Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 12 of 190
Found at i:3633967 original size:13 final size:13
Alignment explanation
Indices: 3633951--3633976 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3633941 GTCAACAAGA
3633951 ACAACCAAATCAT
1 ACAACCAAATCAT
3633964 ACAACCAAATCAT
1 ACAACCAAATCAT
3633977 TCTTACTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
ACAACCAAATCAT
Found at i:3646695 original size:31 final size:31
Alignment explanation
Indices: 3646660--3646720 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3646650 TTAGTAATAT
* * *
3646660 TCTTCTCATATTAATTTGATTGAGAACTTAA
1 TCTTCCCACATTAATTTAATTGAGAACTTAA
3646691 TCTTCCCACATTAATTTAATTGAGAACTTA
1 TCTTCCCACATTAATTTAATTGAGAACTTA
3646721 TCGTAATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (31 bp):
TCTTCCCACATTAATTTAATTGAGAACTTAA
Found at i:3648189 original size:2 final size:2
Alignment explanation
Indices: 3648182--3648212 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3648172 NNNNNNNNNN
3648182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3648213 AAATTTTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3648463 original size:5 final size:5
Alignment explanation
Indices: 3648453--3648482 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3648443 ATAATTTATT
3648453 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
3648483 GATAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:3649521 original size:156 final size:156
Alignment explanation
Indices: 3649237--3649552 Score: 605
Period size: 156 Copynumber: 2.0 Consensus size: 156
3649227 TCGGGCAACA
*
3649237 CTCCTATGATTCCTAATCTACATCTCACAAAAGAAGATGGTGGTTTATTTGAGAACCCTAAGAGG
1 CTCCTATGATTCCTAATCTACATCTCACAAAAGAAGATGGTGGTTTATTTGACAACCCTAAGAGG
3649302 TATAGAAGATTGGTAGAAAAGTTGAACTATCTCACACTAACCTGTCTAGATATCGCACATGCAAC
66 TATAGAAGATTGGTAGAAAAGTTGAACTATCTCACACTAACCTGTCTAGATATCGCACATGCAAC
3649367 CGGTGTTGTTAGCCAATTTATGACAG
131 CGGTGTTGTTAGCCAATTTATGACAG
3649393 CTCCTATGATTCCTAATCTACATCTCACAAAAGAAGATGGTGGTTTATTTGACAACCCTAAGAGG
1 CTCCTATGATTCCTAATCTACATCTCACAAAAGAAGATGGTGGTTTATTTGACAACCCTAAGAGG
* *
3649458 TATAGAAGATTGGTAGAAAAGTTGAACTATCTCACACTAACTTGTCTAGATATCGCATATGCAAC
66 TATAGAAGATTGGTAGAAAAGTTGAACTATCTCACACTAACCTGTCTAGATATCGCACATGCAAC
3649523 CGGTGTTGTTAGCCAATTTATGACAG
131 CGGTGTTGTTAGCCAATTTATGACAG
3649549 CTCC
1 CTCC
3649553 AACCATTCAT
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 157 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (156 bp):
CTCCTATGATTCCTAATCTACATCTCACAAAAGAAGATGGTGGTTTATTTGACAACCCTAAGAGG
TATAGAAGATTGGTAGAAAAGTTGAACTATCTCACACTAACCTGTCTAGATATCGCACATGCAAC
CGGTGTTGTTAGCCAATTTATGACAG
Found at i:3652797 original size:2 final size:2
Alignment explanation
Indices: 3652790--3652815 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3652780 ATTTTCTGCT
3652790 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
3652816 CACACGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3663274 original size:10 final size:10
Alignment explanation
Indices: 3663257--3663304 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
3663247 TAAATTTTAG
3663257 AAAATTTATT
1 AAAATTTATT
* *
3663267 AAATTTTAAT
1 AAAATTTATT
*
3663277 AAAAATT-TT
1 AAAATTTATT
3663286 AAAATTTATT
1 AAAATTTATT
*
3663296 AAAAATTAT
1 AAAATTTAT
3663305 ATTTTTTATA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AAAATTTATT
Found at i:3663287 original size:19 final size:20
Alignment explanation
Indices: 3663247--3663304 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
3663237 TAATAAATAA
* *
3663247 TAAATTTT-AGAAAATTTAT
1 TAAATTTTAATAAAAATTAT
3663266 TAAATTTTAATAAAAATT-T
1 TAAATTTTAATAAAAATTAT
* *
3663285 TAAAATTTATTAAAAATTAT
1 TAAATTTTAATAAAAATTAT
3663305 ATTTTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 25 0.76
20 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAATTTTAATAAAAATTAT
Found at i:3663576 original size:30 final size:31
Alignment explanation
Indices: 3663522--3663579 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3663512 GAAATTTATA
*
3663522 TTTATTTACATTTTGTATATTTTTTTACAAC
1 TTTATTTACATTTTATATATTTTTTTACAAC
*
3663553 TTTATTTATATTTTATA-ATTTTTTTAC
1 TTTATTTACATTTTATATATTTTTTTAC
3663580 GATTTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTATTTACATTTTATATATTTTTTTACAAC
Found at i:3663588 original size:20 final size:20
Alignment explanation
Indices: 3663563--3663637 Score: 75
Period size: 19 Copynumber: 3.8 Consensus size: 20
3663553 TTTATTTATA
3663563 TTTTATAATTTTTTTACGAT
1 TTTTATAATTTTTTTACGAT
** *
3663583 TTTTATAA-AATTTTACAAT
1 TTTTATAATTTTTTTACGAT
*
3663602 TTTT-TATATATTGTTTACGAT
1 TTTTATA-AT-TTTTTTACGAT
3663623 TTTTAT-ATTTTTTTA
1 TTTTATAATTTTTTTA
3663638 TTTTTAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
18 2 0.05
19 19 0.44
20 10 0.23
21 11 0.26
22 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTATAATTTTTTTACGAT
Found at i:3663588 original size:31 final size:30
Alignment explanation
Indices: 3663522--3663606 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
3663512 GAAATTTATA
* *
3663522 TTTATTTACATTTTGTATATTTTTTTACAAC
1 TTTATTTAAATTTTATA-ATTTTTTTACAAC
* *
3663553 TTTATTTATATTTTATAATTTTTTTACGA-
1 TTTATTTAAATTTTATAATTTTTTTACAAC
*
3663582 TTT-TTATAAAATTTTACAATTTTTT
1 TTTATT-T-AAATTTTATAATTTTTT
3663607 ATATATTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.04
29 4 0.09
30 26 0.55
31 15 0.32
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTATTTAAATTTTATAATTTTTTTACAAC
Found at i:3663666 original size:26 final size:28
Alignment explanation
Indices: 3663637--3663688 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
3663627 ATATTTTTTT
*
3663637 ATTTTTAAT-AAATTT-TTAATATTTGG
1 ATTTTTAATAAAATTTAATAATATTTGG
*
3663663 ATTTTTATTAAAATTTAATAATATTT
1 ATTTTTAATAAAATTTAATAATATTT
3663689 ATATCTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 6 0.27
28 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (28 bp):
ATTTTTAATAAAATTTAATAATATTTGG
Found at i:3663881 original size:89 final size:89
Alignment explanation
Indices: 3663745--3663935 Score: 267
Period size: 89 Copynumber: 2.1 Consensus size: 89
3663735 TAATAAAAGC
** * *
3663745 AGGGGCTTAATTGCTTTTTTGAAAAAATTTGAGGGTTTTTTTGATGCATTTTGAAAGTTCAAGGA
1 AGGGGCTTAATTGCTTTTTTGAAAAAATTTGAGGACTTTTTTAATGCATTTTGAAAGTTCAAAGA
* * *
3663810 CCCAATTGAGTGC-AAAAAAAATT
66 CCAAAATGAGTGCAAAAAAAAAAT
** *
3663833 AGGGGCTTAATTGCTTTTCTTGAAAAGGTTTGAGGACTTTTTTAATGCATTTTGAAAGTTCAAAT
1 AGGGGCTTAATTGCTTTT-TTGAAAAAATTTGAGGACTTTTTTAATGCATTTTGAAAGTTCAAAG
3663898 ACCAAAATGAGTGCAAAAAAAAAAAT
65 ACCAAAATGAGTGC-AAAAAAAAAAT
3663924 AGGGGCTTAATT
1 AGGGGCTTAATT
3663936 TTATTTTATT
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
88 18 0.20
89 51 0.57
91 21 0.23
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (89 bp):
AGGGGCTTAATTGCTTTTTTGAAAAAATTTGAGGACTTTTTTAATGCATTTTGAAAGTTCAAAGA
CCAAAATGAGTGCAAAAAAAAAAT
Found at i:3664628 original size:29 final size:29
Alignment explanation
Indices: 3664586--3664644 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3664576 CGTATTAACT
3664586 TTAAGTCATCTAAATCTCAATCAATCTTA
1 TTAAGTCATCTAAATCTCAATCAATCTTA
3664615 TTAAGTCATCTAAATCTCAATCAATCTTA
1 TTAAGTCATCTAAATCTCAATCAATCTTA
3664644 T
1 T
3664645 AAGATGAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.39
Consensus pattern (29 bp):
TTAAGTCATCTAAATCTCAATCAATCTTA
Found at i:3664692 original size:2 final size:2
Alignment explanation
Indices: 3664687--3664731 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3664677 TAACTAAATA
3664687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3664729 AT A
1 AT A
3664732 AACTATGCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3665540 original size:30 final size:31
Alignment explanation
Indices: 3665499--3665559 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
3665489 GGGTTGGGAG
*
3665499 GGGAGAGGAGTAAAAGTTTTGGGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
3665530 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
3665560 AAAAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:3665705 original size:9 final size:9
Alignment explanation
Indices: 3665688--3665718 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3665678 TCGAGTTGAT
3665688 TCGAATAAC
1 TCGAATAAC
*
3665697 TCGATTAAC
1 TCGAATAAC
3665706 TCGAATAAC
1 TCGAATAAC
3665715 TCGA
1 TCGA
3665719 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:3668319 original size:83 final size:83
