Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 20 of 132
Found at i:5852751 original size:3 final size:3
Alignment explanation
Indices: 5852743--5852800 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
5852733 CATAATTTGT
5852743 TTA TTA TTA TTA 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
5852791 TTA TTA TTA T
1 TTA TTA TTA T
5852801 CAACTAAAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5855485 original size:29 final size:29
Alignment explanation
Indices: 5855401--5855485 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
5855391 GATTAAATCA
* *
5855401 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAA-TTTCATGTATACAATTGAACC
* * * *
5855431 ACAACTAGAATTTCATGTGTATAATTGCACC
1 A-AATTA-AATTTCATGTATACAATTGAACC
*
5855462 AAATTAAAATTCATGTATACAATT
1 AAATTAAATTTCATGTATACAATT
5855486 ATACATTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 15 0.35
30 5 0.12
31 21 0.49
32 2 0.05
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.34
Consensus pattern (29 bp):
AAATTAAATTTCATGTATACAATTGAACC
Found at i:5856471 original size:97 final size:96
Alignment explanation
Indices: 5856304--5856489 Score: 234
Period size: 97 Copynumber: 1.9 Consensus size: 96
5856294 GAAAAGGATG
* * * * *
5856304 TTCGATTATCTCGTTTTGAAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTCAGAATCAGA
1 TTCGATTATCTCGTTTTGAAAAAAATCGCACCTAGTAAGTTAACGCACAAATTTTCAAAATCAGA
*
5856369 GATAAATA-AACATTGCCTCGATTTAAAAATA
66 AATAAA-AGAACATTGCCTCGATTTAAAAATA
**
5856400 TTCGATTAT-TCCGTTTTGAAGAAAAATCGTGCCTAGTAAGTTAACGCACAAATTTTCAAAACTC
1 TTCGATTATCT-CGTTTTGAA-AAAAATCGCACCTAGTAAGTTAACGCACAAATTTTCAAAA-TC
*
5856464 -GAAATAAAAGAATATTGCCTCGATTT
63 AGAAATAAAAGAACATTGCCTCGATTT
5856490 TAAATTTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
95 1 0.01
96 19 0.25
97 55 0.71
98 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (96 bp):
TTCGATTATCTCGTTTTGAAAAAAATCGCACCTAGTAAGTTAACGCACAAATTTTCAAAATCAGA
AATAAAAGAACATTGCCTCGATTTAAAAATA
Found at i:5856815 original size:59 final size:59
Alignment explanation
Indices: 5856751--5857028 Score: 197
Period size: 58 Copynumber: 4.7 Consensus size: 59
5856741 ATTCGAGCGC
*
5856751 AAAATGGTAAC-TTTGGGAA-AGTTCAAGGTCAAAAACGGAATTTTTAGACA-TCCGGGGGT
1 AAAATGGT-ACTTTTGGGAAGA-ATCAAGGTCAAAAACGGAATTTTTAGA-AGTCCGGGGGT
* * * * * *
5856810 AAAATGGTACTTTTTGGAAGAATCATGGTCTAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAATGGTACTTTTGGGAAGAATCAAGGTCAAAAACGGAATTTTTAGAAGTCCGGGGGT
** * * * ** ** ****
5856869 AAAATGGTTGTTTT-TGAAAAATCGAGGTCAAAAATTGAATTTTGGGAAGTTTAAGGGT
1 AAAATGGTACTTTTGGGAAGAATCAAGGTCAAAAACGGAATTTTTAGAAGTCCGGGGGT
* * ** *** *
5856927 AAAATGGTAATTTTGGGAAG-ATCAAGGTCAAAAATGGAATTTTGGGAAGTTTAGGGAT
1 AAAATGGTACTTTTGGGAAGAATCAAGGTCAAAAACGGAATTTTTAGAAGTCCGGGGGT
* * * * *
5856985 AAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTT
1 AAAATGGTACTTTTGGGAAGAATCAAGGTCAAAAACGGAATTTT
5857029 CGAAAGTTTG
Statistics
Matches: 184, Mismatches: 30, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
58 101 0.55
59 82 0.45
60 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (59 bp):
AAAATGGTACTTTTGGGAAGAATCAAGGTCAAAAACGGAATTTTTAGAAGTCCGGGGGT
Found at i:5856927 original size:58 final size:59
Alignment explanation
Indices: 5856806--5857105 Score: 313
Period size: 58 Copynumber: 5.1 Consensus size: 59
5856796 AGACATCCGG
* * * * * ***
5856806 GGGTAAAATGGTACTTTTTGGAAGAATCATGGTCTAAAATGGAATTTTTGGAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTGGGAAGTTTAA
** * *
5856865 GGGTAAAATGGTTGTTTTT-GAAAAATCGAGGTCAAAAATTGAATTTTGGGAAGTTTAA
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTGGGAAGTTTAA
* *
5856923 GGGTAAAATGGTAA-TTTTGGGAAGATCAAGGTCAAAAATGGAATTTTGGGAAGTTT-A
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTGGGAAGTTTAA
* * * *
5856980 GGGATAAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTCGAAAGTTTGA
1 GGG-TAAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTGGGAAGTTTAA
* ** ** * *
5857040 GGGTAAAAAT-GTAATTTTTAGAAAGTTTGAGGTC-AAAATGGAATTTTAGAAAGTTTAA
1 GGGT-AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTGGGAAGTTTAA
*
5857098 TGGTAAAA
1 GGGTAAAA
5857106 ATGTAAATTT
Statistics
Matches: 205, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
57 12 0.06
58 111 0.54
59 73 0.36
60 9 0.04
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTGGGAAGTTTAA
Found at i:5856938 original size:29 final size:29
Alignment explanation
Indices: 5856898--5857125 Score: 178
Period size: 29 Copynumber: 7.8 Consensus size: 29
5856888 AATCGAGGTC
* *
5856898 AAAAATTGAATTTTGGGAAGTTTAAGGGT
1 AAAAATGGAATTTTGGAAAGTTTAAGGGT
* * *
5856927 -AAAATGGTAATTTTGGGAAGATCAA-GGT
1 AAAAATGG-AATTTTGGAAAGTTTAAGGGT
*
5856955 CAAAAATGGAATTTTGGGAAGTTT-AGGG-
1 -AAAAATGGAATTTTGGAAAGTTTAAGGGT
** * *
5856983 ATAAAATGGTAATTTTTGGAAAAATCAAGGTT
1 A-AAAATGG-AA-TTTTGGAAAGTTTAAGGGT
* *
5857015 AAAAATGGAATTTTCGAAAGTTTGAGGGT
1 AAAAATGGAATTTTGGAAAGTTTAAGGGT
* * *
5857044 AAAAATGTAATTTTTAGAAAGTTTGA-GGT
1 AAAAATGGAA-TTTTGGAAAGTTTAAGGGT
* * *
5857073 CAAAATGGAATTTTAGAAAGTTTAATGGT
1 AAAAATGGAATTTTGGAAAGTTTAAGGGT
* *
5857102 AAAAATGTAAATTTTAGAAAGTTT
1 AAAAATG-GAATTTTGGAAAGTTT
5857126 GGGGCCAAAC
Statistics
Matches: 164, Mismatches: 23, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.01
28 31 0.19
29 74 0.45
30 47 0.29
31 10 0.06
32 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTTAAGGGT
Found at i:5857078 original size:117 final size:116
Alignment explanation
Indices: 5856806--5857096 Score: 316
Period size: 117 Copynumber: 2.5 Consensus size: 116
5856796 AGACATCCGG
* * * * * * ** *
5856806 GGGTAAAATGGTACTTTTTGGAAGAATCATGGTCTAAAATGGAATTTTTGGAAGTTCGGGGGTAA
1 GGGTAAAATGGTAATTTTAGAAAG-ATCAAGGTCAAAAATGGAATTTTAGGAAGTTTAGGGATAA
** * * * *
5856871 AATGGTTGTTTTTGAAAAATCGAGGTCAAAAATTGAATTTTGGGAAGTTTAA
65 AATGGTAATTTTTGAAAAATCAAGGTCAAAAATGGAATTTTCGAAAGTTTAA
* * *
5856923 GGGTAAAATGGTAATTTTGGGAAGATCAAGGTCAAAAATGGAATTTTGGGAAGTTTAGGGATAAA
1 GGGTAAAATGGTAATTTTAGAAAGATCAAGGTCAAAAATGGAATTTTAGGAAGTTTAGGGATAAA
* *
5856988 ATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTCGAAAGTTTGA
66 ATGGTAATTTTT-GAAAAATCAAGGTCAAAAATGGAATTTTCGAAAGTTTAA
* ** *
5857040 GGGTAAAAAT-GTAATTTTTAGAAAGTTTGAGGTC-AAAATGGAATTTTAGAAAGTTTA
1 GGGT-AAAATGGTAA-TTTTAGAAAGATCAAGGTCAAAAATGGAATTTTAGGAAGTTTA
5857097 ATGGTAAAAA
Statistics
Matches: 148, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
116 45 0.30
117 84 0.57
118 19 0.13
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (116 bp):
GGGTAAAATGGTAATTTTAGAAAGATCAAGGTCAAAAATGGAATTTTAGGAAGTTTAGGGATAAA
ATGGTAATTTTTGAAAAATCAAGGTCAAAAATGGAATTTTCGAAAGTTTAA
Found at i:5857123 original size:58 final size:58
Alignment explanation
Indices: 5857016--5857166 Score: 194
Period size: 58 Copynumber: 2.6 Consensus size: 58
5857006 ATCAAGGTTA
* * * *
5857016 AAAATGGAATTTTCGAAAGTTTGAGGGTAAAAATGTAATTTTTAGAAAGTTTGAGGTC
1 AAAATGGAATTTTAGAAAGTTTAAGGGTAAAAATGTAAATTTTAGAAAGTTTGAGGCC
* *
5857074 AAAATGGAATTTTAGAAAGTTTAATGGTAAAAATGTAAATTTTAGAAAGTTTGGGGCC
1 AAAATGGAATTTTAGAAAGTTTAAGGGTAAAAATGTAAATTTTAGAAAGTTTGAGGCC
* ** * *
5857132 AAACTATAATTTTAGAGAAGTTTAGGGGTCAAAAT
1 AAAATGGAATTTTAGA-AAGTTTAAGGGTAAAAAT
5857167 ATGATTTCTG
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
58 65 0.81
59 15 0.19
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTAGAAAGTTTAAGGGTAAAAATGTAAATTTTAGAAAGTTTGAGGCC
Found at i:5858294 original size:3 final size:3
Alignment explanation
Indices: 5858286--5858363 Score: 95
Period size: 3 Copynumber: 25.3 Consensus size: 3
5858276 CTTTCTTTTC
* *
5858286 ATT ATT ATT ATT ATT AATT AAT ATT ATT ATT AATT ATT A-T ACCT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT -ATT ATT ATT A-TT ATT
*
5858333 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5858364 AAAATCAATG
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
2 2 0.03
3 56 0.85
4 8 0.12
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:5859177 original size:17 final size:17
Alignment explanation
Indices: 5859157--5859237 Score: 65
Period size: 17 Copynumber: 4.7 Consensus size: 17
5859147 TAATTCACAA
*
5859157 TAAATTTAAATTTGAAG
1 TAAATTTAAATTTAAAG
** *
5859174 TAAATTTAAACTAAAAAA
1 TAAATTTAAA-TTTAAAG
*
5859192 TGAATTTAAATTTAGAA-
1 TAAATTTAAATTTA-AAG
* *
5859209 TAAATTCAAACTTAAAG
1 TAAATTTAAATTTAAAG
*
5859226 TAAATTAAAATT
1 TAAATTTAAATT
5859238 AAAAATTAGA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
16 2 0.04
17 33 0.67
18 14 0.29
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:5859666 original size:39 final size:38
Alignment explanation
Indices: 5859612--5860036 Score: 253
Period size: 39 Copynumber: 10.9 Consensus size: 38
5859602 GATAACTACA
*
5859612 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATAGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGAT-GTG
* * * * * *
5859651 ATCTGCCCTAAGCTCGGGGTAAGAGATCGAATGGCTGTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTG-GTTGATGTG
* **
5859690 ATCT-ACCCTGGCTCGGGGTAAGAGATTGGTTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATG-TG
* * *** * * *
5859728 ATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGTTGCG
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT-TGGTTGATGTG
** * * *
5859767 ATCTGCCTTAGGCTAGGGATAAGAGATTGGTTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATG-TG
* * *** * * *
5859806 ATCTGCCTCAAGCTCGGGGTAAAAGATCAAATGGCT-TCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT-TGGTTGATGT-G
* * *
5859845 ATCTGTCCCAGGCTCGGGGTAAGAGATTAGTTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATG-TG
* *** * * * *
5859884 ATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTTTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT-TGGTTGATGTG
*
5859923 ATTTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATG-TG
* * * *** * * *
5859962 ATCTGCCCCAGGCTCGTGGTAAAAGATCAAATGGCT-TCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT-TGGTTGATGT-G
5860001 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATG
5860037 ATGTAACTTC
Statistics
Matches: 276, Mismatches: 96, Indels: 28
0.69 0.24 0.07
Matches are distributed among these distances:
37 4 0.01
38 40 0.14
39 214 0.78
40 18 0.07
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (38 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGTG
Found at i:5859812 original size:78 final size:78
Alignment explanation
Indices: 5859610--5860039 Score: 625
Period size: 78 Copynumber: 5.5 Consensus size: 78
5859600 TGGATAACTA
* *
5859610 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGAT-AGTGATCTGCCCTAAGCTCGGGGTAAG
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGA-TGATCTGCCCCAAGCTCGGGGTAAA
*
5859674 AGATCGAATGGCTGT
65 AGATCAAATGGCT-T
* * *
5859689 -AATCT-ACCCTGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAACTCGGGGTAAAA
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAA
5859752 GATCAAATGG-TT
66 GATCAAATGGCTT
* ** * * *
5859764 GCGATCTGCCTTAGGCTAGGGATAAGAGATTGGTTGATGATGATCTGCCTCAAGCTCGGGGTAAA
1 -CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAA
5859829 AGATCAAATGGCTT
65 AGATCAAATGGCTT
* *
5859843 CAATCTGTCCCAGGCTCGGGGTAAGAGATTAGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAA
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAA
5859908 GATCAAATGGCTT
66 GATCAAATGGCTT
* * * * *
