Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 12 of 16
Found at i:1523339 original size:40 final size:39
Alignment explanation
Indices: 1523263--1523340 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
1523253 GGTAAAAAGA
* *
1523263 CATAATGTATCGATACATTACAGAATATATCGATACATT
1 CATAATGTATCGATACATTACAAAATATATCAATACATT
* *
1523302 CATACATGTATCGATATATTGA-AAAATGTATCAATACAT
1 CATA-ATGTATCGATACATT-ACAAAATATATCAATACAT
1523341 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.12
40 28 0.85
41 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTACAAAATATATCAATACATT
Found at i:1523814 original size:11 final size:11
Alignment explanation
Indices: 1523800--1523825 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1523790 CATCAAATAA
1523800 ATAAAATCAAT
1 ATAAAATCAAT
1523811 ATAAAATCAAT
1 ATAAAATCAAT
1523822 ATAA
1 ATAA
1523826 GCCAATACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAATCAAT
Found at i:1524051 original size:16 final size:16
Alignment explanation
Indices: 1524030--1524064 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1524020 ATTTTCTTAT
* *
1524030 TAATAATTAATTATTA
1 TAATAATAAAATATTA
1524046 TAATAATAAAATATTA
1 TAATAATAAAATATTA
1524062 TAA
1 TAA
1524065 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATAAAATATTA
Found at i:1527722 original size:49 final size:50
Alignment explanation
Indices: 1527647--1527829 Score: 242
Period size: 50 Copynumber: 3.7 Consensus size: 50
1527637 GTTGCCATTG
** *
1527647 TTGACAATAGAGAGAGGTGATCGTAATTGTTGACGATTATTCACCAACCT
1 TTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACCT
* *
1527697 TT-ACAATAGAGAGAGATGGCCGTAATTGTTGACGATTCTTTACCAACCT
1 TTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACCT
* * * * * *
1527746 TTGATAATAAAGAGAGGTGGTCATAATTGTTGATGATTCTTCATCAACCT
1 TTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACCT
* *
1527796 TTGATAATAGAAAGAGGTGGCCGTAATTGTTGAC
1 TTGACAATAGAGAGAGGTGGCCGTAATTGTTGAC
1527830 TCTAAGCAAC
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
49 44 0.39
50 70 0.61
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (50 bp):
TTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACCT
Found at i:1528360 original size:32 final size:33
Alignment explanation
Indices: 1528317--1528389 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 33
1528307 ATTTATATTA
* *
1528317 TTTAAGATTTAAATTTTTTCGAA-TTCGAATCAT
1 TTTAAGATTTAAATTTTTT-AAAGTTCAAATCAT
1528350 TTTAAG-TTTAAATTTTTTAAAGTTCAAATCAT
1 TTTAAGATTTAAATTTTTTAAAGTTCAAATCAT
1528382 TTT-AGATT
1 TTTAAGATT
1528390 CAGGTTACGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 4 0.11
32 26 0.72
33 6 0.17
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (33 bp):
TTTAAGATTTAAATTTTTTAAAGTTCAAATCAT
Found at i:1529345 original size:12 final size:11
Alignment explanation
Indices: 1529323--1529347 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1529313 AAAATCAAAT
1529323 ATTTTAAAAAA
1 ATTTTAAAAAA
1529334 ATTTTAAAAAA
1 ATTTTAAAAAA
1529345 ATT
1 ATT
1529348 ATTTTCAAAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:1530384 original size:29 final size:30
Alignment explanation
Indices: 1530322--1530377 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 30
1530312 TATTTTTATG
1530322 ATAAAAAATTAAAAATTAATTAAAATATAA
1 ATAAAAAATTAAAAATTAATTAAAATATAA
* *
1530352 ATAAAAAA-TAAAATTTAATTTAAATA
1 ATAAAAAATTAAAAATTAATTAAAATA
1530378 ATTATAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (30 bp):
ATAAAAAATTAAAAATTAATTAAAATATAA
Found at i:1530482 original size:15 final size:16
Alignment explanation
Indices: 1530452--1530485 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1530442 AAATTAAACT
*
1530452 AAATTCAATACAAATC
1 AAATTAAATACAAATC
1530468 AAATTAAAT-CAAATC
1 AAATTAAATACAAATC
1530483 AAA
1 AAA
1530486 AATCACAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTAAATACAAATC
Found at i:1530638 original size:6 final size:6
Alignment explanation
Indices: 1530627--1530666 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1530617 GGAAATTCGA
* * *
1530627 TTTTGC TTTTGC TTTTAC TTTTTC TTTTAC TTTTGC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
1530667 TGCCTCGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.72
Consensus pattern (6 bp):
TTTTGC
Found at i:1530647 original size:12 final size:12
Alignment explanation
Indices: 1530627--1530666 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1530617 GGAAATTCGA
*
1530627 TTTTGCTTTTGC
1 TTTTACTTTTGC
*
1530639 TTTTACTTTTTC
1 TTTTACTTTTGC
1530651 TTTTACTTTTGC
1 TTTTACTTTTGC
1530663 TTTT
1 TTTT
1530667 TGCCTCGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTACTTTTGC
Found at i:1530737 original size:22 final size:22
Alignment explanation
Indices: 1530712--1530780 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1530702 TTATTTATAA
1530712 ATATAATTTTTATAATTAATAG
1 ATATAATTTTTATAATTAATAG
*
1530734 ATAT-A-TTTTACTCA-T-AT-G
1 ATATAATTTTTA-TAATTAATAG
*
1530752 AATAATAATTTTTATAATTAATAA
1 -AT-ATAATTTTTATAATTAATAG
1530776 ATATA
1 ATATA
1530781 TCTTACAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 16
0.65 0.05 0.29
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 8 0.22
21 6 0.17
22 13 0.36
23 4 0.11
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (22 bp):
ATATAATTTTTATAATTAATAG
Found at i:1530770 original size:42 final size:42
Alignment explanation
Indices: 1530714--1530798 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
1530704 ATTTATAAAT
* * **
1530714 ATAATTTTTATAATTAATAGATATATTTTACTCATATGAATA
1 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1530756 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1530798 A
1 A
1530799 AAATAGTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (42 bp):
ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
Found at i:1537692 original size:21 final size:21
Alignment explanation
Indices: 1537649--1537693 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1537639 AATTTCAACT
* *
1537649 GGAAACAAGAGCCAACATTCA
1 GGAAACAAGAGACAACATCCA
1537670 GGAAACAAG-GACAAGCATCCA
1 GGAAACAAGAGACAA-CATCCA
1537691 GGA
1 GGA
1537694 TTTAGGCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.47, C:0.22, G:0.24, T:0.07
Consensus pattern (21 bp):
GGAAACAAGAGACAACATCCA
Found at i:1544936 original size:109 final size:109
Alignment explanation
Indices: 1544740--1544958 Score: 411
Period size: 109 Copynumber: 2.0 Consensus size: 109
1544730 GTTTGGTAAG
1544740 ATTGATTTTCATTTAACTTGATAATTTGATTTTTATTTTATATTAATAATTTTGCTTTTATTAAT
1 ATTGATTTTCATTTAACTTGATAATTTGATTTTTATTTTATATTAATAATTTTGCTTTTATTAAT
*
1544805 CGCTTATTTAAATTTTAGTTTTCATTCAAACAATTCGAAAAAAA
66 CGCTTATTTAAATTTTAATTTTCATTCAAACAATTCGAAAAAAA
*
1544849 ATTGATTTTCATTTAACTTGATAATTTGATTTTTATTTTATATTAATAATTTTGTTTTTATTAAT
1 ATTGATTTTCATTTAACTTGATAATTTGATTTTTATTTTATATTAATAATTTTGCTTTTATTAAT
*
1544914 CGCTTATTTAAATTTTAATTTTCATTCAACCAATTCGAAAAAAA
66 CGCTTATTTAAATTTTAATTTTCATTCAAACAATTCGAAAAAAA
1544958 A
1 A
1544959 CCCCTTTTAC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (109 bp):
ATTGATTTTCATTTAACTTGATAATTTGATTTTTATTTTATATTAATAATTTTGCTTTTATTAAT
CGCTTATTTAAATTTTAATTTTCATTCAAACAATTCGAAAAAAA
Found at i:1549146 original size:31 final size:33
Alignment explanation
Indices: 1549105--1549180 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
1549095 ATCAATTCTA
1549105 ATTTAAATCATATT-AG-TTT-AATTTTTTTCAT
1 ATTTAAATCAT-TTAAGATTTGAATTTTTTTCAT
* *
1549136 ATTTAGATCATTTAAGATTTGAATTTTTTTGA-
1 ATTTAAATCATTTAAGATTTGAATTTTTTTCAT
*
1549168 ATTTGAATCATTT
1 ATTTAAATCATTT
1549181 TAAATTCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 2 0.05
31 12 0.32
32 14 0.37
33 10 0.26
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (33 bp):
ATTTAAATCATTTAAGATTTGAATTTTTTTCAT
Found at i:1549819 original size:17 final size:17
Alignment explanation
Indices: 1549797--1549831 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1549787 GTAACACTTT
1549797 TGCTATATATCCCAATA
1 TGCTATATATCCCAATA
1549814 TGCTATATATCCCAATA
1 TGCTATATATCCCAATA
1549831 T
1 T
1549832 TAATTGACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (17 bp):
TGCTATATATCCCAATA
Found at i:1550772 original size:17 final size:17
Alignment explanation
Indices: 1550750--1550784 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1550740 GCAACACTTT
1550750 TGCTATATATCCCAATA
1 TGCTATATATCCCAATA
*
1550767 TGCTATATATCTCAATA
1 TGCTATATATCCCAATA
1550784 T
1 T
1550785 TAATTGACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (17 bp):
TGCTATATATCCCAATA
Found at i:1550910 original size:953 final size:956
Alignment explanation
Indices: 1548763--1551523 Score: 4163
Period size: 953 Copynumber: 2.9 Consensus size: 956
1548753 GTCTAAACAA
* * *
1548763 ATATATATATATATATAAGAAGACCAAATTTAAATTAAATATTTAATTTTAAAATCAATTTAAAC
1 ATATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAAT
* ** *
1548828 ATCTTTTTATATTAATTAATTCAGATAAAATTTTATAACACTTTTAGCTATAAAT-CC------C
66 ATCTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTT-GCTATATATCCCAATATGC
* * * *
1548886 -AT-TAT-T--A-ATT-A---ACCCTATTTTCTTAAATTAAAAATTTTCTATTCAACAAATGAAT
130 TATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAAT
* * * * * * * * *
1548941 TAATTAAACATAATAGCTCTATATTTTTATATCAACTATATGTTGATTATAAAAAGTAACCTGTA
195 TAATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATA
* * * *
1549006 ATTTTCAGACAAAAACTAATTAT-GCA-T--TT-T--A-----GTTACAAAACTTCCTTTTAAAT
260 GTCTTCAGACAAGAATTAATTATAG-ATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAAT
* *
1549059 AAAAGTGGTAGTTGGATGAATTTAGTGAGAAATCTGATCAATTCTAATTTAAATCATATT-AGTT
324 AAAAGTGGTAGTTGGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTGA-TT
