Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 35
Found at i:5320759 original size:29 final size:29
Alignment explanation
Indices: 5320724--5320805 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
5320714 AAACTAAATT
* *
5320724 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
5320753 GATGTCATTGCTTATATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
5320782 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
5320806 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:5325510 original size:29 final size:29
Alignment explanation
Indices: 5325475--5325556 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
5325465 AAACTAAATT
* *
5325475 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
5325504 GATGTCATTGCTTATATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
5325533 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
5325557 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:5326472 original size:31 final size:31
Alignment explanation
Indices: 5326437--5326497 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
5326427 GGGAAAAGAA
5326437 TGGTAATATGGGTTCTTATCTTCGGATCAGT
1 TGGTAATATGGGTTCTTATCTTCGGATCAGT
5326468 TGGTAATATGGGTTCTTATCTTCGGATCAG
1 TGGTAATATGGGTTCTTATCTTCGGATCAG
5326498 GGTGGAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (31 bp):
TGGTAATATGGGTTCTTATCTTCGGATCAGT
Found at i:5331361 original size:45 final size:45
Alignment explanation
Indices: 5331272--5331711 Score: 630
Period size: 45 Copynumber: 9.8 Consensus size: 45
5331262 ACCTCTATTC
* *
5331272 ATGTTTATAATGCA-CCATTATGCATTTTCAACTCTAGCATACTTTT
1 ATGTTGATAATGCACCCA-TATGCA-TTTCAACTATAGCATACTTTT
**
5331318 ATGTTGATAATGCACCCATATGCATTTCAACTATATTATACTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
*
5331363 ATGTTGATAATGCACCCATATGCATTTCAACTATAGGATACTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
*
5331408 ATCTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
* * *
5331453 CTGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
* * * *
5331498 ATATTGATATTGCACCCATATACATTTCAACTATAGCATAATTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
* * * *
5331543 CTATTGATAATGCACCCATATGCATTTAAACTATATCATACTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
*
5331588 ATGTCGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
* * **
5331633 CTGTTGATAATGCACCCATATACATTTCAACTATAATATACTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
* **
5331678 ATGTTGATAATGGAATCATATGCATTTCAACTAT
1 ATGTTGATAATGCACCCATATGCATTTCAACTAT
5331712 GACATCGTTG
Statistics
Matches: 355, Mismatches: 38, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
45 333 0.94
46 19 0.05
47 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (45 bp):
ATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTT
Found at i:5332203 original size:22 final size:22
Alignment explanation
Indices: 5332161--5332231 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 22
5332151 TAGCTTTTCA
*
5332161 GTATCAATAC--CCATACCATG
1 GTATCAATACTACCATACTATG
5332181 GTATCAATACTACCATACTATG
1 GTATCAATACTACCATACTATG
*
5332203 GTA-C-ATA-TACTATACTATG
1 GTATCAATACTACCATACTATG
*
5332222 GTATCGATAC
1 GTATCAATAC
5332232 CATTTTTGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 14 0.32
20 14 0.32
21 4 0.09
22 12 0.27
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (22 bp):
GTATCAATACTACCATACTATG
Found at i:5333206 original size:32 final size:32
Alignment explanation
Indices: 5333165--5333237 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
5333155 CTAAGGTAAT
* *
5333165 CCTTGGGTAGGCTCTT-AGGCCCCAATATACTA
1 CCTTGGGTAGGCT-TTAAGGCCCCAAGACACTA
*
5333197 CCTTGGGTAGGCTTTAAGGCCCCAAGACACTC
1 CCTTGGGTAGGCTTTAAGGCCCCAAGACACTA
5333229 CCTTGGGTA
1 CCTTGGGTA
5333238 AATCATGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 2 0.05
32 35 0.95
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.26
Consensus pattern (32 bp):
CCTTGGGTAGGCTTTAAGGCCCCAAGACACTA
Found at i:5333524 original size:30 final size:32
Alignment explanation
Indices: 5333468--5333553 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 32
5333458 GTAGGCTTTT
* * *
5333468 AGGCTCTAAAGTACTCCCTT-GAGTAGGATCTA
1 AGGCCCTAAGGTATTCCCTTAG-GTAGGATCTA
* *
5333500 AGGCCC-AATGTATT-CCTTAGGTAGGCTCTA
1 AGGCCCTAAGGTATTCCCTTAGGTAGGATCTA
5333530 AGGCCCTAAGGTATTCCCTTAGGT
1 AGGCCCTAAGGTATTCCCTTAGGT
5333554 TGGCTTCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 19 0.41
31 14 0.30
32 13 0.28
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (32 bp):
AGGCCCTAAGGTATTCCCTTAGGTAGGATCTA
Found at i:5335615 original size:23 final size:24
Alignment explanation
Indices: 5335589--5335634 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
5335579 TCAACCATAA
*
5335589 TAACATATTAGGTAGCG-CTTATG
1 TAACATAATAGGTAGCGACTTATG
5335612 TAACATAATAGGTAGCGACTTAT
1 TAACATAATAGGTAGCGACTTAT
5335635 TAAGCTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (24 bp):
TAACATAATAGGTAGCGACTTATG
Found at i:5335920 original size:118 final size:117
Alignment explanation
Indices: 5335739--5337388 Score: 1092
Period size: 118 Copynumber: 14.6 Consensus size: 117
5335729 TATTACCAAA
* * *
5335739 TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACATAACTA-GTCAACTACTTGATTTGTTA
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACA-AACTAGGTTAATTACTTGATTTGTTA
*
5335803 TCAACCATAATAACATATTAGGTAGCCCTTATGTAACATAATAGGTAGCGCAT
65 TCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCAT
* * * * *
5335856 TTTTAAAGCTAATGGGGCCTTAGAAATCTGACGATATA-AAATTAGGTTAATTATTTAATTTGTT
1 TTTT-AAGCTGATGGGGCCTTAGAAATCCGACGATA-ACAAACTAGGTTAATTACTTGATTTGTT
** * * * *
5335920 ATC-AGTATTATCAACATATTAGGTA--AC--ATAT-A-A-AAT-GTTA-C-CAAA
64 ATCAACCATAAT-AACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGC-AT
* * * * *
5335965 GTTTAAGCTGATTGAGCCTTAGAAATCTGACGATAACATAACCA-GTTAATTACTTGATTTGTTA
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACA-AACTAGGTTAATTACTTGATTTGTTA
* * *
5336029 TCAACCATAATAACATATTAGGTATCACTTATGTAACGTAATAGGTAGCGCCT
65 TCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCAT
* ** * *
5336082 TTTTAAAGATGATGGGGCCTTAGAAATTTGACGATATCATAACCA-GTTAATTACTTGATTTGTT
1 TTTT-AAGCTGATGGGGCCTTAGAAATCCGACGATAACA-AACTAGGTTAATTACTTGATTTGTT
* * *
5336146 ATCAACCATAATAACATATTAGGTATCACTTATGTAACGTAATAGGTAGCGCCT
64 ATCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCAT
* * * * * *
5336200 TTTTAAAGATGACGGGGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACATAATTTGTTA
1 TTTT-AAGCTGATGGGGCCTTAGAAATCCGACGATAACAAACTAGGTTAATTACTTGATTTGTTA
** * * * *
5336265 TC-AGTATTATCAACATATTAGGTA--AC-------ACCTAAT-GTTA-C-CAAA
65 TCAACCATAAT-AACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGC-AT
* * * * *
5336307 GTTTAAGATGATGGAGCCTTAGAAATCCGACGATAACTTAA-TTGGTTAATTACTTGATTTGTTA
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAAC-AAACTAGGTTAATTACTTGATTTGTTA
** * *
5336371 TCAACCATAATAACATATTAGGTAATACTTATGTAACGTAAT-GCGTAGCGCCT
65 TCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAG-GTAGCGCAT
* * * * * *
5336424 TTTTAAGCTGATTGGTCCTTAGAAATCCGAAGATAATAAAATAGGTTAATTACTTAATTTGTTAT
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAACTAGGTTAATTACTTGATTTGTTAT
** * * * *
5336489 C-AGTATTATCAACATATTA-G--GCA---ATGCCT-A-A-AAT-GTTACCG-AA
66 CAACCATAAT-AACATATTAGGTAGCACTTATG--TAACATAATAGGTAGCGCAT
* * ** * *
5336532 GTTTAAGTTGATGGATCCTTAGAAATCCGACGATAACATAAC-AAGTTAATTATTTGATTTGTTA
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACA-AACTAGGTTAATTACTTGATTTGTTA
* * *
5336596 TCAACCATAATAACATATTAGGTAGAATTTATGTAACACAATAGGTAGCGTC-T
65 TCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCG-CAT
* * *
5336649 TTTTAAGCTGATGGGGCCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTAATTTGTTAT
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAACTAGGTTAATTACTTGATTTGTTAT
** * * * *
5336714 C-AGTATTATCAACATATTAAGTAAGGC-C-----T-A-A-AAT-GTTA-C-CAAA
66 CAACCATAAT-AACATATTAGGT-A-GCACTTATGTAACATAATAGGTAGCGC-AT
* * * * *
5336757 GTTTAAGCTGATGGAGCCTTAGAAATCTGATGATAACATAAC-CGGTTAATTACTTGATTTGTTA
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACA-AACTAGGTTAATTACTTGATTTGTTA
* * * * *
5336821 TCAACCATAATAACATATTAGGTAACGCTTATGTAACGTAATAGGTAGTGCCT
65 TCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCAT
* * * * *
5336874 TTTTAAAACTGATGGGGCCTTAGAAATCCGAAGATAACAAAATAAGTTAATTACTTAATTTGTTA
1 TTTT-AAGCTGATGGGGCCTTAGAAATCCGACGATAACAAACTAGGTTAATTACTTGATTTGTTA
*** * *** * * *
5336939 T-ATGTATTATCAACATATTAGGTA--A--TGCCT-A-A-AAT-GTTACCG-AA
65 TCAACCATAAT-AACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCAT
* * * * * *
5336983 GTTTAAGCTGATGGAGCCTTAGAAATCCAACGATCACATAACCA-GTTAATTATTTGATTT-TTA
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACA-AACTAGGTTAATTACTTGATTTGTTA
* * * *
5337046 TCAACCATAATAACATATTAGGTAGCGCTTATG-AACGTAATAGGTAGCACCT
65 TCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCAT
* * * *
5337098 TTTTAAGCTGATGGGGCCTTAGAAGTCCGACGATAACAAAATAGGTTAATTACCTAATTTGTTAT
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAACTAGGTTAATTACTTGATTTGTTAT
** * *** * *
5337163 --AGTATTATCAACATATTAGGTA--A--TGCCT-A-A-AAT-GTTA-C-CAAA
66 CAACCATAAT-AACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGC-AT
* ** * * * * *
5337205 GTTTAAGCTGATGAAGCCTTAGAAAACCGATGATAACATAACCA-ATTAATTATTTGATTTGTTA
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACA-AACTAGGTTAATTACTTGATTTGTTA
* * * * * * *
5337269 TAAACCATAATAACATATTATGTAACGCTTATGTAACGTAATAGGTAGTGCCT
65 TCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCAT
* ** * * * *
5337322 TTTTAAGCTTATGGGGCCTTAGAAATAGGATGATATCAAAATAGGTTAATTACTTAATTTGTTAT
1 TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAACTAGGTTAATTACTTGATTTGTTAT
5337387 CA
66 CA
5337389 GTATTATCAA
Statistics
Matches: 1183, Mismatches: 243, Indels: 214
0.72 0.15 0.13
Matches are distributed among these distances:
106 69 0.06
107 81 0.07
108 265 0.22
109 55 0.05
110 16 0.01
111 16 0.01
112 10 0.01
113 11 0.01
114 22 0.02
115 78 0.07
116 41 0.03
117 212 0.18
118 305 0.26
119 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (117 bp):
TTTTAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAACTAGGTTAATTACTTGATTTGTTAT
CAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCAT
Found at i:5336170 original size:226 final size:226
Alignment explanation
Indices: 5335576--5336149 Score: 841
Period size: 226 Copynumber: 2.5 Consensus size: 226
5335566 ACTGGAAACA
* * *
5335576 TTATCAACCATAATAACATATTAGGTAGCGCTTATGTAACATAATAGGTAGCGACTTATT-AAGC
1 TTATCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCCTTTTTAAAGC
* * *
5335640 TGATGGAGACTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTA
66 TGATGGGGCCTTAGAAATCTGACGATATCAAAATAGGTTAATTACTTAATTTGTTATCAGTATTA
* ** * *
5335705 TCAACAT-TTAGGCAATGCCTAAAATATTACCAAATTTTAAGCTGATGGAGCCTTAGAAATCCGA
131 TCAACATATTAGGTAACACATAAAATATTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGA
*
5335769 CGATAACATAACTAGTCAACTACTTGATTTG
196 CGATAACATAACCAGTCAACTACTTGATTTG
* *
5335800 TTATCAACCATAATAACATATTAGGTAGCCCTTATGTAACATAATAGGTAGCGCATTTTTAAAGC
1 TTATCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCCTTTTTAAAGC
* *
5335865 TAATGGGGCCTTAGAAATCTGACGATAT-AAAATTAGGTTAATTATTTAATTTGTTATCAGTATT
66 TGATGGGGCCTTAGAAATCTGACGATATCAAAA-TAGGTTAATTACTTAATTTGTTATCAGTATT
* * * *
5335929 ATCAACATATTAGGTAACATATAAAATGTTACCAAAGTTTAAGCTGATTGAGCCTTAGAAATCTG
130 ATCAACATATTAGGTAACACATAAAATATTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCG
* *
5335994 ACGATAACATAACCAGTTAATTACTTGATTTG
195 ACGATAACATAACCAGTCAACTACTTGATTTG
* * *
5336026 TTATCAACCATAATAACATATTAGGTATCACTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGA
1 TTATCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCCTTTTTAAAGC
* ** *
5336091 TGATGGGGCCTTAGAAATTTGACGATATCATAACCA-GTTAATTACTTGATTTGTTATCA
66 TGATGGGGCCTTAGAAATCTGACGATATCA-AAATAGGTTAATTACTTAATTTGTTATCA
5336150 ACCATAATAA
Statistics
Matches: 313, Mismatches: 32, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
224 60 0.19
225 66 0.21
226 183 0.58
227 2 0.01
228 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (226 bp):
TTATCAACCATAATAACATATTAGGTAGCACTTATGTAACATAATAGGTAGCGCCTTTTTAAAGC
TGATGGGGCCTTAGAAATCTGACGATATCAAAATAGGTTAATTACTTAATTTGTTATCAGTATTA
TCAACATATTAGGTAACACATAAAATATTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGA
CGATAACATAACCAGTCAACTACTTGATTTG
Found at i:5336605 original size:225 final size:225
Alignment explanation
Indices: 5336091--5337514 Score: 2072
Period size: 225 Copynumber: 6.3 Consensus size: 225
5336081 TTTTTAAAGA
* ** *
5336091 TGATGGGGCCTTAGAAATTTGACGATATCATAACCAGTTAATTACTTGATTTGTTATCAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACATAACCAGTTAATTACTTGATTTGTTATCAACCATA
* * *
5336156 ATAACATATTAGGTATCACTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGATGACGGGGCCTT
66 ATAACATATTAGGTAACACTTATGTAACGTAATAGGTAGCGCCTTTTT-AAGCTGATGGGGCCTT
* * *
5336221 AGAAATCTGACGATAACAAAATAGGTTAATTACATAATTTGTTATCAGTATTATCAACATATTAG
130 AGAAATCCGAAGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAG
** *
5336286 GTAACACCT--AATGTTACCAAAGTTTAAGA
195 GTAATGCCTAAAATGTTACCAAAGTTTAAGC
* ***
5336315 TGATGGAGCCTTAGAAATCCGACGATAACTTAATTGGTTAATTACTTGATTTGTTATCAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACATAACCAGTTAATTACTTGATTTGTTATCAACCATA
* * *
5336380 ATAACATATTAGGTAATACTTATGTAACGTAAT-GCGTAGCGCCTTTTTAAGCTGATTGGTCCTT
66 ATAACATATTAGGTAACACTTATGTAACGTAATAG-GTAGCGCCTTTTTAAGCTGATGGGGCCTT
*
5336444 AGAAATCCGAAGATAATAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAG
130 AGAAATCCGAAGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAG
* * *
5336509 GCAATGCCTAAAATGTTACCGAAGTTTAAGT
195 GTAATGCCTAAAATGTTACCAAAGTTTAAGC
* * *
5336540 TGATGGATCCTTAGAAATCCGACGATAACATAACAAGTTAATTATTTGATTTGTTATCAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACATAACCAGTTAATTACTTGATTTGTTATCAACCATA
* ** *
5336605 ATAACATATTAGGTAGA-ATTTATGTAACACAATAGGTAGCGTCTTTTTAAGCTGATGGGGCCTT
66 ATAACATATTAGGTA-ACACTTATGTAACGTAATAGGTAGCGCCTTTTTAAGCTGATGGGGCCTT
* *
5336669 AGAAATCCGATGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAA
130 AGAAATCCGAAGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAG
*
5336734 GTAAGGCCTAAAATGTTACCAAAGTTTAAGC
195 GTAATGCCTAAAATGTTACCAAAGTTTAAGC
* * *
5336765 TGATGGAGCCTTAGAAATCTGATGATAACATAACCGGTTAATTACTTGATTTGTTATCAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACATAACCAGTTAATTACTTGATTTGTTATCAACCATA
* * *
5336830 ATAACATATTAGGTAACGCTTATGTAACGTAATAGGTAGTGCCTTTTTAAAACTGATGGGGCCTT
66 ATAACATATTAGGTAACACTTATGTAACGTAATAGGTAGCGCCTTTTT-AAGCTGATGGGGCCTT
*
5336895 AGAAATCCGAAGATAACAAAATAAGTTAATTACTTAATTTGTTAT-ATGTATTATCAACATATTA
130 AGAAATCCGAAGATAACAAAATAGGTTAATTACTTAATTTGTTATCA-GTATTATCAACATATTA
*
5336959 GGTAATGCCTAAAATGTTACCGAAGTTTAAGC
194 GGTAATGCCTAAAATGTTACCAAAGTTTAAGC
* * *
5336991 TGATGGAGCCTTAGAAATCCAACGATCACATAACCAGTTAATTATTTGATTT-TTATCAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACATAACCAGTTAATTACTTGATTTGTTATCAACCATA
* * *
5337055 ATAACATATTAGGTAGCGCTTATG-AACGTAATAGGTAGCACCTTTTTAAGCTGATGGGGCCTTA
66 ATAACATATTAGGTAACACTTATGTAACGTAATAGGTAGCGCCTTTTTAAGCTGATGGGGCCTTA
* * *
5337119 GAAGTCCGACGATAACAAAATAGGTTAATTACCTAATTTGTTAT-AGTATTATCAACATATTAGG
131 GAAATCCGAAGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGG
5337183 TAATGCCTAAAATGTTACCAAAGTTTAAGC
196 TAATGCCTAAAATGTTACCAAAGTTTAAGC
* * * * * *
5337213 TGATGAAGCCTTAGAAAACCGATGATAACATAACCAATTAATTATTTGATTTGTTATAAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACATAACCAGTTAATTACTTGATTTGTTATCAACCATA
* * * *
5337278 ATAACATATTATGTAACGCTTATGTAACGTAATAGGTAGTGCCTTTTTAAGCTTATGGGGCCTTA
66 ATAACATATTAGGTAACACTTATGTAACGTAATAGGTAGCGCCTTTTTAAGCTGATGGGGCCTTA
** * * *
5337343 GAAATAGGATGATATCAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAATATATTAGG
131 GAAATCCGAAGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGG
* *
5337408 TAAAGCCTAAAATGTTACAAAAGTTTAAGC
196 TAATGCCTAAAATGTTACCAAAGTTTAAGC
* * ** * *
5337438 TAATGGAGCCTTAGAAATCTGACGATAACATAACTGGTTAATTACTTGATTTGTTATCAACCTTT
1 TGATGGAGCCTTAGAAATCCGACGATAACATAACCAGTTAATTACTTGATTTGTTATCAACCATA
5337503 ATCAACATATTA
66 AT-AACATATTA
5337515 CCATGTATAT
Statistics
Matches: 1080, Mismatches: 108, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
222 94 0.09
223 170 0.16
224 198 0.18
225 457 0.42
226 161 0.15
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (225 bp):
TGATGGAGCCTTAGAAATCCGACGATAACATAACCAGTTAATTACTTGATTTGTTATCAACCATA
ATAACATATTAGGTAACACTTATGTAACGTAATAGGTAGCGCCTTTTTAAGCTGATGGGGCCTTA
GAAATCCGAAGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGG
TAATGCCTAAAATGTTACCAAAGTTTAAGC
Found at i:5337435 original size:673 final size:674
Alignment explanation
Indices: 5336091--5337514 Score: 2171
Period size: 673 Copynumber: 2.1 Consensus size: 674
5336081 TTTTTAAAGA
* * * *
5336091 TGATGGGGCCTTAGAAATTTGACGATATCATAACCAGTTAATTACTTGATTTGTTATCAACCATA
1 TGATGGAGCCTTAGAAATCTGACGATAACATAACCGGTTAATTACTTGATTTGTTATCAACCATA
*
5336156 ATAACATATTAGGTATCACTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGATGACGGGGCCTT
66 ATAACATATTAGGTAACACTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGATGACGGGGCCTT
* * *
5336221 AGAAATCTGACGATAACAAAATAGGTTAATTACATAATTTGTTATCAGTATTATCAACATATTAG
131 AGAAATCCGAAGATAACAAAATAAGTTAATTACATAATTTGTTATCAGTATTATCAACATATTAG
* * ***
5336286 GTAACACCTAATGTTACCAAAGTTTAAGATGATGGAGCCTTAGAAATCCGACGATAACTTAATTG
196 GTAACACCTAATGTTACCAAAGTTTAAGATGATGGAGCCTTAGAAATCCAACGATAACATAACCA
*
5336351 GTTAATTACTTGATTTGTTATCAACCATAATAACATATTAGGTAATACTTATGTAACGTAATGCG
261 GTTAATTACTTGATTTGTTATCAACCATAATAACATATTAGGTAACACTTATGTAACGTAATGCG
* * * * *
5336416 TAGCGCCTTTTTAAGCTGATTGGTCCTTAGAAATCCGAAGATAATAAAATAGGTTAATTACTTAA
326 TAGCACCTTTTTAAGCTGATGGGGCCTTAGAAATCCGAAGATAACAAAATAGGTTAATTACCTAA
* * *
5336481 TTTGTTATCAGTATTATCAACATATTAGGCAATGCCTAAAATGTTACCGAAGTTTAAGTTGATGG
391 TTTGTTATCAGTATTATCAACATATTAGGCAATGCCTAAAATGTTACCAAAGTTTAAGCTGATGA
* * *
5336546 ATCCTTAGAAATCCGACGATAACATAACAAGTTAATTATTTGATTTGTTATCAACCATAATAACA
456 AGCCTTAGAAAACCGACGATAACATAACAAGTTAATTATTTGATTTGTTATAAACCATAATAACA
* * *
5336611 TATTAGGTAGAATTTATGTAACACAATAGGTAGCGTCTTTTTAAGCTGATGGGGCCTTAGAAATC
521 TATTAGGTAGAACTTATGTAACACAATAGGTAGCGCCTTTTTAAGCTGATGGGGCCTTAGAAATA
*
5336676 CGATGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAAGTAAGGC
586 CGATGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAAGTAAAGC
*
5336741 CTAAAATGTTACCAAAGTTTAAGC
651 CTAAAATGTTACAAAAGTTTAAGC
*
5336765 TGATGGAGCCTTAGAAATCTGATGATAACATAACCGGTTAATTACTTGATTTGTTATCAACCATA
1 TGATGGAGCCTTAGAAATCTGACGATAACATAACCGGTTAATTACTTGATTTGTTATCAACCATA
* * *
5336830 ATAACATATTAGGTAACGCTTATGTAACGTAATAGGTAGTGCCTTTTTAAA-ACTGATGGGGCCT
66 ATAACATATTAGGTAACACTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGA-TGACGGGGCCT
*
5336894 TAGAAATCCGAAGATAACAAAATAAGTTAATTACTTAATTTGTTAT-ATGTATTATCAACATATT
130 TAGAAATCCGAAGATAACAAAATAAGTTAATTACATAATTTGTTATCA-GTATTATCAACATATT
** * * *
5336958 AGGTAATGCCTAAAATGTTACCGAAGTTTAAGCTGATGGAGCCTTAGAAATCCAACGATCACATA
194 AGGTAACACCT--AATGTTACCAAAGTTTAAGATGATGGAGCCTTAGAAATCCAACGATAACATA
* * *
5337023 ACCAGTTAATTATTTGATTT-TTATCAACCATAATAACATATTAGGTAGCGCTTATG-AACGTAA
257 ACCAGTTAATTACTTGATTTGTTATCAACCATAATAACATATTAGGTAACACTTATGTAACGTAA
* *
5337086 TAG-GTAGCACCTTTTTAAGCTGATGGGGCCTTAGAAGTCCGACGATAACAAAATAGGTTAATTA
322 T-GCGTAGCACCTTTTTAAGCTGATGGGGCCTTAGAAATCCGAAGATAACAAAATAGGTTAATTA
*
5337150 CCTAATTTGTTAT-AGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTTAAGCT
386 CCTAATTTGTTATCAGTATTATCAACATATTAGGCAATGCCTAAAATGTTACCAAAGTTTAAGCT
*
5337214 GATGAAGCCTTAGAAAACCGATGATAACATAACCAA-TTAATTATTTGATTTGTTATAAACCATA
451 GATGAAGCCTTAGAAAACCGACGATAACATAA-CAAGTTAATTATTTGATTTGTTATAAACCATA
* * ** * *
5337278 ATAACATATTATGTA-ACGCTTATGTAACGTAATAGGTAGTGCCTTTTTAAGCTTATGGGGCCTT
515 ATAACATATTAGGTAGA-ACTTATGTAACACAATAGGTAGCGCCTTTTTAAGCTGATGGGGCCTT
* * * *
5337342 AGAAATAGGATGATATCAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAATATATTAG
579 AGAAATACGATGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAA
5337407 GTAAAGCCTAAAATGTTACAAAAGTTTAAGC
644 GTAAAGCCTAAAATGTTACAAAAGTTTAAGC
* * * *
5337438 TAATGGAGCCTTAGAAATCTGACGATAACATAACTGGTTAATTACTTGATTTGTTATCAACCTTT
1 TGATGGAGCCTTAGAAATCTGACGATAACATAACCGGTTAATTACTTGATTTGTTATCAACCATA
5337503 ATCAACATATTA
66 AT-AACATATTA
5337515 CCATGTATAT
Statistics
Matches: 680, Mismatches: 62, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
672 1 0.00
673 310 0.46
674 272 0.40
675 34 0.05
676 63 0.09
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (674 bp):
TGATGGAGCCTTAGAAATCTGACGATAACATAACCGGTTAATTACTTGATTTGTTATCAACCATA
ATAACATATTAGGTAACACTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGATGACGGGGCCTT
AGAAATCCGAAGATAACAAAATAAGTTAATTACATAATTTGTTATCAGTATTATCAACATATTAG
GTAACACCTAATGTTACCAAAGTTTAAGATGATGGAGCCTTAGAAATCCAACGATAACATAACCA
GTTAATTACTTGATTTGTTATCAACCATAATAACATATTAGGTAACACTTATGTAACGTAATGCG
TAGCACCTTTTTAAGCTGATGGGGCCTTAGAAATCCGAAGATAACAAAATAGGTTAATTACCTAA
TTTGTTATCAGTATTATCAACATATTAGGCAATGCCTAAAATGTTACCAAAGTTTAAGCTGATGA
AGCCTTAGAAAACCGACGATAACATAACAAGTTAATTATTTGATTTGTTATAAACCATAATAACA
TATTAGGTAGAACTTATGTAACACAATAGGTAGCGCCTTTTTAAGCTGATGGGGCCTTAGAAATA
CGATGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAAGTAAAGC
CTAAAATGTTACAAAAGTTTAAGC
Found at i:5337703 original size:14 final size:14
Alignment explanation
Indices: 5337684--5337713 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5337674 AGTATGGAAA
5337684 ATATATATGTATGT
1 ATATATATGTATGT
5337698 ATATATATGTATGT
1 ATATATATGTATGT
5337712 AT
1 AT
5337714 GTATCGATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
ATATATATGTATGT
Found at i:5337845 original size:13 final size:14
Alignment explanation
Indices: 5337818--5337847 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5337808 ACTATTATCG
5337818 TTTTACCGATATAC
1 TTTTACCGATATAC
5337832 TTTTACCG-TATAC
1 TTTTACCGATATAC
5337845 TTT
1 TTT
5337848 GTAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTTACCGATATAC
Found at i:5339835 original size:20 final size:19
Alignment explanation
Indices: 5339796--5339836 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5339786 CTTTCTCTTA
* *
5339796 TTTTACTCCAATGCCATTT
1 TTTTACTCCAACGACATTT
5339815 TTTTACTCCAACCGACATTT
1 TTTTACTCCAA-CGACATTT
5339835 TT
1 TT
5339837 AATAAATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.22, C:0.27, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTTACTCCAACGACATTT
Found at i:5340272 original size:2 final size:2
Alignment explanation
Indices: 5340265--5340296 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5340255 GATTCCGAAG
5340265 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
5340297 CCTTCCCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5341345 original size:55 final size:55
Alignment explanation
Indices: 5341204--5341447 Score: 319
Period size: 55 Copynumber: 4.5 Consensus size: 55
5341194 TTGACTCACC
* * **
5341204 TATGAATTTCTTGAGGTTGCACATACAATGACAATACGGAAATTCATAAACTCAT
1 TATGAATTTCTTGAGGTTGCACACACAATGCCAATACAAAAATTCATAAACTCAT
* * * * * *
5341259 TAT-AAATTCGTGAGGTTGCACACATACTGCCAATGCAAAAATTCATAAAATCAT
1 TATGAATTTCTTGAGGTTGCACACACAATGCCAATACAAAAATTCATAAACTCAT
* * * **
5341313 TATGAATTTCTTGAGGTTGCACACATAGTGCCAGTACGGAAATTCATAAACTCAT
1 TATGAATTTCTTGAGGTTGCACACACAATGCCAATACAAAAATTCATAAACTCAT