Alignment explanation
Indices: 3668180--3668346 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
3668170 AAAAAGACTG
*
3668180 TGTATTTCTTATAAGTTCTCCTGTACTGTTACTTTTTTATAATTTATTTAGCTTACTGCCATACA
1 TGTATTTCTTATAAGTTCTCCTGTACTGTAACTTTTTTATAATTTATTTAGCTTACTGCCATACA
3668245 AGATTACAAGTTCAGGAA
66 AGATTACAAGTTCAGGAA
3668263 TGTATTTCTTATAAGTTCTCCTGTACTGTAACTTTTTTATAATTTATTTAGCTTACTGCCATACA
1 TGTATTTCTTATAAGTTCTCCTGTACTGTAACTTTTTTATAATTTATTTAGCTTACTGCCATACA
3668328 AGATTACAAGTTCAGGAA
66 AGATTACAAGTTCAGGAA
3668346 T
1 T
3668347 TTAGTAGCTT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (83 bp):
TGTATTTCTTATAAGTTCTCCTGTACTGTAACTTTTTTATAATTTATTTAGCTTACTGCCATACA
AGATTACAAGTTCAGGAA
Found at i:3675530 original size:27 final size:29
Alignment explanation
Indices: 3675491--3675545 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
3675481 GACTTTATAT
* *
3675491 TTTTTTTCTTAATTTAATG-TTTAATTTC
1 TTTTTATCTTAATTTAATGCTTGAATTTC
3675519 TTTTTATC-TAATTTAATGCTTGAATTT
1 TTTTTATCTTAATTTAATGCTTGAATTT
3675546 GACTCTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (29 bp):
TTTTTATCTTAATTTAATGCTTGAATTTC
Found at i:3676817 original size:20 final size:19
Alignment explanation
Indices: 3676781--3676946 Score: 76
Period size: 20 Copynumber: 8.5 Consensus size: 19
3676771 AATATTTTTC
*
3676781 TCATAAAAA-TATTAAAAAG
1 TCATAAAAATTA-TAAAAAA
3676800 TCATAAAAATTATAAAAAAA
1 TCATAAAAATTAT-AAAAAA
3676820 TCA-AACAAATTATAAAAAA
1 TCATAA-AAATTATAAAAAA
*
3676839 T-AT-AAAATTA-ATAAAAC
1 TCATAAAAATTATA-AAAAA
* *
3676856 TTATTTAAAATTA-AAAAAA
1 TCA-TAAAAATTATAAAAAA
* * *
3676875 ACATATTAGAATTCTTAAAAAA
1 TCATA--AAAATT-ATAAAAAA
* *
3676897 TAATAAAAAATTGTAAAAAATTA
1 TCAT-AAAAATTAT-AAAAA--A
* *
3676920 TTATAAAAATT-TTAAAAA
1 TCATAAAAATTATAAAAAA
3676938 TCATAAAAA
1 TCATAAAAA
3676947 CTTGAGTTGG
Statistics
Matches: 116, Mismatches: 15, Indels: 33
0.71 0.09 0.20
Matches are distributed among these distances:
16 1 0.01
17 11 0.09
18 13 0.11
19 25 0.22
20 35 0.30
21 11 0.09
22 15 0.13
23 5 0.04
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
TCATAAAAATTATAAAAAA
Found at i:3676818 original size:10 final size:10
Alignment explanation
Indices: 3676804--3676946 Score: 59
Period size: 10 Copynumber: 14.4 Consensus size: 10
3676794 AAAAAGTCAT
3676804 AAAAATTATA
1 AAAAATTATA
3676814 AAAAA--ATCA
1 AAAAATTAT-A
3676823 AACAAATTATA
1 AA-AAATTATA
3676834 AAAAA-TAT-
1 AAAAATTATA
3676842 -AAAATTA-A
1 AAAAATTATA
* *
3676850 TAAAACTTATT
1 -AAAAATTATA
*
3676861 TAAAATTA-A
1 AAAAATTATA
**
3676870 AAAAAACATA
1 AAAAATTATA
* * *
3676880 TTAGAATTCTTA
1 -AAAAATT-ATA
*
3676892 AAAAATAATA
1 AAAAATTATA
*
3676902 AAAAATTGTA
1 AAAAATTATA
3676912 AAAAATTATTA
1 AAAAATTA-TA
*
3676923 TAAAAATT-TT
1 -AAAAATTATA
*
3676933 AAAAATCATA
1 AAAAATTATA
3676943 AAAA
1 AAAA
3676947 CTTGAGTTGG
Statistics
Matches: 95, Mismatches: 23, Indels: 30
0.64 0.16 0.20
Matches are distributed among these distances:
7 4 0.04
8 4 0.04
9 17 0.18
10 47 0.49
11 12 0.13
12 11 0.12
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:3676881 original size:21 final size:20
Alignment explanation
Indices: 3676841--3676881 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3676831 ATAAAAAATA
* *
3676841 TAAAATTAATAAAACTTATT
1 TAAAATTAAAAAAACATATT
3676861 TAAAATTAAAAAAAACATATT
1 TAAAATT-AAAAAAACATATT
3676882 AGAATTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAATTAAAAAAACATATT
Found at i:3677389 original size:9 final size:9
Alignment explanation
Indices: 3677375--3677429 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
3677365 AGTTTATTTT
3677375 ATTTTTATA
1 ATTTTTATA
3677384 ATTTTTATA
1 ATTTTTATA
*
3677393 AGTTTATATCA
1 A-TTTTTAT-A
*
3677404 ATTTTAAT-
1 ATTTTTATA
*
3677412 ATTTTT-TT
1 ATTTTTATA
3677420 ATTTTTATA
1 ATTTTTATA
3677429 A
1 A
3677430 AATTTTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
7 1 0.03
8 11 0.30
9 12 0.32
10 11 0.30
11 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:3677446 original size:21 final size:22
Alignment explanation
Indices: 3677421--3677467 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
3677411 TATTTTTTTA
*
3677421 TTTTTAT-AAAATTTTAATACG
1 TTTTTATAAAAATTTAAATACG
*
3677442 TTTTTATAAAAATTTAAATATG
1 TTTTTATAAAAATTTAAATACG
3677464 TTTT
1 TTTT
3677468 ATTAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTTTATAAAAATTTAAATACG
Found at i:3677462 original size:49 final size:48
Alignment explanation
Indices: 3677371--3677482 Score: 113
Period size: 49 Copynumber: 2.3 Consensus size: 48
3677361 TTCAAGTTTA
* ** *
3677371 TTTTATTTTTAT--AATTTTTATAAGTTTATATCAATTTTAATAT-TT
1 TTTTATTTTTATAAAATTTTAATAAGTTTATAAAAATTTAAATATGTT
*
3677416 TTTTATTTTTATAAAATTTTAATACGTTTTTATAAAAATTTAAATATGTT
1 TTTTATTTTTATAAAATTTTAATAAG--TTTATAAAAATTTAAATATGTT
* *
3677466 TTATTAATTATATAAAA
1 TT-TTATTTTTATAAAA
3677483 ATTATAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
45 12 0.22
47 10 0.19
49 16 0.30
50 4 0.07
51 12 0.22
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (48 bp):
TTTTATTTTTATAAAATTTTAATAAGTTTATAAAAATTTAAATATGTT
Found at i:3677521 original size:19 final size:18
Alignment explanation
Indices: 3677486--3677520 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3677476 TATAAAAATT
3677486 ATAAATTTTATTTTTTTG
1 ATAAATTTTATTTTTTTG
*
3677504 ATAAATTTTCTTTTTTT
1 ATAAATTTTATTTTTTT
3677521 TTATTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
ATAAATTTTATTTTTTTG
Found at i:3679118 original size:30 final size:30
Alignment explanation
Indices: 3679082--3679150 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
3679072 AGATGTGCAC
* *
3679082 GGCAACCCCATTCCACTT-ACTGACGAGCAT
1 GGCAACCCCATT-CAATTGACTGACGAACAT
*
3679112 GGCAACCCCGTTCAATTGACTGACGAACAT
1 GGCAACCCCATTCAATTGACTGACGAACAT
*
3679142 GGTAACCCC
1 GGCAACCCC
3679151 GTTTACGTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.28, C:0.35, G:0.19, T:0.19
Consensus pattern (30 bp):
GGCAACCCCATTCAATTGACTGACGAACAT
Found at i:3685337 original size:29 final size:30
Alignment explanation
Indices: 3685283--3685434 Score: 148
Period size: 30 Copynumber: 5.1 Consensus size: 30
3685273 TTAAATTTTT
* *
3685283 TTACATTTTGACCCCTAATCTTT-TCTAAAA
1 TTACATTTTGACCCTTAAACTTTCTC-AAAA
* *
3685313 TTACCTTTTGACCCTTAAACTTTCTCTAAA
1 TTACATTTTGACCCTTAAACTTTCTCAAAA
* *
3685343 TTACATTTTAACCCTTGAAA-TTT-TCTAAA
1 TTACATTTTGACCCTT-AAACTTTCTCAAAA
* * *
3685372 TTACATTTTAACCCCTGAACTTTCTCAAAA
1 TTACATTTTGACCCTTAAACTTTCTCAAAA
* * * *
3685402 TTATATTTTGACCCTGACATTTTCTCAAAA
1 TTACATTTTGACCCTTAAACTTTCTCAAAA
3685432 TTA
1 TTA
3685435 TGTTTCAGCC
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.02
29 24 0.24
30 71 0.70
31 5 0.05
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (30 bp):
TTACATTTTGACCCTTAAACTTTCTCAAAA
Found at i:3685403 original size:59 final size:59
Alignment explanation
Indices: 3685303--3685434 Score: 167
Period size: 59 Copynumber: 2.2 Consensus size: 59
3685293 ACCCCTAATC
* * * *
3685303 TTTTCTAAAATTACCTTTTGACCCTTAAACTTTCTCTAAATTACATTTTAACCCTTGAAA
1 TTTTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACATTTTAACCC-TGAAA
* * * *
3685363 TTTTCT-AAATTACATTTTAACCCCTGAACTTTCTCAAAATTATATTTTGACCCTGACA
1 TTTTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACATTTTAACCCTGAAA
3685421 TTTTCTCAAAATTA
1 TTTTCT-AAAATTA
3685435 TGTTTCAGCC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 10 0.16
59 40 0.65
60 12 0.19
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (59 bp):
TTTTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACATTTTAACCCTGAAA
Found at i:3685758 original size:19 final size:19
Alignment explanation
Indices: 3685736--3685776 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
3685726 AATAAAAACC
3685736 AAAGCAA-AAAGAAAAAGAA
1 AAAGCAACAAAGAAAAA-AA
3685755 AAAGCAAGCAAAGAAAAAAA
1 AAAGCAA-CAAAGAAAAAAA
3685775 AA
1 AA
3685777 TTTCAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 9 0.45
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAGCAACAAAGAAAAAAA
Found at i:3685926 original size:3 final size:3
Alignment explanation
Indices: 3685918--3685972 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
3685908 GGGGGCTGAT
*
3685918 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGT
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3685966 AGA AGA A
1 AGA AGA A
3685973 AAAAAATTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:3686271 original size:6 final size:6
