Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 94 of 173
Found at i:29456112 original size:89 final size:88
Alignment explanation
Indices: 29456009--29456180 Score: 292
Period size: 89 Copynumber: 1.9 Consensus size: 88
29455999 ATTTAATCAA
*
29456009 TAAAAAAACATATATATACATACATATATAAATATAGAAAAATATTCGTTAGAA-AAAAATAAAT
1 TAAAAAAACATATATATACATACATATAT-AATATAGAAAAATAGTCGTTAGAAGAAAAATAAAT
29456073 ATACATACATGTACATATAATTTT
65 ATACATACATGTACATATAATTTT
*
29456097 TAAAGAAAACATATATATATATACATATATAATATAGAAAAATAGTCGTTAGAAGAAAAATAAAT
1 TAAA-AAAACATATATATACATACATATATAATATAGAAAAATAGTCGTTAGAAGAAAAATAAAT
*
29456162 ATACATACATGTACGTATA
65 ATACATACATGTACATATA
29456181 TAAATAAATA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
88 27 0.34
89 52 0.66
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (88 bp):
TAAAAAAACATATATATACATACATATATAATATAGAAAAATAGTCGTTAGAAGAAAAATAAATA
TACATACATGTACATATAATTTT
Found at i:29456258 original size:18 final size:18
Alignment explanation
Indices: 29456237--29456282 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29456227 AAAATATGCG
**
29456237 TATATATATGGAAATAAA
1 TATATATATAAAAATAAA
*
29456255 TATATACATAAAAATAAA
1 TATATATATAAAAATAAA
*
29456273 TATACATATA
1 TATATATATA
29456283 TATATATAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (18 bp):
TATATATATAAAAATAAA
Found at i:29457462 original size:14 final size:14
Alignment explanation
Indices: 29457443--29457478 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
29457433 TGATATTTTT
29457443 TTTGGGCCATTGTA
1 TTTGGGCCATTGTA
29457457 TTTGGGCCATTGTA
1 TTTGGGCCATTGTA
29457471 TTTGGGCC
1 TTTGGGCC
29457479 TATTTCGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.17, G:0.31, T:0.42
Consensus pattern (14 bp):
TTTGGGCCATTGTA
Found at i:29457701 original size:15 final size:16
Alignment explanation
Indices: 29457667--29457704 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29457657 AAAAAAATAT
*
29457667 ATAAATAGACATGAAA
1 ATAAATAAACATGAAA
*
29457683 ATAAATAAAGATG-AA
1 ATAAATAAACATGAAA
29457698 ATAAATA
1 ATAAATA
29457705 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.21
Consensus pattern (16 bp):
ATAAATAAACATGAAA
Found at i:29462493 original size:12 final size:12
Alignment explanation
Indices: 29462460--29462494 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
29462450 TGAGACAAGA
29462460 TATTCTTTAAAT
1 TATTCTTTAAAT
*
29462472 TACTCTTTTAAAT
1 TATTC-TTTAAAT
29462485 TATTCTTTAA
1 TATTCTTTAA
29462495 GTAACCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTCTTTAAAT
Found at i:29462966 original size:16 final size:16
Alignment explanation
Indices: 29462945--29463014 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 16
29462935 AATTGAATTG
**
29462945 CTATTACAGTTCTATT
1 CTATTACAACTCTATT
*
29462961 CTATTATAACTCTATT
1 CTATTACAACTCTATT
* *
29462977 CTATTACAATTCTTTT
1 CTATTACAACTCTATT
* * *
29462993 CCATTACAGCTCTATC
1 CTATTACAACTCTATT
29463009 CTATTA
1 CTATTA
29463015 TACTGAACCA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (16 bp):
CTATTACAACTCTATT
Found at i:29463006 original size:32 final size:32
Alignment explanation
Indices: 29462945--29463014 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
29462935 AATTGAATTG
* * * *
29462945 CTATTACAGTTCTATTCTATTATAACTCTATT
1 CTATTACAATTCTATTCCATTACAACTCTATC
* *
29462977 CTATTACAATTCTTTTCCATTACAGCTCTATC
1 CTATTACAATTCTATTCCATTACAACTCTATC
29463009 CTATTA
1 CTATTA
29463015 TACTGAACCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (32 bp):
CTATTACAATTCTATTCCATTACAACTCTATC
Found at i:29464417 original size:24 final size:24
Alignment explanation
Indices: 29464390--29464445 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
29464380 TATATATATT
29464390 TGAAAAAAATTTCAAAGCAAAATA
1 TGAAAAAAATTTCAAAGCAAAATA
29464414 TGAAAAAAATTTCAAAGCAAAATA
1 TGAAAAAAATTTCAAAGCAAAATA
*
29464438 AGAAAAAA
1 TGAAAAAA
29464446 TACTTTAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.66, C:0.07, G:0.09, T:0.18
Consensus pattern (24 bp):
TGAAAAAAATTTCAAAGCAAAATA
Found at i:29464598 original size:19 final size:20
Alignment explanation
Indices: 29464554--29464619 Score: 82
Period size: 19 Copynumber: 3.3 Consensus size: 20
29464544 TCTTTAGAAT
*
29464554 TTTTTTTAAAATATTTTATA
1 TTTTTTAAAAATATTTTATA
29464574 TATTTTTAAAAATATTTT-TA
1 T-TTTTTAAAAATATTTTATA
*
29464594 TTTTTTAAAATTATTTTGA-A
1 TTTTTTAAAAATATTTT-ATA
29464614 TTTTTT
1 TTTTTT
29464620 TTTGTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 15 0.37
20 11 0.27
21 15 0.37
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTTAAAAATATTTTATA
Found at i:29464616 original size:20 final size:18
Alignment explanation
Indices: 29464555--29464619 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 18
29464545 CTTTAGAATT
29464555 TTTTTTAAAATATTTTATA
1 TTTTTTAAAATATTTTA-A
*
29464574 TATTTTTAAAAATATTTTTA
1 T-TTTTT-AAAATATTTTAA
29464594 TTTTTTAAAATTATTTTGAA
1 TTTTTTAAAA-TATTTT-AA
29464614 TTTTTT
1 TTTTTT
29464620 TTTGTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.10
19 12 0.30
20 14 0.35
21 10 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTTAAAATATTTTAA
Found at i:29472140 original size:27 final size:27
Alignment explanation
Indices: 29472102--29472154 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
29472092 GAAATATATA
29472102 AAAGGTTAAACATTCTGACCACCTTTT
1 AAAGGTTAAACATTCTGACCACCTTTT
*
29472129 AAAGGTTGAACATTCTGACCACCTTT
1 AAAGGTTAAACATTCTGACCACCTTT
29472155 ATAACTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (27 bp):
AAAGGTTAAACATTCTGACCACCTTTT
Found at i:29474930 original size:2 final size:2
Alignment explanation
Indices: 29474919--29475017 Score: 83
Period size: 2 Copynumber: 50.0 Consensus size: 2
29474909 GACTATTGAA
* * * *
29474919 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG TG TG TG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * * *
29474960 TG TG TG TG TG TG TG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
29475002 AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG
29475018 GATCCCCCGA
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
1 1 0.01
2 91 0.99
ACGTcount: A:0.39, C:0.00, G:0.49, T:0.11
Consensus pattern (2 bp):
AG
Found at i:29476350 original size:364 final size:364
Alignment explanation
Indices: 29475674--29476404 Score: 1128
Period size: 364 Copynumber: 2.0 Consensus size: 364
29475664 GTACAGTGTT
* * * *
29475674 AAGCACCGAATTGCAATTGCTTACCATCTGCAAGCCAATGGTTAAGCAGAGGTATCAAACCGTGA
1 AAGCACCGAATTGCAACTGCTTACCATCCGCAAGCCAATGGTTAAGAAGAGGTATCAAACCGAGA
* * *
29475739 GATTAAACAAATCATTGAGAATATAGTGAACTCATCTCGGAAAAATTGGTTGGTTCAATTAGATA
66 GATTAAACAAATCATTGAGAAGAGAGTGAACTCATCTCAGAAAAATTGGTTGGTTCAATTAGATA
*
29475804 ATGCCTTGTGAGCTTATAAGACAACTTATAAAACTCAGTTGGGGATGTCTCCATTCATAGTGTTT
131 ATGCATTGTGAGCTTATAAGACAACTTATAAAACTCAGTTGGGGATGTCTCCATTCATAGTGTTT
*
29475869 ACAGAAAGAACTATCATTTGCCAATAGAGTTAGAAAAGTGAGCATACTGGGCAGTTAAAGAATTG
196 ACAGAAAGAACTATCATTTGCCAATAGAGTTAGAAAAGCGAGCATACTGGGCAGTTAAAGAATTG
* * *
29475934 AATCTTGATCCTAAGTTAGCTAAACATGCTAGGTTGTTTCAACTAAATGAATTGGAGCAATTTAG
261 AATCTTGATCCTAAGTTAGCTAAAAACGCTAGGTTGTTTCAACTAAATGAATTAGAGCAATTTAG
* * *
29475999 ATTTTTGGTATATTAGAATGTCAAGTTGTACAAAGAGAA
326 ATTTTTGGCATATGAGAATGCCAAGTTGTACAAAGAGAA
*
29476038 AAGCACCGAATTGCAACTGCTTACCATCCGCAAGCCAATGGTTAAGAAGAGGTATCAAATC-AGA
1 AAGCACCGAATTGCAACTGCTTACCATCCGCAAGCCAATGGTTAAGAAGAGGTATCAAACCGAGA
** * *
29476102 GATTAAGTAAATCCTTGAGAAGAGAGTGAACTCATCTCAGAAAAATTGGTTGGTTCAATTAGATG
66 GATTAAACAAATCATTGAGAAGAGAGTGAACTCATCTCAGAAAAATTGGTTGGTTCAATTAGATA
*
29476167 ATGCATTGTGAGCTTATAAGACAACTTATAAAACTCCA-TTGGGGATGTCTCCATATCATATTGT
131 ATGCATTGTGAGCTTATAAGACAACTTATAAAACT-CAGTTGGGGATGTCTCCAT-TCATAGTGT
* **
29476231 TTACAGTAAA-AACTATCATTTGCCAATAGAGTTAGAAAAGCGAGCATACTTGGTTGTT-AAGAA
194 TTACAG-AAAGAACTATCATTTGCCAATAGAGTTAGAAAAGCGAGCATACTGGGCAGTTAAAG-A
* * * * *
29476294 ATTGAATCTTGGTCCTAATTTAGCTAAAAACGCTAGGTTGTTTCAACTACATGAATTAGAGTAGT
257 ATTGAATCTTGATCCTAAGTTAGCTAAAAACGCTAGGTTGTTTCAACTAAATGAATTAGAGCAAT
*
29476359 TTAGATTTTTGGCATATGAGAATGCCGAGTTGTACAAAGAGAA
322 TTAGATTTTTGGCATATGAGAATGCCAAGTTGTACAAAGAGAA
29476402 AAG
1 AAG
29476405 AAAATTGTGC
Statistics
Matches: 333, Mismatches: 30, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
363 113 0.34
364 217 0.65
365 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (364 bp):
AAGCACCGAATTGCAACTGCTTACCATCCGCAAGCCAATGGTTAAGAAGAGGTATCAAACCGAGA
GATTAAACAAATCATTGAGAAGAGAGTGAACTCATCTCAGAAAAATTGGTTGGTTCAATTAGATA
ATGCATTGTGAGCTTATAAGACAACTTATAAAACTCAGTTGGGGATGTCTCCATTCATAGTGTTT
ACAGAAAGAACTATCATTTGCCAATAGAGTTAGAAAAGCGAGCATACTGGGCAGTTAAAGAATTG
AATCTTGATCCTAAGTTAGCTAAAAACGCTAGGTTGTTTCAACTAAATGAATTAGAGCAATTTAG
ATTTTTGGCATATGAGAATGCCAAGTTGTACAAAGAGAA
Found at i:29476765 original size:35 final size:35
Alignment explanation
Indices: 29476726--29476795 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
29476716 TGTTGAAGAG
29476726 TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
1 TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
29476761 TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
1 TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
29476796 GATACCACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (35 bp):
TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
Found at i:29479532 original size:23 final size:23
Alignment explanation
Indices: 29479489--29479532 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29479479 GAAATTAAAT
**
29479489 TATAATTTTTACTATAGTAAAAA
1 TATAATTTTTAAAATAGTAAAAA
*
29479512 TATAATTTTTAAAATATTAAA
1 TATAATTTTTAAAATAGTAAA
29479533 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TATAATTTTTAAAATAGTAAAAA
Found at i:29481374 original size:14 final size:14
Alignment explanation
Indices: 29481340--29481368 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29481330 AAATTATAGA
29481340 TTATTATTATAATT
1 TTATTATTATAATT
29481354 TTATTATTA-AATT
1 TTATTATTATAATT
29481367 TT
1 TT
29481369 TTTTATACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATTATTATAATT
Found at i:29487454 original size:62 final size:59
Alignment explanation
Indices: 29487344--29487543 Score: 188
Period size: 62 Copynumber: 3.2 Consensus size: 59
29487334 TCAATTTAAC
* * * *
29487344 ATTAAATTAATATAATATTTATTAAGATAAATATTAGATTAAATTTAATATTAAATATT
1 ATTAAAATAATAAAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATATT
29487403 ATTAAAATAATAAAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAGATAACCA
1 ATTAAAATAATAAAATATTTAT-T--AAGATAAACATTAAATTAAATTTAATATTAA-AT----A
29487468 TTTTAAT
58 ---T--T
* * **
29487475 ATTAAATTAATAAAATA-CTATTAAGATATGCATTAAATTAAATTTAATATTAAA-ATT
1 ATTAAAATAATAAAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATATT
*
29487532 ATTAAGATAATA
1 ATTAAAATAATA
29487544 TTATTTTTGG
Statistics
Matches: 118, Mismatches: 10, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
57 11 0.09
59 21 0.18
60 1 0.01
62 30 0.25
63 2 0.02
67 2 0.02
68 29 0.25
70 2 0.02
71 3 0.03
72 17 0.14
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.41
Consensus pattern (59 bp):
ATTAAAATAATAAAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATATT
Found at i:29487543 original size:68 final size:70
Alignment explanation
Indices: 29487392--29487546 Score: 163
Period size: 68 Copynumber: 2.2 Consensus size: 70
29487382 TTAAATTTAA
* *
29487392 TATTAAATATTATTAAAATAATAAAATATTTATCTACAAGATAAACATTAAATTAAATTTAATAT
1 TATTAAATAATATTAAAATAATAAAATATCTATCTA-AAGATAAACATTAAATTAAATTTAATAT
*
29487457 TAAGAT
65 TAAAAT
* ** ** * **
29487463 AACCATTTTAATATTAAATTAATAAAATA-CTAT-T-AAGATATGCATTAAATTAAATTTAATAT
1 TATTA-AATAATATTAAAATAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATAT
29487525 TAAAAT
65 TAAAAT
29487531 TATTAAGATAATATTA
1 TATTAA-ATAATATTA
29487547 TTTTTGGAAT
Statistics
Matches: 66, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
68 41 0.62
70 1 0.02
71 5 0.08
72 19 0.29
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (70 bp):
TATTAAATAATATTAAAATAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATATT
AAAAT
Found at i:29489437 original size:43 final size:43
Alignment explanation
Indices: 29489268--29489438 Score: 145
Period size: 43 Copynumber: 4.0 Consensus size: 43
29489258 ATAAGATTCT
* * * *
29489268 GATATGTGATTTCGTGTAAGACCACGTTTGGGACGTTGGCATC
1 GATATTTGATTACGTGTAAGACCTCGTCTGGGACGTTGGCATC
* * *
29489311 GAT-TTGAGATTTACGTGTAAGACCAT-GTCTGGGACATTGGCACC
1 GATATT-TGA-TTACGTGTAAGACC-TCGTCTGGGACGTTGGCATC
* ** * *
29489355 G-TATATGATTTTGTGTAATACC-CTGTCTGGGATAG-TGGCATC
1 GATATTTGATTACGTGTAAGACCTC-GTCTGGGA-CGTTGGCATC
*
29489397 GATATTTGATTACATGTAAGACCTCGTCTGGGACGTTGGCAT
1 GATATTTGATTACGTGTAAGACCTCGTCTGGGACGTTGGCAT
29489439 TGTTCGAGCT
Statistics
Matches: 97, Mismatches: 21, Indels: 20
0.70 0.15 0.14
Matches are distributed among these distances:
42 28 0.29
43 38 0.39
44 31 0.32
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
GATATTTGATTACGTGTAAGACCTCGTCTGGGACGTTGGCATC
Found at i:29497525 original size:23 final size:23
Alignment explanation
Indices: 29497482--29497530 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
29497472 GAGACGTGGC
* *
29497482 ATCGCGTCGTCGAGACAAGGGGT
1 ATCGCGTCATCGAGACAAGGGCT
**
29497505 ATCGCGTCATCGAGATGAGGGCT
1 ATCGCGTCATCGAGACAAGGGCT
29497528 ATC
1 ATC
29497531 TTCTCGTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.20
Consensus pattern (23 bp):
ATCGCGTCATCGAGACAAGGGCT
Found at i:29497971 original size:9 final size:9
Alignment explanation
Indices: 29497957--29498035 Score: 51
Period size: 9 Copynumber: 8.6 Consensus size: 9
29497947 ATTAAAAAAT
29497957 ATTTTTATA
1 ATTTTTATA
29497966 ATTTTTA-A
1 ATTTTTATA
*
29497974 ATAATTTTATG
1 AT--TTTTATA
29497985 A-TTTT-TA
1 ATTTTTATA
29497992 ATTTTTAAAATA
1 ATTTTT---ATA
29498004 ATTTTTTATA
1 A-TTTTTATA
29498014 ATTTTTCA-A
1 ATTTTT-ATA
29498023 ATTTTTA-A
1 ATTTTTATA
29498031 ATTTT
1 ATTTT
29498036 CAAAAATTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
7 2 0.03
8 18 0.31
9 19 0.33
10 10 0.17
11 1 0.02
12 3 0.05
13 5 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:29497981 original size:19 final size:19
Alignment explanation
Indices: 29497953--29497992 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29497943 ATATATTAAA
*
29497953 AAATATTTTTATAATTTTT
1 AAATAATTTTATAATTTTT
*
29497972 AAATAATTTTATGATTTTT
1 AAATAATTTTATAATTTTT
29497991 AA
1 AA
29497993 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
AAATAATTTTATAATTTTT
Found at i:29498037 original size:16 final size:18
Alignment explanation
Indices: 29498006--29498039 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
29497996 TTAAAATAAT
29498006 TTTTTATAATTTTTCAAA
1 TTTTTATAATTTTTCAAA
29498024 TTTTTA-AA-TTTTCAAA
1 TTTTTATAATTTTTCAAA
29498040 AATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTATAATTTTTCAAA
Found at i:29500613 original size:20 final size:20
Alignment explanation
Indices: 29500581--29500633 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
29500571 ACCAATTTAT
*
29500581 AGACAAGCCACCAG-ATTCAC
1 AGACAAGCTACCAGAATT-AC
* *
29500601 AGATAAGCTACCAGAATTGC
1 AGACAAGCTACCAGAATTAC
29500621 AGACAAGCTACCA
1 AGACAAGCTACCA
29500634 TAAATGTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.42, C:0.28, G:0.17, T:0.13
Consensus pattern (20 bp):
AGACAAGCTACCAGAATTAC
Found at i:29507743 original size:17 final size:17
Alignment explanation
Indices: 29507721--29507753 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29507711 ACTGCAGGGG
*
29507721 TCACACGGTCATGTGAA
1 TCACACGGTCAAGTGAA
29507738 TCACACGGTCAAGTGA
1 TCACACGGTCAAGTGA
29507754 CACGCTCGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (17 bp):
TCACACGGTCAAGTGAA
Found at i:29509141 original size:25 final size:25
Alignment explanation
Indices: 29509110--29509212 Score: 109
Period size: 25 Copynumber: 4.2 Consensus size: 25
29509100 GTTATAAACA
29509110 GTAAGCTCATCCGAGCTGAATAACG
1 GTAAGCTCATCCGAGCTGAATAACG
* * *
29509135 GTAAGCTCTTCCGAGATGAATAATG
1 GTAAGCTCATCCGAGCTGAATAACG
* * **
29509160 GTAAGCTCATGCGAGCTGAGTATTG
1 GTAAGCTCATCCGAGCTGAATAACG
* * *
29509185 GTAAGCTCATACAAGCTGAA-ATCG
1 GTAAGCTCATCCGAGCTGAATAACG
29509209 GTAA
1 GTAA
29509213 CCCTAATGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
24 7 0.11
25 59 0.89
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (25 bp):
GTAAGCTCATCCGAGCTGAATAACG
Found at i:29510919 original size:21 final size:21
Alignment explanation
Indices: 29510869--29510919 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
29510859 TAGATAGTTC
*
29510869 TTTTATTTTTGTATATTGTTG
1 TTTTATTTTTGTAAATTGTTG
*
29510890 TTTTCTTTTTGTGAAATT-TT-
1 TTTTATTTTTGT-AAATTGTTG
29510910 TATTTATTTT
1 T-TTTATTTT
29510920 CCTTGTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 4 0.16
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTATTTTTGTAAATTGTTG
Found at i:29521468 original size:14 final size:14
Alignment explanation
Indices: 29521449--29521476 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29521439 GTTTAAAGAT
29521449 GGTTAAAAACTAAG
1 GGTTAAAAACTAAG
29521463 GGTTAAAAACTAAG
1 GGTTAAAAACTAAG
29521477 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
GGTTAAAAACTAAG
Found at i:29523958 original size:15 final size:16
Alignment explanation
Indices: 29523935--29523964 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29523925 AAAAATTAAT
29523935 ATATAAATTATAAATA
1 ATATAAATTATAAATA
29523951 ATAT-AATTATAAAT
1 ATATAAATTATAAAT
29523965 TAAAGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAATTATAAATA
Found at i:29523962 original size:22 final size:21
Alignment explanation
Indices: 29523923--29523966 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
29523913 AGCTAAGTTG
29523923 ATAAAAATTAATATATAAATT
1 ATAAAAATTAATATATAAATT
29523944 ATAAATAATATAAT-TATAAATT
1 ATAAA-AAT-TAATATATAAATT
29523966 A
1 A
29523967 AAGTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 12 0.57
23 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAAATTAATATATAAATT
Found at i:29530092 original size:14 final size:14
Alignment explanation
Indices: 29530073--29530100 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29530063 TTTTAAAGAT
29530073 GGTTAAAAACTAAG
1 GGTTAAAAACTAAG
29530087 GGTTAAAAACTAAG
1 GGTTAAAAACTAAG
29530101 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
GGTTAAAAACTAAG
Found at i:29531646 original size:19 final size:20
Alignment explanation
Indices: 29531602--29531646 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
29531592 ATCATGTTCA
29531602 TATTTTTAACATATTTTAAT
1 TATTTTTAACATATTTTAAT
29531622 TA-TTTTATA-ATA-TTTAAT
1 TATTTTTA-ACATATTTTAAT
29531640 TATTTTT
1 TATTTTT
29531647 CGACAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
20 3 0.13
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTTAACATATTTTAAT
Found at i:29537613 original size:30 final size:30
Alignment explanation
Indices: 29537444--29537652 Score: 135
Period size: 29 Copynumber: 7.1 Consensus size: 30
29537434 AGTGGGATCA
* * * *
29537444 CGATGGTCGTCATCGTCCCTTTTCATAGTT
1 CGATAGTCGTCACCATCCCTTTTCATAATT
29537474 -GATAGTCGTCACCATCCCTTTTCATAA-T
1 CGATAGTCGTCACCATCCCTTTTCATAATT
* * * * *
29537502 CGATAGTTG-AAGCTATTCATTTTCATAATT
1 CGATAGTCGTCA-CCATCCCTTTTCATAATT
* * *
29537532 TGATGGTCGTCACCATCCTTTTTCA-ATATT
1 CGATAGTCGTCACCATCCCTTTTCATA-ATT
* * * * *
29537562 TGATAGCCG-AAGCTATACCTTTTCATAATT
1 CGATAGTCGTCA-CCATCCCTTTTCATAATT
* *
29537592 CAATGGTCGTCACCATCCCTTTTCATAA-T
1 CGATAGTCGTCACCATCCCTTTTCATAATT
* * *
29537621 CGATAGCCG-AAGCTATCCCTTTTCATAATT
1 CGATAGTCGTCA-CCATCCCTTTTCATAATT
29537651 CG
1 CG
29537653 GTGATCATCG
Statistics
Matches: 135, Mismatches: 34, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
28 3 0.02
29 67 0.50
30 62 0.46
31 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (30 bp):
CGATAGTCGTCACCATCCCTTTTCATAATT
Found at i:29537651 original size:59 final size:59
Alignment explanation
Indices: 29537459--29537652 Score: 264
Period size: 59 Copynumber: 3.3 Consensus size: 59
29537449 GTCGTCATCG
* * **
29537459 TCCCTTTTCATAGTT-GATAGTCGTCACCATCCCTTTTCATAATCGATAGTTGAAGCTA
1 TCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
* * * * * *
29537517 TTCATTTTCATAATTTGATGGTCGTCACCATCCTTTTTCAATATTTGATAGCCGAAGCTA
1 TCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTC-ATAATCGATAGCCGAAGCTA
* *
29537577 TACCTTTTCATAATTCAATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
1 TCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
29537636 TCCCTTTTCATAATTCG
1 TCCCTTTTCATAATTCG
29537653 GTGATCATCG
Statistics
Matches: 116, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
58 12 0.10
59 54 0.47
60 50 0.43
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (59 bp):
TCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
Found at i:29550200 original size:19 final size:17
Alignment explanation
Indices: 29550165--29550200 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
29550155 TACGAAATAA
29550165 AATAATTACAATTAATT
1 AATAATTACAATTAATT
29550182 AATAATATACAACTTAATT
1 AATAAT-TACAA-TTAATT
29550201 TCATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAATTACAATTAATT
Found at i:29550664 original size:9 final size:9
Alignment explanation
Indices: 29550650--29550675 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29550640 CTTGCTATTT
29550650 TTTTCTTTC
1 TTTTCTTTC
29550659 TTTTCTTTC
1 TTTTCTTTC
29550668 TTTTCTTT
1 TTTTCTTT
29550676 TTAATGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:29563683 original size:40 final size:39
Alignment explanation
Indices: 29563653--29563875 Score: 211
Period size: 40 Copynumber: 5.6 Consensus size: 39
29563643 GCTACTCGTT
*
29563653 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGTTATAGTAACTCGCA
* *
29563693 CAAATGCATTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGG-TTATAGTAACTCGCA
* *
29563733 CAAATGCCTTCGGGCTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGTTA-TAGTAACTCGCA
* *
29563772 CAAATGCCTTCGGGCTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGTTA-TAGTAACTCGCA
** * * * * *
29563811 CAAATGCCTTCAGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTC-GGGCTTAGCCCGGTTATAGTAAC-TCGCA
*
29563852 CAAAT-CCTTCGAGACTTAGCCCGG
1 CAAATGCCTTCG-GGCTTAGCCCGG
29563876 ACATCATTCA
Statistics
