Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 78 of 204
Found at i:24305432 original size:42 final size:42
Alignment explanation
Indices: 24305373--24305461 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
24305363 ATAGCCTAGC
* *
24305373 ACACGGCCTAGAACACGGGTC-TGTGTGGCAACTTAGAGAGTT
1 ACACGGCCTAGAACACGGG-CATGTGGGGCAACTCAGAGAGTT
* *
24305415 ACACGGCCTAGCACACGGGCATGTGGGGCAACTCAGTGAGTT
1 ACACGGCCTAGAACACGGGCATGTGGGGCAACTCAGAGAGTT
24305457 ACACG
1 ACACG
24305462 AATGAAGACA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (42 bp):
ACACGGCCTAGAACACGGGCATGTGGGGCAACTCAGAGAGTT
Found at i:24306963 original size:14 final size:12
Alignment explanation
Indices: 24306944--24307010 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
24306934 TGAACCCCTT
24306944 ATTAAACATAAAAA
1 ATTAAA-AT-AAAA
*
24306958 ATTAAAATTAAA
1 ATTAAAATAAAA
**
24306970 ATTAAAGGAAAA
1 ATTAAAATAAAA
*
24306982 GATAAAAATGAAAA
1 -ATTAAAAT-AAAA
*
24306996 ATAAAAATAAAA
1 ATTAAAATAAAA
24307008 ATT
1 ATT
24307011 TTAAATTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
12 18 0.42
13 15 0.35
14 10 0.23
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (12 bp):
ATTAAAATAAAA
Found at i:24307001 original size:13 final size:13
Alignment explanation
Indices: 24306977--24307009 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
24306967 AAAATTAAAG
24306977 GAAAAGATAAAAAT
1 GAAAA-ATAAAAAT
24306991 GAAAAATAAAAAT
1 GAAAAATAAAAAT
24307004 -AAAAAT
1 GAAAAAT
24307010 TTTAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 8 0.42
14 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (13 bp):
GAAAAATAAAAAT
Found at i:24309377 original size:24 final size:24
Alignment explanation
Indices: 24309275--24309444 Score: 128
Period size: 24 Copynumber: 6.9 Consensus size: 24
24309265 ACACACTGCA
* *
24309275 GCTCTTATGAGCGTCCCATTATATG
1 GCTCTTATGAGCTTCCCGTTA-ATG
* *
24309300 GCTCTTCATGAGCTTTCCGCTTAAAG
1 GCTCTT-ATGAGCTTCCCG-TTAATG
* **
24309326 GCTCTTTGTGAGCTTCCTAATTAATG
1 GCTC-TTATGAGCTTCC-CGTTAATG
24309352 GCTCTCTA-GAGCTTCCCGTTAATG
1 GCTCT-TATGAGCTTCCCGTTAATG
** * * *
24309376 GCTCTTCGGAGCTACCTGTTATTG
1 GCTCTTATGAGCTTCCCGTTAATG
* **
24309400 GCTCGTATGAGCTTCCTAATT-ATG
1 GCTCTTATGAGCTTCC-CGTTAATG
24309424 GCTCTTATGAGCTTCCCGTTA
1 GCTCTTATGAGCTTCCCGTTA
24309445 TACAGCCGAA
Statistics
Matches: 111, Mismatches: 26, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
23 3 0.03
24 53 0.48
25 17 0.15
26 33 0.30
27 5 0.05
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGTTAATG
Found at i:24309412 original size:48 final size:49
Alignment explanation
Indices: 24309293--24309501 Score: 167
Period size: 48 Copynumber: 4.2 Consensus size: 49
24309283 GAGCGTCCCA
* * * * *
24309293 TTATATGGCTCTTCATGAGCTTTCCGCTTAAAGGCTCTTTGTGAGCTTCCTAA
1 TTATATGGCTCGT-ATGAGCTTCCCG-TTAATGGCTCTTCG-GAGCTTCCT-G
* *
24309346 TTA-ATGGCTC-TCTAGAGCTTCCCGTTAATGGCTCTTCGGAGCTACCTG
1 TTATATGGCTCGTAT-GAGCTTCCCGTTAATGGCTCTTCGGAGCTTCCTG
** ** *
24309394 TTAT-TGGCTCGTATGAGCTTCCTAATT-ATGGCTCTTATGAGCTTCCCG
1 TTATATGGCTCGTATGAGCTTCC-CGTTAATGGCTCTTCGGAGCTTCCTG
** * * * *
24309442 TTATACAGC-CGAATAAGCTTCTCGTTAATGGCTCTCCGGAGCTTCCTG
1 TTATATGGCTCGTATGAGCTTCCCGTTAATGGCTCTTCGGAGCTTCCTG
24309490 TTATATGGCTCG
1 TTATATGGCTCG
24309502 AGAGAGGGCT
Statistics
Matches: 123, Mismatches: 26, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
47 2 0.02
48 72 0.59
49 16 0.13
50 13 0.11
51 10 0.08
52 7 0.06
53 3 0.02
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.36
Consensus pattern (49 bp):
TTATATGGCTCGTATGAGCTTCCCGTTAATGGCTCTTCGGAGCTTCCTG
Found at i:24313003 original size:36 final size:36
Alignment explanation
Indices: 24312952--24313024 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
24312942 AGTAAACTCT
*
24312952 ATTCAACTCAATAGCCTTTTAGATCTATTCTAACTA
1 ATTCAACTCAATAGCCTTTCAGATCTATTCTAACTA
* * *
24312988 ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTA
1 ATTCAACTCAATAGCCTTTCAGATCTATTCTAACTA
24313024 A
1 A
24313025 AGCGCTCCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (36 bp):
ATTCAACTCAATAGCCTTTCAGATCTATTCTAACTA
Found at i:24317729 original size:21 final size:21
Alignment explanation
Indices: 24317703--24317742 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
24317693 TGTTGCAACC
24317703 CACACCCTGTGTTGAGCCACA
1 CACACCCTGTGTTGAGCCACA
24317724 CACACCCTGTGTTGAGCCA
1 CACACCCTGTGTTGAGCCA
24317743 TAGCCTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
CACACCCTGTGTTGAGCCACA
Found at i:24318075 original size:13 final size:13
Alignment explanation
Indices: 24318054--24318099 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
24318044 GAGCATTCTC
* *
24318054 TTTACTCTTTTAT
1 TTTATTCTTCTAT
24318067 TTTATTCTTCTAT
1 TTTATTCTTCTAT
24318080 TTTATTCTTCTAT
1 TTTATTCTTCTAT
24318093 TTATATT
1 TT-TATT
24318100 TCGTTAACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATTCTTCTAT
Found at i:24326659 original size:125 final size:125
Alignment explanation
Indices: 24326437--24326753 Score: 537
Period size: 125 Copynumber: 2.5 Consensus size: 125
24326427 GATAAAATCA
*
24326437 AAGCAGGATGCTTTATC-GAAAGAATTTCTGAAATCTCGCCCACGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATCAG-AAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
*
24326501 TTGGTCCTGAAAAAATAATTTCAAGTTGACGTTTTTGAGCGAATAGTATAAAAAACGCTTC
65 TAGGTCCTGAAAAAATAATTTCAAGTTGACGTTTTTGAGCGAATAGTATAAAAAACGCTTC
*
24326562 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
*
24326627 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTTTGAGCGAATAGTATAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCAAGTTGACGTTTTTGAGCGAATAGTATAAAAAACGCTTC
* ** * *
24326687 AAGCAGGATGCTTTATCAGAAAAATTTCTGAAATCGCGCCCTTGTGGGCGCGCTTTTACTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
24326752 AG
66 AG
24326754 CATGTTTGGG
Statistics
Matches: 181, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
125 180 0.99
126 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCAAGTTGACGTTTTTGAGCGAATAGTATAAAAAACGCTTC
Found at i:24329821 original size:58 final size:59
Alignment explanation
Indices: 24329730--24329853 Score: 214
Period size: 58 Copynumber: 2.1 Consensus size: 59
24329720 CATTGTAAAC
*
24329730 AAATTATATTTTTTTGTACCAATCAAAATATTTTGTAAAAACGCAATAGTTTGTTAGTA
1 AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAATAGTTTGTTAGTA
* *
24329789 AAATTATA-TTTTTTGTACCAATGAAAACATTTTGTAAAAACGCTATAGTTTGTTAGTA
1 AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAATAGTTTGTTAGTA
24329847 AAATTAT
1 AAATTAT
24329854 TAATTGTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 54 0.87
59 8 0.13
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (59 bp):
AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAATAGTTTGTTAGTA
Found at i:24329953 original size:21 final size:21
Alignment explanation
Indices: 24329917--24330053 Score: 195
Period size: 21 Copynumber: 6.4 Consensus size: 21
24329907 GGTTAGGTTT
24329917 AGGGTTAGGG-TTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
24329937 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
24329958 AGGGTTTAGGGTTTTTAAGTTG
1 AGGG-TTAGGGTTTTTAAGTTA
***
24329980 TTTGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
24330001 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
24330022 AGGGTTTAGGGTTTTTAAGTTAA
1 AGGG-TTAGGGTTTTTAAGTT-A
*
24330045 AGTGTTAGG
1 AGGGTTAGG
24330054 CTTAGGCTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.10
21 52 0.50
22 38 0.37
23 4 0.04
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:24329987 original size:43 final size:43
Alignment explanation
Indices: 24329917--24330053 Score: 183
Period size: 43 Copynumber: 3.2 Consensus size: 43
24329907 GGTTAGGTTT
*
24329917 AGGGTTAGGG-TTTTAAGTTAAGG-GTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTAGGGTGTTAGGGTTTTTAAGTTA
**
24329958 AGGGTTTAGGGTTTTTAAGTT-GTTTGTTAGGGTTTTTAAGTTA
1 AGGG-TTAGGGTTTTTAAGTTAGGGTGTTAGGGTTTTTAAGTTA
24330001 AGGGTTAGGGTTTTTAAGTTAAGGGT-TTAGGGTTTTTAAGTTAA
1 AGGGTTAGGGTTTTTAAGTT-AGGGTGTTAGGGTTTTTAAGTT-A
*
24330045 AGTGTTAGG
1 AGGGTTAGG
24330054 CTTAGGCTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
41 4 0.05
42 22 0.26
43 47 0.56
44 11 0.13
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (43 bp):
AGGGTTAGGGTTTTTAAGTTAGGGTGTTAGGGTTTTTAAGTTA
Found at i:24330001 original size:64 final size:63
Alignment explanation
Indices: 24329920--24330042 Score: 237
Period size: 64 Copynumber: 1.9 Consensus size: 63
24329910 TAGGTTTAGG
24329920 GTTAGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTGTTT
1 GTTAGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTGTTT
24329983 GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT
1 GTTAGGG-TTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT
24330043 AAAGTGTTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 7 0.12
64 52 0.88
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (63 bp):
GTTAGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTGTTT
Found at i:24330213 original size:12 final size:12
Alignment explanation
Indices: 24330193--24330235 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
24330183 AGGGTTTGTC
