Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 21
Found at i:1476205 original size:63 final size:64
Alignment explanation
Indices: 1476126--1476262 Score: 179
Period size: 64 Copynumber: 2.2 Consensus size: 64
1476116 TATAGAGTGT
* * * *
1476126 ATCGATGCACAGGGAGTGCATCGATGCA-CCCA-TATTAATGGAAACATCGAATGTAATTCGTGC
1 ATCGATGCACAAGGAGTGCATCGATGCATCCCATTA-AAATGAAAACATCGAAGGTAATTCGTGC
* * * *
1476189 ATCGATGCATAAGGAGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGC
1 ATCGATGCACAAGGAGTGCATCGATGCATCCCATTAAAATGAAAACATCGAAGGTAATTCGTGC
1476253 ATCGATGCAC
1 ATCGATGCAC
1476263 TGTTGAATGC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 26 0.41
64 35 0.56
65 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (64 bp):
ATCGATGCACAAGGAGTGCATCGATGCATCCCATTAAAATGAAAACATCGAAGGTAATTCGTGC
Found at i:1481917 original size:34 final size:34
Alignment explanation
Indices: 1481879--1481944 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1481869 ACTACTTGCA
*
1481879 CATTCGGTGCCTACCTTGTTGATTTTTCAACAAT
1 CATTCGGTGCCTACCTTGTTGAATTTTCAACAAT
1481913 CATTCGGTGCCTACCTTGTTGAATTTTCAACA
1 CATTCGGTGCCTACCTTGTTGAATTTTCAACA
1481945 TTTTGTTCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (34 bp):
CATTCGGTGCCTACCTTGTTGAATTTTCAACAAT
Found at i:1487834 original size:23 final size:23
Alignment explanation
Indices: 1487807--1487913 Score: 83
Period size: 23 Copynumber: 4.7 Consensus size: 23
1487797 AAGGTTACCG
* *
1487807 TTCGTTTAGTGTTCGCGAACATA
1 TTCGTTTAATGTTCACGAACATA
* *
1487830 TTCGTTCAATGTTCAC-AACATG
1 TTCGTTTAATGTTCACGAACATA
* ** **
1487852 TTCTTTTAACATTCGTGAACATA
1 TTCGTTTAATGTTCACGAACATA
*
1487875 TTCGTTT-ATCGTTCATGAACATA
1 TTCGTTTAAT-GTTCACGAACATA
* *
1487898 TTTGTTTAATTTTCAC
1 TTCGTTTAATGTTCAC
1487914 AAATATGCTC
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 16 0.25
23 45 0.71
24 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (23 bp):
TTCGTTTAATGTTCACGAACATA
Found at i:1502334 original size:31 final size:31
Alignment explanation
Indices: 1502261--1502324 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1502251 AGTTACGTCG
1502261 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
1502292 GGGACCATATTGCAAACGGACTAAATGTT-A
1 GGGACCATATTGCAAACGGACTAAATGTTGA
1502322 GGG
1 GGG
1502325 GATTATATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:1502799 original size:20 final size:20
Alignment explanation
Indices: 1502755--1502799 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1502745 TCTTAAACGT
*
1502755 AAAATAAATTATATTTTTCA
1 AAAATAAATTATATTTTACA
1502775 AAAATATAATT-TATTTTACA
1 AAAATA-AATTATATTTTACA
*
1502795 TAAAT
1 AAAAT
1502800 TATTTTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATAAATTATATTTTACA
Found at i:1502877 original size:16 final size:17
Alignment explanation
Indices: 1502841--1502878 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1502831 CATTAAAGAA
*
1502841 AATAT-AAAAATAGATT
1 AATATAAAAAATAAATT
1502857 AATATAAAAAATAAATT
1 AATATAAAAAATAAATT
1502874 -ATATA
1 AATATA
1502879 TTTAATCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AATATAAAAAATAAATT
Found at i:1504764 original size:19 final size:20
Alignment explanation
Indices: 1504742--1504785 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1504732 TTATAAATAT
**
1504742 AAATTAAATTATTA-ATAAA
1 AAATTAAAAAATTATATAAA
*
1504761 AAATAAAAAAATTATATAAA
1 AAATTAAAAAATTATATAAA
1504781 AAATT
1 AAATT
1504786 TAGAACAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTAAAAAATTATATAAA
Found at i:1513769 original size:46 final size:45
Alignment explanation
Indices: 1513711--1513816 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 45
1513701 TGCACATACT
*
1513711 ATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCAAATGCATTTG
1 ATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCAAATGCATTTC
* * *
1513757 ATGTATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACTCAGGCTATTTTGAAACATCAAATGCATTTC
*
1513802 ATGCATCGGTGCACT
1 ATGCATCGATGCACT
1513817 AACTAAGGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
45 30 0.58
46 19 0.37
47 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTATTTTGAAACATCAAATGCATTTC
Found at i:1521864 original size:65 final size:63
Alignment explanation
Indices: 1521795--1521954 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 63
1521785 GAATAAATTG
* *
1521795 AACATCAAATGCATTTCATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG
1521858 AA
63 -A
* * * *
1521860 AACATCGAATGCATTTGATACATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGA
*
1521924 AACATCGAATGCATTTCATGCATCGGTGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
1521955 TAACTAAAGG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 48 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGA
Found at i:1524532 original size:2 final size:2
Alignment explanation
Indices: 1524525--1524549 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1524515 TCAATCTACA
1524525 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1524550 ATTTACGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1524732 original size:13 final size:13
Alignment explanation
Indices: 1524713--1524770 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
1524703 CTCAATGCAC
*
1524713 GTCATAAATGTGT
1 GTCATAAATGCGT
*
1524726 GTTATAAATGCGT
1 GTCATAAATGCGT
*
1524739 GTCATAAATGCGC
1 GTCATAAATGCGT
* *
1524752 GTCATAAATACGC
1 GTCATAAATGCGT
1524765 GTCATA
1 GTCATA
1524771 GATTTATGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:1526829 original size:30 final size:30
Alignment explanation
Indices: 1526795--1526855 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1526785 TGATTAGATC
1526795 TTAAAAAGAAAAGGCTATTAGTGATTGGGA
1 TTAAAAAGAAAAGGCTATTAGTGATTGGGA
1526825 TTAAAAAGAAAAGGCTATTAGTGATTGGGA
1 TTAAAAAGAAAAGGCTATTAGTGATTGGGA
1526855 T
1 T
1526856 AAGAGGAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (30 bp):
TTAAAAAGAAAAGGCTATTAGTGATTGGGA
Found at i:1532845 original size:88 final size:88
Alignment explanation
Indices: 1532696--1532873 Score: 356
Period size: 88 Copynumber: 2.0 Consensus size: 88
1532686 TCATACCAAA
1532696 ACTTATCCACTAATTACTGCTACCATATATTAAAATTATTTATTTTTTATTCAAAAGTTTTAATG
1 ACTTATCCACTAATTACTGCTACCATATATTAAAATTATTTATTTTTTATTCAAAAGTTTTAATG
1532761 CTTAAAAAAATAAAAATAGTATT
66 CTTAAAAAAATAAAAATAGTATT
1532784 ACTTATCCACTAATTACTGCTACCATATATTAAAATTATTTATTTTTTATTCAAAAGTTTTAATG
1 ACTTATCCACTAATTACTGCTACCATATATTAAAATTATTTATTTTTTATTCAAAAGTTTTAATG
1532849 CTTAAAAAAATAAAAATAGTATT
66 CTTAAAAAAATAAAAATAGTATT
1532872 AC
1 AC
1532874 ATATATACTG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (88 bp):
ACTTATCCACTAATTACTGCTACCATATATTAAAATTATTTATTTTTTATTCAAAAGTTTTAATG
CTTAAAAAAATAAAAATAGTATT
Found at i:1542677 original size:32 final size:32
Alignment explanation
Indices: 1542636--1542699 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1542626 TCACATTCAT
* * * *
1542636 GAATGTCATGTTATCACAAAGGATTATAAATA
1 GAATATCATGATATCACAAAGAAATATAAATA
1542668 GAATATCATGATATCACAAAGAAATATAAATA
1 GAATATCATGATATCACAAAGAAATATAAATA
1542700 CACTATCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (32 bp):
GAATATCATGATATCACAAAGAAATATAAATA
Found at i:1544084 original size:31 final size:32
Alignment explanation
Indices: 1544046--1544127 Score: 114
Period size: 31 Copynumber: 2.6 Consensus size: 32
1544036 GAGAGTCGCT
* *
1544046 GGGAACACAGT-CCTCTTCCGAGGAAGACGTC
1 GGGAACACAGTGCGTCTTCCGAGGAAGACGCC
* *
1544077 GGGAACACAGTGCGTC-TCCGGGGAAGATGCC
1 GGGAACACAGTGCGTCTTCCGAGGAAGACGCC
1544108 GGGAACACAGTGCGTCTTCC
1 GGGAACACAGTGCGTCTTCC
1544128 CCTTGTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
31 39 0.87
32 6 0.13
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.16
Consensus pattern (32 bp):
GGGAACACAGTGCGTCTTCCGAGGAAGACGCC
Found at i:1544768 original size:22 final size:23
Alignment explanation
Indices: 1544729--1544776 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1544719 AGTTTATTTT
1544729 AATTTTTTAGAATAAAAAT-TAA
1 AATTTTTTAGAATAAAAATATAA
*
1544751 AATTATTTTA-AATTAAAATATAA
1 AATT-TTTTAGAATAAAAATATAA
1544774 AAT
1 AAT
1544777 ATAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AATTTTTTAGAATAAAAATATAA
Found at i:1544810 original size:15 final size:15
Alignment explanation
Indices: 1544773--1544832 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 15
1544763 TTAAAATATA
1544773 AAATA-TAAAAAAATT
1 AAATATTAAAAAAA-T
*
1544788 GAAT-TTAAAAAAAT
1 AAATATTAAAAAAAT
*
1544802 AAATATT-AAAAAGT
1 AAATATTAAAAAAAT
*
1544816 AAA-ATTAAAATAAT
1 AAATATTAAAAAAAT
1544830 AAA
1 AAA
1544833 AAATTATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 3 0.08
14 21 0.57
15 13 0.35
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAATATTAAAAAAAT
Found at i:1544834 original size:15 final size:15
Alignment explanation
Indices: 1544739--1544834 Score: 56
Period size: 15 Copynumber: 6.5 Consensus size: 15
1544729 AATTTTTTAG
1544739 AATAAAAATTAAAATT
1 AATAAAAATTAAAA-T
* **
1544755 ATTTTAAATTAAAAT
1 AATAAAAATTAAAAT
*
1544770 -AT-AAAATATAAAAA
1 AATAAAAAT-TAAAAT
** * *
1544784 AATTGAATTTAAAAA
1 AATAAAAATTAAAAT
*
1544799 AATAAATATTAAAA-
1 AATAAAAATTAAAAT
*
1544813 AGT-AAAATTAAAAT
1 AATAAAAATTAAAAT
1544827 AATAAAAA
1 AATAAAAA
1544835 ATTATATATA
Statistics
Matches: 60, Mismatches: 15, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
13 13 0.22
14 10 0.17
15 23 0.38
16 14 0.23
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAAAAATTAAAAT
Found at i:1544838 original size:29 final size:29
Alignment explanation
Indices: 1544760--1544838 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
1544750 AAATTATTTT
* * *
1544760 AAATTAAAAT-ATAAAATATAAAAAAATTG
1 AAATTAAAATAATAAAATAT-TAAAAAGTA
* *
1544789 AATTTAAAAAAAT-AAATATTAAAAAGTA
1 AAATTAAAATAATAAAATATTAAAAAGTA
*
1544817 AAATTAAAATAATAAAAAATTA
1 AAATTAAAATAATAAAATATTA
1544839 TATATATATA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 17 0.43
29 21 0.52
30 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (29 bp):
AAATTAAAATAATAAAATATTAAAAAGTA
Found at i:1546706 original size:23 final size:23
Alignment explanation
Indices: 1546676--1546722 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1546666 TTTCTGGACT
*
1546676 TCGCTTTATATACTAGCTTATTA
1 TCGCTTTATAAACTAGCTTATTA
1546699 TCGCTTTATAAACTAGCTTATTA
1 TCGCTTTATAAACTAGCTTATTA
1546722 T
1 T
1546723 ATGCAAGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (23 bp):
TCGCTTTATAAACTAGCTTATTA
Found at i:1547033 original size:21 final size:21
Alignment explanation
Indices: 1546975--1547033 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1546965 ATGAATTATG
1546975 ATATATATTTTT-A-TTTTTA
1 ATATATATTTTTAATTTTTTA
** *
1546994 ATA-GCATTTTTAGTATTTTTA
1 ATATATATTTTTAAT-TTTTTA
1547015 ATATATATTTTTAATTTTT
1 ATATATATTTTTAATTTTT
1547034 ATTTAGTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 6 0.20
19 3 0.10
