTAAAAATAAATT
1 TTAAATTTAATAATACATATTTAAAAATAAATT
40668251 TTAAATTTA
1 TTAAATTTA
40668260 GTTATAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 22 0.61
32 1 0.03
33 5 0.14
34 8 0.22
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (33 bp):
TTAAATTTAATAATACATATTTAAAAATAAATT
Found at i:40668365 original size:26 final size:26
Alignment explanation
Indices: 40668315--40668366 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40668305 AATATTAAGA
*
40668315 TAAACAATATTTATCTTAATAATAAT
1 TAAACAATATTTATATTAATAATAAT
* * *
40668341 TAAATAATATTTATATTTATGATAAT
1 TAAACAATATTTATATTAATAATAAT
40668367 ATTTTTTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (26 bp):
TAAACAATATTTATATTAATAATAAT
Found at i:40668367 original size:18 final size:18
Alignment explanation
Indices: 40668344--40668397 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
40668334 TAATAATTAA
40668344 ATAATATTTATATTTATG
1 ATAATATTTATATTTATG
*
40668362 ATAATATTTTTTATCTATATG
1 ATAATA-TTTATAT-T-TATG
40668383 ATAAT-TTATATATTT
1 ATAATATT-TATATTT
40668398 TATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 7 0.23
19 9 0.30
20 5 0.17
21 9 0.30
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
ATAATATTTATATTTATG
Found at i:40668691 original size:22 final size:23
Alignment explanation
Indices: 40668633--40668697 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 23
40668623 TTTATATTAG
*
40668633 ATATGTATAAAATAATAAAATATT
1 ATATATATAAAATAATAAAATA-T
* * *
40668657 ATTGTTTAAAAAATAATAAAATA-
1 A-TATATATAAAATAATAAAATAT
40668680 ATATATATAAAATAATAA
1 ATATATATAAAATAATAA
40668698 GTAAGTTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 14 0.41
23 1 0.03
24 1 0.03
25 18 0.53
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (23 bp):
ATATATATAAAATAATAAAATAT
Found at i:40668696 original size:25 final size:25
Alignment explanation
Indices: 40668641--40668697 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
40668631 AGATATGTAT
* * *
40668641 AAAATAATAAAATATTATTGTTTAA
1 AAAATAATAAAATAATATTATATAA
40668666 AAAATAATAAAATAATA-TATATAA
1 AAAATAATAAAATAATATTATATAA
40668690 AATAATAA
1 AA-AATAA
40668698 GTAAGTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAATAATAAAATAATATTATATAA
Found at i:40668842 original size:7 final size:7
Alignment explanation
Indices: 40668812--40668868 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
40668802 CCCCTAATAT
40668812 TATATAA
1 TATATAA
* *
40668819 AAAATAA
1 TATATAA
*
40668826 TATTAAAA
1 TA-TATAA
40668834 TATATAA
1 TATATAA
40668841 TATATAA
1 TATATAA
*
40668848 TCTATAA
1 TATATAA
*
40668855 TCTATATA
1 TATATA-A
40668863 TATATA
1 TATATA
40668869 TGTATAAGCA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
7 29 0.73
8 11 0.28
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (7 bp):
TATATAA
Found at i:40669386 original size:27 final size:25
Alignment explanation
Indices: 40669335--40669394 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
40669325 ATAATAAAAT
40669335 AAAAGAAAAAGAAATAGGAAAGAAA
1 AAAAGAAAAAGAAATAGGAAAGAAA
* *
40669360 GAAAGAACAAACGAAATA-GAAGGGAAA
1 AAAAGAA-AAA-GAAATAGGAA-AGAAA
40669387 AAAAGAAA
1 AAAAGAAA
40669395 GAAAAGGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.21
26 7 0.24
27 16 0.55
ACGTcount: A:0.72, C:0.03, G:0.22, T:0.03
Consensus pattern (25 bp):
AAAAGAAAAAGAAATAGGAAAGAAA
Found at i:40670095 original size:24 final size:24
Alignment explanation
Indices: 40670068--40670114 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40670058 ATTGAAATGG
40670068 ATTG-ATTTACTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
40670092 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
40670115 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:40675563 original size:38 final size:37
Alignment explanation
Indices: 40675438--40675566 Score: 132
Period size: 38 Copynumber: 3.4 Consensus size: 37
40675428 ATTTGGCACT
**
40675438 CAGTGCCTCATCGAATAATTTGAAGTAATAATTTGACACC
1 CAGTGCCTCATCGAATAATCCGAAGT-A-AA-TTGACACC
* ** * * *
40675478 CAGTGTCTCATCGGCTAAACCAAAGTAAATTGGCACC
1 CAGTGCCTCATCGAATAATCCGAAGTAAATTGACACC
40675515 CAGTGCCTCATCGAATTAATCCGAAGTAAATTGACACC
1 CAGTGCCTCATCGAA-TAATCCGAAGTAAATTGACACC
* *
40675553 TAGTGTCTCATCGA
1 CAGTGCCTCATCGA
40675567 CTCGAAGTAG
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
37 19 0.26
38 33 0.46
39 1 0.01
40 19 0.26
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (37 bp):
CAGTGCCTCATCGAATAATCCGAAGTAAATTGACACC
Found at i:40676908 original size:12 final size:12
Alignment explanation
Indices: 40676891--40676923 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40676881 ATTTCGAAAG
