Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 185 of 226
Found at i:56033722 original size:44 final size:44
Alignment explanation
Indices: 56033624--56033740 Score: 110
Period size: 44 Copynumber: 2.7 Consensus size: 44
56033614 TGGAGAAAAA
* * * * * *
56033624 TAAAGCTACGAATCCTATATCCCTAAAGTGGCAATGGCTCAGGT
1 TAAAGTTACAAATCCTATATCCCTGAAGTGGCAATAGATCAGAT
* * *
56033668 TGAA-TCTACAAATCCTATATCCTTGAAGTGGCAGTAGATCAGAT
1 TAAAGT-TACAAATCCTATATCCCTGAAGTGGCAATAGATCAGAT
* * *
56033712 TAAAGTTACAATTCTTATACCCCTGAAGT
1 TAAAGTTACAAATCCTATATCCCTGAAGT
56033741 TACAGTGGGT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
44 56 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (44 bp):
TAAAGTTACAAATCCTATATCCCTGAAGTGGCAATAGATCAGAT
Found at i:56034492 original size:12 final size:12
Alignment explanation
Indices: 56034467--56034521 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
56034457 TAGATACCTG
56034467 CAAAGAAGAAAAA
1 CAAAGAA-AAAAA
*
56034480 CAAAGACAAAAA
1 CAAAGAAAAAAA
56034492 CAGAAGCAAAAAAA
1 CA-AAG-AAAAAAA
*
56034506 CAAAAAAAAAAA
1 CAAAGAAAAAAA
56034518 CAAA
1 CAAA
56034522 TGATAGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 18 0.49
13 11 0.30
14 8 0.22
ACGTcount: A:0.78, C:0.13, G:0.09, T:0.00
Consensus pattern (12 bp):
CAAAGAAAAAAA
Found at i:56041023 original size:18 final size:18
Alignment explanation
Indices: 56041002--56041062 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
56040992 TTTTTTCGTA
*
56041002 TATAATATTTTTTATTTT
1 TATAATATTTTTAATTTT
* *
56041020 TATAAT-TTTTTGCACTTT
1 TATAATATTTTT-AATTTT
56041038 TAT-ATATTTTATAATTTT
1 TATAATATTTT-TAATTTT
56041056 TA-AATAT
1 TATAATAT
56041063 AAAACCACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 7 0.20
18 27 0.77
19 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (18 bp):
TATAATATTTTTAATTTT
Found at i:56041484 original size:15 final size:14
Alignment explanation
Indices: 56041440--56041489 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
56041430 TTAATAAAAA
56041440 TAAT-TATT-ATAT
1 TAATATATTAATAT
56041452 TAATATATTAATAT
1 TAATATATTAATAT
56041466 TAATACTATTAA-AT
1 TAATA-TATTAATAT
56041480 ATAATA-ATTA
1 -TAATATATTA
56041490 TTTAATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.12
13 8 0.24
14 11 0.32
15 11 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATATATTAATAT
Found at i:56042952 original size:9 final size:9
Alignment explanation
Indices: 56042935--56043015 Score: 81
Period size: 9 Copynumber: 8.6 Consensus size: 9
56042925 TTTGGTTAAA
56042935 AATTACCCG
1 AATTACCCG
*
56042944 AATTGCCCG
1 AATTACCCG
*
56042953 AAAATTACCCA
1 --AATTACCCG
*
56042964 AATTACCTG
1 AATTACCCG
56042973 AATTACCCG
1 AATTACCCG
* *
56042982 AAAATTACTCA
1 --AATTACCCG
56042993 AATTACCCG
1 AATTACCCG
56043002 AATTACCCG
1 AATTACCCG
56043011 AATTA
1 AATTA
56043016 AATCACTACA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
9 44 0.76
11 14 0.24
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:56042976 original size:29 final size:29
Alignment explanation
Indices: 56042934--56043012 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
56042924 TTTTGGTTAA
*
56042934 AAATTACCCGAATTGCCCGAAAATTACCC
1 AAATTACCCGAATTACCCGAAAATTACCC
* *
56042963 AAATTACCTGAATTACCCGAAAATTACTC
1 AAATTACCCGAATTACCCGAAAATTACCC
56042992 AAATTACCCGAATTACCCGAA
1 AAATTACCCGAATTACCCGAA
56043013 TTAAATCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.23
Consensus pattern (29 bp):
AAATTACCCGAATTACCCGAAAATTACCC
Found at i:56043044 original size:17 final size:17
Alignment explanation
Indices: 56043022--56043119 Score: 56
Period size: 17 Copynumber: 5.4 Consensus size: 17
56043012 ATTAAATCAC
*
56043022 TACATAATTAAAAGCAT
1 TACATAATTAAAAACAT
* * *
56043039 TACATAAATCTTTAAATCAC
1 TACAT-AA--TTAAAAACAT
*
56043059 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
*
56043076 TACATAAGTCTTGAATTAAC--
1 TACATAA---TT-AA-AAACAT
56043096 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
56043113 TACATAA
1 TACATAA
56043120 GTCTTGAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
15 3 0.05
16 2 0.03
17 27 0.44
18 2 0.03
19 2 0.03
20 21 0.34
21 2 0.03
22 2 0.03
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:56043064 original size:20 final size:18
Alignment explanation
Indices: 56043013--56043065 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
56043003 ATTACCCGAA
56043013 TTAAATCACTACAT-AAT
1 TTAAATCACTACATAAAT
* * *
56043030 TAAAAGCATTACATAAATCT
1 TTAAATCACTACATAAA--T
56043050 TTAAATCACTACATAA
1 TTAAATCACTACATAA
56043066 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 11 0.41
18 2 0.07
20 14 0.52
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (18 bp):
TTAAATCACTACATAAAT
Found at i:56043125 original size:37 final size:37
Alignment explanation
Indices: 56043020--56043140 Score: 181
Period size: 37 Copynumber: 3.3 Consensus size: 37
56043010 GAATTAAATC
* * * * *
56043020 ACTACATAATTAAAAGCATTACATAAATCTTTAAATC
1 ACTACATAATTAAAAACATTACATAAGTCTTGAATTA
*
56043057 ACTACATAATTAAAAATATTACATAAGTCTTGAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTGAATTA
56043094 ACTACATAATTAAAAACATTACATAAGTCTTGAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTGAATTA
56043131 AC-ACATAATT
1 ACTACATAATT
56043141 GACATGTAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 8 0.10
37 69 0.90
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (37 bp):
ACTACATAATTAAAAACATTACATAAGTCTTGAATTA
Found at i:56045798 original size:23 final size:23
Alignment explanation
Indices: 56045768--56045812 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
56045758 GAGTTAAAGG
*
56045768 AAACTAGAAGTAGGTTCAGCCTA
1 AAACTAGAAGAAGGTTCAGCCTA
*
56045791 AAACTAGAAGAAGGTTCGGCCT
1 AAACTAGAAGAAGGTTCAGCCT
56045813 TGCCAGCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (23 bp):
AAACTAGAAGAAGGTTCAGCCTA
Found at i:56047311 original size:21 final size:21
Alignment explanation
Indices: 56047279--56047319 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56047269 AATAAAAACC
56047279 TAACAATAATAACAAA-AATAT
1 TAACAATAATAA-AAATAATAT
56047300 TAACGAAT-ATAAAAATAATA
1 TAAC-AATAATAAAAATAATA
56047320 ATAGTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.17
21 12 0.67
22 3 0.17
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
TAACAATAATAAAAATAATAT
Found at i:56047321 original size:3 final size:3
Alignment explanation
Indices: 56047308--56047362 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
56047298 ATTAACGAAT
* * *
56047308 ATA AAA ATA ATA ATA GTA A-A GACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
56047353 ATA ATA ATA A
1 ATA ATA ATA A
56047363 AATTGCCCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:56049227 original size:170 final size:170
Alignment explanation
Indices: 56048945--56049899 Score: 1676
Period size: 170 Copynumber: 5.6 Consensus size: 170
56048935 CGCAACGTCG
* ** ** * * *
56048945 GGGAGATAGAATTACTGGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
1 GGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
* * * *
56049010 TTCGGTTTGTTCCACTGTAACCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAATTTC
66 TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTC
56049075 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
131 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
56049115 GGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
1 GGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
* *
56049180 TTTGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAATTTC
66 TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTC
56049245 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
131 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
*
56049285 GGGAGATAGGATTACTATCTTTGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
1 GGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
56049350 TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTC
66 TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTC
56049415 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
131 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
*
56049455 AGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
1 GGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
*
56049520 TTCGGTCTGCTCCACTGTAATATCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTC
66 TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTC
* *
56049585 AAAGAGATAAGATCCTTTAATCCGCTCTACTGTAATCTCA
131 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
* * *
56049625 GGAAGATAGGATTACTATCTTTGATCTGCTCCACTATAATCTCAGGGAGATAAGATCTGCACTTC
1 GGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
*
56049690 TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGTGATCTACTCTGCTGTAACTTC
66 TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTC
*
56049755 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATATCA
131 AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
*
56049795 GGGAGATAGGATTACTATCTTTGATCTGCTTCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
1 GGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
*
56049860 TTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTG
66 TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTG
56049900 TATAATGAAC
Statistics
Matches: 751, Mismatches: 34, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 751 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (170 bp):
GGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTC
TTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTC
AGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCA
Found at i:56062146 original size:21 final size:22
Alignment explanation
Indices: 56062112--56062165 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
56062102 ACATGTGGAT
*
56062112 TATAAAAATA-ACATAAAATAA
1 TATATAAATATACATAAAATAA
***
56062133 TATAT-AATATACATATTTTAA
1 TATATAAATATACATAAAATAA
56062154 TATATAAATATA
1 TATATAAATATA
56062166 TATAGACACG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAATATACATAAAATAA
Found at i:56062357 original size:3 final size:3
Alignment explanation
Indices: 56062344--56062398 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
56062334 ATTAACGATT
* * *
56062344 ATA AAA ATA ATA ATA GTA A-A GACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
56062389 ATA ATA ATA A
1 ATA ATA ATA A
56062399 AATTGCCCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:56064193 original size:16 final size:16
Alignment explanation