* * *
5341368 TATAAATTTCTTGAGGTTGCACACACAATGCCAGTACAAAAACTCATAAACTCAT
1 TATGAATTTCTTGAGGTTGCACACACAATGCCAATACAAAAATTCATAAACTCAT
5341423 TATGAATTTCTTGAGGTTGCACACA
1 TATGAATTTCTTGAGGTTGCACACA
5341448 GTGCCCTAGT
Statistics
Matches: 163, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 44 0.27
55 119 0.73
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (55 bp):
TATGAATTTCTTGAGGTTGCACACACAATGCCAATACAAAAATTCATAAACTCAT
Found at i:5341438 original size:110 final size:109
Alignment explanation
Indices: 5341204--5341447 Score: 371
Period size: 110 Copynumber: 2.2 Consensus size: 109
5341194 TTGACTCACC
*
5341204 TATGAATTTCTTGAGGTTGCACATACAATGACAATACGGAAATTCATAAACTCATTATAAATTCG
1 TATGAATTTCTTGAGGTTGCACACACAATGACAATACGGAAATTCATAAACTCATTATAAATTCG
* * * *
5341269 TGAGGTTGCACACATACTGCCAATGCAAAAATTCATAAAATCAT
66 TGAGGTTGCACACACAATGCCAATACAAAAACTCATAAAATCAT
* * * *
5341313 TATGAATTTCTTGAGGTTGCACACATAGTGCCAGTACGGAAATTCATAAACTCATTATAAATTTC
1 TATGAATTTCTTGAGGTTGCACACACAATGACAATACGGAAATTCATAAACTCATTATAAA-TTC
* * *
5341378 TTGAGGTTGCACACACAATGCCAGTACAAAAACTCATAAACTCAT
65 GTGAGGTTGCACACACAATGCCAATACAAAAACTCATAAAATCAT
5341423 TATGAATTTCTTGAGGTTGCACACA
1 TATGAATTTCTTGAGGTTGCACACA
5341448 GTGCCCTAGT
Statistics
Matches: 122, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
109 56 0.46
110 66 0.54
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (109 bp):
TATGAATTTCTTGAGGTTGCACACACAATGACAATACGGAAATTCATAAACTCATTATAAATTCG
TGAGGTTGCACACACAATGCCAATACAAAAACTCATAAAATCAT
Found at i:5346317 original size:55 final size:55
Alignment explanation
Indices: 5346224--5346496 Score: 366
Period size: 55 Copynumber: 5.0 Consensus size: 55
5346214 TGGTTTTCAA
* * * * * * *
5346224 ACACGTAGTGCCGATACGATAATTTACAAACTCATTATGAATTACGTGGGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
* * * *
5346279 ACACATAGTACCAATATGGAAATTCATAAACTCATTATGAATTTTGTGAGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
* * *
5346334 ACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTGAGGTTGT
1 ACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
* * *
5346389 ACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCGTGAGGTTAC
1 ACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
* * *
5346444 ACACATAGTGCCAATACGAAAATTCATAAACTCGTTATGGATTTCTTGAGGTT
1 ACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTT
5346497 TAACACAGGG
Statistics
Matches: 191, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 191 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (55 bp):
ACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
Found at i:5354867 original size:33 final size:33
Alignment explanation
Indices: 5354828--5354902 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
5354818 TTGCACGTTG
5354828 TACGCTCCAGACCTCCACGGCCACATTGCACGC
1 TACGCTCCAGACCTCCACGGCCACATTGCACGC
5354861 TACGCTCCAGACCTCCACGGCCACATTGCACGC
1 TACGCTCCAGACCTCCACGGCCACATTGCACGC
*
5354894 CACGCTCCA
1 TACGCTCCA
5354903 CCGCTCTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.21, C:0.47, G:0.17, T:0.15
Consensus pattern (33 bp):
TACGCTCCAGACCTCCACGGCCACATTGCACGC
Found at i:5360261 original size:20 final size:20
Alignment explanation
Indices: 5360217--5360269 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
5360207 ACAAATTTTT
* * *
5360217 TATGAATAGTAT-TGTATTG
1 TATGAATAGTATCAGTACTA
5360236 TATGAATAGTATCAGTACTA
1 TATGAATAGTATCAGTACTA
5360256 TATGAATAGTATCA
1 TATGAATAGTATCA
5360270 ATATTGTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (20 bp):
TATGAATAGTATCAGTACTA
Found at i:5368007 original size:39 final size:41
Alignment explanation
Indices: 5367913--5368044 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 41
5367903 CACAGTGACG
*
5367913 AGCACAGGCAACGGTATCCTTGGTGGTACATCTGCAACTACC
1 AGCACAGGCAATGGTATCCTTGGTGGTACA-CTGCAACTACC
* *
5367955 AGCATAGGAAATGGTATCCTTGGTGGTACA-T-CAACTACC
1 AGCACAGGCAATGGTATCCTTGGTGGTACACTGCAACTACC
*
5367994 AGCACAGGCAATGGTATCTTTGGTGGTACACCTGCAACTA-C
1 AGCACAGGCAATGGTATCCTTGGTGGTACA-CTGCAACTACC
5368035 AGGCACAGGC
1 A-GCACAGGC
5368045 TGTAGTACTT
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
39 35 0.44
40 1 0.01
41 3 0.04
42 41 0.51
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (41 bp):
AGCACAGGCAATGGTATCCTTGGTGGTACACTGCAACTACC
Found at i:5370063 original size:46 final size:47
Alignment explanation
Indices: 5369982--5370078 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 47
5369972 GGATACCTAC
** *
5369982 ATTTCCGTGTACCCGAAGTATTAGGTACCCCGTTCTCC-GAGTAGTAT
1 ATTTCCGTGTACCCGAAGTACCAGGAACCCCGTTCTCCAGA-TAGTAT
* * *
5370029 ATTT-CGTGTACTCGAAGTACCAGGAACCCGGTTCTTCAGATAGTAT
1 ATTTCCGTGTACCCGAAGTACCAGGAACCCCGTTCTCCAGATAGTAT
5370075 ATTT
1 ATTT
5370079 GTTGGCATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
46 37 0.86
47 6 0.14
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (47 bp):
ATTTCCGTGTACCCGAAGTACCAGGAACCCCGTTCTCCAGATAGTAT
Found at i:5378437 original size:22 final size:23
Alignment explanation
Indices: 5378412--5378469 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
5378402 TTTATTATTT
*
5378412 AAAA-ATAAAATATTTTAAATTC
1 AAAATATAAAATATTTAAAATTC
*
5378434 AAAATATAAAA-ATTTAAAATTT
1 AAAATATAAAATATTTAAAATTC
*
5378456 AAAATATCAAATAT
1 AAAATATAAAATAT
5378470 ATATATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 23 0.74
23 8 0.26
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATATAAAATATTTAAAATTC
Found at i:5384829 original size:14 final size:17
Alignment explanation
Indices: 5384812--5384847 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
5384802 AAAACTATTT
5384812 ATAAATCA-CTA-AA-A
1 ATAAATCATCTATAACA
5384826 ATAAATCATCTATAACA
1 ATAAATCATCTATAACA
5384843 ATAAA
1 ATAAA
5384848 ATAAAACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.42
15 3 0.16
16 2 0.11
17 6 0.32
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAATCATCTATAACA
Found at i:5384866 original size:21 final size:22
Alignment explanation
Indices: 5384823--5384866 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5384813 TAAATCACTA
* *
5384823 AAAATAAATCATCTATAACAAT
1 AAAATAAAACATCGATAACAAT
*
5384845 AAAATAAAACAT-GATAATAAT
1 AAAATAAAACATCGATAACAAT
5384866 A
1 A
5384867 TGGGTTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATAAAACATCGATAACAAT
Found at i:5394064 original size:20 final size:20
Alignment explanation
Indices: 5394039--5394076 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5394029 GGAAATTAAT
5394039 GTTAGAGTGATG-AATTTGGA
1 GTTAGAGTG-TGAAATTTGGA
5394059 GTTAGAGTGTGAAATTTG
1 GTTAGAGTGTGAAATTTG
5394077 ACTATTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (20 bp):
GTTAGAGTGTGAAATTTGGA
Found at i:5395849 original size:19 final size:18
Alignment explanation
Indices: 5395825--5395887 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
5395815 TATGAATTGG
5395825 GCTATGAACTTGAAAATAA
1 GCTATGAA-TTGAAAATAA
*
5395844 GCTATGAATTTGAAACTAA
1 GCTATGAA-TTGAAAATAA
*
5395863 GTTATGAATCT-AAAATAA
1 GCTATGAAT-TGAAAATAA
*
5395881 GTTATGA
1 GCTATGA
5395888 GTCATGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
18 14 0.36
19 25 0.64
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (18 bp):
GCTATGAATTGAAAATAA
Found at i:5395883 original size:18 final size:19
Alignment explanation
Indices: 5395835--5395887 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
5395825 GCTATGAACT
* *
5395835 TGAAAATAAGCTATGAATT
1 TGAAAATAAGTTATGAATC
*
5395854 TGAAACTAAGTTATGAATC
1 TGAAAATAAGTTATGAATC
5395873 T-AAAATAAGTTATGA
1 TGAAAATAAGTTATGA
5395888 GTCATGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (19 bp):
TGAAAATAAGTTATGAATC
Found at i:5397202 original size:54 final size:54
Alignment explanation
Indices: 5397130--5397673 Score: 707
Period size: 54 Copynumber: 10.1 Consensus size: 54
5397120 ATATGTATTC
* *
5397130 ATTTACTGTATTGACACTATATGTGCAACCTAAGAAATTCATAATAAGTTTATGA
1 ATTTA-TGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* * *
5397185 ATTTATGTATTGGCACTAAGCGTTCAACCTAAGAAATTCATAATAAGTTTATGA
1 ATTTATGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* *
5397239 ATTTATGTATTGGCACTATGCGTGCAACCTAAGAAATTTATAATAAGTTTATGA
1 ATTTATGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* ** * *
5397293 ACTTCCGTATTGTCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGA
1 ATTTATGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* * * * *
5397347 ATTTACGAATTGGCACAATGTATGCAACCTAAGAAATTTATAATAAGTTTATGA
1 ATTTATGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* * *
5397401 ATTTCTGTATTTGCATTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
1 ATTTATGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
*
5397455 ATTT-TCTTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
1 ATTTAT-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* * *
5397509 ATTT-TCGTATTGACACTTTGTGTGCAACCTAAGAAATTCATAATTAGTTTATGA
1 ATTTAT-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
** * * *
5397563 ATTTCCGTTTTGGCACTATGTGTGCAACCTAATAAATTCATAATAAGTTTATAA
1 ATTTATGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
** * * * * *
5397617 ATTTCCGTATTGGCATTATGTGTGC-ACCTTACGTAATTCATAATGAGTTTGTGA
1 ATTTATGTATTGGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGTTTATGA
5397671 ATT
1 ATT
5397674 ACCGTCATGA
Statistics
Matches: 433, Mismatches: 53, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
53 4 0.01
54 424 0.98
55 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (54 bp):
ATTTATGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
Found at i:5401293 original size:13 final size:13
Alignment explanation
Indices: 5401275--5401320 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
5401265 GTCATAAATC
*
5401275 TATGACGCGCATT
1 TATGACGCACATT
*
5401288 TATGACACACATT
1 TATGACGCACATT
*
5401301 TATGACGCTCATT
1 TATGACGCACATT
*
5401314 AATGACG
1 TATGACG
5401321 TTCATTAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:5401325 original size:13 final size:13
Alignment explanation
Indices: 5401297--5401339 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
5401287 TTATGACACA
* *
5401297 CATTTATGACGCT
1 CATTAATGACGTT
5401310 CATTAATGACGTT
1 CATTAATGACGTT
5401323 CATTAATGACGTT
1 CATTAATGACGTT
5401336 CATT
1 CATT
5401340 GAGTGTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (13 bp):
CATTAATGACGTT
Found at i:5405374 original size:91 final size:91
Alignment explanation
Indices: 5405209--5405378 Score: 243
Period size: 91 Copynumber: 1.9 Consensus size: 91
5405199 ACCTTCAAGA
* * * *
5405209 AAAAAACAGCAACAAATGATGTAAAATAGTTGACAAGGAATATATACTTAACATATTTGTTTAAG
1 AAAAAACAACAACAAAAGATGTAAAACAATTGACAAGGAATATATACTTAACATATTTGTTTAAG
5405274 GCCTACATAAAAGAATGAAAGATCAT
66 GCCTACATAAAAGAATGAAAGATCAT
* * * *
5405300 AAAATACAACAACAAAAGATGTCAAACAATTGACATGGAAT-TAATATTTAACATATTTGTTTAA
1 AAAAAACAACAACAAAAGATGTAAAACAATTGACAAGGAATAT-ATACTTAACATATTTGTTTAA
*
5405364 GGCCTGCATAAAAGA
65 GGCCTACATAAAAGA
5405379 TCATAAATAA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
90 1 0.01
91 68 0.99
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.26
Consensus pattern (91 bp):
AAAAAACAACAACAAAAGATGTAAAACAATTGACAAGGAATATATACTTAACATATTTGTTTAAG
GCCTACATAAAAGAATGAAAGATCAT
Found at i:5406571 original size:253 final size:254
Alignment explanation
Indices: 5406110--5406618 Score: 1011
Period size: 253 Copynumber: 2.0 Consensus size: 254
5406100 GTCGGCCCCC
5406110 TCTGCCATTGAGAAAACAAATGATTCATAAGAGATTCGATGAACATCTATTTTTTCTTGGGAGAT
1 TCTGCCATTGAGAAAACAAATGATTCATAAGAGATTCGATGAACATCTATTTTTTCTTGGGAGAT
5406175 TTTTTATTTTTTGAGATGAGAGATTTGGACACACATGTATGTCGGGGAAGAAGCGGGAAAGGATG
66 TTTTTATTTTTTGAGATGAGAGATTTGGACACACATGTATGTCGGGGAAGAAGCGGGAAAGGATG
