Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009300.1 Hibiscus syriacus cultivar Beakdansim tig00113021_pilon, whole genome shotgun sequence
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: 152308
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:1973 original size:11 final size:11
Alignment explanation
Indices: 1957--1991 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1947 AGAATTCAAT
*
1957 TATCAAGCCAA
1 TATCAAGCAAA
1968 TATCAAGCAAA
1 TATCAAGCAAA
*
1979 TATCAAGAAAA
1 TATCAAGCAAA
1990 TA
1 TA
1992 AAATAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (11 bp):
TATCAAGCAAA
Found at i:6195 original size:24 final size:25
Alignment explanation
Indices: 6155--6204 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
6145 AGGTTGATGC
6155 TATTGAATTTCTTGTGCATTTTCTT
1 TATTGAATTTCTTGTGCATTTTCTT
6180 TATTGAA-TTCTTGTGCATTTTCTT
1 TATTGAATTTCTTGTGCATTTTCTT
6204 T
1 T
6205 CTTTTTTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (25 bp):
TATTGAATTTCTTGTGCATTTTCTT
Found at i:9620 original size:81 final size:81
Alignment explanation
Indices: 9485--9647 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
9475 AATGCCAAAA
9485 ACACCTCAAAGATTTCGGTCCTATAAAGAAAGAACAAAAACTAACATTTTACATTTTTGCTTGCT
1 ACACCTCAAAGATTTCGGTCCTATAAAGAAAGAACAAAAACTAACATTTTACATTTTTGCTTGCT
9550 GGGATGCACTTAATGC
66 GGGATGCACTTAATGC
9566 ACACCTCAAAGATTTCGGTCCTATAAAGAAAGAACAAAAACTAACATTTTACATTTTTGCTTGCT
1 ACACCTCAAAGATTTCGGTCCTATAAAGAAAGAACAAAAACTAACATTTTACATTTTTGCTTGCT
9631 GGGATGCACTTAATGC
66 GGGATGCACTTAATGC
9647 A
1 A
9648 TGTGAGGCAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (81 bp):
ACACCTCAAAGATTTCGGTCCTATAAAGAAAGAACAAAAACTAACATTTTACATTTTTGCTTGCT
GGGATGCACTTAATGC
Found at i:10185 original size:31 final size:31
Alignment explanation
Indices: 10142--10213 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
10132 AGCAAAATCA
*
10142 CTAGAAAATCAGAAACAGCTAGATGATTCTT
1 CTAGTAAATCAGAAACAGCTAGATGATTCTT
10173 CTAGTAAATCAGAAACAGCTAGATGATTCTT
1 CTAGTAAATCAGAAACAGCTAGATGATTCTT
10204 CTAGTAAATC
1 CTAGTAAATC
10214 GGATAAACAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (31 bp):
CTAGTAAATCAGAAACAGCTAGATGATTCTT
Found at i:10304 original size:2 final size:2
Alignment explanation
Indices: 10297--10341 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
10287 ATTATAGCAC
10297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10339 TA T
1 TA T
10342 GGTTTATCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10460 original size:23 final size:23
Alignment explanation
Indices: 10433--10483 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
10423 AGACACAGAA
*
10433 GCAAGATCCTGGTAAAGATGATG
1 GCAAGATCCTAGTAAAGATGATG
10456 GCAAGATCCTAGTAAAGATGATG
1 GCAAGATCCTAGTAAAGATGATG
10479 GCAAG
1 GCAAG
10484 TTGGTGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (23 bp):
GCAAGATCCTAGTAAAGATGATG
Found at i:16931 original size:23 final size:23
Alignment explanation
Indices: 16905--16963 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
16895 ATCAAGTACA
**
16905 ATAACATTTTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
16928 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
16951 ATAATAAAATAGG
1 ATAACATAATAGG
16964 CATTTAACCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:17023 original size:87 final size:87
Alignment explanation
Indices: 16877--17039 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
16867 AATGTTATAT
*
16877 CATTTAACCGGAAATATTATCAAGTACAATAACATTTTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
16942 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
16964 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
17029 AGCGCTTATAT
66 AGCGCTTATAT
17040 TAACCTATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:17494 original size:200 final size:197
Alignment explanation
Indices: 17056--17760 Score: 756
Period size: 200 Copynumber: 3.5 Consensus size: 197
17046 ATTTTCGAAG
* * * *
17056 TAAAA-TGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATTATTATCGGTTAT
1 TAAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAAATTATAATTATCGGTT-T
** * ** *
17120 -GATGTTTTTTAGATAGATACAATTT-TAAATGTATCGACACTTTATGCTTGCACCTGGTTGGAC
65 CGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCT-GTT----
** * * * *
17183 ATTCATATTTCATTCTGGAAAAAAGTATCGACACAAACTAACAACATGTCGATACATTAT-TTAG
125 -TTGGTA-TTCATTCTGGACAAAAGTATCGACACAAATTTACAA-GTGTCGATACATTATGTT-G
17247 ACCTA---TTCA
186 ACCTATTTTTCA
* * * *
17256 TAAAACTGGTATATTTATACCGATTACATTGAAAATTTACCTATTAAATTATACTTATGGGTTTC
1 TAAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAAATTATAATTATCGGTTTC
* *
17321 GATATTTTCGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCT-TTTTGGT
66 GATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCA-CCTGTTTTGGT
*
17385 ATTCATTCTGGACCAAAAGTATCGACATAAATTTAGCAAGTGTCGATAC-TTCATGTTGACCTAT
130 ATTCATTCTGGA-CAAAAGTATCGACACAAATTTA-CAAGTGTCGATACATT-ATGTTGACCTAT
17449 TTTATCA
192 TTT-TCA
* * *
17456 TAAAATTGGTATATTTATATCGGTTACATTGTAAATTTACCTAATAAATTATAATTATCGGTTTC
1 TAAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAAATTATAATTATCGGTTTC
*
17521 GATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG-TGCACCTCG-TTTGT
66 GATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATG-GTTGCACCT-GTTTTG-
* *
17584 GCATTCATCCTGGACAATAAGTATCGACACAAATTATACAAGTGTCGATACATTATGTTGACCTA
128 GTATTCATTCTGGACAA-AAGTATCGACACAAATT-TACAAGTGTCGATACATTATGTTGACCTA
17649 -TTTTC-
191 TTTTTCA
* * * * **
17654 TAATTAACCGATATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTTGTT
1 TAA--AACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAAATTATAATTATCGGTT
* * *
17719 TTGATTTTTTTGGG-TCGATAC-TTGTATAAAATGTATCGACAC
64 TCGATGTTTTTGGGATCGATACTTTTTAT-AAATGTATCGACAC
17761 ATATTTAGGT
Statistics
Matches: 435, Mismatches: 48, Indels: 45
0.82 0.09 0.09
Matches are distributed among these distances:
195 13 0.03
196 39 0.09
197 5 0.01
198 7 0.02
199 27 0.06
200 188 0.43
201 123 0.28
202 30 0.07
203 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
TAAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAAATTATAATTATCGGTTTC
GATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCTGTTTTGGTA
TTCATTCTGGACAAAAGTATCGACACAAATTTACAAGTGTCGATACATTATGTTGACCTATTTTT
CA
Found at i:20634 original size:199 final size:200
Alignment explanation
Indices: 20294--20852 Score: 836
Period size: 199 Copynumber: 2.8 Consensus size: 200
20284 TTTATTTACA
* *
20294 AAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
* * *
20359 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTCGGTATCGACACTTTTAATAAAT
66 TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGACACTTTTAATAAAT
* * * *
20424 GTATCGACACTTTGTGCGTTCATCCTTTTTTGCATCCATTCTGGA-AAAAAGTATCGACACAA-A
131 GTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTAGACAAAAAGTATCGACACAATA
20487 TTTAAC
196 -TTAAC
* * *
20493 AAGTGTCGCTACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTACATTG
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
* * *
20558 TAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGATACTTTTTGA-AAA
66 TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGACAC-TTTTAATAAA
* *
20622 TGTATCGACACTTTATGCGTTTACCCTTTTTGGCATCCATTCTAGACAAAAATTATCGACACAAT
130 TGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTAGACAAAAAGTATCGACACAAT
*
20687 ATTAAT
195 ATTAAC
* * * *
20693 AAGTGTCGATACATATTATAGACCTATTCTCTTATAAAACTGGTATATGTATACCGATTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
* *
20758 TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTATAATAAAT
66 TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGACACTTTTAATAAAT
* *
20823 GTATCGAAACTTTATGCGTGCAACCCTTTT
131 GTATCGACACTTTATGCGTTC-ACCCTTTT
20853 GGATCGACAC
Statistics