Indices: 56064172--56064205 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
56064162 TTTTTTTTCT
56064172 TACATTAATTACAATA
1 TACATTAATTACAATA
56064188 TACATTAATTACAATA
1 TACATTAATTACAATA
56064204 TA
1 TA
56064206 TTCAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
TACATTAATTACAATA
Found at i:56064214 original size:18 final size:16
Alignment explanation
Indices: 56064172--56064215 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
56064162 TTTTTTTTCT
*
56064172 TACATTAATTACAATA
1 TACAATAATTACAATA
*
56064188 TACATTAATTACAATA
1 TACAATAATTACAATA
56064204 TATTCAATAATT
1 TA--CAATAATT
56064216 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 18 0.72
18 7 0.28
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (16 bp):
TACAATAATTACAATA
Found at i:56065249 original size:16 final size:16
Alignment explanation
Indices: 56065227--56065264 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
56065217 CTAAGAGAAT
56065227 ATTGGGCTGGATTTAA
1 ATTGGGCTGGATTTAA
* *
56065243 GTTGGGCTGGGTTTAA
1 ATTGGGCTGGATTTAA
56065259 ATTGGG
1 ATTGGG
56065265 GGAGGGTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.18, C:0.05, G:0.39, T:0.37
Consensus pattern (16 bp):
ATTGGGCTGGATTTAA
Found at i:56069736 original size:24 final size:24
Alignment explanation
Indices: 56069709--56069760 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
56069699 TTAGTAAGTC
* *
56069709 AAATAAACTATACTCATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
56069733 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
56069757 AAAT
1 AAAT
56069761 CTTCTAGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:56071340 original size:21 final size:21
Alignment explanation
Indices: 56071273--56071341 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
56071263 TTTTTTTATA
56071273 ATATTATTATAATA-TAATGAAT
1 ATATTA-TATAATATTAAT-AAT
* * *
56071295 -TTTTATATTTATATTTAT-A-
1 ATATTATA-TAATATTAATAAT
56071314 ATATTATATAATATTAATAAT
1 ATATTATATAATATTAATAAT
56071335 ATATTAT
1 ATATTAT
56071342 GTTATGATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
19 8 0.22
20 10 0.28
21 15 0.42
22 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
ATATTATATAATATTAATAAT
Found at i:56073893 original size:97 final size:97
Alignment explanation
Indices: 56073728--56074010 Score: 475
Period size: 97 Copynumber: 2.9 Consensus size: 97
56073718 AAAGAACTCT
* * * *
56073728 TAATATGTTGCTAATATGTCA-CCCTAAAGGTTATC---TTTTTGTCTGTTTTATTAAAAACATT
1 TAATATGTTACTAATATGTCATCCC-ATAGGTCATCTTTTTTTTTTCTGTTTTATTAAAAACATT
*
56073789 GATATTTATGTTGCAAGAATTTATAAACTTTGA
65 GACATTTATGTTGCAAGAATTTATAAACTTTGA
56073822 TAATATGTTACTAATATGTCATCCCATAGGTCATCTTTTTTTTTTCTGTTTTATTAAAAACATTG
1 TAATATGTTACTAATATGTCATCCCATAGGTCATCTTTTTTTTTTCTGTTTTATTAAAAACATTG
56073887 ACATTTATGTTGCAAGAATTTATAAACTTTGA
66 ACATTTATGTTGCAAGAATTTATAAACTTTGA
56073919 TAATATGTTACTAATATGTCATCCCATAGGTCATCTTTTTTTTTTTCTGTTTTATTAAAAACATT
1 TAATATGTTACTAATATGTCATCCCATAGGTCATC-TTTTTTTTTTCTGTTTTATTAAAAACATT
56073984 GACATTTATGTTGCAAGAATTTATAAA
65 GACATTTATGTTGCAAGAATTTATAAA
56074011 TATTTAGGGG
Statistics
Matches: 179, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
94 28 0.16
95 3 0.02
97 92 0.51
98 56 0.31
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (97 bp):
TAATATGTTACTAATATGTCATCCCATAGGTCATCTTTTTTTTTTCTGTTTTATTAAAAACATTG
ACATTTATGTTGCAAGAATTTATAAACTTTGA
Found at i:56082053 original size:21 final size:20
Alignment explanation
Indices: 56082029--56082084 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
56082019 TAATAGAGGG
56082029 TAAAGAAATGAAAT-GATGACA
1 TAAAGAAAT-AAATAGATGA-A
*
56082050 TAAATAAATAAATAGATGAA
1 TAAAGAAATAAATAGATGAA
56082070 TAAAGAAAATAAATA
1 TAAAG-AAATAAATA
56082085 AAAAGATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.21
Consensus pattern (20 bp):
TAAAGAAATAAATAGATGAA
Found at i:56082335 original size:59 final size:58
Alignment explanation
Indices: 56082271--56082588 Score: 191
Period size: 59 Copynumber: 5.4 Consensus size: 58
56082261 ATGAAAAGGA
*
56082271 AATATAAGTAATATCAAATTTAAATATTTAAAAAAAGAATAATCAATAAATAGATAAAT
1 AATATAA-TAATATCAAATTTAAATATTTAAAAAAAGAATAATAAATAAATAGATAAAT
* * *
56082330 AATATAAATAATATTAAATTTAAGTATTTTAAAAAATAAAAGAATAATAAATAAATTGATAAA-
1 AATAT-AATAATATCAAATTTAAATA-TTT---AAA-AAAAGAATAATAAATAAATAGATAAAT
* * *
56082393 ACAAAT-ATAA-AT--AATATTAAATGTTT--AAAAAGCAA-AA-GAATAACA-A-ATAAAT
1 A-ATATAATAATATCAAAT-TTAAATATTTAAAAAAAG-AATAATAAATAA-ATAGATAAAT
* * * *
56082445 -ATA-AAAAATATCCATTTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAA
1 AATATAATAATATCAAATTTAAATATTT--AAA--AAAAGAATAATAAATAAATAGATAAAT
* * * * * *
56082505 AATATAAAGAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAAT-AACAAATAAATAAAT
1 AATAT-AATAATATCAAATTTAAATATTTAAAAAA--AGAATAATAAATAAATAGATAAAT
*
56082565 AA-ATAGATAA-AACAAATTTAAATA
1 AATATA-ATAATATCAAATTTAAATA
56082589 ATATCAAATT
Statistics
Matches: 201, Mismatches: 27, Indels: 63
0.69 0.09 0.22
Matches are distributed among these distances:
50 5 0.02
51 7 0.03
52 14 0.07
53 10 0.05
54 3 0.01
56 1 0.00
57 2 0.01
58 21 0.10
59 41 0.20
60 29 0.14
61 14 0.07
62 4 0.02
63 23 0.11
64 27 0.13
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (58 bp):
AATATAATAATATCAAATTTAAATATTTAAAAAAAGAATAATAAATAAATAGATAAAT
Found at i:56082465 original size:52 final size:53
Alignment explanation
Indices: 56082409--56082509 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 53
56082399 ATAAATAATA
*
56082409 TTAAATGTTTAAAAAGCAAAAGAATAACAAATAAAT-ATAAAAAATATCCATT
1 TTAAATATTTAAAAAGCAAAAGAATAACAAATAAATAATAAAAAATATCCATT
* *
56082461 TTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAAATAT
1 TTAAATATTTAAAAAGCAAAAGAATAACAAATAAATA-ATAAAAAATAT
56082510 AAAGAATATC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 33 0.75
54 11 0.25
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (53 bp):
TTAAATATTTAAAAAGCAAAAGAATAACAAATAAATAATAAAAAATATCCATT
Found at i:56082486 original size:111 final size:116
Alignment explanation
Indices: 56082326--56082688 Score: 325
Period size: 127 Copynumber: 3.1 Consensus size: 116
56082316 ATAAATAGAT
* * * *
56082326 AAAT-AATATAAATAATATTAAATTTAAGTATTTTAAAAAATAAAAGAATAATAAATAAATTGAT
1 AAATAAATATAAAAAATATCAAATTTAAATATTTTAAAAAATAAAAGAATAATAAATAAATAGAT
* *
56082390 AAAACAA-ATATA-AATA-ATA-TTAAATGTTT-AAAAAGCAAAAGAATAAC
66 AAAA-AATATAAAGAATACAAATTTAAATGTTTAAAAAAGCAAAAGAATAAC
* * *
56082437 AAATAAATATAAAAAATATCCATTTTAAATA-TTTAAAAAGTAAAAGAATAATAAATAAATAGAT
1 AAATAAATATAAAAAATATCAAATTTAAATATTTTAAAAAATAAAAGAATAATAAATAAATAGAT
*
56082501 AAAAAATATAAAGAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAAC
66 AAAAAATATAAAGAATA-CAAATTTAAATGTTTAAAAAAGCAAAAGAATAAC
* * **
56082553 AAATAAATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAGTAA-A
1 AAATAAAT--ATAAA-A-A-ATATCAAATTT--A-AATAT----TTTAAA-AAATAAAAG-AATA
* * * * *
56082617 AT-AATAAATA-A-AACAAATTTAAATAATATCAAATTTAAATGTTTAAAAAGGTAAAAGAATAA
52 ATAAATAAATAGATAAAAAATATAAAGAATA-CAAATTTAAATGTTTAAAAAAGCAAAAGAATAA
56082679 C
116 C
56082680 AAATAAATA
1 AAATAAATA
56082689 AATAGATAAA
Statistics
Matches: 210, Mismatches: 20, Indels: 30
0.81 0.08 0.12
Matches are distributed among these distances:
110 2 0.01
111 43 0.20
112 25 0.12
114 2 0.01
115 10 0.05
116 25 0.12
118 5 0.02
119 1 0.00
120 1 0.00
121 7 0.03
123 1 0.00
124 4 0.02
125 1 0.00
127 56 0.27
128 1 0.00
129 14 0.07
130 10 0.05
131 2 0.01
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (116 bp):
AAATAAATATAAAAAATATCAAATTTAAATATTTTAAAAAATAAAAGAATAATAAATAAATAGAT
AAAAAATATAAAGAATACAAATTTAAATGTTTAAAAAAGCAAAAGAATAAC
Found at i:56082495 original size:15 final size:15
Alignment explanation
Indices: 56082470--56082559 Score: 56
Period size: 15 Copynumber: 5.7 Consensus size: 15
56082460 TTTAAATATT
*
56082470 TAAAAAGTAAAAGAA
1 TAAAAAATAAAAGAA
*
56082485 TAATAAATAAATAG-A
1 TAAAAAATAAA-AGAA
56082500 TAAAAAATATAAAGAA
1 TAAAAAATA-AAAGAA
** * **
56082516 TATCAAATTTAAATGTT
1 TA--AAAAATAAAAGAA
56082533 TAAAAAAGTAAAAGAA
1 TAAAAAA-TAAAAGAA
*
56082549 TAACAAATAAA
1 TAAAAAATAAA
56082560 TAAATAAATA
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
15 27 0.49
16 18 0.33
17 5 0.09
18 5 0.09
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (15 bp):
TAAAAAATAAAAGAA
Found at i:56082495 original size:22 final size:21
Alignment explanation
Indices: 56082470--56082512 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
56082460 TTTAAATATT
56082470 TAAAAAG-TAAAAGAATAATAAA
1 TAAAAAGATAAAA-AAT-ATAAA
*
56082492 TAAATAGATAAAAAATATAAA
1 TAAAAAGATAAAAAATATAAA
56082513 GAATATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
TAAAAAGATAAAAAATATAAA
Found at i:56082503 original size:175 final size:174
Alignment explanation
Indices: 56082270--56082839 Score: 575
Period size: 175 Copynumber: 3.2 Consensus size: 174
56082260 AATGAAAAGG
* * *
56082270 AAATATAAGTAATATCAAATTTAAATATTT--AAA--AAAAGAATAATCAATAAATAGATAAATA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAA
*
56082331 ATATAAATAATATTAAATTTAAGTATTTTAAAAAATAAAAGAATAATAAATAAATTGATAAAACA
66 ATATAAATAATATCAAATTTAA-TATTTTAAAAAATAAAAGAATAATAAATAAATTGATAAAACA
*
56082396 AATATAAATAATATTAAATGTTTAAAAAGCAAAAGAATAACAAAT
130 AATATAAATAATATTAAATGTTTAAAAAGTAAAAGAATAACAAAT
* * *
56082441 AAATATAAAAAATATCCATTTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAA
*
56082506 ATATAAAGAATATCAAATTTAA-ATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAATA
66 ATATAAATAATATCAAATTTAATAT-TTTAAAAAA-TAAAAGAAT----AATAAATAAAT---T-
* * * * *
56082570 GATAAAACAAATTTAAATAATATCAAAT-TTAAATATTTAAAAGTAAAATAATAAATAAAAC
121 GATAAAACAAATATAAATAATATTAAATGTT---TA---AAAAGTAAAAGAAT-AA-CAAAT
* *
56082631 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAGGTAAAAGAATAACAAATAAATAAATAGAT
1 AAATATAAATAATATCAAATTTAAATATTTAAAAA-GTAAAAGAAT----AATAAATAAATAGAT
* *
56082696 AAAACGAATATAAATAATATCAAATTTAA-ATATTTAAAAAGTAAAAGAATAATAAATAAATAGA
61 AAAA--AATATAAATAATATCAAATTTAATAT-TTTAAAAAATAAAAGAATAATAAATAAATTGA
* * * *
56082760 TAATATAAATA-ATATCAA-ATTTAAATGTTTAAAGAGTAAAAGAATAACAAAT
123 TAAAACAAATATAAAT-AATA-TTAAATGTTTAAAAAGTAAAAGAATAACAAAT
* *
56082812 AAATAAATAGATAA-AACAAATTTAAATA
1 AAAT--ATAAATAATATCAAATTTAAATA
56082840 ATATCAAATT
Statistics
Matches: 329, Mismatches: 36, Indels: 57
0.78 0.09 0.14
Matches are distributed among these distances:
171 26 0.08
173 5 0.02
174 9 0.03
175 55 0.17
179 11 0.03
181 7 0.02
182 17 0.05
183 44 0.13
185 2 0.01
186 2 0.01
187 4 0.01
188 29 0.09
189 4 0.01
190 33 0.10
191 10 0.03
192 11 0.03