5406240 AAAATAAGGGGGAATTAAAAGACGACTTTTACAGATGACACACAATTAAAACTGTACTCCGTGTT
131 AAAATAAGGGGGAATTAAAAGACGACTTTTACAGATGACACACAATTAAAACTGTACTCCGTGTT
5406305 TTTGCAAATTTTTTGGATTATGACTATTAAATATGACACACATTATTGTAAGTCATAAA
196 TTTGCAAATTTTTTGGATTATGACTATTAAATATGACACACATTATTGTAAGTCATAAA
5406364 TCTGCCATTGAG-AAACAAATGATTCATAAGAGATTCGATGAACATCTATTTTTTCTTGGGAGAT
1 TCTGCCATTGAGAAAACAAATGATTCATAAGAGATTCGATGAACATCTATTTTTTCTTGGGAGAT
5406428 TTTTTATTTTTTGAGATGAGAGATTTGGACACACATGTATGTCGGGGAAGAAGCGGGAAAGGATG
66 TTTTTATTTTTTGAGATGAGAGATTTGGACACACATGTATGTCGGGGAAGAAGCGGGAAAGGATG
5406493 AAAATAAGGGGGAATTAAAAGACGACTTTTACAGATGACACACAATTAAAACTGTACTCCGTGTT
131 AAAATAAGGGGGAATTAAAAGACGACTTTTACAGATGACACACAATTAAAACTGTACTCCGTGTT
5406558 TTTGCAAATTTTTTGGATTATGACTATTAAATATGACACACATTATTGTAAGTCATAAA
196 TTTGCAAATTTTTTGGATTATGACTATTAAATATGACACACATTATTGTAAGTCATAAA
5406617 TC
1 TC
5406619 GTTCAGATTT
Statistics
Matches: 255, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
253 243 0.95
254 12 0.05
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (254 bp):
TCTGCCATTGAGAAAACAAATGATTCATAAGAGATTCGATGAACATCTATTTTTTCTTGGGAGAT
TTTTTATTTTTTGAGATGAGAGATTTGGACACACATGTATGTCGGGGAAGAAGCGGGAAAGGATG
AAAATAAGGGGGAATTAAAAGACGACTTTTACAGATGACACACAATTAAAACTGTACTCCGTGTT
TTTGCAAATTTTTTGGATTATGACTATTAAATATGACACACATTATTGTAAGTCATAAA
Found at i:5409340 original size:54 final size:54
Alignment explanation
Indices: 5409258--5409631 Score: 507
Period size: 54 Copynumber: 6.9 Consensus size: 54
5409248 GCATTTACCA
**
5409258 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCG
* *
5409312 TATTGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAACTTCCG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCG
* * *
5409366 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAACAACTTTATGAATTTCCA
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCG
* **
5409420 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTTG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCG
* * * *
5409474 TATTGACACTATGTGTGTAACCTAAGAAATTTATAATAAGTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCG
* * * * * *
5409528 TATTGGCACTATGTGTACAAGCTAATAAATCCATATTTAGTTTATGAATTTCCG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCG
* * * * *
5409582 TATTGGCACTATGTGTGCAGCCCACA-TAATTCATAATGAGTTTTTGAATT
1 TATTGGCACTATGTGTGCAACCTA-AGAAATTCATAATAAGTTTATGAATT
5409632 ACTATATCGA
Statistics
Matches: 280, Mismatches: 39, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
54 279 1.00
55 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (54 bp):
TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCG
Found at i:5409646 original size:162 final size:162
Alignment explanation
Indices: 5409250--5409631 Score: 568
Period size: 162 Copynumber: 2.4 Consensus size: 162
5409240 TATGTATTGC
5409250 ATTTACCATATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTAT
1 ATTT-CCATATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTAT
5409315 TGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAACTTCCGTATTGGCACTATGT
65 TGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAACTTCCGTATTGGCACTATGT
* *
5409380 GTGCAACCTAAGAAATTCATAACAACTTTATGA
130 GTACAACCTAAGAAATCCATAACAACTTTATGA
*
5409413 ATTTCCATATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTTGTATT
1 ATTTCCATATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATT
* * * *
5409478 GACACTATGTGTGTAACCTAAGAAATTTATAATAAGTTTATGAATTTTCGTATTGGCACTATGTG
66 GACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAACTTCCGTATTGGCACTATGTG
* * *** *
5409543 TACAAGCTAATAAATCCATATTTAGTTTATGA
131 TACAACCTAAGAAATCCATAACAACTTTATGA
* * * * * *
5409575 ATTTCCGTATTGGCACTATGTGTGCAGCCCACA-TAATTCATAATGAGTTTTTGAATT
1 ATTTCCATATTGGCACTATGTGTGCAACCTA-AGAAATTCATAATAAGTTTATGAATT
5409632 ACTATATCGA
Statistics
Matches: 199, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
162 194 0.97
163 5 0.03
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (162 bp):
ATTTCCATATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATT
GACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAACTTCCGTATTGGCACTATGTG
TACAACCTAAGAAATCCATAACAACTTTATGA
Found at i:5410201 original size:19 final size:19
Alignment explanation
Indices: 5410179--5410232 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
5410169 GAGAATGAGT
5410179 TATGAAATATGAAAGTGAA
1 TATGAAATATGAAAGTGAA
* *
5410198 TATGAAA-GTGAAAAATGAA
1 TATGAAATATG-AAAGTGAA
* *
5410217 AATGAGATATGAAAGT
1 TATGAAATATGAAAGT
5410233 CATGTATTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.07
19 23 0.85
20 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (19 bp):
TATGAAATATGAAAGTGAA
Found at i:5410215 original size:13 final size:13
Alignment explanation
Indices: 5410181--5410232 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
5410171 GAATGAGTTA
5410181 TGAAATATGAAAG
1 TGAAATATGAAAG
5410194 TG-AATATGAAAG
1 TGAAATATGAAAG
* *
5410206 TGAAAAATGAAAA
1 TGAAATATGAAAG
*
5410219 TGAGATATGAAAG
1 TGAAATATGAAAG
5410232 T
1 T
5410233 CATGTATTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 12 0.36
13 21 0.64
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
TGAAATATGAAAG
Found at i:5411807 original size:22 final size:22
Alignment explanation
Indices: 5411775--5411819 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5411765 TCGAAATAAA
*
5411775 ATTCATAATAAATATCATATAT
1 ATTCATAATAAACATCATATAT
* *
5411797 ATTCATGATAAACATCGTATAT
1 ATTCATAATAAACATCATATAT
5411819 A
1 A
5411820 AAAACAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (22 bp):
ATTCATAATAAACATCATATAT
Found at i:5414569 original size:76 final size:74
Alignment explanation
Indices: 5414383--5414589 Score: 245
Period size: 75 Copynumber: 2.7 Consensus size: 74
5414373 CAAAGCCAAA
* * * ***
5414383 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAATCGATTCCCCTCCTGAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGA-TCCCCCCATAGGAGGAACCGATTCCCC-CCTAAACAA
5414448 TTTGGCTCCGAG
63 TTTGGCTCCGAG
* *
5414460 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAATT
1 AATTCCAG-ATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAATT
* *
5414525 TTGTTCCGAG
65 TGGCTCCGAG
* *
5414535 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAG-ATGCTCGGAGGGAACCGAT-CCCCCCATAGGAGGAACCGATTCCCCC
5414590 TTGTTCAACG
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
75 58 0.51
76 31 0.27
77 23 0.20
78 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (74 bp):
AATTCCAGATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAATTT
GGCTCCGAG
Found at i:5422279 original size:9 final size:8
Alignment explanation
Indices: 5422257--5422307 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
5422247 TGTTTCAACA
5422257 TTTTGGAT
1 TTTTGGAT
5422265 ATTTTGGAT
1 -TTTTGGAT
5422274 TGTTT-GAT
1 T-TTTGGAT
5422282 TTTGTGGAT
1 TTT-TGGAT
*
5422291 TGTTGGA-
1 TTTTGGAT
5422298 TTTTGGAT
1 TTTTGGAT
5422306 TT
1 TT
5422308 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:5422291 original size:17 final size:17
Alignment explanation
Indices: 5422259--5422302 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
5422249 TTTCAACATT
5422259 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
5422276 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
5422293 TTGGATTTTG
1 TTGGATTTTG
5422303 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:5422603 original size:21 final size:21
Alignment explanation
Indices: 5422577--5422619 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5422567 TGAAGAAGTG
5422577 TTAAAGTAAGGGGGAGTAATT
1 TTAAAGTAAGGGGGAGTAATT
5422598 TTAAAGTAAGGGGGAGTAATT
1 TTAAAGTAAGGGGGAGTAATT
5422619 T
1 T
5422620 CAAAACTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (21 bp):
TTAAAGTAAGGGGGAGTAATT
Found at i:5423068 original size:75 final size:75
Alignment explanation
Indices: 5422906--5423115 Score: 278
Period size: 75 Copynumber: 2.8 Consensus size: 75
5422896 CAATTCAAAG
* * * *
5422906 CCAAAAATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGA
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAA
**
5422971 ATGGTTTGGCT
65 ACAGTTTGGCT
* *
5422982 CCGAGATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAA
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAA
* *
5423047 CAGTTTTGTT
66 CAGTTTGGCT
* * * *
5423057 CCAAGAATTCCAGTATGCTCGGAGGGAACCGATCCCCCCA-AGGGGGTACCGATTCCCCC
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCC
5423116 TTGTTCAACG
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
74 17 0.14
75 72 0.61
76 29 0.25
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.20
Consensus pattern (75 bp):
CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAA
CAGTTTGGCT
Found at i:5426897 original size:11 final size:12
Alignment explanation
Indices: 5426881--5426913 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5426871 TTCCCAAGTA
5426881 CTCTTCATTTC-
1 CTCTTCATTTCT
5426892 CTCTTCATTTCT
1 CTCTTCATTTCT
*
5426904 CTCTTTATTT
1 CTCTTCATTT
5426914 TCCTTCCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (12 bp):
CTCTTCATTTCT
Found at i:5429930 original size:21 final size:21
Alignment explanation
Indices: 5429901--5429983 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 21
5429891 GAAAATATAG
* *
5429901 ATACTCCTTATAGGGGTATCA
1 ATACACCTTACAGGGGTATCA
5429922 ATACACCTTACAGGGGTATCA
1 ATACACCTTACAGGGGTATCA
* *
5429943 ATACACCTTAGAGGGGTATTA
1 ATACACCTTACAGGGGTATCA
* *
5429964 ATACTCCTTACAAGGGTATC
1 ATACACCTTACAGGGGTATC
5429984 GATCCTAGGG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (21 bp):
ATACACCTTACAGGGGTATCA
Found at i:5431017 original size:18 final size:18
Alignment explanation
Indices: 5430994--5431042 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
5430984 TTATGCTAAG
*
5430994 ATAAATATTTTGATGTTT
1 ATAAATGTTTTGATGTTT
5431012 ATAAATGTTTTGATGTTT
1 ATAAATGTTTTGATGTTT
5431030 ATAAATGTTTTGA
1 ATAAATGTTTTGA
5431043 AAAGAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (18 bp):
ATAAATGTTTTGATGTTT
Found at i:5437711 original size:136 final size:138
Alignment explanation
Indices: 5437370--5437777 Score: 480
Period size: 136 Copynumber: 3.0 Consensus size: 138
5437360 AACGAAAATC
* * * * * * *
5437370 ACATGGTTCTTATGTGATGAGGAAGTATGGTTATCTAATGATGACGTTGCTCCTACGCATTGAGG
1 ACATGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTTGCTCCTACGTAATGAGG
* * * * * *
5437435 AGATCTGGTCGTTGGACAACATTGTTCCTACGTGATGAGAACGTCTAGCCATCTTT-AGAGATGA
66 AGATCTAGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTCATCTTTAAG-GATAA
*
5437499 TTTGGAGATA
130 TTT-GAGAAA
*** * * * * *
5437509 ACACAATTCCTACGTGATGAGAAAGCCTGGTTATCTGAGGATGACATTGCTCCTACGTGATAAGG
1 ACATGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTTGCTCCTACGTAATGAGG
* * *
5437574 AGATATAGTCGATAGACGACATTGTTCCTACGTGATGAGGACGTCTAGTCGTCTTTAAGGATAAT
66 AGATCTAGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTCATCTTTAAGGATAAT
5437639 TT-A-AAA
131 TTGAGAAA
* * ** *
5437645 ACATGGTTCCTACATGATGAGGAAGTCTGGTTATCTGAGGATAACGCAGCTCCTACATAATGAGG
1 ACATGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTTGCTCCTACGTAATGAGG
* * *
5437710 AGATCTAGTCGGTGGACGACATTGTTCCTACGTGATGAGGATGTCTAGTCATCTTTAGGGATAAT
66 AGATCTAGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTCATCTTTAAGGATAAT
5437775 TTG
131 TTG
5437778 TAACATCCCA
Statistics
Matches: 223, Mismatches: 44, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
136 115 0.52
137 1 0.00
139 105 0.47
140 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (138 bp):
ACATGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTTGCTCCTACGTAATGAGG
AGATCTAGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTCATCTTTAAGGATAAT
TTGAGAAA
Found at i:5440809 original size:23 final size:24
Alignment explanation
Indices: 5440758--5440815 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
5440748 CTCTCTGGTT
5440758 TCTCTCTTTCTTTTTCTTCTTTGC
1 TCTCTCTTTCTTTTTCTTCTTTGC
* *
5440782 TCTCTCTTTGTTTTT-TTCTTT-T
1 TCTCTCTTTCTTTTTCTTCTTTGC
5440804 TCCTCTCTTTCT
1 T-CTCTCTTTCT
5440816 ATGTAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 15 0.50
24 14 0.47
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (24 bp):
TCTCTCTTTCTTTTTCTTCTTTGC
Found at i:5442135 original size:21 final size:22
Alignment explanation
Indices: 5442092--5442136 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5442082 TAATAATAAG
5442092 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
5442114 AACATATAA-AATTAAA-ATATA
1 AACA-ATAATAATTAAATATATA
5442135 AA
1 AA
5442137 TATAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:5442146 original size:23 final size:23
Alignment explanation
Indices: 5442095--5442146 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
5442085 TAATAAGAAC
5442095 AATAATAATTAAATATATAAACAT
1 AATAA-AATTAAATATATAAACAT
*
5442119 -ATAAAATTAAA-ATATAAATAT
1 AATAAAATTAAATATATAAACAT
5442140 AAATAAA
1 -AATAAA
5442147 CAATGACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.36
22 7 0.28
23 9 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AATAAAATTAAATATATAAACAT
Found at i:5443499 original size:3 final size:3
Alignment explanation
Indices: 5443491--5443558 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
5443481 TTTATTTATC
** *
5443491 TAA TAA TAA TAA TAA TATA TAA TTAA TAA TAA TAA TAA TTT TAA TGA
1 TAA TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TAA TAA TAA TAA TAA
5443538 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
5443559 AAAGTAAACT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 51 0.89
4 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5448842 original size:13 final size:13
Alignment explanation
Indices: 5448824--5448857 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5448814 TGTCACGTAC
5448824 ATATTTTAAAAAA
1 ATATTTTAAAAAA
* *
5448837 ATATTTTTAAATA
1 ATATTTTAAAAAA
5448850 ATATTTTA
1 ATATTTTA
5448858 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATTTTAAAAAA
Found at i:5452015 original size:29 final size:31
Alignment explanation
Indices: 5451965--5452024 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
5451955 AAAAAATTAA
5451965 TTTTTAAAGTTAAATGAGT-AAAT-TGAAAT
1 TTTTTAAAGTTAAATGAGTAAAATATGAAAT
* * *
5451994 TTTTTAAAGTTTAGTGATTAAAATATGAAAT
1 TTTTTAAAGTTAAATGAGTAAAATATGAAAT
5452025 AAAAAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.62
30 4 0.15
31 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTTTAAAGTTAAATGAGTAAAATATGAAAT
Found at i:5452450 original size:17 final size:17
Alignment explanation
Indices: 5452429--5452470 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5452419 TTTTAAATTT
5452429 AAAATATTCAAA-AAAA
1 AAAATATTCAAATAAAA
* *
5452445 ATAAATATACAAATAATA
1 A-AAATATTCAAATAAAA
5452463 AAAATATT
1 AAAATATT
5452471 AATTTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 4 0.19
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATTCAAATAAAA
Found at i:5454610 original size:27 final size:27
Alignment explanation
Indices: 5454570--5454665 Score: 81
Period size: 27 Copynumber: 3.5 Consensus size: 27
5454560 AATAATAGTA
*
5454570 TTTTTATTATTTTAATATATATTTAAT
1 TTTTTATTAATTTAATATATATTTAAT
* * *
5454597 TTTTTAGTAATTTAATTTAATTTTTAGTAT
1 TTTTTATTAATTTAATAT-ATATTTA--AT
*
5454627 TTTTTATTTAATTT-TTA-ATATTTAAT
1 TTTTTA-TTAATTTAATATATATTTAAT
5454653 TTTTT-TTATATTT
1 TTTTTATTA-ATTT
5454666 TCAATTCTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
24 3 0.05
25 4 0.07
26 7 0.12
27 15 0.27
28 12 0.21
30 9 0.16
31 6 0.11
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTTTATTAATTTAATATATATTTAAT
Found at i:5454622 original size:20 final size:20
Alignment explanation
Indices: 5454590--5454654 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
5454580 TTTAATATAT
5454590 ATTTAATTTTTTAGTAATTTA
1 ATTTAA-TTTTTAGTAATTTA
* *
5454611 ATTTAATTTTTAGTATTTTTT
1 ATTTAATTTTTAGTA-ATTTA
*
5454632 ATTTAATTTTTAAT-ATTTA
1 ATTTAATTTTTAGTAATTTA
5454651 ATTT
1 ATTT
5454655 TTTTTATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 7 0.18
20 9 0.24
21 22 0.58
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
ATTTAATTTTTAGTAATTTA
Found at i:5454658 original size:28 final size:26
Alignment explanation
Indices: 5454569--5454661 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 26
5454559 TAATAATAGT
* *
5454569 ATTTTTATTATTTTAATAT-ATATTTA
1 ATTTTTTTTA-TTTAATTTAATATTTA
* *
5454595 ATTTTTTAGTAATTTAATTTAATTTTTA
1 ATTTTTT--TTATTTAATTTAATATTTA
* *
5454623 GTATTTTTTATTTAATTTTTAATATTTA
1 ATTTTTTTTATTTAA--TTTAATATTTA
5454651 ATTTTTTTTAT
1 ATTTTTTTTAT
5454662 ATTTTCAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
26 13 0.25
27 7 0.13
28 32 0.62
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
ATTTTTTTTATTTAATTTAATATTTA
Found at i:5462098 original size:66 final size:66
Alignment explanation
Indices: 5462016--5462147 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
5462006 AACAATCGGG
5462016 ATCTCCAAGAACCTATTACTATTTAATAATACCTTGGTCTGCCGTGAACCAACATTTCTAATTGG
1 ATCTCCAAGAACCTATTACTATTTAATAATACCTTGGTCTGCCGTGAACCAACATTTCTAATTGG
5462081 A
66 A
5462082 ATCTCCAAGAACCTATTACTATTTAATAATACCTTGGTCTGCCGTGAACCAACATTTCTAATTGG
1 ATCTCCAAGAACCTATTACTATTTAATAATACCTTGGTCTGCCGTGAACCAACATTTCTAATTGG
5462147 A
66 A
5462148 GCCAAACGCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (66 bp):
ATCTCCAAGAACCTATTACTATTTAATAATACCTTGGTCTGCCGTGAACCAACATTTCTAATTGG
A
Found at i:5464528 original size:24 final size:24
Alignment explanation
Indices: 5464494--5464542 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5464484 TAAACTAAAT
* *
5464494 ATGAATGTTTATTTACACATTCTG
1 ATGAATATTTATTTACACATCCTG
5464518 ATGAATATTTATTTACACATCCTG
1 ATGAATATTTATTTACACATCCTG
5464542 A
1 A
5464543 ATGATTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (24 bp):
ATGAATATTTATTTACACATCCTG
Found at i:5465704 original size:27 final size:28
Alignment explanation
Indices: 5465655--5465712 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
5465645 AGGGGTGCAC
5465655 AAAAAATCCGAATATCCGATTTTGAGAA
1 AAAAAATCCGAATATCCGATTTTGAGAA
* *
5465683 AAAAATATCCGAA-A-CCGGTTTTGGGAA
1 AAAAA-ATCCGAATATCCGATTTTGAGAA
5465710 AAA
1 AAA
5465713 TCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGAGAA
Found at i:5465734 original size:19 final size:20
Alignment explanation
Indices: 5465712--5465750 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5465702 TTTGGGAAAA
*
5465712 ATCGG-TTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
5465731 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
5465751 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:5465810 original size:12 final size:12
Alignment explanation
Indices: 5465795--5465840 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
5465785 CGGTTTTTTT
*
5465795 ACCGGATAAAAA
1 ACCGGTTAAAAA
5465807 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
5465822 ACCGGTTAAAAA
1 ACCGGTTAAAAA
5465834 ACCGGTT
1 ACCGGTT
5465841 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:5465822 original size:15 final size:13
Alignment explanation
Indices: 5465801--5465841 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
5465791 TTTTACCGGA
5465801 TAAAAAACCGGTT
1 TAAAAAACCGGTT
5465814 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
5465828 TAAAAAACCGGTT
1 TAAAAAACCGGTT
5465841 T
1 T
5465842 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:5468167 original size:21 final size:21
Alignment explanation
Indices: 5468143--5468182 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5468133 TTTATTTTAT
5468143 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
5468164 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
5468183 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:5468230 original size:33 final size:33
Alignment explanation
Indices: 5468177--5468275 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
5468167 TTTGTTTCAA
5468177 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
5468209 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * * *
5468242 TTATCAAATTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
5468275 T
1 T
5468276 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:5468304 original size:13 final size:13
Alignment explanation
Indices: 5468261--5468315 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
5468251 TTGGAAGTAT
5468261 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
5468274 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
5468288 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
5468301 TTAAGTATTTGAA
1 TTAAGTATTTCAA
5468314 TT
1 TT
5468316 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:5468537 original size:21 final size:21
Alignment explanation
Indices: 5468511--5468588 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
5468501 TGGAGCGTGG
5468511 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
*
5468532 GGGAATTGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
*
5468553 GGGAATTGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
*
5468574 GGGAATCGGTTCCCT
1 GGGAATCGGTACCCT
5468589 AAGTGTAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.27
Consensus pattern (21 bp):
GGGAATCGGTACCCTCTCATA
Found at i:5468786 original size:15 final size:15
Alignment explanation
Indices: 5468756--5468810 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 15
5468746 ATCTGGAATA
*
5468756 TTAAAATCGG-TTTT
1 TTAAAACCGGTTTTT
*
5468770 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
5468785 TTAAAAAACCGGTTTTT
1 TT--AAAACCGGTTTTT
5468802 TTAAAACCG
1 TTAAAACCG
5468811 AAACCGGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 8 0.23
15 13 0.37
17 14 0.40
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:5468819 original size:21 final size:17
Alignment explanation
Indices: 5468774--5468807 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5468764 GGTTTTTTAT
5468774 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
5468791 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
5468808 CCGAAACCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
AACCGGTTTTTTTAAAA
Found at i:5468927 original size:15 final size:17
Alignment explanation
Indices: 5468901--5468932 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5468891 TGCTATGAGA
5468901 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
5468917 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
5468933 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:5472412 original size:6 final size:6
Alignment explanation
Indices: 5472403--5472446 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
5472393 CATCTCTTAT
* *
5472403 TCTTCA TCTTCA TCTTCA TATTCA TCTTCA TATTCA TCTTCA TC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TC
5472447 CACTTCTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCA
Found at i:5473881 original size:2 final size:2
Alignment explanation
Indices: 5473874--5473914 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5473864 ATTAGTTCCA
*
5473874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5473915 GCTGAAGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5475608 original size:32 final size:31
Alignment explanation
Indices: 5475534--5475662 Score: 108
Period size: 31 Copynumber: 4.3 Consensus size: 31
5475524 GAAAATATAA
* ** *
5475534 GTTTTGGTCACTTACGTTATTATTTTATTAT
