Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 80 of 210
Found at i:23929520 original size:27 final size:27
Alignment explanation
Indices: 23929472--23929536 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
23929462 ATGGAAGAAG
*
23929472 TACTA-TACTGGTGGCTCTGCCACA-A
1 TACTATTACTGGTGGCTCAGCCACATA
*
23929497 TCACTGTTACTGGTGGCAT-AGCCACATA
1 T-ACTATTACTGGTGGC-TCAGCCACATA
23929525 TACTATTACTGG
1 TACTATTACTGG
23929537 CAGCTTTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.03
26 3 0.09
27 26 0.79
28 3 0.09
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (27 bp):
TACTATTACTGGTGGCTCAGCCACATA
Found at i:23929556 original size:26 final size:26
Alignment explanation
Indices: 23929524--23929577 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
23929514 ATAGCCACAT
23929524 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* *
23929550 ATACTATTGCTGGTAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
23929576 AT
1 AT
23929578 GCTACTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:23929677 original size:32 final size:32
Alignment explanation
Indices: 23929580--23929820 Score: 121
Period size: 32 Copynumber: 7.5 Consensus size: 32
23929570 GCTGCGATGC
* *** * *
23929580 TACTGATGGCTTTGTGTTAATCATAGTACCGT
1 TACTGATGACTTTGTGCCGATCATATTAACGT
* * * * *
23929612 TACTGATGGCTTTGTGCCAACCATAGTACCGT
1 TACTGATGACTTTGTGCCGATCATATTAACGT
* *
23929644 TACTGATGACTTTATACCGATCATATTAACGT
1 TACTGATGACTTTGTGCCGATCATATTAACGT
* * * *
23929676 TA-TCGATGACTATGTGCTGATTAT-TTCACTGT
1 TACT-GATGACTTTGTGCCGATCATATTAAC-GT
* * * *
23929708 TACTGATGACTGTGTGTCGATCATA-TCACTGC
1 TACTGATGACTTTGTGCCGATCATATTAAC-GT
* * * * * *
23929740 CACTAATGGCTTTGTACCGATCATGTTACCGT
1 TACTGATGACTTTGTGCCGATCATATTAACGT
* * * *
23929772 TACTGATGGCTATATGCCGATCATA-TCACTGT
1 TACTGATGACTTTGTGCCGATCATATTAAC-GT
* *
23929804 TACTAATGGCTTTGTGC
1 TACTGATGACTTTGTGC
23929821 TAATCACATT
Statistics
Matches: 161, Mismatches: 42, Indels: 12
0.75 0.20 0.06
Matches are distributed among these distances:
31 7 0.04
32 151 0.94
33 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (32 bp):
TACTGATGACTTTGTGCCGATCATATTAACGT
Found at i:23931113 original size:10 final size:10
Alignment explanation
Indices: 23931070--23931114 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
23931060 CATATGAATA
*
23931070 TGATGAATTT
1 TGATTAATTT
*
23931080 TAATTAATTT
1 TGATTAATTT
23931090 TGTAGTTAATTT
1 TG-A-TTAATTT
23931102 TGATTAATTT
1 TGATTAATTT
23931112 TGA
1 TGA
23931115 CTATTTTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.63
11 2 0.07
12 9 0.30
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (10 bp):
TGATTAATTT
Found at i:23941259 original size:29 final size:29
Alignment explanation
Indices: 23941220--23941291 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
23941210 ATAATTGCAG
*
23941220 AAAATCTACCAAATAAATAATAAATGCGAT
1 AAAATC-ACCAAATAAAGAATAAATGCGAT
* *
23941250 AAAATCACCAAATAACGAATAAATGTGAT
1 AAAATCACCAAATAAAGAATAAATGCGAT
* *
23941279 AAGATCGCCAAAT
1 AAAATCACCAAAT
23941292 CCCGTTGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 31 0.84
30 6 0.16
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (29 bp):
AAAATCACCAAATAAAGAATAAATGCGAT
Found at i:23942246 original size:124 final size:123
Alignment explanation
Indices: 23941995--23942223 Score: 327
Period size: 124 Copynumber: 1.9 Consensus size: 123
23941985 TTTAGCGGTG
** *
23941995 TTTTTGGAAAAGCGCCGCTAATGCTTGGGGCTTTAGCGGCGTTTTTGGAAAAGCGTAGGTAATGC
1 TTTTTGGAAAAGCGCCGCTAATGCTAAGGGCTTTAGCGGCGTTTTTGGAAAAGCGTAGCTAATGC
* *
23942060 TCAGGGCTTTAGCGGCATTTTTGCAAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCG
66 TCAGGGCTTTAGCGGCATTTTTGCAAAAGCGCCGCTAATGCTCAGGGCTTTACCAGCA
* *
23942118 TTTTTGGAAAAGCGCCGCTAATGCTAAGGGCTTTAGCGGTGTTTTTTGGAAAAGCGTCGCTAATG
1 TTTTTGGAAAAGCGCCGCTAATGCTAAGGGCTTTAGCGGCG-TTTTTGGAAAAGCGTAGCTAATG
* **
23942183 CT-AGGGATTTTAGCGGTGTTTTT-CGAAAAGCGCCGCTAATG
65 CTCAGGG-CTTTAGCGGCATTTTTGC-AAAAGCGCCGCTAATG
23942224 GTTGGGGTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
123 43 0.45
124 52 0.55
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (123 bp):
TTTTTGGAAAAGCGCCGCTAATGCTAAGGGCTTTAGCGGCGTTTTTGGAAAAGCGTAGCTAATGC
TCAGGGCTTTAGCGGCATTTTTGCAAAAGCGCCGCTAATGCTCAGGGCTTTACCAGCA
Found at i:23942247 original size:41 final size:41
Alignment explanation
Indices: 23941982--23942223 Score: 315
Period size: 41 Copynumber: 5.9 Consensus size: 41
23941972 GAACTTTCGA
* **
23941982 GGCTTTAGCGGTGTTTTTGGAAAAGCGCCGCTAATGCTTGG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAG
** * *
23942023 GGCTTTAGCGGCGTTTTTGGAAAAGCGTAGGTAATGCTCAG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAG
* * *
23942064 GGCTTTAGCGGCATTTTTGCAAAAGCGCCGCTAATGCTCAG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAG
*
23942105 GGCTTTAGCAGCGTTTTTGGAAAAGCGCCGCTAATGCTAAG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAG
* *
23942146 GGCTTTAGCGGTGTTTTTTGGAAAAGCGTCGCTAATGCT-AG
1 GGCTTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAATGCTAAG
* * *
23942187 GGATTTTAGCGGTGTTTTTCGAAAAGCGCCGCTAATG
1 GG-CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATG
23942224 GTTGGGGTTT
Statistics
Matches: 178, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
41 144 0.81
42 34 0.19
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAG
Found at i:23942258 original size:124 final size:123
Alignment explanation
Indices: 23942002--23942262 Score: 312
Period size: 124 Copynumber: 2.1 Consensus size: 123
23941992 GTGTTTTTGG
** *
23942002 AAAAGCGCCGCTAATGCTTGGGGCTTTAGCGGCGTTTTTGGAAAAGCGTAGGTAATGCTCAGGGC
1 AAAAGCGCCGCTAATGCTAAGGGCTTTAGCGGCGTTTTTGGAAAAGCGTAGCTAATGCTCAGGGC
* * **
23942067 TTTAGCGGCATTTTTGCAAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGG
66 TTTAGCGGCATTTTTGCAAAAGCGCCGCTAATGCTCAGGGCTTTACCAGCATTTTTCC
* *
23942125 AAAAGCGCCGCTAATGCTAAGGGCTTTAGCGGTGTTTTTTGGAAAAGCGTCGCTAATGCT-AGGG
1 AAAAGCGCCGCTAATGCTAAGGGCTTTAGCGGCG-TTTTTGGAAAAGCGTAGCTAATGCTCAGGG
* ** * ** *
23942189 ATTTTAGCGGTGTTTTT-CGAAAAGCGCCGCTAATGGTTGGGGTTTTACC-GACATTTTTCC
65 -CTTTAGCGGCATTTTTGC-AAAAGCGCCGCTAATGCTCAGGGCTTTACCAG-CATTTTTCC
*
23942249 AAAAACGCCGCTAA
1 AAAAGCGCCGCTAA
23942263 AAATATTTTA
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
123 37 0.32
124 80 0.68
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (123 bp):
AAAAGCGCCGCTAATGCTAAGGGCTTTAGCGGCGTTTTTGGAAAAGCGTAGCTAATGCTCAGGGC
TTTAGCGGCATTTTTGCAAAAGCGCCGCTAATGCTCAGGGCTTTACCAGCATTTTTCC
Found at i:23942650 original size:14 final size:15
Alignment explanation
Indices: 23942620--23942660 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
23942610 GTTTAGAGAG
23942620 TATGGATTTAAGGAT
1 TATGGATTTAAGGAT
*
23942635 TATGGA-TTAGGGAT
1 TATGGATTTAAGGAT
23942649 TATGG-TTTAAGG
1 TATGGATTTAAGG
23942661 GTTGGGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:23942853 original size:14 final size:15
Alignment explanation
Indices: 23942827--23942870 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
23942817 GGTTTAAGCA
23942827 GGTTTAGGGGTTA-G
1 GGTTTAGGGGTTATG
* *
23942841 GGGTTATGGGTTATG
1 GGTTTAGGGGTTATG
*
23942856 GGTTTAGGGTTTATG
1 GGTTTAGGGGTTATG
23942871 TTTTATGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (15 bp):
GGTTTAGGGGTTATG
Found at i:23942865 original size:7 final size:7
Alignment explanation
Indices: 23942776--23942919 Score: 62
Period size: 7 Copynumber: 19.9 Consensus size: 7
23942766 GGGATTATGT
23942776 GTTTAGG
1 GTTTAGG
* *
23942783 GATTATG
1 GTTTAGG
* *
23942790 GATTACG
1 GTTTAGG
*
23942797 GTTTATG
1 GTTTAGG
23942804 GTTTAAGG
1 GTTT-AGG
*
23942812 G-TTGGG
1 GTTTAGG
23942818 GTTTAAGCAG
1 GTTT-AG--G
23942828 GTTTAGG
1 GTTTAGG
*
23942835 GGTTAGG
1 GTTTAGG
*
23942842 GGTTATGG
1 GTTTA-GG
23942850 G-TTATGG
1 GTTTA-GG
23942857 GTTTAGG
1 GTTTAGG
*
23942864 GTTTATG
1 GTTTAGG
* *
23942871 TTTTATG
1 GTTTAGG
*
23942878 ATTTAGG
1 GTTTAGG
23942885 GTTTAGG
1 GTTTAGG
*
23942892 AGATT-GG
1 -GTTTAGG
23942899 AG-TTAGGG
1 -GTTTA-GG
23942907 GTTTAGG
1 GTTTAGG
23942914 GTTTAG
1 GTTTAG
23942920 ATTAATTGGT
Statistics
Matches: 111, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
6 5 0.05
7 81 0.73
8 18 0.16
9 2 0.02
10 5 0.05
ACGTcount: A:0.19, C:0.01, G:0.39, T:0.41
Consensus pattern (7 bp):
GTTTAGG
Found at i:23945318 original size:6 final size:6
Alignment explanation
Indices: 23945307--23945343 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
23945297 AACTACTTCA
23945307 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT-TTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
23945344 GTGAAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTCTTT
Found at i:23948233 original size:43 final size:43
Alignment explanation
Indices: 23948173--23948263 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
23948163 CTTTGAGTTC
* * *
23948173 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
23948215 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
23948258 ATTACC
1 ATTACC
23948264 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:23948721 original size:43 final size:43
Alignment explanation
Indices: 23948629--23948934 Score: 409
Period size: 43 Copynumber: 7.2 Consensus size: 43
23948619 TGTTTTTAGT
* * * * *
23948629 GGCGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
*
23948671 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
*
23948714 GGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* * *
23948757 GGCGTTTGTGGGAAAAGCTCCGCTAGAGGTCTTGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* * *
23948800 GGAGTTTGT-GCAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* * * *
23948842 GGCGTTTGTGGAAAAATCACCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
** * *
23948885 AACGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
23948928 GGCGTTT
1 GGCGTTT
23948935 ATTTCTAAAA
Statistics
Matches: 231, Mismatches: 31, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
