Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_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: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 7 of 12
Found at i:1672298 original size:2 final size:2
Alignment explanation
Indices: 1672291--1672318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1672281 CTTGAAGACG
1672291 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
1672319 GAAAGTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1675876 original size:17 final size:17
Alignment explanation
Indices: 1675854--1675886 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1675844 AATGATAGGC
*
1675854 AAAAAAAGGACTTCTTA
1 AAAAAAAAGACTTCTTA
1675871 AAAAAAAAGACTTCTT
1 AAAAAAAAGACTTCTT
1675887 CTTCTTCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAAAAAGACTTCTTA
Found at i:1679762 original size:26 final size:26
Alignment explanation
Indices: 1679650--1679763 Score: 210
Period size: 26 Copynumber: 4.4 Consensus size: 26
1679640 TTCACTAAGA
*
1679650 CTAGCGCCGAAAGCAATGCAAGAGTT
1 CTAGCGCCTAAAGCAATGCAAGAGTT
*
1679676 CTAGCGCCGAAAGCAATGCAAGAGTT
1 CTAGCGCCTAAAGCAATGCAAGAGTT
1679702 CTAGCGCCTAAAGCAATGCAAGAGTT
1 CTAGCGCCTAAAGCAATGCAAGAGTT
1679728 CTAGCGCCTAAAGCAATGCAAGAGTT
1 CTAGCGCCTAAAGCAATGCAAGAGTT
1679754 CTAGCGCCTA
1 CTAGCGCCTA
1679764 GACACACTTA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 87 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.18
Consensus pattern (26 bp):
CTAGCGCCTAAAGCAATGCAAGAGTT
Found at i:1688705 original size:182 final size:182
Alignment explanation
Indices: 1688302--1689155 Score: 1182
Period size: 182 Copynumber: 4.7 Consensus size: 182
1688292 TGTTGGTTTA
* * * *
1688302 TGTCGATACTTTATAAAAACTGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACC
* * * * *
1688367 GGTCTCGAAAAGACAAAACTGGTACAGCG-GTACTGGATATATTGAAAGTGTCGATACTTTAATA
65 GGTCTCTAAAAGACAAAACCGGTATAGAGCG-ACCGGATATATTGAAAGTGTCGATACTTTAATA
*
1688431 TAAGTAT---CACTTTGTGAATTTAAAAGAGAAACTGTTTTAGCGCCTATAAAG
129 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
** * *
1688482 TGTCGATGTTTTATAACAATGTATCGTTCCACAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * *
1688547 GTCTCTAAAAGATAAAACCGATATAGAGCGATCGGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAAGACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
1688612 AGTATCGACACTTTGTGAATTTAAAAGAGAAAC-GATTTTAGAGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAG-TTTTAGCGCCTATAAAG
* **
1688664 TGTCGATACTTTATAACAATGTATTGATCCACAACGATATAACAAGTAAAAATATGACAAAATTG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * *
1688729 GTCTCTAAATGACAAAATCGGTATAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAAGACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
* *
1688794 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATACAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * * *
1688846 TGTCGATACTTTATAACAATGTATCGATTCTCAACGATATAACAAGTAAAAATATGATAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * *
1688911 GTCTCTAAAGGACAAAATCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAAGACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
* * * * * *
1688976 AGTATCGACACTTTGTGAATTTAAAAGATAAGCAGCTTTAGCGTCAATAAAA
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * *
1689028 TGTCGATACTTTATAAAAATGTATCGATCAATAACGATATAACATA-TAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACA-AGTAAAAATATGACAAAACC
* * * * * *
1689092 AGTCTC-AAAATGAAAAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATA
65 GGTCTCTAAAA-GACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATA
1689156 AGTATGCGTA
Statistics
Matches: 605, Mismatches: 61, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
179 103 0.17
180 17 0.03
181 4 0.01
182 479 0.79
183 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (182 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
GTCTCTAAAAGACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
Found at i:1691412 original size:17 final size:18
Alignment explanation
Indices: 1691390--1691425 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1691380 GAAGATTATT
*
1691390 GGCAATG-AGGTAGAGGA
1 GGCAATGAAGGCAGAGGA
1691407 GGCAATGAAGGCAGAGGA
1 GGCAATGAAGGCAGAGGA
1691425 G
1 G
1691426 AAGGAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.36, C:0.08, G:0.47, T:0.08
Consensus pattern (18 bp):
GGCAATGAAGGCAGAGGA
Found at i:1691714 original size:198 final size:198
Alignment explanation
Indices: 1691446--1691968 Score: 643
Period size: 198 Copynumber: 2.7 Consensus size: 198
1691436 AGATGGTTGT
* * *
1691446 ATTTGTGTCGATATTTATTGTCCGTAATGAATGCCCAAATGAGGTGCACACATAAAGTGTCGATA
1 ATTTGTGTCGATACTT-TTGTCCATAATGAATGCCCAAACGAGGTGCACACATAAAGTGTCGATA
* *
1691511 CATTTATTAAAAGTATCGATCCCAATAAA-ATCG-AACCTGATAATTATATTGTAATATGTAAAT
65 CATTTATTAAAAGTATCGATCCCAA-AAACATCGAAACC-GATAATTATAATGTAATAGGTAAAT
* * **
1691574 TTACAATGTAACATATATAAATATACCGGTTTTATGAGAAAATAGGTCA-GCATAAAGTATCGA-
128 TTACAATGTAACAGATAGAAATATACCGG-TTTATGAGAAAATA-GT-ATAAATAAAGTATCGAT
1691637 ACTTGTTAA
190 ACTTGTTAA
* *
1691646 ATTTGTGTTGATACATTTTGTCCATAATGAATG-CCAAACG-GGTGCACGCATAAAGTGTCGATA
1 ATTTGTGTCGATAC-TTTTGTCCATAATGAATGCCCAAACGAGGTGCACACATAAAGTGTCGATA
* * * *
1691709 CATTTATTAAAAGTGTCGATCTCAAAAACATCGAAACCGATAATTATAATATGATAGGTAAATTT
65 CATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTT
* * * * *
1691774 ACAATGTACCCGATAGAAATATACTGGTTTATGAGAAAATAGTATAAATAATGTATCGATACTTT
130 ACAATGTAACAGATAGAAATATACCGGTTTATGAGAAAATAGTATAAATAAAGTATCGATACTTG
1691839 TTAA
195 TTAA
* * * * *
1691843 GTTTGTGTCGATGCTTTT-TCCAGAATGAATGTCC-AACGAGGTGCACACATAAAGTATCGATAC
1 ATTTGTGTCGATACTTTTGTCCATAATGAATGCCCAAACGAGGTGCACACATAAAGTGTCGATAC
** * *
1691906 ATTTCA--AATTGTATCGATCCAAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTT
66 ATTT-ATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTT
1691969 GTAATTTTAC
Statistics
Matches: 281, Mismatches: 34, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
195 66 0.23
196 45 0.16
197 37 0.13
198 94 0.33
199 10 0.04
200 27 0.10
201 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (198 bp):
ATTTGTGTCGATACTTTTGTCCATAATGAATGCCCAAACGAGGTGCACACATAAAGTGTCGATAC
ATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTA
CAATGTAACAGATAGAAATATACCGGTTTATGAGAAAATAGTATAAATAAAGTATCGATACTTGT
TAA
Found at i:1692126 original size:86 final size:85
Alignment explanation
Indices: 1692016--1692176 Score: 313
Period size: 86 Copynumber: 1.9 Consensus size: 85
1692006 AAATAGGTCA
1692016 ATATAAGCGCTACTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTC
1 ATATAAGCGCTACTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTC
1692081 CGGTTAAATGTCTATTTTAT
66 CGGTTAAATGTCTATTTTAT
1692101 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTA-CTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1692166 CCGGTTAAATG
65 CCGGTTAAATG
1692177 ATATAACATA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 12 0.16
86 63 0.84
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (85 bp):
ATATAAGCGCTACTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTC
CGGTTAAATGTCTATTTTAT
Found at i:1698025 original size:20 final size:20
Alignment explanation
Indices: 1698000--1698051 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1697990 GATTTTCCAG
* *
1698000 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
*
1698020 AATCGCAACCCGAACACATA
1 AATCGCAACGCGAACACATA
1698040 AATCGCAACGCG
1 AATCGCAACGCG
1698052 TATCCGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.42, C:0.29, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1698061 original size:20 final size:20
Alignment explanation
Indices: 1698038--1698191 Score: 213
Period size: 20 Copynumber: 7.7 Consensus size: 20
1698028 CCCGAACACA
1698038 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
1698058 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
1698078 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1698098 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1698118 TAAATCGCAACGCGTGTCCG
1 TAAATCGCAACGCGTATCCG
* *
1698138 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
*
1698158 TAAAATCGCAACGCATATCCG
1 T-AAATCGCAACGCGTATCCG
1698179 TAAATCGC-ACGCG
1 TAAATCGCAACGCG
1698192 ATTTTTAAAG
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.03
20 97 0.82
21 17 0.14
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:1698067 original size:40 final size:40
Alignment explanation
Indices: 1698000--1698191 Score: 194
Period size: 40 Copynumber: 4.8 Consensus size: 40
1697990 GATTTTCCAG
* ** * * *
1698000 AATCGCAACGCGAATATGAAAATCGCAACCCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAAC-CGTA
* * *
1698040 AATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
* *
1698080 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
* *
1698120 AATCGCAACGCGTGTCCGTAAATCGCAACGAC--AATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGTAA-CCGT-A
*
1698161 AATCGCAACGCATATCCGTAAATCGC-ACGCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG
1698192 ATTTTTAAAG
Statistics
Matches: 129, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
39 2 0.02
40 99 0.77
41 28 0.22
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.18
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
Found at i:1698088 original size:60 final size:60
Alignment explanation
Indices: 1698000--1698191 Score: 210
Period size: 60 Copynumber: 3.2 Consensus size: 60
1697990 GATTTTCCAG
* ** * * *
1698000 AATCGCAACGCGAATATGAAAATCGCAACCCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACACGAACACGTAAATCGCAACGCGTATCCGTA
* * * * *
1698060 AACCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACACG-AACACGTAAATCGCAACGCGTATCCGTA
* * *
1698120 AATCGCAACGCGTGTCCGTAAATCGCAACGAC-AATACGTAAAATCGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAAC-ACGAACACGT-AAATCGCAACGCGTATCCGTA
1698181 AATCGC-ACGCG
1 AATCGCAACGCG
1698192 ATTTTTAAAG
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
59 1 0.01
60 81 0.74
61 28 0.25
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.18
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACACGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:1698584 original size:14 final size:14
Alignment explanation
