Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008075.1 Hibiscus syriacus cultivar Beakdansim tig00110577_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: 1947163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1505949 original size:24 final size:26
Alignment explanation
Indices: 1505921--1505989 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 26
1505911 CAACTCGTAT
1505921 AAATTTGCACCGAAGTGCCACG-TAG
1 AAATTTGCACCGAAGTGCCACGATAG
*
1505946 -AATTTGTC-CCGAA-TGAC-CGTATAG
1 AAATTTG-CACCGAAGTGCCACG-ATAG
*
1505970 AAATTTGCACCGTAGTGCCA
1 AAATTTGCACCGAAGTGCCA
1505990 TATAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
22 2 0.06
23 3 0.09
24 15 0.44
25 11 0.32
26 3 0.09
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (26 bp):
AAATTTGCACCGAAGTGCCACGATAG
Found at i:1505993 original size:25 final size:24
Alignment explanation
Indices: 1505921--1505999 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
1505911 CAACTCGTAT
**
1505921 AAATTTGCACCGAAGTGCCACGTAG
1 AAATTTGCACCG-AGTGCCATATAG
* *
1505946 -AATTTGTC-CCGAATGACCGTATAG
1 AAATTTG-CACCGAGTG-CCATATAG
1505970 AAATTTGCACCGTAGTGCCATATA-
1 AAATTTGCACCG-AGTGCCATATAG
1505994 AAATTT
1 AAATTT
1506000 TCCATAAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
23 3 0.07
24 21 0.49
25 16 0.37
26 3 0.07
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (24 bp):
AAATTTGCACCGAGTGCCATATAG
Found at i:1506029 original size:22 final size:23
Alignment explanation
Indices: 1505987--1506038 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1505977 CACCGTAGTG
* *
1505987 CCATATAAAATTTTCCATAAGGA
1 CCATATAAAATATTCCATAAGAA
*
1506010 CCATATAAAA-ATTCCTTAAGAA
1 CCATATAAAATATTCCATAAGAA
*
1506032 TCATATA
1 CCATATA
1506039 CATATATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (23 bp):
CCATATAAAATATTCCATAAGAA
Found at i:1506286 original size:31 final size:31
Alignment explanation
Indices: 1506232--1506310 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
1506222 TTATATCGCG
* *
1506232 TAGACATATCATTTCT-ATACCTTTATCACA
1 TAGACATATAATTTTTCATACCTTTATCACA
1506262 TAGACATATAATTTTTCATACCTTTATCACA
1 TAGACATATAATTTTTCATACCTTTATCACA
* *
1506293 TAGCTCATATAACTTTTC
1 TAG-ACATATAATTTTTC
1506311 CTGCATATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 14 0.33
31 17 0.40
32 12 0.28
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.42
Consensus pattern (31 bp):
TAGACATATAATTTTTCATACCTTTATCACA
Found at i:1506365 original size:25 final size:25
Alignment explanation
Indices: 1506337--1506398 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
1506327 AATAATACAT
1506337 ATAATATGAATTCAT-ATCATGTATC
1 ATAATATGAATT-ATGATCATGTATC
1506362 ATAATATGGAA-TATGATCATGTATC
1 ATAATAT-GAATTATGATCATGTATC
*
1506387 AAAATATTGAAT
1 ATAATA-TGAAT
1506399 ATAGACTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.06
25 26 0.81
26 4 0.12
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (25 bp):
ATAATATGAATTATGATCATGTATC
Found at i:1506399 original size:25 final size:25
Alignment explanation
Indices: 1506352--1506400 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1506342 ATGAATTCAT
*
1506352 ATCATGTATCATAATATGGAATATG
1 ATCATGTATCAAAATATGGAATATG
*
1506377 ATCATGTATCAAAATATTGAATAT
1 ATCATGTATCAAAATATGGAATAT
1506401 AGACTTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (25 bp):
ATCATGTATCAAAATATGGAATATG
Found at i:1507700 original size:18 final size:18
Alignment explanation
Indices: 1507677--1507737 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
1507667 GTTCTTAATG
*
1507677 AGTGGTCCTACGGGATAT
1 AGTGGTCCTACGGGACAT
*
1507695 AGTGGTCCTACGAGACAT
1 AGTGGTCCTACGGGACAT
* *
1507713 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTACGGGACAT
1507731 AGTGGTC
1 AGTGGTC
1507738 ATTCGAGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:1507742 original size:18 final size:18
Alignment explanation
Indices: 1507708--1507742 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1507698 GGTCCTACGA
* *
1507708 GACATAGTGGTCCTTCGG
1 GACAAAGTGGTCATTCGG
1507726 GACAAAGTGGTCATTCG
1 GACAAAGTGGTCATTCG
1507743 AGATAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (18 bp):
GACAAAGTGGTCATTCGG
Found at i:1507745 original size:36 final size:36
Alignment explanation
Indices: 1507677--1507745 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
1507667 GTTCTTAATG
* * *
1507677 AGTGGTCCTACGGGATATAGTGGTCCTACGAGACAT
1 AGTGGTCCTACGGGACAAAGTGGTCATACGAGACAT
* *
1507713 AGTGGTCCTTCGGGACAAAGTGGTCATTCGAGA
1 AGTGGTCCTACGGGACAAAGTGGTCATACGAGA
1507746 TAAATATTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (36 bp):
AGTGGTCCTACGGGACAAAGTGGTCATACGAGACAT
Found at i:1510511 original size:31 final size:31
Alignment explanation
Indices: 1510387--1510511 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
1510377 GTCGAGGGTA
* *
1510387 TACCTATGTTCTACGGAACATATTGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
1510419 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
1510450 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
1510481 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
1510512 GCCAAGGATC
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
31 53 0.68
32 25 0.32
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:1510552 original size:30 final size:30
Alignment explanation
Indices: 1510498--1510569 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
1510488 GTTCTTCGGA
* * *
1510498 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
1510528 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
1510558 ACCTCTGGATAG
1 ACCTCTGGATAG
1510570 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:1515347 original size:31 final size:31
Alignment explanation
Indices: 1515223--1515347 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 31
1515213 GTCGAGGGTA
*
1515223 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
1515255 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
1515286 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
1515317 TACCTAGGTTCTTCGGAACAAATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
1515348 GCCAAGGATC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:1519432 original size:20 final size:20
Alignment explanation
Indices: 1519409--1519448 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1519399 CACTGAAATA
1519409 TTGGTATCGAGACTGACAAG
1 TTGGTATCGAGACTGACAAG
* *
1519429 TTGGTCTCTAGACTGACAAG
1 TTGGTATCGAGACTGACAAG
1519449 GGTTTTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGGTATCGAGACTGACAAG
Found at i:1526592 original size:20 final size:20
Alignment explanation
Indices: 1526567--1526608 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1526557 GACTTGTATG
1526567 AGCATAACTCCCCTTATGTT
1 AGCATAACTCCCCTTATGTT
1526587 AGCATAACTCCCCTTATGTT
1 AGCATAACTCCCCTTATGTT
1526607 AG
1 AG
1526609 TTTAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (20 bp):
AGCATAACTCCCCTTATGTT
Found at i:1532200 original size:2 final size:2
Alignment explanation
Indices: 1532193--1532219 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1532183 GCAGTGAGGA
1532193 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 A
1532220 CACACACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1532803 original size:9 final size:10
Alignment explanation
Indices: 1532778--1532814 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1532768 ATTGTGTTGT
1532778 TAATCTTTTTA
1 TAAT-TTTTTA
1532789 TAATTTTTTA
1 TAATTTTTTA
*
1532799 TATTTTTTTA
1 TAATTTTTTA
1532809 TAATTT
1 TAATTT
1532815 AAATACATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:1536596 original size:60 final size:60
Alignment explanation
Indices: 1536487--1536599 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
1536477 TCGGGTGACA
***
1536487 ATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGTAATATTTTATAATCGGATAATC
1 ATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGTAATACACTATAATCGGATAATC
* * * **
1536547 ATTTTGTAATTTTTAATAGTTGATAGACTTAATAAAGTTGTACACTATAATCG
1 ATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGTAATACACTATAATCG
1536600 AGTGACTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGTAATACACTATAATCGGATAATC
Found at i:1536630 original size:2 final size:2
Alignment explanation
Indices: 1536623--1536648 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1536613 GTATTTTAAT