195 19 0.06
196 9 0.03
197 32 0.10
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (174 bp):
AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAA
ATATAAATAATATCAAATTTAATATTTTAAAAAATAAAAGAATAATAAATAAATTGATAAAACAA
ATATAAATAATATTAAATGTTTAAAAAGTAAAAGAATAACAAAT
Found at i:56082506 original size:31 final size:31
Alignment explanation
Indices: 56082471--56082567 Score: 101
Period size: 31 Copynumber: 3.1 Consensus size: 31
56082461 TTAAATATTT
56082471 AAAAAGTAAAAGAATAATAAATAAATAGATA
1 AAAAAGTAAAAGAATAATAAATAAATAGATA
*
56082502 AAAAA-TATAAAGAAT-ATCAAATTTAAAT-GTTTA
1 AAAAAGTA-AAAGAATAAT-AAA--TAAATAG-ATA
* *
56082535 AAAAAGTAAAAGAATAACAAATAAATAAATA
1 AAAAAGTAAAAGAATAATAAATAAATAGATA
56082566 AA
1 AA
56082568 TAGATAAAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
30 4 0.07
31 24 0.44
32 1 0.02
33 22 0.41
34 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (31 bp):
AAAAAGTAAAAGAATAATAAATAAATAGATA
Found at i:56082518 original size:72 final size:70
Alignment explanation
Indices: 56082441--56082628 Score: 160
Period size: 64 Copynumber: 2.7 Consensus size: 70
56082431 AATAACAAAT
*
56082441 AAATATAAAAAATATCCATTTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAA-A
1 AAATAT-AAAAATAT-CA-TTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAAATAAATA
56082505 AATATAAA-
63 AATA-AAAC
* * * * *
56082513 GAATAT---CA-A--ATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAATAGA
1 AAATATAAAAATATCATTTAAATATTT-AAAAAGTAAAAGAATAATAAATAAATAAATAAATAAA
56082572 TAAAAC
65 TAAAAC
* *
56082578 AAATTTAAATAATATCAAATTTAAATATTT-AAAAGTAAAATAATAAATAAA
1 AAATATAAA-AATATC--ATTTAAATATTTAAAAAGTAAAAGAAT-AATAAA
56082629 ACAAATTTAA
Statistics
Matches: 91, Mismatches: 12, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
63 10 0.11
64 35 0.38
65 8 0.09
67 1 0.01
68 1 0.01
69 1 0.01
70 1 0.01
72 18 0.20
73 5 0.05
74 11 0.12
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (70 bp):
AAATATAAAAATATCATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAAATAAATAAAT
AAAAC
Found at i:56082537 original size:33 final size:32
Alignment explanation
Indices: 56082445--56082556 Score: 99
Period size: 33 Copynumber: 3.5 Consensus size: 32
56082435 ACAAATAAAT
* * *
56082445 ATAAAA-AATATCCATTTTAAATATTTAAAAA
1 ATAAAAGAATATCAAATTTAAATGTTTAAAAA
* *
56082476 GTAAAAGAATAAT-AAA--TAAATAG-ATAAAAA
1 ATAAAAGAAT-ATCAAATTTAAAT-GTTTAAAAA
56082506 ATATAAAGAATATCAAATTTAAATGTTTAAAAA
1 ATA-AAAGAATATCAAATTTAAATGTTTAAAAA
*
56082539 AGTAAAAGAATAACAAAT
1 A-TAAAAGAATATCAAAT
56082557 AAATAAATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
30 15 0.23
31 15 0.23
32 5 0.08
33 27 0.42
34 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (32 bp):
ATAAAAGAATATCAAATTTAAATGTTTAAAAA
Found at i:56082598 original size:16 final size:16
Alignment explanation
Indices: 56082577--56082656 Score: 63
Period size: 16 Copynumber: 4.7 Consensus size: 16
56082567 ATAGATAAAA
56082577 CAAATTTAAATAATAT
1 CAAATTTAAATAATAT
*
56082593 CAAATTTAAATATTTAAAAGT
1 CAAATTT-AA-A--TAATA-T
* * *
56082614 AAAATAATAAATAA-AA
1 CAAAT-TTAAATAATAT
56082630 CAAATTTAAATAATAT
1 CAAATTTAAATAATAT
56082646 CAAATTTAAAT
1 CAAATTTAAAT
56082657 GTTTAAAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
15 7 0.14
16 23 0.46
17 3 0.06
18 4 0.08
20 5 0.10
21 7 0.14
22 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (16 bp):
CAAATTTAAATAATAT
Found at i:56082609 original size:74 final size:70
Alignment explanation
Indices: 56082486--56082900 Score: 209
Period size: 69 Copynumber: 6.3 Consensus size: 70
56082476 GTAAAAGAAT
*
56082486 AATAAATAAATAGATAAAAAATATAAAGAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATA
1 AATAAATAAATAGATAAAAAATATAAAGAATATCAAATTTAAATATTT--AAAAGTAAAAGAATA
56082551 ACAAATA
64 ACAAATA
* *
56082558 AATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAGT--AA-AATA
1 AATAAATAAATAGAT-AAA-AAATATAAAGAATATCAAATTTAAATATTTAAAAGTAAAAGAATA
*
56082620 ATAAAT-
64 ACAAATA
* * * * * * ** *
56082626 -A-AAACAAAT--TTAAATAATAT-CA-AAT-TTAAATGTTTAAAAAGGTAAAAG-AATAA-CA-
1 AATAAATAAATAGATAAAAAATATAAAGAATATCAAA--TTTAAATATTTAAAAGTAA-AAGAAT
*
56082681 AATAAATA
63 AACAAATA
* *
56082689 AATAGATAAA-ACG------AATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATA
1 AATAAATAAATA-GATAAAAAATATAAAGAATATCAAATTTAAATATTT-AAAAGTAAAAGAATA
*
56082747 ATAAATA
64 ACAAATA
* * * * * *
56082754 AATAGAT-AAT--ATAAATAATAT-CA-AAT-TTAAATGTTTAAAGA-GTAAAAG------AATA
1 AATAAATAAATAGATAAAAAATATAAAGAATATCAAA--TTTAAATATTTAAAAGTAAAAGAATA
56082806 ACAAATA
64 ACAAATA
* * * * * *
56082813 AATAAATAGATA-A-AACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAA
1 AATAAATAAATAGATAAAAAATATAAAGAATATCAAATTTAAATATTT-AAAAGTAAAAGAATAA
56082876 CAAATA
65 CAAATA
56082882 AATAAATAAATAGATAAAA
1 AATAAATAAATAGATAAAA
56082901 CAACTCATAA
Statistics
Matches: 261, Mismatches: 38, Indels: 89
0.67 0.10 0.23
Matches are distributed among these distances:
59 20 0.08
60 11 0.04
61 28 0.11
62 24 0.09
63 25 0.10
64 11 0.04
65 29 0.11
66 11 0.04
67 9 0.03
68 5 0.02
69 31 0.12
70 3 0.01
71 3 0.01
72 21 0.08
73 3 0.01
74 27 0.10
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (70 bp):
AATAAATAAATAGATAAAAAATATAAAGAATATCAAATTTAAATATTTAAAAGTAAAAGAATAAC
AAATA
Found at i:56082640 original size:53 final size:55
Alignment explanation
Indices: 56082561--56082678 Score: 186
Period size: 53 Copynumber: 2.2 Consensus size: 55
56082551 ACAAATAAAT
*
56082561 AAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTT-AAAA-GTA
1 AAAT-AATAAATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGGTA
*
56082615 AAATAATAAATAAAACAAATTTAAATAATATCAAATTTAAATGTTTAAAAAGGTA
1 AAATAATAAATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGGTA
*
56082670 AAAGAATAA
1 AAATAATAA
56082679 CAAATAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
53 40 0.68
54 8 0.14
55 11 0.19
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (55 bp):
AAATAATAAATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGGTA
Found at i:56082688 original size:69 final size:68
Alignment explanation
Indices: 56082615--56082893 Score: 351
Period size: 69 Copynumber: 4.2 Consensus size: 68
56082605 TTTAAAAGTA
* *
56082615 AAATAATAAATAAAACAAATTTAAATAATATCAAATTTAAATGTTTAAAAAGGTAAAAGAATAAC
1 AAATAATAAATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAA-GTAAAAGAATAAC
56082680 AAAT
65 AAAT
* *
56082684 AAATAAATAGATAAAACGAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT---
1 AAAT-AATAAATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAAC
56082746 -AAT
65 AAAT
* * * *
56082749 --A-AATAAAT-AGA-TAATATAAATAATATCAAATTTAAATGTTTAAAGAGTAAAAGAATAACA
1 AAATAATAAATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACA
56082809 AAT
66 AAT
* * * *
56082812 AAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAAC
1 AAAT-AATAAATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAAC
56082877 AAAT
65 AAAT
56082881 AAATAAATAAATA
1 AAAT-AATAAATA
56082894 GATAAAACAA
Statistics
Matches: 181, Mismatches: 18, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
59 42 0.23
60 2 0.01
61 6 0.03
63 4 0.02
65 4 0.02
67 6 0.03
68 2 0.01
69 72 0.40
70 43 0.24
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (68 bp):
AAATAATAAATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACA
AAT
Found at i:56082691 original size:35 final size:35
Alignment explanation
Indices: 56082652--56082757 Score: 85
Period size: 35 Copynumber: 3.1 Consensus size: 35
56082642 ATATCAAATT
56082652 TAAATGTTTAAAAAGGTAAAAGAATAACAAATAAA
1 TAAATGTTTAAAAAGGTAAAAGAATAACAAATAAA
* * * * * *
56082687 TAAATAG-ATAAAACGAATATAAATAATATCAAAT--T
1 TAAAT-GTTTAAAAAG-GTA-AAAGAATAACAAATAAA
* *
56082722 TAAATATTTAAAAA-GTAAAAGAATAATAAATAAA
1 TAAATGTTTAAAAAGGTAAAAGAATAACAAATAAA
56082756 TA
1 TA
56082758 GATAATATAA
Statistics
Matches: 51, Mismatches: 14, Indels: 13
0.65 0.18 0.17
Matches are distributed among these distances:
32 11 0.22
33 2 0.04
34 2 0.04
35 21 0.41
36 3 0.06
37 12 0.24
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (35 bp):
TAAATGTTTAAAAAGGTAAAAGAATAACAAATAAA
Found at i:56082776 original size:59 final size:59
Alignment explanation
Indices: 56082702--56082898 Score: 225
Period size: 59 Copynumber: 3.2 Consensus size: 59
56082692 AGATAAAACG
56082702 AATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGAT
1 AATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGAT
* *
56082761 AATATAAATAATATCAAATTTAAATGTTTAAAGAGTAAAAGAATAACAAATAAATAAATAGAT
1 AATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT----AATAAATAAATAGAT
* * * * *
56082824 AAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAAT
1 ------AATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGAT
*
56082889 AA-ATAGATAA
1 AATATAAATAA
56082899 AACAACTCAT
Statistics
Matches: 117, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
58 6 0.05
59 44 0.38
63 15 0.13
65 13 0.11
69 39 0.33
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (59 bp):
AATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGAT
Found at i:56082838 original size:128 final size:128
Alignment explanation
Indices: 56082441--56082898 Score: 642
Period size: 128 Copynumber: 3.6 Consensus size: 128
56082431 AATAACAAAT
* * *
56082441 AAATATAAAAAATATCCATTTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGAT----A
*
56082506 ATATAAAGAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAATAG
62 ATATAAATAATATCAAATTTAAATGTTT-AAAAAGTAAAAGAATAAC----AAATAAATAAATAG
56082571 ATAAAAC
122 ATAAAAC
* * *
56082578 AAATTTAAATAATATCAAATTTAAATATTT-AAAAGT--AA-AATAATAAATAAA-ACA-AATTT
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAATAT
56082637 AAATAATATCAAATTTAAATGTTTAAAAAGGTAAAAGAATAACAAATAAATAAATAGATAAAAC
66 AAATAATATCAAATTTAAATGTTTAAAAA-GTAAAAGAATAACAAATAAATAAATAGATAAAAC
*
56082701 GAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAATAT
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAATAT
*
56082766 AAATAATATCAAATTTAAATGTTTAAAGAGTAAAAGAATAACAAATAAATAAATAGATAAAAC
66 AAATAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATAAATAGATAAAAC
* * * * *
56082829 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAATAA-AT
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAATAT
*
56082893 AGATAA
66 AAATAA
56082899 AACAACTCAT
Statistics
Matches: 295, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
123 49 0.17
124 6 0.02
126 7 0.02
127 60 0.20
128 92 0.31
129 32 0.11
132 2 0.01
133 13 0.04
134 2 0.01
136 6 0.02
137 26 0.09
