Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008548.1 Hibiscus syriacus cultivar Beakdansim tig00111440_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: 1170587
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:610495 original size:32 final size:31
Alignment explanation
Indices: 610441--610503 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
610431 AAATAGAAGG
610441 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTT-AGGGTGA
***
610473 AGTGGTGAAAGAAGTTTCGGTGTTAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAGGGTGA
610504 TATTAAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.25
32 21 0.75
ACGTcount: A:0.29, C:0.02, G:0.44, T:0.25
Consensus pattern (31 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAGGGTGA
Found at i:612258 original size:183 final size:184
Alignment explanation
Indices: 611928--612428 Score: 977
Period size: 183 Copynumber: 2.7 Consensus size: 184
611918 AGAAAGCTTA
611928 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
1 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
611993 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
66 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
612058 TAAATCGTATCGACACATTTTTCTTCCAATATGGATATAAAGTACCGACACAAT
131 TAAATCGTATCGACACATTTTTCTTCCAATATGGATATAAAGTACCGACACAAT
612112 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
1 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
612177 ATATTAC-AAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
66 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
612241 TAAATCGTATCGACACATTTTTCTTCCAATATGGATATAAAGTACCGACACAAT
131 TAAATCGTATCGACACATTTTTCTTCCAATATGGATATAAAGTACCGACACAAT
*
612295 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
1 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
612360 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTG
66 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
612425 TAAA
131 TAAA
612429 AAGTGTCCAT
Statistics
Matches: 314, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
183 182 0.58
184 132 0.42
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (184 bp):
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
TAAATCGTATCGACACATTTTTCTTCCAATATGGATATAAAGTACCGACACAAT
Found at i:612450 original size:22 final size:22
Alignment explanation
Indices: 612420--612472 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
612410 ATGTCGACAC
*
612420 TTTTGTAAAAAGTG-TCCATACT
1 TTTTATAAAAAG-GATCCATACT
*
612442 TTTTATAAAAAGGATCGATACT
1 TTTTATAAAAAGGATCCATACT
*
612464 TTTTTTAAA
1 TTTTATAAA
612473 GATATGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (22 bp):
TTTTATAAAAAGGATCCATACT
Found at i:613887 original size:3 final size:3
Alignment explanation
Indices: 613879--613952 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
613869 ACTTGTTTGG
* * * **
613879 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
613927 AGC TTC ATC GTC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
613953 TGTCATCTTC
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:613946 original size:42 final size:42
Alignment explanation
Indices: 613887--613977 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
613877 GGATCATCAT
*
613887 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* ** * *
613929 CTTCATCGTCATCATCATCATCATTGTCATCTTCATTGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
613971 CTTCATC
1 CTTCATC
613978 TTCTGCGACC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.37
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:613958 original size:9 final size:9
Alignment explanation
Indices: 613892--613959 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 9
613882 ATCATCTTCA
*
613892 TCATCATCA
1 TCATCATCG
613901 TCATCATCG
1 TCATCATCG
*
613910 TCATCATCT
1 TCATCATCG
**
613919 TCATCGCCAG
1 TCATCATC-G
*
613929 -CTTCATCG
1 TCATCATCG
*
613937 TCATCATCA
1 TCATCATCG
*
613946 TCATCATTG
1 TCATCATCG
613955 TCATC
1 TCATC
613960 TTCATTGTCA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
8 1 0.02
9 44 0.98
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.35
Consensus pattern (9 bp):
TCATCATCG
Found at i:613980 original size:6 final size:6
Alignment explanation
Indices: 613883--613980 Score: 56
Period size: 6 Copynumber: 16.3 Consensus size: 6
613873 GTTTGGATCA
* * * * * * * *
613883 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
613931 TCATCG TCATCA TCATCA TCAT-T GTCATCT TCAT-T GTCAGCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT -TCATCT TCATCT -TCATCT TCATCT
613979 TC
1 TC
613981 TGCGACCGAT
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
5 1 0.01
6 70 0.96
7 2 0.03
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:615791 original size:197 final size:198
Alignment explanation
Indices: 615415--616564 Score: 2076
Period size: 197 Copynumber: 5.8 Consensus size: 198
615405 TTTAAATTAG
615415 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
615480 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
615545 CGACACTTTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAA
131 CGAC-TTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAA
615609 AAAA
195 AAAA
615613 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
615678 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * **
615742 CGACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
131 CGACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAAA
615807 AAA
196 AAA
*
615810 TATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
615875 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
615939 CGACACTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAAA
131 CGACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAAA
616004 AAA
196 AAA
616007 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
616072 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * **
616137 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CG--ACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAA
616202 AAAAA
194 AAAAA
616207 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
616272 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
616337 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGT--AA
131 CGAC-TTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAA
616400 AAAA
195 AAAA
616404 TATCGACAACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTAT
1 TATCGAC-ACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTAT
616469 AATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
616534 TCGACACTTTTTTATATATGGATCGACACTT
130 TCG--ACTTTTTTATATATGGATCGACACTT
616565 AATGCAGTAT
Statistics
Matches: 918, Mismatches: 26, Indels: 15
0.96 0.03 0.02
Matches are distributed among these distances:
196 5 0.01
197 388 0.42
198 257 0.28
199 75 0.08
200 193 0.21
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAAA
AAA
Found at i:618182 original size:18 final size:19
Alignment explanation
Indices: 618159--618196 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
618149 GTTAAATTAC
*
618159 ATTA-GGTTAATATTTATT
1 ATTAGGGTTAATATTAATT
*
618177 ATTAGGGTTTATATTAATT
1 ATTAGGGTTAATATTAATT
618196 A
1 A
618197 AGATTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
ATTAGGGTTAATATTAATT
Found at i:620091 original size:35 final size:35
Alignment explanation
Indices: 620045--620114 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
620035 TTTCATTTAG
620045 GGGGAATCGATACCCCCCAGGGAGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGAGAATCTGTTCCC
* *
620080 GGGGAATCGATACCCCCTAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGAGAATCTGTTCCC
620115 CCTGCACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGAGAATCTGTTCCC
Found at i:623180 original size:2 final size:2
Alignment explanation
Indices: 623173--623238 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
623163 TCAATCAAAT
623173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
623215 TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
623239 TTTTCCAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:626696 original size:30 final size:33
Alignment explanation
Indices: 626660--626723 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 33
626650 TTATTGTAGG
* *
626660 TATCTAATGTTT-TTTC-GTTATCA-TTTAAGA
1 TATCTAAAGTTTCTTTCTATTATCATTTTAAGA
626690 TATCTAAAGTTTCTTTCTATTATCATTTTAAGA
1 TATCTAAAGTTTCTTTCTATTATCATTTTAAGA