1536623 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1536649 ATGGACCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1542942 original size:29 final size:30
Alignment explanation
Indices: 1542854--1542957 Score: 124
Period size: 32 Copynumber: 3.5 Consensus size: 30
1542844 TTTCATTTAA
*
1542854 GTACCTAAAGTATTTTTTTGGTCAAAATAA
1 GTACCTAAAGTATTTTTTTGGTCAAAATAG
* **
1542884 ATACCTAAAGTTATCTTTTTTAATCAAAATAG
1 GTACCTAAAG-TAT-TTTTTTGGTCAAAATAG
1542916 GTACCTTAAA-TATTTTTTTGGTC-AAATAG
1 GTACC-TAAAGTATTTTTTTGGTCAAAATAG
1542945 GTACCT-AAGTATT
1 GTACCTAAAGTATT
1542958 CCGTTTTTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.03
28 5 0.08
29 11 0.17
30 17 0.27
31 6 0.10
32 18 0.29
33 4 0.06
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (30 bp):
GTACCTAAAGTATTTTTTTGGTCAAAATAG
Found at i:1543089 original size:28 final size:27
Alignment explanation
Indices: 1543040--1543137 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 27
1543030 AAAAAGTTTG
* * *
1543040 AATAGTTTAGGTATCTACTTTGACATAA
1 AATACTTTAGGTA-CTATTTTGACAAAA
*
1543068 AATACTTTACGTACCTATTTTGACCAAAA
1 AATACTTTAGGTA-CTATTTTGA-CAAAA
*
1543097 ATATAACTTTAGGTATTCATTTTGACAAAA
1 A-AT-ACTTTAGGTACT-ATTTTGACAAAA
*
1543127 AAAACTTTAGG
1 AATACTTTAGG
1543138 CACTTAAATG
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 27 0.47
29 6 0.10
30 9 0.16
31 16 0.28
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (27 bp):
AATACTTTAGGTACTATTTTGACAAAA
Found at i:1545424 original size:31 final size:31
Alignment explanation
Indices: 1545366--1545431 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1545356 TGTAATATAA
* *
1545366 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCATTTACAATATGG
* *
1545397 TCCCTCAACATTTAGTCTATTTACAATATGG
1 TCCCCCAACATTTAGTCCATTTACAATATGG
1545428 TCCC
1 TCCC
1545432 GACGTAACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCATTTACAATATGG
Found at i:1546070 original size:2 final size:2
Alignment explanation
Indices: 1546063--1546119 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1546053 GCTGTAACTT
1546063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1546105 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1546120 TTTAATTTGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1547195 original size:36 final size:36
Alignment explanation
Indices: 1547145--1547218 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
1547135 TTGAGGTAAT
*
1547145 ATGTTGAAGAGTAAGGCTTTATAATATTCATGCAAC
1 ATGTTGAAGAGTAAGCCTTTATAATATTCATGCAAC
*
1547181 ATGTTGAAGTGTAAGCCTTTATAATATTCATGCAAC
1 ATGTTGAAGAGTAAGCCTTTATAATATTCATGCAAC
1547217 AT
1 AT
1547219 TTATGAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
ATGTTGAAGAGTAAGCCTTTATAATATTCATGCAAC
Found at i:1548032 original size:31 final size:31
Alignment explanation
Indices: 1547972--1548039 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1547962 TTGCAATACA
*
1547972 GTCCCCCAACATTTAGTCTATTTACAATATG
1 GTCCCCCAACATTTAGTCCATTTACAATATG
*
1548003 GTCCCCCAACATTTAGTCCGTTTGA-AATATG
1 GTCCCCCAACATTTAGTCCATTT-ACAATATG
*
1548034 ATCCCC
1 GTCCCC
1548040 AATATAACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCATTTACAATATG
Found at i:1549140 original size:122 final size:123
Alignment explanation
Indices: 1549003--1549248 Score: 449
Period size: 123 Copynumber: 2.0 Consensus size: 123
1548993 CATAGCCGAG
*
1549003 TTTGTGCTG-TTTTTTTCAGTGTTTTAGTGCGGTTATTGCTTGGCTGTAGTTTGAGTCACGCGAC
1 TTTGTGCTGTTTTTTTTCAGTGTTTTAGTGCGGTTATTGCTTGGCTGTAGTTTGAGCCACGCGAC
1549067 TCAAGACGATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGAGGACCCCTTTGGC
66 TCAAGACGATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGAGGACCCCTTTGGC
*
1549125 TTTGTGCTGTTTTTTTTCAGTGTTTTAGTGTGGTTATTGCTTGGCTGTAGTTTGAGCCACGCGAC
1 TTTGTGCTGTTTTTTTTCAGTGTTTTAGTGCGGTTATTGCTTGGCTGTAGTTTGAGCCACGCGAC
* *
1549190 TCAAGACTATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGTGGACCCCTTTGGC
66 TCAAGACGATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGAGGACCCCTTTGGC
1549248 T
1 T
1549249 ACTTAAATTC
Statistics
Matches: 119, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
122 9 0.08
123 110 0.92
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (123 bp):
TTTGTGCTGTTTTTTTTCAGTGTTTTAGTGCGGTTATTGCTTGGCTGTAGTTTGAGCCACGCGAC
TCAAGACGATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGAGGACCCCTTTGGC
Found at i:1552589 original size:23 final size:26
Alignment explanation
Indices: 1552559--1552637 Score: 110
Period size: 27 Copynumber: 3.1 Consensus size: 26
1552549 GACAATCGTC
*
1552559 CTCCATTAAAAAA-TA-T-TTAATGT
1 CTCCATTAAAAAAGCATTGTTAATGT
1552582 CTCCATTAAAAAAGGCATTGTTAATGT
1 CTCCATTAAAAAA-GCATTGTTAATGT
1552609 CTCCATTAAAAAAGGCATTGTTAATGT
1 CTCCATTAAAAAA-GCATTGTTAATGT
1552636 CT
1 CT
1552638 ACCTGTCATA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
23 13 0.25
25 1 0.02
26 1 0.02
27 36 0.71
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (26 bp):
CTCCATTAAAAAAGCATTGTTAATGT
Found at i:1552606 original size:27 final size:27
Alignment explanation
Indices: 1552575--1552637 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
1552565 TAAAAAATAT
1552575 TTAATGTCTCCATTAAAAAAGGCATTG
1 TTAATGTCTCCATTAAAAAAGGCATTG
1552602 TTAATGTCTCCATTAAAAAAGGCATTG
1 TTAATGTCTCCATTAAAAAAGGCATTG
1552629 TTAATGTCT
1 TTAATGTCT
1552638 ACCTGTCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (27 bp):
TTAATGTCTCCATTAAAAAAGGCATTG
Found at i:1555860 original size:20 final size:20
Alignment explanation
Indices: 1555837--1555884 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1555827 AAAATTATAG
1555837 AAAATATAAAAAGTATAAATA
1 AAAATATAAAAAGTA-AAATA
* *
1555858 AAAA-ATAATAATTAAAATA
1 AAAATATAAAAAGTAAAATA
1555877 AAAATATA
1 AAAATATA
1555885 TTTTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 11 0.46
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATATAAAAAGTAAAATA
Found at i:1560992 original size:30 final size:30
Alignment explanation
Indices: 1560956--1561026 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
1560946 ATACATTCCC
1560956 GAACCATACCCCGAGTTGTAGTTTAAGCCA
1 GAACCATACCCCGAGTTGTAGTTTAAGCCA
*
1560986 GAACCATACCCCGAGTTGTGGTTTAAGCCA
1 GAACCATACCCCGAGTTGTAGTTTAAGCCA
1561016 GAACCATACCC
1 GAACCATACCC
1561027 TGCATCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (30 bp):
GAACCATACCCCGAGTTGTAGTTTAAGCCA
Found at i:1561562 original size:18 final size:17
Alignment explanation
Indices: 1561539--1561580 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1561529 AGGAAAAAAA
1561539 CAACTAATCAAACCGAAG
1 CAACTAATCAAACC-AAG
* *
1561557 CAACTAAACAAATCAAG
1 CAACTAATCAAACCAAG
1561574 CAA-TAAT
1 CAACTAAT
1561581 AACTGAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 6 0.29
18 12 0.57
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (17 bp):
CAACTAATCAAACCAAG
Found at i:1562774 original size:31 final size:31
Alignment explanation
Indices: 1562733--1562805 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
1562723 TACACGGTTT
* *
1562733 CTAACATTATCAATTCGTTCGATTATAGTAC
1 CTAACGTTATCAATTCGTTCGAATATAGTAC
* *
1562764 CTAACGTTATCAATTCGTTCGAATATGGTCC
1 CTAACGTTATCAATTCGTTCGAATATAGTAC
1562795 CTAACGTTATC
1 CTAACGTTATC
1562806 GATCCATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (31 bp):
CTAACGTTATCAATTCGTTCGAATATAGTAC
Found at i:1562822 original size:31 final size:31
Alignment explanation
Indices: 1562733--1562822 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 31
1562723 TACACGGTTT
* * * *
1562733 CTAACATTATCAATTCGTTCGATTATAGTAC
1 CTAACGTTATCAATCCATTCGATTATGGTAC
* * * *
1562764 CTAACGTTATCAATTCGTTCGAATATGGTCC
1 CTAACGTTATCAATCCATTCGATTATGGTAC
* *
1562795 CTAACGTTATCGATCCATTTGATTATGG
1 CTAACGTTATCAATCCATTCGATTATGG
1562823 CTCCAACATT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (31 bp):
CTAACGTTATCAATCCATTCGATTATGGTAC
Found at i:1565722 original size:9 final size:9
Alignment explanation
Indices: 1565708--1565750 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
1565698 TAATATTTTG
1565708 TATTTAATT
1 TATTTAATT
1565717 TATTTAATT
1 TATTTAATT
*
1565726 TATTTAA-G
1 TATTTAATT
*
1565734 TATTTAAAT
1 TATTTAATT
1565743 TATTTAAT
1 TATTTAAT
1565751 ATTGTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
TATTTAATT
Found at i:1565738 original size:21 final size:20
Alignment explanation