Matches: 322, Mismatches: 33, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
199 157 0.49
200 156 0.48
201 9 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (200 bp):
AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGACACTTTTAATAAAT
GTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTAGACAAAAAGTATCGACACAATA
TTAAC
Found at i:20881 original size:200 final size:197
Alignment explanation
Indices: 20294--20883 Score: 792
Period size: 200 Copynumber: 3.0 Consensus size: 197
20284 TTTATTTACA
* *
20294 AAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
* * *
20359 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTCGGTATCGACACTTTTAATAAAT
66 TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGACACTTTTAATAAAT
* * * * * *
20424 GTATCGACACTTTGTGCGTTCATCCTTTTTTGCATCCATTCTGGAAAAAAGTATCGACACAAATT
131 GTATCGACACTTTATGCG-TCAACC-CTTTTGGATCCATTCTAGAAAAATGTATCGACACAAATT
20489 TAAC
194 TAAC
* * *
20493 AAGTGTCGCTACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTACATTG
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
* * *
20558 TAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGATACTTTTTGA-AAA
66 TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGACAC-TTTTAATAAA
**
20622 TGTATCGACACTTTATGCGTTTACCCTTTTTGGCATCCATTCTAGACAAAAAT-TATCGACAC-A
130 TGTATCGACACTTTATGCGTCAACCC-TTTTGG-ATCCATTCTAG--AAAAATGTATCGACACAA
*
20685 ATATTAAT
191 AT-TTAAC
* * * *
20693 AAGTGTCGATACATATTATAGACCTATTCTCTTATAAAACTGGTATATGTATACCGATTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
* *
20758 TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTATAATAAAT
66 TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGACACTTTTAATAAAT
* *
20823 GTATCGAAACTTTATGCGTGCAACCCTTTTGGATCGACACTCTATG-AAAATGTATCGACAC
131 GTATCGACACTTTATGCGT-CAACCCTTTTGGATC--CATTCTA-GAAAAATGTATCGACAC
20884 TTTGTATGTT
Statistics
Matches: 343, Mismatches: 36, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
198 8 0.02
199 155 0.45
200 164 0.48
201 15 0.04
202 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (197 bp):
AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
TAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGTATCGACACTTTTAATAAAT
GTATCGACACTTTATGCGTCAACCCTTTTGGATCCATTCTAGAAAAATGTATCGACACAAATTTA
AC
Found at i:20904 original size:51 final size:52
Alignment explanation
Indices: 20796--20905 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 52
20786 GGTTTTGATG
*
20796 TTTTTGGGATCGACACTTATAATAAATGTATCGAAACTTTATGCGTGCAACCC
1 TTTTT-GGATCGACACTTATAATAAATGTATCGAAACTTTATACGTGCAACCC
* * * * *
20849 -TTTTGGATCGACACTCTATGA-AAATGTATCGACACTTTGTATGT-TAACCC
1 TTTTTGGATCGACACT-TATAATAAATGTATCGAAACTTTATACGTGCAACCC
20899 TTTTTGG
1 TTTTTGG
20906 CATCCATTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
50 5 0.10
51 36 0.73
52 8 0.16
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (52 bp):
TTTTTGGATCGACACTTATAATAAATGTATCGAAACTTTATACGTGCAACCC
Found at i:21107 original size:251 final size:251
Alignment explanation
Indices: 20597--21088 Score: 650
Period size: 251 Copynumber: 2.0 Consensus size: 251
20587 GTTTTGATGT
* * * * *
20597 TTTTGGTATCGATACTTTTTGAAAATGTATCGACACTTTATGCGTTTACCCTTTTTGGCATCCAT
1 TTTTGG-ATCGACACTCTATGAAAATGTATCGACACTTTATACGTTAACCCTTTTTGGCATCCAT
** * * *
20662 TCTAGACAAAAATTATCGACACAATATTAATAAGTGTCGATACATATTATAGACCTATTCTCTTA
65 TCTAGACAAAAAGCATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTTA
* * * *
20727 TAAAACTGGTATATGTATACCGATTATATTATAAAATTACCTATTACATTATAATTATGGGTTTT
130 TAAAACCGGTATATGTATACCGATTACATTATAAAATTACCCATTACATTATAATTATGGGTTTC
* *
20792 GATGTTTTTGGGATCGACACTTATAATAAATGTATCGAAACTTTATGCGTGCAACCC
195 GATGTTTTTGGGATCGACACTTATAATAAATGGATCGAAACTTTATGCGTGAAACCC
* *
20849 TTTTGGATCGACACTCTATGAAAATGTATCGACACTTTGTATGTTAACCCTTTTTGGCATCCATT
1 TTTTGGATCGACACTCTATGAAAATGTATCGACACTTTATACGTTAACCCTTTTTGGCATCCATT
* * *
20914 CTGGACAAAAAGCATCGACACAATACTAATAAGTGTCGATAAATGTTGTAGACATATT-T-TTCA
66 CTAGACAAAAAGCATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTT-A
* *
20977 TAAAACCGGTATATTTATACCGGTTACATTGA-AAAATTACCCATTACATTATAATTATGGGTTT
130 TAAAACCGGTATATGTATACCGATTACATT-ATAAAATTACCCATTACATTATAATTATGGGTTT
* ** * * * *
21041 CGATATTTTTTGGG-TCGTTACTTTTTATATATGGATCGACACTTTATG
194 CGAT-GTTTTTGGGATCGACACTTATAATAAATGGATCGAAACTTTATG
21089 GGAAACTTTA
Statistics
Matches: 208, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
249 2 0.01
250 89 0.43
251 111 0.53
252 6 0.03
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (251 bp):
TTTTGGATCGACACTCTATGAAAATGTATCGACACTTTATACGTTAACCCTTTTTGGCATCCATT
CTAGACAAAAAGCATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTTAT
AAAACCGGTATATGTATACCGATTACATTATAAAATTACCCATTACATTATAATTATGGGTTTCG
ATGTTTTTGGGATCGACACTTATAATAAATGGATCGAAACTTTATGCGTGAAACCC
Found at i:22377 original size:18 final size:18
Alignment explanation
Indices: 22356--22391 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22346 ATCATCATCA
22356 TCATCATCATCGTCATTG
1 TCATCATCATCGTCATTG
* *
22374 TCATCTTCATCTTCATTG
1 TCATCATCATCGTCATTG
22392 ACCGTTTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.28, G:0.08, T:0.44
Consensus pattern (18 bp):
TCATCATCATCGTCATTG
Found at i:23540 original size:201 final size:201
Alignment explanation
Indices: 23195--23916 Score: 1189
Period size: 201 Copynumber: 3.6 Consensus size: 201
23185 GTATCGACAC
* * * **
23195 AAAGTGTCGATACATATTGTAGACCTATTCTCCCATAAAACCGGTATATTTATACCCATTACATT
1 AAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATT
* * *
23260 GAAAATTTACCTATTATATTATACTTATGGATGCGTATGTTTATG-GGATCGATACTTTTTATAA
66 GAAAATTTACCTATTACATTATACTTATGGATGCATATGTTT-CGAGGATCGATACTTTTTATAA
*
23324 ATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTTTGGACCAAAAGTATCGACACAA
130 ATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAA
23389 AATTAAA
195 AATTAAA
*
23396 AAAGTGTCGATACATGTTGTAGATCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATT
1 AAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATT
*
23461 GAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCGAGAATCGATACTTTTTATAAA
66 GAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCGAGGATCGATACTTTTTATAAA
*
23526 TGTATCGACACTTTATGATTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAA
131 TGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAA
23591 ATTAAA
196 ATTAAA
* * * *
23597 AAAGTGTTGATACATGTTGTAGACATATTCTCTCATAAAACCGGTATATTTATACTGGTTACATT
1 AAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATT
* *
23662 GAAAATTTACCTATTACATTATATTTATGGATGCATATGTTTCTAGGATCGATACTTTTTATAAA
66 GAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCGAGGATCGATACTTTTTATAAA
** **
23727 TGTATCGACACTTTATGGTTAAACCCTTTTTGGCATTCATTCTGGACCAAAAGTATTAACACAAA
131 TGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAA
*
23792 ATTTAA
196 ATTAAA
23798 AAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAAG-ATATTTATACCGGTTACAT
1 AAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACC-AGTATATTTATACCGGTTACAT
23862 TGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG-GGATCGATA
65 TGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTC-GAGGATCGATA
23917 AATTTTACCT
Statistics
Matches: 486, Mismatches: 32, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
200 1 0.00
201 484 1.00
202 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (201 bp):
AAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATT
GAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCGAGGATCGATACTTTTTATAAA
TGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAA
ATTAAA
Found at i:24203 original size:19 final size:19
Alignment explanation
Indices: 24179--24227 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
24169 TTACATTCAC
24179 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
*
24198 ATACAAAATTATAAATTTT