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (128 bp):
AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAATAT
AAATAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATAAATAGATAAAAC
Found at i:56083906 original size:21 final size:20
Alignment explanation
Indices: 56083868--56083907 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
56083858 AATTACAATG
* *
56083868 TTATTTTTCTATTTTTTCTA
1 TTATTTTTCTACTATTTCTA
56083888 TTATTCTTTCTACTATTTCT
1 TTATT-TTTCTACTATTTCT
56083908 TTCGTGTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTTCTACTATTTCTA
Found at i:56084603 original size:43 final size:44
Alignment explanation
Indices: 56084402--56084889 Score: 474
Period size: 44 Copynumber: 11.1 Consensus size: 44
56084392 GGATTTGTCT
*
56084402 CTTCAATTTGCTCCACTGCAACTTCAGGGAGATAAGACTTAC-TA-
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT-CGTAG
* * *
56084446 CTTCAATCTTGCTCCACTACAACTTCAGGGAGATAAGACTCACTA-
1 CTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTC-GTAG
* **
56084491 CTTCAATCTTGCTCCACTACAACTTCAGGGAGATAAGATTTATAG
1 CTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAG
* *
56084536 CTTCAACCTGCTCCACTGCAACTTCAGGGAGACAA-ATTCGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAG
* * * *
56084579 CTTTAATCTGCTCCATTGCGACTTCAGGGAGATAAGGTTC--A-
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAG
* * *
56084620 CTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAG
* ** * * *
56084664 CCTCAATCTGCTCCACCACAACTTCAAGGATATTAGATTCGT-G
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAG
* * * * *
56084707 ACTTTAATCTACTCCACTGCAACTTCAAGGAGATAAGACTCACTA-
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GTAG
* * * *
56084752 TTTCAATCTGCTCCAATGCAACTTCAGGGAGATAATATTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAG
* * * * *
56084796 CTTC-ATCTTGCTCCACTGCATCTTTAGGAAGATAAGATTTGCTAT
1 CTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTCG-TAG
* * *
56084841 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAG
56084885 CTTCA
1 CTTCA
56084890 CTGAACTGTT
Statistics
Matches: 368, Mismatches: 61, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
41 36 0.10
42 1 0.00
43 43 0.12
44 173 0.47
45 112 0.30
46 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAG
Found at i:56085398 original size:18 final size:18
Alignment explanation
Indices: 56085356--56085398 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
56085346 ATGCCTGAAA
56085356 AAGATTGTATCAATAGAC
1 AAGATTGTATCAATAGAC
* * *
56085374 AATATTGTATTAATAGAT
1 AAGATTGTATCAATAGAC
56085392 AAGATTG
1 AAGATTG
56085399 AAATTTATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (18 bp):
AAGATTGTATCAATAGAC
Found at i:56096096 original size:25 final size:26
Alignment explanation
Indices: 56096085--56096133 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
56096075 ATAATGACAT
*
56096085 AAATAAATAAATAGATG-AATAAAGA
1 AAATAAATAAATAAATGAAATAAAGA
* *
56096110 AAATAAATAAATAGATAAAATAAA
1 AAATAAATAAATAAATGAAATAAA
56096134 AATGTCATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.20
Consensus pattern (26 bp):
AAATAAATAAATAAATGAAATAAAGA
Found at i:56096113 original size:21 final size:20
Alignment explanation
Indices: 56096063--56096119 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
56096053 TAATAGAGGG
56096063 TAAAGAAATGAAATAATGACA
1 TAAAGAAAT-AAATAATGACA
*
56096084 TAAATAAATAAATAGATGA-A
1 TAAAGAAATAAATA-ATGACA
56096104 TAAAGAAAATAAATAA
1 TAAAG-AAATAAATAA
56096120 ATAGATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.21
Consensus pattern (20 bp):
TAAAGAAATAAATAATGACA
Found at i:56096302 original size:14 final size:14
Alignment explanation
Indices: 56096283--56096312 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56096273 ATATATATAT
56096283 AAATGCTTAATGAA
1 AAATGCTTAATGAA
56096297 AAATGCTTAATGAA
1 AAATGCTTAATGAA
56096311 AA
1 AA
56096313 GGAAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
AAATGCTTAATGAA
Found at i:56096623 original size:43 final size:41
Alignment explanation
Indices: 56096576--56096700 Score: 122
Period size: 43 Copynumber: 3.1 Consensus size: 41
56096566 AATAAATAGA
56096576 TAAAACAAATATAAATAATATCAAATTTAAATGTTTAAAAAAG
1 TAAAACAAATATAAATAATATCAAATTTAAAT-TTT-AAAAAG
* * *
56096619 TAAAA-GAATAACAAATAA-AT-AAA--TAAA---TAAATAG
1 TAAAACAAAT-ATAAATAATATCAAATTTAAATTTTAAAAAG
56096653 ATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAG
1 -TAAAACAAATATAAATAATATCAAATTTAAAT-TTTAAAAAG
56096696 TAAAA
1 TAAAA
56096701 GAATAATGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
34 5 0.08
35 13 0.20
36 5 0.08
37 3 0.05
39 8 0.12
41 3 0.05
42 10 0.15
43 18 0.28
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (41 bp):
TAAAACAAATATAAATAATATCAAATTTAAATTTTAAAAAG
Found at i:56096648 original size:78 final size:73
Alignment explanation
Indices: 56096426--56096742 Score: 413
Period size: 78 Copynumber: 4.4 Consensus size: 73
56096416 GTAAAAGAAT
* *
56096426 AATAAATAAATAGATAAAAACAAATATAAAT-A-AT---A-TTAAATGTTTAAAAAGCAAAAGAA
1 AATAAATAAATAGAT-AAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAA
*
56096485 TAACAAATA
65 TAATAAATA
* *
56096494 AATAAATAAATAGATAAAATAAATATAAA-AATATCAATTTTAAATATTTAAAAAGTAAAAG---
1 AATAAATAAATAGATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT
56096555 AAT-AATA
66 AATAAATA
*
56096562 AATAAATAAATAGATAAAACAAATATAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAA
1 AATAAATAAATAGATAAAACAAATATAAATAATATCAAATTTAAATATTT-AAAAAGTAAAAGAA
56096627 TAACAAATAAATA
65 T----AATAAATA
56096640 AATAAATAAATAGATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT
1 AATAAATAAATAGATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT
*
56096705 AATGAATA
66 AATAAATA
* * *
56096713 AATACATAGATAGATAAAACAAATTTAAAT
1 AATAAATAAATAGATAAAACAAATATAAAT
56096743 GTTTAAAAAA
Statistics
Matches: 220, Mismatches: 13, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
67 14 0.06
68 49 0.22
69 20 0.09
70 12 0.05
72 20 0.09
73 34 0.15
77 18 0.08
78 53 0.24
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.26
Consensus pattern (73 bp):
AATAAATAAATAGATAAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT
AATAAATA
Found at i:56096649 original size:27 final size:28
Alignment explanation
Indices: 56096611--56096671 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
56096601 TTTAAATGTT
*
56096611 TAAA-AAAGTAAA-AGA-ATAACAAATAAA
1 TAAATAAAGTAAATAGATAAAACAAAT--A
56096638 TAAATAAA-TAAATAGATAAAACAAATA
1 TAAATAAAGTAAATAGATAAAACAAATA
56096665 TAAATAA
1 TAAATAA
56096672 TATCAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 16 0.53
28 6 0.20
29 8 0.27
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (28 bp):
TAAATAAAGTAAATAGATAAAACAAATA
Found at i:56096665 original size:69 final size:67
Alignment explanation
Indices: 56096426--56096978 Score: 422
Period size: 69 Copynumber: 8.1 Consensus size: 67
56096416 GTAAAAGAAT
* * *
56096426 AATAAATAAATAGATAAAAACAAATATAAATAATATTAAATGTTTAAAAAGCAAAAGAATAACAA
1 AATAAATAAATAAAT-AAAA-AAATAT-CA-AAT-TTAAATGTTTAAAAAGTAAAAGAATAACAA
56096491 ATAAATA
61 ATAAATA
* * * *
56096498 AATAAATAGATAAAATAAATATAAAAATATCAATTTTAAATATTTAAAAAGTAAAAGAATAATAA
1 AAT--A-A-AT-AAATAAATAAAAAAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAA
56096563 ATAAATA
61 ATAAATA
* * *
56096570 AATAGATAAAACAAATATAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAAT
1 AATAAAT-AAATAAATA-AAAAAATATCAAATTTAAATGTTT-AAAAAGTAAAAGAATAACAAAT
56096635 AAATA
63 AAATA
* ** * *
56096640 AATAAATAAATAGATAAAACAAATAT-AAATAATATCAAA--TTTAAATATTTAAAA-AGTAAAA
1 AATAAATAAATAAATAAAA-AAATATCAAAT--T-T-AAATGTTTAAA-AAGTAAAAGAATAACA
*
56096701 GAAT-AATG
60 -AATAAATA
* * * *
56096709 AATAAATACATAGATAGATAAA-A-CAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAA
1 AATAAATAAATAAATAAAAAAATATCAAATTTAAATGTTT-AAAAAGTAAAAGAATAACAAATAA
56096772 ATA
65 ATA
* * * * * *
56096775 GAT--A-AAACAAATATAAATAATTTAAATATTTAAATATTTAAAAAGTAAAAGAAT----AATA
1 AATAAATAAATAAATA-AAAAAATATCAA-ATTTAAATGTTTAAAAAGTAAAAGAATAACAAATA
56096833 AATA
64 AATA
* * *
56096837 AATAGAT-AAT--AT-AAATAATATCAAATTTAAATGTTTAAAAAGTAAAAGGATAACAAATAAA
1 AATAAATAAATAAATAAAAAAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAA
56096898 TA
66 TA
* * * * * * *
56096900 AATATATTAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAATAGAGGAATAACAAATA
1 AATA-AATAAATAAATA-AAAAAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATA
56096965 AATA
64 AATA
*
56096969 AATAGATAAA
1 AATAAATAAA
56096979 ACAACTCATA
Statistics
Matches: 387, Mismatches: 57, Indels: 78
0.74 0.11 0.15
Matches are distributed among these distances:
59 25 0.06
60 10 0.03
62 12 0.03
63 21 0.05
64 9 0.02
65 15 0.04
66 30 0.08
67 18 0.05
68 25 0.06
69 109 0.28
70 46 0.12
71 1 0.00
72 43 0.11
73 2 0.01
74 2 0.01
75 7 0.02
76 5 0.01
77 7 0.02
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (67 bp):
AATAAATAAATAAATAAAAAAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAA
TA
Found at i:56096856 original size:9 final size:9
Alignment explanation
Indices: 56096784--56096862 Score: 51
Period size: 8 Copynumber: 9.0 Consensus size: 9
56096774 AGATAAAACA
56096784 AATATAAAT
1 AATATAAAT
*
56096793 AATTTAAAT
1 AATATAAAT
*
56096802 -ATTTAAAT
1 AATATAAAT
*
56096810 -ATTTAAA-
1 AATATAAAT
*
56096817 AAGTA-AAAG
1 AA-TATAAAT
56096826 AATAATAAAT
1 AAT-ATAAAT
*
56096836 AA-ATAGAT
1 AATATAAAT
56096844 AATATAAAT
1 AATATAAAT
56096853 AATATCAAAT
1 AATAT-AAAT
56096863 TTAAATGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
8 27 0.47
9 22 0.38
10 9 0.16
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (9 bp):
AATATAAAT
Found at i:56096895 original size:59 final size:60
Alignment explanation
Indices: 56096661--56096968 Score: 259
Period size: 59 Copynumber: 5.0 Consensus size: 60
56096651 AGATAAAACA
* ** *
56096661 AATATAAATAATATCAA-ATTTAAATATTTAAAAAGTAAAAGAATAATGAATAAATACAT
1 AATATAAATAATATAAATATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAGAT
* * *
56096720 -AGATAGATAA-A-ACAA-ATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAGAT
1 AATATAAATAATATA-AATATTTAAATATTT-AAAAAGTAAAAGAATAACAAATAAATAGAT
* *
56096778 AAAACAAATATAAATAATTTAAATATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGA
1 ------AATATAAATAATATAAATATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAGA
56096843 T
60 T
* * * *
56096844 AATATAAATAATATCAA-ATTTAAATGTTTAAAAAGTAAAAGGATAACAAATAAATAAAT
1 AATATAAATAATATAAATATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAGAT
* * * * *