Indices: 1565714--1565763 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 20
1565704 TTTGTATTTA
1565714 ATTTATTTAATTTATTTAAGT
1 ATTTATTTAATTTATTTAA-T
1565735 ATTTA---AA-TTATTTAAT
1 ATTTATTTAATTTATTTAAT
1565751 ATTGTATTTAATT
1 ATT-TATTTAATT
1565764 ATTATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
16 4 0.17
17 10 0.42
18 2 0.08
20 2 0.08
21 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
ATTTATTTAATTTATTTAAT
Found at i:1565739 original size:17 final size:16
Alignment explanation
Indices: 1565717--1565753 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1565707 GTATTTAATT
*
1565717 TATTTAATTTATTTAA
1 TATTTAAATTATTTAA
1565733 GTATTTAAATTATTTAA
1 -TATTTAAATTATTTAA
1565750 TATT
1 TATT
1565754 GTATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TATTTAAATTATTTAA
Found at i:1579692 original size:18 final size:16
Alignment explanation
Indices: 1579661--1579695 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1579651 CATCTTGTTT
1579661 TCGTTCTCATGGTAAA
1 TCGTTCTCATGGTAAA
1579677 TCGTATCTCTATGGTAAA
1 TCGT-TCTC-ATGGTAAA
1579695 T
1 T
1579696 AGGAAGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 9 0.53
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (16 bp):
TCGTTCTCATGGTAAA
Found at i:1582754 original size:14 final size:14
Alignment explanation
Indices: 1582735--1582761 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1582725 ATAGCTTAAG
1582735 ATCTGAGAGCAAGA
1 ATCTGAGAGCAAGA
1582749 ATCTGAGAGCAAG
1 ATCTGAGAGCAAG
1582762 TGTCAGGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.30, T:0.15
Consensus pattern (14 bp):
ATCTGAGAGCAAGA
Found at i:1588524 original size:13 final size:13
Alignment explanation
Indices: 1588508--1588532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1588498 GGAATTGATT
1588508 TTGAGTGTTTTTA
1 TTGAGTGTTTTTA
1588521 TTGAGTGTTTTT
1 TTGAGTGTTTTT
1588533 TCTTTCGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (13 bp):
TTGAGTGTTTTTA
Found at i:1598691 original size:9 final size:9
Alignment explanation
Indices: 1598679--1598784 Score: 52
Period size: 9 Copynumber: 12.4 Consensus size: 9
1598669 AATAAAAGAG
1598679 AAAATGAAA
1 AAAATGAAA
1598688 AAAATGAAA
1 AAAATGAAA
1598697 AAAAT-AATA
1 AAAATGAA-A
*
1598706 ATAAT--AA
1 AAAATGAAA
*
1598713 AAAATGAGA
1 AAAATGAAA
*
1598722 AGAA-G-AA
1 AAAATGAAA
*
1598729 AAAA--AAG
1 AAAATGAAA
1598736 AAAA-G-AA
1 AAAATGAAA
1598743 AAAATGAGAA
1 AAAATGA-AA
1598753 AAAA-GAAA
1 AAAATGAAA
*
1598761 AAATGATGGAA
1 AAA--ATGAAA
*
1598772 AAAACGAAA
1 AAAATGAAA
1598781 AAAA
1 AAAA
1598785 AAGAAGAGAA
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
7 19 0.25
8 10 0.13
9 33 0.44
10 7 0.09
11 6 0.08
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.09
Consensus pattern (9 bp):
AAAATGAAA
Found at i:1598703 original size:30 final size:29
Alignment explanation
Indices: 1598663--1598817 Score: 92
Period size: 29 Copynumber: 5.3 Consensus size: 29
1598653 TTTCGCTTGA
*
1598663 AGAAGAAATAAAAGAGAAAATGAAAAAA--
1 AGAA-AAAAAAAAGAGAAAATGAAAAAATG
* * *
1598691 ATGAAAAAAATAATA-ATAAT-AAAAAATG
1 A-GAAAAAAAAAAGAGAAAATGAAAAAATG
*
1598719 AGAAGAAGAAAAAAAAGAAAA-GAAAAAATG
1 AGAA-AA-AAAAAAGAGAAAATGAAAAAATG
** *
1598749 AGAAAAAAGAAAA-A-ATGATGGAAAAAACG
1 AGAAAAAA-AAAAGAGAAAAT-GAAAAAATG
*
1598778 A-AAAAAAAAGAAGAGAAAAATGAAAAAAAG
1 AGAAAAAAAA-AAGAG-AAAATGAAAAAATG
*
1598808 AGAAATAAAA
1 AGAAAAAAAA
1598818 GGAGGGTTCA
Statistics
Matches: 98, Mismatches: 14, Indels: 27
0.71 0.10 0.19
Matches are distributed among these distances:
26 6 0.06
27 11 0.11
28 22 0.22
29 25 0.26
30 24 0.24
31 10 0.10
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (29 bp):
AGAAAAAAAAAAGAGAAAATGAAAAAATG
Found at i:1598773 original size:18 final size:17
Alignment explanation
Indices: 1598672--1598783 Score: 76
Period size: 16 Copynumber: 6.6 Consensus size: 17
1598662 AAGAAGAAAT
*
1598672 AAAAGAGAAAATGA-AA
1 AAAAGAAAAAATGAGAA
1598688 AAAATGAAAAAAAT-A-ATA
1 AAAA-G-AAAAAATGAGA-A
* *
1598706 ATAATAAAAAATGAG-A
1 AAAAGAAAAAATGAGAA
* *
1598722 AGAAGAAAAAA--A-AG
1 AAAAGAAAAAATGAGAA
1598736 AAAAGAAAAAATGAGAA
1 AAAAGAAAAAATGAGAA
1598753 AAAAGAAAAAATGATGGAA
1 AAAAGAAAAAATGA--GAA
1598772 AAAACGAAAAAA
1 AAAA-GAAAAAA
1598784 AAAGAAGAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 11 0.14
16 22 0.29
17 19 0.25
18 10 0.13
19 7 0.09
20 7 0.09
ACGTcount: A:0.75, C:0.01, G:0.15, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAAATGAGAA
Found at i:1598796 original size:22 final size:21
Alignment explanation
Indices: 1598721--1598811 Score: 62
Period size: 22 Copynumber: 4.2 Consensus size: 21
1598711 AAAAAATGAG
*
1598721 AAGAAGAAAAAAAAGAAAAGAAA
1 AAGAAG-AGAAAAAGAAAA-AAA
* *
1598744 AA-ATGAGAAAAA-AGAAAAA
1 AAGAAGAGAAAAAGAAAAAAA
* *
1598763 ATGATG-GAAAAAACGAAAAAAA
1 AAGAAGAG-AAAAA-GAAAAAAA
1598785 AAGAAGAGAAAAATGAAAAAAA
1 AAGAAGAGAAAAA-GAAAAAAA
*
1598807 GAGAA
1 AAGAA
1598812 ATAAAAGGAG
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
19 5 0.09
20 11 0.20
21 6 0.11
22 29 0.54
23 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (21 bp):
AAGAAGAGAAAAAGAAAAAAA
Found at i:1598812 original size:17 final size:16
Alignment explanation
Indices: 1598667--1598808 Score: 89
Period size: 17 Copynumber: 8.6 Consensus size: 16
1598657 GCTTGAAGAA
*
1598667 GAAATAAAAGAGAAAAT
1 GAAA-AAAAGAAAAAAT
1598684 GAAAAAAATGAAAAAAAT
1 GAAAAAAA-G-AAAAAAT
* *
1598702 -AATAATAATAAAAAAT
1 GAA-AAAAAGAAAAAAT
* *
1598718 GAGAAGAAGAAAAAA-
1 GAAAAAAAGAAAAAAT
*
1598733 -AAGAAAAGAAAAAAT
1 GAAAAAAAGAAAAAAT
1598748 GAGAAAAAAGAAAAAAT
1 GA-AAAAAAGAAAAAAT
1598765 GATGGAAAAAACG-AAAAA-
1 GA---AAAAAA-GAAAAAAT
*
1598783 -AAAAGAAGAGAAAAAT
1 GAAAAAAAGA-AAAAAT
1598799 GAAAAAAAGA
1 GAAAAAAAGA
1598809 GAAATAAAAG
Statistics
Matches: 99, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
13 1 0.01
14 16 0.16
15 5 0.05
16 22 0.22
17 32 0.32
18 10 0.10
19 12 0.12
20 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (16 bp):
GAAAAAAAGAAAAAAT
Found at i:1600520 original size:486 final size:486
Alignment explanation
Indices: 1599609--1600580 Score: 1899
Period size: 486 Copynumber: 2.0 Consensus size: 486
1599599 GAAAAGAAAG
1599609 AGTCAAGGTTCTGTTAAGGCGAGAGATATGGAATTGAGATTGTCAACTGGGGTGAACTGGTCAAA
1 AGTCAAGGTTCTGTTAAGGCGAGAGATATGGAATTGAGATTGTCAACTGGGGTGAACTGGTCAAA
1599674 CGTTCTGTGCCCAAGATGAAGCCGAGTTCCATCGAGATCAAAAGGAGATAGAGTTCCTTCAAAGA
66 CGTTCTGTGCCCAAGATGAAGCCGAGTTCCATCGAGATCAAAAGGAGATAGAGTTCCTTCAAAGA
1599739 AAAAAACGCATTGAATTGCATAATTGCATACATTTTAGGCATGAGTAGGATCATGGCATTCATAA
131 AAAAAACGCATTGAATTGCATAATTGCATACATTTTAGGCATGAGTAGGATCATGGCATTCATAA
1599804 TCGCATGATGGCTTAAATATCTACAGGTTTCCCATGAATAGTTGAAGATTGAAGATATGAAAGCA
196 TCGCATGATGGCTTAAATATCTACAGGTTTCCCATGAATAGTTGAAGATTGAAGATATGAAAGCA
*
1599869 TCGAACTGGTCTTGAGATTTTGACAAGAATGATGTTTATACGAAAATTGAGTCAAAGCAGATTCA
261 TCAAACTGGTCTTGAGATTTTGACAAGAATGATGTTTATACGAAAATTGAGTCAAAGCAGATTCA
1599934 AATATCCAATGGCTCCAGACAAGTTTTCACGATGGAGATGGATTTTCAAAAATTTTCTCAACTTC
326 AATATCCAATGGCTCCAGACAAGTTTTCACGATGGAGATGGATTTTCAAAAATTTTCTCAACTTC
1599999 TAAATTATTTTTTAGTATAATATTTTTCAAATATACATTCATGATGAATAATGTTTGATTTTCAG
391 TAAATTATTTTTTAGTATAATATTTTTCAAATATACATTCATGATGAATAATGTTTGATTTTCAG
1600064 GTTTGACCTTTGAAGCAAATCATCTATAAGC
456 GTTTGACCTTTGAAGCAAATCATCTATAAGC
1600095 AGTCAAGGTTCTGTTAAGGCGAGAGATATGGAATTGAGATTGTCAACTGGGGTGAACTGGTCAAA
1 AGTCAAGGTTCTGTTAAGGCGAGAGATATGGAATTGAGATTGTCAACTGGGGTGAACTGGTCAAA
*
1600160 CGTTTTGTGCCCAAGATGAAGCCGAGTTCCATCGAGATCAAAAGGAGATAGAGTTCCTTCAAAGA
66 CGTTCTGTGCCCAAGATGAAGCCGAGTTCCATCGAGATCAAAAGGAGATAGAGTTCCTTCAAAGA
*
1600225 AGAAAACGCATTGAATTGCATAATTGCATACATTTTAGGCATGAGTAGGATCATGGCATTCATAA
131 AAAAAACGCATTGAATTGCATAATTGCATACATTTTAGGCATGAGTAGGATCATGGCATTCATAA
1600290 TCGCATGATGGCTTAAATATCTACAGGTTTCCCATGAATAGTTGAAGATTGAAGATATGAAAGCA
196 TCGCATGATGGCTTAAATATCTACAGGTTTCCCATGAATAGTTGAAGATTGAAGATATGAAAGCA
*
1600355 TCAAACTGGTCTTGAGATTTTGACAAGAATGATGTTTATACGAAAATTGAGTCAAAGCATATTCA
261 TCAAACTGGTCTTGAGATTTTGACAAGAATGATGTTTATACGAAAATTGAGTCAAAGCAGATTCA
*
1600420 AATATCCAATGGCTTCAGACAAGTTTTCACGATGGAGATGGATTTTCAAAAATTTTCTCAACTTC
326 AATATCCAATGGCTCCAGACAAGTTTTCACGATGGAGATGGATTTTCAAAAATTTTCTCAACTTC
1600485 TAAATTATTTTTTAGTATAATATTTTTCAAATATACATTCATGATGAATAATGTTTGATTTTCAG
391 TAAATTATTTTTTAGTATAATATTTTTCAAATATACATTCATGATGAATAATGTTTGATTTTCAG
1600550 GTTTGACCTTTGAAGCAAATCATCTATAAGC
456 GTTTGACCTTTGAAGCAAATCATCTATAAGC