Indices: 1698565--1698621 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1698555 ATTCATTTCG
1698565 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1698579 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
*
1698598 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
1698612 CGTTGCGATT
1 CGTTGCGATT
1698622 TTCAAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 9 0.26
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1698600 original size:33 final size:33
Alignment explanation
Indices: 1698558--1698622 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1698548 CACTTAGATT
1698558 CATTTCGCGTTGCGATTCTCTCGTTGCGATTTC
1 CATTTCGCGTTGCGATTCTCTCGTTGCGATTTC
*
1698591 CATTTCGCGTTGCTATTCTCTCGTTGCGATTT
1 CATTTCGCGTTGCGATTCTCTCGTTGCGATTT
1698623 TCAAGTTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.09, C:0.26, G:0.20, T:0.45
Consensus pattern (33 bp):
CATTTCGCGTTGCGATTCTCTCGTTGCGATTTC
Found at i:1699820 original size:20 final size:20
Alignment explanation
Indices: 1699795--1699834 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1699785 TAGTTGTATA
*
1699795 CTATTCTTATCTCATTAACG
1 CTATTCTTATCTCATCAACG
*
1699815 CTATTCTTGTCTCATCAACG
1 CTATTCTTATCTCATCAACG
1699835 ATGAAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (20 bp):
CTATTCTTATCTCATCAACG
Found at i:1700587 original size:179 final size:177
Alignment explanation
Indices: 1700199--1700684 Score: 548
Period size: 179 Copynumber: 2.7 Consensus size: 177
1700189 GATACAAATG
* * * * *
1700199 AAAAATGTATCGCTCCATAGCAATATAACAGATAAAAATATAATAAAACCGGTTTC-ATTATGAT
1 AAAAATGTATCGATCCATAGCAATATAACAG-T-AAAATATGACAAAA-CGGTCTCGA-AATGAT
** * * *
1700263 AAAACCGGTAAACCGCTACTGAATATATCGAAAGTATCGATTAGATTTAA-ATAAGTATCGACAC
62 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTATCGA-TAG--TTAATATAAGTATCGACAC
1700327 TTTTGGAATTTAAAAGAGAAGAAGTAATAACGCCTATAAAGTGTCGATACTTTAT
124 TTTTGGAATTTAAAAGAGAAGAAGTAATAACGCCTAT-AAGTGTCGATACTTTAT
* * * *
1700382 AAAAACGTATCGATCCATAACAATATAACATGTATAAGTATGACAAAATCGGTCACGAAATGATA
1 AAAAATGTATCGATCCATAGCAATATAACA-GTA-AAATATGACAAAA-CGGTCTCGAAATGATA
* * *
1700447 AAATCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACGTTAATATAAGTATCGACACTTT
63 AAACCGGTAAAAAGCTACCGGATATATTGAAAGTATCGATA-GTTAATATAAGTATCGACACTTT
* * *
1700512 TTGAATTTAAAAGAG-AGAAGTTATAGCGCCTAT-AGTGTCGATACTTTAT
127 TGGAATTTAAAAGAGAAGAAGTAATAACGCCTATAAGTGTCGATACTTTAT
* *
1700561 ACAAATGTATCGATCCATAGCAATATAACAGGTAAGAATATGACAAAACATGTCTCGAAATGATA
1 AAAAATGTATCGATCCATAGCAATATAACA-GTAA-AATATGACAAAAC-GGTCTCGAAATGATA
* * * * * *
1700626 AAACCAGTAAAAAGTTATCGGATATATTGAAAGTATTGATAAATTAATATAAGTGTCGA
63 AAACCGGTAAAAAGCTACCGGATATATTGAAAGTATCGAT-AGTTAATATAAGTATCGA
1700685 TAAATTAATA
Statistics
Matches: 259, Mismatches: 36, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
178 2 0.01
179 118 0.46
180 1 0.00
181 20 0.08
182 34 0.13
183 82 0.32
184 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (177 bp):
AAAAATGTATCGATCCATAGCAATATAACAGTAAAATATGACAAAACGGTCTCGAAATGATAAAA
CCGGTAAAAAGCTACCGGATATATTGAAAGTATCGATAGTTAATATAAGTATCGACACTTTTGGA
ATTTAAAAGAGAAGAAGTAATAACGCCTATAAGTGTCGATACTTTAT
Found at i:1700686 original size:20 final size:20
Alignment explanation
Indices: 1700656--1700704 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1700646 GATATATTGA
*
1700656 AAGTATTGATAAATTAATAT
1 AAGTATCGATAAATTAATAT
*
1700676 AAGTGTCGATAAATTAATAT
1 AAGTATCGATAAATTAATAT
1700696 AAGTATCGA
1 AAGTATCGA
1700705 CACTTTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (20 bp):
AAGTATCGATAAATTAATAT
Found at i:1702703 original size:22 final size:22
Alignment explanation
Indices: 1702653--1702707 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1702643 AATGTTTTTG
1702653 TTTT-TTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
1702675 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
1702698 TTTTATTATA
1 TTTTATTATA
1702708 AATTCAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 10 0.36
23 4 0.14
24 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:1703386 original size:18 final size:18
Alignment explanation
Indices: 1703363--1703401 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1703353 GAGAAAATTT
1703363 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1703381 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1703399 GAA
1 GAA
1703402 ATGAGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1703725 original size:17 final size:17
Alignment explanation
Indices: 1703703--1703738 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1703693 TTTAAATATT
1703703 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
* *
1703720 TCATGAAAATATTTTAA
1 TCATGAAAAGATATTAA
1703737 TC
1 TC
1703739 CTAATGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:1704103 original size:15 final size:15
Alignment explanation
Indices: 1704083--1704112 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1704073 TGGACAACAA
*
1704083 CGGTAATGTTGAGGG
1 CGGTAATATTGAGGG
1704098 CGGTAATATTGAGGG
1 CGGTAATATTGAGGG
1704113 TATTGCGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.43, T:0.27
Consensus pattern (15 bp):
CGGTAATATTGAGGG
Found at i:1705529 original size:198 final size:198
Alignment explanation
Indices: 1705191--1706118 Score: 1468
Period size: 198 Copynumber: 4.6 Consensus size: 198
1705181 TATGGTAAAC
*
1705191 ATGTGTCGATACATTTATAAAAAGTATCGATTCCAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
* * * *
1705256 TAGGTAAATTATGAATCTAAACGATCTAAATACACCGATTTATGAGAAAACAAGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
1705321 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCAT
131 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-
**
1705385 GGA-A
194 CCATA
*
1705389 ATGTGTCGATACATTTATAAAAAGTCTCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
* *
1705454 TAGGTAAATTATGAATCTAATCGGTCTAAAAACACCGGTTTATGAGAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
1705519 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCAT
131 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-
**
1705583 GGA-A
194 CCATA
* *
1705587 ATGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAGACTCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
*
1705652 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
*
1705717 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCTAGAATGATTTCCTTACCAAGGTCACC
131 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACC
1705782 ATA
196 ATA
*
1705785 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
* * *
1705850 TAGGTAAATTATCAATCTAACCGGTATATCCGGTCTAAATATACCGGTTTATGAGAAAATAGGTG
66 TAGGTAAATTATGAA--T---C--TA-A-CCGGTCTAAATACACCGGTTTATGAGAAAACAGGTG
*
1705915 TACATAAAGTATCGACACTTGTTTAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACC
122 TACATAAAGTATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACC
1705980 AAGGTCACCATA
187 AAGGTCACCATA
* *
1705992 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAAACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
* * * *
1706057 TAGGTAAATTATGAATCTAACCGGTTTAAATACACCGATTTATGATAAAACATGTGTACATA
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATA
1706119 TACGTTTTGT
Statistics
Matches: 684, Mismatches: 35, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
197 1 0.00
198 487 0.71
199 3 0.00
200 3 0.00
202 1 0.00
203 1 0.00
205 3 0.00
206 1 0.00
207 184 0.27
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
TAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACC
ATA
Found at i:1706624 original size:15 final size:15
Alignment explanation
Indices: 1706604--1706655 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
1706594 AGAATTGAGG
*
1706604 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAA
1706619 CTCTTCTCAA-CCAA
1 CTCTTCTCAACCCAA
1706633 CATCTTCTCAACCCAA
1 C-TCTTCTCAACCCAA
1706649 CTCTTCT
1 CTCTTCT
1706656 GAGGAAATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
14 4 0.12
15 25 0.74
16 5 0.15
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (15 bp):
CTCTTCTCAACCCAA
Found at i:1710613 original size:200 final size:200
Alignment explanation
Indices: 1709953--1711275 Score: 1708
Period size: 200 Copynumber: 6.5 Consensus size: 200
1709943 GTGCATGAAC
* * * * *
1709953 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGCA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
*
1710018 ATAGGTAAAATAACAATGTAACCGGTCTAAATATACCGATT-TATAAGAAAAG--AGGTATACAT
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTAT-TAA-AAAAGAAAGGTATACAT
* * * * **
1710080 AAAGTATCGAAACTTTATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAA
129 AATGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTT----CC-AAA
1710145 CAAGTTCACAAA
189 CAAGTTCACAAA
* * * * * *
1710157 TAAGTGTCTATACATTTATATCAAGTGTCGATCCCAAAAACATCGAAACCCGTAACTATAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* * * * * * * * *
1710222 ATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTT-TTATGAGAAA-ATAGGTCTACA-
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTA--AAAAAGAAAGGTATACAT
* * * * * **
1710284 ATATGTATCGACACTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCA
129 A-ATGTATCGATACTTTATACATTTGTGTCGACAC-TTTATGTCCATAATAAATTTTCCAAA-CA
*
1710347 AGTGCACGAAA
191 AGTTCAC-AAA
1710358 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
*
1710423 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAAAGGTATACGTAA
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAAAGGTATACATAA
1710488 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
131 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
1710553 ACAAA
196 ACAAA
* *
1710558 AAAGTGTTGATACATTTATAACAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* *
1710623 ATAGGTAACATTACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAA
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAAAGGTATACATAA
1710688 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
131 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
*
1710753 ACGAA
196 ACAAA
1710758 AAAGTGTCGATACATTTATAACAAGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATC
1 AAAGTGTCGATACATTTATAACAA--GT-G---------T--C--G-AT----CCCAAAAACATC
1710823 GAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATT
45 GAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATT
* *
1710888 AAAAAAGAATGGTATACATAATGTATCAATACTTTATACATTTGTGTCGACACTTTATGTCCATA
110 AAAAAAGAAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATA
* **
1710953 ATAAATTTTCCAAACAATTTCATGAA
175 ATAAATTTTCCAAACAAGTTCACAAA
* *
1710979 AAAGTGTCGATACATTTATAACAAGTGTTGATCCCAAAAACATCGAAACACATAATTTTAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* *
1711044 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACGTAA
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAAAGGTATACATAA
* *
1711109 TGTATCGATACTTTATACATTTATGTTGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
131 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
*
1711174 ACGAA
196 ACAAA
* * * * * * *
1711179 AAAGTGTTGATACATTTAGAAAAAGTGTCGATCCTAAAAACATCGAAACTCGTCATTATAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* * * *
1711244 ATAGGTCACTTTACAATGTAACCGGTTTAAAT
66 ATAGGTAACATAACAATGTAACCGGTCTAAAT
1711276 TTTCCGGTTT
Statistics
Matches: 1000, Mismatches: 85, Indels: 72
0.86 0.07 0.06
Matches are distributed among these distances:
199 3 0.00
200 479 0.48
201 153 0.15
202 14 0.01
203 3 0.00
204 100 0.10
205 52 0.05
206 2 0.00
209 1 0.00
212 1 0.00
216 1 0.00
217 2 0.00
218 1 0.00
219 2 0.00
221 186 0.19
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (200 bp):
AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAAAGGTATACATAA
TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
ACAAA
Found at i:1710705 original size:22 final size:21
Alignment explanation
Indices: 1710679--1710724 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1710669 AAAAGAAAGG
*
1710679 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
1710701 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
1710722 TAT
1 TAT
1710725 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:1710785 original size:21 final size:21
Alignment explanation
Indices: 1710759--1710810 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1710749 GTTCACGAAA
1710759 AAGTGTCGATACATTTATAAC
1 AAGTGTCGATACATTTATAAC
1710780 AAGTGTCGATACATTTATAAC
1 AAGTGTCGATACATTTATAAC
*
1710801 AAGTATCGAT
1 AAGTGTCGAT
1710811 CCCAAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
AAGTGTCGATACATTTATAAC
Found at i:1710880 original size:221 final size:221
Alignment explanation
Indices: 1710559--1711210 Score: 864
Period size: 221 Copynumber: 3.0 Consensus size: 221
1710549 GTTCACAAAA
* * *
1710559 AAGTGTTGATACATTTATAACAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATGTAA
1 AAGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAA
*
1710624 TAGGTAACATTACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAAT
66 TAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAAT
1710689 GTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCA
131 GTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCA
1710754 CGAAAAAGTGTCGATACATTTATAAC
196 CGAAAAAGTGTCGATACATTTATAAC
1710780 AAGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAA
1 AAGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAA
* *
1710845 TAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAATGGTATACATAAT
66 TAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAAT
* *
1710910 GTATCAATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAATTTCA
131 GTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCA
*
1710975 TGAAAAAGTGTCGATACATTTATAAC
196 CGAAAAAGTGTCGATACATTTATAAC
* ** * * *** *
1711001 AAGTGTTGAT-C----CCAA-AA--A-C-AT-CGAAACACAT---AA-TTTTAATGTA-ATAGGT
1 AAGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACACATAAT-TATA-ATGT
* ** * * *
1711050 AACA--TAAC--AA-TGT-AAC-CGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACGTA
64 AATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATA
* *
1711108 ATGTATCGATACTTTATACATTTATGTTGACACTTTATGTCCATAATAAATTTTCCAAACAAGTT
129 ATGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTT
* * *
1711173 CACGAAAAAGTGTTGATACATTTAGAAA
194 CACGAAAAAGTGTCGATACATTTATAAC
1711201 AAGTGTCGAT
1 AAGTGTCGAT
1711211 CCTAAAAACA
Statistics
Matches: 394, Mismatches: 35, Indels: 25
0.87 0.08 0.06
Matches are distributed among these distances:
200 133 0.34
201 1 0.00
202 1 0.00
203 2 0.01
205 4 0.01
206 5 0.01
207 10 0.03
210 8 0.02
211 2 0.01
212 1 0.00
213 1 0.00
215 2 0.01
216 2 0.01
220 1 0.00
221 221 0.56
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (221 bp):
AAGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAA
TAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAAT
GTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCA
CGAAAAAGTGTCGATACATTTATAAC
Found at i:1711073 original size:621 final size:604
Alignment explanation
Indices: 1709953--1711343 Score: 1864
Period size: 621 Copynumber: 2.3 Consensus size: 604
1709943 GTGCATGAAC
* * * * *
1709953 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGCA
1 AAAGTGTTGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* * *
1710018 ATAGGTAAAATAACAATGTAACCGGTCTAAATATACCGATTTATAAGAAAAG-AGGTATACATAA
66 ATAGGTAACATTACAATGTAACCGGTCTAAATATACCGGTTT-TAA-AAAAGAAGGTATACATAA
* * **
1710082 AGTATCGAAACTTTATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAACA
129 TGTATCGAAACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAACCAAAACA
* * * * * *
1710147 AGTTCACAAATAAGTGTCTATACATTTATATCAAGTGTCGATCCCAAAAACATCGAAACCCGTAA
194 AGTTCACAAACAAGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACACATAA
* * * * * * * *
1710212 CTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAG
259 CTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTTTATAAAAAAATAG
* * * * **
1710277 GTCTACAATATGTATCGACACTTTATTCATTTGTGTCGATACATGTTGTCCAGAATGTATTTCCA
324 GTATACAATATGTATCAACACTTTATACATTTGTGTCGACACATGTTGTCCAGAATAAATTTCCA
1710342 AACCAAGTGCACGAAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAC
389 AACCAAGTGCACGAAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAC
1710407 ACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAA
454 ACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAA
*
1710472 AGAAAGGTATACGTAATGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAA
519 AGAAAGGTATACGTAATGTATCGATACTTTATACATTTATGTCGACACTTTATGTCCATAATAAA
1710537 TTTTCCAAACAAGTTCACAAA
584 TTTTCCAAACAAGTTCACAAA
* *
1710558 AAAGTGTTGATACATTTATAACAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATGTA
1 AAAGTGTTGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
1710623 ATAGGTAACATTACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAA
66 ATAGGTAACATTACAATGTAACCGGTCTAAATATACCGGTT-TTAAAAAAG-AAGGTATACATAA
* *
1710688 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
129 TGTATCGAAACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCC-AAC-----C
1710753 ACGAAA-AAGTGTCGATACATTTATAACAAGTGTCGATACATTTATAACAAGTATCGATCCCAAA
188 A--AAACAAGT-TC---AC----A-AACAAGTGTCGATACATTTATAACAAGTATCGATCCCAAA
*
1710817 AACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCG
242 AACATCGAAACACATAACTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCG
* *
1710882 ATTATTA-AAAAAGAAT-GGTATAC-ATAATGTATCAATACTTTATACATTTGTGTCGACAC-TT
307 ATT-TTATAAAAA-AATAGGTATACAAT-ATGTATCAACACTTTATACATTTGTGTCGACACATG
* * * *
1710943 TATGTCCATAATAAATTTTCCAAA-CAATTTCATG-AAAAAGTGTCGATACATTTATAACAAGTG
369 T-TGTCCAGAATAAA-TTTCCAAACCAAGTGCACGAAAAAAGTGTCGATACATTTATAACAAGTG
* *
1711006 TTGATCCCAAAAACATCGAAACACATAATTTTAATGTAATAGGTAACATAACAATGTAACCGGTC
432 TCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTC
* *
1711071 TAAATATACCGGTTATTAAAAAAGAAAGGTATACGTAATGTATCGATACTTTATACATTTATGTT
497 TAAATATACCGATTATTAAAAAAGAAAGGTATACGTAATGTATCGATACTTTATACATTTATGTC
*
1711136 GACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAA
562 GACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACAAA
* * * * *
1711179 AAAGTGTTGATACATTTAGAAAAAGTGTCGATCCTAAAAACATCGAAACTCGTCATTATAATGTA
1 AAAGTGTTGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* * * * * * *
1711244 ATAGGTCACTTTACAATGTAACCGGTTTAAATTTTCCGGTTTTATGAGAAAA-TAGGTCTACATA
66 ATAGGTAACATTACAATGTAACCGGTCTAAATATACCGGTTTTA--A-AAAAGAAGGTATACATA
* * * * *
1711308 ATGTATAGACACTTTTTAAATTAGTGTCGATACTTT
128 ATGTATCGAAACTTTATACATTTGTGTCGATACTTT
1711344 TTAAAATTAC
Statistics
Matches: 689, Mismatches: 69, Indels: 40
0.86 0.09 0.05
Matches are distributed among these distances:
604 5 0.01
605 99 0.14
606 62 0.09
607 3 0.00
612 2 0.00
613 4 0.01
614 5 0.01
617 2 0.00
620 3 0.00
621 335 0.49
622 151 0.22
623 18 0.03
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (604 bp):
AAAGTGTTGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
ATAGGTAACATTACAATGTAACCGGTCTAAATATACCGGTTTTAAAAAAGAAGGTATACATAATG
TATCGAAACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAACCAAAACAAG
TTCACAAACAAGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACACATAACT
ATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTTTATAAAAAAATAGGT
ATACAATATGTATCAACACTTTATACATTTGTGTCGACACATGTTGTCCAGAATAAATTTCCAAA
CCAAGTGCACGAAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACAC
ATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAG
AAAGGTATACGTAATGTATCGATACTTTATACATTTATGTCGACACTTTATGTCCATAATAAATT
TTCCAAACAAGTTCACAAA
Found at i:1711343 original size:421 final size:407
Alignment explanation
Indices: 1709969--1711275 Score: 1668
Period size: 421 Copynumber: 3.2 Consensus size: 407
1709959 TCGATACATT
* * * * *
1709969 TATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGCAATAGGTAAAATAACAA
1 TATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAA
* *
1710034 TGTAACCGGTCTAAATATACCGATTTAT-AAGAAAAG-A-GGTATACATAAAGTATCGAAACTTT
66 TGTAACCGGTCTAAATATACCGA-TTATGAA-AAAAGAATGGTATACATAATGTATCGATACTTT
* * ** *
1710096 ATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAACAAGTTCACAAATAAG
129 ATACATTTGTGTCGACACTTTATGTCCATAATAAATTTT----CC-AAACAAGTTCACAAAAAAG
* * * * * *
1710161 TGTCTATACATTTATATCAAGTGTCGATCCCAAAAACATCGAAACCCGTAACTATAATGTAATAG
189 TGTCGATACATTTATAACAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATGTAATAG
* * * * * * * *
1710226 GTCACTTTACAATGTAACCGGTTTAAATTTACCGGTT-TTATGAGAAA-ATAGGTCTACA-ATAT
254 GTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTA--AAAAAGAAAGGTATACATA-AT