* * * * *
1549123 TAATTTTTTTCATATTTAGATCATTTAAGATTTGAATTTTTTTGAATTTGAATCATTTTAAATTC
388 TAATTTTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTC
* * * *
1549188 ATA-TTTTTTAAGTTTAAACCATTTTAGATTCAGATTAAGTATGAGTAAATTTTATTATATTTTT
453 ATACTTTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTA-TATATATTT
* * * *
1549252 TTTAATTTTATGTTTTATATAATCATTTTTATATAATTTAATTATTAAAATTTTAAAATTCATTA
517 TTTAATTTTATGTTATATATAGTCATTTTTATATAATTTAAATATTAAAATTTAAAAATTCATTA
1549317 TTATGTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATT
582 TTATGTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATT
* *
1549382 AATGTCAACATTTGTTATCACAAATATTTTTTGGTTGCTAATTTCTTAATTAATTAAGGCCTTAC
647 AATGTCAACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCTTAC
*
1549447 TTCATTTAATTTAGGAAATACATTAGCAAAATGAAACTTACTTTCTGGTTCATATAGAGTAGCA-
712 TTCATTTAATTTAGGAAATACATTAGCAAAATG-AA---ACTTGCT-GTTCATATAGAGTAGCAC
* * * *
1549511 TTTTTTTTATAAAAAATTTCAACATTCAAAAATTCATTAAGCATCAATAAATTCAATTCAAGCTA
772 TTTTTTTTATAAAAAAATTCAACATTAAAAAATTCATTAAACATCAATTAATTCAATTCAAGCTA
* * ** ** *
1549576 AAATAATTTATTATAAATATAAAACTTTTTTCAACAATGATTTTCGTATAGAGTAACGCTATTCA
837 AAATAATTTATTATAAAAATAAAATTTTTTTCAACGCTGATTTTAATATAAAGTAACGCTATTCA
* ** *
1549641 ATTACCTTATCAAAAAGTCGTTTGATGGAGACCCGAACCTGCACAAAAGCAAGGG
902 ATTACCTTATCAAAAAGTCGTTCGATACAGACCCAAACCTGCACAAAAGCAAGGG
1549696 --------ATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAAT
1 ATATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAAT
1549753 ATCTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTTGCTATATATCCCAATATGCT
66 ATCTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTTGCTATATATCCCAATATGCT
*
1549818 ATATATCCCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATT
131 ATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATT
1549883 AATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAG
196 AATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAG
1549948 TCTTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAA
261 TCTTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAA
*
1550013 AAGTGGTAGTTGGATGAATTTAGTTAGAAATTTGATCAATTCTAATTCAAATCATATTGATTTAA
326 AAGTGGTAGTTGGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTGATTTAA
*
1550078 TTTTTTT-AGATTTAAATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATA
391 TTTTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATA
1550142 CTTTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATATTTTTTA
456 CTTTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATATTTTTTA
* *
1550207 ATTTTATGTTATATATAGTCATTTTTACATAATTTAAATATTAAAATTTAAAAATTCATTATTTT
521 ATTTTATGTTATATATAGTCATTTTTATATAATTTAAATATTAAAATTTAAAAATTCATTATTAT
1550272 GTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAATG
586 GTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAATG
* * *
1550337 TCAACATTTGTTGTCACTAATATTTTTGGGTTGCTAATTTTTTAATTAATTAAGACCTTACTTCA
651 TCAACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCTTACTTCA
* *
1550402 TTTAATTTAGGAAATACATTAGCAAAATGAAACTTGCT-TTCA-AAAAAGTAGCACTTTTTTTTA
716 TTTAATTTAGGAAATACATTAGCAAAATGAAACTTGCTGTTCATATAGAGTAGCACTTTTTTTTA
* * * ** * *
1550465 TAAAAAAATTCAGCATTTAAAAATTTATTAAATGTCAATTAATACAATTCGAGCTAAAATAACTT
781 TAAAAAAATTCAACATTAAAAAATTCATTAAACATCAATTAATTCAATTCAAGCTAAAATAA-TT
1550530 T-TTATAAAAATAAAATTTTTTTCAACGCTGATTTTAATATAAAGTAACGCTATTCAATTACCTG
845 TATTATAAAAATAAAATTTTTTTCAACGCTGATTTTAATATAAAGTAACGCTATTCAATTACCT-
* * *** *
1550594 T-TGAAAAGGTCGTTCGATACCTTCCCAAATCTGCACAAAAGCAAGGG
909 TATCAAAAAGTCGTTCGATACAGACCCAAACCTGCACAAAAGCAAGGG
*
1550641 ATATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAGT
1 ATATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAAT
*
1550706 ATCTATTTATATTAATTAATTCAGATAAAATTTGGCAACACTTTTGCTATATATCCCAATATGCT
66 ATCTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTTGCTATATATCCCAATATGCT
1550771 ATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATT
131 ATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATT
1550836 AATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAG
196 AATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAG
1550901 TCTTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAA
261 TCTTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAA
*
1550966 AAGTGGTAGTTAGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTGATTTAA
326 AAGTGGTAGTTGGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTGATTTAA
*
1551031 TTTTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTGATA
391 TTTTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATA
* *
1551096 CTTTTTTAAATTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATATTTTTTT
456 CTTTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATATTTTTTA
* *
1551161 ATTTTATGTTATATATAGTCATTTTTATATAATTTAAATGTTAAAATTCAAAAATTCATTATTAT
521 ATTTTATGTTATATATAGTCATTTTTATATAATTTAAATATTAAAATTTAAAAATTCATTATTAT
1551226 GTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAATG
586 GTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAATG
1551291 TCAACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCTTACTTCA
651 TCAACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCTTACTTCA
** * *
1551356 TTTAATTTATAAAATACATTAGCAACATGAAACTTGCTTTCTTGTTCATATAGAGTAGCACTTCT
716 TTTAATTTAGGAAATACATTAGCAAAATGAAACTTG----C-TGTTCATATAGAGTAGCACTTTT
* * * * *
1551421 TTTTATAAAAAAATTTCAACATTCAAAAAATCCACTAAACATCAACTAATTTAATTTAAGCTAAA
776 TTTTATAAAAAAA-TTCAACATT-AAAAAATTCATTAAACATCAATTAATTCAATTCAAGCTAAA
*
1551486 ATAATTTATTATAAAAATAAAATTTCTTTCAACGCTGA
839 ATAATTTATTATAAAAATAAAATTTTTTTCAACGCTGA
1551524 GAGTAACGTT
Statistics
Matches: 1661, Mismatches: 114, Indels: 76
0.90 0.06 0.04
Matches are distributed among these distances:
924 8 0.00
925 98 0.06
931 1 0.00
932 2 0.00
933 3 0.00
936 1 0.00
937 3 0.00
938 1 0.00
941 116 0.07
942 2 0.00
944 11 0.01
945 157 0.09
946 4 0.00
947 7 0.00
950 2 0.00
951 276 0.17
952 139 0.08
953 385 0.23
954 339 0.20
958 1 0.00
959 1 0.00
960 4 0.00
961 26 0.02
962 11 0.01
963 63 0.04
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (956 bp):
ATATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAAT
ATCTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTTGCTATATATCCCAATATGCT
ATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATT
AATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAG
TCTTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAA
AAGTGGTAGTTGGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTGATTTAA
TTTTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATA
CTTTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATATTTTTTA
ATTTTATGTTATATATAGTCATTTTTATATAATTTAAATATTAAAATTTAAAAATTCATTATTAT
GTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAATG
TCAACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCTTACTTCA
TTTAATTTAGGAAATACATTAGCAAAATGAAACTTGCTGTTCATATAGAGTAGCACTTTTTTTTA
TAAAAAAATTCAACATTAAAAAATTCATTAAACATCAATTAATTCAATTCAAGCTAAAATAATTT
ATTATAAAAATAAAATTTTTTTCAACGCTGATTTTAATATAAAGTAACGCTATTCAATTACCTTA
TCAAAAAGTCGTTCGATACAGACCCAAACCTGCACAAAAGCAAGGG
Found at i:1551083 original size:32 final size:33
Alignment explanation
Indices: 1551047--1551123 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
1551037 TCAGATTTAG
* * *
1551047 ATCATTTAAGATTTGA-ACTCTTTTGAATTCGA
1 ATCATTTTAGATTTGATACTCTTTTAAATTCAA
* *
1551079 ATCATTTTAGA-TTGATACTTTTTTAAATTTAA
1 ATCATTTTAGATTTGATACTCTTTTAAATTCAA
1551111 ATCATTTTAGATT
1 ATCATTTTAGATT
1551124 CAGATTAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 4 0.11
32 33 0.87
33 1 0.03
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.49
Consensus pattern (33 bp):
ATCATTTTAGATTTGATACTCTTTTAAATTCAA
Found at i:1551580 original size:15 final size:15
Alignment explanation
Indices: 1551560--1551589 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1551550 ATGTTTTACA
1551560 TCAGACGCGGGGACG
1 TCAGACGCGGGGACG
1551575 TCAGACGCGGGGACG
1 TCAGACGCGGGGACG
1551590 GGAGGTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.47, T:0.07
Consensus pattern (15 bp):
TCAGACGCGGGGACG
Found at i:1552555 original size:22 final size:24
Alignment explanation
Indices: 1552503--1552558 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
1552493 CAAATTTTAA
*
1552503 TAATATTATATAATTTATTTATAT
1 TAATATTATAAAATTTATTTATAT
1552527 T-AT-TTATAAAATTT-TTTAT-T
1 TAATATTATAAAATTTATTTATAT
1552547 TAATATTATAAA
1 TAATATTATAAA
1552559 TTAAATGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
21 7 0.24
22 17 0.59
23 2 0.07
24 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATATTATAAAATTTATTTATAT
Found at i:1552564 original size:26 final size:25
Alignment explanation
Indices: 1552516--1552564 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1552506 TATTATATAA
**
1552516 TTTATTTATATTATTTATAAAATTT
1 TTTATTTATATTATAAATAAAATTT
*
1552541 TTTATTTAATATTATAAATTAAAT
1 TTTATTT-ATATTATAAATAAAAT
1552565 GATATTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTATTTATATTATAAATAAAATTT
Found at i:1553177 original size:22 final size:22
Alignment explanation
Indices: 1553152--1553193 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1553142 TTTTTTTAAA
* *
1553152 ATTAAATGAAATTGAATCAAAT
1 ATTAAATAAAATTAAATCAAAT
*
1553174 ATTAAGTAAAATTAAATCAA
1 ATTAAATAAAATTAAATCAA
1553194 TTTGAACTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (22 bp):
ATTAAATAAAATTAAATCAAAT
Found at i:1553717 original size:22 final size:22
Alignment explanation
Indices: 1553692--1553764 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
1553682 ATCATTATTT
1553692 ATAAATATAATTTTTATAATTA
1 ATAAATATAATTTTTATAATTA
*
1553714 ATAAATAT-A-TTTTACTCA-T-
1 ATAAATATAATTTTTA-TAATTA