24330193 AATTAAATTATA
1 AATTAAATTATA
*
24330205 AATTTAATTATAA
1 AATTAAATTAT-A
24330218 AATATAAATTTATA
1 AAT-TAAA-TTATA
24330232 AATT
1 AATT
24330236 TTTAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 10 0.38
13 5 0.19
14 7 0.27
15 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAAATTATA
Found at i:24330750 original size:17 final size:19
Alignment explanation
Indices: 24330718--24330761 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
24330708 GACTCGAAAA
*
24330718 AGGAAACATATAA-GGGTT
1 AGGATACATATAAGGGGTT
*
24330736 ATGATACAT-TAAGGGGTT
1 AGGATACATATAAGGGGTT
24330754 AGGATACA
1 AGGATACA
24330762 CACCTGGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.25
Consensus pattern (19 bp):
AGGATACATATAAGGGGTT
Found at i:24332598 original size:51 final size:50
Alignment explanation
Indices: 24332542--24332646 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 50
24332532 TAATTTTTTT
24332542 AAAAT-AATTAAAATTAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGC
1 AAAATAAATT-AAA-TAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGC
* * *
24332593 AAAATAAAATTAAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGC
1 AAAAT-AAATTAAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGC
24332644 AAA
1 AAA
24332647 TTGAGAGCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
51 40 0.83
52 4 0.08
53 4 0.08
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.25
Consensus pattern (50 bp):
AAAATAAATTAAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGC
Found at i:24332649 original size:11 final size:11
Alignment explanation
Indices: 24332633--24332674 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
24332623 ATTTGGAAGG
24332633 AAATTGAGAGC
1 AAATTGAGAGC
24332644 AAATTGAGAGC
1 AAATTGAGAGC
* *
24332655 AATTTGAGAGA
1 AAATTGAGAGC
24332666 AAATTGAGA
1 AAATTGAGA
24332675 AAATAATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.26, T:0.21
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:24332651 original size:33 final size:34
Alignment explanation
Indices: 24332614--24332688 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
24332604 AAATATGGAT
* **
24332614 TTGAGAGAAATTTG-GAAGGAAATTGAGAGCA-AA
1 TTGAGAGAAATTTGAG-AGAAAATTGAGAAAATAA
*
24332647 TTGAGAGCAATTTGAGAGAAAATTGAGAAAATAA
1 TTGAGAGAAATTTGAGAGAAAATTGAGAAAATAA
24332681 TTGAGAGA
1 TTGAGAGA
24332689 GGATTAGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 25 0.71
34 10 0.29
ACGTcount: A:0.47, C:0.03, G:0.28, T:0.23
Consensus pattern (34 bp):
TTGAGAGAAATTTGAGAGAAAATTGAGAAAATAA
Found at i:24337080 original size:20 final size:20
Alignment explanation
Indices: 24337040--24337094 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
24337030 AAGATTTTTT
24337040 TTTTTTA-AAAAT-TA-AAA
1 TTTTTTATAAAATATATAAA
*
24337057 TTTTTTATAAAATATATAAG
1 TTTTTTATAAAATATATAAA
*
24337077 TTTTGTGATAAAA-ATATA
1 TTTT-TTATAAAATATATA
24337095 TGGGCTCCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 7 0.22
18 5 0.16
19 2 0.06
20 11 0.34
21 7 0.22
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTTTATAAAATATATAAA
Found at i:24344194 original size:104 final size:109
Alignment explanation
Indices: 24344061--24344263 Score: 308
Period size: 110 Copynumber: 1.9 Consensus size: 109
24344051 TTTTTATTGT
*
24344061 AATTTTTATGTTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAA-CT-ATTA-TAAATTATT
1 AATTTTTATGTTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATATGATTAGTAAATTATT
*
24344123 TGTTTATTTTAATATTTATTGTGATTTGTTAGGTTATGAATGTA
66 TGTTTAGTTTAATATTTATTGTGATTTGTTAGGTTATGAATGTA
* *
24344167 AATTTTTATGTT-TTTTT-ATTTATTTTAAATTTATTTTGTTAGTAATTTATGATTAGGTTAATT
1 AATTTTTATGTTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAA--TATGATTA-GTAAATT
24344230 ATTTGTTTAGTTTAATATTTATTGTGATTTGTTA
63 ATTTGTTTAGTTTAATATTTATTGTGATTTGTTA
24344264 TGAATGCAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
104 27 0.31
105 5 0.06
106 12 0.14
107 1 0.01
108 4 0.05
110 38 0.44
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (109 bp):
AATTTTTATGTTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATATGATTAGTAAATTATT
TGTTTAGTTTAATATTTATTGTGATTTGTTAGGTTATGAATGTA
Found at i:24346705 original size:33 final size:35
Alignment explanation
Indices: 24346639--24346720 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 35
24346629 TGGAACAAGC
* *
24346639 TTGGAACAAACTTTGTATTTATTTAATTGAGATTCA
1 TTGGAACAAACTTTGTA-TTATTTAAATAAGATTCA
*
24346675 TTGGAACAAATTTTGTA-T-TTTAAATAAGATTCA
1 TTGGAACAAACTTTGTATTATTTAAATAAGATTCA
*
24346708 TTGGTACAAACTT
1 TTGGAACAAACTT
24346721 GGAACAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 24 0.59
34 1 0.02
36 16 0.39
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (35 bp):
TTGGAACAAACTTTGTATTATTTAAATAAGATTCA
Found at i:24350430 original size:16 final size:16
Alignment explanation
Indices: 24350378--24350430 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
24350368 GTGGCCCCTC
24350378 AGTAAAATTTTAATTT
1 AGTAAAATTTTAATTT
**
24350394 AG-ACCATTTATAATTT
1 AGTAAAATTT-TAATTT
*
24350410 A-TAAAATTTTAAATT
1 AGTAAAATTTTAATTT
24350425 AGTAAA
1 AGTAAA
24350431 GATAATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (16 bp):
AGTAAAATTTTAATTT
Found at i:24357148 original size:3 final size:3
Alignment explanation
Indices: 24357140--24357168 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
24357130 ATTGTTAATG
24357140 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
24357169 GTCCAATTAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:24361865 original size:2 final size:2
Alignment explanation
Indices: 24361858--24361896 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24361848 CCTCCCGACA
24361858 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
24361897 GTGTCTTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:24365484 original size:41 final size:41
Alignment explanation
Indices: 24365433--24365529 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
24365423 AAATATATCT
* *
24365433 TTTTCAACCTTTTCATGTGTTATCCTTTTCGGGTAATTTCC
1 TTTTCAACCTTTTCATGTGTTATCCCTTTCGGGTAACTTCC
*
24365474 TTTTCAACCTTTCCATGTGTTATCCCTTTCGGGTAACTTCC
1 TTTTCAACCTTTTCATGTGTTATCCCTTTCGGGTAACTTCC
24365515 TTTTCAACCTTTTCA
1 TTTTCAACCTTTTCA
24365530 AGAATTCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.15, C:0.26, G:0.10, T:0.48
Consensus pattern (41 bp):
TTTTCAACCTTTTCATGTGTTATCCCTTTCGGGTAACTTCC
Found at i:24366688 original size:41 final size:41
Alignment explanation
Indices: 24366556--24366691 Score: 104
Period size: 41 Copynumber: 3.4 Consensus size: 41
24366546 ACCAGTTTGG
* *
24366556 CACCCGGTGCCTCATC-AAATAAT-TCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAAATAATCT-GAAGTAGTAAATTGA
* * ** * * * *
24366596 CACTCAGTGTCTCATCG-GCTAAAC-CAA--AGTGAATTGG
1 CACCCAGTGCCTCATCGAAATAATCTGAAGTAGTAAATTGA
* *
24366633 CACCGAGTGCCTCATCGAATTAATCTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAAATAATCTGAAGTAGTAAATTGA
*
24366674 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
24366692 CTCGAAGTCG
Statistics
Matches: 69, Mismatches: 21, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
37 21 0.30
38 4 0.06
39 4 0.06
40 16 0.23
41 24 0.35
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAAATAATCTGAAGTAGTAAATTGA
Found at i:24366892 original size:24 final size:24
Alignment explanation
Indices: 24366847--24366903 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
24366837 TATATATACC
24366847 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
24366871 AATTC-ATCACATACTAAA-TCAATA
1 AATTCAATCA-ATA-TAAATTCAATA
*
24366895 CATTTCAAT
1 -AATTCAAT
24366904 TGTAAAACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 4 0.14
24 14 0.50
25 8 0.29
26 2 0.07
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:24367660 original size:7 final size:7
Alignment explanation
Indices: 24367648--24367677 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
24367638 CTTTATTATA
24367648 ATATAAT
1 ATATAAT
24367655 ATATAAT
1 ATATAAT
24367662 ATATAAT
1 ATATAAT
24367669 ATAT-AT
1 ATATAAT
24367675 ATA
1 ATA
24367678 CTTAACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:24367667 original size:14 final size:13
Alignment explanation
Indices: 24367644--24367677 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
24367634 CTTTCTTTAT
24367644 TATA-ATATAATA
1 TATATATATAATA
24367656 TATAATATATAATA
1 TAT-ATATATAATA
24367670 TATATATA
1 TATATATA
24367678 CTTAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 6 0.30
14 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATATAATA
Found at i:24367738 original size:28 final size:30
Alignment explanation
Indices: 24367689--24367747 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
24367679 TTAACATTTA
* *
24367689 ATTTTTACTATTACAATATTATAAT-ATAT
1 ATTTTAACTATTAAAATATTATAATAATAT
*
24367718 ATTTTAACT-TTAAAATTTTATAATAATAT
1 ATTTTAACTATTAAAATATTATAATAATAT
24367747 A
1 A
24367748 CTTATGCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTTAACTATTAAAATATTATAATAATAT
Found at i:24369984 original size:31 final size:32
Alignment explanation
Indices: 24369949--24370008 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