56096903 ATATTAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAATAGAGGAATAACAAATAAAT
1 A-A-T--ATAAATA-ATATAA-AT---ATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAAT
56096968 A
57 A
56096969 AATAGATAAA
Statistics
Matches: 201, Mismatches: 26, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
57 14 0.07
58 35 0.17
59 39 0.19
60 16 0.08
61 1 0.00
63 6 0.03
64 4 0.02
65 9 0.04
66 31 0.15
67 12 0.06
69 34 0.17
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (60 bp):
AATATAAATAATATAAATATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAGAT
Found at i:56098582 original size:9 final size:9
Alignment explanation
Indices: 56098568--56098643 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
56098558 GTAGTGATTC
56098568 AATTCGGTT
1 AATTCGGTT
*
56098577 AATTCGGGT
1 AATTCGGTT
*
56098586 AATTCGGGT
1 AATTCGGTT
*
56098595 AATTCGATT
1 AATTCGGTT
*
56098604 AATTCGGGT
1 AATTCGGTT
* * *
56098613 ATTTAGATT
1 AATTCGGTT
56098622 AATTCGGTT
1 AATTCGGTT
56098631 AATTCGGTT
1 AATTCGGTT
56098640 AATT
1 AATT
56098644 TTTAACCAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:56098600 original size:27 final size:27
Alignment explanation
Indices: 56098568--56098643 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
56098558 GTAGTGATTC
* *
56098568 AATTCGGTTAATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCGGGTAATTAGAGT
* * *
56098595 AATTCGATTAATTCGGGTATTTAGATT
1 AATTCGGTTAATTCGGGTAATTAGAGT
*
56098622 AATTCGGTTAATTCGGTTAATT
1 AATTCGGTTAATTCGGGTAATT
56098644 TTTAACCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (27 bp):
AATTCGGTTAATTCGGGTAATTAGAGT
Found at i:56099951 original size:19 final size:20
Alignment explanation
Indices: 56099907--56099951 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
56099897 CAAAAATTAC
56099907 ATAAAAATATAAAATAATTT
1 ATAAAAATATAAAATAATTT
*
56099927 -TTAAAAT-TCAAAAT-ATTT
1 ATAAAAATAT-AAAATAATTT
56099945 ATAAAAA
1 ATAAAAA
56099952 AATCTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAAATATAAAATAATTT
Found at i:56101001 original size:26 final size:26
Alignment explanation
Indices: 56100972--56101022 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
56100962 AAGTCATCAA
56100972 TAAGTCAACTTTTGACTCCAAATTTT
1 TAAGTCAACTTTTGACTCCAAATTTT
* *
56100998 TAAGTCAACTTTTGATTCGAAATTT
1 TAAGTCAACTTTTGACTCCAAATTT
56101023 GTATGTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (26 bp):
TAAGTCAACTTTTGACTCCAAATTTT
Found at i:56101759 original size:20 final size:19
Alignment explanation
Indices: 56101730--56101776 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
56101720 AGTTTTTAAA
*
56101730 TTTT-ATAACATTTAATACT
1 TTTTAATAACATTT-ATAAT
56101749 TTTTAATAACATTTATAAT
1 TTTTAATAACATTTATAAT
56101768 TTTCTAATA
1 TTT-TAATA
56101777 TTTTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATAACATTTATAAT
Found at i:56101770 original size:19 final size:20
Alignment explanation
Indices: 56101730--56101795 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
56101720 AGTTTTTAAA
*
56101730 TTTT-ATAACATTTAATACT
1 TTTTAATAACATTTAATAAT
56101749 TTTTAATAACATTT-ATAAT
1 TTTTAATAACATTTAATAAT
*
56101768 TTTCTAAT-A-TTTTAATAAT
1 TTT-TAATAACATTTAATAAT
*
56101787 TTCTAATAA
1 TTTTAATAA
56101796 TTTTTAAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.17
19 20 0.50
20 13 0.32
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTAATAACATTTAATAAT
Found at i:56101783 original size:38 final size:36
Alignment explanation
Indices: 56101724--56101795 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 36
56101714 AGTAGTAGTT
* *
56101724 TTTAAATTTTATAACATTTAATACTTTTTAATAACA
1 TTTAAATTTTATAACATTTAATAATTTCTAATAACA
* *
56101760 TTTATAATTTTCTAATATTTTAATAATTTCTAATAA
1 TTTA-AATTTTATAACA-TTTAATAATTTCTAATAA
56101796 TTTTTAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 4 0.13
37 10 0.33
38 16 0.53
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (36 bp):
TTTAAATTTTATAACATTTAATAATTTCTAATAACA
Found at i:56107395 original size:22 final size:22
Alignment explanation
Indices: 56107365--56107408 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
56107355 ATAGTTTATC
56107365 TTTTATTTGCTTGATGAGAAAA
1 TTTTATTTGCTTGATGAGAAAA
* *
56107387 TTTTGTTTGTTTGATGAGAAAA
1 TTTTATTTGCTTGATGAGAAAA
56107409 ATTGGAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (22 bp):
TTTTATTTGCTTGATGAGAAAA
Found at i:56107982 original size:17 final size:18
Alignment explanation
Indices: 56107960--56107993 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56107950 GCTAAGCATA
*
56107960 CCAAAA-CACATTTCCAG
1 CCAAAAGCACATCTCCAG
56107977 CCAAAAGCACATCTCCA
1 CCAAAAGCACATCTCCA
56107994 ATAGGTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.38, G:0.06, T:0.15
Consensus pattern (18 bp):
CCAAAAGCACATCTCCAG
Found at i:56126338 original size:35 final size:35
Alignment explanation
Indices: 56126276--56126361 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
56126266 TTTTATTTGT
*
56126276 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
56126309 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
56126345 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
56126362 ATAAATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:56126347 original size:25 final size:23
Alignment explanation
Indices: 56126303--56126363 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
56126293 TGATATTTAA
*
56126303 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
56126327 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
56126352 ATATTATTAAAT
1 ATATAATTAAAT
56126364 AAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:56126791 original size:19 final size:19
Alignment explanation
Indices: 56126751--56126805 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
56126741 CTTGTGTTAT
* * *
56126751 AATTAAAAGA-TATTTATT
1 AATTAAATGATTATTAATA
56126769 AATTAAATGATTATTAATA
1 AATTAAATGATTATTAATA
* *
56126788 AATTATATTATTA-TAATA
1 AATTAAATGATTATTAATA
56126806 TAAAGTAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
AATTAAATGATTATTAATA
Found at i:56127925 original size:45 final size:46
Alignment explanation
Indices: 56127874--56127974 Score: 118
Period size: 45 Copynumber: 2.2 Consensus size: 46
56127864 GCCGACTACT
56127874 GTTACTGTTACCA-AATC-GACACTTTGTATGTCGAATACTGTTACC
1 GTTACTGTTACCAGAATCAG-CACTTTGTATGTCGAATACTGTTACC
* * * * *
56127919 GTTACTGTTA-CAGATTCAGCACTTTGTGTGTTGAATATTGTTACT
1 GTTACTGTTACCAGAATCAGCACTTTGTATGTCGAATACTGTTACC
*
56127964 ATTACTGTTAC
1 GTTACTGTTAC
56127975 TGTTACCGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
44 2 0.04
45 44 0.94
46 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.41
Consensus pattern (46 bp):
GTTACTGTTACCAGAATCAGCACTTTGTATGTCGAATACTGTTACC
Found at i:56127974 original size:6 final size:6
Alignment explanation
Indices: 56127957--56127997 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
56127947 TGTTGAATAT
* *
56127957 TGTTAC TATTAC TGTTAC TGTTAC CGTTAC TGATTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TG-TTAC TGTT
56127998 TAGGTACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
TGTTAC
Found at i:56133424 original size:41 final size:41
Alignment explanation
Indices: 56133379--56133505 Score: 182
Period size: 41 Copynumber: 3.1 Consensus size: 41
56133369 ACAAATCCAA
* * ** *
56133379 ATATGATACACCGACACAAAGCCTGCTAGGCATAATGCCTG
1 ATATGGTACACCGGCATGAAGCCTGCTAGGCATAAAGCCTG
*
56133420 ATATGGTACACCGGCATGAAGCCTGCTAGACATAAAGCCTG
1 ATATGGTACACCGGCATGAAGCCTGCTAGGCATAAAGCCTG
* *
56133461 ATATGGTACACCGGCATGAAGCATGCTAGGCATAAAGCCTA
1 ATATGGTACACCGGCATGAAGCCTGCTAGGCATAAAGCCTG
56133502 ATAT
1 ATAT
56133506 AATTCACTAG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 77 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (41 bp):
ATATGGTACACCGGCATGAAGCCTGCTAGGCATAAAGCCTG
Found at i:56133488 original size:82 final size:82
Alignment explanation
Indices: 56133349--56133505 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 82
56133339 GATACCACAT
* *
56133349 CGGCATAAAGCCTACTAGACACAAATCCAAATATGATACACCGACACAAAGCCTGCTAGGCATAA
1 CGGCATAAAGCCTACTAGACACAAAGCCAAATATGATACACCGACACAAAGCATGCTAGGCATAA
* *
56133414 TGCCTGATATGGTACAC
66 AGCCTAATATGGTACAC
* * * ** * * **
56133431 CGGCATGAAGCCTGCTAGACATAAAGCCTGATATGGTACACCGGCATGAAGCATGCTAGGCATAA
1 CGGCATAAAGCCTACTAGACACAAAGCCAAATATGATACACCGACACAAAGCATGCTAGGCATAA
56133496 AGCCTAATAT
66 AGCCTAATAT
56133506 AATTCACTAG
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
82 62 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (82 bp):
CGGCATAAAGCCTACTAGACACAAAGCCAAATATGATACACCGACACAAAGCATGCTAGGCATAA
AGCCTAATATGGTACAC
Found at i:56133524 original size:82 final size:82
Alignment explanation
Indices: 56133351--56133526 Score: 190
Period size: 82 Copynumber: 2.1 Consensus size: 82
56133341 TACCACATCG
* * * *
56133351 GCATAAAGCCTACTAGACACAAATCCAAATATGATACACCGACACAAAGCCTGCTAGGCATAATG
1 GCATAAAGCCTGCTAGACACAAAGCCAAATATGATACACCGACACAAAGCATGCTAGGCATAAAG
* ** *
56133416 CCTGATATGGTACACCG
66 CCTAATATAATACACCA
* * ** * * **
56133433 GCATGAAGCCTGCTAGACATAAAGCCTGATATGGTACACCGGCATGAAGCATGCTAGGCATAAAG
1 GCATAAAGCCTGCTAGACACAAAGCCAAATATGATACACCGACACAAAGCATGCTAGGCATAAAG
* *
56133498 CCTAATATAATTCACTA
66 CCTAATATAATACACCA
56133515 GCATAAAGCCTG
1 GCATAAAGCCTG
56133527 AATATCACTG
Statistics
Matches: 75, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (82 bp):
GCATAAAGCCTGCTAGACACAAAGCCAAATATGATACACCGACACAAAGCATGCTAGGCATAAAG
CCTAATATAATACACCA
Found at i:56135816 original size:41 final size:41
Alignment explanation
Indices: 56135701--56135898 Score: 127
Period size: 41 Copynumber: 4.9 Consensus size: 41
56135691 GATTTTTTGA
*
56135701 GCCTTTAGCGGCGTTTTTGTAA--AAGCGACGCTAATGCTC-G
1 GCCTTTAGCGGCG-TTTT-TAACTAAGCGCCGCTAATGCTCTG
** * * ** * *
56135741 AATCTTTAGCGGCGTTTCTATCTGGGCGCTGCTAATTCTCTG
1 -GCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAATGCTCTG
*
56135783 GCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAATGGT-TG
1 GCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAATGCTCTG
* *** ** *
56135823 GCCTTTAGTGGCGTTTTTGTTTGTGCGCCGCTAATGCAT-TT
1 GCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAATGC-TCTG
* * ** *
56135864 ACCTTTAGTGGCGTTTTTGCCAAAGCGCCGCTAAT
1 GCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAAT
56135899 AGTAAAAAAA
Statistics
Matches: 121, Mismatches: 32, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
39 2 0.02
40 35 0.29
41 83 0.69
42 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (41 bp):
GCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAATGCTCTG
Found at i:56135836 original size:40 final size:41
Alignment explanation
Indices: 56135781--56135898 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 41
56135771 GCTAATTCTC
* * *
56135781 TGGCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAATG-GT
1 TGGCCTTTAGTGGCGTTTTTGACTAAGCGCCGCTAATGCAT
** **
56135821 TGGCCTTTAGTGGCGTTTTTGTTTGTGCGCCGCTAATGCAT
1 TGGCCTTTAGTGGCGTTTTTGACTAAGCGCCGCTAATGCAT
** * *
56135862 TTACCTTTAGTGGCGTTTTTGCCAAAGCGCCGCTAAT
1 TGGCCTTTAGTGGCGTTTTTGACTAAGCGCCGCTAAT
56135899 AGTAAAAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 32 0.51
41 31 0.49
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.36
Consensus pattern (41 bp):
TGGCCTTTAGTGGCGTTTTTGACTAAGCGCCGCTAATGCAT
Found at i:56136432 original size:15 final size:15
Alignment explanation
Indices: 56136384--56136450 Score: 56
Period size: 15 Copynumber: 4.9 Consensus size: 15
56136374 TACGTGGTAT
* *
56136384 AGATTTAAGGTTTGG
1 AGATTTAAGGGTTAG
56136399 A-ATTTAA-GGTT--
1 AGATTTAAGGGTTAG
56136410 A-ATTTAAGGGTTAG
1 AGATTTAAGGGTTAG
* *
56136424 AGGTTTAAGGGTTTG
1 AGATTTAAGGGTTAG
56136439 AGATTT-AGGGTT
1 AGATTTAAGGGTT
56136451 TCAACGGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 7 0.16
12 4 0.09
13 3 0.07
14 13 0.30
15 17 0.39
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.40
Consensus pattern (15 bp):
AGATTTAAGGGTTAG
Found at i:56136742 original size:12 final size:10
Alignment explanation
Indices: 56136713--56136741 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
56136703 TGATTTTTTT
56136713 GATATATATG
1 GATATATATG
56136723 GATATATATG
1 GATATATATG
56136733 GATATATAT
1 GATATATAT
56136742 AGTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (10 bp):
GATATATATG
Found at i:56139889 original size:43 final size:42
Alignment explanation
Indices: 56139799--56139940 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 42
56139789 GCGTCGCTAA
* * * * * *
56139799 CTTTAGCGGCGCTTCTCCAACAAACGCCGCTATAGATCAGGAT
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTATAG-TAAAGAC
*
56139842 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTAAAGAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTATAG-TAAAGAC
* * * ** *
56139885 CTTTAGCAACACTTTTACCACAAATACCGCTATAG-AACAAAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGTAA-AGAC
56139927 CTTTAGCGACGCTT
1 CTTTAGCGACGCTT
56139941 CTTGCAAAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.02
42 15 0.18
43 66 0.80
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (42 bp):
CTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGTAAAGAC
Found at i:56146529 original size:21 final size:22
Alignment explanation
Indices: 56146496--56146536 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
56146486 TCTGAAATCC
56146496 TAAACCCCTAACCCCTAAACTT
1 TAAACCCCTAACCCCTAAACTT
* *
56146518 TAAATCCC-AACCCTTAAAC
1 TAAACCCCTAACCCCTAAAC
56146537 AATAACCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACCCCTAACCCCTAAACTT
Found at i:56146983 original size:35 final size:36
Alignment explanation
Indices: 56146937--56147021 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 36
56146927 ATCTATACCT
*
56146937 TTAAACCATAAACCGTAACCCTTAAACCCTAAA-TC
1 TTAAACCATAAACCGTAACCCATAAACCCTAAACTC
** *
56146972 TTAAACCATAAAGTGTAACCCATAACCCCTAAACTC
1 TTAAACCATAAACCGTAACCCATAAACCCTAAACTC
* *
56147008 ATAATCCATAAACC
1 TTAAACCATAAACC
56147022 TTAAAATAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 29 0.71
36 12 0.29
ACGTcount: A:0.44, C:0.31, G:0.04, T:0.22
Consensus pattern (36 bp):
TTAAACCATAAACCGTAACCCATAAACCCTAAACTC
Found at i:56147026 original size:22 final size:24
Alignment explanation
Indices: 56146986--56147051 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 24
56146976 ACCATAAAGT
* *
56146986 GTAAC-CCATAACCCCTAAACTCA
1 GTAACTCCATAAACCTTAAACTCA
*
56147009 -TAA-TCCATAAACCTTAAAAT-A
1 GTAACTCCATAAACCTTAAACTCA
*
56147030 GTAACTTC-TAAACCTTAAACTC
1 GTAACTCCATAAACCTTAAACTC
56147052 TAAATCATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 1 0.03
22 31 0.91
23 2 0.06
ACGTcount: A:0.42, C:0.29, G:0.03, T:0.26
Consensus pattern (24 bp):
GTAACTCCATAAACCTTAAACTCA
Found at i:56147452 original size:41 final size:41
Alignment explanation
Indices: 56147395--56147709 Score: 479
Period size: 41 Copynumber: 7.7 Consensus size: 41
56147385 ATATTTTTGT
*
56147395 GGCGCTTCCCCAAAAACGCCGCTAAAGATCAGAGCATTAGC
1 GGCGCTTCCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
**
56147436 GGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCATTAGC
1 GGCGCTTCCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
*
56147477 GGCGCTTTCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
1 GGCGCTTCCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
* * *
56147518 GGCGCTTCCCCAAAAACGCCGTTAAAGACCAAAGTATTAGC
1 GGCGCTTCCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
*
56147559 GGCGCTTCCCCAAAAACGCCGCTAAAGACCAGAGCATTAAC
1 GGCGCTTCCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
**
56147600 GGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
1 GGCGCTTCCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
*
56147641 GGCGCTTCCCCAAAAACGCCGCTAAA-ACCCTGAGCATTAGC
1 GGCGCTTCCCCAAAAACGCCGCTAAAGA-CCAGAGCATTAGC
* **
56147682 GGCGCTTTTCTAAAAAACGCCGCTAAAG
1 GGCGC-TTCCCCAAAAACGCCGCTAAAG
56147710 CCCCGAATGG
Statistics
Matches: 248, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
40 1 0.00
41 229 0.92
42 18 0.07
ACGTcount: A:0.32, C:0.31, G:0.21, T:0.16
Consensus pattern (41 bp):
GGCGCTTCCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
Found at i:56148142 original size:13 final size:13
Alignment explanation
Indices: 56148136--56148160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56148126 ATTTTTTTGT
56148136 TATATTTTAGTTG
1 TATATTTTAGTTG
56148149 TATATTTTAGTT
1 TATATTTTAGTT
56148161 TTAATTACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TATATTTTAGTTG
Found at i:56148669 original size:21 final size:21
Alignment explanation
Indices: 56148640--56148692 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
56148630 ATCTTTGATA
* *
56148640 TATATATATTTATATACAGTTT
1 TATATATATTTAT-TAAAATTT
56148662 TA-ATATATTTATTAAAATTT
1 TATATATATTTATTAAAATTT
56148682 TATATATATTT
1 TATATATATTT
56148693 GAAAAGCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATATATTTATTAAAATTT
Found at i:56148782 original size:12 final size:12
Alignment explanation
Indices: 56148765--56148789 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56148755 TACACAACAC
56148765 ATAACTTACATA
1 ATAACTTACATA
56148777 ATAACTTACATA
1 ATAACTTACATA
56148789 A
1 A
56148790 GTTATATATA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:56148789 original size:21 final size:21
Alignment explanation
Indices: 56148763--56148829 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
56148753 CTTACACAAC
56148763 ACATAACTTACATAATAACTT
1 ACATAACTTACATAATAACTT
* *
56148784 ACATAAGTTATAT-ATAAACTTAT
1 ACATAACTTACATAAT-AAC-T-T
*
56148807 ATATAACTTACATACATAACTT
1 ACATAACTTACATA-ATAACTT
56148829 A
1 A
56148830 AACCAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
20 2 0.06
21 14 0.39
22 3 0.08
23 12 0.33
24 3 0.08
25 2 0.06
ACGTcount: A:0.48, C:0.15, G:0.01, T:0.36
Consensus pattern (21 bp):
ACATAACTTACATAATAACTT
Found at i:56148846 original size:48 final size:45
Alignment explanation
Indices: 56148765--56148854 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 45
56148755 TACACAACAC
*
56148765 ATAACTTACATAATAACTTACATAAGTTATATAT-AAACTTATAT
1 ATAACTTACATAATAACTTACAAAAGTTATATATAAAACTTATAT
* *
56148809 ATAACTTACATACATAACTTAAACCAAAATTTTTATATAAAACTTA
1 ATAACTTACATA-ATAACTT--A-CAAAAGTTATATATAAAACTTA
56148855 CATACATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
44 12 0.32
45 7 0.18
47 1 0.03
48 11 0.29
49 7 0.18
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (45 bp):
ATAACTTACATAATAACTTACAAAAGTTATATATAAAACTTATAT
Found at i:56148889 original size:20 final size:17
Alignment explanation
Indices: 56148847--56148933 Score: 61
Period size: 17 Copynumber: 4.9 Consensus size: 17
56148837 ATTTTTATAT
56148847 AAAACTTACATACATAC
1 AAAACTTACATACATAC
*
56148864 ATAACTTACATGCACAATAC
1 AAAACTTACAT--AC-ATAC
* *
56148884 AAAACTTAAAT-CAAAC
1 AAAACTTACATACATAC
* *
56148900 TTATAA-TAACATACATAC
1 --AAAACTTACATACATAC
*
56148918 ATAACTTACATACATA
1 AAAACTTACATACATA
56148934 ATACATAACT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
16 7 0.13
17 25 0.46
18 7 0.13
19 2 0.04
20 13 0.24
ACGTcount: A:0.52, C:0.21, G:0.01, T:0.26
Consensus pattern (17 bp):
AAAACTTACATACATAC
Found at i:56148927 original size:13 final size:13
Alignment explanation
Indices: 56148905--56148934 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56148895 CAAACTTATA
56148905 ATAACATACATAC
1 ATAACATACATAC
*
56148918 ATAACTTACATAC
1 ATAACATACATAC
56148931 ATAA
1 ATAA
56148935 TACATAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (13 bp):
ATAACATACATAC
Found at i:56149042 original size:9 final size:9
Alignment explanation
Indices: 56149024--56149348 Score: 186
Period size: 9 Copynumber: 37.8 Consensus size: 9
56149014 CTTATATTTA
*
56149024 AACTTGCAT
1 AACTTACAT
56149033 AACTTACAT
1 AACTTACAT
*
56149042 AA-TAACAT
1 AACTTACAT
56149050 AACAACTTACAT
1 ---AACTTACAT
56149062 AA--TACAT
1 AACTTACAT
* *
56149069 AGCATACAT
1 AACTTACAT
56149078 AACTTACAT
1 AACTTACAT
*
56149087 AA--TACAA
1 AACTTACAT
56149094 AACTTACAT
1 AACTTACAT
*
56149103 AACTTAAAT
1 AACTTACAT
* *
56149112 ATCTTACAC
1 AACTTACAT
56149121 AACTTACAT
1 AACTTACAT
*
56149130 AACCTACAT
1 AACTTACAT
56149139 AA--TACAT
1 AACTTACAT
56149146 AACTTACAT
1 AACTTACAT
*
56149155 AACTTACCT
1 AACTTACAT
56149164 AACTTACAT
1 AACTTACAT
*
56149173 AATACATA-AT
1 -A-ACTTACAT
56149183 AACTTAC--
1 AACTTACAT
56149190 AACTTAC--
1 AACTTACAT
56149197 AACTTACAT
1 AACTTACAT
*
56149206 AACATACAT
1 AACTTACAT
* **
56149215 TACTTTGAT
1 AACTTACAT
56149224 AACTTACAT
1 AACTTACAT
*
56149233 AAGTTACAT
1 AACTTACAT
** *
56149242 AAAATATAT
1 AACTTACAT
*
56149251 AACTGAC--
1 AACTTACAT
56149258 AACTTACAT
1 AACTTACAT
*
56149267 AACATACAT
1 AACTTACAT
* **
56149276 TACTTTGAT
1 AACTTACAT
*
56149285 AAC-TA-TT
1 AACTTACAT
**
56149292 AAAATACAT
1 AACTTACAT
*
56149301 AA--TACAC
1 AACTTACAT
56149308 AACTTACAT
1 AACTTACAT
* *
56149317 AGCTTACTT
1 AACTTACAT
56149326 AA--TACAT
1 AACTTACAT
56149333 AACTTACAT
1 AACTTACAT
*
56149342 AATTTAC
1 AACTTAC
56149349 TTAATACATA
Statistics