Matches: 158, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
39 71 0.45
40 75 0.47
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGTTATAGTAACTCGCA
Found at i:29563770 original size:39 final size:40
Alignment explanation
Indices: 29563653--29563876 Score: 253
Period size: 39 Copynumber: 5.7 Consensus size: 40
29563643 GCTACTCGTT
* *
29563653 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * *
29563693 CAAATGCATTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
29563733 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
29563772 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * * *
29563811 CAAATGCCTTC-AGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
*
29563852 CAAAT-CCTTCGAGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29563877 CATCATTCAA
Statistics
Matches: 163, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
38 1 0.01
39 74 0.45
40 74 0.45
41 14 0.09
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:29563830 original size:79 final size:79
Alignment explanation
Indices: 29563653--29563836 Score: 228
Period size: 79 Copynumber: 2.3 Consensus size: 79
29563643 GCTACTCGTT
* * *
29563653 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCATTCGGGACTTAACCCG
1 CAAATGCCTTCGAG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCATTCGGGACTTAACCCG
*
29563717 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
* * * *
29563733 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGAGCTTAGCCCGGAATTAGTAACTCGCACAAATGCATTCGGGACTTAACCCGGA
*
29563797 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* *
29563811 CAAATGCCTTCAGATCTTAGTCCGGA
1 CAAATGCCTTC-GAGCTTAGCCCGGA
29563837 TATGGTCACT
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 33 0.36
79 44 0.48
80 15 0.16
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGAGCTTAGCCCGGAATTAGTAACTCGCACAAATGCATTCGGGACTTAACCCGGA
ATTAGTAACTCGCA
Found at i:29571766 original size:79 final size:82
Alignment explanation
Indices: 29571655--29571839 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
29571645 GCTACTCGTT
* *
29571655 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
29571718 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
29571735 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
29571798 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
29571815 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29571840 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:29571839 original size:40 final size:40
Alignment explanation
Indices: 29571636--29571839 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
29571626 CGGAATTTAA
** *
29571636 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29571676 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
29571716 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29571755 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
29571795 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29571835 CCGGA
1 CCGGA
29571840 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29574546 original size:112 final size:112
Alignment explanation
Indices: 29574092--29574641 Score: 776
Period size: 114 Copynumber: 4.9 Consensus size: 112
29574082 AAAATAAGCA
** * ** ** *
29574092 TTAGCGGCGTTTTCCAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCAGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
* * *
29574157 TGGGAATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGGTTAGGGCT
66 TGGG-ATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
* *
29574205 TTAGCAGCGTTTTTGAGAAAGCGCCGCAAAAAAATATAAGCCCAACGACGTCGTTTTGTGGGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAA-ATAAGCCCAACGACGCCGTTTTGTGGGCTT
* *
29574270 TTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGCT
65 TT-GGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
* * *
29574319 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACATAAGCCCAACGGCGCCGTTTTATGGGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAA-ATAAGCCCAACGACGCCGTTTTGTGGGCTT
*
29574384 TTGAGGATTTAGCGACGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
65 TTG-GGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
* *
29574433 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGTCATTTTGTGGGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
* * *
29574498 TGGGATTTAGCGGCGCTTTTAAGAAAGCGCCACTAATGCTTAGTGCT
66 TGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
** * *
29574545 TTAGCTACGTTTTTTAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCTGTTTTGTGGGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
**
29574610 TGGGGATTTAGCAACGTTTTTAAGAAAGCGCC
66 T-GGGATTTAGCGGCGTTTTTAAGAAAGCGCC
29574642 GCAAAAAAAC
Statistics
Matches: 395, Mismatches: 38, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
112 101 0.26
113 86 0.22
114 205 0.52
115 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (112 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
TGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
Found at i:29574682 original size:73 final size:72
Alignment explanation
Indices: 29574544--29574694 Score: 239
Period size: 73 Copynumber: 2.1 Consensus size: 72
29574534 TGCTTAGTGC
* * * * *
29574544 TTTAGCTACGTTTTTTAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCTGTTTTGTGGGCTT
1 TTTAGCAACGTTTTTAAGAAAGCGCCGCAAAAAAAATAAGCCAAACGACGCCGTTTTGTGAGCTT
*
29574609 TTGGGGA
66 TCGGGGA
29574616 TTTAGCAACGTTTTTAAGAAAGCGCCGCAAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCT
1 TTTAGCAACGTTTTTAAGAAAGCGCCGCAAAAAAA-ATAAGCCAAACGACGCCGTTTTGTGAGCT
29574681 TTCGGGGA
65 TTCGGGGA
29574689 TTTAGC
1 TTTAGC
29574695 GGCCAAAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 33 0.46
73 39 0.54
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (72 bp):
TTTAGCAACGTTTTTAAGAAAGCGCCGCAAAAAAAATAAGCCAAACGACGCCGTTTTGTGAGCTT
TCGGGGA
Found at i:29574889 original size:14 final size:14
Alignment explanation
Indices: 29574872--29574902 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29574862 GGTTTAGAGT
29574872 TTATGGATTAGGGA
1 TTATGGATTAGGGA
*
29574886 TTATGGATTATGGA
1 TTATGGATTAGGGA
29574900 TTA
1 TTA
29574903 AGGGTTGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (14 bp):
TTATGGATTAGGGA
Found at i:29575253 original size:14 final size:13
Alignment explanation
Indices: 29575219--29575267 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
29575209 GATTTAAGGT
29575219 TTAGGGGTTAGGAG
1 TTAGGGGTTA-GAG
29575233 TTTAGGGGTTAGATG
1 -TTAGGGGTTAGA-G
29575248 TTAGGGGTTAAGAG
1 TTAGGGGTT-AGAG
29575262 TTAGGG
1 TTAGGG
29575268 ATTTAAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 18 0.56
15 14 0.44
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:29575287 original size:15 final size:14
Alignment explanation
Indices: 29575212--29575282 Score: 65
Period size: 15 Copynumber: 4.9 Consensus size: 14
29575202 GTGTTGGGAT
29575212 TTAAGGTTTAGGGG
1 TTAAGGTTTAGGGG
*
29575226 TTAGGAGTTTAGGGG
1 TTAAG-GTTTAGGGG
*
29575241 TT-AGATGTTAGGGG
1 TTAAGGT-TTAGGGG
*
29575255 TTAAGAG-TTAGGGAT
1 TTAAG-GTTTAGGG-G
29575270 TTAAGGTTTAGGG
1 TTAAGGTTTAGGG
29575283 ATTTAGGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
13 1 0.02
14 21 0.46
15 24 0.52
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (14 bp):
TTAAGGTTTAGGGG
Found at i:29576090 original size:106 final size:108
Alignment explanation
Indices: 29575974--29576319 Score: 385
Period size: 107 Copynumber: 3.1 Consensus size: 108
29575964 AGCAATAGCA
** * *
29575974 GCGTTTTTATAA-AAAATGCCATAAAATAATTTTACTTTAAAAAAATAGCCCCTTTTAGCATAGC
1 GCGTTTTTATAAGAAAACACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCATAGC
29576038 ATAGCAAAACGGCATAGTTTTGTTCAAAAT-AAATTTTTTGCG
66 ATAGCAAAACGGCATAGTTTTGTTCAAAATGAAATTTTTTGCG
29576080 GCGTTTTTATAAGAAAACACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCATAGC
1 GCGTTTTTATAAGAAAACACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCATAGC
*
29576145 ATAGCAAAACGGCATAGTTTTGTTCAAAATGAAATTTTTTTCTAAAGGTAAGCAATA
66 ATAGCAAAACGGCATAGTTTTGTTCAAAATGAAA---TTTT-T-----T--GC---G
* * * * * * *
29576202 GCGGTGTTTTTATAAAAAACGCCACAAAATAATTTTAC-TTTAAAAAATAG-CCCTTTTAGCATA
1 GCGTTTTTATAAGAAAA--CACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCATA
* *
29576265 GCATAGCAAAACGGCGTAGTTTTGTTTAAAATGAAAATTTTTTGCG
64 GCATAGCAAAACGGCATAGTTTTGTTCAAAATG-AAATTTTTTGCG
29576311 GCGTTTTTA
1 GCGTTTTTA
29576320 CCGCTAAAGA
Statistics
Matches: 203, Mismatches: 18, Indels: 35
0.79 0.07 0.14
Matches are distributed among these distances:
106 12 0.06
107 78 0.38
108 3 0.01
109 6 0.03
111 4 0.02
112 3 0.01
114 1 0.00
117 1 0.00
119 3 0.01
120 4 0.02
122 56 0.28
123 14 0.07
124 18 0.09
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (108 bp):
GCGTTTTTATAAGAAAACACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCATAGC
ATAGCAAAACGGCATAGTTTTGTTCAAAATGAAATTTTTTGCG
Found at i:29576276 original size:122 final size:125
Alignment explanation
Indices: 29576077--29576307 Score: 387
Period size: 122 Copynumber: 1.9 Consensus size: 125
29576067 TAAATTTTTT
29576077 GCGGCGTTTTTATAAGAAAACACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCAT
1 GCGGCGTTTTTATAAGAAAACACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCAT
*
29576142 AGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAAATTTTTTTCTAAAGGTAAGCAATA
66 AGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAAAATTTTTTCTAAAGGTAAGCAATA
* * *
29576202 GCGGTGTTTTTATAA-AAAACGCCACAAAATAATTTTAC-TTTAAAAAATAG-CCCTTTTAGCAT
1 GCGGCGTTTTTATAAGAAAACACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCAT
* *
29576264 AGCATAGCAAAACGGCGTAGTTTTGTTTAAAATGAAAATTTTTT
66 AGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAAAATTTTTT
29576308 GCGGCGTTTT
Statistics
Matches: 100, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
122 53 0.53
123 11 0.11
124 22 0.22
125 14 0.14
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (125 bp):
GCGGCGTTTTTATAAGAAAACACCACAAAATAATTTTACGTTAAAAAAATAGCCCCTTTTAGCAT
AGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAAAATTTTTTCTAAAGGTAAGCAATA
Found at i:29581192 original size:23 final size:22
Alignment explanation
Indices: 29581140--29581192 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
29581130 TCCACGTCTT
*
29581140 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
29581162 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
29581185 TTTCTTTT
1 TTTCTTTT
29581193 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:29585192 original size:43 final size:43
Alignment explanation
Indices: 29585103--29585223 Score: 149
Period size: 43 Copynumber: 2.8 Consensus size: 43
29585093 TTTTTGCTAC
* *
29585103 AAGCGTCGCTAAAGGT-TTGCTTGTTT-GCGGCATTTGTGAAAG
1 AAGCGTCGCTAAAGGTCTTG-TTCTTTAGCGGCGTTTGTGAAAG
* *
29585145 AAGCGTCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAA-
1 AAGCGTCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTGT-GAAAG
* *
29585188 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 AAGCGTCGCTAAAGGTCTTGTTCTTTAGCGGCGTTT
29585224 TTCTCTAAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
42 21 0.30
43 45 0.65
44 3 0.04