*
40676891 GGCACATGGTTT
1 GGCACACGGTTT
40676903 GGCACACGGTTT
1 GGCACACGGTTT
40676915 GGCACACGG
1 GGCACACGG
40676924 GCGTGTGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.21
Consensus pattern (12 bp):
GGCACACGGTTT
Found at i:40677381 original size:20 final size:20
Alignment explanation
Indices: 40677358--40677426 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
40677348 AAAAATAATT
40677358 ATAATTTAATAGAAATTATG
1 ATAATTTAATAGAAATTATG
* * *
40677378 ATAATTATACATTAAAAATAATT
1 ATAATT-TA-A-TAGAAATTATG
* *
40677401 ATAGTTTAATAGAAATTGTG
1 ATAATTTAATAGAAATTATG
40677421 ATAATT
1 ATAATT
40677427 ACACATTTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 18 0.49
21 3 0.08
22 3 0.08
23 13 0.35
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (20 bp):
ATAATTTAATAGAAATTATG
Found at i:40677409 original size:43 final size:44
Alignment explanation
Indices: 40677321--40677452 Score: 198
Period size: 43 Copynumber: 3.0 Consensus size: 44
40677311 ATTAAAATAA
*
40677321 AATAGAAGTTGTGATAATTATACATTTAAAAATAATTATAATTT
1 AATAGAAATTGTGATAATTATACATTTAAAAATAATTATAATTT
* *
40677365 AATAGAAATTATGATAATTATACA-TTAAAAATAATTATAGTTT
1 AATAGAAATTGTGATAATTATACATTTAAAAATAATTATAATTT
*
40677408 AATAGAAATTGTGATAATTACACATTTAAAAA-AATTCA-AATTT
1 AATAGAAATTGTGATAATTATACATTTAAAAATAATT-ATAATTT
40677451 AA
1 AA
40677453 ATTACAATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
43 50 0.62
44 30 0.38
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (44 bp):
AATAGAAATTGTGATAATTATACATTTAAAAATAATTATAATTT
Found at i:40677563 original size:12 final size:12
Alignment explanation
Indices: 40677546--40677571 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40677536 AAAAGTTGTG
40677546 ATAAATATAATT
1 ATAAATATAATT
40677558 ATAAATATAATT
1 ATAAATATAATT
40677570 AT
1 AT
40677572 TAGTTTAAAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAAATATAATT
Found at i:40677691 original size:11 final size:11
Alignment explanation
Indices: 40677654--40677691 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
40677644 AAGTATCTTG
40677654 ATTATCACTTA
1 ATTATCACTTA
40677665 ATTAT-ACTTATA
1 ATTATCAC-T-TA
40677677 ATTATCACTTA
1 ATTATCACTTA
40677688 ATTA
1 ATTA
40677692 AACGACTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.08
11 12 0.50
12 8 0.33
13 2 0.08
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTATCACTTA
Found at i:40679016 original size:10 final size:10
Alignment explanation
Indices: 40679001--40679035 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
40678991 ATTAGGGGAA
40679001 AAAGTAAAAC
1 AAAGTAAAAC
40679011 AAAGTAAAAC
1 AAAGTAAAAC
40679021 AAAGTAAAAC
1 AAAGTAAAAC
40679031 AAAGT
1 AAAGT
40679036 GAACATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAGTAAAAC
Found at i:40679696 original size:25 final size:25
Alignment explanation
Indices: 40679668--40679719 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
40679658 TTTGGCTTGG
*
40679668 CATTTACTAAG-CAATATCAGATATT
1 CATTTA-TAAGACAATATCAAATATT
*
40679693 CATTTATTAGACAATATCAAATATT
1 CATTTATAAGACAATATCAAATATT
40679718 CA
1 CA
40679720 AATTATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (25 bp):
CATTTATAAGACAATATCAAATATT
Found at i:40696088 original size:25 final size:26
Alignment explanation
Indices: 40696060--40696115 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
40696050 AATTATGAGT
40696060 GATATC-TTGACGAGAAAAGTATGTA
1 GATATCTTTGACGAGAAAAGTATGTA
*
40696085 GATATCTTTGATGAGAAAAGTATGTA
1 GATATCTTTGACGAGAAAAGTATGTA
*
40696111 CATAT
1 GATAT
40696116 TTATAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (26 bp):
GATATCTTTGACGAGAAAAGTATGTA
Found at i:40711285 original size:15 final size:15
Alignment explanation
Indices: 40711265--40711294 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40711255 ATACACTAAG
40711265 GAACAACTAGAGCAT
1 GAACAACTAGAGCAT
40711280 GAACAACTAGAGCAT
1 GAACAACTAGAGCAT
40711295 CTACACAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (15 bp):
GAACAACTAGAGCAT
Found at i:40713578 original size:40 final size:40
Alignment explanation
Indices: 40713494--40713655 Score: 218
Period size: 40 Copynumber: 4.0 Consensus size: 40
40713484 CGGATGATAA
* * *
40713494 CCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * *
40713534 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
40713574 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
40713614 CCGGGCTAAGACCCGAGGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
40713654 CC
1 CC
40713656 AGCTAAATCC
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 2 0.02
40 101 0.96
