Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008512.1 Hibiscus syriacus cultivar Beakdansim tig00111372_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: 1759229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1232618 original size:84 final size:84
Alignment explanation
Indices: 1232477--1232821 Score: 602
Period size: 84 Copynumber: 4.1 Consensus size: 84
1232467 AAATAAGTGT
* * *
1232477 TCTGATTTGGCAAAACCAATCATTGAATCTGAAAGATGAATTTGCTCAATAGCATCTTCTGGAAG
1 TCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAG
1232542 TGTTCTTTGAGTTATCTGA
66 TGTTCTTTGAGTTATCTGA
*
1232561 TCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTCGAAG
1 TCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAG
1232626 TGTTCTTTGAGTTATCTGA
66 TGTTCTTTGAGTTATCTGA
1232645 TCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAG
1 TCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAG
1232710 TGTTCTTTGAGTTATCTGA
66 TGTTCTTTGAGTTATCTGA
* * *
1232729 TCTGATTTGGCAGAACTAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTTTGAAAG
1 TCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAG
*
1232793 TGTTCTTTGAGTTATCTAA
66 TGTTCTTTGAGTTATCTGA
*
1232812 TCTGGTTTGG
1 TCTGATTTGG
1232822 TAAAAATTAC
Statistics
Matches: 251, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
83 44 0.18
84 207 0.82
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (84 bp):
TCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAG
TGTTCTTTGAGTTATCTGA
Found at i:1233872 original size:113 final size:113
Alignment explanation
Indices: 1233551--1234228 Score: 1020
Period size: 113 Copynumber: 6.0 Consensus size: 113
1233541 CAAAGATTCA
* * * *
1233551 AATCTATCATTTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCATCTGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGA
* **
1233616 AGGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTG
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
1233667 AATTCATCACTTGATGGATTA-TTTTTGCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAA
1 AATCCATCATTTGATGGATCAGCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
1233730 AAGGAAGAAGAAGTCCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
1233779 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1233844 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
1233892 AATCCATCATTTGATGGATCAGCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1233957 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
1234005 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1234070 AGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
1234118 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTG
* * * *
1234182 AAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1234229 GCATAATTCT
Statistics
Matches: 522, Mismatches: 33, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
112 79 0.15
113 347 0.66
115 23 0.04
116 73 0.14
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:1234555 original size:3 final size:3
Alignment explanation
Indices: 1234547--1234650 Score: 190
Period size: 3 Copynumber: 34.7 Consensus size: 3
1234537 TTTTTATCCA
*
1234547 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1234595 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1234643 TAT TAT TA
1 TAT TAT TA
1234651 AATATATATT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1235145 original size:18 final size:18
Alignment explanation
Indices: 1235124--1235160 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1235114 AGAACGGGAC
*
1235124 AGAGAGACAGAAAAAAAA
1 AGAGAGACACAAAAAAAA
*
1235142 AGAGAGAGACAAAAAAAA
1 AGAGAGACACAAAAAAAA
1235160 A
1 A
1235161 ACAGAGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.22, T:0.00
Consensus pattern (18 bp):
AGAGAGACACAAAAAAAA
Found at i:1235147 original size:20 final size:19
Alignment explanation
Indices: 1235122--1235167 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1235112 AGAGAACGGG
1235122 ACAGAGAGACAGAAAAAAAA
1 ACAGAGAGACA-AAAAAAAA
*
1235142 AGAGAGAGACAAAAAAAAA
1 ACAGAGAGACAAAAAAAAA
1235161 ACAGAGA
1 ACAGAGA
1235168 AGATACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.70, C:0.09, G:0.22, T:0.00
Consensus pattern (19 bp):
ACAGAGAGACAAAAAAAAA
Found at i:1235155 original size:16 final size:16
Alignment explanation
Indices: 1235126--1235159 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1235116 AACGGGACAG
1235126 AGAGACAGAAAAAAAA
1 AGAGACAGAAAAAAAA
*
1235142 AGAGAGAGACAAAAAAA
1 AGAGACAGA-AAAAAAA
1235159 A
1 A
1235160 AACAGAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.74, C:0.06, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAGACAGAAAAAAAA
Found at i:1236032 original size:17 final size:17
Alignment explanation
Indices: 1236001--1236035 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1235991 GTATTTTTAT
**
1236001 TTTTATATTGTTAAATA
1 TTTTATATTCATAAATA
1236018 TTTTATATTCATAAATA
1 TTTTATATTCATAAATA
1236035 T
1 T
1236036 ATAATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTATATTCATAAATA
Found at i:1238774 original size:18 final size:19
Alignment explanation
Indices: 1238747--1238796 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
1238737 AATCTACTTG
1238747 AATTAAAAAAAA-CAGAAA
1 AATTAAAAAAAATCAGAAA
*
1238765 AATTACAAAAAATCAGAAA
1 AATTAAAAAAAATCAGAAA
1238784 AATTATAAAAAAA
1 AATTA-AAAAAAA
1238797 AAATTAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.39
19 11 0.39
20 6 0.21
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.16
Consensus pattern (19 bp):
AATTAAAAAAAATCAGAAA
Found at i:1238776 original size:19 final size:18
Alignment explanation
Indices: 1238747--1238796 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1238737 AATCTACTTG
1238747 AATTAAAAAAAACAGAAA
1 AATTAAAAAAAACAGAAA
*
1238765 AATTACAAAAAATCAGAAA
1 AATTA-AAAAAAACAGAAA
1238784 AATTATAAAAAAA
1 AATTA-AAAAAAA
1238797 AAATTAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.16
Consensus pattern (18 bp):
AATTAAAAAAAACAGAAA
Found at i:1246078 original size:16 final size:17
Alignment explanation
Indices: 1246059--1246092 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1246049 TTTAAAATAG
1246059 TAATATA-ATATATTTA
1 TAATATACATATATTTA
1246075 TAATATATCATATATTTA
1 TAATATA-CATATATTTA
1246093 CAGAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATACATATATTTA
Found at i:1248231 original size:28 final size:28
Alignment explanation
Indices: 1248174--1248246 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 28
1248164 TTAAAAATAT
*
1248174 ATCTTAAATTTAATATTTAAGTTTTAAA
1 ATCTTAAATTTAATATTTAAGATTTAAA
* * *
1248202 ATCTATAATTTTAATCTTTAA-ATTTGAA
1 ATCT-TAAATTTAATATTTAAGATTTAAA
* * *
1248230 ATATTACATTTGATATT
1 ATCTTAAATTTAATATT
1248247 ATTTAAATCT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
27 9 0.26
28 12 0.34
29 14 0.40
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (28 bp):
ATCTTAAATTTAATATTTAAGATTTAAA
Found at i:1249841 original size:2 final size:2
Alignment explanation
Indices: 1249834--1249870 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1249824 ATAGGCCGGC
1249834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1249871 CTGAGAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1253377 original size:21 final size:21
Alignment explanation
Indices: 1253351--1253405 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1253341 TATCCTATCG
1253351 AAAGTATCGACACCTGACATA
1 AAAGTATCGACACCTGACATA
1253372 AAAGTATCGACACCTGACATA
1 AAAGTATCGACACCTGACATA
1253393 AAAGTATCGACAC
1 AAAGTATCGACAC
1253406 TTTGGTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (21 bp):
AAAGTATCGACACCTGACATA
Found at i:1256222 original size:202 final size:201
Alignment explanation
Indices: 1255599--1256341 Score: 1333
Period size: 201 Copynumber: 3.7 Consensus size: 201
1255589 AGGTAAAATT
* * *
1255599 TATCGATCCCAAAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGA
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGG
*
1255664 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTGATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTGATTTTGT
* *
1255729 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTACAACCATAAAGTATCGATACATTTAT
131 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
1255794 AAAAAG
196 AAAAAG
1255800 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGG
* *
1255865 TATAAATATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACGTTTTTGATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTGATTTTGT
1255930 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
131 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
1255995 AAAAAG
196 AAAAAG
* *
1256001 TATCGATCCCAGAAACATATGAATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTAG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGG
* *
1256066 TATAAATATATCGGTTTTATGAGAGAATAAGTCTACAACATGTATCGACACATTTTTTGATTTTG
66 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACAC-TTTTTTGATTTTG
1256131 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
130 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
*
1256196 TAAAATG
195 TAAAAAG
*
1256203 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGG
* *
1256268 TATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTTATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTGATTTTGT
1256333 GTCGATACT
131 GTCGATACT
1256342 AATTTAAATA
Statistics
Matches: 519, Mismatches: 22, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
201 326 0.63
202 193 0.37
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (201 bp):
TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGG
TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTGATTTTGT
GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
AAAAAG
Found at i:1257856 original size:3 final size:3
Alignment explanation
Indices: 1257815--1257885 Score: 70
Period size: 3 Copynumber: 23.7 Consensus size: 3
1257805 CAAGCGGTCA
* * * * * * * *
1257815 ATG AAG ATG AAG ATG ACG ATG AAG AAG ACG ATG AAG ATG ATG ATG ATA
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1257863 ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG AT
1257886 CCAAACAAGT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.42, C:0.03, G:0.31, T:0.24
Consensus pattern (3 bp):
ATG
Found at i:1257885 original size:12 final size:12
Alignment explanation
Indices: 1257815--1257884 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1257805 CAAGCGGTCA
*
1257815 ATGAAGATGAAG
1 ATGATGATGAAG
*
1257827 ATGACGATGAAG
1 ATGATGATGAAG
* *
