Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 105 of 113
Found at i:20626575 original size:33 final size:34
Alignment explanation
Indices: 20626533--20626596 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
20626523 TTTTATTTAT
*
20626533 TTATTTATTT-TTGTTCTTTATTTATT-TTATCTC
1 TTATTTATTTATT-TTATTTATTTATTGTTATCTC
20626566 TTATTTATTTATTTTATTTATTTATTGTTAT
1 TTATTTATTTATTTTATTTATTTATTGTTAT
20626597 AATATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 22 0.79
34 6 0.21
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (34 bp):
TTATTTATTTATTTTATTTATTTATTGTTATCTC
Found at i:20630011 original size:13 final size:12
Alignment explanation
Indices: 20629978--20630016 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
20629968 ATATTTAAAT
20629978 TTTCATATCAT-
1 TTTCATATCATA
*
20629989 TTTTATATCATA
1 TTTCATATCATA
20630001 TTATCATATCATA
1 TT-TCATATCATA
20630014 TTT
1 TTT
20630017 AAAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 3 0.12
13 11 0.46
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTCATATCATA
Found at i:20631000 original size:29 final size:30
Alignment explanation
Indices: 20630963--20631022 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
20630953 AATTTACAAA
* *
20630963 TTTATAATTCAAATGTTACATTAAA-AATT
1 TTTAAAATTCAAATATTACATTAAATAATT
* *
20630992 TTTAAAATTTAAATATTAGATTAAATAATT
1 TTTAAAATTCAAATATTACATTAAATAATT
20631022 T
1 T
20631023 ATTTTAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTAAAATTCAAATATTACATTAAATAATT
Found at i:20632823 original size:17 final size:17
Alignment explanation
Indices: 20632801--20632853 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
20632791 TTGATTATTA
20632801 TCGAGTCGAGCTCAAGT
1 TCGAGTCGAGCTCAAGT
*
20632818 TCGAGT--AGCTCAACGCA
1 TCGAGTCGAGCTCAA-G-T
20632835 TCGA-TCGAGC-CAAGT
1 TCGAGTCGAGCTCAAGT
20632850 TCGA
1 TCGA
20632854 ATATTCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 11 0.37
16 3 0.10
17 13 0.43
18 3 0.10
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (17 bp):
TCGAGTCGAGCTCAAGT
Found at i:20633531 original size:37 final size:37
Alignment explanation
Indices: 20633481--20633553 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
20633471 ATTTTGAGTT
* *
20633481 AATTTTTTTTTATCTCTTTATTGTTCCTATTGACCTA
1 AATTTCTTTTTATCTCTTTATTGTACCTATTGACCTA
*
20633518 AATTTCTTTTTATCTCTTTATTGTACCTTTTGACCT
1 AATTTCTTTTTATCTCTTTATTGTACCTATTGACCT
20633554 TATGTCTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (37 bp):
AATTTCTTTTTATCTCTTTATTGTACCTATTGACCTA
Found at i:20633788 original size:36 final size:35
Alignment explanation
Indices: 20633748--20633815 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 35
20633738 TAATGAATTA
*
20633748 TACTTATTTAAATCTCAAAATAATTTTAATATTTAG
1 TACTTATTTAAATATCAAAAT-ATTTTAATATTTAG
*
20633784 TACTTATTTAAATATCAAAATTTTTTAATATT
1 TACTTATTTAAATATCAAAATATTTTAATATT
20633816 AATATATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 10 0.33
36 20 0.67
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.50
Consensus pattern (35 bp):
TACTTATTTAAATATCAAAATATTTTAATATTTAG
Found at i:20634501 original size:48 final size:48
Alignment explanation
Indices: 20634425--20634521 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
20634415 CTAAATCATT
* *
20634425 ATCACCTCAAATTATAAGTTTGTATCCATGCTTCAAAGGTGAAGAGCC
1 ATCACCTCAAATCATAAGTTTGTATCCATGCTTAAAAGGTGAAGAGCC
* *
20634473 ATCACCTCAAATCATGAGTTTGTGTCCATGCTTAAAAGGTGAAGAGCC
1 ATCACCTCAAATCATAAGTTTGTATCCATGCTTAAAAGGTGAAGAGCC
20634521 A
1 A
20634522 CATTTTTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (48 bp):
ATCACCTCAAATCATAAGTTTGTATCCATGCTTAAAAGGTGAAGAGCC
Found at i:20634785 original size:30 final size:31
Alignment explanation
Indices: 20634751--20634809 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
20634741 GACAATTTTC
* * *
20634751 TCCTTATATATTTAGTTA-ATTATAAATTTG
1 TCCTTACATATTTAATTATATAATAAATTTG
20634781 TCCTTACATATTTAATTATATAATAAATT
1 TCCTTACATATTTAATTATATAATAAATT
20634810 AATATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.51
Consensus pattern (31 bp):
TCCTTACATATTTAATTATATAATAAATTTG
Found at i:20634835 original size:17 final size:15
Alignment explanation
Indices: 20634804--20634840 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
20634794 AATTATATAA
20634804 TAAATTAATATTAAT
1 TAAATTAATATTAAT
20634819 TAAATTAAATAATTAAT
1 TAAATT-AAT-ATTAAT
20634836 TAAAT
1 TAAAT
20634841 AATGTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 3 0.15
17 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATTAATATTAAT
Found at i:20634920 original size:22 final size:22
Alignment explanation
Indices: 20634894--20634944 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
20634884 ATATTTCATA
20634894 TATAATATTATTCAAA-CAATAT
1 TATAATATTATT-AAATCAATAT
*
20634916 TATAATATTATTAAATTAATAT
1 TATAATATTATTAAATCAATAT
20634938 T-TAATAT
1 TATAATAT
20634945 CAAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAATATTATTAAATCAATAT
Found at i:20635492 original size:21 final size:21
Alignment explanation
Indices: 20635468--20635509 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20635458 TTTTTCATAT
20635468 TTTTAATAAAAATC-TTTTTTA
1 TTTTAA-AAAAATCATTTTTTA
*
20635489 TTTTAAAAATATCATTTTTTA
1 TTTTAAAAAAATCATTTTTTA
20635510 ATTATGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAAAAAAATCATTTTTTA
Found at i:20635507 original size:152 final size:152
Alignment explanation
Indices: 20635202--20635508 Score: 329
Period size: 152 Copynumber: 2.0 Consensus size: 152
20635192 TTTTTTTATA
* *
20635202 TTTTCAATAAAAACTACATTTTTTATTTTAAAAAATTTCTCTTTAAAAAAAATACATTTTTATCT
1 TTTTCAACAAAAACTACATTTTTTATTTTAAAAAATTTATCTTTAAAAAAAATACATTTTTATCT
* * * *
20635267 TAGAAACATCATCTTTATTGAATTCTAAAAAATTTATTTTTTATATTTTCAACAAAAGACTGCTT
66 TAAAAACATCATCTTTATTAAATTCTAAAAAATATATTTTTCATATTTTCAACAAAAGACTGCTT
* * *
20635332 TTTTGTCTTAGAAACATCTTTT
131 TTTTATCTTAAAAACATCATTT
* * *
20635354 TTTTCAACAAAAACTGCA-TTTTTATTTTAAAAATTTTATCTTTTCAACAAAAATTA-AGTTTTT
1 TTTTCAACAAAAACTACATTTTTTATTTTAAAAAATTTATC-TTT-AA-AAAAAATACA-TTTTT
* ** * * * *
20635417 ATCTTAAAAACGTGGTCTTTGTTAAAATT-TGAAAAATAATATTTTTCATATTTTTAATAAAA-A
62 ATCTTAAAAACATCATCTTTATT-AAATTCTAAAAAAT-ATATTTTTCATATTTTCAACAAAAGA
* *
20635480 -T-CTTTTTTATTTTAAAAATATCATTT
125 CTGCTTTTTTATCTTAAAAACATCATTT
20635506 TTT
1 TTT
20635509 AATTATGAAA
Statistics
Matches: 128, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
151 20 0.16
152 42 0.33
153 4 0.03
154 38 0.30
155 24 0.19
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (152 bp):
TTTTCAACAAAAACTACATTTTTTATTTTAAAAAATTTATCTTTAAAAAAAATACATTTTTATCT
TAAAAACATCATCTTTATTAAATTCTAAAAAATATATTTTTCATATTTTCAACAAAAGACTGCTT
TTTTATCTTAAAAACATCATTT
Found at i:20635834 original size:75 final size:76
Alignment explanation
Indices: 20635709--20635849 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 76
20635699 AAAATTATAT
* *
20635709 TTTTATCTTAAAAATATCATTTTTGTTAAATTCTGAAAAATAA-ATATTTTTCATATTTTTAACA
1 TTTTATCTTAAAAATATCATTTTTGTTAAATTATGAAAAATAATATATTTTTCATATTTTCAACA
20635773 AAAGCCACACA
66 AAAGCCACACA
* ** * * *
20635784 TTTTATTTTAAAAATATCATTTTTGTTGGATTATGAAAAATAGTTTTTTTTTCATATTTTCAACA
1 TTTTATCTTAAAAATATCATTTTTGTTAAATTATGAAAAATAATATATTTTTCATATTTTCAACA
20635849 A
66 A
20635850 GGACTGCATT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
75 38 0.67
76 19 0.33
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.48
Consensus pattern (76 bp):
TTTTATCTTAAAAATATCATTTTTGTTAAATTATGAAAAATAATATATTTTTCATATTTTCAACA
AAAGCCACACA
Found at i:20636054 original size:26 final size:26
Alignment explanation
Indices: 20636022--20636072 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
20636012 TGGGAATCTT
* *
20636022 AAAAATCTTAGTAATCACATTCTAAA
1 AAAAATCGTAATAATCACATTCTAAA
20636048 AAAAATCGTAATAATCACATTCTAA
1 AAAAATCGTAATAATCACATTCTAA
20636073 TGAACCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (26 bp):
AAAAATCGTAATAATCACATTCTAAA
Found at i:20636243 original size:22 final size:23
Alignment explanation
Indices: 20636203--20636246 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20636193 GTTTGAATTA
*
20636203 TATTTATCTTTTTAATTAATTTT
1 TATTTATCTTTATAATTAATTTT
*
20636226 TATTTAT-TTTATATTTAATTT
1 TATTTATCTTTATAATTAATTT
20636247 AAAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATCTTTATAATTAATTTT
Found at i:20636422 original size:11 final size:11
Alignment explanation
Indices: 20636406--20636511 Score: 55
Period size: 11 Copynumber: 10.1 Consensus size: 11
20636396 GTGTATACTT
20636406 AAATAATATTA
1 AAATAATATTA
20636417 AAATAATA--A
1 AAATAATATTA
* *
20636426 GAA-AATATGA
1 AAATAATATTA
* *
20636436 TAATATTAGTT-
1 AAATAATA-TTA
20636447 AAATAATATTA
1 AAATAATATTA
*
20636458 AAATATTATTA
1 AAATAATATTA
** *
20636469 AGTTAACATTA
1 AAATAATATTA
*
20636480 AAAT-A-A-TG
1 AAATAATATTA
*
20636488 AAATACTATTA
1 AAATAATATTA
20636499 AAATAATACTTA
1 AAATAATA-TTA
20636511 A
1 A
20636512 TATTCAAACA
Statistics
Matches: 69, Mismatches: 17, Indels: 17
0.67 0.17 0.17
Matches are distributed among these distances:
8 9 0.13
9 4 0.06
10 7 0.10
11 44 0.64
12 5 0.07
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (11 bp):
AAATAATATTA
Found at i:20636462 original size:22 final size:22
Alignment explanation
Indices: 20636404--20636484 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 22
20636394 TAGTGTATAC
20636404 TTAA-ATAATATTAAAATA--A
1 TTAAGATAATATTAAAATATTA
* * *
20636423 -TAAGAAAATATGATAATATTA
1 TTAAGATAATATTAAAATATTA
20636444 GTTAA-ATAATATTAAAATATTA
1 -TTAAGATAATATTAAAATATTA
* *
20636466 TTAAGTTAACATTAAAATA
1 TTAAGATAATATTAAAATA
20636485 ATGAAATACT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
18 3 0.06
19 11 0.23