21 13 0.43
22 8 0.27
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (21 bp):
ATATATATTTTTAATTTTTTA
Found at i:1551905 original size:182 final size:180
Alignment explanation
Indices: 1551416--1552380 Score: 1258
Period size: 182 Copynumber: 5.3 Consensus size: 180
1551406 GATACAAATG
* * * * *
1551416 AAAAATGTATCGCTCCATAGCAATATTACAGGTAAAAATATGGCAAAACCGGTTTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
*
1551481 AAACCGGTAAA-ACGCTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
66 AAACCGGTAAATA-ACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
*
1551545 TCTGAATTTAAAAGAGAAGAAGTTATAACGCCTAAAAAGTGTCGATACTTTAAA
130 T-TGAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTT-AA
* * * * * ** *
1551599 AAAAATGTATCGATCTATAATAATATAACATGTAAAAATAGGATAAAACAAGTCTAAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* *
1551664 AAACCGGTAAATAACTACCGGATATGTTGAAAGTCTCGATAATTTAATATAAATATCGACACTTT
66 AAACCGGTAAATAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* *
1551729 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAACGTGTCGACACTTTAT
131 -TGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTGTCGATACTTTAA
** **
1551781 GCAAATGTATCGATCCATAACAATATAACAACCT-AAAATATGACAAAACCGGTCTCAAAATGAC
1 AAAAATGTATCGATCCATAACAATATAAC-AGGTAAAAATATGACAAAACCGGTCTCAAAATGAC
** * * *
1551845 AAAACATGTAAATAACTACCGGATATGTTAAAAGTGTCTATACTTTAATATAAGTATCGACACTT
65 AAAACCGGTAAATAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
* *
1551910 TTGGAATTTAAAAGATAAGAAGTTATAGCGCCTATAAAATGTCGATACTTTAA
130 TT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTA-AAAGTGTCGATACTTTAA
* * ** * *
1551963 AAAAATGTATCGATCCATAACAATATAATAGGTTAAAATATGACAAAACAAGTCTAAAAAATGAA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCT-CAAAATGAC
* *
1552028 AAAACCGGT-AA-AACGATATCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
65 AAAACCGGTAAATAAC--TACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* * *
1552091 TTTATGAATTTAAAAGAAAAGAAGTTATAGCGCCTAAAACGTGTCGACACTTTAT
128 TTT-TGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTGTCGATACTTTAA
** ** * *
1552146 GCAAATGTATCGATCCATAACAATATAACAACCT-AAAATATGAAAAAATCGGTCTCAAAATGAC
1 AAAAATGTATCGATCCATAACAATATAAC-AGGTAAAAATATGACAAAACCGGTCTCAAAATGAC
* * * *
1552210 AAAACAGGTAAATAACTATCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATTGACACTT
65 AAAACCGGTAAATAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
*
1552275 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTACAAAGTGTTGATACTTTAA
130 TT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTA-AAAGTGTCGATACTTTAA
1552328 AAAAATGTATCGATCCATAGA-AATATAACAGGTAAAAATATGACAAAACCGGT
1 AAAAATGTATCGATCCATA-ACAATATAACAGGTAAAAATATGACAAAACCGGT
1552381 AAAGCGCTAC
Statistics
Matches: 678, Mismatches: 86, Indels: 37
0.85 0.11 0.05
Matches are distributed among these distances:
181 9 0.01
182 352 0.52
183 310 0.46
184 7 0.01
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (180 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
AAACCGGTAAATAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
TGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTGTCGATACTTTAA
Found at i:1552071 original size:365 final size:362
Alignment explanation
Indices: 1551418--1552376 Score: 1460
Period size: 365 Copynumber: 2.6 Consensus size: 362
1551408 TACAAATGAA
* * * ** * *
1551418 AAATGTATCGCTCCATAGCAATATTAC-AGGTAAAAATATGGCAAAACCGGTTTCAAAATGACAA
1 AAATGTATCGATCCATAACAATATAACAACCT-AAAATATGACAAAACCGGTCTCAAAATGACAA
* * *
1551482 AACCGGTAAA-ACGCTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
65 AACAGGTAAATA-ACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
*
1551546 CT-GAATTTAAAAGAGAAGAAGTTATAACGCCTAAAAAGTGTCGATACTTTAAAAAAAATGTATC
129 -TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAA-TGTCGATACTTT-AAAAAAATGTATC
* * * * *
1551610 GATCTATAATAATATAACATGTAAAAATAGGATAAAACAAGTCTAAAAATGACAAAACCGGTAAA
191 GATCCATAA-AATATAACAGGTAAAAATATGACAAAACAAGTCTAAAAATGAAAAAACCGGTAAA
* *
1551675 TAACTACCGGATATGTTGAAAGTCTCGATAATTTAATATAAATATCGACACTTTCTGAATTTAAA
255 TAACTACCAGATATGTTGAAAGTCTCGATAATTTAATATAAATATCGACACTTTATGAATTTAAA
*
1551740 AGAGAAGAAGTTATAGCGCCTAAAACGTGTCGACACTTTATGC
320 AGAAAAGAAGTTATAGCGCCTAAAACGTGTCGACACTTTATGC
1551783 AAATGTATCGATCCATAACAATATAACAACCTAAAATATGACAAAACCGGTCTCAAAATGACAAA
1 AAATGTATCGATCCATAACAATATAACAACCTAAAATATGACAAAACCGGTCTCAAAATGACAAA
* * *
1551848 ACATGTAAATAACTACCGGATATGTTAAAAGTGTCTATACTTTAATATAAGTATCGACACTTTTG
66 ACAGGTAAATAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTG
*
1551913 GAATTTAAAAGATAAGAAGTTATAGCGCCTATAAAATGTCGATACTTTAAAAAAATGTATCGATC
131 GAATTTAAAAGAGAAGAAGTTATAGCGCCTA-AAAATGTCGATACTTTAAAAAAATGTATCGATC
* *
1551978 CATAACAATATAATAGGTTAAAATATGACAAAACAAGTCTAAAAAATGAAAAAACCGGT-AA-AA
195 CATAA-AATATAACAGGTAAAAATATGACAAAACAAGTCT-AAAAATGAAAAAACCGGTAAATAA
* * *
1552041 CGATATCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTATGAATTTAAAA
258 C--TACCAGATATGTTGAAAGTCTCGATAATTTAATATAAATATCGACACTTTATGAATTTAAAA
1552106 GAAAAGAAGTTATAGCGCCTAAAACGTGTCGACACTTTATGC
321 GAAAAGAAGTTATAGCGCCTAAAACGTGTCGACACTTTATGC
* *
1552148 AAATGTATCGATCCATAACAATATAACAACCTAAAATATGAAAAAATCGGTCTCAAAATGACAAA
1 AAATGTATCGATCCATAACAATATAACAACCTAAAATATGACAAAACCGGTCTCAAAATGACAAA
* *
1552213 ACAGGTAAATAACTATCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATTGACACTTTTG
66 ACAGGTAAATAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTG
* *
1552278 GAATTTAAAAGAGAAGAAGTTATAGCGCCTACAAAGTGTTGATACTTTAAAAAAATGTATCGATC
131 GAATTTAAAAGAGAAGAAGTTATAGCGCCTA-AAAATGTCGATACTTTAAAAAAATGTATCGATC
1552343 CATAGAAATATAACAGGTAAAAATATGACAAAAC
195 CATA-AAATATAACAGGTAAAAATATGACAAAAC
1552377 CGGTAAAGCG
Statistics
Matches: 544, Mismatches: 42, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
363 3 0.01
364 53 0.10
365 480 0.88
366 8 0.01
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (362 bp):
AAATGTATCGATCCATAACAATATAACAACCTAAAATATGACAAAACCGGTCTCAAAATGACAAA
ACAGGTAAATAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTG
GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAATGTCGATACTTTAAAAAAATGTATCGATCC
ATAAAATATAACAGGTAAAAATATGACAAAACAAGTCTAAAAATGAAAAAACCGGTAAATAACTA
CCAGATATGTTGAAAGTCTCGATAATTTAATATAAATATCGACACTTTATGAATTTAAAAGAAAA
GAAGTTATAGCGCCTAAAACGTGTCGACACTTTATGC
Found at i:1552715 original size:157 final size:157
Alignment explanation
Indices: 1552429--1552730 Score: 568
Period size: 157 Copynumber: 1.9 Consensus size: 157
1552419 ATAAGTACGC
1552429 GTAATAAATTATCGATACTTTCAAAGAAATAGGTAAATATCATATCGAAAGTATCGACACTTGAC
1 GTAATAAATTATCGATACTTTCAAAGAAATAGGTAAATATCATATCGAAAGTATCGACACTTGAC
* *
1552494 ATAAAAGTATCGACACTTAGGTAGTTGTATCGATTAAATATAAATAACATATCCAGTTTAAAAAT
66 ATAAAAATATCGACACTTAGGTAGTTGTATCGATTAAATATAAATAACATATCCAGTGTAAAAAT
1552559 AAAGACATAGCTAAAATAACATCCGGT
131 AAAGACATAGCTAAAATAACATCCGGT
* *
1552586 GTAATAAATTATCTATACTTTCAAAGAAATAGGTAAATATCCTATCGAAAGTATCGACACTTGAC
1 GTAATAAATTATCGATACTTTCAAAGAAATAGGTAAATATCATATCGAAAGTATCGACACTTGAC
1552651 ATAAAAATATCGACACTTAGGTAGTTGTATCGATTAAATATAAATAACATATCCAGTGTAAAAAT
66 ATAAAAATATCGACACTTAGGTAGTTGTATCGATTAAATATAAATAACATATCCAGTGTAAAAAT
1552716 AAAGACATAGCTAAA
131 AAAGACATAGCTAAA
1552731 TTTCCTCTGA
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 141 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (157 bp):
GTAATAAATTATCGATACTTTCAAAGAAATAGGTAAATATCATATCGAAAGTATCGACACTTGAC
ATAAAAATATCGACACTTAGGTAGTTGTATCGATTAAATATAAATAACATATCCAGTGTAAAAAT
AAAGACATAGCTAAAATAACATCCGGT
Found at i:1553020 original size:21 final size:19
Alignment explanation
Indices: 1552966--1553033 Score: 100
Period size: 19 Copynumber: 3.6 Consensus size: 19
1552956 CTTTTATTTA
* *
1552966 ATATTATATGTAAAAAATT
1 ATATTATAGGTAAAAAATG
1552985 ATATTATAGGTAAAAAATG
1 ATATTATAGGTAAAAAATG
*
1553004 ATATTATAGGTAGAAAATG
1 ATATTATAGGTAAAAAATG
*
1553023 ATATTTTAGGT
1 ATATTATAGGT
1553034 TGTATAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (19 bp):
ATATTATAGGTAAAAAATG
Found at i:1554336 original size:22 final size:21
Alignment explanation
Indices: 1554285--1554340 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 21
1554275 AATGTTTTTG
*
1554285 TTTTTTTATATAAAATGATAA
1 TTTTATTATATAAAATGATAA
1554306 TATAGTTATTATATAAAATGATAA
1 T-T--TTATTATATAAAATGATAA
1554330 CTTTTATTATA
1 -TTTTATTATA
1554341 AATGTAGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 1 0.03
22 9 0.30
24 19 0.63
25 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTATTATATAAAATGATAA
Found at i:1555003 original size:18 final size:18
Alignment explanation
Indices: 1554980--1555018 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1554970 TGAAAAATTT
*
1554980 GAAGAAGACAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1554998 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1555016 GAA
1 GAA
1555019 ATGGGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1556396 original size:19 final size:19
Alignment explanation
Indices: 1556372--1556421 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
1556362 AAATGTAGGG
1556372 TTAATTTTGTATA-AGATTT
1 TTAATTTTGTATATA-ATTT
1556391 TTAATTTTGTATATAATTT
1 TTAATTTTGTATATAATTT
*
1556410 ATAATTTTGTAT
1 TTAATTTTGTAT
1556422 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (19 bp):
TTAATTTTGTATATAATTT
Found at i:1557328 original size:198 final size:199
Alignment explanation
Indices: 1556787--1558082 Score: 1970
Period size: 199 Copynumber: 6.5 Consensus size: 199
1556777 GTAAACTTAT
* * * * *
1556787 GTGTCGATACATTTATAAGAAGTGTCGATCTCAAAAACATCGAAACCCATTATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGTAATA
* * * *
1556852 GGTAAATTAACAATGTAACCGGTCTAAATATATCAGTTTTTTAGAAAACAGGTGTACAAAACGTA
66 GGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
*
1556917 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACTA
1556982 AAAA
196 AAAA
* * * * * *
1556986 GTGTCGATACATTTATAATAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATTTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGTAATA
* * *
1557051 GGTAAATTAACAATATAACCGATCTAAATATACCAGTTTTTGAGAAAACATGTGTACAAAAAGTA
66 GGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
1557116 TCGACATAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACTA
1557181 AAAA
196 AAAA
* * *
1557185 GTGTCGATACATTTATAAGAAGTATTGATCCCAGAAA-ATCGAAACCCATAATTATGATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGTAATA
* *
1557249 GGTAAATTAACAATTTAACCGGTCTAAGTATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * * *
1557314 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATATATTTCCAAACCAAGGGCACGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACTA
1557379 AAAA
196 AAAA
* * * *
1557383 GTCTTGATACATTTCTAACAAGTGTCGATCACAGAAACATCGAAACCCATAATTATGATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGTAATA
* *
1557448 GGTAAATTAACAATTTAACCGGTCTAAGTATACCAGTTTTTAAGAAAACAGGTGTAC-AAAAGTA