626723 T
1 T
626724 TATTTTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.38
31 4 0.14
32 6 0.21
33 8 0.28
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (33 bp):
TATCTAAAGTTTCTTTCTATTATCATTTTAAGA
Found at i:628858 original size:28 final size:28
Alignment explanation
Indices: 628805--628860 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
628795 ACCATTGTTG
**
628805 CTTTCAAGCACTGACTCGACGGTATAAT
1 CTTTCAAGCACTGACTCGACAATATAAT
* *
628833 CTTTCAAGCACTGGCTCGATAATATAAT
1 CTTTCAAGCACTGACTCGACAATATAAT
628861 ATAAACAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (28 bp):
CTTTCAAGCACTGACTCGACAATATAAT
Found at i:629783 original size:21 final size:20
Alignment explanation
Indices: 629740--629782 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
629730 TTCGATACAA
629740 TTAATAGAAAATGCAGTATTT
1 TTAATAGAAAAT-CAGTATTT
629761 TTAATGAGAAAAT-AGTATTT
1 TTAAT-AGAAAATCAGTATTT
629781 TT
1 TT
629783 TTAGTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 5 0.24
22 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (20 bp):
TTAATAGAAAATCAGTATTT
Found at i:630561 original size:7 final size:7
Alignment explanation
Indices: 630549--630573 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
630539 CTCCAACTTA
630549 GCAAATT
1 GCAAATT
630556 GCAAATT
1 GCAAATT
630563 GCAAATT
1 GCAAATT
630570 GCAA
1 GCAA
630574 TTAGCATGGT
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (7 bp):
GCAAATT
Found at i:631336 original size:20 final size:20
Alignment explanation
Indices: 631311--631533 Score: 167
Period size: 20 Copynumber: 11.1 Consensus size: 20
631301 TAAACGCGCT
* *
631311 TTGCGAATTTAACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
* **
631331 TTGCGAATTTGAAATTCACTG
1 TTGCGAATTTG-ACTTCTGTG
*
631352 TTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCTGTG
631372 TTGCGAATTTGACTAT-TGTG
1 TTGCGAATTTGACT-TCTGTG
631392 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
631412 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
** *
631432 TTATG-ATTT-ACAAATTC-GCG
1 TTGCGAATTTGAC---TTCTGTG
*
631452 TTGCG-ATTT-ACAGATTC-GCG
1 TTGCGAATTTGAC---TTCTGTG
*
631472 TTGCGAATTTGACTTCAGTG
1 TTGCGAATTTGACTTCTGTG
* **
631492 TTGCGCATTTGACTATC-GCA
1 TTGCGAATTTGACT-TCTGTG
631512 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
631532 TT
1 TT
631534 ACAACTTACA
Statistics
Matches: 169, Mismatches: 22, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
18 2 0.01
19 10 0.06
20 128 0.76
21 27 0.16
22 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:631485 original size:100 final size:100
Alignment explanation
Indices: 631367--631582 Score: 337
Period size: 100 Copynumber: 2.2 Consensus size: 100
631357 AATTTGACTA
* **
631367 TCGCGTTGCGAATTTGACTAT-TGTGTTGCGAATTTGACT-TCTGTGTTGCGAATTTGACTTCTG
1 TCGCGTTGCGAATTTGACT-TCAGTGTTGCGAATTTGACTATC-GCATTGCGAATTTGACTTCTG
** *
631430 TGTTATGATTTACAAATTCGCGTTGCGATTTACAGAT
64 TGTTACAACTTACAAATTCGCGTTGCGATTTACAGAT
*
631467 TCGCGTTGCGAATTTGACTTCAGTGTTGCGCATTTGACTATCGCATTGCGAATTTGACTTCTGTG
1 TCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTATCGCATTGCGAATTTGACTTCTGTG
631532 TTACAACTTACAAATTCGCGTTGCGATTTACAGAT
66 TTACAACTTACAAATTCGCGTTGCGATTTACAGAT
631567 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
631583 GAAACCGGGT
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
99 1 0.01
100 104 0.97
101 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (100 bp):
TCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTATCGCATTGCGAATTTGACTTCTGTG
TTACAACTTACAAATTCGCGTTGCGATTTACAGAT
Found at i:631556 original size:40 final size:41
Alignment explanation
Indices: 631459--631557 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 41
631449 GCGTTGCGAT
* * * *
631459 TTACAGATTCGCGTTGCGAATTTGACTTCAGTGTTGCGCAT
1 TTACAAATTCGCGTTGCGAATTTGACTTCAGTGTTACGAAC
* * *
631500 TTGAC-TA-TCGCATTGCGAATTTGACTTCTGTGTTAC-AAC
1 TT-ACAAATTCGCGTTGCGAATTTGACTTCAGTGTTACGAAC
631539 TTACAAATTCGCGTTGCGA
1 TTACAAATTCGCGTTGCGA
631558 TTTACAGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
38 2 0.04
39 4 0.09
40 36 0.77
41 3 0.06
42 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (41 bp):
TTACAAATTCGCGTTGCGAATTTGACTTCAGTGTTACGAAC
Found at i:631568 original size:20 final size:20
Alignment explanation
Indices: 631539--631577 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
631529 GTGTTACAAC
631539 TTACAAATTCGCGTTGCGAT
1 TTACAAATTCGCGTTGCGAT
*
631559 TTACAGATTCGCGTTGCGA
1 TTACAAATTCGCGTTGCGA
631578 ATTTGGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (20 bp):
TTACAAATTCGCGTTGCGAT
Found at i:631616 original size:100 final size:100
Alignment explanation
Indices: 631367--631622 Score: 293
Period size: 100 Copynumber: 2.6 Consensus size: 100
631357 AATTTGACTA
* ** * * * *
631367 TCGCGTTGCGAATTTGACTATTGTGTTGCGAATTTGACT-TCTGTGTTGCGAATTTGACTTCTGT
1 TCGCGTTGCGAATTTGACAACAGGGTTGCAAATTGGACTATC-GCGTTGCGAATTTGACTTCTGT
** *
631431 GTTATGATTTACAAATTCGCGTTGCGATTTACAGAT
65 GTTACAACTTACAAATTCGCGTTGCGATTTACAGAT
** * ** * *
631467 TCGCGTTGCGAATTTGACTTCAGTGTTGCGCATTTGACTATCGCATTGCGAATTTGACTTCTGTG
1 TCGCGTTGCGAATTTGACAACAGGGTTGCAAATTGGACTATCGCGTTGCGAATTTGACTTCTGTG
631532 TTACAACTTACAAATTCGCGTTGCGATTTACAGAT
66 TTACAACTTACAAATTCGCGTTGCGATTTACAGAT
* *
631567 TCGCGTTGCGAATTTGGA-AACCGGGTTGCAAAATTGGAGT-TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTT-GACAACAGGGTTGC-AAATTGGACTATCGCGTTGCGAATTTG
631623 TTGGTCATTT
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
100 125 0.93
101 10 0.07
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (100 bp):
TCGCGTTGCGAATTTGACAACAGGGTTGCAAATTGGACTATCGCGTTGCGAATTTGACTTCTGTG
TTACAACTTACAAATTCGCGTTGCGATTTACAGAT
Found at i:632668 original size:14 final size:14
Alignment explanation
Indices: 632649--632675 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
632639 TGTTTCATTG
632649 AAAATATTTTTAAA
1 AAAATATTTTTAAA
632663 AAAATATTTTTAA
1 AAAATATTTTTAA
632676 CTGAAACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATATTTTTAAA
Found at i:632742 original size:83 final size:83
Alignment explanation
Indices: 632603--632756 Score: 254
Period size: 83 Copynumber: 1.9 Consensus size: 83
632593 GTCGAACCAG
* * * *
632603 CTAAGTCAGAAACTGTAGTAATATTAGCTGTATGTTTGTTTCATTGAAAATATTTTTAAAAAAAT
1 CTAAGTCAAAAACTGCAGTAATACTAGCTGTATGTTTGTTTCACTGAAAATATTTTTAAAAAAAT
632668 ATTTTTAACTGAAACTGT
66 ATTTTTAACTGAAACTGT
* *
632686 CTAAGTCAAAAACTGCAGTAATACTAGCTGTTTGTTTGTTTCACTGAAAATATTTTTTAAAAAAT
1 CTAAGTCAAAAACTGCAGTAATACTAGCTGTATGTTTGTTTCACTGAAAATATTTTTAAAAAAAT
632751 ATTTTT
66 ATTTTT
632757 TGTAAAATGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (83 bp):
CTAAGTCAAAAACTGCAGTAATACTAGCTGTATGTTTGTTTCACTGAAAATATTTTTAAAAAAAT
ATTTTTAACTGAAACTGT
Found at i:632804 original size:13 final size:14
Alignment explanation
Indices: 632774--632803 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
632764 TGAATTATAC
632774 TTTCTGAAAAACAT
1 TTTCTGAAAAACAT
*
632788 TTTCTGAAAAATAT
1 TTTCTGAAAAACAT
632802 TT
1 TT
632804 CATGGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTCTGAAAAACAT
Found at i:632937 original size:22 final size:22
Alignment explanation
Indices: 632894--632958 Score: 112
Period size: 22 Copynumber: 2.9 Consensus size: 22
632884 ATATAATAAA
*
632894 TAATATTATTAATTATAAAAACT
1 TAATATTATT-ATTTTAAAAACT
632917 TAATATTATTATTTTAAAAACT
1 TAATATTATTATTTTAAAAACT
632939 TAATATTATTATTTTAAAAA
1 TAATATTATTATTTTAAAAA
632959 TATTATAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
22 31 0.76
23 10 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATATTATTATTTTAAAAACT
Found at i:633395 original size:24 final size:24
Alignment explanation
Indices: 633361--633418 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
633351 ATAATATTAT
*
633361 TATATTATTAAAAATATTAATAAA
1 TATATTTTTAAAAATATTAATAAA
* * *
633385 TATATTTTT-AACATGTTAATAAT
1 TATATTTTTAAAAATATTAATAAA
633408 TAATATTTTTA
1 T-ATATTTTTA
633419 TTAAAATGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TATATTTTTAAAAATATTAATAAA
Found at i:635802 original size:3 final size:3
Alignment explanation
Indices: 635796--635876 Score: 60
Period size: 3 Copynumber: 27.0 Consensus size: 3
635786 ATGATGGGAG
* * *
635796 TGA TGA TGA TTA TGA TGA TGA -GT TCGA TGA TGAA T-T TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA T-GA TGA TG-A TGA TGA TGA TGA
* * *