*
1553733 ATGAATAATAATTTTTATAATTA
1 ATAAAT-ATAATTTTTATAATTA
1553756 ATAAATATA
1 ATAAATATA
1553765 TCTTACAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 5 0.12
20 8 0.20
21 6 0.15
22 17 0.41
23 5 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (22 bp):
ATAAATATAATTTTTATAATTA
Found at i:1553754 original size:42 final size:42
Alignment explanation
Indices: 1553698--1553782 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
1553688 ATTTATAAAT
* **
1553698 ATAATTTTTATAATTAATAAATATATTTTACTCATATGAATA
1 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1553740 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1553782 A
1 A
1553783 AAATAGTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (42 bp):
ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
Found at i:1554642 original size:13 final size:13
Alignment explanation
Indices: 1554621--1554667 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
1554611 ATATTATATA
1554621 TTTTT-AATTTAT
1 TTTTTAAATTTAT
1554633 TTTTTAAATTATAT
1 TTTTTAAATT-TAT
*
1554647 ATTTTTAAATTTAA
1 -TTTTTAAATTTAT
1554661 TTTTTAA
1 TTTTTAA
1554668 TAATTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 5 0.16
13 11 0.35
14 5 0.16
15 10 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTTAAATTTAT
Found at i:1554644 original size:27 final size:28
Alignment explanation
Indices: 1554613--1554667 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
1554603 ATTTGTCCAT
*
1554613 ATTATATATTTTT-AATTTATTTTTTAA
1 ATTATATATTTTTAAATTTAATTTTTAA
1554640 ATTATATATTTTTAAATTTAATTTTTAA
1 ATTATATATTTTTAAATTTAATTTTTAA
1554668 TAATTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTATATATTTTTAAATTTAATTTTTAA
Found at i:1554651 original size:16 final size:15
Alignment explanation
Indices: 1554614--1554684 Score: 62
Period size: 15 Copynumber: 4.8 Consensus size: 15
1554604 TTTGTCCATA
1554614 TTATATATTTTT-AA-
1 TTATAT-TTTTTAAAT
1554628 TT-TATTTTTTAAA-
1 TTATATTTTTTAAAT
1554641 TTATATATTTTTAAAT
1 TTATAT-TTTTTAAAT
*
1554657 TTA-ATTTTTAATAAT
1 TTATATTTTTTA-AAT
1554672 TTAATATTTTTTA
1 TT-ATATTTTTTA
1554685 TTAAAATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.10
13 7 0.15
14 10 0.21
15 15 0.31
16 4 0.08
17 7 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTTTTAAAT
Found at i:1554672 original size:15 final size:13
Alignment explanation
Indices: 1554620--1554681 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 13
1554610 CATATTATAT
1554620 ATTTTT-AATTTA
1 ATTTTTAAATTTA
*
1554632 TTTTTTAAATTATA
1 ATTTTTAAATT-TA
1554646 TATTTTTAAATTTA
1 -ATTTTTAAATTTA
1554660 ATTTTTAATAATTTA
1 ATTTTT-A-AATTTA
1554675 ATATTTT
1 AT-TTTT
1554682 TTATTAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 5 0.12
13 10 0.24
14 5 0.12
15 18 0.43
16 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTTAAATTTA
Found at i:1556592 original size:27 final size:27
Alignment explanation
Indices: 1556526--1556630 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 27
1556516 TAAAAATTAG
* *
1556526 CCACCAATTTTGACAAAACAACAA-G--
1 CCACCATTTTTGAC-AAACAAAAAGGAA
*
1556551 CCACAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * * *
1556578 TCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
1556605 CCACCATTTTTTACAAACACAAAAGG
1 CCACCATTTTTGACAAACA-AAAAGG
1556631 TGGCTTTTGT
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
24 8 0.13
25 13 0.21
27 38 0.60
28 4 0.06
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:1562093 original size:19 final size:19
Alignment explanation
Indices: 1562069--1562108 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1562059 AAATAATGGG
*
1562069 AATGAATAGCAAGAAAAAA
1 AATGAACAGCAAGAAAAAA
* *
1562088 AATGAACATCAATAAAAAA
1 AATGAACAGCAAGAAAAAA
1562107 AA
1 AA
1562109 ATGGCCCTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.12
Consensus pattern (19 bp):
AATGAACAGCAAGAAAAAA
Found at i:1566401 original size:20 final size:19
Alignment explanation
Indices: 1566351--1566428 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
1566341 GGTAAAAAGA
1566351 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
1566370 GCAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
*
1566390 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* * *
1566410 GAAAAATGTATCAATACAT
1 -CATAATGTATCGATACAT
1566429 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.06
20 42 0.89
21 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:1566427 original size:40 final size:39
Alignment explanation
Indices: 1566351--1566428 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1566341 GGTAAAAAGA
* * *
1566351 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCAATACATT
* *
1566390 CATACATGTATCGATATATTGAAAAATGTATCAATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCAATACAT
1566429 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCAATACATT
Found at i:1566900 original size:11 final size:11
Alignment explanation
Indices: 1566886--1566911 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1566876 CATCAAATAA
1566886 ATAAAATCAAT
1 ATAAAATCAAT
1566897 ATAAAATCAAT
1 ATAAAATCAAT
1566908 ATAA
1 ATAA
1566912 GCCAATACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAATCAAT
Found at i:1567137 original size:16 final size:16
Alignment explanation
Indices: 1567116--1567150 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1567106 AATTTCTTAT
* *
1567116 TAATAATTAATTATTA
1 TAATAATAAAATATTA
1567132 TAATAATAAAATATTA
1 TAATAATAAAATATTA
1567148 TAA
1 TAA
1567151 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATAAAATATTA
Found at i:1568832 original size:2 final size:2
Alignment explanation
Indices: 1568825--1568854 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1568815 CTTCTATTTA
1568825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1568855 GGTAAATCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1568883 original size:15 final size:15
Alignment explanation
Indices: 1568863--1568892 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1568853 ATGGTAAATC
1568863 GCCTAATCAATGGAT
1 GCCTAATCAATGGAT
1568878 GCCTAATCAATGGAT
1 GCCTAATCAATGGAT
1568893 AATTTCTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
GCCTAATCAATGGAT
Found at i:1570423 original size:14 final size:14
Alignment explanation
Indices: 1570406--1570437 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1570396 TTTTCAAATT
1570406 GAAGTTTTAATAAG
1 GAAGTTTTAATAAG
1570420 GAAGTTTTAATAAG
1 GAAGTTTTAATAAG
1570434 GAAG
1 GAAG
1570438 AAAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (14 bp):
GAAGTTTTAATAAG
Found at i:1574330 original size:34 final size:34
Alignment explanation
Indices: 1574287--1574370 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
1574277 AATAACATAT
1574287 ATATATATATATATATCATTTAAGTTGTTTAATA
1 ATATATATATATATATCATTTAAGTTGTTTAATA
1574321 ATATATATATATATATCATTTAAGTTGTTTAATA
1 ATATATATATATATATCATTTAAGTTGTTTAATA
*
1574355 GTATATATATATATAT
1 ATATATATATATATAT
1574371 ATGCCATAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (34 bp):
ATATATATATATATATCATTTAAGTTGTTTAATA
Found at i:1576745 original size:50 final size:50
Alignment explanation
Indices: 1576670--1576853 Score: 278
Period size: 50 Copynumber: 3.7 Consensus size: 50
1576660 GTTGCCATTA
** *
1576670 TTGACAATAGAGAGAGGTGGTCGTAATTGTTGACGATTCTTCATCAACCT
1 TTGACAATAGAGAGAGGTGACCGTAATTGTTGACGATTCTTCACCAACCT
1576720 TTGACAATAGAGAGAGGTGACCGTAATTGTTGACGATTCTTCACCAACCT
1 TTGACAATAGAGAGAGGTGACCGTAATTGTTGACGATTCTTCACCAACCT
* ** * *
1576770 TTGACAATAAAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACCC
1 TTGACAATAGAGAGAGGTGACCGTAATTGTTGACGATTCTTCACCAACCT
* *
1576820 TTGATAATAGAAAGAGGTGACCGTAATTGTTGAC
1 TTGACAATAGAGAGAGGTGACCGTAATTGTTGAC
1576854 TCTAAGCAAC
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 120 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (50 bp):
TTGACAATAGAGAGAGGTGACCGTAATTGTTGACGATTCTTCACCAACCT
Found at i:1576843 original size:100 final size:100
Alignment explanation
Indices: 1576670--1576853 Score: 314
Period size: 100 Copynumber: 1.8 Consensus size: 100
1576660 GTTGCCATTA
* * * * *
1576670 TTGACAATAGAGAGAGGTGGTCGTAATTGTTGACGATTCTTCATCAACCTTTGACAATAGAGAGA
1 TTGACAATAAAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACCCTTGACAATAGAAAGA
1576735 GGTGACCGTAATTGTTGACGATTCTTCACCAACCT
66 GGTGACCGTAATTGTTGACGATTCTTCACCAACCT
*
1576770 TTGACAATAAAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACCCTTGATAATAGAAAGA
1 TTGACAATAAAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACCCTTGACAATAGAAAGA
1576835 GGTGACCGTAATTGTTGAC
66 GGTGACCGTAATTGTTGAC
1576854 TCTAAGCAAC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (100 bp):
TTGACAATAAAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACCCTTGACAATAGAAAGA
GGTGACCGTAATTGTTGACGATTCTTCACCAACCT
Found at i:1577998 original size:17 final size:17
Alignment explanation
Indices: 1577976--1578010 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1577966 GTAACACTTT
1577976 TGCTATATATCTCAATA
1 TGCTATATATCTCAATA
1577993 TGCTATATATCTCAATA
1 TGCTATATATCTCAATA
1578010 T
1 T
1578011 TAATTGACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (17 bp):
TGCTATATATCTCAATA
Found at i:1578952 original size:17 final size:17
Alignment explanation
Indices: 1578930--1578964 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1578920 GTAACACTTT
1578930 TGCTATATATCCCAATA
1 TGCTATATATCCCAATA
*
1578947 TGCTATATATCTCAATA
1 TGCTATATATCCCAATA
1578964 T
1 T
1578965 TAATTGACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (17 bp):
TGCTATATATCCCAATA
Found at i:1579268 original size:954 final size:954
Alignment explanation
Indices: 1577202--1579734 Score: 4511