66 GGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
*
1557512 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACAA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACTA
1557577 AAAA
196 AAAA
* *
1557581 GTGTCGATACATTTCTAACAAGTGTCGATCCCATAAACATCGAAACCCATAATTATGATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGTAATA
* * * * * * * *
1557646 GGCAAATTAAAAATTTAACCGGTCTAAGTTTATCGGTTTTTGAGAAAACATGTGTATAAAAAGTA
66 GGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
1557711 TTGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACTA
1557776 AAAA
196 AAAA
* * * *
1557780 GTGTCGATATATTTATAAGAATTGTCGATCCCAGAAACATCAAAACCCATAATTATGATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGTAATA
* *
1557845 AGTAAATTAATAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
1557910 TCGATACAAATAAAACAAGTGTGGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACTA
1557975 AAAA
196 AAAA
1557979 GTGTCGATACATTTATAACAAGTGTCGATCCCA-AGAACATCGAAACCCATAATTAT-ATTGTAA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAGA-AACATCGAAACCCATAATTATGA-TGTAA
* * * * * *
1558042 TATGTAAATTAACAATGTAACCGATATAAAAATACCGGTTT
64 TAGGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTT
1558083 AATTTGAAAA
Statistics
Matches: 1005, Mismatches: 88, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
198 362 0.36
199 643 0.64
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (199 bp):
GTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGTAATA
GGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACTA
AAAA
Found at i:1557625 original size:397 final size:397
Alignment explanation
Indices: 1556787--1558082 Score: 2004
Period size: 397 Copynumber: 3.3 Consensus size: 397
1556777 GTAAACTTAT
* * * *
1556787 GTGTCGATACATTTATAAGAAGTGTCGATCTCAAAAACATCGAAACCCATTATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATC-CCAAAACATCGAAACCCATAATTATGATGTAATA
* * * *
1556852 GGTAAATTAACAATGTAACCGGTCTAAATATATCAGTTTTTTAGAAAACAGGTGTACAAAACGTA
65 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
1556917 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACGA
* * * * * *
1556982 AAAAGTGTCGATACATTTATAATAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATTT
195 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGT
* * *
1557047 AATAGGTAAATTAACAATATAACCGATCTAAATATACCAGTTTTTGAGAAAACATGTGTACAAAA
260 AATAGGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAA
*
1557112 AGTATCGACATAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGC
325 AGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGC
1557177 ACTAAAAA
390 ACTAAAAA
* * *
1557185 GTGTCGATACATTTATAAGAAGTATTGATCCCAGAAA-ATCGAAACCCATAATTATGATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCA-AAACATCGAAACCCATAATTATGATGTAATA
* *
1557249 GGTAAATTAACAATTTAACCGGTCTAAGTATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
65 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
1557314 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATATATTTCCAAACCAAGGGCACGA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACGA
* * * *
1557379 AAAAGTCTTGATACATTTCTAACAAGTGTCGATCACAGAAACATCGAAACCCATAATTATGATGT
195 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGT
* *
1557444 AATAGGTAAATTAACAATTTAACCGGTCTAAGTATACCAGTTTTTAAGAAAACAGGTGTAC-AAA
260 AATAGGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAA
*
1557508 AGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGC
325 AGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGC
*
1557573 ACAAAAAA
390 ACTAAAAA
*
1557581 GTGTCGATACATTTCTAACAAGTGTCGATCCCATAAACATCGAAACCCATAATTATGATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCA-AAACATCGAAACCCATAATTATGATGTAATA
* * * * * * * *
1557646 GGCAAATTAAAAATTTAACCGGTCTAAGTTTATCGGTTTTTGAGAAAACATGTGTATAAAAAGTA
65 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
*
1557711 TTGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACGA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACGA
* * * *
1557776 AAAAGTGTCGATATATTTATAAGAATTGTCGATCCCAGAAACATCAAAACCCATAATTATGATGT
195 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGT
* *
1557841 AATAAGTAAATTAATAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAA
260 AATAGGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAA
* *
1557906 AGTATCGATACAAATAAAACAAGTGTGGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGC
325 AGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGC
1557971 ACTAAAAA
390 ACTAAAAA
1557979 GTGTCGATACATTTATAACAAGTGTCGATCCCAAGAACATCGAAACCCATAATTAT-ATTGTAAT
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAA-AACATCGAAACCCATAATTATGA-TGTAAT
* * * *
1558043 ATGTAAATTAACAATGTAACCGATATAAAAATACCGGTTT
64 AGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTT
1558083 AATTTGAAAA
Statistics
Matches: 817, Mismatches: 76, Indels: 10
0.90 0.08 0.01
Matches are distributed among these distances:
396 105 0.13
397 520 0.64
398 192 0.24
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (397 bp):
GTGTCGATACATTTATAACAAGTGTCGATCCCAAAACATCGAAACCCATAATTATGATGTAATAG
GTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTAT
CGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGGGCACGAA
AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATGATGTA
ATAGGTAAATTAACAATTTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAA
GTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCA
CTAAAAA
Found at i:1558447 original size:15 final size:15
Alignment explanation
Indices: 1558427--1558484 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
1558417 TTTCTCAAAG
1558427 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
* *
1558442 CTCTTCCCAGCCCAC
1 CTCTTCTCAACCCAC
1558457 CTCTTCTCAACCACAAC
1 CTCTTCTCAACC-C-AC
1558474 CTCCTTCTCAA
1 CT-CTTCTCAA
1558485 ACAATTGCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 23 0.64
16 1 0.03
17 4 0.11
18 8 0.22
ACGTcount: A:0.21, C:0.52, G:0.02, T:0.26
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:1559649 original size:3 final size:3
Alignment explanation
Indices: 1559618--1559661 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1559608 CAAGCGGTCA
* * * *
1559618 ATG AAG ATG ACG ATG AAG ATG AAG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1559662 CCAAACAAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.41, C:0.02, G:0.32, T:0.25
Consensus pattern (3 bp):
ATG
Found at i:1561247 original size:200 final size:197
Alignment explanation
Indices: 1560903--1561649 Score: 967
Period size: 200 Copynumber: 3.8 Consensus size: 197
1560893 TATTCATTCA
* * *
1560903 TGTCGATACATGTT-GTCCATAATGTATTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTT
1 TGTCGATAC-TTTTGGTCCAGAATGTATTTCAAAACCAAGTGCAC-AAAAAGTGTCGATACATTT
* *
1560967 ATAAGAAGTGTCGATACTAAAAACATCGAAATACATAGATATAATGTAATAGGTAAAATAACAAT
64 ATAAGAAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAATTAACAAT
* * * * *
1561032 GTAACCGGCCTAAATATATCGGTTTTTGAGAAAACATGTATACATAAAGTATCGACACAAATACA
129 GTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACA-AAAGTATCGACACAAATAAA
*
1561097 ATAAG
193 ACAAG
* ** *
1561102 TGTCGATACTTTTTGTCCAGCGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTT
1 TGTCGATACTTTTGGTCCAGAATGTA-TTTCAAAACCAAGTGCACAA-AAAGTGTCGATACATTT
* * * *
1561167 ATAACAAGTGTCGAT-CTCAAAAACATTGAAACCCATA-ATTATGAA-GTAATAAGTAAATTAAC
64 ATAAGAAGTGTCGATACT-AAAAACATCGAAACACATAGA-TAT-AATGTAATAGGTAAATTAAC
* *
1561229 AATTTAACTGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAGTATCGACACAAATA
126 AATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAGTATCGACACAAATA
1561294 AAACAAG
191 AAACAAG
* * *
1561301 TGTCGATACTTTTGGTCCATAATGTATTTCAAAACCAAATGCACTAAAAGTGTCGATACATTTAT
1 TGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACAAAAAGTGTCGATACATTTAT
* * * *
1561366 AAGAAGTGTCGATCCCAAAAACTTC-AGAACCCATA-ATTATGAA-GTAATAGGTAAATTAACAA
66 AAGAAGTGTCGATACTAAAAACATCGA-AACACATAGA-TAT-AATGTAATAGGTAAATTAACAA
* * *
1561428 TGTAATCGGTCT--A-A-ACTGGTTTATGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAA
128 TGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAC-AAAAGTATCGACACAAATAA
1561489 AACAAG
192 AACAAG
* * * *
1561495 TGTCGATACATTTGGTCCAGAATGTATTTCAAAACCAATTGCATTAAAACGTGTCGATACATTTA
1 TGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCA-CAAAAAGTGTCGATACATTTA
* *
1561560 TAAGAAGTGTCGATACTAAAAACATCGAAATATATAGATATAATGTAATAGGTAAATTAACAATG
65 TAAGAAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAATTAACAATG
1561625 TAACCGGTCTAAATATACCGGTTTT
130 TAACCGGTCTAAATATACCGGTTTT
1561650 ATGAACAAAT
Statistics
Matches: 479, Mismatches: 52, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
193 24 0.05
194 69 0.14
195 80 0.17
196 3 0.01
197 82 0.17
198 22 0.05
199 75 0.16
200 122 0.25
201 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (197 bp):
TGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACAAAAAGTGTCGATACATTTAT
AAGAAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAATTAACAATGT
AACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAGTATCGACACAAATAAAACA
AG
Found at i:1561636 original size:392 final size:398
Alignment explanation
Indices: 1560903--1561649 Score: 1009
Period size: 392 Copynumber: 1.9 Consensus size: 398
1560893 TATTCATTCA
* *
1560903 TGTCGATACATGTTGTCCATAATGTATTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTA
1 TGTCGATACATGTTGTCCATAATGTATTTCAAAACCAAATGCACGAAAAAGTGTCGATACATTTA
* *
1560968 TAAGAAGTGTCGATACTAAAAACATCGAAATACATAGATATAATGTAATAGGTAAAATAACAATG
66 TAAGAAGTGTCGATACCAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATG
* * * *
1561033 TAACCGGCCTAAATATATCGGTTTTTGAGAAAACATGTATACATAAAGTATCGACACAAATACAA
131 TAACCGGCCTAAATATATCGGTTTATGAGAAAACAGGTATACAAAAAGTATCGACACAAATAAAA
* * * **
1561098 TAAGTGTCGATACTTTTTGTCCAGCGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATAC
196 CAAGTGTCGATACATTTGGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATAC
* *
1561163 ATTTATAACAAGTGTCGATCTCAAAAACATTGAAACCCATAATTATGAAGTAATAAGTAAATTAA
261 ATTTATAACAAGTGTCGATCTCAAAAACATCGAAACACATAATTATGAAGTAATAAGTAAATTAA
* *
1561228 CAATTTAACTGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAGTATCGACACAAAT
326 CAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAGTATCGACACAAAT
1561293 AAAACAAG
391 AAAACAAG
* *
1561301 TGTCGATAC-TTTTGGTCCATAATGTATTTCAAAACCAAATGCAC-TAAAAGTGTCGATACATTT
1 TGTCGATACATGTT-GTCCATAATGTATTTCAAAACCAAATGCACGAAAAAGTGTCGATACATTT
* * * *
1561364 ATAAGAAGTGTCGATCCCAAAAACTTC-AGAACCCATA-ATTATGAA-GTAATAGGTAAATTAAC
65 ATAAGAAGTGTCGATACCAAAAACATCGA-AACACATAGA-TAT-AATGTAATAGGTAAAATAAC
* * * *
1561426 AATGTAATCGGTCT-AA-A-CT-GGTTTATGAGAAAACAGGTGTACAAAAAGTATCGACACAAAT
127 AATGTAACCGGCCTAAATATATCGGTTTATGAGAAAACAGGTATACAAAAAGTATCGACACAAAT
* * * *
1561487 AAAACAAGTGTCGATACATTTGGTCCAGAATGTA-TTTCAAAACCAATTGCATTAA-AACGTGTC
192 AAAACAAGTGTCGATACATTTGGTCCAGAATGTATTTTAAAAACCAAGTGCA-CAACAAAGTGTC
* * * *