41 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:40715768 original size:25 final size:26
Alignment explanation
Indices: 40715716--40715768 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
40715706 TAGGGTTAGG
*
40715716 TTTTCTTTTCATTTTTAGAGTAGGTT
1 TTTTCTTTTCATTTTTAGAGTAGATT
40715742 TTTTCTTTTC-TTTTTAG-GTTAGATT
1 TTTTCTTTTCATTTTTAGAG-TAGATT
40715767 TT
1 TT
40715769 AATTTTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 1 0.04
25 14 0.56
26 10 0.40
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.66
Consensus pattern (26 bp):
TTTTCTTTTCATTTTTAGAGTAGATT
Found at i:40725166 original size:11 final size:11
Alignment explanation
Indices: 40725152--40725203 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
40725142 ATTTGGTTGT
40725152 TGTTTTGGCAC
1 TGTTTTGGCAC
****
40725163 TGTTTCAATAC
1 TGTTTTGGCAC
* *
40725174 TATTTTGGTAC
1 TGTTTTGGCAC
40725185 TGTTTTGGCAC
1 TGTTTTGGCAC
40725196 TGTTTTGG
1 TGTTTTGG
40725204 GCTCTTCTTC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.50
Consensus pattern (11 bp):
TGTTTTGGCAC
Found at i:40729346 original size:65 final size:65
Alignment explanation
Indices: 40729245--40729373 Score: 186
Period size: 65 Copynumber: 2.0 Consensus size: 65
40729235 ACTTTTGAAA
* * * *
40729245 GAGTTTTTCCTCGATACATTAGAGTATTCATATCTAATTTCATCATGGTATCTGATTTTTTATCT
1 GAGTGTTTCCTCGATACATTAGAGTATTCATATCTAATTTCAGCATGGTAACAGATTTTTTATCT
* * * *
40729310 GAGTGTTTCCTCGATACATTATAGTATTTATCTCTAATTTCAGCATGGTAACAGTTTTTTTATC
1 GAGTGTTTCCTCGATACATTAGAGTATTCATATCTAATTTCAGCATGGTAACAGATTTTTTATC
40729374 CTGTTTTGGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.47
Consensus pattern (65 bp):
GAGTGTTTCCTCGATACATTAGAGTATTCATATCTAATTTCAGCATGGTAACAGATTTTTTATCT
Found at i:40733524 original size:16 final size:16
Alignment explanation
Indices: 40733503--40733534 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40733493 GCTGTAAAAG
40733503 GTATTGGAAGAGCTAA
1 GTATTGGAAGAGCTAA
40733519 GTATTGGAAGAGCTAA
1 GTATTGGAAGAGCTAA
40733535 AGTTGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25
Consensus pattern (16 bp):
GTATTGGAAGAGCTAA
Found at i:40741343 original size:18 final size:19
Alignment explanation
Indices: 40741303--40741343 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
40741293 CAATCTCCTT
40741303 TTGAACAGTAGTCTCTCCC
1 TTGAACAGTAGTCTCTCCC
40741322 -TGAACAGTAG-CTC-CCTC
1 TTGAACAGTAGTCTCTCC-C
40741339 TTGAA
1 TTGAA
40741344 TAATAGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 4 0.20
18 14 0.70
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (19 bp):
TTGAACAGTAGTCTCTCCC
Found at i:40747102 original size:31 final size:31
Alignment explanation
Indices: 40747064--40747126 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
40747054 TGTAAAGAAG
40747064 ACTGAATTTAAATCTTTTTATTTCATAGGAA
1 ACTGAATTTAAATCTTTTTATTTCATAGGAA
40747095 ACTGAATTTAAATCTTTTTATTTCATAGGAA
1 ACTGAATTTAAATCTTTTTATTTCATAGGAA
40747126 A
1 A
40747127 ATTAAAATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (31 bp):
ACTGAATTTAAATCTTTTTATTTCATAGGAA
Found at i:40754105 original size:16 final size:16
Alignment explanation
Indices: 40754079--40754127 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
40754069 ACTTAAGTAT
*
40754079 ATAATAAAATAATATA
1 ATAATATAATAATATA
* * *
40754095 TTAATTTAATAATTTA
1 ATAATATAATAATATA
*
40754111 ATAATATAATAAAATA
1 ATAATATAATAATATA
40754127 A
1 A
40754128 ATAAAATAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATATAATAATATA
Found at i:40754199 original size:14 final size:15
Alignment explanation
Indices: 40754180--40754209 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
40754170 GAAATTGGGG
40754180 AGAAAAAG-AAAGAA
1 AGAAAAAGAAAAGAA
40754194 AGAAAAAGAAAAGAA
1 AGAAAAAGAAAAGAA
40754209 A
1 A
40754210 AAATTAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAAGAA
Found at i:40760762 original size:44 final size:43
Alignment explanation
Indices: 40760629--40760766 Score: 129
Period size: 42 Copynumber: 3.2 Consensus size: 43
40760619 TCCTAGACGT
* * * *
40760629 GGTCTTACATGT-AATTCAGTATCGATGCCTCTATCCCAAACAG
1 GGTCTTACATGTAAATTCA-AATCGATGCCTATGTCCCAAACAC
* * * *
40760672 GGTCTTACACG-AAATT-AGATACGATGCCTATGTCCCACACAT
1 GGTCTTACATGTAAATTCAAAT-CGATGCCTATGTCCCAAACAC
* * *
40760714 GGTCTTACATGTAAATCTCAAATCGAGGCCTGTGTCCCAGACAC
1 GGTCTTACATGTAAAT-TCAAATCGATGCCTATGTCCCAAACAC
40760758 GGTCTTACA
1 GGTCTTACA
40760767 CAATATCTCA
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.03
42 28 0.36
43 18 0.23
44 27 0.35
45 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (43 bp):
GGTCTTACATGTAAATTCAAATCGATGCCTATGTCCCAAACAC
Found at i:40763454 original size:35 final size:35