Period size: 954 Copynumber: 2.7 Consensus size: 954
1577192 AGACAAGAAC
** * * *
1577202 TAATTATGCATTCTAGTTACAAAACTTCCTTTTAAATAAAAGTGGTCGTTGGATGAATTTAGTCA
1 TAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAAAAGTGGTAGTTGAATGAATTTAGTTA
* *
1577267 GAAATCTGATCAATTCTAATTCAAATCATATT-AGTTTAATTTTTTTCAGATTTAGATCATTTAA
66 TAAATTTGATCAATTCTAATTCAAATCATATTGA-TTTAATTTTTTTCAGATTTAGATCATTTAA
* * * * * * * *
1577331 GATTTAAATTTTTTTGACTTTGAATAATTTTAAATTCATA-TTTTTTAAGTTTAAACCATTTTAG
130 GATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACTTTTTTAAGTTTAAATCATTTTAG
* * * *
1577395 ATTCAGATTAAGTATGAGTAGATTTTATATAT-T-TTTTTAATTTTATGTTTTATATAATCATTT
195 ATTCAGATTAAGTATGAATAGATTTTATATATATATTTTTTATTTTATGTTATATATAGTCATTT
* *
1577458 TTATATAATTTAAATATTAAAATTTAAAAATTCATTATTATGTCTTTTAAAATAGGCTCTGGTAT
260 TTATATAATTTAAATATTAAAATTCAAAAATTCATTATTATGTCTTTTAAAATAGGCTTTGGTAT
1577523 AATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTCAATATTTGTTATCACAAATATT
325 AATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTCAATATTTGTTATCACAAATATT
1577588 TTTGGGTTGCTAATTTCTTAATTAATTAAGGCCTTACTTCATTTAATTTAGGAAATACATTAGCA
390 TTTGGGTTGCTAATTTCTTAATTAATTAAGGCCTTACTTCATTTAATTTAGGAAATACATTAGCA
*
1577653 AAACAAAACTTGCTTTCTGGTTCATATAGAGTAACATTTCCTTTTATAAAAAATTTCAACATTCA
455 AAACGAAACTTGCTTTCTGGTTCATATAGAGTAACATTTCCTTTTATAAAAAATTTCAACATTCA
1577718 AAAATTCATTAAGCATCAATCAATTCAATTCAAGCTAAAATAATTTATTATAAATATAAAACTTT
520 AAAATTCATTAAGCATCAATCAATTCAATTCAAGCTAAAATAATTTATTATAAATATAAAACTTT
*
1577783 TTTCAACAATTATTTTCATATAAAGTAACGCTATTCAATTACCTCATCAAAAGTTTGTACGATGG
585 TTTCAACAATAATTTTCATATAAAGTAACGCTATTCAATTACCTCATCAAAAGTTTGTACGATGG
1577848 AGCTCAAAACCTGCACAAAAGCAAGGGATATATATAAGAATACCAAATTTAAATTAAATATTTAA
650 AGCTCAAAACCTGCACAAAAGCAAGGGATATATATAAGAATACCAAATTTAAATTAAATATTTAA
1577913 TTCTAAAATCAATTTAAATATCTATTTATATTAATTAATTTAGATAAAATTTGGTAACACTTTTG
715 TTCTAAAATCAATTTAAATATCTATTTATATTAATTAATTTAGATAAAATTTGGTAACACTTTTG
*
1577978 CTATATATCTCAATATGCTATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTT
780 CTATATATCCCAATATGCTATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTT
*
1578043 TCTATTCAACAAATAAATTAATTAAACACAATAGCTGTCTATTTTTATATCAACTAAATGTTAAT
845 TCTATTCAACAAATAAATTAATTAAACACAATAGCTGTCTATTTTTATATCAACTAAATATTAAT
1578108 TATAAAAGGTAGCTTATAGTCTTCAGACAAGAATTAATTATAGAT
910 TATAAAAGGTAGCTTATAGTCTTCAGACAAGAATTAATTATAGAT
*
1578153 TAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAAAAGTGATAGTTGAATGAATTTAGTTA
1 TAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAAAAGTGGTAGTTGAATGAATTTAGTTA
1578218 TAAATTTGATCAATTCTAATTCAAATCATATTGATTTAATTTTTTTCAGATTTAGATCATTTAAG
66 TAAATTTGATCAATTCTAATTCAAATCATATTGATTTAATTTTTTTCAGATTTAGATCATTTAAG
1578283 ATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACTTTTTTAAGTTTAAATCATTTTAGA
131 ATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACTTTTTTAAGTTTAAATCATTTTAGA
1578348 TTCAGATTAAGTATGAATAGATTTTATATATATATTTTTTATTTTATGTTATATATAGTCATTTT
196 TTCAGATTAAGTATGAATAGATTTTATATATATATTTTTTATTTTATGTTATATATAGTCATTTT
1578413 TATATAATTTAAATATTAAAATTCAAAAATTCATTATTATGTCTTTTAAAATAGGCTTTGGTATA
261 TATATAATTTAAATATTAAAATTCAAAAATTCATTATTATGTCTTTTAAAATAGGCTTTGGTATA
1578478 ATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTCAATATTTGTTATCACAAATATTT
326 ATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTCAATATTTGTTATCACAAATATTT
1578543 TTGGGTTGCTAATTTCTTAATTAATTAAGGCCTTACTTCATTTAATTTAGGAAATACATTAGCAA
391 TTGGGTTGCTAATTTCTTAATTAATTAAGGCCTTACTTCATTTAATTTAGGAAATACATTAGCAA
1578608 AACGAAACTTGCTTTCTGGTTCATATAGAGTAACATTTCCTTTTATAAAAAATTTCAACATTCAA
456 AACGAAACTTGCTTTCTGGTTCATATAGAGTAACATTTCCTTTTATAAAAAATTTCAACATTCAA
1578673 AAATTCATTAAGCATCAATCAATTCAATTCAAGCTAAAATAATTTATTATAAATATAAAACTTTT
521 AAATTCATTAAGCATCAATCAATTCAATTCAAGCTAAAATAATTTATTATAAATATAAAACTTTT
* *
1578738 TTCAACAATGATTTTCGTATAAAGTAACGCTATTCAATTACCTCATCAAAAGTTTGTACGATGGA
586 TTCAACAATAATTTTCATATAAAGTAACGCTATTCAATTACCTCATCAAAAGTTTGTACGATGGA
1578803 GCTCAAAACCTGCACAAAAGCAAGGGATATATATAAGAATACCAAATTTAAATTAAATATTTAAT
651 GCTCAAAACCTGCACAAAAGCAAGGGATATATATAAGAATACCAAATTTAAATTAAATATTTAAT
1578868 TCTAAAATCAATTTAAATATCTATTTATATTAATTAATTTAGATAAAATTTGGTAACACTTTTGC
716 TCTAAAATCAATTTAAATATCTATTTATATTAATTAATTTAGATAAAATTTGGTAACACTTTTGC
1578933 TATATATCCCAATATGCTATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTT
781 TATATATCCCAATATGCTATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTT
*
1578998 CTATTTAACAAATAAATTAATTAAACACAATAGCTGTCTATTTTTATATCAACTAAATATTAATT
846 CTATTCAACAAATAAATTAATTAAACACAATAGCTGTCTATTTTTATATCAACTAAATATTAATT
1579063 ATAAAAGGTAGCTTATAGTCTTCAGACAAGAATTAATTATAGAT
911 ATAAAAGGTAGCTTATAGTCTTCAGACAAGAATTAATTATAGAT
*
1579107 TAATTATGCATTCCGGTTACAAAACTTCATTTTAAATAAAAGTGGTAGTTGAATGAATTTAGTTA
1 TAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAAAAGTGGTAGTTGAATGAATTTAGTTA
1579172 TAAATTTGATCAATTCTAATTCAAATCATATTGATTTAATTTTTTTCAGATTTAGATCATTTAAG
66 TAAATTTGATCAATTCTAATTCAAATCATATTGATTTAATTTTTTTCAGATTTAGATCATTTAAG
1579237 ATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACTTTTTTAAGTTTAAATCATTTTAGA
131 ATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACTTTTTTAAGTTTAAATCATTTTAGA
1579302 TTCAGATTAAGTATGAATAGATTTTATATATATATTTTTTATTTTATGTTATATATAGTCATTTT
196 TTCAGATTAAGTATGAATAGATTTTATATATATATTTTTTATTTTATGTTATATATAGTCATTTT
*
1579367 TATATAATTTAAATATTAAAATTCAAAAATTTATTATTATGTCTTTTAAAATAGGCTTTGGTATA
261 TATATAATTTAAATATTAAAATTCAAAAATTCATTATTATGTCTTTTAAAATAGGCTTTGGTATA
*
1579432 ATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTCAACATTTGTTATCACAAATATTT
326 ATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTCAATATTTGTTATCACAAATATTT
* * *
1579497 TTGGGTTGCTAATTTCTTAATTAATTAAGACCTTACTTCATTTAATTTATGAAATACACTAGCAA
391 TTGGGTTGCTAATTTCTTAATTAATTAAGGCCTTACTTCATTTAATTTAGGAAATACATTAGCAA
* * * * * * *
1579562 CATGAAACTTGCTTTCTCGTTCATATAGAGTAGCACTTCTTTTTATAAAAAATTTCAGCATTCAA
456 AACGAAACTTGCTTTCTGGTTCATATAGAGTAACATTTCCTTTTATAAAAAATTTCAACATTCAA
* * * * * *
1579627 AAAATCTACTAAACATCAA-CTAATTTAATTTAAGCTAAAATAATTTATTATAAAAATAAAA-TT
521 AAATTC-ATTAAGCATCAATC-AATTCAATTCAAGCTAAAATAATTTATTATAAATATAAAACTT
* ** * *
1579690 TCTTTCGACGTTAATTTTTATATAAAGTAACGTTATTCAATTACC
584 T-TTTCAACAATAATTTTCATATAAAGTAACGCTATTCAATTACC
1579735 ATTACAAAAT
Statistics
Matches: 1520, Mismatches: 55, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
951 152 0.10
952 55 0.04
953 1 0.00
954 1229 0.81
955 83 0.05
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (954 bp):
TAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAAAAGTGGTAGTTGAATGAATTTAGTTA
TAAATTTGATCAATTCTAATTCAAATCATATTGATTTAATTTTTTTCAGATTTAGATCATTTAAG
ATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACTTTTTTAAGTTTAAATCATTTTAGA
TTCAGATTAAGTATGAATAGATTTTATATATATATTTTTTATTTTATGTTATATATAGTCATTTT
TATATAATTTAAATATTAAAATTCAAAAATTCATTATTATGTCTTTTAAAATAGGCTTTGGTATA
ATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTCAATATTTGTTATCACAAATATTT
TTGGGTTGCTAATTTCTTAATTAATTAAGGCCTTACTTCATTTAATTTAGGAAATACATTAGCAA
AACGAAACTTGCTTTCTGGTTCATATAGAGTAACATTTCCTTTTATAAAAAATTTCAACATTCAA
AAATTCATTAAGCATCAATCAATTCAATTCAAGCTAAAATAATTTATTATAAATATAAAACTTTT
TTCAACAATAATTTTCATATAAAGTAACGCTATTCAATTACCTCATCAAAAGTTTGTACGATGGA
GCTCAAAACCTGCACAAAAGCAAGGGATATATATAAGAATACCAAATTTAAATTAAATATTTAAT
TCTAAAATCAATTTAAATATCTATTTATATTAATTAATTTAGATAAAATTTGGTAACACTTTTGC
TATATATCCCAATATGCTATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTT
CTATTCAACAAATAAATTAATTAAACACAATAGCTGTCTATTTTTATATCAACTAAATATTAATT
ATAAAAGGTAGCTTATAGTCTTCAGACAAGAATTAATTATAGAT
Found at i:1580700 original size:22 final size:23
Alignment explanation
Indices: 1580652--1580703 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
1580642 TTTTAATAAC
*
1580652 ATTATATAATTTATTTATATTAT
1 ATTATAAAATTTATTTATATTAT
1580675 -TTATAAAATTT-TTTAT-TTAAT
1 ATTATAAAATTTATTTATATT-AT
1580696 ATTATAAA
1 ATTATAAA
1580704 TTAAATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 7 0.27
22 17 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTATAAAATTTATTTATATTAT
Found at i:1580709 original size:26 final size:25
Alignment explanation
Indices: 1580661--1580709 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1580651 CATTATATAA
**
1580661 TTTATTTATATTATTTATAAAATTT
1 TTTATTTATATTATAAATAAAATTT
*
1580686 TTTATTTAATATTATAAATTAAAT
1 TTTATTT-ATATTATAAATAAAAT
1580710 GATATTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTATTTATATTATAAATAAAATTT
Found at i:1580857 original size:32 final size:32
Alignment explanation
Indices: 1580784--1580857 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1580774 TTTTTATAAA
1580784 TTAAAAAAAAACAACTATTAATCTTTTTACAC
1 TTAAAAAAAAACAACTATTAATCTTTTTACAC
** * * *
1580816 ACAACAAAAAATAACTATTAATTTTTTTA-AC
1 TTAAAAAAAAACAACTATTAATCTTTTTACAC
*
1580847 TTTAAAAAAAA
1 TTAAAAAAAAA
1580858 TAATTCCTAT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (32 bp):
TTAAAAAAAAACAACTATTAATCTTTTTACAC
Found at i:1580971 original size:2 final size:2
Alignment explanation
Indices: 1580960--1581006 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1580950 AAAATAATTA
1580960 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1581001 AT AT AT
1 AT AT AT
1581007 GCAATTAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1581815 original size:6 final size:6
Alignment explanation
Indices: 1581804--1581843 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1581794 GGAAATTCGA
* * *
1581804 TTTTGC TTTTGC TTTTAC TTTTTC TTTTAC TTTTGC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
1581844 TGCCTCGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.72
Consensus pattern (6 bp):
TTTTGC
Found at i:1581824 original size:12 final size:12