24369939 AAAAATAACA
*
24369949 AAATTGGGTTTTAGGTT-CTTAAAAGTTGAAG
1 AAATTGGGTTTTAAGTTCCTTAAAAGTTGAAG
***
24369980 AAATTTTTTTTTAAGTTCCTTAAAAGTTG
1 AAATTGGGTTTTAAGTTCCTTAAAAGTTG
24370009 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 13 0.54
32 11 0.46
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (32 bp):
AAATTGGGTTTTAAGTTCCTTAAAAGTTGAAG
Found at i:24380216 original size:16 final size:17
Alignment explanation
Indices: 24380189--24380223 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
24380179 AGAGAGTTGA
24380189 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
24380206 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
24380222 GA
1 GA
24380224 TGTGAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:24382571 original size:51 final size:51
Alignment explanation
Indices: 24382516--24382799 Score: 211
Period size: 51 Copynumber: 5.6 Consensus size: 51
24382506 GATGAACACG
* *
24382516 TGTGTAGTATTGTGTGAAGGCTACTACGTGAATCAATAA-ATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAGAT-ATGGTCACA
* * * * * * * * * * *
24382567 TGTGTAGCACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAGATATGGTCACA
* *
24382618 TGTGTAGTA-TGGTGTGAAGGCTACTACGTGAATCGATAA-ATGATGGTCACA
1 TGTGTAGTACT-ATGTGAAGGCTACTACGTGAATCAATAAGAT-ATGGTCACA
* * * * * * * *
24382669 TGTGTAGAACTAAGTGAAGGCTACTATGTGTACTGAA-AAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTG-AATCAATAAGATATGGTCACA
* ** * * *
24382720 TGTGTAGTGCTATGTGAAGGCTACTACGTGAA-CCGTAAAACT-TGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAGA-TATGGTCACA
*
24382770 TGCGTAGTACTATGTGAAGGCTACTACGTG
1 TGTGTAGTACTATGTGAAGGCTACTACGTG
24382800 TATCGAATGA
Statistics
Matches: 178, Mismatches: 47, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
50 40 0.22
51 132 0.74
52 6 0.03
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAGATATGGTCACA
Found at i:24382688 original size:102 final size:101
Alignment explanation
Indices: 24382512--24382751 Score: 390
Period size: 102 Copynumber: 2.3 Consensus size: 101
24382502 TATCGATGAA
*
24382512 CACGTGTGTAGTATTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGCAC
1 CACGTGTGTAGTA-TGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGAAC
*
24382577 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
65 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
*
24382614 CACGTGTGTAGTATGGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGAAC
1 CACGTGTGTAGTAT-GTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGAAC
* *
24382679 TAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTGGT
65 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* *
24382716 CACGTGTGTAGTGCTATGTGAAGGCTACTACGTGAA
1 CACGTGTGTAGT-ATGTGTGAAGGCTACTACGTGAA
24382752 CCGTAAAACT
Statistics
Matches: 129, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
101 1 0.01
102 127 0.98
103 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (101 bp):
CACGTGTGTAGTATGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGAACT
AAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:24385841 original size:20 final size:20
Alignment explanation
Indices: 24385816--24385853 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24385806 ACCCCCTTTA
24385816 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
24385836 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
24385854 CGAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:24387886 original size:43 final size:43
Alignment explanation
Indices: 24387825--24387908 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
24387815 GGCTGTAATT
*
24387825 AACCGATTCTTTAGATCTTCAAAAGCTTCCAAACAAATTGAAC
1 AACCGATTCTTTAGATCTTAAAAAGCTTCCAAACAAATTGAAC
24387868 AACCGATTCTTTAGATCTTAAAAAGCTTCCAAACAAATTGA
1 AACCGATTCTTTAGATCTTAAAAAGCTTCCAAACAAATTGA
24387909 GCATTGTATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (43 bp):
AACCGATTCTTTAGATCTTAAAAAGCTTCCAAACAAATTGAAC
Found at i:24391116 original size:39 final size:34
Alignment explanation
Indices: 24391051--24391129 Score: 88
Period size: 39 Copynumber: 2.2 Consensus size: 34
24391041 AAGTAAGTGT
*
24391051 AGAAAAATAAACTCTAAAACTAAGAAAGAA-TAAG
1 AGAAAAAAAAACTCTAAAACTAAGAAA-AACTAAG
24391085 AGAAAATAAAAACTCTAAAAAACTTATAGAAAAACTAAG
1 AGAAAA-AAAAACTCT--AAAAC-TA-AGAAAAACTAAG
24391124 AGAAAA
1 AGAAAA
24391130 CCTAGAGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
34 6 0.16
35 8 0.21
37 5 0.13
38 4 0.11
39 15 0.39
ACGTcount: A:0.66, C:0.09, G:0.10, T:0.15
Consensus pattern (34 bp):
AGAAAAAAAAACTCTAAAACTAAGAAAAACTAAG
Found at i:24395198 original size:6 final size:6
Alignment explanation
Indices: 24395179--24395208 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
24395169 TATTCAGATA
24395179 AATATT AA-ATT AATATT AATATT AATATT A
1 AATATT AATATT AATATT AATATT AATATT A
24395209 TATCTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATATT
Found at i:24395198 original size:68 final size:72
Alignment explanation
Indices: 24395073--24395203 Score: 173
Period size: 68 Copynumber: 1.9 Consensus size: 72
24395063 ACTTAATGAG
* * * *
24395073 TTTAATATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAGTTAAATTTAATATTAAGA
1 TTTAAAATTAAATTAATAAAATATATATCTACAAGATAAACATTAAATTAAATTTAATATTAAGA
24395138 TATTCAC
66 TATTCAC
*
24395145 TTTAAAATTAAATTAATAAAATA-ATAT-T-C-AGATAAATATTAAATT-AATATTAATATTAA
1 TTTAAAATTAAATTAATAAAATATATATCTACAAGATAAACATTAAATTAAAT-TTAATATTAA
24395204 TATTATATCT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
67 3 0.06
68 24 0.45
69 1 0.02
70 1 0.02
71 3 0.06
72 21 0.40
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (72 bp):
TTTAAAATTAAATTAATAAAATATATATCTACAAGATAAACATTAAATTAAATTTAATATTAAGA
TATTCAC
Found at i:24395202 original size:12 final size:11
Alignment explanation
Indices: 24395146--24395208 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
24395136 GATATTCACT
*
24395146 TTAAAATTAAA
1 TTAATATTAAA
24395157 TTAATA--AAA
1 TTAATATTAAA
*
24395166 -TAATATTCAGA
1 TTAATATT-AAA
*
24395177 TAAATATTAAA
1 TTAATATTAAA
24395188 TTAATATTAATA
1 TTAATATTAA-A
24395200 TTAATATTA
1 TTAATATTA
24395209 TATCTATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 5 0.12
9 3 0.07
11 18 0.43
12 16 0.38
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:24395641 original size:24 final size:25
Alignment explanation
Indices: 24395612--24395662 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
24395602 AAATATCATA
*
24395612 TTAATTTTAATTAATT-TGATTAAT
1 TTAATTTTAATTAATTAAGATTAAT
* *
24395636 TTAATTTTACTTGATTAAGATTAAT
1 TTAATTTTAATTAATTAAGATTAAT
24395661 TT
1 TT
24395663 TCTTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (25 bp):
TTAATTTTAATTAATTAAGATTAAT
Found at i:24396175 original size:5 final size:5
Alignment explanation
Indices: 24396167--24396192 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
24396157 TTTCATCCGA
24396167 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
24396193 ACCGATTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:24398947 original size:2 final size:2
Alignment explanation
Indices: 24398940--24398975 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24398930 TAATTGACTG
24398940 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
24398976 CTAAATCTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24399417 original size:37 final size:37
Alignment explanation
Indices: 24399376--24399457 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
24399366 AAATATTTAT
* *
24399376 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
*
24399413 TAATCAATGTTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
24399450 TAATCAAT
1 TAATCAAT
24399458 ATATTTATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (37 bp):
TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
Found at i:24399537 original size:33 final size:33
Alignment explanation
Indices: 24399500--24399575 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
24399490 TTAAAACTTG
*
24399500 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
24399533 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
24399566 AATTATACAT
1 AATTATACAT
24399576 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:24402793 original size:92 final size:91
Alignment explanation
Indices: 24402636--24402844 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
24402626 TTGATTTTAG
* * *
24402636 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
24402701 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
24402728 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
24402792 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
24402820 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
24402845 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:24402807 original size:24 final size:25
Alignment explanation
Indices: 24402772--24402819 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
24402762 TTATGAAATT
24402772 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
24402796 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
24402820 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:24406219 original size:16 final size:17