Alignment explanation
Indices: 40763410--40763603 Score: 270
Period size: 34 Copynumber: 5.6 Consensus size: 35
40763400 TCCTTATTGA
*
40763410 AATACCATACCTACATTTCACAACTCAGTATGGGA-
1 AATACCATACCTACGTTTCACAACTCAGTAT-GGAT
* **
40763445 AATGCCATACCTACG-TTCTTAACTCAGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* *
40763479 AATACCATACCTACGTTTCACAACTCGGTATGGTT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
40763514 AATACCATACCTAC-TTTCACAACTCAGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* *
40763548 GATA-CATACCTACGTTTCACAACTCGGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
*
40763582 GATACCATACCTACGTTTCACA
1 AATACCATACCTACGTTTCACA
40763604 CTTTGCCACG
Statistics
Matches: 142, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
33 12 0.08
34 71 0.50
35 59 0.42
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (35 bp):
AATACCATACCTACGTTTCACAACTCAGTATGGAT
Found at i:40763491 original size:69 final size:69
Alignment explanation
Indices: 40763410--40763603 Score: 266
Period size: 69 Copynumber: 2.8 Consensus size: 69
40763400 TCCTTATTGA
* * * **
40763410 AATACCATACCTACATTTCACAACTCAGTATGGGAAATGCCATACCTACGTTCTTAACTCAGTAT
1 AATACCATACCTACGTTTCACAACTCGGTATGGGAAATACCATACCTACGTTCACAACTCAGTAT
40763475 GGAT
66 GGAT
** *
40763479 AATACCATACCTACGTTTCACAACTCGGTATGGTTAATACCATACCTACTTTCACAACTCAGTAT
1 AATACCATACCTACGTTTCACAACTCGGTATGGGAAATACCATACCTACGTTCACAACTCAGTAT
40763544 GGAT
66 GGAT
* *
40763548 GATA-CATACCTACGTTTCACAACTCGGTAT-GGATGATACCATACCTACGTTTCACA
1 AATACCATACCTACGTTTCACAACTCGGTATGGGA-AATACCATACCTACG-TTCACA
40763604 CTTTGCCACG
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
67 1 0.01
68 39 0.35
69 70 0.64
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (69 bp):
AATACCATACCTACGTTTCACAACTCGGTATGGGAAATACCATACCTACGTTCACAACTCAGTAT
GGAT
Found at i:40763936 original size:2 final size:2
Alignment explanation
Indices: 40763929--40763958 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40763919 ACAAGTCATT
40763929 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
40763959 TATATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:40769823 original size:35 final size:34
Alignment explanation
Indices: 40769777--40770008 Score: 270
Period size: 35 Copynumber: 6.7 Consensus size: 34
40769767 TTTCCTTATT
* *
40769777 GAAATACCATACCTACATTTCACAACTCGGTATGG
1 GAAATACCATACCTACGTTTCACAACTCAGTAT-G
* **
40769812 GAAATGCCATACCTACG-TTCTTAACTCAGTATG
1 GAAATACCATACCTACGTTTCACAACTCAGTATG
40769845 GATAATACCATACCTACGTTTCACAACTCAGTATG
1 GA-AATACCATACCTACGTTTCACAACTCAGTATG
* *
40769880 GTTAATACCATACCTAC-TTTCACAACTCGGTATG
1 G-AAATACCATACCTACGTTTCACAACTCAGTATG
* *
40769914 GATGATACCATACTTACGTTTCACAACTCAGTATG
1 GA-AATACCATACCTACGTTTCACAACTCAGTATG
* * * *
40769949 GTTAATACCATACCTACATTTCACAGCTCGGTATG
1 G-AAATACCATACCTACGTTTCACAACTCAGTATG
*
40769984 GATGATACCATACCTACGTTTCACA
1 GA-AATACCATACCTACGTTTCACA
40770009 CTTTGCCACG
Statistics
Matches: 167, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
33 3 0.02
34 55 0.33
35 109 0.65
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30
Consensus pattern (34 bp):
GAAATACCATACCTACGTTTCACAACTCAGTATG
Found at i:40769959 original size:104 final size:104
Alignment explanation
Indices: 40769779--40770008 Score: 320
Period size: 104 Copynumber: 2.2 Consensus size: 104
40769769 TCCTTATTGA
* **
40769779 AATACCATACCTACATTTCACAACTCGGTATGGGAAATGCCATACCTACGTTCTTAACTCAGTAT
1 AATACCATACCTACATTTCACAACTCGGTATGGGAAATACCATACCTACGTTCACAACTCAGTAT
* *
40769844 GGATAATACCATACCTACGTTTCACAACTCAGTATGGTT
66 GGATAATACCATACCTACATTTCACAACTCAGTATGGAT
* *
40769883 AATACCATACCTAC-TTTCACAACTCGGTAT-GGATGATACCATACTTACGTTTCACAACTCAGT
1 AATACCATACCTACATTTCACAACTCGGTATGGGA-AATACCATACCTACG-TTCACAACTCAGT
* * *
40769946 ATGGTTAATACCATACCTACATTTCACAGCTCGGTATGGAT
64 ATGGATAATACCATACCTACATTTCACAACTCAGTATGGAT
* *
40769987 GATACCATACCTACGTTTCACA
1 AATACCATACCTACATTTCACA
40770009 CTTTGCCACG
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
102 3 0.03
103 28 0.25
104 74 0.66
105 7 0.06
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (104 bp):
AATACCATACCTACATTTCACAACTCGGTATGGGAAATACCATACCTACGTTCACAACTCAGTAT
GGATAATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:40770028 original size:69 final size:69
Alignment explanation
Indices: 40769780--40770008 Score: 341
Period size: 69 Copynumber: 3.3 Consensus size: 69
40769770 CCTTATTGAA
* * ** * * ** *
40769780 ATACCATACCTACATTTCACAACTCGGTATGGGAAATGCCATACCTACGTTCTTAACTCAGTATG
1 ATACCATACCTACGTTTCACAACTCAGTATGGTTAATACCATACCTACTTTCACAACTCGGTATG
*
40769845 GATA
66 GATG