Alignment explanation
Indices: 1581804--1581843 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1581794 GGAAATTCGA
*
1581804 TTTTGCTTTTGC
1 TTTTACTTTTGC
*
1581816 TTTTACTTTTTC
1 TTTTACTTTTGC
1581828 TTTTACTTTTGC
1 TTTTACTTTTGC
1581840 TTTT
1 TTTT
1581844 TGCCTCGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTACTTTTGC
Found at i:1581951 original size:19 final size:19
Alignment explanation
Indices: 1581894--1581951 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 19
1581884 TATAAATCTA
*
1581894 ATTTTTATAATTAATAAAT
1 ATTTTTATAATTAATAAAC
* *
1581913 ATATTTTACTCATATAAATAACC
1 AT-TTTTA-T-A-ATTAATAAAC
1581936 ATTTTTATAATTAATA
1 ATTTTTATAATTAATA
1581952 TATATATCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 8 0.26
20 6 0.19
21 2 0.06
22 6 0.19
23 9 0.29
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTTATAATTAATAAAC
Found at i:1582847 original size:16 final size:15
Alignment explanation
Indices: 1582794--1582838 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 15
1582784 ATCCGTCTAT
*
1582794 ATTATATA-TTTTCA
1 ATTATATATTTTTAA
*
1582808 AGT-TAT-TTTTTAA
1 ATTATATATTTTTAA
1582821 ATTATATATTTTTAA
1 ATTATATATTTTTAA
1582836 ATT
1 ATT
1582839 TAATAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 10 0.40
14 5 0.20
15 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTATATATTTTTAA
Found at i:1582848 original size:29 final size:29
Alignment explanation
Indices: 1582816--1582897 Score: 68
Period size: 29 Copynumber: 2.9 Consensus size: 29
1582806 CAAGTTATTT
1582816 TTTAAATTATATATTTTTAAATTTAATAA
1 TTTAAATTATATATTTTTAAATTTAATAA
* *
1582845 TTTAATATT-T-T-TTATTAAAATATAAATAA
1 TTTAA-ATTATATATT-TTTAAAT-TTAATAA
1582874 TTT-AA-TATA-ATTTTTAATATTTAA
1 TTTAAATTATATATTTTTAA-ATTTAA
1582898 GTTAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 16
0.68 0.06 0.26
Matches are distributed among these distances:
26 1 0.02
27 11 0.26
28 12 0.29
29 15 0.36
30 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAAATTATATATTTTTAAATTTAATAA
Found at i:1585483 original size:27 final size:27
Alignment explanation
Indices: 1585443--1585511 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
1585433 AGCCACCATT
*
1585443 TATTTGTCAAAAATGGTTGTTACTTTG
1 TATTTGTCAAAAATGGTAGTTACTTTG
* * * *
1585470 TGTTTGTAAAAAATGGTAGTTTCTTTT
1 TATTTGTCAAAAATGGTAGTTACTTTG
1585497 TATTTGTCAAAAATG
1 TATTTGTCAAAAATG
1585512 ATGGCATATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTAGTTACTTTG
Found at i:1590037 original size:27 final size:27
Alignment explanation
Indices: 1590006--1590078 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
1589996 AGCCATCATT
1590006 TGTTTGTCAAAAATGGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
1590033 TGTTTGTCAAAAATGGTGGTTCCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
1590060 TATTTGTCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
1590079 CATGTTGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:1590089 original size:24 final size:25
Alignment explanation
Indices: 1590004--1590095 Score: 105
Period size: 27 Copynumber: 3.6 Consensus size: 25
1589994 AAAGCCATCA
*
1590004 TTTGTTTGTCAAAAATGGTGGTTACT
1 TTTGTTTGTCAAAAATGGTGGTCA-T
*
1590030 TTGTGTTTGTCAAAAATGGTGGTTCCTT
1 TT-TGTTTGTCAAAAATGGTGG-T-CAT
*
1590058 TTTATTTGTCAAAAATGGTGG-CAT
1 TTTGTTTGTCAAAAATGGTGGTCAT
*
1590082 GTTGTTTGTCAAAA
1 TTTGTTTGTCAAAA
1590096 TTTGTGGCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
24 14 0.25
26 2 0.04
27 37 0.65
28 4 0.07
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.45
Consensus pattern (25 bp):
TTTGTTTGTCAAAAATGGTGGTCAT
Found at i:1590111 original size:51 final size:54
Alignment explanation
Indices: 1590008--1590114 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 54
1589998 CCATCATTTG
* * * **
1590008 TTTGTCAAAAATGGTGGTTACTTTGTGTTTGTCAAAAATGGTGGTTCCTTTTTA
1 TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTCAAAAATGGTGGCTAATTTTTA
* *
1590062 TTTGTCAAAAATGGTGG-CA-TGT-TGTTTGTCAAAATTTGTGGCTAATTTTTA
1 TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTCAAAAATGGTGGCTAATTTTTA
1590113 TT
1 TT
1590115 ACAAAATAGG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
51 26 0.57
52 2 0.04
53 1 0.02
54 17 0.37
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.47
Consensus pattern (54 bp):
TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTCAAAAATGGTGGCTAATTTTTA
Found at i:1591906 original size:27 final size:28
Alignment explanation
Indices: 1591876--1591928 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1591866 TAATTTCTTT
* *
1591876 TTTAAGCAATTAAA-ATTTATTTAAAAA
1 TTTAAGAAATTAAATATTTAATTAAAAA
*
1591903 TTTAATAAATTAAATATTTAATTAAA
1 TTTAAGAAATTAAATATTTAATTAAA
1591929 TTATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TTTAAGAAATTAAATATTTAATTAAAAA
Found at i:1591921 original size:16 final size:17
Alignment explanation
Indices: 1591896--1591931 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1591886 TAAAATTTAT
1591896 TTAAAAATTTAA-TAAA
1 TTAAAAATTTAATTAAA
*
1591912 TTAAATATTTAATTAAA
1 TTAAAAATTTAATTAAA
1591929 TTA
1 TTA
1591932 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAAATTTAATTAAA
Found at i:1592020 original size:20 final size:22
Alignment explanation
Indices: 1591985--1592025 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1591975 AATAAATGAA
1591985 ATTTTAAAATAATTAAAAAATT
1 ATTTTAAAATAATTAAAAAATT
1592007 ATTTT-AAA-AATTAAAAAAT
1 ATTTTAAAATAATTAAAAAAT
1592026 GAAATAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTTAAAATAATTAAAAAATT
Found at i:1592069 original size:13 final size:13
Alignment explanation
Indices: 1592053--1592098 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1592043 TATTTTAATA
1592053 TATTAAAAATATT
1 TATTAAAAATATT
1592066 TATT---AA-ATT
1 TATTAAAAATATT
1592075 TATTAAAAATATT
1 TATTAAAAATATT
*
1592088 TATGAAAAATA
1 TATTAAAAATA
1592099 AAAAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
12 2 0.07
13 17 0.61
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
TATTAAAAATATT
Found at i:1592549 original size:2 final size:2
Alignment explanation
Indices: 1592542--1592589 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1592532 ACCTTTCAAA
*
1592542 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1592584 AT AT AT
1 AT AT AT
1592590 CTAACGAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1595131 original size:50 final size:50
Alignment explanation
Indices: 1595072--1595330 Score: 428
Period size: 50 Copynumber: 5.2 Consensus size: 50
1595062 TATACTTAGA
*
1595072 GTCAACAATTATGGCCACCTCCCTTTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1595122 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
** * *
1595172 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTAATGAAGGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1595222 GTCAACAATTATGGCCACCTCCCTCTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
1595272 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1595322 GTCAACAAT
1 GTCAACAAT
1595331 GGCAACAACT
Statistics
Matches: 193, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 193 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1596001 original size:13 final size:13
Alignment explanation
Indices: 1595983--1596007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1595973 ACACAAAGTA
1595983 TGTATCGATACAT
1 TGTATCGATACAT
1595996 TGTATCGATACA
1 TGTATCGATACA
1596008 CCAAAAAATT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1596004 original size:32 final size:34
Alignment explanation
Indices: 1595963--1596031 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
1595953 GTAGCCAAAC
**
1595963 TTGTATCGATACA-CAAAGTA-TGTATCGATACA
1 TTGTATCGATACACCAAAAAATTGTATCGATACA
1595995 TTGTATCGATACACCAAAAAATTGTATCGATACA
1 TTGTATCGATACACCAAAAAATTGTATCGATACA
1596029 TTG
1 TTG
1596032 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 13 0.39
33 5 0.15
34 15 0.45
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (34 bp):
TTGTATCGATACACCAAAAAATTGTATCGATACA
Found at i:1596093 original size:20 final size:22
Alignment explanation
Indices: 1596062--1596105 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1596052 GCTATATTTT
1596062 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
1596083 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
1596104 CA
1 CA
1596106 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:1602207 original size:13 final size:13
Alignment explanation
Indices: 1602189--1602226 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1602179 CATAATTCTT
1602189 TGTATCGATACAC
1 TGTATCGATACAC
* *
1602202 TGTATCGATAGAT
1 TGTATCGATACAC
1602215 TGTATCGATACA
1 TGTATCGATACA
1602227 AGGGGATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1604085 original size:38 final size:38
Alignment explanation
Indices: 1604034--1604119 Score: 138
Period size: 38 Copynumber: 2.3 Consensus size: 38
1604024 GCTATAACAA
* *
1604034 AAAGGGAGAGAGAATACAAGCAAATAAATTTTATGATT
1 AAAGGGGGAGAGAATACAAACAAATAAATTTTATGATT
*
1604072 AAAGGGGGAGAGAATACAAACAAATGAATTTTATGATT
1 AAAGGGGGAGAGAATACAAACAAATAAATTTTATGATT
1604110 -AAGGGGGAGA
1 AAAGGGGGAGA
1604120 AAGAAATTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 10 0.22
38 35 0.78
ACGTcount: A:0.48, C:0.05, G:0.27, T:0.21
Consensus pattern (38 bp):
AAAGGGGGAGAGAATACAAACAAATAAATTTTATGATT
Found at i:1604782 original size:20 final size:20
Alignment explanation
Indices: 1604757--1604811 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1604747 AAAACCCTTA
1604757 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
1604777 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATTGC
*
1604797 AATGTATCGATACAT