635841 -GTT TGA TGA TGA CGA TGA TGA TTA TGA TGA TGA TGA
1 TG-A TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
635877 GGAATTTGGT
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
2 3 0.05
3 52 0.87
4 5 0.08
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (3 bp):
TGA
Found at i:635811 original size:12 final size:11
Alignment explanation
Indices: 635796--635874 Score: 81
Period size: 12 Copynumber: 6.9 Consensus size: 11
635786 ATGATGGGAG
635796 TGATGATGATT
1 TGATGATGATT
635807 ATGATGATGAGTT
1 -TGATGATGA-TT
*
635820 CGATGATGAATT
1 TGATGATG-ATT
635832 TGATGATGAGTT
1 TGATGATGA-TT
635844 TGATGATGA--
1 TGATGATGATT
*
635853 CGATGATGATT
1 TGATGATGATT
635864 ATGATGATGAT
1 -TGATGATGAT
635875 GAGGAATTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
9 8 0.14
11 1 0.02
12 45 0.79
13 3 0.05
ACGTcount: A:0.30, C:0.03, G:0.29, T:0.38
Consensus pattern (11 bp):
TGATGATGATT
Found at i:635815 original size:24 final size:23
Alignment explanation
Indices: 635785--635874 Score: 64
Period size: 24 Copynumber: 3.9 Consensus size: 23
635775 CTTGCCCGAG
635785 GATGATGGGAGTGATGATGATTAT
1 GATGAT-GGAGTGATGATGATTAT
635809 GATGAT-GAGTTCGATGATGAATT-T
1 GATGATGGAG-T-GATGATG-ATTAT
**
635833 GATGAT-GAGTTTGATGATGACGAT
1 GATGATGGAG--TGATGATGATTAT
*
635857 GATGAT-TA-TGATGATGAT
1 GATGATGGAGTGATGATGAT
635875 GAGGAATTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
21 9 0.16
22 3 0.05
23 2 0.04
24 38 0.67
25 5 0.09
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (23 bp):
GATGATGGAGTGATGATGATTAT
Found at i:639937 original size:11 final size:11
Alignment explanation
Indices: 639923--639947 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
639913 TATATAAACT
639923 AATAATAAATA
1 AATAATAAATA
639934 AATAATAAATA
1 AATAATAAATA
639945 AAT
1 AAT
639948 TATTACTAAT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAAATA
Found at i:640605 original size:16 final size:16
Alignment explanation
Indices: 640584--640615 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
640574 CGCCTAAACT
640584 CTCACATGAGCAATGC
1 CTCACATGAGCAATGC
640600 CTCACATGAGCAATGC
1 CTCACATGAGCAATGC
640616 TTTTAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (16 bp):
CTCACATGAGCAATGC
Found at i:642702 original size:6 final size:7
Alignment explanation
Indices: 642684--642709 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
642674 AGAATTTATT
642684 TAAAAAA
1 TAAAAAA
642691 TAAAAAA
1 TAAAAAA
642698 TAAAAAA
1 TAAAAAA
642705 TAAAA
1 TAAAA
642710 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:647079 original size:45 final size:45
Alignment explanation
Indices: 646965--647082 Score: 173
Period size: 45 Copynumber: 2.6 Consensus size: 45
646955 ATATGATTTC
* *
646965 ATGAAAATGTGATATAAGCTATGTAATATTGACCTATGTGATTAT
1 ATGAAAATGTGATATAAGCTATGTGACATTGACCTATGTGATTAT
* * * *
647010 ATGAAAAAGTGATAAAAACTATGTGGCATTGACCTATGTGATTAT
1 ATGAAAATGTGATATAAGCTATGTGACATTGACCTATGTGATTAT
*
647055 ATGAACATGTGATATAAGCTATGTGACA
1 ATGAAAATGTGATATAAGCTATGTGACA
647083 AGAATATATG
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (45 bp):
ATGAAAATGTGATATAAGCTATGTGACATTGACCTATGTGATTAT
Found at i:647277 original size:23 final size:22
Alignment explanation
Indices: 647218--647280 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
647208 TAGTCGAGGG
*
647218 TTCTATGCGGTCCTTTGAGACAA
1 TTCTATGC-GTCCTTCGAGACAA
*
647241 TTCTACATG-GTCCTTCGAGACAT
1 TTCT--ATGCGTCCTTCGAGACAA
647264 TTCTATGCGTTCCTTCG
1 TTCTATGCG-TCCTTCG
647281 GGATAATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.09
22 1 0.03
23 27 0.79
25 3 0.09
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (22 bp):
TTCTATGCGTCCTTCGAGACAA
Found at i:647330 original size:24 final size:24
Alignment explanation
Indices: 647321--647401 Score: 153
Period size: 24 Copynumber: 3.4 Consensus size: 24
647311 TGGTACTTTG
647321 GTGCAATTTCTACGCGGCACTTCA
1 GTGCAATTTCTACGCGGCACTTCA
647345 GTGCAATTTCTACGCGGCACTTCA
1 GTGCAATTTCTACGCGGCACTTCA
*
647369 GTGCAATTTCTACGCGGCACTTCT
1 GTGCAATTTCTACGCGGCACTTCA
647393 GTGCAATTT
1 GTGCAATTT
647402 ATATGAGCTG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (24 bp):
GTGCAATTTCTACGCGGCACTTCA
Found at i:647537 original size:21 final size:21
Alignment explanation
Indices: 647512--647573 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
647502 TGAACAATGT
647512 ATGATAATGATGTTGATGATA
1 ATGATAATGATGTTGATGATA
* * *
647533 ATGATAACGTTGTTGATGTTA
1 ATGATAATGATGTTGATGATA
*
647554 ATGATAATGATGATGATGAT
1 ATGATAATGATGTTGATGAT
647574 TTGTATATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (21 bp):
ATGATAATGATGTTGATGATA
Found at i:651477 original size:23 final size:23
Alignment explanation
Indices: 651415--651478 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
651405 CATTATTATA
* * *
651415 TGGCACTACGGTGCAATTCTATG
1 TGGCACTTCAGTGCAATTCTACG
* * *
651438 CGGCAC-TCTGATTCAATTCTACG
1 TGGCACTTCAG-TGCAATTCTACG
651461 TGGCACTTCAGTGCAATT
1 TGGCACTTCAGTGCAATT
651479 ATACTAGCTG
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
22 2 0.06
23 26 0.84
24 3 0.10
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (23 bp):
TGGCACTTCAGTGCAATTCTACG
Found at i:652929 original size:26 final size:26
Alignment explanation
Indices: 652806--652916 Score: 204
Period size: 26 Copynumber: 4.3 Consensus size: 26
652796 GAACAAGTTA
652806 TGAGTGATTAAGTAAAAAAGGGTTTT
1 TGAGTGATTAAGTAAAAAAGGGTTTT
*
652832 TGAGTGATTAAGTAAAAAATGGTTTT
1 TGAGTGATTAAGTAAAAAAGGGTTTT
*
652858 TGAGTGATTAAGTAAAAAATGGTTTT
1 TGAGTGATTAAGTAAAAAAGGGTTTT
652884 TGAGTGATTAAGTAAAAAAGGGTTTT
1 TGAGTGATTAAGTAAAAAAGGGTTTT
652910 TGAGTGA
1 TGAGTGA
652917 ATTGATGAGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 83 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (26 bp):
TGAGTGATTAAGTAAAAAAGGGTTTT
Found at i:653941 original size:15 final size:15
Alignment explanation
Indices: 653891--653962 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
653881 CATTTCATCC
*
653891 TATGTGATTTCATGAA
1 TATGTGATAT-ATGAA
* * *
653907 AATGTGATATAAG-T
1 TATGTGATATATGAA
653921 TATGTGATAT-TGACA
1 TATGTGATATATGA-A
653936 TATGTGATTATATGAA
1 TATGTGA-TATATGAA
*
653952 AATGTGATATA
1 TATGTGATATA
653963 AGCTATGTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.02
14 9 0.20
15 13 0.30
16 18 0.41
17 3 0.07
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (15 bp):
TATGTGATATATGAA
Found at i:653941 original size:45 final size:46
Alignment explanation
Indices: 653891--654017 Score: 188
Period size: 45 Copynumber: 2.8 Consensus size: 46
653881 CATTTCATCC
*
653891 TATGTGATT-TCATGAAAATGTGATATAAGTTATGTGAT-ATTGACA
1 TATGTGATTAT-ATGAAAATGTGATATAAGCTATGTGATCATTGACA
*
653936 TATGTGATTATATGAAAATGTGATATAAGCTATGTG-TCATTGACC
1 TATGTGATTATATGAAAATGTGATATAAGCTATGTGATCATTGACA
* *
653981 TATATGATTATATGAACATGTGATATAAGCTATGTGA
1 TATGTGATTATATGAAAATGTGATATAAGCTATGTGA
654018 CAAGAATCTA
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
44 1 0.01
45 73 0.97
46 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (46 bp):
TATGTGATTATATGAAAATGTGATATAAGCTATGTGATCATTGACA
Found at i:654051 original size:45 final size:45
Alignment explanation
Indices: 653902--654039 Score: 143
Period size: 45 Copynumber: 3.1 Consensus size: 45
653892 ATGTGATTTC
* * * * * **
653902 ATGAAAATGTGATATAAGTTATGTGATATTGACATATGTGATTAT
1 ATGAACATGTGATATAAGCTATGTGACATAGACCTATACGATTAT
* * * *
653947 ATGAAAATGTGATATAAGCTATGTGTCATTGACCTATATGATTAT
1 ATGAACATGTGATATAAGCTATGTGACATAGACCTATACGATTAT
* *
653992 ATGAACATGTGATATAAGCTATGTGACA-AGAATCTATGCGATTAT
1 ATGAACATGTGATATAAGCTATGTGACATAG-ACCTATACGATTAT
654037 ATG
1 ATG
654040 TCTATGTGAT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 1 0.01
45 80 0.99
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (45 bp):
ATGAACATGTGATATAAGCTATGTGACATAGACCTATACGATTAT
Found at i:657685 original size:19 final size:19
Alignment explanation
Indices: 657643--657686 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
657633 AGTTAACTCT
657643 GGTCAAAGTCAACAGGTCG
1 GGTCAAAGTCAACAGGTCG
* * *
657662 AGTCAAAGTCAACGGGTTG
1 GGTCAAAGTCAACAGGTCG
657681 GGTCAA
1 GGTCAA
657687 GCAGTTTGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (19 bp):
GGTCAAAGTCAACAGGTCG
Found at i:658454 original size:20 final size:20
Alignment explanation
Indices: 658429--658470 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
658419 CTGCCACTAC
658429 ATTATTTTATTCTTAGTGCT