5859921 TAATTTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGTGGTAAAA
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAA
5859986 GATCAAATGGCTT
66 GATCAAATGGCTT
*
5859999 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATG
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATG
5860040 TAACTTCACT
Statistics
Matches: 314, Mismatches: 32, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
75 1 0.00
76 1 0.00
77 64 0.20
78 246 0.78
79 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (78 bp):
CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAA
GATCAAATGGCTT
Found at i:5860207 original size:101 final size:101
Alignment explanation
Indices: 5860094--5860295 Score: 282
Period size: 101 Copynumber: 2.0 Consensus size: 101
5860084 GCTGTTGTAA
* * * * *
5860094 TTTTAATCCAACTTCGCTGCAACTTC-AGAAAGAT-GAGATTTGATGTTGAAGTTTCATCTTGCT
1 TTTTAATCCAACTTCACTGCAACTTCAAG-AAGATAG-GAATTGACGTTAAAGCTTCATCTTGCT
*
5860157 CTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
64 CTTACTACAACTTCAGAGAGATAAAGACTTGCCATTGT
* *
5860195 TTTTAATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
* *
5860260 TACTGCAACTTTAGAGAGATAAAGACTTGCCATTGT
66 TACTACAACTTCAGAGAGATAAAGACTTGCCATTGT
5860296 AGTTTTGATC
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 86 0.97
102 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (101 bp):
TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
TACTACAACTTCAGAGAGATAAAGACTTGCCATTGT
Found at i:5860478 original size:48 final size:48
Alignment explanation
Indices: 5860423--5861469 Score: 309
Period size: 50 Copynumber: 21.1 Consensus size: 48
5860413 AAATCTTCAT
* *
5860423 GGTACTGGATCCGCCGTTGCGGCTTAGATCTTTTCCTTGTGTCTTTGT
1 GGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTTGA
*
5860471 GGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTAATGTCTTTGA
1 GGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTT-GTGTCTTTGA
* * *** * * * * * *
5860520 GGTATTACG-TTTTCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGC
1 GGTACT-GGATCCGCCGTTGCGGCTTAGATCTTTCCC--TTGTGTCTTTGA
* * * ** *
5860570 GGTACTAGATCCGCCATTGCGGTCTTAGATCTTTCTCGTCATGTCTCTGA
1 GGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTC-CCTTGTGTCTTTGA
* * * * * * * * *
5860620 GGTACAAGG-TTCGCCGTTGTGACTTAAACCCTTCCCTTTTGTATCTTTGC
1 GGTAC-TGGATCCGCCGTTGCGGCTTAGATCTTTCCC--TTGTGTCTTTGA
* ** * *
5860670 GGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGTCTCTAA
1 GGTACTGGATCCGCCGTTGCGG-CTTAGATC-TTTCCCTTGTGTCTTTGA
* * * * * * * *
5860720 GGTA-TAAGG-TTCGCTGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGC
1 GGTACT--GGATCCGCCGTTGCGGCTTAGATCTTTCCC--TTGTGTCTTTGA
* * *** **
5860770 GGTACTGGATCCGCCGTTACGGTATTAGATCTTTTTAGTCATGTCTTTGA
1 GGTACTGGATCCGCCGTTGCGG-CTTAGATC-TTTCCCTTGTGTCTTTGA
* * * * * * * *
5860820 GGTA-T-AATGTTCGTCATTGCGACTTAAACCTTTCCCTT-TGCATCTTTGC
1 GGTACTGGA--TCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG--TCTTTGA
* * * * *
5860869 GGTACTAGATCCGCCTTTGCGGTCTTAGATCTTT-CCTGTCATGTCTCTAA
1 GGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCT-T-GTGTCTTTGA
* * * * * * * *
5860919 GGTA-TAAGG-TTCACCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGC
1 GGTACT--GGATCCGCCGTTGCGGCTTAGATCTTTCCC--TTGTGTCTTTGA
* ** *
5860969 GGTATTGGATCCGCCGTTAG-GGTCTTAGATCTTTCCCATCATGTCTCTGA
1 GGTACTGGATCCGCCGTT-GCGG-CTTAGATCTTTCCC-TTGTGTCTTTGA
* * * * * *
5861019 GGTA-TAAGG-TTCGCCGTTGCGACTTAAACCTTT-CCTTTTGCATCTTTGC
1 GGTACT--GGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG--TCTTTGA
* * ** *
5861068 GGTACTGGATCCGCCGTTACGGTCTTAGATCTTTCTCGTCATGTCTCTGA
1 GGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTC-CCTTGTGTCTTTGA
* * ** * * * *
5861118 GGTACAAGG-TTCGCCGTTGCGATTTAAACCCTTCCCTTTTGTATCTTT-A
1 GGTAC-TGGATCCGCCGTTGCGGCTTAGATCTTTCCC--TTGTGTCTTTGA
* * ** *
5861167 CGGTACTGTATCCGCCGTTACGGTCTTAGATCTTTCCCGTCATGTCTCTGA
1 -GGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCC-TTGTGTCTTTGA
* * * * * * * * * *
5861218 AGTACTAGG-TTCGTCGTTGTGACTTAAACCCTTCCCTTTTGTATCTTTGC
1 GGTACT-GGATCCGCCGTTGCGGCTTAGATCTTTCCC--TTGTGTCTTTGA
* * * ** *
5861268 GGTATTGGATCCGTCGTTGCAGTCTTAGATCTTTCCCGTCATGTTTTTGA
1 GGTACTGGATCCGCCGTTGC-GGCTTAGATCTTTCCC-TTGTGTCTTTGA
** * * * *
5861318 GGTA-TAAGGAT-CGTTGTTGCGACTTAAACCTTTCCCTT-TGCATCTTTGC
1 GGTACT--GGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG--TCTTTGA
* * * * *
5861367 GGTACTGGATCCGCCGTCGCGGCTTAGATCTTTCCTTTCATG-CTTCGT
1 GGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTT-GTGTCTTTGA
* * *
5861415 GGTACTGGATCCGCCGTTGCGGCTTAGATCATTCCCTTAATGTCTCTGA
1 GGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTT-GTGTCTTTGA
5861464 GGTACT
1 GGTACT
5861470 AGGTTTGCCA
Statistics
Matches: 696, Mismatches: 233, Indels: 139
0.65 0.22 0.13
Matches are distributed among these distances:
47 7 0.01
48 99 0.14
49 198 0.28
50 301 0.43
51 77 0.11
52 14 0.02
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.38
Consensus pattern (48 bp):
GGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTTGA
Found at i:5860644 original size:100 final size:100
Alignment explanation
Indices: 5860459--5861401 Score: 1279
Period size: 100 Copynumber: 9.5 Consensus size: 100
5860449 GATCTTTTCC
* * * * *
5860459 TTGTGTCTTTGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCTTAATGTCTTTGAGGT
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
* * ** * *
5860523 ATTACGTTTTCCATTGCGACTTAAACCTTTCCCTT
66 ATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* * *
5860558 TTGTATCTTTGCGGTACTAGATCCGCCATTGCGGTCTTAGATCTTTCTCGTCATGTCTCTGAGGT
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
* *
5860623 ACAAGGTTCGCCGTTGTGACTTAAACCCTTCCCTT
66 ATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* *
5860658 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGTCTCTAAGGT
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
*
5860723 ATAAGGTTCGCTGTTGCGACTTAAACCCTTCCCTT
66 ATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* * *** *
5860758 TTGTATCTTTGCGGTACTGGATCCGCCGTTACGGTATTAGATCTTTTTAGTCATGTCTTTGAGGT
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
* * * *
5860823 ATAATGTTCGTCATTGCGACTTAAACCTTTCCC-T
66 ATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* * * * *
5860857 TTGCATCTTTGCGGTACTAGATCCGCCTTTGCGGTCTTAGATCTTTCCTGTCATGTCTCTAAGGT
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
*
5860922 ATAAGGTTCACCGTTGCGACTTAAACCCTTCCCTT
66 ATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* *
5860957 TTGTATCTTTGCGGTATTGGATCCGCCGTTAG-GGTCTTAGATCTTTCCCATCATGTCTCTGAGG
1 TTGTATCTTTGCGGTACTGGATCCGCCGTT-GCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGG
*
5861021 TATAAGGTTCGCCGTTGCGACTTAAA-CCTTTCCTT
65 TATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* * *
5861056 TTGCATCTTTGCGGTACTGGATCCGCCGTTACGGTCTTAGATCTTTCTCGTCATGTCTCTGAGGT
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
* *
5861121 ACAAGGTTCGCCGTTGCGATTTAAACCCTTCCCTT
66 ATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* * * *
5861156 TTGTATCTTTACGGTACTGTATCCGCCGTTACGGTCTTAGATCTTTCCCGTCATGTCTCTGAAGT
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
* *
5861221 ACT-AGGTTCGTCGTTGTGACTTAAACCCTTCCCTT
66 A-TAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* * * * *
5861256 TTGTATCTTTGCGGTATTGGATCCGTCGTTGCAGTCTTAGATCTTTCCCGTCATGTTTTTGAGGT
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
* ** *
5861321 ATAAGGATCGTTGTTGCGACTTAAACCTTTCCC-T
66 ATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
* *
5861355 TTGCATCTTTGCGGTACTGGATCCGCCGTCGCGG-CTTAGATCTTTCC
1 TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCC
5861402 TTTCATGCTT
Statistics
Matches: 743, Mismatches: 94, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
98 13 0.02
99 235 0.32
100 494 0.66
101 1 0.00
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (100 bp):
TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
ATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
Found at i:5860949 original size:199 final size:200
Alignment explanation
Indices: 5860464--5861401 Score: 1250
Period size: 199 Copynumber: 4.7 Consensus size: 200
5860454 TTTCCTTGTG
* * * *
5860464 TCTTTGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCT-TAATGTCTTTGAGGTATTA
1 TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTT-CCTGTCATGTCTCTGAGGTATAA
* ** * * * * *
5860527 CGTTTTCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTAGATCCGCCATTGCGG
65 GGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGG
* *
5860592 TCTTAGATCTTTCTC-GTCATGTCTCTGAGGTACAAGGTTCGCCGTTGTGACTTAAACCCTTCCC
130 TCTTAGATCTTTC-CAGTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCCTTCCC
*
5860656 TTTTGTA
194 TTTTGCA
*
5860663 TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCC-GTCATGTCTCTAAGGTATAA
1 TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATC-TTTCCTGTCATGTCTCTGAGGTATAA
*
5860727 GGTTCGCTGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGG
65 GGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGG
* ** * * * * *
5860792 TATTAGATCTTTTTAGTCATGTCTTTGAGGTATAATGTTCGTCATTGCGACTTAAACCTTTCCC-
130 TCTTAGATCTTTCCAGTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCT
5860856 TTTGCA
195 TTTGCA
* * *
5860862 TCTTTGCGGTACTAGATCCGCCTTTGCGGTCTTAGATCTTTCCTGTCATGTCTCTAAGGTATAAG
1 TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCTGTCATGTCTCTGAGGTATAAG
* * *
5860927 GTTCACCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTATTGGATCCGCCGTTAGGGT
66 GTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGGT
*
5860992 CTTAGATCTTTCCCA-TCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAA-CCTTTCCT
131 CTTAGATCTTT-CCAGTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCT
5861055 TTTGCA
195 TTTGCA
* *
5861061 TCTTTGCGGTACTGGATCCGCCGTTACGGTCTTAGATCTTT-CTCGTCATGTCTCTGAGGTACAA
1 TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCT-GTCATGTCTCTGAGGTATAA
* * *
5861125 GGTTCGCCGTTGCGATTTAAACCCTTCCCTTTTGTATCTTTACGGTACTGTATCCGCCGTTACGG
65 GGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGG
* * * *
5861190 TCTTAGATCTTTCCCGTCATGTCTCTGAAGTACT-AGGTTCGTCGTTGTGACTTAAACCCTTCCC
130 TCTTAGATCTTTCCAGTCATGTCTCTGAGGTA-TAAGGTTCGCCGTTGCGACTTAAACCCTTCCC
*
5861254 TTTTGTA
194 TTTTGCA
* * * * * *
5861261 TCTTTGCGGTATTGGATCCGTCGTTGCAGTCTTAGATCTTTCCCGTCATGTTTTTGAGGTATAAG
1 TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCTGTCATGTCTCTGAGGTATAAG
* ** * * **
5861326 GATCGTTGTTGCGACTTAAACCTTTCCC-TTTGCATCTTTGCGGTACTGGATCCGCCGTCGCGG-
66 GTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGGT
5861389 CTTAGATCTTTCC
131 CTTAGATCTTTCC
5861402 TTTCATGCTT
Statistics
Matches: 652, Mismatches: 75, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
198 27 0.04
199 395 0.61
200 226 0.35
201 4 0.01
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.39
Consensus pattern (200 bp):
TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCTGTCATGTCTCTGAGGTATAAG
GTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGGT
CTTAGATCTTTCCAGTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTT
TTGCA
Found at i:5861013 original size:299 final size:300
Alignment explanation
Indices: 5860464--5861400 Score: 1338
Period size: 299 Copynumber: 3.1 Consensus size: 300
5860454 TTTCCTTGTG
* * * * * *