1561550 GATACATTTATAAGAAGTGTCGATACT-AAAAACATCGAAATATATAGA-TAT-AATGTAATAGG
256 GATACATTTATAACAAGTGTCGAT-CTCAAAAACATCGAAACACATA-ATTATGAA-GTAATAAG
1561612 TAAATTAACAATGTAACCGGTCTAAATATACCGGTTTT
318 TAAATTAACAATGTAACCGGTCTAAATATACCGGTTTT
1561650 ATGAACAAAT
Statistics
Matches: 306, Mismatches: 35, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
391 2 0.01
392 106 0.35
393 71 0.23
394 1 0.00
395 1 0.00
396 4 0.01
397 82 0.27
398 39 0.13
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (398 bp):
TGTCGATACATGTTGTCCATAATGTATTTCAAAACCAAATGCACGAAAAAGTGTCGATACATTTA
TAAGAAGTGTCGATACCAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATG
TAACCGGCCTAAATATATCGGTTTATGAGAAAACAGGTATACAAAAAGTATCGACACAAATAAAA
CAAGTGTCGATACATTTGGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATAC
ATTTATAACAAGTGTCGATCTCAAAAACATCGAAACACATAATTATGAAGTAATAAGTAAATTAA
CAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAGTATCGACACAAAT
AAAACAAG
Found at i:1563422 original size:130 final size:130
Alignment explanation
Indices: 1563189--1563452 Score: 474
Period size: 130 Copynumber: 2.0 Consensus size: 130
1563179 CGTAGAGAAG
* *
1563189 CAAACCTTTCCATTTGCATTATTTCTGGAGGCACATTCAAATCAACAAAATTGGGTGCAGAAGCC
1 CAAACCTTGCCATTTGCATTATTTCTGGAGGCACATTCAAATCAACAAAACTGGGTGCAGAAGCC
* * *
1563254 TTCGCATCCTTAGTCCACCTACTTTGAATCAAAGACCCGGGCAAATATGTGTAATCTAATTGCTT
66 TTCGCATCCTTAGTCCACCTACTTTGAATCAAAGACCCGGGAAAATATGTGTAATCCAAGTGCTT
*
1563319 CAAACCTTGCCATTTGTATTATTTCTGGAGGCACATTCAAATCAACAAAACTGGGTGCAGAAGCC
1 CAAACCTTGCCATTTGCATTATTTCTGGAGGCACATTCAAATCAACAAAACTGGGTGCAGAAGCC
1563384 TTCGCATCCTTAGTCCACCTACTTTGAATCAAAGACCCGGGAAAATATGTGTAATCCAAGTGCTT
66 TTCGCATCCTTAGTCCACCTACTTTGAATCAAAGACCCGGGAAAATATGTGTAATCCAAGTGCTT
1563449 CAAA
1 CAAA
1563453 ACGTGAAGTT
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (130 bp):
CAAACCTTGCCATTTGCATTATTTCTGGAGGCACATTCAAATCAACAAAACTGGGTGCAGAAGCC
TTCGCATCCTTAGTCCACCTACTTTGAATCAAAGACCCGGGAAAATATGTGTAATCCAAGTGCTT
Found at i:1565854 original size:182 final size:182
Alignment explanation
Indices: 1565510--1566188 Score: 1035
Period size: 182 Copynumber: 3.7 Consensus size: 182
1565500 GTAAATTAAC
* * *
1565510 AGTGTCGATACTTTAATATAAGTATCGACACTTT-TGGAAATAAAAAGAGAAGAAGTTATAGCGC
1 AGTGTCGATAATTTAATATAAGTATCGACACTTTCT-GAATTTAAAAGAGAAGAAGTTATAGCGC
* * *
1565574 CTAAAAAGTGTCGATACTTTA-AAAAATGTATCGATCCATAATAATATTACATGTAAAAATATGA
65 CTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGA
* * * *
1565638 CAAAACCAGTCTCAAAATGACAAAATCAGTAAAACGATACCGGATATGTTTCA
130 CAAAACCGGTCTCAAAATGACAAAACCGGTAAAACGATACCGGATATGTTGCA
*
1565691 AGTGTCAATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
1 AGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
* *
1565756 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCTATAACAATATAACATGTAAAAATATGAC
66 TAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
1565821 AAAACCGGTCTCAAAATGACAAAACCGGTAAAAC-ACTACCGGATATGTTGCA
131 AAAACCGGTCTCAAAATGACAAAACCGGTAAAACGA-TACCGGATATGTTGCA
*
1565873 AGTGTCGATAATTTAATATAAGTATCAACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
1 AGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
* *
1565938 TAAACAGTGTCGACACTTT-TAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
66 TAAAAAGTGTCGACACTTTAT-AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGA
* * * *
1566002 CAAAACCGGTCTCAAAATGAAAAAACCGGTAAAAGGATACCGTATATGTTGAA
130 CAAAACCGGTCTCAAAATGACAAAACCGGTAAAACGATACCGGATATGTTGCA
* * *
1566055 AGTGTCGCTAATTTAATATAAGTATCGACACTTTCCGAATTTAAAAGAGAAGGAGTTATAGCGCC
1 AGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
* * **
1566120 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCGATAATTATATAACA-GCTAAAAATATGA
66 TAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCATAACAATATAACATG-TAAAAATATGA
*
1566184 GAAAA
130 CAAAA
1566189 TAGGTTAACA
Statistics
Matches: 458, Mismatches: 33, Indels: 13
0.91 0.07 0.03
Matches are distributed among these distances:
181 81 0.18
182 375 0.82
183 2 0.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
TAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
AAAACCGGTCTCAAAATGACAAAACCGGTAAAACGATACCGGATATGTTGCA
Found at i:1566707 original size:64 final size:64
Alignment explanation
Indices: 1566590--1566709 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 64
1566580 TACCTATTAC
* * *
1566590 ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAGTATTTTCGGTTAAATGCCTATTTT
1 ATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTTCGATTAAATGCCTATTTT
* *
1566654 ATTATATAAGTGCTACCTAATATATTATTGTGCTTGATAATA-TTTCTGATTAAATG
1 ATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTTC-GATTAAATG
1566710 ATATAACATA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
63 4 0.08
64 46 0.92
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (64 bp):
ATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTTCGATTAAATGCCTATTTT
Found at i:1582148 original size:21 final size:21
Alignment explanation
Indices: 1582106--1582148 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1582096 TTTCTGGGCT
* *
1582106 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1582127 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1582148 A
1 A
1582149 ATGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1582831 original size:23 final size:23
Alignment explanation
Indices: 1582797--1582888 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
1582787 CATTATTATA
* *
1582797 TGGCACTACGGTGCAATTCTACA
1 TGGCACTCCGGTGCAATTCTACG
* *
1582820 CGGCACTCCGGTGTAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
*
1582843 TGGCACTCCGGTGTAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
* *
1582866 TGGCACTTCGGTGCAATTATACG
1 TGGCACTCCGGTGCAATTCTACG
1582889 AGCTGTGGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTACG
Found at i:1586044 original size:50 final size:47
Alignment explanation
Indices: 1585981--1586078 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 47
1585971 CCAACAGCCA
1585981 TTCTTACATAATATCTCCATCAAGAAAATATCCAGCAGACCATTGCTTC
1 TTCTTACATAATATCTCCATCAAGAAAATATCCAGCAG-CCATT-CTTC
1586030 TTCTATACATAATATCTCCATCAAGAAAATATCCAGCAGCCATTCTTC
1 TTCT-TACATAATATCTCCATCAAGAAAATATCCAGCAGCCATTCTTC
1586078 T
1 T
1586079 CAAGGTTCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
48 5 0.10
49 9 0.19
50 34 0.71
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.32
Consensus pattern (47 bp):
TTCTTACATAATATCTCCATCAAGAAAATATCCAGCAGCCATTCTTC
Found at i:1597278 original size:28 final size:28
Alignment explanation
Indices: 1597245--1597308 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
1597235 CTGGGATCTG
1597245 TTCTCTGTCCTTTTTTTTTGTATCTTGT
1 TTCTCTGTCCTTTTTTTTTGTATCTTGT
1597273 TTCTCTGTCCTTTTTTTTTGTATCTTGT
1 TTCTCTGTCCTTTTTTTTTGTATCTTGT
1597301 TTCTCTGT
1 TTCTCTGT
1597309 ATCTCTCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.03, C:0.19, G:0.11, T:0.67
Consensus pattern (28 bp):
TTCTCTGTCCTTTTTTTTTGTATCTTGT
Found at i:1597311 original size:15 final size:15
Alignment explanation
Indices: 1597263--1597312 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
1597253 CCTTTTTTTT
1597263 TGTATCTTGTTTCTC
1 TGTATCTTGTTTCTC
* * *
1597278 TGT-CCTT-TTTTTT
1 TGTATCTTGTTTCTC
1597291 TGTATCTTGTTTCTC
1 TGTATCTTGTTTCTC
1597306 TGTATCT
1 TGTATCT
1597313 CTCTCTGTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 7 0.26
14 6 0.22
15 14 0.52
ACGTcount: A:0.06, C:0.18, G:0.12, T:0.64
Consensus pattern (15 bp):
TGTATCTTGTTTCTC
Found at i:1597739 original size:3 final size:3
Alignment explanation
Indices: 1597723--1597803 Score: 87
Period size: 3 Copynumber: 27.7 Consensus size: 3
1597713 TGTAATATTA
* * * *
1597723 AAT AAT -AT ATT AAT AAT AAT AAT AAT TAT AAT TAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1597770 AAT AAT TAT AAT AAT AAT AAT -AT AAAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
1597804 AAATGAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 6 0.09
3 56 0.88
4 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1603810 original size:57 final size:53
Alignment explanation
Indices: 1603748--1603851 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 53
1603738 AAATTAACCC
* * *
1603748 TTATTATTATTATATATATAATTATTTTTTATTTATTTTCTATATTTTTTTGTTTAT
1 TTATTATTATTATAT-TAT-ACTA-TTTTTATTT-TTTACTATATTGTTTTGTTTAT
1603805 TTATTATTATTATATTATACTATTTTTATTTTTTACTATATTGTTTT
1 TTATTATTATTATATTATACTATTTTTATTTTTTACTATATTGTTTT
1603852 CATTACTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
53 14 0.32
54 9 0.20
55 3 0.07
56 3 0.07
57 15 0.34
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (53 bp):
TTATTATTATTATATTATACTATTTTTATTTTTTACTATATTGTTTTGTTTAT
Found at i:1603909 original size:2 final size:2
Alignment explanation
Indices: 1603902--1603938 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1603892 TATTATCATT
1603902 TA TA TA TA TA TA TA TA 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 TA TA TA T
1603939 TTGTTTTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1603993 original size:21 final size:20
Alignment explanation
Indices: 1603956--1604000 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1603946 CTACACATTT
* * *
1603956 TTTTTCAATCTTCTTTCAGC
1 TTTTTCAATTTTATTTCAAC
1603976 TTTTTCAATTTTTATTTCAAC
1 TTTTTCAA-TTTTATTTCAAC
1603997 TTTT
1 TTTT
1604001 CAACTTTTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.18, C:0.18, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTCAATTTTATTTCAAC
Found at i:1606911 original size:20 final size:19
Alignment explanation
Indices: 1606887--1606976 Score: 67
Period size: 19 Copynumber: 4.5 Consensus size: 19
1606877 AATCAAGAAC
1606887 AAAAAGAGAAGGAAAAAAGAG
1 AAAAAGA-AA-GAAAAAAGAG
*
1606908 AAAAACAAAGAAAAAA-AG
1 AAAAAGAAAGAAAAAAGAG
*
1606926 CAAAAAGAAAAGAAAAAAG-C
1 -AAAAAG-AAAGAAAAAAGAG
* *
1606946 AAAAACAAAGGAAAAATATAG
1 AAAAAGAAA-GAAAAA-AGAG
1606967 AAAAAAGAAA
1 -AAAAAGAAA
1606977 ACAAGACGCA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
18 5 0.09
19 23 0.42
20 13 0.24
21 6 0.11
22 8 0.15
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAAGAG
Found at i:1606922 original size:19 final size:19
Alignment explanation
Indices: 1606898--1606971 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
1606888 AAAAGAGAAG
1606898 GAAAAAAGAGAAAAACAAA
1 GAAAAAAGAGAAAAACAAA
*
1606917 GAAAAAA-AGCAAAAAGAAAA
1 GAAAAAAGAG-AAAAA-CAAA
*
1606937 GAAAAAAG-CAAAAACAAA
1 GAAAAAAGAGAAAAACAAA
*
1606955 GGAAAAATATAGAAAAA
1 -GAAAAA-AGAGAAAAA
1606972 AGAAAACAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.11
19 23 0.52
20 11 0.25
21 5 0.11
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (19 bp):
GAAAAAAGAGAAAAACAAA
Found at i:1606951 original size:38 final size:42
Alignment explanation
Indices: 1606886--1606977 Score: 120
Period size: 39 Copynumber: 2.3 Consensus size: 42
1606876 CAATCAAGAA
* *
1606886 CAAAAAGAGAAGGAAAAAAGAGAAAAACAAA-GAAAAA-A-AG