1600581 CTTCACGAAA
Statistics
Matches: 481, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
486 481 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (486 bp):
AGTCAAGGTTCTGTTAAGGCGAGAGATATGGAATTGAGATTGTCAACTGGGGTGAACTGGTCAAA
CGTTCTGTGCCCAAGATGAAGCCGAGTTCCATCGAGATCAAAAGGAGATAGAGTTCCTTCAAAGA
AAAAAACGCATTGAATTGCATAATTGCATACATTTTAGGCATGAGTAGGATCATGGCATTCATAA
TCGCATGATGGCTTAAATATCTACAGGTTTCCCATGAATAGTTGAAGATTGAAGATATGAAAGCA
TCAAACTGGTCTTGAGATTTTGACAAGAATGATGTTTATACGAAAATTGAGTCAAAGCAGATTCA
AATATCCAATGGCTCCAGACAAGTTTTCACGATGGAGATGGATTTTCAAAAATTTTCTCAACTTC
TAAATTATTTTTTAGTATAATATTTTTCAAATATACATTCATGATGAATAATGTTTGATTTTCAG
GTTTGACCTTTGAAGCAAATCATCTATAAGC
Found at i:1600674 original size:51 final size:51
Alignment explanation
Indices: 1600613--1600965 Score: 598
Period size: 51 Copynumber: 6.8 Consensus size: 51
1600603 AAATTCGTTT
1600613 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1600664 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1600715 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1600766 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1600817 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * ** *
1600868 GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* *
1600920 GTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCG
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCG
1600966 AACCCGTTTT
Statistics
Matches: 292, Mismatches: 5, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
51 248 0.85
52 10 0.03
55 2 0.01
56 32 0.11
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:1600954 original size:56 final size:51
Alignment explanation
Indices: 1600613--1601077 Score: 583
Period size: 51 Copynumber: 8.8 Consensus size: 51
1600603 AAATTCGTTT
*
1600613 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1600664 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1600715 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1600766 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1600817 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* ** *
1600868 GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * ** *
1600920 GTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTT
1 GTTGAAGA---TT-GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * ** *
1600976 GTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTT
1 GTTGAAGA---TT-GAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACAAG-TTC
*
1601032 GTTGAAGATTGTTAGAGTTCTATACTCCCTGAACGG-ATAGGGAGCG
1 GTTGAAGA---TT-GAGTTCTATACTCTCTGAA-GGAATAGGGAGCG
1601078 AACCCGTTTT
Statistics
Matches: 399, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
51 248 0.62
52 10 0.03
55 2 0.01
56 137 0.34
57 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:1601143 original size:55 final size:56
Alignment explanation
Indices: 1600623--1601180 Score: 444
Period size: 51 Copynumber: 10.4 Consensus size: 56
1600613 GTTGAAGATT
* * * ** *
1600623 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
* * * ** *
1600674 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
* * * ** *
1600725 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
* * * ** *
1600776 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
* * * ** *
1600827 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
*
1600878 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
1600934 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
* * *
1600990 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTTGTTGAAGATTGTTA
1 GAGTTCTATACTCTCTGAA-GGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
* * * *
1601046 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTT-ATGAAAATTGTTC
1 GAGTTCTATACTCTCTGAA-GGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
* * * * *
1601101 AAG-TCTTATACTCTCTGAATGAATAGAGAGC-AGACACATTTT-ATGAAGATTGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGA-ACCCGTTTTGTTGAAGATTGTTC
1601156 GAG-TCTTATACT-TCCTGAAGGAATA
1 GAGTTC-TATACTCT-CTGAAGGAATA
1601181 CGGAGCAGAC
Statistics
Matches: 476, Mismatches: 21, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
51 238 0.50
52 10 0.02
54 5 0.01
55 74 0.16
56 147 0.31
57 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (56 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
Found at i:1601190 original size:55 final size:55
Alignment explanation
Indices: 1600878--1601186 Score: 314
Period size: 56 Copynumber: 5.5 Consensus size: 55
1600868 GTTGAAGATT
* *
1600878 GAGTTCTATAC-TCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTTC-CTGAAGGAATAG-GAGCGAACCCGTTTTGATGAAGATTGTTC
*
1600934 GAGTTCTATAC-TCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTTC-CTGAAGGAATAG-GAGCGAACCCGTTTTGATGAAGATTGTTC
* * *
1600990 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTTGTTGAAGATTGTTA
1 GAGTTCTATACTTCCTGAA-GGAATA-GGAGCGAACCCGTTTTGATGAAGATTGTTC
* *
1601046 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTT-ATGAAAATTGTTC
1 GAGTTCTATACTTCCTGAA-GGAATA-GGAGCGAACCCGTTTTGATGAAGATTGTTC
* * * *
1601101 AAG-TCTTATAC-TCTCTGAATGAATAGAGAGC-AGACACATTTT-ATGAAGATTGTTC
1 GAGTTC-TATACTTC-CTGAAGGAATAG-GAGCGA-ACCCGTTTTGATGAAGATTGTTC
1601156 GAG-TCTTATACTTCCTGAAGGAATACGGAGC
1 GAGTTC-TATACTTCCTGAAGGAATA-GGAGC
1601187 AGACTCCTCA
Statistics
Matches: 229, Mismatches: 14, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
54 6 0.03
55 72 0.31
56 147 0.64
57 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (55 bp):
GAGTTCTATACTTCCTGAAGGAATAGGAGCGAACCCGTTTTGATGAAGATTGTTC
Found at i:1606052 original size:11 final size:12
Alignment explanation
Indices: 1606012--1606055 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1606002 TATTTAAACG
*
1606012 GGTATTGGGCCA
1 GGTATTGGGTCA
*
1606024 GGTATTGGGTCG
1 GGTATTGGGTCA
1606036 GGTATTGGGTC-
1 GGTATTGGGTCA
1606047 GGTATTGGG
1 GGTATTGGG
1606056 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:1606054 original size:23 final size:24
Alignment explanation
Indices: 1606010--1606055 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1606000 ATTATTTAAA
1606010 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
1606034 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
1606056 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:1606133 original size:24 final size:25
Alignment explanation
Indices: 1606073--1606156 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 25
1606063 TCGGGCCGGG
1606073 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
1606096 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
1606120 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
1606145 TATATATATATA
1 TATATAT-TATA
1606157 ATAATTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 4 0.08
23 8 0.17
24 24 0.50
25 4 0.08
26 1 0.02
27 6 0.12
28 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:1606138 original size:2 final size:2
Alignment explanation
Indices: 1606127--1606156 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1606117 AAATTTATTA
1606127 AT AT -T 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 A
1606157 ATAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1606206 original size:13 final size:12
Alignment explanation
Indices: 1606175--1606211 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1606165 TTTTAATATT
*
1606175 TATCGGGTCGGG
1 TATCGGGGCGGG
1606187 TATCGGGGCGGG
1 TATCGGGGCGGG
1606199 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
1606212 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:1615360 original size:17 final size:19
Alignment explanation
Indices: 1615338--1615372 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1615328 GCTTTTGTTC
1615338 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
1615355 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
1615373 GAGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:1623169 original size:23 final size:23
Alignment explanation
Indices: 1623142--1623197 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
1623132 TGTACTTTTG
1623142 TGCTGAATCATTCAACACTGTTT
1 TGCTGAATCATTCAACACTGTTT
*
1623165 TGCTGAATCATTCATCACTGTTT
1 TGCTGAATCATTCAACACTGTTT
1623188 TGCTGAATCA
1 TGCTGAATCA
1623198 GTCAGTACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (23 bp):
TGCTGAATCATTCAACACTGTTT
Found at i:1623207 original size:23 final size:23
Alignment explanation