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.31
Consensus pattern (43 bp):
AAGCGTCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTGTGAAAG
Found at i:29585256 original size:42 final size:42
Alignment explanation
Indices: 29585188--29585351 Score: 229
Period size: 42 Copynumber: 3.9 Consensus size: 42
29585178 TTTGTGGGAA
** * *
29585188 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTTTCTCT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
* * * * *
29585230 AAACGTCGTTAAAGAACATGGTCTTTAGTGGCGTTTTTTTGT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
* *
29585272 AAGCGCCGCTAAAGAACATGGTCTTTAACGGTGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
29585314 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
29585352 GTTTGTAAAC
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 104 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
Found at i:29585308 original size:84 final size:84
Alignment explanation
Indices: 29585151--29585351 Score: 240
Period size: 84 Copynumber: 2.4 Consensus size: 84
29585141 AAAGAAGCGT
** * * ** * ** * *
29585151 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAG
1 CGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTG-TAAGCGCCGCTAAAGAACATGGTCTTTAA
*
29585216 CGGCGTTTTTCTCTAAACGT
65 CGGCGTTTTTCTCTAAACGC
* *
29585236 CGTTAAAGAACATGGTCTTTAGTGGCGTTTTTTTGTAAGCGCCGCTAAAGAACATGGTCTTTAAC
1 CGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTGTAAGCGCCGCTAAAGAACATGGTCTTTAAC
* * *
29585301 GGTGTTTTTTTCTAAGCGC
66 GGCGTTTTTCTCTAAACGC
29585320 CGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 CGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
29585352 GTTTGTAAAC
Statistics
Matches: 97, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
84 70 0.72
85 27 0.28
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (84 bp):
CGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTGTAAGCGCCGCTAAAGAACATGGTCTTTAAC
GGCGTTTTTCTCTAAACGC
Found at i:29585468 original size:21 final size:22
Alignment explanation
Indices: 29585443--29585485 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29585433 TAGTAGCGTT
*
29585443 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAGACCTA
*
29585465 AAAAAATGCCGCTAAAGACCT
1 AAAAAACGCCGCTAAAGACCT
29585486 GTTTTGGTGT
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:0.47, C:0.26, G:0.16, T:0.12
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAGACCTA
Found at i:29586162 original size:40 final size:40
Alignment explanation
Indices: 29586118--29586295 Score: 184
Period size: 40 Copynumber: 4.5 Consensus size: 40
29586108 GTATAAATAG
* * *
29586118 GGGCACGTAAGTGCATTCCGAGGTACCGAAGTACAAACAA
1 GGGCACGTATGTGCATTCAGAGGTACCAAAGTACAAACAA
**
29586158 GGGCACGTATGTGCATTCA-AGGGTATTAAAGTACAAAC-A
1 GGGCACGTATGTGCATTCAGA-GGTACCAAAGTACAAACAA
* * *
29586197 GGGTCACGTATGTGCATTCAGGGGTACAAAAGTACAATCAA
1 GGG-CACGTATGTGCATTCAGAGGTACCAAAGTACAAACAA
* * * *
29586238 GGGCACATATGTGCATTTAG-GGTACCGAAGTACAAA-TA
1 GGGCACGTATGTGCATTCAGAGGTACCAAAGTACAAACAA
*
29586276 GGAGCACGTATGTGTATTCA
1 GG-GCACGTATGTGCATTCA
29586296 TTCAATAATT
Statistics
Matches: 115, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
38 3 0.03
39 32 0.28
40 76 0.66
41 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (40 bp):
GGGCACGTATGTGCATTCAGAGGTACCAAAGTACAAACAA
Found at i:29586230 original size:80 final size:78
Alignment explanation
Indices: 29586107--29586295 Score: 216
Period size: 80 Copynumber: 2.4 Consensus size: 78
29586097 GAGTTACCGG
* * * ** *
29586107 AGTATAAATAGGGGCACGTAAGTGCATTCCGAGGTACCGAAGTACAAACAAGGGCACGTATGTGC
1 AGTACAAATA-GGGCACGTATGTGCATTCAGAGGTACAAAAGTACAAACAAGGGCACATATGTGC
**
29586172 ATTCAAGGGTATTAA
65 ATT-AAGGGTACCAA
* * *
29586187 AGTACAAACAGGGTCACGTATGTGCATTCAGGGGTACAAAAGTACAATCAAGGGCACATATGTGC
1 AGTACAAATAGGG-CACGTATGTGCATTCAGAGGTACAAAAGTACAAACAAGGGCACATATGTGC
* *
29586252 ATTTAGGGTACCGA
65 ATTAAGGGTACCAA
*
29586266 AGTACAAATAGGAGCACGTATGTGTATTCA
1 AGTACAAATAGG-GCACGTATGTGCATTCA
29586296 TTCAATAATT
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
79 36 0.39
80 56 0.61
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (78 bp):
AGTACAAATAGGGCACGTATGTGCATTCAGAGGTACAAAAGTACAAACAAGGGCACATATGTGCA
TTAAGGGTACCAA
Found at i:29587803 original size:82 final size:82
Alignment explanation
Indices: 29587679--29587835 Score: 296
Period size: 82 Copynumber: 1.9 Consensus size: 82
29587669 AATCTATACT
*
29587679 GTCTTAGCATTGAAACGTGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
1 GTCTTAGCATTGAAACATGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
29587744 TAAGCTATAGCATTGAA
66 TAAGCTATAGCATTGAA
29587761 GTCTTAGCATTGAAACATGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
1 GTCTTAGCATTGAAACATGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
*
29587826 TAAGGTATAG
66 TAAGCTATAG
29587836 ACTGATTCTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (82 bp):
GTCTTAGCATTGAAACATGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
TAAGCTATAGCATTGAA
Found at i:29607599 original size:23 final size:24
Alignment explanation
Indices: 29607543--29607602 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
29607533 TTATTAACAT
*
29607543 TGTTCGTGAATATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
* *
29607567 TGTTCATGAACATGTTCATTTA-A
1 TGTTCGTGAACATGTTCAATTATA
29607590 TGTTCGTGAACAT
1 TGTTCGTGAACAT
29607603 TAAATAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:29608337 original size:40 final size:40
Alignment explanation
Indices: 29608252--29608341 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 40
29608242 GGGACGTGTT
* * *
29608252 AGCAAATCGCATCCACGTCAGCGCGATTACTTACGTGGCA
1 AGCAAATCGCGTCCACGTAAGCGCGATTACTAACGTGGCA
29608292 A-CAAATCGCGTCCACGTAAGCGCGATTTACTAACGTGG-A
1 AGCAAATCGCGTCCACGTAAGCGCGA-TTACTAACGTGGCA
29608331 AGCAAATCGCG
1 AGCAAATCGCG
29608342 CTTACGTGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 24 0.53
40 21 0.47
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (40 bp):
AGCAAATCGCGTCCACGTAAGCGCGATTACTAACGTGGCA
Found at i:29610589 original size:12 final size:12
Alignment explanation
Indices: 29610574--29610601 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29610564 TGTTATCATG
29610574 GTGGTTATAATA
1 GTGGTTATAATA
29610586 GTGGTTATAATA
1 GTGGTTATAATA
29610598 GTGG
1 GTGG
29610602 AACTTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (12 bp):
GTGGTTATAATA
Found at i:29615324 original size:28 final size:28
Alignment explanation
Indices: 29615290--29615345 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
29615280 TAACATAGTT
29615290 TTTCTATGTTTTCCATTTGTTAAAACTA
1 TTTCTATGTTTTCCATTTGTTAAAACTA
29615318 TTTCTATGTTTTCCATTTGTTAAAACTA
1 TTTCTATGTTTTCCATTTGTTAAAACTA
29615346 ATCCCTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (28 bp):
TTTCTATGTTTTCCATTTGTTAAAACTA
Found at i:29615897 original size:5 final size:6
Alignment explanation
Indices: 29615868--29615901 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
29615858 TTTGACTTTA
29615868 AAAAAT AAAGAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT -AA-AAAT AAAAAT AAAAAT AAAAAT AA
29615902 TTAAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.69
7 4 0.15
8 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:29620026 original size:16 final size:16
Alignment explanation
Indices: 29620003--29620052 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
29619993 TAAAAAGTAA
29620003 TTAGAATATATAATAT
1 TTAGAATATATAATAT
* *
29620019 TTCA-AATA-AAAATAA
1 TT-AGAATATATAATAT
29620034 TTAGAATATATAATAT
1 TTAGAATATATAATAT
29620050 TTA
1 TTA
29620053 AAAATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.41
16 14 0.52
17 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (16 bp):
TTAGAATATATAATAT
Found at i:29620038 original size:31 final size:32
Alignment explanation
Indices: 29619988--29620060 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
29619978 AGATACTAAC
29619988 TCAAATAAAAAGTAATTAGAATATATAATATT
1 TCAAATAAAAAGTAATTAGAATATATAATATT
29620020 TCAAATAAAAA-TAATTAGAATATATAATATT
1 TCAAATAAAAAGTAATTAGAATATATAATATT
*
29620051 TAAAAATAAA
1 T-CAAATAAA
29620061 TTTTAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 21 0.54
32 18 0.46
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (32 bp):
TCAAATAAAAAGTAATTAGAATATATAATATT
Found at i:29620041 original size:15 final size:15
Alignment explanation
Indices: 29619991--29620041 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
29619981 TACTAACTCA
29619991 AATAAAAAGTAATTAG
1 AATAAAAA-TAATTAG
* *
29620007 AATATATAATATTTCA-
1 AATA-AAAATAATT-AG
29620023 AATAAAAATAATTAG
1 AATAAAAATAATTAG
29620038 AATA
1 AATA
29620042 TATAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 1 0.04
15 11 0.39
16 12 0.43
17 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (15 bp):
AATAAAAATAATTAG
Found at i:29620217 original size:17 final size:17
Alignment explanation
Indices: 29620176--29620217 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
29620166 TTTCATTGCT
29620176 ATTATTTTGATTGTCAA
1 ATTATTTTGATTGTCAA
29620193 ATTAATTTTGA-TGTCTAA
1 ATT-ATTTTGATTGTC-AA
29620211 ATTATTT
1 ATTATTT
29620218 AAACAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (17 bp):
ATTATTTTGATTGTCAA
Found at i:29621488 original size:27 final size:27
Alignment explanation
Indices: 29621404--29621493 Score: 94
Period size: 27 Copynumber: 3.3 Consensus size: 27
29621394 TCGCGAGGTG
*
29621404 GGGTTCGCCAGTTGGTTTGGC-AAGCTA
1 GGGTTTGCCAGTTGGTTTGGCGAA-CTA
* * * *
29621431 AGGTTTGCTAGTTGGTTTGGTG-AGTA
1 GGGTTTGCCAGTTGGTTTGGCGAACTA
*
29621457 GGGGTTTGCCAATTGGTTTGGCGAACTA
1 -GGGTTTGCCAGTTGGTTTGGCGAACTA
29621485 GGGTTTGCC
1 GGGTTTGCC
29621494 GGTATAAATC
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
26 2 0.04
27 45 0.90
28 3 0.06
ACGTcount: A:0.14, C:0.13, G:0.38, T:0.34
Consensus pattern (27 bp):
GGGTTTGCCAGTTGGTTTGGCGAACTA
Found at i:29623966 original size:33 final size:33
Alignment explanation
Indices: 29623922--29624082 Score: 148
Period size: 33 Copynumber: 4.9 Consensus size: 33
29623912 CATGGCATCC
* * *
29623922 ATAGAGGTAGTCCGCTGAGACAGTAAACACAGA
1 ATAGAGATAGTCCACTGAGACAATAAACACAGA
* * *
29623955 ATAGAGATAGTCCGCTGGGACAATAAACACAAA
1 ATAGAGATAGTCCACTGAGACAATAAACACAGA
* * * *
29623988 ATAGAGATAGTCCACTGGGATAGTAAACATAGA
1 ATAGAGATAGTCCACTGAGACAATAAACACAGA
* * * *
29624021 ATAAAGATAGTCCATTGAGACAATAAATATA-A
1 ATAGAGATAGTCCACTGAGACAATAAACACAGA
* *
29624053 A-ATAGATAGTCCA-TTAGGACAATAAACACA
1 ATAGAGATAGTCCACTGA-GACAATAAACACA
29624083 TAACAAATAA
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
30 2 0.02
31 22 0.20
32 2 0.02
33 82 0.76
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (33 bp):
ATAGAGATAGTCCACTGAGACAATAAACACAGA
Found at i:29624029 original size:66 final size:66
Alignment explanation
Indices: 29623922--29624082 Score: 175
Period size: 66 Copynumber: 2.5 Consensus size: 66
29623912 CATGGCATCC
* * * * *
29623922 ATAGAGGTAGTCCGCTGAGACAGTAAACACAGAATAGAGATAGTCCGCTGGGACAATAAACACAA
1 ATAGAGATAGTCCACTGAGACAGTAAACACAGAATAAAGATAGTCCACTGAGACAATAAACACAA
29623987 A
66 A
* * * * * *