1257839 AAGACGATGAAG
1 ATGATGATGAAG
1257851 ATGATGATGATA-
1 ATGATGATGA-AG
*
1257863 ATGATGATGATG
1 ATGATGATGAAG
1257875 ATGATGATGA
1 ATGATGATGA
1257885 TCCAAACAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
12 50 0.98
13 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.31, T:0.23
Consensus pattern (12 bp):
ATGATGATGAAG
Found at i:1259052 original size:23 final size:23
Alignment explanation
Indices: 1259009--1259052 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1258999 ACTAGTTATT
*
1259009 AATGTATTTTACATCTGTGTGCA
1 AATGTATTTTACATCTATGTGCA
*
1259032 AATGTATTTTACATTTATGTG
1 AATGTATTTTACATCTATGTG
1259053 ATGATGCGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (23 bp):
AATGTATTTTACATCTATGTGCA
Found at i:1261999 original size:200 final size:197
Alignment explanation
Indices: 1261439--1262170 Score: 592
Period size: 200 Copynumber: 3.6 Consensus size: 197
1261429 ACCTAAATAT
*
1261439 GTGTCGATACATTT-TATACAAGTATCGA-CCCTAAAAACATCAAAACTAATAATTATAATGTAA
1 GTGTCGATACATTTATA-AAAAGTATCGATCCC-AAAAACATCAAAACTAATAATTATAATGTAA
*
1261502 TAGGTAAATTAAT-AATGTAACCGATATAAATATACCGG-TTTATTAGAAAATAGGTCAACATAA
64 TAGGTAAA-T-ATCAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAA-ATAA
** * * ** * *
1261565 TGTATTAACACTTGTGTAATTTGTGTCAATACTTATTGTCTAGGATGAACGCACAAACGAGGTGT
126 TGTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCAAAATGAACGCACAAAAGAGGTGA
1261630 ACGCATAAA
189 ACGCATAAA
* * * * *
1261639 GTGTCGATACATTTATTAAAAGTATCGATCACAAAAACATCGAAACTGATAATTATAATGTATTA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACTAATAATTATAATGTAATA
* * * * *
1261704 GGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGATAAAATAAGTCAGCATCAA-G
66 GGTAAATAT-CAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCA-AAT-AATG
* * *
1261768 GATCGACACTTGCTAAATTTCTGTCGATACTTTTGGTCCAAAATGAATAC-CA-AAAAG-GGTGC
128 TATCGACACTTG-TTAATTTGTGTCGATACTTTT-GTCCAAAATG-A-ACGCACAAAAGAGGTG-
1261830 AAC-CATAAA
188 AACGCATAAA
* ** ** *
1261839 GTGTCGATACATTTATAAAAAATATCGATCCCGGAAACATCAAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACTAATAATTATAATGTAATA
* * * *
1261904 GGTAAATGCTCAATGTAACCGGTATAAATATACTGGTTTTATGAGATAATAGGTCTAAATAATGT
66 GGTAAAT-ATCAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTC-AAATAATGT
* * * * * **
1261969 ATCGACACGTTGTTAGTTTGTGTTGATACTTTTTTCCTAAATGAAATATGAATGC-CCAACCAGG
129 ATCGACAC-TTGTTAATTTGTGTCGATACTTTTGTCC------AAA-ATGAACGCACAAAAGAGG
1262033 TGCAA-GCATAAA
186 TG-AACGCATAAA
* ** ** ** ** * *
1262045 GTATCGATACATTTA-AAATTGTATCGATCTAAAAAACATCGTAACCGATAATAATATTGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACTAATAATTATAATGTAATA
* * * **
1262109 GGTAAATTTACAATATTACC-AGTATAAATATACCGG-TTTACTTCGAAAATAGGTCAATATAA
66 GGTAAATAT-CAATGTAACCGA-TATAAATATACCGGTTTTA-TGAGAAAATAGGTCAA-ATAA
1262171 GCGCTACCTA
Statistics
Matches: 428, Mismatches: 73, Indels: 57
0.77 0.13 0.10
Matches are distributed among these distances:
198 1 0.00
199 6 0.01
200 225 0.53
201 64 0.15
202 6 0.01
203 2 0.00
204 8 0.02
205 86 0.20
206 30 0.07
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (197 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACTAATAATTATAATGTAATA
GGTAAATATCAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAAATAATGTAT
CGACACTTGTTAATTTGTGTCGATACTTTTGTCCAAAATGAACGCACAAAAGAGGTGAACGCATA
AA
Found at i:1266369 original size:82 final size:82
Alignment explanation
Indices: 1266264--1266417 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 82
1266254 GGAATAGAAC
* * * * *
1266264 TGTTTATAGTGGCGTTTTTCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTT-TTATAC
1 TGTTTATAGTGGCATTTTTCAACAAACGACGCAATAGAGAAGTAATTTAGCGGCGTTTATCAAAC
1266328 AAACGCCATAATAGGGT
66 AAACGCCATAATAGGGT
* *
1266345 TGTTTATAGTGGCATTTTTCCAACAAACGATGCTATAGAGAAGTAATTTAGCGGCGTTTATCAAA
1 TGTTTATAGTGGCATTTTT-CAACAAACGACGCAATAGAGAAGTAATTTAGCGGCGTTTATCAAA
1266410 CAAACGCC
65 CAAACGCC
1266418 GCAATAGAGC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 18 0.28
82 35 0.55
83 11 0.17
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (82 bp):
TGTTTATAGTGGCATTTTTCAACAAACGACGCAATAGAGAAGTAATTTAGCGGCGTTTATCAAAC
AAACGCCATAATAGGGT
Found at i:1266425 original size:42 final size:42
Alignment explanation
Indices: 1266274--1266426 Score: 152
Period size: 41 Copynumber: 3.7 Consensus size: 42
1266264 TGTTTATAGT
1266274 GGCGTTTTTC-AACAAACGCCGCAATAGAGTAGTAATTTAGC
1 GGCGTTTTTCAAACAAACGCCGCAATAGAGTAGTAATTTAGC
* ** * * *
1266315 GGCGTTTTT-ATACAAACGCCATAATAGGGTTGT--TTATAGT
1 GGCGTTTTTCAAACAAACGCCGCAATAGAGTAGTAATT-TAGC
* * ** * *
1266355 GGCATTTTTCCAACAAACGATGCTATAGAGAAGTAATTTAGC
1 GGCGTTTTTCAAACAAACGCCGCAATAGAGTAGTAATTTAGC
*
1266397 GGCGTTTATCAAACAAACGCCGCAATAGAG
1 GGCGTTTTTCAAACAAACGCCGCAATAGAG
1266427 CAATAATATA
Statistics
Matches: 83, Mismatches: 24, Indels: 9
0.72 0.21 0.08
Matches are distributed among these distances:
39 2 0.02
40 11 0.13
41 41 0.49
42 27 0.33
43 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (42 bp):
GGCGTTTTTCAAACAAACGCCGCAATAGAGTAGTAATTTAGC
Found at i:1267390 original size:82 final size:82
Alignment explanation
Indices: 1267254--1267484 Score: 209
Period size: 82 Copynumber: 2.8 Consensus size: 82
1267244 GCGGGGTTGC
** * * *** *
1267254 TATATAGTGGCGTTTTTTCAAACAAACGCCGCAACAAAAAGAAATTTTGCGGCGTTTTT-TATAA
1 TATATAGTGGCGTTTTAGCAAACAAACGCCGCAA-AGAAAGTAATTTAAAGGCGTTTTTATACAA
1267318 ACGA-TGCAATAGGGTTAT
65 AC-ACTGCAATAGGGTTAT
* * *
1267336 TATTTCGTGGCGTTTTAGCAAACAAACGCCGCTGAAGAAAGTAATTTAAAGGCGTTTTTATACAA
1 TATATAGTGGCGTTTTAGCAAACAAACGCCGC-AAAGAAAGTAATTTAAAGGCGTTTTTATACAA
** *
1267401 ACACTGCAATTTGTTTAT
65 ACACTGCAATAGGGTTAT
** ** * *
1267419 TATATAGTGGCGTTTTATG-TTAC-AACGCCGCAAAAGAAAGTAATTTAGCGGTGTTTTTAAACA
1 TATATAGTGGCGTTTTA-GCAAACAAACGCCGC-AAAGAAAGTAATTTAAAGGCGTTTTTATACA
1267482 AAC
64 AAC
1267485 GCCGTGATAA
Statistics
Matches: 121, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
82 85 0.70
83 35 0.29
84 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (82 bp):
TATATAGTGGCGTTTTAGCAAACAAACGCCGCAAAGAAAGTAATTTAAAGGCGTTTTTATACAAA
CACTGCAATAGGGTTAT
Found at i:1275241 original size:20 final size:20
Alignment explanation
Indices: 1275216--1275265 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1275206 TTTGAAGGTA
1275216 CATCGATGCAGTAAGGGGTG
1 CATCGATGCAGTAAGGGGTG
1275236 CATCGATGCAGTAAGGGGTG
1 CATCGATGCAGTAAGGGGTG
1275256 CATCGATGCA
1 CATCGATGCA
1275266 TCAATACTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (20 bp):
CATCGATGCAGTAAGGGGTG
Found at i:1276826 original size:23 final size:23
Alignment explanation
Indices: 1276758--1276826 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1276748 ACATATTATA
1276758 CGGCACTTCAGTGCATTTCTACG
1 CGGCACTTCAGTGCATTTCTACG
* * * *
1276781 CGGAACTACACTGCAATTCTACG
1 CGGCACTTCAGTGCATTTCTACG
* * *
1276804 TGGCACTTCGGTGCATTTATACG
1 CGGCACTTCAGTGCATTTCTACG
1276827 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (23 bp):
CGGCACTTCAGTGCATTTCTACG
Found at i:1278879 original size:30 final size:28
Alignment explanation
Indices: 1278785--1278882 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 28
1278775 ACCGTTGACC
* * ***
1278785 GGTGCTATTCTGGGAATTTATTCGATTTT
1 GGTGCTATTTTGGGAATTAATTC-AAAAT
* *
1278814 GGTCCTATTATGGGAATTAATTCAAAAT
1 GGTGCTATTTTGGGAATTAATTCAAAAT
* *
1278842 GGGTGCTATTTTGGTAATTAATTTGAAAAGT
1 -GGTGCTATTTTGGGAATTAA-TTCAAAA-T
1278873 GGTGCTATTT
1 GGTGCTATTT
1278883 CTGTAAAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
28 2 0.04
29 37 0.66
30 16 0.29
31 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTAATTCAAAAT
Found at i:1284917 original size:18 final size:18
Alignment explanation
Indices: 1284894--1284936 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1284884 TGACCGATCA
*
1284894 CGACCCGACCCGTTGACC
1 CGACCCGACCCATTGACC
*
1284912 CGACCCAACCCATTGACC
1 CGACCCGACCCATTGACC
1284930 CGACCCG
1 CGACCCG
1284937 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.51, G:0.19, T:0.09
Consensus pattern (18 bp):
CGACCCGACCCATTGACC
Found at i:1285015 original size:29 final size:29
Alignment explanation
Indices: 1284950--1285046 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
1284940 ACCGTTGACC
* * * ** *
1284950 GGTGCTATTCTGGGAATTTATTCGATTTT
1 GGTGCTATTATGGGAATTAATTCAAAATG
*
1284979 GGTTCTATTATGGGAATTAATTCAAAATG
1 GGTGCTATTATGGGAATTAATTCAAAATG
* * *
1285008 GGTGCTATTTTGGTAATTAATTCGAAAAGG
1 GGTGCTATTATGGGAATTAATTC-AAAATG
1285038 GGTGCTATT
1 GGTGCTATT
1285047 TCTGAAAATG
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
29 42 0.75
30 14 0.25
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (29 bp):
GGTGCTATTATGGGAATTAATTCAAAATG
Found at i:1286727 original size:164 final size:164
Alignment explanation
Indices: 1286455--1286752 Score: 578
Period size: 164 Copynumber: 1.8 Consensus size: 164
1286445 TGCCCGCTTA
1286455 GTATATGAAGCCAGAGTTTATGAGTTTGATACAGAGGGAAATCGTAATGTGTATGGACAAGAGTA
1 GTATATGAAGCCAGAGTTTATGAGTTTGATACAGAGGGAAATCGTAATGTGTATGGACAAGAGTA
* *
1286520 TAGTTTGATGAGTAGAGTGAAAGGTTGTGAAGCAAATTTAAATGAAAATGATGCATGCAAGTAAG
66 CAGTTTGATGAGTAGAGTGAAAGGTTGTGAAGCAAACTTAAATGAAAATGATGCATGCAAGTAAG
1286585 GTGTGGATAAGTGCATCAGCGATAAGTGTATAAG
131 GTGTGGATAAGTGCATCAGCGATAAGTGTATAAG
1286619 GTATATGAAGCCAGAGTTTATGAGTTTGATACAGAGGGAAATCGTAATGTGTATGGACAAGAGTA
1 GTATATGAAGCCAGAGTTTATGAGTTTGATACAGAGGGAAATCGTAATGTGTATGGACAAGAGTA
1286684 CAGTTTGATGAGTAGAGTGAAAGGTTGTGAAGCAAACTTAAATGAAAATGATGCATGCAAGTAAG
66 CAGTTTGATGAGTAGAGTGAAAGGTTGTGAAGCAAACTTAAATGAAAATGATGCATGCAAGTAAG
1286749 GTGT
131 GTGT
1286753 AGAGGGCTGG
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 132 1.00
ACGTcount: A:0.37, C:0.07, G:0.29, T:0.27
Consensus pattern (164 bp):
GTATATGAAGCCAGAGTTTATGAGTTTGATACAGAGGGAAATCGTAATGTGTATGGACAAGAGTA
CAGTTTGATGAGTAGAGTGAAAGGTTGTGAAGCAAACTTAAATGAAAATGATGCATGCAAGTAAG
GTGTGGATAAGTGCATCAGCGATAAGTGTATAAG
Found at i:1289192 original size:16 final size:17
Alignment explanation
Indices: 1289157--1289193 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1289147 TGATATGAGT
1289157 ATATGTGTTGTATGTTG
1 ATATGTGTTGTATGTTG
*
1289174 ATATGTTTTGTAT-TTG
1 ATATGTGTTGTATGTTG
1289190 ATAT
1 ATAT
1289194 ATGATATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.57
Consensus pattern (17 bp):
ATATGTGTTGTATGTTG
Found at i:1290303 original size:23 final size:23
Alignment explanation
Indices: 1290277--1290338 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1290267 ATATTATACG
1290277 GCACTTCGGTGCATTTCTACGCA
1 GCACTTCGGTGCATTTCTACGCA
* **
1290300 GCACTAT-GGTGCAATTCTACGTG