1 GTTTTGGTCACTTATGTTATCGTTTTATTAG
* *
5475565 GCTTTGGTCACTTGTGTTATCGTTTTATTAAG
1 GTTTTGGTCACTTATGTTATCGTTTTATT-AG
*
5475597 GTTTTGGTCACTTATATTATCG---TA--A-
1 GTTTTGGTCACTTATGTTATCGTTTTATTAG
* * *
5475622 GCTTTGGTCACTTATATTATCGTTTTATTAA
1 GTTTTGGTCACTTATGTTATCGTTTTATTAG
*
5475653 GCTTTGGTCA
1 GTTTTGGTCA
5475663 ATAGGATGTT
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
25 21 0.26
26 1 0.01
28 2 0.02
29 2 0.02
30 1 0.01
31 34 0.42
32 20 0.25
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.51
Consensus pattern (31 bp):
GTTTTGGTCACTTATGTTATCGTTTTATTAG
Found at i:5480209 original size:19 final size:19
Alignment explanation
Indices: 5480187--5480235 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
5480177 TCTCAAAATC
*
5480187 ATTTTCAAAACCTCATTTT
1 ATTTTCAAAACCTAATTTT
**
5480206 ATTTTTCAAAGTCTAATTTT
1 A-TTTTCAAAACCTAATTTT
*
5480226 GTTTTCAAAA
1 ATTTTCAAAA
5480236 GAAAACCATG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (19 bp):
ATTTTCAAAACCTAATTTT
Found at i:5487093 original size:15 final size:15
Alignment explanation
Indices: 5487075--5487105 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5487065 TGGGAAGGTG
5487075 GTACCGATACCATAA
1 GTACCGATACCATAA
5487090 GTACCGATACCATAA
1 GTACCGATACCATAA
5487105 G
1 G
5487106 GGAGGTATCG
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:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (15 bp):
GTACCGATACCATAA
Found at i:5498008 original size:14 final size:14
Alignment explanation
Indices: 5497991--5498022 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5497981 TAAAATCCTA
5497991 TTTATAAATTTAAT
1 TTTATAAATTTAAT
5498005 TTTATAAATTTAAT
1 TTTATAAATTTAAT
5498019 TTTA
1 TTTA
5498023 AATATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATAAATTTAAT
Found at i:5498033 original size:18 final size:18
Alignment explanation
Indices: 5498007--5498045 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5497997 AATTTAATTT
5498007 TATAAATTTAATTTTAAA
1 TATAAATTTAATTTTAAA
* * *
5498025 TATATATTTATTTTTCAA
1 TATAAATTTAATTTTAAA
5498043 TAT
1 TAT
5498046 TAAGAAAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATAAATTTAATTTTAAA
Found at i:5510991 original size:182 final size:182
Alignment explanation
Indices: 5510636--5511660 Score: 1589
Period size: 182 Copynumber: 5.6 Consensus size: 182
5510626 ATCGATACAA
* * *
5510636 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATC-AAACCGGTTTC-ATTAT
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-CAAAACCAGTCTCGA-AAT
* * *
5510699 GACAAAACCGGTAAAGTGCTACCTA-ATATGGTT-AAAGTATCGATTCCAC-TGAA-ATAAGTAT
64 GACAAAACCGGTAAAGCGCTACC-AGATAT-GTTCAAAGTGTCGA-T--ACTTTAATATAAGTAT
* * *
5510760 CAACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAAGTGTCGATACTTT
124 CGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
* *
5510819 ATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCAATCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGA
* * *
5510884 CAAAACCAGTAAAGCGCTACCAGATATGTTCAAAGTATCGATACTTTAATATAAGTATCAACACT
66 CAAAACCGGTAAAGCGCTACCAGATATGTTCAAAGTGTCGATACTTTAATATAAGTATCGACACT
* *
5510949 TTTGGAATTTAAAAGGGAAGCAGTAATATCGCCTATAAAGTGTCGATACTTT
131 TTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
* *
5511001 ATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAATTTGACAAAACCAGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGA
* *
5511066 CAAAACCGGTAAAGTGCTACCAGATATGTTCAAAGTGTCGATACTTTAATATAAGTATCGACACC
66 CAAAACCGGTAAAGCGCTACCAGATATGTTCAAAGTGTCGATACTTTAATATAAGTATCGACACT
5511131 TTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
131 TTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
* *
5511183 ATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATTTGACAAAACCAGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGA
* * * *
5511248 CAAAATCGGTAAAGTGCTACCGGATATGTTCAAAGTGTCGATACTTTAATATAAGTATTGACACT
66 CAAAACCGGTAAAGCGCTACCAGATATGTTCAAAGTGTCGATACTTTAATATAAGTATCGACACT
* *
5511313 TTTGGAATTTAAAAGAGAAGCAATAATAGCGCCTATAAAGTGTCGATAATTT
131 TTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
*
5511365 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAGCCAGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGA
* * *
5511430 CAAAACTGGTAAAGCGCTACCGGATATGTTCAAAGTGTCGATACTTTAATATAAGGATCGACACT
66 CAAAACCGGTAAAGCGCTACCAGATATGTTCAAAGTGTCGATACTTTAATATAAGTATCGACACT
*
5511495 TTTGGAATTTAAAAGAGAAGCAGTAATAGCACCTATAAAGTGTCGATACTTT
131 TTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
* * *
5511547 ATAAAAATATATCGATCCATAATAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGA
* *
5511612 C--AATCGGTAAAGCGCTACCGGATATGTTCAAAGTGTCGATACTTTAATA
66 CAAAACCGGTAAAGCGCTACCAGATATGTTCAAAGTGTCGATACTTTAATA
5511661 AGTACGCGTA
Statistics
Matches: 788, Mismatches: 48, Indels: 15
0.93 0.06 0.02
Matches are distributed among these distances:
180 48 0.06
181 3 0.00
182 647 0.82
183 89 0.11
184 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (182 bp):
ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGA
CAAAACCGGTAAAGCGCTACCAGATATGTTCAAAGTGTCGATACTTTAATATAAGTATCGACACT
TTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
Found at i:5517744 original size:23 final size:23
Alignment explanation
Indices: 5517696--5517745 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5517686 ACATATTTTA
*
5517696 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
5517719 TTATATAAGCGTTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
5517742 TTAT
1 TTAT
5517746 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:5517861 original size:158 final size:157
Alignment explanation
Indices: 5517573--5518091 Score: 828
Period size: 158 Copynumber: 3.3 Consensus size: 157
5517563 ACAGAAGCTC
* * * * * *
5517573 TACCTAATATGTTATTATGCTTTATAATGTTTTCAGTAATTAACCGGTTTTGTTATACTTGGTAA
1 TACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAACCGATTATGTTAT-CTTGGTAA
*
5517638 CATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACATATTTTATTATATA
65 CATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATA
5517703 AGCGCTACCTATTACGTTATATAAGCGT
130 AGCGCTACCTATTACGTTATATAAGCGT
5517731 TACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAACCGATTATGTTATCTTTGGTAA
1 TACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAACCGATTATGTTATC-TTGGTAA
* * *
5517796 CATTTTAGGCGTTTATCTAATATGTTATAATAACAAATTAAATAATTAACCTATTTTATTATATA
65 CATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATA
5517861 AGCGCTACCTATTACGTTATATAAGC-T
130 AGCGCTACCTATTACGTTATATAAGCGT
*
5517888 CTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAACC-AGTTATGTTATCCTTGAT
1 -TACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAACCGA-TTATGTTAT-CTTGGT
*
5517952 AACATTTTAGGCGTTTACCTAATATGTTGTAATGAA-AAAATAAGTAATTAACCTATTTTATTAT
63 AACATTTTAGGCGTTTACCTAATATGTTGTAAT-AACAAATTAAGTAATTAACCTATTTTATTAT
*
5518016 ATAAGCGCTACCTATTACGTTATATAAGCGC
127 ATAAGCGCTACCTATTACGTTATATAAGCGT
* *
5518047 TACCTAATATGTTATTGTGCTTGATAATGTTTACAGTAATTAACC
1 TACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAACC
5518092 TATTTTATTA
Statistics
Matches: 337, Mismatches: 18, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
157 3 0.01
158 331 0.98
159 3 0.01
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (157 bp):
TACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAACCGATTATGTTATCTTGGTAAC
ATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAA
GCGCTACCTATTACGTTATATAAGCGT
Found at i:5517880 original size:23 final size:23
Alignment explanation
Indices: 5517854--5517903 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5517844 ACCTATTTTA
*
5517854 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
5517877 TTATATAAGCTCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
5517900 TTAT
1 TTAT
5517904 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:5518029 original size:23 final size:23
Alignment explanation
Indices: 5518002--5518052 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5517992 TAAGTAATTA
**
5518002 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
5518025 ACCTATTACGTTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
5518048 ACCTA
1 ACCTA
5518053 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:5518060 original size:23 final size:23
Alignment explanation
Indices: 5518012--5518061 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
5518002 ACCTATTTTA
*
5518012 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
5518035 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
5518058 TTAT
1 TTAT
5518062 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:5518124 original size:23 final size:23
Alignment explanation
Indices: 5518089--5518139 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5518079 ACAGTAATTA
** *
5518089 ACCTATTTTATTATATAAGTGCT
1 ACCTATTACATTATATAAGCGCT
5518112 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
5518135 ACCTA
1 ACCTA
5518140 ATATTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:5518140 original size:87 final size:87
Alignment explanation
Indices: 5517994--5518161 Score: 300
Period size: 87 Copynumber: 1.9 Consensus size: 87
5517984 TGAAAAAATA
*
5517994 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGT
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGT
*
5518059 TATTGTGCTTGATAATGTTTAC
66 TATTGTACTTGATAATGTTTAC
* *
5518081 AGTAATTAACCTATTTTATTATATAAGTGCTACCTATTACATTATATAAGCGCTACCTAATATTT
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGT
5518146 TATTGTACTTGATAAT
66 TATTGTACTTGATAAT
5518162 ATTTCCATTT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (87 bp):
AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGT
TATTGTACTTGATAATGTTTAC
Found at i:5520012 original size:16 final size:15
Alignment explanation
Indices: 5519991--5520024 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5519981 TCAAACAGTG
5519991 AACTGGTCTGACCCTA
1 AACTGGTCTGACCC-A
*
5520007 AACTGGTTTGACCCA
1 AACTGGTCTGACCCA
5520022 AAC
1 AAC
5520025 AATTTAACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (15 bp):
AACTGGTCTGACCCA
Found at i:5521325 original size:2 final size:2
Alignment explanation
Indices: 5521318--5521356 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5521308 TTCTGATTCC
5521318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5521357 ACATTTGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5522424 original size:41 final size:41
Alignment explanation
Indices: 5522378--5522460 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
5522368 TAATTTAGAG
5522378 AGGATTTGGTAGATTGTAAACAATACATTAGTAAAATAGGT
1 AGGATTTGGTAGATTGTAAACAATACATTAGTAAAATAGGT
5522419 AGGATTTGGTAGATTGTAAACAATACATTAGTAAAATAGGT
1 AGGATTTGGTAGATTGTAAACAATACATTAGTAAAATAGGT
5522460 A
1 A
5522461 AAACTGGACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (41 bp):
AGGATTTGGTAGATTGTAAACAATACATTAGTAAAATAGGT
Found at i:5523327 original size:118 final size:117
Alignment explanation
Indices: 5523196--5523544 Score: 439
Period size: 118 Copynumber: 2.9 Consensus size: 117
5523186 GAACTATGTC
** * *
5523196 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTAAGTCAAATTATGAATTATTGTATGTTGC
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTAAGTTGAATTGTGAATTATTGTATGTTAC
* *
5523261 CATGATCGAATTAAGTTGAATTGTGAATTATTGCATGTTGCCATGATTGAATT
66 CATGATTGAATTAA-TCGAATTGTGAATTATTGCATGTTGCCATGATTGAATT
* * *
5523314 GAATTGTGAATTATTGCATGCTGCCATGATTGAATTAAGTTGAATTGTGAATTATTGCATGCTAC
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTAAGTTGAATTGTGAATTATTGTATGTTAC
*
5523379 CATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTTCCATGATTGAATT
66 CATGATTGAATT-AATCGAATTGTGAATTATTGCATGTTGCCATGATTGAATT