* * * * * * ** *
1710288 GTATCGACACTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCAAGTG
316 GTATCGATACTTTATACATTTATGTCGACAC-TTTATGTCCATAATAAATTTTCCAAA-CAAGTT
1710351 CACGAAAAAAGTGTCGATACA--T-T----
379 CACG-AAAAAGTGTCGATACATTTATAAGG
*
1710374 TATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAA
1 TATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAA
* * *
1710439 TGTAACCGGTCTAAATATACCGATTATTAAAAAAGAAAGGTATACGTAATGTATCGATACTTTAT
66 TGTAACCGGTCTAAATATACCGATTATGAAAAAAGAATGGTATACATAATGTATCGATACTTTAT
*
1710504 ACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACAAAAAAGTGTTGAT
131 ACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACAAAAAAGTGTCGAT
1710569 ACATTTATAACAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACAT
196 ACATTTATAACAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACAT
*
1710634 TACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATAC
261 AACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATAC
*
1710699 TTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTG
326 TTTATACATTTATGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTG
1710764 TCGATACATTTATAACAAGTGTCG
391 TCGATACATTTAT---AA--G--G
1710788 ATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAAC
1 -------TATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAAC
* *
1710853 ATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAATGGTATACATAATGTATCAAT
59 ATAACAATGTAACCGGTCTAAATATACCGATTATGAAAAAAGAATGGTATACATAATGTATCGAT
* **
1710918 ACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAATTTCATGAAAAAG
124 ACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACAAAAAAG
* *
1710983 TGTCGATACATTTATAACAAGTGTTGATCCCAAAAACATCGAAACACATAATTTTAATGTAATAG
189 TGTCGATACATTTATAACAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATGTAATAG
*
1711048 GTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACGTAATGTA
254 GTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTA
*
1711113 TCGATACTTTATACATTTATGTTGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGA
319 TCGATACTTTATACATTTATGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGA
*
1711178 AAAAGTGTTGATACA-TT-T-A-G
384 AAAAGTGTCGATACATTTATAAGG
* * * * * * * *
1711198 -A-AA-AAGTGTCGATCCTAAAAACATCGAAACTCGTCATTATAATGTAATAGGTCACTTTACAA
1 TATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAA
*
1711260 TGTAACCGGTTTAAAT
66 TGTAACCGGTCTAAAT
1711276 TTTCCGGTTT
Statistics
Matches: 813, Mismatches: 60, Indels: 63
0.87 0.06 0.07
Matches are distributed among these distances:
400 88 0.11
401 169 0.21
402 16 0.02
403 1 0.00
404 9 0.01
405 85 0.10
406 57 0.07
410 1 0.00
415 1 0.00
419 1 0.00
420 2 0.00
421 383 0.47
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (407 bp):
TATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAA
TGTAACCGGTCTAAATATACCGATTATGAAAAAAGAATGGTATACATAATGTATCGATACTTTAT
ACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACAAAAAAGTGTCGAT
ACATTTATAACAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACAT
AACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATAC
TTTATACATTTATGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTG
TCGATACATTTATAAGG
Found at i:1715051 original size:87 final size:86
Alignment explanation
Indices: 1714960--1715118 Score: 264
Period size: 87 Copynumber: 1.8 Consensus size: 86
1714950 CAATATAAGC
*
1714960 GCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTTCCGGTTAA
1 GCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAA
1715025 ATGCATATTTTATTATATAATT
66 ATG-ATATTTTATTATATAATT
* * * *
1715047 GCTACCTATTACATTATATAAGCGTTATCTAATATGTTATTGTGCTTGATAATATTTTCGGTTAA
1 GCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAA
1715112 ATGATAT
66 ATGATAT
1715119 AACATAACCG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 4 0.06
87 63 0.94
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.45
Consensus pattern (86 bp):
GCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAA
ATGATATTTTATTATATAATT
Found at i:1726460 original size:20 final size:20
Alignment explanation
Indices: 1726384--1726453 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1726374 TCATATTCTC
1726384 TGGTAATCTTTTATTCCCAT
1 TGGTAATCTTTTATTCCCAT
1726404 TGGTAATCTTTTATTCCCAT
1 TGGTAATCTTTTATTCCCAT
1726424 TGGTAATCTTTTATTCCCAT
1 TGGTAATCTTTTATTCCCAT
*
1726444 TGATAATCTT
1 TGGTAATCTT
1726454 ACATTCCGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (20 bp):
TGGTAATCTTTTATTCCCAT
Found at i:1727115 original size:17 final size:17
Alignment explanation
Indices: 1727090--1727135 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1727080 TTACTCGTAT
*
1727090 AAAAGTTATAATTAATA
1 AAAAATTATAATTAATA
1727107 AAAAATTAT-ATTAATA
1 AAAAATTATAATTAATA
* *
1727123 TAAAATTAAAATT
1 AAAAATTATAATT
1727136 TTGAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAAATTATAATTAATA
Found at i:1739268 original size:20 final size:21
Alignment explanation
Indices: 1739243--1739294 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1739233 TTTTCCCAAT
*
1739243 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1739263 TCGCAACGCGAATTGCGAAAA
1 TCGCAATGCGAATTAAGAAAA
1739284 TCGCAATGCGA
1 TCGCAATGCGA
1739295 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1739308 original size:20 final size:20
Alignment explanation
Indices: 1739283--1739396 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
1739273 AATTGCGAAA
*
1739283 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1739303 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1739323 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1739344 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1739364 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1739384 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1739397 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1739327 original size:61 final size:61
Alignment explanation
Indices: 1739262--1739396 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
1739252 GAATAAGTAA
* * * * * *
1739262 ATCGCAACGCGA-ATTGCGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGATAATAC-AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* * *
1739323 ATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
*
1739384 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1739397 TTACATAGCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 59 0.95
62 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (61 bp):
ATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
Found at i:1739948 original size:19 final size:19
Alignment explanation
Indices: 1739910--1739976 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1739900 TTCGAGAATG
1739910 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1739930 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
1739949 AAAATAGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1739968 AAAATCGCA
1 AAAATCGCA
1739977 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1739994 original size:19 final size:18
Alignment explanation
Indices: 1739972--1740088 Score: 140
Period size: 19 Copynumber: 6.7 Consensus size: 18
1739962 GAAACCAAAA
*
1739972 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTT-ATT
1739991 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTT-ATT
*
1740010 TCGCGTTGCGATTTTTTT
1 TCGCGTTGCGATTTTATT
1740028 TCGCGTTGCGA-TTT-TT
1 TCGCGTTGCGATTTTATT
1740044 TCGCGTTGCG-----ATT
1 TCGCGTTGCGATTTTATT
1740057 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTT-ATT
1740076 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1740089 GTCTGGTCGC
Statistics
Matches: 89, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
13 12 0.13
16 12 0.13
17 3 0.03
18 13 0.15
19 49 0.55
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTATT
Found at i:1740060 original size:13 final size:13
Alignment explanation
Indices: 1740026--1740070 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 13
1740016 TGCGATTTTT
1740026 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
1740039 TTTTTTCGCGTTGCGA
1 ---TTTCGCGTTGCGA
1740055 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
1740068 TTT
1 TTT
1740071 TCATTTCGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 16 0.55
16 13 0.45
ACGTcount: A:0.07, C:0.20, G:0.27, T:0.47
Consensus pattern (13 bp):
TTTCGCGTTGCGA
Found at i:1740108 original size:33 final size:32
Alignment explanation
Indices: 1740042--1740155 Score: 149
Period size: 33 Copynumber: 3.5 Consensus size: 32
1740032 GTTGCGATTT
**
1740042 TTTCGCGTTGCGATTTC-GCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTCTG-GTTGCGATAGTCA
*
1740074 TTTCGCGTTGCGATTGTCTGGTCGCGATAGTCA
1 TTTCGCGTTGCGATT-TCTGGTTGCGATAGTCA
*
1740107 TTTCGCGTTGCGATTCTCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATT-TCTGGTTGCGATAGTCA
1740140 TTTCCGCGTTGCGATT
1 TTT-CGCGTTGCGATT
1740156 CTCATTATCT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
32 15 0.21
33 45 0.62
34 13 0.18
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTCTGGTTGCGATAGTCA
Found at i:1740130 original size:66 final size:66
Alignment explanation
Indices: 1739988--1740155 Score: 205
Period size: 66 Copynumber: 2.5 Consensus size: 66
1739978 TGCGATTTTC
* ** * * **
1739988 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTTTTTCGCGTTGCGATTTTTTCGCGTTGC
1 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCTGGTCGCGATGAGATCATTTCGCGTTGC
1740053 G
66 G
1740054 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCTGGTCGCGAT-AG-TCATTTCGCGTTG
1 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATT-TCTGGTCGCGATGAGATCATTTCGCGTTG
1740117 CG
65 CG
* **
1740119 ATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATT
1 ATT-TCGCGTTGCGATTTTCATTT-CGCGTTGCGATT
1740156 CTCATTATCT
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
65 16 0.18
66 53 0.60
67 20 0.22
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.43
Consensus pattern (66 bp):
ATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCTGGTCGCGATGAGATCATTTCGCGTTGC
G
Found at i:1740160 original size:20 final size:20
Alignment explanation
Indices: 1740126--1740183 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1740116 GCGATTCTCT