1 CAAAAAGA-AAAGAAAAAAGACAAAAACAAAGGAAAAATATAG
1606926 CAAAAAGAAAAGAAAAAAG-CAAAAACAAAGGAAAAATATAG
1 CAAAAAGAAAAGAAAAAAGACAAAAACAAAGGAAAAATATAG
*
1606967 AAAAAAGAAAA
1 CAAAAAGAAAA
1606978 CAAGACGCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
38 9 0.20
39 16 0.35
40 9 0.20
41 12 0.26
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.02
Consensus pattern (42 bp):
CAAAAAGAAAAGAAAAAAGACAAAAACAAAGGAAAAATATAG
Found at i:1608068 original size:31 final size:32
Alignment explanation
Indices: 1608001--1608072 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
1607991 GGAACAATGG
* * *
1608001 GGGCACCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTA
* *
1608033 GGGCATCTTTGGAGATT-AACATCGAATATTA
1 GGGCATCTTTGAAGATTCAACATCAAATATTA
1608064 GGGCATCTT
1 GGGCATCTT
1608073 CGGGGATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 20 0.57
32 15 0.43
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTGAAGATTCAACATCAAATATTA
Found at i:1608810 original size:60 final size:60
Alignment explanation
Indices: 1608737--1608873 Score: 220
Period size: 60 Copynumber: 2.3 Consensus size: 60
1608727 TTACTCGAGA
* *
1608737 TTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAATAC
1 TTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAACAC
* * * *
1608797 TTGGATTTCAACTTCACAACAAATGATATCCAACTCAAAGTCGATTTGTTGAAACAACAC
1 TTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAACAC
1608857 TTGGATTTCAACTTCAC
1 TTGGATTTCAACTTCAC
1608874 GAAGAAGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (60 bp):
TTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAACAC
Found at i:1609189 original size:37 final size:36
Alignment explanation
Indices: 1609137--1609329 Score: 172
Period size: 37 Copynumber: 5.1 Consensus size: 36
1609127 GTTTTACATT
* * * ***
1609137 AAACAAATTTCGTCTCCCTTGAGACAGTTTTTTTTG
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
1609173 GAACTAAGTTTTGTCTCTCTTGAGATAG-TTCCTCTTT
1 AAAC-AAGTTTTGTCTCTCTTGAGACAGTTTCC-CTTG
* *
1609210 AAACAAATTTTGTGTTTGTCTCTCTTGAGATAGTTTCTCTTG
1 AAAC-AA----GT-TTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1609252 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
1609288 CAACATAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACA-AGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1609325 AAACA
1 AAACA
1609330 CCAATCTTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
36 35 0.27
37 60 0.47
41 4 0.03
42 26 0.20
43 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (36 bp):
AAACAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1609241 original size:42 final size:42
Alignment explanation
Indices: 1609182--1609264 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1609172 GGAACTAAGT
*
1609182 TTTGTCTCTCTTGAGATAGTTCCTCTTTAAACAAATTTTGTG
1 TTTGTCTCTCTTGAGATAGTTCCTCTTGAAACAAATTTTGTG
*
1609224 TTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTTGT
1 TTTGTCTCTCTTGAGATAGTTCCTCTTGAAACAAATTTTGT
1609265 CTCTCTTGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (42 bp):
TTTGTCTCTCTTGAGATAGTTCCTCTTGAAACAAATTTTGTG
Found at i:1609466 original size:35 final size:36
Alignment explanation
Indices: 1609391--1609496 Score: 160
Period size: 35 Copynumber: 2.9 Consensus size: 36
1609381 AGTTTCTCTT
* *
1609391 AAAAAAACCTTTTAAATCGTTTCTCTTGAAACACAAA
1 AAAAAAACCTTTGAAATTGTTTCTCTTGAAACAC-AA
*
1609428 AAAAAAACCTTTGAAATTTTTTCTCTTGAAACAC-A
1 AAAAAAACCTTTGAAATTGTTTCTCTTGAAACACAA
*
1609463 AAAAAAACCTTTGAAAATGTTTCTCTTGAAACAC
1 AAAAAAACCTTTGAAATTGTTTCTCTTGAAACAC
1609497 GAAGACTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 33 0.52
37 31 0.48
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (36 bp):
AAAAAAACCTTTGAAATTGTTTCTCTTGAAACACAA
Found at i:1610895 original size:28 final size:30
Alignment explanation
Indices: 1610867--1610938 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
1610857 TTAACCCTTA
1610867 TTATTATTATATATATAATT-ATTTTTTAT
1 TTATTATTATATATATAATTGATTTTTTAT
* **
1610896 TTATT-TTCTATAT-TTTTTGATTTTTTAT
1 TTATTATTATATATATAATTGATTTTTTAT
*
1610924 TTATTAATAT-TATAT
1 TTATTATTATATATAT
1610939 TATACTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.09
28 24 0.69
29 8 0.23
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (30 bp):
TTATTATTATATATATAATTGATTTTTTAT
Found at i:1616865 original size:21 final size:21
Alignment explanation
Indices: 1616852--1616974 Score: 153
Period size: 21 Copynumber: 5.9 Consensus size: 21
1616842 CAATACGATT
*
1616852 TTGGACTATCGCAATACGAAC
1 TTGGACTATCGCAATGCGAAC
1616873 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
1616894 TTGGACTATCGCAATGCGAA-
1 TTGGACTATCGCAATGCGAAC
* *
1616914 TATGTA-AATCGCAATGCGATA-
1 T-TGGACTATCGCAATGCGA-AC
* *
1616935 GTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
1616956 TTCGACTATCGCAATGCGA
1 TTGGACTATCGCAATGCGA
1616975 TTTACATATT
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.18
21 74 0.82
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:1616988 original size:41 final size:39
Alignment explanation
Indices: 1616858--1616994 Score: 102
Period size: 41 Copynumber: 3.3 Consensus size: 39
1616848 GATTTTGGAC
* *
1616858 TATCGCAATACGAACTTGGACTATCGCAATGCGAACTTGGAC-
1 TATCGCAATGCGAACTT-GACTATCGCAATGCG-A-TT-TACA
* *
1616900 TATCGCAATGCGAA-TATGTA-AATCGCAATGCGATAGT-CGA
1 TATCGCAATGCGAACT-TG-ACTATCGCAATGCGAT-TTAC-A
1616940 CTATCGCAATGCGAACTTCGACTATCGCAATGCGATTTACA
1 -TATCGCAATGCGAACTT-GACTATCGCAATGCGATTTACA
*
1616981 TATTCGCATTGCGA
1 TA-TCGCAATGCGA
1616995 TAGTCGAAGT
Statistics
Matches: 77, Mismatches: 7, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 3 0.04
41 41 0.53
42 31 0.40
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (39 bp):
TATCGCAATGCGAACTTGACTATCGCAATGCGATTTACA
Found at i:1617009 original size:20 final size:21
Alignment explanation
Indices: 1616984--1617050 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
1616974 ATTTACATAT
* *
1616984 TCGCATTGCGATAGTC-GAAG
1 TCGCATTGCGATAGTCAAAAA
*
1617004 TTGCATTGCGATAGTCAAAAA
1 TCGCATTGCGATAGTCAAAAA
*
1617025 TCGCATTGCGATAGTCTAAAA
1 TCGCATTGCGATAGTCAAAAA
1617046 TCGCA
1 TCGCA
1617051 ACGACTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGATAGTCAAAAA
Found at i:1617765 original size:21 final size:21
Alignment explanation
Indices: 1617750--1617869 Score: 106
Period size: 21 Copynumber: 5.8 Consensus size: 21
1617740 GCGATTTTGG
1617750 ACTATCGCAATGCGATAGTCA
1 ACTATCGCAATGCGATAGTCA
1617771 ACTATCGCAATGCGAATATGT-A
1 ACTATCGCAATGCG-ATA-GTCA
*
1617793 A--ATCGCAATGCAATAGTCGA
1 ACTATCGCAATGCGATAGTC-A
* *
1617813 AGT-TCGCATTGCGATAGTCCA
1 ACTATCGCAATGCGATAGT-CA
* * *
1617834 AGT-TCGCATTGCGATAGTCG
1 ACTATCGCAATGCGATAGTCA
*
1617854 ACTATCGCATTGCGAT
1 ACTATCGCAATGCGAT
1617870 TTACATATTC
Statistics
Matches: 86, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 15 0.17
21 58 0.67
22 6 0.07
23 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (21 bp):
ACTATCGCAATGCGATAGTCA
Found at i:1617882 original size:83 final size:83
Alignment explanation
Indices: 1617753--1617930 Score: 227
Period size: 83 Copynumber: 2.1 Consensus size: 83
1617743 ATTTTGGACT
* * *
1617753 ATCGCAATGCGATAGTCAACTATCGCAATGCGAATATGTAAATCGCAATGCAATAGTCGAAGTTC
1 ATCGCATTGCGATAGTCAACTATCGCAATGCGAATATGTAAATCGCAATGCAATAATCCAAGTTC
*
1617818 GCATTGCGATAGTCCAAG
66 GCATTGCGATAGTCCAAA
* * * * *
1617836 TTCGCATTGCGATAGTCGACTATCGCATTGCG-AT-T-TACATATTCGCATTGCGATAATCCAAG
1 ATCGCATTGCGATAGTCAACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCAATAATCCAAG
1617898 TTCGCATTGCGATAGTCCAAA
63 TTCGCATTGCGATAGTCCAAA
1617919 ATCGCATTGCGA
1 ATCGCATTGCGA
1617931 ATCTGGAAAC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
80 2 0.02
81 2 0.02
82 3 0.04
83 75 0.91
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (83 bp):
ATCGCATTGCGATAGTCAACTATCGCAATGCGAATATGTAAATCGCAATGCAATAATCCAAGTTC
GCATTGCGATAGTCCAAA
Found at i:1617903 original size:21 final size:21
Alignment explanation
Indices: 1617795--1617930 Score: 143
Period size: 21 Copynumber: 6.5 Consensus size: 21
1617785 AATATGTAAA
* * *
1617795 TCGCAATGCAATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
1617816 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
1617837 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
1617857 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
*
1617878 TCGCATTGCGATAATCCAAGT
1 TCGCATTGCGATAGTCCAAGT
**
1617899 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAGT
1617920 TCGCATTGCGA
1 TCGCATTGCGA
1617931 ATCTGGAAAC
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
20 17 0.17
21 80 0.82
22 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:1617903 original size:41 final size:41
Alignment explanation
Indices: 1617812--1617930 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
1617802 GCAATAGTCG
* *
1617812 AAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 AAGTTCGCATTGCGATAGTACAAGTTCGCATTGCGATAATC
* * *
1617853 GACTATCGCATTGCGAT-TTACATA-TTCGCATTGCGATAATCC
1 AAGT-TCGCATTGCGATAGTACA-AGTTCGCATTGCGATAAT-C
* **
1617895 AAGTTCGCATTGCGATAGTCCAAAATCGCATTGCGA
1 AAGTTCGCATTGCGATAGTACAAGTTCGCATTGCGA
1617931 ATCTGGAAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
41 33 0.52
42 30 0.48
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (41 bp):
AAGTTCGCATTGCGATAGTACAAGTTCGCATTGCGATAATC
Found at i:1627762 original size:20 final size:20
Alignment explanation
Indices: 1627737--1627778 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1627727 ATGGATGGTC
1627737 TAATTTCTTTCTATTAAAAA
1 TAATTTCTTTCTATTAAAAA
1627757 TAATTTCTTTCTATTAAAAA
1 TAATTTCTTTCTATTAAAAA
1627777 TA
1 TA
1627779 CCAAGGAATG
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:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTTCTTTCTATTAAAAA
Found at i:1630209 original size:60 final size:60
Alignment explanation
Indices: 1630097--1630209 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
1630087 GAAGAATTTG
* * * * * *
1630097 GAATATTTAAAAGTATGAGGATCAATTTAGAATGTGACTCACGATTTGAGGATAAAATTA
1 GAATATTAAAAAGTATGAGGACCAATTTAGAATGAGAATCACAATTTAAGGATAAAATTA
* *
1630157 GAATATTAAAAAGT-TTAGGGACCAATTTAGAATGAGAATCATAATTTAAGGAT
1 GAATATTAAAAAGTATGA-GGACCAATTTAGAATGAGAATCACAATTTAAGGAT
1630210 GTACGGTGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 2 0.05
60 42 0.95
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.31
Consensus pattern (60 bp):
GAATATTAAAAAGTATGAGGACCAATTTAGAATGAGAATCACAATTTAAGGATAAAATTA
Found at i:1633380 original size:13 final size:13
Alignment explanation
Indices: 1633362--1633386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1633352 ATGATAACTG
1633362 AAAAATAAAAATA
1 AAAAATAAAAATA
1633375 AAAAATAAAAAT
1 AAAAATAAAAAT
1633387 GATGACAGCT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:1640454 original size:3 final size:3
Alignment explanation
Indices: 1640441--1640517 Score: 63