1 ATTATTTTATTCTTAGTGCT
658449 ATTATTTTATTCTTAGTGCT
1 ATTATTTTATTCTTAGTGCT
658469 AT
1 AT
658471 AAGATATATT
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:0.21, C:0.10, G:0.10, T:0.60
Consensus pattern (20 bp):
ATTATTTTATTCTTAGTGCT
Found at i:664921 original size:20 final size:20
Alignment explanation
Indices: 664896--664934 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
664886 TTTTCAAAGG
664896 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
*
664916 CATGCATCGATGCACCAAT
1 CATGCACCGATGCACCAAT
664935 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.36, G:0.15, T:0.18
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:665020 original size:65 final size:64
Alignment explanation
Indices: 664948--665130 Score: 199
Period size: 64 Copynumber: 2.8 Consensus size: 64
664938 TAAATTGAAT
* * * *
664948 ATCAAATGTATTTTATACATTGATGCACTCTTCATGCATCGATGCACTTAGGGT-TTTATGAAAA
1 ATCAAATGCATTTTATGCATCGATGCACTCTTCATGCATCGATGCACTAAGGGTATTT-T-AAAA
665012 A
64 A
* **** * * *
665013 ATCAAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAAAAC
1 ATCAAATGCATTTTATGCATCGATGCACTCTTCATGCATCGATGCACTAAGGGTATTTTAAAAA
* *
665077 ATCGAATGCATTTTATGCATCGATGCACTCTT-AGTGCATCGATACACTAAGGGT
1 ATCAAATGCATTTTATGCATCGATGCACTCTTCA-TGCATCGATGCACTAAGGGT
665131 CCAACGGTAA
Statistics
Matches: 96, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
63 1 0.01
64 47 0.49
65 45 0.47
66 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (64 bp):
ATCAAATGCATTTTATGCATCGATGCACTCTTCATGCATCGATGCACTAAGGGTATTTTAAAAA
Found at i:665099 original size:18 final size:20
Alignment explanation
Indices: 665076--665118 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
665066 TATTTTAAAA
*
665076 CATCGAATGCA-TTTTA-TG
1 CATCGAATGCACTCTTAGTG
665094 CATCG-ATGCACTCTTAGTG
1 CATCGAATGCACTCTTAGTG
665113 CATCGA
1 CATCGA
665119 TACACTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (20 bp):
CATCGAATGCACTCTTAGTG
Found at i:665115 original size:64 final size:64
Alignment explanation
Indices: 664948--665124 Score: 189
Period size: 65 Copynumber: 2.7 Consensus size: 64
664938 TAAATTGAAT
* * * * *
664948 ATCAAATGTATTTTATACATTGATGCACTCTTCATGCATCGATGCACTTAGGGTTTTATGAAAAA
1 ATCAAATGCATTTTATGCATCGATGCACTCTT-ATGCATCGATGCACTCAGGCTTTTATGAAAAA
* * *
665013 ATCAAATGCATTTGATGCATCGATGCACAAGC-CATGCATCGATGCACTCAGGCTATTT-T-AAA
1 ATCAAATGCATTTTATGCATCGATGCAC--TCTTATGCATCGATGCACTCAGGCT-TTTATGAAA
*
665075 AC
63 AA
* *
665077 ATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCATCGATACACT
1 ATCAAATGCATTTTATGCATCGATGCACTCTTA-TGCATCGATGCACT
665125 AAGGGTCCAA
Statistics
Matches: 93, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 43 0.46
65 44 0.47
66 3 0.03
67 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (64 bp):
ATCAAATGCATTTTATGCATCGATGCACTCTTATGCATCGATGCACTCAGGCTTTTATGAAAAA
Found at i:670978 original size:23 final size:23
Alignment explanation
Indices: 670908--670989 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
670898 CACTTAACAA
*
670908 TGCATCGATACATC-CCTTTGAATG
1 TGCATCGATGCA-CACC-TTGAATG
* *
670932 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACACCTTGAATG
* *
670953 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
670976 TGCATCGATGCACA
1 TGCATCGATGCACA
670990 AGGCCATGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
21 14 0.30
22 3 0.06
23 21 0.45
24 9 0.19
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:673672 original size:19 final size:19
Alignment explanation
Indices: 673648--673717 Score: 140
Period size: 19 Copynumber: 3.7 Consensus size: 19
673638 GCATTTTATA
673648 CATCGATGCACTCTCCATG
1 CATCGATGCACTCTCCATG
673667 CATCGATGCACTCTCCATG
1 CATCGATGCACTCTCCATG
673686 CATCGATGCACTCTCCATG
1 CATCGATGCACTCTCCATG
673705 CATCGATGCACTC
1 CATCGATGCACTC
673718 AGGGTTTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (19 bp):
CATCGATGCACTCTCCATG
Found at i:673759 original size:65 final size:64
Alignment explanation
Indices: 673683--673851 Score: 216
Period size: 64 Copynumber: 2.6 Consensus size: 64
673673 TGCACTCTCC
*
673683 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGGTATTT-T-AAAACATCAAATGCATTT
673747 G
64 G
*** * *
673748 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAAAACATCAAATGCATTTT
1 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGGTATTTTAAAACATCAAATGCATTTG
* * *
673812 ATGCATCGATGCACTCT-TAGTGCACCGATGCACTAAGGGT
1 ATGCATCGATGCACTCTCCA-TGCATCGATGCACTCAGGGT
673852 CCAATGGTCA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 48 0.54
65 37 0.42
66 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGGTATTTTAAAACATCAAATGCATTTG
Found at i:678129 original size:3 final size:3
Alignment explanation
Indices: 678113--678194 Score: 150
Period size: 3 Copynumber: 28.0 Consensus size: 3
678103 GGCCTACAAA
678113 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
678159 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
678195 TTGGCCACCG
Statistics
Matches: 77, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 73 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:679334 original size:22 final size:22
Alignment explanation
Indices: 679308--679351 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
679298 ATTTTTTCAA
*
679308 AATTTAACTTGTTTCACGTATC
1 AATTTAACTTGTATCACGTATC
679330 AATTTAACTTGTATCACGTATC
1 AATTTAACTTGTATCACGTATC
679352 TTGACCGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (22 bp):
AATTTAACTTGTATCACGTATC
Found at i:680112 original size:15 final size:15
Alignment explanation
Indices: 680086--680128 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
680076 ATTTTGGATG
680086 TTTAAGTTTATTTTAA
1 TTTAA-TTTATTTTAA
680102 TTTAATTTATTTTAA
1 TTTAATTTATTTTAA
*
680117 TAT-ATTTATTTT
1 TTTAATTTATTTT
680129 TCACTAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 9 0.35
15 12 0.46
16 5 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTAATTTATTTTAA
Found at i:680466 original size:59 final size:58
Alignment explanation
Indices: 680347--680528 Score: 149
Period size: 59 Copynumber: 3.1 Consensus size: 58
680337 TATATCTTTA
** * * * * *
680347 AAAATATATTTTATTTTTATCTTAACTTATT--AAATATATTT-TCTCATTAACCTAATTT
1 AAAATATATTTTATAATTATTTTAAGTT-TTAAAAATATATTTAT-TC-TTATCTTAACTT
* *
680405 AAAA-ATGTTTTATAATTATTTTAA-TTTTAAAAACATATATTTTATTCTTATTTTAACTT
1 AAAATATATTTTATAATTATTTTAAGTTTT-AAAA-ATATA-TTTATTCTTATCTTAACTT
** * *
680464 AAAAATATATTTTATTCTTATTTTAAGTTTTAAAAATATATTTATTTTTATCTTAATTT
1 -AAAATATATTTTATAATTATTTTAAGTTTTAAAAATATATTTATTCTTATCTTAACTT
680523 AAAATA
1 AAAATA
680529 ATAATAAAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
55 2 0.02
56 2 0.02
57 16 0.16
58 12 0.12
59 29 0.29
60 14 0.14
61 22 0.22
62 4 0.04
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (58 bp):
AAAATATATTTTATAATTATTTTAAGTTTTAAAAATATATTTATTCTTATCTTAACTT
Found at i:680497 original size:31 final size:29
Alignment explanation
Indices: 680343--680526 Score: 151
Period size: 30 Copynumber: 6.2 Consensus size: 29
680333 TTTATATATC
* *
680343 TTTAAAAATATATTTTATTTTTATCTTAA
1 TTTAAAAATATATTTTATTCTTATTTTAA
* * * ***
680372 CTTATTAAATATATTTT-CTCATTAACCTAA
1 TTTA-AAAATATATTTTATTC-TTATTTTAA
* **
680402 TTT-AAAA-ATGTTTTATAATTATTTTAA
1 TTTAAAAATATATTTTATTCTTATTTTAA
680429 TTTTAAAAACATATATTTTATTCTTATTTTAA
1 -TTT-AAAA-ATATATTTTATTCTTATTTTAA
*
680461 CTTAAAAATATATTTTATTCTTATTTTAA
1 TTTAAAAATATATTTTATTCTTATTTTAA
* *
680490 GTTTTAAAAATATA-TTTATTTTTATCTTAA
1 --TTTAAAAATATATTTTATTCTTATTTTAA
680520 TTTAAAA
1 TTTAAAA
680527 TAATAATAAA
Statistics
Matches: 123, Mismatches: 22, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
27 12 0.10
28 13 0.11
29 26 0.21
30 41 0.33
31 14 0.11
32 17 0.14
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTAAAAATATATTTTATTCTTATTTTAA
Found at i:686308 original size:21 final size:20
Alignment explanation
Indices: 686279--686318 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
686269 TATTATAAAA
*
686279 AAAAGTAAATATTTTTATTAT
1 AAAAGTAAAT-TATTTATTAT
*
686300 AAAATTAAATTATTTATTA
1 AAAAGTAAATTATTTATTA
686319 ATTTTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AAAAGTAAATTATTTATTAT
Found at i:689055 original size:93 final size:94
Alignment explanation
Indices: 688882--689072 Score: 339
Period size: 93 Copynumber: 2.0 Consensus size: 94
688872 ACATATAGTC
688882 AATTTGTTGAGTTAATCGATCGACGGAATTGACCAAGAGGGGGGTGAATTGGCAATTAAAAATTT