Matches: 240, Mismatches: 53, Indels: 46
0.71 0.16 0.14
Matches are distributed among these distances:
7 54 0.22
8 12 0.05
9 160 0.67
10 3 0.01
11 6 0.03
12 5 0.02
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:56149084 original size:25 final size:25
Alignment explanation
Indices: 56149053--56149344 Score: 140
Period size: 25 Copynumber: 11.5 Consensus size: 25
56149043 ATAACATAAC
* *
56149053 AACTTACATAATACATAGCATACAT
1 AACTTACATAATACATAACTTACAT
*
56149078 AACTTACATAATACAAAACTTACAT
1 AACTTACATAATACATAACTTACAT
* * *
56149103 AACTTAAATATCTTACACAACTTACAT
1 AACTTACATA--ATACATAACTTACAT
*
56149130 AACCTACATAATACATAACTTACAT
1 AACTTACATAATACATAACTTACAT
* *
56149155 AACTTACCTAACTTACATAATACATA-AT
1 AACTTACATAA--TACAT-A-ACTTACAT
*
56149183 AACTTACA-ACTTAC--AACTTACAT
1 AACTTACATA-ATACATAACTTACAT
* * **
56149206 AACATACATTACTTTGATAACTTACAT
1 AACTTACA-TA-ATACATAACTTACAT
* * *
56149233 AAGTTACATAAAATATATAACTGAC--
1 AACTTACAT--AATACATAACTTACAT
* **
56149258 AACTTACATAACATACATTACTTTGAT
1 AACTTACAT-A-ATACATAACTTACAT
*
56149285 AACTATTA-A-AATACATAA--TACAC
1 AAC--TTACATAATACATAACTTACAT
* *
56149308 AACTTACATAGCTTACTTAA--TACAT
1 AACTTACATA--ATACATAACTTACAT
56149333 AACTTACATAAT
1 AACTTACATAAT
56149345 TTACTTAATA
Statistics
Matches: 205, Mismatches: 39, Indels: 48
0.70 0.13 0.16
Matches are distributed among these distances:
21 3 0.01
22 5 0.02
23 17 0.08
24 2 0.01
25 100 0.49
26 5 0.02
27 54 0.26
28 12 0.06
29 7 0.03
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:56149145 original size:43 final size:41
Alignment explanation
Indices: 56149073--56149183 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 41
56149063 ATACATAGCA
* * *
56149073 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCT
1 TACACAACTTACATAATACATAA--TACATAACTTAAATAACT
*
56149116 TACACAACTTACATAACCTACATAATACATAACTTACATAACT
1 TACACAACTTACATAA--TACATAATACATAACTTAAATAACT
56149159 TAC-CTAACTTACATAATACATAATA
1 TACAC-AACTTACATAATACATAATA
56149184 ACTTACAACT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
41 9 0.15
42 1 0.02
43 45 0.74
45 6 0.10
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.31
Consensus pattern (41 bp):
TACACAACTTACATAATACATAATACATAACTTAAATAACT
Found at i:56149152 original size:34 final size:34
Alignment explanation
Indices: 56149024--56149275 Score: 154
Period size: 34 Copynumber: 7.5 Consensus size: 34
56149014 CTTATATTTA
* *
56149024 AACTTGCATAACTTAC---ATA-ATAACATA-AC
1 AACTTACATAACTTACATAATACATAACTTACAC
*
56149053 AACTTACATAA--TACATAGCATACATAACTTACAT
1 AACTTACATAACTTACATA--ATACATAACTTACAC
* * *
56149087 AA--TACAAAACTTACATAACTTAAATATCTTACAC
1 AACTTACATAACTTACATAA--TACATAACTTACAC
* *
56149121 AACTTACATAACCTACATAATACATAACTTACAT
1 AACTTACATAACTTACATAATACATAACTTACAC
* *
56149155 AACTTACCTAACTTACATAATACATAA-TAACTTAC
1 AACTTACATAACTTACATAATACATAACTTAC--AC
* ** *
56149190 AACTTAC--AACTTACATAACATACATTACTTTGAT
1 AACTTACATAACTTACAT-A-ATACATAACTTACAC
* * *
56149224 AACTTACATAAGTTACATAAAATATATAAC-T-GAC
1 AACTTACATAACTTACAT--AATACATAACTTACAC
*
56149258 AACTTACATAACATACAT
1 AACTTACATAACTTACAT
56149276 TACTTTGATA
Statistics
Matches: 175, Mismatches: 27, Indels: 37
0.73 0.11 0.15
Matches are distributed among these distances:
27 3 0.02
29 10 0.06
32 10 0.06
33 19 0.11
34 85 0.49
35 16 0.09
36 30 0.17
37 2 0.01
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (34 bp):
AACTTACATAACTTACATAATACATAACTTACAC
Found at i:56149170 original size:52 final size:52
Alignment explanation
Indices: 56149073--56149171 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 52
56149063 ATACATAGCA
* *
56149073 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACT
1 TACATAACCTACATAATACAAAACTTACATAACTTAAATAACTTACACAACT
* **
56149125 TACATAACCTACATAATACATAACTTACATAACTTACCTAACTTACA
1 TACATAACCTACATAATACAAAACTTACATAACTTAAATAACTTACA
56149172 TAATACATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.30
Consensus pattern (52 bp):
TACATAACCTACATAATACAAAACTTACATAACTTAAATAACTTACACAACT
Found at i:56149272 original size:61 final size:60
Alignment explanation
Indices: 56149163--56149304 Score: 193
Period size: 61 Copynumber: 2.4 Consensus size: 60
56149153 ATAACTTACC
*
56149163 TAACTTACATAATACATAATAACTTACAACTTACAACTTACATAACATACATTACTTTGA
1 TAACTTACATAATACATAATAACTTACAACTGACAACTTACATAACATACATTACTTTGA
*
56149223 TAACTTACATAAGTTACATAA-AA-TATATAACTGACAACTTACATAACATACATTACTTTGA
1 TAACTTACATAA--TACATAATAACT-TACAACTGACAACTTACATAACATACATTACTTTGA
56149284 TAACTATTA-A-AATACATAATA
1 TAAC--TTACATAATACATAATA
56149305 CACAACTTAC
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
59 7 0.09
60 14 0.19
61 42 0.57
62 8 0.11
63 3 0.04
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (60 bp):
TAACTTACATAATACATAATAACTTACAACTGACAACTTACATAACATACATTACTTTGA
Found at i:56149348 original size:25 final size:25
Alignment explanation
Indices: 56149300--56149359 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
56149290 TTAAAATACA
* *
56149300 TAATACACAACTTACATAGCTTACT
1 TAATACATAACTTACATAACTTACT
*
56149325 TAATACATAACTTACATAATTTACT
1 TAATACATAACTTACATAACTTACT
56149350 TAATACATAA
1 TAATACATAA
56149360 ATTATGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (25 bp):
TAATACATAACTTACATAACTTACT
Found at i:56154891 original size:12 final size:12
Alignment explanation
Indices: 56154876--56154906 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
56154866 GGCAGTGAGG
56154876 GAAGCAGCGAGA
1 GAAGCAGCGAGA
*
56154888 GAAGCAGCGATA
1 GAAGCAGCGAGA
56154900 GAAGCAG
1 GAAGCAG
56154907 AGGTTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.39, T:0.03
Consensus pattern (12 bp):
GAAGCAGCGAGA
Found at i:56155375 original size:43 final size:40
Alignment explanation
Indices: 56155341--56155609 Score: 256
Period size: 43 Copynumber: 6.4 Consensus size: 40
56155331 GTTTGTGAAA
56155341 TAAGCGCCGCTAAAGAACACTA-CTTTTAGCGGCGTTTTTGAC
1 TAAGCGCCGCTAAAGAACA-TATC-TTTAGCGGCGTTTTT-AC
* * *
56155383 CAAGCGCCGCTACAGAACAT-TACTTTTAGCGGCGTTCTATTTC
1 TAAGCGCCGCTAAAGAACATAT-C-TTTAGCGGCGTT-T-TTAC
* * *
56155426 TAAGCGCCGCTAAAGAATAGGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACA-TATCTTTAGCGGCG-TTTTTAC
56155468 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-C
1 TAAGCGCCGCTAAAGAACAT-ATCTTTAGCGGCGTTTTTAC
* * *
56155508 ATAAGCGCCGCTAAAGAATAGGATCTTTAGCGGCGTTTATTTCC
1 -TAAGCGCCGCTAAAGAACA-TATCTTTAGCGGCG-TT-TTTAC
* *
56155552 TTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC
1 TAAGCGCCGCTAAAGAACAT-ATCTTTAGCGGCGTTTTTAC
*
56155593 TGTAAGCGCCGCAAAAG
1 --TAAGCGCCGCTAAAG
56155610 TTAGCGACGT
Statistics
Matches: 193, Mismatches: 18, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
40 1 0.01
41 41 0.21
42 69 0.36
43 75 0.39
44 6 0.03
45 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (40 bp):
TAAGCGCCGCTAAAGAACATATCTTTAGCGGCGTTTTTAC
Found at i:56155400 original size:42 final size:40
Alignment explanation
Indices: 56155342--56155592 Score: 265
Period size: 42 Copynumber: 6.0 Consensus size: 40
56155332 TTTGTGAAAT
*
56155342 AAGCGCCGCTAAAGAACACTA-CTTTTAGCGGCGTTTTTGACC
1 AAGCGCCGCTAAAGAACA-TATC-TTTAGCGGCGTTTTT-TCC
* *
56155384 AAGCGCCGCTACAGAACAT-TACTTTTAGCGGCGTTCTATTTCT
1 AAGCGCCGCTAAAGAACATAT-C-TTTAGCGGCGTT-T-TTTCC
* *
56155427 AAGCGCCGCTAAAGAATAGGATCTTTAGCGGCGTTTTTTCC
1 AAGCGCCGCTAAAGAACA-TATCTTTAGCGGCGTTTTTTCC
*
56155468 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTCAT
1 -AAGCGCCGCTAAAGAACAT-ATCTTTAGCGGCGTTTTTTC-C
* *
56155510 AAGCGCCGCTAAAGAATAGGATCTTTAGCGGCGTTTATTTCC
1 AAGCGCCGCTAAAGAACA-TATCTTTAGCGGCGTTT-TTTCC
*
56155552 TTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC
1 -AAGCGCCGCTAAAGAACAT-ATCTTTAGCGGCGTTTTTTC
56155593 TGTAAGCGCC
Statistics
Matches: 179, Mismatches: 16, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
41 41 0.23
42 68 0.38
43 66 0.37
44 3 0.02
45 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (40 bp):
AAGCGCCGCTAAAGAACATATCTTTAGCGGCGTTTTTTCC
Found at i:56155564 original size:126 final size:128
Alignment explanation
Indices: 56155341--56155609 Score: 361
Period size: 126 Copynumber: 2.1 Consensus size: 128
56155331 GTTTGTGAAA
* * **
56155341 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGACCAAGCGCCGCTACAGAACATTAC
1 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTCACCAAGCGCCGCTAAAGAACAGGAC
*
56155406 TTTTAGCGGCGTTCTATTTCTAAGCGCCGCTAAAGAATAGGATCTTTAGCGGCGTTTTTTC-C
66 TTTTAGCGGCGTTCTATTTCTAAGCGCCGCTAAAGAACAGGATCTTTAGCGGCGTTTTTTCTC
* *
56155468 TAAGCGCCGCTAAAGAACA-TGA-TCTTTAGCGGCGTTTTTCA-TAAGCGCCGCTAAAGAATAGG
1 TAAGCGCCGCTAAAGAACACT-ACT-TTTAGCGGCGTTTTTCACCAAGCGCCGCTAAAGAACAGG
* *
56155530 A-TCTTTAGCGGCGTT-TATTTCCTTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC
64 ACT-TTTAGCGGCGTTCTATTT-CTAAGCGCCGCTAAAGAACAGGATCTTTAGCGGCGTTTTTTC
*
56155593 TG
127 TC
*
56155595 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
56155610 TTAGCGACGT
Statistics
Matches: 126, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
125 6 0.05
126 70 0.56
127 50 0.40
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (128 bp):
TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTCACCAAGCGCCGCTAAAGAACAGGAC
TTTTAGCGGCGTTCTATTTCTAAGCGCCGCTAAAGAACAGGATCTTTAGCGGCGTTTTTTCTC
Found at i:56157778 original size:158 final size:157
Alignment explanation
Indices: 56157490--56157802 Score: 608
Period size: 158 Copynumber: 2.0 Consensus size: 157
56157480 TTCCTATGGA
56157490 TGGCGTCACTGTTAATGAAGACTGGAGAGTAGTTTGGGAGAATGATTTACCACCGAGAATTAAAC
1 TGGCGTCACTGTTAATGAAGACTGGAGAGTAGTTTGGGAGAATGATTTACCACCGAGAATTAAAC
56157555 ATTTCATGTGATTGGTAATGCATCGGAAATGTCAAACGAACGAAGAAAGAGCTAGGAGGAATTTA
66 ATTTCATGTGATTGGTAATGCATCGGAAATGTCAAACGAACGAAGAAAGAGCTAGGAGGAATTT-
56157620 AAAAATGATGCCGGATGTGCACTGTGAG
130 AAAAATGATGCCGGATGTGCACTGTGAG
*
56157648 TGGCGTCACTGTTAATGAAGACTGGAGAGTAGTTTGGGAGAATGATTTACCACCGAGACTTAAAC
1 TGGCGTCACTGTTAATGAAGACTGGAGAGTAGTTTGGGAGAATGATTTACCACCGAGAATTAAAC
56157713 ATTTCATGTGATTGGTAATGCATCGGAAATGTCAAACGAACGAAGAAAGAGCTAGGAGGAATTTA
66 ATTTCATGTGATTGGTAATGCATCGGAAATGTCAAACGAACGAAGAAAGAGCTAGGAGGAATTTA
56157778 AAAATGATGCCGGATGTGCACTGTG
131 AAAATGATGCCGGATGTGCACTGTG
56157803 TGAGGCGACA
Statistics
Matches: 154, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
157 26 0.17
158 128 0.83
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (157 bp):
TGGCGTCACTGTTAATGAAGACTGGAGAGTAGTTTGGGAGAATGATTTACCACCGAGAATTAAAC
ATTTCATGTGATTGGTAATGCATCGGAAATGTCAAACGAACGAAGAAAGAGCTAGGAGGAATTTA
AAAATGATGCCGGATGTGCACTGTGAG