1 GCACT-TCGGTGCATTTCTACGCA
*
1290323 GCACTTCAGTGCATTT
1 GCACTTCGGTGCATTT
1290339 ATATGAGCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCA
Found at i:1292995 original size:21 final size:21
Alignment explanation
Indices: 1292978--1293028 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1292968 TGAAGCAGAA
*
1292978 AGAGAAGTAGCGGCAGCATAG
1 AGAGAAGCAGCGGCAGCATAG
1292999 AGAGAAGCAGCGGCAGCATAG
1 AGAGAAGCAGCGGCAGCATAG
1293020 AGAGAAGCA
1 AGAGAAGCA
1293029 ACATATCAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.37, T:0.06
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCATAG
Found at i:1293441 original size:43 final size:43
Alignment explanation
Indices: 1293346--1293457 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 43
1293336 ATTATGTGTT
* * * *
1293346 CTTTAGCGGCATTTGTAACAAAAAATGCCGCAATATACCATAC
1 CTTTAGCGGCGTTTGTATCCAAAAACGCCGCAATATACCATAC
* * *
1293389 ATTTTGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCA-AC
1 CTTTAGCGGCGTTTGTATCC-AAAAACGCCGCAATATACCATAC
1293432 CTTTAGCGGCGTTTGTATCCAAAAAC
1 CTTTAGCGGCGTTTGTATCCAAAAAC
1293458 CACCACGAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 6 0.10
43 35 0.59
44 18 0.31
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTATCCAAAAACGCCGCAATATACCATAC
Found at i:1293573 original size:43 final size:43
Alignment explanation
Indices: 1293520--1293778 Score: 232
Period size: 43 Copynumber: 6.0 Consensus size: 43
1293510 CATACGCATT
* * * *
1293520 TTACGACGTTTGTGGGGAAAACGCCACTAAATATCAACACCTA
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTA
* * *** * * *
1293563 TTACAACGTTTTTCTCAAAAATGCCGTTAAATCTCAAAACCTA
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTA
* * *
1293606 TTACGACGTTTGTGTGAAAAACACCGTTAAATCTCAACACCTA
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTA
* * * *
1293649 TTGCTACGTTTGTGAGAAAAACG-CGCTAAATATCAAAACCTA
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTA
* * * *
1293691 TTGCGTCGTCTGTGAGAAAAACGTCGCTAAATCTCAACACCTA
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTA
* * * * * * * *
1293734 TTGCGGCATTTATGGGGAAAACGCCGCTATACCTCAACACCTA
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTA
1293777 TT
1 TT
1293779 GTGGCGTTTG
Statistics
Matches: 176, Mismatches: 39, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
42 36 0.20
43 140 0.80
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTA
Found at i:1293612 original size:86 final size:85
Alignment explanation
Indices: 1293520--1293735 Score: 243
Period size: 85 Copynumber: 2.5 Consensus size: 85
1293510 CATACGCATT
* * * * * * *
1293520 TTACGACGTTTGTGGGGAAAACGCCACTAAATATCAACACCTATTACAACGTTTTTCTCAAAAAT
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTACAACGTTTGTCACAAAAAC
* *
1293585 GCCGTTAAATCTCAAAACCTA
66 G-CGCTAAATATCAAAACCTA
* * * * * * *
1293606 TTACGACGTTTGTGTGAAAAACACCGTTAAATCTCAACACCTATTGCTACGTTTGTGAGAAAAAC
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTACAACGTTTGTCACAAAAAC
1293671 GCGCTAAATATCAAAACCTA
66 GCGCTAAATATCAAAACCTA
* * * *
1293691 TTGCGTCGTCTGTGAGAAAAACGTCGCTAAATCTCAACACCTATT
1 TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATT
1293736 GCGGCATTTA
Statistics
Matches: 108, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
85 55 0.51
86 53 0.49
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (85 bp):
TTACGACGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTACAACGTTTGTCACAAAAAC
GCGCTAAATATCAAAACCTA
Found at i:1293755 original size:85 final size:86
Alignment explanation
Indices: 1293520--1293762 Score: 218
Period size: 85 Copynumber: 2.8 Consensus size: 86
1293510 CATACGCATT
* * * * * * * * * * *** *
1293520 TTACGACGTTTGTGGGGAAAACGCCACTAAATATCAACACCTATTACAACGTTTTTCTCAAAAAT
1 TTACGACGTCTGTGAGAAAAACACCGCTAAATCTCAACACCTATTGCGACATTTATGAGAAAAAC
* *
1293585 GCCGTTAAATCTCAAAACCTA
66 GCCGCTAAATATCAAAACCTA
* * * * * *
1293606 TTACGACGTTTGTGTGAAAAACACCGTTAAATCTCAACACCTATTGCTACGTTTGTGAGAAAAAC
1 TTACGACGTCTGTGAGAAAAACACCGCTAAATCTCAACACCTATTGCGACATTTATGAGAAAAAC
1293671 G-CGCTAAATATCAAAACCTA
66 GCCGCTAAATATCAAAACCTA
* * ** * * *
1293691 TTGCGTCGTCTGTGAGAAAAACGTCGCTAAATCTCAACACCTATTGCGGCATTTATGGGGAAAAC
1 TTACGACGTCTGTGAGAAAAACACCGCTAAATCTCAACACCTATTGCGACATTTATGAGAAAAAC
1293756 GCCGCTA
66 GCCGCTA
1293763 TACCTCAACA
Statistics
Matches: 128, Mismatches: 28, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
85 70 0.55
86 58 0.45
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (86 bp):
TTACGACGTCTGTGAGAAAAACACCGCTAAATCTCAACACCTATTGCGACATTTATGAGAAAAAC
GCCGCTAAATATCAAAACCTA
Found at i:1296281 original size:7 final size:7
Alignment explanation
Indices: 1296249--1296282 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1296239 ATATTTTTAG
1296249 TAAATTT
1 TAAATTT
*
1296256 TAATTTT
1 TAAATTT
1296263 TAATATTT
1 TAA-ATTT
1296271 TAAATTT
1 TAAATTT
1296278 TAAAT
1 TAAAT
1296283 AATTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAAATTT
Found at i:1297221 original size:24 final size:23
Alignment explanation
Indices: 1297173--1297240 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
1297163 ATTTCAGTAA
*
1297173 TATGTTCGTTTATTATTAT-TTGTT
1 TATGTTCGTTCA-T-TTATGTTGTT
1297197 TATGTTCGTTCATTTATGTTCGTT
1 TATGTTCGTTCATTTATGTT-GTT
*
1297221 TATGTGT-GTTCAATTATGTT
1 TATGT-TCGTTCATTTATGTT
1297241 TAGCCAAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.10
23 3 0.08
24 31 0.79
25 1 0.03
ACGTcount: A:0.16, C:0.07, G:0.16, T:0.60
Consensus pattern (23 bp):
TATGTTCGTTCATTTATGTTGTT
Found at i:1297412 original size:10 final size:10
Alignment explanation
Indices: 1297397--1297435 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1297387 AAAATCTATT
1297397 TTCATTTATG
1 TTCATTTATG
*
1297407 TTCATTTACG
1 TTCATTTATG
* *
1297417 TTCGTTTATA
1 TTCATTTATG
1297427 TTCATTTAT
1 TTCATTTAT
1297436 TGTGTTCGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:1297467 original size:24 final size:23
Alignment explanation
Indices: 1297416--1297471 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1297406 GTTCATTTAC
*
1297416 GTTCGTTTATATTCATTTATTGT
1 GTTCGTTTACATTCATTTATTGT
* *
1297439 GTTCGTTTACATTCGTTCTTTTGT
1 GTTCGTTTACATTCATT-TATTGT
1297463 GTTCGTTTA
1 GTTCGTTTA
1297472 TATCCGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (23 bp):
GTTCGTTTACATTCATTTATTGT
Found at i:1297489 original size:24 final size:23
Alignment explanation
Indices: 1297416--1297494 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
1297406 GTTCATTTAC
* *
1297416 GTTCGTTTATATTCATTTATTGT
1 GTTCGTTTATATTCGTTTTTTGT
*
1297439 GTTCGTTTACATTCGTTCTTTTGT
1 GTTCGTTTATATTCGTT-TTTTGT
* *
1297463 GTTCGTTTATATCCGTTTGTTTTT
1 GTTCGTTTATATTCGTTT-TTTGT
*
1297487 GTTTGTTT
1 GTTCGTTT
1297495 GTTTATCATT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
23 16 0.34
24 31 0.66
ACGTcount: A:0.10, C:0.11, G:0.16, T:0.62
Consensus pattern (23 bp):
GTTCGTTTATATTCGTTTTTTGT
Found at i:1312452 original size:32 final size:32
Alignment explanation
Indices: 1312416--1312487 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
1312406 ACAAAGTTAA
*
1312416 TATTGCTTGGGGGAACAAGTCCAAGTTACTAG
1 TATTGCTTGGGGGAACAAGTACAAGTTACTAG
*
1312448 TATTGCTTGGGTGAACAAGTACAAGTTACTAG
1 TATTGCTTGGGGGAACAAGTACAAGTTACTAG
1312480 TATTGCTT
1 TATTGCTT
1312488 CACATGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (32 bp):
TATTGCTTGGGGGAACAAGTACAAGTTACTAG
Found at i:1321583 original size:19 final size:20
Alignment explanation
Indices: 1321544--1321611 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
1321534 TCGGGTCGGG
* *
1321544 TCAG-ACCGGTCAAAACAGT
1 TCAGAACCGGTCAAACCGGT
1321563 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
*
1321582 TC-GAACCGGTTGAAACCGG-
1 TCAGAACCGG-TCAAACCGGT
1321601 TCAGAACCGGT
1 TCAGAACCGGT
1321612 TGAAAACCGG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 27 0.63
20 15 0.35
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (20 bp):
TCAGAACCGGTCAAACCGGT
Found at i:1321599 original size:20 final size:22
Alignment explanation
Indices: 1321574--1321623 Score: 79
Period size: 20 Copynumber: 2.4 Consensus size: 22
1321564 CAGACCGGTC
1321574 AAACCGGTTC-GAACCGGTTG-
1 AAACCGGTTCAGAACCGGTTGA
1321594 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTCAGAACCGGTTGA
1321615 AAACCGGTT
1 AAACCGGTT
1321624 AAATCAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 7 0.26
22 1 0.04
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (22 bp):
AAACCGGTTCAGAACCGGTTGA
Found at i:1328010 original size:22 final size:22
Alignment explanation
Indices: 1327978--1328042 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
1327968 AACGGTCAAC
* *
1327978 GGTCAATGGTCCGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1328000 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
* *
1328022 GGTTAACGGTCGGGTTGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1328043 AGATCGATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.09, C:0.20, G:0.48, T:0.23
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1328096 original size:20 final size:20
Alignment explanation
Indices: 1328052--1328120 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
1328042 CAGATCGATC
1328052 AAACCGGTTC-AGACCGGTT-
1 AAACCGGTTCGA-ACCGGTTG
1328071 AAACCGGTTCGAACCGGTTG
1 AAACCGGTTCGAACCGGTTG
*
1328091 AAACCGG-TCAGAACAGGTTG
1 AAACCGGTTC-GAACCGGTTG
1328111 AAAACCGGTT
1 -AAACCGGTT
1328121 AAATCGGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
19 19 0.43
20 17 0.39
21 7 0.16
22 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (20 bp):
AAACCGGTTCGAACCGGTTG
Found at i:1328117 original size:21 final size:19
Alignment explanation
Indices: 1328067--1328119 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1328057 GGTTCAGACC
*
1328067 GGTT-AAACCGGTTCGAACC
1 GGTTGAAACCGG-TCGAACA
1328086 GGTTGAAACCGGTCAGAACA
1 GGTTGAAACCGGTC-GAACA
1328106 GGTTGAAAACCGGT
1 GGTTG-AAACCGGT
1328120 TAAATCGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 6 0.20
20 16 0.53
21 8 0.27
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (19 bp):
GGTTGAAACCGGTCGAACA
Found at i:1328129 original size:20 final size:18
Alignment explanation
Indices: 1328052--1328129 Score: 50
Period size: 20 Copynumber: 3.9 Consensus size: 18
1328042 CAGATCGATC
*
1328052 AAACCGGTTCAGACCGGTT-
1 AAACCGGTT-A-AACGGTTG
*
1328071 AAACCGGTTCGAACCGGTTG
1 AAACCGGTT--AAACGGTTG
*
1328091 AAACCGGTCAGAACAGGTTG
1 AAACCGGTTA-AAC-GGTTG
1328111 AAAACCGGTTAAATCGGTT
1 -AAACCGGTTAAA-CGGTT