Period size: 3 Copynumber: 26.0 Consensus size: 3
1640431 TTTAGGCCTG
*
1640441 TAA TAA T-A TAA TAA TTAA TAA TAA TAA -AA TAA TAA T-A TAG TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1640484 TAAA TAAA TAA TAA -AA TTA TTA TTA TAA TAA TAA
1 T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1640518 AAACAAATGG
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 8 0.12
3 46 0.72
4 10 0.16
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1640454 original size:8 final size:8
Alignment explanation
Indices: 1640441--1640516 Score: 63
Period size: 8 Copynumber: 10.0 Consensus size: 8
1640431 TTTAGGCCTG
1640441 TAATAATA
1 TAATAATA
1640449 TAATAAT-
1 TAATAATA
1640456 TAAT-A-A
1 TAATAATA
*
1640462 TAATAAAA
1 TAATAATA
1640470 TAATAATA
1 TAATAATA
*
1640478 TAGTAATA
1 TAATAATA
1640486 -AATAA-A
1 TAATAATA
*
1640492 TAATAAAA
1 TAATAATA
* *
1640500 TTATTATTA
1 -TAATAATA
1640509 TAATAATA
1 TAATAATA
1640517 AAAACAAATG
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
6 6 0.11
7 14 0.26
8 29 0.54
9 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (8 bp):
TAATAATA
Found at i:1640498 original size:11 final size:10
Alignment explanation
Indices: 1640441--1640497 Score: 60
Period size: 11 Copynumber: 5.3 Consensus size: 10
1640431 TTTAGGCCTG
1640441 TAATAATATAA
1 TAATAA-ATAA
*
1640452 TAATTAATAA
1 TAATAAATAA
1640462 TAATAAAATAA
1 TAAT-AAATAA
*
1640473 TAATATAGTAA
1 TAATA-AATAA
1640484 TAAATAAATAA
1 T-AATAAATAA
1640495 TAA
1 TAA
1640498 AATTATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 11 0.28
11 24 0.62
12 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
TAATAAATAA
Found at i:1640960 original size:123 final size:121
Alignment explanation
Indices: 1640809--1641292 Score: 521
Period size: 123 Copynumber: 3.9 Consensus size: 121
1640799 AACTCCATAG
* * *
1640809 GTGAT-GAATCAAGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
1 GTGATAGAGTCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
* * *
1640873 AAGTTCTTCTCATTATGAACTTTATCTGGAAATGTTGATGTTGATTTATCTCCTTCT
66 GAGTTCTTCTCATTATGAACTCT-TCTGGAAATGTTGATATTGATTTATCTCCTTCT
1640930 GTGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
1 GTGATAGAGTCAAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
** * *
1640995 TGAGTTCTTCTCATTATGAACTCCTT-TGGAAATACTAATCTTCAAAAGAGGGGTTGTTAAT-TC
65 TGAGTTCTTCTCATTATGAACT-CTTCTGGAAATGTTGATATT-----GA-----T-TT-ATCTC
1641058 AGCTTCATAT
117 --CTTC---T
* * **
1641068 GTGAT-GAATTAAGGC-AAGGTTGAACAAGTTCTCATCTCATTATGAACTTCTTCTTATTCTTCA
1 GTGATAGAGTCAA-GCAAAGGTTGAACAAGTTCT--TCTCATTATGAACTTCTTCTTCCTCTTCA
* * *
1641131 GATGAGTTCTTCTCATTATG-ACTCTTCTGGAAATGTTGATATTGATCTATCTTCTTAT
63 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATATTGATTTATCTCCTTCT
* * *
1641189 ATGATAGCGTCGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
1 GTGATAGAGTCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
*
1641254 GAGTTCTTCTCATTATGAACTTTATCTGGAAATGTTGAT
66 GAGTTCTTCTCATTATGAACTCT-TCTGGAAATGTTGAT
1641293 CAATCGAGTG
Statistics
Matches: 306, Mismatches: 28, Indels: 57
0.78 0.07 0.15
Matches are distributed among these distances:
120 47 0.15
121 16 0.05
122 55 0.18
123 69 0.23
124 4 0.01
125 2 0.01
126 2 0.01
127 3 0.01
132 3 0.01
133 4 0.01
134 2 0.01
135 4 0.01
136 20 0.07
137 20 0.07
138 55 0.18
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (121 bp):
GTGATAGAGTCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATATTGATTTATCTCCTTCT
Found at i:1641267 original size:258 final size:259
Alignment explanation
Indices: 1640795--1641274 Score: 761
Period size: 259 Copynumber: 1.9 Consensus size: 259
1640785 TTCTTCTTTC
1640795 ATTCAACTCCATAGGTGATGAATCAAGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTC
1 ATTCAACTCCATAGGTGATGAATCAAGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTC
* * * *
1640860 TTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTATCTGGAAATGTTGATGTTGATTTATCTC
66 TTACTCTTCAGATAAGTTCTTCTCATTATGAACTCTATCTGGAAATGTTGATATTGATCTATCTC
* *
1640925 CTTCTGTGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCT
131 CTTATATGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCT
1640990 TCAGATGAGTTCTTCTCATTATGAACTCCTTTGGAAATACTAATCTTCAAAAGAGGGGTTGTTA
196 TCAGATGAGTTCTTCTCATTATGAACTCCTTTGGAAATACTAATCTTCAAAAGAGGGGTTGTTA
* * * * *
1641054 ATTCAGCTTCATATGTGATGAATTAAGGC-AAGGTTGAACAAGTTCTCATCTCATTATGAACTTC
1 ATTCAACTCCATAGGTGATGAATCAA-GCTAAGGTCGAACAAGTTCT--TCTCATTATGAACTTC
* *
1641118 TTCTTATTCTTCAGATGAGTTCTTCTCATTATG-ACTCT-TCTGGAAATGTTGATATTGATCTAT
63 TTCTTACTCTTCAGATAAGTTCTTCTCATTATGAACTCTATCTGGAAATGTTGATATTGATCTAT
* * *
1641181 CTTCTTATATGATAGCGTCGAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
128 CTCCTTATATGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
1641245 TCTTCAGATGAGTTCTTCTCATTATGAACT
193 TCTTCAGATGAGTTCTTCTCATTATGAACT
1641275 TTATCTGGAA
Statistics
Matches: 202, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
258 71 0.35
259 79 0.39
260 6 0.03
261 46 0.23
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (259 bp):
ATTCAACTCCATAGGTGATGAATCAAGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTC
TTACTCTTCAGATAAGTTCTTCTCATTATGAACTCTATCTGGAAATGTTGATATTGATCTATCTC
CTTATATGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCT
TCAGATGAGTTCTTCTCATTATGAACTCCTTTGGAAATACTAATCTTCAAAAGAGGGGTTGTTA
Found at i:1642358 original size:18 final size:19
Alignment explanation
Indices: 1642325--1642364 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1642315 ATAAAAGAAC
1642325 AAATTGAATTTCAAAA-AT
1 AAATTGAATTTCAAAAGAT
1642343 AAATTGAA-TTCGAAAAGAT
1 AAATTGAATTTC-AAAAGAT
1642362 AAA
1 AAA
1642365 CTTGGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.15
18 12 0.60
19 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (19 bp):
AAATTGAATTTCAAAAGAT
Found at i:1642737 original size:17 final size:17
Alignment explanation
Indices: 1642702--1642747 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
1642692 CTTGACCCTC
1642702 TTTTTTCTATTATTATTT
1 TTTTTTCT-TTATTATTT
* *
1642720 TTTTTTCTTTTTTCTTT
1 TTTTTTCTTTATTATTT
1642737 TTTTTTCTTTA
1 TTTTTTCTTTA
1642748 AGCATAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTTATTATTT
Found at i:1650645 original size:18 final size:19
Alignment explanation
Indices: 1650605--1650652 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1650595 AGAGAAGAAA
*
1650605 CATCAATGCATAAGGAGTG
1 CATCGATGCATAAGGAGTG
1650624 CATCGATGCATAAGGA-TG
1 CATCGATGCATAAGGAGTG
1650642 CATCGATGCAT
1 CATCGATGCAT
1650653 CCCTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (19 bp):
CATCGATGCATAAGGAGTG
Found at i:1656864 original size:26 final size:26
Alignment explanation
Indices: 1656802--1656865 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
1656792 GAAATTTAAA
1656802 TATTAAAT-TAAATATAAATAAATAG
1 TATTAAATATAAATATAAATAAATAG
*
1656827 TGACTAAA-ATAAATA-AAA-AATTATAG
1 T-ATTAAATATAAATATAAATAA--ATAG
1656853 TATTAAATATAAA
1 TATTAAATATAAA
1656866 AAAGTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 2 0.06
25 9 0.28
26 21 0.66
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
TATTAAATATAAATATAAATAAATAG
Found at i:1658190 original size:3 final size:3
Alignment explanation
Indices: 1658182--1658290 Score: 154
Period size: 3 Copynumber: 37.0 Consensus size: 3
1658172 TTTGGGCCTG
1658182 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
1658231 TAC TAA -AA TAA TAA TAA -AA TAA TAA TAA TAG T-A TAAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
1658273 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1658291 AAACAAATGG
Statistics
Matches: 96, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
2 7 0.07
3 84 0.88
4 5 0.05
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1661053 original size:16 final size:16
Alignment explanation
Indices: 1661029--1661059 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1661019 CTTATTGTTT
*
1661029 ATTTTATTTAAAAATA
1 ATTTAATTTAAAAATA
1661045 ATTTAATTTAAAAAT
1 ATTTAATTTAAAAAT
1661060 TTTAATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAATTTAAAAATA
Found at i:1661387 original size:2 final size:2
Alignment explanation
Indices: 1661380--1661412 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1661370 GACGGAATTG
1661380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1661413 AACAAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1661755 original size:9 final size:10
Alignment explanation
Indices: 1661728--1661757 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1661718 GATTCGGTAA
1661728 TTCTTTTCTTT
1 TTCTTTT-TTT
1661739 TTCTTTTTTT
1 TTCTTTTTTT
1661749 TTCTTTTTT
1 TTCTTTTTT
1661758 ATTTGACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:1666637 original size:5 final size:5
Alignment explanation
Indices: 1666627--1666653 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1666617 AAAAATGAAA
1666627 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1666654 GAAAGAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1668377 original size:11 final size:11
Alignment explanation
Indices: 1668361--1668385 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1668351 TGGTCTCTTG
1668361 ACAATTTTGGA
1 ACAATTTTGGA
1668372 ACAATTTTGGA
1 ACAATTTTGGA
1668383 ACA
1 ACA
1668386 TATGAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (11 bp):
ACAATTTTGGA
Found at i:1669922 original size:32 final size:32
Alignment explanation
Indices: 1669866--1669928 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1669856 GGTTGCTCCA
* *
1669866 CCCACATCTGATCCGAAAGCTACTGAAATTAT
1 CCCACAGCTGAGCCGAAAGCTACTGAAATTAT
1669898 CCCACAGCTGAGCCGACAAG-TACTGAAATTA
1 CCCACAGCTGAGCCGA-AAGCTACTGAAATTA
1669929 ACTCACATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.21
Consensus pattern (32 bp):
CCCACAGCTGAGCCGAAAGCTACTGAAATTAT
Found at i:1680210 original size:10 final size:9
Alignment explanation
Indices: 1680189--1680230 Score: 66
Period size: 10 Copynumber: 4.4 Consensus size: 9
1680179 GGCTGAAAAT
1680189 CGGTTTGAC
1 CGGTTTGAC
1680198 CGGTTTCGAC
1 CGGTTT-GAC
1680208 CGGTTTGAAC
1 CGGTTTG-AC
1680218 CGGTTTGAC
1 CGGTTTGAC
1680227 CGGT
1 CGGT
1680231 CTGAACCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 13 0.42
10 18 0.58
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:1680213 original size:19 final size:19
Alignment explanation
Indices: 1680189--1680238 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
1680179 GGCTGAAAAT
1680189 CGGTTTG-ACCGGTTTCGAC
1 CGGTTTGAACCGGTTT-GAC
1680208 CGGTTTGAACCGGTTTGAC
1 CGGTTTGAACCGGTTTGAC
*
1680227 CGGTCTGAACCG
1 CGGTTTGAACCG
1680239 ATCCGACCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.14, C:0.26, G:0.32, T:0.28
Consensus pattern (19 bp):
CGGTTTGAACCGGTTTGAC
Found at i:1680238 original size:10 final size:10
Alignment explanation
Indices: 1680189--1680238 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
1680179 GGCTGAAAAT