**
1740126 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1740146 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1740166 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1740184 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1742262 original size:21 final size:21
Alignment explanation
Indices: 1742238--1742304 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1742228 TCATTCCTCG
1742238 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1742259 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1742280 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1742301 AGAG
1 AGAG
1742305 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1742262 original size:42 final size:42
Alignment explanation
Indices: 1742182--1742304 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
1742172 GCCCGACTCG
* * * ** * *
1742182 CCTATCATCCCTCAAGAGTCCACTCTTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1742224 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
1742266 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1742305 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:1743683 original size:14 final size:14
Alignment explanation
Indices: 1743664--1743699 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1743654 ATTGTTTAAT
1743664 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1743678 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1743692 TGATTTGT
1 TGATTTGT
1743700 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1743943 original size:12 final size:12
Alignment explanation
Indices: 1743926--1743950 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1743916 TCTTCGGGGA
1743926 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1743938 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1743950 C
1 C
1743951 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1744159 original size:24 final size:24
Alignment explanation
Indices: 1744125--1744178 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1744115 CTAAAACATC
* *
1744125 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1744149 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1744173 ATCAAA
1 ATCAAA
1744179 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1745149 original size:20 final size:20
Alignment explanation
Indices: 1745112--1745149 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1745102 ATTCATTTGA
*
1745112 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
1745132 CTATCGCAACGAGGAAAT
1 CTATCGCAACGAGAAAAT
1745150 CGCAATGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:1745192 original size:14 final size:16
Alignment explanation
Indices: 1745172--1745245 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1745162 TGAAAATCGC
1745172 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1745187 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1745204 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1745223 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1745239 -TTGCGAT
1 ATTGCGAT
1745246 AGCCATTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1745209 original size:19 final size:19
Alignment explanation
Indices: 1745168--1745235 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1745158 GAAATGAAAA
1745168 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1745184 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1745201 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1745220 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1745236 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1745255 original size:20 final size:20
Alignment explanation
Indices: 1745230--1745267 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1745220 TCGCATTGCG
*
1745230 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1745250 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1745268 TCTGTTTTGC
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:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1745372 original size:14 final size:14
Alignment explanation
Indices: 1745353--1745389 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1745343 CATCAATTAA
1745353 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1745367 ACAAATCATCTTTT
1 ACAAATCAACATTT
1745381 ACAAATCAA
1 ACAAATCAA
1745390 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1747283 original size:20 final size:19
Alignment explanation
Indices: 1747248--1747314 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1747238 GAAACTTAAA
1747248 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1747267 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1747287 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1747306 ATCGCAACG
1 ATCGCAACG
1747315 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1747322 original size:14 final size:14
Alignment explanation
Indices: 1747303--1747360 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1747293 ATGCGAAATG
1747303 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1747317 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1747333 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1747349 AAAATCGCAACG
1 AAAATCGCAACG
1747361 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1747345 original size:32 final size:33
Alignment explanation
Indices: 1747287--1747365 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1747277 GGAAATGGCT
*
1747287 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1747320 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1747352 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1747366 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1747398 original size:18 final size:19
Alignment explanation
Indices: 1747372--1747436 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 19
1747362 GAAACACAAA
*
1747372 TCGCATTGC-ATTTTCATT
1 TCGCGTTGCGATTTTCATT
1747390 TCGCGTTGCGATTTT-A--
1 TCGCGTTGCGATTTTCATT
1747406 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
1747422 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1747437 GTCGTTGCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 3 0.08
14 9 0.23
16 2 0.05
18 17 0.44
19 8 0.21
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1747412 original size:14 final size:14
Alignment explanation
Indices: 1747393--1747449 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
1747383 TTTCATTTCG
1747393 CGTTGCGATTTTAT
1 CGTTGCGATTTTAT
*
1747407 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TAT
*
1747423 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTAT
1747439 CGTTGCGATTT
1 CGTTGCGATTT
1747450 CATTCGCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:1747424 original size:32 final size:32
Alignment explanation
Indices: 1747383--1747462 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
1747373 CGCATTGCAT
1747383 TTTCATTTCGCGTTGCGATTTTATCGTTGCGA
1 TTTCATTTCGCGTTGCGATTTTATCGTTGCGA
*
1747415 TTTCATTTCGCGTTGCGATTTTGTCGTTGCGA
1 TTTCATTTCGCGTTGCGATTTTATCGTTGCGA
*
1747447 TTTCA-TTCGCATTGCG
1 TTTCATTTCGCGTTGCG
1747463 TAGCCATTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 10 0.22
32 36 0.78
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (32 bp):
TTTCATTTCGCGTTGCGATTTTATCGTTGCGA
Found at i:1747499 original size:20 final size:20
Alignment explanation
Indices: 1747458--1747502 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1747448 TTCATTCGCA
1747458 TTGCG-TAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
1747477 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
1747497 TTGCGA
1 TTGCGA
1747503 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1748008 original size:18 final size:18
Alignment explanation
Indices: 1747982--1748026 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1747972 GTCGATCAGA
*
1747982 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1748000 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1748018 TGATGGCTC
1 TGATGGCTC
1748027 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1749891 original size:20 final size:20
Alignment explanation
Indices: 1749866--1749959 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1749856 GATTATGTAT
1749866 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1749886 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1749906 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1749927 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1749947 TATCGCATTGCGA
1 TATCGCGTTGCGA
1749960 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1749960 original size:20 final size:20
Alignment explanation
Indices: 1749846--1749960 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1749836 CGCTTTGAAA
*
1749846 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1749867 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1749887 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1749907 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1749928 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1749948 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1749961 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1749978 original size:21 final size:21
Alignment explanation
Indices: 1749949--1750041 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
1749939 ATAGTCAGTA
1749949 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1749970 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1749990 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1750011 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1750031 TCGCATTGCGA
1 TCGCATTGCGA
1750042 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1749979 original size:41 final size:41
Alignment explanation
Indices: 1749888--1750022 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1749878 AAAGTCAGTA
* * * ** *
1749888 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1749928 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1749970 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1750011 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1750023 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1750023 original size:41 final size:41
Alignment explanation