Alignment explanation
Indices: 24406190--24406222 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24406180 ATTAGAATAA
*
24406190 AATAAAGTTCTAATATT
1 AATAAACTTCTAATATT
24406207 AATAAACTT-TAATATT
1 AATAAACTTCTAATATT
24406223 TTGATATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAAACTTCTAATATT
Found at i:24418457 original size:20 final size:20
Alignment explanation
Indices: 24418432--24418469 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24418422 CTATTTCAAC
*
24418432 TTGAAACATCGAGTAGTTAT
1 TTGAAACATCGAGCAGTTAT
24418452 TTGAAACATCGAGCAGTT
1 TTGAAACATCGAGCAGTT
24418470 TGATCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TTGAAACATCGAGCAGTTAT
Found at i:24423798 original size:42 final size:42
Alignment explanation
Indices: 24423740--24423851 Score: 161
Period size: 42 Copynumber: 2.7 Consensus size: 42
24423730 GATGCAAGGG
24423740 ACACACGGCCAAAACACACGCCCATGTGCTAAGTCATGTGTC
1 ACACACGGCCAAAACACACGCCCATGTGCTAAGTCATGTGTC
* *
24423782 ACACATGGCCAAAACACACGCCCATGTGCTAGGTCATGTGTC
1 ACACACGGCCAAAACACACGCCCATGTGCTAAGTCATGTGTC
* ** * *
24423824 ACATACGGCTGAGACACACGCCCGTGTG
1 ACACACGGCCAAAACACACGCCCATGTG
24423852 GACAAAATAG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.29, C:0.32, G:0.22, T:0.17
Consensus pattern (42 bp):
ACACACGGCCAAAACACACGCCCATGTGCTAAGTCATGTGTC
Found at i:24426276 original size:50 final size:50
Alignment explanation
Indices: 24426165--24426362 Score: 227
Period size: 50 Copynumber: 3.8 Consensus size: 50
24426155 ATTTGGGTAA
* *
24426165 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA--G-G---ATG
* *
24426221 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGTACCAGGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAGGATG
** *
24426271 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATTGGCACCTA-TATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACC-AGGATG
** * *
24426321 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
24426363 GTACAAGAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
50 82 0.65
51 1 0.01
53 1 0.01
54 1 0.01
56 41 0.33
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAGGATG
Found at i:24426312 original size:106 final size:100
Alignment explanation
Indices: 24426176--24426360 Score: 262
Period size: 100 Copynumber: 1.8 Consensus size: 100
24426166 GAGATCCCAT
* **
24426176 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-C-CT---A-TATGAGAACTCCCATGTAAGACCA
* *
24426241 TGTCTGGGACATGGCGTTGGTACCAGGATGAGAGGTCCCCC
60 TATCTGGGACATGGCATTGGTACCAGGATGAGAGGTCCCCC
24426282 GTAAGACCATGTCTGGGACATGGCATTGGCACCTATATGAGAACTCCCATGTAAGACCATATCTG
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCTATATGAGAACTCCCATGTAAGACCATATCTG
*
24426347 GGATATGGCATTGG
66 GGACATGGCATTGG
24426361 CAGTACAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
100 39 0.53
101 1 0.01
104 1 0.01
105 1 0.01
106 31 0.42
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (100 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCTATATGAGAACTCCCATGTAAGACCATATCTG
GGACATGGCATTGGTACCAGGATGAGAGGTCCCCC
Found at i:24429562 original size:16 final size:17
Alignment explanation
Indices: 24429537--24429569 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24429527 ATACCTTTAT
*
24429537 TTTTACTAA-TTTAAAA
1 TTTTAATAATTTTAAAA
24429553 TTTTAATAATTTTAAAA
1 TTTTAATAATTTTAAAA
24429570 AATTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAATAATTTTAAAA
Found at i:24435640 original size:3 final size:3
Alignment explanation
Indices: 24435632--24435663 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
24435622 CAAAATCATT
*
24435632 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24435664 GCCATGGCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:24445440 original size:2 final size:2
Alignment explanation
Indices: 24445435--24445469 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24445425 ATTTTATATA
24445435 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
24445470 CATATTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:24454194 original size:12 final size:12
Alignment explanation
Indices: 24454177--24454201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24454167 AAAATGCATT
24454177 ATTAATAAAATA
1 ATTAATAAAATA
24454189 ATTAATAAAATA
1 ATTAATAAAATA
24454201 A
1 A
24454202 CACATGAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAATAAAATA
Found at i:24457742 original size:20 final size:20
Alignment explanation
Indices: 24457717--24457795 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
24457707 TAAAATTTTC
24457717 CACAAAGGCTAACATAATAG
1 CACAAAGGCTAACATAATAG
* * *
24457737 CACAAAGGCAATATATAAAGTACAC
1 CACAAAGGCTA-ACAT-AA-T--AG
24457762 CACAAAGGCTAACATAATAG
1 CACAAAGGCTAACATAATAG
*
24457782 CATAAAGGCTAACA
1 CACAAAGGCTAACA
24457796 GAATGCCATA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 24 0.51
21 3 0.06
22 3 0.06
23 3 0.06
24 3 0.06
25 11 0.23
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.15
Consensus pattern (20 bp):
CACAAAGGCTAACATAATAG
Found at i:24457805 original size:20 final size:21
Alignment explanation
Indices: 24457765--24457847 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 21
24457755 AGTACACCAC
*
24457765 AAAGGCTAACATAATAG-CAT
1 AAAGGCTAACAGAATAGCCAT
24457785 AAAGGCTAACAGAAT-GCCAT
1 AAAGGCTAACAGAATAGCCAT
* * *
24457805 AAAGGCCCATTCAGAATACGCCAC
1 AAAGG-CTA-ACAGAATA-GCCAT
*
24457829 ATAGGCTAACAGAAT-GCCA
1 AAAGGCTAACAGAATAGCCA
24457848 CCTATGTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 26 0.51
21 2 0.04
22 12 0.24
23 2 0.04
24 8 0.16
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (21 bp):
AAAGGCTAACAGAATAGCCAT
Found at i:24458777 original size:8 final size:8
Alignment explanation
Indices: 24458764--24458792 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
24458754 CACTAGAGAC
24458764 CAGTGTTA
1 CAGTGTTA
24458772 CAGTGTTA
1 CAGTGTTA
24458780 CAGTGTTA
1 CAGTGTTA
24458788 CAGTG
1 CAGTG
24458793 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:24458906 original size:23 final size:23
Alignment explanation
Indices: 24458879--24458954 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
24458869 AGTGTTATTG
24458879 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
24458902 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
24458925 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
24458948 ATCAGTG
1 ATCAGTG
24458955 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:24463458 original size:36 final size:37
Alignment explanation
Indices: 24463418--24463514 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 37
24463408 GTCTCCAATT
* * *
24463418 TCACATTTCAGTTCAATTTCACTTTTTCACTTTCAA-
1 TCACATTTCAATTCAATTTCACATTTCCACTTTCAAG
* * *
24463454 TCACAATTCAATTCAAAATTCACATTTCCATTTTCAAG
1 TCACATTTCAATTC-AATTTCACATTTCCACTTTCAAG
* *
24463492 TCA-ATATTCATTTCAATTCCACA
1 TCACAT-TTCAATTCAATTTCACA
24463515 CTTATATTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
36 12 0.25
37 26 0.54
38 10 0.21
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.41
Consensus pattern (37 bp):
TCACATTTCAATTCAATTTCACATTTCCACTTTCAAG
Found at i:24464705 original size:23 final size:24
Alignment explanation
Indices: 24464678--24464722 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
24464668 GAAAAATATT
*
24464678 AAATAT-ATATTTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
24464701 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
24464723 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:24464833 original size:9 final size:9
Alignment explanation
Indices: 24464819--24464846 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
24464809 TTTTGTTACA
24464819 ACAATTAAT
1 ACAATTAAT
24464828 ACAATTAAT
1 ACAATTAAT
24464837 ACAATTAAT
1 ACAATTAAT
24464846 A
1 A
24464847 ATTTGATAAA
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:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:24464868 original size:68 final size:68
Alignment explanation
Indices: 24464789--24464998 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
24464779 TCAAGTTTGT
*
24464789 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
24464854 AAA
66 AAA
24464857 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
24464922 AAA
66 AAA
*
24464925 TTTACTAATCAAATATTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
24464988 AAT
66 AAA
24464991 TTTACTAA
1 TTTACTAA
24464999 CAATTAATTT
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 111 0.80
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:24464899 original size:9 final size:9
Alignment explanation
Indices: 24464887--24464914 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
24464877 TTTTATTACA
24464887 ACAATTAAT
1 ACAATTAAT
24464896 ACAATTAAT
1 ACAATTAAT
24464905 ACAATTAAT
1 ACAATTAAT
24464914 A
1 A
24464915 ATTTGATAAA
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:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:24465008 original size:16 final size:16
Alignment explanation
Indices: 24464987--24465028 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
24464977 AATAATTTGA
*
24464987 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