42 62 0.27
43 169 0.73
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
Found at i:23948857 original size:128 final size:129
Alignment explanation
Indices: 23948664--23948934 Score: 409
Period size: 128 Copynumber: 2.1 Consensus size: 129
23948654 AAGGTTTGTT
* *
23948664 CTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAAA
1 CTATAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAAAA
* * ** * * * *
23948729 AGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCTCCGCTAGAGGTCTTGAG
66 AGCACCGCTAAAGGTCCTGATCTATAGCAACGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGAG
* *
23948793 CTATAGCGGAGTTTGT-GCAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAAA
1 CTATAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAAAA
* *
23948857 ATCACCGCTAAAGGTCCTGATCTATAGCAACGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGAT
66 AGCACCGCTAAAGGTCCTGATCTATAGCAACGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGAG
23948921 CTATAGCGGCGTTT
1 CTATAGCGGCGTTT
23948935 ATTTCTAAAA
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
128 112 0.88
129 15 0.12
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (129 bp):
CTATAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAAAA
AGCACCGCTAAAGGTCCTGATCTATAGCAACGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGAG
Found at i:23956607 original size:27 final size:27
Alignment explanation
Indices: 23956567--23956619 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
23956557 TGGAGGCGGT
*
23956567 ATATAACCACTTCATACATCTATTTCC
1 ATATAACCACTTCATACATCCATTTCC
* * *
23956594 ATATAAGCATTTCATATATCCATTTC
1 ATATAACCACTTCATACATCCATTTC
23956620 TGTTTACACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATAACCACTTCATACATCCATTTCC
Found at i:23958425 original size:20 final size:20
Alignment explanation
Indices: 23958400--23958445 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
23958390 TTCTCTCTAT
23958400 TTTTGGCGT-TGGCTCCTTGA
1 TTTTGG-GTGTGGCTCCTTGA
*
23958420 TTTTGGGTGGTGGTTCCTTGA
1 TTTTGGGT-GTGGCTCCTTGA
23958441 TTTTG
1 TTTTG
23958446 TCCATGTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 6 0.26
21 15 0.65
ACGTcount: A:0.04, C:0.13, G:0.33, T:0.50
Consensus pattern (20 bp):
TTTTGGGTGTGGCTCCTTGA
Found at i:23961456 original size:17 final size:17
Alignment explanation
Indices: 23961434--23961474 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
23961424 AATACGAATT
**
23961434 ATATATACATATTTACA
1 ATATATACATAAGTACA
*
23961451 ATATATATATAAGTACA
1 ATATATACATAAGTACA
23961468 ATATATA
1 ATATATA
23961475 AGTAAATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (17 bp):
ATATATACATAAGTACA
Found at i:23961936 original size:3 final size:3
Alignment explanation
Indices: 23961928--23961997 Score: 65
Period size: 3 Copynumber: 24.3 Consensus size: 3
23961918 TGTATATAGA
* * *
23961928 AAT AAT AAT AAT AAT AAT AAT AAC GAT -AT AAT -AT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
23961974 AAC ATT AAA AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
23961998 GCTAAGAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
2 6 0.11
3 47 0.89
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:23963743 original size:44 final size:44
Alignment explanation
Indices: 23963642--23964017 Score: 226
Period size: 44 Copynumber: 8.7 Consensus size: 44
23963632 CTTTCTTGGG
*** ***
23963642 TCTGCTCCACTGCAACTTCAGGGAGATAAG--ACCCGA-TGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGATTTTAA
* *
23963683 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATATGTGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGATTTTAA
* * **
23963726 TCTACTCCACTGCAACTTCAGGGAGATAGGATTAT-TGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TATGTGATTTTAA
* * ** * *
23963770 TCTGCTCCAGTGTAACTTCAGGGAGATAAGAT-TCGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATAT-GTGAT-TTTAA
* * * * * * *
23963815 TTTGC-CTTACTACAACTTCA-GGAGGATAAGGCT-TGCTTA-CTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAA-GATATG-TGATTTTAA
**
23963859 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTA---GA-TGCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TATGTGATTTTAA
* * *
23963900 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGATTTTAA
* * * * * **
23963943 TCCGCTCCATTGCGACTTTAGGGAGATAGGATTAT-TGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TATGTGATTTTAA
23963987 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
23964018 GTCGCCATCT
Statistics
Matches: 250, Mismatches: 63, Indels: 41
0.71 0.18 0.12
Matches are distributed among these distances:
39 1 0.00
40 43 0.17
41 14 0.06
42 6 0.02
43 17 0.07
44 134 0.54
45 31 0.12
46 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGATTTTAA
Found at i:23963905 original size:217 final size:218
Alignment explanation
Indices: 23963609--23964028 Score: 673
Period size: 217 Copynumber: 1.9 Consensus size: 218
23963599 TGCTCCACTG
* *
23963609 CAACTTCAAGGAGATAAGACTCGCTTTCTTGGGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
1 CAACTTCAAGGAGATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * *
23963674 CCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATATGTGATTTTAATCTACTCCACTGC
66 CAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATATGTGATTTTAATCCACTCCACTGC
* * *
23963739 AACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCAGTGTAACTTCAGGGAGATAAGATTC
131 AACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAGTC
23963804 GCCATCTTCAGTTTGCCTTACTA
196 GCCATCTTCAGTTTGCCTTACTA
* *
23963827 CAACTTC-AGGAGGATAAGGCTTGCTTACTT-AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CAACTTCAAGGA-GATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * *
23963890 CTAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCATTG
65 CCAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATATGTGATTTTAATCCACTCCACTG
* *
23963955 CGACTTTAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAGT
130 CAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAGT
23964020 CGCCATCTT
195 CGCCATCTT
23964029 TGGTCTTTTA
Statistics
Matches: 185, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
217 163 0.88
218 22 0.12
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (218 bp):
CAACTTCAAGGAGATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
CAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATATGTGATTTTAATCCACTCCACTGC
AACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAGTC
GCCATCTTCAGTTTGCCTTACTA
Found at i:23964441 original size:44 final size:44
Alignment explanation
Indices: 23964383--23964504 Score: 167
Period size: 44 Copynumber: 2.8 Consensus size: 44
23964373 ATCTGCTATT
* *
23964383 TTCAACCTACTCCACTGTTGCTCAGGTAGATAGGA-TTCACAATC
1 TTCAACCTATTCCACTGTTGCTCAGGGAGATAGGACTT-ACAATC
*
23964427 TTCAACATATTCCACTGTTGAC-CAGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGTTG-CTCAGGGAGATAGGACTTACAATC
* *
23964471 TTCAACCTATTCCACTGCTGTTCAGGGAGATAGG
1 TTCAACCTATTCCACTGTTGCTCAGGGAGATAGG
23964505 GCTGGGGTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
44 66 0.96
45 3 0.04
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
TTCAACCTATTCCACTGTTGCTCAGGGAGATAGGACTTACAATC
Found at i:23964566 original size:88 final size:87
Alignment explanation
Indices: 23964515--23965077 Score: 727
Period size: 88 Copynumber: 6.4 Consensus size: 87
23964505 GCTGGGGTTA
* *
23964515 TCGATCTGCTTCACTGTCGGTGCAGAAAGGTAAGATCTGCTATTTTTAACCTACTT-CGCTACAA
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTA-TTCCGCTACAA
*
23964579 CCCAGGAAGGCAAGGCTGGTGTCT
65 -CCAGGGAGGCAAGGCTGGTGTCT
* **
23964603 TCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTATTCCGCTACAAC
*
23964668 CTAGGGAGGCAAGGTTGGTGTCT
66 C-AGGGAGGCAAGGCTGGTGTCT
* ** *
23964691 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTGCTCCCCTACAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTATTCCGCTACAA-
* *
23964756 CCAAGGAGGCAAGG-TTGTGTCT
65 CCAGGGAGGCAAGGCTGGTGTCT
* * * *** * *
23964778 TCGATCTACTTCGA-TGTCGGTGCAGGAAGGCAAGATCTACAATTTTTAACCTGCACCGTTGCAA
1 TCGATCTGCTTC-ACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTATTCCGCTACAA
23964842 CCTAGGGAGGCAAGGCTGGTGTCT
65 CC-AGGGAGGCAAGGCTGGTGTCT
* * * **
23964866 TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTATTCCGCTACAA-
*
23964931 CCAGGGAGGCAAGGCTAGTGTCT
65 CCAGGGAGGCAAGGCTGGTGTCT
* * *
23964954 TCGATCTCCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGTTCCGCTACAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTATTCCGCTACAA-
*
23965019 CCAGGGAGGCAAGGTTGGTGTCT
65 CCAGGGAGGCAAGGCTGGTGTCT
* * *
23965042 TCGATCTGTTTCACTGTCAGTGCGGGAAGGCAAGAT
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGAT
23965078 TTGTTGTCTT
Statistics
Matches: 426, Mismatches: 41, Indels: 16
0.88 0.08 0.03
Matches are distributed among these distances:
86 2 0.00
87 77 0.18
88 343 0.81
89 4 0.01
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (87 bp):
TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTATTCCGCTACAAC
CAGGGAGGCAAGGCTGGTGTCT
Found at i:23964722 original size:44 final size:44
Alignment explanation
Indices: 23964581--23964724 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 44
23964571 CGCTACAACC
*
23964581 CAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGGTTGGTGTCTTCAATCTGCTTCACTGTCGGTG
* * * * * * * * * ***
23964625 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCT-AC-AAC
1 CAGGAAGGCAAGGT-TGGTGTCTTCAATCTGCTTCACTGTCGGTG
* *
23964668 CTAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCACTGTCGGTG
1 C-AGGAAGGCAAGGTTGGTGTCTTCAATCTGCTTCACTGTCGGTG
23964713 CAGGAAGGCAAG
1 CAGGAAGGCAAG
23964725 ATCTACTATT
Statistics
Matches: 68, Mismatches: 28, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
43 16 0.24
44 35 0.51
45 17 0.25
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGTTGGTGTCTTCAATCTGCTTCACTGTCGGTG
Found at i:23964862 original size:263 final size:264
Alignment explanation
Indices: 23964515--23965077 Score: 869