1680189 CGGTTTG-AC
1 CGGTTTGAAC
1680198 CGGTTTCG-AC
1 CGGTTT-GAAC
1680208 CGGTTTGAAC
1 CGGTTTGAAC
1680218 CGGTTTG-AC
1 CGGTTTGAAC
*
1680227 CGGTCTGAAC
1 CGGTTTGAAC
1680237 CG
1 CG
1680239 ATCCGACCCG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 15 0.41
10 22 0.59
ACGTcount: A:0.14, C:0.26, G:0.32, T:0.28
Consensus pattern (10 bp):
CGGTTTGAAC
Found at i:1680246 original size:19 final size:19
Alignment explanation
Indices: 1680204--1680246 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1680194 TGACCGGTTT
* * *
1680204 CGACCGGTTTGAACCGGTT
1 CGACCGGTCTGAACCGATC
*
1680223 TGACCGGTCTGAACCGATC
1 CGACCGGTCTGAACCGATC
1680242 CGACC
1 CGACC
1680247 CGACCCGACC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.19, C:0.33, G:0.28, T:0.21
Consensus pattern (19 bp):
CGACCGGTCTGAACCGATC
Found at i:1680260 original size:14 final size:15
Alignment explanation
Indices: 1680236--1680265 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1680226 CCGGTCTGAA
1680236 CCGATCCGACCCGAC
1 CCGATCCGACCCGAC
1680251 CCGA-CCGACCCGAC
1 CCGATCCGACCCGAC
1680265 C
1 C
1680266 GTTGACCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.20, C:0.57, G:0.20, T:0.03
Consensus pattern (15 bp):
CCGATCCGACCCGAC
Found at i:1687566 original size:13 final size:13
Alignment explanation
Indices: 1687548--1687572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1687538 CCGGTCTGAC
1687548 CCGACCCGACCGA
1 CCGACCCGACCGA
1687561 CCGACCCGACCG
1 CCGACCCGACCG
1687573 TTGACCGTTG
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:0.20, C:0.56, G:0.24, T:0.00
Consensus pattern (13 bp):
CCGACCCGACCGA
Found at i:1687580 original size:7 final size:7
Alignment explanation
Indices: 1687568--1687592 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1687558 CGACCGACCC
1687568 GACCGTT
1 GACCGTT
1687575 GACCGTT
1 GACCGTT
1687582 GACCGTT
1 GACCGTT
1687589 GACC
1 GACC
1687593 TCCTTTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:1691914 original size:15 final size:16
Alignment explanation
Indices: 1691891--1691921 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1691881 TTATCTTTGG
1691891 ATTGCTTTTCTTCTCC
1 ATTGCTTTTCTTCTCC
1691907 ATTG-TTTTCTTCTCC
1 ATTGCTTTTCTTCTCC
1691922 TCTCTTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.06, C:0.29, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTGCTTTTCTTCTCC
Found at i:1706041 original size:30 final size:30
Alignment explanation
Indices: 1706005--1706090 Score: 118
Period size: 30 Copynumber: 2.9 Consensus size: 30
1705995 AGAGTTTCAC
1706005 TCAAATTCCCATCAATACCCTCATTCTCCT
1 TCAAATTCCCATCAATACCCTCATTCTCCT
* *
1706035 TCAAATTCCCATCAATAACCTCATCCTCCT
1 TCAAATTCCCATCAATACCCTCATTCTCCT
* * * *
1706065 TCAAATCCCCAGCAAAACCTTCATTC
1 TCAAATTCCCATCAATACCCTCATTC
1706091 AGATCAACAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.30, C:0.40, G:0.01, T:0.29
Consensus pattern (30 bp):
TCAAATTCCCATCAATACCCTCATTCTCCT
Found at i:1707709 original size:78 final size:79
Alignment explanation
Indices: 1707612--1707782 Score: 186
Period size: 79 Copynumber: 2.2 Consensus size: 79
1707602 ACTTAGTCGT
* * * *
1707612 GTTTAGATGATCAAGTCCTCTAC-ACA-AAAAGTCAAATTGAGGATGGCATTACTCATTCTCTTC
1 GTTTAGATGATCGACTCCTCGACGACAGAAAA-TCAAATTGAGGATGACATTACTCATTCTCTT-
1707675 AAAG-CAACTAATCAA
64 AAAGACAACTAATCAA
* ** * * * * *
1707690 GTTTGGATGATCGACTCCTCGACGTGAGAAAATTAAATTGTGGATGATATTGCTCATTCTCTTGA
1 GTTTAGATGATCGACTCCTCGACGACAGAAAATCAAATTGAGGATGACATTACTCATTCTCTTAA
1707755 AGACAACTAATCAA
66 AGACAACTAATCAA
*
1707769 TTTTAGATGATCGA
1 GTTTAGATGATCGA
1707783 TTATTCGGTG
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
78 22 0.29
79 50 0.66
80 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (79 bp):
GTTTAGATGATCGACTCCTCGACGACAGAAAATCAAATTGAGGATGACATTACTCATTCTCTTAA
AGACAACTAATCAA
Found at i:1708256 original size:2 final size:2
Alignment explanation
Indices: 1708249--1708287 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1708239 AATTGGGATA
1708249 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
1708288 GCGCTTTTAT
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:1713873 original size:19 final size:19
Alignment explanation
Indices: 1713849--1713898 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1713839 AATACGTATT
*
1713849 TATGAACAATATTATACGG
1 TATGAACAATACTATACGG
* *
1713868 TATGAACAGTACTATATGG
1 TATGAACAATACTATACGG
1713887 TATGAACAATAC
1 TATGAACAATAC
1713899 CGTGAACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (19 bp):
TATGAACAATACTATACGG
Found at i:1714973 original size:49 final size:49
Alignment explanation
Indices: 1714901--1715003 Score: 197
Period size: 49 Copynumber: 2.1 Consensus size: 49
1714891 TTATACATTT
*
1714901 CATATCACTTGTTCTTTCTCTTCTGTCACATACCACATGTATGTGTAAC
1 CATATCACTTGTTCTTTCTCTTCTGTCACATACCACATGTATGTATAAC
1714950 CATATCACTTGTTCTTTCTCTTCTGTCACATACCACATGTATGTATAAC
1 CATATCACTTGTTCTTTCTCTTCTGTCACATACCACATGTATGTATAAC
1714999 CATAT
1 CATAT
1715004 ATCTCATATC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.41
Consensus pattern (49 bp):
CATATCACTTGTTCTTTCTCTTCTGTCACATACCACATGTATGTATAAC
Found at i:1716621 original size:29 final size:28
Alignment explanation
Indices: 1716532--1716710 Score: 137
Period size: 28 Copynumber: 6.4 Consensus size: 28
1716522 CATTTTACAC
* * * * *
1716532 AAATAGTACCTTTTTAAAATAATTACCA
1 AAATAGCACCATTTTGAATTAATTCCCA
*
1716560 AAATAGCACC-TTTTCGAATTAATTTCCA
1 AAATAGCACCATTTT-GAATTAATTCCCA
1716588 AAATAGCACCAATTTTGAATTAATTCCCA
1 AAATAGCACC-ATTTTGAATTAATTCCCA
* * ** * *
1716617 GAATATCACTTTTTTGAA-AAATTACCA
1 AAATAGCACCATTTTGAATTAATTCCCA
* *
1716644 AAATAGCACCATTTCGAATTAATTCACA
1 AAATAGCACCATTTTGAATTAATTCCCA
* ** ** *
1716672 GAATAGCACCAAAATCAAATAAATTCCCA
1 AAATAGCACC-ATTTTGAATTAATTCCCA
1716701 AAATAGCACC
1 AAATAGCACC
1716711 GGTAAACGGG
Statistics
Matches: 120, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
27 24 0.20
28 51 0.43
29 41 0.34
30 4 0.03
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.30
Consensus pattern (28 bp):
AAATAGCACCATTTTGAATTAATTCCCA
Found at i:1716682 original size:28 final size:28
Alignment explanation
Indices: 1716558--1716710 Score: 114
Period size: 29 Copynumber: 5.4 Consensus size: 28
1716548 AAATAATTAC
*
1716558 CAAAATAGCACCTTTTCGAATTAATTTC-
1 CAAAATAGCACCATTTCGAATTAA-TTCA
* *
1716586 CAAAATAGCACCAATTTTGAATTAATTCC
1 CAAAATAGCACC-ATTTCGAATTAATTCA
* * ** * *
1716615 CAGAATATCACTTTTTTGAA-AAATT-A
1 CAAAATAGCACCATTTCGAATTAATTCA
1716641 CCAAAATAGCACCATTTCGAATTAATTCA
1 -CAAAATAGCACCATTTCGAATTAATTCA
* ** * * *
1716670 CAGAATAGCACCAAAATCAAATAAATTCC
1 CAAAATAGCACC-ATTTCGAATTAATTCA
1716699 CAAAATAGCACC
1 CAAAATAGCACC
1716711 GGTAAACGGG
Statistics
Matches: 98, Mismatches: 21, Indels: 11
0.75 0.16 0.08
Matches are distributed among these distances:
27 19 0.19
28 37 0.38
29 42 0.43
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (28 bp):
CAAAATAGCACCATTTCGAATTAATTCA
Found at i:1716697 original size:84 final size:85
Alignment explanation
Indices: 1716542--1716705 Score: 224
Period size: 84 Copynumber: 1.9 Consensus size: 85
1716532 AAATAGTACC
* ** **
1716542 TTTTTAAAATAATTACCAAAATAGCACCTTTTCGAATTAATTTCCAAAATAGCACCAATTTTGAA
1 TTTTTAAAATAATTACCAAAATAGCACCATTTCGAATTAATTTCCAAAATAGCACCAAAATCAAA
* *
1716607 TTAATTCCCAGAATATCACT
66 TAAATTCCCAAAATATCACT
* *
1716627 TTTTTGAAA-AATTACCAAAATAGCACCATTTCGAATTAA-TTCACAGAATAGCACCAAAATCAA
1 TTTTTAAAATAATTACCAAAATAGCACCATTTCGAATTAATTTC-CAAAATAGCACCAAAATCAA
1716690 ATAAATTCCCAAAATA
65 ATAAATTCCCAAAATA
1716706 GCACCGGTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
83 3 0.04
84 58 0.84
85 8 0.12
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (85 bp):
TTTTTAAAATAATTACCAAAATAGCACCATTTCGAATTAATTTCCAAAATAGCACCAAAATCAAA
TAAATTCCCAAAATATCACT
Found at i:1716743 original size:18 final size:18
Alignment explanation
Indices: 1716720--1716754 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1716710 CGGTAAACGG
1716720 GTCGGGTCAACGGGTCGA
1 GTCGGGTCAACGGGTCGA
*
1716738 GTCGGGTTAACGGGTCG
1 GTCGGGTCAACGGGTCG
1716755 GATCGTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.46, T:0.20
Consensus pattern (18 bp):
GTCGGGTCAACGGGTCGA
Found at i:1723736 original size:29 final size:29
Alignment explanation
Indices: 1723700--1723847 Score: 115
Period size: 29 Copynumber: 5.2 Consensus size: 29
1723690 CATTTTACAC
*
1723700 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
* * *
1723729 AAATAGCACCCTTTTCGAATTAATTTCCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
** * *
1723758 AAATAGCACCAATTTCGAATTAATT-CTCA
1 AAATAGCACCCTTTTCAAAATAATTAC-CA
* * *
1723787 GAATATCA--CTTTTGAAAA-AATTACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
* * * *
1723813 AAATAACACCCATTTCAAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
*
1723842 GAATAG
1 AAATAG
1723848 TACCAAAATC
Statistics
Matches: 93, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
26 12 0.13
27 6 0.06
28 8 0.09
29 67 0.72
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAAATAATTACCA
Found at i:1723867 original size:84 final size:85
Alignment explanation
Indices: 1723710--1723875 Score: 226
Period size: 84 Copynumber: 2.0 Consensus size: 85
1723700 AAATAGCACC
* * * * * **
1723710 CTTTTTAAAATAATTACCAAAATAGCACCCTTTTCGAATTAATTTCCAAAATAGCACCAATTTCG
1 CTTTTGAAAATAATTACCAAAATAACACCCATTTCAAATTAATTCCCAAAATAGCACCAAAATCG
* *
1723775 AATTAATTCTCAGAATATCA
66 AATAAATTCCCAGAATATCA
* *
1723795 CTTTTGAAAA-AATTACCAAAATAACACCCATTTCAAATTAATTCCCAGAATAGTACCAAAATCG
1 CTTTTGAAAATAATTACCAAAATAACACCCATTTCAAATTAATTCCCAAAATAGCACCAAAATCG
1723859 AATAAATTCCCAGAATA
66 AATAAATTCCCAGAATA
1723876 ACACCGGTCA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
84 61 0.87
85 9 0.13
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.30
Consensus pattern (85 bp):
CTTTTGAAAATAATTACCAAAATAACACCCATTTCAAATTAATTCCCAAAATAGCACCAAAATCG
AATAAATTCCCAGAATATCA
Found at i:1726891 original size:7 final size:7
Alignment explanation
Indices: 1726881--1726909 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1726871 AATTTATATT
1726881 TTTTTTA
1 TTTTTTA
1726888 TTTTTTA
1 TTTTTTA
1726895 -TTTTTA
1 TTTTTTA
1726901 TTTTTTA
1 TTTTTTA
1726908 TT
1 TT
1726910 AATGGAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:1726900 original size:13 final size:13
Alignment explanation
Indices: 1726882--1726909 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1726872 ATTTATATTT
1726882 TTTTTATTTTTTA
1 TTTTTATTTTTTA
1726895 TTTTTATTTTTTA
1 TTTTTATTTTTTA
1726908 TT
1 TT
1726910 AATGGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:1727169 original size:75 final size:69
Alignment explanation
Indices: 1727076--1727232 Score: 210
Period size: 69 Copynumber: 2.2 Consensus size: 69
1727066 ATCGAATAAA
*
1727076 TAATTATAATTTACAA-TTTTTATATTTTATATTTTAAAATTTTAATT-GAATAAATAATTATTG
1 TAATTATAATTTACAATTTTTTATATTTT-T-TATT----TTTT-ATTCGAATAAATAATTATTG