Alignment explanation
Indices: 3686258--3686319 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
3686248 GAAGAGAAAG
3686258 AAAG-A AAAGAA AAA-AA AAAG-- AAAGAA AAAGAA AAAGTGAA GCAAA-AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA--GAA --AAAGAA
3686305 AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAA
3686320 AGGGGGTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
4 4 0.08
5 12 0.25
6 24 0.50
7 2 0.04
8 3 0.06
10 3 0.06
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:3686288 original size:21 final size:21
Alignment explanation
Indices: 3686254--3686319 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
3686244 AAAAGAAGAG
3686254 AAAGAAAG-AAAAGAAAAAAA
1 AAAGAAAGAAAAAGAAAAAAA
**
3686274 AAAGAAAGAAAAAGAAAAAGT
1 AAAGAAAGAAAAAGAAAAAAA
*
3686295 GAAGCAAA-AAAAAGAAAAAGAA
1 AAAG-AAAGAAAAAGAAAAA-AA
3686317 AAA
1 AAA
3686320 AGGGGGTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 8 0.22
21 24 0.65
22 5 0.14
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAAAGAAAAAAA
Found at i:3686292 original size:27 final size:28
Alignment explanation
Indices: 3686243--3686319 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
3686233 CAACAGGCCG
3686243 AAAAAGAAGAGAAAGAA-AGAAAAG-AAAAA
1 AAAAAGAA-AGAAA-AAGA-AAAAGTAAAAA
* **
3686272 AAAAAGAAAGAAAAAGAAAAAGTGAAGC
1 AAAAAGAAAGAAAAAGAAAAAGTAAAAA
3686300 AAAAA-AAAGAAAAAGAAAAA
1 AAAAAGAAAGAAAAAGAAAAA
3686320 AGGGGGTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
27 22 0.51
28 13 0.30
29 8 0.19
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (28 bp):
AAAAAGAAAGAAAAAGAAAAAGTAAAAA
Found at i:3686320 original size:15 final size:15
Alignment explanation
Indices: 3686242--3686319 Score: 61
Period size: 15 Copynumber: 5.0 Consensus size: 15
3686232 CCAACAGGCC
* *
3686242 GAAAAAGAAGAGAAA
1 GAAAAAAAAGAAAAA
*
3686257 GAAAGAAAAGAAAAA
1 GAAAAAAAAGAAAAA
3686272 -AAAAAGAAAGAAAAA
1 GAAAAA-AAAGAAAAA
*
3686287 GAAAAAGTGAAGCAAAAA
1 GAAAAA--AAAG-AAAAA
3686305 -AAAGAAAAAGAAAAA
1 GAAA-AAAAAGAAAAA
3686320 AGGGGGTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
14 4 0.08
15 26 0.51
16 8 0.16
17 6 0.12
18 7 0.14
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:3686510 original size:28 final size:28
Alignment explanation
Indices: 3686470--3686527 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
3686460 ATATTTTTGT
*
3686470 ATTTATATTTTAAATTTAATTTAATTTCA
1 ATTTATATTTTAAATTTAA-ATAATTTCA
3686499 ATTT-TATTTTAAATTTAAATAATTTCA
1 ATTTATATTTTAAATTTAAATAATTTCA
3686526 AT
1 AT
3686528 AAATAAGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 10 0.36
28 14 0.50
29 4 0.14
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTATATTTTAAATTTAAATAATTTCA
Found at i:3686827 original size:35 final size:34
Alignment explanation
Indices: 3686782--3686879 Score: 119
Period size: 37 Copynumber: 2.8 Consensus size: 34
3686772 AATACGGTAC
*
3686782 TTCTTAAAAAAATCTCGTGTTTCAAAATT-TTCGTG
1 TTCTTAAAAAAAT-TCGTGTTTCAAAATTCTT-GTA
3686817 TTCTTTAAAAAAAATTCGTGTTTCTAAAATTCTTGTA
1 TTC-TT-AAAAAAATTCGTGTTTC-AAAATTCTTGTA
3686854 TT-TTAAAAAAATTCGTGTTTTCAAAA
1 TTCTTAAAAAAATTCGTG-TTTCAAAA
3686880 AAAGAAAAAG
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
34 17 0.30
35 9 0.16
36 11 0.19
37 18 0.32
38 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (34 bp):
TTCTTAAAAAAATTCGTGTTTCAAAATTCTTGTA
Found at i:3686836 original size:36 final size:33
Alignment explanation
Indices: 3686785--3686879 Score: 111
Period size: 34 Copynumber: 2.7 Consensus size: 33
3686775 ACGGTACTTC
*
3686785 TTAAAAAAATCTCGTGTTTCAAAATT-TTCGTGTTCT
1 TTAAAAAAAT-TCGTGTTTCAAAATTCTT-GT-AT-T
3686821 TTAAAAAAAATTCGTGTTTCTAAAATTCTTGTATT
1 TT-AAAAAAATTCGTGTTTC-AAAATTCTTGTATT
3686856 TTAAAAAAATTCGTGTTTTCAAAA
1 TTAAAAAAATTCGTG-TTTCAAAA
3686880 AAAGAAAAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
34 17 0.31
35 7 0.13
36 12 0.22
37 16 0.30
38 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (33 bp):
TTAAAAAAATTCGTGTTTCAAAATTCTTGTATT
Found at i:3686864 original size:19 final size:18
Alignment explanation
Indices: 3686787--3686882 Score: 67
Period size: 19 Copynumber: 5.4 Consensus size: 18
3686777 GGTACTTCTT
3686787 AAAAAAATCTCGTG-TTTC
1 AAAAAAAT-TCGTGTTTTC
** *
3686805 -AAAATTTTCGTGTTCTTTA
1 AAAAAAATTCGTG-T-TTTC
3686824 AAAAAAATTCGTG-TTTC
1 AAAAAAATTCGTGTTTTC
* * *
3686841 --TAAAATTCTTGTATTTT
1 AAAAAAATTCGTGT-TTTC
3686858 AAAAAAATTCGTGTTTTC
1 AAAAAAATTCGTGTTTTC
3686876 AAAAAAA
1 AAAAAAA
3686883 GAAAAAGTTG
Statistics
Matches: 58, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
15 9 0.16
16 5 0.09
17 11 0.19
18 10 0.17
19 13 0.22
20 10 0.17
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (18 bp):
AAAAAAATTCGTGTTTTC
Found at i:3692132 original size:43 final size:43
Alignment explanation
Indices: 3692084--3692205 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 43
3692074 TTTTAGAAAT
3692084 AAACGCCGCTAAAAGTCATGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAAGTCATGACCTTTAGCGGCGCTTCTCCCAC
* * * * *
3692127 AAACGCCGCT-ATAGATCATGACTTTTAGCTGCGCTTTTCCTAC
1 AAACGCCGCTAAAAG-TCATGACCTTTAGCGGCGCTTCTCCCAC
*
3692170 AAACGCCGCTAAAGAAT-ATGACCTTTAGCGGCGCTT
1 AAACGCCGCTAAA-AGTCATGACCTTTAGCGGCGCTT
3692206 GTTGGCTAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
42 3 0.04
43 61 0.91
44 2 0.03
45 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAAGTCATGACCTTTAGCGGCGCTTCTCCCAC
Found at i:3701993 original size:30 final size:30
Alignment explanation
Indices: 3701958--3702016 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3701948 CCGCCATTAG
*
3701958 GAAAGTTCCTCTAAACTACTGGAAATAAAA
1 GAAAGTTCCTCTAAACTACAGGAAATAAAA
*
3701988 GAAAGTTCCTCTAAAGTACAGGAAATAAA
1 GAAAGTTCCTCTAAACTACAGGAAATAAA
3702017 CGGTTCAGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.22
Consensus pattern (30 bp):
GAAAGTTCCTCTAAACTACAGGAAATAAAA
Found at i:3705600 original size:25 final size:25
Alignment explanation
Indices: 3705566--3705650 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
3705556 AGCATGTAAT
3705566 CGGGAAGCTC-TTTCAAGCCATATAA
1 CGGGAAGCTCATTT-AAGCCATATAA
* * *
3705591 CGGGAAGCTCATTTGAGCTATGTAA
1 CGGGAAGCTCATTTAAGCCATATAA
* * *
3705616 CGGGAAGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATTTAAGCCATATAA
**
3705641 CTAGAAGCTC
1 CGGGAAGCTC
3705651 CGGAGAGCCA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
25 49 0.94
26 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (25 bp):
CGGGAAGCTCATTTAAGCCATATAA
Found at i:3705635 original size:50 final size:50
Alignment explanation
Indices: 3705555--3705650 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 50
3705545 TATGCCATAC
* *
3705555 GAGCATGTAATCGGGAAGCTCTTTCAAGCCATATAACGGGAAGCTCATTT
1 GAGCATGTAATCGGGAAGCTCTGTCAAGCCATATAACGAGAAGCTCATTT
* * *
3705605 GAGCTATGTAA-CGGGAAGCTCATGT-GAGCCATGTAACTAGAAGCTC
1 GAGC-ATGTAATCGGGAAGCTC-TGTCAAGCCATATAACGAGAAGCTC
3705651 CGGAGAGCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
50 31 0.79
51 8 0.21
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (50 bp):
GAGCATGTAATCGGGAAGCTCTGTCAAGCCATATAACGAGAAGCTCATTT
Found at i:3705671 original size:24 final size:24
Alignment explanation
Indices: 3705581--3705785 Score: 99
Period size: 25 Copynumber: 8.4 Consensus size: 24
3705571 AGCTCTTTCA
***
3705581 AGCCATATAACGGGAAGCTCATTTG
1 AGCCAT-TAACGGGAAGCTCAGGAG
* * *
3705606 AGCTATGTAACGGGAAGCTCATGTG
1 AGCCAT-TAACGGGAAGCTCAGGAG
** *
3705631 AGCCATGTAACTAGAAGCTCCGGAG
1 AGCCAT-TAACGGGAAGCTCAGGAG
* *
3705656 AGCCATTAACGGGAAGTTCAAGTA-
1 AGCCATTAACGGGAAGCTC-AGGAG
* * *
3705680 AGCCAATATCGAGAAGCTC-GGAG
1 AGCCATTAACGGGAAGCTCAGGAG
* * **
3705703 AGCCATTAACAGGAATCTCATAAG
1 AGCCATTAACGGGAAGCTCAGGAG
* * * *
3705727 AGCCATTTATCGAGAAGCTCCGAAG
1 AGCCA-TTAACGGGAAGCTCAGGAG
* ** **
3705752 AGCAACAAACGGGAAGCTCAAAAAG
1 AGCCATTAACGGGAAGCTC-AGGAG
3705777 AGCCATTAA
1 AGCCATTAA
3705786 TCAAGAAGCT
Statistics
Matches: 133, Mismatches: 42, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
22 2 0.02
23 14 0.11
24 42 0.32
25 75 0.56
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (24 bp):
AGCCATTAACGGGAAGCTCAGGAG
Found at i:3705684 original size:49 final size:47
Alignment explanation
Indices: 3705613--3705722 Score: 130
Period size: 47 Copynumber: 2.3 Consensus size: 47
3705603 TTGAGCTATG
* * * *
3705613 TAACGGGAAGCTCATGTGAGCCATGTAACTAGAAGCTCCGGAGAGCCAT