21 5 0.10
22 26 0.54
23 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (22 bp):
TTAAGATAATATTAAAATATTA
Found at i:20636563 original size:28 final size:27
Alignment explanation
Indices: 20636451--20636669 Score: 118
Period size: 28 Copynumber: 7.6 Consensus size: 27
20636441 TTAGTTAAAT
* *
20636451 AATATTAAAATATTATTAAGTTAACATTAA
1 AATA-TAAAATATTATTAA-ATAATATT-A
* *
20636481 AATAATGAAATACTATTAAAATAATACTT-
1 AAT-ATAAAATATTATT-AAATAATA-TTA
* * *
20636510 AATATTCAAACATTACTAAA-ATATATTA
1 AATA-TAAAATATTATTAAATA-ATATTA
* * *
20636538 AATATTAAATAATATTAAAGCAATATTA
1 AATATAAAATATTATTAAA-TAATATTA
* * *
20636566 AATATGAAAATAGTAACTAAATTAATATTT
1 AATAT-AAAATA-TTATTAAA-TAATATTA
* *
20636596 AGTATAAAATATTATTCAAATAATACTA
1 AATATAAAATATTATT-AAATAATATTA
* *
20636624 AATATTAAATATTATTAAAATAATATTT
1 AATATAAAATATTATT-AAATAATATTA
**
20636652 GGTATTAAAATATTATTA
1 AATA-TAAAATATTATTA
20636670 TTTATTCAGT
Statistics
Matches: 145, Mismatches: 32, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
27 14 0.10
28 57 0.39
29 37 0.26
30 32 0.22
31 5 0.03
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (27 bp):
AATATAAAATATTATTAAATAATATTA
Found at i:20636732 original size:17 final size:17
Alignment explanation
Indices: 20636712--20636877 Score: 66
Period size: 17 Copynumber: 9.8 Consensus size: 17
20636702 TGATAAATTT
20636712 ATATTAATATTAAAATA
1 ATATTAATATTAAAATA
*
20636729 ATATTAAAATATTACAA-A
1 ATATT--AATATTAAAATA
*
20636747 AT-TT--TGTT-AAATA
1 ATATTAATATTAAAATA
*
20636760 ATATTAAATTATTTTAAATTA
1 ATATT-AA-TA--TTAAAATA
*
20636781 ACAATTAATATT-AAA-A
1 A-TATTAATATTAAAATA
*
20636797 ATA-TAA-A-TAATATA
1 ATATTAATATTAAAATA
*
20636811 ATAATTAAAATTAAAA-A
1 AT-ATTAATATTAAAATA
* * *
20636828 TTTATTAAAATTAAATTTA
1 -ATATTAATATTAAA-ATA
20636847 ATACTTAATATTAAAATA
1 ATA-TTAATATTAAAATA
*
20636865 TTATTAATATTAA
1 ATATTAATATTAA
20636878 TATTTAATAT
Statistics
Matches: 111, Mismatches: 16, Indels: 44
0.65 0.09 0.26
Matches are distributed among these distances:
12 3 0.03
13 9 0.08
14 8 0.07
15 2 0.02
16 5 0.05
17 33 0.30
18 17 0.15
19 20 0.18
20 4 0.04
21 7 0.06
22 3 0.03
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATTAATATTAAAATA
Found at i:20636849 original size:36 final size:37
Alignment explanation
Indices: 20636809--20636886 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 37
20636799 ATAAATAATA
20636809 TAATAATTAAAATTAAAA-ATTTATTAAAATTAA-ATT
1 TAATAATTAAAATTAAAATA-TTATTAAAATTAATATT
* * *
20636845 TAATACTTAATATTAAAATATTATTAATATTAATATT
1 TAATAATTAAAATTAAAATATTATTAAAATTAATATT
20636882 TAATA
1 TAATA
20636887 TAAATATTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 28 0.76
37 9 0.24
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (37 bp):
TAATAATTAAAATTAAAATATTATTAAAATTAATATT
Found at i:20636859 original size:19 final size:18
Alignment explanation
Indices: 20636830--20636895 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
20636820 ATTAAAAATT
*
20636830 TATTAAAATTAAATTTAA
1 TATTAATATTAAATTTAA
* *
20636848 TACTTAATATTAAA-ATAT
1 TA-TTAATATTAAATTTAA
20636866 TATTAATATTAATATTTAA
1 TATTAATATTAA-ATTTAA
*
20636885 TATAAATATTA
1 TATTAATATTA
20636896 CTAAAATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 10 0.26
18 7 0.18
19 22 0.56
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAATATTAAATTTAA
Found at i:20636860 original size:13 final size:12
Alignment explanation
Indices: 20636830--20636895 Score: 55
Period size: 13 Copynumber: 5.4 Consensus size: 12
20636820 ATTAAAAATT
*
20636830 TATTAAAATTAA
1 TATTAATATTAA
20636842 -ATTTAATACTTAA
1 TA-TTAATA-TTAA
* *
20636855 TATTAA-AATAT
1 TATTAATATTAA
20636866 TATTAATATTAA
1 TATTAATATTAA
*
20636878 TATTTAATATAAA
1 TA-TTAATATTAA
20636891 TATTA
1 TATTA
20636896 CTAAAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 9 0.21
12 14 0.33
13 19 0.44
14 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TATTAATATTAA
Found at i:20636871 original size:30 final size:30
Alignment explanation
Indices: 20636727--20636900 Score: 99
Period size: 30 Copynumber: 5.7 Consensus size: 30
20636717 AATATTAAAA
** ** *
20636727 TAATATTAAAATATTACAAAATTTTGTTAAA
1 TAATATTAAAATATTATTAAA-TTTAATAAT
* *
20636758 TAATATTAAATTATT-TTAAA-TTAACAAT
1 TAATATTAAAATATTATTAAATTTAATAAT
* * *
20636786 TAATATTAAAAATATAAAT-AATATAATAAT
1 TAATATT-AAAATATTATTAAATTTAATAAT
* *
20636816 TAAAATTAAAAATTTATTAAAATTAAATTTAATACT
1 TAATATT-AAAA--TATT---ATTAAATTTAATAAT
*
20636852 TAATATTAAAATATTATT-AATATTAATATT
1 TAATATTAAAATATTATTAAAT-TTAATAAT
*
20636882 TAATA-T-AAATATTACTAAA
1 TAATATTAAAATATTATTAAA
20636901 ATATTTACTA
Statistics
Matches: 112, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
28 20 0.18
29 14 0.12
30 36 0.32
31 14 0.12
32 3 0.03
33 4 0.04
35 6 0.05
36 15 0.13
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (30 bp):
TAATATTAAAATATTATTAAATTTAATAAT
Found at i:20636875 original size:6 final size:6
Alignment explanation
Indices: 20636830--20636895 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
20636820 ATTAAAAATT
* * *
20636830 TATTAA AATTAA -ATTTAA TACTTAA TATTAA -AATAT TATTAA TATTAA
1 TATTAA TATTAA TA-TTAA TA-TTAA TATTAA TATTAA TATTAA TATTAA
*
20636878 TATTTAA TATAAA TATTA
1 TA-TTAA TATTAA TATTA
20636896 CTAAAATATT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
5 4 0.08
6 31 0.65
7 13 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TATTAA
Found at i:20636953 original size:21 final size:20
Alignment explanation
Indices: 20636927--20636984 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
20636917 AATTGAATTT
20636927 TTAATATTGTTAAACTAAGAA
1 TTAATATTGTTAAA-TAAGAA
* * *
20636948 TTAATATTGTTCAATAATAT
1 TTAATATTGTTAAATAAGAA
*
20636968 TTAATATTATTAAATAA
1 TTAATATTGTTAAATAA
20636985 TAGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAATATTGTTAAATAAGAA
Found at i:20637011 original size:41 final size:40
Alignment explanation
Indices: 20636966--20637157 Score: 135
Period size: 41 Copynumber: 4.7 Consensus size: 40
20636956 GTTCAATAAT
20636966 ATTTAATATTATTAAA-TAATAGTTAATTTTATGAAATTAAA
1 ATTTAATATTATTAAATTAATA-TTAATTTTAT-AAATTAAA
* * * *
20637007 ATTTAATAATATTAAATTAATATTGAATATTATTAATTAAT
1 ATTTAATATTATTAAATTAATATT-AATTTTATAAATTAAA
* * *
20637048 ATATAATATGATTAAATTAATATTTAATTTTTATTAAACT-AA
1 ATTTAATATTATTAAATTAATA-TTAA-TTTTA-TAAATTAAA
* * * * * *
20637090 TTTCTAATTTTATGAAATTAATCTTAA--TTAAAATATTAAT
1 ATT-TAATATTATTAAATTAATATTAATTTTATAA-ATTAAA
20637130 ATTTAATATTACTT-AA-TAATATATAATT
1 ATTTAATATTA-TTAAATTAATAT-TAATT
20637158 ATTTAATATA
Statistics
Matches: 115, Mismatches: 24, Indels: 24
0.71 0.15 0.15
Matches are distributed among these distances:
38 7 0.06
39 17 0.15
40 4 0.03
41 44 0.38
42 24 0.21
43 19 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (40 bp):
ATTTAATATTATTAAATTAATATTAATTTTATAAATTAAA
Found at i:20637023 original size:21 final size:21
Alignment explanation
Indices: 20636900--20637145 Score: 193
Period size: 21 Copynumber: 11.9 Consensus size: 21
20636890 ATATTACTAA
*
20636900 AATATTTACTATTATTAAATT
1 AATATTTAATATTATTAAATT
* * *
20636921 GAATTTTTAATATTGTTAAACT
1 -AATATTTAATATTATTAAATT
* * * *
20636943 AAGAATTAATATTGTTCAA-T
1 AATATTTAATATTATTAAATT
20636963 AATATTTAATATTATTAAA-T
1 AATATTTAATATTATTAAATT
* * *
20636983 AATAGTTAATTTTATGAAATT
1 AATATTTAATATTATTAAATT
* *
20637004 AAAATTTAATAATATTAAATT
1 AATATTTAATATTATTAAATT
*
20637025 AATATTGAATATTATT-AATT
1 AATATTTAATATTATTAAATT
* *
20637045 AATATATAATATGATTAAATT
1 AATATTTAATATTATTAAATT
* *
20637066 AATATTTAATTTTTATTAAACT
1 AATATTTAA-TATTATTAAATT
* *
20637088 AAT-TTCTAATTTTATGAAATT
1 AATATT-TAATATTATTAAATT
* *
20637109 AAT-CTT-A-ATTA-AAATATT
1 AATATTTAATATTATTAA-ATT
20637127 AATATTTAATATTACTTAA
1 AATATTTAATATTA-TTAA
20637146 TAATATATAA
Statistics
Matches: 177, Mismatches: 37, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
17 2 0.01
18 9 0.05
19 3 0.02
20 52 0.29
21 77 0.44
22 32 0.18
23 2 0.01
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (21 bp):
AATATTTAATATTATTAAATT
Found at i:20637161 original size:28 final size:25
Alignment explanation
Indices: 20637107--20637166 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
20637097 TTTTATGAAA
*
20637107 TTAATCTTAATTAAAATATTAATAT
1 TTAATATTAATTAAAATATTAATAT
*
20637132 TTAATATTACTTAATAATATATAATTAT
1 TTAATATTAATTAA-AATAT-TAA-TAT
20637160 TTAATAT
1 TTAATAT
20637167 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 12 0.40
26 5 0.17
27 3 0.10
28 10 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAATATTAATTAAAATATTAATAT
Found at i:20637168 original size:15 final size:14
Alignment explanation
Indices: 20637121--20637166 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
20637111 TCTTAATTAA
20637121 AATATTAA-TATTT
1 AATATTAATTATTT
* *
20637134 AATATTACTTA-AT
1 AATATTAATTATTT
20637147 AATATATAATTATTT
1 AATAT-TAATTATTT
20637162 AATAT
1 AATAT
20637167 ATTATTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 13 0.50
14 7 0.27
15 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTAATTATTT
Found at i:20637173 original size:15 final size:15
Alignment explanation
Indices: 20637117--20637175 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
20637107 TTAATCTTAA
* *
20637117 TTAAAATATTAATAT
1 TTAATATATTATTAT
20637132 TT-A-ATATTACTTA-
1 TTAATATATTA-TTAT
* *
20637145 ATAATATATAATTAT
1 TTAATATATTATTAT
20637160 TTAATATATTATTAT
1 TTAATATATTATTAT
20637175 T
1 T
20637176 AATTTGTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
13 7 0.20
14 7 0.20
15 21 0.60
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATATATTATTAT
Found at i:20637176 original size:18 final size:18
Alignment explanation
Indices: 20637125--20637176 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