1 ATACAAAATTATAAATCTT
*
24217 ATAAAAAATTA
1 ATACAAAATTA
24228 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:24797 original size:4 final size:4
Alignment explanation
Indices: 24788--25488 Score: 1275
Period size: 4 Copynumber: 178.5 Consensus size: 4
24778 CATTATAATT
24788 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
24836 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
24884 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
24929 TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
24975 TACA TACA TACA TACA TACA TACA T--A TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
25021 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
25069 CACA TACA TACA TACA TACA TACA TACA TACA T--A TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
25114 -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
25161 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
25209 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
25257 TATA CATA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
25304 TACA -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
25351 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
25399 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
25447 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
25489 AATATCAATC
Statistics
Matches: 678, Mismatches: 6, Indels: 26
0.95 0.01 0.04
Matches are distributed among these distances:
2 10 0.01
3 9 0.01
4 659 0.97
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:26734 original size:33 final size:33
Alignment explanation
Indices: 26688--26753 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
26678 CATCTTAAGA
*
26688 TCACCCCTTAACACCTCAACTTATTTCACCACT
1 TCACCCCTCAACACCTCAACTTATTTCACCACT
* *
26721 TCACCCCTCAACACCTCAACTTCTTTTACCACT
1 TCACCCCTCAACACCTCAACTTATTTCACCACT
26754 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.44, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTATTTCACCACT
Found at i:26812 original size:21 final size:21
Alignment explanation
Indices: 26787--26830 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
26777 CCCCTTATGC
26787 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
26808 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
26829 CT
1 CT
26831 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:29376 original size:182 final size:182
Alignment explanation
Indices: 29050--29518 Score: 624
Period size: 182 Copynumber: 2.6 Consensus size: 182
29040 ATGAAAGTAT
* *
29050 CGACACTTTCAATATAT-CAGGTAGCGCTTTACCGGTTTTATCATTTTGATACC-AGTTTTATCA
1 CGACACTTTCAATATATCCA-GTAGCACTTTACCGGTTTTATCATTTCGATACCGA-TTTTATCA
*
29113 TAGTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCG
64 TATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCG
* *
29178 CTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTCGAT-ACTTATATTAAACTGC
129 CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCA-TTATATTAAACTAC
* * *
29232 CGACACTTTAAATATATCCAGTAGCTCTTTACCGGTTTTATCATTTCGATACCGATTTTGTCATA
1 CGACACTTTCAATATATCCAGTAGCACTTTACCGGTTTTATCATTTCGATACCGATTTTATCATA
* * * *
29297 TTTTTACCTGTTATATCGTTGTGGATCAATACATTTTTATAAAGTATCGACACTTTATAGGCGTT
66 TTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCT
* * *
29362 AAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATTAAAGTAT
131 AAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATTAAACTAC
* * * * * * *
29414 AGACACGTTCAATATATCCGGTAAG-AATTTACCGGTATTGTCTTTTCG-TGACCGATTTTATCA
1 CGACACTTTCAATATATCCAGT-AGCACTTTACCGGTTTTATCATTTCGAT-ACCGATTTTATC-
* * *
29477 ATATTTTTACCTATTATATTGATATGGATCGATACATTTTTA
63 ATATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTA
29519 ATTTGGATCG
Statistics
Matches: 252, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
181 1 0.00
182 208 0.83
183 43 0.17
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (182 bp):
CGACACTTTCAATATATCCAGTAGCACTTTACCGGTTTTATCATTTCGATACCGATTTTATCATA
TTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCT
AAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATTAAACTAC
Found at i:38560 original size:13 final size:13
Alignment explanation
Indices: 38542--38567 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38532 TTAACATTTA
38542 ATATGCTCACTAG
1 ATATGCTCACTAG
38555 ATATGCTCACTAG
1 ATATGCTCACTAG
38568 TTATAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
ATATGCTCACTAG
Found at i:43340 original size:21 final size:20
Alignment explanation
Indices: 43316--43378 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
43306 TTAATAAAAC
43316 ATTTATCTAAAAATATATATA
1 ATTTAT-TAAAAATATATATA
* *
43337 ATTTA-TAAAAATAAGATATTT
1 ATTTATTAAAAAT-ATATA-TA
43358 ATTTATTTAAAAATATA-ATA
1 ATTTA-TTAAAAATATATATA
43378 A
1 A
43379 AATACACATC
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 7 0.21
20 6 0.18
21 12 0.35
22 2 0.06
23 7 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTATTAAAAATATATATA
Found at i:43359 original size:17 final size:19
Alignment explanation
Indices: 43323--43359 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
43313 AACATTTATC
*
43323 TAAAAATATATATAATTTA
1 TAAAAATATAGATAATTTA
43342 TAAAAATA-AGAT-ATTTA
1 TAAAAATATAGATAATTTA
43359 T
1 T
43360 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAAATATAGATAATTTA
Found at i:47669 original size:20 final size:20
Alignment explanation
Indices: 47613--47669 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
47603 AATCAGATTG
*
47613 CCCAGGGGGTACAAATTCCC
1 CCCAGGGGGTACAGATTCCC
*
47633 CCCAGGGGGAACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
47653 CCCAGGGGGTACCGATT
1 CCCAGGGGGTACAGATT
47670 TCTCCTGTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:48536 original size:3 final size:3
Alignment explanation
Indices: 48530--48605 Score: 86
Period size: 3 Copynumber: 26.0 Consensus size: 3
48520 TTTTTTTTAT
*
48530 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAG T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
48576 TAAA TAA -AA TAA TAT TAA TAT TAA AAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48606 AAAACAAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 5 0.08
3 54 0.89
4 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:48557 original size:20 final size:20
Alignment explanation
Indices: 48532--48589 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
48522 TTTTTTATTA
48532 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
48552 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
48572 AGT-ATAAATAA-AATAATA
1 A-TAAT-AATAATAATAATA
48590 TTAATATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 30 0.83
21 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:48560 original size:23 final size:23
Alignment explanation
Indices: 48530--48595 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
48520 TTTTTTTTAT
48530 TAATAATAATAATAATAATAATA
1 TAATAATAATAATAATAATAATA
*
48553 TAATAATAATAATAATAATAGTA
1 TAATAATAATAATAATAATAATA
*
48576 TAAATAA-AATAATATTAATA
1 T-AATAATAATAATAATAATA
48596 TTAAAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 35 0.88
24 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAATAATAATAATAATAATAATA
Found at i:48603 original size:23 final size:23
Alignment explanation
Indices: 48527--48607 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
48517 TAATTTTTTT
*
48527 TATTAATAATAATAATAATAATAA
1 TATTAAAAATAA-AATAATAATAA
*
48551 TA-TAATAAT--AATAATAATAA
1 TATTAAAAATAAAATAATAATAA
* * *
48571 TAGTATAAATAAAATAATATTAA
1 TATTAAAAATAAAATAATAATAA
48594 TATTAAAAATAAAA
1 TATTAAAAATAAAA
48608 AACAAATGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
20 13 0.27
21 5 0.10
23 29 0.59
24 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (23 bp):
TATTAAAAATAAAATAATAATAA
Found at i:48997 original size:138 final size:138