5860464 TCTTTGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCTTAATGTCTTTGAGGTATTAC
1 TCTTTGCGGTACTGGATCCGCCGTTACGGTCTTAGATCTTTCTCGTCATGTCTTTGAGGTATAAC
*
5860528 GTT-TTCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTAGATCCGCCATTGCGG
66 GTTCGT-CATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTAGATCCGCCATTGCGG
* *
5860592 TCTTAGATCTTT-CTCGTCATGTCTCTGAGGTACAAGGTTCGCCGTTGTGACTTAAACCCTTCCC
130 TCTTAGATCTTTCCT-GTCATGTCTCTAAGGTATAAGGTTCGCCGTTGTGACTTAAACCCTTCCC
* * *
5860656 TTTTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGTCTCTAAG
194 TTTTGTATCTTTGCGGTATTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAG
*
5860721 GTATAAGGTTCGCTGTTGCGACTTAAACCCTTCCCTTTTGTA
259 GTATAAGGTTCGCTGTTGCGACTTAAACCCTTCCCTTTTGCA
* * * *
5860763 TCTTTGCGGTACTGGATCCGCCGTTACGGTATTAGATCTTTTTAGTCATGTCTTTGAGGTATAAT
1 TCTTTGCGGTACTGGATCCGCCGTTACGGTCTTAGATCTTTCTCGTCATGTCTTTGAGGTATAAC
* *
5860828 GTTCGTCATTGCGACTTAAACCTTTCCC-TTTGCATCTTTGCGGTACTAGATCCGCCTTTGCGGT
66 GTTCGTCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTAGATCCGCCATTGCGGT
* *
5860892 CTTAGATCTTTCCTGTCATGTCTCTAAGGTATAAGGTTCACCGTTGCGACTTAAACCCTTCCCTT
131 CTTAGATCTTTCCTGTCATGTCTCTAAGGTATAAGGTTCGCCGTTGTGACTTAAACCCTTCCCTT
*
5860957 TTGTATCTTTGCGGTATTGGATCCGCCGTTAG-GGTCTTAGATCTTTCCCATCATGTCTCTGAGG
196 TTGTATCTTTGCGGTATTGGATCCGCCGTT-GCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGG
* *
5861021 TATAAGGTTCGCCGTTGCGACTTAAA-CCTTTCCTTTTGCA
260 TATAAGGTTCGCTGTTGCGACTTAAACCCTTCCCTTTTGCA
* * *
5861061 TCTTTGCGGTACTGGATCCGCCGTTACGGTCTTAGATCTTTCTCGTCATGTCTCTGAGGTACAAG
1 TCTTTGCGGTACTGGATCCGCCGTTACGGTCTTAGATCTTTCTCGTCATGTCTTTGAGGTATAAC
* * * * * * *
5861126 GTTCGCCGTTGCGATTTAAACCCTTCCCTTTTGTATCTTTACGGTACT-GTATCCGCCGTTACGG
66 GTTCGTCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTAG-ATCCGCCATTGCGG
* *
5861190 TCTTAGATCTTTCCCGTCATGTCTCTGAA-GTACT-AGGTTCGTCGTTGTGACTTAAACCCTTCC
130 TCTTAGATCTTTCCTGTCATGTCTCT-AAGGTA-TAAGGTTCGCCGTTGTGACTTAAACCCTTCC
* * * *
5861253 CTTTTGTATCTTTGCGGTATTGGATCCGTCGTTGCAGTCTTAGATCTTTCCCGTCATGTTTTTGA
193 CTTTTGTATCTTTGCGGTATTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGA
* * *
5861318 GGTATAAGGATCGTTGTTGCGACTTAAACCTTTCCC-TTTGCA
258 GGTATAAGGTTCGCTGTTGCGACTTAAACCCTTCCCTTTTGCA
**
5861360 TCTTTGCGGTACTGGATCCGCCGTCGCGG-CTTAGATCTTTC
1 TCTTTGCGGTACTGGATCCGCCGTTACGGTCTTAGATCTTTC
5861401 CTTTCATGCT
Statistics
Matches: 574, Mismatches: 54, Indels: 21
0.88 0.08 0.03
Matches are distributed among these distances:
298 109 0.19
299 401 0.70
300 63 0.11
301 1 0.00
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.39
Consensus pattern (300 bp):
TCTTTGCGGTACTGGATCCGCCGTTACGGTCTTAGATCTTTCTCGTCATGTCTTTGAGGTATAAC
GTTCGTCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTAGATCCGCCATTGCGGT
CTTAGATCTTTCCTGTCATGTCTCTAAGGTATAAGGTTCGCCGTTGTGACTTAAACCCTTCCCTT
TTGTATCTTTGCGGTATTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGT
ATAAGGTTCGCTGTTGCGACTTAAACCCTTCCCTTTTGCA
Found at i:5867981 original size:29 final size:31
Alignment explanation
Indices: 5867948--5868083 Score: 114
Period size: 29 Copynumber: 4.7 Consensus size: 31
5867938 TCTAAAATGA
5867948 AATTTTT-GAAAGTTTGAGGGT-AAAATGGT
1 AATTTTTAGAAAGTTTGAGGGTAAAAATGGT
* * **
5867977 CATTTTTAAAAAAATT-AGGGTTAAAAATGG-
1 AATTTTTAGAAAGTTTGAGGG-TAAAAATGGT
5868007 AATTTTT-GAAA-TTTGAGGGTAAAAAT-GT
1 AATTTTTAGAAAGTTTGAGGGTAAAAATGGT
*
5868035 AATTTTTAGAAAGTTT-AAGGTCAAAAAT-G-
1 AATTTTTAGAAAGTTTGAGGGT-AAAAATGGT
* *
5868064 AAATTTTGGAAAGTTT-AGGG
1 AATTTTTAGAAAGTTTGAGGG
5868084 GCCAAAATAT
Statistics
Matches: 88, Mismatches: 11, Indels: 16
0.77 0.10 0.14
Matches are distributed among these distances:
27 1 0.01
28 16 0.18
29 42 0.48
30 22 0.25
31 7 0.08
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.36
Consensus pattern (31 bp):
AATTTTTAGAAAGTTTGAGGGTAAAAATGGT
Found at i:5867984 original size:59 final size:59
Alignment explanation
Indices: 5867911--5868083 Score: 187
Period size: 58 Copynumber: 2.9 Consensus size: 59
5867901 ATTCGGGGCT
*
5867911 AAATGG-CACTTTTTAGAAGAATCAAGGTCTAAAATGAAATTTTTGAAAGTTTGAGGGT-A
1 AAATGGTCA-TTTTTAGAA-AATTAAGGTCTAAAATGAAATTTTTGAAAGTTTGAGGGTAA
* * *
5867970 AAATGGTCATTTTTAAAAAAATTAGGGT-TAAAAATGGAATTTTTGAAA-TTTGAGGGTAA
1 AAATGGTCATTTTT-AGAAAATTAAGGTCT-AAAATGAAATTTTTGAAAGTTTGAGGGTAA
* * * *
5868029 AAAT-GTAATTTTTAGAAAGTTTAAGGTCAAAAATGAAATTTTGGAAAGTTT-AGGG
1 AAATGGTCATTTTTAGAAA-ATTAAGGTCTAAAATGAAATTTTTGAAAGTTTGAGGG
5868084 GCCAAAATAT
Statistics
Matches: 96, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
57 4 0.04
58 44 0.46
59 43 0.45
60 5 0.05
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (59 bp):
AAATGGTCATTTTTAGAAAATTAAGGTCTAAAATGAAATTTTTGAAAGTTTGAGGGTAA
Found at i:5868012 original size:30 final size:29
Alignment explanation
Indices: 5867941--5868070 Score: 88
Period size: 30 Copynumber: 4.4 Consensus size: 29
5867931 ATCAAGGTCT
* * *
5867941 AAAATGAAATTTTTGAAAGTTTGAGGG-T-
1 AAAATGGAATTTTTAAAAATTT-AGGGTTA
* *
5867969 AAAATGGTCATTTTTAAAAAAATTAGGGTTA
1 AAAATGG-AATTTTT-AAAAATTTAGGGTTA
*
5868000 AAAATGGAATTTTT-GAAATTTGAGGG-TA
1 AAAATGGAATTTTTAAAAATTT-AGGGTTA
* * * *
5868028 AAAATGTAATTTTTAGAAAGTTTAAGGTCA
1 AAAATGGAATTTTTA-AAAATTTAGGGTTA
*
5868058 AAAATGAAATTTT
1 AAAATGGAATTTT
5868071 GGAAAGTTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
28 26 0.32
29 17 0.21
30 30 0.38
31 7 0.09
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTAAAAATTTAGGGTTA
Found at i:5868090 original size:30 final size:30
Alignment explanation
Indices: 5867994--5868140 Score: 110
Period size: 29 Copynumber: 5.0 Consensus size: 30
5867984 AAAAAAATTA
* * *
5867994 GGGTTAAAAATGGAATTTTTGAAA-TTT-G
1 GGGTCAAAAATGAAATTTTGGAAAGTTTAG
* *
5868022 AGGGT-AAAAATGTAATTTTTAGAAAGTTTA-
1 -GGGTCAAAAATG-AAATTTTGGAAAGTTTAG
*
5868052 AGGTCAAAAATGAAATTTTGGAAAGTTTAG
1 GGGTCAAAAATGAAATTTTGGAAAGTTTAG
*
5868082 GGG-CCAAAAT-ATAATTTTGGAGAAGTTTAG
1 GGGTCAAAAATGA-AATTTTGGA-AAGTTTAG
* * *
5868112 GGGTTAAAATATG-ATTTTTGGATAGTTTA
1 GGGTCAAAA-ATGAAATTTTGGAAAGTTTA
5868141 AGGACTTCCA
Statistics
Matches: 96, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
28 8 0.08
29 46 0.48
30 29 0.30
31 11 0.11
32 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGTCAAAAATGAAATTTTGGAAAGTTTAG
Found at i:5869294 original size:3 final size:3
Alignment explanation
Indices: 5869265--5869345 Score: 92
Period size: 3 Copynumber: 26.3 Consensus size: 3
5869255 CTTTCTTTTC
* * * *
5869265 ATT ATC ATT AAT ATT AATT AAT ATT ATT ATT AATT ATT A-T ACCT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT -ATT ATT ATT A-TT ATT
5869312 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5869346 AAAATCAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
2 2 0.03
3 57 0.85
4 8 0.12
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:5870150 original size:17 final size:16
Alignment explanation
Indices: 5870124--5870236 Score: 64
Period size: 17 Copynumber: 6.6 Consensus size: 16
5870114 CTTTTTAATT
*
5870124 AATTTTAATTTACAATA
1 AATTTAAATTTA-AATA
**
5870141 AATTTAAATTTATTGTA
1 AATTTAAATTTA-AATA
*
5870158 AATTAAAATTTAAAGTA
1 AATTTAAATTTAAA-TA
** *
5870175 AATTTAAACTCAAAAATG
1 AATTTAAA-T-TTAAATA
*
5870193 AATTTAAATTTAGAACA
1 AATTTAAATTTA-AATA
* *
5870210 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAA-TA
*
5870227 AATTAAAATT
1 AATTTAAATT
5870237 AAAAATTGGA
Statistics
Matches: 71, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
16 3 0.04
17 55 0.77
18 10 0.14
19 3 0.04
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.38
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:5870698 original size:31 final size:30
Alignment explanation
Indices: 5870660--5870760 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 30
5870650 TTCATATCAC
5870660 ATTTGATACCTGAACTTGACACTTTTTCCTA
1 ATTTGATACCTGAACTTGACA-TTTTTCCTA
* * *
5870691 ATTTGATATCTAAACTT----TTTTTGACCCA
1 ATTTGATACCTGAACTTGACATTTTT--CCTA
* *
5870719 ATTTGGTACATGAACTTGACATTTTTTCCTA
1 ATTTGATACCTGAACTTGACA-TTTTTCCTA
*
5870750 ATTTGGTACCT
1 ATTTGATACCT
5870761 AAATTTATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
26 5 0.09
28 16 0.30
31 28 0.52
33 5 0.09
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (30 bp):
ATTTGATACCTGAACTTGACATTTTTCCTA
Found at i:5871050 original size:17 final size:17
Alignment explanation
Indices: 5871030--5871063 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5871020 TTATATTTTT
*
5871030 TAAAAAATATTTTTAAA
1 TAAAAAATAATTTTAAA
*
5871047 TAAAAACTAATTTTAAA
1 TAAAAAATAATTTTAAA
5871064 AAATCAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAATAATTTTAAA
Found at i:5872415 original size:17 final size:17
Alignment explanation
Indices: 5872393--5872426 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5872383 CTGAGGTTCA
5872393 ATAATATTATTTA-ATTT
1 ATAATA-TATTTATATTT
5872410 ATAATATATTTATATTT
1 ATAATATATTTATATTT
5872427 GAATTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATATATTTATATTT
Found at i:5874426 original size:31 final size:31
Alignment explanation
Indices: 5874391--5874488 Score: 98
Period size: 29 Copynumber: 3.3 Consensus size: 31
5874381 AAAATTTAGG
5874391 TACCAAATTAGGAAAAAGTGTCAAGTTCAGA
1 TACCAAATTAGGAAAAAGTGTCAAGTTCAGA
* * * * *
5874422 TACCAAGTTGAGTCAAAAA----AAAGTTTAAA
1 TACCAAATT-AG-GAAAAAGTGTCAAGTTCAGA
5874451 TACCAAATTAGGAAAAAGTGTCAAGTTCAGA
1 TACCAAATTAGGAAAAAGTGTCAAGTTCAGA
5874482 -ACCAAAT
1 TACCAAAT
5874489 GTTATATTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 13
0.69 0.14 0.18
Matches are distributed among these distances:
27 5 0.10
28 2 0.04
29 15 0.29
30 7 0.14
31 15 0.29
32 2 0.04
33 5 0.10
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.22
Consensus pattern (31 bp):
TACCAAATTAGGAAAAAGTGTCAAGTTCAGA
Found at i:5874441 original size:59 final size:59
Alignment explanation
Indices: 5874302--5874488 Score: 227
Period size: 60 Copynumber: 3.1 Consensus size: 59
5874292 TACATTTAAG
* * * *
5874302 TACCAAATTGAATCTAAAAAAAACTTAGGTGCCAAATTAGGAAAAAATG-CAAAGTTCA-A
1 TACCAAATTGAGTC-AAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGTC-AAGTTCAGA
* *
5874361 GTACCAAAATGTGTCCAAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGA
1 -TACCAAATTGAGT-CAAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGA
* **
5874422 TACCAAGTTGAGTCAAAAAAAAGTTTAAATACCAAATTAGGAAAAAGTGTCAAGTTCAGA
1 TACCAAATTGAGTCAAAAAAAA-TTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGA
5874482 -ACCAAAT
1 TACCAAAT
5874489 GTTATATTAA
Statistics
Matches: 111, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
59 15 0.14
60 93 0.84
61 3 0.03
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (59 bp):
TACCAAATTGAGTCAAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGA
Found at i:5879013 original size:21 final size:20
Alignment explanation
Indices: 5878989--5879046 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
5878979 TATCTGGGAT
*
5878989 CATCACATGACATTCTTGCTG
1 CATCA-ATGACATCCTTGCTG
* *
5879010 CATCTAAAGACATCCTTGGTG
1 CATC-AATGACATCCTTGCTG
5879031 CATCAAATGACATCCT
1 CATC-AATGACATCCT
5879047 CCCAGCATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (20 bp):
CATCAATGACATCCTTGCTG
Found at i:5883140 original size:16 final size:17
Alignment explanation
Indices: 5883107--5883141 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5883097 TTTAAATTTC