20637115 AATTAAAATA
*
20637125 TTAATAT-TTAATATTAC
1 TTAATATATTATTATTAC
* *
20637142 TTAATA-ATATATAATTAT
1 TTAATATAT-TATTATTAC
20637160 TTAATATATTATTATTA
1 TTAATATATTATTATTA
20637177 ATTTGTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 7 0.25
18 19 0.68
19 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATATATTATTATTAC
Found at i:20638403 original size:3 final size:3
Alignment explanation
Indices: 20638395--20638424 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20638385 CACATAGACA
20638395 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20638425 GATTAACCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20647946 original size:18 final size:18
Alignment explanation
Indices: 20647919--20647953 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20647909 GGATTGAACA
20647919 TTTTCTTTTT-TTTTTTT
1 TTTTCTTTTTGTTTTTTT
20647936 TTTTGCTTTTTGTTTTTT
1 TTTT-CTTTTTGTTTTTT
20647954 CACAAGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (18 bp):
TTTTCTTTTTGTTTTTTT
Found at i:20649166 original size:28 final size:27
Alignment explanation
Indices: 20649114--20649168 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
20649104 ATAAGTAAAA
* *
20649114 TTTGATAACTTTTTATATAATTTTGAT
1 TTTGATAACTTTTTATAAAAGTTTGAT
*
20649141 TTTGATAAATTTTTTATAAAAGTTTGAT
1 TTTGAT-AACTTTTTATAAAAGTTTGAT
20649169 AATATTCGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (27 bp):
TTTGATAACTTTTTATAAAAGTTTGAT
Found at i:20649645 original size:44 final size:44
Alignment explanation
Indices: 20649595--20649704 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 44
20649585 TTGACAATTG
* * * ** *
20649595 AATTATCATTGATTTATTATTATATTATTAGTGATTTACTATTC
1 AATTATCATTGATTTATTACTAAAATATTAACGATTTACTATTA
* * *
20649639 AATTATCAATGATATATTGCTAAAATATTAACGATTTACTATTA
1 AATTATCATTGATTTATTACTAAAATATTAACGATTTACTATTA
* *
20649683 AATTAGCATTGA-TTACTACTAA
1 AATTATCATTGATTTATTACTAA
20649705 TTTATGAATA
Statistics
Matches: 52, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
43 7 0.13
44 45 0.87
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (44 bp):
AATTATCATTGATTTATTACTAAAATATTAACGATTTACTATTA
Found at i:20649753 original size:22 final size:21
Alignment explanation
Indices: 20649580--20649763 Score: 75
Period size: 22 Copynumber: 8.4 Consensus size: 21
20649570 AAAAATGATC
* * *
20649580 AATGATTGACAATTGAATTATC
1 AATGATTTACTATT-AATTATG
* * *
20649602 ATTGATTTATTATTATATTATT
1 AATGATTTACTATTA-ATTATG
* *
20649624 AGTGATTTACTATTCAATTATC
1 AATGATTTACTATT-AATTATG
* * * * * *
20649646 AATGATATATTGCTAAAATATT
1 AATGATTTACT-ATTAATTATG
*
20649668 AACGATTTACTATTAAATTA-G
1 AATGATTTACTATT-AATTATG
* *
20649689 CATTGA-TTACTACTAATTTATG
1 -AATGATTTACTATTAA-TTATG
* * *
20649711 AATAATTTATTACTAAGTTATG
1 AATGATTTACTATTAA-TTATG
*
20649733 AATGATTTACTATTATATTATT
1 AATGATTTACTATTA-ATTATG
*
20649755 ATTGATTTA
1 AATGATTTA
20649764 GTTTTAGTTT
Statistics
Matches: 119, Mismatches: 34, Indels: 18
0.70 0.20 0.11
Matches are distributed among these distances:
20 2 0.02
21 15 0.13
22 99 0.83
23 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (21 bp):
AATGATTTACTATTAATTATG
Found at i:20656132 original size:29 final size:29
Alignment explanation
Indices: 20656067--20656137 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
20656057 GAATGATTTT
* *
20656067 TAAATTATAATTAAATATTTAATGTGATATA
1 TAAATTATAA--AAATATTTAATATGATACA
* * *
20656098 TGAATTTTAAAAATTTTTAATATGATACA
1 TAAATTATAAAAATATTTAATATGATACA
20656127 TAAATTATAAA
1 TAAATTATAAA
20656138 TTTATTAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 25 0.76
31 8 0.24
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (29 bp):
TAAATTATAAAAATATTTAATATGATACA
Found at i:20661803 original size:10 final size:10
Alignment explanation
Indices: 20661788--20661836 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
20661778 ATAATAATTT
20661788 TATATTAAAA
1 TATATTAAAA
*
20661798 TATATTTAAA
1 TATATTAAAA
20661808 TATATT-AAA
1 TATATTAAAA
20661817 TAATATATAAAA
1 T-ATAT-TAAAA
20661829 -A-ATTAAAA
1 TATATTAAAA
20661837 ATTAATGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 5 0.14
9 6 0.17
10 20 0.57
11 1 0.03
12 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATATTAAAA
Found at i:20661822 original size:20 final size:20
Alignment explanation
Indices: 20661788--20661836 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
20661778 ATAATAATTT
*
20661788 TATATTAAAATATATTTAAA
1 TATATTAAAATATATATAAA
20661808 TATATT-AAATAATATATAAA
1 TATATTAAAAT-ATATATAAA
*
20661828 -AAATTAAAA
1 TATATTAAAA
20661837 ATTAATGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATATTAAAATATATATAAA
Found at i:20662478 original size:19 final size:18
Alignment explanation
Indices: 20662450--20662487 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
20662440 ATGTAATAAA
*
20662450 AGTTTTAAATTATTTAAT
1 AGTTTTAAATTAATTAAT
20662468 AGTTATTAAATTAATTAAT
1 AGTT-TTAAATTAATTAAT
20662487 A
1 A
20662488 ATTAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
AGTTTTAAATTAATTAAT
Found at i:20662509 original size:45 final size:42
Alignment explanation
Indices: 20662454--20662538 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
20662444 AATAAAAGTT
*
20662454 TTAAATTATTTAATAGTTATTAAATTAATT-AATAATTAAAAATGG
1 TTAAATTATTT-ATA-TT-TCAAA-TAATTAAATAATTAAAAATGG
*
20662499 TTAAATTATTTTTATTTCAAATAATTAAATAATTAAAAAT
1 TTAAATTATTTATATTTCAAATAATTAAATAATTAAAAAT
20662539 TAATAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
41 5 0.14
42 17 0.46
43 2 0.05
44 2 0.05
45 11 0.30
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (42 bp):
TTAAATTATTTATATTTCAAATAATTAAATAATTAAAAATGG
Found at i:20663477 original size:2 final size:2
Alignment explanation
Indices: 20663472--20663501 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20663462 TATATATATA
*
20663472 TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
20663502 ATATAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:20663817 original size:20 final size:21
Alignment explanation
Indices: 20663792--20663834 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20663782 TTATTAATAT
*
20663792 ATAAATTATA-TATATTATCA
1 ATAAATGATATTATATTATCA
*
20663812 ATAAATGATATTATTTTATCA
1 ATAAATGATATTATATTATCA
20663833 AT
1 AT
20663835 GAAAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (21 bp):
ATAAATGATATTATATTATCA
Found at i:20668105 original size:20 final size:20
Alignment explanation
Indices: 20668067--20668103 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
20668057 CCATTTTATT
*
20668067 TATTATTATTTATATTTTTA
1 TATTATTATATATATTTTTA
20668087 TATT-TT-TATATATTTTT
1 TATTATTATATATATTTTT
20668104 TTCCTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 10 0.62
19 2 0.12
20 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTATTATATATATTTTTA
Found at i:20668250 original size:8 final size:8
Alignment explanation
Indices: 20668239--20668445 Score: 67
Period size: 8 Copynumber: 25.5 Consensus size: 8
20668229 TTTTTGCCCC
20668239 TATTATTA
1 TATTATTA
*
20668247 TATTACTA
1 TATTATTA
*
20668255 CTA-TACTA
1 -TATTATTA
20668263 TCATTA-TA
1 T-ATTATTA
* *
20668271 TTATTGTTG
1 -TATTATTA
*
20668280 TAGTATTA
1 TATTATTA
20668288 TATTA-TA
1 TATTATTA
* *
20668295 TTATTGTAA
1 -TATTATTA
20668304 TA-TATTGA
1 TATTATT-A
20668312 TATTATATTA
1 TA-T-TATTA
*
20668322 CATTATTA
1 TATTATTA
20668330 TATTATGT-
1 TATTAT-TA
20668338 TA-TATTA
1 TATTATTA
20668345 T-TATATTA
1 TAT-TATTA
**
20668353 TATTAGGA
1 TATTATTA
20668361 TATTATTA
1 TATTATTA
*
20668369 TACTA-T-
1 TATTATTA
*
20668375 TCTTA-TA
1 TATTATTA
*
20668382 GCATTA-TA
1 -TATTATTA
20668390 TTATTATTA
1 -TATTATTA
20668399 TATTATTA
1 TATTATTA
20668407 TATTATATTA
1 TA-T-TATTA
* *
20668417 GATTATTTT
1 TATTA-TTA
*
20668426 TATTATAA
1 TATTATTA
20668434 TATTATTA
1 TATTATTA
20668442 TATT
1 TATT
20668446 TGAAATTATT
Statistics
Matches: 147, Mismatches: 30, Indels: 44
0.67 0.14 0.20
Matches are distributed among these distances:
6 5 0.03
7 10 0.07
8 100 0.68
9 20 0.14
10 8 0.05
11 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (8 bp):
TATTATTA
Found at i:20668273 original size:5 final size:5
Alignment explanation
Indices: 20668242--20668445 Score: 88
Period size: 5 Copynumber: 39.8 Consensus size: 5
20668232 TTGCCCCTAT
* * *
20668242 TATTA TATTA CTACTA TACTA TCATTA TATTA TTGTTGTA GTATTA TATTA
1 TATTA TATTA -TATTA TATTA T-ATTA TATTA -T-AT-TA -TATTA TATTA
* *
20668293 TATTA T-TGTA -A-TA TATTGA TATTA TATTA CA-T- TATTA TATTA TGTTA
1 TATTA TAT-TA TATTA TATT-A TATTA TATTA TATTA TATTA TATTA TATTA
* * *
20668340 TA-T- TATTA TATTA TATTA GGA-TA TTATTA TACTA TTCTTA TAGCATTA
1 TATTA TATTA TATTA TATTA -TATTA -TATTA TATTA -TATTA T---ATTA
* * *
20668388 TATTA TTATTA TA-T- TATTA TATTA TATTA GATTA T-TTT TATTA TAATA
1 TATTA -TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
20668436 TTATTA TATT
1 -TATTA TATT
20668446 TGAAATTATT
Statistics
Matches: 152, Mismatches: 22, Indels: 50
0.68 0.10 0.22
Matches are distributed among these distances:
3 7 0.05
4 11 0.07
5 94 0.62
6 31 0.20
7 2 0.01
8 7 0.05
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:20668295 original size:24 final size:24
Alignment explanation
Indices: 20668265--20668366 Score: 84
Period size: 24 Copynumber: 4.2 Consensus size: 24
20668255 CTATACTATC
**
20668265 ATTATATTATTGTTGTAGTATT-AT
1 ATTATATTATTGTAATA-TATTGAT
20668289 ATTATATTATTGTAATATATTGAT
1 ATTATATTATTGTAATATATTGAT
* *
20668313 ATTATATTACAT-TATTATATT-AT
1 ATTATATTA-TTGTAATATATTGAT
* * *
20668336 GTTATATTATTATATTATATTAGGAT
1 ATTATATTATTGTAATATATT--GAT
20668362 ATTAT
1 ATTAT
20668367 TATACTATTC
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 23 0.35
24 34 0.52
25 1 0.02
26 6 0.09