Indices: 1623133--1623207 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
1623123 CATTCAGAAT
1623133 GTACT-TTTGTGCTGAATCATTCA
1 GTACTGTTT-TGCTGAATCATTCA
**
1623156 ACACTGTTTTGCTGAATCATTCA
1 GTACTGTTTTGCTGAATCATTCA
*
1623179 -TCACTGTTTTGCTGAATCAGTCA
1 GT-ACTGTTTTGCTGAATCATTCA
1623202 GTACTG
1 GTACTG
1623208 AATCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (23 bp):
GTACTGTTTTGCTGAATCATTCA
Found at i:1624414 original size:15 final size:15
Alignment explanation
Indices: 1624396--1624426 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1624386 AAATTCCAAA
1624396 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1624411 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1624426 T
1 T
1624427 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1635132 original size:20 final size:20
Alignment explanation
Indices: 1635107--1635200 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1635097 AATTGGGAAA
*
1635107 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1635127 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1635148 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1635168 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1635188 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1635201 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1635755 original size:19 final size:19
Alignment explanation
Indices: 1635713--1635783 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
1635703 TAGTTTCGAG
1635713 AATAAAAATCGCAACGCGGA
1 AATAAAAATCGCAACGC-GA
**
1635733 AATAACTATCGCAACGCGA
1 AATAAAAATCGCAACGCGA
*
1635752 AATAAAAATCGCAATGCGA
1 AATAAAAATCGCAACGCGA
**
1635771 AACCAAAATCGCA
1 AATAAAAATCGCA
1635784 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.66
20 15 0.34
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.13
Consensus pattern (19 bp):
AATAAAAATCGCAACGCGA
Found at i:1635801 original size:19 final size:19
Alignment explanation
Indices: 1635779--1635817 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1635769 GAAACCAAAA
1635779 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1635798 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1635817 T
1 T
1635818 TGCGTTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1635822 original size:19 final size:19
Alignment explanation
Indices: 1635784--1635923 Score: 77
Period size: 19 Copynumber: 7.8 Consensus size: 19
1635774 CAAAATCGCA
*
1635784 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTTGCG
1635803 TTGCGATTTTCATTTTGCG
1 TTGCGATTTTCATTTTGCG
* *
1635822 TTGC-A-ATTC--TCT-CG
1 TTGCGATTTTCATTTTGCG
* **
1635836 TCGCGATAGTCATTTTGCG
1 TTGCGATTTTCATTTTGCG
*
1635855 TTGCGA--TTC--TCT-CG
1 TTGCGATTTTCATTTTGCG
** *
1635869 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-TGCG
*
1635889 TTGCGATTCTCATTATCT-CG
1 TTGCGATTTTCATT-T-TGCG
1635909 TTGCGATTTTCATTT
1 TTGCGATTTTCATTT
1635924 CAACCAAAAG
Statistics
Matches: 93, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
14 13 0.14
15 5 0.05
16 5 0.05
17 5 0.05
18 4 0.04
19 30 0.32
20 29 0.31
21 2 0.02
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTTGCG
Found at i:1635842 original size:33 final size:33
Alignment explanation
Indices: 1635812--1635899 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1635802 GTTGCGATTT
*
1635812 TCATTTTGCGTTGCAATTCTCTCGTCGCGATAG
1 TCATTTTGCGTTGCGATTCTCTCGTCGCGATAG
*
1635845 TCATTTTGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTTGCGTTGCGATTCTCTCGTCGCGATAG
*
1635878 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-TGCGTTGCGATTCTC
1635900 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (33 bp):
TCATTTTGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1635901 original size:20 final size:20
Alignment explanation
Indices: 1635867--1635924 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1635857 GCGATTCTCT
**
1635867 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1635887 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1635907 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1635925 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1638062 original size:42 final size:42
Alignment explanation
Indices: 1637996--1638188 Score: 194
Period size: 42 Copynumber: 4.6 Consensus size: 42
1637986 AGACACCGCA
* * * * *
1637996 AGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCG
1 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
* * *
1638038 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCCCTCA
1 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
* * * *
1638080 AGAGTCCACTCCTATCGTTGAAGAGGCC-CATATCATTCCTCG
1 AGAGTCCCCTCCCACCGTTCAAGAGGCCAC-TATCATTCCTCG
* * *
1638122 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCA-TCGTTG
1 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
*
1638163 AAGAGGT-CCCTCCCACCATTCAAGAG
1 -AGA-GTCCCCTCCCACCGTTCAAGAG
1638189 CCCGATTCAC
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
41 5 0.04
42 116 0.94
43 3 0.02
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (42 bp):
AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
Found at i:1638161 original size:21 final size:21
Alignment explanation
Indices: 1638053--1638168 Score: 58
Period size: 21 Copynumber: 5.5 Consensus size: 21
1638043 CCCCTCCCAC
1638053 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
1638074 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* *
1638095 CGTTGAAGAGGCC-CATATCATT
1 CGTTCAAGAGGCCAC-TGTCA-T
* * * * ** *
1638117 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
1638137 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
*
1638158 CGTTGAAGAGG
1 CGTTCAAGAGG
1638169 TCCCTCCCAC
Statistics
Matches: 65, Mismatches: 24, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
20 3 0.05
21 58 0.89
22 4 0.06
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:1638167 original size:84 final size:84
Alignment explanation
Indices: 1637994--1638158 Score: 321
Period size: 84 Copynumber: 2.0 Consensus size: 84
1637984 GAAGACACCG
*
1637994 CAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1 CAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1638059 AGAGGCCACTGTCATCCCT
66 AGAGGCCACTGTCATCCCT
1638078 CAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1 CAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1638143 AGAGGCCACTGTCATC
66 AGAGGCCACTGTCATC
1638159 GTTGAAGAGG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.22
Consensus pattern (84 bp):
CAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
AGAGGCCACTGTCATCCCT
Found at i:1638187 original size:21 final size:20
Alignment explanation
Indices: 1638128--1638188 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1638118 CTCGAGAGTC
1638128 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
1638148 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
1638169 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
1638189 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:1638188 original size:84 final size:84
Alignment explanation
Indices: 1637994--1638188 Score: 266
Period size: 84 Copynumber: 2.3 Consensus size: 84
1637984 GAAGACACCG
* * * * *
1637994 CAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1 CAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1638059 AGAGGCCACTGTCATCCCT
66 AGAGGCCACTGTCATCCCT
* * * *
1638078 CAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1 CAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
**
1638143 AGAGGCCACTGTCATCGTT
66 AGAGGCCACTGTCATCCCT
*
1638162 GAAGAGGTCC-CTCCCACCATTCAAGAG
1 CAAGA-GTCCACTCCCACCATTCAAGAG
1638189 CCCGATTCAC
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 98 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (84 bp):
CAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
AGAGGCCACTGTCATCCCT
Found at i:1639539 original size:14 final size:14
Alignment explanation
Indices: 1639520--1639553 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1639510 ATTATTGCTT
1639520 ATTTGTAAAAGGTG
1 ATTTGTAAAAGGTG
*
1639534 ATTTGTAAAAGTTG
1 ATTTGTAAAAGGTG
1639548 ATTTGT
1 ATTTGT
1639554 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGGTG
Found at i:1639684 original size:19 final size:19
Alignment explanation
Indices: 1639660--1639704 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1639650 AAAAAGTACT
*
1639660 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