Alignment explanation
Indices: 48834--49143 Score: 557
Period size: 138 Copynumber: 2.2 Consensus size: 138
48824 CTAGCAAAAA
* * *
48834 GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
48899 CTCCTTCTGGAAATGCTGATCTTCAAAAGAGGTATTGTTGATTCAATTTCAATATGTGATGAATC
66 CTCCTTCTGAAAATGCTGATCTTCAAAAGAGGTATTGTTGATTCAATTTCAATATGTGATGAATC
48964 AAATTAAG
131 AAATTAAG
48972 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
49037 CTTCTTCTGAAAATGTTGATCTTCAAAAGAGGTATTGTTGATTCAATTTCAATATGTGATGAATC
66 CTCCTTCTGAAAATGCTGATCTTCAAAAGAGGTATTGTTGATTCAATTTCAATATGTGATGAATC
49102 AAATTAAG
131 AAATTAAG
*
49110 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCT
49144 GGAAAAGTCG
Statistics
Matches: 165, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 165 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (138 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTCCTTCTGAAAATGCTGATCTTCAAAAGAGGTATTGTTGATTCAATTTCAATATGTGATGAATC
AAATTAAG
Found at i:49004 original size:17 final size:17
Alignment explanation
Indices: 48982--49044 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
48972 GTTGAACAAA
48982 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* * *
48999 TTCTTCTCCTTCTTCAGATGAG
1 TTCTTCTCATT-AT--GA--AC
49021 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
49038 TTCTTCT
1 TTCTTCT
49045 GAAAATGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 18 0.51
18 1 0.03
19 2 0.06
20 2 0.06
21 1 0.03
22 11 0.31
ACGTcount: A:0.17, C:0.25, G:0.08, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:49261 original size:123 final size:121
Alignment explanation
Indices: 49117--49507 Score: 469
Period size: 123 Copynumber: 3.3 Consensus size: 121
49107 AAGGTTGAAC
*
49117 AAGTTCTTCTCATTATGAAC-TTCTTCTGGAAAAGTCGATGCTGATCTATCTCCTTCTGTGATAA
1 AAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGT-GATG-TGATCTATCTCCTTATGTGATAA
* * *
49181 AATCAAGCAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCATCTTCAGAT
63 AATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT
* * * * * *
49240 AAGTTCTTCACATTATGAACTTTCTCTAGAAAA--G-T-TGATCCA--T-C-GA-GTGATGAATT
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGATGTGATCTATCTCCTTATGTGATAAAAT
* * * *
49296 CGAGGAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTTAGAT
66 CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGAT
* * * * *
49353 GAGTTCTTCTCATTATGAACTTTATCTGGAAATGTTGATGATGATCTATCCCCTTATGTGATAGA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-TGATG-TGATCTATCTCCTTATGTGATAAA
*
49418 ATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGAT
64 ATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT
*
49476 GAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAA
49508 GGTTGATCCA
Statistics
Matches: 224, Mismatches: 31, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
112 48 0.21
113 37 0.17
114 1 0.00
115 1 0.00
116 1 0.00
117 7 0.03
119 7 0.03
120 1 0.00
122 1 0.00
123 69 0.31
124 51 0.23
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (121 bp):
AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGATGTGATCTATCTCCTTATGTGATAAAAT
CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT
Found at i:51081 original size:20 final size:21
Alignment explanation
Indices: 51022--51082 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
51012 CTTGACCCTC
*
51022 ATTTTCTATTTTTTCTTTTTT
1 ATTTTCTATTTTTTCTTCTTT
51043 ATTTTC-ATTTTTTCATTCTTT
1 ATTTTCTATTTTTTC-TTCTTT
*
51064 -TTTTCTTTTTTTTCTTCTT
1 ATTTTCTATTTTTTCTTCTT
51083 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (21 bp):
ATTTTCTATTTTTTCTTCTTT
Found at i:54623 original size:11 final size:10
Alignment explanation
Indices: 54599--54645 Score: 60
Period size: 11 Copynumber: 4.5 Consensus size: 10
54589 AAATAAATAT
54599 AAAAAATG-A
1 AAAAAATGTA
54608 GAAAAGAATGTA
1 -AAAA-AATGTA
54620 AAAAAATGTAA
1 AAAAAATGT-A
54631 AAAAAATGTA
1 AAAAAATGTA
54641 AAAAA
1 AAAAA
54646 TGATTGCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 15 0.44
11 18 0.53
12 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (10 bp):
AAAAAATGTA
Found at i:54625 original size:21 final size:21
Alignment explanation
Indices: 54599--54645 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
54589 AAATAAATAT
*
54599 AAAAAATG-AGAAAAGAATGTA
1 AAAAAATGTA-AAAAAAATGTA
54620 AAAAAATGTAAAAAAAATGTA
1 AAAAAATGTAAAAAAAATGTA
54641 AAAAA
1 AAAAA
54646 TGATTGCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (21 bp):
AAAAAATGTAAAAAAAATGTA
Found at i:58455 original size:15 final size:15
Alignment explanation
Indices: 58435--58466 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
58425 TGCAATGAAT
58435 AATGAATGTATGCAA
1 AATGAATGTATGCAA
58450 AATGAATGTATGCAA
1 AATGAATGTATGCAA
58465 AA
1 AA
58467 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:62594 original size:21 final size:21
Alignment explanation
Indices: 62570--62627 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
62560 TTAATAAAAC
62570 ATTTATCTAAAAATATATA-TA
1 ATTTAT-TAAAAATATATATTA
* *
62591 ATTTA-TAAAAATAAGATATTT
1 ATTTATTAAAAAT-ATATATTA
62612 ATTTATTTAAAAATAT
1 ATTTA-TTAAAAATAT
62628 CAGAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 11 0.37
22 1 0.03
23 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTTATTAAAAATATATATTA
Found at i:62613 original size:17 final size:19
Alignment explanation
Indices: 62577--62613 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
62567 AACATTTATC
*
62577 TAAAAATATATATAATTTA
1 TAAAAATATAGATAATTTA
62596 TAAAAATA-AGAT-ATTTA
1 TAAAAATATAGATAATTTA
62613 T
1 T
62614 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAAATATAGATAATTTA
Found at i:62811 original size:3 final size:3
Alignment explanation
Indices: 62797--62837 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
62787 ATATATATTT
*
62797 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
62838 TAAATATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:63524 original size:22 final size:22
Alignment explanation
Indices: 63499--63549 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
63489 AGTCGTCCGC
63499 CACCGCCAACCTCGCCGCCGAT
1 CACCGCCAACCTCGCCGCCGAT
* *
63521 CACCGCCAACCTCGCTGCCGTT
1 CACCGCCAACCTCGCCGCCGAT
63543 CACCGCC
1 CACCGCC
63550 TCCGGTGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.55, G:0.18, T:0.12
Consensus pattern (22 bp):
CACCGCCAACCTCGCCGCCGAT
Found at i:64132 original size:17 final size:17
Alignment explanation
Indices: 64112--64159 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
64102 AATTTTTTAT
64112 TAATAATAATAATAATA
1 TAATAATAATAATAATA
**
64129 TAATAATAATAATTGTA
1 TAATAATAATAATAATA
64146 TAAATAA-AATAATA
1 T-AATAATAATAATA
64160 TTAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TAATAATAATAATAATA
Found at i:64148 original size:14 final size:14
Alignment explanation
Indices: 64114--64141 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64104 TTTTTTATTA
64114 ATAATAATAATAAT
1 ATAATAATAATAAT
64128 ATAATAATAATAAT
1 ATAATAATAATAAT
64142 TGTATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:64159 original size:3 final size:3
Alignment explanation
Indices: 64112--64141 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
64102 AATTTTTTAT
64112 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
64142 TGTATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:64170 original size:17 final size:18
Alignment explanation
Indices: 64109--64175 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
64099 TATAATTTTT
*
64109 TATTAATAATAATAATAA
1 TATTAATAATAATATTAA
*
64127 TA-TAATAATAATAATT-G
1 TATTAATAATAAT-ATTAA
*
64144 TATAAATAAAATAATATTAA
1 TATTAAT--AATAATATTAA
*
64164 TATTAAAAATAA
1 TATTAATAATAA
64176 AAAACAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 12 0.32