29623988 ATAGAGATAGTCCACTGGGATAGTAAACATAGAATAAAGATAGTCCATTGAGACAATAAATATAA
1 ATAGAGATAGTCCACTGAGACAGTAAACACAGAATAAAGATAGTCCACTGAGACAATAAACACAA
29624053 A
66 A
* *
29624054 AT--AGATAGTCCA-TTAGGACAATAAACACA
1 ATAGAGATAGTCCACTGA-GACAGTAAACACA
29624083 TAACAAATAA
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
63 1 0.01
64 20 0.26
66 57 0.73
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (66 bp):
ATAGAGATAGTCCACTGAGACAGTAAACACAGAATAAAGATAGTCCACTGAGACAATAAACACAA
A
Found at i:29632050 original size:22 final size:21
Alignment explanation
Indices: 29632025--29632068 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
29632015 TGATAAACTT
29632025 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
29632047 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
29632068 T
1 T
29632069 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:29644651 original size:45 final size:45
Alignment explanation
Indices: 29644602--29644793 Score: 208
Period size: 45 Copynumber: 4.3 Consensus size: 45
29644592 ATCATAAATT
*
29644602 AGTAAGACCATGACTAAAAGACGTTATGACATCATGATTCTATCG
1 AGTAAGACCATGACTAAAAGACGTTATGACATCACGATTCTATCG
* * * *
29644647 AGTAAGACCATGATTGAAAGACGTTATGGCATCACGACTCTATCG
1 AGTAAGACCATGACTAAAAGACGTTATGACATCACGATTCTATCG
* * * **
29644692 AGTAAGACCATGAC-AGAAAAACGTTATGGCATCATGATTCTATAT
1 AGTAAGACCATGACTA-AAAGACGTTATGACATCACGATTCTATCG
* * * * *
29644737 AGTAAGACCAT-AGCTAAAAGATGATATGACATCACGAATCAAACG
1 AGTAAGACCATGA-CTAAAAGACGTTATGACATCACGATTCTATCG
*
29644782 AATAAGACCATG
1 AGTAAGACCATG
29644794 GTTGAAAGAC
Statistics
Matches: 120, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
44 1 0.01
45 118 0.98
46 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTAAGACCATGACTAAAAGACGTTATGACATCACGATTCTATCG
Found at i:29644757 original size:90 final size:90
Alignment explanation
Indices: 29644602--29644793 Score: 235
Period size: 90 Copynumber: 2.1 Consensus size: 90
29644592 ATCATAAATT
* * * *
29644602 AGTAAGACCATGACTAAAAGACGTTATGACATCATGATTCTATCGAGTAAGACCATGATTGAAAG
1 AGTAAGACCATGACTAAAAAACGTTATGACATCATGATTCTATAGAGTAAGACCATGACTAAAAG
* * * * *
29644667 ACGTTATGGCATCACGACTCTATCG
66 ACGATATGACATCACGAATCAAACG
* *
29644692 AGTAAGACCATGAC-AGAAAAACGTTATGGCATCATGATTCTATATAGTAAGACCAT-AGCTAAA
1 AGTAAGACCATGACTA-AAAAACGTTATGACATCATGATTCTATAGAGTAAGACCATGA-CTAAA
*
29644755 AGATGATATGACATCACGAATCAAACG
64 AGACGATATGACATCACGAATCAAACG
*
29644782 AATAAGACCATG
1 AGTAAGACCATG
29644794 GTTGAAAGAC
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 2 0.02
90 85 0.98
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (90 bp):
AGTAAGACCATGACTAAAAAACGTTATGACATCATGATTCTATAGAGTAAGACCATGACTAAAAG
ACGATATGACATCACGAATCAAACG
Found at i:29645701 original size:20 final size:20
Alignment explanation
Indices: 29645676--29645729 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
29645666 TATTTAAGCT
*
29645676 AAAGTAAGTAAATGCACTGA
1 AAAGTAAGTAAATGCAATGA
*
29645696 AAAGTAAGTAAATGCAATGG
1 AAAGTAAGTAAATGCAATGA
29645716 AAAGTAAGTAAATG
1 AAAGTAAGTAAATG
29645730 GAAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAGTAAGTAAATGCAATGA
Found at i:29647243 original size:13 final size:13
Alignment explanation
Indices: 29647225--29647267 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
29647215 TACATTTTTC
29647225 CTAAATATTATCA
1 CTAAATATTATCA
29647238 CTAAATA--ATC-
1 CTAAATATTATCA
*
29647248 CTAAATGTTATCA
1 CTAAATATTATCA
29647261 CTAAATA
1 CTAAATA
29647268 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:29647250 original size:23 final size:23
Alignment explanation
Indices: 29647223--29647269 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
29647213 GCTACATTTT
29647223 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
29647246 TCCTAAATGTTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
29647269 T
1 T
29647270 TCAAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:29647276 original size:23 final size:23
Alignment explanation
Indices: 29647227--29647276 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
29647217 CATTTTTCCT
*
29647227 AAATATTATCACTAAATAATCCT
1 AAATATTATCACTAAATAATCCA
* *
29647250 AAATGTTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATCCA
29647273 AAAT
1 AAAT
29647277 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCCA
Found at i:29651757 original size:20 final size:20
Alignment explanation
Indices: 29651710--29651764 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
29651700 AAAATAAAAT
*
29651710 AAAATAAAAACAAATTCAAA
1 AAAATAAAAATAAATTCAAA
** *
29651730 AATGTAAAAATAAATTTAAA
1 AAAATAAAAATAAATTCAAA
29651750 AAAAT-AAAATAAATT
1 AAAATAAAAATAAATT
29651765 GGTAAATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATAAAAATAAATTCAAA
Found at i:29652637 original size:13 final size:13
Alignment explanation
Indices: 29652619--29652684 Score: 81
Period size: 13 Copynumber: 5.5 Consensus size: 13
29652609 TAGATTTTTC
29652619 CTAAATATTATCA
1 CTAAATATTATCA
29652632 CTAAATA--ATC-
1 CTAAATATTATCA
29652642 CTAAATATTATCA
1 CTAAATATTATCA
*
29652655 CTAAATA--AT-T
1 CTAAATATTATCA
29652665 CTAAATATTATCA
1 CTAAATATTATCA
29652678 CTAAATA
1 CTAAATA
29652685 ATACAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
10 14 0.31
11 5 0.11
12 5 0.11
13 21 0.47
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:29652647 original size:23 final size:23
Alignment explanation
Indices: 29652617--29652686 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
29652607 GCTAGATTTT
29652617 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
29652640 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
29652663 TTCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
29652686 T
1 T
29652687 ACAAAATTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:29663425 original size:49 final size:49
Alignment explanation
Indices: 29663255--29663438 Score: 185
Period size: 50 Copynumber: 3.7 Consensus size: 49
29663245 GGGAATGAGA
* * * **
29663255 TCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCA-AGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATA-A-GAGAAC
** * * *
29663305 TCCCCCGTAAGACCATGTCTGAGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATAAGAGAAC
* *
29663355 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTATAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-ATAAGAGAAC
*
29663403 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGG
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
29663439 TATGTTATTA
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
48 4 0.04
49 37 0.34
50 66 0.60
51 2 0.02
52 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATAAGAGAAC
Found at i:29693097 original size:17 final size:18
Alignment explanation
Indices: 29693075--29693108 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29693065 CGTCCGCGAC
29693075 AAACGCGA-CGCGACCGA
1 AAACGCGACCGCGACCGA
29693092 AAACGCGACCGCGACCG
1 AAACGCGACCGCGACCG
29693109 CAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.38, G:0.29, T:0.00
Consensus pattern (18 bp):
AAACGCGACCGCGACCGA
Found at i:29696341 original size:16 final size:16
Alignment explanation
Indices: 29696322--29696360 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
29696312 ATAAATAAAT
*
29696322 AAAATTATATTATATA
1 AAAATTACATTATATA
29696338 AAAATTACATTATATA
1 AAAATTACATTATATA
29696354 AAAATTA
1 AAAATTA
29696361 AATGAGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTACATTATATA
Found at i:29696699 original size:55 final size:55
Alignment explanation
Indices: 29696615--29696782 Score: 209
Period size: 52 Copynumber: 3.1 Consensus size: 55
29696605 TTATTTAAAC
29696615 AAAAAATATTTTTTAATAT-AAAAATTGATTCGCGCCTGTCAAATAGGCGCGATT
1 AAAAAATATTTTTTAATATAAAAAATTGATTCGCGCCTGTCAAATAGGCGCGATT
** * *
29696669 AAAAAATATTTTTTAATATAAAAAATTGATTCGCGTTTGTCATATAGGCGCAATT
1 AAAAAATATTTTTTAATATAAAAAATTGATTCGCGCCTGTCAAATAGGCGCGATT
* * * * * *
29696724 --AAAGT-TTTTTTAATATAAAAAATTGATTGGTGCCTGCCAGATAGGCACGATT
1 AAAAAATATTTTTTAATATAAAAAATTGATTCGCGCCTGTCAAATAGGCGCGATT
29696776 ACAAAAA
1 A-AAAAA
29696783 ACATACCATT
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
52 39 0.41
53 4 0.04
54 19 0.20
55 34 0.35
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (55 bp):
AAAAAATATTTTTTAATATAAAAAATTGATTCGCGCCTGTCAAATAGGCGCGATT
Found at i:29697489 original size:60 final size:60
Alignment explanation
Indices: 29697360--29697490 Score: 133
Period size: 60 Copynumber: 2.2 Consensus size: 60
29697350 CTTACAAATT
* * * * *
29697360 TAAATTACTAATAAATTAATTTTAAAATAATTAAAAACACAAAAAATTATAACATAATCC
1 TAAAATACTAACAAATAAATTTTAAAATAATTAAAAACACAAAAAATAATAACATAATAC
* * * *
29697420 TAAATTACTAACAAATAAATTTTAAAATAATTATAAAA-AGTAAAAAA-AATTACATTCATAC
1 TAAAATACTAACAAATAAATTTTAAAATAATTA-AAAACA-CAAAAAATAATAACA-TAATAC
29697481 -AAAATACTAA
1 TAAAATACTAA
29697491 TCCAAAACTA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
60 46 0.77
61 14 0.23
ACGTcount: A:0.60, C:0.09, G:0.01, T:0.31
Consensus pattern (60 bp):
TAAAATACTAACAAATAAATTTTAAAATAATTAAAAACACAAAAAATAATAACATAATAC
Found at i:29697759 original size:20 final size:20
Alignment explanation
Indices: 29697734--29697782 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
29697724 TTTTCCCATT
*
29697734 GAAGGGACAATAGCC-TGGTG
1 GAAGGGACAACA-CCATGGTG
29697754 GAAGGGACAACACCATGGTG
1 GAAGGGACAACACCATGGTG
29697774 GAAGGGACA
1 GAAGGGACA
29697783 GAGGCAACAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.35, C:0.16, G:0.39, T:0.10
Consensus pattern (20 bp):
GAAGGGACAACACCATGGTG
Found at i:29698609 original size:88 final size:88
Alignment explanation
Indices: 29698491--29698660 Score: 277
Period size: 88 Copynumber: 1.9 Consensus size: 88
29698481 AGCGCACTTC
* * * *
29698491 TCTCACAAACGCCGCTAAAGCCCTTGTTCTTTAGCGGCGCTTTTCTCAAAAACACCACTAAACGT
1 TCTCAAAAACGCCGCTAAAACCCTTGTTCTTTAGCGACGCCTTTCTCAAAAACACCACTAAACGT
29698556 CATGTTCTTTAGCGGCGGTTTTT
66 CATGTTCTTTAGCGGCGGTTTTT
* * *
29698579 TCTCAAAAACGCCGCTAAAACCCTTGTTCTTTAGCGACGCCTTTCTCAAAAATACCGCTAAAGGT
1 TCTCAAAAACGCCGCTAAAACCCTTGTTCTTTAGCGACGCCTTTCTCAAAAACACCACTAAACGT
29698644 CATGTTCTTTAGCGGCG
66 CATGTTCTTTAGCGGCG
29698661 CTTCCCTAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (88 bp):
TCTCAAAAACGCCGCTAAAACCCTTGTTCTTTAGCGACGCCTTTCTCAAAAACACCACTAAACGT
CATGTTCTTTAGCGGCGGTTTTT
Found at i:29698680 original size:43 final size:43
Alignment explanation
Indices: 29698455--29698680 Score: 199
Period size: 43 Copynumber: 5.2 Consensus size: 43
29698445 TTATTAATAT
* ** * *
29698455 AAACGTCGCTAAAGAACATGTTCTTTAGC-GCACTTCTCTCAC
1 AAACGCCGCTAAAGCCCATGTTCTTTAGCGGCGCTTCTCTCAA
* *
29698497 AAACGCCGCTAAAGCCCTTGTTCTTTAGCGGCGCTTTTCTCAA
1 AAACGCCGCTAAAGCCCATGTTCTTTAGCGGCGCTTCTCTCAA
* * * * *
29698540 AAACACCACTAAA-CGTCATGTTCTTTAGCGGCGGTTTTTTCTCAA
1 AAACGCCGCTAAAGC-CCATGTTCTTTAGCGGC-G-CTTCTCTCAA
* * *
29698585 AAACGCCGCTAAAACCCTTGTTCTTTAGCGACGCCTT-TCTCAA
1 AAACGCCGCTAAAGCCCATGTTCTTTAGCGGCG-CTTCTCTCAA
** ** *
29698628 AAATACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCCCT-AA
1 AAACGCCGCTAAAGCCCATGTTCTTTAGCGGCGCTTCTCTCAA
29698670 GAAACGCCGCT
1 -AAACGCCGCT
29698681 CTTGTTTGAT
Statistics