Period size: 263 Copynumber: 2.1 Consensus size: 264
23964505 GCTGGGGTTA
* * * * **
23964515 TCGATCTGCTTCACTGTCGGTGCAGAAAGGTAAGATCTGCTATTTTTAACCTACTTCGCTACAAC
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTACAATTTTTAACCTACACCGCTACAAC
*
23964580 CCAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTA
66 CCAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCAA
* * * *
23964645 TTTTTAACCTGCTCCGCTACAACCTAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCACTGTCG
131 TTTTTAACCTGCTCCGCTACAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTCCTTCACTGTCG
*
23964710 GTGCAGGAAGGCAAGATCTACTATTTTTAACCTGCTCCCCTACAACCCAAGGAGGCAAGGTT-GT
196 ATGCAGGAAGGCAAGATCTACTATTTTTAACCTGCTCCCCTACAACCCAAGGAGGCAAGGTTGGT
23964774 GTCT
261 GTCT
* * * *
23964778 TCGATCTACTTCGA-TGTCGGTGCAGGAAGGCAAGATCTACAATTTTTAACCTGCACCGTTGCAA
1 TCGATCTGCTTC-ACTGTCGGTGCAGGAAGGCAAGATCTACAATTTTTAACCTACACCGCTACAA
* * *
23964842 CCTAGGGAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCA
65 CCCAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCA
23964907 ATTTTTAACCTGCTCCGCTACAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTCCTTCACTGTC
130 ATTTTTAACCTGCTCCGCTACAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTCCTTCACTGTC
* * * *
23964972 GATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGTTCCGCTACAACCCAGGGAGGCAAGGTTGG
195 GATGCAGGAAGGCAAGATCTACTATTTTTAACCTGCTCCCCTACAACCCAAGGAGGCAAGGTTGG
23965037 TGTCT
260 TGTCT
* * *
23965042 TCGATCTGTTTCACTGTCAGTGCGGGAAGGCAAGAT
1 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGAT
23965078 TTGTTGTCTT
Statistics
Matches: 270, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
263 233 0.86
264 37 0.14
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (264 bp):
TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTACAATTTTTAACCTACACCGCTACAAC
CCAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCAA
TTTTTAACCTGCTCCGCTACAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTCCTTCACTGTCG
ATGCAGGAAGGCAAGATCTACTATTTTTAACCTGCTCCCCTACAACCCAAGGAGGCAAGGTTGGT
GTCT
Found at i:23970468 original size:25 final size:26
Alignment explanation
Indices: 23970433--23970489 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
23970423 CATTTTCTCG
* * *
23970433 AATTTTTTCAAGGG-AAAATTGTTAT
1 AATTTTATCAAGGGTAAAATTGTCAA
23970458 AATTTTATCAAGGGTAAAATTGTCAA
1 AATTTTATCAAGGGTAAAATTGTCAA
23970484 AATTTT
1 AATTTT
23970490 GGTGAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (26 bp):
AATTTTATCAAGGGTAAAATTGTCAA
Found at i:23975149 original size:17 final size:17
Alignment explanation
Indices: 23975127--23975162 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
23975117 CCTTGACAAC
23975127 CTCCTTAACAGGCAGCT
1 CTCCTTAACAGGCAGCT
23975144 CTCCTTAACAGGCAGCT
1 CTCCTTAACAGGCAGCT
23975161 CT
1 CT
23975163 AGAAGAGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (17 bp):
CTCCTTAACAGGCAGCT
Found at i:23975674 original size:10 final size:10
Alignment explanation
Indices: 23975639--23975681 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
23975629 AAACAATTCT
23975639 ATAACAAAAA
1 ATAACAAAAA
*
23975649 GATAACAAAAC
1 -ATAACAAAAA
*
23975660 TTAACAAAAA
1 ATAACAAAAA
23975670 ATAACAACAAA
1 ATAACAA-AAA
23975681 A
1 A
23975682 GCAAAATGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.72, C:0.14, G:0.02, T:0.12
Consensus pattern (10 bp):
ATAACAAAAA
Found at i:23976549 original size:16 final size:18
Alignment explanation
Indices: 23976510--23976543 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23976500 TAAGTTTCTA
23976510 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
23976527 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
23976544 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:23976645 original size:26 final size:27
Alignment explanation
Indices: 23976616--23976674 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
23976606 ATTAAAAACT
*
23976616 TTAAATATATATATAAT-TATTA-AATA
1 TTAAATATA-ATATAATATAATATAATA
23976642 TT-AATATAATATAATATAATATAATA
1 TTAAATATAATATAATATAATATAATA
23976668 -TAAATAT
1 TTAAATAT
23976675 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 7 0.24
25 11 0.38
26 11 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAAATATAATATAATATAATATAATA
Found at i:23976653 original size:5 final size:5
Alignment explanation
Indices: 23976619--23976670 Score: 63
Period size: 5 Copynumber: 10.4 Consensus size: 5
23976609 AAAAACTTTA
*
23976619 AATAT ATATAT AAT-T ATTA- AATATT AATAT AATAT AATAT AATAT AATAT
1 AATAT A-ATAT AATAT AATAT AATA-T AATAT AATAT AATAT AATAT AATAT
23976669 AA
1 AA
23976671 ATATTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 6 0.15
5 26 0.63
6 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:23977058 original size:4 final size:4
Alignment explanation
Indices: 23977049--23977203 Score: 135
Period size: 4 Copynumber: 38.2 Consensus size: 4
23977039 GGGCAGAAGG
*
23977049 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGGAGA GGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A-GA-A AGAA
* * *
23977099 AGAA AG-A A-AA AGAA GGAA AGAAA AGGAA AG-G AGAA GAGAA AAAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AG-AA A-GAA AGAA AGAA -AGAA AGAA AGAA
23977147 AGAA AG-A AG-A AG-A AGAAA AGGAAA AGAGA AGAA A-AA AGAA AGAA
1 AGAA AGAA AGAA AGAA AG-AA A-G-AA AGA-A AGAA AGAA AGAA AGAA
*
23977191 AGAA GGAA AGAA A
1 AGAA AGAA AGAA A
23977204 AGGAAAGGAG
Statistics
Matches: 128, Mismatches: 10, Indels: 26
0.78 0.06 0.16
Matches are distributed among these distances:
3 18 0.14
4 82 0.64
5 21 0.16
6 7 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:23977119 original size:48 final size:46
Alignment explanation
Indices: 23977050--23977232 Score: 131
Period size: 48 Copynumber: 3.8 Consensus size: 46
23977040 GGCAGAAGGA
* *
23977050 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-GAG-AG
1 GAAAGAAAG-AA-AAAGAAGGAAAGAAAGAAAGAAAGAAAGAAAGAAG
* * *
23977096 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG-GAGAAGAGAAAAAAA
1 GAAAGAAAGAAAAAGAAGGAAAG-AAA-GAAAGAAAGAA-AGAAAGAAG
* * *
23977144 GAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAA-AAAGAAAGAAA
1 GAAAGAAAGAAAAAGAAGGAAA-G-AAAGA-AAGAAAGAAAGAAAGAAG
* * * *
23977192 GAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAA
1 GAAAGAAAGAAAAAG-AAGGA-AAGA-AAGAAAGAAAGAAA
23977233 AAGAAGAGGG
Statistics
Matches: 110, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
44 11 0.10
45 9 0.08
46 16 0.15
47 1 0.01
48 49 0.45
49 21 0.19
50 3 0.03
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (46 bp):
GAAAGAAAGAAAAAGAAGGAAAGAAAGAAAGAAAGAAAGAAAGAAG
Found at i:23977194 original size:82 final size:80
Alignment explanation
Indices: 23977045--23977239 Score: 274
Period size: 82 Copynumber: 2.4 Consensus size: 80
23977035 TGGGGGGCAG
* * *
23977045 AAGGAGAA-AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAAAA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAG-AAG-AAGAAAGAAAGAAAAGAGAAGAAAGAAAGAAAA
23977109 AGAAGGAAAGAAAAGGA
64 AGAAGGAAAGAAAAGGA
23977126 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAG-AAGAAAAGGAAAAGAGAAGAAA-AAAGAAAG
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAG-AAA-GAAAAGAGAAGAAAGAAAG-AA-
23977189 AAAGAAGGAAAGAAAAGGA
62 AAAGAAGGAAAGAAAAGGA
23977208 AAGGAGAAGAGAAAAAAA-AAAGAAA-AAGAAGA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGA
23977240 GGGAAGGAAG
Statistics
Matches: 105, Mismatches: 3, Indels: 12
0.88 0.03 0.10
Matches are distributed among these distances:
79 3 0.03
80 16 0.15
81 32 0.30
82 54 0.51
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (80 bp):
AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAGAAAGAAAAGAGAAGAAAGAAAGAAAAAG
AAGGAAAGAAAAGGA
Found at i:23977252 original size:44 final size:41
Alignment explanation
Indices: 23977045--23977240 Score: 196
Period size: 41 Copynumber: 4.8 Consensus size: 41
23977035 TGGGGGGCAG
* *
23977045 AAGGAGAA-AGAAAGAAAGAAAGAAAGAAAGAA-AGAAAGAAAGA
1 AAGGAGAAGAGAAA-AAAAAAAGAAAG-AAGAAGAG-AA-AAGGA
* *
23977088 AAGGAG-AG-GAAAGAAAGAA-AAAGAAGGAA-AGAAAAGGA
1 AAGGAGAAGAGAAAAAAAAAAGAAAGAA-GAAGAGAAAAGGA
23977126 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAGAAAAGGA
1 AAGGAGAAGAGAAAAAAA-AAAGAAAGAAGAAG-AGAAAAGGA
* *
23977169 AAAGAG-A-AGAAAAAAGAAAGAAAGAAGGAA-AGAAAAGGA
1 AAGGAGAAGAGAAAAAAAAAAGAAAGAA-GAAGAGAAAAGGA
23977208 AAGGAGAAGAGAAAAAAAAAAGAAA-AAGAAGAG
1 AAGGAGAAGAGAAAAAAAAAAGAAAGAAGAAGAG
23977241 GGAAGGAAGG
Statistics
Matches: 131, Mismatches: 10, Indels: 27
0.78 0.06 0.16
Matches are distributed among these distances:
38 10 0.08
39 23 0.18
40 31 0.24
41 35 0.27
42 12 0.09
43 20 0.15
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (41 bp):
AAGGAGAAGAGAAAAAAAAAAGAAAGAAGAAGAGAAAAGGA
Found at i:23981799 original size:27 final size:27
Alignment explanation
Indices: 23981729--23981800 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
23981719 TTTTATTTTT
* * *
23981729 TTAT-ATATTTTGGTAAATAAAATATA
1 TTATAATATTTTGATAAATAAAAAAAA
*
23981755 -TATATATATATT-AGTAAATAAAAAAAA
1 TTATA-ATATTTTGA-TAAATAAAAAAAA
23981782 TTATAATATTTTGATAAAT
1 TTATAATATTTTGATAAAT
23981801 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
25 3 0.08
27 28 0.78
28 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (27 bp):
TTATAATATTTTGATAAATAAAAAAAA
Found at i:23999192 original size:16 final size:16
Alignment explanation
Indices: 23999174--23999238 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
23999164 TTCGCTATAT
* *
23999174 TGGATTAGAGGTGTAT
1 TGGAATAGAGGTGTAA
*
23999190 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
*
23999206 TGGAATAGAAGTGTAA
1 TGGAATAGAGGTGTAA
23999222 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
23999238 T
1 T
23999239 AGCAAATCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.34, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:23999493 original size:18 final size:17
Alignment explanation