1 AAAGTATCGATACAT
1604812 GAAAAAGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:1604901 original size:13 final size:13
Alignment explanation
Indices: 1604883--1604907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1604873 ACACAAAGTA
1604883 TGTATCGATACAT
1 TGTATCGATACAT
1604896 TGTATCGATACA
1 TGTATCGATACA
1604908 CCAAAAAATT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1604904 original size:32 final size:34
Alignment explanation
Indices: 1604863--1604931 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
1604853 GTAGCCAAAC
**
1604863 TTGTATCGATACA-CAAAGTA-TGTATCGATACA
1 TTGTATCGATACACCAAAAAATTGTATCGATACA
1604895 TTGTATCGATACACCAAAAAATTGTATCGATACA
1 TTGTATCGATACACCAAAAAATTGTATCGATACA
1604929 TTG
1 TTG
1604932 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 13 0.39
33 5 0.15
34 15 0.45
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (34 bp):
TTGTATCGATACACCAAAAAATTGTATCGATACA
Found at i:1604997 original size:20 final size:22
Alignment explanation
Indices: 1604962--1605005 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
1604952 GCTATATTTT
1604962 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
*
1604983 CAAAT-TGTATTGATACATTCA
1 CAAATATGTATCGATACATTCA
1605004 CA
1 CA
1605006 TGGGAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:1609882 original size:50 final size:50
Alignment explanation
Indices: 1609823--1610081 Score: 385
Period size: 50 Copynumber: 5.2 Consensus size: 50
1609813 TATACTTAGA
1609823 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
1609873 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTCGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
1609923 GTCAACAATTATGACCACCTCCCTCTATTGTCAAAGGTTAGT-AAAAGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGA-ATC
* *
1609973 GTCAACAATTATGGTCACCTCCCTCTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * * *
1610023 GTCAACAATTATAGCTACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1610073 GTCAACAAT
1 GTCAACAAT
1610082 GGCAACAACT
Statistics
Matches: 187, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
49 3 0.02
50 181 0.97
51 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1610617 original size:30 final size:30
Alignment explanation
Indices: 1610543--1610620 Score: 113
Period size: 31 Copynumber: 2.6 Consensus size: 30
1610533 GCTCTATATT
1610543 TTTTTAACTT-AAAAAAACAACTATTAATC
1 TTTTTAACTTAAAAAAAACAACTATTAATC
** *
1610572 TTTTTACACACAAAAAAAATAACTATTAATC
1 TTTTTA-ACTTAAAAAAAACAACTATTAATC
1610603 TTTTTAACTTAAAAAAAA
1 TTTTTAACTTAAAAAAAA
1610621 AATAACTCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 6 0.14
30 12 0.29
31 24 0.57
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (30 bp):
TTTTTAACTTAAAAAAAACAACTATTAATC
Found at i:1611297 original size:26 final size:24
Alignment explanation
Indices: 1611241--1611297 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
1611231 GAATTTATTT
*
1611241 TTATAATAAAAATTAATTAAAATA
1 TTATAAAAAAAATTAATTAAAATA
* *
1611265 TAAATAAAAAAAATTTAATTCAAATAA
1 T-TATAAAAAAAA-TTAATTAAAAT-A
1611292 TTATAA
1 TTATAA
1611298 GTTATTAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.04
25 9 0.35
26 14 0.54
27 2 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TTATAAAAAAAATTAATTAAAATA
Found at i:1611555 original size:12 final size:12
Alignment explanation
Indices: 1611540--1611573 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1611530 TCGATTTTGC
1611540 TTTTGCTTTTAA
1 TTTTGCTTTTAA
* *
1611552 TTTTTCTTTTAC
1 TTTTGCTTTTAA
1611564 TTTTGCTTTT
1 TTTTGCTTTT
1611574 TGCCTCCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTGCTTTTAA
Found at i:1611560 original size:18 final size:18
Alignment explanation
Indices: 1611533--1611567 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1611523 AGGAAATTCG
*
1611533 ATTTTGCTTTTGCTTTTA
1 ATTTTGCTTTTACTTTTA
*
1611551 ATTTTTCTTTTACTTTT
1 ATTTTGCTTTTACTTTT
1611568 GCTTTTTGCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.71
Consensus pattern (18 bp):
ATTTTGCTTTTACTTTTA
Found at i:1611685 original size:42 final size:42
Alignment explanation
Indices: 1611624--1611705 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
1611614 TATAAATCTA
**
1611624 ATTTTTATAATTAAAAAATATATTTTACTCATATGAATAATC
1 ATTTTTATAATTAAAAAATATATTTTACAAATATGAATAATC
*
1611666 ATTTTTATAATTAATAAATATATTTTACAAATATGAATAA
1 ATTTTTATAATTAAAAAATATATTTTACAAATATGAATAA
1611706 AAATAGTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (42 bp):
ATTTTTATAATTAAAAAATATATTTTACAAATATGAATAATC
Found at i:1611704 original size:23 final size:23
Alignment explanation
Indices: 1611639--1611706 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 23
1611629 TATAATTAAA
*
1611639 AAATATATTTTACTCATATGAAT
1 AAATATATTTTACTAATATGAAT
1611662 -AATCAT-TTTTA-TAAT-T-AAT
1 AAAT-ATATTTTACTAATATGAAT
*
1611681 AAATATATTTTACAAATATGAAT
1 AAATATATTTTACTAATATGAAT
1611704 AAA
1 AAA
1611707 AATAGTAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
19 5 0.14
20 9 0.24
21 6 0.16
22 9 0.24
23 8 0.22
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (23 bp):
AAATATATTTTACTAATATGAAT
Found at i:1616383 original size:27 final size:27
Alignment explanation
Indices: 1616353--1616409 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1616343 CAATTGTTGC
1616353 CAGCCAATTTTGAAATTCAATTTGAAA
1 CAGCCAATTTTGAAATTCAATTTGAAA
1616380 CAGCCAATTTTGAAATTCAATTTGAAA
1 CAGCCAATTTTGAAATTCAATTTGAAA
1616407 CAG
1 CAG
1616410 TGAAGGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (27 bp):
CAGCCAATTTTGAAATTCAATTTGAAA
Found at i:1620803 original size:17 final size:18
Alignment explanation
Indices: 1620778--1620825 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
1620768 TAACAAAAAA
1620778 ATAAT-TAAAAC-ATAAT
1 ATAATATAAAACAATAAT
1620794 ATAATAT-AAACAATAAT
1 ATAATATAAAACAATAAT
*
1620811 ATAAATATAATACAA
1 AT-AATATAAAACAA
1620826 ATACATAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.33
17 8 0.30
18 5 0.19
19 5 0.19
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAATATAAAACAATAAT
Found at i:1620828 original size:17 final size:17
Alignment explanation
Indices: 1620785--1620825 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1620775 AAAATAATTA
1620785 AAAC-ATAATATAATAT
1 AAACAATAATATAATAT
1620801 AAACAATAATATAAATAT
1 AAACAATAATAT-AATAT
1620819 AATACAA
1 AA-ACAA
1620826 ATACATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 7 0.32
19 4 0.18
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (17 bp):
AAACAATAATATAATAT
Found at i:1621690 original size:6 final size:6
Alignment explanation
Indices: 1621679--1621705 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1621669 ATTTTGGTTG
1621679 TTTTGC TTTTGC TTTTGC TTTTGC TTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTT
1621706 AAAATCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:1623124 original size:17 final size:17
Alignment explanation
Indices: 1623089--1623127 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1623079 ATTTAGATAA
1623089 TTTAAGATTTGAATTTT
1 TTTAAGATTTGAATTTT
*
1623106 TTTAA-ATTTGAATTAT
1 TTTAAGATTTGAATTTT
1623122 TTTAAG
1 TTTAAG
1623128 TTCACACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (17 bp):
TTTAAGATTTGAATTTT
Found at i:1624441 original size:31 final size:31
Alignment explanation
Indices: 1624364--1624448 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
1624354 GCTCTATATT
1624364 TTTTTAACTT--AAAAAAACAACTATTAATC
1 TTTTTAACTTAAAAAAAAACAACTATTAATC
* *
1624393 TTTTTACAC--ACACAAAAAATAACTATTAATC
1 TTTTTA-ACTTA-AAAAAAAACAACTATTAATC
1624424 TTTTTAACTTAAAAAAAAAACAACT
1 TTTTTAACTT-AAAAAAAAACAACT
1624449 CCTATTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
29 6 0.13
30 4 0.09
31 23 0.51
32 11 0.24
33 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTTTAACTTAAAAAAAAACAACTATTAATC
Found at i:1624749 original size:7 final size:7
Alignment explanation
Indices: 1624739--1624768 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1624729 ATGAGAAAGA
*
1624739 GAAGGAT
1 GAAGAAT
1624746 GAAGAAT
1 GAAGAAT
1624753 GAAGAAT
1 GAAGAAT
1624760 GAAGAAT
1 GAAGAAT
1624767 GA
1 GA
1624769 TGAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (7 bp):
GAAGAAT
Found at i:1625382 original size:12 final size:12
Alignment explanation
Indices: 1625362--1625395 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1625352 TGAAATTCGA
1625362 TTTTGCTTTTAC
1 TTTTGCTTTTAC
*
1625374 TTTTTCTTTTAC
1 TTTTGCTTTTAC
1625386 TTTTGCTTTT
1 TTTTGCTTTT
1625396 TGACTCGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTGCTTTTAC
Found at i:1625388 original size:18 final size:18
Alignment explanation
Indices: 1625362--1625396 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1625352 TGAAATTCGA
*
1625362 TTTTGCTTTTACTTTTTC
1 TTTTACTTTTACTTTTTC
*
1625380 TTTTACTTTTGCTTTTT
1 TTTTACTTTTACTTTTT
1625397 GACTCGTCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTACTTTTACTTTTTC
Found at i:1626128 original size:14 final size:14
Alignment explanation
Indices: 1626111--1626149 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1626101 TAAAATTTAA
*
1626111 TAAAATAAAAAAAC
1 TAAATTAAAAAAAC
* *
1626125 TAAATTACAAAAGC
1 TAAATTAAAAAAAC
1626139 TAAATTAAAAA
1 TAAATTAAAAA
1626150 TAACATCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.21
Consensus pattern (14 bp):
TAAATTAAAAAAAC
Found at i:1626371 original size:12 final size:14
Alignment explanation
Indices: 1626350--1626415 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 14
1626340 GTCCATATTA
1626350 TATATTTTT-AATT
1 TATATTTTTAAATT
1626363 TAT-TTTTTAAATT
1 TATATTTTTAAATT
1626376 ATATATTTTTAAATT
1 -TATATTTTTAAATT
*
1626391 TA-ATCTTTAATAATT