1639679 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
1639698 ATCGCAA
1 ATCGCAA
1639705 CGAGAGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:1639779 original size:33 final size:32
Alignment explanation
Indices: 1639736--1639861 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 32
1639726 TTAAATTCGT
1639736 GTTGCGATTTTCATTTCGCATTGCGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATT-CCTC
* **
1639769 GTTGCAATTTTCATTTCGCATTGCGAAATT-AGC
1 GTTGCGATTTTCATTTCGCATTGCG--ATTCCTC
1639802 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTC-CTC
1639835 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
1639862 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCTC
Found at i:1639815 original size:66 final size:66
Alignment explanation
Indices: 1639736--1639860 Score: 232
Period size: 66 Copynumber: 1.9 Consensus size: 66
1639726 TTAAATTCGT
1639736 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGCGAAATTAG
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGCGAAATTAG
1639801 C
66 C
* *
1639802 GTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGCGA
1639861 TAGTAATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGCGAAATTAG
C
Found at i:1642174 original size:12 final size:12
Alignment explanation
Indices: 1642157--1642189 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1642147 CGGGGACTTG
1642157 TTCTTCTTCTTT
1 TTCTTCTTCTTT
1642169 TTCTTCTTCTTT
1 TTCTTCTTCTTT
1642181 TTCTTCTTC
1 TTCTTCTTC
1642190 AGGATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:1642398 original size:24 final size:24
Alignment explanation
Indices: 1642364--1642417 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1642354 CTGAAACATC
*
1642364 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1642388 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1642412 ATCAAA
1 ATCAAA
1642418 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1643235 original size:20 final size:20
Alignment explanation
Indices: 1643210--1643267 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1643200 AATTTGGAAA
* *
1643210 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
*
1643230 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
1643250 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
1643268 AAATCGCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:1643274 original size:20 final size:20
Alignment explanation
Indices: 1643206--1643276 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1643196 TGCGAATTTG
* * *
1643206 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATTCT
**
1643226 GACTATCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
***
1643246 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
1643266 GAAAATCGCAA
1 GAAAATCGCAA
1643277 TCATCTTCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:1643583 original size:20 final size:20
Alignment explanation
Indices: 1643490--1643585 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
1643480 CAACGGGGAA
*
1643490 ATCGCAACGCGAAAATGGCT
1 ATCGCAACTCGAAAATGGCT
*
1643510 ATCACAACGT-GAAAATGGCT
1 ATCGCAAC-TCGAAAATGGCT
* ***
1643530 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACTCGAAAATG-GCT
*
1643550 ATCGCAACGCGAAAATGGCT
1 ATCGCAACTCGAAAATGGCT
*
1643570 ATCGCAACTAGAAAAT
1 ATCGCAACTCGAAAAT
1643586 CGCAATGCGA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
19 6 0.10
20 47 0.81
21 5 0.09
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACTCGAAAATGGCT
Found at i:1643808 original size:14 final size:14
Alignment explanation
Indices: 1643789--1643825 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1643779 CATCAATTAA
1643789 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1643803 ACAAATCATCTTTT
1 ACAAATCAACATTT
1643817 ACAAATCAA
1 ACAAATCAA
1643826 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1645671 original size:20 final size:20
Alignment explanation
Indices: 1645648--1645715 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1645638 GAAACTTAAA
1645648 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1645668 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
* **
1645688 ATCGCAATGC-AAAATGAAA
1 ATCGCAACGCGAAAATGACT
1645707 ATCGCAACG
1 ATCGCAACG
1645716 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1645721 original size:14 final size:14
Alignment explanation
Indices: 1645704--1645761 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1645694 ATGCAAAATG
1645704 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1645718 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1645734 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1645750 AAAATCGCAACG
1 AAAATCGCAACG
1645762 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1645746 original size:32 final size:33
Alignment explanation
Indices: 1645688--1645766 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1645678 GGAAATGGCT
*
1645688 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1645721 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1645753 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1645767 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1645814 original size:14 final size:14
Alignment explanation
Indices: 1645795--1645852 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1645785 TTTCATTTCG
1645795 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1645809 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1645825 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1645841 CGTTGCGATTTT
1 CGTTGCGATTTT
1645853 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1645859 original size:33 final size:33
Alignment explanation
Indices: 1645778--1645868 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1645768 ACAAATCGCA
*
1645778 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1645811 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1645843 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1645869 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1645907 original size:20 final size:20
Alignment explanation
Indices: 1645853--1645896 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1645843 TTGCGATTTT
*
1645853 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
1645872 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
1645892 CATTT
1 CATTT
1645897 TTGTGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1646415 original size:18 final size:18
Alignment explanation
Indices: 1646389--1646433 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1646379 GTCGATCAGA
*
1646389 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1646407 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1646425 TGATGGCTC
1 TGATGGCTC
1646434 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1647801 original size:20 final size:20
Alignment explanation
Indices: 1647753--1647811 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1647743 AATAGTTTCT
** *
1647753 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1647773 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1647793 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1647812 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1648102 original size:22 final size:22
Alignment explanation
Indices: 1648075--1648118 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1648065 GATGGAGATA
1648075 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1648097 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1648119 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1648350 original size:42 final size:41
Alignment explanation
Indices: 1648292--1648400 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 41
1648282 GAAAATCGCA
* *
1648292 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCG
1 TTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCTCG
* * *
1648333 TTGCGATTTTTGTATTATCGCATTGCGATAGTAAGTAT-TGCA
1 TTGCGA-TTATGTATTATCGCATTGCGAAAGTAAGTATCT-CG
*
1648375 TTGCGA-TA-GTCAGTATCGCATTGCGA
1 TTGCGATTATGT-ATTATCGCATTGCGA
1648401 TTTTCCTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
39 2 0.03
40 15 0.26
41 7 0.12
42 34 0.59
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.38
Consensus pattern (41 bp):
TTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCTCG
Found at i:1648377 original size:20 final size:20