24465003 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
24465019 TAGTTTTAAT
1 TAATTTTAAT
24465029 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:24465046 original size:19 final size:20
Alignment explanation
Indices: 24465022--24465059 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
24465012 TAACAATTAG
24465022 TTTTAATTTT-ATTAAAAAA
1 TTTTAATTTTAATTAAAAAA
24465041 TTTTAATTTTAATTAAAAA
1 TTTTAATTTTAATTAAAAA
24465060 CGGGCCGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTAATTTTAATTAAAAAA
Found at i:24470079 original size:13 final size:13
Alignment explanation
Indices: 24470061--24470085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24470051 CACAAACGAT
24470061 AAAATTTTCACAC
1 AAAATTTTCACAC
24470074 AAAATTTTCACA
1 AAAATTTTCACA
24470086 AATATAAATT
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:24483090 original size:87 final size:89
Alignment explanation
Indices: 24482965--24483133 Score: 193
Period size: 87 Copynumber: 1.9 Consensus size: 89
24482955 TAATTAAGTC
* *
24482965 CTTTTTTTTACACTCAATTAAGTATTTAAACTTTTAAAATACATCAAAAAAGCCCT-AAA-ATTT
1 CTTTTTTTTACACTCAATTAAGTACTTAAACTTCTAAAATACATCAAAAAAGCCCTCAAACATTT
24483028 AAAAAAAAAACAATTAAGCCCCTA
66 AAAAAAAAAACAATTAAGCCCCTA
* * ** * * *
24483052 CTTTTTTTTGCACTCAATTGAA-TACTTGAA-TTGCTAAAATGTATCAAAAAGGTCCTCAAACTT
1 CTTTTTTTTACACTCAATT-AAGTACTTAAACTT-CTAAAATACATCAAAAAAGCCCTCAAACAT
* *
24483115 TTTAAAAAAACACAATTAA
64 TTAAAAAAAAAACAATTAA
24483134 ACAATTGTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
86 2 0.03
87 42 0.63
88 5 0.07
89 18 0.27
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.34
Consensus pattern (89 bp):
CTTTTTTTTACACTCAATTAAGTACTTAAACTTCTAAAATACATCAAAAAAGCCCTCAAACATTT
AAAAAAAAAACAATTAAGCCCCTA
Found at i:24483285 original size:19 final size:19
Alignment explanation
Indices: 24483262--24483307 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
24483252 AATTATAATA
*
24483262 AATAAATATTATTAAATTT
1 AATAAAAATTATTAAATTT
*
24483281 TATAAAAATTATTAAATTT
1 AATAAAAATTATTAAATTT
24483300 AATAAAAA
1 AATAAAAA
24483308 ATATAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAAAAATTATTAAATTT
Found at i:24483368 original size:10 final size:10
Alignment explanation
Indices: 24483355--24483402 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
24483345 TAAAAAAGTG
*
24483355 TAAAATTTTA
1 TAAAATATTA
* *
24483365 TAAAAAATCA
1 TAAAATATTA
24483375 TAAAATATTA
1 TAAAATATTA
24483385 TAAAATA-TA
1 TAAAATATTA
24483394 TAGAAATAT
1 TA-AAATAT
24483403 AGAAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 4 0.13
10 27 0.87
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
TAAAATATTA
Found at i:24483369 original size:20 final size:20
Alignment explanation
Indices: 24483355--24483402 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
24483345 TAAAAAAGTG
*
24483355 TAAAATTTTATAAAAAATCA
1 TAAAATATTATAAAAAATCA
*
24483375 TAAAATATTATAAAATAT-A
1 TAAAATATTATAAAAAATCA
24483394 TAGAAATAT
1 TA-AAATAT
24483403 AGAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAAATATTATAAAAAATCA
Found at i:24483403 original size:10 final size:9
Alignment explanation
Indices: 24483363--24483410 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
24483353 TGTAAAATTT
*
24483363 TATAAAAAA
1 TATAAAATA
24483372 TCATAAAATA
1 T-ATAAAATA
24483382 TTATAAAATA
1 -TATAAAATA
24483392 TATAGAAATA
1 TATA-AAATA
*
24483402 TAGAAAATA
1 TATAAAATA
24483411 AATTTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 10 0.29
10 23 0.68
11 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
TATAAAATA
Found at i:24483653 original size:9 final size:9
Alignment explanation
Indices: 24483641--24483727 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
24483631 TTTTTATGCA
24483641 TTTTATATT
1 TTTTATATT
24483650 TTTT-TATGAT
1 TTTTATAT--T
**
24483660 TTTTATAAAA
1 TTTTAT-ATT
* *
24483670 TTTTACAGT
1 TTTTATATT
24483679 TTTTATATT
1 TTTTATATT
* *
24483688 TTTTACAAT
1 TTTTATATT
24483697 TTTTATATT
1 TTTTATATT
24483706 TTTTATATT
1 TTTTATATT
24483715 TTTTAATATT
1 TTTT-ATATT
24483725 TTT
1 TTT
24483728 ATTAAAATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
8 3 0.05
9 39 0.63
10 18 0.29
11 1 0.02
12 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (9 bp):
TTTTATATT
Found at i:24483663 original size:19 final size:18
Alignment explanation
Indices: 24483630--24483727 Score: 76
Period size: 19 Copynumber: 5.3 Consensus size: 18
24483620 CTAAATAGTC
24483630 TTTTTTATGCA-TTTTATA
1 TTTTTTATG-ATTTTTATA
24483648 TTTTTTTATGATTTTTATAA
1 -TTTTTTATGATTTTTAT-A
** *
24483668 AATTTTA-CAGTTTTTATA
1 TTTTTTATGA-TTTTTATA
**
24483686 TTTTTTACAATTTTTATA
1 TTTTTTATGATTTTTATA
24483704 TTTTTTAT-ATTTTTTAATA
1 TTTTTTATGA-TTTTT-ATA
24483723 TTTTT
1 TTTTT
24483728 ATTAAAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.02
18 28 0.42
19 36 0.55
20 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTTATGATTTTTATA
Found at i:24483729 original size:27 final size:26
Alignment explanation
Indices: 24483641--24483729 Score: 106
Period size: 27 Copynumber: 3.2 Consensus size: 26
24483631 TTTTTATGCA
*
24483641 TTTTATATTTTTTTATGATTTTTATAAAA
1 TTTTATA-TTTTTTAT-ATTTTT-TAAAT
* *
24483670 TTTTACAGTTTTTATATTTTTTACAAT
1 TTTTATATTTTTTATATTTTTTA-AAT
24483697 TTTTATATTTTTTATATTTTTTAATAT
1 TTTTATATTTTTTATATTTTTTAA-AT
24483724 TTTTAT
1 TTTTAT
24483730 TAAAATTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
26 3 0.06
27 37 0.70
28 7 0.13
29 6 0.11
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTATATTTTTTATATTTTTTAAAT
Found at i:24483753 original size:9 final size:9
Alignment explanation
Indices: 24483650--24483756 Score: 81
Period size: 9 Copynumber: 11.6 Consensus size: 9
24483640 ATTTTATATT
*
24483650 TTTTTATGA
1 TTTTTATAA
24483659 TTTTTATAAA
1 TTTTTAT-AA
* * *
24483669 ATTTTACAG
1 TTTTTATAA
*
24483678 TTTTTATAT
1 TTTTTATAA
*
24483687 TTTTTACAA
1 TTTTTATAA
*
24483696 TTTTTATAT
1 TTTTTATAA
*
24483705 TTTTTATAT
1 TTTTTATAA
24483714 TTTTTA-ATA
1 TTTTTATA-A
24483723 TTTTTATTAAA
1 TTTTTA-T-AA
* *
24483734 ATTTAATAA
1 TTTTTATAA
24483743 TTTTTATAA
1 TTTTTATAA
24483752 TTTTT
1 TTTTT
24483757 TGTCACATGC
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
8 1 0.01
9 63 0.82
10 7 0.09
11 5 0.06
12 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:24485028 original size:15 final size:16
Alignment explanation
Indices: 24484996--24485030 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
24484986 CATTAACATG
24484996 TATTTTTTAATATATT
1 TATTTTTTAATATATT
24485012 TATTTTTTAATAT-TT
1 TATTTTTTAATATATT
24485027 TATT
1 TATT
24485031 ATATCTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTTAATATATT
Found at i:24487366 original size:2 final size:2
Alignment explanation
Indices: 24487359--24487385 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24487349 CTTGAGGTAC
24487359 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
24487386 ATCCTTATTA
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:24490064 original size:36 final size:35
Alignment explanation
Indices: 24489981--24490102 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 35
24489971 GATCCGATTA
*
24489981 AAACACGAGAATTTTTTTAAAAAACACGAGAATTTTG
1 AAACACGAG-ATTTTTTTAAAAAA-ACGAAAATTTTG
* *
24490018 -GACAC-A-ATTTTTTTTAAAAAACGAAAATTTATG
1 AAACACGAGATTTTTTTAAAAAAACGAAAATTT-TG
* * *
24490051 AAACACGAGATTTTTTTGAAAACACGAAAATTTTCA
1 AAACACGAGATTTTTTTAAAAAAACGAAAATTTT-G
*
24490087 AAACATCGAAATTTTT
1 AAACA-CGAGATTTTT
24490103 GAAAACACGA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
32 9 0.13
33 15 0.21
34 4 0.06
35 3 0.04
36 31 0.44
37 9 0.13
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (35 bp):
AAACACGAGATTTTTTTAAAAAAACGAAAATTTTG
Found at i:24490084 original size:18 final size:18
Alignment explanation
Indices: 24490027--24490314 Score: 218
Period size: 17 Copynumber: 16.3 Consensus size: 18
24490017 GGACACAATT
* *
24490027 TTTTTTAAAAAACGAAAA
1 TTTTTGAAAACACGAAAA
* **
24490045 TTTATG-AAACACGAGATT
1 TTTTTGAAAACACGA-AAA
24490063 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
24490081 -TTTTCAAAACATCG-AAA
1 TTTTTGAAAACA-CGAAAA
**
24490098 TTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAAAA
* *
24490116 TTTTT-TAAATACGAAAA
1 TTTTTGAAAACACGAAAA
* *
24490133 -ATTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
*
24490150 TTTTTG-AAATACGAAAA
1 TTTTTGAAAACACGAAAA
*
24490167 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
24490184 TTTTTG-AAACAC-AGAAG
1 TTTTTGAAAACACGA-AAA
24490201 TTTTTAGAAAACACGAAAA
1 TTTTT-GAAAACACGAAAA
* *** **
24490220 ATTTTGAAAATTGGAATT
1 TTTTTGAAAACACGAAAA
*
24490238 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
24490256 TTTTTGAAAAACATGAAAA
1 TTTTTG-AAAACACGAAAA
* **
24490275 TTTTTG-CAACACGGGAA
1 TTTTTGAAAACACGAAAA
24490292 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
24490310 ATTTT
1 TTTTT
24490315 CCGATTTTTT
Statistics
Matches: 206, Mismatches: 51, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
16 4 0.02
17 94 0.46
18 71 0.34
19 36 0.17
20 1 0.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:24490152 original size:52 final size:54
Alignment explanation