* ** * *
5523432 GAATCTAATTGTGGATTATTGCATGCTTTCATGATCGAATTGAGTTGAATGGTGAATTATT-TCA
1 G-----AATTGTGAATTATTGCATGCTGCCATGATCGAATTAAGTTGAATTGTGAATTATTGT-A
* * * *
5523496 TGTTTCCATGATTGAACTGAATCGAATTGTGAATTAGTGCATGCTGCCA
60 TGTTACCATGATTGAA-TTAATCGAATTGTGAATTATTGCATGTTGCCA
5523545 AGATCGAACT
Statistics
Matches: 200, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
118 106 0.53
119 2 0.01
123 91 0.46
124 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (117 bp):
GAATTGTGAATTATTGCATGCTGCCATGATCGAATTAAGTTGAATTGTGAATTATTGTATGTTAC
CATGATTGAATTAATCGAATTGTGAATTATTGCATGTTGCCATGATTGAATT
Found at i:5523564 original size:41 final size:41
Alignment explanation
Indices: 5523196--5523565 Score: 389
Period size: 41 Copynumber: 9.1 Consensus size: 41
5523186 GAACTATGTC
*
5523196 GAATTGTGAATTATTGCATGCTGCCATGATCGAATT-AAGTC
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAA-TT
* * * *
5523237 AAATTATGAATTATTGTATGTTGCCATGATCGAATT-AAGTT
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAA-TT
*
5523278 GAATTGTGAATTATTGCATGTTGCC---AT-G-ATTGAATT
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAATT
*
5523314 GAATTGTGAATTATTGCATGCTGCCATGATTGAATT-AAGTT
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAA-TT
* * *
5523355 GAATTGTGAATTATTGCATGCTACCATGATTGAATTGAATC
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAATT
* * *
5523396 GAATTGTGAATTATTGCATGTTTCCATGATTGAATTGAATCT
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAAT-T
* ** *
5523438 -AATTGTGGATTATTGCATGCTTTCATGATCGAATTGAGTT
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAATT
* * * * * * *
5523478 GAATGGTGAATTATTTCATGTTTCCATGATTGAACTGAATC
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAATT
* * * *
5523519 GAATTGTGAATTAGTGCATGCTGCCAAGATCGAACTCAATT
1 GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAATT
5523560 GAATTG
1 GAATTG
5523566 AAATCTTAAA
Statistics
Matches: 282, Mismatches: 37, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
36 29 0.10
37 3 0.01
38 2 0.01
39 2 0.01
40 4 0.01
41 240 0.85
42 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (41 bp):
GAATTGTGAATTATTGCATGCTGCCATGATCGAATTGAATT
Found at i:5535223 original size:20 final size:20
Alignment explanation
Indices: 5535198--5535242 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5535188 TTCAATTATG
*
5535198 GCATCCGTTCATGCCTTAAT
1 GCATCCGTTCATACCTTAAT
*
5535218 GCATCCTTTCATACCTTAAT
1 GCATCCGTTCATACCTTAAT
5535238 GCATC
1 GCATC
5535243 ATTTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.36
Consensus pattern (20 bp):
GCATCCGTTCATACCTTAAT
Found at i:5535247 original size:20 final size:20
Alignment explanation
Indices: 5535205--5535249 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5535195 ATGGCATCCG
* *
5535205 TTCATGCCTTAATGCATCCT
1 TTCATACCTTAATGCATCAT
5535225 TTCATACCTTAATGCATCAT
1 TTCATACCTTAATGCATCAT
5535245 TTCAT
1 TTCAT
5535250 GCATTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.07, T:0.42
Consensus pattern (20 bp):
TTCATACCTTAATGCATCAT
Found at i:5535652 original size:19 final size:20
Alignment explanation
Indices: 5535610--5535661 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
5535600 GATGTTTTAT
*
5535610 TGGTATCGATA-CCCTTACAA
1 TGGTATCGATACCCCCTA-AA
5535630 TGGTATCGATACCCCCT-AA
1 TGGTATCGATACCCCCTAAA
*
5535649 TGGTATCAATACC
1 TGGTATCGATACC
5535662 AAAATTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 11 0.38
21 4 0.14
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (20 bp):
TGGTATCGATACCCCCTAAA
Found at i:5535669 original size:74 final size:74
Alignment explanation
Indices: 5535560--5535788 Score: 388
Period size: 74 Copynumber: 3.1 Consensus size: 74
5535550 TATGCTATAT
* * * * *
5535560 TATCAATACCCCCT-ACGATATCGATCCCAAAATTAGATTCGATGTTTTATTGGTATCGATACCC
1 TATCGATACCCCCTAACGGTATCAATACCAAAATTAGATTCGATGTTTTCTTGGTATCGATACCC
5535624 TTACAATGG
66 TTACAATGG
* *
5535633 TATCGATACCCCCTAATGGTATCAATACCAAAATTAGATTCAATGTTTTCTTGGTATCGATACCC
1 TATCGATACCCCCTAACGGTATCAATACCAAAATTAGATTCGATGTTTTCTTGGTATCGATACCC
5535698 TTACAATGG
66 TTACAATGG
5535707 TATCGATACCCCCTAACGGTATCAATACCAAAATTAGATTCGATGTTTTCTTGGTATCGATACCC
1 TATCGATACCCCCTAACGGTATCAATACCAAAATTAGATTCGATGTTTTCTTGGTATCGATACCC
5535772 TTACAATGG
66 TTACAATGG
5535781 TATCGATA
1 TATCGATA
5535789 TTTCCTCAAT
Statistics
Matches: 146, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
73 13 0.09
74 133 0.91
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (74 bp):
TATCGATACCCCCTAACGGTATCAATACCAAAATTAGATTCGATGTTTTCTTGGTATCGATACCC
TTACAATGG
Found at i:5537001 original size:247 final size:246
Alignment explanation
Indices: 5536566--5537059 Score: 979
Period size: 247 Copynumber: 2.0 Consensus size: 246
5536556 CGAAATTTTT
5536566 CCTCTTATTTTAAATCATTTAAATAAAGTCCCTAATTCAATATTTGGGATACTACAATTCTCCCC
1 CCTCTTATTTTAAATCATTTAAATAAAGTCCCTAATTCAATATTTGGGATACTACAATTCTCCCC
5536631 TTAAGAAAATTCATCATCAACTTTAAATAAATACCTGAAGTAAAAAGGTAGGGAAACTGTATTCT
66 TTAAGAAAATTCATCATCAACTTTAAATAAATACCTGAAGTAAAAAGGTAGGGAAACTGTATTCT
5536696 CATGTCCTCATCTCTTTCCCAAGTAGCCTTTTCCACCTTATGATTTTTCCAGAGTACCTTAAGTA
131 CATGTCCTCATCTCTTTCCCAAGTAGCCTTTTCCACCTTATGATTTTTCCAGAGTACCTTAAGTA
5536761 AGGGAATTTGTGTGTTGCACAACTCTTTGATTTTTCTAGTTAAGATTCGCA
196 AGGGAATTTGTGTGTTGCACAACTCTTTGATTTTTCTAGTTAAGATTCGCA
5536812 CCTCTTATTTTAAATCATTTAAATAAAGTCCCTAATTCAATATTTGGGATACTACAATTCTCCCC
1 CCTCTTATTTTAAATCATTTAAATAAAGTCCCTAATTCAATATTTGGGATACTACAATTCTCCCC
5536877 TTAAGAAAATTCATCATCAACTTTAAAATAAATACCTGAAGTAAAAAGGTAGGGAAACTGTATTC
66 TTAAGAAAATTCATCATCAACTTT-AAATAAATACCTGAAGTAAAAAGGTAGGGAAACTGTATTC
5536942 TCATGTCCTCATCTCTTTCCCAAGTAGCCTTTTCCACCTTATGATTTTTCCAGAGTACCTTAAGT
130 TCATGTCCTCATCTCTTTCCCAAGTAGCCTTTTCCACCTTATGATTTTTCCAGAGTACCTTAAGT
5537007 AAGGGAATTTGTGTGTTGCACAACTCTTTGATTTTTCTAGTTAAGATTCGCA
195 AAGGGAATTTGTGTGTTGCACAACTCTTTGATTTTTCTAGTTAAGATTCGCA
5537059 C
1 C
5537060 TAGTTCTACT
Statistics
Matches: 247, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
246 89 0.36
247 158 0.64
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (246 bp):
CCTCTTATTTTAAATCATTTAAATAAAGTCCCTAATTCAATATTTGGGATACTACAATTCTCCCC
TTAAGAAAATTCATCATCAACTTTAAATAAATACCTGAAGTAAAAAGGTAGGGAAACTGTATTCT
CATGTCCTCATCTCTTTCCCAAGTAGCCTTTTCCACCTTATGATTTTTCCAGAGTACCTTAAGTA
AGGGAATTTGTGTGTTGCACAACTCTTTGATTTTTCTAGTTAAGATTCGCA
Found at i:5541209 original size:27 final size:27
Alignment explanation
Indices: 5541169--5541290 Score: 67
Period size: 27 Copynumber: 5.0 Consensus size: 27
5541159 ATGCTTTAAT
* *
5541169 GCATCCTTTTATGCATTTTCAATTATG
1 GCATCCATTCATGCATTTTCAATTATG
* *
5541196 GCATCCGTTCATGC--CTT-AA-TA--
1 GCATCCATTCATGCATTTTCAATTATG
5541217 -CAT-CATTCCATGCATTTTCAATTATG
1 GCATCCATT-CATGCATTTTCAATTATG
* *
5541243 CCATCCATTCATGC--CTT--A--AT-
1 GCATCCATTCATGCATTTTCAATTATG
*
5541263 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCATTCATGCATTTTCAATTATG
5541290 G
1 G
5541291 AATCTGTTCA
Statistics
Matches: 70, Mismatches: 9, Indels: 32
0.63 0.08 0.29
Matches are distributed among these distances:
19 3 0.04
20 20 0.29
21 2 0.03
22 4 0.06
23 5 0.07
24 5 0.07
25 4 0.06
26 2 0.03
27 21 0.30
28 4 0.06
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.41
Consensus pattern (27 bp):
GCATCCATTCATGCATTTTCAATTATG
Found at i:5541209 original size:47 final size:47
Alignment explanation
Indices: 5541121--5541336 Score: 299
Period size: 47 Copynumber: 4.6 Consensus size: 47
5541111 CATATTAAGA
* * *
5541121 CATCCATTT-ATGCATTTTAATATATATGGCATCCTTTCATGCTTTAATG
1 CATCC-TTTCATGCATTTTCA-AT-TATGGCATCCGTTCATGCCTTAATG
* *
5541170 CATCCTTTTATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATA
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
* * * *
5541217 CATCATTCCATGCATTTTCAATTATGCCATCCATTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
* *
5541264 CATCCTTTCATGCATTTTCAATTATGGAATCTGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
5541311 CATCCTTTCATGCATTTTCAATTATG
1 CATCCTTTCATGCATTTTCAATTATG
5541337 AATTTGATTT
Statistics
Matches: 150, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
47 130 0.87
48 5 0.03
49 15 0.10
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.43
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
Found at i:5541846 original size:20 final size:21
Alignment explanation
Indices: 5541821--5541874 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
5541811 ATGTTGCCTA
5541821 GTATCGATACCCT-TACCATG
1 GTATCGATACCCTATACCATG
* *
5541841 GTATCGATACTACTATACTATG
1 GTATCGATAC-CCTATACCATG
*
5541863 GTACCGATACCC
1 GTATCGATACCC
5541875 CATTACGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 15 0.54
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
GTATCGATACCCTATACCATG
Found at i:5541888 original size:95 final size:96
Alignment explanation
Indices: 5541750--5541947 Score: 238
Period size: 95 Copynumber: 2.1 Consensus size: 96
5541740 ACGCTAGTAC
* * * ** ** **
5541750 CGATACTTCTATACTATAGTACTGATACCACATCCCGGTATCGATACTGAAATTATCTTCGATG-
1 CGATACTACTATACTATAGTACCGATACCACATCACGACATCGATACCAAAATTAGATTCGATGT
*
5541814 TTGCCTAG-TATCGATACCCTTACCATGGTAT
66 TTG-CTAGATATCGATACCCTTACAATGGTAT
* * *
5541845 CGATACTACTATACTATGGTACCGATACCCCATTACGACATCGATACCAAAATTAGATTCGATGT
1 CGATACTACTATACTATAGTACCGATACCACATCACGACATCGATACCAAAATTAGATTCGATGT
*
5541910 TTGCTTGATATCGATACCCTTACAATGGTAT
66 TTGCTAGATATCGATACCCTTACAATGGTAT
*
5541941 CAATACT
1 CGATACT
5541948 TCCTCAACCG
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
95 55 0.64
96 31 0.36
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (96 bp):
CGATACTACTATACTATAGTACCGATACCACATCACGACATCGATACCAAAATTAGATTCGATGT
TTGCTAGATATCGATACCCTTACAATGGTAT
Found at i:5552162 original size:216 final size:217
Alignment explanation
Indices: 5551754--5552203 Score: 618
Period size: 216 Copynumber: 2.1 Consensus size: 217
5551744 AAAGGATTTA
* *
5551754 ATCATCATGCTCGAAAGACTTAATGATGGCCTAAAGGACTTACCAATTTTGGAAATAGTTTAATG
1 ATCATCTTGCTTGAAAGACTTAATGATGGCC-AAAGGACTTACCAATTTTGGAAATAGTTTAATG
* **
5551819 TGTAAGAAACTTTAGAAATCACTTTCTTACTTTCCAAAAATTTAATTTTCTGAAAGTACCAAATG
65 TGTAAGAAACTTTAGAAATCACTTTCTTACTTTCCAAAAATTTAATTTTATGAAAACACCAAATG
** *
5551884 AGAAACATTGAAAATCACTTTCTTTTTTTTCACAAACATCATATGAAAGCATCTTTCCCAATGGT
130 AGAAACATTGAAAATCACTTTCTAATTTTTCACAAACATCATATGAAAGCATCTTGCCCAATGGT
** *
5551949 CTTATAGATGGCTTGAAGGAC-T
195 CTTATAGATGGCCCGAAGAACTT
* * *
5551971 ATCATCTTGCTTGAAAGACTTACTGATGGACC-GAGGACTTACCAATTTTGGAAATAGTTTACTA
1 ATCATCTTGCTTGAAAGACTTAATGATGG-CCAAAGGACTTACCAATTTTGGAAATAGTTTAAT-
* * * * **
5552035 G-GTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTATGAAAACATTAAAT
64 GTGTAAGAAACTTTAGAAATCACTTTCTTACTTTCCAAAAATTTAATTTTATGAAAACACCAAAT
* * ***
5552099 GGGAAACTTTGAAAATTGTTTTCTAATTTTTCACAAACATCATATGAAAGCATCTTGCCCAATGG
129 GAGAAACATTGAAAATCACTTTCTAATTTTTCACAAACATCATATGAAAGCATCTTGCCCAATGG
5552164 TCTTATAGATGGCCCGAAGAACTT
194 TCTTATAGATGGCCCGAAGAACTT
*
5552188 ATCATCTTGATTGAAA
1 ATCATCTTGCTTGAAA
5552204 TACTAACATA
Statistics
Matches: 204, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
216 159 0.78
217 43 0.21
218 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (217 bp):
ATCATCTTGCTTGAAAGACTTAATGATGGCCAAAGGACTTACCAATTTTGGAAATAGTTTAATGT
GTAAGAAACTTTAGAAATCACTTTCTTACTTTCCAAAAATTTAATTTTATGAAAACACCAAATGA
GAAACATTGAAAATCACTTTCTAATTTTTCACAAACATCATATGAAAGCATCTTGCCCAATGGTC
TTATAGATGGCCCGAAGAACTT
Found at i:5560244 original size:7 final size:7
Alignment explanation
Indices: 5560234--5560281 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
5560224 TTTTAAAAAA
5560234 TTAATTT
1 TTAATTT
5560241 TTAATTT
1 TTAATTT
*
5560248 ATAA-TT
1 TTAATTT
*
5560254 TTAAATT
1 TTAATTT
*
5560261 TTAAATT