1 TAACGGGAAGCTCAAGTAAGCCA-ATAACGAGAAGCT-CGGAGAGCCAT
* *
3705662 TAACGGGAAGTTCAAGTAAGCCAATATCGAGAAGCTCGGAGAGCCAT
1 TAACGGGAAGCTCAAGTAAGCCAATAACGAGAAGCTCGGAGAGCCAT
* *
3705709 TAACAGGAATCTCA
1 TAACGGGAAGCTCA
3705723 TAAGAGCCAT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 22 0.42
48 10 0.19
49 20 0.38
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (47 bp):
TAACGGGAAGCTCAAGTAAGCCAATAACGAGAAGCTCGGAGAGCCAT
Found at i:3705731 original size:47 final size:47
Alignment explanation
Indices: 3705643--3705746 Score: 124
Period size: 47 Copynumber: 2.2 Consensus size: 47
3705633 CCATGTAACT
*
3705643 AGAAGCTCCGGAGAGCCATTAACGGGAAGTTCAAGTAAGCCA-ATATCG
1 AGAAGCT-CGGAGAGCCATTAACAGGAAGTTCAAG-AAGCCATATATCG
*
3705691 AGAAGCTCGGAGAGCCATTAACAGGAA-TCTCATA-AGAGCCATTTATCG
1 AGAAGCTCGGAGAGCCATTAACAGGAAGT-TCA-AGA-AGCCATATATCG
3705739 AGAAGCTC
1 AGAAGCTC
3705747 CGAAGAGCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
46 2 0.04
47 27 0.54
48 21 0.42
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (47 bp):
AGAAGCTCGGAGAGCCATTAACAGGAAGTTCAAGAAGCCATATATCG
Found at i:3712702 original size:18 final size:19
Alignment explanation
Indices: 3712663--3712703 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3712653 AATTACAAAA
*
3712663 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
3712682 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
3712700 AAAA
1 AAAA
3712704 AAATCCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:3713934 original size:40 final size:40
Alignment explanation
Indices: 3713890--3713975 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
3713880 ACGACTAATG
* * * ** *
3713890 TTTTTATTAGTTTATTGCATATAAATTGTTGAAATATTAA
1 TTTTTATTAATTCATTGCAGATAAATAATTAAAATATTAA
*
3713930 TTTTTCTTAATTCATTGCAGATAAATAATTAAAATATTAA
1 TTTTTATTAATTCATTGCAGATAAATAATTAAAATATTAA
3713970 TTTTTA
1 TTTTTA
3713976 ACAATAAGGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (40 bp):
TTTTTATTAATTCATTGCAGATAAATAATTAAAATATTAA
Found at i:3716985 original size:3 final size:3
Alignment explanation
Indices: 3716967--3717028 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
3716957 GTTGTCTTCT
* *
3716967 TTA TTG TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3717015 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
3717029 TGCTTTCTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3718209 original size:26 final size:28
Alignment explanation
Indices: 3718180--3718237 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 28
3718170 TAATCATGAT
3718180 TTAAACAAATATTCATA-TTTATA-TA-A
1 TTAAA-AAATATTCATATTTTATACTAGA
3718206 TT--AAAATATTCATATTTTATACTAGA
1 TTAAAAAATATTCATATTTTATACTAGA
3718232 TTAAAA
1 TTAAAA
3718238 TATGTGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
23 11 0.41
24 7 0.26
25 2 0.07
26 5 0.19
28 2 0.07
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (28 bp):
TTAAAAAATATTCATATTTTATACTAGA
Found at i:3718213 original size:23 final size:26
Alignment explanation
Indices: 3718186--3718240 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 26
3718176 TGATTTAAAC
3718186 AAATATTCATA-TTTATA-TA-ATTA
1 AAATATTCATATTTTATACTAGATTA
3718209 AAATATTCATATTTTATACTAGATTA
1 AAATATTCATATTTTATACTAGATTA
3718235 AAATAT
1 AAATAT
3718241 GTGATAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 11 0.38
24 6 0.21
25 2 0.07
26 10 0.34
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATATTCATATTTTATACTAGATTA
Found at i:3728357 original size:9 final size:9
Alignment explanation
Indices: 3728343--3728444 Score: 55
Period size: 9 Copynumber: 10.8 Consensus size: 9
3728333 TATTTTTCTC
3728343 ATAAAAAAT
1 ATAAAAAAT
3728352 ATAAAAAA-
1 ATAAAAAAT
*
3728360 ATTAAATAAAA
1 A-TAAA-AAAT
*
3728371 ATTAAAAAT
1 ATAAAAAAT
**
3728380 GGATATAAACTT
1 --ATA-AAAAAT
* *
3728392 ATTAAAATT
1 ATAAAAAAT
*
3728401 ATAAAAATT
1 ATAAAAAAT
3728410 ATAAAAAAT
1 ATAAAAAAT
*
3728419 TTATAAAAAT
1 ATA-AAAAAT
3728429 -TATAAAAAT
1 ATA-AAAAAT
3728438 ATAAAAA
1 ATAAAAA
3728445 CCTAATAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
8 1 0.01
9 51 0.68
10 16 0.21
11 3 0.04
12 4 0.05
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:3728405 original size:29 final size:27
Alignment explanation
Indices: 3728395--3728461 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
3728385 TAAACTTATT
* *
3728395 AAAATTATAAAAATTATAAAAAATTTATA
1 AAAATTATAAAAA-TAT-AAAAACTTATT
* *
3728424 AAAATTATAAAAATATAAAAACCTAAT
1 AAAATTATAAAAATATAAAAACTTATT
3728451 -AAATTATAAAA
1 AAAATTATAAAA
3728462 TTAATAACGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.32
27 7 0.21
28 3 0.09
29 13 0.38
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAATTATAAAAATATAAAAACTTATT
Found at i:3728424 original size:20 final size:19
Alignment explanation
Indices: 3728395--3728444 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
3728385 TAAACTTATT
3728395 AAAATTATAAAAATTATAA
1 AAAATTATAAAAATTATAA
3728414 AAAATTTATAAAAATTAT-A
1 AAAA-TTATAAAAATTATAA
3728433 AAAA-TATAAAAA
1 AAAATTATAAAAA
3728445 CCTAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.27
19 9 0.30
20 13 0.43
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATTATAAAAATTATAA
Found at i:3728555 original size:29 final size:30
Alignment explanation
Indices: 3728478--3728556 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 30
3728468 ACGCTTACTT
* *
3728478 AAAATATTTAAAATTAAAAAATGTATTACA
1 AAAATATTAAAAATTAAAAAATGTAGTACA
** * *
3728508 ATTATTTTAAAAAAATAAAAAAT-T-GTACA
1 AAAATATT-AAAAATTAAAAAATGTAGTACA
*
3728537 AAAATATTAAAAATTTAAAA
1 AAAATATTAAAAATTAAAAA
3728557 GTATTAAAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
28 10 0.27
29 9 0.24
30 6 0.16
31 12 0.32
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAATATTAAAAATTAAAAAATGTAGTACA
Found at i:3729153 original size:9 final size:9
Alignment explanation
Indices: 3729106--3729268 Score: 82
Period size: 9 Copynumber: 17.6 Consensus size: 9
3729096 TTCTTAACTT
*
3729106 TTTTTAGAA
1 TTTTTATAA
3729115 CTTTTTATAA
1 -TTTTTATAA
**
3729125 TTTATTA-GG
1 TTT-TTATAA
3729134 TTTTTAT-A
1 TTTTTATAA
3729142 TTTTTATAA
1 TTTTTATAA
3729151 TTTTTATAA
1 TTTTTATAA
*
3729160 GTTTATATCAA
1 -TTTTTAT-AA
* **
3729171 TTTTCATGC
1 TTTTTATAA
*
3729180 TTTTTTTAA
1 TTTTTATAA
*
3729189 TATTTAATAA
1 T-TTTTATAA
3729199 TTTTTAT-A
1 TTTTTATAA
*
3729207 TTATTGAT-A
1 TT-TTTATAA
* *
3729216 TTTTTTTTA
1 TTTTTATAA
3729225 TTTTTATAA
1 TTTTTATAA
* *
3729234 TATTTTCTTATT
1 T-TTTT-ATA-A
3729246 TTTTTATAA
1 TTTTTATAA
*
3729255 TTTTTATGA
1 TTTTTATAA
3729264 TTTTT
1 TTTTT
3729269 TATTCTTTTT
Statistics
Matches: 116, Mismatches: 26, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
8 16 0.14
9 56 0.48
10 35 0.30
11 8 0.07
12 1 0.01
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3729258 original size:30 final size:28
Alignment explanation
Indices: 3729198--3729279 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 28
3729188 ATATTTAATA
* *
3729198 ATTTTTATATTA-TTGA-TATTTTTTTT
1 ATTTTTATAATATTTTATTATTTTTTTT
*
3729224 ATTTTTATAATATTTTCTTATTTTTTTAT
1 ATTTTTATAATATTTTATTATTTTTTT-T
* * *
3729253 AATTTTTATGATTTTTTATTCTTTTTT
1 -ATTTTTATAATATTTTATTATTTTTT
3729280 ATGGGAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 11 0.24
27 2 0.04
28 9 0.20
29 1 0.02
30 22 0.49
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (28 bp):
ATTTTTATAATATTTTATTATTTTTTTT
Found at i:3733076 original size:41 final size:41
Alignment explanation
Indices: 3733019--3733102 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
3733009 GTTTAGAGAA
3733019 TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
1 TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
3733060 TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
1 TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
3733101 TT
1 TT
3733103 AGTACAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (41 bp):
TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
Found at i:3737732 original size:13 final size:13
Alignment explanation
Indices: 3737714--3737746 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3737704 TAATTTTGGT
*
3737714 GCCACACAGTCTG
1 GCCACACAGTCTA
3737727 GCCACACAGTCTA
1 GCCACACAGTCTA
3737740 GCCACAC
1 GCCACAC
3737747 GGTCGTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.42, G:0.18, T:0.12
Consensus pattern (13 bp):
GCCACACAGTCTA
Found at i:3748860 original size:3 final size:3