40769849 ATACCATACCTACGTTTCACAACTCAGTATGGTTAATACCATACCTACTTTCACAACTCGGTATG
1 ATACCATACCTACGTTTCACAACTCAGTATGGTTAATACCATACCTACTTTCACAACTCGGTATG
40769914 GATG
66 GATG
* *
40769918 ATACCATACTTACGTTTCACAACTCAGTATGGTTAATACCATACCTACATTTCACAGCTCGGTAT
1 ATACCATACCTACGTTTCACAACTCAGTATGGTTAATACCATACCTAC-TTTCACAACTCGGTAT
40769983 GGATG
65 GGATG
40769988 ATACCATACCTACGTTTCACA
1 ATACCATACCTACGTTTCACA
40770009 CTTTGCCACG
Statistics
Matches: 146, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
69 106 0.73
70 40 0.27
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (69 bp):
ATACCATACCTACGTTTCACAACTCAGTATGGTTAATACCATACCTACTTTCACAACTCGGTATG
GATG
Found at i:40770341 original size:2 final size:2
Alignment explanation
Indices: 40770334--40770365 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40770324 ACAAGTCATT
40770334 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
40770366 TATATATATT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:40772243 original size:20 final size:20
Alignment explanation
Indices: 40772198--40772244 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40772188 GCCGGATTCT
* * *
40772198 CCTTGAAGACTGAAGATTTT
1 CCTTCAAGACTAAAGATTTC
*
40772218 CTTTCAAGACTAAAGATTTC
1 CCTTCAAGACTAAAGATTTC
40772238 CCTTCAA
1 CCTTCAA
40772245 TTTCCTTCAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
CCTTCAAGACTAAAGATTTC
Found at i:40777508 original size:33 final size:33
Alignment explanation
Indices: 40777471--40777538 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
40777461 ACTGAATTAT
40777471 ACAATGTTTAATTTTATTTGATTTGTGTTATAA
1 ACAATGTTTAATTTTATTTGATTTGTGTTATAA
40777504 ACAATGTTTAATTTTATTTGATTTGTGTTATAA
1 ACAATGTTTAATTTTATTTGATTTGTGTTATAA
40777537 AC
1 AC
40777539 CGTAGTGACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (33 bp):
ACAATGTTTAATTTTATTTGATTTGTGTTATAA
Found at i:40778818 original size:40 final size:41
Alignment explanation
Indices: 40778742--40778852 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 41
40778732 CAATAAACTG
** *
40778742 AAGCTATCTCGGTATCGCACACTTAGTGCCACATATAGCCA
1 AAGCTATCTCGCAATCGCACACTAAGTGCCACATATAGCCA
* * *
40778783 AAGCTAT-TC-CAATTCGCACACTAAGTGCTATATATAGCCG
1 AAGCTATCTCGCAA-TCGCACACTAAGTGCCACATATAGCCA
*
40778823 AAGCTATCTCGGAAT-GCACACTAAGTGCCA
1 AAGCTATCTCGCAATCGCACACTAAGTGCCA
40778853 AACATAGTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.02
40 46 0.78
41 10 0.17
42 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (41 bp):
AAGCTATCTCGCAATCGCACACTAAGTGCCACATATAGCCA
Found at i:40782540 original size:38 final size:38
Alignment explanation
Indices: 40782491--40783027 Score: 885
Period size: 38 Copynumber: 13.9 Consensus size: 38
40782481 TGATATGAAA
* *
40782491 TGTGTAAGACCATGGTTGAAAGATACCATGACAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782529 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782567 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782605 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782643 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782681 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782719 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782757 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782795 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782833 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
40782871 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
* ** *****
40782909 TGTGTAAGACCATGGTTGAAAGATACCATGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
* *
40782947 TGTGTAAGACCATGGTTGAAAGATACCATGGAAACCTAATATGAG
1 TGTGTAAGACCATGGTTGAAAGATACCACGGCAACC-----T--G
*
40782992 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 -TGTGTAAGACCATGGTTGAAAGATACCACGGCAAC
40783028 GTGACATGAA
Statistics
Matches: 473, Mismatches: 18, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
38 439 0.93
46 34 0.07
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (38 bp):
TGTGTAAGACCATGGTTGAAAGATACCACGGCAACCTG
Found at i:40782938 original size:16 final size:16
Alignment explanation
Indices: 40782917--40782977 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 16
40782907 TGTGTGTAAG
40782917 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
* *
40782933 ACCATGATATGAAATGTGTAAG
1 ACCATGGT-TGAAA---G--AT
40782955 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
40782971 ACCATGG
1 ACCATGG
40782978 AAACCTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 15 0.43
17 5 0.14
18 1 0.03
20 1 0.03
21 5 0.14
22 8 0.23
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (16 bp):
ACCATGGTTGAAAGAT
Found at i:40783116 original size:46 final size:46