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTATATTATTGTAATATATTGAT
Found at i:20668319 original size:13 final size:12
Alignment explanation
Indices: 20668283--20668439 Score: 81
Period size: 13 Copynumber: 12.5 Consensus size: 12
20668273 ATTGTTGTAG
20668283 TATTATATTATA
1 TATTATATTATA
*
20668295 TTATTGTA--ATA
1 -TATTATATTATA
20668306 TATTGATA-T-TA
1 TATT-ATATTATA
*
20668317 TATTACATTATTA
1 TATTATATTA-TA
*
20668330 TATTATGTTATA
1 TATTATATTATA
20668342 TTATTATATTATA
1 -TATTATATTATA
**
20668355 TTAGGATATTATTA
1 -TATTATATTA-TA
* *
20668369 TACTATTCTTATA
1 TATTA-TATTATA
*
20668382 GCATTATATTAT-
1 -TATTATATTATA
20668394 TATTATATTATTA
1 TATTATATTA-TA
*
20668407 TATTATATTAGA
1 TATTATATTATA
*
20668419 TTATTTTTATTATAA
1 -TA-TTATATTAT-A
20668434 TATTAT
1 TATTAT
20668440 TATATTTGAA
Statistics
Matches: 111, Mismatches: 19, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
10 6 0.05
11 21 0.19
12 4 0.04
13 61 0.55
14 18 0.16
15 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (12 bp):
TATTATATTATA
Found at i:20668346 original size:3 final size:3
Alignment explanation
Indices: 20668323--20668442 Score: 52
Period size: 3 Copynumber: 44.7 Consensus size: 3
20668313 ATTATATTAC
* **
20668323 ATT ATT A-T ATT A-T GTT A-T ATT ATT A-T ATT A-T ATT AGG A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * **
20668365 ATT A-T ACT ATT CTT A-T AGC ATT A-T ATT ATT ATT A-T ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
20668408 ATT A-T ATT A-G ATT ATT TTT ATT A-T AAT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20668443 ATTTGAAATT
Statistics
Matches: 87, Mismatches: 16, Indels: 28
0.66 0.12 0.21
Matches are distributed among these distances:
2 25 0.29
3 62 0.71
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:20668375 original size:11 final size:10
Alignment explanation
Indices: 20668239--20668444 Score: 68
Period size: 11 Copynumber: 19.1 Consensus size: 10
20668229 TTTTTGCCCC
20668239 TATTATTATA
1 TATTATTATA
* *
20668249 TTACTACTATA
1 -TATTATTATA
*
20668260 CTATCATTATA
1 -TATTATTATA
* *
20668271 TTATTGTTGTA
1 -TATTATTATA
20668282 GTATTA-TATTA
1 -TATTATTA-TA
20668293 TATTATTGTAATA
1 TATTA-T-T-ATA
20668306 TATTGA-TATTA
1 TATT-ATTA-TA
20668317 TATTACATTATTA
1 TATT--ATTA-TA
20668330 TATTATGT-TA
1 TATTAT-TATA
20668340 TATTATTATA
1 TATTATTATA
*
20668350 T-TATATTAGGA
1 TAT-TATTA-TA
20668361 TATTATTATA
1 TATTATTATA
*
20668371 CTATTCTTATA
1 -TATTATTATA
*
20668382 GCATTA-TAT-
1 -TATTATTATA
20668391 TATTATTATA
1 TATTATTATA
20668401 TTATTA-TATTA
1 -TATTATTA-TA
20668412 TATTAGATTAT-
1 TATT--ATTATA
*
20668423 TTTTATTATAA
1 TATTATTAT-A
20668434 TATTATTATA
1 TATTATTATA
20668444 T
1 T
20668445 TTGAAATTAT
Statistics
Matches: 148, Mismatches: 23, Indels: 49
0.67 0.10 0.22
Matches are distributed among these distances:
8 4 0.03
9 10 0.07
10 35 0.24
11 74 0.50
12 5 0.03
13 18 0.12
14 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (10 bp):
TATTATTATA
Found at i:20669384 original size:21 final size:21
Alignment explanation
Indices: 20669349--20669390 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20669339 ACTTTTTTAT
20669349 TTTTACTGACTATTTTATAAAA
1 TTTTACTGACTATTTT-TAAAA
*
20669371 TTTTA-TGGCTATTTTTAAAA
1 TTTTACTGACTATTTTTAAAA
20669391 AAAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTACTGACTATTTTTAAAA
Found at i:20683747 original size:41 final size:42
Alignment explanation
Indices: 20683684--20683795 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 42
20683674 ACCATCGAAA
* * * *
20683684 AAAATAATAATAATAGATAAATATACAT-TGATAGATAAATAT
1 AAAA-AATATTAATAGATAAATAAAAATATAATAGATAAATAT
20683726 AAAAAATATTAATAGATAAATAAAAATAATAATAGATAAATAT
1 AAAAAATATTAATAGATAAATAAAAAT-ATAATAGATAAATAT
20683769 AAAAAATATATATTAATAGATAAATAA
1 --AAAA-A-ATATTAATAGATAAATAA
20683796 TAAAAAAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
41 20 0.33
42 4 0.07
43 13 0.22
45 4 0.07
46 1 0.02
47 18 0.30
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (42 bp):
AAAAAATATTAATAGATAAATAAAAATATAATAGATAAATAT
Found at i:20683786 original size:27 final size:27
Alignment explanation
Indices: 20683755--20683912 Score: 128
Period size: 27 Copynumber: 5.8 Consensus size: 27
20683745 ATAAAAATAA
20683755 TAATAGATAAATATAAAAAATATATAT
1 TAATAGATAAATATAAAAAATATATAT
20683782 TAATAGATAAATAATAAAAAA-ATATAT
1 TAATAGATAAAT-ATAAAAAATATATAT
* **
20683809 TAATAAAT-AATA-AAACGTATATATAT
1 TAATAGATAAATATAAA-AAATATATAT
*
20683835 TAATAGATAAATA-AAAAAGATTAATAGAT
1 TAATAGATAAATATAAAAA-A-T-ATATAT
* * * *
20683864 AAATA-ATAATAAAAAAAAAATATTTAT
1 TAATAGATAA-ATATAAAAAATATATAT
* * *
20683891 AAATAAATAAAAATAAAAAATA
1 TAATAGATAAATATAAAAAATA
20683913 AAAATAAAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
24 3 0.03
25 2 0.02
26 16 0.15
27 53 0.49
28 18 0.17
29 12 0.11
30 5 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (27 bp):
TAATAGATAAATATAAAAAATATATAT
Found at i:20683844 original size:53 final size:48
Alignment explanation
Indices: 20683714--20683912 Score: 178
Period size: 52 Copynumber: 4.1 Consensus size: 48
20683704 ATATACATTG
*
20683714 ATAGATAAATAT--AAAA-A-ATATTAATAGATAAAT-AAAAATAATA
1 ATAGATAAATATAAAAAATATATATTAATAGATAAATAAAAAAAAATA
20683757 ATAGATAAATATAAAAAATATATATTAATAGATAAATAATAAAAAAATA
1 ATAGATAAATATAAAAAATATATATTAATAGATAAATAA-AAAAAAATA
* * *
20683806 TATTA-ATAAATAATAAAACGTATATATATTAATAGATAAATAAAAAAGATTA
1 -A-TAGATAAAT-ATAAAA--AATATATATTAATAGATAAATAAAAAAAAATA
* * * *
20683858 ATAGATAAATAATAATAAAAAAAAAATATTTATAAATAAATAAAAATAAAA-A
1 ATAGAT--A-AAT-ATAAAAAATATATATTAATAGATAAATAAAAA-AAAATA
20683910 ATA
1 ATA
20683913 AAAATAAAAA
Statistics
Matches: 129, Mismatches: 11, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
43 12 0.09
45 4 0.03
46 1 0.01
47 16 0.12
48 1 0.01
49 8 0.06
50 9 0.07
51 11 0.09
52 32 0.25
53 25 0.19
54 10 0.08
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.29
Consensus pattern (48 bp):
ATAGATAAATATAAAAAATATATATTAATAGATAAATAAAAAAAAATA
Found at i:20683866 original size:51 final size:48
Alignment explanation
Indices: 20683731--20683877 Score: 174
Period size: 50 Copynumber: 2.9 Consensus size: 48
20683721 AATATAAAAA
20683731 ATATTAATAGATAAATAAAAATAA-TAATAGATAAAT-ATAAAAAATAT
1 ATATTAATAGATAAATAAAAA-AATTAATAGATAAATAATAAAAAATAT
* *
20683778 ATATTAATAGATAAATAATAAAAAAATATATTA-ATAAATAATAAAACGTATAT
1 ATATTAATAGAT--A-AATAAAAAAAT-TAATAGATAAATAATAAAA--AATAT
20683831 ATATTAATAGATAAATAAAAAAGATTAATAGATAAATAATAATAAAA
1 ATATTAATAGATAAATAAAAAA-ATTAATAGATAAATAATAA-AAAA
20683878 AAAAAATATT
Statistics
Matches: 85, Mismatches: 4, Indels: 19
0.79 0.04 0.18
Matches are distributed among these distances:
47 12 0.14
49 3 0.04
50 28 0.33
51 24 0.28
52 2 0.02
53 16 0.19
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.30
Consensus pattern (48 bp):
ATATTAATAGATAAATAAAAAAATTAATAGATAAATAATAAAAAATAT
Found at i:20683882 original size:31 final size:31
Alignment explanation
Indices: 20683835--20683915 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 31
20683825 GTATATATAT
* *
20683835 TAATAGATAAATAAAAAAGATTAATAGATAAA
1 TAATA-ATAAAAAAAAAAGATTAATAAATAAA
* *
20683867 TAATAATAAAAAAAAAATATTTATAAATAAA
1 TAATAATAAAAAAAAAAGATTAATAAATAAA
*
20683898 TAAAAATAAAAAATAAAA
1 TAATAATAAAAAA-AAAA
20683916 ATAAAAATGC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 34 0.79
32 9 0.21
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (31 bp):
TAATAATAAAAAAAAAAGATTAATAAATAAA
Found at i:20683913 original size:13 final size:13
Alignment explanation
Indices: 20683889--20683922 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
20683879 AAAAATATTT
20683889 ATAAATAAATAAAA
1 ATAAA-AAATAAAA
20683903 ATAAAAAATAAAA
1 ATAAAAAATAAAA
20683916 ATAAAAA
1 ATAAAAA
20683923 TGCAAATGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:20684090 original size:5 final size:5
Alignment explanation
Indices: 20684082--20684114 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
20684072 TTTTACCTTT
*
20684082 TTTTG TTTTT TTTTG TTTTG -TTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
20684115 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:20684175 original size:44 final size:43
Alignment explanation
Indices: 20684140--20684645 Score: 501
Period size: 44 Copynumber: 11.5 Consensus size: 43
20684130 AATTTTGATC
* * *
20684140 AAAGCTCCTCTAAACAGAGACTCAACGACTTTAAAAAATATAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAA-ATAAAT
* * ** * * * * *
20684185 AAAGTTTCTCTACTCAAAGGCTTAACGATTTTGGAAAAGTAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAAT
* ** * * *
20684229 AGAGCTCCTCTAATTAGAGGCTCAATGACTTTTAGAAAGATAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGAC-TTT-GAAAAATAAAT
20684274 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* *
20684317 AAAGCTCCTCTAAATAGAGGCTCAATGACTTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGAC-TTTGAAAAATAAAT
* * *
20684361 AAAGCTTCTCTAAACAGAGACTCAACAACTTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGAC-TTTGAAAAATAAAT
*
20684405 AAAGCTCTTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAAATAAAT
* * * *
20684449 AAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGGAAAAGTAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAAT
* ** * * *
20684493 AAAGCTCTTCTAATTAGAGGCTCAATGACTTGGAAAAATAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * * *
20684536 AAAGCTCTTCTAAGCAGAGGCTCCACAACTTTAGAAAAATAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAAT
* * * *
20684580 AAAGCTCCTCTAAGCAAAGGCTCAACGAC-CTGAAAAAATAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAAATAAAT
**
20684623 AAAGCTCCTCTAAGTAGAGGCTC
1 AAAGCTCCTCTAAACAGAGGCTC
20684646 CATAACTTTT
Statistics
Matches: 392, Mismatches: 63, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.00