1328130 TCCAGCAGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
18 1 0.02
19 18 0.37
20 20 0.41
21 10 0.20
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.21
Consensus pattern (18 bp):
AAACCGGTTAAACGGTTG
Found at i:1335204 original size:22 final size:22
Alignment explanation
Indices: 1335176--1335218 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1335166 AACGGTCAAC
1335176 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCG
*
1335198 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCCGGTCGGGTC
1335219 AGACCGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.26, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCCGGTCGGGTCG
Found at i:1335207 original size:17 final size:17
Alignment explanation
Indices: 1335187--1335219 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1335177 GTCAACGGTC
1335187 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
1335204 CGGTCGGGTCGGGTCA
1 CGGTCGGGTCGGGTCA
1335220 GACCGGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.48, T:0.18
Consensus pattern (17 bp):
CGGTCGGGTCGGGTCAA
Found at i:1338789 original size:4 final size:4
Alignment explanation
Indices: 1338780--1338805 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1338770 ATAGAATACC
1338780 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
1338806 GCAGTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1340716 original size:2 final size:2
Alignment explanation
Indices: 1340709--1340761 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1340699 AAACTACTTT
1340709 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
1340751 TA -A TA TA TA TA
1 TA TA TA TA TA TA
1340762 AAAGTAGTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1344034 original size:3 final size:3
Alignment explanation
Indices: 1344026--1344095 Score: 88
Period size: 3 Copynumber: 23.7 Consensus size: 3
1344016 TTTTTATTCG
* * *
1344026 TAT TAT TAT TAT TAT T-T TAT CAA TAT TAT TAT TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1344073 TAT TAT TAA TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
1344096 CAGGCCATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1346954 original size:148 final size:149
Alignment explanation
Indices: 1346765--1347062 Score: 589
Period size: 148 Copynumber: 2.0 Consensus size: 149
1346755 GGATATTTTC
1346765 TTTCCATTAATTGGTACTAACCATTTTATTTTTTTTATTTTTTTTATCTATTTTGTAGATACATT
1 TTTCCATTAATTGGTACTAACCATTTTATTTTTTTTATTTTTTTTATCTATTTTGTAGATACATT
1346830 TTATTTTGTTCTAACTTGTTATAGTGATTTCTTTTGTTTGCATGATCATGACATGATTAGAAGGT
66 TTATTTTGTTCTAACTTGTTATAGTGATTTCTTTTGTTTGCATGATCATGACATGATTAGAAGGT
1346895 GTTGA-TTGTGAGTGGTCA
131 GTTGATTTGTGAGTGGTCA
1346913 TTTCCATTAATTGGTACTAACCATTTTATTTTTTTTATTTTTTTTATCTATTTTGTAGATACATT
1 TTTCCATTAATTGGTACTAACCATTTTATTTTTTTTATTTTTTTTATCTATTTTGTAGATACATT
1346978 TTATTTTGTTCTAACTTGTTATAGTGATTTCTTTTGTTTGCATGATCATGACATGATTAGAAGGT
66 TTATTTTGTTCTAACTTGTTATAGTGATTTCTTTTGTTTGCATGATCATGACATGATTAGAAGGT
1347043 GTTGATTTGTGAGTGGTCA
131 GTTGATTTGTGAGTGGTCA
1347062 T
1 T
1347063 CAAATTGAAA
Statistics
Matches: 149, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 135 0.91
149 14 0.09
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.53
Consensus pattern (149 bp):
TTTCCATTAATTGGTACTAACCATTTTATTTTTTTTATTTTTTTTATCTATTTTGTAGATACATT
TTATTTTGTTCTAACTTGTTATAGTGATTTCTTTTGTTTGCATGATCATGACATGATTAGAAGGT
GTTGATTTGTGAGTGGTCA
Found at i:1347600 original size:19 final size:19
Alignment explanation
Indices: 1347576--1347621 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1347566 AAGAGTTGTA
1347576 CGAGAAGCTACTTAAAGCG
1 CGAGAAGCTACTTAAAGCG
1347595 CGAGAAGCTACTTAAAGCG
1 CGAGAAGCTACTTAAAGCG
*
1347614 CAAGAAGC
1 CGAGAAGC
1347622 GGCTCCACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (19 bp):
CGAGAAGCTACTTAAAGCG
Found at i:1348712 original size:20 final size:18
Alignment explanation
Indices: 1348672--1348757 Score: 73
Period size: 19 Copynumber: 4.4 Consensus size: 18
1348662 ACACCTTTGC
1348672 TGCATTTGCATTTTCATTT
1 TGCATTTGCATTTT-ATTT
*
1348691 TGCATTTGTACTTTTATGTT
1 TGCATTTGCA-TTTTAT-TT
1348711 TGCATTTGCAGTTTTTATATT
1 TGCATTTGCA--TTTTAT-TT
* *
1348732 TTCATTTGTATTTTCATTT
1 TGCATTTGCATTTT-ATTT
*
1348751 TACATTT
1 TGCATTT
1348758 TGCTACATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
19 23 0.41
20 17 0.30
21 16 0.29
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (18 bp):
TGCATTTGCATTTTATTT
Found at i:1348759 original size:20 final size:21
Alignment explanation
Indices: 1348672--1348757 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 21
1348662 ACACCTTTGC
1348672 TGCATTTGCA-TTTTCAT-TT
1 TGCATTTGCACTTTTCATATT
* *
1348691 TGCATTTGTACTTTT-ATGTT
1 TGCATTTGCACTTTTCATATT
* *
1348711 TGCATTTGCAGTTTTTATATT
1 TGCATTTGCACTTTTCATATT
* *
1348732 TTCATTTGTA-TTTTCAT-TT
1 TGCATTTGCACTTTTCATATT
*
1348751 TACATTT
1 TGCATTT
1348758 TGCTACATTG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 19 0.34
20 25 0.45
21 12 0.21
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (21 bp):
TGCATTTGCACTTTTCATATT
Found at i:1350690 original size:23 final size:23
Alignment explanation
Indices: 1350664--1350724 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1350654 CTCGTATAAA
*
1350664 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1350687 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1350710 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1350725 TATAAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1351260 original size:2 final size:2
Alignment explanation
Indices: 1351248--1351328 Score: 132
Period size: 2 Copynumber: 41.5 Consensus size: 2
1351238 ACTTGATAAC
1351248 AT AT AT CAT AT AT AT A- AT AT AT AT A- 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
1351289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1351329 ATCGTCATAT
Statistics
Matches: 75, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.04
2 70 0.93
3 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1352324 original size:20 final size:20
Alignment explanation
Indices: 1352299--1352336 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1352289 TTCCCTTTGA
1352299 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
1352319 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
1352337 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:1352986 original size:15 final size:14
Alignment explanation
Indices: 1352962--1352993 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1352952 GGCTTCACGT
1352962 GAAAAAGAAGAAGA
1 GAAAAAGAAGAAGA
1352976 GAAAGAAGAAGAAGA
1 GAAA-AAGAAGAAGA
1352991 GAA
1 GAA
1352994 CTCTGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAGAAGA
Found at i:1356209 original size:52 final size:52
Alignment explanation
Indices: 1356147--1356250 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
1356137 TGAAAGCTCA
1356147 CATTAGTATGAAAATTTGGGACATTTTGAAGGCCCATTTTAGATAAGAATGG
1 CATTAGTATGAAAATTTGGGACATTTTGAAGGCCCATTTTAGATAAGAATGG
1356199 CATTAGTATGAAAATTTGGGACATTTTGAAGGCCCATTTTAGATAAGAATGG
1 CATTAGTATGAAAATTTGGGACATTTTGAAGGCCCATTTTAGATAAGAATGG
1356251 TCCATGTGGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (52 bp):
CATTAGTATGAAAATTTGGGACATTTTGAAGGCCCATTTTAGATAAGAATGG
Found at i:1357336 original size:77 final size:77
Alignment explanation
Indices: 1357244--1357397 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
1357234 TGAAGAAAAC
* *
1357244 CCTGGAAATGAATGATCAAGTGGAAAAAGACTGAGTTCGCCACTTTGAAGTCAAATGAAGATTGC
1 CCTGGAAATGAATGATCAAGTGGAAAAAGACCGAGTTCACCACTTTGAAGTCAAATGAAGATTGC
1357309 ATCCACATTCAT
66 ATCCACATTCAT
1357321 CCTGGAAATGAATGATCAAGTGGAAAAAGACCGAGTTCACCACTTTGAAGTCAAATGAAGATTGC
1 CCTGGAAATGAATGATCAAGTGGAAAAAGACCGAGTTCACCACTTTGAAGTCAAATGAAGATTGC
1357386 ATCCACATTCAT
66 ATCCACATTCAT
1357398 GCATTCATAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (77 bp):
CCTGGAAATGAATGATCAAGTGGAAAAAGACCGAGTTCACCACTTTGAAGTCAAATGAAGATTGC
ATCCACATTCAT
Found at i:1358119 original size:42 final size:42
Alignment explanation
Indices: 1358048--1358129 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1358038 TCTTGCTTTG
** *
1358048 TAAATCCTTCGGGTTATCAGTAATTCTTTCAAGCATGATGCT
1 TAAATCCTTCGGGTTATCAGTAAGACTTTCAAGCAAGATGCT
* *
1358090 TAAATCCTTCGGGTTATCTGTAAGACTTTCGAGCAAGATG
1 TAAATCCTTCGGGTTATCAGTAAGACTTTCAAGCAAGATG
1358130 ATAAGTTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (42 bp):
TAAATCCTTCGGGTTATCAGTAAGACTTTCAAGCAAGATGCT
Found at i:1358581 original size:123 final size:123
Alignment explanation
Indices: 1358400--1359335 Score: 1355
Period size: 123 Copynumber: 7.7 Consensus size: 123
1358390 CAGAATGTTT
** * * * * * *
1358400 TCAACATTTCCAGTGGAGAGTTCATAATAAGAAGAACTCGTCCGAAGAGGAATAAGAAGTTCAGA
1 TCAACATTTCCAGAAG-GAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATA
* * *
1358465 ATCTGAAGAACTTATTCAACCTTTTGTTTGATTCTATCGCAGAAGGAGATAGAGTAGCA
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
* * * *
1358524 TCAATATTTACAAAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
* *
1358589 TCTAAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCATAAGGAGATAGAGCAGCA
66 TCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
* * *
1358647 TCAACATTTACAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
*
1358712 TCTGAAGAATTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
66 TCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
1358770 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
* * * *
1358835 TTTGAAGAACTTATTCAACCTTATGCTCGATTCTATCACAGAAGGAGATAGAGCAACA
66 TCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
* * *
1358893 TCAACATTTCTAGAAGGAGTTTGTAATAAGAAGAACTCATCTGAAGATAAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
* * *
1358958 TCTGAATAACTTATTCAACCTTTTGCTCGATTTTATCGCAGAAGAAGATAGAGCAGCA
66 TCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
*
1359016 TCAACATTTCTAGAAGGAGTTCGTAAT---AAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
* * * * *
1359078 TCTGAAGAACTTATTCAACATTTTTCTTGATTCTATCGCAGAAGAAGATAGAGTAGCA
66 TCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
* * * * *
1359136 TCAATATTTCCATAATGAGTTCGTGAT---AAGAACTCATCTGAAGATAAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
* * *
1359198 TCTGAAGAACTTATTCAACCTTTTACTCGATTTTATCGCAGAAGAAGATAGAGCAGCA
66 TCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
* *
1359256 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCGTCTGAAGAGGAAGAA-AATGTTCATA
1 TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAA-GTTCATA
** *
1359320 ATAAGAAGAGCTTATT