5883107 ATTATTAGATTGGTTTT
1 ATTATTAGATTGGTTTT
5883124 ATTATTAGATT-GTTTT
1 ATTATTAGATTGGTTTT
5883140 AT
1 AT
5883142 AGCATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (17 bp):
ATTATTAGATTGGTTTT
Found at i:5883843 original size:3 final size:3
Alignment explanation
Indices: 5883835--5883874 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5883825 ATCTCTCCTT
5883835 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5883875 ATTATTAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5884406 original size:2 final size:2
Alignment explanation
Indices: 5884401--5884434 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5884391 TTTTTTGTAA
5884401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5884435 AAATCTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5891407 original size:5 final size:5
Alignment explanation
Indices: 5891396--5891449 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
5891386 AGACAAAAAA
* * * * * *
5891396 AGCAT GGCAT GGCAT GGCAT AGCAT AGCAT AGCAT AGCAG AGCAG AGCAG
1 AGCAT AGCAT AGCAT AGCAT AGCAT AGCAT AGCAT AGCAT AGCAT AGCAT
5891446 AGCA
1 AGCA
5891450 GAGGGGGCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.35, C:0.20, G:0.31, T:0.13
Consensus pattern (5 bp):
AGCAT
Found at i:5891778 original size:5 final size:5
Alignment explanation
Indices: 5891768--5891802 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
5891758 TGCTTTTTCA
*
5891768 TCTTT TCTTT TC-TT TCTTT TCTTT TCTTC TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
5891803 TTCAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:5891785 original size:14 final size:15
Alignment explanation
Indices: 5891768--5891802 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
5891758 TGCTTTTTCA
5891768 TCTTTTCTTTTCTT-
1 TCTTTTCTTTTCTTC
5891782 TCTTTTCTTTTCTTC
1 TCTTTTCTTTTCTTC
5891797 TCTTTT
1 TCTTTT
5891803 TTCAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTTTTCTTTTCTTC
Found at i:5894359 original size:2 final size:2
Alignment explanation
Indices: 5894352--5894383 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5894342 ATCATACCAA
5894352 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
5894384 TGAAAAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5897630 original size:33 final size:33
Alignment explanation
Indices: 5897593--5897658 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
5897583 TCTCCCAGGA
5897593 CTTGTTCCATTATGTTCTTCAGTGCTTCCCACT
1 CTTGTTCCATTATGTTCTTCAGTGCTTCCCACT
5897626 CTTGTTCCATTATGTTCTTCAGTGCTTCCCACT
1 CTTGTTCCATTATGTTCTTCAGTGCTTCCCACT
5897659 GCTTCAGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.12, C:0.30, G:0.12, T:0.45
Consensus pattern (33 bp):
CTTGTTCCATTATGTTCTTCAGTGCTTCCCACT
Found at i:5907551 original size:312 final size:311
Alignment explanation
Indices: 5906987--5907556 Score: 946
Period size: 312 Copynumber: 1.8 Consensus size: 311
5906977 TGTATAATAA
* *
5906987 TATGAACACACTGATTTTTCATAAATGCAAGAAACAATTGCTCACAACTCTGCTAAATATAAGAA
1 TATGAACACACTGATTTTTCATAAAAGAAAGAAACAATTGCTCACAACTCTGCTAAATATAAGAA
* *
5907052 AATATAACAATTGCCTTGCACAAGAGAAAAAAATTTCTAATATCATAAATATACAAGATATAATG
66 AATATAACAATTGCCTTGCACAAGAGAAAAAAATTTCTAATATAATAAATATACAAGAGATAATG
5907117 CCTCAGTGTGTTATCAGTCATCCATGTTACCTAGCCAATAAGTAGATATTACCCAGAATATCAAC
131 CCTCAGTGTGTTATCAGTCATCCATGTTACCTAGCCAATAAGTAGATATTACCCAGAATATCAAC
*
5907182 TACATTAACACAGACAACTTCAACACATCATATGCACATGAATCCAATAACATTTGTCTTAGCGA
196 TACATTAACACAGACAACTTCAACACACCATATGCACATGAATCCAATAACATTTGTCTTAGCGA
5907247 AAGCACTACCTCGTCTACCCCTCAATGTGCATGTACAATAACAATCAAAAT
261 AAGCACTACCTCGTCTACCCCTCAATGTGCATGTACAATAACAATCAAAAT
* *
5907298 TATGAACACAACT-ATTTTTTATAAAAGAAAGGAACAATTGCTCACAACTCTGCTAAATATAAGA
1 TATGAACAC-ACTGATTTTTCATAAAAGAAAGAAACAATTGCTCACAACTCTGCTAAATATAAGA
* * * * * *
5907362 AGATCTAAACAATTGCCTTGCACAAGAGAAAACATTTTCTAGTATAATGAATATACAAGAGATAA
65 AAATAT-AACAATTGCCTTGCACAAGAGAAAAAAATTTCTAATATAATAAATATACAAGAGATAA
* *
5907427 TGCCTCAGTGTGTTATCAGTCATCCATGTTACCTTGCCAATAAGTAGCTATTACCCAGACA-ATC
129 TGCCTCAGTGTGTTATCAGTCATCCATGTTACCTAGCCAATAAGTAGATATTACCCAGA-ATATC
* *
5907491 AACTACATTAACACGGACAACTTCAACACACCATATGCACATGAATCCAATAATATTTGTCTTAG
193 AACTACATTAACACAGACAACTTCAACACACCATATGCACATGAATCCAATAACATTTGTCTTAG
5907556 C
258 C
5907557 TACAGCCTAT
Statistics
Matches: 239, Mismatches: 17, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
311 60 0.25
312 178 0.74
313 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.27
Consensus pattern (311 bp):
TATGAACACACTGATTTTTCATAAAAGAAAGAAACAATTGCTCACAACTCTGCTAAATATAAGAA
AATATAACAATTGCCTTGCACAAGAGAAAAAAATTTCTAATATAATAAATATACAAGAGATAATG
CCTCAGTGTGTTATCAGTCATCCATGTTACCTAGCCAATAAGTAGATATTACCCAGAATATCAAC
TACATTAACACAGACAACTTCAACACACCATATGCACATGAATCCAATAACATTTGTCTTAGCGA
AAGCACTACCTCGTCTACCCCTCAATGTGCATGTACAATAACAATCAAAAT
Found at i:5908974 original size:51 final size:51
Alignment explanation
Indices: 5908919--5909015 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
5908909 TTTTGTAGTT
5908919 TATTTTAAAGAAGTATTTTTGGGATAAAAATCA-ATTTTTGAAAAAAAGTGA
1 TATTTTAAAGAAGTATTTTTGGGATAAAAAT-ATATTTTTGAAAAAAAGTGA
*
5908970 TATTTTAAAGAAGTATTTTTGGGATAAAAATATTTTTTTGAAAAAA
1 TATTTTAAAGAAGTATTTTTGGGATAAAAATATATTTTTGAAAAAA
5909016 GTGTTTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 1 0.02
51 43 0.98
ACGTcount: A:0.44, C:0.01, G:0.14, T:0.40
Consensus pattern (51 bp):
TATTTTAAAGAAGTATTTTTGGGATAAAAATATATTTTTGAAAAAAAGTGA
Found at i:5913242 original size:18 final size:18
Alignment explanation
Indices: 5913216--5913250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5913206 GTTTTCTTCC
5913216 ATTTAAGTTTTCAATTTA
1 ATTTAAGTTTTCAATTTA
* *
5913234 ATTTTAGTTTTCTATTT
1 ATTTAAGTTTTCAATTT
5913251 CATAACCCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (18 bp):
ATTTAAGTTTTCAATTTA
Found at i:5915666 original size:30 final size:31
Alignment explanation
Indices: 5915589--5915666 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 31
5915579 TGGATGAATG
5915589 AAATTTTT-AATAAAAAAAACTAATTTACTCTT
1 AAATTTTTAAAT-AAAAAAACTAATTTACTC-T
* * * *
5915621 TAA-TCTTACAT-AAAAAATTAATTTACTC-
1 AAATTTTTAAATAAAAAAACTAATTTACTCT
5915649 AAATTTTTAAATAAAAAA
1 AAATTTTTAAATAAAAAA
5915667 GATAATAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
28 2 0.06
29 6 0.17
30 21 0.58
31 3 0.08
32 4 0.11
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATTTTTAAATAAAAAAACTAATTTACTCT
Found at i:5915837 original size:16 final size:16
Alignment explanation
Indices: 5915792--5915842 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
5915782 CTCTAAAATA
5915792 ATAAAATTTT-AATTT
1 ATAAAATTTTAAATTT
* *
5915807 A-GATATTTTATAATTT
1 ATAAAATTTTA-AATTT
*
5915823 ATAAAATTTTAAATTA
1 ATAAAATTTTAAATTT
5915839 ATAA
1 ATAA
5915843 TAATAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 6 0.21
15 1 0.04
16 14 0.50
17 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATAAAATTTTAAATTT
Found at i:5915916 original size:22 final size:22
Alignment explanation
Indices: 5915891--5915962 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
5915881 ATTTGATTTA
5915891 ATATTTTAAAAATAATAAAAAT
1 ATATTTTAAAAATAATAAAAAT
* * **
5915913 ATATACTATTCAAAAT--TTAATTT
1 ATAT--T-TTAAAAATAATAAAAAT
5915936 AATATTTTAAAAATAATAAAAAT
1 -ATATTTTAAAAATAATAAAAAT
5915959 ATAT
1 ATAT
5915963 ATTCAAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
21 7 0.19
22 9 0.25
23 8 0.22
24 5 0.14
25 7 0.19
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATTTTAAAAATAATAAAAAT
Found at i:5915965 original size:24 final size:24
Alignment explanation
Indices: 5915891--5915965 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 24
5915881 ATTTGATTTA
5915891 ATATTTTAAAAATAATAAAAATAT
1 ATATTTTAAAAATAATAAAAATAT
* * * **
5915915 ATACTATTCAAAAT--TTAATTTA-
1 ATA-TTTTAAAAATAATAAAAATAT
5915937 ATATTTTAAAAATAATAAAAATAT
1 ATATTTTAAAAATAATAAAAATAT
5915961 ATATT
1 ATATT
5915966 CAAATAATGA
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 8 0.22
22 3 0.08
23 10 0.27
24 8 0.22
25 8 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATTTTAAAAATAATAAAAATAT
Found at i:5917776 original size:28 final size:28
Alignment explanation
Indices: 5917736--5917795 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
5917726 AAGCGATGGC
5917736 ATACTCTCACAAAATGGTTGAAGGTGCA
1 ATACTCTCACAAAATGGTTGAAGGTGCA
5917764 ATACTCTCACAAAATGGTTGAAGGTGCA
1 ATACTCTCACAAAATGGTTGAAGGTGCA
5917792 ATAC
1 ATAC
5917796 CTTTTTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (28 bp):
ATACTCTCACAAAATGGTTGAAGGTGCA
Found at i:5923013 original size:3 final size:3
Alignment explanation
Indices: 5923005--5923033 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5922995 AGCAAAAGAA
5923005 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5923034 AGAAAACTCC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5928557 original size:14 final size:15
Alignment explanation
Indices: 5928540--5928572 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5928530 CTAATAATCA
*
5928540 TTTATTAATATA-TT
1 TTTATAAATATAGTT
5928554 TTTATAAATATAGTT
1 TTTATAAATATAGTT
5928569 TTTA
1 TTTA
5928573 ATGGGGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTATAAATATAGTT
Found at i:5928639 original size:20 final size:20
Alignment explanation
Indices: 5928614--5928657 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5928604 TTTGCATCAG
*
5928614 GTTACATTTTAATCACTTAT
1 GTTACATTCTAATCACTTAT
*
5928634 GTTACATTCTAGTCACTTAT
1 GTTACATTCTAATCACTTAT
5928654 GTTA
1 GTTA
5928658 TTATTTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (20 bp):
GTTACATTCTAATCACTTAT
Found at i:5929608 original size:30 final size:30
Alignment explanation
Indices: 5929524--5929618 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
5929514 GTGCAATTTG
* *
5929524 ATACAT-AAACTTTAATTTAGTGT-AATTAT
1 ATACATAAAACTTTAATTTGGT-TCAAATAT
* * **
5929553 ACACATGAAACTTTGGTTGTGGTTCAAATAT
1 ATACATAAAACTTTAATT-TGGTTCAAATAT
5929584 ATACATAAAACTTTAATTTGGTTC-AATA-
1 ATACATAAAACTTTAATTTGGTTCAAATAT
5929612 ATACATA
1 ATACATA
5929619 TTTAAAGAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
28 7 0.13
29 9 0.17
30 16 0.30
31 22 0.41
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (30 bp):
ATACATAAAACTTTAATTTGGTTCAAATAT
Found at i:5931336 original size:15 final size:18
Alignment explanation
Indices: 5931316--5931354 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
5931306 TTCAATTGGT
5931316 CTCATATTTT-T-C-TTC
1 CTCATATTTTCTCCTTTC
5931331 CTCATATTTTCTCCTTTC
1 CTCATATTTTCTCCTTTC
5931349 CTCATA
1 CTCATA
5931355 AACAAGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 1 0.05
17 1 0.05
18 9 0.43
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (18 bp):
CTCATATTTTCTCCTTTC
Found at i:5931406 original size:14 final size:14
Alignment explanation
Indices: 5931385--5931419 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5931375 ACTAAACTTA
5931385 ACTTGAAGATTTCC
1 ACTTGAAGATTTCC
*
5931399 ATTTGAAGATTTCC
1 ACTTGAAGATTTCC
5931413 ACTTGAA
1 ACTTGAA
5931420 TTATAAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (14 bp):
ACTTGAAGATTTCC
Found at i:5932652 original size:16 final size:16
Alignment explanation
Indices: 5932631--5932680 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