43 108 0.28
44 217 0.55
45 66 0.17
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (43 bp):
AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
Found at i:20684438 original size:87 final size:87
Alignment explanation
Indices: 20684139--20684665 Score: 540
Period size: 87 Copynumber: 6.0 Consensus size: 87
20684129 AAATTTTGAT
* * * * ** *
20684139 CAAAGCTCCTCTAAACAGAGACTCAACGACTTTAAAAAATATAAACAAAGTTTCTCTACTCAAAG
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAA-ATAAACAAAGCTCCTCTAAGCAGAG
* * *
20684204 GCTTAACGA-TTTTGGAAAAGTAAA
64 GCTCAACAACTTTT-GAAAAATAAA
* ** * * *
20684228 CAGAGCTCCTCTAATTAGAGGCTCAATGACTTTTAGAAAGATAAACAAAGCTCCTCTAAACAGAG
1 CAAAGCTCCTCTAAACAGAGGCTCAACGAC-TTT-GAAAAATAAACAAAGCTCCTCTAAGCAGAG
*
20684293 GCTCAACGAC-TTTGAAAAATAAA
64 GCTCAACAACTTTTGAAAAATAAA
* * * * * * *
20684316 TAAAGCTCCTCTAAATAGAGGCTCAATGACTTTTGAAAAATAAATAAAGCTTCTCTAAACAGAGA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGAC-TTTGAAAAATAAACAAAGCTCCTCTAAGCAGAGG
20684381 CTCAACAACTTTTGAAAAATAAA
65 CTCAACAACTTTTGAAAAATAAA
* * *
20684404 TAAAGCTCTTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAATAAAGCTCCTCTAAGCAGAGG
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAAATAAACAAAGCTCCTCTAAGCAGAGG
** * *
20684469 CTCAATGACTTTGGAAAAGTAAA
65 CTCAACAACTTTTGAAAAATAAA
* ** * * *
20684492 CAAAGCTCTTCTAATTAGAGGCTCAATGACTTGGAAAAATAAACAAAGCTCTTCTAAGCAGAGGC
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAGCAGAGGC
* *
20684557 TCCACAACTTTAGAAAAATAAA
66 TCAACAACTTTTGAAAAATAAA
* * * *
20684579 CAAAGCTCCTCTAAGCAAAGGCTCAACGAC-CTGAAAAAATAAACAAAGCTCCTCTAAGTAGAGG
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAAATAAACAAAGCTCCTCTAAGCAGAGG
* *
20684643 CTCCATAACTTTT-AAACAATAAA
65 CTCAACAACTTTTGAAA-AATAAA
20684666 TTGCTCCTAA
Statistics
Matches: 377, Mismatches: 55, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
86 4 0.01
87 155 0.41
88 155 0.41
89 56 0.15
90 7 0.02
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (87 bp):
CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAGCAGAGGC
TCAACAACTTTTGAAAAATAAA
Found at i:20686315 original size:10 final size:10
Alignment explanation
Indices: 20686286--20686341 Score: 62
Period size: 9 Copynumber: 5.7 Consensus size: 10
20686276 CTTTTTCTCC
*
20686286 TTTCATCTTT
1 TTTCATTTTT
*
20686296 TTACATTTTTT
1 TTTCA-TTTTT
20686307 TTTCATTTTT
1 TTTCATTTTT
*
20686317 TTT-ATTTGT
1 TTTCATTTTT
20686326 TTTCA-TTTT
1 TTTCATTTTT
20686335 TTTCATT
1 TTTCATT
20686342 CTTTCACCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 16 0.42
10 14 0.37
11 8 0.21
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:20687226 original size:19 final size:19
Alignment explanation
Indices: 20687202--20687247 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
20687192 ATACCAAATG
20687202 AAATCCTACTACCTAAAAA
1 AAATCCTACTACCTAAAAA
*
20687221 AAATCCTACTACCTAAAAG
1 AAATCCTACTACCTAAAAA
20687240 AAATCCTA
1 AAATCCTA
20687248 ACATTACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.22
Consensus pattern (19 bp):
AAATCCTACTACCTAAAAA
Found at i:20691589 original size:24 final size:24
Alignment explanation
Indices: 20691562--20691607 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
20691552 GGTTGTTCCT
*
20691562 ATGTGTTTCTGACCTCTTTGTTTC
1 ATGTGTTTCTGACCTCTCTGTTTC
20691586 ATGTGTTTCTGACCTCTCTGTT
1 ATGTGTTTCTGACCTCTCTGTT
20691608 CCCCTTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.09, C:0.22, G:0.17, T:0.52
Consensus pattern (24 bp):
ATGTGTTTCTGACCTCTCTGTTTC
Found at i:20692160 original size:29 final size:29
Alignment explanation
Indices: 20692139--20692283 Score: 84
Period size: 27 Copynumber: 5.4 Consensus size: 29
20692129 AATATACATT
* *
20692139 GATAGATAAATATAAAAAAAATATTAATA
1 GATAAATAAAAATAAAAAAAATATTAATA
20692168 GATAAATAAAAAT----AAAA-A-TAATA
1 GATAAATAAAAATAAAAAAAATATTAATA
* * * *
20692191 GATAAAT-ATAA-AAAATATACATTAATA
1 GATAAATAAAAATAAAAAAAATATTAATA
20692218 GATAAAT---AATAAAAAAATATATTAATA
1 GATAAATAAAAATAAAAAAA-ATATTAATA
** * *
20692245 -A-ACAATAAAAAT-GTATATATATTAATA
1 GATA-AATAAAAATAAAAAAAATATTAATA
20692272 GATAAATAAAAA
1 GATAAATAAAAA
20692284 AATTAATAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
22 3 0.03
23 12 0.13
24 1 0.01
25 9 0.10
26 10 0.11
27 29 0.32
28 11 0.12
29 15 0.17
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (29 bp):
GATAAATAAAAATAAAAAAAATATTAATA
Found at i:20692205 original size:27 final size:26
Alignment explanation
Indices: 20692140--20692233 Score: 115
Period size: 27 Copynumber: 3.7 Consensus size: 26
20692130 ATATACATTG
*
20692140 ATAGATAAATATAAAAAA-AATATTA
1 ATAGATAAATATAAAAAATAAAATTA
*
20692165 ATAGAT-AA-AT-AAAAATAAAAATA
1 ATAGATAAATATAAAAAATAAAATTA
*
20692188 ATAGATAAATATAAAAAATATACATTA
1 ATAGATAAATATAAAAAATA-AAATTA
20692215 ATAGATAAATAATAAAAAA
1 ATAGATAAAT-ATAAAAAA
20692234 ATATATTAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.08
23 13 0.22
24 4 0.07
25 8 0.14
26 7 0.12
27 14 0.24
28 8 0.14
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (26 bp):
ATAGATAAATATAAAAAATAAAATTA
Found at i:20692246 original size:50 final size:49
Alignment explanation
Indices: 20692144--20692333 Score: 192
Period size: 50 Copynumber: 3.8 Consensus size: 49
20692134 ACATTGATAG
*
20692144 ATAAATATAAAAAA-A-ATATTAATAGATAAATAAAAATAAAA-ATAATA
1 ATAAATATAAAAAATATATATTAATAGATAAATAAAAA-AAAATATATTA
*
20692191 GATAAATATAAAAAATATACATTAATAGATAAATAATAAAAAAATATATTA
1 -ATAAATATAAAAAATATATATTAATAGATAAATAA-AAAAAAATATATTA
* * *
20692242 ATAAACAATAAAAATGTATATATATTAATAGATAAAT-AAAAAAATTA-ATAA
1 ATAAA-TATAAAAA---ATATATATTAATAGATAAATAAAAAAAAATATATTA
* *
20692293 ATAAATAATAATAATAATATATATTTATAAATAAATAAAAA
1 ATAAAT-ATAA-AA-AATATATATTAATAGATAAATAAAAA
20692334 TACAAATAGG
Statistics
Matches: 121, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
48 14 0.12
49 1 0.01
50 44 0.36
51 31 0.26
52 10 0.08
53 2 0.02
54 19 0.16
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (49 bp):
ATAAATATAAAAAATATATATTAATAGATAAATAAAAAAAAATATATTA
Found at i:20694617 original size:50 final size:50
Alignment explanation
Indices: 20694550--20694688 Score: 172
Period size: 50 Copynumber: 2.8 Consensus size: 50
20694540 AGTTTTGAGA
* *
20694550 AAGATGAAATTTATAAAGTTGTTGAGCCTCTACTTAGAGGAGGTTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGATTTTTTC
* * * * *
20694600 AAGATGAAATTTTTAAAGTTATTAAGTCTCTACCTAGAGGAGATTTTTTT
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGATTTTTTC
* * *
20694650 AAGAT-TAATTTTTAAAAGTTGTTGAGCCTTTGCTTAGAG
1 AAGATGAAATTTTT-AAAGTTGTTGAGCCTCTACTTAGAG
20694689 AAGCTTATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
49 7 0.09
50 67 0.91
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (50 bp):
AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGATTTTTTC
Found at i:20694816 original size:49 final size:49
Alignment explanation
Indices: 20694717--20694980 Score: 168
Period size: 49 Copynumber: 5.4 Consensus size: 49
20694707 AAAAGCCTTC
* * * *
20694717 AAACCTCTGTTTAGAGGAGCCTTTTTCCAAGATGAAATCTTTAAAGTTGTT
1 AAACCTCTGCTTAAAGGAG-CTTTTTTCAAGAT-AAATTTTTAAAGTTGTT
* *
20694768 AAATCTTTGCTTAAAGGAGCTTTTTTCAAGATAAATTTTTAAAGTTGTT
1 AAACCTCTGCTTAAAGGAGCTTTTTTCAAGATAAATTTTTAAAGTTGTT
* ** * *** * *
20694817 GATTCTCTGCTTAGAGGAGCCCATTT----AT--ATTTTCAAAAGTCGTT
1 AAACCTCTGCTTAAAGGAGCTTTTTTCAAGATAAATTTT-TAAAGTTGTT
* *
20694861 GAGCCTCTGCTTAGAA-GA-CTCTTTTTCCAAGATAAATTCTTTAAAGTTGTT
1 AAACCTCTGCTTA-AAGGAGCT-TTTTT-CAAGATAAATT-TTTAAAGTTGTT
* * * * * * *
20694912 GAGCTTCTACTTAGAGGAGC-TTTTCCAAGATGAAAATTTTAAAGTTGTT
1 AAACCTCTGCTTAAAGGAGCTTTTTTCAAGAT-AAATTTTTAAAGTTGTT
*
20694961 AAACCTATGCTTAAAGGAGC
1 AAACCTCTGCTTAAAGGAGC
20694981 CAATTTATAT
Statistics
Matches: 165, Mismatches: 34, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
43 6 0.04
44 24 0.15
45 3 0.02
49 69 0.42
50 21 0.13
51 39 0.24
52 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (49 bp):
AAACCTCTGCTTAAAGGAGCTTTTTTCAAGATAAATTTTTAAAGTTGTT
Found at i:20695002 original size:144 final size:145
Alignment explanation
Indices: 20694564--20695023 Score: 481
Period size: 144 Copynumber: 3.2 Consensus size: 145
20694554 TGAAATTTAT
* * * * *
20694564 AAAGTTGTTGAGCCTCTACTTAGAGGAGGT-TTTTT-CAAGATGAAATT-TTTAAAGTTATTAAG
1 AAAGTCGTTGAGCCTCTGCTTAGAAGAGCTCTTTTTCCAAGATGAAATTCTTTAAAGTTGTTAAG
* * * * * * *
20694626 -TCTCTACCTAGAGGAGATTTTTTTAAGATTAATTTTTAAAAGTTGTTGAGCCTTTGCTTAGAGA
66 CT-TCTACTTAGAGGAG-CTTTTTCAAGATAAATTTTT-AAAGTTGTTGAACCTATGCTTAGAGG
**
20694690 AGCTTATTTATATTTTCA
128 AGCCAATTTATATTTTCA
* * * * *
20694708 AAAG-CCTTCAAACCTCTGTTTAGAGGAGC-CTTTTTCCAAGATGAAA-TCTTTAAAGTTGTTAA
1 AAAGTCGTT-GAGCCTCTGCTTAGAAGAGCTCTTTTTCCAAGATGAAATTCTTTAAAGTTGTT-A
* * * ** *
20694770 ATCTT-TGCTTAAAGGAGCTTTTTTCAAGATAAATTTTTAAAGTTGTTGATTCTCTGCTTAGAGG
64 AGCTTCTACTTAGAGGAGC-TTTTTCAAGATAAATTTTTAAAGTTGTTGAACCTATGCTTAGAGG
*
20694834 AGCCCATTTATATTTTCA
128 AGCCAATTTATATTTTCA
*
20694852 AAAGTCGTTGAGCCTCTGCTTAGAAGA-CTCTTTTTCCAAGAT-AAATTCTTTAAAGTTGTTGAG
1 AAAGTCGTTGAGCCTCTGCTTAGAAGAGCTCTTTTTCCAAGATGAAATTCTTTAAAGTTGTTAAG
* * * *
20694915 CTTCTACTTAGAGGAGCTTTTCCAAGATGAAAATTTTAAAGTTGTTAAACCTATGCTTAAAGGAG
66 CTTCTACTTAGAGGAGCTTTTTCAAGAT-AAATTTTTAAAGTTGTTGAACCTATGCTTAGAGGAG
20694980 CCAATTTATATTTTCA
130 CCAATTTATATTTTCA
* * *
20694996 AAAGTCGTTGGGCCTTTCCTTAGAAGAG
1 AAAGTCGTTGAGCCTCTGCTTAGAAGAG
20695024 TCCATTTATA
Statistics
Matches: 262, Mismatches: 41, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
143 20 0.08
144 188 0.72
145 50 0.19
146 3 0.01
147 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (145 bp):
AAAGTCGTTGAGCCTCTGCTTAGAAGAGCTCTTTTTCCAAGATGAAATTCTTTAAAGTTGTTAAG
CTTCTACTTAGAGGAGCTTTTTCAAGATAAATTTTTAAAGTTGTTGAACCTATGCTTAGAGGAGC