Alignment explanation
Indices: 1648348--1648401 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1648338 ATTTTTGTAT
1648348 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
1648368 TATTGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1648388 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1648402 TTTCCTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1648388 original size:62 final size:63
Alignment explanation
Indices: 1648286--1648404 Score: 161
Period size: 62 Copynumber: 1.9 Consensus size: 63
1648276 CACTTTGAAA
* * * *
1648286 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTTGTATT
* *
1648349 ATCGCATTGCGA-TA-GTAAGTATTGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1648405 CCTAATTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
61 2 0.04
62 35 0.71
63 12 0.24
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (63 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTTGTATT
Found at i:1648434 original size:20 final size:21
Alignment explanation
Indices: 1648390--1648441 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1648380 ATAGTCAGTA
*
1648390 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTACTAAT
* *
1648411 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACTAAT
1648431 TCGCATTGCGA
1 TCGCATTGCGA
1648442 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACTAAT
Found at i:1654453 original size:22 final size:22
Alignment explanation
Indices: 1654428--1654473 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1654418 GTTTACAAAT
*
1654428 AGGGAATCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
*
1654450 AGGGAACCTATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
1654472 AG
1 AG
1654474 TACTGCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.22
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:1655035 original size:21 final size:21
Alignment explanation
Indices: 1654986--1655049 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
1654976 CATATGAAAT
*
1654986 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
1655007 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
1655029 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
1655050 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:1665929 original size:12 final size:11
Alignment explanation
Indices: 1665864--1665930 Score: 50
Period size: 11 Copynumber: 6.3 Consensus size: 11
1665854 AAAATTACAT
1665864 TATTAAAAATA
1 TATTAAAAATA
1665875 TATTAAAAATA
1 TATTAAAAATA
* ***
1665886 CATTATTGATA
1 TATTAAAAATA
**
1665897 -ATTATGAA-A
1 TATTAAAAATA
1665906 T-TTAAAAATA
1 TATTAAAAATA
1665916 TATTAAAAATTA
1 TATTAAAAA-TA
1665928 TAT
1 TAT
1665931 AATACAACTA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
9 6 0.14
10 8 0.18
11 25 0.57
12 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1665963 original size:19 final size:19
Alignment explanation
Indices: 1665939--1665977 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1665929 ATAATACAAC
1665939 TAAACCATATTGTAATGCA
1 TAAACCATATTGTAATGCA
1665958 TAAACCATATTGTAATGCA
1 TAAACCATATTGTAATGCA
1665977 T
1 T
1665978 TTAATATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (19 bp):
TAAACCATATTGTAATGCA
Found at i:1666911 original size:22 final size:22
Alignment explanation
Indices: 1666883--1666960 Score: 147
Period size: 22 Copynumber: 3.5 Consensus size: 22
1666873 GGACTATTAT
*
1666883 GTCCCGAAAGACCACTGGATAC
1 GTCCCGAATGACCACTGGATAC
1666905 GTCCCGAATGACCACTGGATAC
1 GTCCCGAATGACCACTGGATAC
1666927 GTCCCGAATGACCACTGGATAC
1 GTCCCGAATGACCACTGGATAC
1666949 GTCCCGAATGAC
1 GTCCCGAATGAC
1666961 TAATATACCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (22 bp):
GTCCCGAATGACCACTGGATAC
Found at i:1670429 original size:17 final size:16
Alignment explanation
Indices: 1670407--1670475 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
1670397 CCGTGTCCCG
*
1670407 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
* *
1670424 ACCCGG-TAATCGAGT
1 ACCCGGATATTCGGGT
*
1670439 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
1670456 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
1670471 ACCCG
1 ACCCG
1670476 ATACCCGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:1670442 original size:15 final size:15
Alignment explanation
Indices: 1670419--1670475 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
1670409 CCGGATGTTA
1670419 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
1670434 CGAGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
1670450 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
1670466 CGGGTACCCG
1 CGGGTACCCG
1670476 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:1670443 original size:32 final size:32
Alignment explanation
Indices: 1670407--1670475 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
1670397 CCGTGTCCCG
1670407 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
* * *
1670439 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
1670471 ACCCG
1 ACCCG
1670476 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGAGT
Found at i:1672557 original size:22 final size:22
Alignment explanation
Indices: 1672505--1672560 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1672495 GGACTATTAT
*
1672505 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAATGACCACTGGATAC
1672527 GTCCCGAATGACCACTGGATAC
1 GTCCCGAATGACCACTGGATAC
1672549 GTCCCGAATGAC
1 GTCCCGAATGAC
1672561 TAATATACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.16
Consensus pattern (22 bp):
GTCCCGAATGACCACTGGATAC
Found at i:1672819 original size:21 final size:21
Alignment explanation
Indices: 1672795--1672862 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
1672785 AACTCGCATG
1672795 TCATATCTTGTTCACATATGT
1 TCATATCTTGTTCACATATGT
* ***
1672816 TCATATATACATCACATATG-
1 TCATATCTTGTTCACATATGT
1672836 TCATATCTTGTTCACATATGT
1 TCATATCTTGTTCACATATGT
1672857 TCATAT
1 TCATAT
1672863 ATACATCACA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.44
Consensus pattern (21 bp):
TCATATCTTGTTCACATATGT
Found at i:1672839 original size:41 final size:41
Alignment explanation
Indices: 1672792--1672873 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1672782 GTAAACTCGC
1672792 ATGTCATATCTTGTTCACATATGTTCATATATACATCACAT
1 ATGTCATATCTTGTTCACATATGTTCATATATACATCACAT
1672833 ATGTCATATCTTGTTCACATATGTTCATATATACATCACAT
1 ATGTCATATCTTGTTCACATATGTTCATATATACATCACAT
1672874 TATATTTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (41 bp):
ATGTCATATCTTGTTCACATATGTTCATATATACATCACAT
Found at i:1672871 original size:21 final size:21
Alignment explanation
Indices: 1672806--1672873 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
1672796 CATATCTTGT
1672806 TCACATATGTTCATATATACA
1 TCACATATGTTCATATATACA
* ***
1672827 TCACATATG-TCATATCTTGT
1 TCACATATGTTCATATATACA
1672847 TCACATATGTTCATATATACA
1 TCACATATGTTCATATATACA
1672868 TCACAT
1 TCACAT
1672874 TATATTTTAG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.40
Consensus pattern (21 bp):
TCACATATGTTCATATATACA
Found at i:1673196 original size:2 final size:2
Alignment explanation
Indices: 1673189--1673220 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1673179 TACCAATTCC
1673189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1673221 ACTCATGTAA
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):
TA
Found at i:1681326 original size:11 final size:11
Alignment explanation
Indices: 1681312--1681425 Score: 147
Period size: 11 Copynumber: 10.3 Consensus size: 11
1681302 TTAAAATCCG
1681312 TCGAGCTTGAA
1 TCGAGCTTGAA
*
1681323 TCGAGTTTGAA
1 TCGAGCTTGAA
1681334 TCGAGCTTGAA
1 TCGAGCTTGAA
*
1681345 TCGAGTTTGAA
1 TCGAGCTTGAA
*
1681356 TCGAGCTTAAA
1 TCGAGCTTGAA
*
1681367 TCGAGTTTGAA
1 TCGAGCTTGAA
1681378 TCGAGCTTGAA
1 TCGAGCTTGAA
* *
1681389 TCGAGTTTAAAA
1 TCGAGCTT-GAA
*
1681401 TTGAGCTTGAA
1 TCGAGCTTGAA
*
1681412 TTGAGCTTGAA
1 TCGAGCTTGAA
1681423 TCG
1 TCG
1681426 GGTTTAAAAT
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
11 80 0.91
12 8 0.09
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:1681337 original size:22 final size:22
Alignment explanation
Indices: 1681312--1681425 Score: 174
Period size: 22 Copynumber: 5.1 Consensus size: 22
1681302 TTAAAATCCG
1681312 TCGAGCTTGAATCGAGTTTGAA
1 TCGAGCTTGAATCGAGTTTGAA
1681334 TCGAGCTTGAATCGAGTTTGAA
1 TCGAGCTTGAATCGAGTTTGAA