5932621 TGATGGAGAT
5932631 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
5932647 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
5932662 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
5932677 ATTA
1 ATTA
5932681 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:5932905 original size:25 final size:26
Alignment explanation
Indices: 5932857--5932925 Score: 113
Period size: 25 Copynumber: 2.7 Consensus size: 26
5932847 AAAAATATTT
5932857 AAAATTTTATATTAATTTTGTATAACA
1 AAAATTTTAT-TTAATTTTGTATAACA
5932884 AAAATTTTATTTAATTTT-TATAACA
1 AAAATTTTATTTAATTTTGTATAACA
*
5932909 AAAATTTTATTTTATTT
1 AAAATTTTATTTAATTT
5932926 AAATTTTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 23 0.56
26 8 0.20
27 10 0.24
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (26 bp):
AAAATTTTATTTAATTTTGTATAACA
Found at i:5939514 original size:13 final size:13
Alignment explanation
Indices: 5939496--5939520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5939486 TTTTATCAAA
5939496 AAAGTATTTTTTC
1 AAAGTATTTTTTC
5939509 AAAGTATTTTTT
1 AAAGTATTTTTT
5939521 GTGTCAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
AAAGTATTTTTTC
Found at i:5939593 original size:19 final size:20
Alignment explanation
Indices: 5939569--5939609 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5939559 TTTAGCAATA
5939569 TTTTTATCCCAAAAATA-TT
1 TTTTTATCCCAAAAATACTT
*
5939588 TTTTTATCTCAAAAATACTT
1 TTTTTATCCCAAAAATACTT
5939608 TT
1 TT
5939610 GAGCAATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTATCCCAAAAATACTT
Found at i:5940915 original size:29 final size:28
Alignment explanation
Indices: 5940882--5940945 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
5940872 TATTTGGAAT
*
5940882 TTAATCTTTACATTTTA-ATTTGATATAAG
1 TTAATCTTTAC-TTTTACA-ATGATATAAG
*
5940911 TTAATCCTTTACTTTTACAATGATATTAG
1 TTAAT-CTTTACTTTTACAATGATATAAG
5940940 TTAATC
1 TTAATC
5940946 CAAATAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 23 0.74
30 7 0.23
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (28 bp):
TTAATCTTTACTTTTACAATGATATAAG
Found at i:5947281 original size:500 final size:508
Alignment explanation
Indices: 5946322--5947290 Score: 1157
Period size: 500 Copynumber: 1.9 Consensus size: 508
5946312 TCACGCATAG
* *
5946322 ATAGTCCATCATCCACTCAGAATTAAGGTATGTCACACTATTAACGTCACAAGTGAATAAATTCA
1 ATAGTCCATCATCCACTCAGAATTAAGGTATGTCACACTATAAACGTCACAAGTGAATAAATCCA
* *
5946387 TAAACCAATCTAAGATCTATTTTACTAGGGTACTGTCCAAAGTACTATCAGTCGAGTCAATCACA
66 TAAACCAATCTAAGATCTATTCTACTAGGGTACTGTCCAAAGTACAATCAGTCGAG-CAATCACA
* * * * *
5946452 TTTATTTTATCTTCTAAGAGACATCTGCTCCGATGTCCAAGATAAAGCATCTTCCTAATTGGACT
130 TGTACTCTATCTTCTAAGAGACATCCGCTCCGATGTCCAAGACAAAGCATCTTCCTAATTGGACT
* * * *
5946517 TGATAGACGACATATTAGTCTTTCAATCGGTTTGCTTATTTTCGATTAGACTAAGGATATATTTA
195 TGATAGACGACATATTAATC-TTCAATCGGTTTGCTTATTTCCGATTAAACTAAGGACATATTTA
* * * *
5946582 GGTTCATCTACTAATACAAGTTATTTTTCAATATTACGATCCGACCATATAATACTACTTAATAT
259 GGTTCATCTACTAATACAAGTTATTTTTCAATATTACAATACGACCATATAATACCACTTAAGAT
* * * * * * *
5946647 TAGTTAAATATTATATAACCAGTGAACCAATATTTGCTTCCATTTTACTTTGCGTAGAAGAATAT
324 TAGTTAAATATTAGATAACCAATGAACCAATATTTCCTTCCATTTTACTTTACATAGAAAAACAT
* ** * * **
5946712 TGAGGACAATATATAAACGGTATTAATGTAATTAATTGATATTATTGTTAAATCAATTTGTTCAA
389 TAAAAACAATATATAAACGATATTAATGTAATTAATTGATATTATTGTTAAATCAATTTCTAAAA
5946777 AAAATACAAGTATACAAAAAGAATATACTACACTTAGGACATTAGATCCAACAAC
454 AAAATACAAGTATACAAAAAGAATATACTACACTTAGGACATTAGATCCAACAAC
* * *
5946832 ATAGTTCATCATCCACTCA-AGATTAAGGTATGTCACACTATAAATGTTACAAGTGAATAAATCC
1 ATAGTCCATCATCCACTCAGA-ATTAAGGTATGTCACACTATAAACGTCACAAGTGAATAAATCC
* * * *
5946896 ATAAA-CAGATCTAGGATTTATTCTACTTGGGTTA-TGTCC-AA-TCCAATCAGTC-A-C-AT-A
65 ATAAACCA-ATCTAAGATCTATTCTACTAGGG-TACTGTCCAAAGTACAATCAGTCGAGCAATCA
* * * * * * *
5946953 TATGT-CTCTATCTTTTGAGAGTCATCCGCTTCGATGTTCAAGACAAAGTAT-TTCCCTAATTGG
128 CATGTACTCTATCTTCTAAGAGACATCCGCTCCGATGTCCAAGACAAAGCATCTT-CCTAATTGG
** *
5947016 ACTTGATAGACGACATATTAATC-T-AATTTGTTTGCTTGTTTCCGATTAAACTAAGGACATATT
192 ACTTGATAGACGACATATTAATCTTCAATCGGTTTGCTTATTTCCGATTAAACTAAGGACATATT
* * * * *
5947079 TAGGTTCATCTACTAATATAAGTTGTTTTTTTC-GTATTACAATATGACCATATAATACCGCTTA
257 TAGGTTCATCTACTAATACAAG-T-TATTTTTCAATATTACAATACGACCATATAATACCACTTA
* * **
5947143 GGATTAGTTAAATGTTAGATAACCAATGAACTGATATTTCCTTCCATTTTACTTTACAT-GCAAA
320 AGATTAGTTAAATATTAGATAACCAATGAACCAATATTTCCTTCCATTTTACTTTACATAG-AAA
*
5947207 AACATTAAAAATAATATATAAA-GAATATTAATGTAATTAA-TGAATATT-TT-TTAAATCAATA
384 AACATTAAAAACAATATATAAACG-ATATTAATGTAATTAATTG-ATATTATTGTTAAATCAAT-
*
5947268 TATCTAAAAAAAATACAATTATA
446 T-TCTAAAAAAAATACAAGTATA
5947291 TTTAGACAGA
Statistics
Matches: 389, Mismatches: 59, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
498 10 0.03
499 61 0.16
500 132 0.34
501 9 0.02
502 67 0.17
503 4 0.01
504 2 0.01
505 1 0.00
507 1 0.00
508 9 0.02
509 5 0.01
510 86 0.22
511 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (508 bp):
ATAGTCCATCATCCACTCAGAATTAAGGTATGTCACACTATAAACGTCACAAGTGAATAAATCCA
TAAACCAATCTAAGATCTATTCTACTAGGGTACTGTCCAAAGTACAATCAGTCGAGCAATCACAT
GTACTCTATCTTCTAAGAGACATCCGCTCCGATGTCCAAGACAAAGCATCTTCCTAATTGGACTT
GATAGACGACATATTAATCTTCAATCGGTTTGCTTATTTCCGATTAAACTAAGGACATATTTAGG
TTCATCTACTAATACAAGTTATTTTTCAATATTACAATACGACCATATAATACCACTTAAGATTA
GTTAAATATTAGATAACCAATGAACCAATATTTCCTTCCATTTTACTTTACATAGAAAAACATTA
AAAACAATATATAAACGATATTAATGTAATTAATTGATATTATTGTTAAATCAATTTCTAAAAAA
AATACAAGTATACAAAAAGAATATACTACACTTAGGACATTAGATCCAACAAC
Found at i:5947669 original size:20 final size:19
Alignment explanation
Indices: 5947620--5947670 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
5947610 TTTATATTGA
*
5947620 AATTTAT-TTTTTAAAATT
1 AATTTATATATTTAAAATT
* *
5947638 TATTTTTAATATTTAAAATAT
1 AATTTAT-ATATTTAAAAT-T
5947659 AATTTATATATT
1 AATTTATATATT
5947671 CAAATTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTATATATTTAAAATT
Found at i:5956178 original size:20 final size:20
Alignment explanation
Indices: 5956147--5956199 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
5956137 CTTTCAAAAA
5956147 AAAAATTT-AAAATAATTT-T
1 AAAAATTTCAAAAT-ATTTAT
*
5956166 CAAAATTTCAAAATATTTAT
1 AAAAATTTCAAAATATTTAT
5956186 AAAAATTTCAAAAT
1 AAAAATTTCAAAAT
5956200 TTATATTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:5956206 original size:24 final size:25
Alignment explanation
Indices: 5956178--5956225 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5956168 AAATTTCAAA
*
5956178 ATATT-TATAAAAATT-TCAAAATTT
1 ATATTCTA-AAAAATTATAAAAATTT
5956202 ATATTCTAAAAAATTATAAAAATT
1 ATATTCTAAAAAATTATAAAAATT
5956226 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATTCTAAAAAATTATAAAAATTT
Found at i:5956442 original size:24 final size:25
Alignment explanation
Indices: 5956415--5956466 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
5956405 CTTTAATTTT
5956415 AATTTAACTCGAA-TAATTTCACTC
1 AATTTAACTCGAATTAATTTCACTC
* *
5956439 AATTTGACTCGAATTTCATTTCACTC
1 AATTTAACTCGAA-TTAATTTCACTC
5956465 AA
1 AA
5956467 CTTGATTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.50
26 12 0.50
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (25 bp):
AATTTAACTCGAATTAATTTCACTC
Found at i:5983864 original size:17 final size:17
Alignment explanation
Indices: 5983842--5983874 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5983832 CAATACTTTA
*
5983842 ATTCGATTAATTTTTTC
1 ATTCGAGTAATTTTTTC
5983859 ATTCGAGTAATTTTTT
1 ATTCGAGTAATTTTTT
5983875 ATACTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (17 bp):
ATTCGAGTAATTTTTTC
Found at i:5984452 original size:19 final size:22
Alignment explanation
Indices: 5984428--5984469 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5984418 ATAGTCTGAT
5984428 AAGTAT-A-AAAAT-ATTCAAA
1 AAGTATAATAAAATAATTCAAA
5984447 AAGTATAATAAAATAATTCAAA
1 AAGTATAATAAAATAATTCAAA
5984469 A
1 A
5984470 TTCAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 1 0.05
21 5 0.25
22 8 0.40
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (22 bp):
AAGTATAATAAAATAATTCAAA
Found at i:5988731 original size:13 final size:13
Alignment explanation
Indices: 5988713--5988751 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
5988703 AACTTTGAAC
5988713 CCCAAACTTAAAA
1 CCCAAACTTAAAA
5988726 CCCAAACTT-AAA
1 CCCAAACTTAAAA
5988738 CCCTAAACTTAAAA
1 CCC-AAACTTAAAA
5988752 TCTTGAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 15 0.62
14 3 0.12
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (13 bp):
CCCAAACTTAAAA
Found at i:5990324 original size:21 final size:21
Alignment explanation
Indices: 5990298--5990339 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5990288 TTTGACGAAC
5990298 AAAACAAAATCAAAAAACAAA
1 AAAACAAAATCAAAAAACAAA
* *
5990319 AAAACAAAGTCTAAAAACAAA
1 AAAACAAAATCAAAAAACAAA
5990340 TTTTCAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.76, C:0.14, G:0.02, T:0.07
Consensus pattern (21 bp):
AAAACAAAATCAAAAAACAAA
Found at i:5993964 original size:55 final size:55
Alignment explanation
Indices: 5993880--5993990 Score: 159
Period size: 55 Copynumber: 2.0 Consensus size: 55
5993870 ATTGGAAGAC
** *
5993880 TGTAACACCCCTACACCCGATTCACACGTATAAACCCGGTATAAGAGTATTACAT
1 TGTAACACCCCTACACCCGATTCACACGTATAAACCCAATATAAGAGCATTACAT
* * * *
5993935 TGTAACACCCCTATACCCGATTTATACGTATAAACCCAATATAGGAGCATTACAT
1 TGTAACACCCCTACACCCGATTCACACGTATAAACCCAATATAAGAGCATTACAT
5993990 T
1 T
5993991 ACAGTACGGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (55 bp):
TGTAACACCCCTACACCCGATTCACACGTATAAACCCAATATAAGAGCATTACAT
Found at i:5994813 original size:23 final size:23
Alignment explanation
Indices: 5994739--5994952 Score: 144
Period size: 23 Copynumber: 9.5 Consensus size: 23
5994729 TAAACGGAAC
* * *
5994739 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
5994761 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
5994783 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
5994809 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
5994829 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
5994848 AATCAGAGAGCACA-AGAAGTGCT
1 AAACAGAGAGCACACA-AAGTGCT
* * *
5994871 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
5994894 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
5994919 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
5994942 AATCAGAGAGC
1 AAACAGAGAGC
5994953 GCGCTAGTGT
Statistics
Matches: 151, Mismatches: 23, Indels: 35
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 19 0.13
23 76 0.50
24 3 0.02
25 28 0.19
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:5994906 original size:48 final size:46
Alignment explanation
Indices: 5994832--5994952 Score: 179
Period size: 48 Copynumber: 2.6 Consensus size: 46
5994822 ACAAAGTACT
* * *
5994832 GAGCACACAAAGTGCTAATCAGAGAGCACAAGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACAAGAAGTGCTAAACAGA
* *
5994878 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACAAGAAGTGCTAAACAGA
5994926 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
5994953 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
46 26 0.38
48 42 0.62
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACAAGAAGTGCTAAACAGA
Found at i:5997645 original size:18 final size:18
Alignment explanation