Matches: 148, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
42 31 0.21
43 78 0.53
44 4 0.03
45 34 0.23
46 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGCCCATGTTCTTTAGCGGCGCTTCTCTCAA
Found at i:29699053 original size:21 final size:21
Alignment explanation
Indices: 29699029--29699099 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
29699019 TTCTGCTCTG
*
29699029 CTCTGCTTCCCTTACTGCCGC
1 CTCTGCTTCCCTCACTGCCGC
*
29699050 CTCTGCTTCCCTCACTACCGC
1 CTCTGCTTCCCTCACTGCCGC
*
29699071 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCACTGCCGC
29699092 CTCTGCTT
1 CTCTGCTT
29699100 TAAGTTGTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.04, C:0.49, G:0.14, T:0.32
Consensus pattern (21 bp):
CTCTGCTTCCCTCACTGCCGC
Found at i:29700807 original size:44 final size:44
Alignment explanation
Indices: 29700747--29701571 Score: 1410
Period size: 44 Copynumber: 18.7 Consensus size: 44
29700737 AAACAGCACA
* *
29700747 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACATTATA
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
*
29700791 TATAATATTAATTAAGTTGTGTATTATGTATTATGTATGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
*
29700835 TATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
*
29700879 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
29700923 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTAT-
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
*
29700966 T-TAATATTAATTAAGTTGTGTATTATGTATTATGTATGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
*
29701009 TATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
* *
29701053 TATAATATTAATTAAGTTGTGTAATATGTATTATGTATGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
*
29701097 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
29701141 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTAT-
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
29701184 T-TAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
*
29701227 TATAATATTAATTAAGTTGTGTATTATGTATTATGTATTATGTATGTTATG
1 TATAATATTAATTAAG-T-TG-----TGTATTATGTATTATGTACGTTATG
*
29701278 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
29701322 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTAT-
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
*
29701365 T-TAATATTAATTAAGTTGTGTATTATGTATTATGTATGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
* *
29701408 TATAATATTAATTAAGTTGTGTAATATGTTTTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
29701452 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
29701496 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
29701540 TATAATATTAATTAAGTTGTGTATTATGTATT
1 TATAATATTAATTAAGTTGTGTATTATGTATT
29701572 TAAGTTGTGT
Statistics
Matches: 742, Mismatches: 26, Indels: 26
0.93 0.03 0.03
Matches are distributed among these distances:
42 121 0.16
43 6 0.01
44 569 0.77
45 1 0.00
46 2 0.00
49 2 0.00
50 1 0.00
51 40 0.05
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.50
Consensus pattern (44 bp):
TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATG
Found at i:29701039 original size:174 final size:176
Alignment explanation
Indices: 29700747--29701571 Score: 1419
Period size: 174 Copynumber: 4.7 Consensus size: 176
29700737 AAACAGCACA
* *
29700747 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACATTATATATAATATTAATTAAGTTGTG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTG
* *
29700812 TATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTA
66 TATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTA
* *
29700877 TGTATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATG
131 TGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
29700923 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTAT-T-TAATATTAATTAAGTTGTG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTG
* *
29700986 TATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTA
66 TATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTA
*
29701051 TGTATAATATTAATTAAGTTGTGTAATATGTATTATGTATGTTATG
131 TGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
*
29701097 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTAAGTTGTG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTG
29701162 TATTATGTATTATGTACGTTAT-T-TAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTA
66 TATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTA
*
29701225 TGTATAATATTAATTAAGTTGTGTATTATGTATTATGTATTATGTATGTTATG
131 TGTATAATATTAATTAAGTTGTG---TA---A-TATGTATTATGTACGTTATG
*
29701278 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTAAGTTGTG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTG
*
29701343 TATTATGTATTATGTACGTTAT-T-TAATATTAATTAAGTTGTGTATTATGTATTATGTATGTTA
66 TATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTA
*
29701406 TGTATAATATTAATTAAGTTGTGTAATATGTTTTATGTACGTTATG
131 TGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
29701452 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTG
29701517 TATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATT
66 TATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATT
29701572 TAAGTTGTGT
Statistics
Matches: 627, Mismatches: 11, Indels: 22
0.95 0.02 0.03
Matches are distributed among these distances:
174 335 0.53
175 5 0.01
176 112 0.18
177 2 0.00
178 2 0.00
180 1 0.00
181 170 0.27
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.50
Consensus pattern (176 bp):
TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTG
TATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTA
TGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
Found at i:29701214 original size:7 final size:7
Alignment explanation
Indices: 29701202--29701271 Score: 56
Period size: 7 Copynumber: 9.7 Consensus size: 7
29701192 AATTAAGTTG
29701202 TGTATTA
1 TGTATTA
29701209 TGTATTA
1 TGTATTA
29701216 TGTACGTTA
1 TGTA--TTA
29701225 TGTA-TA
1 TGTATTA
*
29701231 -ATATTAA
1 TGTATT-A
*
29701238 T-TAAGTTG
1 TGT-A-TTA
29701246 TGTATTA
1 TGTATTA
29701253 TGTATTA
1 TGTATTA
29701260 TGTATTA
1 TGTATTA
29701267 TGTAT
1 TGTAT
29701272 GTTATGTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
5 2 0.04
6 3 0.06
7 34 0.65
8 3 0.06
9 10 0.19
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.53
Consensus pattern (7 bp):
TGTATTA
Found at i:29701225 original size:16 final size:15
Alignment explanation
Indices: 29701160--29701410 Score: 61
Period size: 16 Copynumber: 16.9 Consensus size: 15
29701150 AATTAAGTTG
29701160 TGTA-TTATGTATTA
1 TGTAGTTATGTATTA
* *
29701174 TGTACGTTATTTAATA
1 TGTA-GTTATGTATTA
* * *
29701190 T-TAATTAAG--TTG
1 TGTAGTTATGTATTA
29701202 TGTA-TTATGTATTA
1 TGTAGTTATGTATTA
29701216 TGTACGTTATGTATAATA
1 TGTA-GTTATGTAT--TA
* *
29701234 TTAATTAAGTTGTGTATTA
1 -T--GT-AGTTATGTATTA
29701253 TGTA-TTATGTATTA
1 TGTAGTTATGTATTA
29701267 TGTATGTTATGTATAATA
1 TGTA-GTTATGTAT--TA
* * *
29701285 T-TAATTAAG--TTG
1 TGTAGTTATGTATTA
*
29701297 TGTA-TTATGCATTA
1 TGTAGTTATGTATTA
29701311 TGTACGTTATGTATAATA
1 TGTA-GTTATGTAT--TA
* * *
29701329 T-TAATTAAG--TTG
1 TGTAGTTATGTATTA
29701341 TGTA-TTATGTATTA
1 TGTAGTTATGTATTA
* *
29701355 TGTACGTTATTTAATA
1 TGTA-GTTATGTATTA
* * *
29701371 T-TAATTAAG--TTG
1 TGTAGTTATGTATTA
29701383 TGTA-TTATGTATTA
1 TGTAGTTATGTATTA
29701397 TGTATGTTATGTAT
1 TGTA-GTTATGTAT
29701411 AATATTAATT
Statistics
Matches: 170, Mismatches: 33, Indels: 66
0.63 0.12 0.25
Matches are distributed among these distances:
12 24 0.14
13 8 0.05
14 49 0.29
15 5 0.03
16 58 0.34
17 4 0.02
18 9 0.05
19 3 0.02
21 9 0.05
22 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.52
Consensus pattern (15 bp):
TGTAGTTATGTATTA
Found at i:29701568 original size:218 final size:218
Alignment explanation
Indices: 29700749--29701567 Score: 1417
Period size: 218 Copynumber: 3.7 Consensus size: 218
29700739 ACAGCACATA
* *
29700749 TAATATTAATTAAGTTGTGTATTATGTATTATGTACATTATATATAATATTAATTAAGTTGTGTA
1 TAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTA
*
29700814 TTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
66 TTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
29700879 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTAAGTTGTG
131 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTAAGTTGTG
29700944 TATTATGTATTATGTACGTTATT
196 TATTATGTATTATGTACGTTATT
*
29700967 TAATATTAATTAAGTTGTGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTA
1 TAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTA
* *
29701032 ATATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTATGTTATG
66 TTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
29701097 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTAAGTTGTG
131 TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTAAGTTGTG
29701162 TATTATGTATTATGTACGTTATT
196 TATTATGTATTATGTACGTTATT
29701185 TAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTA
1 TAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAG-T-TG--
* * *
29701250 TTATGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTATGCATTATGTA
62 ---TGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTA
*
29701315 CGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTAT-T-TAATATTAATTA
124 CGTTATGTATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTA
*
29701378 AGTTGTGTATTATGTATTATGTATGTTATGT
189 AGTTGTGTATTATGTATTATGTACGTTAT-T
* *
29701409 ATAATATTAATTAAGTTGTGTAATATGTTTTATGTACGTTATGTATAATATTAATTAAGTTGTGT
1 -TAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGT
*
29701474 ATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTAT
65 ATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTAT
29701539 GTATAATATTAATTAAGTTGTGTATTATG
130 GTATAATATTAATTAAGTTGTGTATTATG
29701568 TATTTAAGTT
Statistics
Matches: 574, Mismatches: 18, Indels: 18
0.94 0.03 0.03
Matches are distributed among these distances:
218 364 0.63
219 1 0.00
220 2 0.00
223 42 0.07
224 3 0.01
225 162 0.28
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.50
Consensus pattern (218 bp):
TAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTA
TTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATG
TATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTAAGTTGTG
TATTATGTATTATGTACGTTATT
Found at i:29701593 original size:16 final size:17
Alignment explanation
Indices: 29701551--29701598 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 17
29701541 ATAATATTAA
29701551 TTAAGTTGTGTATTATG
1 TTAAGTTGTGTATTATG
29701568 TATTTAAGTTGTGTATTATG
1 ---TTAAGTTGTGTATTATG
*
29701588 -TAAGTTATGTA
1 TTAAGTTGTGTA
29701599 AGAAATGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
20 17 0.63
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (17 bp):
TTAAGTTGTGTATTATG
Found at i:29701597 original size:9 final size:9
Alignment explanation
Indices: 29701583--29701756 Score: 51
Period size: 9 Copynumber: 19.1 Consensus size: 9
29701573 AAGTTGTGTA
29701583 TTATGTAAG
1 TTATGTAAG
29701592 TTATGTAAG
1 TTATGTAAG
**
29701601 AAATGT-A-
1 TTATGTAAG
29701608 TTATGTAAG
1 TTATGTAAG
*
29701617 TTGTGT-A-
1 TTATGTAAG
* *
29701624 TAATGTTAG
1 TTATGTAAG
**
29701633 TTATCAAAG
1 TTATGTAAG
29701642 TTATGT-A-
1 TTATGTAAG
*
29701649 CTATGTAATTAG