Found at i:56159166 original size:24 final size:24
Alignment explanation
Indices: 56159122--56159168 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
56159112 TTTATACTTT
* *
56159122 AAAATATATTTTTAAGGTTAAATA
1 AAAATATATTTTCAAGATTAAATA
56159146 AAAATATATTATTCAA-ATTAAAT
1 AAAATATATT-TTCAAGATTAAAT
56159169 TTTCTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
AAAATATATTTTCAAGATTAAATA
Found at i:56160879 original size:18 final size:20
Alignment explanation
Indices: 56160853--56160890 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
56160843 TTTTCTATTA
56160853 TTTATTTCT-TTTTAATTTT
1 TTTATTTCTCTTTTAATTTT
*
56160872 TTTA-TTCTCTTTTACTTTT
1 TTTATTTCTCTTTTAATTTT
56160891 CTAGTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTCTCTTTTAATTTT
Found at i:56161527 original size:13 final size:13
Alignment explanation
Indices: 56161509--56161543 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
56161499 ACCAAACGTT
56161509 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
56161522 TCAAAAGTACTTT
1 TCAAAAGCACTTC
56161535 TCAAAAGCA
1 TCAAAAGCA
56161544 TTGTCAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:56162521 original size:18 final size:20
Alignment explanation
Indices: 56162495--56162532 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
56162485 TTTTCTATTA
56162495 TTTATTTCT-TTTTAATTTT
1 TTTATTTCTCTTTTAATTTT
*
56162514 TTTA-TTCTCTTTTACTTTT
1 TTTATTTCTCTTTTAATTTT
56162533 ATAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTCTCTTTTAATTTT
Found at i:56163619 original size:19 final size:22
Alignment explanation
Indices: 56163595--56163660 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 22
56163585 TATTTAATCT
56163595 TTTTATTT-C-TTTA-TTTTCC
1 TTTTATTTCCATTTATTTTTCC
56163614 TTTTATTCTTCCATTTATTTTTCC
1 TTTTA-T-TTCCATTTATTTTTCC
56163638 TTTTATTCTTCCATTTATTTTTC
1 TTTTA-T-TTCCATTTATTTTTC
56163661 TCTCTTCTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.12
20 1 0.02
21 2 0.05
22 1 0.02
23 4 0.10
24 29 0.69
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATTTCCATTTATTTTTCC
Found at i:56163630 original size:12 final size:12
Alignment explanation
Indices: 56163604--56163656 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
56163594 TTTTTATTTC
*
56163604 TTTATT-TTCCT
1 TTTATTCTTCCA
56163615 TTTATTCTTCCA
1 TTTATTCTTCCA
* *
56163627 TTTATTTTTCCT
1 TTTATTCTTCCA
56163639 TTTATTCTTCCA
1 TTTATTCTTCCA
56163651 TTTATT
1 TTTATT
56163657 TTTCTCTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
11 6 0.17
12 30 0.83
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTCTTCCA
Found at i:56163639 original size:24 final size:24
Alignment explanation
Indices: 56163604--56163660 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
56163594 TTTTTATTTC
56163604 TTTA-TTTTCCTTTTATTCTTCCA
1 TTTATTTTTCCTTTTATTCTTCCA
56163627 TTTATTTTTCCTTTTATTCTTCCA
1 TTTATTTTTCCTTTTATTCTTCCA
56163651 TTTATTTTTC
1 TTTATTTTTC
56163661 TCTCTTCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTTTTCCTTTTATTCTTCCA
Found at i:56164386 original size:17 final size:16
Alignment explanation
Indices: 56164343--56164385 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
56164333 AAAGGGAAGA
56164343 AAAAGAAAAAGAAAAG
1 AAAAGAAAAAGAAAAG
* * *
56164359 AAAAGTTAAAAGAACAT
1 AAAAG-AAAAAGAAAAG
56164376 AAAAGAAAAA
1 AAAAGAAAAA
56164386 AATTAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:56178573 original size:8 final size:8
Alignment explanation
Indices: 56178560--56178589 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
56178550 GTAATTTGTT
56178560 AAAAAAGA
1 AAAAAAGA
56178568 AAAAAAGA
1 AAAAAAGA
56178576 AAAAAAGA
1 AAAAAAGA
56178584 AAAAAA
1 AAAAAA
56178590 AATTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:56180311 original size:5 final size:5
Alignment explanation
Indices: 56180303--56180331 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
56180293 TTAAATAGTA
56180303 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
56180332 ATCGATTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:56184784 original size:6 final size:6
Alignment explanation
Indices: 56184773--56184799 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56184763 AGAAGGCATC
56184773 AGATAG AGATAG AGATAG AGATAG AGA
1 AGATAG AGATAG AGATAG AGATAG AGA
56184800 AAGGGCAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (6 bp):
AGATAG
Found at i:56185260 original size:3 final size:3
Alignment explanation
Indices: 56185252--56185277 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56185242 TTGATAATCT
56185252 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
56185278 CTTGGTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:56185551 original size:2 final size:2
Alignment explanation
Indices: 56185544--56185576 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56185534 GTTGTTAATA
56185544 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
56185577 AAAGGGATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56185924 original size:3 final size:3
Alignment explanation
Indices: 56185891--56185934 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
56185881 AAGCTGAGAA
* * * *
56185891 TCC TCC ACC TCC ACC TCC ACC TCC ACC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
56185935 ATCATCATCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.09, C:0.66, G:0.00, T:0.25
Consensus pattern (3 bp):
TCC
Found at i:56185934 original size:6 final size:6
Alignment explanation
Indices: 56185892--56185932 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
56185882 AGCTGAGAAT
* *
56185892 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCT CCTCCT CCTCC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCC
56185933 TCATCATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.10, C:0.68, G:0.00, T:0.22
Consensus pattern (6 bp):
CCTCCA
Found at i:56205015 original size:75 final size:75
Alignment explanation
Indices: 56204900--56205043 Score: 193
Period size: 75 Copynumber: 1.9 Consensus size: 75
56204890 CAACTTTTAA
* * * *
56204900 ATTTGAATTATAATCACTAGATTATTGCAATTATAGTTACTCCAAATCTAGAATTCAAACTTC-A
1 ATTTGAAATATAATCACTAGATTATTGCAATAATAATTACTCCAAATCTAAAATTCAAAC-TCAA
56204964 GAAAATTCTAG
65 GAAAATTCTAG
** *
56204975 ATTTGAAATATAAT-AGCTAGATTATTGCAATAATAATTACTCTGAATTTAAAATTCAAACTCAA
1 ATTTGAAATATAATCA-CTAGATTATTGCAATAATAATTACTCCAAATCTAAAATTCAAACTCAA
56205039 GAAAA
65 GAAAA
56205044 ATAGATCTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
74 3 0.05
75 57 0.95
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (75 bp):
ATTTGAAATATAATCACTAGATTATTGCAATAATAATTACTCCAAATCTAAAATTCAAACTCAAG
AAAATTCTAG
Found at i:56209380 original size:22 final size:22
Alignment explanation
Indices: 56209329--56209383 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
56209319 AGAAATTTAT
*
56209329 TGTTTTGATGTTATTTTTCCAC
1 TGTTTTGTTGTTATTTTTCCAC
* *
56209351 TATTTTGTTGTTGTTTTTCCAC
1 TGTTTTGTTGTTATTTTTCCAC
56209373 TGTTTTGTTGT
1 TGTTTTGTTGT
56209384 CATGTCACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.09, C:0.11, G:0.16, T:0.64
Consensus pattern (22 bp):
TGTTTTGTTGTTATTTTTCCAC
Found at i:56221930 original size:15 final size:16
Alignment explanation
Indices: 56221905--56221934 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56221895 TTGAACTAAT
56221905 TTTATAATTTTTTTAC
1 TTTATAATTTTTTTAC
56221921 TTTA-AATTTTTTTA
1 TTTATAATTTTTTTA
56221935 GAATTTTTAA
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:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATAATTTTTTTAC
Found at i:56222090 original size:20 final size:20
Alignment explanation
Indices: 56222065--56222102 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56222055 TCTGAGTTAA
56222065 AAAGTTTCTATACT-ATTTAT
1 AAAGTTT-TATACTGATTTAT
56222085 AAAGTTTTATACTGATTT
1 AAAGTTTTATACTGATTT
56222103 GGTGTCATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (20 bp):
AAAGTTTTATACTGATTTAT
Found at i:56224801 original size:5 final size:6
Alignment explanation
Indices: 56224771--56224800 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
56224761 ACATTACAGC
56224771 GAAAAA GAAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA G-AAAAA GAAAAA GAAAAA GAAAA
56224801 GTTGGCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:56236281 original size:2 final size:2
Alignment explanation
Indices: 56236274--56236311 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56236264 CGCCTGCATT
56236274 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
56236312 TATGGTGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:56240804 original size:27 final size:27
Alignment explanation
Indices: 56240774--56240831 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
56240764 CAACACGAAA
* *
56240774 CTAACATAATTAACAATACTTTAAGAC
1 CTAACATAATAAACAATACTTCAAGAC
*
56240801 CTAACATAATAAACAATACTTCAATAC
1 CTAACATAATAAACAATACTTCAAGAC
56240828 CTAA
1 CTAA
56240832 ATTCTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.28
Consensus pattern (27 bp):
CTAACATAATAAACAATACTTCAAGAC
Found at i:56241249 original size:24 final size:25
Alignment explanation
Indices: 56241222--56241278 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
56241212 ATTATATATT
*
56241222 AAATATATTTTTTTA-TTTTTAATC
1 AAATATATTTTTTAACTTTTTAATC
*
56241246 AAATATACTTTTTAACTTTTTAATC
1 AAATATATTTTTTAACTTTTTAATC
56241271 AAATATAT
1 AAATATAT
56241279 ATTTAGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATATATTTTTTAACTTTTTAATC
Found at i:56241291 original size:25 final size:25
Alignment explanation
Indices: 56241237--56241283 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
56241227 TATTTTTTTA
*
56241237 TTTTTAATCAAATATACTTTTTAAC
1 TTTTTAATCAAATATACTATTTAAC
56241262 TTTTTAATCAAATATA-TATTTA
1 TTTTTAATCAAATATACTATTTA
56241284 GGTTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTTTAATCAAATATACTATTTAAC
Found at i:56241891 original size:31 final size:30
Alignment explanation
Indices: 56241856--56241935 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
56241846 AGAAAATTTG
56241856 AGGATCAAATTGATAGAATT-TTTA-AATGT
1 AGGATCAAATTGATAGAATTATTTAGAAT-T
* * *
56241885 GAAGGATTAAATTTATTGAATTATTTAGAATT
1 --AGGATCAAATTGATAGAATTATTTAGAATT
*
56241917 CGGATCAAATTGATAGAAT
1 AGGATCAAATTGATAGAAT
56241936 ATGTAAGTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 15 0.38
31 17 0.43
32 5 0.12
33 3 0.08
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.38
Consensus pattern (30 bp):
AGGATCAAATTGATAGAATTATTTAGAATT
Done.