Indices: 5997622--5997657 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5997612 AATTCATATC
5997622 ACTTTCAATTCCAATTTT
1 ACTTTCAATTCCAATTTT
* *
5997640 ACTTTCACTTTCAATTTT
1 ACTTTCAATTCCAATTTT
5997658 GATCACAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (18 bp):
ACTTTCAATTCCAATTTT
Found at i:6000709 original size:24 final size:24
Alignment explanation
Indices: 6000689--6000736 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6000679 CTCTTAAGAG
*
6000689 CTCAAACCCATTAAAATTTAAAAC
1 CTCAAACACATTAAAATTTAAAAC
* *
6000713 CTCATACACATTAATATTTAAAAC
1 CTCAAACACATTAAAATTTAAAAC
6000737 ACAAATTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (24 bp):
CTCAAACACATTAAAATTTAAAAC
Found at i:6001873 original size:22 final size:22
Alignment explanation
Indices: 6001832--6001873 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6001822 TCACTACTTA
***
6001832 TGTGAATGTGTGATCTTGAATT
1 TGTGAATGTGTGAGAGTGAATT
6001854 TGTGAATGTGTGAGAGTGAA
1 TGTGAATGTGTGAGAGTGAA
6001874 GTGAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.02, G:0.33, T:0.38
Consensus pattern (22 bp):
TGTGAATGTGTGAGAGTGAATT
Found at i:6005259 original size:24 final size:25
Alignment explanation
Indices: 6005232--6005287 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
6005222 CCGATGTATC
6005232 ATTAATTTTTTTTAAAAAT-TTATG
1 ATTAATTTTTTTTAAAAATATTATG
* * *
6005256 ATT-ATTCTTTTTAATAATATTATT
1 ATTAATTTTTTTTAAAAATATTATG
*
6005280 TTTAATTT
1 ATTAATTT
6005288 AAATTTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 13 0.52
24 9 0.36
25 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTAATTTTTTTTAAAAATATTATG
Found at i:6009490 original size:43 final size:42
Alignment explanation
Indices: 6009382--6009510 Score: 150
Period size: 43 Copynumber: 3.0 Consensus size: 42
6009372 TCTATTAATG
* * *
6009382 TTAGCGGCGTTTGTGGAAAAAACACTGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGG-AAAAGCGCTGCTAAAGACCATGTTCT
* * *
6009425 TTAGCAGCGTTTGTGGGGAAAGCGCTGCTAAAAACCATGTTCT
1 TTAGCGGCGTTTGT-GGAAAAGCGCTGCTAAAGACCATGTTCT
* * *
6009468 TTAGCGGCGTTTGTGAGAAAAGCGCCGTTAAAGACCATTTTCT
1 TTAGCGGCGTTTGTG-GAAAAGCGCTGCTAAAGACCATGTTCT
6009511 ATAGTGCGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
42 1 0.01
43 69 0.96
44 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGAAAAGCGCTGCTAAAGACCATGTTCT
Found at i:6009535 original size:31 final size:32
Alignment explanation
Indices: 6009497--6009557 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
6009487 AAGCGCCGTT
6009497 AAAGACCATTTTCTATAGT-GCGTTTTTTCTA
1 AAAGACCATTTTCTATAGTGGCGTTTTTTCTA
* *
6009528 AAAGACCATTTTTTATAGTGGTGTTTTTTC
1 AAAGACCATTTTCTATAGTGGCGTTTTTTC
6009558 CAATAAACGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.48
Consensus pattern (32 bp):
AAAGACCATTTTCTATAGTGGCGTTTTTTCTA
Found at i:6015700 original size:23 final size:22
Alignment explanation
Indices: 6015674--6015716 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
6015664 ATCTTGATTT
6015674 TTTTTTAGATAAT-TTATGTAAAG
1 TTTTTT-GA-AATATTATGTAAAG
6015697 TTTTTTGAAATATTATGTAA
1 TTTTTTGAAATATTATGTAA
6015717 TTCATTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 10 0.53
23 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TTTTTTGAAATATTATGTAAAG
Found at i:6016284 original size:6 final size:6
Alignment explanation
Indices: 6016273--6016323 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
6016263 TATGAGGATT
* * **
6016273 AAATAA AAATAA AAATAA AAATAA AAATAA AATTTA AAGCAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
6016321 AAA
1 AAA
6016324 AACAGAAAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:6027077 original size:39 final size:36
Alignment explanation
Indices: 6027033--6027128 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 36
6027023 TAGGACAAGT
6027033 CTCTTCCAAAAGGTATGTCCAATATGAAAAGCG-TTGTGA
1 CTCTT-CAAAAGGT-TGTCCAATATG-AAAG-GATTGTGA
*
6027072 CTCTTCAAAAGGTGTCCATCCAATATGAAAGGATTGTGA
1 CTCTTCAAAAGGT-T--GTCCAATATGAAAGGATTGTGA
6027111 CTCTTCAAAA-GTTGTCCA
1 CTCTTCAAAAGGTTGTCCA
6027129 TTGAGTGTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
35 4 0.08
37 1 0.02
38 12 0.24
39 25 0.49
40 9 0.18
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (36 bp):
CTCTTCAAAAGGTTGTCCAATATGAAAGGATTGTGA
Found at i:6027129 original size:39 final size:40
Alignment explanation
Indices: 6027050--6027129 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
6027040 AAAAGGTATG
6027050 TCCAATATGAAAAGCGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGCGTTGTGACTCTTCAAAAGGTGTCCA
*
6027090 TCCAATATG-AAAG-GATTGTGACTCTTCAAAAGTTGTCCA
1 TCCAATATGAAAAGCG-TTGTGACTCTTCAAAAGGTGTCCA
6027129 T
1 T
6027130 TGAGTGTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 1 0.03
39 28 0.74
40 9 0.24
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (40 bp):
TCCAATATGAAAAGCGTTGTGACTCTTCAAAAGGTGTCCA
Found at i:6035391 original size:39 final size:40
Alignment explanation
Indices: 6035338--6035414 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
6035328 AAAAGGTATG
* *
6035338 TCCATTATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCTA
1 TCCAATATGAAAAGGGTTATGACTCTTCAAAAGGTGTCTA
6035378 TCCAATATG-AAAGGGTTATGACTCTTCAAAAGGTGTC
1 TCCAATATGAAAAGGGTTATGACTCTTCAAAAGGTGTC
6035415 CGTTAAGTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 27 0.77
40 8 0.23
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTATGACTCTTCAAAAGGTGTCTA
Found at i:6039098 original size:18 final size:20
Alignment explanation
Indices: 6039075--6039120 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6039065 CTAATATAAC
*
6039075 TTTTTAT-ATTTTTTAA-TA
1 TTTTTATGAATTTTTAATTA
6039093 TTTTTATGAATTTTTAATTA
1 TTTTTATGAATTTTTAATTA
6039113 TTTATTAT
1 TTT-TTAT
6039121 TGTTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 8 0.33
20 5 0.21
21 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTATGAATTTTTAATTA
Found at i:6040115 original size:5 final size:5
Alignment explanation
Indices: 6040105--6040129 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6040095 ATTTAATTAT
6040105 TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA
6040130 ATAAACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:6053420 original size:11 final size:11
Alignment explanation
Indices: 6053398--6053430 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6053388 TTTTTAAGCA
6053398 TAATAAATAAT
1 TAATAAATAAT
6053409 T-ATAATATAAT
1 TAATAA-ATAAT
6053420 TAATAAATAAT
1 TAATAAATAAT
6053431 AAAAAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.20
11 12 0.60
12 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATAAATAAT
Found at i:6054613 original size:58 final size:59
Alignment explanation
Indices: 6054545--6054666 Score: 142
Period size: 58 Copynumber: 2.1 Consensus size: 59
6054535 TAAAAACTAT
* * *
6054545 ATTTTTACCCCTAAA-TTTCTTAAAAATTACA-TTTTGCCCCCGAACATCT-AAAATTACC
1 ATTTTGACCCC-AAACTTT-TTAAAAATTACATTTTTACCCCCAAACATCTAAAAATTACC
** * *
6054603 ATTTTGACCCCAAACTTTTTTGAAATTGCATTTTTACCCCTAAACATCTAAAAATTACC
1 ATTTTGACCCCAAACTTTTTAAAAATTACATTTTTACCCCCAAACATCTAAAAATTACC
6054662 ATTTT
1 ATTTT
6054667 TAACCTCGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
57 12 0.22
58 28 0.52
59 14 0.26
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (59 bp):
ATTTTGACCCCAAACTTTTTAAAAATTACATTTTTACCCCCAAACATCTAAAAATTACC
Found at i:6054657 original size:29 final size:30
Alignment explanation
Indices: 6054545--6054843 Score: 128
Period size: 29 Copynumber: 10.3 Consensus size: 30
6054535 TAAAAACTAT
**
6054545 ATTTTTACCCCTAAATTTCTTAAAAATTA-C
1 ATTTTTACCCCTAAACATC-TAAAAATTACC
* **
6054575 A-TTTTGCCCCCGAACATCT-AAAATTACC
1 ATTTTTACCCCTAAACATCTAAAAATTACC
* * * ** *
6054603 ATTTTGACCCC-AAACTTTTTTGAAATT-GC
1 ATTTTTACCCCTAAAC-ATCTAAAAATTACC
6054632 ATTTTTACCCCTAAACATCTAAAAATTACC
1 ATTTTTACCCCTAAACATCTAAAAATTACC
* * * *
6054662 ATTTTTA-ACCTCGAACATC-CAAAATTATC
1 ATTTTTACCCCT-AAACATCTAAAAATTACC
* * * * * *
6054691 A-TATTATCCTTGAACATCCAAATATTA-C
1 ATTTTTACCCCTAAACATCTAAAAATTACC
* *
6054719 -TGTTTTGCCCTTAAACATCTAAAAATTACC
1 AT-TTTTACCCCTAAACATCTAAAAATTACC
* * * *
6054749 A-TTTTACCCTTGAA-ATTTCAAAAATTATC
1 ATTTTTACCCCTAAACATCT-AAAAATTACC
* * *
6054778 A-TTTT-GCCCTCGAACATCCAAAAATTACC
1 ATTTTTACCCCT-AAACATCTAAAAATTACC
* * *
6054807 A-TTTTACCCTTGAA-ATCCAAAAATTACC
1 ATTTTTACCCCTAAACATCTAAAAATTACC
6054835 A-TTTTACCC
1 ATTTTTACCC
6054844 TCAAATTTCC
Statistics
Matches: 208, Mismatches: 44, Indels: 36
0.72 0.15 0.12
Matches are distributed among these distances:
27 7 0.03
28 47 0.23
29 124 0.60
30 30 0.14
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
ATTTTTACCCCTAAACATCTAAAAATTACC
Found at i:6054707 original size:58 final size:57
Alignment explanation
Indices: 6054634--6054839 Score: 211
Period size: 58 Copynumber: 3.6 Consensus size: 57
6054624 GAAATTGCAT
* * * ** *
6054634 TTTTACCCCTAAACATCTAAAAATTACCATTTTTAACCTCGAACATCCAAAATTATCA
1 TTTTACCCTTGAA-ATCCAAAAATTACCATTTTTGCCCTCGAACATCCAAAATTACCA
* * * ** *
6054692 TATTATCCTTGAACATCCAAATATTA-C-TGTTTTGCCCTTAAACATCTAAAAATTACCA
1 TTTTACCCTTGAA-ATCCAAAAATTACCAT-TTTTGCCCTCGAACATC-CAAAATTACCA
* *
6054750 TTTTACCCTTGAAATTTCAAAAATTATCA-TTTTGCCCTCGAACATCCAAAAATTACCA
1 TTTTACCCTTGAAA-TCCAAAAATTACCATTTTTGCCCTCGAACATCC-AAAATTACCA
6054808 TTTTACCCTTGAAATCCAAAAATTACCATTTT
1 TTTTACCCTTGAAATCCAAAAATTACCATTTT
6054840 ACCCTCAAAT
Statistics
Matches: 120, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
56 1 0.01
57 27 0.22
58 91 0.76
59 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (57 bp):
TTTTACCCTTGAAATCCAAAAATTACCATTTTTGCCCTCGAACATCCAAAATTACCA
Found at i:6054738 original size:87 final size:87
Alignment explanation
Indices: 6054634--6054839 Score: 247
Period size: 87 Copynumber: 2.4 Consensus size: 87
6054624 GAAATTGCAT
* * *
6054634 TTTTACCCCTAAACATCTAAAAATTACCATTTTTAACCTCGAACA-TCCAAAATTATCATATTAT
1 TTTTACCCTTAAACATCTAAAAATTACCATTTTTAACCTCGAA-ATTCAAAAATTATCATATTAC
* * **
6054698 CCTTGAACATCCAAATATTACTG
65 CCTCGAACATCCAAAAATTACCA
* * * * *
6054721 TTTTGCCCTTAAACATCTAAAAATTACCA-TTTTACCCTTGAAATTTCAAAAATTATCATTTTGC
1 TTTTACCCTTAAACATCTAAAAATTACCATTTTTAACCTCGAAA-TTCAAAAATTATCATATTAC
6054785 CCTCGAACATCCAAAAATTACCA
65 CCTCGAACATCCAAAAATTACCA
* *
6054808 TTTTACCCTTGAA-ATCCAAAAATTACCATTTT
1 TTTTACCCTTAAACATCTAAAAATTACCATTTT
6054840 ACCCTCAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
85 1 0.01
86 25 0.25
87 75 0.74
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (87 bp):
TTTTACCCTTAAACATCTAAAAATTACCATTTTTAACCTCGAAATTCAAAAATTATCATATTACC
CTCGAACATCCAAAAATTACCA
Found at i:6066849 original size:25 final size:25
Alignment explanation
Indices: 6066817--6066874 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
6066807 GTTTTATATT
*
6066817 TATTTATT-ACATATATAAATAATTA
1 TATTTATTCA-ATATAAAAATAATTA
*
6066842 TATTTATTCAATATAAAAATATTTA
1 TATTTATTCAATATAAAAATAATTA
*
6066867 AATTTATT
1 TATTTATT
6066875 TATATTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTTATTCAATATAAAAATAATTA
Found at i:6070585 original size:17 final size:17
Alignment explanation
Indices: 6070547--6070585 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6070537 AGGTGGAGAA
* *
6070547 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
*
6070564 TTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