18 12 0.32
19 3 0.08
20 11 0.29
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (18 bp):
TATTAATAATAATATTAA
Found at i:64173 original size:23 final size:23
Alignment explanation
Indices: 64109--64177 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 23
64099 TATAATTTTT
* * *
64109 TATTAATAATAATAATAATATAA
1 TATTAATATTAAAAATAAAATAA
* *
64132 TAATAATAATTGTATAAATAAAATAA
1 TATTAAT-A-T-TAAAAATAAAATAA
64158 TATTAATATTAAAAATAAAA
1 TATTAATATTAAAAATAAAA
64178 AACAAATGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
23 16 0.44
24 2 0.06
25 1 0.03
26 17 0.47
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (23 bp):
TATTAATATTAAAAATAAAATAA
Found at i:64558 original size:15 final size:15
Alignment explanation
Indices: 64538--64572 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
64528 TTTGTTTCAA
64538 GTTTTAACAGAAAAG
1 GTTTTAACAGAAAAG
* *
64553 GTTTTAACGGAAAAT
1 GTTTTAACAGAAAAG
64568 GTTTT
1 GTTTT
64573 CTCTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (15 bp):
GTTTTAACAGAAAAG
Found at i:69569 original size:55 final size:55
Alignment explanation
Indices: 69510--69932 Score: 433
Period size: 55 Copynumber: 7.7 Consensus size: 55
69500 TCGAATGACA
* * * * * *
69510 GGTCCGTTCCCTATTCCTTCAGGGAGTATA-AGACTTGAACAATCTTTAATAAATG
1 GGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACG
* * * *
69565 GGTCCGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAATG
1 GGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACG
* ** * * * ** *
69620 TGTATGATCCCTATTCGTTCAGGGAGTATA-AGACTTTAACAATCTTCAATAAACG
1 GGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACG
* * * *
69675 GGTCCTCTCCCTATTCGTTCAGGGAGTATGGAACTCGAACAATCTTCAACAAACG
1 GGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
* ** * * *
69730 TGTCCGCTCTTTATTCCTTCAGAAAGTATAGAACTTGAACAAACTTCAACAAACG
1 GGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
* *
69785 GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTT-AATAAAACG
1 GGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-CAAACG
* *
69840 GGTCCGCTCTCC-ATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAATG
1 GGTCCGCTC-CCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
* * * *
69895 GGTTCACTCTCTATTCCTTTAGAGAGTATAGAACTCGA
1 GGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGA
69933 TCTTCATAAA
Statistics
Matches: 314, Mismatches: 49, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
54 3 0.01
55 307 0.98
56 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (55 bp):
GGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
Found at i:69998 original size:37 final size:37
Alignment explanation
Indices: 69943--70018 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
69933 TCTTCATAAA
69943 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAG
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTA-AG
69981 ATGA-TTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
70017 AT
1 AT
70019 TGACTTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 4 0.11
37 30 0.79
38 4 0.11
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (37 bp):
ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
Found at i:71319 original size:7 final size:7
Alignment explanation
Indices: 71303--71474 Score: 56
Period size: 7 Copynumber: 24.4 Consensus size: 7
71293 CTTTCTTTTA
*
71303 TTTTCTT
1 TTTTCAT
71310 TTTTCA-
1 TTTTCAT
71316 TTTTCA-
1 TTTTCAT
*
71322 TTTTCTT
1 TTTTCAT
71329 TTTTCA-
1 TTTTCAT
*
71335 TTTTCTTT
1 TTTTC-AT
*
71343 TTTCTCTT
1 TTT-TCAT
*
71351 TTTTCTCT
1 TTTTC-AT
*
71359 TTCTTCTT
1 TT-TTCAT
71367 TTTTCAT
1 TTTTCAT
*
71374 ATTT-AT
1 TTTTCAT
*
71380 TATTGT-TT
1 T-TT-TCAT
*
71388 TTTTC-C
1 TTTTCAT
71394 TTTTCAT
1 TTTTCAT
*
71401 TTTTC-C
1 TTTTCAT
* *
71407 TTTACCT
1 TTTTCAT
71414 TTTTCATTT
1 TTTTCA--T
71423 TTTCTCAT
1 TTT-TCAT
*
71431 TTTTCCT
1 TTTTCAT
71438 TTCTTCAT
1 TT-TTCAT
71446 TTTTC--
1 TTTTCAT
*
71451 TTTTAAT
1 TTTTCAT
*
71458 TTTTAAT
1 TTTTCAT
71465 TTTTCAT
1 TTTTCAT
71472 TTT
1 TTT
71475 CAGGCGAAAT
Statistics
Matches: 127, Mismatches: 21, Indels: 34
0.70 0.12 0.19
Matches are distributed among these distances:
5 4 0.03
6 28 0.22
7 56 0.44
8 27 0.21
9 9 0.07
10 3 0.02
ACGTcount: A:0.10, C:0.17, G:0.01, T:0.73
Consensus pattern (7 bp):
TTTTCAT
Found at i:71320 original size:13 final size:13
Alignment explanation
Indices: 71316--71373 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
71306 TCTTTTTTCA
71316 TTTTCATTTTCTT
1 TTTTCATTTTCTT
71329 TTTTCATTTTCTT
1 TTTTCATTTTCTT
*
71342 TTTTC-TCTT-TT
1 TTTTCATTTTCTT
* *
71353 TTCTCTTTCTTCTT
1 TTTTCATT-TTCTT
71367 TTTTCAT
1 TTTTCAT
71374 ATTTATTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 6 0.16
12 4 0.11
13 20 0.54
14 7 0.19
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCATTTTCTT
Found at i:71352 original size:9 final size:9
Alignment explanation
Indices: 71338--71370 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
71328 TTTTTCATTT
71338 TCTTTTTTC
1 TCTTTTTTC
71347 TCTTTTTTC
1 TCTTTTTTC
*
71356 TCTTTCTTC
1 TCTTTTTTC
71365 T-TTTTT
1 TCTTTTT
71371 CATATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TCTTTTTTC
Found at i:71377 original size:72 final size:70
Alignment explanation
Indices: 71292--71474 Score: 160
Period size: 72 Copynumber: 2.6 Consensus size: 70
71282 TCATATTGAA
* * * * *
71292 CCTTTCTT-TTATTTTCTTTTTTCATTTTCATTTTCTTTTTTCATTTTCTTTTTTCTCTTTTTTC
1 CCTTTCTTCATATTTTCTTTTTT--TTTTCATTTTCATTTTTCATTTACCTTTTTC-ATTTTTTC
71356 TC-TTTCTT
63 TCATTT-TT
* * *
71364 -CTTTTTTCATATTTAT-TATTGTTTTTTTCCTTTTCATTTTTCCTTTACCTTTTTCATTTTTTC
1 CCTTTCTTCATATTT-TCT-TT-TTTTTTTCATTTTCATTTTTCATTTACCTTTTTCATTTTTTC
71427 TCATTTTT
63 TCATTTTT
* *
71435 CCTTTCTTCAT-TTTTCTTTTAATTTTTAATTTTTCATTTT
1 CCTTTCTTCATATTTTCTTTT-TTTTTTCA-TTTTCATTTT
71475 CAGGCGAAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
69 1 0.01
70 8 0.09
71 31 0.34
72 44 0.49
73 3 0.03
74 3 0.03
ACGTcount: A:0.10, C:0.17, G:0.01, T:0.72
Consensus pattern (70 bp):
CCTTTCTTCATATTTTCTTTTTTTTTTCATTTTCATTTTTCATTTACCTTTTTCATTTTTTCTCA
TTTTT
Found at i:71447 original size:15 final size:14
Alignment explanation
Indices: 71387--71450 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 14
71377 TATTATTGTT
71387 TTTTTCCTTT-TCA
1 TTTTTCCTTTCTCA
71400 TTTTTCCTTTAC-C-
1 TTTTTCCTTT-CTCA
*
71413 TTTTTCATTTTTTCTCA
1 TTTTTC---CTTTCTCA
71430 TTTTTCCTTTCTTCA
1 TTTTTCCTTTC-TCA
71445 TTTTTC
1 TTTTTC
71451 TTTTAATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 16 0.39
14 5 0.12
15 10 0.24
16 4 0.10
17 6 0.15
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTCCTTTCTCA
Found at i:71469 original size:43 final size:43
Alignment explanation
Indices: 71387--71469 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
71377 TATTATTGTT
* *
71387 TTTTTCCTTTTCATTTTTCCTTTACCTTTTTCATTTTTTCTCA
1 TTTTTCCTTTTCATTTTTCCTTTACATTTTTCAATTTTTCTCA
*
71430 TTTTTCCTTTCTTCATTTTTCTTTTA-ATTTTT-AATTTTTC
1 TTTTTCC-TT-TTCATTTTTCCTTTACATTTTTCAATTTTTC
71470 ATTTTCAGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 14 0.40
44 7 0.20
45 14 0.40
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (43 bp):
TTTTTCCTTTTCATTTTTCCTTTACATTTTTCAATTTTTCTCA
Found at i:75204 original size:45 final size:47
Alignment explanation
Indices: 75138--75246 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 47
75128 CCATGTTTTG
* *
75138 TTATTC-AAAAAGAAATCCTAACCGCATAATATTTAATTCGCATGC-
1 TTATTCGAAAAAGAAATCCTAACCACATAATATCTAATTCGCATGCA
* * * *
75183 TTGTTCGAAAAATAAA-CCTAACCACATGATATCTAGTTCGCATGCA
1 TTATTCGAAAAAGAAATCCTAACCACATAATATCTAATTCGCATGCA
75229 TTTATTCGAAAAACGAAA
1 -TTATTCGAAAAA-GAAA
75247 ATAAATGACT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
45 30 0.58
46 8 0.15
47 11 0.21
48 3 0.06
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.29