65 ATCTGAAGAACTTATT
1359336 AGAGATTCCA
Statistics
Matches: 740, Mismatches: 68, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
120 218 0.29
122 2 0.00
123 509 0.69
124 11 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (123 bp):
TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
TCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCA
Found at i:1359592 original size:3 final size:3
Alignment explanation
Indices: 1359584--1359646 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
1359574 TTTTTATTCG
* * *
1359584 TAT TAT TAT TAT T-T TAT CAA TAT TAT TAT T-T TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1359630 TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1359647 CAGGCCGTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1359600 original size:20 final size:19
Alignment explanation
Indices: 1359575--1359631 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 19
1359565 TTATCACATT
1359575 TTTTATTCGTATTATTATTA
1 TTTTATTC-TATTATTATTA
*
1359595 TTTTA-TC-AATATTATTA
1 TTTTATTCTATTATTATTA
*
1359612 TTTTATTAATATTATTATTA
1 TTTTATT-CTATTATTATTA
1359632 ATATTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 14 0.45
18 1 0.03
19 2 0.06
20 14 0.45
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATTCTATTATTATTA
Found at i:1359609 original size:17 final size:17
Alignment explanation
Indices: 1359587--1359630 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
1359577 TTATTCGTAT
1359587 TATTATTATTTTATCAA
1 TATTATTATTTTATCAA
*
1359604 TATTATTATTTTATTAA
1 TATTATTATTTTATCAA
1359621 TATTATTATT
1 TATTATTATT
1359631 AATATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTATTTTATCAA
Found at i:1362633 original size:111 final size:111
Alignment explanation
Indices: 1362439--1362662 Score: 448
Period size: 111 Copynumber: 2.0 Consensus size: 111
1362429 GTTTCATATC
1362439 CTTAAGTTAGAGGAATTTTATTTTCTTCGAATAAAACAAGTGATGTCAATGGGTCGGGTTTCGTG
1 CTTAAGTTAGAGGAATTTTATTTTCTTCGAATAAAACAAGTGATGTCAATGGGTCGGGTTTCGTG
1362504 AGTACCCGTACTTGCACCAATTAGAGGTGAGCAAAACTCGACACAA
66 AGTACCCGTACTTGCACCAATTAGAGGTGAGCAAAACTCGACACAA
1362550 CTTAAGTTAGAGGAATTTTATTTTCTTCGAATAAAACAAGTGATGTCAATGGGTCGGGTTTCGTG
1 CTTAAGTTAGAGGAATTTTATTTTCTTCGAATAAAACAAGTGATGTCAATGGGTCGGGTTTCGTG
1362615 AGTACCCGTACTTGCACCAATTAGAGGTGAGCAAAACTCGACACAA
66 AGTACCCGTACTTGCACCAATTAGAGGTGAGCAAAACTCGACACAA
1362661 CT
1 CT
1362663 CAAAAAATTG
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (111 bp):
CTTAAGTTAGAGGAATTTTATTTTCTTCGAATAAAACAAGTGATGTCAATGGGTCGGGTTTCGTG
AGTACCCGTACTTGCACCAATTAGAGGTGAGCAAAACTCGACACAA
Found at i:1363287 original size:20 final size:20
Alignment explanation
Indices: 1363257--1363363 Score: 180
Period size: 20 Copynumber: 5.3 Consensus size: 20
1363247 TAAATATATT
1363257 TTATAATTTTATAATTTTAAA
1 TTAT-ATTTTATAATTTTAAA
1363278 TTATATTTTATAATTTTAAA
1 TTATATTTTATAATTTTAAA
1363298 TTATATTTTATAATTTTAAA
1 TTATATTTTATAATTTTAAA
1363318 TTATATTTTATAATTTTAAA
1 TTATATTTTATAATTTTAAA
*
1363338 TTATATTTTAT-ATATTAAA
1 TTATATTTTATAATTTTAAA
*
1363357 TAATATT
1 TTATATT
1363364 ACAATGTGAA
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
19 13 0.15
20 67 0.80
21 4 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATTTTATAATTTTAAA
Found at i:1363292 original size:13 final size:13
Alignment explanation
Indices: 1363244--1363332 Score: 74
Period size: 13 Copynumber: 6.6 Consensus size: 13
1363234 AAATATAATA
*
1363244 TTATAAATATATT
1 TTATAATTATATT
1363257 TTATAATTTTATAATT
1 TTATAA--TTAT-ATT
1363273 TTA-AATTATATT
1 TTATAATTATATT
* **
1363285 TTATAATTTTAAA
1 TTATAATTATATT
*
1363298 TTATATTTTATAATT
1 TTATA-ATTAT-ATT
1363313 TTA-AATTATATT
1 TTATAATTATATT
1363325 TTATAATT
1 TTATAATT
1363333 TTAAATTATA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
12 12 0.20
13 29 0.48
14 4 0.07
15 9 0.15
16 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATAATTATATT
Found at i:1363342 original size:13 final size:13
Alignment explanation
Indices: 1363230--1363332 Score: 61
Period size: 13 Copynumber: 7.6 Consensus size: 13
1363220 AAATATATTC
*
1363230 TTTAAAATATAAT
1 TTTAAATTATAAT
1363243 ATTATAAA-TAT-AT
1 -TT-TAAATTATAAT
1363256 TTTATAATTTTATAAT
1 TTTA-AA--TTATAAT
1363272 TTTAAATTAT-AT
1 TTTAAATTATAAT
*
1363284 TTTATAATTTTAAAT
1 TTTA-AATTAT-AAT
* **
1363299 TATATTTTATAAT
1 TTTAAATTATAAT
1363312 TTTAAATTAT-AT
1 TTTAAATTATAAT
1363324 TTTATAATT
1 TTTA-AATT
1363333 TTAAATTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.03
12 16 0.23
13 25 0.35
14 8 0.11
15 14 0.20
16 6 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTAAATTATAAT
Found at i:1363348 original size:7 final size:7
Alignment explanation
Indices: 1363251--1363350 Score: 63
Period size: 8 Copynumber: 14.7 Consensus size: 7
1363241 ATATTATAAA
1363251 TATATTT
1 TATATTT
1363258 TATAATTT
1 TAT-ATTT
1363266 TATAATTT
1 TAT-ATTT
*
1363274 TA-A-AT
1 TATATTT
1363279 TATATTT
1 TATATTT
1363286 TATAATTT
1 TAT-ATTT
*
1363294 TA-A-AT
1 TATATTT
1363299 TATATTT
1 TATATTT
1363306 TATAATTT
1 TAT-ATTT
*
1363314 TA-A-AT
1 TATATTT
1363319 TATATTT
1 TATATTT
1363326 TATAATTT
1 TAT-ATTT
*
1363334 TA-A-AT
1 TATATTT
1363339 TATATTT
1 TATATTT
1363346 TATAT
1 TATAT
1363351 ATTAAATAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
5 12 0.16
6 8 0.11
7 21 0.29
8 32 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TATATTT
Found at i:1366908 original size:2 final size:2
Alignment explanation
Indices: 1366889--1366922 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1366879 TTCTTTTGTT
* *
1366889 TA TA TA TC TA TA TC 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
1366923 CATGTTAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1368494 original size:315 final size:315
Alignment explanation
Indices: 1367908--1368539 Score: 962
Period size: 315 Copynumber: 2.0 Consensus size: 315
1367898 AGGGTTGCTC
* * *
1367908 AACTAGAGGAGAAACTAGCGCTGTCTGAAGAAGAAAAGTTGGAATTGCAGATGGCTTTAACCGAA
1 AACTAGAGGAGAAACTAGCGCTGACCGAAGAAGAAAAGTCGGAATTGCAGATGGCTTTAACCGAA
* *
1367973 TCTCAAAAACAGCTTAAAACATTGCAGAATCAACTAAGCGAAGCCGAGACAAGGTTCAAAGATGT
66 TCTCAAAAACAGCTTAAAACATTGCAGAACCAACTAAGCGAAGCCGAGACAAGGTTCAAAGATGA
* * *
1368038 GCAAACTCAACTAGCTCTTGATGACAACTCAAAGAAATCCGTAGAGGAGGAAGCAAAAGTTGCAA
131 GCAAACTCAACTAACTCTTGATGACAAATCAAAGAAAGCCGTAGAGGAGGAAGCAAAAGTTGCAA
* * * * * * * *
1368103 ACATGAATAGAGAAGTGGCGGTATCAAGACTTAGAGATGCTGAAATTGAAATAAAGACTTTAATT
196 ACATGAATAGACAAGAGGCAGAATCAAGACTTACAGAGGCAGAAACTGAAATAAAGACTTTAATT
* *
1368168 TCCAAAGTTACTTCGTTAGAAGAAGTGTTCAGAAAGGAACAAGCACTGTCAGCTG
261 TCCAAAGTTACTTCGTTAGAAGAAGTGTTCAAAAAGGAAAAAGCACTGTCAGCTG
* * * *
1368223 AACTAGGGGAGAAGCTAGCGCTGACCGAAGAA-AAAATGTCGGAATTGCAGATGGCTTTCACTGA
1 AACTAGAGGAGAAACTAGCGCTGACCGAAGAAGAAAA-GTCGGAATTGCAGATGGCTTTAACCGA
1368287 ATCTCAAAAACAGCTTAAAACATTGCAGAACCAACTAA-CTGAAGCCGAGACAAGGTTCAAAGAT
65 ATCTCAAAAACAGCTTAAAACATTGCAGAACCAACTAAGC-GAAGCCGAGACAAGGTTCAAAGAT
* * * *
1368351 GAGCAAACTCAATTAACTCTTGCTGACAAATCAAAGAAAGCCTTAGAGGAGGAAGTAAAAGTTGC
129 GAGCAAACTCAACTAACTCTTGATGACAAATCAAAGAAAGCCGTAGAGGAGGAAGCAAAAGTTGC
1368416 AAACATGAATAGACAAGAGGCAGAATCAAGACTTACAGAGGCAGAAACTGAAATAAAGACTTTAA
194 AAACATGAATAGACAAGAGGCAGAATCAAGACTTACAGAGGCAGAAACTGAAATAAAGACTTTAA
** * *
1368481 TTTCCAAAGTTACTTCGTTAGAAGATTTGTTCAAAAAGGAAAAAGCATTGTCCGCTG
259 TTTCCAAAGTTACTTCGTTAGAAGAAGTGTTCAAAAAGGAAAAAGCACTGTCAGCTG
1368538 AA
1 AA
1368540 AACATGAGTA
Statistics
Matches: 285, Mismatches: 30, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
314 5 0.02
315 280 0.98
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.21
Consensus pattern (315 bp):
AACTAGAGGAGAAACTAGCGCTGACCGAAGAAGAAAAGTCGGAATTGCAGATGGCTTTAACCGAA
TCTCAAAAACAGCTTAAAACATTGCAGAACCAACTAAGCGAAGCCGAGACAAGGTTCAAAGATGA
GCAAACTCAACTAACTCTTGATGACAAATCAAAGAAAGCCGTAGAGGAGGAAGCAAAAGTTGCAA
ACATGAATAGACAAGAGGCAGAATCAAGACTTACAGAGGCAGAAACTGAAATAAAGACTTTAATT
TCCAAAGTTACTTCGTTAGAAGAAGTGTTCAAAAAGGAAAAAGCACTGTCAGCTG
Found at i:1392932 original size:27 final size:27
Alignment explanation
Indices: 1392902--1392980 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
1392892 AATATAAATT
1392902 ATATTTTTCTATTAAAGTAGATGTCTA
1 ATATTTTTCTATTAAAGTAGATGTCTA
* *
1392929 ATATTTAT-T-TT--AG-AAAT-T-T-
1 ATATTTTTCTATTAAAGTAGATGTCTA
*
1392948 ATTTTTTTCTATTAAAGTAGATGTCTA
1 ATATTTTTCTATTAAAGTAGATGTCTA
1392975 ATATTT
1 ATATTT
1392981 ATTTCATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
19 6 0.16
20 2 0.05
21 3 0.08
22 3 0.08
23 4 0.11
24 3 0.08
25 3 0.08
26 2 0.05
27 12 0.32
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (27 bp):
ATATTTTTCTATTAAAGTAGATGTCTA
Found at i:1396707 original size:12 final size:12
Alignment explanation
Indices: 1396690--1396725 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1396680 ATTATTTCAC
1396690 TATCAATTATAT
1 TATCAATTATAT
1396702 TATCAATTATAT
1 TATCAATTATAT
*
1396714 TATCATTTATAT
1 TATCAATTATAT
1396726 CTCGTAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (12 bp):
TATCAATTATAT
Found at i:1397024 original size:23 final size:23
Alignment explanation
Indices: 1396998--1397044 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1396988 CACCACATCT
*
1396998 TGTATAAATGCACCGAAGTGCCA
1 TGTAGAAATGCACCGAAGTGCCA
*
1397021 TGTAGAATTGCACCGAAGTGCCA
1 TGTAGAAATGCACCGAAGTGCCA
1397044 T
1 T
1397045 ATAAGATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (23 bp):
TGTAGAAATGCACCGAAGTGCCA
Found at i:1397555 original size:2 final size:2
Alignment explanation
Indices: 1397548--1397603 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1397538 ACTCATAGTC
1397548 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
1397590 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1397604 CCTTTTACCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1398181 original size:18 final size:18
Alignment explanation
Indices: 1398160--1398194 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1398150 GTAATAAGAA
1398160 CAATTAAA-TAAATAAAAG
1 CAATTAAAGTAAA-AAAAG
1398178 CAATTAAAGTAAAAAAA
1 CAATTAAAGTAAAAAAA
1398195 AATAAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (18 bp):
CAATTAAAGTAAAAAAAG
Found at i:1411467 original size:2 final size:2
Alignment explanation
Indices: 1411458--1411516 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
1411448 ATTTAAAAAA
*
1411458 AT AT -T AT AT AC 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
1411499 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1411517 GTCTATCCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1411642 original size:80 final size:80