1 AATTTGTTGAGTTAATCGATCGACGGAATTGACCAAGAGGGGGGTGAATTGGCAATTAAAAATTT
*
688947 GGTGGAAGCTTTTGCAAAAAATTGAAAGT
66 GGTAGAAGCTTTTGCAAAAAATTGAAAGT
* *
688976 AATTTGTTGAGTTAATCGATTGACGGAATTGGCCAAGA-GGGGGTGAATTGGCAATTAAAAATTT
1 AATTTGTTGAGTTAATCGATCGACGGAATTGACCAAGAGGGGGGTGAATTGGCAATTAAAAATTT
*
689040 GGTAGAAGCTTTTGCAGAAAATTGAAAGT
66 GGTAGAAGCTTTTGCAAAAAATTGAAAGT
689069 AATT
1 AATT
689073 GCACAGTGAT
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
93 57 0.61
94 36 0.39
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (94 bp):
AATTTGTTGAGTTAATCGATCGACGGAATTGACCAAGAGGGGGGTGAATTGGCAATTAAAAATTT
GGTAGAAGCTTTTGCAAAAAATTGAAAGT
Found at i:698170 original size:22 final size:21
Alignment explanation
Indices: 698120--698174 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
698110 CTTGGAGCGT
*
698120 GGGGGGAATCGGAACCCCCTA
1 GGGGGGAATCGGTACCCCCTA
*
698141 -TGGGGAATCGGTACCCCCTTA
1 GGGGGGAATCGGTACCCCC-TA
698162 GGGGGGAATCGGT
1 GGGGGGAATCGGT
698175 TCCCTCTGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.55
21 2 0.07
22 11 0.38
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTA
Found at i:699172 original size:20 final size:20
Alignment explanation
Indices: 699147--699185 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
699137 CAATTTATTC
699147 ATTGGTGCATCGATGCATAG
1 ATTGGTGCATCGATGCATAG
*
699167 ATTGGTGCATCGGTGCATA
1 ATTGGTGCATCGATGCATA
699186 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATAG
Found at i:701858 original size:23 final size:22
Alignment explanation
Indices: 701832--701910 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
701822 ACATGGCCTT
*
701832 GTGCATTGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
701854 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
701876 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
701899 GATGCATCGATG
1 G-TGCATCGATG
701911 TACTGTTAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
21 15 0.34
22 2 0.05
23 18 0.41
24 9 0.20
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:707470 original size:65 final size:65
Alignment explanation
Indices: 707306--707429 Score: 160
Period size: 65 Copynumber: 1.9 Consensus size: 65
707296 TGACCGTTGG
* * * * *
707306 AACACTTAGTGCATCGGTGCACCA-AGTGTGCATCGATGCATAAAATGAATTCGATGTTTTCATA
1 AACACTGAGTGCATCGATGCA-TAGAGAGTGCATCGATGCATAAAATGAATTCGATGTTTTAATA
707370 A
65 A
* * *
707371 AACCCTGAGTGCATCGATGCATGGAGAGTGCATCGATGCATAAAATGCATTCGATGTTT
1 AACACTGAGTGCATCGATGCATAGAGAGTGCATCGATGCATAAAATGAATTCGATGTTT
707430 AATTTATTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 51 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (65 bp):
AACACTGAGTGCATCGATGCATAGAGAGTGCATCGATGCATAAAATGAATTCGATGTTTTAATAA
Found at i:716039 original size:29 final size:29
Alignment explanation
Indices: 716006--716264 Score: 343
Period size: 29 Copynumber: 9.0 Consensus size: 29
715996 AATTATCACC
*
716006 CCTTTTAAAAATATTTACGAAACTAACAA
1 CCTTTTAAAAATATTTACGAAAATAACAA
* *
716035 CC-TTTCAAAATATTTACAAAAATAAC-A
1 CCTTTTAAAAATATTTACGAAAATAACAA
716062 CCATTTTAAAAATATTTACGAAAATAAC-A
1 CC-TTTTAAAAATATTTACGAAAATAACAA
716091 CCATTTTAAAAATATTTACGAAAATAAC-A
1 CC-TTTTAAAAATATTTACGAAAATAACAA
* *
716120 CACTTTTAAAAATATTTACAAAAATAACAC
1 C-CTTTTAAAAATATTTACGAAAATAACAA
*
716150 CCTTTTAAAAATATTTACGAAAATAACAC
1 CCTTTTAAAAATATTTACGAAAATAACAA
*
716179 CCTTTTAAAAATATTTACGAAAATAACAC
1 CCTTTTAAAAATATTTACGAAAATAACAA
716208 CCTTTTAAAAATATTTAC-AAAACTAAC-A
1 CCTTTTAAAAATATTTACGAAAA-TAACAA
*
716236 CTCTTTTAAAAATAATTAC-AAAACTAACA
1 C-CTTTTAAAAATATTTACGAAAA-TAACA
716265 CCCGGTCAAC
Statistics
Matches: 213, Mismatches: 10, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
27 3 0.01
28 26 0.12
29 182 0.85
30 2 0.01
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.31
Consensus pattern (29 bp):
CCTTTTAAAAATATTTACGAAAATAACAA
Found at i:716127 original size:58 final size:57
Alignment explanation
Indices: 716006--716267 Score: 386
Period size: 58 Copynumber: 4.5 Consensus size: 57
715996 AATTATCACC
* * * *
716006 CCTTTTAAAAATATTTACGAAACTAACAACC-TTTCAAAATATTTACAAAAATAACA
1 CCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACGAAAATAACA
*
716062 CCATTTTAAAAATATTTACGAAAATAACACCATTTTAAAAATATTTACGAAAATAACA
1 CC-TTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACGAAAATAACA
*
716120 CACTTTTAAAAATATTTACAAAAATAACACCCTTTTAAAAATATTTACGAAAATAACA
1 C-CTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACGAAAATAACA
716178 CCCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTAC-AAAACTAACA
1 -CCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACGAAAA-TAACA
*
716236 CTCTTTTAAAAATAATTAC-AAAACTAACACCC
1 C-CTTTTAAAAATATTTACGAAAA-TAACACCC
716268 GGTCAACGGT
Statistics
Matches: 190, Mismatches: 9, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
56 2 0.01
57 35 0.18
58 151 0.79
59 2 0.01
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.31
Consensus pattern (57 bp):
CCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACGAAAATAACA
Found at i:716267 original size:87 final size:86
Alignment explanation
Indices: 716005--716267 Score: 413
Period size: 87 Copynumber: 3.0 Consensus size: 86
715995 CAATTATCAC
* * *
716005 CCCTTTTAAAAATATTTACGAAACTAACAACC-TTTCAAAATATTTACAAAAATAACACCATTTT
1 CCCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACAAAAATAACACC-TTTT
716069 AAAAATATTTACGAAAATAACA
65 AAAAATATTTACGAAAATAACA
* *
716091 CCATTTTAAAAATATTTACGAAAATAACACACTTTTAAAAATATTTACAAAAATAACACCCTTTT
1 CCCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACAAAAATAACA-CCTTTT
716156 AAAAATATTTACGAAAATAACA
65 AAAAATATTTACGAAAATAACA
*
716178 CCCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACAAAACTAACACTCTTTT
1 CCCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACAAAAATAACAC-CTTTT
*
716243 AAAAATAATTAC-AAAACTAACA
65 AAAAATATTTACGAAAA-TAACA
716265 CCC
1 CCC
716268 GGTCAACGGT
Statistics
Matches: 164, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
86 33 0.20
87 129 0.79
88 2 0.01
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (86 bp):
CCCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACAAAAATAACACCTTTTA
AAAATATTTACGAAAATAACA
Found at i:724485 original size:29 final size:29
Alignment explanation
Indices: 724443--724606 Score: 229
Period size: 29 Copynumber: 5.7 Consensus size: 29
724433 CCATTGATCG
724443 GGTGATATTTTAGTAATTAATTCGAAATA
1 GGTGATATTTTAGTAATTAATTCGAAATA
* * * *
724472 GGTGTTATTCTAGTAATTAATTCAAAATG
1 GGTGATATTTTAGTAATTAATTCGAAATA
* *
724501 GGTGCTATTTTAGTAATTAATTCAAAATA
1 GGTGATATTTTAGTAATTAATTCGAAATA
724530 GGTGATATTTTAGTAATTAATTCGAAATA
1 GGTGATATTTTAGTAATTAATTCGAAATA
* * * *
724559 GGTGTTATTTCAGTAATTCATTCGAAATG
1 GGTGATATTTTAGTAATTAATTCGAAATA
*
724588 GGTGCTATTTTAGTAATTA
1 GGTGATATTTTAGTAATTA
724607 TTTAAAAAAG
Statistics
Matches: 119, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 119 1.00
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTAATTCGAAATA
Found at i:724589 original size:87 final size:87
Alignment explanation
Indices: 724443--724606 Score: 294
Period size: 87 Copynumber: 1.9 Consensus size: 87
724433 CCATTGATCG
724443 GGTGATATTTTAGTAATTAATTCGAAATAGGTGTTATTCTAGTAATTAATTCAAAATGGGTGCTA
1 GGTGATATTTTAGTAATTAATTCGAAATAGGTGTTATTCTAGTAATTAATTCAAAATGGGTGCTA
724508 TTTTAGTAATTAATTCAAAATA
66 TTTTAGTAATTAATTCAAAATA
* *
724530 GGTGATATTTTAGTAATTAATTCGAAATAGGTGTTATT-TCAGTAATTCATTCGAAATGGGTGCT
1 GGTGATATTTTAGTAATTAATTCGAAATAGGTGTTATTCT-AGTAATTAATTCAAAATGGGTGCT
724594 ATTTTAGTAATTA
65 ATTTTAGTAATTA
724607 TTTAAAAAAG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
86 1 0.01
87 73 0.99
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (87 bp):
GGTGATATTTTAGTAATTAATTCGAAATAGGTGTTATTCTAGTAATTAATTCAAAATGGGTGCTA
TTTTAGTAATTAATTCAAAATA
Found at i:724626 original size:58 final size:57
Alignment explanation
Indices: 724443--724632 Score: 191
Period size: 58 Copynumber: 3.3 Consensus size: 57
724433 CCATTGATCG
* * * * * **
724443 GGTGATATTTTAGTAATTAATTCGAAATAGGTGTTATTCTAGTAATTAATTCAAAATG
1 GGTGCTATTTCAGTAATTAATTCGAAATAGGTGATATTTTAGTAATT-ATTTAAAAAA
* * ** *
724501 GGTGCTATTTTAGTAATTAATTCAAAATAGGTGATATTTTAGTAATTAATTCGAAATA
1 GGTGCTATTTCAGTAATTAATTCGAAATAGGTGATATTTTAGTAATT-ATTTAAAAAA
* * * *
724559 GGTGTTATTTCAGTAATTCATTCGAAATGGGTGCTATTTTAGTAATTATTTAAAAAA
1 GGTGCTATTTCAGTAATTAATTCGAAATAGGTGATATTTTAGTAATTATTTAAAAAA
* *
724616 GAGTACTATTTCTGTAA
1 G-GTGCTATTTCAGTAA