Alignment explanation
Indices: 40782935--40783117 Score: 215
Period size: 46 Copynumber: 4.0 Consensus size: 46
40782925 TGAAAGATAC
* * * *
40782935 CATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGAAA
1 CATGACATGAAAAGAGTAAGACCATGGTTGAAAGATACCATGGCAA
* * * * * *
40782981 CCTAATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CATGACATGAAAAGAGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
40783027 CGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAA
1 CATGACATGAAAAGAGTAAGACCATGGTTGAAAGATACCATGGCAA
* * *
40783073 CATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CATGACATGAAAA-GAGTAAGACCATGGTTGAAAGATACCATGGCA
40783118 TCACGTCAAA
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 5 0.04
46 115 0.96
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
CATGACATGAAAAGAGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:40786509 original size:32 final size:32
Alignment explanation
Indices: 40786473--40786537 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
40786463 TGATAGATCA
40786473 ATAAAATAAAACCAAATCAAACATATATTTAT
1 ATAAAATAAAACCAAATCAAACATATATTTAT
40786505 ATAAAATAAAACCAAATCAAACATATATTTAT
1 ATAAAATAAAACCAAATCAAACATATATTTAT
40786537 A
1 A
40786538 CTCATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (32 bp):
ATAAAATAAAACCAAATCAAACATATATTTAT
Found at i:40786982 original size:42 final size:42
Alignment explanation
Indices: 40786873--40787097 Score: 289
Period size: 42 Copynumber: 5.4 Consensus size: 42
40786863 ATAAAATTTA
* *
40786873 CTAGGC-ATAAAGCCT-AGTATAATACACCAGCACAGAA-CCTG
1 CTAGGCAATAAAGCCTGA-TATAATACACTAGCATA-AAGCCTG
* * ** *
40786914 CTAGGCAAT-AGGCCTGACATAATACACCGGCATAAAGCCTA
1 CTAGGCAATAAAGCCTGATATAATACACTAGCATAAAGCCTG
*
40786955 CTAGGCAATAAAGCCTGATATAATACACTAACATAAAGCCTG
1 CTAGGCAATAAAGCCTGATATAATACACTAGCATAAAGCCTG
* *
40786997 CTAGGCAATAAAGCCCGATATAATACACTAGCATAAAGCGTG
1 CTAGGCAATAAAGCCTGATATAATACACTAGCATAAAGCCTG
* *
40787039 CTAGGCAAT-AAGCCCGATATAATACACTATCATAAAGCCTG
1 CTAGGCAATAAAGCCTGATATAATACACTAGCATAAAGCCTG
40787080 CTAGGCAATAAAGCCTGA
1 CTAGGCAATAAAGCCTGA
40787098 ATATCACTGA
Statistics
Matches: 162, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
40 2 0.01
41 76 0.47
42 84 0.52
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (42 bp):
CTAGGCAATAAAGCCTGATATAATACACTAGCATAAAGCCTG
Found at i:40787045 original size:125 final size:124
Alignment explanation
Indices: 40786873--40787097 Score: 310
Period size: 125 Copynumber: 1.8 Consensus size: 124
40786863 ATAAAATTTA
* * *
40786873 CTAGGCATAAAGCCTAGTATAATACACCAGCACAGAACCTGCTAGGCAATAGGCCTGACATAATA
1 CTAGGCATAAAGCCGAGTATAATACACCAGCACAGAACCTGCTAGGCAATAAGCCCGACATAATA
*
40786938 CACCGGCATAAAGCCTACTAGGCAATAAAGCCTGATATAATACACTAACATAAAGCCTG
66 CACCAGCATAAAGCCTACTAGGCAATAAAGCCTGATATAATACACTAACATAAAGCCTG
* * * *
40786997 CTAGGCAATAAAGCCCGA-TATAATACACTAGCATA-AAGCGTGCTAGGCAATAAGCCCGATATA
1 CTAGGC-ATAAAG-CCGAGTATAATACACCAGCACAGAA-CCTGCTAGGCAATAAGCCCGACATA
* * *
40787060 ATACACTATCATAAAGCCTGCTAGGCAATAAAGCCTGA
63 ATACACCAGCATAAAGCCTACTAGGCAATAAAGCCTGA
40787098 ATATCACTGA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
124 8 0.09
125 76 0.87
126 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (124 bp):
CTAGGCATAAAGCCGAGTATAATACACCAGCACAGAACCTGCTAGGCAATAAGCCCGACATAATA
CACCAGCATAAAGCCTACTAGGCAATAAAGCCTGATATAATACACTAACATAAAGCCTG
Found at i:40787091 original size:83 final size:84
Alignment explanation
Indices: 40786871--40787094 Score: 278
Period size: 83 Copynumber: 2.7 Consensus size: 84
40786861 ACATAAAATT
* * * * * *
40786871 TACTAGGC-ATAAAG-CCTAGTATAATACACCAGCACAGAA-CCTGCTAGGCAAT-AGGCCTGAC
1 TACTAGGCAATAAAGCCCGA-TATAATACACTAACATA-AAGCCTGCTAGGCAATAAAGCCCGAC
*
40786932 ATAATACACCGGCATAAAGCC
64 ATAATACACCAGCATAAAGCC
* *
40786953 TACTAGGCAATAAAGCCTGATATAATACACTAACATAAAGCCTGCTAGGCAATAAAGCCCGATAT
1 TACTAGGCAATAAAGCCCGATATAATACACTAACATAAAGCCTGCTAGGCAATAAAGCCCGACAT
* *
40787018 AATACACTAGCATAAAGCG
66 AATACACCAGCATAAAGCC
* *
40787037 TGCTAGGCAAT-AAGCCCGATATAATACACTATCATAAAGCCTGCTAGGCAATAAAGCC
1 TACTAGGCAATAAAGCCCGATATAATACACTAACATAAAGCCTGCTAGGCAATAAAGCC
40787095 TGAATATCAC
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
82 10 0.08
83 78 0.63
84 36 0.29
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (84 bp):
TACTAGGCAATAAAGCCCGATATAATACACTAACATAAAGCCTGCTAGGCAATAAAGCCCGACAT
AATACACCAGCATAAAGCC
Found at i:40791628 original size:38 final size:39
Alignment explanation
Indices: 40791569--40791818 Score: 243
Period size: 46 Copynumber: 5.9 Consensus size: 39
40791559 CTGATATGAA
*
40791569 ATGTGTAAGACAATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
40791608 -TGTGTAAGACCATGGCTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
40791646 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
40791684 ATATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAG
1 --ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAACC-----T--G
*
40791737 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
* *
40791776 ACATGAAAAGAATAAGACCATGGTTGAAAGATATCATGGCAAC
1 --ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
40791819 ATGACAGAAA
Statistics
Matches: 181, Mismatches: 8, Indels: 37
0.80 0.04 0.16
Matches are distributed among these distances:
38 73 0.40
39 1 0.01
41 6 0.03
44 2 0.01
46 93 0.51
48 1 0.01
51 4 0.02
53 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.22
Consensus pattern (39 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:40791717 original size:46 final size:46
Alignment explanation
Indices: 40791650--40791862 Score: 284
Period size: 46 Copynumber: 4.6 Consensus size: 46
40791640 AACCTGTGTG
*
40791650 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAA
* * * **
40791696 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAA
*
40791742 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAA
* * *
40791788 TAAGACCATGGTTGAAAGATATCATGGCAACATGACA-GAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAA-GAA
** * *
40791834 TAAGACCACAGTTGAAAGACACTATGGCA
1 TAAGACCATGGTTGAAAGATACCATGGCA
40791863 TCACGTCAAA
Statistics
Matches: 148, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 5 0.03
46 143 0.97
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAA
Found at i:40791803 original size:92 final size:92
Alignment explanation
Indices: 40791646--40791862 Score: 319
Period size: 92 Copynumber: 2.4 Consensus size: 92
40791636 TGGCAACCTG
*
40791646 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAAGAATAAGACCATGGTTGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGA
* * *
40791711 AAGATACCATGGCAACCTGATATG-AGA
66 AAGATACCATGGCAACATGACA-GAAAA
*
40791738 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGA
*
40791803 AAGATATCATGGCAACATGACAGAAAA
66 AAGATACCATGGCAACATGACAGAAAA
* ** * *
40791830 TGAGTAAGACCACAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
40791863 TCACGTCAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
91 1 0.01
92 112 0.99
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (92 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGA
AAGATACCATGGCAACATGACAGAAAA
Found at i:40791848 original size:138 final size:130
Alignment explanation
Indices: 40791608--40791862 Score: 323
Period size: 138 Copynumber: 1.9 Consensus size: 130
40791598 TGGCAACCTG
*
40791608 TGTGTAAGACCATGGCTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGTTGAAAGATACC
1 TGTGTAAGACCATGGCTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGTTGAAAGATACC
* * ** *
40791673 ATGGCAACCTGATATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
66 ATGGCAACATGACATGAAAAGAATAAGACCACAGTTGAAAGACACCATGGCAACCTGATATGAGA
* *
40791738 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGA
1 TGTGTAAGACCATGGCTGAAAGATACCATGGCAACCTG---TG---AG--TAAGACCATGGTTGA
* * *
40791803 AAGATATCATGGCAACATGACA-GAAAATGAGTAAGACCACAGTTGAAAGACACTATGGCA
58 AAGATACCATGGCAACATGACATGAAAA-GAATAAGACCACAGTTGAAAGACACCATGGCA
40791863 TCACGTCAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
130 36 0.34
133 2 0.02
136 1 0.01
137 5 0.05
138 61 0.58
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (130 bp):
TGTGTAAGACCATGGCTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGTTGAAAGATACC
ATGGCAACATGACATGAAAAGAATAAGACCACAGTTGAAAGACACCATGGCAACCTGATATGAGA
Found at i:40794644 original size:56 final size:56
Alignment explanation
Indices: 40794577--40794686 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
40794567 ACTAAATTAA
40794577 GACCAAATTGAATAGATGAAGAACTATGAGGGACTAAATTAAAATTTTACCAAAAG
1 GACCAAATTGAATAGATGAAGAACTATGAGGGACTAAATTAAAATTTTACCAAAAG
*
40794633 GACCAAATTGAATAGATGAAGAACTATGAGGGACTAAATTACAATTTTACCAAA
1 GACCAAATTGAATAGATGAAGAACTATGAGGGACTAAATTAAAATTTTACCAAA
40794687 TTAAATGATG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (56 bp):
GACCAAATTGAATAGATGAAGAACTATGAGGGACTAAATTAAAATTTTACCAAAAG
Found at i:40818804 original size:42 final size:42
Alignment explanation
Indices: 40818688--40818868 Score: 226
Period size: 42 Copynumber: 4.4 Consensus size: 42
40818678 ATAAAATTTA
* *
40818688 CTAGGC-ATAAAG-CCTAGTATAATACACCAGCACAGAA-CCTG
1 CTAGGCAATAAAGCCCGA-TATAATACACCAGCATA-AAGCCTG
* * * * *
40818729 CTAGGCAAT-AGGTCTGACATAATACACCGGCATAAAGCCTG
1 CTAGGCAATAAAGCCCGATATAATACACCAGCATAAAGCCTG
40818770 CTAGGCAATAAAGCCCGATATAATACACCAGCATAAAGCCTG