*
1681356 TCGAGCTTAAATCGAGTTTGAA
1 TCGAGCTTGAATCGAGTTTGAA
*
1681378 TCGAGCTTGAATCGAGTTTAAAA
1 TCGAGCTTGAATCGAGTTT-GAA
* * *
1681401 TTGAGCTTGAATTGAGCTTGAA
1 TCGAGCTTGAATCGAGTTTGAA
1681423 TCG
1 TCG
1681426 GGTTTAAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
22 65 0.78
23 18 0.22
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (22 bp):
TCGAGCTTGAATCGAGTTTGAA
Found at i:1681613 original size:32 final size:32
Alignment explanation
Indices: 1681576--1681652 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
1681566 CTTGCGAGTT
*
1681576 TTCGAGTCGAGCTTGTTCATATAATTTTCGAG
1 TTCGAGTCGAGCTTGTTCATATAATTTTAGAG
*
1681608 TTCGAGTCGAGCTTGTTCATATAGTTTTAGAG
1 TTCGAGTCGAGCTTGTTCATATAATTTTAGAG
*
1681640 TTCGAGCCGAGCT
1 TTCGAGTCGAGCT
1681653 CAGCAATACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (32 bp):
TTCGAGTCGAGCTTGTTCATATAATTTTAGAG
Found at i:1681771 original size:2 final size:2
Alignment explanation
Indices: 1681709--1681754 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1681699 CCATTGAAAC
1681709 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1681750 TA TA T
1 TA TA T
1681755 TGGAATTAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1702973 original size:2 final size:2
Alignment explanation
Indices: 1702966--1702996 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1702956 TTGTCTAAAC
*
1702966 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1702997 TTAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1703517 original size:49 final size:49
Alignment explanation
Indices: 1703462--1703563 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
1703452 TAAAAATAAA
1703462 AATTCTACAAAGTATAAGTGAACTCTAACTTCATATAAATTTTTGACTT
1 AATTCTACAAAGTATAAGTGAACTCTAACTTCATATAAATTTTTGACTT
1703511 AATTCTACAAAGTATAAGTGAACTCTAACTTCATATAAATTTTTGACTT
1 AATTCTACAAAGTATAAGTGAACTCTAACTTCATATAAATTTTTGACTT
1703560 AATT
1 AATT
1703564 AAAAAATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (49 bp):
AATTCTACAAAGTATAAGTGAACTCTAACTTCATATAAATTTTTGACTT
Found at i:1706316 original size:79 final size:79
Alignment explanation
Indices: 1706233--1706389 Score: 251
Period size: 79 Copynumber: 2.0 Consensus size: 79
1706223 AAAAAATAAT
* * * *
1706233 ATTTTAGATATCTCCCAATATTAATATTTTAGGTAAAAAAAATAATATTTTAGATAGCGTTTTAC
1 ATTTTAGATAGCACCCAATATTAACATTTTAGGTAAAAAAAATAATATTTTAGATAGCGCTTTAC
*
1706298 CGGAAATGTTAAAC
66 CGAAAATGTTAAAC
* *
1706312 ATTTTAGGTAGCACCCAATATTAACATTTTCGGTAAAAAAAATAATATTTTAGATAGCGCTTTAC
1 ATTTTAGATAGCACCCAATATTAACATTTTAGGTAAAAAAAATAATATTTTAGATAGCGCTTTAC
1706377 CGAAAATGTTAAA
66 CGAAAATGTTAAA
1706390 AAATATTAAC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (79 bp):
ATTTTAGATAGCACCCAATATTAACATTTTAGGTAAAAAAAATAATATTTTAGATAGCGCTTTAC
CGAAAATGTTAAAC
Found at i:1707191 original size:65 final size:64
Alignment explanation
Indices: 1706990--1707191 Score: 194
Period size: 64 Copynumber: 3.1 Consensus size: 64
1706980 AGTAGTGTAC
** * * ** * * *
1706990 CGATGCACTATATAATGCATCGATGCAC-CCTTGAATAAATTGAATTTTGAATGCATTTTGTGTA
1 CGATGCAC-ATACCATGCATCGATGCACTCC-TAAATAATTTGAACATCGAATGCATTTTATGCA
*
1707054 C
64 T
**
1707055 CGATGCACA-AGGAATGCATCGATGCACTCCTAAATAATTTGAACATCGAATGCATTTTATGCAT
1 CGATGCACATA-CCATGCATCGATGCACTCCTAAATAATTTGAACATCGAATGCATTTTATGCAT
** * *
1707119 CGATGCACATACCATGCATCGATGCACTCC-AGGCTTATTTGAAACATCGAATGTATTTTATGCA
1 CGATGCACATACCATGCATCGATGCACTCCTA-AATAATTTG-AACATCGAATGCATTTTATGCA
1707183 T
64 T
1707184 CGATGCAC
1 CGATGCAC
1707192 CCCAAGTGTA
Statistics
Matches: 117, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 74 0.63
65 41 0.35
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (64 bp):
CGATGCACATACCATGCATCGATGCACTCCTAAATAATTTGAACATCGAATGCATTTTATGCAT
Found at i:1712975 original size:23 final size:21
Alignment explanation
Indices: 1712949--1713001 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
1712939 GAAGATGTAC
1712949 CAATGCACTCCTTGAATGTGCAT
1 CAATGCACTCC-TG-ATGTGCAT
*
1712972 CAATGCACT-CTGTTGTGCAT
1 CAATGCACTCCTGATGTGCAT
*
1712992 CAATACACTC
1 CAATGCACTC
1713002 GTTGGGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 15 0.56
21 2 0.07
22 1 0.04
23 9 0.33
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
CAATGCACTCCTGATGTGCAT
Found at i:1712990 original size:20 final size:19
Alignment explanation
Indices: 1712965--1713005 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1712955 ACTCCTTGAA
*
1712965 TGTGCATCAATGCACTCTGT
1 TGTGCATCAATACACTC-GT
1712985 TGTGCATCAATACACTCGT
1 TGTGCATCAATACACTCGT
1713004 TG
1 TG
1713006 GGTTTTGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (19 bp):
TGTGCATCAATACACTCGT
Found at i:1723161 original size:3 final size:3
Alignment explanation
Indices: 1723155--1723183 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1723145 TCTTCTTCTT
1723155 CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1723184 GAATCATCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:1727391 original size:19 final size:18
Alignment explanation
Indices: 1727367--1727435 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
1727357 GTATTATTAA
1727367 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
1727386 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
1727404 ATTAATCTAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
1727426 ATT-TTAATAA
1 ATTATTAATAA
1727436 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:1727539 original size:28 final size:28
Alignment explanation
Indices: 1727488--1727593 Score: 76
Period size: 28 Copynumber: 3.7 Consensus size: 28
1727478 ATTATAAAAA
* * *
1727488 TAATA-TTTAATAATAAATAAATTATTT
1 TAATATTTTAAAAATAATTATATTATTT
*
1727515 TAATATTTTAAAAATAATTATATTAAGTT
1 TAATATTTTAAAAATAATTATATT-ATTT
*
1727544 T--TATTATAAATAAT-ATTATTTATTATATT
1 TAATATTTTAAA-AATAATTA--TATTAT-TT
1727573 TAATATTTGTAATAAATAATT
1 TAATATTT-TAA-AAATAATT
1727594 TTTAAAAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
27 17 0.28
28 19 0.31
29 11 0.18
31 4 0.07
32 6 0.10
33 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
TAATATTTTAAAAATAATTATATTATTT
Found at i:1727540 original size:23 final size:26
Alignment explanation
Indices: 1727488--1727562 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 26
1727478 ATTATAAAAA
*
1727488 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATAT
1727515 TAATATTT-TAA-AAAT-AATTATAT
1 TAATATTTATAATAAATAAATTATAT
*
1727538 TAAGT-TTTATTATAAATAATATTAT
1 TAA-TATTTATAATAAATAA-ATTAT
1727563 TTATTATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 13 0.32
24 7 0.17
25 7 0.17
26 1 0.02
27 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATAT
Found at i:1730871 original size:151 final size:149
Alignment explanation
Indices: 1730579--1730875 Score: 406
Period size: 151 Copynumber: 2.0 Consensus size: 149
1730569 GGTCCAAAAA
*
1730579 GGATAGGAATTTATCTTGATTAAGAAGTCAACTTATCAACCACACCAAATTGTCCCCATAAACTG
1 GGATAGGAATTTATCTTGATTAAGAAGTCAACTTATCAACCACACCAAAGTGTCCCCATAAACTG
* **
1730644 GAACAAACAGAAAAGCAATGGACATTTGCAGGCTTCTCAGAACAGTAACATAAAAAGTTTGAAAA
66 GAACAAAAAGAAAAGCAATGGACATTTGCAGGCTTCTCAGAACAGTAACATAAAAAGAATGAAAA
* *
1730709 GGGTAGCAAAATCATCCTG
131 GAGAAGCAAAATCATCCTG
* *
1730728 GGATAGGAATTTATCTTGA-TAAGAAG-CACATTTATCAACCACACCAAAGTGTCCCCCTAAACT
1 GGATAGGAATTTATCTTGATTAAGAAGTCA-ACTTATCAACCACACCAAAGTGTCCCCATAAACT
* *
1730791 GGAAGAAGCAGAAGAACAAG-AACTGG-CATTTGCGGGCTTCTCAGAACAGTAACATAAAAA-AA
65 GGAACAA--A-AAGAA-AAGCAA-TGGACATTTGCAGGCTTCTCAGAACAGTAACATAAAAAGAA
1730853 TGAAAAAGAGAAGCAAAATCATC
125 TG-AAAAGAGAAGCAAAATCATC
1730876 ATAGATTGAA
Statistics
Matches: 131, Mismatches: 10, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
147 2 0.02
148 44 0.34
149 19 0.15
150 3 0.02
151 57 0.44
152 6 0.05
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (149 bp):
GGATAGGAATTTATCTTGATTAAGAAGTCAACTTATCAACCACACCAAAGTGTCCCCATAAACTG
GAACAAAAAGAAAAGCAATGGACATTTGCAGGCTTCTCAGAACAGTAACATAAAAAGAATGAAAA
GAGAAGCAAAATCATCCTG
Found at i:1738370 original size:16 final size:17
Alignment explanation
Indices: 1738333--1738370 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1738323 TTATTGATCT
*
1738333 AAAATGAAAAGCAATAG
1 AAAATGAAAAGCAATAA
*
1738350 GAAATG-AAAGCAATAA
1 AAAATGAAAAGCAATAA
1738366 AAAAT
1 AAAAT
1738371 TATATCGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.13
Consensus pattern (17 bp):
AAAATGAAAAGCAATAA
Done.