Alignment explanation
Indices: 1411554--1411707 Score: 281
Period size: 80 Copynumber: 1.9 Consensus size: 80
1411544 CCCCATTGGT
* *
1411554 CGACCGCCATTACCACCTATAGCTTGTAAACGATATAAGATAAATCGCGAGTTACTCCAGATTGA
1 CGACCGCCATTACCACCTACAGCTTGTAAACGATACAAGATAAATCGCGAGTTACTCCAGATTGA
1411619 CTTAGTTAACAATGG
66 CTTAGTTAACAATGG
*
1411634 CGACCGCCATTACCACCTACAGCTTGTAAACGATACAAGATAAATCGCGAGTTACTCGAGATTGA
1 CGACCGCCATTACCACCTACAGCTTGTAAACGATACAAGATAAATCGCGAGTTACTCCAGATTGA
1411699 CTTAGTTAA
66 CTTAGTTAA
1411708 AGTTAAGTCA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (80 bp):
CGACCGCCATTACCACCTACAGCTTGTAAACGATACAAGATAAATCGCGAGTTACTCCAGATTGA
CTTAGTTAACAATGG
Found at i:1414223 original size:2 final size:2
Alignment explanation
Indices: 1414216--1414264 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1414206 GCACAATTGA
1414216 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1414258 AG AG AG A
1 AG AG AG A
1414265 ACTTTTTGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1423099 original size:25 final size:27
Alignment explanation
Indices: 1423071--1423122 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1423061 GTTTATGTTG
*
1423071 TATCATATG-TG-TGACATGATTAATT
1 TATCATATGATGATGACATGAGTAATT
*
1423096 TATCATATGATGATTACATGAGTAATT
1 TATCATATGATGATGACATGAGTAATT
1423123 ATTTGCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 2 0.09
27 12 0.52
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (27 bp):
TATCATATGATGATGACATGAGTAATT
Found at i:1425734 original size:17 final size:18
Alignment explanation
Indices: 1425712--1425753 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1425702 TACCTATATA
1425712 CTTTTA-GTATCGATACC
1 CTTTTACGTATCGATACC
1425729 CTTTTACGGTATCGATACC
1 CTTTTAC-GTATCGATACC
1425748 CATTTT
1 C-TTTT
1425754 CGATTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
19 12 0.55
20 4 0.18
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (18 bp):
CTTTTACGTATCGATACC
Found at i:1427485 original size:25 final size:25
Alignment explanation
Indices: 1427466--1427537 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
1427456 ATATTTTTGA
1427466 TAAAATAATATAATAATATTATTAT
1 TAAAATAATATAATAATATTATTAT
* * *
1427491 TACAATAATATACTCA-ATTA-TAT
1 TAAAATAATATAATAATATTATTAT
* *
1427514 TATATTAATATATGATAATATTAT
1 TAAAATAATATA--ATAATATTAT
1427538 ATTCTTATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
23 13 0.36
24 4 0.11
25 15 0.42
26 4 0.11
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (25 bp):
TAAAATAATATAATAATATTATTAT
Found at i:1427820 original size:28 final size:33
Alignment explanation
Indices: 1427764--1427831 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 33
1427754 ATAATTTATC
**
1427764 ATATTTTTATTTTAATAGAATATACTAGAGTTA
1 ATATTTTTATTTTAATAGAATATACTAGAAATA
1427797 ATATTTTTA-TTT-ATA-AAT-TA-TAGAAATA
1 ATATTTTTATTTTAATAGAATATACTAGAAATA
1427825 ATATTTT
1 ATATTTT
1427832 AATAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 13 0.39
29 2 0.06
30 3 0.09
31 3 0.09
32 3 0.09
33 9 0.27
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (33 bp):
ATATTTTTATTTTAATAGAATATACTAGAAATA
Found at i:1428027 original size:123 final size:122
Alignment explanation
Indices: 1427891--1428134 Score: 393
Period size: 123 Copynumber: 2.0 Consensus size: 122
1427881 TAAAATAATA
1427891 ATATTAAGCTTTTATAATAATTAAAATTATTTATTATATTTTATATTTGCAATAAATAATTTCTA
1 ATATTAAGCTTTTATAATAATTAAAATTATTTATTATATTTTATATTTGCAATAAATAATTTCT-
* *
1427956 AAAAAAATTATCAACTAGTGAAAAATGGTTTACAC-ACAT-TTTTCAAACACCATAAAAC
65 AAAAAAATTATCAACTAGTG-AAAATGATTTACACAACATCTTCT-AAACACCATAAAAC
* * *
1428014 ATATTAAGTTTTTATAATAATTAATATTATTTATTATATTTTATATTTGTAATAAATAATTTCTA
1 ATATTAAGCTTTTATAATAATTAAAATTATTTATTATATTTTATATTTGCAATAAATAATTTCTA
*
1428079 AAAAAATTATCAACTAGTGAAAATGATTTACACAACATCTTCTAAATACCATAAAA
66 AAAAAATTATCAACTAGTGAAAATGATTTACACAACATCTTCTAAACACCATAAAA
1428135 TATTTTTCAA
Statistics
Matches: 113, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
121 13 0.12
122 36 0.32
123 64 0.57
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (122 bp):
ATATTAAGCTTTTATAATAATTAAAATTATTTATTATATTTTATATTTGCAATAAATAATTTCTA
AAAAAATTATCAACTAGTGAAAATGATTTACACAACATCTTCTAAACACCATAAAAC
Found at i:1428150 original size:14 final size:14
Alignment explanation
Indices: 1428131--1428160 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1428121 TAAATACCAT
1428131 AAAATATTTTTCAA
1 AAAATATTTTTCAA
*
1428145 AAAATATTTTTTAA
1 AAAATATTTTTCAA
1428159 AA
1 AA
1428161 GACGTAGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATATTTTTCAA
Found at i:1430434 original size:3 final size:3
Alignment explanation
Indices: 1430426--1430466 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
1430416 AGACAAAAAC
1430426 AAT AAT AAT AAT AAT AAAT AAAT AA- AAT AAT AA- AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AA
1430467 ATCAAATGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 24 0.69
4 7 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1430451 original size:8 final size:8
Alignment explanation
Indices: 1430426--1430467 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
1430416 AGACAAAAAC
1430426 AATAATAA
1 AATAATAA
1430434 TAATAAT-A
1 -AATAATAA
1430442 AATAAATAA
1 AAT-AATAA
1430451 AATAATAA
1 AATAATAA
1430459 AATAATAA
1 AATAATAA
1430467 A
1 A
1430468 TCAAATGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 3 0.10
8 18 0.58
9 10 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:1430500 original size:20 final size:21
Alignment explanation
Indices: 1430441--1430503 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
1430431 TAATAATAAT
*
1430441 AAATAAATAAAATAATAAA-A
1 AAATAAATAAAATAAAAAAGA
* *
1430461 TAATAAATCAAATGGGAAAAAAGA
1 AAATAAATAAAAT---AAAAAAGA
1430485 AAATAAAT-AAATAAAAAAG
1 AAATAAATAAAATAAAAAAG
1430504 CCAAAAGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 18 0.51
23 9 0.26
24 8 0.23
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (21 bp):
AAATAAATAAAATAAAAAAGA
Found at i:1430591 original size:16 final size:15
Alignment explanation
Indices: 1430560--1430615 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
1430550 AGGAAAATAC
1430560 AAATAAAAAAAGAAT
1 AAATAAAAAAAGAAT
1430575 AAATCAAAAGAAA-AAT
1 AAAT-AAAA-AAAGAAT
* *
1430591 AAGTAAAAATAGAA-
1 AAATAAAAAAAGAAT
1430605 AAATAGAAAAA
1 AAATA-AAAAA
1430616 TATATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 6 0.18
15 14 0.42
16 10 0.30
17 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (15 bp):
AAATAAAAAAAGAAT
Found at i:1430604 original size:18 final size:16
Alignment explanation
Indices: 1430583--1430617 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1430573 ATAAATCAAA
1430583 AGAAAAATAAGTAAAAAT
1 AGAAAAAT-AG-AAAAAT
1430601 AGAAAAATAGAAAAAT
1 AGAAAAATAGAAAAAT
1430617 A
1 A
1430618 TATATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 2 0.12
18 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
AGAAAAATAGAAAAAT
Found at i:1430614 original size:7 final size:8
Alignment explanation
Indices: 1430583--1430617 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
1430573 ATAAATCAAA
1430583 AGAAAAAT
1 AGAAAAAT
1430591 AAGTAAAAAT
1 -AG-AAAAAT
1430601 AGAAAAAT
1 AGAAAAAT
1430609 AGAAAAAT
1 AGAAAAAT
1430617 A
1 A
1430618 TATATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 15 0.60
9 4 0.16
10 6 0.24
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (8 bp):
AGAAAAAT
Found at i:1431840 original size:2 final size:2
Alignment explanation
Indices: 1431833--1431881 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
1431823 TAAAATAAAT
* * *
1431833 TA TA TA TA TA TA TA TA TA TA TA TT TA AA AA CTA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
1431875 TA TA TA T
1 TA TA TA T
1431882 TTCAAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1431879 original size:26 final size:28
Alignment explanation
Indices: 1431837--1431889 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
1431827 ATAAATTATA
1431837 TATATATATATATATATATTT-AAAAAC
1 TATATATATATATATATATTTCAAAAAC
1431864 TATATA-ATATATATATATTTCAAAAA
1 TATATATATATATATATATTTCAAAAA
1431890 AGTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
TATATATATATATATATATTTCAAAAAC
Found at i:1431905 original size:27 final size:27
Alignment explanation
Indices: 1431875--1432021 Score: 77
Period size: 27 Copynumber: 5.4 Consensus size: 27
1431865 ATATAATATA
1431875 TATATATT-TCAAAAAAGTTTTAAAAAC
1 TATATATTAT-AAAAAAGTTTTAAAAAC
* *
1431902 TATATATTATATATAAGTTTTAAAAAC
1 TATATATTATAAAAAAGTTTTAAAAAC
* * * * * *
1431929 TCAAAATGTTTTTAAAAAA-CTAT-ATAA-
1 T--ATAT-ATTATAAAAAAGTTTTAAAAAC
* * * *
1431956 TATATATTTTCAAAATGTTTTTTAAAAC
1 TATATATTATAAAAAAG-TTTTAAAAAC
* * * *
1431984 TATATAATATATAAATGTTTTCAAAAC
1 TATATATTATAAAAAAGTTTTAAAAAC
1432011 TATATATTATA
1 TATATATTATA
1432022 TCTATTTTAA
Statistics
Matches: 89, Mismatches: 23, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
24 8 0.09
25 3 0.03
26 2 0.02
27 47 0.53
28 17 0.19
29 5 0.06
30 7 0.08
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (27 bp):
TATATATTATAAAAAAGTTTTAAAAAC
Found at i:1431990 original size:35 final size:36
Alignment explanation
Indices: 1431929--1432061 Score: 124
Period size: 35 Copynumber: 3.9 Consensus size: 36
1431919 TTTTAAAAAC
1431929 TCAAAATGTTTTTAAAAAACTATATAATATATATTT
1 TCAAAATGTTTTTAAAAAACTATATAATATATATTT
*
1431965 TCAAAATGTTTTT-TAAAACTATAT-A-ATATA---
1 TCAAAATGTTTTTAAAAAACTATATAATATATATTT
* * * *
1431995 T--AAATGTTTTCAAAACTA-TATATTATATCTATTT
1 TCAAAATGTTTTTAAAA-AACTATATAATATATATTT
* *
1432029 TAAAAATG-TTTTCAAAAACTATATAATATATAT
1 TCAAAATGTTTTTAAAAAACTATATAATATATAT
1432062 ATATTCGAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
28 9 0.12
29 7 0.09
30 3 0.04
31 4 0.05
33 5 0.06
34 3 0.04
35 28 0.36
36 18 0.23
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
TCAAAATGTTTTTAAAAAACTATATAATATATATTT
Found at i:1431995 original size:82 final size:85
Alignment explanation
Indices: 1431858--1432011 Score: 219
Period size: 82 Copynumber: 1.8 Consensus size: 85
1431848 ATATATATTT
*
1431858 AAAAACTATATAATATATATATATTTCAAAAAAGTTTTAAAAACTATATATTATATATAA-GTTT
1 AAAAACTATATAATATATATATATTTCAAAAAAGTTTTAAAAACTATATAATATATA-AATGTTT
1431922 TAAAAACTCAAAATGTTTTTA
65 TAAAAACTCAAAATGTTTTTA
* *
1431943 AAAAACTATAT-A-ATATATAT-TTTC-AAAATGTTTTTTAAAACTATATAATATATAAATGTTT
1 AAAAACTATATAATATATATATATTTCAAAAAAG-TTTTAAAAACTATATAATATATAAATGTTT
*
1432004 TCAAAACT
65 TAAAAACT
1432012 ATATATTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