1 TATAT-TTTTA-AATT
1626406 TAATATTTTT
1 T-ATATTTTT
1626416 CATTAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
12 5 0.11
13 9 0.20
14 9 0.20
15 15 0.34
16 4 0.09
17 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTTTTAAATT
Found at i:1626384 original size:15 final size:15
Alignment explanation
Indices: 1626346--1626390 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
1626336 ATCCGTCCAT
1626346 ATTATATATTTTT-A
1 ATTATATATTTTTAA
1626360 ATT-TAT-TTTTTAA
1 ATTATATATTTTTAA
1626373 ATTATATATTTTTAA
1 ATTATATATTTTTAA
1626388 ATT
1 ATT
1626391 TAATCTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.18
13 7 0.25
14 6 0.21
15 10 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTATATATTTTTAA
Found at i:1626987 original size:22 final size:22
Alignment explanation
Indices: 1626945--1626988 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1626935 ACATCTTTAA
* *
1626945 TTATTATTAATACATATAATTT
1 TTATAATTAATACATAAAATTT
1626967 TTATAATTAATGA-ATAAAATTT
1 TTATAATTAAT-ACATAAAATTT
1626989 ACATTTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTATAATTAATACATAAAATTT
Found at i:1629048 original size:27 final size:27
Alignment explanation
Indices: 1629004--1629066 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
1628994 TCAATTTGTC
* *
1629004 AAAAATGGTGGTTACTTTGTGTTTATA
1 AAAAATGGTAGTTACTTTGTATTTATA
* * *
1629031 AAAAATGGTAGTTTCTTTTTATTTGTA
1 AAAAATGGTAGTTACTTTGTATTTATA
1629058 AAAAATGGT
1 AAAAATGGT
1629067 GGCATATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.44
Consensus pattern (27 bp):
AAAAATGGTAGTTACTTTGTATTTATA
Found at i:1629076 original size:27 final size:26
Alignment explanation
Indices: 1628997--1629077 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
1628987 GCCACCATCA
* *
1628997 ATTTGTCAAAAATGGTGGTTACTTTGT
1 ATTTGTAAAAAATGGTGGTTA-TTTTT
* * * *
1629024 GTTTATAAAAAATGGTAGTTTCTTTTT
1 ATTTGTAAAAAATGGT-GGTTATTTTT
*
1629051 ATTTGTAAAAAATGGTGGCATATTTTT
1 ATTTGTAAAAAATGGTGG-TTATTTTT
1629078 TGTCAAAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
26 1 0.02
27 37 0.90
28 3 0.07
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (26 bp):
ATTTGTAAAAAATGGTGGTTATTTTT
Found at i:1629085 original size:24 final size:24
Alignment explanation
Indices: 1629052--1629109 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1629042 TTTCTTTTTA
* *
1629052 TTTGTAAAAAATGGTGGCATATTT
1 TTTGTCAAAAATGGTGGCATATTG
* *
1629076 TTTGTCAAAATTTGTGGCATATTG
1 TTTGTCAAAAATGGTGGCATATTG
1629100 TTTGTCAAAA
1 TTTGTCAAAA
1629110 TTTGTGGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCATATTG
Found at i:1629110 original size:24 final size:24
Alignment explanation
Indices: 1629065--1629117 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1629055 GTAAAAAATG
*
1629065 GTGGCATATTTTTTGTCAAAATTT
1 GTGGCATATTGTTTGTCAAAATTT
1629089 GTGGCATATTGTTTGTCAAAATTT
1 GTGGCATATTGTTTGTCAAAATTT
1629113 GTGGC
1 GTGGC
1629118 TAATTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (24 bp):
GTGGCATATTGTTTGTCAAAATTT
Found at i:1631684 original size:21 final size:22
Alignment explanation
Indices: 1631655--1631700 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1631645 TGTTCAGACA
** *
1631655 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1631677 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1631698 AGT
1 AGT
1631701 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1633614 original size:27 final size:27
Alignment explanation
Indices: 1633583--1633655 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
1633573 AGCCACCATT
*
1633583 TGTTTGTCAAAAATAGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
1633610 TGTTTGTCAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
1633637 TATTTGTCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
1633656 CATATTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:1633666 original size:24 final size:25
Alignment explanation
Indices: 1633581--1633672 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 25
1633571 AAAGCCACCA
* *
1633581 TTTGTTTGTCAAAAATAGTGGTTACT
1 TTTGTTTGTCAAAAATGGTGGTCA-T
*
1633607 TTGTGTTTGTCAAAAATGGTGGTTTCTT
1 TT-TGTTTGTCAAAAATGGTGG--TCAT
*
1633635 TTTATTTGTCAAAAATGGTGG-CAT
1 TTTGTTTGTCAAAAATGGTGGTCAT
*
1633659 ATTGTTTGTCAAAA
1 TTTGTTTGTCAAAA
1633673 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
24 14 0.25
26 2 0.04
27 36 0.64
28 3 0.05
29 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (25 bp):
TTTGTTTGTCAAAAATGGTGGTCAT
Found at i:1634291 original size:25 final size:25
Alignment explanation
Indices: 1634238--1634294 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
1634228 TATTTTAAAT
*
1634238 ATAATAAATATTATTATAATTAATT
1 ATAATAAATATTATTATAATTAATA
1634263 ATAATAAATATTAATTATAA-TAATA
1 ATAATAAATATT-ATTATAATTAATA
1634288 ATAATAA
1 ATAATAA
1634295 TTTTAACCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATAAATATTATTATAATTAATA
Found at i:1635479 original size:16 final size:17
Alignment explanation
Indices: 1635454--1635489 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1635444 AAAATTTTAT
1635454 TTAAAAATTTAA-TAAA
1 TTAAAAATTTAATTAAA
*
1635470 TTAAATATTTAATTAAA
1 TTAAAAATTTAATTAAA
1635487 TTA
1 TTA
1635490 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAAATTTAATTAAA
Found at i:1636831 original size:12 final size:12
Alignment explanation
Indices: 1636814--1636850 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1636804 TTGAACTGAA
1636814 AATATTTTAAAG
1 AATATTTTAAAG
1636826 AATATTTTAAAG
1 AATATTTTAAAG
1636838 AATATTTTAAAG
1 AATATTTTAAAG
1636850 A
1 A
1636851 GTTGAACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AATATTTTAAAG
Found at i:1636865 original size:24 final size:23
Alignment explanation
Indices: 1636799--1636872 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
1636789 GAGAAAAAAA
1636799 AAAGATTGAACTGAAAATATTTT
1 AAAGATTGAACTGAAAATATTTT
* ** *
1636822 AAAGAAT-ATTTTAAAGAATATTTT
1 AAAGATTGA-ACTGAA-AATATTTT
1636846 AAAGAGTTGAACTGAAAATATTTT
1 AAAGA-TTGAACTGAAAATATTTT
1636870 AAA
1 AAA
1636873 AAATATCTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
22 1 0.03
23 9 0.23
24 24 0.62
25 4 0.10
26 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (23 bp):
AAAGATTGAACTGAAAATATTTT
Found at i:1637795 original size:2 final size:2
Alignment explanation
Indices: 1637788--1637821 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1637778 ATGATTCTTC
1637788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1637822 TATTTGTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1640104 original size:36 final size:37
Alignment explanation
Indices: 1640043--1640156 Score: 133
Period size: 36 Copynumber: 3.1 Consensus size: 37
1640033 GCAAAATCAA
* * *
1640043 ATTATGAAGATTACGATCTTTGTAATTATAATTAGAAT
1 ATTATGAAGATTACAAT-TTTGTAATCATAATCAGAAT
*
1640081 ATTATGAA-ATTACAATTTTGTAATCATAATCAAAAT
1 ATTATGAAGATTACAATTTTGTAATCATAATCAGAAT
* * * *
1640117 ATTAT-AAGATTACTATTCTATAATCATAATCAGGAT
1 ATTATGAAGATTACAATTTTGTAATCATAATCAGAAT
1640153 ATTA
1 ATTA
1640157 AAAAATCCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.03
36 49 0.74
37 7 0.11
38 8 0.12
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (37 bp):
ATTATGAAGATTACAATTTTGTAATCATAATCAGAAT
Found at i:1640831 original size:3 final size:3
Alignment explanation
Indices: 1640823--1640849 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1640813 ATGGTTCAGT
1640823 AGC AGC AGC AGC AGC AGC AGC AGC AGC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC
1640850 TTGTGCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:1641180 original size:5 final size:5
Alignment explanation
Indices: 1641170--1641217 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
1641160 GCTAAAACTG
1641170 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1641218 AAATAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:1646462 original size:20 final size:21
Alignment explanation
Indices: 1646437--1646475 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1646427 AACCGAATTA
*
1646437 ATATTTAA-AATATATAAAAT
1 ATATTTAATAAAATATAAAAT
1646457 ATATTTAATAAAATATAAA
1 ATATTTAATAAAATATAAA
1646476 TTTAAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATTTAATAAAATATAAAAT
Found at i:1647573 original size:2 final size:2
Alignment explanation
Indices: 1647566--1647613 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1647556 AAATAAGAAC
* * * *
1647566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AC AT GT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1647608 AT AT AT
1 AT AT AT
1647614 GATACACATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1649300 original size:2 final size:2
Alignment explanation
Indices: 1649295--1649319 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1649285 AAAAAATTGA
1649295 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
1649320 GAGAGAGAGA
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:1649324 original size:2 final size:2
Alignment explanation
Indices: 1649319--1649360 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1649309 ATATATATAT
* *
1649319 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1649361 CAGTTAAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1651647 original size:13 final size:14
Alignment explanation
Indices: 1651622--1651694 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 14
1651612 TTATTTTTGT
1651622 GTAATTAGTTTATA
1 GTAATTAGTTTATA
1651636 GTAATT-GTTTATTA
1 GTAATTAGTTTA-TA
**
1651650 TGTGAAATTAGGTTTAGC
1 -GT--AATTA-GTTTATA
*
1651668 GTAATTAGTTTAGGA
1 GTAATTAGTTTA-TA
1651683 GTAATTAGTTTA
1 GTAATTAGTTTA
1651695 AAGCCTATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.10