Indices: 24490040--24490158 Score: 140
Period size: 52 Copynumber: 2.3 Consensus size: 54
24490030 TTTAAAAAAC
* * *
24490040 GAAAATTTATG-AAACACGAGATTTTTTTGAAAACACGAAAATTTTCAAAACATC
1 GAAAATTTTTGAAAACACGAGATTTTTTT-AAAACACGAAAAATTTCAAAACATA
* *
24490094 G-AAATTTTTGAAAACACGAGGA-TTTTTT-AAATACGAAAAATTTGAAAACA-A
1 GAAAATTTTTGAAAACACGA-GATTTTTTTAAAACACGAAAAATTTCAAAACATA
24490145 GAAAATTTTTGAAA
1 GAAAATTTTTGAAA
24490159 TACGAAAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
51 1 0.02
52 31 0.54
53 8 0.14
54 15 0.26
55 2 0.04
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (54 bp):
GAAAATTTTTGAAAACACGAGATTTTTTTAAAACACGAAAAATTTCAAAACATA
Found at i:24490286 original size:36 final size:36
Alignment explanation
Indices: 24490027--24490314 Score: 193
Period size: 36 Copynumber: 8.1 Consensus size: 36
24490017 GGACACAATT
* * * * **
24490027 TTTTTTAAAAAACGAAAATTTATGAAACAC-GAGATT
1 TTTTTGAAAACACGAAAATTTTTGAAAAACAGA-AAA
*
24490063 TTTTTGAAAACACGAAAA-TTTT-CAAAACATCG-AAA
1 TTTTTGAAAACACGAAAATTTTTGAAAAACA--GAAAA
** * *
24490098 TTTTTGAAAACACGAGGATTTTTTAAATAC-GAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAAACAGAAAA
* * *
24490133 -ATTTGAAAACAAGAAAATTTTTGAAATAC-GAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAAACAGAAAA
* * *
24490167 TTTTAG-AAACACGAAAATTTTTGAAACACAG-AAG
1 TTTTTGAAAACACGAAAATTTTTGAAAAACAGAAAA
* *** **
24490201 TTTTTAGAAAACACGAAAAATTTTGAAAATTGGAATT
1 TTTTT-GAAAACACGAAAATTTTTGAAAAACAGAAAA
*
24490238 TTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAAACA-GAAAA
* **
24490275 TTTTTG-CAACACGGGAATTTTTG-AAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAAACA-GAAAA
*
24490310 ATTTT
1 TTTTT
24490315 CCGATTTTTT
Statistics
Matches: 200, Mismatches: 40, Indels: 25
0.75 0.15 0.09
Matches are distributed among these distances:
34 61 0.31
35 43 0.22
36 76 0.38
37 20 0.10
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (36 bp):
TTTTTGAAAACACGAAAATTTTTGAAAAACAGAAAA
Found at i:24490446 original size:21 final size:20
Alignment explanation
Indices: 24490420--24490461 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
24490410 TGTTACCTTA
24490420 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
24490441 TTTTTGAAGACACGAAAATT
1 TTTTTGAAAACACGAAAATT
24490461 T
1 T
24490462 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:24490654 original size:16 final size:17
Alignment explanation
Indices: 24490629--24490678 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
24490619 AAAATTATTT
24490629 AAAATAAAA-TAAAATA
1 AAAATAAAATTAAAATA
* *
24490645 AAAATCAAATTAAATTA
1 AAAATAAAATTAAAATA
24490662 AAAATATAAATATAAAA
1 AAAATA-AAAT-TAAAA
24490679 ATGCATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 4 0.15
19 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAAAATTAAAATA
Found at i:24490690 original size:9 final size:9
Alignment explanation
Indices: 24490676--24490700 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
24490666 TATAAATATA
24490676 AAAATGCAT
1 AAAATGCAT
24490685 AAAATGCAT
1 AAAATGCAT
24490694 AAAATGC
1 AAAATGC
24490701 TAATAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (9 bp):
AAAATGCAT
Found at i:24491678 original size:29 final size:29
Alignment explanation
Indices: 24491607--24491720 Score: 165
Period size: 29 Copynumber: 3.9 Consensus size: 29
24491597 TAATTTTGAG
* * *
24491607 AAAGTTTAGAGGTCAAAATGTAATTTTTAG
1 AAAGTTTAGGGGTCAAAATGTAA-TTTCAA
*
24491637 AAAGTTTAGGGGTTAAAATGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
24491666 AAAGTTTATGGGTCAAAATGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
24491695 AAAGTTTAGGGGTCAAAATGCAATTT
1 AAAGTTTAGGGGTCAAAATGTAATTT
24491721 TTTATTTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
29 55 0.72
30 21 0.28
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTCAA
Found at i:24492013 original size:74 final size:79
Alignment explanation
Indices: 24491912--24492617 Score: 815
Period size: 78 Copynumber: 8.9 Consensus size: 79
24491902 CGAAAATGCT
* * * *
24491912 TCGGCGTGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTGAAATACAGAAA
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAA
*
24491976 -TTGAA-AAATACC
66 TTTAAAGAAATACC
* *
24491988 TC-G-ACGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACA-AAA
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAA
* *
24492049 ATTGAA-AAATACC
66 TTTAAAGAAATACC
* * *
24492062 TC-G-ACGTGACTCAAGGCTCAACTCACCTCTCGCAATAAGAGTTGATTTTTTTTTTGAAAATAC
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAA-AC
24492125 A-AAATTTAAAAGAAATACC
61 AGAAATTT-AAAGAAATACC
* * * *
24492144 TCAGCATGTGACCCGAGGCTCAACTCACCTCTTGCATTATGAGTTGATTTTTTGAAAAACAGAAA
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAA
*
24492209 TTTAAACGAAATACT
66 TTTAAA-GAAATACC
*
24492224 TCGGC--GTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAATAC-G
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAA-ACAG
24492286 AAATTTAAAAGAAATACC
63 AAATTT-AAAGAAATACC
* *
24492304 TCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAA
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAA
24492369 TTTAAATGAAATACC
66 TTTAAA-GAAATACC
* * * *
24492384 TCGGCATGTGTC-CGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAGAGCAGAAA
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAA
24492447 TTTAAAAGAAATACC
66 TTT-AAAGAAATACC
*
24492462 TCGGCATGTGTC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGATTTTTTTTTTG-AA
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGA---G-TTGA----TTTTTTGAAA
24492525 AACAGAAATTTAAAAGAAATACC
58 AACAGAAATTT-AAAGAAATACC
* *
24492548 TCGGCATG-GTC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTAAGAAAACAGAA
1 TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA-AAAACAGAA
24492610 ATTTAAAG
65 ATTTAAAG
24492618 NNNNNNNNNN
Statistics
Matches: 565, Mismatches: 32, Indels: 65
0.85 0.05 0.10
Matches are distributed among these distances:
73 3 0.01
74 105 0.19
75 1 0.00
76 7 0.01
77 4 0.01
78 115 0.20
79 58 0.10
80 103 0.18
81 12 0.02
82 51 0.09
83 1 0.00
84 36 0.06
85 32 0.06
86 31 0.05
87 6 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (79 bp):
TCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAA
TTTAAAGAAATACC
Found at i:24492318 original size:160 final size:160
Alignment explanation
Indices: 24491927--24492597 Score: 837
Period size: 160 Copynumber: 4.2 Consensus size: 160
24491917 GTGTGACCCG
* *
24491927 AGGCTCAACTCACCTCTCACAATATGAGTTGA---TTTTTG-AAATACAGAAA-TT-GAA-AAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAATACAGAAATTTAAAAGAAAT
* * *
24491985 ACCTC-G-ACGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACA-
66 ACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAG
* * *
24492046 AAAATTGAA-AAATACCTCGACGTGACTCA
131 AAATTTAAAGAAATACCTCGGCGTGACTCA
*
24492075 AGGCTCAACTCACCTCTCGCAATAAGAGTTGATTTTTTTTTTGAAAATACA-AAATTTAAAAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTGAAAATACAGAAATTTAAAAGAA
* * *
24492139 ATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTTGCATTATGAGTTGATTTTTTGAAAAAC
64 ATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC
*
24492204 AGAAATTTAAACGAAATACTTCGGCGTGACTCA
129 AGAAATTTAAA-GAAATACCTCGGCGTGACTCA
24492237 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAATAC-GAAATTTAAAAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAATACAGAAATTTAAAAGAAAT
*
24492301 ACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAG
66 ACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAG
* *
24492366 AAATTTAAATGAAATACCTCGGCATGTGTC-CG
131 AAATTTAAA-GAAATACCTCGGC--GTGACTCA
* * *
24492398 AGGCTCAACTCACCTCTCGCATTATGAGTTGA---TTTTTGAAGA-GCAGAAATTTAAAAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAATACAGAAATTTAAAAGAAAT
*
24492459 ACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGATTTTTTTTTTG
66 ACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA---G-TTGA----TTTTTTG
* * *
24492523 -AAAACAGAAATTTAAAAGAAATACCTCGGCATG-GTCCG
123 AAAAACAGAAATTT-AAAGAAATACCTCGGCGTGACT-CA
24492561 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
24492598 AAGAAAACAG
Statistics
Matches: 463, Mismatches: 27, Indels: 48
0.86 0.05 0.09
Matches are distributed among these distances:
148 30 0.06
153 9 0.02
154 9 0.02
155 2 0.00
156 9 0.02
157 31 0.07
158 75 0.16
159 13 0.03
160 123 0.27
161 36 0.08
162 55 0.12
163 33 0.07
164 26 0.06
165 10 0.02
166 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (160 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAATACAGAAATTTAAAAGAAAT
ACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAG
AAATTTAAAGAAATACCTCGGCGTGACTCA
Found at i:24492581 original size:85 final size:87
Alignment explanation
Indices: 24492430--24492594 Score: 307
Period size: 85 Copynumber: 1.9 Consensus size: 87
24492420 TATGAGTTGA
*
24492430 TTTTTGAAGAGCAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCG
1 TTTTTGAAGAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCG
24492495 CAATATGAGTTGATTGATTTTT
66 CAATATGAGTTGATTGATTTTT
24492517 TTTTTGAA-AACAGAAATTTAAAAGAAATACCTCGGCATG-GTCCGAGGCTCAACTCACCTCTCG
1 TTTTTGAAGAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCG
24492580 CAATATGAGTTGATT
66 CAATATGAGTTGATT