Alignment explanation
Indices: 3748852--3748894 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3748842 CCCTGTTTCT
3748852 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3748895 ATCTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3760875 original size:16 final size:16
Alignment explanation
Indices: 3760838--3760877 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3760828 TTAATAAAAT
* *
3760838 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3760854 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3760870 TAAAATTA
1 TAAAATTA
3760878 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3760877 original size:22 final size:22
Alignment explanation
Indices: 3760810--3760862 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
3760800 TAATTAAAAT
* * *
3760810 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
3760832 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
3760854 TAAAATTAA
1 TAAAATTAA
3760863 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:3760936 original size:66 final size:59
Alignment explanation
Indices: 3760880--3760999 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
3760870 TAAAATTATC
* * *
3760880 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
3760938 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
3760997 AAA
1 AAA
3761000 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:3761112 original size:23 final size:24
Alignment explanation
Indices: 3761065--3761110 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
3761055 AAATAAACTT
3761065 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
3761089 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
3761111 AATATTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:3761601 original size:20 final size:22
Alignment explanation
Indices: 3761578--3761617 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3761568 TAAAAAATAT
3761578 ATTAAAAT-AT-TAAATATTAA
1 ATTAAAATAATATAAATATTAA
3761598 ATTAAAATAATATAAATATT
1 ATTAAAATAATATAAATATT
3761618 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTAAAATAATATAAATATTAA
Found at i:3761624 original size:20 final size:19
Alignment explanation
Indices: 3761572--3761623 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 19
3761562 AATAAATAAA
*
3761572 AAATATATTAAAAT-AT-T
1 AAATATTTTAAAATAATAT
3761589 AAATATTAAATTAAAATAATAT
1 AAATATT---TTAAAATAATAT
3761611 AAATATTTTAAAA
1 AAATATTTTAAAA
3761624 AAAATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 6 0.21
19 6 0.21
20 7 0.24
21 2 0.07
22 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATTTTAAAATAATAT
Found at i:3773276 original size:16 final size:16
Alignment explanation
Indices: 3773255--3773323 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
3773245 TTTGGTTCGC
3773255 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3773271 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3773287 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
3773304 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3773320 TGTA
1 TGTA
3773324 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3773301 original size:33 final size:32
Alignment explanation
Indices: 3773255--3773323 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
3773245 TTTGGTTCGC
3773255 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
3773287 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
3773320 TGTA
1 TGTA
3773324 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:3773388 original size:44 final size:45
Alignment explanation
Indices: 3773304--3773394 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
3773294 GGATTAGAGG
* * *
3773304 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
3773349 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
3773393 TG
1 TG
3773395 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:3773579 original size:18 final size:17
Alignment explanation
Indices: 3773558--3773592 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3773548 TTATTATTAA
*
3773558 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3773576 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3773593 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3773676 original size:120 final size:119
Alignment explanation
Indices: 3773536--3773801 Score: 442
Period size: 120 Copynumber: 2.2 Consensus size: 119
3773526 ATTTAATCAT
3773536 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
3773601 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATAAATATTCTTATATGAATTTACTAAAATCAT-ATATATAATACTATAAAATATA
* *
3773657 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
3773722 TAAATATTCTTATATGAATTTACTAAAATTATATATATAATAGTATAAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATATATATAATACTATAAAATATA
*
3773776 ATATAACATAATTATTATTAAATATA
1 ATTTAACATAATTATTATTAAATATA
3773802 ATCAATTTTT
Statistics
Matches: 137, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
119 45 0.33
120 88 0.64
121 4 0.03
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (119 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
TAAATATTCTTATATGAATTTACTAAAATCATATATATAATACTATAAAATATA
Found at i:3773699 original size:18 final size:17
Alignment explanation
Indices: 3773676--3773712 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
3773666 AATTATTATT
3773676 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
3773692 AAATATATGATTTAATA
1 AAATATATGATTTAATA
3773709 AAAT
1 AAAT
3773713 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:3777621 original size:22 final size:21
Alignment explanation
Indices: 3777596--3777643 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
3777586 ATAAACTTTT
3777596 AAAAATTATAAAAGATTCATA-A
1 AAAAATTAT--AAGATTCATATA
*
3777618 AAAAGTTATAAGATTCATATA
1 AAAAATTATAAGATTCATATA
3777639 AAAAA
1 AAAAA
3777644 AAAGTATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 10 0.43
21 5 0.22
22 8 0.35
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (21 bp):
AAAAATTATAAGATTCATATA
Found at i:3779569 original size:62 final size:62
Alignment explanation
Indices: 3779472--3779588 Score: 234
Period size: 62 Copynumber: 1.9 Consensus size: 62
3779462 CTGCCTGGAA
3779472 CTCTCCAATACTCCCATAGCTTCTAGAAGAGCATTCATTGTTGCACAATAGAACTCTCCAAT
1 CTCTCCAATACTCCCATAGCTTCTAGAAGAGCATTCATTGTTGCACAATAGAACTCTCCAAT
3779534 CTCTCCAATACTCCCATAGCTTCTAGAAGAGCATTCATTGTTGCACAATAGAACT
1 CTCTCCAATACTCCCATAGCTTCTAGAAGAGCATTCATTGTTGCACAATAGAACT
3779589 GTTCAGAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (62 bp):
CTCTCCAATACTCCCATAGCTTCTAGAAGAGCATTCATTGTTGCACAATAGAACTCTCCAAT
Found at i:3779803 original size:2 final size:2
Alignment explanation
Indices: 3779791--3779826 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3779781 CCTCCCTCCT
* *
3779791 GA GA GA TA GA GA GA GA GA GA GA TA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3779827 TTAGTGGAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06
Consensus pattern (2 bp):
GA
Found at i:3779812 original size:16 final size:16
Alignment explanation
Indices: 3779791--3779826 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3779781 CCTCCCTCCT
3779791 GAGAGATAGAGAGAGA
1 GAGAGATAGAGAGAGA
3779807 GAGAGATAGAGAGAGA
1 GAGAGATAGAGAGAGA
3779823 GAGA
1 GAGA
3779827 TTAGTGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06
Consensus pattern (16 bp):
GAGAGATAGAGAGAGA
Found at i:3782530 original size:2 final size:2
Alignment explanation
Indices: 3782525--3782561 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3782515 ACTATATAAC
3782525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3782562 CCAAACAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3785275 original size:25 final size:25
Alignment explanation
Indices: 3785238--3785293 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
3785228 CATATATGAA
*
3785238 ATAATCTTGTTGTTTAATGTAGT-GG
1 ATAATCTTATTGTTTAATGTA-TAGG
*
3785263 ATAATCTTATTGTTTGATGTATAGG
1 ATAATCTTATTGTTTAATGTATAGG
3785288 ATAATC
1 ATAATC
3785294 ATTTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (25 bp):
ATAATCTTATTGTTTAATGTATAGG
Found at i:3788458 original size:17 final size:17
Alignment explanation
Indices: 3788421--3788459 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3788411 TTATTTGTTC
*
3788421 TATTGTTGGAATTGAAT
1 TATTGTTGGAATTGAAA
3788438 TATTGTTGGAATT-ATAA