724633 AATGGTTGAC
Statistics
Matches: 113, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
57 8 0.07
58 105 0.93
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (57 bp):
GGTGCTATTTCAGTAATTAATTCGAAATAGGTGATATTTTAGTAATTATTTAAAAAA
Found at i:725756 original size:117 final size:117
Alignment explanation
Indices: 725545--725832 Score: 454
Period size: 117 Copynumber: 2.5 Consensus size: 117
725535 GGAAGTATTT
* *
725545 CAGGCTCCTTTGTTGTGTTCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* *
725610 GGAACCTACACGTTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTG
66 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGAGAAGTTATTACTG
725662 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* *
725727 GGAACCTACACATTGTAGTGA-TGGAAGTGACTGGATGGAGACGTTATTATTG
66 GGAACCTACACATTGTAGTGATTGG-AGTGACTGGATGGAGAAGTTATTACTG
** * *
725779 CAGGCTCCTCGGCT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGCATGTGGGTG
1 CAGGCTCCTTTGCTGT-GTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTG
725833 CATGTTTCGA
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
116 4 0.03
117 155 0.97
ACGTcount: A:0.17, C:0.16, G:0.35, T:0.32
Consensus pattern (117 bp):
CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGAGAAGTTATTACTG
Found at i:728126 original size:19 final size:19
Alignment explanation
Indices: 728084--728126 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
728074 AAGATAATTT
* *
728084 TTTTAAAAAATATTTTTTA
1 TTTTAAAAAATATTTATGA
* *
728103 ATTTAATAAATATTTATGA
1 TTTTAAAAAATATTTATGA
728122 TTTTA
1 TTTTA
728127 TTTTATATAT
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:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTAAAAAATATTTATGA
Found at i:729084 original size:41 final size:41
Alignment explanation
Indices: 729030--729108 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
729020 GTACCGCGGG
729030 AAAAAAAGCCGAAAGCAAGTGTATCATTCTCTGATTTTGGA
1 AAAAAAAGCCGAAAGCAAGTGTATCATTCTCTGATTTTGGA
729071 AAAAAAAGCCGAAAGCAAGTGTATCATTCTCTGATTTT
1 AAAAAAAGCCGAAAGCAAGTGTATCATTCTCTGATTTT
729109 ACTATTGACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (41 bp):
AAAAAAAGCCGAAAGCAAGTGTATCATTCTCTGATTTTGGA
Found at i:729612 original size:32 final size:33
Alignment explanation
Indices: 729571--729633 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
729561 ATTTATTATG
* *
729571 TAAGTCTAATTATGGACTGATC-AATTTTAGTA
1 TAAGTCTAATTATAGACTAATCAAATTTTAGTA
729603 TAAGTCTAATTATAGACTAATCAAATTTTAG
1 TAAGTCTAATTATAGACTAATCAAATTTTAG
729634 GAATATAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.40
Consensus pattern (33 bp):
TAAGTCTAATTATAGACTAATCAAATTTTAGTA
Found at i:730448 original size:14 final size:14
Alignment explanation
Indices: 730399--730454 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
730389 CGATTTCATG
*
730399 ATTGTTTTATATTA
1 ATTGTTATATATTA
* *
730413 AAT-TTATATA-AA
1 ATTGTTATATATTA
*
730425 ATTTGGTATATATTA
1 A-TTGTTATATATTA
730440 ATTGTTATATATTA
1 ATTGTTATATATTA
730454 A
1 A
730455 ATTTATTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
12 2 0.06
13 7 0.22
14 21 0.66
15 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (14 bp):
ATTGTTATATATTA
Found at i:730463 original size:16 final size:16
Alignment explanation
Indices: 730417--730465 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
730407 ATATTAAATT
* *
730417 TATATAAAATTTGGTA
1 TATATTAAATTTGTTA
730433 TATATT-AA-TTGTTA
1 TATATTAAATTTGTTA
*
730447 TATATTAAATTTATTA
1 TATATTAAATTTGTTA
730463 TAT
1 TAT
730466 TTATAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 11 0.39
15 4 0.14
16 13 0.46
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TATATTAAATTTGTTA
Found at i:730464 original size:14 final size:14
Alignment explanation
Indices: 730405--730466 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
730395 CATGATTGTT
730405 TTATATTAAATTTA
1 TTATATTAAATTTA
*
730419 -TATA--AAATTTGG
1 TTATATTAAATTT-A
*
730431 TATATATTAATTGTTA
1 T-TATATTAAAT-TTA
730447 -TATATTAAATTTA
1 TTATATTAAATTTA
730460 TTATATT
1 TTATATT
730467 TATAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
11 6 0.16
13 7 0.19
14 19 0.51
16 3 0.08
17 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (14 bp):
TTATATTAAATTTA
Found at i:733314 original size:16 final size:16
Alignment explanation
Indices: 733295--733346 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
733285 AATTGAGGAT
733295 CATTTATATACTTTAC
1 CATTTATATACTTTAC
* *
733311 CATTGAT-TAGTTTAC
1 CATTTATATACTTTAC
733326 TCATTTATATACTTTAC
1 -CATTTATATACTTTAC
733343 CATT
1 CATT
733347 GATTAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 7 0.23
16 16 0.53
17 7 0.23
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (16 bp):
CATTTATATACTTTAC
Found at i:733335 original size:32 final size:32
Alignment explanation
Indices: 733294--733360 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
733284 TAATTGAGGA
*
733294 TCATTTATATACTTTACCATTGATTAGTTTAC
1 TCATTTATATACTTTACCATTGATTAATTTAC
733326 TCATTTATATACTTTACCATTGATTAATTTAC
1 TCATTTATATACTTTACCATTGATTAATTTAC
733358 TCA
1 TCA
733361 ATTACTCGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.49
Consensus pattern (32 bp):
TCATTTATATACTTTACCATTGATTAATTTAC
Found at i:734027 original size:30 final size:29
Alignment explanation
Indices: 733993--734504 Score: 194
Period size: 30 Copynumber: 17.2 Consensus size: 29
733983 ATTGAATTTC
733993 TTTTATTCTTATCTTAATTAAAAAATTATA
1 TTTTATTCTTATCTTAATTAAAAAA-TATA
* *
734023 TTTTAATCTTATCTTAACTTATAAAATATA
1 TTTTATTCTTATCTTAA-TTAAAAAATATA
* *
734053 TTTTATTCCTACCTTAACTT-AAAAATATA
1 TTTTATTCTTATCTTAA-TTAAAAAATATA
* *** *
734082 TTTTATTTTTATCTTAACTTGTTACATATA
1 TTTTATTCTTATCTTAA-TTAAAAAATATA
* * **
734112 TTATATTCTTAACTTAAATTATTAAATATA
1 TTTTATTCTTATCTT-AATTAAAAAATATA
* * **
734142 TTATATTCTTACCTTAAATTATTAAATATA
1 TTTTATTCTTATCTT-AATTAAAAAATATA
** * *
734172 TTAAATTGTTATCTTAACTTGAAAATATATA
1 TTTTATTCTTATCTTAA-TT-AAAAAATATA
* * **
734203 TCTTATT-TTAATTTTAAAAAATATATTAATATA
1 TTTTATTCTT-ATCTTAATTAA-A-A--AATATA
* * *
734236 TTTTATTCTTATTTTAATTTAGAAATATA
1 TTTTATTCTTATCTTAATTAAAAAATATA
734265 TTTT-TT-TTATCTTAATTATGAAAAAATATA
1 TTTTATTCTTATCTTAA-T-T-AAAAAATATA
* *
734295 TTTTTTATT-TTAATTTTAAAATATTATAAAAATAAA
1 --TTTTATTCTT-ATCTT---A-ATTA-AAAAATATA
* ** *
734331 ATTTA--AATAT-TTAAGTTAAGGTAAAAAATA
1 TTTTATTCTTATCTTAA-TTAA---AAAATATA
* *
734361 TTTT-TT-ATAAC---ATT-AAAAATATA
1 TTTTATTCTTATCTTAATTAAAAAATATA
* *** *
734384 TTTTATT-TT-TTTTAACTTATTGAATTTA
1 TTTTATTCTTATCTTAA-TTAAAAAATATA
* **
734412 TTTTATTCTTATCTTAACTGGAAAATATA
1 TTTTATTCTTATCTTAATTAAAAAATATA
* *
734441 TTTTAATCTTATCTTAACTTATAAAATATA
1 TTTTATTCTTATCTTAA-TTAAAAAATATA
* *
734471 TTTTATTCCTACCTTAACTT-AAAAATATA
1 TTTTATTCTTATCTTAA-TTAAAAAATATA
734500 TTTTA
1 TTTTA
734505 ATTTTAAAAT
Statistics
Matches: 372, Mismatches: 70, Indels: 81
0.71 0.13 0.15
Matches are distributed among these distances:
23 11 0.03
24 3 0.01
26 2 0.01
27 14 0.04
28 20 0.05
29 77 0.21
30 162 0.44
31 30 0.08
32 6 0.02
33 24 0.06
34 10 0.03
35 1 0.00
36 9 0.02
37 2 0.01
38 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (29 bp):
TTTTATTCTTATCTTAATTAAAAAATATA
Found at i:734112 original size:89 final size:90
Alignment explanation
Indices: 734019--734192 Score: 233
Period size: 89 Copynumber: 1.9 Consensus size: 90
734009 ATTAAAAAAT
* * * * *
734019 TATATTTTAATCTTATCTTAACTTATAAAATATATTTTATTCCTACCTTAACTTA-AAAATATAT
1 TATATTATAATCTTAACTTAAATTATAAAATATATTATATTCCTACCTTAAATTATAAAATATAT
** *
734083 TTTATTTTTATCTTAACTTGTTACA
66 TAAATTGTTATCTTAACTTGTTACA
* * * *
734108 TATATTATATTCTTAACTTAAATTATTAAATATATTATATTCTTACCTTAAATTATTAAATATAT
1 TATATTATAATCTTAACTTAAATTATAAAATATATTATATTCCTACCTTAAATTATAAAATATAT
734173 TAAATTGTTATCTTAACTTG
66 TAAATTGTTATCTTAACTTG
734193 AAAATATATA
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 47 0.65
90 25 0.35
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (90 bp):
TATATTATAATCTTAACTTAAATTATAAAATATATTATATTCCTACCTTAAATTATAAAATATAT
TAAATTGTTATCTTAACTTGTTACA
Found at i:734122 original size:119 final size:117
Alignment explanation
Indices: 733948--734211 Score: 273
Period size: 119 Copynumber: 2.2 Consensus size: 117
733938 AAAATCACAT
* * * * *
733948 CTTAACATTAAAAATATATTTT-TATTTTTTAACTTATTGAATTTCTTTTATTCTTATCTT-AAT
1 CTTAAC-TTAAAAATATATTTTATTTTTTTTAACTTATTGAATATATTATATTCTTAACTTAAAT
* * * **