CAATTTATATTTTCA
Found at i:20696874 original size:8 final size:8
Alignment explanation
Indices: 20696851--20696888 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
20696841 TCAAATATTT
20696851 AAATAA-A
1 AAATAATA
20696858 AAATAAATA
1 AAAT-AATA
20696867 AAATAATA
1 AAATAATA
20696875 AAATAATA
1 AAATAATA
20696883 AAATAA
1 AAATAA
20696889 AATGTGCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 4 0.14
8 20 0.69
9 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAATAATA
Found at i:20699823 original size:2 final size:2
Alignment explanation
Indices: 20699816--20699860 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
20699806 GACAATAATT
* * *
20699816 TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20699858 TA T
1 TA T
20699861 TAAATAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:20701332 original size:8 final size:8
Alignment explanation
Indices: 20701309--20701342 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
20701299 TTAAGAAAGC
20701309 TATAAAAA
1 TATAAAAA
20701317 T-TATAAAA
1 TATA-AAAA
20701325 TATAAAAA
1 TATAAAAA
20701333 TATAAAAA
1 TATAAAAA
20701341 TA
1 TA
20701343 CATAAACAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 2 0.08
8 20 0.83
9 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TATAAAAA
Found at i:20705494 original size:13 final size:14
Alignment explanation
Indices: 20705466--20705498 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20705456 AAGTCCATTT
*
20705466 TGATTAAATATGAA
1 TGATCAAATATGAA
20705480 TGATCAAAT-TGAA
1 TGATCAAATATGAA
20705493 TGATCA
1 TGATCA
20705499 TGTATTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (14 bp):
TGATCAAATATGAA
Found at i:20706923 original size:24 final size:24
Alignment explanation
Indices: 20706888--20707119 Score: 202
Period size: 24 Copynumber: 9.5 Consensus size: 24
20706878 AGTTCAAAAT
*
20706888 AATGAGAATCTTTAAGGAGTTTTA
1 AATGAGAATCTTTAAGAAGTTTTA
*
20706912 AATGAGATTCTTTAAGAAGTTTTA
1 AATGAGAATCTTTAAGAAGTTTTA
***
20706936 AATGAGAATCTTTGTCTTTAAGTTTTA
1 AATGAGAATC-TT-T-AAGAAGTTTTA
*
20706963 AATGAGAATCTTTAAGGAGTTTTA
1 AATGAGAATCTTTAAGAAGTTTTA
* *
20706987 AATGAGATTCTTTATGAAGTTTTA
1 AATGAGAATCTTTAAGAAGTTTTA
***
20707011 AATGAGAATCTTTTTCTTTAAGTTTTA
1 AATGAGAATC--TTT-AAGAAGTTTTA
* * * *
20707038 AATAAGAATCTGTAA-AGTGTTTTG
1 AATGAGAATCTTTAAGA-AGTTTTA
* *
20707062 AATGAGAAACTTT---ATGTTTTA
1 AATGAGAATCTTTAAGAAGTTTTA
*
20707083 AATGAGAATCTTTAAGAAGTTTTG
1 AATGAGAATCTTTAAGAAGTTTTA
*
20707107 AATGAGAACCTTT
1 AATGAGAATCTTT
20707120 GAATTTAGAT
Statistics
Matches: 168, Mismatches: 30, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
21 18 0.11
22 1 0.01
23 1 0.01
24 101 0.60
25 5 0.03
26 6 0.04
27 36 0.21
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (24 bp):
AATGAGAATCTTTAAGAAGTTTTA
Found at i:20706963 original size:51 final size:48
Alignment explanation
Indices: 20706888--20707119 Score: 195
Period size: 51 Copynumber: 4.8 Consensus size: 48
20706878 AGTTCAAAAT
* * *
20706888 AATGAGAATCTTTAAGGAGTTTTAAATGAGATTCTTTAAGAAGTTTTA
1 AATGAGAATCTTTATGAAGTTTTAAATGAGAATCTTTAAGAAGTTTTA
* * *
20706936 AATGAGAATCTTTGTCTTTAAGTTTTAAATGAGAATCTTTAAGGAGTTTTA
1 AATGAGAATC-TT-T-ATGAAGTTTTAAATGAGAATCTTTAAGAAGTTTTA
* ***
20706987 AATGAGATTCTTTATGAAGTTTTAAATGAGAATCTTTTTCTTTAAGTTTTA
1 AATGAGAATCTTTATGAAGTTTTAAATGAGAATC--TTT-AAGAAGTTTTA
* * * * *
20707038 AATAAGAATCTGTA--AAGTGTTTTGAATGAGAAACTTT---ATGTTTTA
1 AATGAGAATCTTTATGAA--GTTTTAAATGAGAATCTTTAAGAAGTTTTA
* * *
20707083 AATGAGAATCTTTAAGAAGTTTTGAATGAGAACCTTT
1 AATGAGAATCTTTATGAAGTTTTAAATGAGAATCTTT
20707120 GAATTTAGAT
Statistics
Matches: 152, Mismatches: 22, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
45 37 0.24
47 2 0.01
48 29 0.19
49 8 0.05
50 6 0.04
51 70 0.46
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (48 bp):
AATGAGAATCTTTATGAAGTTTTAAATGAGAATCTTTAAGAAGTTTTA
Found at i:20706973 original size:75 final size:74
Alignment explanation
Indices: 20706888--20707095 Score: 303
Period size: 75 Copynumber: 2.8 Consensus size: 74
20706878 AGTTCAAAAT
20706888 AATGAGAATCTTTAAGGAGTTTTAAATGAGATTCTTTAAGAAGTTTTAAATGAGAATCTTTGTCT
1 AATGAGAATCTTTAAGGAGTTTTAAATGAGATTCTTT-AGAAGTTTTAAATGAGAATCTTTGTCT
20706953 TTAAGTTTTA
65 TTAAGTTTTA
*
20706963 AATGAGAATCTTTAAGGAGTTTTAAATGAGATTCTTTATGAAGTTTTAAATGAGAATCTTTTTCT
1 AATGAGAATCTTTAAGGAGTTTTAAATGAGATTCTTTA-GAAGTTTTAAATGAGAATCTTTGTCT
20707028 TTAAGTTTTA
65 TTAAGTTTTA
* * * * * ** *
20707038 AATAAGAATCTGTAAAGTGTTTTGAATGAGAAACTTT--ATGTTTTAAATGAGAATCTTT
1 AATGAGAATCTTTAAGGAGTTTTAAATGAGATTCTTTAGAAGTTTTAAATGAGAATCTTT
20707096 AAGAAGTTTT
Statistics
Matches: 123, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
72 20 0.16
74 1 0.01
75 102 0.83
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (74 bp):
AATGAGAATCTTTAAGGAGTTTTAAATGAGATTCTTTAGAAGTTTTAAATGAGAATCTTTGTCTT
TAAGTTTTA
Found at i:20707091 original size:45 final size:45
Alignment explanation
Indices: 20707026--20707119 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
20707016 GAATCTTTTT
*
20707026 CTTTAAGTTTTAAATAAGAATCTGTAAAG-TGTTTTGAATGAGAAA
1 CTTTAAGTTTTAAATAAGAATCT-TAAAGAAGTTTTGAATGAGAAA
* * * *
20707071 CTTTATGTTTTAAATGAGAATCTTTAAGAAGTTTTGAATGAGAAC
1 CTTTAAGTTTTAAATAAGAATCTTAAAGAAGTTTTGAATGAGAAA
20707116 CTTT
1 CTTT
20707120 GAATTTAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 4 0.09
45 39 0.91
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (45 bp):
CTTTAAGTTTTAAATAAGAATCTTAAAGAAGTTTTGAATGAGAAA
Found at i:20707584 original size:18 final size:18
Alignment explanation
Indices: 20707563--20707602 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20707553 TTTTTGAATT
*
20707563 TGAAAATTTTTGTGAAAC
1 TGAAAATTCTTGTGAAAC
*
20707581 TGAAAATTCTTGTGAATC
1 TGAAAATTCTTGTGAAAC
20707599 TGAA
1 TGAA
20707603 TATCTTGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (18 bp):
TGAAAATTCTTGTGAAAC
Found at i:20707630 original size:16 final size:16
Alignment explanation
Indices: 20707606--20707636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20707596 ATCTGAATAT
20707606 CTTGCGAATCTTTGAC
1 CTTGCGAATCTTTGAC
*
20707622 CTTGTGAATCTTTGA
1 CTTGCGAATCTTTGA
20707637 ATTACAAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (16 bp):
CTTGCGAATCTTTGAC
Found at i:20707859 original size:83 final size:83
Alignment explanation
Indices: 20707720--20707877 Score: 298
Period size: 83 Copynumber: 1.9 Consensus size: 83
20707710 TACTGATTAT
*
20707720 TGGATTGAAAAGTTCTTGAATATTTCAAATTGTGAAACTTTGGAGTTTTGAGATTTAGTAATTGT
1 TGGATTGAAAAGTTCTTGAATATTTCAAATTGTGAAACTTTGGAGTTTCGAGATTTAGTAATTGT
20707785 TGTTAAGCTATAATCAGA
66 TGTTAAGCTATAATCAGA
*
20707803 TGGATTGCAAAGTTCTTGAATATTTCAAATTGTGAAACTTTGGAGTTTCGAGATTTAGTAATTGT
1 TGGATTGAAAAGTTCTTGAATATTTCAAATTGTGAAACTTTGGAGTTTCGAGATTTAGTAATTGT
20707868 TGTTAAGCTA
66 TGTTAAGCTA
20707878 CAACTAGACG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (83 bp):
TGGATTGAAAAGTTCTTGAATATTTCAAATTGTGAAACTTTGGAGTTTCGAGATTTAGTAATTGT
TGTTAAGCTATAATCAGA
Found at i:20708880 original size:4 final size:4
Alignment explanation
Indices: 20708871--20708917 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
20708861 ATCGAGCCCT
* * *
20708871 TTTA TTTA TTTA TGGT- TTTA TTTG TTTA GTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
20708918 TAGTTTTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 1 0.03
4 33 0.94
5 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:20708891 original size:16 final size:16
Alignment explanation
Indices: 20708870--20708915 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
20708860 AATCGAGCCC
20708870 TTTTATTTATTTATGG
1 TTTTATTTATTTATGG
* *
20708886 TTTTATTTGTTTA-GT
1 TTTTATTTATTTATGG
20708901 TATTTATTTATTTAT
1 T-TTTATTTATTTAT
20708916 TTTAGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (16 bp):
TTTTATTTATTTATGG
Found at i:20708975 original size:16 final size:16
Alignment explanation
Indices: 20708954--20708985 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20708944 TAGGAAAGCT
*
20708954 ATAAAAATTATAAAAA
1 ATAAAAAATATAAAAA
20708970 ATAAAAAATATAAAAA
1 ATAAAAAATATAAAAA
20708986 TACATAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAAAAATATAAAAA
Found at i:20710996 original size:14 final size:15
Alignment explanation
Indices: 20710971--20710999 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20710961 AGCAATGCCT
20710971 CTTCCATTTTCTTTC
1 CTTCCATTTTCTTTC
20710986 CTTCC-TTTTCTTTC
1 CTTCCATTTTCTTTC
20711000 AAGTCAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTCCATTTTCTTTC
Found at i:20713682 original size:28 final size:29
Alignment explanation
Indices: 20713651--20713709 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
20713641 AAAAAGTAAC
* *
20713651 TTATTATTTGATTACATTGAAGCAT-AAT
1 TTATTATATGATTACAATGAAGCATGAAT
20713679 TTATTATATGATTACAATGAAGCATGAAT
1 TTATTATATGATTACAATGAAGCATGAAT
20713708 TT
1 TT
20713710 GGAAGAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (29 bp):
TTATTATATGATTACAATGAAGCATGAAT
Found at i:20714278 original size:2 final size:2
Alignment explanation
Indices: 20714273--20714300 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20714263 ATGTTAAATG
20714273 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
20714301 ACATAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20721590 original size:19 final size:19
Alignment explanation
Indices: 20721552--20721590 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20721542 TATTTAATAT
* **
20721552 TAAAATTTAAATTTTTTAA
1 TAAAATTAAAATTTCATAA
20721571 TAAAATTAAAATTTCATAA
1 TAAAATTAAAATTTCATAA
20721590 T
1 T
20721591 TTTTAATGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAATTAAAATTTCATAA
Found at i:20721685 original size:25 final size:26