Consensus pattern (47 bp):
TTATTCGAAAAAGAAATCCTAACCACATAATATCTAATTCGCATGCA
Found at i:92042 original size:8 final size:8
Alignment explanation
Indices: 92029--92054 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
92019 GGTACAAGGT
92029 TAATTATG
1 TAATTATG
92037 TAATTATG
1 TAATTATG
92045 TAATTATG
1 TAATTATG
92053 TA
1 TA
92055 TCAGGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
TAATTATG
Found at i:92987 original size:3 final size:3
Alignment explanation
Indices: 92965--93028 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
92955 CTCGAAAAAA
*
92965 TAT TAT TAAT TA- TAT GAT TAT TAT TAAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* *
93011 AAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT
93029 CATTTTACAG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:92988 original size:18 final size:17
Alignment explanation
Indices: 92965--93021 Score: 84
Period size: 15 Copynumber: 3.5 Consensus size: 17
92955 CTCGAAAAAA
92965 TATTATTAATTATATGAT
1 TATTATTAATTATAT-AT
92983 TATTATTAATTAT-TAT
1 TATTATTAATTATATAT
92999 TATTATT-ATTATA-AT
1 TATTATTAATTATATAT
93014 TATTATTA
1 TATTATTA
93022 GTATTATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.38
16 9 0.24
17 1 0.03
18 13 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATTAATTATATAT
Found at i:94567 original size:2 final size:2
Alignment explanation
Indices: 94562--94620 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
94552 AAATCATCAT
94562 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
94604 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
94621 TAAAAATTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:94806 original size:6 final size:5
Alignment explanation
Indices: 94763--94805 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
94753 ATTTTTTACC
* *
94763 TATTT TCATTT TCATTT TATTT AATTT TAGTT TATTT TATTT T
1 TATTT T-ATTT T-ATTT TATTT TATTT TATTT TATTT TATTT T
94806 TGTGAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 22 0.67
6 11 0.33
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:99768 original size:37 final size:37
Alignment explanation
Indices: 99736--99822 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 37
99726 GTTGTCGCCT
* *
99736 TTGAGACAATTTCTTTTAAAAATAAATTTTGTCTCAC
1 TTGAGACAATTTCTTATAAAAACAAATTTTGTCTCAC
* *
99773 TTAAGACAATTT-TTATCAAAACAAATTTTGTCTCAC
1 TTGAGACAATTTCTTATAAAAACAAATTTTGTCTCAC
*
99809 TTGAGACAGTTTCT
1 TTGAGACAATTTCT
99823 CTCGAAATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 31 0.72
37 12 0.28
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (37 bp):
TTGAGACAATTTCTTATAAAAACAAATTTTGTCTCAC
Found at i:100118 original size:64 final size:66
Alignment explanation
Indices: 99959--100119 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 66
99949 AGAAACAAAA
* * * * *
99959 CCATCTTTGAGAT-TGTTTCCCTTAAAACAAGTTTGTCTCTCTTGATACAGTTTCTCTTGAAACA
1 CCATCTTTGAGATCTGTTTCCCTTGAAACAAATTTGTCCCTCTTGAGACAGCTTCTCTTGAAACA
100023 C
66 C
*
100024 CCATCTTTGAGATC-GTTTCCCTTGAAACAAATTTGTCCCTCTTGAGACAGCTTCTCTTGAAGCA
1 CCATCTTTGAGATCTGTTTCCCTTGAAACAAATTTGTCCCTCTTGAGACAGCTTCTCTTGAAACA
100088 -
66 C
*
100088 TCATCTTTGAG-TCTGTTTCCCTTGAAACAAAT
1 CCATCTTTGAGATCTGTTTCCCTTGAAACAAAT
100120 CCCTAAAGAT
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
63 2 0.02
64 28 0.32
65 57 0.66
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (66 bp):
CCATCTTTGAGATCTGTTTCCCTTGAAACAAATTTGTCCCTCTTGAGACAGCTTCTCTTGAAACA
C
Found at i:100425 original size:134 final size:129
Alignment explanation
Indices: 100118--100588 Score: 409
Period size: 130 Copynumber: 3.6 Consensus size: 129
100108 CTTGAAACAA
** * * * * *
100118 ATCCCTAAAGATGGCCTATCGTTCTCATCGTGTAGGAACCGTGTCATCCCCCGACCATA-CTCCT
1 ATCCCTAAAGATGGAATATCATCCTCATCGCGTAGGAACCGTGTCAT-CCCAGACCAGACCTCCT
* *
100182 CATCACGTAGGAGCCGTGTCAACCTAGATAATCAGTCATCCTCATCACGTAGGAACTGCGATTAT
65 CATCACGTAGGAGCCGTGTC-ACCTAGATAACCAGTCATCCTCATCACGTAGGAACTGAGATTAT
100247 C
129 C
* * *
100248 ATCCCTAAAGATGGTATATCATCCTCATCGCATAGGAACCGTGTCATCTACAGACCAGACCTCCT
1 ATCCCTAAAGATGGAATATCATCCTCATCGCGTAGGAACCGTGTCATC-CCAGACCAGACCTCCT
* * * *
100313 CATCACGTAGGAGCCGTGTCACCCATAGATAACCAGTCGTCCTCATCGCGTATGAACTTAG-TTA
65 CATCACGTAGGAGCCGTGTCA-CC-TAGATAACCAGTCATCCTCATCACGTAGGAACTGAGATTA
100377 TCAC
128 T--C
* *
100381 AATTCCTAAAGAT-GAAT-TGCCTTCCTCATCGCGTAGGAACCGTGTCATCCCATGACCAGACCT
1 -ATCCCTAAAGATGGAATAT--CATCCTCATCGCGTAGGAACCGTGTCATCCCA-GACCAGACCT
* * * ** * * ** * *
100444 CCTCATAACGTCGGAGCCATGTCACCTTAGATAACCAACCGTCTTCAAT-ATATAGAAAC-CATG
62 CCTCATCACGTAGGAGCCGTGTCACC-TAGATAACCAGTCATCCTC-ATCACGTAGGAACTGA-G
100507 -TTATC
124 ATTATC
* * * ** * *
100512 ATCCCTAAAGAT-TATCTACCATCCTCATCATGTAGGAATCGTGTCATCCACCGACCAGACCTCC
1 ATCCCTAAAGATGGA-ATATCATCCTCATCGCGTAGGAACCGTGTCATCC-CAGACCAGACCTCC
*
100576 TTATCACGTAGGA
64 TCATCACGTAGGA
100589 ACCATGTTAT
Statistics
Matches: 281, Mismatches: 45, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
129 1 0.00
130 109 0.39
131 34 0.12
132 32 0.11
133 34 0.12
134 71 0.25
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (129 bp):
ATCCCTAAAGATGGAATATCATCCTCATCGCGTAGGAACCGTGTCATCCCAGACCAGACCTCCTC
ATCACGTAGGAGCCGTGTCACCTAGATAACCAGTCATCCTCATCACGTAGGAACTGAGATTATC
Found at i:100609 original size:88 final size:88
Alignment explanation
Indices: 100500--100676 Score: 237
Period size: 88 Copynumber: 2.0 Consensus size: 88
100490 AATATATAGA
* * ** *
100500 AACCATGTTATCATCCCTAAAGATTATCTACCATCCTCATCATGTAGGAATCGTGTCATCCACCG
1 AACCATGTTATCACCCCTAAAGATGATCTACCATCCTCATCACATAGAAATCGTGTCATCCACCG
*
100565 ACCAGACCTCCTTATCACGTAGG
66 ACCAGACCTCCTCATCACGTAGG
* * ** *
100588 AACCATGTTATCACCCCTAAAGATGGTTTTTCATCCTCATCACATAGAAATCGTGTCATCCATCG
1 AACCATGTTATCACCCCTAAAGATGATCTACCATCCTCATCACATAGAAATCGTGTCATCCACCG
* *
100653 ACCATACCTTCTCATCACGTAGG
66 ACCAGACCTCCTCATCACGTAGG
100676 A
1 A
100677 GCCGTGTCAC
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 76 1.00
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.28
Consensus pattern (88 bp):
AACCATGTTATCACCCCTAAAGATGATCTACCATCCTCATCACATAGAAATCGTGTCATCCACCG
ACCAGACCTCCTCATCACGTAGG
Found at i:103641 original size:27 final size:27
Alignment explanation
Indices: 103609--103674 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
103599 AAAACATTGT
*
103609 TGAATGATTCAGCACATAAGTACATTC
1 TGAATGATTCAGCACAGAAGTACATTC
*
103636 TGAATGATTCAGCACAGAAGTAGATTC
1 TGAATGATTCAGCACAGAAGTACATTC
103663 TGAATGATTCAG
1 TGAATGATTCAG
103675 AACCATTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (27 bp):
TGAATGATTCAGCACAGAAGTACATTC
Found at i:103747 original size:16 final size:16
Alignment explanation
Indices: 103726--103785 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
103716 ACAGAGCCTC
*
103726 TGAATCATTCAATATT
1 TGAATCATTCAACATT
* **
103742 TGAATCTTTCAACGCT
1 TGAATCATTCAACATT
*
103758 T-AATCATTCAGCATT
1 TGAATCATTCAACATT
103773 TGAATCATTCAAC
1 TGAATCATTCAAC
103786 GCTTAATCAT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 11 0.32
16 23 0.68
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:103764 original size:31 final size:31
Alignment explanation
Indices: 103728--103797 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
103718 AGAGCCTCTG
* *
103728 AATCATTCAATATTTGAATCTTTCAACGCTT
1 AATCATTCAACATTTGAATCATTCAACGCTT
*
103759 AATCATTCAGCATTTGAATCATTCAACGCTT
1 AATCATTCAACATTTGAATCATTCAACGCTT
103790 AATCATTC
1 AATCATTC
103798 TGAAGTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (31 bp):
AATCATTCAACATTTGAATCATTCAACGCTT
Found at i:103767 original size:15 final size:15
Alignment explanation
Indices: 103744--103797 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
103734 TCAATATTTG
*
103744 AATCTTTCAACGCTT
1 AATCATTCAACGCTT
* **
103759 AATCATTCAGCATTT
1 AATCATTCAACGCTT