734011 TAAAAAATTATATTTTAATCTTATCTTAACTTATAAAATATATTTTATTCCTAC
65 TAAAAAA-TATATTATAATCTTACCTTAAATTATAAAATATATTAAATTCCTAC
*
734065 CTTAACTTAAAAATATATTTTATTTTTATCTTAACTTGTT-ACATATATTATATTCTTAACTTAA
1 CTTAACTTAAAAATATATTTTATTTTT-T-TTAACTTATTGA-ATATATTATATTCTTAACTTAA
** * * ** *
734129 ATTATTAAATATATTATATTCTTACCTTAAATTATTAAATATATTAAATTGTTAT
63 ATTAAAAAATATATTATAATCTTACCTTAAATTATAAAATATATTAAATTCCTAC
*
734184 CTTAACTTGAAAATATATATCTTATTTT
1 CTTAACTT-AAAA-ATATATTTTATTTT
734212 AATTTTAAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
116 15 0.12
117 10 0.08
118 2 0.02
119 69 0.57
120 12 0.10
121 13 0.11
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (117 bp):
CTTAACTTAAAAATATATTTTATTTTTTTTAACTTATTGAATATATTATATTCTTAACTTAAATT
AAAAAATATATTATAATCTTACCTTAAATTATAAAATATATTAAATTCCTAC
Found at i:734200 original size:89 final size:88
Alignment explanation
Indices: 734001--734201 Score: 224
Period size: 89 Copynumber: 2.2 Consensus size: 88
733991 TCTTTTATTC
* * * * *
734001 TTATCTTAA-TTAAAAAATTATATTTTAATCTTATCTTAACTTATAAAATATATTTTATTCCTAC
1 TTATCTTAACTT-GAAAA-TATATTATAATCTTAACTTAAATTATAAAATATATTATATTCCTAC
* ** *
734065 CTTAACTTAAAAATATATTTTATTT
64 CTTAAATTAAAAATATATTAAATTG
* * * * *
734090 TTATCTTAACTTGTTACATATATTATATTCTTAACTTAAATTATTAAATATATTATATTCTTACC
1 TTATCTTAACTTG-AAAATATATTATAATCTTAACTTAAATTATAAAATATATTATATTCCTACC
*
734155 TTAAATTATTAAATATATTAAATTG
65 TTAAATTA-AAAATATATTAAATTG
734180 TTATCTTAACTTGAAAATATAT
1 TTATCTTAACTTGAAAATATAT
734202 ATCTTATTTT
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
89 63 0.68
90 29 0.32
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.50
Consensus pattern (88 bp):
TTATCTTAACTTGAAAATATATTATAATCTTAACTTAAATTATAAAATATATTATATTCCTACCT
TAAATTAAAAATATATTAAATTG
Found at i:734208 original size:25 final size:25
Alignment explanation
Indices: 734180--734228 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
734170 TATTAAATTG
*
734180 TTATCTTAACTTGAAAATATATATC
1 TTATCTTAACTTGAAAAAATATATC
* * *
734205 TTATTTTAATTTTAAAAAATATAT
1 TTATCTTAACTTGAAAAAATATAT
734229 TAATATATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (25 bp):
TTATCTTAACTTGAAAAAATATATC
Found at i:734273 original size:33 final size:37
Alignment explanation
Indices: 734201--734278 Score: 94
Period size: 39 Copynumber: 2.2 Consensus size: 37
734191 TGAAAATATA
734201 TATCTTATTTTAATTTTAAAAAATATATTAATATATTT
1 TATCTTATTTTAATTTTAAAAAATATATT-ATATATTT
*
734239 TATTCTTATTTTAA-TTT-AGAAATATATT-T-T-TTT
1 TA-TCTTATTTTAATTTTAAAAAATATATTATATATTT
734272 TATCTTA
1 TATCTTA
734279 ATTATGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
32 5 0.13
33 5 0.13
34 1 0.03
35 1 0.03
37 10 0.26
38 5 0.13
39 11 0.29
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (37 bp):
TATCTTATTTTAATTTTAAAAAATATATTATATATTT
Found at i:734274 original size:27 final size:27
Alignment explanation
Indices: 734230--734318 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 27
734220 AAAATATATT
734230 AATATATTTTATTCTTATTTTAATTTAGA
1 AATATATTTT-TT-TTATTTTAATTTAGA
*
734259 AATATATTTTTTTTATCTTAA-TTATGAA
1 AATATATTTTTTTTATTTTAATTTA-G-A
* *
734287 AAAATATATTTTTTATTTTAATTTTA-A
1 AATATATTTTTTTTATTTTAA-TTTAGA
734314 AATAT
1 AATAT
734319 TATAAAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
26 3 0.06
27 14 0.27
28 21 0.41
29 10 0.20
30 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
AATATATTTTTTTTATTTTAATTTAGA
Found at i:734452 original size:29 final size:29
Alignment explanation
Indices: 734410--734506 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
734400 TTATTGAATT
* **
734410 TATTTTATTCTTATCTTAACTGGAAAATA
1 TATTTTAATCTTATCTTAACTAAAAAATA
*
734439 TATTTTAATCTTATCTTAACTTATAAAATA
1 TATTTTAATCTTATCTTAAC-TAAAAAATA
* * * *
734469 TATTTTATTCCTACCTTAACTTAAAAATA
1 TATTTTAATCTTATCTTAACTAAAAAATA
734498 TATTTTAAT
1 TATTTTAAT
734507 TTTAAAATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 34 0.59
30 24 0.41
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.49
Consensus pattern (29 bp):
TATTTTAATCTTATCTTAACTAAAAAATA
Found at i:734473 original size:59 final size:58
Alignment explanation
Indices: 734375--734508 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 58
734365 TTATAACATT
* * ** * * *
734375 AAAAATATATTTT-ATTTTTTTTAACTTATTGAATTTATTTTATTCTTATCTTAACTG
1 AAAAATATATTTTAATTTATCTTAACTTATAAAATATATTTTATTCCTACCTTAACTG
* *
734432 GAAAATATATTTTAATCTTATCTTAACTTATAAAATATATTTTATTCCTACCTTAACTT
1 AAAAATATATTTTAAT-TTATCTTAACTTATAAAATATATTTTATTCCTACCTTAACTG
734491 AAAAATATATTTTAATTT
1 AAAAATATATTTTAATTT
734509 TAAAATATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
57 12 0.18
58 4 0.06
59 49 0.75
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (58 bp):
AAAAATATATTTTAATTTATCTTAACTTATAAAATATATTTTATTCCTACCTTAACTG
Found at i:735424 original size:23 final size:22
Alignment explanation
Indices: 735381--735429 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
735371 ATAAAATTTG
735381 ACAAGCACTAAACACAACAACA
1 ACAAGCACTAAACACAACAACA
735403 ACAAGCACTAAACAACAACAACA
1 ACAAGCACTAAAC-ACAACAACA
735426 ACAA
1 ACAA
735430 CAAGCACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.61, C:0.31, G:0.04, T:0.04
Consensus pattern (22 bp):
ACAAGCACTAAACACAACAACA
Found at i:738547 original size:43 final size:43
Alignment explanation
Indices: 738500--738584 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
738490 ACACTAAATT
* *
738500 CCAAAATAATACTCCACAAATACATCAAACTAACATATTAAAG
1 CCAAAATAACAATCCACAAATACATCAAACTAACATATTAAAG
* *
738543 CCAAAATAACAATTCACAAATACATTAAACTAACATATTAAA
1 CCAAAATAACAATCCACAAATACATCAAACTAACATATTAAA
738585 AATATTCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.55, C:0.21, G:0.01, T:0.22
Consensus pattern (43 bp):
CCAAAATAACAATCCACAAATACATCAAACTAACATATTAAAG
Found at i:739421 original size:23 final size:23
Alignment explanation
Indices: 739380--739425 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
739370 TTTTAAAAAC
*
739380 ATAATAATATATTCAATTATATT
1 ATAATAATATATTAAATTATATT
739403 ATAATAATATA-TAATATTATATT
1 ATAATAATATATTAA-ATTATATT
739426 CATATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAATAATATATTAAATTATATT
Found at i:739430 original size:18 final size:18
Alignment explanation
Indices: 739380--739430 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
739370 TTTTAAAAAC
*
739380 ATAATAATATATTCA-AT
1 ATAATATTATATTCATAT
* *
739397 -T-ATATTATAATAATAT
1 ATAATATTATATTCATAT
739413 ATAATATTATATTCATAT
1 ATAATATTATATTCATAT
739431 TTTAATAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 1 0.04
18 13 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATATTATATTCATAT
Found at i:739437 original size:29 final size:29
Alignment explanation
Indices: 739352--739447 Score: 97
Period size: 29 Copynumber: 3.2 Consensus size: 29
739342 ATATTTTTTA
* * *
739352 ATAATTTTATATTTATATTTTTAA-AA-AC
1 ATAATATTATATTCATA-TTTTAATAATAT
*
739380 ATAATAATATATTCAATTATATTATAATAATAT
1 ATAATATTATATTC-A-TAT-TT-TAATAATAT
739413 ATAATATTATATTCATATTTTAATAATAT
1 ATAATATTATATTCATATTTTAATAATAT
739442 ATAATA
1 ATAATA
739448 AATTGTTAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
28 11 0.19
29 17 0.30
30 6 0.11
31 6 0.11
32 3 0.05
33 14 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAATATTATATTCATATTTTAATAATAT
Found at i:739509 original size:22 final size:23
Alignment explanation
Indices: 739484--739542 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
739474 ATTAGGTTTA
739484 TAAAATAATATTATTAA-ATATT
1 TAAAATAATATTATTAAGATATT
*
739506 TAAAAT-ATATTTATTAATGATTTT
1 TAAAATAATA-TTATTAA-GATATT
739530 TAAATATAATATT
1 TAAA-ATAATATT
739543 CTCATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.10
22 13 0.42
24 8 0.26
25 4 0.13
26 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAATAATATTATTAAGATATT
Found at i:739570 original size:15 final size:15
Alignment explanation
Indices: 739547--739576 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
739537 AATATTCTCA
739547 TTTTAATATTATAAT
1 TTTTAATATTATAAT
*
739562 TTTTGATATTATAAT
1 TTTTAATATTATAAT
739577 AATGTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTTAATATTATAAT
Found at i:756982 original size:66 final size:66
Alignment explanation
Indices: 756876--757007 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
756866 TTGACAGCCA
756876 ATTTCTGGCAAAGATCCTGGTATAGGGGGTTATCAAACTTCATGGAATACCAAGATCTGTAGTAA