14 13 0.27
15 20 0.41
17 6 0.12
19 5 0.10
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.47
Consensus pattern (14 bp):
GTAATTAGTTTATA
Found at i:1651648 original size:32 final size:33
Alignment explanation
Indices: 1651619--1651679 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
1651609 TTATTATTTT
* *
1651619 TGTGTAATTA-GTTTATAGTAATT-GTTTATTA
1 TGTGAAATTAGGTTTAGAGTAATTAGTTTATTA
*
1651650 TGTGAAATTAGGTTTAGCGTAATTAGTTTA
1 TGTGAAATTAGGTTTAGAGTAATTAGTTTA
1651680 GGAGTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
32 11 0.44
33 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.49
Consensus pattern (33 bp):
TGTGAAATTAGGTTTAGAGTAATTAGTTTATTA
Found at i:1657124 original size:402 final size:403
Alignment explanation
Indices: 1655860--1657478 Score: 2483
Period size: 402 Copynumber: 4.0 Consensus size: 403
1655850 GGCATCAGCC
* * *
1655860 AGATAGGGTTTTACGTCAGTTCGGGCTAGATCAACCTATTCCTAAAACCCCAG-AATAGCCGTAG
1 AGATAGGGTCTTACGTCAGTTCGAGCTAGATCAACCTATTCCTAAAACCCC-GCAACAGCCGTAG
1655924 AAGTTACATACTATCACATTGGCTAGGAGAATTGACGAGTTTTGGCCTTCTATACATAGGCAGTA
65 AAGTTACATACTATCACATTGGCTAGGAGAATTGACGAGTTTTGGCCTTCTATACATAGGCAGTA
* *
1655989 TATTGAATTGTGGAACAATCATGCTAAGAGAA-TGGTTATTGGCACACCATTATAGCGACCTTTA
130 TATTGAATTGTGGGACAATCATGCTAAGA-AAGTGGTTATTGGCACACCATTACAGCGACCTTTA
* * * * *
1656053 TCAACACAGTCAAAGTATATGTGCTGGTATAGAAAAATCACGAGACACTAGATTGCTAAAAGTAT
194 TCAGCACAGTCAGAGTATATGCGCTGGTATAGAAAAATCACGAGACACTGGATTGCTAAAAGTAC
* * * *
1656118 TGCCCATACTGGAGTCGTAGTTAGTAATTTGGTTTTGTAAGTTTAATTTAACTCATACTTTGGTA
259 TGCCCATGCTGGAGTCGCAGTTAGTAATTTGGTTTTGTAAG---GATTTAAATCATACTTTGGTA
*
1656183 ATTTTTTATTTGATTATATTATTTTTTAGGTTGATGAAGTGGCACAACTTAATTCATTAGCTGCT
321 ATTTTTTATTTGATTATATTATTTTTTAGGTTGACGAAGTGGCACAACTTAATTCATTAGCTGCT
*
1656248 GATCCTGAGTACATGCTG
386 GATCCTGGGTACATGCTG
* * * *
1656266 AGATAAGGTCTTACGTCAGTTCGGGCTAAATCAACCTATTCCTAAAACCCCACAACAGCCGTAGA
1 AGATAGGGTCTTACGTCAGTTCGAGCTAGATCAACCTATTCCTAAAACCCCGCAACAGCCGTAGA
* * * *
1656331 AGTTACATACTATCACATTGGTTGGGAGAATTGACGAGTTTTAGCCTTCTATACATAGGTAGTAT
66 AGTTACATACTATCACATTGGCTAGGAGAATTGACGAGTTTTGGCCTTCTATACATAGGCAGTAT
* * * * *
1656396 ATTGAATTGTGAGACAATCGTGCTAAGAGAGTGGTTATTGGCACACCATTATAGCAACCTTTATC
131 ATTGAATTGTGGGACAATCATGCTAAGAAAGTGGTTATTGGCACACCATTACAGCGACCTTTATC
* ** *
1656461 AGCAC-GTCAGAGTATATGCGCTGGTATAGAAAAATTACGAGATGCTGGATTGCTAAAAGTACTA
196 AGCACAGTCAGAGTATATGCGCTGGTATAGAAAAATCACGAGACACTGGATTGCTAAAAGTACTG
* * *
1656525 CACATGCTGGAGTCGCGGTTAGTAATTTGGTTTTGTAAGGTTAATTTAAATCATACTTTAGTAA-
261 CCCATGCTGGAGTCGCAGTTAGTAATTTGGTTTTGTAAGG---ATTTAAATCATACTTTGGTAAT
* * *
1656589 TTTTTATTTGATTATATTGTTTTTTAGATTGACGAAGTGGCACAACTTAATTCATTAGCTACTGA
323 TTTTTATTTGATTATATTATTTTTTAGGTTGACGAAGTGGCACAACTTAATTCATTAGCTGCTGA
*
1656654 TCCTAGGTACATGCTG
388 TCCTGGGTACATGCTG
* *
1656670 AGATAGGGTCTTACGTCAGTTCGAGCTAGATCAACCTATTCTTAAAACCCCGCAACAACCGTAGA
1 AGATAGGGTCTTACGTCAGTTCGAGCTAGATCAACCTATTCCTAAAACCCCGCAACAGCCGTAGA
* * *
1656735 AGTTACATACTATCACATTGGCTGGGAGAATTGACAAGTTTTGGCCTTCTATACATAGGCAATAT
66 AGTTACATACTATCACATTGGCTAGGAGAATTGACGAGTTTTGGCCTTCTATACATAGGCAGTAT
1656800 ATTGAATTGTGGGACAATCATGCTAAGAAAGTGGTTATTGGCACACCATTACAGCGACCTTTATC
131 ATTGAATTGTGGGACAATCATGCTAAGAAAGTGGTTATTGGCACACCATTACAGCGACCTTTATC
* * ** * * *
1656865 AGTACAGTTAGAGTATATGCATTAGTATAGAAAAATCACAAGACAATGGATTGCTAAAAGTACTG
196 AGCACAGTCAGAGTATATGCGCTGGTATAGAAAAATCACGAGACACTGGATTGCTAAAAGTACTG
1656930 CCCATGCTGGAGTCGCAGTTAGTAATTTGGTTTTGTAAGG-TTTAAATCATACTTTGGTAATTTT
261 CCCATGCTGGAGTCGCAGTTAGTAATTTGGTTTTGTAAGGATTTAAATCATACTTTGGTAATTTT
**
1656994 TTATTTGATTATATTATTTTTTAGGTTGACGAAGTGGCACAACTTAATTCATTAGCTGCTGATGT
326 TTATTTGATTATATTATTTTTTAGGTTGACGAAGTGGCACAACTTAATTCATTAGCTGCTGATCC
1657059 TGGGTACATGCTG
391 TGGGTACATGCTG
* * *
1657072 AGATAGGGTCTTACGTCAGTTTGAGCTAGATCAACCTATTCTTAAAACCCCGCAACAGCCATAGA
1 AGATAGGGTCTTACGTCAGTTCGAGCTAGATCAACCTATTCCTAAAACCCCGCAACAGCCGTAGA
* *
1657137 AGTTACATACTATCACATTGGCTATGAGAATTGATGAGTTTTGGCCTTCTATACATAGGCAGTAT
66 AGTTACATACTATCACATTGGCTAGGAGAATTGACGAGTTTTGGCCTTCTATACATAGGCAGTAT
* * * *
1657202 ATTGAATTGTGGGACAATCGTGCTAAGAGAGTAGTTATTGGCACACCATTACAACGACCTTTATC
131 ATTGAATTGTGGGACAATCATGCTAAGAAAGTGGTTATTGGCACACCATTACAGCGACCTTTATC
** * *
1657267 AGCACAGTCAGAGTATATGCGCTGGTATAGAAAAATCACGAGATGCTGGATTGCAAAAAGTGCTG
196 AGCACAGTCAGAGTATATGCGCTGGTATAGAAAAATCACGAGACACTGGATTGCTAAAAGTACTG
*
1657332 CCCATGCTGGAGTCGCGGTTAGTAATTTGGTTTTGTAAGGTTAATTTAAATCATACTTTGGTAAT
261 CCCATGCTGGAGTCGCAGTTAGTAATTTGGTTTTGTAAGG---ATTTAAATCATACTTTGGTAAT
*
1657397 TTTTTATTTGATTATATTATTTTTTAGGTTGAGGAAGTGGCACAACTTAATTCATTAGCTGCTGA
323 TTTTTATTTGATTATATTATTTTTTAGGTTGACGAAGTGGCACAACTTAATTCATTAGCTGCTGA
1657462 TCCTGGGTACATGCTG
388 TCCTGGGTACATGCTG
1657478 A
1 A
1657479 CTAATGACGA
Statistics
Matches: 1103, Mismatches: 99, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
401 19 0.02
402 351 0.32
404 258 0.23
405 193 0.17
406 282 0.26
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (403 bp):
AGATAGGGTCTTACGTCAGTTCGAGCTAGATCAACCTATTCCTAAAACCCCGCAACAGCCGTAGA
AGTTACATACTATCACATTGGCTAGGAGAATTGACGAGTTTTGGCCTTCTATACATAGGCAGTAT
ATTGAATTGTGGGACAATCATGCTAAGAAAGTGGTTATTGGCACACCATTACAGCGACCTTTATC
AGCACAGTCAGAGTATATGCGCTGGTATAGAAAAATCACGAGACACTGGATTGCTAAAAGTACTG
CCCATGCTGGAGTCGCAGTTAGTAATTTGGTTTTGTAAGGATTTAAATCATACTTTGGTAATTTT
TTATTTGATTATATTATTTTTTAGGTTGACGAAGTGGCACAACTTAATTCATTAGCTGCTGATCC
TGGGTACATGCTG
Found at i:1657903 original size:30 final size:28
Alignment explanation
Indices: 1657868--1657936 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
1657858 ATTTTATGCT
* *
1657868 TACCCACCATATTTCCCTACTCAATCTCCA
1 TACCCAACATA-TT-CCTACTCAACCTCCA
* *
1657898 TACCCATCATA-TCTTACTCAACCTCCA
1 TACCCAACATATTCCTACTCAACCTCCA
1657925 TACCCAACATAT
1 TACCCAACATAT
1657937 CCTGCCACGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 23 0.68
28 1 0.03
30 10 0.29
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.29
Consensus pattern (28 bp):
TACCCAACATATTCCTACTCAACCTCCA
Found at i:1657915 original size:27 final size:27
Alignment explanation
Indices: 1657885--1657937 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1657875 CATATTTCCC
* *
1657885 TACTCAATCTCCATACCCATCATATCT
1 TACTCAACCTCCATACCCAACATATCT
1657912 TACTCAACCTCCATACCCAACATATC
1 TACTCAACCTCCATACCCAACATATC
1657938 CTGCCACGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (27 bp):
TACTCAACCTCCATACCCAACATATCT
Found at i:1658315 original size:36 final size:36
Alignment explanation
Indices: 1658266--1658459 Score: 122
Period size: 36 Copynumber: 5.2 Consensus size: 36
1658256 TAGTTATTAG
1658266 TTGTTGATAGTAGTAATGTGAAATATGCAGAAATAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAATAT
* * * * *
1658302 TTGTTGATTGTAGTTATCGTGCAGATTAT-CTTGGAATAT
1 TTGTTGATAGTAGTAAT-GTG-A-AATATGC-AGAAATAT
* * *
1658341 TTGTTAATAGTAGCAATGTGAAATATGCAGAAACAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAATAT
* * * * * * * *
1658377 TTATTGATTGTAGTTATCGTGCAGATTAT-CTCGGATTAG
1 TTGTTGATAGTAGTAAT-GTG-A-AATATGC-AGAAATAT
* * * *
1658416 TTGTTGATAGTAGTACTATGAAATATGCTGAAACAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAATAT
1658452 TTGTTGAT
1 TTGTTGAT
1658460 TGTAATTATC
Statistics
Matches: 113, Mismatches: 35, Indels: 20
0.67 0.21 0.12
Matches are distributed among these distances:
36 51 0.45
37 10 0.09
38 9 0.08
39 43 0.38
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (36 bp):
TTGTTGATAGTAGTAATGTGAAATATGCAGAAATAT
Found at i:1658345 original size:39 final size:39
Alignment explanation
Indices: 1658297--1658429 Score: 112
Period size: 39 Copynumber: 3.5 Consensus size: 39
1658287 AATATGCAGA
* *
1658297 AATATTTGTTGATTGTAGTTATCGTGCAGATTATCTTGG
1 AATATTTGTTGATAGTAGTTATCGTGCAGATTATCTAGG
* ** * *
1658336 AATATTTGTTAATAGTAGCAAT-GTG-A-AATATGC-AGA
1 AATATTTGTTGATAGTAGTTATCGTGCAGATTAT-CTAGG
* * * *
1658372 AACATTTATTGATTGTAGTTATCGTGCAGATTATCTCGG
1 AATATTTGTTGATAGTAGTTATCGTGCAGATTATCTAGG
* *
1658411 ATTAGTTGTTGATAGTAGT
1 AATATTTGTTGATAGTAGT
1658430 ACTATGAAAT
Statistics
Matches: 68, Mismatches: 21, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
36 21 0.31
37 5 0.07
38 5 0.07
39 37 0.54
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (39 bp):
AATATTTGTTGATAGTAGTTATCGTGCAGATTATCTAGG
Found at i:1658489 original size:75 final size:75
Alignment explanation
Indices: 1658261--1658489 Score: 332
Period size: 75 Copynumber: 3.1 Consensus size: 75
1658251 CGGATTAGTT
*
1658261 ATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAATATTTGTTGATTGTAGTTATCGTGCAG
1 ATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGTTATCGTGCAG
*
1658326 ATTATCTTGG
66 ATTATCTCGG
* * * * *
1658336 AATATTTGTTAATAGTAGCAATGTGAAATATGCAGAAACATTTATTGATTGTAGTTATCGTGCAG
1 ATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGTTATCGTGCAG
1658401 ATTATCTCGG
66 ATTATCTCGG
* * * * * *
1658411 ATTAGTTGTTGATAGTAGTACTATGAAATATGCTGAAACATTTGTTGATTGTAATTATCATGTAG
1 ATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGTTATCGTGCAG
*
1658476 ATTATCTCAG
66 ATTATCTCGG
1658486 ATTA
1 ATTA
1658490 TCGTTTCATC
Statistics
Matches: 135, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 135 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (75 bp):
ATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGTTATCGTGCAG
ATTATCTCGG
Found at i:1663706 original size:18 final size:17
Alignment explanation
Indices: 1663685--1663720 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1663675 ATTAAACTCG
1663685 AAAAATTAATTTAACAAA
1 AAAAATTAATTTAA-AAA
*
1663703 AAAAATTTATTTAAAAA
1 AAAAATTAATTTAAAAA
1663720 A
1 A
1663721 TGAGTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTAATTTAAAAA
Done.