24492595 TTTAAGAAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
85 39 0.51
86 30 0.39
87 8 0.10
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (87 bp):
TTTTTGAAGAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCG
CAATATGAGTTGATTGATTTTT
Found at i:24494429 original size:11 final size:10
Alignment explanation
Indices: 24494413--24494492 Score: 65
Period size: 11 Copynumber: 7.5 Consensus size: 10
24494403 TTCATCTTGA
24494413 TTTTTCTTTCT
1 TTTTTCTTT-T
24494424 TTTTTCTTTT
1 TTTTTCTTTT
*
24494434 TTTTCCTTTT
1 TTTTTCTTTT
24494444 TTCTTGT-TTTT
1 TT-TT-TCTTTT
*
24494455 TTTGTTGTTTT
1 TTT-TTCTTTT
24494466 TTTTT-TGTTT
1 TTTTTCT-TTT
24494476 TTTTGTCTATTT
1 TTTT-TCT-TTT
24494488 TTTTT
1 TTTTT
24494493 TTCAGGCATA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
9 1 0.02
10 23 0.39
11 27 0.46
12 8 0.14
ACGTcount: A:0.01, C:0.09, G:0.06, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:24494433 original size:17 final size:17
Alignment explanation
Indices: 24494413--24494455 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
24494403 TTCATCTTGA
24494413 TTTTTCTTT-CTTTTTTC
1 TTTTT-TTTCCTTTTTTC
24494430 TTTTTTTTCCTTTTTTC
1 TTTTTTTTCCTTTTTTC
24494447 TTGTTTTTT
1 TT-TTTTTT
24494456 TTGTTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCCTTTTTTC
Found at i:24494442 original size:10 final size:9
Alignment explanation
Indices: 24494413--24494491 Score: 56
Period size: 8 Copynumber: 8.6 Consensus size: 9
24494403 TTCATCTTGA
24494413 TTTTTCTTTCT
1 TTTTTC-TT-T
24494424 TTTTTCTTT
1 TTTTTCTTT
*
24494433 TTTTTC-CT
1 TTTTTCTTT
24494441 TTTTTCTTGT
1 TTTTTCTT-T
*
24494451 TTTTT-TTG
1 TTTTTCTTT
*
24494459 TTGTT-TTT
1 TTTTTCTTT
*
24494467 TTTTTGTTT
1 TTTTTCTTT
24494476 TTTTGTCTATT
1 TTTT-TCT-TT
24494487 TTTTT
1 TTTTT
24494492 TTTCAGGCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
8 17 0.30
9 16 0.29
10 11 0.20
11 12 0.21
ACGTcount: A:0.01, C:0.09, G:0.06, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:24494455 original size:12 final size:12
Alignment explanation
Indices: 24494440--24494495 Score: 69
Period size: 12 Copynumber: 4.6 Consensus size: 12
24494430 TTTTTTTTCC
24494440 TTTTTTCTTGTT
1 TTTTTTCTTGTT
*
24494452 TTTTTTGTTGTT
1 TTTTTTCTTGTT
24494464 TTTTTT-TTGTT
1 TTTTTTCTTGTT
*
24494475 TTTTTGTCTATTTT
1 TTTTT-TCT-TGTT
24494489 TTTTTTC
1 TTTTTTC
24494496 AGGCATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.26
12 18 0.46
13 3 0.08
14 8 0.21
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (12 bp):
TTTTTTCTTGTT
Found at i:24494467 original size:14 final size:13
Alignment explanation
Indices: 24494423--24494479 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 13
24494413 TTTTTCTTTC
*
24494423 TTTTTTCTTTTTT
1 TTTTTTGTTTTTT
24494436 TTCCTTTT-TTCTTGTT
1 TT--TTTTGTT-TT-TT
24494452 TTTTTTGTTGTTTT
1 TTTTTTGTT-TTTT
24494466 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
24494479 T
1 T
24494480 GTCTATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 7 0.18
14 17 0.45
15 10 0.26
16 4 0.11
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:24494471 original size:28 final size:27
Alignment explanation
Indices: 24494413--24494491 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 27
24494403 TTCATCTTGA
24494413 TTTTTCTTTCTTTTTTCTTTTTTTTCCT
1 TTTTTCTTTCTTTTTTCTTTTTTTT-CT
*
24494441 TTTTTCTTGT-TTTTTT-TGTTGTTTT-T
1 TTTTTCTT-TCTTTTTTCT-TTTTTTTCT
* *
24494467 TTTTTGTTT-TTTTGTCTATTTTTTT
1 TTTTTCTTTCTTTTTTCT-TTTTTTT
24494492 TTTCAGGCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 6 0.14
26 15 0.35
27 1 0.02
28 20 0.47
29 1 0.02
ACGTcount: A:0.01, C:0.09, G:0.06, T:0.84
Consensus pattern (27 bp):
TTTTTCTTTCTTTTTTCTTTTTTTTCT
Found at i:24494480 original size:22 final size:24
Alignment explanation
Indices: 24494440--24494494 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
24494430 TTTTTTTTCC
* *
24494440 TTTTTTCTTGTTTTTTTTGT-TGT
1 TTTTTTTTTGTTTTTTTTGTCTAT
24494463 TTTTTTTTTG-TTTTTTTGTCTAT
1 TTTTTTTTTGTTTTTTTTGTCTAT
24494486 TTTTTTTTT
1 TTTTTTTTT
24494495 CAGGCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (24 bp):
TTTTTTTTTGTTTTTTTTGTCTAT
Found at i:24500525 original size:36 final size:35
Alignment explanation
Indices: 24500442--24500563 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 35
24500432 GATCCGATTA
*
24500442 AAACACGAGAATTTTTTTAAAAAACACGAGAATTTTG
1 AAACACGAG-ATTTTTTTAAAAAA-ACGAAAATTTTG
* *
24500479 -GACAC-A-ATTTTTTTTAAAAAACGAAAATTTATG
1 AAACACGAGATTTTTTTAAAAAAACGAAAATTT-TG
* * *
24500512 AAACACGAGATTTTTTTGAAAACACGAAAATTTTCA
1 AAACACGAGATTTTTTTAAAAAAACGAAAATTTT-G
*
24500548 AAACATCGAAATTTTT
1 AAACA-CGAGATTTTT
24500564 GAAAACACGA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
32 9 0.13
33 15 0.21
34 4 0.06
35 3 0.04
36 31 0.44
37 9 0.13
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (35 bp):
AAACACGAGATTTTTTTAAAAAAACGAAAATTTTG
Found at i:24500545 original size:18 final size:18
Alignment explanation
Indices: 24500488--24500775 Score: 202
Period size: 17 Copynumber: 16.3 Consensus size: 18
24500478 GGACACAATT
* *
24500488 TTTTTTAAAAAACGAAAA
1 TTTTTGAAAACACGAAAA
* **
24500506 TTTATG-AAACACGAGATT
1 TTTTTGAAAACACGA-AAA
24500524 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
24500542 -TTTTCAAAACATCG-AAA
1 TTTTTGAAAACA-CGAAAA
**
24500559 TTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAAAA
* *
24500577 TTTTT-TAAATACGAAAA
1 TTTTTGAAAACACGAAAA
* *
24500594 -ATTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
*
24500611 TTTTT-AAAATACGAAAA
1 TTTTTGAAAACACGAAAA
*
24500628 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
24500645 TTTTTG-AAACAC-AGAAG
1 TTTTTGAAAACACGA-AAA
24500662 TTTTTAGAAAACACGAAAA
1 TTTTT-GAAAACACGAAAA
* *** ***
24500681 ATTTTGAAAATTGGATTT
1 TTTTTGAAAACACGAAAA
*
24500699 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
24500717 TTTTTGAAAAACATGAAAA
1 TTTTTG-AAAACACGAAAA
* *
24500736 TTTTTG-CAACACTG-GAA
1 TTTTTGAAAACAC-GAAAA
24500753 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
24500771 ATTTT
1 TTTTT
24500776 CCGATTTTTT
Statistics
Matches: 204, Mismatches: 50, Indels: 32
0.71 0.17 0.11
Matches are distributed among these distances:
16 4 0.02
17 94 0.46
18 69 0.34
19 36 0.18
20 1 0.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:24500679 original size:36 final size:35
Alignment explanation
Indices: 24500489--24500725 Score: 189
Period size: 36 Copynumber: 6.8 Consensus size: 35
24500479 GACACAATTT
* *
24500489 TTTTTA-AAAA-ACGAAAATTTATGAAACACGAGAT
1 TTTTTAGAAAACACGAAAATTTTTGAAACACGA-AA
* **
24500523 TTTTTTGAAAACACGAAAATTTTCAAAACATCGAAA
1 TTTTTAGAAAACACGAAAATTTTTGAAACA-CGAAA
** * *
24500559 TTTTT-GAAAACACGAGGATTTTTTAAATACGAAA
1 TTTTTAGAAAACACGAAAATTTTTGAAACACGAAA
** * * *
24500593 AATTT-GAAAACAAGAAAATTTTTAAAATACGAAA
1 TTTTTAGAAAACACGAAAATTTTTGAAACACGAAA
* *
24500627 ATTTTAG-AAACACGAAAATTTTTGAAACACAGAAG
1 TTTTTAGAAAACACGAAAATTTTTGAAACAC-GAAA
* * **
24500662 TTTTTAGAAAACACGAAAAATTTTGAAA-ATTGGATT
1 TTTTTAGAAAACACGAAAATTTTTGAAACA--CGAAA
* *
24500698 TTTTTTGAAAACACGAGAATTTTTGAAA
1 TTTTTAGAAAACACGAAAATTTTTGAAA
24500726 AACATGAAAA
Statistics
Matches: 166, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
34 62 0.37
35 34 0.20
36 67 0.40
37 3 0.02
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (35 bp):
TTTTTAGAAAACACGAAAATTTTTGAAACACGAAA
Found at i:24501096 original size:16 final size:17
Alignment explanation
Indices: 24501068--24501106 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
24501058 AAAATTATTT
24501068 AAAATAAATTTAAA-TA
1 AAAATAAATTTAAATTA
24501084 AAAATCAAA-TTAAATTA
1 AAAAT-AAATTTAAATTA
24501101 AAAATA
1 AAAATA
24501107 TAAATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATAAATTTAAATTA
Found at i:24501118 original size:14 final size:13
Alignment explanation
Indices: 24501090--24501124 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
24501080 AATAAAAATC
24501090 AAAT-TAAATTAA
1 AAATATAAATTAA
24501102 AAATATAAATATAA
1 AAATATAAAT-TAA
24501116 AAATATAAA
1 AAATATAAA
24501125 AATGCATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 5 0.24
14 12 0.57
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAAATTAA
Found at i:24501271 original size:7 final size:7
Alignment explanation
Indices: 24501259--24501345 Score: 63
Period size: 8 Copynumber: 11.9 Consensus size: 7
24501249 GAATTGAACC
24501259 TCTTTTT
1 TCTTTTT
24501266 TCTTTTTT
1 TC-TTTTT
24501274 CTCTTTTT
1 -TCTTTTT
24501282 TCTTTTT
1 TCTTTTT
24501289 TCTTTTTT
1 TC-TTTTT
24501297 TCCTTCTTT
1 T-CTT-TTT
**
24501306 T-TTCCT
1 TCTTTTT
24501312 TCTCTTTT
1 TCT-TTTT
24501320 TCTTCTTT
1 TCTT-TTT
*
24501328 T-TCTTT
1 TCTTTTT
24501334 TCTTTTT
1 TCTTTTT
24501341 T-TTTT
1 TCTTTT
24501346 CTCTGCTGGG
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
6 10 0.15
7 21 0.32
8 27 0.42
9 7 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:24501279 original size:16 final size:16
Alignment explanation
Indices: 24501258--24501349 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 16
24501248 CGAATTGAAC
24501258 CTCTTTTTTCTTTTTT
1 CTCTTTTTTCTTTTTT
24501274 CTCTTTTTTCTTTTTT
1 CTCTTTTTTCTTTTTT
*
24501290 CTTTTTTTCCTTCTTTTTT