Alignment explanation
Indices: 20721624--20721687 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 26
20721614 AATATATTAT
*
20721624 ATAATTTTAAA-ATA-TAAAAAAAATT
1 ATAA-TTTAAAGATATTAAAAAAAATC
* *
20721649 AAAATTT-TAGATATTAAAAAAAA-C
1 ATAATTTAAAGATATTAAAAAAAATC
20721673 ATAATTTAAAGATAT
1 ATAATTTAAAGATAT
20721688 CCCAAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.03
24 12 0.39
25 18 0.58
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (26 bp):
ATAATTTAAAGATATTAAAAAAAATC
Found at i:20723178 original size:8 final size:7
Alignment explanation
Indices: 20723152--20723176 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20723142 TTTATTAATT
20723152 TTTTAAA
1 TTTTAAA
20723159 TTTTAAA
1 TTTTAAA
20723166 TTTTAAA
1 TTTTAAA
20723173 TTTT
1 TTTT
20723177 TATATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:20723194 original size:13 final size:13
Alignment explanation
Indices: 20723172--20723210 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
20723162 TAAATTTTAA
*
20723172 ATTTTTATATATT
1 ATTTTAATATATT
**
20723185 ATTTTAATATAAA
1 ATTTTAATATATT
20723198 ATTTTAATATATT
1 ATTTTAATATATT
20723211 TAAGTAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:20723291 original size:17 final size:18
Alignment explanation
Indices: 20723247--20723289 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
20723237 ATTTTTATTT
* *
20723247 TATAAAAATTTAAAAATA
1 TATATAAATTAAAAAATA
20723265 TATATAAATTAAAAAATA
1 TATATAAATTAAAAAATA
20723283 TATATAA
1 TATATAA
20723290 TTCGATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATATAAATTAAAAAATA
Found at i:20724106 original size:8 final size:7
Alignment explanation
Indices: 20724055--20724105 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
20724045 AAATAAAATT
20724055 AAAAGTA
1 AAAAGTA
20724062 AAAA--A
1 AAAAGTA
*
20724067 AAAAGTC
1 AAAAGTA
* *
20724074 AAATGTC
1 AAAAGTA
*
20724081 AAAGGTA
1 AAAAGTA
20724088 AAAAGTA
1 AAAAGTA
20724095 AAAAGTA
1 AAAAGTA
20724102 AAAA
1 AAAA
20724106 AAAAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 5 0.14
7 32 0.86
ACGTcount: A:0.69, C:0.04, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAGTA
Found at i:20725185 original size:21 final size:21
Alignment explanation
Indices: 20725155--20725198 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20725145 ATAATTATTA
20725155 ATTAAGTGCATGATAATTGAT
1 ATTAAGTGCATGATAATTGAT
* * *
20725176 ATTAATTGCATTATAATTTAT
1 ATTAAGTGCATGATAATTGAT
20725197 AT
1 AT
20725199 GTTATGTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTAAGTGCATGATAATTGAT
Found at i:20725232 original size:21 final size:24
Alignment explanation
Indices: 20725208--20725262 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
20725198 TGTTATGTTA
*
20725208 TTGCATGATA-TAC-T-ATATTTT
1 TTGCATGATATTACATGATATTAT
*
20725229 TTGCATGATATTGCATGATATTAT
1 TTGCATGATATTACATGATATTAT
20725253 TTGCATGATA
1 TTGCATGATA
20725263 ATTTTTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
22 2 0.07
23 1 0.03
24 16 0.55
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (24 bp):
TTGCATGATATTACATGATATTAT
Found at i:20726586 original size:21 final size:21
Alignment explanation
Indices: 20726562--20726609 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
20726552 ACTAACCCTT
*
20726562 TTATGTTGTTCTTTGCATATA
1 TTATGTTGTTATTTGCATATA
* *
20726583 TTATATTGTTATTTGTATATA
1 TTATGTTGTTATTTGCATATA
20726604 TTATGT
1 TTATGT
20726610 GTATACTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.12, T:0.60
Consensus pattern (21 bp):
TTATGTTGTTATTTGCATATA
Found at i:20729235 original size:38 final size:38
Alignment explanation
Indices: 20729193--20729308 Score: 124
Period size: 38 Copynumber: 3.3 Consensus size: 38
20729183 ACTTGTCATT
20729193 TTAGGATTTCTTTGGAATAATGGACTTATTTTATTGTA
1 TTAGGATTTCTTTGGAATAATGGACTTATTTTATTGTA
* * *
20729231 TTAGGATTTCATTT-G-A-AAT-TAC-T-TGTCA-T-T-
1 TTAGGATTTC-TTTGGAATAATGGACTTATTTTATTGTA
*
20729261 TTAGGATTTCTTTGGAATAATGGGCTTATTTTATTGTA
1 TTAGGATTTCTTTGGAATAATGGACTTATTTTATTGTA
20729299 TTAGGATTTC
1 TTAGGATTTC
20729309 ATTTTATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
29 3 0.05
30 11 0.18
31 2 0.03
32 4 0.07
33 4 0.07
34 2 0.03
35 5 0.08
36 4 0.07
37 2 0.03
38 21 0.34
39 3 0.05
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (38 bp):
TTAGGATTTCTTTGGAATAATGGACTTATTTTATTGTA
Found at i:20729260 original size:68 final size:68
Alignment explanation
Indices: 20729175--20729312 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
20729165 AAAAGGCTGA
20729175 TTGAAACTACTTGTCATTTTAGGATTTCTTTGGAATAATGGACTTATTTTATTGTATTAGGATTT
1 TTGAAACTACTTGTCATTTTAGGATTTCTTTGGAATAATGGACTTATTTTATTGTATTAGGATTT
20729240 CAT
66 CAT
* *
20729243 TTGAAATTACTTGTCATTTTAGGATTTCTTTGGAATAATGGGCTTATTTTATTGTATTAGGATTT
1 TTGAAACTACTTGTCATTTTAGGATTTCTTTGGAATAATGGACTTATTTTATTGTATTAGGATTT
20729308 CAT
66 CAT
20729311 TT
1 TT
20729313 TATTTTATAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (68 bp):
TTGAAACTACTTGTCATTTTAGGATTTCTTTGGAATAATGGACTTATTTTATTGTATTAGGATTT
CAT
Found at i:20731341 original size:22 final size:22
Alignment explanation
Indices: 20731316--20731428 Score: 73
Period size: 24 Copynumber: 5.0 Consensus size: 22
20731306 GAAAAAGAAC
*
20731316 CTTTGAAACTTTGGATGTGAAT
1 CTTTGAAATTTTGGATGTGAAT
* ** *
20731338 CTTTAAAAGTTTTCAAATGTGGAT
1 CTTTGAAA-TTTT-GGATGTGAAT
*
20731362 CTTTGAAATTTTGGATGTGAAA
1 CTTTGAAATTTTGGATGTGAAT
** * * *
20731384 CCATAAAATTTTTTAGATGAGAAT
1 CTTTGAAA--TTTTGGATGTGAAT
* *
20731408 ATTTGAAATTTTGGTTGTGAA
1 CTTTGAAATTTTGGATGTGAA
20731429 ATTTTAAAGT
Statistics
Matches: 64, Mismatches: 23, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
22 28 0.44
23 7 0.11
24 29 0.45
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (22 bp):
CTTTGAAATTTTGGATGTGAAT
Found at i:20731391 original size:46 final size:46
Alignment explanation
Indices: 20731280--20731429 Score: 133
Period size: 46 Copynumber: 3.3 Consensus size: 46
20731270 AATGAGAATC
* * * * * *
20731280 TTTGGGTGTGAAGCCAT-AAAGTTTTTGAAA-AAGAACCTTTGAAAC
1 TTTGGATGTGAAACCATAAAAG-TTTTCAAATGAGAATCTTTGAAAT
* ** * *
20731325 TTTGGATGTGAATCTTTAAAAGTTTTCAAATGTGGATCTTTGAAAT
1 TTTGGATGTGAAACCATAAAAGTTTTCAAATGAGAATCTTTGAAAT
* * * *
20731371 TTTGGATGTGAAACCATAAAATTTTTTAGATGAGAATATTTGAAAT
1 TTTGGATGTGAAACCATAAAAGTTTTCAAATGAGAATCTTTGAAAT
*
20731417 TTTGGTTGTGAAA
1 TTTGGATGTGAAA
20731430 TTTTAAAGTT
Statistics
Matches: 83, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
45 20 0.24
46 63 0.76
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.39
Consensus pattern (46 bp):
TTTGGATGTGAAACCATAAAAGTTTTCAAATGAGAATCTTTGAAAT
Found at i:20731707 original size:35 final size:38
Alignment explanation
Indices: 20731644--20731713 Score: 92
Period size: 35 Copynumber: 1.9 Consensus size: 38
20731634 TTCTTATAAA
* *
20731644 TATGAAACTCTTACGAATTCTTGGGAATTTAAAAATCT
1 TATGAAACTCTTACGAACTCTTGAGAATTTAAAAATCT
*
20731682 TATGAAACT-TTA-G-ACTCTTGAGAATTTGAAAA
1 TATGAAACTCTTACGAACTCTTGAGAATTTAAAAA
20731714 GCCTAAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 16 0.55
36 1 0.03
37 3 0.10
38 9 0.31
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (38 bp):
TATGAAACTCTTACGAACTCTTGAGAATTTAAAAATCT
Found at i:20731871 original size:18 final size:18
Alignment explanation
Indices: 20731848--20731891 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20731838 TGCAAACTTG
*
20731848 AAATTCTTACGAATTTAA
1 AAATTCTTACGAATATAA
* *
20731866 AAATTCTTATGAATATGA
1 AAATTCTTACGAATATAA
20731884 AAATTCTT
1 AAATTCTT
20731892 GCAAATCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (18 bp):
AAATTCTTACGAATATAA
Found at i:20731927 original size:16 final size:17
Alignment explanation
Indices: 20731902--20731940 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
20731892 GCAAATCCAA
*
20731902 AAATCCTTGTGAA-TTG
1 AAATCTTTGTGAATTTG
20731918 AAATCTTTGTGAATTTG
1 AAATCTTTGTGAATTTG
20731935 AAATCT
1 AAATCT
20731941 CTACAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (17 bp):
AAATCTTTGTGAATTTG
Found at i:20732668 original size:23 final size:24
Alignment explanation
Indices: 20732642--20732704 Score: 101
Period size: 23 Copynumber: 2.6 Consensus size: 24
20732632 AAAAGGTCAA
*
20732642 AAAATTAAAAAAAAATCAAAA-TC
1 AAAAGTAAAAAAAAATCAAAAGTC
20732665 AAAAGTAAAAAAAAATCAAAAGTC
1 AAAAGTAAAAAAAAATCAAAAGTC
20732689 AAAAGTACAAAAAAAA
1 AAAAGTA-AAAAAAAA
20732705 GAAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
23 20 0.54
24 9 0.24
25 8 0.22
ACGTcount: A:0.75, C:0.08, G:0.05, T:0.13
Consensus pattern (24 bp):
AAAAGTAAAAAAAAATCAAAAGTC
Found at i:20732679 original size:17 final size:18
Alignment explanation
Indices: 20732659--20732692 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
20732649 AAAAAAAATC
20732659 AAAATCAAAAGT-AAAAA
1 AAAATCAAAAGTCAAAAA
20732676 AAAATCAAAAGTCAAAA
1 AAAATCAAAAGTCAAAA
20732693 GTACAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAATCAAAAGTCAAAAA
Found at i:20733718 original size:3 final size:3
Alignment explanation
Indices: 20733710--20733738 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20733700 GTTTGTTTGT
20733710 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20733739 TAGTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20735070 original size:163 final size:162
Alignment explanation
Indices: 20734822--20735276 Score: 433
Period size: 147 Copynumber: 2.9 Consensus size: 162
20734812 TTAAACACAG
* * * * * * *
20734822 TAGACTTTTGGTTACCTAATTTTTTTTAT-GAGTTTTTGACTTTTCATTTTCTTTTATTCACGTT
1 TAGACTTTTGGTTGCATAA-CTTTTTTATGGA-TTTTTGACTTTTGATTTTCTTCTATTTATGTT
* * *
20734886 CTTTACAACTGTTATTTGTTAAAATTTATTGAAACTTTTAGTTTCTAATATTAGTGTTTTTAACT