1 CTAGGCAATAAAGCCCGATATAATACACCAGCATAAAGCCTG
* * *
40818812 CTAGGCAATGAAGCCCAATATAATACACTAGCATAAAGCCTG
1 CTAGGCAATAAAGCCCGATATAATACACCAGCATAAAGCCTG
40818854 CTAGGCAATAAAGCC
1 CTAGGCAATAAAGCC
40818869 AGAGTATCAC
Statistics
Matches: 121, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.02
41 35 0.29
42 84 0.69
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (42 bp):
CTAGGCAATAAAGCCCGATATAATACACCAGCATAAAGCCTG
Found at i:40821077 original size:23 final size:23
Alignment explanation
Indices: 40821039--40821157 Score: 95
Period size: 23 Copynumber: 5.2 Consensus size: 23
40821029 CTCCTGAGCT
40821039 GCTG-AACAGTAAGCTCTAATGA
1 GCTGAAACAGTAAGCTCTAATGA
* *
40821061 GCTGAAACGGTAAGCTCT-ATCAA
1 GCTGAAACAGTAAGCTCTAAT-GA
*
40821084 GCTG-AACAGTAAGCTC-ATACGA
1 GCTGAAACAGTAAGCTCTA-ATGA
* * *
40821106 GCTAAAAC-GATAAGCTCCACTGA
1 GCTGAAACAG-TAAGCTCTAATGA
* *
40821129 GCTGAAAACAGTAAGCTCTTACGA
1 GCTG-AAACAGTAAGCTCTAATGA
40821153 GCTGA
1 GCTGA
40821158 TATATCGGTA
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
22 22 0.29
23 34 0.45
24 18 0.24
25 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (23 bp):
GCTGAAACAGTAAGCTCTAATGA
Found at i:40821093 original size:45 final size:45
Alignment explanation
Indices: 40821039--40821173 Score: 139
Period size: 45 Copynumber: 2.9 Consensus size: 45
40821029 CTCCTGAGCT
*
40821039 GCTGAACAGTAAGCTCTAATGAGCTGAAACGGTAAGCTCTA-TCAA
1 GCTGAACAGTAAGCTCTAACGAGCTGAAACGGTAAGCTCTACT-AA
* * * *
40821084 GCTGAACAGTAAGCTC-ATACGAGCTAAAACGATAAGCTCCACTGA
1 GCTGAACAGTAAGCTCTA-ACGAGCTGAAACGGTAAGCTCTACTAA
*
40821129 GCTGAAAACAGTAAGCTCTTACGAGCTGATATATCGGTAAGCTCT
1 GCTG--AACAGTAAGCTCTAACGAGCTGA-A-A-CGGTAAGCTCT
40821174 TATGAGTTGT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
44 1 0.01
45 40 0.55
46 1 0.01
47 20 0.27
48 1 0.01
49 1 0.01
50 9 0.12
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (45 bp):
GCTGAACAGTAAGCTCTAACGAGCTGAAACGGTAAGCTCTACTAA
Found at i:40821098 original size:22 final size:22
Alignment explanation
Indices: 40821039--40821099 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
40821029 CTCCTGAGCT
*
40821039 GCTGAACAGTAAGCTCTAATGA
1 GCTGAACAGTAAGCTCTAATAA
*
40821061 GCTGAAACGGTAAGCTCT-ATCAA
1 GCTG-AACAGTAAGCTCTAAT-AA
40821084 GCTGAACAGTAAGCTC
1 GCTGAACAGTAAGCTC
40821100 ATACGAGCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (22 bp):
GCTGAACAGTAAGCTCTAATAA
Found at i:40823776 original size:19 final size:19
Alignment explanation
Indices: 40823754--40823793 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
40823744 TCTGTACACA
**
40823754 AATTCTATTTCGTAACATT
1 AATTCTATTTCAAAACATT
40823773 AATTCTATTTCAAAACATT
1 AATTCTATTTCAAAACATT
40823792 AA
1 AA
40823794 ACGGTCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (19 bp):
AATTCTATTTCAAAACATT
Found at i:40825999 original size:12 final size:12
Alignment explanation
Indices: 40825982--40826006 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40825972 GGAGAAAGAG
40825982 AAAAAATAAAAT
1 AAAAAATAAAAT
40825994 AAAAAATAAAAT
1 AAAAAATAAAAT
40826006 A
1 A
40826007 TTTAATTTTA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:40833124 original size:5 final size:6
Alignment explanation
Indices: 40833109--40833133 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40833099 GAGAAAGAGA
40833109 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
40833134 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:40835843 original size:10 final size:10
Alignment explanation
Indices: 40835828--40835860 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
40835818 TTGCTTGGCT
*
40835828 TGGAAATGGA
1 TGGAAAAGGA
40835838 TGGAAAAGGA
1 TGGAAAAGGA
40835848 TGGAAAAGGA
1 TGGAAAAGGA
40835858 TGG
1 TGG
40835861 TTTCTCATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.42, T:0.15
Consensus pattern (10 bp):
TGGAAAAGGA
Found at i:40838037 original size:17 final size:17
Alignment explanation
Indices: 40838015--40838058 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
40838005 TTCTAAGAAG
40838015 TATTTTTAAAATAAAAA
1 TATTTTTAAAATAAAAA
*
40838032 TATTTTTAAGATAAAAA
1 TATTTTTAAAATAAAAA
40838049 TATTTTTAAA
1 TATTTTTAAA
40838059 TAAGTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TATTTTTAAAATAAAAA
Found at i:40843469 original size:11 final size:11
Alignment explanation
Indices: 40843453--40843483 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40843443 ATCGTAGACC
40843453 ATAAAAATATA
1 ATAAAAATATA
40843464 ATAAAAATATA
1 ATAAAAATATA
*
40843475 ATAGAAATA
1 ATAAAAATA
40843484 AATTTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
ATAAAAATATA
Done.