Indices: 23999472--23999506 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23999462 TTATTATTAA
*
23999472 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
23999490 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
23999507 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:23999850 original size:120 final size:120
Alignment explanation
Indices: 23999637--23999852 Score: 314
Period size: 120 Copynumber: 1.8 Consensus size: 120
23999627 NNNNNNNNNN
* *
23999637 ATCATAATATATGATACTGTAAAATATAAATTAACATAATAATTATTAAATATATTATAATTAAA
1 ATCATAATATATGATACTATAAAAGATAAATTAACATAATAATTATTAAATATATTATAATTAAA
*
23999702 ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAA
66 ATATATAATTTAATAAAATTCTAAATAATTAATATTCTTATATGAATTTACTCAA
* *
23999757 ATCATAATATATGATACTATAAAAGA-AAATTTGAA-ATAATTCA-TATTAAATATATTTTAATT
1 ATCATAATATATGATACTATAAAAGATAAA-TT-AACATAA-TAATTATTAAATATATTATAATT
*
23999819 AAAATATATGATTTAATAAAATT-TAAAATAATTA
63 AAAATATATAATTTAATAAAATTCT-AAATAATTA
23999853 TAACCAATAA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
119 4 0.05
120 78 0.91
121 4 0.05
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (120 bp):
ATCATAATATATGATACTATAAAAGATAAATTAACATAATAATTATTAAATATATTATAATTAAA
ATATATAATTTAATAAAATTCTAAATAATTAATATTCTTATATGAATTTACTCAA
Found at i:23999953 original size:91 final size:91
Alignment explanation
Indices: 23999858--24000064 Score: 285
Period size: 91 Copynumber: 2.3 Consensus size: 91
23999848 AATTATAACC
* * *
23999858 AATAAATTATATTT-TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 AATAAATT-TATTTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
23999921 TAATATATAATTTCATAAAATTCTTGAT
64 TAATATATAATTTCATAAAATTCTTAAT
* * *
23999949 AATAAATTTTTTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGTG
1 AATAAATTTATTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
24000014 ATATATAATTTCATAAAATTCTTAAT
66 ATATATAATTTCATAAAATTCTTAAT
*
24000040 AATAAAATGTT-CTTATATGAATTTA
1 AAT-AAAT-TTATTTATATGAATTTA
24000065 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
90 4 0.04
91 78 0.75
92 20 0.19
93 2 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
AATAAATTTATTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAAT
Found at i:23999980 original size:47 final size:47
Alignment explanation
Indices: 23999924--24000064 Score: 123
Period size: 44 Copynumber: 3.0 Consensus size: 47
23999914 TTAATAATAA
*
23999924 TATATAATTTCATAAAATTCTTGATAATAAATTTTTTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTTTTATATGAATT
* ** * * *
23999971 TATACAA-TT--TAAAATAATTAATATTAAATATAATTTAATAGTG-A--
1 TATATAATTTCATAAAATTCTTAATAATAAAT-T-TTTTTATA-TGAATT
* *
24000015 TATATAATTTCATAAAATTCTTAATAATAAAATGTTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAAT-AAATTTTTTTATATGAATT
24000063 TA
1 TA
24000065 CTAAAATCAA
Statistics
Matches: 69, Mismatches: 15, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
44 22 0.32
45 5 0.07
46 15 0.22
47 21 0.30
48 6 0.09
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (47 bp):
TATATAATTTCATAAAATTCTTAATAATAAATTTTTTTATATGAATT
Found at i:24000024 original size:44 final size:43
Alignment explanation
Indices: 23999882--24000024 Score: 103
Period size: 44 Copynumber: 3.2 Consensus size: 43
23999872 TATGAATTTG
* *
23999882 TATAATTTAAAATAA-TAATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAA-TATTAAATATAATTTAAT-ATGATA
** * * * *
23999926 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTTTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAATTTAATATG-A--TA
*
23999973 TACAATTTAAAATAATTAATATTAAATATAATTTAATAGTGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATA-TGATA
24000017 TATAATTT
1 TATAATTT
24000025 CATAAAATTC
Statistics
Matches: 73, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
44 32 0.44
45 9 0.12
46 10 0.14
47 20 0.27
48 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATATGATA
Found at i:24001485 original size:11 final size:11
Alignment explanation
Indices: 24001469--24001495 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
24001459 AAAACTCAAT
24001469 ACAAAAGTTTC
1 ACAAAAGTTTC
24001480 ACAAAAGTTTC
1 ACAAAAGTTTC
24001491 ACAAA
1 ACAAA
24001496 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:24005982 original size:41 final size:40
Alignment explanation
Indices: 24005904--24005982 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
24005894 GATTGAACAT
*
24005904 AATTAAAGGTTGAACATAATTATTATTATTTGAATAATATC
1 AATTAAAGGTTGAACATAATTATTATTATAT-AATAATATC
24005945 AATTAAAGGTTGAACATAATTATATATTAGTAT-ATAAT
1 AATTAAAGGTTGAACATAATTAT-TATTA-TATAATAAT
24005983 TTGTATGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
41 28 0.80
42 5 0.14
43 2 0.06
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.41
Consensus pattern (40 bp):
AATTAAAGGTTGAACATAATTATTATTATATAATAATATC
Found at i:24006823 original size:2 final size:2
Alignment explanation
Indices: 24006818--24006843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24006808 TTTTTCTTTA
24006818 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
24006844 TGCATTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24011066 original size:36 final size:35
Alignment explanation
Indices: 24011013--24011089 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 35
24011003 TAACCTTATC
* *
24011013 AATTGATTACTTGAATTTAATAGCTAATAACTAATT
1 AATTGATTAATTGAATTTAATAACTAAT-ACTAATT
* * * *
24011049 AATTGATTAATTTAATTTGATAACTCATACTGATT
1 AATTGATTAATTGAATTTAATAACTAATACTAATT
24011084 AATTGA
1 AATTGA
24011090 ACTTGTTAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 12 0.34
36 23 0.66
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (35 bp):
AATTGATTAATTGAATTTAATAACTAATACTAATT
Found at i:24015428 original size:31 final size:31
Alignment explanation
Indices: 24015393--24015460 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
24015383 TACACTGGTA
24015393 GTCACCCAACTATT-AGTAAA-TTTCATTTTTG
1 GTCACCCAACTATTCA--AAATTTTCATTTTTG
24015424 GTCACCCAACTATTCAAAATTTTCATTTTTG
1 GTCACCCAACTATTCAAAATTTTCATTTTTG
24015455 GTCACC
1 GTCACC
24015461 AACCGTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
30 3 0.09
31 31 0.89
32 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.40
Consensus pattern (31 bp):
GTCACCCAACTATTCAAAATTTTCATTTTTG
Found at i:24015470 original size:30 final size:31
Alignment explanation
Indices: 24015413--24015470 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
24015403 TATTAGTAAA
*
24015413 TTTCATTTTTGGTCACCCAACTATTCAAAAT
1 TTTCATTTTTGGTCACCCAACCATTCAAAAT
*
24015444 TTTCATTTTTGGTCA-CCAACCGTTCAA
1 TTTCATTTTTGGTCACCCAACCATTCAA
24015471 GTACTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (31 bp):
TTTCATTTTTGGTCACCCAACCATTCAAAAT
Found at i:24024444 original size:21 final size:21
Alignment explanation
Indices: 24024419--24024458 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
24024409 AAATAATATT
*
24024419 AAATTTTTATATATTTTTTTA
1 AAATTTTCATATATTTTTTTA
24024440 AAATTTTCATATATTTTTT
1 AAATTTTCATATATTTTTT
24024459 ATTTTTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
AAATTTTCATATATTTTTTTA
Found at i:24027377 original size:25 final size:25
Alignment explanation
Indices: 24027343--24027426 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
24027333 AACTTTGGAG
24027343 TTTTTT-TTTTATATTTTTAAGTTT
1 TTTTTTATTTTATATTTTTAAGTTT
* **
24027367 TTTTTTATTTTGA-ATTTTAAAGAGT
1 TTTTTTATTTT-ATATTTTTAAGTTT
* *
24027392 TTTTTTATTTT-TATTTTTTA-TGTA
1 TTTTTTATTTTATATTTTTAAGT-TT
24027416 TTTTTTATTTT
1 TTTTTTATTTT
24027427 TAAAAATATA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
24 23 0.48
25 24 0.50
26 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (25 bp):
TTTTTTATTTTATATTTTTAAGTTT
Found at i:24027443 original size:23 final size:23
Alignment explanation
Indices: 24027417--24027475 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
24027407 TTTTATGTAT
24027417 TTTTTAT-TTTTAAAAATATAAAA
1 TTTTTATCTTTTAAAAATAT-AAA
* *
24027440 TTTTGATCTTTTTAAAATATAAA
1 TTTTTATCTTTTAAAAATATAAA
*
24027463 TTTTTATGTTTTA
1 TTTTTATCTTTTA
24027476 TTTAAAAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (23 bp):
TTTTTATCTTTTAAAAATATAAA
Found at i:24027919 original size:16 final size:15
Alignment explanation
Indices: 24027903--24027957 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
24027893 TTTTGGAAAT
24027903 TTTTATTTTTTTTAA
1 TTTTATTTTTTTTAA
*
24027918 TTTTAGATTTTTTTAA
1 TTTTA-TTTTTTTTAA
*
24027934 TTTTTCATGTTTTTT-A
1 -TTTT-ATTTTTTTTAA
24027950 TTTTATTT
1 TTTTATTT
24027958 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 3 0.09
15 9 0.27
16 10 0.30
17 10 0.30
18 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (15 bp):
TTTTATTTTTTTTAA
Found at i:24027992 original size:23 final size:25
Alignment explanation
Indices: 24027954--24027999 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
24027944 TTTTTATTTT
24027954 ATTTAAAAAAATTAT-AATTTTTGA
1 ATTTAAAAAAATTATAAATTTTTGA
24027978 ATTTAAAAAAA-TATAAATTTTT
1 ATTTAAAAAAATTATAAATTTTT
24028000 ATGTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTAAAAAAATTATAAATTTTTGA
Found at i:24032279 original size:2 final size:2
Alignment explanation
Indices: 24032272--24032303 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24032262 ATTGAGTGGT
24032272 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24032304 ATTTACTTCT
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):
TA
Found at i:24035966 original size:13 final size:13
Alignment explanation
Indices: 24035948--24035972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24035938 AAATTCAATG
24035948 TCAATTTCATATA
1 TCAATTTCATATA
24035961 TCAATTTCATAT
1 TCAATTTCATAT
24035973 CCAAACATAT
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:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAATTTCATATA
Found at i:24036832 original size:34 final size:34
Alignment explanation