1 TTAATTT
5560268 TTAATTTT
1 TTAA-TTT
5560276 TTAATT
1 TTAATT
5560282 AAATAATGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 5 0.14
7 25 0.69
8 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTAATTT
Found at i:5560252 original size:14 final size:13
Alignment explanation
Indices: 5560234--5560275 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
5560224 TTTTAAAAAA
5560234 TTAATTTTTAATT
1 TTAATTTTTAATT
*
5560247 TATAATTTTAAATT
1 T-TAATTTTTAATT
*
5560261 TTAAATTTTAATT
1 TTAATTTTTAATT
5560274 TT
1 TT
5560276 TTAATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATTTTTAATT
Found at i:5560276 original size:21 final size:21
Alignment explanation
Indices: 5560236--5560275 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5560226 TTAAAAAATT
*
5560236 AATTTTTAATTTATAATTTTA
1 AATTTTAAATTTATAATTTTA
5560257 AATTTTAAATTT-TAATTTT
1 AATTTTAAATTTATAATTTT
5560276 TTAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTTAAATTTATAATTTTA
Found at i:5567775 original size:20 final size:20
Alignment explanation
Indices: 5567736--5567775 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5567726 TATTATTTCA
*
5567736 AATTAATGAAATCTATATTT
1 AATTAATGAAATCTAAATTT
5567756 AATTAATTGAAAT-TAAATTT
1 AATTAA-TGAAATCTAAATTT
5567776 TCGATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
AATTAATGAAATCTAAATTT
Found at i:5574493 original size:90 final size:89
Alignment explanation
Indices: 5574339--5574514 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 89
5574329 CTAACACACT
* *
5574339 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
1 CTTTTATAGCAAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATAT
* *
5574404 TTAAATAATTGGAATTTAATAATC
66 TTAAATAATTGAAATTAAATAATC
* *
5574428 CTTTTATATCAAAGTTACCCTAATCATATTAGAGATTTTATTATTTCAAATTAATTAAATTTATA
1 CTTTTATAGCAAAGTTACCCTAATCATATTAG-GATTTTATTATTTCAAATTAATTAAATCTATA
*
5574493 TTTAATTAATTGAAATTAAATA
65 TTTAAATAATTGAAATTAAATA
5574515 TTAATTAACT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (89 bp):
CTTTTATAGCAAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAAATAATTGAAATTAAATAATC
Found at i:5574518 original size:21 final size:20
Alignment explanation
Indices: 5574476--5574522 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
5574466 TATTATTTCA
*
5574476 AATTAATTAAATTTATATTT
1 AATTAATTAAATTAATATTT
5574496 AATTAATTGAAATTAA-ATATT
1 AATTAATT-AAATTAATAT-TT
5574517 AATTAA
1 AATTAA
5574523 CTATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATTAATTAAATTAATATTT
Found at i:5596129 original size:23 final size:25
Alignment explanation
Indices: 5596088--5596135 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
5596078 TATAAATAGC
5596088 ACATTATATACTCCAT-AAAGAAAG
1 ACATTATATACTCCATAAAAGAAAG
5596112 ACATATATATAC-CC-TAAAAGAAAG
1 ACAT-TATATACTCCATAAAAGAAAG
5596136 GCTTGGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 1 0.05
24 14 0.64
25 7 0.32
ACGTcount: A:0.52, C:0.17, G:0.08, T:0.23
Consensus pattern (25 bp):
ACATTATATACTCCATAAAAGAAAG
Found at i:5602809 original size:221 final size:222
Alignment explanation
Indices: 5602424--5602846 Score: 548
Period size: 221 Copynumber: 1.9 Consensus size: 222
5602414 GGCCACTCTG
* * * * *
5602424 CTAAAATCAATAAGTTTATAAATTAAAGGTAATTTCAAACAGGTGTTGAGGTAAGTCTAAGCTTC
1 CTAAAATCAATAAGCTCATAAATTAAAGGTAATTTCAAACAGCTATTGAGGTAAGTCTAAGATTC
* * * * *
5602489 ATGAAGTGATTATATTCAAACCGTGACATTAATTGTGACATGATAAATTTACCAAATGAGGGAAA
66 ATGAAGTGATTATATTCAAACCATGACATTAATCGTGACACGATAAATTCACCAAAGGAGGGAAA
* *
5602554 GAAATGAGGTAAAAATAAGGATAATAATTTTAATA-AGGGTGGTAATGCCT-AAGATTAAGATAA
131 GAAACGAGGTAAAAATAAGGATAATAAGTTTAATATA-GGTGGTAATGCCTAAAG-TTAAGATAA
*
5602617 AATGAGTGTAATAAAATAGGGCTACTCCA
194 AATAAGTGTAATAAAATAGGGCTACTCCA
* *
5602646 CTAAAAGT-AATAAGCTCATAAATTGAAGGTAATTTCAAATAGCTATTGAGGTAAGTCTAAGATT
1 CTAAAA-TCAATAAGCTCATAAATTAAAGGTAATTTCAAACAGCTATTGAGGTAAGTCTAAGATT
* * * * * * * *
5602710 CGTTAAGTG-TTATATTCAAACCATGGCATTAATCGTGGCGCGATGAATTCCCCAAGGGAGGGAA
65 CATGAAGTGATTATATTCAAACCATGACATTAATCGTGACACGATAAATTCACCAAAGGAGGGAA
* * * *
5602774 AGAAACGAGGTAAAAGTGAGGATGATAAGTTTAATATAGGTGGTAATGCCTAAAGTTGAGATAAA
130 AGAAACGAGGTAAAAATAAGGATAATAAGTTTAATATAGGTGGTAATGCCTAAAGTTAAGATAAA
5602839 ATAAGTGT
195 ATAAGTGT
5602847 TTGTTGTCTA
Statistics
Matches: 171, Mismatches: 27, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
221 104 0.61
222 66 0.39
223 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (222 bp):
CTAAAATCAATAAGCTCATAAATTAAAGGTAATTTCAAACAGCTATTGAGGTAAGTCTAAGATTC
ATGAAGTGATTATATTCAAACCATGACATTAATCGTGACACGATAAATTCACCAAAGGAGGGAAA
GAAACGAGGTAAAAATAAGGATAATAAGTTTAATATAGGTGGTAATGCCTAAAGTTAAGATAAAA
TAAGTGTAATAAAATAGGGCTACTCCA
Found at i:5604179 original size:13 final size:14
Alignment explanation
Indices: 5604156--5604233 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 14
5604146 AATATCATTA
5604156 CTTTGATATGATGT
1 CTTTGATATGATGT
5604170 CTTT-ATATGAT-T
1 CTTTGATATGATGT
* * *
5604182 TTTTGATATGTTGCC
1 CTTTGATATGATG-T
**
5604197 CGAT-ATATGATGT
1 CTTTGATATGATGT
*
5604210 -TTTGATATGGTGT
1 CTTTGATATGATGT
5604223 CTTT-ATATGAT
1 CTTTGATATGAT
5604234 ATTTGTGAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
12 5 0.11
13 27 0.57
14 14 0.30
15 1 0.02
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (14 bp):
CTTTGATATGATGT
Found at i:5613001 original size:54 final size:54
Alignment explanation
Indices: 5612937--5613044 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
5612927 GTGCTTGAAA
5612937 TCAACATCAAACATTATTAAACCAATGAGAAGCTTGAGGATGAAATGGGGAATT
1 TCAACATCAAACATTATTAAACCAATGAGAAGCTTGAGGATGAAATGGGGAATT
5612991 TCAACATCAAACATTATTAAACCAATGAGAAGCTTGAGGATGAAATGGGGAATT
1 TCAACATCAAACATTATTAAACCAATGAGAAGCTTGAGGATGAAATGGGGAATT
5613045 CTAAAGAAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (54 bp):
TCAACATCAAACATTATTAAACCAATGAGAAGCTTGAGGATGAAATGGGGAATT
Found at i:5615519 original size:67 final size:67
Alignment explanation
Indices: 5615440--5615574 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
5615430 TAAAACATTC
5615440 TGATAGAATTGATCTTAAGTGACGTGTGCGTCTAACCCTTTAGGCTTGAATGCGAGGCTGAATAG
1 TGATAGAATTGATCTTAAGTGACGTGTGCGTCTAACCCTTTAGGCTTGAATGCGAGGCTGAATAG
5615505 TA
66 TA
5615507 TGATAGAATTGATCTTAAGTGACGTGTGCGTCTAACCCTTTAGGCTTGAATGCGAGGCTGAATAG
1 TGATAGAATTGATCTTAAGTGACGTGTGCGTCTAACCCTTTAGGCTTGAATGCGAGGCTGAATAG
5615572 TA
66 TA
5615574 T
1 T
5615575 TTGTAGACAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (67 bp):
TGATAGAATTGATCTTAAGTGACGTGTGCGTCTAACCCTTTAGGCTTGAATGCGAGGCTGAATAG
TA
Found at i:5628361 original size:149 final size:149
Alignment explanation
Indices: 5628091--5628386 Score: 592
Period size: 149 Copynumber: 2.0 Consensus size: 149
5628081 TTCACAATTT
5628091 CTGCTAATTTAAATTGTTGTGATCTTCGATATTCAGTTGTAATGTCTGGGCTAAGTCTAGAGGGT
1 CTGCTAATTTAAATTGTTGTGATCTTCGATATTCAGTTGTAATGTCTGGGCTAAGTCTAGAGGGT
5628156 TACAGAGCTAGCTTGGTGGTGGTGGTGGTGGTGTATGATTGAAGAGCAATAGAGGTAACATTAGT
66 TACAGAGCTAGCTTGGTGGTGGTGGTGGTGGTGTATGATTGAAGAGCAATAGAGGTAACATTAGT
5628221 GATCCTTATAGTCTAATGG
131 GATCCTTATAGTCTAATGG
5628240 CTGCTAATTTAAATTGTTGTGATCTTCGATATTCAGTTGTAATGTCTGGGCTAAGTCTAGAGGGT
1 CTGCTAATTTAAATTGTTGTGATCTTCGATATTCAGTTGTAATGTCTGGGCTAAGTCTAGAGGGT
5628305 TACAGAGCTAGCTTGGTGGTGGTGGTGGTGGTGTATGATTGAAGAGCAATAGAGGTAACATTAGT
66 TACAGAGCTAGCTTGGTGGTGGTGGTGGTGGTGTATGATTGAAGAGCAATAGAGGTAACATTAGT
5628370 GATCCTTATAGTCTAAT
131 GATCCTTATAGTCTAAT
5628387 TGGTGAAAAG
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (149 bp):
CTGCTAATTTAAATTGTTGTGATCTTCGATATTCAGTTGTAATGTCTGGGCTAAGTCTAGAGGGT
TACAGAGCTAGCTTGGTGGTGGTGGTGGTGGTGTATGATTGAAGAGCAATAGAGGTAACATTAGT
GATCCTTATAGTCTAATGG
Found at i:5629904 original size:2 final size:2
Alignment explanation
Indices: 5629897--5629932 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5629887 ATTGAAATTA
5629897 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
5629933 TAAAAAAGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5637730 original size:170 final size:172
Alignment explanation
Indices: 5637448--5637788 Score: 668
Period size: 170 Copynumber: 2.0 Consensus size: 172
5637438 TGATGTTATC
5637448 TTGCAACCGTTGTCACGATCAATAAATTTGTCTTTAATTTCAACATGAATGAAATTAACAAGAAT
1 TTGCAACCGTTGTCACGATCAATAAATTTGTCTTTAATTTCAACATGAATGAAATTAACAAGAAT
5637513 TTACCACAATTACTTGGCATGTTACAAACTGCTGAAAGTAACATGCAAAAGGTTGGACCTAAGCC
66 TTACCACAATTACTTGGCATGTTACAAACTGCTGAAAGTAACATGCAAAAGGTTGGACCTAAGCC
5637578 CATTTTGATGGTCCGCAA-GAT-AAGGAAAGATAAAGAAAAG
131 CATTTTGATGGTCCGCAAGGATAAAGGAAAGATAAAGAAAAG
5637618 TTGCAACCGTTGTCACGATCAATAAATTTGTCTTTAATTTCAACATGAATGAAATTAACAAGAAT
1 TTGCAACCGTTGTCACGATCAATAAATTTGTCTTTAATTTCAACATGAATGAAATTAACAAGAAT
5637683 TTACCACAATTACTTGGCATGTTACAAACTGCTGAAAGTAACATGCAAAAGGTTGGACCTAAGCC
66 TTACCACAATTACTTGGCATGTTACAAACTGCTGAAAGTAACATGCAAAAGGTTGGACCTAAGCC
5637748 CATTTTGATGGTCCGCAAGGATAAAGGAAAGATAAAGAAAA
131 CATTTTGATGGTCCGCAAGGATAAAGGAAAGATAAAGAAAA
5637789 AGATAGTGGA
Statistics
Matches: 169, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
170 148 0.88
171 3 0.02
172 18 0.11
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (172 bp):
TTGCAACCGTTGTCACGATCAATAAATTTGTCTTTAATTTCAACATGAATGAAATTAACAAGAAT
TTACCACAATTACTTGGCATGTTACAAACTGCTGAAAGTAACATGCAAAAGGTTGGACCTAAGCC
CATTTTGATGGTCCGCAAGGATAAAGGAAAGATAAAGAAAAG
Found at i:5643955 original size:18 final size:19
Alignment explanation
Indices: 5643926--5643964 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5643916 ACTTGAATTG
*
5643926 AATTTATTCAAAGTTTTCA
1 AATTTATTCAAAATTTTCA
5643945 AATTT-TTCAAAATTTTCA
1 AATTTATTCAAAATTTTCA
5643963 AA
1 AA
5643965 AATAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTTATTCAAAATTTTCA
Found at i:5643959 original size:10 final size:9
Alignment explanation
Indices: 5643926--5643964 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
5643916 ACTTGAATTG
5643926 AATTTATTCA
1 AATTT-TTCA
*
5643936 AAGTTTTCA
1 AATTTTTCA
5643945 AATTTTTCA
1 AATTTTTCA
*
5643954 AAATTTTCA
1 AATTTTTCA
5643963 AA
1 AA
5643965 AATAATTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (9 bp):
AATTTTTCA
Found at i:5652623 original size:20 final size:20
Alignment explanation
Indices: 5652598--5652655 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
5652588 CAATTTATTC
5652598 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
5652618 ATTGGTGCATTGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
5652638 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
5652656 CCCTTTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.14, G:0.34, T:0.33
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:5666339 original size:38 final size:38
Alignment explanation
Indices: 5666297--5666406 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 38
5666287 ATTATTATAT
5666297 TTTATTAAAATAAAATTATTATAAAATTATATTAATTA
1 TTTATTAAAATAAAATTATTATAAAATTATATTAATTA
* * *
5666335 TTTATTAAAATAAGAATAATATATTATGAATTATATTATTTA
1 TTTATTAAAATAA-AATTAT-TA-TA-AAATTATATTAATTA
* *
5666377 CTTATTAAAAATAATATTATTA-AAATATTA
1 TTTATT-AAAATAAAATTATTATAAA-ATTA
5666407 AAAATATTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
38 14 0.24
39 10 0.17
40 2 0.03
41 4 0.07
42 22 0.37
43 7 0.12
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (38 bp):
TTTATTAAAATAAAATTATTATAAAATTATATTAATTA
Found at i:5676608 original size:13 final size:15
Alignment explanation
Indices: 5676590--5676621 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5676580 AGCATATAGT
5676590 GAACTTA-G-AACCC
1 GAACTTAGGTAACCC
5676603 GAACTTAGGTAACCC
1 GAACTTAGGTAACCC
5676618 GAAC
1 GAAC
5676622 CTTAAGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (15 bp):
GAACTTAGGTAACCC
Done.