6070581 CTTGT
1 CTTGT
6070586 CAAGGTGGAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:6073285 original size:51 final size:51
Alignment explanation
Indices: 6073179--6073275 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
6073169 TGTCAGCAAA
* **
6073179 AAATTTAATTATTTTTTTAAAATATAAAATTTTTAAAAATATTTTAAAGTT
1 AAATTTAATTATTTTTTTAAAATATAAAATTATTAAAAATATCATAAAGTT
6073230 -AATTTAAATT-TATTTTTTAAAATATAAAATTATT-AAAATCATCATA
1 AAATTT-AATTAT-TTTTTTAAAATATAAAATTATTAAAAAT-ATCATA
6073276 TTTTAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 11 0.28
51 29 0.73
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (51 bp):
AAATTTAATTATTTTTTTAAAATATAAAATTATTAAAAATATCATAAAGTT
Found at i:6073353 original size:15 final size:15
Alignment explanation
Indices: 6073333--6073362 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6073323 GACCCTTCCC
*
6073333 CTTTTTATTTTCCTT
1 CTTTTTATTTACCTT
6073348 CTTTTTATTTACCTT
1 CTTTTTATTTACCTT
6073363 TTCTGTATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (15 bp):
CTTTTTATTTACCTT
Found at i:6074437 original size:15 final size:15
Alignment explanation
Indices: 6074394--6074440 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
6074384 TTTAATAATT
6074394 TTATA-TTT-AAAAA
1 TTATATTTTAAAAAA
6074407 TTAAATATTTTAAAAAAA
1 TT--ATATTTT-AAAAAA
6074425 TTATATTTTAAAAAA
1 TTATATTTTAAAAAA
6074440 T
1 T
6074441 AATTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.07
15 10 0.34
16 10 0.34
18 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTATATTTTAAAAAA
Found at i:6074444 original size:18 final size:18
Alignment explanation
Indices: 6074387--6074450 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 18
6074377 TGATGATTTT
*
6074387 AATAATTTTATATTTAAAA
1 AATAATTATAT-TTTAAAA
*
6074406 ATTAA--ATATTTT-AAA
1 AATAATTATATTTTAAAA
6074421 AA-AATTATATTTTAAAA
1 AATAATTATATTTTAAAA
6074438 AATAATTA-ATTTT
1 AATAATTATATTTT
6074451 TTTGCTGACG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 2 0.05
15 4 0.11
16 10 0.26
17 13 0.34
18 5 0.13
19 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAATTATATTTTAAAA
Found at i:6077855 original size:27 final size:27
Alignment explanation
Indices: 6077731--6077946 Score: 107
Period size: 27 Copynumber: 7.9 Consensus size: 27
6077721 AATTTTTTAG
* * * *
6077731 ATTTTATAGTTTTGCCCCTGTTTTTCAA
1 ATTTTACAGTTTT-CCCTTATTTTCCAA
* * *
6077759 ATTTTATAGTTTTTTCCTGACTTTT-CAA
1 ATTTTACAG-TTTTCCCTTA-TTTTCCAA
* * * * *
6077787 ATTTTATAGTTCTACCCTTGTTTTTCAG
1 ATTTTACAGTT-TTCCCTTATTTTCCAA
* * *
6077815 TTTTTGCAAG-TTTCCCTTATTTTCCAG
1 ATTTTAC-AGTTTTCCCTTATTTTCCAA
*
6077842 ATTTTACAGTTTTCCCGTATTTTCCAA
1 ATTTTACAGTTTTCCCTTATTTTCCAA
* * * * *
6077869 AATTTATAGTTTTGCCTT-TTTT-TAG
1 ATTTTACAGTTTTCCCTTATTTTCCAA
* **
6077894 ATTTTACAGTTTTGCCTCTATTTTTTAAA
1 ATTTTACAGTTTTCCCT-TA-TTTTCCAA
*
6077923 ATTTTACAGTGTTTCCTTTATTTT
1 ATTTTACAGT-TTTCCCTTATTTT
6077947 TATTGATTTT
Statistics
Matches: 146, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
25 16 0.11
26 7 0.05
27 53 0.36
28 42 0.29
29 23 0.16
30 5 0.03
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.55
Consensus pattern (27 bp):
ATTTTACAGTTTTCCCTTATTTTCCAA
Found at i:6077927 original size:29 final size:27
Alignment explanation
Indices: 6077842--6077947 Score: 92
Period size: 29 Copynumber: 3.9 Consensus size: 27
6077832 TATTTTCCAG
**
6077842 ATTTTACAGTTTTCCCGTATTTTCCAAA
1 ATTTTACAGTTTTCCC-TATTTTTTAAA
* * *
6077870 A-TTTATAGTTTTGCCT-TTTTTT-AG
1 ATTTTACAGTTTTCCCTATTTTTTAAA
6077894 ATTTTACAGTTTTGCCTCTATTTTTTAAA
1 ATTTTACAGTTTT-CC-CTATTTTTTAAA
*
6077923 ATTTTACAGTGTTTCCTTTATTTTT
1 ATTTTACAGT-TTTCC-CTATTTTT
6077948 ATTGATTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
24 2 0.03
25 14 0.22
26 2 0.03
27 14 0.22
28 7 0.11
29 21 0.33
30 3 0.05
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.57
Consensus pattern (27 bp):
ATTTTACAGTTTTCCCTATTTTTTAAA
Found at i:6077955 original size:29 final size:28
Alignment explanation
Indices: 6077885--6077956 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
6077875 TAGTTTTGCC
6077885 TTTTTTTAGATTTTACAGTTTTGCCTCTA
1 TTTTTTT-GATTTTACAGTTTTGCCTCTA
** *
6077914 TTTTTTAAAATTTTACAGTGTTT-CCTTTA
1 TTTTTT-TGATTTTACAGT-TTTGCCTCTA
6077943 TTTTTATTGATTTT
1 TTTTT-TTGATTTT
6077957 TCAATTTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.19, C:0.10, G:0.08, T:0.62
Consensus pattern (28 bp):
TTTTTTTGATTTTACAGTTTTGCCTCTA
Found at i:6085187 original size:22 final size:22
Alignment explanation
Indices: 6085152--6085193 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6085142 ATATTGTTCT
*
6085152 ATTTTTATTAATAACCTATGTA
1 ATTTTTATCAATAACCTATGTA
* *
6085174 ATTTTTATCCATAACTTATG
1 ATTTTTATCAATAACCTATG
6085194 AAAATTGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTTTTATCAATAACCTATGTA
Found at i:6091943 original size:30 final size:29
Alignment explanation
Indices: 6091903--6092068 Score: 96
Period size: 30 Copynumber: 5.6 Consensus size: 29
6091893 TGACTTTTAG
*
6091903 GGGTAAAAATGTAATTTTTGGTGAAATCA
1 GGGTAAAAATGGAATTTTTGGTGAAATCA
*
6091932 GGGTCAAAAATGGGA-TTTT-G-GAAAGTTCGA
1 GGGT-AAAAATGGAATTTTTGGTGAAA--TC-A
*
6091962 GGGT-AAAGTGGTAATTTTTGGGTGAAATCA
1 GGGTAAAAATGG-AATTTTT-GGTGAAATCA
* * *
6091992 GGGTTAAAATGGAA-TTTT--AGAAAGTTTGA
1 GGGTAAAAATGGAATTTTTGGTGAAA---TCA
* *
6092021 GGGT-AAAATGGTAATTTTGGGTGAAATTA
1 GGGTAAAAATGG-AATTTTTGGTGAAATCA
*
6092050 GGGTTAATAATGGAATTTT
1 GGG-TAAAAATGGAATTTT
6092069 AGAAAGTTTG
Statistics
Matches: 107, Mismatches: 11, Indels: 37
0.69 0.07 0.24
Matches are distributed among these distances:
26 4 0.04
27 4 0.04
28 14 0.13
29 28 0.26
30 34 0.32
31 14 0.13
32 5 0.05
33 4 0.04
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGTGAAATCA
Found at i:6092024 original size:29 final size:28
Alignment explanation
Indices: 6091991--6092089 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 28
6091981 GGGTGAAATC
6091991 AGGGTTAAAATGGAATTTTAGAAAGTTTG
1 AGGG-TAAAATGGAATTTTAGAAAGTTTG
*
6092020 AGGGTAAAATGGTAATTTTGGGTGAAA--TT-
1 AGGGTAAAATGG-AATTTT---AGAAAGTTTG
6092049 AGGGTTAATAATGGAATTTTAGAAAGTTTG
1 AGGG-TAA-AATGGAATTTTAGAAAGTTTG
6092079 -GGGTAAAATGG
1 AGGGTAAAATGG
6092090 TTATTCTGGG
Statistics
Matches: 59, Mismatches: 2, Indels: 20
0.73 0.02 0.25
Matches are distributed among these distances:
27 9 0.15
28 11 0.19
29 19 0.32
30 11 0.19
31 5 0.08
32 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (28 bp):
AGGGTAAAATGGAATTTTAGAAAGTTTG
Found at i:6092083 original size:58 final size:58
Alignment explanation
Indices: 6091902--6092198 Score: 409
Period size: 59 Copynumber: 5.1 Consensus size: 58
6091892 TTGACTTTTA
* * * * *
6091902 GGGGTAAAAAT-GTAATTTTTGGTGAAATCAGGGTCAAAAATGGGATTTTGGAAAGTTC
1 GGGGT-AAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTT
*
6091960 GAGGGTAAAGTGGTAATTTTTGGGTGAAATCAGGGTT-AAAATGGAATTTTAGAAAGTTT
1 G-GGGTAAAATGGTAA-TTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTT
* *
6092019 GAGGGTAAAATGGTAATTTTGGGTGAAATTAGGGTTAATAATGGAATTTTAGAAAGTTT
1 G-GGGTAAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTT
* * * *
6092078 GGGGTAAAATGGTTATTCTGGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTT
1 GGGGTAAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTT
* *
6092136 GGGAGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAAGTTT
1 GGG-GTAAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTT
6092195 GGGG
1 GGGG
6092199 ACTAGAATAA
Statistics
Matches: 215, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
58 79 0.37
59 118 0.55
60 18 0.08
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTT
Found at i:6092144 original size:117 final size:117
Alignment explanation
Indices: 6091903--6092198 Score: 409
Period size: 117 Copynumber: 2.5 Consensus size: 117
6091893 TGACTTTTAG
* * * * *
6091903 GGGTAAAAAT-GTAATTTTTGGTGAAATCAGGGTCAAAAATGGGATTTTGGAAAGTTCGAGGGTA
1 GGGT-AAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTG-GGGTA
* * *
6091967 AAGTGGTAATTTTTGGGTGAAATCAGGGTTAAAATGGAATTTTAGAAAGTTTGA
64 AAATGGTAATTTCTGGGTGAAATCAGGGTTAAAATAGAATTTTAGAAAGTTTGA
* *
6092021 GGGTAAAATGGTAATTTTGGGTGAAATTAGGGTTAATAATGGAATTTTAGAAAGTTTGGGGTAAA
1 GGGTAAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGTAAA
* *
6092086 ATGGTTA-TTCTGGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTTG-
66 ATGGTAATTTCTGGGTGAAATCAGGGTT-AAAATAGAATTTTAGAAAGTTTGA
* *
6092137 GGAGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAAGTTTGGGG
1 GG-GTAAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTGGGG
6092199 ACTAGAATAA
Statistics
Matches: 159, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
116 20 0.13
117 94 0.59
118 45 0.28
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGTAAA
ATGGTAATTTCTGGGTGAAATCAGGGTTAAAATAGAATTTTAGAAAGTTTGA
Found at i:6092895 original size:13 final size:14
Alignment explanation
Indices: 6092875--6092912 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
6092865 AAAAGTCCCT
6092875 TTCCTTTTCTTCT-
1 TTCCTTTTCTTCTA
* *
6092888 TTCTTTTTCTTTTA
1 TTCCTTTTCTTCTA
6092902 TTCCTTTTCTT
1 TTCCTTTTCTT
6092913 TTGTTCTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCCTTTTCTTCTA
Found at i:6092911 original size:14 final size:13
Alignment explanation
Indices: 6092874--6092933 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 13
6092864 TAAAAGTCCC
*
6092874 TTTCCTTTTCTTC
1 TTTCCTTTTCTTT
*
6092887 TTTCTTTTTCTTT
1 TTTCCTTTTCTTT
6092900 TATTCCTTTTCTTT
1 T-TTCCTTTTCTTT
*
6092914 TGTTCTTTATTCTTT
1 T-TTCCTT-TTCTTT
6092929 ATTTC
1 -TTTC
6092934 AAACAACAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
13 12 0.31
14 17 0.44
15 9 0.23
16 1 0.03
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTCCTTTTCTTT
Found at i:6093258 original size:24 final size:26
Alignment explanation
Indices: 6093231--6093278 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
6093221 TTTTTTTATA
6093231 TTATTAGT-AAATA-TCATTATTACC
1 TTATTAGTAAAATATTCATTATTACC
*
6093255 TTATTATTAAAATATTCATTATTA
1 TTATTAGTAAAATATTCATTATTA
6093279 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (26 bp):
TTATTAGTAAAATATTCATTATTACC
Found at i:6093298 original size:20 final size:19
Alignment explanation
Indices: 6093255--6093305 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
6093245 CATTATTACC
6093255 TTATTATTAAAA-TATTCA
1 TTATTATTAAAATTATTCA
**
6093273 TTATTATTAAAATTATTTTT
1 TTATTATTAAAATTA-TTCA
6093293 TTATTATTAAAAT
1 TTATTATTAAAAT
6093306 GTTATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.41
19 2 0.07
20 15 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATTAAAATTATTCA
Found at i:6094075 original size:42 final size:41
Alignment explanation
Indices: 6094027--6094108 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
6094017 ATATTTAAGC
* *
6094027 TAAATTTAAATTTAGAAAAAAAATTCAAATCTAAATCTAAAT
1 TAAATTTAAACTTAGAAAAAAAATTCAAA-CCAAATCTAAAT
* * *
6094069 TAAATTTAAACTTAGAAATAAATTTGAAACCAAATCTAAA
1 TAAATTTAAACTTAGAAAAAAAATTCAAACCAAATCTAAA
6094109 CTCAAGAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.32
Consensus pattern (41 bp):
TAAATTTAAACTTAGAAAAAAAATTCAAACCAAATCTAAAT
Found at i:6094809 original size:200 final size:199
Alignment explanation
Indices: 6094460--6095095 Score: 1004
Period size: 200 Copynumber: 3.2 Consensus size: 199