Indices: 24036789--24036908 Score: 195
Period size: 34 Copynumber: 3.5 Consensus size: 34
24036779 CATATAACAA
* * *
24036789 ATAATCCATGTAAATTATGTATTTCATGTAGCTT
1 ATAAACCATGTAAATCATGTATTTCATGTAACTT
*
24036823 ATAAACCATGTAAATCATGAATTTCATGTAACTT
1 ATAAACCATGTAAATCATGTATTTCATGTAACTT
*
24036857 ATAAACTATGTAAATCATGTATTTCATGTAACTT
1 ATAAACCATGTAAATCATGTATTTCATGTAACTT
24036891 ATAAACCATGTAAATCAT
1 ATAAACCATGTAAATCAT
24036909 ATAACTTTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 79 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (34 bp):
ATAAACCATGTAAATCATGTATTTCATGTAACTT
Found at i:24041235 original size:21 final size:21
Alignment explanation
Indices: 24041209--24041263 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
24041199 AACAGTGGTG
*
24041209 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
24041230 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
24041251 GCAGTGAGATTAG
1 GCGGTGAGATTAG
24041264 AAACAGCGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:24048543 original size:22 final size:22
Alignment explanation
Indices: 24048500--24048544 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
24048490 TTACAGTTAT
* *
24048500 AGAATAGAACAAATATAGATGC
1 AGAACAGAACAAATACAGATGC
* *
24048522 AGAACAGATCAAATACATATGC
1 AGAACAGAACAAATACAGATGC
24048544 A
1 A
24048545 ATTTCCTACC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (22 bp):
AGAACAGAACAAATACAGATGC
Found at i:24049976 original size:27 final size:27
Alignment explanation
Indices: 24049916--24049997 Score: 71
Period size: 26 Copynumber: 3.1 Consensus size: 27
24049906 AAGAAAAGGA
* * * *
24049916 AAGAAGGAAAAAAAATGATAGACCAAAG
1 AAGAAAGAAAAAAAATGTTTGA-AAAAG
24049944 AA-AAAGAAAAAAAATGTTTGAAAAAG
1 AAGAAAGAAAAAAAATGTTTGAAAAAG
* *
24049970 AAGAAAG-TAAAAGAT-TTTGGAAAAAG
1 AAGAAAGAAAAAAAATGTTT-GAAAAAG
24049996 AA
1 AA
24049998 AGACTTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
25 3 0.07
26 21 0.46
27 20 0.43
28 2 0.04
ACGTcount: A:0.65, C:0.02, G:0.20, T:0.13
Consensus pattern (27 bp):
AAGAAAGAAAAAAAATGTTTGAAAAAG
Found at i:24050403 original size:20 final size:19
Alignment explanation
Indices: 24050360--24050396 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
24050350 GGAGAAAGAT
24050360 TAATTTATTTTCCTATAAAA
1 TAATTTATTTT-CTATAAAA
24050380 TAATTTATTTT-TATAAA
1 TAATTTATTTTCTATAAA
24050397 GTATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTTATTTTCTATAAAA
Found at i:24059806 original size:20 final size:20
Alignment explanation
Indices: 24059768--24059807 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
24059758 TTTCTCAACC
* *
24059768 TCAAAATCTTCCATAAACAT
1 TCAAAAACTTCAATAAACAT
*
24059788 TCAAAAACTTCAATTAACAT
1 TCAAAAACTTCAATAAACAT
24059808 AAATGGTAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (20 bp):
TCAAAAACTTCAATAAACAT
Found at i:24063588 original size:31 final size:30
Alignment explanation
Indices: 24063543--24063630 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 30
24063533 AAATATTTTA
* * *
24063543 TTTTTTTATTTTTTAATTTTAAAATACATAC
1 TTTTTTAAATTTTAAATTTTAAAATAC-TAC
*
24063574 TTTTATTAAATTTTAAATTTTTTAAA-ACTAC
1 TTTT-TTAAATTTTAAA-TTTTAAAATACTAC
*
24063605 TTTTTTAATTTTTAAAATTTTAAAAT
1 TTTTTTAAATTTT-AAATTTTAAAAT
24063631 TTTTTTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
30 15 0.32
31 14 0.30
32 11 0.23
33 7 0.15
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTTTAAATTTTAAATTTTAAAATACTAC
Found at i:24063623 original size:38 final size:38
Alignment explanation
Indices: 24063581--24063656 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
24063571 TACTTTTATT
24063581 AAATTTT-AAA-TTTTTTAAAACTACTTTTTTAATTTTTA
1 AAATTTTAAAATTTTTTTAAAA-TAC-TTTTTAATTTTTA
24063619 AAATTTTAAAATTTTTTTAAAATACTTTTTAATTTTTA
1 AAATTTTAAAATTTTTTTAAAATACTTTTTAATTTTTA
24063657 TTTTAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
38 20 0.56
39 6 0.17
40 10 0.28
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (38 bp):
AAATTTTAAAATTTTTTTAAAATACTTTTTAATTTTTA
Found at i:24064359 original size:27 final size:27
Alignment explanation
Indices: 24064329--24064386 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
24064319 AACAGAATTG
24064329 CCAGAATTGCCACAGAAGACGAATCGA
1 CCAGAATTGCCACAGAAGACGAATCGA
24064356 CCAGAATTGCCACAGAAGACGAATCGA
1 CCAGAATTGCCACAGAAGACGAATCGA
24064383 CCAG
1 CCAG
24064387 TTCTATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.28, G:0.22, T:0.10
Consensus pattern (27 bp):
CCAGAATTGCCACAGAAGACGAATCGA
Found at i:24068800 original size:9 final size:9
Alignment explanation
Indices: 24068786--24068813 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
24068776 TAAAATTCAC
24068786 CCACTTTTT
1 CCACTTTTT
24068795 CCACTTTTT
1 CCACTTTTT
24068804 CCACTTTTT
1 CCACTTTTT
24068813 C
1 C
24068814 ACACCACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.36, G:0.00, T:0.54
Consensus pattern (9 bp):
CCACTTTTT
Found at i:24069311 original size:17 final size:18
Alignment explanation
Indices: 24069282--24069316 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
24069272 TTCTCCTAAA
*
24069282 TTTCAATTTTATTTAATT
1 TTTCAATTTTATTGAATT
24069300 TTTCAA-TTTATTGAATT
1 TTTCAATTTTATTGAATT
24069317 ATTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTCAATTTTATTGAATT
Found at i:24071533 original size:22 final size:21
Alignment explanation
Indices: 24071495--24071544 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
24071485 TGAAGAATGT
*
24071495 AATTTTATGCTATTTTACATTA
1 AATTTTATGCTAATTTA-ATTA
24071517 AATTTT-TGCATAATTTAATT-
1 AATTTTATGC-TAATTTAATTA
24071537 -ATTTTATG
1 AATTTTATG
24071545 TGACATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 5 0.20
20 2 0.08
21 6 0.24
22 12 0.48
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (21 bp):
AATTTTATGCTAATTTAATTA
Found at i:24075292 original size:33 final size:33
Alignment explanation
Indices: 24075250--24075315 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
24075240 ATTCAAGTAA
24075250 ATCATCCCCATCAGTAGGAGATTCCAAAACCTC
1 ATCATCCCCATCAGTAGGAGATTCCAAAACCTC
24075283 ATCATCCCCATCAGTAGGAGATTCCAAAACCTC
1 ATCATCCCCATCAGTAGGAGATTCCAAAACCTC
24075316 TTCCATACTA
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:0.33, C:0.33, G:0.12, T:0.21
Consensus pattern (33 bp):
ATCATCCCCATCAGTAGGAGATTCCAAAACCTC
Found at i:24083932 original size:20 final size:20
Alignment explanation
Indices: 24083881--24083921 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
24083871 CTACCATGTG
24083881 AATTTAACCCTTAAAACCTT
1 AATTTAACCCTTAAAACCTT
*
24083901 AATTTAACCCTTGAAACCTT
1 AATTTAACCCTTAAAACCTT
24083921 A
1 A
24083922 GTTTGAGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.34
Consensus pattern (20 bp):
AATTTAACCCTTAAAACCTT
Found at i:24086138 original size:92 final size:92
Alignment explanation
Indices: 24085976--24086174 Score: 317
Period size: 92 Copynumber: 2.2 Consensus size: 92
24085966 GCATCACAAG
* *
24085976 TTAACCAAAATGACACAATCTAGCAAGGTATCCAATGGTACCAAGCCAAGATAACATCCATAACT
1 TTAA-CAAAATGACACAATCTAGCAAGGTATCAAATGGTACCAAACCAAGATAACATCCATAACT
*
24086041 TATACAAGCCAATTCACCAACTAACTAT
65 TATACAAGCCAATTCACCAACTAACCAT
* * * * *
24086069 TTAACAAAATGACACCATTTAGCAAGGTATCAAATGGTACTAAACCAAGATAATATCTATAACTT
1 TTAACAAAATGACACAATCTAGCAAGGTATCAAATGGTACCAAACCAAGATAACATCCATAACTT
24086134 ATACAAGCCAATTCACCAACTAACCAT
66 ATACAAGCCAATTCACCAACTAACCAT
24086161 TTAACAAAATGACA
1 TTAACAAAATGACA
24086175 TTACAATTCA
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
92 94 0.96
93 4 0.04
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (92 bp):
TTAACAAAATGACACAATCTAGCAAGGTATCAAATGGTACCAAACCAAGATAACATCCATAACTT
ATACAAGCCAATTCACCAACTAACCAT
Found at i:24101304 original size:2 final size:2
Alignment explanation
Indices: 24101299--24101325 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24101289 CTCTCCATCC
24101299 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
24101326 ACCTTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24102726 original size:12 final size:12
Alignment explanation
Indices: 24102709--24102737 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
24102699 ACATGCCTAC
24102709 ACATGTATATCT
1 ACATGTATATCT
24102721 ACATGTATATCT
1 ACATGTATATCT
24102733 ACATG
1 ACATG
24102738 GAGGAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (12 bp):
ACATGTATATCT
Found at i:24109257 original size:25 final size:25
Alignment explanation
Indices: 24109245--24109298 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
24109235 AATAGTTTTA
24109245 TAAACCATATTAAGAAGAATTATTT
1 TAAACCATATTAAGAAGAATTATTT
* *
24109270 TAAACCATATTAAGAGGAACTATTT
1 TAAACCATATTAAGAAGAATTATTT
24109295 TAAA
1 TAAA
24109299 TTGTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (25 bp):
TAAACCATATTAAGAAGAATTATTT
Found at i:24114655 original size:21 final size:22
Alignment explanation
Indices: 24114624--24114708 Score: 93
Period size: 21 Copynumber: 3.9 Consensus size: 22
24114614 ATTAAAGCTT
*
24114624 CTAATACGGTGTAGGTAAACCA
1 CTAATACGGTGTAGATAAACCA
**
24114646 CTAAT-CGGTGTAGATAAAATTTA
1 CTAATACGGTGTAGAT-AAA-CCA
* *
24114669 CTAATACAGTGTGGATAAACCA
1 CTAATACGGTGTAGATAAACCA
24114691 CTAA-ACGGTGTAGATAAA
1 CTAATACGGTGTAGATAAA
24114709 AGTTGTTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 21 0.41
22 13 0.25
23 9 0.18
24 8 0.16
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (22 bp):
CTAATACGGTGTAGATAAACCA
Found at i:24114688 original size:45 final size:45
Alignment explanation
Indices: 24114624--24114709 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
24114614 ATTAAAGCTT
* *
24114624 CTAATACGGTGTAGGTAAACCACTAATCGGTGTAGATAAAATTTA
1 CTAATACAGTGTAGGTAAACCACTAAACGGTGTAGATAAAATTTA
24114669 CTAATACAGTGT-GGATAAACCACTAAACGGTGTAGATAAAA
1 CTAATACAGTGTAGG-TAAACCACTAAACGGTGTAGATAAAA
24114710 GTTGTTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (45 bp):
CTAATACAGTGTAGGTAAACCACTAAACGGTGTAGATAAAATTTA