Indices: 1749949--1750041 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1749939 ATAGTCAGTA
1749949 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1749990 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1750031 TCGCATTGCGA
1 TCGCATTGCGA
1750042 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1750411 original size:16 final size:17
Alignment explanation
Indices: 1750390--1750425 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1750380 ACGAATAAAA
1750390 ATATTTATA-TAAATGT
1 ATATTTATATTAAATGT
*
1750406 ATATTTATATTAGATGT
1 ATATTTATATTAAATGT
1750423 ATA
1 ATA
1750426 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
ATATTTATATTAAATGT
Found at i:1750487 original size:16 final size:18
Alignment explanation
Indices: 1750455--1750487 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1750445 TATTAATGTA
1750455 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1750473 TGAAT-ATTT-TATTTT
1 TGAATCATTTATATTTT
1750488 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1751198 original size:129 final size:127
Alignment explanation
Indices: 1750940--1751184 Score: 391
Period size: 129 Copynumber: 1.9 Consensus size: 127
1750930 TAATTTCTTC
* *
1750940 TAATTAGGTGGTGACATGTGTCACCAAACATATATCATGATCATGTGTTAACACATGTCAGATCC
1 TAATTAGGTGGTGACATGTGTCACCAAACACATATCATGATCATGTGCTAACACATGTCAGATCC
** * *
1751005 TGGTTAAATGATTAATTTATTAAATTTTATTAATTTAGGACCAAATTGATAGCATATATAAA
66 TAATTAAATGATTAATTTATTAAATTCTATTAATTTAGGACCAAATTGATAGCATAAATAAA
* *
1751067 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAA--ACACATATCATGATCATGTGCTAACACATGTCAGAT
1751132 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
64 CCTAATTAAATGATTAATTTATTAAATTCTA-TTAATTTAGGACCAAATTGAT
1751185 TATATAAATA
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
127 27 0.25
129 60 0.56
130 21 0.19
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (127 bp):
TAATTAGGTGGTGACATGTGTCACCAAACACATATCATGATCATGTGCTAACACATGTCAGATCC
TAATTAAATGATTAATTTATTAAATTCTATTAATTTAGGACCAAATTGATAGCATAAATAAA
Found at i:1751631 original size:35 final size:35
Alignment explanation
Indices: 1751581--1751656 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
1751571 AATTGAATTT
* *
1751581 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1751616 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1751651 AATTGA
1 AATTGA
1751657 GGACTGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1767359 original size:24 final size:24
Alignment explanation
Indices: 1767332--1767389 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1767322 GATTATGAAA
*
1767332 TTAAATTTATATT-ATATTTAAATT
1 TTAAATTTAAATTGATATTT-AATT
* *
1767356 TTAAAATTAAATTGATATTTTATT
1 TTAAATTTAAATTGATATTTAATT
*
1767380 TAAAATTTAA
1 TTAAATTTAA
1767390 GAAACAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTAAATTTAAATTGATATTTAATT
Found at i:1767363 original size:30 final size:30
Alignment explanation
Indices: 1767329--1767389 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1767319 TTAGATTATG
* *
1767329 AAATTAAATTTATATTATATTTAAATTTTA
1 AAATTAAATTGATATTATATTTAAAATTTA
*
1767359 AAATTAAATTGATATTTTATTTAAAATTTA
1 AAATTAAATTGATATTATATTTAAAATTTA
1767389 A
1 A
1767390 GAAACAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
AAATTAAATTGATATTATATTTAAAATTTA
Found at i:1767399 original size:31 final size:30
Alignment explanation
Indices: 1767334--1767413 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
1767324 TTATGAAATT
* * **
1767334 AAATTTATATTATATTTAAATTTTAAAATT
1 AAATTGATATTATATTTAAAATTTAAAAAC
*
1767364 AAATTGATATTTTATTTAAAATTTAAGAAAC
1 AAATTGATATTATATTTAAAATTTAA-AAAC
*
1767395 AAATTAGAAATTAATATTT
1 AAATT-GATATT-ATATTT
1767414 TTATTGTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 23 0.57
31 7 0.17
32 5 0.12
33 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (30 bp):
AAATTGATATTATATTTAAAATTTAAAAAC
Found at i:1773906 original size:28 final size:28
Alignment explanation
Indices: 1773850--1773907 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1773840 ATATATTTAA
1773850 TTTTTTCAAAAATTTATGATTTTCATCT
1 TTTTTTCAAAAATTTATGATTTTCATCT
* * *
1773878 TTTTTTTAAAATTTCTATTATTTTC-TCT
1 TTTTTTCAAAAATT-TATGATTTTCATCT
1773906 TT
1 TT
1773908 AAAAGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTTTCAAAAATTTATGATTTTCATCT
Found at i:1775612 original size:28 final size:28
Alignment explanation
Indices: 1775572--1775633 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1775562 CTCCCTAAAT
*
1775572 TTTTTTGGAATTTT-TAGGAATTT-AGGAG
1 TTTTTTGAAATTTTATA-GAATTTAAGG-G
1775600 TTTTTTGAAATTTTATAGAATTTAAGGG
1 TTTTTTGAAATTTTATAGAATTTAAGGG
1775628 TTTTTT
1 TTTTTT
1775634 TTTTGGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (28 bp):
TTTTTTGAAATTTTATAGAATTTAAGGG
Found at i:1775663 original size:31 final size:32
Alignment explanation
Indices: 1775600--1775664 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
1775590 AATTTAGGAG
*
1775600 TTTTTTGAAATTTTATAGAATTTAAGGGTTTT
1 TTTTTTGAAATTTTATAGAATTTAAGGATTTT
* * * *
1775632 TTTTTTGGAATTTTA-ATAATTTCATGATTTT
1 TTTTTTGAAATTTTATAGAATTTAAGGATTTT
1775663 TT
1 TT
1775665 AGAAAATAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (32 bp):
TTTTTTGAAATTTTATAGAATTTAAGGATTTT
Found at i:1778487 original size:20 final size:21
Alignment explanation
Indices: 1778462--1778506 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1778452 AAAATGTTTT
1778462 AGAAAATTCTA-AATTTTTCC
1 AGAAAATTCTAGAATTTTTCC
* *
1778482 AGAAAATTTTAGAATTTTTCT
1 AGAAAATTCTAGAATTTTTCC
1778503 AGAA
1 AGAA
1778507 CCTCTCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (21 bp):
AGAAAATTCTAGAATTTTTCC
Found at i:1797929 original size:2 final size:2
Alignment explanation
Indices: 1797922--1797952 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1797912 CACCCCTATT
*
1797922 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1797953 TAAATAGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1797933 original size:10 final size:10
Alignment explanation
Indices: 1797918--1797950 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1797908 TAAACACCCC
1797918 TATTTATATA
1 TATTTATATA
1797928 TATTTATATA
1 TATTTATATA
*
1797938 TATATATATA
1 TATTTATATA
1797948 TAT
1 TAT
1797951 ATTAAATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTTATATA
Found at i:1811704 original size:43 final size:43
Alignment explanation
Indices: 1811657--1811791 Score: 143
Period size: 42 Copynumber: 3.2 Consensus size: 43
1811647 TTACAACATA
*
1811657 TAGCGGCGATTGT-TCAACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATT-TATCAACAAACGCCGCAATAGGTATTGATATT
** *
1811700 TAGCGGCG-TTTATCATTAAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGATTTATCAACAAACGCCGCAATAGGTATTGATATT
* ** * *
1811742 TAACGGC-ATTTGGCAGACAAACGCCGCAATA-GTCTTGATGTT
1 TAGCGGCGATTTATCA-ACAAACGCCGCAATAGGTATTGATATT
1811784 TAGCGGCG
1 TAGCGGCG
1811792 TTTTCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 54 0.71
43 21 0.28
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (43 bp):
TAGCGGCGATTTATCAACAAACGCCGCAATAGGTATTGATATT
Found at i:1811738 original size:42 final size:41
Alignment explanation
Indices: 1811657--1811879 Score: 139
Period size: 42 Copynumber: 5.3 Consensus size: 41
1811647 TTACAACATA
** *
1811657 TAGCGGCGATTGTTCAACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCG-TT-TTCATTAAACGCCGCAATAGGTATTGATATT
*
1811700 TAGCGGCGTTTATCATTAAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGTTT-TCATTAAACGCCGCAATAGGTATTGATATT
* * * ** * *
1811742 TAACGGCATTTGGCAGACAAACGCCGCAATA-GTCTTGATGTT
1 TAGCGGCGTTT-TCA-TTAAACGCCGCAATAGGTATTGATATT
* * * *
1811784 TAGCGGCGTTTTC-TTCAAAACGCCGCAGTAGATTTTTAT-TT
1 TAGCGGCGTTTTCATT--AAACGCCGCAATAGGTATTGATATT
* * * * *
1811825 TATCGGCGTTTTC-CTACAACGCCGCAGGATATGTTTTGAGATT
1 TAGCGGCGTTTTCATTA-AACGCCGCA--ATAGGTATTGATATT
*
1811868 TTGCGGCGTTTT
1 TAGCGGCGTTTT
1811880 TATCAAAAAC
Statistics
Matches: 141, Mismatches: 30, Indels: 18
0.75 0.16 0.10
Matches are distributed among these distances:
39 1 0.01
40 9 0.06
41 29 0.21
42 69 0.49
43 33 0.23
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (41 bp):
TAGCGGCGTTTTCATTAAACGCCGCAATAGGTATTGATATT
Found at i:1812286 original size:21 final size:21
Alignment explanation
Indices: 1812225--1812333 Score: 69
Period size: 21 Copynumber: 5.2 Consensus size: 21
1812215 TGATATATTA
* * * *
1812225 CTTCTCTCTGTTCTGCCGATG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
1812246 CCTCTCTCTGTGC-GCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
1812266 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* ** *
1812287 CTGCTCTAGCTGCTTTCTGCTG
1 CTTCTCTCTCTGC-TTCCGCTG
* *
1812309 CTGCTCTCTCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
1812330 CTTC
1 CTTC
1812334 ATTTTCCGCT
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
20 18 0.26
21 35 0.50
22 17 0.24
ACGTcount: A:0.02, C:0.39, G:0.18, T:0.41
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:1812672 original size:20 final size:19
Alignment explanation
Indices: 1812639--1812676 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1812629 GAATAATTTA
1812639 AAATAAAAATGTCATGGTAC
1 AAATAAAAATGTCA-GGTAC
1812659 AAATAAATAA-GTCAGGTA
1 AAATAAA-AATGTCAGGTA
1812677 ATTTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 11 0.65
21 2 0.12
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATAAAAATGTCAGGTAC
Found at i:1815699 original size:26 final size:27
Alignment explanation
Indices: 1815670--1815726 Score: 107
Period size: 26 Copynumber: 2.1 Consensus size: 27
1815660 ATATTAGGGG
1815670 TTTTAGAAAATATTTTTTATTTTT-GT
1 TTTTAGAAAATATTTTTTATTTTTAGT
1815696 TTTTAGAAAATATTTTTTATTTTTAGT
1 TTTTAGAAAATATTTTTTATTTTTAGT
1815723 TTTT
1 TTTT
1815727 CGTAAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (27 bp):
TTTTAGAAAATATTTTTTATTTTTAGT
Found at i:1816604 original size:28 final size:28
Alignment explanation
Indices: 1816547--1816610 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 28
1816537 CTTTTTTTAA
1816547 TAAAATAAAAAATACAAAATTAATATAT
1 TAAAATAAAAAATACAAAATTAATATAT
1816575 TAAATATAAAAATACTACAAAATTAA-ATTAT
1 TAAA-ATAAAAA-A-TACAAAATTAATA-TAT
1816606 TAAAA
1 TAAAA
1816611 ATCAATTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 4 0.12