103774 GAATCATTCAACGCTT
1 -AATCATTCAACGCTT
103790 AATCATTC
1 AATCATTC
103798 TGAAGTAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.37
Consensus pattern (15 bp):
AATCATTCAACGCTT
Found at i:104032 original size:30 final size:30
Alignment explanation
Indices: 103997--104053 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
103987 TATGTTAGGC
*
103997 TAAATTTAAATTTATAAAATTTTAAGAAAA
1 TAAATTTAAATTCATAAAATTTTAAGAAAA
*
104027 TAAATTTGAATTCATAAAATTTTAAGA
1 TAAATTTAAATTCATAAAATTTTAAGA
104054 GTTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (30 bp):
TAAATTTAAATTCATAAAATTTTAAGAAAA
Found at i:105124 original size:38 final size:38
Alignment explanation
Indices: 105045--105130 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 38
105035 TTACAACCTT
* * *
105045 AAATATTATGTTTTTATAATAACTTTAAATTACACTAA
1 AAATATTATATTTTTATAATAACATTAAATTACAATAA
* * *
105083 AAATATTATATTTTTATACT-TCATTAAATTACAATCGA
1 AAATATTATATTTTTATAATAACATTAAATTACAAT-AA
105121 AAATATTATA
1 AAATATTATA
105131 AAAATAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 12 0.29
38 29 0.71
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (38 bp):
AAATATTATATTTTTATAATAACATTAAATTACAATAA
Found at i:105174 original size:9 final size:9
Alignment explanation
Indices: 105160--105190 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
105150 CATCAAACTT
105160 AAAAAATTA
1 AAAAAATTA
105169 AAAAAATTAA
1 AAAAAATT-A
105179 AAAAAATTA
1 AAAAAATTA
105188 AAA
1 AAA
105191 CATTTTCGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAAATTA
Found at i:105181 original size:10 final size:10
Alignment explanation
Indices: 105160--105190 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
105150 CATCAAACTT
105160 AAAAAATT-A
1 AAAAAATTAA
105169 AAAAAATTAA
1 AAAAAATTAA
105179 AAAAAATTAA
1 AAAAAATTAA
105189 AA
1 AA
105191 CATTTTCGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:111222 original size:12 final size:12
Alignment explanation
Indices: 111205--111230 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
111195 CCGGGTTTAT
111205 TTTTTCATTTGA
1 TTTTTCATTTGA
111217 TTTTTCATTTGA
1 TTTTTCATTTGA
111229 TT
1 TT
111231 ATCAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTTCATTTGA
Found at i:112536 original size:2 final size:2
Alignment explanation
Indices: 112529--112596 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
112519 TCAATCTACA
112529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112571 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
112597 TTTCCGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112974 original size:85 final size:85
Alignment explanation
Indices: 112652--112975 Score: 488
Period size: 85 Copynumber: 3.8 Consensus size: 85
112642 AATGACTTGT
* * *
112652 GCTTCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
** *
112717 CA-AACAGATTTATAACGGGG
66 CATATTA-ATTTATGACGGGG
* *
112737 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAACGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
*
112802 CATCTTAATTTATGACGGGG
66 CATATTAATTTATGACGGGG
* *
112822 GCTTTAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATATGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
*
112887 CATATTAATTTATGACGGAG
66 CATATTAATTTATGACGGGG
* * * *
112907 GCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAGATTTATGACACACAATTGCGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
112972 CATA
66 CATA
112976 AAAAATTCAT
Statistics
Matches: 217, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
85 216 1.00
86 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
CATATTAATTTATGACGGGG
Found at i:113497 original size:155 final size:154
Alignment explanation
Indices: 113187--113488 Score: 326
Period size: 154 Copynumber: 1.9 Consensus size: 154
113177 TATATATAAG
* * * * *
113187 ATATTTATTTACTTAGAAATATCTGAAAATGACTTCTAGGTGCTTTAAGACATCCCCTTTCTTGA
1 ATATTTAGTTACTTAGAAATATCAGAAAATAACTTCTAGGTGCTTTAAGACAT-CCATTTCTTAA
*
113252 TATTAAAAAATAAATAAATATTAATAAAATATTTCTCTAAAAATAATTAAAATAAATTAAATTAA
65 TATTAAAAAATAAATAAATATAAATAAAATATTTCTCTAAAAATAATTAAAATAAATTAAATTAA
* *
113317 TATATATATAATTTATAAAAGTAGA
130 TAAATAGATAATTTATAAAAGTAGA
* *
113342 ATATTTAGTTATTTAGAAATATCAGAAAA-AACTTCTAGTTGCTTTAAGACAAT-CATTTCCTTA
1 ATATTTAGTTACTTAGAAATATCAGAAAATAACTTCTAGGTGCTTTAAGAC-ATCCATTT-CTTA
** * * * * * *
113405 ATA-TAAATAAATAAATATTTA-AAATATGATTATTTTTCCTAAAAGTAATTTATATAAAATTAA
64 ATATTAAA-AAATAAATAAATATAAATA-AAATATTTCT-CTAAAAATAATTAAAAT-AAATTAA
*
113468 ATTTATAAATAAGAT-ATTTAT
125 ATTAATAAAT-AGATAATTTAT
113489 TTAATAGAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
153 12 0.10
154 43 0.36
155 42 0.35
156 21 0.17
157 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (154 bp):
ATATTTAGTTACTTAGAAATATCAGAAAATAACTTCTAGGTGCTTTAAGACATCCATTTCTTAAT
ATTAAAAAATAAATAAATATAAATAAAATATTTCTCTAAAAATAATTAAAATAAATTAAATTAAT
AAATAGATAATTTATAAAAGTAGA
Found at i:113926 original size:26 final size:26
Alignment explanation
Indices: 113871--113927 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
113861 TTTATTTTCG
* *
113871 AAAAAAATAAAATAAAATACTAAGTA
1 AAAAAAATAAAATAAAATACCAAATA
*
113897 AAAAAAATAAAATGAAA-ACCAAATA
1 AAAAAAATAAAATAAAATACCAAATA
*
113922 TAAAAA
1 AAAAAA
113928 TAACCATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (26 bp):
AAAAAAATAAAATAAAATACCAAATA
Found at i:115067 original size:123 final size:119
Alignment explanation
Indices: 114682--115701 Score: 822
Period size: 113 Copynumber: 8.7 Consensus size: 119
114672 GAATTGAACT
* *
114682 AAGGTTGAACAAGTTCTTCTCATTGTGAACTTCTACTTCTTCTTCTTCTTCAAATGAGTTCTTCT
1 AAGGTTGAACAAGTTCTTCTCATTATGAAC-T-T-CTTCTTC--C-TCTTCAGATGAGTTCTTCT
* * *
114747 CATTATGAAC-TCCTTCTGGAAATGTTGATGTTGA-TCTATCT-CTT-TATGCGATAGAGTCGAG
60 CATTATGAACTTTC-TCTGGAAA-ATTGA---T-ACTCTATCTCCTTCGAT--GATAGAGTCGAG
*
114808 TAA
117 CAA
* * * *
114811 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTTTCATATGAGTTCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
** * *
114876 GAACACT-TCTGGAAATGTTGATGTTGA-TCTATCTCCTTCTG-TGTTAGAGTC-ATGCAA
66 GAACTTTCTCTGGAAA-ATTGA---T-ACTCTATCTCCTTC-GATGATAGAGTCGA-GCAA
* * *
114933 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
114998 GAACTTTCTCTGGAAAAGTTGATGCTACTCTATCTCCTTCTATGATAGAGTC-ATGCAA
66 GAACTTTCTCTGGAAAA-TTGA---TACTCTATCTCCTTCGATGATAGAGTCGA-GCAA
115056 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * *
115121 GAACTTTCTTTGG--AA---ATACT-GA--TCCATCGAGTGAT-GAATTCGAGCAA
66 GAACTTTCTCTGGAAAATTGATACTCTATCTCCTTCGA-TGATAG-AGTCGAGCAA
115168 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * *
115233 GAACTTTCTCT--AGAA---ATACT-GA--TCCATCGAGTGAT-GAATTCGAGCAA
66 GAACTTTCTCTGGAAAATTGATACTCTATCTCCTTCGA-TGATAG-AGTCGAGCAA
115280 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* * *** *
115345 TGAACTCTAC-CTGGCAATATTGAT-C-C-ATC-GAGT-GATG--A-ATTCGAGCAA
65 TGAACT-TTCTCTGG-AAAATTGATACTCTATCTCCTTCGATGATAGAGTCGAGCAA
115393 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* * * * * *
115458 TGAACTCTAC-CTGG-CAA-TG-T--T-GA--TCCATCGAGTGAT-GAATTTGAGCAA
65 TGAACT-TTCTCTGGAAAATTGATACTCTATCTCCTTCGA-TGATAG-AGTCGAGCAA
*
115506 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* * * * * * *
115571 TAAACTCTAC-CTGG-CAA-TG-T--T-GA--TCCATCGAGTAAT-GAATTCGAGCAA
65 TGAACT-TTCTCTGGAAAATTGATACTCTATCTCCTTCGA-TGATAG-AGTCGAGCAA
* *
115619 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGTTGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATTA
115684 TGAACTCTT-TCTGGAAAA
65 TGAACT-TTCTCTGGAAAA
115702 GTGTTGATCC
Statistics
Matches: 799, Mismatches: 54, Indels: 91
0.85 0.06 0.10
Matches are distributed among these distances:
108 1 0.00
109 4 0.01
110 4 0.01
111 8 0.01
112 160 0.20
113 313 0.39
114 8 0.01
116 4 0.01
117 4 0.01
118 2 0.00
119 2 0.00
121 3 0.00
122 102 0.13
123 145 0.18