1 TATTGTTGGAATTGA-AA
3788455 TATTG
1 TATTG
3788460 AATTGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTGAAA
Found at i:3788624 original size:21 final size:20
Alignment explanation
Indices: 3788598--3788705 Score: 94
Period size: 21 Copynumber: 5.3 Consensus size: 20
3788588 GTGTTTTACT
*
3788598 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCT-TTACGAGC
* * * *
3788619 TTCTGTTCAACTGTAATGAGT
1 TTCTGTTCAGCT-TTACGAGC
*
3788640 TTCTGTTTAGCTCTTACGAGC
1 TTCTGTTCAGCT-TTACGAGC
*
3788661 TTCTATTCAGCTTT-CGAGC
1 TTCTGTTCAGCTTTACGAGC
* *
3788680 TTCTATTAAGCTTT-CGAGC
1 TTCTGTTCAGCTTTACGAGC
3788699 TTCTGTT
1 TTCTGTT
3788706 GGCATATTCA
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
19 29 0.40
20 2 0.03
21 42 0.58
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (20 bp):
TTCTGTTCAGCTTTACGAGC
Found at i:3788680 original size:19 final size:19
Alignment explanation
Indices: 3788656--3788702 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3788646 TTAGCTCTTA
*
3788656 CGAGCTTCTATTCAGCTTT
1 CGAGCTTCTATTAAGCTTT
3788675 CGAGCTTCTATTAAGCTTT
1 CGAGCTTCTATTAAGCTTT
3788694 CGAGCTTCT
1 CGAGCTTCT
3788703 GTTGGCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (19 bp):
CGAGCTTCTATTAAGCTTT
Found at i:3792008 original size:21 final size:20
Alignment explanation
Indices: 3791980--3792031 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
3791970 ATTAATAGAA
3791980 GTTATGAATGACAGGAAATT
1 GTTATGAATGACAGGAAATT
*
3792000 GTTAGTGAATGACAGGGAATT
1 GTTA-TGAATGACAGGAAATT
**
3792021 GACATGAATGA
1 GTTATGAATGA
3792032 TTTTATTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.27
Consensus pattern (20 bp):
GTTATGAATGACAGGAAATT
Found at i:3794259 original size:21 final size:22
Alignment explanation
Indices: 3794231--3794294 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
3794221 CAGAAACAGT
*
3794231 ATACGACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
** *
3794253 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
3794273 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
3794295 TTGACAAAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:3797114 original size:17 final size:18
Alignment explanation
Indices: 3797080--3797115 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3797070 TGAACTTTTA
3797080 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
3797098 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
3797115 T
1 T
3797116 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:3797886 original size:14 final size:17
Alignment explanation
Indices: 3797867--3797904 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
3797857 ATTTATTTCT
3797867 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
3797881 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
3797898 TAATATA
1 TAATATA
3797905 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:3797912 original size:12 final size:11
Alignment explanation
Indices: 3797884--3797935 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
3797874 ATATTTATAA
3797884 TATAATTAATT
1 TATAATTAATT
*
3797895 TAATAATATACTT
1 T-ATAAT-TAATT
3797908 TATAATTAATT
1 TATAATTAATT
3797919 TAT-A-T-ATT
1 TATAATTAATT
3797927 TATAATTAA
1 TATAATTAA
3797936 ATCATGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 2 0.06
11 9 0.26
12 10 0.29
13 5 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:3801300 original size:90 final size:89
Alignment explanation
Indices: 3801188--3801373 Score: 320
Period size: 90 Copynumber: 2.1 Consensus size: 89
3801178 TGAATTTTTT
*
3801188 TAATTTTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTTTA
1 TAATTTTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTTTA
3801253 GTGTTTTGTGATTTTTTATGAATG
66 GTGTTTTGTGATTTTTTATGAATG
* *
3801277 TAATTTTTTCAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATCGTTTGTGTTTAGTTT
1 TAATTTTTT-AAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTTT
*
3801342 AGTGTTTTGTGATTTGTTATGAATG
65 AGTGTTTTGTGATTTTTTATGAATG
3801367 T-ATTTTT
1 TAATTTTT
3801374 ATATTATTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 15 0.16
90 77 0.84
ACGTcount: A:0.24, C:0.01, G:0.17, T:0.58
Consensus pattern (89 bp):
TAATTTTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTTTA
GTGTTTTGTGATTTTTTATGAATG
Found at i:3801508 original size:114 final size:113
Alignment explanation
Indices: 3801369--3801590 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 113
3801359 TATGAATGTA
*
3801369 TTTTTATATTATTTTAAAGTCATTTTGTTAGTAATTTATGGTTAGGTTATAAATTATTTGTATTT
1 TTTTTATATTATTTTAAAGTCATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTATTT
* * *
3801434 AGTTTAATG-TTATTGTGATTTTTTTATAAATGTAAATTTTTTTTGCTT
66 AGTTTAATGTTTATTGTGA-ATTGTCATAAATGTAAATTTTTTTTGCTT
* * *
3801482 TTTTTATAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTT
1 TTTTTAT-ATTATTTTAAAGTCATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTATT
*
3801547 TAGTTTAATGTTTATTGTGAATTGTCATAAATGTAAGTTTTTTT
65 TAGTTTAATGTTTATTGTGAATTGTCATAAATGTAAATTTTTTT
3801591 GTATTTTTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
113 7 0.07
114 83 0.84
115 9 0.09
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (113 bp):
TTTTTATATTATTTTAAAGTCATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTATTT
AGTTTAATGTTTATTGTGAATTGTCATAAATGTAAATTTTTTTTGCTT
Found at i:3801610 original size:92 final size:87
Alignment explanation
Indices: 3801505--3801685 Score: 263
Period size: 92 Copynumber: 2.0 Consensus size: 87
3801495 TTTAAAGTTA
* **
3801505 TTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTAATGTTTATTGTGAATT
1 TTTTGTTAGTAATTTATGATTAGGTTATAAATT-ATT-TGTTTAGTTTAATGTAAATTGTGAATT
*
3801570 GTCATAAATGTAAGTTTTTTTGTATTT
64 GTCAT-AATGTAA-TTTTATT-TATTT
*
3801597 TTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTAAATTGTGATTTGT
1 TTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTAAATTGTGAATTGT
*
3801662 TATAATGTAATTTTATTTATTT
66 CATAATGTAATTTTATTTATTT
3801684 TT
1 TT
3801686 GATTTATTTC
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
87 7 0.08
88 6 0.07
89 7 0.08
90 28 0.34
91 2 0.02
92 33 0.40
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.57
Consensus pattern (87 bp):
TTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTAAATTGTGAATTGT
CATAATGTAATTTTATTTATTT
Found at i:3802232 original size:21 final size:21
Alignment explanation
Indices: 3802206--3802258 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3802196 CATTGTTTCT
* * *
3802206 AATCTCACTGCTATAGTATCC
1 AATCTCACCGCTACAGTAACC
*
3802227 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
3802248 AATCTCACCGC
1 AATCTCACCGC
3802259 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:3806719 original size:54 final size:54
Alignment explanation
Indices: 3806571--3806721 Score: 143
Period size: 54 Copynumber: 2.9 Consensus size: 54
3806561 AACTAATAAT
* * * *
3806571 TAATTTATAATACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATT-AAAATAAACAAA
* * * *
3806626 -AATTTATATTAATAACCTAAC-AAATCAC---AATAA-ACATTAAACTAAACAAA
1 TAATTTATAATAATAA-CTAACAAAATAACTTTAA-AATAAATTAAAATAAACAAA
* *
3806676 TAATTTATAATAGTAACTAACAAAATGACTTTAAAATAAATTAAAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAA
3806722 ACAACATAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
50 14 0.19
51 25 0.33
52 2 0.03
53 2 0.03
54 27 0.36
55 5 0.07
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.31
Consensus pattern (54 bp):
TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAATAAACAAA
Found at i:3806724 original size:51 final size:51
Alignment explanation
Indices: 3806571--3806730 Score: 137
Period size: 51 Copynumber: 3.1 Consensus size: 51
3806561 AACTAATAAT
* * *
3806571 TAATTTATAATACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAA--CA-AA
* * * ** *
3806625 AAATTTATATTAATAACCTAAC-AAATCACAATAAACATTAAACT--AAACAAA
1 TAATTTATAATAATAA-CTAACAAAATAACTTTAAA-A-TAAATTAAAAACAAA
* *
3806676 TAATTTATAATAGTAACTAACAAAATGACTTTAAAATAAATTAAAAACAACA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAACAA-A
3806728 TAA
1 TAA
3806731 AAACAACAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
49 5 0.06
50 6 0.07
51 31 0.37
52 5 0.06
54 25 0.30
55 6 0.07
56 5 0.06
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (51 bp):
TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAACAAA
Found at i:3807045 original size:24 final size:25
Alignment explanation