29 7 0.22
30 3 0.09
31 18 0.56
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (28 bp):
TAAAATAAAAAATACAAAATTAATATAT
Found at i:1818275 original size:15 final size:15
Alignment explanation
Indices: 1818255--1818289 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1818245 TAACAAAATG
*
1818255 AAATTTGATCATAAA
1 AAATTTAATCATAAA
1818270 AAATTTAATCATAAA
1 AAATTTAATCATAAA
*
1818285 TAATT
1 AAATT
1818290 AATTAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (15 bp):
AAATTTAATCATAAA
Found at i:1823968 original size:18 final size:18
Alignment explanation
Indices: 1823945--1823988 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1823935 CAGAATGTAA
*
1823945 GATTACCGAAGGGAATAT
1 GATTACCGAAGGGAATAG
1823963 GATTACCGAAGGGAATAG
1 GATTACCGAAGGGAATAG
1823981 GATTACCG
1 GATTACCG
1823989 GAATGTAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (18 bp):
GATTACCGAAGGGAATAG
Found at i:1826627 original size:20 final size:21
Alignment explanation
Indices: 1826589--1826630 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1826579 TGTATATTTT
* *
1826589 ATATTGAAATTTAATAAATTA
1 ATATTGAAAATTAAGAAATTA
1826610 ATATT-AAAATTAAGAAATTA
1 ATATTGAAAATTAAGAAATTA
1826630 A
1 A
1826631 AAATCTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATATTGAAAATTAAGAAATTA
Found at i:1827502 original size:2 final size:2
Alignment explanation
Indices: 1827495--1827557 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
1827485 TTTAAAACAA
1827495 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
1827537 -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1827558 TCATATCCGA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1828111 original size:66 final size:67
Alignment explanation
Indices: 1828005--1828137 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 67
1827995 CCTGAAAAAG
*
1828005 AGAAGAGTGCTTGCTTTTACGAGTTCAGGTATCTACACTTACACCGTTATGTTTGGAATTC-ACT
1 AGAAGAGTGCTTGCTTTTACGAGTTCAGGTATATACACTTACACCGTTATGTTTGGAATTCAACT
1828069 CT
66 CT
1828071 AGAAGAGTGCTTGCTTTTACGAGTTCAGGTATATACACTTACACCGTTATGTTTGGAATTCAACT
1 AGAAGAGTGCTTGCTTTTACGAGTTCAGGTATATACACTTACACCGTTATGTTTGGAATTCAACT
1828136 CT
66 CT
1828138 TTCTTGCATG
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
66 60 0.92
67 5 0.08
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (67 bp):
AGAAGAGTGCTTGCTTTTACGAGTTCAGGTATATACACTTACACCGTTATGTTTGGAATTCAACT
CT
Found at i:1835774 original size:18 final size:18
Alignment explanation
Indices: 1835715--1835785 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 18
1835705 TGGTATATTA
1835715 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
* **
1835733 GTCATTCGAAACGTATCCAGTG
1 GTCCTTCGGGAC--AT--AGTG
*
1835755 GTCCTTTGGGACATAGTG
1 GTCCTTCGGGACATAGTG
1835773 GTCCTTCGGGACA
1 GTCCTTCGGGACA
1835786 AATACTGAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
18 25 0.61
20 4 0.10
22 12 0.29
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.28
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:1841047 original size:2 final size:2
Alignment explanation
Indices: 1841040--1841086 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1841030 TAGTATAAAG
1841040 AT AT AT AT AT AT AT AT AT AT AT A- 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
1841081 AT AT AT
1 AT AT AT
1841087 GATTGTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1842512 original size:22 final size:22
Alignment explanation
Indices: 1842485--1842544 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
1842475 TCGGGGACAT
*
1842485 AGTGGTCATTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
1842507 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
1842529 AGTGGTCCTTCGGGAC
1 AGTGGTCCTTCGGGAC
1842545 ATAGTGGTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.27
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATCC
Found at i:1842552 original size:18 final size:18
Alignment explanation
Indices: 1842452--1842556 Score: 93
Period size: 22 Copynumber: 5.3 Consensus size: 18
1842442 GGATATATTA
* *
1842452 GTCCTTCAGGATATAGTG
1 GTCCTTCGGGACATAGTG
*
1842470 GTCTTTCGGGGACATAGTG
1 GTCCTTC-GGGACATAGTG
*
1842489 GTCATTCGGGACGTATCCAGTG
1 GTCCTTCGGGAC--AT--AGTG
1842511 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGAC--AT--AGTG
1842533 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
1842551 GTCCTT
1 GTCCTT
1842557 AAGGACAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
18 21 0.27
19 15 0.19
20 4 0.05
22 37 0.48
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.30
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:1842562 original size:18 final size:18
Alignment explanation
Indices: 1842529--1842563 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1842519 GGACGTATCC
**
1842529 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTAAGGACAT
1842547 AGTGGTCCTTAAGGACA
1 AGTGGTCCTTAAGGACA
1842564 AATACTGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTAAGGACAT
Found at i:1846287 original size:24 final size:24
Alignment explanation
Indices: 1846260--1846352 Score: 125
Period size: 24 Copynumber: 3.9 Consensus size: 24
1846250 ATTTCCGACT
* *
1846260 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
1846284 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
1846308 TGGATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
1846332 T-AGATTCTGTTCTGATATCTG
1 TGA-ATTCTGTTCTGATATCTG
1846353 TTTTGATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:1846302 original size:48 final size:48
Alignment explanation
Indices: 1846246--1846347 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 48
1846236 AAATATTTTA
1846246 TCTGATTTCCGA-CTTGAATTCTGTTCTGATATATGACCT-GAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTCTGATATATGACCTAG-ATTCTGT
* * * * *
1846294 TCTGATTTCTGATCTGGATTCTGTTCTGATTTCTGATCTAGATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTCTGATATATGACCTAGATTCTGT
1846342 TCTGAT
1 TCTGAT
1846348 ATCTGTTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 45 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTCTGATATATGACCTAGATTCTGT
Found at i:1846305 original size:7 final size:6
Alignment explanation
Indices: 1846287--1846352 Score: 52
Period size: 7 Copynumber: 11.0 Consensus size: 6
1846277 TATGACCTGA
1846287 ATTCTG -TTCTG ATTTCTG A-TCTGG ATTCTG -TTCTG ATTTCTG A-TCTAG
1 ATTCTG ATTCTG A-TTCTG ATTCT-G ATTCTG ATTCTG A-TTCTG ATTCT-G
1846335 ATTCTG -TTCTG ATATCTG
1 ATTCTG ATTCTG AT-TCTG
1846353 TTTTGATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
5 21 0.42
6 7 0.14
7 22 0.44
ACGTcount: A:0.15, C:0.17, G:0.18, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:1846328 original size:36 final size:36
Alignment explanation
Indices: 1846246--1846366 Score: 95
Period size: 36 Copynumber: 3.4 Consensus size: 36
1846236 AAATATTTTA
* * * * *
1846246 TCTGATTTCCGA-CTTGAATTCTGTTCTGATATATGA
1 TCTGATTTCTGATCTAG-ATTCTGATCTGATATCTGT
* * *
1846282 CCTGAATTCTGTTCT-GATTTCTGATCTGGAT-TCTGT
1 TCTGATTTCTGATCTAGA-TTCTGATCT-GATATCTGT
*
1846318 TCTGATTTCTGATCTAGATTCTGTTCTGATATCTGT
1 TCTGATTTCTGATCTAGATTCTGATCTGATATCTGT
* *
1846354 TTTGATTTTTGAT
1 TCTGATTTCTGAT
1846367 ATCTACTTTT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
35 4 0.06
36 56 0.84
37 7 0.10
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (36 bp):
TCTGATTTCTGATCTAGATTCTGATCTGATATCTGT
Found at i:1846352 original size:12 final size:12
Alignment explanation
Indices: 1846265--1846359 Score: 70
Period size: 12 Copynumber: 7.9 Consensus size: 12
1846255 CGACTTGAAT
1846265 TCTGTTCTGATA
1 TCTGTTCTGATA
* **
1846277 TATGACCTGA-A
1 TCTGTTCTGATA
*
1846288 TTCTGTTCTGATT
1 -TCTGTTCTGATA
*
1846301 TCTGATCTGGAT-
1 TCTGTTCT-GATA
*
1846313 TCTGTTCTGATT
1 TCTGTTCTGATA
*
1846325 TCTGATCTAGAT-
1 TCTGTTCT-GATA
1846337 TCTGTTCTGATA
1 TCTGTTCTGATA
*
1846349 TCTGTTTTGAT
1 TCTGTTCTGAT
1846360 TTTTGATATC
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
11 7 0.11
12 52 0.80
13 6 0.09
ACGTcount: A:0.17, C:0.16, G:0.18, T:0.49
Consensus pattern (12 bp):
TCTGTTCTGATA
Found at i:1848408 original size:14 final size:15
Alignment explanation
Indices: 1848375--1848405 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1848365 CAACAAATAG
1848375 AATTTTTATATAAAT
1 AATTTTTATATAAAT
1848390 AATTTTTATATAAAT
1 AATTTTTATATAAAT
1848405 A
1 A
1848406 TTTAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1848512 original size:29 final size:30
Alignment explanation
Indices: 1848470--1848547 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 30
1848460 TACACATTCA
* *
1848470 GTAATCTTTTATTCCTT-TAACCAAACACT
1 GTAATCTTATATTCCTTACAACCAAACACT
1848499 GTAATCTTATATTCCTTCCAAACCAACCAAACACT
1 GTAATCTTATATTCCTT----A-CAACCAAACACT
1848534 GTAATCTTATATTC
1 GTAATCTTATATTC
1848548 TTGCCAAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 16 0.39
35 25 0.61
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
GTAATCTTATATTCCTTACAACCAAACACT
Found at i:1848530 original size:35 final size:35
Alignment explanation
Indices: 1848488--1848568 Score: 146
Period size: 35 Copynumber: 2.3 Consensus size: 35
1848478 TTATTCCTTT
1848488 AACCAAACACTGTAATCTTATATTCCTT-CCAAACC
1 AACCAAACACTGTAATCTTATATT-CTTGCCAAACC
1848523 AACCAAACACTGTAATCTTATATTCTTGCCAAACC
1 AACCAAACACTGTAATCTTATATTCTTGCCAAACC
1848558 AACCAAACACT
1 AACCAAACACT
1848569 ACAATGTAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 3 0.07
35 42 0.93
ACGTcount: A:0.40, C:0.31, G:0.04, T:0.26
Consensus pattern (35 bp):
AACCAAACACTGTAATCTTATATTCTTGCCAAACC
Found at i:1848635 original size:20 final size:20
Alignment explanation
Indices: 1848599--1848636 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1848589 ATCCTATTTT
**
1848599 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1848619 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1848637 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1849449 original size:27 final size:26
Alignment explanation
Indices: 1849394--1849450 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
1849384 ATGTATATTA
*
1849394 AAATTATCTATAATATAATTTTCAAAG
1 AAATTATCTATAATATAA-TTGCAAAG
*
1849421 AAATTATCTATTAATATCAA-TGCATAG
1 AAATTATCTA-TAATAT-AATTGCAAAG
1849448 AAA
1 AAA