1 TTATGT-A--AG
*
29701661 TTATTTAAG
1 TTATGTAAG
29701670 TTATGTAAG
1 TTATGTAAG
*
29701679 TT-TGTGTA-
1 TTATGT-AAG
*
29701687 TTATATAAG
1 TTATGTAAG
*
29701696 TTAT-TATG
1 TTATGTAAG
29701704 TTATTATGTAAG
1 ---TTATGTAAG
*
29701716 TTATGCAAG
1 TTATGTAAG
*
29701725 TTTATATAAG
1 -TTATGTAAG
*
29701735 TTTAAATATAAG
1 -TT--ATGTAAG
29701747 TTATGTAAG
1 TTATGTAAG
29701756 T
1 T
29701757 ATATCACTTT
Statistics
Matches: 120, Mismatches: 26, Indels: 38
0.65 0.14 0.21
Matches are distributed among these distances:
7 13 0.11
8 14 0.12
9 61 0.51
10 10 0.08
11 8 0.07
12 14 0.12
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29701600 original size:25 final size:24
Alignment explanation
Indices: 29701552--29701623 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 24
29701542 TAATATTAAT
29701552 TAAGTTGTGTATTATGT-A--TT-
1 TAAGTTGTGTATTATGTAAGTTTG
29701572 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTT-TG
***
29701597 TAAGAAATGTATTATGTAAGTTGTG
1 TAAGTTGTGTATTATGTAAGTT-TG
29701622 TA
1 TA
29701624 TAATGTTAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 17 0.40
21 1 0.02
23 1 0.02
24 1 0.02
25 23 0.53
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (24 bp):
TAAGTTGTGTATTATGTAAGTTTG
Found at i:29701648 original size:41 final size:41
Alignment explanation
Indices: 29701572--29701656 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 41
29701562 ATTATGTATT
* ** *
29701572 TAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATG
1 TAAGTTGTGTATAATGTAAGTTATCAAAGAAATGTACTATG
* **
29701613 TAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTACTATG
1 TAAGTTGTGTATAATGTAAGTTATCAAAGAAATGTACTATG
29701654 TAA
1 TAA
29701657 TTAGTTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (41 bp):
TAAGTTGTGTATAATGTAAGTTATCAAAGAAATGTACTATG
Found at i:29701713 original size:399 final size:398
Alignment explanation
Indices: 29700747--29701676 Score: 1386
Period size: 399 Copynumber: 2.3 Consensus size: 398
29700737 AAACAGCACA
* * *
29700747 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACATTATATATAATATTAATTAAGTTGTG
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTA-AGT-TATGTAATATTAATTAAGTTATG
** * * * *
29700812 TATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTA--A--TA-TGT-ATTATGT
64 TAAAATGTATTATGTAAGTTATGTATAATATTAATAAAGTTATGTACTATGTATTATGATTATGT
* *
29700871 ACGTTATGTATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATT
129 AAGTTATGTATAATATTAATTAAGTAGTGTATTATGCATTATGTACGTTATGTATAATATTAATT
29700936 AAGTTGTGTATTATGTATTATGTACGTTATTTAATATTAATTAAGTTGTGTATTATGTATTATGT
194 AAGTTGTGTATTATGTATTATGTACGTTATTTAATATTAATTAAGTTGTGTATTATGTATTATGT
29701001 ATGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATGTATAATATTAATT
259 ATGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATGTATAATATTAATT
*
29701066 AAGTTGTGTAATATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTATGCATTAT
324 AAGTTGTGTAATATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGCATTAT
29701131 GTACGTTATG
389 GTACGTTATG
* * *
29701141 TATAATATTAATTAAGTTGTGTATTATGTATTATGTACGTTATTTAATATTAATTAAGTTGTGTA
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTAAGTTATGTAATATTAATTAAGTTATGTA
** * * * *
29701206 TTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTATTATGTA
66 AAATGTATTATGTAAGTTATGTATAATATTAATAAAGTTATGTACTATGTATTATG-ATTATGTA
* *
29701271 TGTTATGTATAATATTAATTAAGTTGTGTATTATGCATTATGTACGTTATGTATAATATTAATTA
130 AGTTATGTATAATATTAATTAAGTAGTGTATTATGCATTATGTACGTTATGTATAATATTAATTA
29701336 AGTTGTGTATTATGTATTATGTACGTTATTTAATATTAATTAAGTTGTGTATTATGTATTATGTA
195 AGTTGTGTATTATGTATTATGTACGTTATTTAATATTAATTAAGTTGTGTATTATGTATTATGTA
*
29701401 TGTTATGTATAATATTAATTAAGTTGTGTAATATGTTTTATGTACGTTATGTATAATATTAATTA
260 TGTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATGTATAATATTAATTA
* *
29701466 AGTTGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGTATTATG
325 AGTTGTGTAATATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGCATTATG
29701531 TACGTTATG
390 TACGTTATG
*
29701540 TATAATATTAATTAAGTTGTGTATTATGTA-T-T-TAAG-T-TGT-GTATT-ATGTAAGTTATGT
1 TATAATATTAATTAAGTTGTGTATTATGTATTATGTAAGTTATGTAATATTAAT-TAAGTTATGT
* *
29701598 AAGAAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTACTATGTAATTA-G-
65 -A-AAATGTATTATGTAAGTTATGTATAATATTA---AT-AAAGTTATGTACTATGT-ATTATGA
*
29701661 TTATTTAAGTTATGTA
123 TTATGTAAGTTATGTA
29701677 AGTTTGTGTA
Statistics
Matches: 497, Mismatches: 24, Indels: 27
0.91 0.04 0.05
Matches are distributed among these distances:
392 69 0.14
393 14 0.03
394 41 0.08
395 27 0.05
396 5 0.01
397 17 0.03
398 3 0.01
399 317 0.64
400 4 0.01
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (398 bp):
TATAATATTAATTAAGTTGTGTATTATGTATTATGTAAGTTATGTAATATTAATTAAGTTATGTA
AAATGTATTATGTAAGTTATGTATAATATTAATAAAGTTATGTACTATGTATTATGATTATGTAA
GTTATGTATAATATTAATTAAGTAGTGTATTATGCATTATGTACGTTATGTATAATATTAATTAA
GTTGTGTATTATGTATTATGTACGTTATTTAATATTAATTAAGTTGTGTATTATGTATTATGTAT
GTTATGTATAATATTAATTAAGTTGTGTAATATGTATTATGTACGTTATGTATAATATTAATTAA
GTTGTGTAATATGTATTATGTACGTTATGTATAATATTAATTAAGTTGTGTATTATGCATTATGT
ACGTTATG
Found at i:29701719 original size:17 final size:18
Alignment explanation
Indices: 29701670--29701720 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
29701660 GTTATTTAAG
29701670 TTATGTAAGTT-TGTGTA
1 TTATGTAAGTTATGTGTA
* *
29701687 TTATATAAGTTATTATGTTA
1 TTATGTAAGTTA-TGTG-TA
29701707 TTATGTAAGTTATG
1 TTATGTAAGTTATG
29701721 CAAGTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 10 0.37
19 4 0.15
20 13 0.48
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (18 bp):
TTATGTAAGTTATGTGTA
Found at i:29702935 original size:146 final size:147
Alignment explanation
Indices: 29702708--29703025 Score: 406
Period size: 146 Copynumber: 2.2 Consensus size: 147
29702698 GTTTATATAT
* * * *
29702708 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGTTTCATCAACAAATAGCTCAAACCTGTGGCAT
1 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGCTTCATCAACAAATACCTCAAACCCGTGACAT
** * * * * *
29702773 TTTTGAATAAATGCCACTAAT-A-ATATAGCAAAACAGCATCGTATCAATAAATGTTAAAACATT
66 TTTCAAAAAAACGCCACTAATAACATATA-AAAAACAGCAGCGTATCAATAAATGTTAAAACAAT
*
29702836 TTTGCGGCATTTTAAGCA
130 TTTGCAGCATTTTAAGCA
** *
29702854 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGCTTCATCAACACTTACCTCAAACCCGTGACGT
1 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGCTTCATCAACAAATACCTCAAACCCGTGACAT
* * * * *
29702919 TTTCAAAAAAACGCCACTAATAACATTTAAAAAACGGCAGCGTTTCTATAAATGTTAGAACAATT
66 TTTCAAAAAAACGCCACTAATAACATATAAAAAACAGCAGCGTATCAATAAATGTTAAAACAATT
* *
29702984 TTGCAGCGTTTTAAGTA
131 TTGCAGCATTTTAAGCA
29703001 AAGCGCCACTAACTATAAGTTCAAA
1 AAGCGCCACTAACTATAAG-TCAAA
29703026 CGAGGTCGTT
Statistics
Matches: 147, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
146 75 0.51
147 63 0.43
148 9 0.06
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (147 bp):
AAGCGCCACTAACTATAAGTCAAAACGCAGTCGCTTCATCAACAAATACCTCAAACCCGTGACAT
TTTCAAAAAAACGCCACTAATAACATATAAAAAACAGCAGCGTATCAATAAATGTTAAAACAATT
TTGCAGCATTTTAAGCA
Found at i:29703100 original size:147 final size:147
Alignment explanation
Indices: 29702708--29703117 Score: 452
Period size: 147 Copynumber: 2.8 Consensus size: 147
29702698 GTTTATATAT
* *
29702708 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGTTTCATCAACAAATAGCTCAAACCTGTGGC-A
1 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGTTTCATCAACAATTAACTCAAACCTGTGGCGA
* * * * * *
29702772 TTTTTGAATAAATGCCACTAATAATATAG-CAAAACAGCATCGTATCAATAAATGTTAAAACATT
66 TTTTAGAA-AAACGCCACTAATAACATAGACAAAACGGCAGCGTATCAATAAATGTTAAAACAAT
*
29702836 TTTGCGGCATTTTAAGCA
130 TTTGCAGCATTTTAAGCA
* * * * *
29702854 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGCTTCATCAACACTTACCTCAAACCCGTGACG-
1 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGTTTCATCAACAATTAACTCAAACCTGTGGCGA
* ** * * * *
29702918 TTTTCAAAAAAACGCCACTAATAACATTTAAAAAACGGCAGCGTTTCTATAAATGTTAGAACAAT
66 TTTT-AGAAAAACGCCACTAATAACATAGACAAAACGGCAGCGTATCAATAAATGTTAAAACAAT
* *
29702983 TTTGCAGCGTTTTAAGTA
130 TTTGCAGCATTTTAAGCA
** * * *
29703001 AAGCGCCACTAACTATAAGTTC-AAACG-AGGTCGTTTCCCCAACAGTTAACTCAAGCTTGTGGC
1 AAGCGCCACTAACTATAAG-TCAAAACGCA-GTCGTTTCATCAACAATTAACTCAAACCTGTGGC
* * * * *
29703064 GATTCTAGAAAAACGCCACTAATACCATAGACAAAACGACAACATATCAATAAA
64 GATTTTAGAAAAACGCCACTAATAACATAGACAAAACGGCAGCGTATCAATAAA
29703118 CATAATTACA
Statistics
Matches: 216, Mismatches: 42, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
146 78 0.36
147 133 0.62
148 5 0.02
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (147 bp):
AAGCGCCACTAACTATAAGTCAAAACGCAGTCGTTTCATCAACAATTAACTCAAACCTGTGGCGA
TTTTAGAAAAACGCCACTAATAACATAGACAAAACGGCAGCGTATCAATAAATGTTAAAACAATT
TTGCAGCATTTTAAGCA
Found at i:29704640 original size:72 final size:72
Alignment explanation
Indices: 29704330--29704992 Score: 813
Period size: 73 Copynumber: 9.2 Consensus size: 72
29704320 TTTTCCAGAA
* * * * * *
29704330 AAGCGCCGCTAATACCACTGCATCTCAAATCAAAACGATGCATTTT-GATTATTTTTGCGGCG-T
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTGTGGCGCT
29704393 TTTCACAG
66 TTT-ACAG
*
29704401 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAATGATGCGTTTTGGTTTTTTTCTTGTGGCGC
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTT-TTGTGGCGC
29704466 TTTTACAG
65 TTTTACAG
*
29704474 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAATGATGCGTTTTGGTTTTTTTTTTGTGGCGC
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGG-TTTTTTTTTGTGGCGC
29704539 TTTTACAG
65 TTTTACAG
*
29704547 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTTTTTTTTGTGGCGCT
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTGTGGCGCT
29704612 TTTACAG
66 TTTACAG
* * *
29704619 AAGCACCGCTAACGCCACTACATCTCAAATCAAAATGATGCGTTTTGG-TTTTTTTTGTGGCGCT
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTGTGGCGCT
29704683 TTTACAG
66 TTTACAG
* * * *
29704690 AAGCGCTGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTT-G-ATTTTTTTGCGGCGCT
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTGTGGCGCT
**
29704753 TTTATGG
66 TTTACAG
** * * * * *
29704760 AAGCGTTGTTAATGCCACTGCATCTCAAATCAAAACGATGTGTTTTGATTATTTTTTGCT-GCGC
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTG-TGGCGC
**
29704824 TTTTATGG
65 TTTTACAG
* * * * ** **
29704832 AAGCGCCGCTAGTGCCACAACATCTCAAATCAAAACGAAGCGTTTGGGTTATTTTTTTGCAGCAT
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTT-TTTTTTTGTGGCGC
*
29704897 TTTTACGG
65 TTTTACAG
* * *
29704905 AATCACCGCTAATGCCACTACATTTCAAATCAAAACGATGCG-TTTGGATTATTTTTTTGCT-GC
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGG-TT-TTTTTTTG-TGGC
29704968 G-TTTCTACAG
63 GCTTT-TACAG
**
29704978 AATTGCCGCTAATGC
1 AAGCGCCGCTAATGC
29704993 TCAATTTTTA
Statistics
Matches: 524, Mismatches: 56, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
70 63 0.12
71 106 0.20
72 140 0.27
73 204 0.39
74 11 0.02
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (72 bp):
AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTGTGGCGCT
TTTACAG
Found at i:29704651 original size:145 final size:144
Alignment explanation
Indices: 29704330--29704992 Score: 813
Period size: 145 Copynumber: 4.6 Consensus size: 144