1727139 ACTTTTATTTAT
59 A-TTTTATTTAT
*
1727151 TAATTATAATTTATAATTTTTTATATTTTTTATTTTTTATTCGAATAAATAATTATTGATTTTAT
1 TAATTATAATTTACAATTTTTTATATTTTTTATTTTTTATTCGAATAAATAATTATTGATTTTAT
1727216 TTAT
66 TTAT
1727220 TAATTATAATTTA
1 TAATTATAATTTA
1727233 ATAGATATAT
Statistics
Matches: 78, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
69 26 0.33
70 21 0.27
74 3 0.04
75 16 0.21
76 12 0.15
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (69 bp):
TAATTATAATTTACAATTTTTTATATTTTTTATTTTTTATTCGAATAAATAATTATTGATTTTAT
TTAT
Found at i:1727215 original size:69 final size:69
Alignment explanation
Indices: 1727100--1727232 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 69
1727090 AATTTTTATA
1727100 TTTTATATTTTAAAATTTTAATTGAATAAATAATTATTGACTTTTATTTATTAATTATAATTTAT
1 TTTTATATTTTAAAATTTTAATTGAATAAATAATTATTGACTTTTATTTATTAATTATAATTTAT
1727165 AATT
66 AATT
** * *
1727169 TTTTATATTTTTTATTTTTTATTCGAATAAATAATTATTGA-TTTTATTTATTAATTATAATTTA
1 TTTTATATTTTAAAATTTTAATT-GAATAAATAATTATTGACTTTTATTTATTAATTATAATTTA
1727233 ATAGATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 42 0.71
70 17 0.29
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (69 bp):
TTTTATATTTTAAAATTTTAATTGAATAAATAATTATTGACTTTTATTTATTAATTATAATTTAT
AATT
Found at i:1727297 original size:27 final size:30
Alignment explanation
Indices: 1727267--1727334 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 30
1727257 TAATTATCAT
*
1727267 ATAAAAATTAAAG-ATTATTT-TT-TATTA
1 ATAAAAATTAAAGAATTATTTCTTCCATTA
*
1727294 AT-AAAATTTAAGAATTATTTCTTCCATTA
1 ATAAAAATTAAAGAATTATTTCTTCCATTA
1727323 ATAAAAATTAAA
1 ATAAAAATTAAA
1727335 AACATTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.26
27 9 0.26
28 2 0.06
29 6 0.18
30 8 0.24
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAAAAATTAAAGAATTATTTCTTCCATTA
Found at i:1727306 original size:26 final size:29
Alignment explanation
Indices: 1727270--1727333 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
1727260 TTATCATATA
* *
1727270 AAAATTAAAG-ATTATTT-TT-TATTAAT
1 AAAATTTAAGAATTATTTCTTCCATTAAT
1727296 AAAATTTAAGAATTATTTCTTCCATTAAT
1 AAAATTTAAGAATTATTTCTTCCATTAAT
*
1727325 AAAAATTAA
1 AAAATTTAA
1727334 AAACATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.28
27 7 0.22
28 2 0.06
29 14 0.44
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (29 bp):
AAAATTTAAGAATTATTTCTTCCATTAAT
Found at i:1728640 original size:11 final size:11
Alignment explanation
Indices: 1728624--1728666 Score: 86
Period size: 11 Copynumber: 3.9 Consensus size: 11
1728614 TGCTATTGTC
1728624 AATTTCTATTA
1 AATTTCTATTA
1728635 AATTTCTATTA
1 AATTTCTATTA
1728646 AATTTCTATTA
1 AATTTCTATTA
1728657 AATTTCTATT
1 AATTTCTATT
1728667 GTTTCATGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTCTATTA
Found at i:1745563 original size:60 final size:60
Alignment explanation
Indices: 1745470--1745582 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
1745460 TATGATTATA
*
1745470 ATTTTAAATTAGTTCCTAAATTTTTAAATATTTC-ATTTTCATCCCTAAACTATAACTATC
1 ATTTTAAATTAGTTCCTAAATTTTTAAATATTTCAATTTT-ATCCCCAAACTATAACTATC
1745530 ATTTTAAATTAG-TCCTCAAACTTTTT-AATATTTCAATTTTATCCCCAAACTAT
1 ATTTTAAATTAGTTCCT-AAA-TTTTTAAATATTTCAATTTTATCCCCAAACTAT
1745583 GATTTTTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
59 4 0.08
60 35 0.71
61 10 0.20
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (60 bp):
ATTTTAAATTAGTTCCTAAATTTTTAAATATTTCAATTTTATCCCCAAACTATAACTATC
Found at i:1748540 original size:21 final size:20
Alignment explanation
Indices: 1748511--1748604 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 20
1748501 ATTCTGACTA
1748511 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTT-CCAAAT
* *
1748532 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTCCAAAT
* **
1748553 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTCCAAAT
* *
1748573 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTCCA-AAT
*
1748594 TCGCAATGCGA
1 TCGCATTGCGA
1748605 ATACGTAAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
20 20 0.34
21 36 0.61
22 3 0.05
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTCCAAAT
Found at i:1748543 original size:41 final size:41
Alignment explanation
Indices: 1748498--1748604 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 41
1748488 GATTCGCAAC
*
1748498 GCGATTCTGACT-A-TCGCATTGCGATTTCCCAAATTCGCGTT
1 GCGATT-TGACTAATTCGCATTGCGATTT-ACAAATTCGCGTT
** **
1748539 GCGATTTTCCTAATTCGCATTGCGATTTACGTATTCGCGTT
1 GCGATTTGACTAATTCGCATTGCGATTTACAAATTCGCGTT
* *
1748580 GCGATTT-TCATAATTCGCAATGCGA
1 GCGATTTGAC-TAATTCGCATTGCGA
1748605 ATACGTAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 4 0.07
41 38 0.68
42 14 0.25
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (41 bp):
GCGATTTGACTAATTCGCATTGCGATTTACAAATTCGCGTT
Found at i:1748619 original size:20 final size:20
Alignment explanation
Indices: 1748594--1748687 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
1748584 TTTTCATAAT
1748594 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1748614 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1748634 TCACAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1748655 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1748675 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1748688 CTGACTATCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1748625 original size:41 final size:41
Alignment explanation
Indices: 1748539--1748626 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
1748529 AATTCGCGTT
* * * * ***
1748539 GCGATTTTCCTAATTCGCATTGCGATTTACGTATTCGCGTT
1 GCGATTTTCATAATTCGCAATGCGATATACGTAATCGCAAC
1748580 GCGATTTTCATAATTCGCAATGCGA-ATACGTAAATCGCAAC
1 GCGATTTTCATAATTCGCAATGCGATATACGT-AATCGCAAC
1748621 GCGATT
1 GCGATT
1748627 AAGTAAATCA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 5 0.13
41 34 0.87
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (41 bp):
GCGATTTTCATAATTCGCAATGCGATATACGTAATCGCAAC
Found at i:1748656 original size:41 final size:41
Alignment explanation
Indices: 1748597--1748687 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
1748587 TCATAATTCG
* *
1748597 CAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAATCA
1 CAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATCA
* * * *
1748637 CAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCG
1 CAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATCA
1748678 CAATGCGAAT
1 CAATGCGAAT
1748688 CTGACTATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 9 0.20
41 35 0.80
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.20
Consensus pattern (41 bp):
CAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATCA
Found at i:1749276 original size:14 final size:14
Alignment explanation
Indices: 1749257--1749293 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1749247 GGAAATGACT
*
1749257 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
*
1749271 ATCGCAACGAGATA
1 ATCGCAACGAGAGA
1749285 ATCGCAACG
1 ATCGCAACG
1749294 CGAAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1749355 original size:33 final size:33
Alignment explanation
Indices: 1749313--1749412 Score: 110
Period size: 33 Copynumber: 2.8 Consensus size: 33
1749303 AATCGCATTA
1749313 CGATTCTCTCGTTGCGATTTTCATTTCGTGTTG
1 CGATTCTCTCGTTGCGATTTTCATTTCGTGTTG
**
1749346 CGATTCTCTCGTTGCGATAGTCATTTCCGTGTTG
1 CGATTCTCTCGTTGCGATTTTCATTT-CGTGTTG
*
1749380 CTATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 C------GATTCTCTCGTTGCGATTTTCATTTC
1749413 AACCAAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
33 24 0.44
34 8 0.15
39 1 0.02
40 22 0.40
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
CGATTCTCTCGTTGCGATTTTCATTTCGTGTTG
Found at i:1749389 original size:20 final size:21
Alignment explanation
Indices: 1749349--1749412 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 21
1749339 CGTGTTGCGA
**
1749349 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1749370 TTC-CGT-GTTGCTATTTTCA-
1 TTCTC-TCGTTGCGATTTTCAT
1749389 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1749410 TTC
1 TTC
1749413 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.11
20 24 0.69
21 7 0.20
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1751249 original size:90 final size:92
Alignment explanation
Indices: 1751096--1751367 Score: 380
Period size: 94 Copynumber: 3.0 Consensus size: 92
1751086 CTTAGTGAAT
* * *
1751096 TTATTCTGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGTATTTGTC
1 TTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTC
1751157 TTTTGTTTTGTCTTTTGGTTGAAA-T-A
66 -TTTGTTTTGTCTTTTGGTTGAAAGTAA
1751183 -TATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTC
1 TTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTC
1751247 TTTGTTTTGTCTTTTGGTTGAAAGTAAA
66 TTTGTTTTGTCTTTTGGTTGAAAGT-AA
* * * * * *
1751275 TTTGTTCGTTTGCTACCAATTCTACTAAACTGTGTATTCTTTAATACTTTGAAGTTAGTATTTGT
1 -TTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGT
1751340 CTTTGTTTTGTCTTTTGGTTG-AAGTAA
65 CTTTGTTTTGTCTTTTGGTTGAAAGTAA
1751367 T
1 T
1751368 GCAATCCATT
Statistics
Matches: 167, Mismatches: 9, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
86 26 0.16
88 3 0.02
89 25 0.15
90 27 0.16
91 1 0.01
92 3 0.02
93 4 0.02
94 78 0.47
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (92 bp):
TTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTC
TTTGTTTTGTCTTTTGGTTGAAAGTAA
Found at i:1751482 original size:20 final size:19
Alignment explanation
Indices: 1751455--1751516 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
1751445 CCTTTTGGTT
1751455 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1751474 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
*
1751494 GAAACGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
1751513 GAAA
1 GAAA
1751517 CTATAATCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
19 21 0.54
20 18 0.46
ACGTcount: A:0.52, C:0.18, G:0.23, T:0.08
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1751524 original size:19 final size:19
Alignment explanation
Indices: 1751461--1751526 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
1751451 GGTTGAAATG
1751461 AAAATCGCAACGAGAGAA-T
1 AAAATCGCAACGAGA-AACT
* *
1751480 GAAAATCGCAACGCGAAACG
1 -AAAATCGCAACGAGAAACT
1751500 AAAATCGCAACGAGAAACT
1 AAAATCGCAACGAGAAACT
*
1751519 ATAATCGC
1 AAAATCGC
1751527 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
19 26 0.65
20 14 0.35
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGAGAAACT
Found at i:1753498 original size:14 final size:14
Alignment explanation
Indices: 1753479--1753514 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1753469 ATTGTTTAAT
1753479 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1753493 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1753507 TGATTTGT
1 TGATTTGT
1753515 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Done.