6094450 TTCATTGACC
* * * * * * *
6094460 TGGTCTTCTTCTCTGTGTCTCATCAGGAAGATGACTGCGATCA-TCTATTTTAATTCGTTTCTCT
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGC-CTCACT-TGTTTTGATTCGCTTCTCT
* * *
6094524 GGATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTA
64 GGATCTCCTC-AGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA
* * * *
6094589 TTGCTTCGACCTGTTTCTCAGTGCCTCATCAGGAAGCTGGATTCGAAGATTGGCTCGTGTTGAGT
128 TTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGC
*
6094654 GCTGAGT
193 GTTGAGT
*
6094661 TGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTTGATTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTGATTCGCTTCTCTGG
*
6094726 ATCTCCTCAGTAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCCAACCATTTTATT
66 ATCTCCTCAG-AAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
*
6094791 GCTTCGACCTGCTTCTCAGTGTCTCATCCGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGT
130 GCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGT
6094856 TGAGT
195 TGAGT
*
6094861 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTGATTCGCTTCTCTGG
*
6094926 ATCTCCTCAGGAAGACAAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
66 ATCTCCTCA-GAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* * *
6094991 GCTTGGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGATGAGCAT
130 GCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGT
6095056 TGAGT
195 TGAGT
*
6095061 TGGTATTCTTCTCTGTATCTCATTAGGAAGATGAC
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGAC
6095096 TGTCTCAATG
Statistics
Matches: 405, Mismatches: 27, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
199 2 0.00
200 367 0.91
201 36 0.09
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (199 bp):
TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTGATTCGCTTCTCTGG
ATCTCCTCAGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTG
CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGTT
GAGT
Found at i:6107333 original size:30 final size:29
Alignment explanation
Indices: 6107299--6107449 Score: 78
Period size: 29 Copynumber: 5.1 Consensus size: 29
6107289 AAAAATGGGA
6107299 TTTTGGAAGGTTCGGGGGTAAAATGGTAAT
1 TTTTGGAA-GTTCGGGGGTAAAATGGTAAT
* * *
6107329 TTTTGGTGAA-ATC-AGGGTCAAAATGG-GAT
1 TTTT-G-GAAGTTCGGGGGT-AAAATGGTAAT
* * *
6107358 TTTAGAAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGGAAGTTCGGGGGTAAAATGGTAAT
* * *
6107387 TTTTGGGTGAAATT-GTGGTTAAAAATGG-AAT
1 TTTT--G-GAAGTTCGGGGGT-AAAATGGTAAT
* * * *
6107418 TTTAGAAAGTTTGGGGGTAAAATAGTAAT
1 TTTTGGAAGTTCGGGGGTAAAATGGTAAT
6107447 TTT
1 TTT
6107450 GGGTGAAATC
Statistics
Matches: 89, Mismatches: 20, Indels: 25
0.66 0.15 0.19
Matches are distributed among these distances:
27 2 0.02
28 19 0.21
29 29 0.33
30 13 0.15
31 12 0.13
32 14 0.16
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (29 bp):
TTTTGGAAGTTCGGGGGTAAAATGGTAAT
Found at i:6107355 original size:58 final size:58
Alignment explanation
Indices: 6107266--6107608 Score: 379
Period size: 58 Copynumber: 5.8 Consensus size: 58
6107256 GGTAAAAATT
* * *
6107266 TAATTTTTGGTGAAAT-AGGGGTCAAAAATGGGATTTTGGAAGGTTCGGGGGTAAAATGG
1 TAATTTTTGGTGAAATCA-GGGT-AAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGG
*
6107325 TAATTTTTGGTGAAATCAGGGTCAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGG
1 TAATTTTTGGTGAAATCAGGGTAAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGG
* * *
6107383 TAATTTTTGGGTGAAAT-TGTGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATAG
1 TAATTTTT-GGTGAAATCAG-GG-TAAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGG
* ** * * *
6107443 TAATTTTGGGTGAAATCAGGGTTAAAAATGAAAATTTAAAAAGTTTAGGGGTAAAATGG
1 TAATTTTTGGTGAAATCAGGG-TAAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGG
* * * * *
6107502 TAATTTTGGGTGAAATCGGGGTTAAAAT-GGACTTTTAGAAAGTTTAGGGGTAAAATGA
1 TAATTTTTGGTGAAATCAGGGTAAAAATGGGA-TTTTAGAAAGTTTGGGGGTAAAATGG
* * * * *
6107560 TAA-TTTTGGATAAAATTAGGGTTAAAATAGAATTTTAGAAAGTTTGGGG
1 TAATTTTTGG-TGAAATCAGGGTAAAAATGGGATTTTAGAAAGTTTGGGG
6107609 ACTAAAGAGC
Statistics
Matches: 248, Mismatches: 28, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
57 6 0.02
58 104 0.42
59 95 0.38
60 43 0.17
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (58 bp):
TAATTTTTGGTGAAATCAGGGTAAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGG
Found at i:6107434 original size:118 final size:118
Alignment explanation
Indices: 6107266--6107608 Score: 433
Period size: 118 Copynumber: 2.9 Consensus size: 118
6107256 GGTAAAAATT
* * * * *
6107266 TAATTTTT-GGTGAAATAGGGGTCAAAAATGGGATTTTGGAAGGTTCGGGGGTAAAATGGTAATT
1 TAATTTTTGGGTGAAATAGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATT
* *
6107330 TTTGGTGAAATCAGGGTCAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGG
66 TTTGGTGAAATCAGGGTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGG
* * *
6107383 TAATTTTTGGGTGAAATTGTGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATAGTAATT
1 TAATTTTTGGGTGAAATAGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATT
* * * * *
6107448 TTGGGTGAAATCAGGGTTAAAAATGAAAATTTAAAAAGTTTAGGGGTAAAATGG
66 TTTGGTGAAATCAGGG-TAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGG
* * * *
6107502 TAA-TTTTGGGTGAAATCGGGGTT-AAAATGGACTTTTAGAAAGTTTAGGGGTAAAATGATAA-T
1 TAATTTTTGGGTGAAATAGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATT
* * * *
6107564 TTTGGATAAAATTAGGGTTAAAATAGAATTTTAGAAAGTTTGGGG
66 TTTGG-TGAAATCAGGGTAAAAATGGAATTTTAGAAAGTTTGGGG
6107609 ACTAAAGAGC
Statistics
Matches: 193, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
116 27 0.14
117 51 0.26
118 81 0.42
119 34 0.18
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (118 bp):
TAATTTTTGGGTGAAATAGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATT
TTTGGTGAAATCAGGGTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGG
Found at i:6107586 original size:30 final size:30
Alignment explanation
Indices: 6107487--6107595 Score: 84
Period size: 29 Copynumber: 3.7 Consensus size: 30
6107477 TTTAAAAAGT
* *
6107487 TTAGGGGTAAAATG-GTAATTTTGGGTGAAA
1 TTAGGGGTAAAATGAG-AATTTTGGATAAAA
* * * **
6107517 -TCGGGGTTAAAATG-GACTTTTAGA-AAGT
1 TTAGGGG-TAAAATGAGAATTTTGGATAAAA
*
6107545 TTAGGGGTAAAATGATAATTTTGGATAAAA
1 TTAGGGGTAAAATGAGAATTTTGGATAAAA
*
6107575 TTAGGGTTAAAAT-AGAATTTT
1 TTAGGGGTAAAATGAGAATTTT
6107596 AGAAAGTTTG
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
28 8 0.13
29 30 0.50
30 22 0.37
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.35
Consensus pattern (30 bp):
TTAGGGGTAAAATGAGAATTTTGGATAAAA
Found at i:6108326 original size:20 final size:18
Alignment explanation
Indices: 6108292--6108342 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
6108282 AGTCCCTTGC
6108292 CTTTTATTCTTTCTTTTT
1 CTTTTATTCTTTCTTTTT
6108310 CTTTTATTCCTTTTCTTTTGT
1 CTTTTATT-C-TTTCTTTT-T
6108331 -TCTTTATTCTTT
1 CT-TTTATTCTTT
6108343 ATTTCAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.28
19 4 0.14
20 10 0.34
21 7 0.24
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.75
Consensus pattern (18 bp):
CTTTTATTCTTTCTTTTT
Found at i:6108340 original size:15 final size:14
Alignment explanation
Indices: 6108302--6108342 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6108292 CTTTTATTCT
6108302 TTCTTTTTCTTTTA
1 TTCTTTTTCTTTTA
* *
6108316 TTCCTTTTCTTTTG
1 TTCTTTTTCTTTTA
6108330 TTCTTTATTCTTT
1 TTCTTT-TTCTTT
6108343 ATTTCAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (14 bp):
TTCTTTTTCTTTTA
Found at i:6108672 original size:24 final size:26
Alignment explanation
Indices: 6108645--6108692 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
6108635 TTTTTTTATA
6108645 TTATTAAT-AAATA-TCATTATTACC
1 TTATTAATAAAATATTCATTATTACC
*
6108669 TTATTATTAAAATATTCATTATTA
1 TTATTAATAAAATATTCATTATTA
6108693 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (26 bp):
TTATTAATAAAATATTCATTATTACC
Found at i:6108692 original size:18 final size:19
Alignment explanation
Indices: 6108669--6108714 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
6108659 CATTATTACC
6108669 TTATTATTAAAA-TATTCA
1 TTATTATTAAAATTATTCA
**
6108687 TTATTATTAAAATTATTTT
1 TTATTATTAAAATTATTCA
6108706 TTATTATTA
1 TTATTATTA
6108715 TTAAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATTAAAATTATTCA
Found at i:6109485 original size:19 final size:19
Alignment explanation
Indices: 6109461--6109529 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 19
6109451 TATTTAAGCT
6109461 AAATTTAAATTTAGAAAA-A
1 AAATTTAAATTTA-AAAATA
6109480 AAATTT-AATTTAAAAATA
1 AAATTTAAATTTAAAAATA
* * **
6109498 AATTTTAAATTCAAATCT-
1 AAATTTAAATTTAAAAATA
6109516 AAA-TTAAATTTAAA
1 AAATTTAAATTTAAA
6109530 CTTAGAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 14 0.33
18 14 0.33
19 14 0.33
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (19 bp):
AAATTTAAATTTAAAAATA
Found at i:6109491 original size:18 final size:18
Alignment explanation
Indices: 6109461--6109508 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
6109451 TATTTAAGCT
6109461 AAATTTAAATTTAGAAAAA
1 AAATTTAAATTTA-AAAAA
6109480 AAATTT-AATTTAAAAATA
1 AAATTTAAATTTAAAAA-A
*
6109498 AATTTTAAATT
1 AAATTTAAATT
6109509 CAAATCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.15
18 12 0.46
19 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATTTAAATTTAAAAAA
Found at i:6109501 original size:12 final size:12
Alignment explanation
Indices: 6109479--6109529 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
6109469 ATTTAGAAAA
*
6109479 AAAATTTAATTT
1 AAAATTAAATTT
*
6109491 AAAAATAAATTT
1 AAAATTAAATTT
* *
6109503 TAAATTCAAATCT
1 AAAATT-AAATTT
6109516 -AAATTAAATTT
1 AAAATTAAATTT
6109527 AAA
1 AAA
6109530 CTTAGAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 5 0.16
12 21 0.68
13 5 0.16
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATTAAATTT
Found at i:6109985 original size:15 final size:14
Alignment explanation
Indices: 6109967--6110019 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
6109957 AAAAATTTTA
6109967 ATAAATAAAAAATGT
1 ATAAATAAAAAAT-T
6109982 ATAAATATATTAAATATT
1 ATAAATA-A--AAA-ATT
6110000 A-AAATAAAAAATT
1 ATAAATAAAAAATT
6110013 ATAAATA
1 ATAAATA
6110020 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 4 0.12
14 8 0.24
15 7 0.21
16 2 0.06
17 5 0.15
18 5 0.15
19 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (14 bp):
ATAAATAAAAAATT
Found at i:6120000 original size:37 final size:37
Alignment explanation
Indices: 6119958--6120045 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
6119948 TTTGATTACA
*
6119958 TGTTAAACATGCCCTACATGATATTATTCGATTTGCT
1 TGTTAAACATGCCCTACATGATATTATCCGATTTGCT
* * *
6119995 TGTTAAACATGTCATACATTATATTATCCGATTTGCT
1 TGTTAAACATGCCCTACATGATATTATCCGATTTGCT
**
6120032 TGTTCGACATGCCC
1 TGTTAAACATGCCC
6120046 ATTCTGGCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (37 bp):
TGTTAAACATGCCCTACATGATATTATCCGATTTGCT
Found at i:6120226 original size:26 final size:26
Alignment explanation
Indices: 6120197--6120248 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6120187 TTGGTGGCTT
6120197 CGTCCACATTGGAGTGTTTGGATGGA
1 CGTCCACATTGGAGTGTTTGGATGGA
6120223 CGTCCACATTGGAGTGTTTGGATGGA
1 CGTCCACATTGGAGTGTTTGGATGGA
6120249 TGAATTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (26 bp):
CGTCCACATTGGAGTGTTTGGATGGA
Done.