64 CTTTAAAATTATTATTTGTTAAAATTTATTGAAACTTTTAGTTTCTAATATTAGTGTTTTT--CT
*
20734951 ATTGATTTTCTTGTAATTTAAGATTTTTCATTACAA
127 ATTGATTTTCTTGTAATTTAAGATTTTTCATGACAA
* *
20734987 TAGA-TTTTGGTTGTC-TAACTTTTTTATGGATTTTTGAGTTTTGATTTTCTTCTATTTATATTC
1 TAGACTTTTGGTTG-CATAACTTTTTTATGGATTTTTGACTTTTGATTTTCTTCTATTTATGTTC
* * *
20735050 TATAAAATTATTAATTGTTAAAATTTATTG-AA-----A----CT--T-TTAGTGTTTTT-GATT
65 TTTAAAATTATTATTTGTTAAAATTTATTGAAACTTTTAGTTTCTAATATTAGTGTTTTTCTATT
* ***
20735101 GATTTTCTTGTGATTTTTTATTTTTCATGACAA
130 GATTTTCTTGTAATTTAAGATTTTTCATGACAA
* * * * *
20735134 TTGACTTTTGGTTGCATAAC-TTTTTATGGATTTTTTATTTTTGATTTTTTTCTATTTGTGTTCT
1 TAGACTTTTGGTTGCATAACTTTTTTATGGATTTTTGACTTTTGATTTTCTTCTATTTATGTTCT
* * * * *
20735198 TTAAAATCATTATTTGTTAAAATTTATTAAAACTTTTAGTTTTTTTAATATTAATATTTTTTTCT
66 TTAAAATTATTATTTGTTAAAATTTATTGAAACTTTTAG--TTTCTAATATT-A-GTGTTTTTCT
20735263 ATTGATTTTCTTGT
127 ATTGATTTTCTTGT
20735277 GACTTATAAT
Statistics
Matches: 235, Mismatches: 33, Indels: 44
0.75 0.11 0.14
Matches are distributed among these distances:
147 99 0.42
148 15 0.06
150 11 0.05
151 1 0.00
153 3 0.01
157 1 0.00
159 1 0.00
161 1 0.00
162 4 0.02
163 61 0.26
164 19 0.08
165 19 0.08
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (162 bp):
TAGACTTTTGGTTGCATAACTTTTTTATGGATTTTTGACTTTTGATTTTCTTCTATTTATGTTCT
TTAAAATTATTATTTGTTAAAATTTATTGAAACTTTTAGTTTCTAATATTAGTGTTTTTCTATTG
ATTTTCTTGTAATTTAAGATTTTTCATGACAA
Found at i:20736693 original size:8 final size:7
Alignment explanation
Indices: 20736675--20736712 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
20736665 TACATATATA
20736675 TAAAAAT
1 TAAAAAT
20736682 TAAAAAT
1 TAAAAAT
20736689 GTAAAAAT
1 -TAAAAAT
20736697 TAAAAA-
1 TAAAAAT
20736703 TAAAAAT
1 TAAAAAT
20736710 TAA
1 TAA
20736713 GTTTAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (7 bp):
TAAAAAT
Found at i:20736695 original size:15 final size:13
Alignment explanation
Indices: 20736674--20736712 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 13
20736664 TTACATATAT
20736674 ATAAAAATTAAAA
1 ATAAAAATTAAAA
20736687 ATGTAAAAATTAAAA
1 A--TAAAAATTAAAA
20736702 ATAAAAATTAA
1 ATAAAAATTAA
20736713 GTTTAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
ATAAAAATTAAAA
Found at i:20739203 original size:16 final size:15
Alignment explanation
Indices: 20739179--20739215 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
20739169 GTTCCATTTC
*
20739179 TTTTTTTTCTTTTAT
1 TTTTTTTTCATTTAT
20739194 TTTTTGTTTCATTTAT
1 TTTTT-TTTCATTTAT
20739210 TTTTTT
1 TTTTTT
20739216 ATTTGCTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.08, C:0.05, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTTTTTCATTTAT
Found at i:20745110 original size:21 final size:21
Alignment explanation
Indices: 20745084--20745150 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
20745074 CCTTTGAAAC
*
20745084 TTTGAATATGAACTTCTAATT
1 TTTGAATGTGAACTTCTAATT
**
20745105 TTTGAATGTGAATCTT-TGAAAC
1 TTTGAATGTGAA-CTTCT-AATT
*
20745127 TTTGAATGTGAATTTCTAATT
1 TTTGAATGTGAACTTCTAATT
20745148 TTT
1 TTT
20745151 TAAATACGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.49
Consensus pattern (21 bp):
TTTGAATGTGAACTTCTAATT
Found at i:20745139 original size:22 final size:22
Alignment explanation
Indices: 20745075--20745139 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
20745065 GAAAAAGAAC
*
20745075 CTTTGAAACTTTGAATATGAA-
1 CTTTGAAACTTTGAATGTGAAT
**
20745096 CTTCT-AATTTTTGAATGTGAAT
1 CTT-TGAAACTTTGAATGTGAAT
20745118 CTTTGAAACTTTGAATGTGAAT
1 CTTTGAAACTTTGAATGTGAAT
20745140 TTCTAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.43
Consensus pattern (22 bp):
CTTTGAAACTTTGAATGTGAAT
Found at i:20745167 original size:44 final size:44
Alignment explanation
Indices: 20745075--20745218 Score: 173
Period size: 44 Copynumber: 3.3 Consensus size: 44
20745065 GAAAAAGAAC
* * * *
20745075 CTTTGAAACTTTGAATATGAACTTCTAA-TTTTTGAATGTGAAT
1 CTTTGAAACTTTGAATGTGAATTTCTAATTTTTTGAATATGAGT
* *
20745118 CTTTGAAACTTTGAATGTGAATTTCTAATTTTTTAAATACGAGT
1 CTTTGAAACTTTGAATGTGAATTTCTAATTTTTTGAATATGAGT
* ** * * *
20745162 CTTTGAAAATTCAAATGTAAATCTCTAATTTTTTGAATATAAGT
1 CTTTGAAACTTTGAATGTGAATTTCTAATTTTTTGAATATGAGT
20745206 CTTTGAAACTTTG
1 CTTTGAAACTTTG
20745219 GATATAAATC
Statistics
Matches: 83, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
43 26 0.31
44 57 0.69
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44
Consensus pattern (44 bp):
CTTTGAAACTTTGAATGTGAATTTCTAATTTTTTGAATATGAGT
Found at i:20745365 original size:46 final size:46
Alignment explanation
Indices: 20745233--20745365 Score: 144
Period size: 46 Copynumber: 2.9 Consensus size: 46
20745223 TAAATCTTTA
* * * **
20745233 AAAATTTTTGAAGT-TGAATATTTGAAATTTTGGATGGGAATTCCT
1 AAAATTTTTCAAATATGAATATTTGAAATTTTGGATGTGAAACCCT
* * *
20745278 AAAATTTTTCAAATATGAATATTTGAAATTCTAGATATGAAACCCT
1 AAAATTTTTCAAATATGAATATTTGAAATTTTGGATGTGAAACCCT
* * *
20745324 AAAATTTTTCATATGA-GAATTTTTGAAATTTTGGTTGTGAAA
1 AAAATTTTTCAAAT-ATGAATATTTGAAATTTTGGATGTGAAA
20745366 TGTTTAAGGT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
45 12 0.17
46 59 0.82
47 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (46 bp):
AAAATTTTTCAAATATGAATATTTGAAATTTTGGATGTGAAACCCT
Found at i:20745883 original size:17 final size:18
Alignment explanation
Indices: 20745863--20745902 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
20745853 AACCTTTGCA
*
20745863 AATTTTGACA-TTTTGTG
1 AATTTTGAAATTTTTGTG
20745880 AATTTTGAAATTTTTGTG
1 AATTTTGAAATTTTTGTG
20745898 -ATTTT
1 AATTTT
20745903 TTTGTGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (18 bp):
AATTTTGAAATTTTTGTG
Found at i:20746143 original size:65 final size:66
Alignment explanation
Indices: 20746027--20746180 Score: 166
Period size: 65 Copynumber: 2.3 Consensus size: 66
20746017 TTTTTTGACT
** * *
20746027 TGTAGTTCAATCTTGGTCACTCATCTTCAATCTTGGTTCAATTCAAATCA-TTTATTTTTCTAAC
1 TGTAGTTCAATCTCAGTCACTCATCTTCAACCTTGGCTCAATTCAAATCATTTTATTTTTCTAAC
20746091 C
66 C
* ** * ** * *
20746092 TGTAATTCAATCTCAGTCACTCATCTTCAACCTTGGCTCGGTTTAGGTCATTTTATTTTTTTGAC
1 TGTAGTTCAATCTCAGTCACTCATCTTCAACCTTGGCTCAATTCAAATCATTTTATTTTTCTAAC
20746157 C
66 C
* * *
20746158 TATGGTTCAATCTCAGTTACTCA
1 TGTAGTTCAATCTCAGTCACTCA
20746181 GTTTTTATAT
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
65 40 0.56
66 32 0.44
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (66 bp):
TGTAGTTCAATCTCAGTCACTCATCTTCAACCTTGGCTCAATTCAAATCATTTTATTTTTCTAAC
C
Found at i:20749783 original size:97 final size:97
Alignment explanation
Indices: 20749611--20749871 Score: 262
Period size: 97 Copynumber: 2.7 Consensus size: 97
20749601 TTGAAATTAG
* * * *
20749611 ATCCTATCAAA-TGATTGGAGGATTTAAATCTTGAATTATGAAT-TGTACCAAACTATT-GGAGA
1 ATCCTACCAAACT-ATTGAAGGATTTAAATCTTAAATTA--AATCT-TACCAAACTATTAGAAG-
* * * *
20749673 ATTTCATAATTTTTTTGATAAAAT-A-AAATTTTTTA
61 ACTTAATAAATTTTTTGAAAAAATAACAAATTTTTTA
* * ** * * * *
20749708 ATCTTGCCAAGTTATTGAAGGATTTAAATCTTAAATTAAGTTTTACTAAATTATTAGAAGACTTA
1 ATCCTACCAAACTATTGAAGGATTTAAATCTTAAATTAAATCTTACCAAACTATTAGAAGACTTA
20749773 ATAAATTTTTTGAAAAAATAACAAATTTTTTA
66 ATAAATTTTTTGAAAAAATAACAAATTTTTTA
* * * *
20749805 ATCCTACCAAACTATTGGAGGATTTAAATCTTGAATTAAATCTTACCAAACTATTATAAGATTTA
1 ATCCTACCAAACTATTGAAGGATTTAAATCTTAAATTAAATCTTACCAAACTATTAGAAGACTTA
20749870 AT
66 AT
20749872 GAGTTTTCTT
Statistics
Matches: 133, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
95 32 0.24
96 5 0.04
97 95 0.71
98 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (97 bp):
ATCCTACCAAACTATTGAAGGATTTAAATCTTAAATTAAATCTTACCAAACTATTAGAAGACTTA
ATAAATTTTTTGAAAAAATAACAAATTTTTTA
Found at i:20752939 original size:21 final size:22
Alignment explanation
Indices: 20752913--20752967 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
20752903 TTAGAAAAAA
*
20752913 GATCGATCCCCTCACA-T-AGAG
1 GATCGATCCCCTCAAACTAAG-G
*
20752934 GATCGATCACCT-AAACTAAGG
1 GATCGATCCCCTCAAACTAAGG
20752955 GATCGATCCCCTC
1 GATCGATCCCCTC
20752968 TTAAAGGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (22 bp):
GATCGATCCCCTCAAACTAAGG
Found at i:20758406 original size:73 final size:72
Alignment explanation
Indices: 20758337--20758514 Score: 212
Period size: 73 Copynumber: 2.4 Consensus size: 72
20758327 ATAAGAAACT
* *
20758337 GATCGATCCCCTTTGGACAAGATCGATCGGGTGTAAAGGTAGTAGCCAATTTCGTTAAACCCAAA
1 GATCGATCCCCTTTGGACAAGATCGATCGGGTGTAAAGGCAGTAGCCAATTTCGCTAAACCCAAA
20758402 AAGAACC
66 AAGAACC
* * ** * * *
20758409 GATCGACCCCCTTTAGGACAGGATCGATCAAGTGTGAAGGCAGTAGCCAATTTTGCTGAACCCAA
1 GATCGATCCCCTTT-GGACAAGATCGATCGGGTGTAAAGGCAGTAGCCAATTTCGCTAAACCCAA
*
20758474 GAAGAACC
65 AAAGAACC
* ** *
20758482 GATCGATCCCTTTTTTAACATGATCGATCGGGT
1 GATCGATCCC-CTTTGGACAAGATCGATCGGGT
20758515 ATTCAACTAG
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
72 13 0.15
73 71 0.82
74 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (72 bp):
GATCGATCCCCTTTGGACAAGATCGATCGGGTGTAAAGGCAGTAGCCAATTTCGCTAAACCCAAA
AAGAACC
Found at i:20760326 original size:20 final size:20
Alignment explanation
Indices: 20760301--20760339 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
20760291 TGAAAATTTG
20760301 ATGATGTTTTGATATTGATA
1 ATGATGTTTTGATATTGATA
20760321 ATGATGTTTTGATATTGAT
1 ATGATGTTTTGATATTGAT
20760340 GATATATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (20 bp):
ATGATGTTTTGATATTGATA
Found at i:20764364 original size:20 final size:20
Alignment explanation
Indices: 20764339--20764377 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20764329 TGAGAATTTG
*
20764339 ATGATGTTTTGATATTGATA
1 ATGATGCTTTGATATTGATA
20764359 ATGATGCTTTGATATTGAT
1 ATGATGCTTTGATATTGAT
20764378 GTTATATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (20 bp):
ATGATGCTTTGATATTGATA
Done.