124 2 0.00
126 6 0.01
127 1 0.00
128 1 0.00
129 29 0.04
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (119 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAATTGATACTCTATCTCCTTCGATGATAGAGTCGAGCAA
Found at i:115406 original size:113 final size:113
Alignment explanation
Indices: 115052--115722 Score: 1098
Period size: 113 Copynumber: 5.9 Consensus size: 113
115042 ATAGAGTCAT
115052 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
115116 ATTATGAACT-TTCTTTGGAAATACTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTCTAC-CTGGAAATATTGATCCATCGAGTGATGAATTCGA
115164 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
115228 ATTATGAACT-TTCTCTAGAAATACTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTCTAC-CTGGAAATATTGATCCATCGAGTGATGAATTCGA
115276 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
115341 ATTATGAACTCTACCTGGCAATATTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTCTACCTGGAAATATTGATCCATCGAGTGATGAATTCGA
115389 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
115454 ATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTTGA
66 ATTATGAACTCTACCTGGAAATATTGATCCATCGAGTGATGAATTCGA
*
115502 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
115567 ATTATAAACTCTACCTGGCAATGTTGATCCATCGAGTAATGAATTCGA
66 ATTATGAACTCTACCTGGAAATATTGATCCATCGAGTGATGAATTCGA
* *
115615 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGTTGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** *
115680 ATTATGAACTCTTTCTGGAAAAGTGTTGATCCATCGAGTGATG
66 ATTATGAACTCTACCTGG-AAA-TATTGATCCATCGAGTGATG
115723 GTTTTGAATC
Statistics
Matches: 535, Mismatches: 20, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
112 154 0.29
113 358 0.67
114 4 0.01
115 19 0.04
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTACCTGGAAATATTGATCCATCGAGTGATGAATTCGA
Found at i:116147 original size:22 final size:22
Alignment explanation
Indices: 116091--116147 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
116081 AATAAAGCTT
*
116091 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
116113 TCATCTTTAAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
116135 TCATCTTTGAAGA
1 TCATCTTTGAAGA
116148 ATGTAGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:116594 original size:54 final size:54
Alignment explanation
Indices: 116511--116665 Score: 161
Period size: 54 Copynumber: 2.9 Consensus size: 54
116501 AGAATAACTA
* * *
116511 GTTCGTAAAACATTTGAAAACACATTCAT-CATCTCATGTGGTTTCTGCT-CAGAT
1 GTTCGTAAAACATTTGACAACACACTCATCCATCTC-TGTGGTTTATG-TACAGAT
* * * *
116565 GTTCGTAAAATATTTGACAACACACTCATCCTTTTCTGTTGTTTATGTACAGAT
1 GTTCGTAAAACATTTGACAACACACTCATCCATCTCTGTGGTTTATGTACAGAT
* * * * * *
116619 GTTCGTAAAGCATTTGACAACACATTTATTCTTTTCTGTGGTTTATG
1 GTTCGTAAAACATTTGACAACACACTCATCCATCTCTGTGGTTTATG
116666 CACAAATTTC
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 81 0.94
55 4 0.05
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACACTCATCCATCTCTGTGGTTTATGTACAGAT
Found at i:118355 original size:31 final size:32
Alignment explanation
Indices: 118314--118450 Score: 111
Period size: 31 Copynumber: 4.2 Consensus size: 32
118304 TAAAATACCC
118314 TTCTTTTCCCGTGAGCTTGCCTCTGCG-ATAT
1 TTCTTTTCCCGTGAGCTTGCCTCTGCGAATAT
* * * *
118345 TTCTTCTCCCGTGAGCTTGTCTCTACGAAAAT
1 TTCTTTTCCCGTGAGCTTGCCTCTGCGAATAT
* * *
118377 TCATCGTTTTCCCAGTGATCTT-CTTCTG-GTAAGAT
1 T--TC-TTTTCCC-GTGAGCTTGCCTCTGCG-AATAT
* *
118412 TTCTTATCCCGTGAACTTGCCTCTGCG-ATAT
1 TTCTTTTCCCGTGAGCTTGCCTCTGCGAATAT
118443 CTTCTTTT
1 -TTCTTTT
118451 TAAGGTTTTG
Statistics
Matches: 82, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
31 34 0.41
32 21 0.26
33 3 0.04
34 3 0.04
35 14 0.17
36 7 0.09
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (32 bp):
TTCTTTTCCCGTGAGCTTGCCTCTGCGAATAT
Found at i:121969 original size:15 final size:15
Alignment explanation
Indices: 121949--121979 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
121939 CTACAGATAG
121949 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
121964 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
121979 A
1 A
121980 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:127734 original size:43 final size:44
Alignment explanation
Indices: 127669--127752 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
127659 TGCATCAAAC
*
127669 AAAACTTTTACATACAGGGGATAGCTTTCAGTCCTAACTTCAAT
1 AAAACTTTTACATACAGGGGATAACTTTCAGTCCTAACTTCAAT
* * **
127713 AAAAC-TTTATATATAGGGGATAACTTTCCTTCCTAACTTC
1 AAAACTTTTACATACAGGGGATAACTTTCAGTCCTAACTTC
127753 TCTAAAGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 30 0.86
44 5 0.14
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (44 bp):
AAAACTTTTACATACAGGGGATAACTTTCAGTCCTAACTTCAAT
Found at i:129034 original size:11 final size:11
Alignment explanation
Indices: 129018--129053 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
129008 TTAATACTTG
129018 AAAATAAAATA
1 AAAATAAAATA
129029 AAAATAAAATA
1 AAAATAAAATA
*
129040 AAAACAATAATA
1 AAAATAA-AATA
129052 AA
1 AA
129054 GAAGAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:129613 original size:2 final size:2
Alignment explanation
Indices: 129606--129630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
129596 AAATCTATTA
129606 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
129631 AATAAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:129837 original size:156 final size:158
Alignment explanation
Indices: 129602--129888 Score: 365
Period size: 156 Copynumber: 1.8 Consensus size: 158
129592 AAGAAAATCT
* * * *
129602 ATTAATATATATATATATATATATATATAAATAAGATATTTATTTATTTATAAATATCTGAAAAT
1 ATTAATATATATATATATATATATATATAAATAAGATATTTAGTTATTTAGAAATATCTAAAAAA
* * * *
129667 GACTTCTAGGTGCTTTAAGACAGCCCCTTT-CTTGATATTAAAAAA-TAAATAAATATTAATAAA
66 GACTTCGAGGTGCTTTAAGACAG-CCATTTCCTTAATATAAAAAAATTAAA-AAATATT--TAAA
129730 ATATTTCTCTAAAAATAATTAAAAAAAATTAA
127 ATATTTCTCTAAAAATAATTAAAAAAAATTAA
129762 ATTAATATATATATATA-AT-T-TATA-AAAGT-AGAATATTTAGTTATTTAGAAATATC-AAAA
1 ATTAATATATATATATATATATATATATAAA-TAAG-ATATTTAGTTATTTAGAAATATCTAAAA
* * *
129821 AAGACTTGGAGTTGCTTTAAGACAGTCATTTCCTTAATATAAAAAAATTAAAAAATATTTAAAAT
64 AAGACTTCGAGGTGCTTTAAGACAGCCATTTCCTTAATATAAAAAAATTAAAAAATATTTAAAAT
129886 ATT
129 ATT
129889 ATTATTTTTC
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
154 9 0.08
155 4 0.04
156 49 0.44
157 30 0.27
158 1 0.01
159 2 0.02
160 17 0.15
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (158 bp):
ATTAATATATATATATATATATATATATAAATAAGATATTTAGTTATTTAGAAATATCTAAAAAA
GACTTCGAGGTGCTTTAAGACAGCCATTTCCTTAATATAAAAAAATTAAAAAATATTTAAAATAT
TTCTCTAAAAATAATTAAAAAAAATTAA
Found at i:130013 original size:3 final size:3
Alignment explanation
Indices: 130005--130053 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
129995 TGTATGACTA
130005 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
130053 A
1 A
130054 GTTAAATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:130959 original size:25 final size:25
Alignment explanation
Indices: 130905--130963 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
130895 TTTTTTTTCG
*
130905 AAAAAAATAAAATAAAATACTAAGT
1 AAAAAAATAAAATAAAATACTAAAT
130930 AAAAAAATAAAATGAAAAT-C-AAAT
1 AAAAAAATAAAAT-AAAATACTAAAT
*
130954 ATAAAAATAA
1 AAAAAAATAA
130964 CCTTTGATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 12 0.39
25 14 0.45
26 5 0.16
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (25 bp):
AAAAAAATAAAATAAAATACTAAAT
Found at i:131090 original size:2 final size:2
Alignment explanation
Indices: 131072--131121 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
131062 TACATGTAAA
* *
131072 AT AT GT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131114 AT AT AT AT
1 AT AT AT AT
131122 TTGTTGTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Done.