Found at i:24114887 original size:34 final size:34
Alignment explanation
Indices: 24114810--24114891 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
24114800 TTTAACAAAA
* *
24114810 CAATACAGTAACAATCAATATGCTTACAACAGTT
1 CAATACAATAGCAATCAATATGCTTACAACAGTT
* * *
24114844 CAATACAATAGCAATTAATATGTTTATAACAGTT
1 CAATACAATAGCAATCAATATGCTTACAACAGTT
24114878 CAACT-CAATAGCAA
1 CAA-TACAATAGCAA
24114892 AAGTCATGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 41 0.98
35 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (34 bp):
CAATACAATAGCAATCAATATGCTTACAACAGTT
Found at i:24114901 original size:34 final size:33
Alignment explanation
Indices: 24114810--24114904 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 33
24114800 TTTAACAAAA
* * * *
24114810 CAATACAGTAACAATCAATATGCTTACAACAGTT
1 CAATACAATAGCAAT-AATATGTTTATAACAGTT
24114844 CAATACAATAGCAATTAATATGTTTATAACAGTT
1 CAATACAATAGCAA-TAATATGTTTATAACAGTT
24114878 CAACT-CAATAGCAA-AAGTCATGTTTAT
1 CAA-TACAATAGCAATAA-T-ATGTTTAT
24114905 TAAGTGTTCG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.04
33 1 0.02
34 48 0.91
35 2 0.04
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (33 bp):
CAATACAATAGCAATAATATGTTTATAACAGTT
Found at i:24117395 original size:13 final size:13
Alignment explanation
Indices: 24117377--24117407 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
24117367 NNNNNNNNNC
24117377 TATGAATTTATTT
1 TATGAATTTATTT
24117390 TATGAATTTATTT
1 TATGAATTTATTT
*
24117403 GATGA
1 TATGA
24117408 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:24117580 original size:50 final size:50
Alignment explanation
Indices: 24117502--24117644 Score: 205
Period size: 50 Copynumber: 2.8 Consensus size: 50
24117492 ATTTGGGTAA
*
24117502 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
24117552 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
24117602 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
24117645 TGTTATTATC
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 47 0.58
51 34 0.42
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:24132907 original size:2 final size:2
Alignment explanation
Indices: 24132902--24132962 Score: 97
Period size: 2 Copynumber: 30.5 Consensus size: 2
24132892 TTCAAAATTA
24132902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
24132944 AT AT ACT AC A- AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT A
24132963 ACTTAACACC
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
1 1 0.02
2 53 0.95
3 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:24138873 original size:50 final size:51
Alignment explanation
Indices: 24138789--24138920 Score: 169
Period size: 50 Copynumber: 2.6 Consensus size: 51
24138779 AAAGTGATGG
* *
24138789 TCACGTGTTTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATAA-G-
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGATAATGA
* * * *
24138839 TCGCATGTGTAGTATTATGTGCAGGCTACTACGTGTATCTGATGGTAATGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATAATGA
* *
24138890 TCATATGTGTAGTACTATGTGTAGGCTACTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA
24138921 TGTGAACTGA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 6 0.09
50 37 0.53
51 27 0.39
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATAATGA
Found at i:24138910 original size:12 final size:14
Alignment explanation
Indices: 24138893--24138924 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24138883 GTAATGATCA
24138893 TATGTGTA-G-TAC
1 TATGTGTAGGCTAC
24138905 TATGTGTAGGCTAC
1 TATGTGTAGGCTAC
24138919 TATGTG
1 TATGTG
24138925 AACTGAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 1 0.06
14 9 0.50
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (14 bp):
TATGTGTAGGCTAC
Found at i:24138980 original size:45 final size:45
Alignment explanation
Indices: 24138931--24139016 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
24138921 TGTGAACTGA
* * *
24138931 ACATCATTGATTAGTAAGGTGGCTGCTATGTGCTGATTCCATCGG
1 ACATCATTGATTAATAAGGTGGCTGCTATGCGCTGAATCCATCGG
*
24138976 ACATCATTGATTAATAAGGTGGTTGCTATGCGCTGAATCCA
1 ACATCATTGATTAATAAGGTGGCTGCTATGCGCTGAATCCA
24139017 CTGAGTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGCTGCTATGCGCTGAATCCATCGG
Found at i:24142743 original size:29 final size:29
Alignment explanation
Indices: 24142682--24142760 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
24142672 ATTCTTAAAT
* * *
24142682 GATAGTCACTGCCAGACTCTTGTTTGGCG
1 GATAGTCACTGACAGACTCTTGTTTGACA
* *
24142711 GATAGTCACTG-CAGACTCTTGATTTTATA
1 GATAGTCACTGACAGACTCTTG-TTTGACA
* *
24142740 GATATTCATTGACAGACTCTT
1 GATAGTCACTGACAGACTCTT
24142761 AAATAAAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.24
29 23 0.55
30 9 0.21
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (29 bp):
GATAGTCACTGACAGACTCTTGTTTGACA
Found at i:24145445 original size:43 final size:43
Alignment explanation
Indices: 24145384--24145542 Score: 201
Period size: 43 Copynumber: 3.7 Consensus size: 43
24145374 TTATGTGGAA
* *
24145384 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTCCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCTAC
* * *** * *
24145427 AAACGCCGCTAAAAAACATAACCTTTAGCGTTGCTTTTCCTAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCTAC
* * *
24145470 AAACGCCACTAAAGAACATCACCTTTAGTGGCACTTTCCCTAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCTAC
*
24145513 AAACGCTGCTAAAGAACATGACCTTTAGCG
1 AAACGCCGCTAAAGAACATGACCTTTAGCG
24145543 ACGCTTTTCC
Statistics
Matches: 94, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCTAC
Found at i:24145531 original size:86 final size:86
Alignment explanation
Indices: 24145384--24145552 Score: 248
Period size: 86 Copynumber: 2.0 Consensus size: 86
24145374 TTATGTGGAA
* * *
24145384 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAAAACATAAC
1 AAACGCCACTAAAGAACATCACCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAAAACATAAC
**
24145449 CTTTAGCGTTGCTTTTCCTAT
66 CTTTAGCGACGCTTTTCCTAT
* * * * *
24145470 AAACGCCACTAAAGAACATCACCTTTAGTGGCACTTTCCCTACAAACGCTGCTAAAGAACATGAC
1 AAACGCCACTAAAGAACATCACCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAAAACATAAC
24145535 CTTTAGCGACGCTTTTCC
66 CTTTAGCGACGCTTTTCC
24145553 CAAAAATGCT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (86 bp):
AAACGCCACTAAAGAACATCACCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAAAACATAAC
CTTTAGCGACGCTTTTCCTAT
Found at i:24146053 original size:66 final size:65
Alignment explanation
Indices: 24145926--24146055 Score: 154
Period size: 66 Copynumber: 2.0 Consensus size: 65
24145916 ATTCTGAAGC
* * ** * *
24145926 TGTAGCTGGAGTTCGTCATATTTTCTACTTGCCTTTGCTTCCCTCGCTACTGCCTCTGCTTTAAC
1 TGTAGCTGGAGTTCATCATATTTTCTA-TTGCCTCTGCTTCCCTCAATACTACCTCCGCTTTAAC
24145991 T
65 T
* *
24145992 TGTAGCTGGAGTTCATCATATTTTCT-TTAAGCCTCTGCTTCTCTCAATGCTACCTCCGCTTTAA
1 TGTAGCTGGAGTTCATCATATTTTCTATT--GCCTCTGCTTCCCTCAATACTACCTCCGCTTTAA
24146056 GTTGAGCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
64 2 0.04
66 52 0.96
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.42
Consensus pattern (65 bp):
TGTAGCTGGAGTTCATCATATTTTCTATTGCCTCTGCTTCCCTCAATACTACCTCCGCTTTAACT
Found at i:24151666 original size:43 final size:43
Alignment explanation
Indices: 24151619--24151720 Score: 195
Period size: 43 Copynumber: 2.4 Consensus size: 43
24151609 ATTCAAAGAT
24151619 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
24151662 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
*
24151705 TTACGTAAGTTATGAT
1 TTATGTAAGTTATGAT
24151721 CCAAAGTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (43 bp):
TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
Found at i:24151667 original size:9 final size:9
Alignment explanation
Indices: 24151619--24151718 Score: 59
Period size: 9 Copynumber: 11.6 Consensus size: 9
24151609 ATTCAAAGAT
24151619 TTATGTAAG
1 TTATGTAAG
*
24151628 TTATGATATG
1 TTATG-TAAG
* * *
24151638 ATATAT-AT
1 TTATGTAAG
24151646 TTATGT-A-
1 TTATGTAAG
24151653 TTATGTAAG
1 TTATGTAAG
24151662 TTATGTAAG
1 TTATGTAAG
*
24151671 TTATGATATG
1 TTATG-TAAG
* * *
24151681 ATATAT-AT
1 TTATGTAAG
24151689 TTATGT-A-
1 TTATGTAAG
24151696 TTATGTAAG
1 TTATGTAAG
*
24151705 TTACGTAAG
1 TTATGTAAG
24151714 TTATG
1 TTATG
24151719 ATCCAAAGTT
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
7 12 0.17
8 12 0.17
9 33 0.48
10 12 0.17
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:24155912 original size:71 final size:72
Alignment explanation
Indices: 24155831--24156048 Score: 217
Period size: 71 Copynumber: 3.1 Consensus size: 72
24155821 AAATGGTTCC
*
24155831 ACTTAATATCAAAACTCAATAAATTGAACTAAA-TAACCTTTTTAAAAATTCATAATTGAACAAA
1 ACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAAACAAA
*
24155895 CATTTTT
66 CAATTTT
** ** * * * *
24155902 ACTTAATATCAAATTTCAATAAATCAAACTAAATTAAGC-TTTTGAAAATGT-ATAACTAAATAA
1 ACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAAT-TCATAATTAAACAA
**** *
24155965 ATGGGTTC
65 ACAATTTT
* * * * **
24155973 GCGTAATATAAAAACTTAATAAATTGAACTAAATTAACCTTTTTAAAAACACATAATTAAACAAA
1 ACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAAACAAA
24156038 CAATTTT
66 CAATTTT
24156045 ACTT
1 ACTT
24156049 GATAATTAAT
Statistics
Matches: 108, Mismatches: 35, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
71 80 0.74
72 28 0.26
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (72 bp):
ACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAAACAAA
CAATTTT
Found at i:24158013 original size:21 final size:19
Alignment explanation
Indices: 24157988--24158035 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
24157978 GTGGGAAATT
*
24157988 TTTAGGGGAAAACTTTAAGGA
1 TTTAGGGGAAAA--TAAAGGA
24158009 TTTA-GGGAAAATAAAGGA
1 TTTAGGGGAAAATAAAGGA
*
24158027 TTTCGGGGA
1 TTTAGGGGA
24158036 TATGAGTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 9 0.38
19 4 0.17
20 7 0.29
21 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.31, T:0.27
Consensus pattern (19 bp):