Indices: 3807015--3807063 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
3807005 ACCATTAAAT
*
3807015 AAAATAAATTTTA-TAAAAATATAA
1 AAAATAAATTTTATTAAAAAAATAA
3807039 AAAATAAATTTTATTAAAAAAATAA
1 AAAATAAATTTTATTAAAAAAATAA
3807064 CGGTATTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATAAATTTTATTAAAAAAATAA
Found at i:3814739 original size:18 final size:20
Alignment explanation
Indices: 3814702--3814742 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3814692 AAATTTTTCA
*
3814702 AAATTTTTGAAAAACTAATT
1 AAATTTTTGAAAAACAAATT
3814722 AAATTTTT-AAAAA-AAATT
1 AAATTTTTGAAAAACAAATT
3814740 AAA
1 AAA
3814743 AAGCTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATTTTTGAAAAACAAATT
Found at i:3814750 original size:30 final size:28
Alignment explanation
Indices: 3814711--3814768 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
3814701 AAAATTTTTG
* *
3814711 AAAAACTAATTAAATTTTTAAAAAAAATT
1 AAAAACTAATGAAA-ATTTAAAAAAAATT
*
3814740 AAAAAGCTAATGAAAATTTAAAAATAATT
1 AAAAA-CTAATGAAAATTTAAAAAAAATT
3814769 CAGATTGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAACTAATGAAAATTTAAAAAAAATT
Found at i:3817755 original size:64 final size:63
Alignment explanation
Indices: 3817619--3817824 Score: 168
Period size: 69 Copynumber: 3.1 Consensus size: 63
3817609 CACTCACATG
* * * * *
3817619 CTCACACTTACTCT-ATAAATAAGTGTCAGTTTCTTAACTATTTTCTTTAACAACTTAGTTTTAA
1 CTCACATTTA-TCTGATAAATAAGTGT-AATTTCTT-ACTATTTTCATTAAAAACTTAATTTTAA
3817683 T
63 T
*
3817684 C-CTACATTTATCTGATAAATAAGTGATAATTTCTTACTATTTTCATTAAAAATTTAATTTTAAT
1 CTC-ACATTTATCTGATAAATAAGTG-TAATTTCTTACTATTTTCATTAAAAACTTAATTTTAAT
* * * * *
3817748 CTCACATTGAT-TAGAGAATACTCTCATAG-CTAACTTTTTTACTATTTTCATTAAAAAGTTAAT
1 CTCACATTTATCT-GATAA-A---T-A-AGTGTAA-TTTCTTACTATTTTCATTAAAAACTTAAT
3817811 TTTAAT
58 TTTAAT
3817817 CTCACATT
1 CTCACATT
3817825 AACTAAAATA
Statistics
Matches: 118, Mismatches: 11, Indels: 20
0.79 0.07 0.13
Matches are distributed among these distances:
63 1 0.01
64 41 0.35
65 27 0.23
66 1 0.01
68 4 0.03
69 42 0.36
70 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.45
Consensus pattern (63 bp):
CTCACATTTATCTGATAAATAAGTGTAATTTCTTACTATTTTCATTAAAAACTTAATTTTAAT
Found at i:3817798 original size:69 final size:68
Alignment explanation
Indices: 3817717--3817893 Score: 241
Period size: 69 Copynumber: 2.6 Consensus size: 68
3817707 TGATAATTTC
* *
3817717 TTACTATTTTCATTAAAAATTTAATTTTAATCTCACATTGATTAGAGA-ATACTCTCATAGCTAA
1 TTACTATTTTCATTAAAAA-TTAATTTTAATCTCACATTGACTA-AAATATACTCTCATAGCTAA
* *
3817781 CTTTT
64 CGTAT
* *
3817786 TTACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTAACTAAAATATACTCTCATAGCTCAC
1 TTACTATTTTCATTAAAAA-TTAATTTTAATCTCACATTGACTAAAATATACTCTCATAGCTAAC
3817851 GTAT
65 GTAT
*
3817855 TCACTATTTTCATTAAAAATTAATTTTAAT-TCCACATTG
1 TTACTATTTTCATTAAAAATTAATTTTAATCT-CACATTG
3817894 GCTAGACAAC
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
67 1 0.01
68 19 0.20
69 77 0.79
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.44
Consensus pattern (68 bp):
TTACTATTTTCATTAAAAATTAATTTTAATCTCACATTGACTAAAATATACTCTCATAGCTAACG
TAT
Found at i:3819457 original size:19 final size:18
Alignment explanation
Indices: 3819424--3819459 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3819414 ACATTCAAAG
*
3819424 CCAAACAAACTTATCAAT
1 CCAAACAAAATTATCAAT
3819442 CCAAACAAAATATATCAA
1 CCAAACAAAAT-TATCAA
3819460 CTTATGGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (18 bp):
CCAAACAAAATTATCAAT
Found at i:3821133 original size:69 final size:69
Alignment explanation
Indices: 3821020--3821168 Score: 192
Period size: 69 Copynumber: 2.2 Consensus size: 69
3821010 AAGTGACAAT
* ** * * *
3821020 TTCTTCACTATTTTTATTAAAAAATTAATTTTAATCCTACATTGACTAGAGAATACTCTCATAGA
1 TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATA-A
3821085 -TAAC
65 CTAAC
* *
3821089 TTCTTCACTATATCCATTAAAAAGTCAATTTTAATCCCAAATTGACTAGAGAATACTTTCATAAC
1 TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATAAC
*
3821154 TCAC
66 TAAC
*
3821158 TTATTCACTAT
1 TTCTTCACTAT
3821169 TAAAAATTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
68 1 0.01
69 68 0.99
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (69 bp):
TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATAAC
TAAC
Found at i:3821191 original size:21 final size:22
Alignment explanation
Indices: 3821165--3821208 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3821155 CACTTATTCA
3821165 CTATTAAAAATT-AATTTTAAT
1 CTATTAAAAATTAAATTTTAAT
*
3821186 CTATTAAAACTTAAATTTTAAT
1 CTATTAAAAATTAAATTTTAAT
3821208 C
1 C
3821209 CCACATTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (22 bp):
CTATTAAAAATTAAATTTTAAT
Found at i:3837157 original size:17 final size:18
Alignment explanation
Indices: 3837115--3837158 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3837105 ATATCAGGAC
3837115 AAAATTATAAAAATTATTG
1 AAAATTA-AAAAATTATTG
* *
3837134 AATATTAAAATATTATT-
1 AAAATTAAAAAATTATTG
3837151 AAAATTAA
1 AAAATTAA
3837159 TATAAGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTAAAAAATTATTG
Found at i:3837188 original size:20 final size:20
Alignment explanation
Indices: 3837160--3837234 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 20
3837150 TAAAATTAAT
3837160 ATAAGATTATAAAAATTGTTA
1 ATAAGATTATAAAAATT-TTA
3837181 ATAA-ATTAT-AAAATTTT-
1 ATAAGATTATAAAAATTTTA
*
3837198 ATAAAATTAATAAAACATATTTA
1 ATAAGATT-ATAAAA-AT-TTTA
*
3837221 A-AATATTATAAAAA
1 ATAAGATTATAAAAA
3837235 CGTATAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.09
18 5 0.11
19 8 0.17
20 9 0.19
21 12 0.26
22 8 0.17
23 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (20 bp):
ATAAGATTATAAAAATTTTA
Found at i:3837262 original size:10 final size:9
Alignment explanation
Indices: 3837115--3837343 Score: 104
Period size: 10 Copynumber: 23.4 Consensus size: 9
3837105 ATATCAGGAC
3837115 AAAATTATA
1 AAAATTATA
*
3837124 AAAATTATTG
1 AAAATTA-TA
*
3837134 AATATTA-A
1 AAAATTATA
* *
3837142 AATATTATT
1 AAAATTATA
3837151 AAAATTAATA
1 AAAATT-ATA
*
3837161 TAAGATTATA
1 -AAAATTATA
*
3837171 AAAATTGTTA
1 AAAATT-ATA
3837181 ATAAATTAT-
1 A-AAATTATA
*
3837190 AAAATTTTA
1 AAAATTATA
3837199 TAAAATTAATA
1 -AAAATT-ATA
*
3837210 AAACATATTTA
1 AAA-AT-TATA
3837221 AAATATTATA
1 AAA-ATTATA
*
3837231 AAAACGTATA
1 AAAA-TTATA
*
3837241 AAAATTCTTA
1 AAAATT-ATA
3837251 AAAACTTATAA
1 AAAA-TTAT-A
* *
3837262 AAAATAAAA
1 AAAATTATA
3837271 AAAATTACTA
1 AAAATTA-TA
3837281 AAAATTATA
1 AAAATTATA
* *
3837290 AAAGTTATTC
1 AAAATTA-TA
*
3837300 AAAA-TATT
1 AAAATTATA
3837308 AAAATTGATA
1 AAAATT-ATA
*
3837318 TAAACTTATA
1 -AAAATTATA
3837328 TAAATATATATA
1 -AAA-AT-TATA
3837340 AAAA
1 AAAA
3837344 AGTCATAAAA
Statistics
Matches: 168, Mismatches: 30, Indels: 43
0.70 0.12 0.18
Matches are distributed among these distances:
8 18 0.11
9 38 0.23
10 70 0.42
11 37 0.22
12 5 0.03
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:3838013 original size:19 final size:19
Alignment explanation
Indices: 3837932--3838013 Score: 51
Period size: 19 Copynumber: 4.2 Consensus size: 19
3837922 ATTTTAATAG
*
3837932 TTTAAATATTTTTA-TGATT
1 TTTAAAT-TTTTTATTAATT
**
3837951 TATTATAATTGTTTTAAGAA-T
1 T-TTA-AATT-TTTTATTAATT
* * *
3837972 TTTAAACGTTTTTATCAAAT
1 TTTAAA-TTTTTTATTAATT
3837992 TTTAAATTTTTTATTAATT
1 TTTAAATTTTTTATTAATT
3838011 TTT
1 TTT
3838014 TATAATTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
19 23 0.47
20 15 0.31
21 10 0.20
22 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTAAATTTTTTATTAATT
Found at i:3838072 original size:29 final size:31
Alignment explanation
Indices: 3838039--3838118 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
3838029 TTTATCAGAT
**
3838039 TTTTTAATAATATTTATAAGCATA-TATTAA
1 TTTTTAATAATATTTATAAAAATATTATTAA
* * *
3838069 -TTTTAATAGTATTTTAAAAAAATATTTTTAA
1 TTTTTAATAATA-TTTATAAAAATATTATTAA
*
3838100 TTTTTAATAATTTTTATAA
1 TTTTTAATAATATTTATAA
3838119 TTTTCCTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
29 10 0.26
30 9 0.23
31 11 0.28
32 9 0.23
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTTTAATAATATTTATAAAAATATTATTAA
Found at i:3844575 original size:33 final size:35
Alignment explanation
Indices: 3844480--3844576 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
3844470 TTAATATTTT
*
3844480 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
3844515 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
3844548 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