29704320 TTTTCCAGAA
* * * * * *
29704330 AAGCGCCGCTAATACCACTGCATCTCAAATCAAAACGATGCATTTT-GATTATTTTTGCGGCG-T
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTGTGGCGCT
*
29704393 TTTCACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAATGATGCGTTTTGGTTTTTTTCT
66 TTT-ACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTT-T
*
29704458 TGTGGCGCTTTTACAG
129 TGCGGCGCTTTTACAG
*
29704474 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAATGATGCGTTTTGGTTTTTTTTTTGTGGCGC
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGG-TTTTTTTTTGTGGCGC
*
29704539 TTTTACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTTTTTTTT
65 TTTTACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTT
*
29704604 GTGGCGCTTTTACAG
130 GCGGCGCTTTTACAG
* * *
29704619 AAGCACCGCTAACGCCACTACATCTCAAATCAAAATGATGCGTTTTGG-TTTTTTTTGTGGCGCT
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTGTGGCGCT
* * *
29704683 TTTACAGAAGCGCTGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTT-G-ATTTTTTTG
66 TTTACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTG
**
29704746 CGGCGCTTTTATGG
131 CGGCGCTTTTACAG
** * * * * *
29704760 AAGCGTTGTTAATGCCACTGCATCTCAAATCAAAACGATGTGTTTTGATTATTTTTTGCT-GCGC
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTG-TGGCGC
** * * * *
29704824 TTTTATGGAAGCGCCGCTAGTGCCACAACATCTCAAATCAAAACGAAGCGTTTGGGTTATTTTTT
65 TTTTACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTT-TTTTTT
* ** *
29704889 TGCAGCATTTTTACGG
129 TGCGGCGCTTTTACAG
* * *
29704905 AATCACCGCTAATGCCACTACATTTCAAATCAAAACGATGCG-TTTGGATTATTTTTTTGCT-GC
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGG-TT-TTTTTTTG-TGGC
**
29704968 G-TTTCTACAGAATTGCCGCTAATGC
63 GCTTT-TACAGAAGCGCCGCTAATGC
29704993 TCAATTTTTA
Statistics
Matches: 454, Mismatches: 54, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
141 58 0.13
142 59 0.13
143 70 0.15
144 46 0.10
145 121 0.27
146 96 0.21
147 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (144 bp):
AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTGTGGCGCT
TTTACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTTTTTTTTG
CGGCGCTTTTACAG
Found at i:29705800 original size:20 final size:20
Alignment explanation
Indices: 29705777--29705842 Score: 116
Period size: 20 Copynumber: 3.3 Consensus size: 20
29705767 ATTTTATAAT
29705777 TTTTTTATAAA-TATTTTGAA
1 TTTTTTA-AAATTATTTTGAA
29705797 TTTTTTAAAATTATTTTGAA
1 TTTTTTAAAATTATTTTGAA
29705817 TTTTTTAAAATTATTTTGAA
1 TTTTTTAAAATTATTTTGAA
29705837 TTTTTT
1 TTTTTT
29705843 TGTTGAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTTTAAAATTATTTTGAA
Found at i:29705818 original size:10 final size:10
Alignment explanation
Indices: 29705788--29705844 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
29705778 TTTTTATAAA
29705788 TATTTTGAAT
1 TATTTTGAAT
*
29705798 T-TTTTAAAAT
1 TATTTT-GAAT
29705808 TATTTTGAAT
1 TATTTTGAAT
*
29705818 T-TTTTAAAAT
1 TATTTT-GAAT
29705828 TATTTTGAAT
1 TATTTTGAAT
*
29705838 TTTTTTG
1 TATTTTG
29705845 TTGAAAGAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
9 8 0.21
10 22 0.58
11 8 0.21
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (10 bp):
TATTTTGAAT
Found at i:29711200 original size:8 final size:8
Alignment explanation
Indices: 29711187--29711217 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
29711177 AATGCTTTAA
29711187 AAATTGTC
1 AAATTGTC
29711195 AAATTGTC
1 AAATTGTC
29711203 AAATTGTC
1 AAATTGTC
29711211 AAATTGT
1 AAATTGT
29711218 ATTTTCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (8 bp):
AAATTGTC
Found at i:29712357 original size:25 final size:25
Alignment explanation
Indices: 29712301--29712357 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
29712291 GAAGTTTCTT
* *
29712301 TTATTTAATGTTTTCTATCTGATTA
1 TTATTTTATGTTTTATATCTGATTA
29712326 TTATTTTATGTTTTATATCTGATTA
1 TTATTTTATGTTTTATATCTGATTA
29712351 TTATTTT
1 TTATTTT
29712358 TCATTCTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (25 bp):
TTATTTTATGTTTTATATCTGATTA
Found at i:29718469 original size:12 final size:12
Alignment explanation
Indices: 29718452--29718476 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29718442 AAGACGAATC
29718452 AATCTGTCAACG
1 AATCTGTCAACG
29718464 AATCTGTCAACG
1 AATCTGTCAACG
29718476 A
1 A
29718477 GTGGGTACAT
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:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
AATCTGTCAACG
Found at i:29720741 original size:18 final size:19
Alignment explanation
Indices: 29720705--29720746 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
29720695 ATCTTAAAAG
29720705 ATAAAAAAAATTAATAACT
1 ATAAAAAAAATTAATAACT
29720724 ATAAAATAAAATT-A-AACT
1 ATAAAA-AAAATTAATAACT
29720742 ATAAA
1 ATAAA
29720747 CATTAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAAAAATTAATAACT
Found at i:29724814 original size:28 final size:28
Alignment explanation
Indices: 29724781--29724835 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
29724771 TATTGCTGTC
29724781 TCAAAACTGATTCACTACCAATTTTTAA
1 TCAAAACTGATTCACTACCAATTTTTAA
29724809 TCAAAACTGATTCACTACCAATTTTTA
1 TCAAAACTGATTCACTACCAATTTTTA
29724836 CTTTTTCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (28 bp):
TCAAAACTGATTCACTACCAATTTTTAA
Found at i:29725581 original size:50 final size:50
Alignment explanation
Indices: 29725513--29725695 Score: 240
Period size: 50 Copynumber: 3.7 Consensus size: 50
29725503 TTTTTTGTAC
* * * ** *
29725513 TGCCAATGCCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAAACATAGTCTTACATGGGACCTCTCATCTCGG
* * * *
29725563 TGCCCATGCCATGTCCCAGACATAGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATAGTCTTACATGGGACCTCTCATCTCGG
* *
29725613 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAAACATAGTCTTACATGGGACCTCTCATCTCGG
* *
29725663 TGCCAATGTCATGTCCCAAACATGGTCTTACAT
1 TGCCAATGCCATGTCCCAAACATAGTCTTACAT
29725696 CCCAAACATG
Statistics
Matches: 118, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 118 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATAGTCTTACATGGGACCTCTCATCTCGG
Found at i:29725700 original size:19 final size:19
Alignment explanation
Indices: 29725676--29725714 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29725666 CAATGTCATG
29725676 TCCCAAACATGGTCTTACA
1 TCCCAAACATGGTCTTACA
29725695 TCCCAAACATGGTCTTACA
1 TCCCAAACATGGTCTTACA
29725714 T
1 T
29725715 GGGACCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.28
Consensus pattern (19 bp):
TCCCAAACATGGTCTTACA
Found at i:29725737 original size:69 final size:69
Alignment explanation
Indices: 29725626--29725764 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 69
29725616 CAATGCCATG
* *
29725626 TCCCAAACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAATGTCATGTCCCAAACATGGTCT
1 TCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAAACATGGTCT
29725691 TACA
66 TACA
*
29725695 TCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCT
1 TCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAAACATGGTCT
29725760 TACA
66 TACA
29725764 T
1 T
29725765 GGGACCTCTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (69 bp):
TCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAAACATGGTCT
TACA
Found at i:29727599 original size:18 final size:18
Alignment explanation
Indices: 29727576--29727611 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29727566 ATCACTGTCA
29727576 CCCACCGTAATCAAATTT
1 CCCACCGTAATCAAATTT
29727594 CCCACCGTAATCAAATTT
1 CCCACCGTAATCAAATTT
29727612 ATTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (18 bp):
CCCACCGTAATCAAATTT
Found at i:29728194 original size:30 final size:32
Alignment explanation
Indices: 29728152--29728212 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 32
29728142 GGGGGTGGGA
29728152 TGGGAGGGGAGTAAAAGTTTCT-GGGGAAAGG
1 TGGGAGGGGAGTAAAAGTTTCTAGGGGAAAGG
*
29728183 TGGGA-GGGAGTAAAAGTTTTTAGGGGAAAG
1 TGGGAGGGGAGTAAAAGTTTCTAGGGGAAAG
29728213 TAAGGAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.31, C:0.02, G:0.46, T:0.21
Consensus pattern (32 bp):
TGGGAGGGGAGTAAAAGTTTCTAGGGGAAAGG
Found at i:29728220 original size:31 final size:30
Alignment explanation
Indices: 29728158--29728220 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
29728148 GGGATGGGAG
*
29728158 GGGAGTAAAAGTTTCTGGGGAAAGGTGGGA
1 GGGAGTAAAAGTTTCTGGGGAAAGGTAGGA
*
29728188 GGGAGTAAAAGTTTTTAGGGGAAA-GTAAGGA
1 GGGAGTAAAAGTTTCT-GGGGAAAGGT-AGGA
29728219 GG
1 GG
29728221 TTTGGGAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.33, C:0.02, G:0.44, T:0.21
Consensus pattern (30 bp):
GGGAGTAAAAGTTTCTGGGGAAAGGTAGGA
Found at i:29731022 original size:9 final size:9
Alignment explanation
Indices: 29731008--29731056 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
29730998 TTTGGTTAAA
29731008 AATTAACCG
1 AATTAACCG
29731017 AATTAACCG
1 AATTAACCG
*
29731026 AATTACCCG
1 AATTAACCG
*
29731035 AATTACCCG
1 AATTAACCG
29731044 AATTAACCG
1 AATTAACCG
29731053 AATT
1 AATT
29731057 GAATCACTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:29741934 original size:35 final size:35
Alignment explanation
Indices: 29741879--29742027 Score: 145
Period size: 35 Copynumber: 4.2 Consensus size: 35
29741869 TACTATCTAT
* **
29741879 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
1 TTGGTGTGCTTCGGTTGGACTAGCTCTTATGAGCA
**
29741914 TTGACGTGCTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGCTTCGGTTGGACTAGCTCTTATGAGCA
* * ** *
29741949 TTGGTGTGGTTCTGTTGGACTTTCTCTTCTGAGCA
1 TTGGTGTGCTTCGGTTGGACTAGCTCTTATGAGCA
* * * * * *
29741984 TTGGTGTGTTTCGATTGGACTTGTTGTTGTGAGCA
1 TTGGTGTGCTTCGGTTGGACTAGCTCTTATGAGCA
29742019 TCTGGTGTG
1 T-TGGTGTG
29742028 ATTTGGAGGG
Statistics
Matches: 94, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 87 0.93
36 7 0.07
ACGTcount: A:0.13, C:0.15, G:0.32, T:0.40
Consensus pattern (35 bp):
TTGGTGTGCTTCGGTTGGACTAGCTCTTATGAGCA
Found at i:29748173 original size:22 final size:21
Alignment explanation
Indices: 29748126--29748175 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
29748116 TTTCTTAAAC
* *
29748126 TTTCCAAATGTTTCTAATTTA
1 TTTCCAAATATTTCTAATGTA
* *
29748147 GTTCCAAATTATTTTTAATGTA
1 TTTCCAAA-TATTTCTAATGTA
29748169 TTTCCAA
1 TTTCCAA
29748176 GGCCTCGAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (21 bp):
TTTCCAAATATTTCTAATGTA
Found at i:29749776 original size:26 final size:26
Alignment explanation
Indices: 29749746--29749800 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
29749736 AATCCGATAG
*
29749746 TAAAACTTAAAAATGTTTGAATTGCT
1 TAAAACTTAAAAATGCTTGAATTGCT
29749772 TAAAACTTAAAAATGCTTGAATTGCT
1 TAAAACTTAAAAATGCTTGAATTGCT
29749798 TAA
1 TAA
29749801 CTGTTGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (26 bp):
TAAAACTTAAAAATGCTTGAATTGCT
Found at i:29750108 original size:21 final size:21
Alignment explanation
Indices: 29750060--29750108 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29750050 TGGATATGTT
* *
29750060 GCGACACGGAACCCCTGTGTC
1 GCGACATGAAACCCCTGTGTC
*
29750081 GCGACATGAAACCCTTGTGTC
1 GCGACATGAAACCCCTGTGTC
*
29750102 GTGACAT
1 GCGACAT
29750109 CACTGTAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (21 bp):
GCGACATGAAACCCCTGTGTC
Done.