TTTAGGGGAAAATAAAGGA
Found at i:24158216 original size:41 final size:40
Alignment explanation
Indices: 24158100--24158236 Score: 132
Period size: 41 Copynumber: 3.4 Consensus size: 40
24158090 TAAATGATAC
* * *
24158100 TTTGTGGCCTTTTTCTCAT-AGTGCCTCTAATGCTTGACCT
1 TTTGCGGCATTTTTCTCATAAATG-CTCTAATGCTTGACCT
** * * *
24158140 TTTGCGGTGTTTTTATCATAAACGCCGCTAATGCTTGACCT
1 TTTGCGGCATTTTTCTCATAAATG-CTCTAATGCTTGACCT
* * *
24158181 TTTGAGGCATTTTTCTCATAAATGCTACTACTGCTTTACCT
1 TTTGCGGCATTTTTCTCATAAATGCT-CTAATGCTTGACCT
*
24158222 ATTGCGGCATTTTTC
1 TTTGCGGCATTTTTC
24158237 CATCCAAACG
Statistics
Matches: 78, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
40 16 0.21
41 62 0.79
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.43
Consensus pattern (40 bp):
TTTGCGGCATTTTTCTCATAAATGCTCTAATGCTTGACCT
Found at i:24159662 original size:21 final size:21
Alignment explanation
Indices: 24159638--24159679 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
24159628 CATTTTCTTC
*
24159638 AATTCAATTCTCAACTCTCAA
1 AATTCAACTCTCAACTCTCAA
24159659 AATTCAACTCTCAACTCTCAA
1 AATTCAACTCTCAACTCTCAA
24159680 TTTATTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTCAACTCTCAACTCTCAA
Found at i:24164342 original size:63 final size:63
Alignment explanation
Indices: 24164223--24164403 Score: 170
Period size: 63 Copynumber: 2.9 Consensus size: 63
24164213 ACACATACGA
* * * * *
24164223 CACCAGTTTATTT-ACACGAA-CACCACATCACGCA-CAATCATTCCCTACACCAACACATTCAT
1 CACCAATTTATTTCACAC-AAGCACCACAACATG-AGCAACCATTCCCTACACCGACACATTCAT
* * ** * *
24164285 CACTACTTTATTTCACACAAGCACCATTACATGAGTAACCATTTCCTACACCGACACATTCAT
1 CACCAATTTATTTCACACAAGCACCACAACATGAGCAACCATTCCCTACACCGACACATTCAT
** * * * *
24164348 TGCCAATTTATTTCACATAAGCATCACAACATGCGCAATCATTCCCTACACCGACA
1 CACCAATTTATTTCACACAAGCACCACAACATGAGCAACCATTCCCTACACCGACA
24164404 ACATCAGCAG
Statistics
Matches: 94, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
62 14 0.15
63 80 0.85
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (63 bp):
CACCAATTTATTTCACACAAGCACCACAACATGAGCAACCATTCCCTACACCGACACATTCAT
Found at i:24181236 original size:17 final size:18
Alignment explanation
Indices: 24181204--24181238 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24181194 ATTTTTTTTA
24181204 TTTTAGTCTCTATTTAAT
1 TTTTAGTCTCTATTTAAT
*
24181222 TTTTTGTCTCT-TTTAAT
1 TTTTAGTCTCTATTTAAT
24181239 ACTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTAGTCTCTATTTAAT
Found at i:24183245 original size:14 final size:14
Alignment explanation
Indices: 24183226--24183252 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24183216 TTAAAAAAAT
24183226 TTAAGTTTGATTTA
1 TTAAGTTTGATTTA
24183240 TTAAGTTTGATTT
1 TTAAGTTTGATTT
24183253 TAAACCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (14 bp):
TTAAGTTTGATTTA
Found at i:24191941 original size:44 final size:43
Alignment explanation
Indices: 24191893--24192098 Score: 157
Period size: 43 Copynumber: 4.8 Consensus size: 43
24191883 AGTGCTGCTA
* * * *
24191893 TTTAGCGGCG-TTTATGTGAAAAAATGCCGCTAAAGATCATGGCC
1 TTTAGCGGCGCTTT-TAT-AAAAAACGCCGCTAAAGATCACGACC
* * *
24191937 TTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGATCACGACT
1 TTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGATCACGACC
* * * * * * *
24191980 TTTAGCGGCGCTTTTTTCACAAACACTGTTAAAGATCATGACC
1 TTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGATCACGACC
* * * * * *
24192023 TTTAGCGGCACTTTTTATCACAAACGCCGCTATAGAACA-AACC
1 TTTAGCGGCGC-TTTTATAAAAAACGCCGCTAAAGATCACGACC
* *
24192066 TTTAGCGGCGCTTCTCA-CAAAAACGCCGCTAAA
1 TTTAGCGGCGCTT-TTATAAAAAACGCCGCTAAA
24192099 AACATAACCT
Statistics
Matches: 134, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
42 16 0.12
43 82 0.61
44 33 0.25
45 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGATCACGACC
Found at i:24191970 original size:43 final size:43
Alignment explanation
Indices: 24191918--24192111 Score: 214
Period size: 43 Copynumber: 4.5 Consensus size: 43
24191908 GTGAAAAAAT
*
24191918 GCCGCTAAAGATCATGGCCTTTAGCGGCGCTTTTATCACAAAC
1 GCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAAAC
* * *
24191961 GCCGCTAAAGATCACGACTTTTAGCGGCGCTTTTTTCACAAAC
1 GCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAAAC
* * * *
24192004 ACTGTTAAAGATCATGACCTTTAGCGGCACTTTTTATCACAAAC
1 GCCGCTAAAGATCATGACCTTTAGCGGCGC-TTTTATCACAAAC
* * * * *
24192048 GCCGCTATAGAACA-AACCTTTAGCGGCGCTTCTCA-CAAAAAC
1 GCCGCTAAAGATCATGACCTTTAGCGGCGCTT-TTATCACAAAC
* *
24192090 GCCGCTAAA-AACATAACCTTTA
1 GCCGCTAAAGATCATGACCTTTA
24192112 AAAAAAATTA
Statistics
Matches: 127, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
41 4 0.03
42 24 0.19
43 78 0.61
44 21 0.17
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAAAC
Found at i:24195106 original size:14 final size:14
Alignment explanation
Indices: 24195087--24195132 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
24195077 AAAAAAATCA
*
24195087 TAATCCCTAATCCC
1 TAATCCATAATCCC
*
24195101 TAATCCATAATCCG
1 TAATCCATAATCCC
*
24195115 TAAATCCATACTCCC
1 T-AATCCATAATCCC
24195130 TAA
1 TAA
24195133 ACCAGCCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.35, C:0.35, G:0.02, T:0.28
Consensus pattern (14 bp):
TAATCCATAATCCC
Found at i:24195133 original size:15 final size:15
Alignment explanation
Indices: 24195088--24195133 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
24195078 AAAAAATCAT
*
24195088 AATCCCTAATCCCT-
1 AATCCATAATCCCTA
*
24195102 AATCCATAATCCGTA
1 AATCCATAATCCCTA
*
24195117 AATCCATACTCCCTA
1 AATCCATAATCCCTA
24195132 AA
1 AA
24195134 CCAGCCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.37, C:0.35, G:0.02, T:0.26
Consensus pattern (15 bp):
AATCCATAATCCCTA
Found at i:24195590 original size:39 final size:40
Alignment explanation
Indices: 24195547--24195653 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 40
24195537 TGGCGTTTTT
24195547 TAATGCTC-ATTTTTAGCGGCGTTTTTTGAAAAACGCCGC
1 TAATGCTCAATTTTTAGCGGCGTTTTTTGAAAAACGCCGC
* * ** * * **
24195586 TAATGCTCAATCTTTAGTGGCAATTTCTGTAAAGTGCCGC
1 TAATGCTCAATTTTTAGCGGCGTTTTTTGAAAAACGCCGC
* * *
24195626 TAATGCTCGATTTTTACCTGCGTTTTTT
1 TAATGCTCAATTTTTAGCGGCGTTTTTT
24195654 TGTCCAAACG
Statistics
Matches: 51, Mismatches: 16, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
39 8 0.16
40 43 0.84
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (40 bp):
TAATGCTCAATTTTTAGCGGCGTTTTTTGAAAAACGCCGC
Found at i:24203689 original size:9 final size:9
Alignment explanation
Indices: 24203675--24203788 Score: 156
Period size: 9 Copynumber: 12.4 Consensus size: 9
24203665 TTTGGTTAAA
24203675 AATTACCCG
1 AATTACCCG
24203684 AATTACCCG
1 AATTACCCG
24203693 AATTACCCG
1 AATTACCCG
*
24203702 ACTTACCCG
1 AATTACCCG
24203711 AATTACCCG
1 AATTACCCG
*
24203720 AATTACTCG
1 AATTACCCG
*
24203729 ACTTACCCG
1 AATTACCCG
24203738 AATTACCCG
1 AATTACCCG
* *
24203747 AATTAACTG
1 AATTACCCG
24203756 AAAATTACCCG
1 --AATTACCCG
*
24203767 AATTACCCA
1 AATTACCCG
24203776 AATTACCCG
1 AATTACCCG
24203785 AATT
1 AATT
24203789 GACACTTTGA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
9 84 0.92
11 7 0.08
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:24204439 original size:20 final size:20
Alignment explanation
Indices: 24204414--24204514 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
24204404 TTTAAAACAT
24204414 TACATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
24204434 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
24204451 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
24204471 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
24204488 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
24204508 TACATAA
1 TACATAA
24204515 TTAAAAACAT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 12 0.21
18 12 0.21
19 13 0.23
20 19 0.34
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.35
Consensus pattern (20 bp):
TACATAAATCTTTGAATCAC
Found at i:24204454 original size:37 final size:37
Alignment explanation
Indices: 24204407--24204540 Score: 234
Period size: 37 Copynumber: 3.6 Consensus size: 37
24204397 GATGAGGTTT
*
24204407 AAAACATTACATAAATCTTTGAATCACTACATAATTA
1 AAAACATTACATAAGTCTTTGAATCACTACATAATTA
*
24204444 AAAATATTACATAAGTCTTTGAATCACTACATAATTA
1 AAAACATTACATAAGTCTTTGAATCACTACATAATTA
*
24204481 AAAATATTACATAAGTCTTTGAATCACTACATAATTA
1 AAAACATTACATAAGTCTTTGAATCACTACATAATTA
24204518 AAAACATTACATAAGTC-TTGAAT
1 AAAACATTACATAAGTCTTTGAAT
24204541 TAACACATAA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
36 6 0.06
37 88 0.94
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (37 bp):
AAAACATTACATAAGTCTTTGAATCACTACATAATTA
Found at i:24204456 original size:17 final size:17
Alignment explanation
Indices: 24204434--24204531 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
24204424 TTTGAATCAC
24204434 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
24204451 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
24204471 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
24204488 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
24204508 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
24204525 TACATAA
1 TACATAA
24204532 GTCTTGAATT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 23 0.40
18 9 0.16
19 10 0.17
20 16 0.28
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:24208896 original size:21 final size:19
Alignment explanation
Indices: 24208864--24208911 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
24208854 TTTTTTTTGT
*
24208864 AAAATCAAATTTTTGTTTAA
1 AAAATCAAATTTTT-CTTAA
*
24208884 AAAATCATTATTTTTCTT-A
1 AAAATCA-AATTTTTCTTAA
24208903 AAAATCAAA
1 AAAATCAAA
24208912 ACTTTATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 8 0.33
20 9 0.38
21 6 0.25
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAATCAAATTTTTCTTAA
Found at i:24209178 original size:146 final size:147
Alignment explanation
Indices: 24208893--24209181 Score: 399