1 C-TCTTTT--TTCTTTTTT
24501309 CCTTCTCTTTTTCTTCTTTT
1 -C-TCT-TTTTTCTT-TTTT
*
24501329 -TCTTTTCTTTTTTTTTT
1 CTC-TTT-TTTCTTTTTT
24501346 CTCT
1 CTCT
24501350 GCTGGGCCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
16 17 0.27
17 14 0.22
18 8 0.12
19 14 0.22
20 8 0.12
21 3 0.05
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTCTTTTTTCTTTTTT
Found at i:24501308 original size:11 final size:11
Alignment explanation
Indices: 24501265--24501329 Score: 62
Period size: 11 Copynumber: 5.7 Consensus size: 11
24501255 AACCTCTTTT
24501265 TTCTTTTTTCTC
1 TTCTTTTTTC-C
**
24501277 TT-TTTTCTTTT
1 TTCTTTT-TTCC
24501288 TTCTTTTTTTCC
1 TTC-TTTTTTCC
24501300 TTCTTTTTTCC
1 TTCTTTTTTCC
24501311 TTCTCTTTTT-C
1 TTCT-TTTTTCC
24501322 TTCTTTTT
1 TTCTTTTT
24501330 CTTTTCTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
10 4 0.09
11 23 0.51
12 14 0.31
13 4 0.09
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCTTTTTTCC
Found at i:24501336 original size:11 final size:11
Alignment explanation
Indices: 24501263--24501347 Score: 54
Period size: 11 Copynumber: 7.5 Consensus size: 11
24501253 TGAACCTCTT
24501263 TTTTCTTTTTTC
1 TTTTC-TTTTTC
24501275 TCTTT-TTTCTT-
1 T-TTTCTTT-TTC
24501286 TTTTCTTTTT-
1 TTTTCTTTTTC
24501296 TTCCTTCTTTTTTCC
1 TT--TTC-TTTTT-C
*
24501311 TTCTCTTTTTC
1 TTTTCTTTTTC
24501322 --TTCTTTTTC
1 TTTTCTTTTTC
*
24501331 TTTTCTTTTTT
1 TTTTCTTTTTC
24501342 TTTTCT
1 TTTTCT
24501348 CTGCTGGGCC
Statistics
Matches: 60, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
9 8 0.13
10 7 0.12
11 22 0.37
12 11 0.18
13 10 0.17
15 2 0.03
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:24501532 original size:6 final size:6
Alignment explanation
Indices: 24501498--24501577 Score: 115
Period size: 6 Copynumber: 12.8 Consensus size: 6
24501488 TTTTTTGGGC
* *
24501498 TTGTTT CTTTTTT TTGTTT CTTTTTT TTGTTT TTGCTTT TTGTTT TTGTTT
1 TTGTTT -TTGTTT TTGTTT -TTGTTT TTGTTT TTG-TTT TTGTTT TTGTTT
24501549 TTGTTT TTGTTT TTGTTT TTGTTT TTGTT
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTT
24501578 GTTTTTTTCT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
6 51 0.76
7 16 0.24
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (6 bp):
TTGTTT
Found at i:24501805 original size:16 final size:16
Alignment explanation
Indices: 24501786--24501816 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24501776 TTCTCCTTCC
24501786 TCTTTTCTTTCTCTCT
1 TCTTTTCTTTCTCTCT
*
24501802 TCTTTTCTTTTTCTC
1 TCTTTTCTTTCTCTC
24501817 GAAGCTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TCTTTTCTTTCTCTCT
Found at i:24502128 original size:29 final size:29
Alignment explanation
Indices: 24502057--24502170 Score: 165
Period size: 29 Copynumber: 3.9 Consensus size: 29
24502047 TAATTTTGAG
* * *
24502057 AAAGTTTAGAGGTCAAAATGTAATTTTTAT
1 AAAGTTTAGGGGTCAAAATGTAA-TTTCAA
*
24502087 AAAGTTTAGGGGTTAAAATGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
24502116 AAAGTTTATGGGTCAAAATGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
24502145 AAAGTTTAGGGGTCAAAATGCAATTT
1 AAAGTTTAGGGGTCAAAATGTAATTT
24502171 TTTATTTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
29 55 0.72
30 21 0.28
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTCAA
Found at i:24504570 original size:37 final size:35
Alignment explanation
Indices: 24504519--24504626 Score: 96
Period size: 37 Copynumber: 3.0 Consensus size: 35
24504509 TTCCAAAAAG
*
24504519 TAATATTATTTTAATAGT-TTAATATTAAATTTAATA
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATA
*
24504555 TAATACTTATCTTAATAGTATTTTATTAATTTAATA
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATA
* *
24504591 TTAAAGTGATTATCTTAATATTA-AAT-TTAATTTAAT
1 -T-AA-T-ATTATCTTAATAGTATTATATTAATTTAAT
24504627 GTTTATCTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
36 14 0.23
37 27 0.44
38 5 0.08
39 14 0.23
40 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (35 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATA
Found at i:24504662 original size:92 final size:92
Alignment explanation
Indices: 24504566--24504744 Score: 349
Period size: 92 Copynumber: 1.9 Consensus size: 92
24504556 AATACTTATC
*
24504566 TTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATTTAATGTTT
1 TTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATTTAATATTT
24504631 ATCTACAAGATAAACATTCTATAAGAT
66 ATCTACAAGATAAACATTCTATAAGAT
24504658 TTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATTTAATATTT
1 TTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATTTAATATTT
24504723 ATCTACAAGATAAACATTCTAT
66 ATCTACAAGATAAACATTCTAT
24504745 TATTTTAATA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 86 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (92 bp):
TTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATTTAATATTT
ATCTACAAGATAAACATTCTATAAGAT
Found at i:24506507 original size:38 final size:37
Alignment explanation
Indices: 24506465--24506539 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
24506455 AATATATAAT
24506465 AAATAAATATTTTTATTC-TTTAATTTTAAAATATTTTA
1 AAAT-AAT-TTTTTATTCTTTTAATTTTAAAATATTTTA
* *
24506503 AAATACTTTTTTATTCTTTTTATTTTTAAAATATTTT
1 AAATAATTTTTTATTC-TTTTAATTTTAAAATATTTT
24506540 TTTTGGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 9 0.27
37 2 0.06
38 22 0.67
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (37 bp):
AAATAATTTTTTATTCTTTTAATTTTAAAATATTTTA
Found at i:24510042 original size:3 final size:3
Alignment explanation
Indices: 24510036--24510067 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
24510026 TCATGATGAT
*
24510036 GAG GAG GAG GAG GAG GAG GAG GAG GAA GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
24510068 TAAGCAGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:24513160 original size:2 final size:2
Alignment explanation
Indices: 24513149--24513186 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
24513139 ATTCAAAGCA
*
24513149 AT AT AT -T AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24513187 ATTATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24518343 original size:20 final size:23
Alignment explanation
Indices: 24518308--24518348 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
24518298 GTGACGGAGC
24518308 GATCATCTTGCTTGAA-AGCATT
1 GATCATCTTGCTTGAAGAGCATT
24518330 GATC-TCTT-CTTGAAGAGCA
1 GATCATCTTGCTTGAAGAGCA
24518349 GAAATGCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (23 bp):
GATCATCTTGCTTGAAGAGCATT
Found at i:24519402 original size:31 final size:30
Alignment explanation
Indices: 24519352--24519434 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
24519342 TCCATCTCTC
24519352 ACATTTTGGATAATTTTAATTTT-AATATAT
1 ACATTTTGGATAATTTTAATTTTAAATA-AT
*
24519382 ACATTTTGTATATATTTTAATTTTAAATAAT
1 ACATTTTGGATA-ATTTTAATTTTAAATAAT
24519413 A-ATTTTGGATAATTTTAATTTT
1 ACATTTTGGATAATTTTAATTTT
24519435 GTTCAGTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
29 11 0.22
30 20 0.41
31 14 0.29
32 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (30 bp):
ACATTTTGGATAATTTTAATTTTAAATAAT
Found at i:24523759 original size:30 final size:30
Alignment explanation
Indices: 24523713--24523801 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
24523703 ATTTCTTATG
*
24523713 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
24523744 CCAATATTTGATACCCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
24523773 ----TATTTGATACCCATATATTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
24523799 CCA
1 CCA
24523802 TAAATATGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
25 22 0.42
26 2 0.04
29 2 0.04
30 19 0.37
31 7 0.13
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:24523768 original size:15 final size:15
Alignment explanation
Indices: 24523723--24523769 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
24523713 CCAATATCTC
24523723 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
24523738 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
24523753 GATACCCATATCTTT
1 GATACCCATATCTTT
24523768 GA
1 GA
24523770 CTTTATTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:24528421 original size:30 final size:29
Alignment explanation
Indices: 24528387--24528467 Score: 125
Period size: 25 Copynumber: 2.9 Consensus size: 29
24528377 CCAGTATCTC
24528387 GATACCCATATCTTTGACTTTCCAATATTT
1 GATACCCATATCTTTGACTTTCC-ATATTT
24528417 GATACCCATATCTTTGAC-TT---TATTT
1 GATACCCATATCTTTGACTTTCCATATTT
24528442 GATACCCATATCTTTGACTTTCCATA
1 GATACCCATATCTTTGACTTTCCATA
24528468 AATATGGATG
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
25 23 0.49
26 2 0.04
29 4 0.09
30 18 0.38
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.43
Consensus pattern (29 bp):
GATACCCATATCTTTGACTTTCCATATTT
Found at i:24528432 original size:15 final size:15
Alignment explanation
Indices: 24528387--24528433 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
24528377 CCAGTATCTC
24528387 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
24528402 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
24528417 GATACCCATATCTTT
1 GATACCCATATCTTT
24528432 GA
1 GA
24528434 CTTTATTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Done.