81 7 0.11
82 36 0.57
83 8 0.13
84 1 0.02
85 11 0.17
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (85 bp):
AAAAACTATATAATATATATATATTTCAAAAAAGTTTTAAAAACTATATAATATATAAATGTTTT
AAAAACTCAAAATGTTTTTA
Found at i:1432022 original size:27 final size:28
Alignment explanation
Indices: 1431968--1432022 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1431958 TATATTTTCA
*
1431968 AAATGTTTTTTAAAACTATATAATATAT
1 AAATGTTTTTCAAAACTATATAATATAT
*
1431996 AAATG-TTTTCAAAACTATATATTATAT
1 AAATGTTTTTCAAAACTATATAATATAT
1432023 CTATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (28 bp):
AAATGTTTTTCAAAACTATATAATATAT
Found at i:1432029 original size:25 final size:27
Alignment explanation
Indices: 1431974--1432034 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
1431964 TTCAAAATGT
* *
1431974 TTTTTAAAACTATATAATATATAAATG
1 TTTTAAAAACTATATAATATATAAATA
* **
1432001 TTTTCAAAACTATAT-AT-TATATCTA
1 TTTTAAAAACTATATAATATATAAATA
1432026 TTTTAAAAA
1 TTTTAAAAA
1432035 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 13 0.45
26 2 0.07
27 14 0.48
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (27 bp):
TTTTAAAAACTATATAATATATAAATA
Found at i:1432079 original size:39 final size:38
Alignment explanation
Indices: 1432000--1432121 Score: 101
Period size: 39 Copynumber: 3.3 Consensus size: 38
1431990 ATATATAAAT
* ** *
1432000 GTTTTCAAAACTATAT-AT-TATATCTATTTTAAAAAT
1 GTTTTCAAAACTATATAATATATATATATTCGAAAAAC
*
1432036 GTTTTCAAAAACTATATAATATATATATATTCGAAAACC
1 GTTTTC-AAAACTATATAATATATATATATTCGAAAAAC
* * *
1432075 GTTTTCTGAAAATTATAT-AT-TATATTTTTTC-AAAAAC
1 GTTTTC--AAAACTATATAATATATATATATTCGAAAAAC
*
1432112 ATTTTCAAAA
1 GTTTTCAAAA
1432122 ATTATACTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
35 4 0.06
36 6 0.08
37 20 0.28
38 11 0.15
39 21 0.30
40 9 0.13
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (38 bp):
GTTTTCAAAACTATATAATATATATATATTCGAAAAAC
Found at i:1432817 original size:84 final size:85
Alignment explanation
Indices: 1432701--1433571 Score: 337
Period size: 84 Copynumber: 10.3 Consensus size: 85
1432691 ATGCGTCACC
* ** * **
1432701 GAGCTGAATGGAATCGAACTC-AATAATTTTTGTTAACAGATAGCTTTTATCGACTTAAACTATG
1 GAGCTGAATGTAATCGAACTCGAA-GGTATTTGTTAACAGATAGCCCTTATCGACTTAAACTATG
*
1432765 TTGTAAATCT-GACATGCCCTT
65 CTGTAAAT-TGGACATGCCCTT
* * * * * * **
1432786 GAGTTGAATG-AATCGAACTCGAAGGTATTTGTTGACATATAGCCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTATTTGTTAACAGATAGCCCTTATCGACTTAAACTATGC
* *
1432850 TGTAAATTGGATATGCCTTT
66 TGTAAATTGGACATGCCCTT
* ** * * * * * *
1432870 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTGAGCTATA
1 GAGCTGAATGTAATCGAACTCGAAGGT-ATTTGTTAACAGATAGCCCTTATCGACTTAAACTATG
* * ** *
1432935 CTGCAAA--CGATGTGCCTTT
65 CTGTAAATTGGACATGCCCTT
* * * ** * * * * * *
1432954 GAGCTGAGTGTACTCGAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGTCATGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGT-ATTTGTTAACAGATAGCCCTTATCGACTTAAACTATG
* * *
1433019 CTGCAAATT--ATATGCCTTT
65 CTGTAAATTGGACATGCCCTT
* * * * * * * * **
1433038 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTATTTGTTAACAGATAGCCCTTATCGACTTAAACTATGC
** *
1433103 TGTAAATTGGATGTGCCTTT
66 TGTAAATTGGACATGCCCTT
* * * *** * * * * *
1433123 GAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGT-ATTTGTTAACAGATAGCCCTTATCGACTTAAACTATG
* * ** *
1433188 TTGCAAA-T-GATGTGCCTTT
65 CTGTAAATTGGACATGCCCTT
* * * * * * * * * * **
1433207 GAGCTGAGTGTAATTGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTTGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTATTTGTTAACAGATAGCCCTTATCGACTTAAACTATGC
** *
1433272 TGTAAATTGGATGTGCCATT
66 TGTAAATTGGACATGCCCTT
* * * ** * * ** * * * * * *
1433292 AAGCTGAGTGTAATCAAACTTTAAGGTCTTTTATTGGCATATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGT-ATTTGTTAACAGATAGCCCTTATCGACTTAAACTATG
* * ** *
1433357 CTGGAAA--CGATGTGCCTTT
65 CTGTAAATTGGACATGCCCTT
* * * ** * * * *
1433376 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGT-ATTTGTTAACAGATAGCCCTTATCGACTTAAACTATG
* * ** *
1433441 TTGCAAA-T-GATGTGCCTTT
65 CTGTAAATTGGACATGCCCTT
* * * * * * * * ****
1433460 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGTGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTATTTGTTAACAGATAGCCCTTATCGACTTAAACTATGC
** *
1433525 TGTAAATTGGATGTGCCTTT
66 TGTAAATTGGACATGCCCTT
*
1433545 GAGCTGAGTGTAATCGAACTCGAAGGT
1 GAGCTGAATGTAATCGAACTCGAAGGT
1433572 CTTTTGTTGA
Statistics
Matches: 673, Mismatches: 98, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
83 110 0.16
84 322 0.48
85 133 0.20
86 108 0.16
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTATTTGTTAACAGATAGCCCTTATCGACTTAAACTATGC
TGTAAATTGGACATGCCCTT
Found at i:1432980 original size:169 final size:170
Alignment explanation
Indices: 1432779--1433581 Score: 1041
Period size: 169 Copynumber: 4.8 Consensus size: 170
1432769 AAATCTGACA
* * * * * * *
1432779 TGCCCTTGAGTTGAATG-AATCGAACTCGAAGGT-ATTTGTTGACATATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* * * * *
1432842 AGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGG
66 AGCTATGCTGCAAATT-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGA
* * * *
1432907 CAGATAACCCTTCTTGACTTGAGCTATACTGCAAA-CGATG
130 CAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGGATG
* * * *
1432947 TGCCTTTGAGCTGAGTGTACTCGAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGTCATG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* *
1433012 AGCTATGCTGCAAATT-ATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGAC
66 AGCTATGCTGCAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGAC
* *
1433075 AGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATG
131 AGATAACCCTTCTCGCCTTGAGCTATGCTGCAAA-TGGATG
* *
1433116 TGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* * *
1433181 AGCTATGTTGCAAA-TGATGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TTGGTTGAC
66 AGCTATGCTGCAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGAC
* * *
1433244 AGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATTGGATG
131 AGATAACCCTTCTCGCCTTGAGCTATGCTGCAAA-TGGATG
* * * ** * *
1433285 TGCCATTAAGCTGAGTGTAATCAAACTTTAAGGTCTTTTATTGGCATATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* * * *
1433350 AGCTATGCTGGAAA-CGATGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGC
66 AGCTATGCTGCAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGAC
* *
1433414 AGATAACCCTTATCGCCTTGAGCTATGTTGCAAAT-GATG
131 AGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGGATG
* * *
1433453 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAAATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* * *
1433517 TGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGA
66 AGCTATGCTGCAAATT-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGA
1433582 ATATGCTTTT
Statistics
Matches: 560, Mismatches: 67, Indels: 15
0.87 0.10 0.02
Matches are distributed among these distances:
167 72 0.13
168 86 0.15
169 328 0.59
170 74 0.13
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (170 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
AGCTATGCTGCAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGAC
AGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGGATG
Found at i:1433154 original size:253 final size:253
Alignment explanation
Indices: 1432761--1433585 Score: 1165
Period size: 253 Copynumber: 3.3 Consensus size: 253
1432751 CGACTTAAAC
* * * * * *
1432761 TATGTTGTAAATCTGACATGCCCTTGAGTTGAATG-AATCGAACTCGAAGGTATTTGTTGACATA
1 TATGCTGTAAAT-TGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACATA
* * *
1432825 TAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCGAACT
65 TAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACT
* * ** *
1432890 CGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTGAGCTATACTGCAAACGATGTGCCTTTG
130 CGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGTTGCAAATGATGTGCCTTTG
* * * * * * *
1432955 AGCTGAGTGTACTCGAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGTCATGAGC
195 AGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGT
* * *
1433015 TATGCTGCAAATT-ATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGAT
1 TATGCTGTAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACATAT
1433079 AACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
66 AACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
1433144 GAATGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
131 GAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
* *
1433209 GCTGAGTGTAATTGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTTGCCTTGAGT
196 GCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGT
* * * * ** * *
1433267 TATGCTGTAAATTGGATGTGCCATTAAGCTGAGTGTAATCAAACTTTAAGGTCTTTTATTGGCAT
1 TATGCTGTAAATT-GATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAT
* * * *
1433332 ATAACCCTTCTCGCCTTGAGCTATGCTGGAAA--CGATGTGCCTTTAAGCTGAGTGTAATCGAAC
64 ATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
1433395 TCGAAGGTCTTTTGTTGGCAGATAACCCTTATCGCCTTGAGCTATGTTGCAAATGATGTGCCTTT
129 TCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGTTGCAAATGATGTGCCTTT
* *
1433460 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGTGT
194 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGT
*
1433520 TATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGA-AT
1 TATGCTGTAAATT-GATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAT
1433584 AT
64 AT
1433586 GCTTTTGAAT
Statistics
Matches: 510, Mismatches: 57, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
252 57 0.11
253 374 0.73
254 42 0.08
255 37 0.07
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (253 bp):
TATGCTGTAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACATAT
AACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
GCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGT
Found at i:1433485 original size:422 final size:422
Alignment explanation
Indices: 1432800--1433580 Score: 1292
Period size: 422 Copynumber: 1.9 Consensus size: 422
1432790 TGAATGAATC
* * *
1432800 GAACTCGAAGGTATTTGTTGACATATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATG
1 GAACTCGAAGGTATTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATG
* * * * *
1432865 CCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTGAG
66 CCATTAAGCTGAATGTAATCAAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGACTTGAG
* *
1432930 CTATACTGCAAACGATGTGCCTTTGAGCTGAGTGTACTCGAACTCGAAGGTCTTTTGTTGGCAGA
131 CTATACTGCAAACGATGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGA
* * * *
1432995 TATCCCTTCTCGTCATGAGCTATGCTGCAAATTATATGCCTTTGAGCTGAGTGTAATCGAACTCG
196 TAACCCTTATCGCCATGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCG
*
1433060 AAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGA
261 AAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGA
*
1433125 GCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTATGTT
326 GCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTATGTT
1433190 GCAAATGATGTGCCTTTGAGCTGAGTGTAATT
391 GCAAATGATGTGCCTTTGAGCTGAGTGTAATT
* * *
1433222 GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATTGGATGTG
1 GAACTCGAAGGTATTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATG
* ** * *
1433287 CCATTAAGCTGAGTGTAATCAAACTTTAAGGTCTTTTATTGGCATATAACCCTTCTCGCCTTGAG
66 CCATTAAGCTGAATGTAATCAAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGACTTGAG
* *
1433352 CTATGCTGGAAACGATGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGA
131 CTATACTGCAAACGATGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGA
* * *
1433417 TAACCCTTATCGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCG
196 TAACCCTTATCGCCATGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCG
*
1433482 AAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGTGTTATGCTGTAAATTGGATGTGCCTTTGA
261 AAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGA
1433547 GCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
326 GCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
1433581 AATATGCTTT
Statistics
Matches: 329, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
422 329 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (422 bp):
GAACTCGAAGGTATTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATG
CCATTAAGCTGAATGTAATCAAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGACTTGAG
CTATACTGCAAACGATGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGA
TAACCCTTATCGCCATGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCG
AAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGA
GCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTATGTT
GCAAATGATGTGCCTTTGAGCTGAGTGTAATT
Found at i:1437362 original size:23 final size:23
Alignment explanation
Indices: 1437294--1437362 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1437284 ATATCTTATA
*
1437294 TGGCACTTCGGTGCATTTCTACA
1 TGGCACTTCGGTGCATTTCTACG
* * * *
1437317 CGGCACTACAGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
1437340 TGGCACTTCGGTACATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1437363 AGTTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1437673 original size:16 final size:16
Alignment explanation
Indices: 1437645--1437680 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1437635 GACCATAGGA
1437645 ATAAAGAGATAAGAGAT
1 ATAAAGAGATAAGAG-T
1437662 ATAAAG-GATAAGAGT
1 ATAAAGAGATAAGAGT
1437677 ATAA
1 ATAA
1437681 GAGTATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 8 0.42
17 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.22, T:0.19
Consensus pattern (16 bp):
ATAAAGAGATAAGAGT
Found at i:1442383 original size:23 final size:23
Alignment explanation
Indices: 1442315--1442383 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1442305 ACATCTTATA
*
1442315 TGGCACTTCT-GTCCATTTCTACG
1 TGGCACTT-TGGTGCATTTCTACG
** *
1442338 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTTGGTGCATTTCTACG
*
1442361 TGGCACTTTGGTGCATTTATACG
1 TGGCACTTTGGTGCATTTCTACG
1442384 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (23 bp):
TGGCACTTTGGTGCATTTCTACG
Found at i:1446386 original size:12 final size:12
Alignment explanation
Indices: 1446369--1446393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1446359 CGAAAAGTGA
1446369 AAAATTTAAATT
1 AAAATTTAAATT
1446381 AAAATTTAAATT
1 AAAATTTAAATT
1446393 A
1 A
1446394 CTCGATTCGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:1446780 original size:29 final size:32
Alignment explanation
Indices: 1446720--1446787 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 32
1446710 ATAATGATAA
1446720 TAAAAAATAAATAAATGAAGATAAATAAAATT
1 TAAAAAATAAATAAATGAAGATAAATAAAATT
1446752 TAAAAAAT-AAT-AAT-AATGA-AAATAAAATT
1 TAAAAAATAAATAAATGAA-GATAAATAAAATT
1446781 TAAAAAA
1 TAAAAAA
1446788 CCAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 19 0.54
30 5 0.14
31 3 0.09
32 8 0.23
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (32 bp):
TAAAAAATAAATAAATGAAGATAAATAAAATT
Found at i:1448090 original size:38 final size:36
Alignment explanation
Indices: 1448036--1448216 Score: 202
Period size: 38 Copynumber: 4.8 Consensus size: 36
1448026 TTCAAAAAAA
* * *
1448036 AAAAAGTTTTACAAACTATATATTATATACATTTTC
1 AAAATGTTTTAAAAACTATATAATATATACATTTTC
*
1448072 AAAATGTTTTTAAAAAACTATATAATATATATATTTTC
1 AAAATG-TTTT-AAAAACTATATAATATATACATTTTC
*
1448110 AAAATGTTTTTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAATG---TTTTAAAAACTATATAATATATACA--TTTTC
* * *
1448151 AAAATGTTTTCAAAACTATATATTATAT-CTATTTTA
1 AAAATGTTTTAAAAACTATATAATATATAC-ATTTTC
1448187 AAAATGTTTTCAAAAACTATATAATATATA
1 AAAATGTTTT-AAAAACTATATAATATATA
1448217 TTTTTGAAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
36 19 0.15
37 20 0.16
38 50 0.40
39 20 0.16
40 5 0.04
41 11 0.09
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATAATATATACATTTTC
Found at i:1448157 original size:11 final size:11
Alignment explanation
Indices: 1448141--1448165 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1448131 TATAATATAT
1448141 AAATGTTTTCA
1 AAATGTTTTCA
1448152 AAATGTTTTCA
1 AAATGTTTTCA
1448163 AAA
1 AAA
1448166 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:1448166 original size:77 final size:75
Alignment explanation
Indices: 1448042--1448216 Score: 228
Period size: 77 Copynumber: 2.3 Consensus size: 75
1448032 AAAAAAAAAG
* * *
1448042 TTTTACAAACTATATATTATATACATTTTCAAAATGTTTTTAAAAAACTATATAATATATATATT
1 TTTTAAAAACTATATAATATATAAATTTTCAAAATGTTTTTAAAAAACTATATAATATATATATT
*
1448107 TTCAAAATGTTT
66 TTAAAAATG--T
* * *
1448119 TTTTAAAAACTATATAATATATAAATGTTTTCAAAATG-TTTT-CAAAACTATATATTATATCTA
1 TTTTAAAAACTATATAATATATAAA--TTTTCAAAATGTTTTTAAAAAACTATATAATATATATA
1448182 TTTTAAAAATGT
64 TTTTAAAAATGT
*
1448194 TTTCAAAAACTATATAATATATA
1 TTTTAAAAACTATATAATATATA
1448217 TTTTTGAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
75 23 0.26
77 50 0.57
78 4 0.05
79 11 0.12
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (75 bp):
TTTTAAAAACTATATAATATATAAATTTTCAAAATGTTTTTAAAAAACTATATAATATATATATT
TTAAAAATGT
Found at i:1449025 original size:19 final size:17
Alignment explanation
Indices: 1448984--1449030 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
1448974 GCATATGAGT
1448984 TTTTAATATTTTTAAAA
1 TTTTAATATTTTTAAAA
1449001 TTTTAATAATTTCTT-AAA
1 TTTTAAT-ATTT-TTAAAA
1449019 TTATTAAT-TTTT
1 TT-TTAATATTTT
1449031 ACTTAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 10 0.37
18 9 0.33
19 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATATTTTTAAAA
Found at i:1449427 original size:42 final size:42
Alignment explanation
Indices: 1449380--1449495 Score: 196
Period size: 42 Copynumber: 2.8 Consensus size: 42
1449370 TCCGAAATTT
*
1449380 CGTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTCC
*
1449422 CGTGTTTGTTTCACGTAATTCATTTTTCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTCC
* *
1449464 AGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTTCGGAA
1449496 CGTAATTCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.47
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTCC
Found at i:1449729 original size:22 final size:22
Alignment explanation
Indices: 1449704--1449777 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
1449694 ATATATTTAT
1449704 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* *
1449726 TAATATTTTTAATATTATATAAAA
1 TAATATTTATAATA--ATATAATA
*
1449750 TAATCAATTATATTATAATAATAATA
1 TAAT--ATT-TATAATAAT-ATAATA
1449776 TA
1 TA
1449778 TGATATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 13 0.32
24 11 0.27
25 2 0.05
26 10 0.24
27 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:1449739 original size:31 final size:31
Alignment explanation
Indices: 1449696--1449839 Score: 96
Period size: 31 Copynumber: 4.8 Consensus size: 31
1449686 TATTTAAAAT
1449696 ATATTTATTAATATTTATAATAATATAATATA
1 ATATTT-TTAATATTTATAATAATATAATATA
1449728 ATATTTTTAATATTATATAA-AATAATCAAT-T-
1 ATATTTTTAATATT-TATAATAAT-AT-AATATA
* * *
1449759 ATA-TTATAATA---ATAAT-ATATGATATT
1 ATATTTTTAATATTTATAATAATATAATATA
1449785 ATATTTTT-AT-TTTAATAAT-ATATAATA-A
1 ATATTTTTAATATTT-ATAATAATATAATATA
*
1449813 ATTTTTTTATATATTTAATAATGAATA
1 ATATTTTTA-ATATTT-ATAAT-AATA
1449840 ATTTTATTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
24 2 0.02
25 3 0.03
26 11 0.12
27 3 0.03
28 7 0.08
29 12 0.13
30 9 0.10
31 23 0.26
32 14 0.16
33 6 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
ATATTTTTAATATTTATAATAATATAATATA
Found at i:1449752 original size:34 final size:34
Alignment explanation
Indices: 1449676--1449753 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 34
1449666 CAAAATATTA
*
1449676 ATTAT-TAAAAT-ATTTAAAATATATTTATTAAT
1 ATTATATAAAATAATATAAAATATATTTATTAAT
*
1449708 ATT-TAT--AATAATATAATATAATATTT-TTAAT
1 ATTATATAAAATAATATAAAAT-ATATTTATTAAT
1449739 ATTATATAAAATAAT
1 ATTATATAAAATAAT
1449754 CAATTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 3 0.08
31 16 0.42
32 13 0.34
34 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTATATAAAATAATATAAAATATATTTATTAAT
Found at i:1449789 original size:26 final size:22
Alignment explanation
Indices: 1449737--1449788 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1449727 AATATTTTTA
1449737 ATATTATATAAAATAATCAATT
1 ATATTATATAAAATAATCAATT
* *
1449759 ATATTATA-ATAATAAT-ATATG
1 ATATTATATAAAATAATCA-ATT
1449780 ATATTATAT
1 ATATTATAT
1449789 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 17 0.65
22 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTATATAAAATAATCAATT
Found at i:1449867 original size:24 final size:26
Alignment explanation
Indices: 1449806--1449869 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 26
1449796 TTAATAATAT
1449806 ATAATAA-ATTTT-TTTATATATTTA
1 ATAATAATATTTTATTTATATATTTA
1449830 ATAATGAATAATTTTATTTATATATTT-
1 ATAAT-AAT-ATTTTATTTATATATTTA
1449857 A-AATAATATTTTA
1 ATAATAATATTTTA
1449870 GTAAAGATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
24 11 0.31
25 5 0.14
26 3 0.08
27 6 0.17
28 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
ATAATAATATTTTATTTATATATTTA
Done.