3844577 AAATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:3848437 original size:243 final size:243
Alignment explanation
Indices: 3848009--3848500 Score: 867
Period size: 243 Copynumber: 2.0 Consensus size: 243
3847999 ATCTTCTTGT
*
3848009 CATTCCAGTGGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
1 CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
** *
3848074 CCCAGCTGCAATTTCTTCAGGAAGACTCTGCTGAAATGTTTTGGGGAGATCCTTTCCAACCCACC
66 CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
*
3848139 TACAAGGAGAATGAAAGAAAGGATAGTGCTGTTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
131 TACAAGGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
*
3848204 AGAGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
196 AGAGATGAATTCATCAACAGCGGATATCTTCAAGGTATGGGATTTGGA
*
3848252 CATTCCAGTAGATGGGGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
1 CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
** * * *
3848317 CTGAGCTGCAATTTCTTCAGGAAGATTCCACTGAAGTGTTTCGGGGAGATCCTTTCCGACCCACC
66 CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
3848382 TACAAGGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
131 TACAAGGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
*
3848447 AGAGATGAATTCATCAACAGTGGATATCTTCAAGGTATGGGATTTGGA
196 AGAGATGAATTCATCAACAGCGGATATCTTCAAGGTATGGGATTTGGA
3848495 CATTCC
1 CATTCC
3848501 GGATGAGGAA
Statistics
Matches: 236, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
243 236 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (243 bp):
CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
TACAAGGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
AGAGATGAATTCATCAACAGCGGATATCTTCAAGGTATGGGATTTGGA
Found at i:3851434 original size:177 final size:177
Alignment explanation
Indices: 3851138--3851495 Score: 689
Period size: 177 Copynumber: 2.0 Consensus size: 177
3851128 AAATGGACCC
3851138 CACGAATGGTTTAATTACGAATTGTAGATTAAATCAGCCCTAAATAAAAATTCTAGAAAAATAGG
1 CACGAATGGTTTAATTACGAATTGTAGATTAAATCAGCCCTAAATAAAAATTCTAGAAAAATAGG
*
3851203 CCACATGCCTAAGTGGATTTACACAATCCAAATGACTAGCCCATGTGGCCCACAGGGTTACCTAT
66 CCACATGCCTAAGTGGATTTACACAACCCAAATGACTAGCCCATGTGGCCCACAGGGTTACCTAT
*
3851268 CCTGCCTGTGTGATTTCACACGCTCGTGTGTCCGACATGGCCAGCCA
131 CCTGCCTATGTGATTTCACACGCTCGTGTGTCCGACATGGCCAGCCA
3851315 CACGAATGGTTTAATTACGAATTGTAGATTAAATCAGCCCTAAATAAAAATTCTAGAAAAATAGG
1 CACGAATGGTTTAATTACGAATTGTAGATTAAATCAGCCCTAAATAAAAATTCTAGAAAAATAGG
*
3851380 CCACATGCCTAAGTGGATTTACACGACCCAAATGACTAGCCCATGTGGCCCACAGGGTTACCTAT
66 CCACATGCCTAAGTGGATTTACACAACCCAAATGACTAGCCCATGTGGCCCACAGGGTTACCTAT
3851445 CCTGCCTATGTGATTTCACACGCTCGTGTGTCCGACATGGCCAGCCA
131 CCTGCCTATGTGATTTCACACGCTCGTGTGTCCGACATGGCCAGCCA
3851492 CACG
1 CACG
3851496 GCCATGTGAC
Statistics
Matches: 178, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 178 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (177 bp):
CACGAATGGTTTAATTACGAATTGTAGATTAAATCAGCCCTAAATAAAAATTCTAGAAAAATAGG
CCACATGCCTAAGTGGATTTACACAACCCAAATGACTAGCCCATGTGGCCCACAGGGTTACCTAT
CCTGCCTATGTGATTTCACACGCTCGTGTGTCCGACATGGCCAGCCA
Found at i:3864201 original size:28 final size:28
Alignment explanation
Indices: 3864163--3864231 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
3864153 CCAAAAAATT
3864163 CAACGGCCATATTGCAACGA-CTAGATTC
1 CAACGGCCATATTGCAACGATC-AGATTC
* *
3864191 CAACGGTCATATTGTAACGATCAGATTC
1 CAACGGCCATATTGCAACGATCAGATTC
**
3864219 CAACTACCATATT
1 CAACGGCCATATT
3864232 ATAACGGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 34 0.97
29 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (28 bp):
CAACGGCCATATTGCAACGATCAGATTC
Found at i:3864244 original size:28 final size:28
Alignment explanation
Indices: 3864163--3864245 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 28
3864153 CCAAAAAATT
* ** *
3864163 CAACGGCCATATTGCAACGACTAGATTC
1 CAACGACCATATTATAACGATTAGATTC
** * *
3864191 CAACGGTCATATTGTAACGATCAGATTC
1 CAACGACCATATTATAACGATTAGATTC
* *
3864219 CAACTACCATATTATAACGGTTAGATT
1 CAACGACCATATTATAACGATTAGATT
3864246 TTTGCATTAC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.28
Consensus pattern (28 bp):
CAACGACCATATTATAACGATTAGATTC
Found at i:3865657 original size:12 final size:12
Alignment explanation
Indices: 3865640--3865664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3865630 GACTAAATTG
3865640 AAATAAAATAAA
1 AAATAAAATAAA
3865652 AAATAAAATAAA
1 AAATAAAATAAA
3865664 A
1 A
3865665 CCCTAAAATA
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):
AAATAAAATAAA
Found at i:3870495 original size:12 final size:11
Alignment explanation
Indices: 3870478--3870511 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
3870468 ACCTTGTGTG
3870478 TGTTCTTTCTGT
1 TGTTCTTT-TGT
3870490 TGTTCTTTTGT
1 TGTTCTTTTGT
3870501 TGCTTCTTTTG
1 TG-TTCTTTTG
3870512 GCATAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.00, C:0.15, G:0.18, T:0.68
Consensus pattern (11 bp):
TGTTCTTTTGT
Found at i:3876484 original size:21 final size:20
Alignment explanation
Indices: 3876448--3876486 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3876438 CTTTGACCGA
*
3876448 TCATTGACTAGTGTTGACTG
1 TCATTGACTAGCGTTGACTG
3876468 TCATTGACTATGCGTTGAC
1 TCATTGACTA-GCGTTGAC
3876487 CAACCACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
TCATTGACTAGCGTTGACTG
Found at i:3876599 original size:21 final size:22
Alignment explanation
Indices: 3876575--3876622 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3876565 AAATAATCAT
3876575 ATATAATATATAAAAATTT-AA
1 ATATAATATATAAAAATTTAAA
** * *
3876596 ATATTTTTTATAAAATTTTAAA
1 ATATAATATATAAAAATTTAAA
3876618 ATATA
1 ATATA
3876623 TAATTTTAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATAATATATAAAAATTTAAA
Found at i:3876668 original size:20 final size:18
Alignment explanation
Indices: 3876636--3876685 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 18
3876626 TTTTAAATTT
3876636 TAAAAAGTT-AAAATCATATA
1 TAAAAA-TTAAAAAT-AT-TA
*
3876656 TAAAAATTAAAAATGTTA
1 TAAAAATTAAAAATATTA
3876674 T-AAAATTAAAAA
1 TAAAAATTAAAAA
3876686 AAAGTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 11 0.39
18 3 0.11
19 3 0.11
20 11 0.39
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (18 bp):
TAAAAATTAAAAATATTA
Found at i:3876833 original size:30 final size:30
Alignment explanation
Indices: 3876798--3876863 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
3876788 TTTAAGCATT
3876798 TTAATTT-TTTAC-ATTTTTGTAATAATATTA
1 TTAATTTCTTT-CTATTTTT-TAATAATATTA
* *
3876828 TTAATTTCTTTCTATTTTTTAATTATTTTA
1 TTAATTTCTTTCTATTTTTTAATAATATTA
3876858 -TAATTT
1 TTAATTT
3876864 ATATGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.19
30 17 0.53
31 9 0.28
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (30 bp):
TTAATTTCTTTCTATTTTTTAATAATATTA
Found at i:3877262 original size:22 final size:22
Alignment explanation
Indices: 3877237--3877285 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3877227 TTTATTTACA
3877237 ATTTTA-CTCGTTTTTTTAAATT
1 ATTTTATCTC-TTTTTTTAAATT
*
3877259 ATTTTATGTCTTTTTTTAAA--
1 ATTTTATCTCTTTTTTTAAATT
3877279 ATTTTAT
1 ATTTTAT
3877286 ATATTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (22 bp):
ATTTTATCTCTTTTTTTAAATT
Found at i:3880954 original size:13 final size:13
Alignment explanation
Indices: 3880936--3880965 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3880926 TATTTGGTAG
3880936 TACAAATTGTAAT
1 TACAAATTGTAAT
3880949 TACAAATTGTAAT
1 TACAAATTGTAAT
3880962 TACA
1 TACA
3880966 TAGTTACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (13 bp):
TACAAATTGTAAT
Found at i:3885071 original size:15 final size:16
Alignment explanation
Indices: 3885041--3885073 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3885031 TAGTTACTTA
*
3885041 TTTGGGTCATTTCGAG
1 TTTGGATCATTTCGAG
3885057 TTTGGATCA-TTCGAG
1 TTTGGATCATTTCGAG
3885072 TT
1 TT
3885074 AGTTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.45
Consensus pattern (16 bp):
TTTGGATCATTTCGAG
Found at i:3886065 original size:19 final size:19
Alignment explanation
Indices: 3886041--3886077 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3886031 CTCGTTCTTG
*
3886041 CTGGTTTCTCCCTTGTTTA
1 CTGGTTTCTCCCTCGTTTA
*
3886060 CTGGTTTGTCCCTCGTTT
1 CTGGTTTCTCCCTCGTTT
3886078 TTGCCAGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.27, G:0.19, T:0.51
Consensus pattern (19 bp):
CTGGTTTCTCCCTCGTTTA
Done.