1849451 ATAATTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 18 0.69
28 6 0.23
29 2 0.08
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (26 bp):
AAATTATCTATAATATAATTGCAAAG
Found at i:1854536 original size:35 final size:35
Alignment explanation
Indices: 1854462--1854529 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1854452 TTCATATTCA
* *
1854462 AAATTCCAAAATATTTTAATTATATTCTAAACCCC
1 AAATTCCAAAACACTTTAATTATATTCTAAACCCC
1854497 AAATTCCAAAACACTTTAATTATATTCTAAACC
1 AAATTCCAAAACACTTTAATTATATTCTAAACC
1854530 TTAAATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTTAATTATATTCTAAACCCC
Found at i:1854607 original size:35 final size:34
Alignment explanation
Indices: 1854531--1854608 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 34
1854521 TTCTAAACCT
1854531 TAAATTGAACTATTTTAGAATTTAAGGTTTAAAA
1 TAAATTGAACTATTTTAGAATTTAAGGTTTAAAA
* * *
1854565 TATAATTGAATTATTTTAGAATTTAGGGTTTAGAA
1 TA-AATTGAACTATTTTAGAATTTAAGGTTTAAAA
1854600 TGAAATTGA
1 T-AAATTGA
1854609 GGACTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
34 2 0.05
35 36 0.92
36 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.42
Consensus pattern (34 bp):
TAAATTGAACTATTTTAGAATTTAAGGTTTAAAA
Found at i:1869418 original size:3 final size:3
Alignment explanation
Indices: 1869402--1869463 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
1869392 TAATATTATT
* *
1869402 TAA TATA TAT TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1869448 TGA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
1869464 TATTATTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1869437 original size:18 final size:18
Alignment explanation
Indices: 1869414--1869463 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1869404 ATATATATTA
1869414 ATAATAATAATAATAATG
1 ATAATAATAATAATAATG
1869432 ATAATAATAATAATAATG
1 ATAATAATAATAATAATG
1869450 ATAATAATAATAAT
1 ATAATAATAATAAT
1869464 TATTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (18 bp):
ATAATAATAATAATAATG
Found at i:1869939 original size:116 final size:115
Alignment explanation
Indices: 1869802--1870467 Score: 961
Period size: 114 Copynumber: 5.8 Consensus size: 115
1869792 GATAGAATTA
* * *
1869802 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTTTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * * ***
1869867 GAACTCTAC-CTGGCAATGTTGATACATCAA-ATGATGAATTCAAACAAAAGG
63 GAACTCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
1869918 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * * * *
1869983 GAACTCTAC-CTGGCAATGTTGATCCATCAA-ATGATGAATTCAAGCAAAAGA
63 GAACTCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
* *
1870034 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1870099 CT-TTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
1870148 TTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1870213 CT-TTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
1870262 TTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1870327 C-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
1870376 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
1870441 C-CTTCTCTGGAAAAGCTAATCTATCAA
66 CTCTTCTCTGGAAAAGATAATCCATCAA
1870468 ATGATAGATT
Statistics
Matches: 521, Mismatches: 26, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
112 2 0.00
113 37 0.07
114 327 0.63
116 155 0.30
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (115 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
Found at i:1871344 original size:83 final size:83
Alignment explanation
Indices: 1871205--1871431 Score: 427
Period size: 83 Copynumber: 2.7 Consensus size: 83
1871195 GTAGTTCTTA
* * *
1871205 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCATCTTTTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
1871270 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
1871288 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
1871353 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
1871371 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1871432 CCAGTTAATG
Statistics
Matches: 141, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 141 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
ATTCAATGATTGGTTCTG
Found at i:1872237 original size:18 final size:19
Alignment explanation
Indices: 1872194--1872230 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1872184 TTCATAGAAG
*
1872194 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTCTCAAA
1872213 AATAAATTGAA-TCTCAAA
1 AATAAATTGAATTCTCAAA
1872231 TAAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAAATTGAATTCTCAAA
Found at i:1883228 original size:15 final size:13
Alignment explanation
Indices: 1883196--1883233 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
1883186 TTTGACAGCA
1883196 AAAT-AAATAATG
1 AAATAAAATAATG
1883208 AAATAAAATAATTG
1 AAATAAAATAA-TG
1883222 CAAATAAAATAA
1 -AAATAAAATAA
1883234 AACATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:1885390 original size:3 final size:3
Alignment explanation
Indices: 1885384--1885460 Score: 118
Period size: 3 Copynumber: 25.7 Consensus size: 3
1885374 TATATGTATT
* * *
1885384 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TGA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1885432 TAA TAA TAA TAA TAA TAA TAA TTA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1885461 TGGGTAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1886865 original size:15 final size:15
Alignment explanation
Indices: 1886845--1886873 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1886835 TGGCTGACCG
1886845 AACCGAATTAATCAT
1 AACCGAATTAATCAT
1886860 AACCGAATTAATCA
1 AACCGAATTAATCA
1886874 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AACCGAATTAATCAT
Found at i:1887383 original size:183 final size:184
Alignment explanation
Indices: 1887000--1887385 Score: 638
Period size: 182 Copynumber: 2.1 Consensus size: 184
1886990 TTTTCTAATT
* * * * *
1887000 TATATAA-AAATTAAATATTTTTTAATTCAAAAAATGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
*
1887064 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
1887129 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
131 GGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGCTTAGCCCATATGTTA
1887183 TATATAATATA-TTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAA
*
1887246 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
1887310 TGGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGCTT-AGCCCATATGTTA
1887365 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1887386 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
181 2 0.01
182 109 0.57
183 77 0.41
184 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGCTTAGCCCATATGTTA
Found at i:1889632 original size:20 final size:20
Alignment explanation
Indices: 1889609--1889646 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1889599 TTGACCTTTC
1889609 ATATA-TTCAACA-GTGAAT
1 ATATATTTCAACATGTGAAT
1889627 ATATATTTCAACATGTGAAT
1 ATATATTTCAACATGTGAAT
1889647 TCGGCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (20 bp):
ATATATTTCAACATGTGAAT
Found at i:1894797 original size:27 final size:26
Alignment explanation
Indices: 1894747--1894798 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1894737 GTGTGTTAGA
*
1894747 CTGTTAAAGAACATGCACGTGTATTG
1 CTGTTAAAGAACATGCACATGTATTG
*
1894773 CTGTTAAAGAAATATGCACATGTATT
1 CTGTTAAAG-AACATGCACATGTATT
1894799 AAGCAGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (26 bp):
CTGTTAAAGAACATGCACATGTATTG
Found at i:1896227 original size:32 final size:31
Alignment explanation
Indices: 1896169--1896241 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
1896159 ATATCATGAC
*
1896169 ATGATATATATCAGATTATCACTTTGAATAAT
1 ATGATATATATCAGATCATCACTTTG-ATAAT
* *
1896201 ATGATGTATATCACG-TCATCATTTTGATAAT
1 ATGATATATATCA-GATCATCACTTTGATAAT
* *
1896232 GTAATATATA
1 ATGATATATA
1896242 GATTATGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 12 0.35
32 21 0.62
33 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (31 bp):
ATGATATATATCAGATCATCACTTTGATAAT
Found at i:1896272 original size:2 final size:2
Alignment explanation
Indices: 1896265--1896297 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1896255 CATCAATTAC
1896265 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 A
1896298 AAATTATGCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1896389 original size:16 final size:15
Alignment explanation
Indices: 1896356--1896412 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1896346 TTATTTTAAC
**
1896356 TAAAAATTAAAACGT
1 TAAAAATTAAAATAT
1896371 TAAAAATTAAAATATT
1 TAAAAATTAAAATA-T
*
1896387 TAAAAA-T-ATATAT
1 TAAAAATTAAAATAT
1896400 T-AAAATTAAAATA
1 TAAAAATTAAAATA
1896413 ACCATTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.11
13 3 0.09
14 8 0.23
15 13 0.37
16 7 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAAAATTAAAATAT
Found at i:1905297 original size:105 final size:104
Alignment explanation
Indices: 1905117--1905317 Score: 348
Period size: 105 Copynumber: 1.9 Consensus size: 104
1905107 ACATCAACCA
*
1905117 AAATCACATGAACAAAGTAAGAATCGGATAATTAAGATTCCAAGAAAAGCCTAACAGATGATAGA
1 AAATCACATGAACAAAGTAAGAATCGGATAATTAAGATTCCAAGAAAAGCCTAACAGATGATAAA
*
1905182 ACTAACATCAAATGCATAAAGAAAAGCCAAATGTATACC
66 ACTAACATCAAATGCATAAAGAAAAACCAAATGTATACC
*
1905221 AAATACACATGAACAAATTAAGAATCGGATAATTAAGATTCCAAGAAAAGCCTAACAGATGATAA
1 AAAT-CACATGAACAAAGTAAGAATCGGATAATTAAGATTCCAAGAAAAGCCTAACAGATGATAA
* *
1905286 AAGTAAGATCAAATGCATAAAGAAAAACCAAA
65 AACTAACATCAAATGCATAAAGAAAAACCAAA
1905318 GCAAGCCTAA
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
104 4 0.04
105 87 0.96
ACGTcount: A:0.53, C:0.15, G:0.14, T:0.18
Consensus pattern (104 bp):
AAATCACATGAACAAAGTAAGAATCGGATAATTAAGATTCCAAGAAAAGCCTAACAGATGATAAA
ACTAACATCAAATGCATAAAGAAAAACCAAATGTATACC
Found at i:1906965 original size:20 final size:19
Alignment explanation
Indices: 1906942--1906988 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1906932 CGATATAACA
1906942 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
1906962 GGTATCAAAATGATGAAACC
1 GGTA-AAAAATGATAAAACC
1906982 GGTAAAA
1 GGTAAAA
1906989 CGCTACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Done.