Period size: 146 Copynumber: 2.0 Consensus size: 147
24208883 AAAAATCATT
24208893 ATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAATTGAGAAAAAAATCAAAACTTTGTTTTAA
1 ATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAATTGAGAAAAAAATCAAAACTTTGTTTTAA
** * *
24208958 AAATTTTAAACTTTTGTTTTAAAATGAATAAAAAACATATTTTTATTTTAAAAATATAAAGTTTC
66 AAATTTTAAACTTTTCCTTTAAAATGAATAAAAAACAGATTTTTATTTTAAAAATATAAACTTTC
24209023 TCTTTAAAAAAAACACA
131 TCTTTAAAAAAAACACA
** * * *
24209040 ATTTTTCTTAAAGTTCAAAGCTTTTATTTTGAAATAGTT-A-AAAAAAATCAAAACTTTGTTTTA
1 ATTTTTCTTAAAAATCAAAAC-TTTATTTCGAAATAATTGAGAAAAAAATCAAAACTTTGTTTTA
* *
24209103 AAAA-TTTAAAC-TTTCCTTTAAAATGATTAAAAAA-AGATTTTTATTTTTAAAATATAAACTCC
65 AAAATTTTAAACTTTTCCTTTAAAATGAATAAAAAACAGATTTTTATTTTAAAAATATAAACT--
* *
24209165 TTTTTTTTAAAAAAAAC
128 TTCTCTTTAAAAAAAAC
24209182 CAAAACTTTG
Statistics
Matches: 126, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
143 23 0.18
144 20 0.16
145 22 0.17
146 27 0.21
147 19 0.15
148 15 0.12
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (147 bp):
ATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAATTGAGAAAAAAATCAAAACTTTGTTTTAA
AAATTTTAAACTTTTCCTTTAAAATGAATAAAAAACAGATTTTTATTTTAAAAATATAAACTTTC
TCTTTAAAAAAAACACA
Found at i:24216218 original size:22 final size:22
Alignment explanation
Indices: 24216188--24216230 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24216178 TATACTTATA
* *
24216188 GATATAACACAACTTGGCTCAT
1 GATAGAACACAACCTGGCTCAT
24216210 GATAGAACACAACCTGGCTCA
1 GATAGAACACAACCTGGCTCA
24216231 CGATTATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (22 bp):
GATAGAACACAACCTGGCTCAT
Found at i:24216755 original size:14 final size:12
Alignment explanation
Indices: 24216734--24216771 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
24216724 ACTTAATCAC
24216734 TTTAATATTAAA
1 TTTAATATTAAA
24216746 TTTATTATATT-AA
1 TTTA--ATATTAAA
24216759 TTTAATATTAAA
1 TTTAATATTAAA
24216771 T
1 T
24216772 CTTCTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 5 0.22
12 7 0.30
13 6 0.26
14 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:24216837 original size:18 final size:19
Alignment explanation
Indices: 24216810--24216857 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
24216800 GTAGATAAAC
*
24216810 ATTAAATTAA-ATTTTAAT
1 ATTAAATTAACACTTTAAT
*
24216828 ATTAACTTAATCACTTTAAT
1 ATTAAATTAA-CACTTTAAT
*
24216848 ATTAGATTAA
1 ATTAAATTAA
24216858 TAAAATACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTAAATTAACACTTTAAT
Found at i:24220276 original size:35 final size:37
Alignment explanation
Indices: 24220204--24220279 Score: 95
Period size: 35 Copynumber: 2.1 Consensus size: 37
24220194 TAACAAATAG
24220204 AATTAAAATATTATAATTATAAAATAACAATAAATAAT
1 AATTAAAATATTAT-ATTATAAAATAACAATAAATAAT
* *
24220242 AATTAAAATATT-T-TTATAATATTAA-AATATATAAT
1 AATTAAAATATTATATTATAA-AATAACAATAAATAAT
24220277 AAT
1 AAT
24220280 GGAATTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 18 0.51
36 4 0.11
37 1 0.03
38 12 0.34
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (37 bp):
AATTAAAATATTATATTATAAAATAACAATAAATAAT
Found at i:24221277 original size:40 final size:40
Alignment explanation
Indices: 24221216--24221327 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
24221206 GGGTACGTAA
* * *
24221216 GTGCAATCAAGGATACTGAAGTACAAATAGGGGCACATAT
1 GTGCAATCAGGGGTACTGAAGTACAAACAGGGGCACATAT
* * *
24221256 GTGCAATCAGGGGTACCGAAGTACAAACAAGGGCACGTAT
1 GTGCAATCAGGGGTACTGAAGTACAAACAGGGGCACATAT
* *
24221296 GTGCAATCAGGAGTATTGAAGTACAAACAGGG
1 GTGCAATCAGGGGTACTGAAGTACAAACAGGG
24221328 TATAATTTAC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.18
Consensus pattern (40 bp):
GTGCAATCAGGGGTACTGAAGTACAAACAGGGGCACATAT
Found at i:24222545 original size:21 final size:21
Alignment explanation
Indices: 24222488--24222545 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
24222478 TGATGCAATG
* *
24222488 TCCTACAATACTAAA-ATAATT
1 TCCTAAAATAC-AAATATAATA
**
24222509 TCCTAAAATATGAATATAATA
1 TCCTAAAATACAAATATAATA
*
24222530 TCCTAAAATGCAAATA
1 TCCTAAAATACAAATA
24222546 CATCTACTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (21 bp):
TCCTAAAATACAAATATAATA
Found at i:24224506 original size:41 final size:40
Alignment explanation
Indices: 24224421--24224536 Score: 115
Period size: 41 Copynumber: 2.8 Consensus size: 40
24224411 TTGAGTTTTA
* * *
24224421 GGGGCTTTAGTGGCGTTTTTTAGAAAGCGTCGCTAAAGCAT
1 GGGGCTTTAGCGGCG-TTTTTGGAAAGCGCCGCTAAAGCAT
** *
24224462 GGGGCTTTAGCGGCGTTTTTGGATAAGCGCCGCTAATTCTT
1 GGGGCTTTAGCGGCGTTTTTGGA-AAGCGCCGCTAAAGCAT
* * *
24224503 GGGGATTTTAGCTGCGCTTTTGGAAAAGCGCCGC
1 GGGG-CTTTAGCGGCGTTTTTGG-AAAGCGCCGC
24224537 AAAAAATAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
40 7 0.11
41 31 0.49
42 24 0.38
43 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (40 bp):
GGGGCTTTAGCGGCGTTTTTGGAAAGCGCCGCTAAAGCAT
Found at i:24224809 original size:14 final size:14
Alignment explanation
Indices: 24224764--24224812 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
24224754 TATTATTATT
24224764 GTTTAGGGTTT-AG
1 GTTTAGGGTTTAAG
* *
24224777 GTTTAAGGGTATATG
1 GTTT-AGGGTTTAAG
*
24224792 GTTTAGGGTTTAAA
1 GTTTAGGGTTTAAG
24224806 GTTTAGG
1 GTTTAGG
24224813 AGTTACTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 4 0.14
14 20 0.69
15 5 0.17
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:24224853 original size:14 final size:14
Alignment explanation
Indices: 24224834--24224877 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
24224824 GAAGGGCTAT
24224834 AGATTATGGGTTTA
1 AGATTATGGGTTTA
24224848 AGATTAT-GGTTTA
1 AGATTATGGGTTTA
* *
24224861 TAGTTTATGCGTTTA
1 -AGATTATGGGTTTA
24224876 AG
1 AG
24224878 GTTTAAGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 6 0.23
14 15 0.58
15 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (14 bp):
AGATTATGGGTTTA
Found at i:24224881 original size:7 final size:7
Alignment explanation
Indices: 24224871--24225024 Score: 69
Period size: 7 Copynumber: 21.7 Consensus size: 7
24224861 TAGTTTATGC
24224871 GTTTAAG
1 GTTTAAG
24224878 GTTTAAG
1 GTTTAAG
* *
24224885 GGTTACG
1 GTTTAAG
*
24224892 GTTTATG
1 GTTTAAG
24224899 GTTTAAG
1 GTTTAAG
24224906 GTTTATA-
1 GTTTA-AG
*
24224913 GATTAAG
1 GTTTAAG
* *
24224920 GGTTAGG
1 GTTTAAG
24224927 GTTTAAAG
1 GTTT-AAG
24224935 GTTTAAG
1 GTTTAAG
*
24224942 GGTTAAG
1 GTTTAAG
*
24224949 AG-TTGAG
1 -GTTTAAG
* *
24224956 GGTTATG
1 GTTTAAG
* *
24224963 GGTTATG
1 GTTTAAG
*
24224970 GTTTATG
1 GTTTAAG
*
24224977 ATTTAAG
1 GTTTAAG
* **
24224984 GGTTGGG
1 GTTTAAG
*
24224991 GTTTAAT
1 GTTTAAG
*
24224998 GTTTAGG
1 GTTTAAG
* *
24225005 GGTTAGGG
1 GTTTA-AG
24225013 GTTTAAG
1 GTTTAAG
24225020 GTTTA
1 GTTTA
24225025 TGTTTTATGA
Statistics
Matches: 111, Mismatches: 30, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
6 2 0.02
7 95 0.86
8 14 0.13
ACGTcount: A:0.23, C:0.01, G:0.35, T:0.41
Consensus pattern (7 bp):
GTTTAAG
Found at i:24224901 original size:21 final size:21
Alignment explanation
Indices: 24224872--24225024 Score: 87
Period size: 21 Copynumber: 7.2 Consensus size: 21
24224862 AGTTTATGCG
* *
24224872 TTTAAGGTTTAAGGG-TTACGG
1 TTTAAGGGTT-AGGGTTTATGG
* * * *
24224893 TTTATGGTTTAAGGTTTATAG
1 TTTAAGGGTTAGGGTTTATGG
* *
24224914 ATTAAGGGTTAGGGTTTAAAGG
1 TTTAAGGGTTAGGGTTT-ATGG
* *
24224936 TTTAAGGGTTAAGAGTTGA-GG
1 TTTAAGGGTT-AGGGTTTATGG
* * * *
24224957 GTTATGGGTTATGGTTTATGA
1 TTTAAGGGTTAGGGTTTATGG
*
24224978 TTTAAGGGTTGGGGTTTAAT-G
1 TTTAAGGGTTAGGGTTT-ATGG
* *
24224999 TTTAGGGGTTAGGGGTTTAAGG
1 TTTAAGGGTTA-GGGTTTATGG
24225021 TTTA
1 TTTA
24225025 TGTTTTATGA
Statistics
Matches: 98, Mismatches: 27, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
20 8 0.08
21 60 0.61
22 25 0.26
23 5 0.05
ACGTcount: A:0.24, C:0.01, G:0.35, T:0.41
Consensus pattern (21 bp):
TTTAAGGGTTAGGGTTTATGG
Found at i:24225033 original size:64 final size:64
Alignment explanation
Indices: 24224871--24225033 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
24224861 TAGTTTATGC
* * * *
24224871 GTTTAAGGTTTAAGGGTTACGGTTTATGGTTTAAGGTTTATAGATTAAGGGTTAGGGTTTAAAG
1 GTTTAAGGGTTAAGAGTTAAGGTTTATGGTTTATGGTTTATAGATTAAGGGTTAGGGTTTAAAG
* * * * *
24224935 GTTTAAGGGTTAAGAGTTGAGGGTTATGGGTTATGGTTTAT-GATTTAAGGGTTGGGGTTT-AAT
1 GTTTAAGGGTTAAGAGTTAAGGTTTATGGTTTATGGTTTATAGA-TTAAGGGTTAGGGTTTAAAG
* * * *
24224998 GTTTAGGGGTTAGGGGTTTAAGGTTTATGTTTTATG
1 GTTTAAGGGTTAAGAG-TTAAGGTTTATGGTTTATG
24225034 ATTCAAGGTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
63 17 0.21
64 64 0.79
ACGTcount: A:0.23, C:0.01, G:0.34, T:0.42
Consensus pattern (64 bp):
GTTTAAGGGTTAAGAGTTAAGGTTTATGGTTTATGGTTTATAGATTAAGGGTTAGGGTTTAAAG
Found at i:24225073 original size:7 final size:7
Alignment explanation
Indices: 24224871--24225075 Score: 51
Period size: 7 Copynumber: 28.9 Consensus size: 7
24224861 TAGTTTATGC
*
24224871 GTTTAAG
1 GTTTAGG
24224878 GTTTAAGG
1 GTTT-AGG
*
24224886 G-TTACG
1 GTTTAGG
*
24224892 GTTTATG
1 GTTTAGG
*
24224899 GTTTAAG
1 GTTTAGG
*
24224906 GTTTATAG
1 GTTTA-GG
* *
24224914 ATTAAGG
1 GTTTAGG
24224921 G-TTAGG
1 GTTTAGG
*
24224927 GTTTAAAG
1 GTTT-AGG
24224935 GTTTAAGG
1 GTTT-AGG
* *
24224943 GTTAAGA
1 GTTTAGG
*
24224950 GTTGAGG
1 GTTTAGG
24224957 G-TTATGG
1 GTTTA-GG
*
24224964 G-TTATG
1 GTTTAGG
*
24224970 GTTTATG
1 GTTTAGG
*
24224977 ATTTAAGG
1 GTTT-AGG
*
24224985 G-TTGGG
1 GTTTAGG
**
24224991 GTTTAAT
1 GTTTAGG
24224998 GTTTAGG
1 GTTTAGG
*
24225005 GGTTAGGG
1 GTTTA-GG
*
24225013 GTTTAAG
1 GTTTAGG
*
24225020 GTTTATG
1 GTTTAGG
* *
24225027 TTTTATG
1 GTTTAGG
* * *
24225034 ATTCAAG
1 GTTTAGG
24225041 GTTTAGG
1 GTTTAGG
**
24225048 GGATAGGG
1 GTTTA-GG
*
24225056 GTTAAGG
1 GTTTAGG
24225063 GTTTAGG
1 GTTTAGG
24225070 GTTTAG
1 GTTTAG
24225076 AGTAATTAGT
Statistics
Matches: 144, Mismatches: 43, Indels: 22
0.69 0.21 0.11
Matches are distributed among these distances:
6 15 0.10
7 97 0.67
8 32 0.22
ACGTcount: A:0.23, C:0.01, G:0.36, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Done.