1 ATTTCTGGCAAAGATCCTGGTATAGGGGGTTATCAAACTTCATGGAATACCAAGATCTGTAGTAA
756941 G
66 G
756942 ATTTCTGGCAAAGATCCTGGTATAGGGGGTTATCAAACTTCATGGAATACCAAGATCTGTAGTAA
1 ATTTCTGGCAAAGATCCTGGTATAGGGGGTTATCAAACTTCATGGAATACCAAGATCTGTAGTAA
757007 G
66 G
757008 TGACCGTGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (66 bp):
ATTTCTGGCAAAGATCCTGGTATAGGGGGTTATCAAACTTCATGGAATACCAAGATCTGTAGTAA
G
Found at i:757691 original size:158 final size:157
Alignment explanation
Indices: 757369--757692 Score: 612
Period size: 158 Copynumber: 2.0 Consensus size: 157
757359 TTCATCGAAG
757369 AAAAGAATACAAAACTGCTTATATACAACTACAATATTCTAACTAACAAAGCTTAACAGAAAGCT
1 AAAA-AATACAAAACTGCTTATATACAACTACAATATTCTAACTAACAAAGCTTAACAGAAAGCT
757434 AACCAACCATAACTGATCAACTAATTATAATTAATATAACCTATACCCTCAAGATGGGACTGCAT
65 AACCAACCATAACTGATCAACTAATTATAATTAATATAACCTATACCCTCAAGATGGGACTGCAT
757499 GAATATTAAGAAGACCCAGCTTGTCAAT
130 GAATATTAAGAAGACCCAGCTTGTCAAT
757527 AAAAAAATACAAAACTGCTTATATACAACTACAATATTCTAACTAACAAAGCTTAACAGAAAGCT
1 -AAAAAATACAAAACTGCTTATATACAACTACAATATTCTAACTAACAAAGCTTAACAGAAAGCT
757592 AACCAACCATAACTGATCAACTAATTATAATTAATATAACCTAATACCCCTCAAGATGGGACTGC
65 AACCAACCATAACTGATCAACTAATTATAATTAATATAACCT-ATA-CCCTCAAGATGGGACTGC
757657 ATGAATATTAAGAAGACCCAGCTTGTCAAT
128 ATGAATATTAAGAAGACCCAGCTTGTCAAT
757687 AAAAAA
1 AAAAAA
757693 ACGATGCACG
Statistics
Matches: 163, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
158 102 0.63
159 13 0.08
160 48 0.29
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (157 bp):
AAAAAATACAAAACTGCTTATATACAACTACAATATTCTAACTAACAAAGCTTAACAGAAAGCTA
ACCAACCATAACTGATCAACTAATTATAATTAATATAACCTATACCCTCAAGATGGGACTGCATG
AATATTAAGAAGACCCAGCTTGTCAAT
Found at i:766746 original size:24 final size:24
Alignment explanation
Indices: 766714--766770 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
766704 AACCATCAAC
*
766714 GAGAACAAGTTTGTTCTTGGCGCA
1 GAGAGCAAGTTTGTTCTTGGCGCA
766738 GAGAGCAAGTTTGTTCTTGGCGCA
1 GAGAGCAAGTTTGTTCTTGGCGCA
766762 GAGAGCAAG
1 GAGAGCAAG
766771 CATCATCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (24 bp):
GAGAGCAAGTTTGTTCTTGGCGCA
Found at i:778111 original size:25 final size:25
Alignment explanation
Indices: 778072--778120 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
778062 TAAACTATTA
*
778072 AAATAGATACTTTGAGTCACAAGCG
1 AAATAGATACTTTGAATCACAAGCG
*
778097 AAATAGATAGC-TTGAATGACAAGC
1 AAATAGATA-CTTTGAATCACAAGC
778121 AATGGGGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (25 bp):
AAATAGATACTTTGAATCACAAGCG
Found at i:780960 original size:139 final size:138
Alignment explanation
Indices: 780722--781188 Score: 386
Period size: 139 Copynumber: 3.4 Consensus size: 138
780712 TATTGGGTCG
* * * * *
780722 AATAGTTAAAATGGAACCTCGAGCAAAAGCGATGACCAAATAAAAAATTCTCCTAAATTAAAAGG
1 AATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACAAAATAAAAAATTCTCATAAATTAAAAGA
** * * * * *
780787 CTACGTTTGAAATTAGACCTAAAATGAAGGCTCTAA-ATATTAATCTATTCAATTTTAATCAATT
66 CTAAATTTGAAATTAGACCTAAAATGAAGACTCTAATA-ATTAACCTAGTAAATTTTAACCAATT
780851 GCTAAGTTA
130 GCTAAGTTA
* * * * *
780860 AATAATTAAAATGGAGCCTCTAGC-AAAGTCGAGGATAAAATTAAGAATTCTCATAAATTAAAAT
1 AATAATTAAAATGGAACCTCGAGCAAAAG-CGAGGACAAAATAAAAAATTCTCATAAATTAAAA-
* *
780924 GACTAAATTTGAAATTAGGCCTAAAGTGAAGACTCTAATAATTAACCTAGTAAATTTTAACCAAT
64 GACTAAATTTGAAATTAGACCTAAAATGAAGACTCTAATAATTAACCTAGTAAATTTTAACCAA-
** * *
780989 TTTTTTTA-TTCG
128 -TTGCTAAGTT-A
* * * * * ** * * *
781001 AATAACTAAATTGGAACCTCGAGCAAAAGCGAGGACCATATTAAAAATTGACCTAAATTTAAGGA
1 AATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACAAAATAAAAAATTCTCATAAATTAAAAGA
* * * * * * * *
781066 CTAAGTTTGAAATTA-AGCCTACAATGGAGGCTCCAATTATTAACCTAATTAATTTTAACCAATT
66 CTAAATTTGAAATTAGA-CCTAAAATGAAGACTCTAATAATTAACCTAGTAAATTTTAACCAATT
* **
781130 -ATTTGATTCA
130 GCTAAG-TT-A
* * * *
781140 AAAAATTAAAATGGAACCTCGAGCAAAAGCGATGACTAAATTAAAAATT
1 AATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACAAAATAAAAAATT
781189 ACCCTAAATT
Statistics
Matches: 264, Mismatches: 55, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
137 6 0.02
138 51 0.19
139 98 0.37
140 56 0.21
141 49 0.19
142 4 0.02
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (138 bp):
AATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACAAAATAAAAAATTCTCATAAATTAAAAGA
CTAAATTTGAAATTAGACCTAAAATGAAGACTCTAATAATTAACCTAGTAAATTTTAACCAATTG
CTAAGTTA
Found at i:781401 original size:28 final size:28
Alignment explanation
Indices: 781331--781410 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
781321 AAGCAATTAA
781331 TAAATATAAAGGGACTAAATTAAAATAAAT
1 TAAA-ATAAAGGG-CTAAATTAAAATAAAT
* **
781361 TAAAATACAGGGCTGAAATTAAAATTTA-
1 TAAAATAAAGGGCT-AAATTAAAATAAAT
* *
781389 TCAAATAAAGGGCTAAAATAAA
1 TAAAATAAAGGGCTAAATTAAA
781411 TGAAAACTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 7 0.16
28 14 0.33
29 18 0.42
30 4 0.09
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (28 bp):
TAAAATAAAGGGCTAAATTAAAATAAAT
Found at i:781579 original size:282 final size:284
Alignment explanation
Indices: 781177--781742 Score: 1109
Period size: 282 Copynumber: 2.0 Consensus size: 284
781167 AGCGATGACT
781177 AAATTAAAAATTACCCTAAATTACCTAAAATCTGAGTAATCTAGATTAGGACTAAAATTATAAAA
1 AAATTAAAAATTACCCTAAATTACCTAAAATCTGAGTAATCTAGATTAGGACTAAAA-TATAAAA
781242 ATCTAAATCAAAAGGTTTAATTTAAAATCTAAAATTCTAGGACTAAATTTAAAGAAATTGAAATT
65 ATCTAAATCAAAAGGTTTAATTTAAAATCTAAAATTCTAGGACTAAATTTAAAGAAATTGAAATT
781307 AAAGACAAAATTAAAAGCAATTAATAAATATAAAGGGACTAAATTAAAATAAATTAAAATACAGG
130 AAAGACAAAATTAAAAGCAATTAATAAATATAAAGGGACTAAATTAAAATAAATTAAAATACAGG
781372 GCTGAAATTAAAATTTATCAAATAAAGGGCTAAAATAAATGAAAACTTATATTAAAGCTTAAGTT
195 GCTGAAATTAAAATTTATCAAATAAAGGGCTAAAATAAATGAAAACTTATATTAAAGCTTAAGTT
781437 AAGAAGTTGCAGAAAATTCAAAAAA
260 AAGAAGTTGCAGAAAATTCAAAAAA
781462 AAATTAAAAATTACCCTAAATTACCTAAAATCTGAGTAATCTAGATTAGGACT-AAA-ATAAAAA
1 AAATTAAAAATTACCCTAAATTACCTAAAATCTGAGTAATCTAGATTAGGACTAAAATATAAAAA
781525 TCTAAATCAAAAGGTTTAATTTAAAATCTAAAATTCTAGGACTAAATTTAAAGAAATTGAAATTA
66 TCTAAATCAAAAGGTTTAATTTAAAATCTAAAATTCTAGGACTAAATTTAAAGAAATTGAAATTA
781590 AAGACAAAATTAAAAGCAATTAATAAATATAAAGGGACTAAATTAAAATAAATTAAAATACAGGG
131 AAGACAAAATTAAAAGCAATTAATAAATATAAAGGGACTAAATTAAAATAAATTAAAATACAGGG
781655 CTGAAATTAAAATTTATCAAATAAAGGGCTAAAATAAATGAAAACTTATATTAAAGCTTAAGTTA
196 CTGAAATTAAAATTTATCAAATAAAGGGCTAAAATAAATGAAAACTTATATTAAAGCTTAAGTTA
781720 AGAAGTTGCAGAAAATTCAAAAA
261 AGAAGTTGCAGAAAATTCAAAAA
781743 TTAGTGTTTA
Statistics
Matches: 281, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
282 225 0.80
284 3 0.01
285 53 0.19
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (284 bp):
AAATTAAAAATTACCCTAAATTACCTAAAATCTGAGTAATCTAGATTAGGACTAAAATATAAAAA
TCTAAATCAAAAGGTTTAATTTAAAATCTAAAATTCTAGGACTAAATTTAAAGAAATTGAAATTA
AAGACAAAATTAAAAGCAATTAATAAATATAAAGGGACTAAATTAAAATAAATTAAAATACAGGG
CTGAAATTAAAATTTATCAAATAAAGGGCTAAAATAAATGAAAACTTATATTAAAGCTTAAGTTA
AGAAGTTGCAGAAAATTCAAAAAA
Found at i:781683 original size:28 final size:28
Alignment explanation
Indices: 781613--781692 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
781603 AAGCAATTAA
781613 TAAATATAAAGGGACTAAATTAAAATAAAT
1 TAAA-ATAAAGGG-CTAAATTAAAATAAAT
* **
781643 TAAAATACAGGGCTGAAATTAAAATTTA-
1 TAAAATAAAGGGCT-AAATTAAAATAAAT
* *
781671 TCAAATAAAGGGCTAAAATAAA
1 TAAAATAAAGGGCTAAATTAAA
781693 TGAAAACTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 7 0.16
28 14 0.33
29 18 0.42
30 4 0.09
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (28 bp):
TAAAATAAAGGGCTAAATTAAAATAAAT
Found at i:781840 original size:29 final size:28
Alignment explanation
Indices: 781774--781837 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
781764 TGTAAATGTT
*
781774 GAAAATTAAAGGCATAAATTAAAATAAA
1 GAAAATTAAAGGCAGAAATTAAAATAAA
*
781802 AAAAATTAAAGGGCAGAAATGT-AAATAACA
1 GAAAATTAAA-GGCAGAAAT-TAAAATAA-A
781832 GAAAAT
1 GAAAAT
781838 AAATCAATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 9 0.30
29 14 0.47
30 7 0.23
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (28 bp):
GAAAATTAAAGGCAGAAATTAAAATAAA
Found at i:782055 original size:47 final size:47
Alignment explanation
Indices: 782002--782093 Score: 184
Period size: 47 Copynumber: 2.0 Consensus size: 47
781992 TTGCGGTTAA
782002 GTTAGAAATTTACCTGGACCATAAATAACGGGAATCATACCCCAGAG
1 GTTAGAAATTTACCTGGACCATAAATAACGGGAATCATACCCCAGAG
782049 GTTAGAAATTTACCTGGACCATAAATAACGGGAATCATACCCCAG
1 GTTAGAAATTTACCTGGACCATAAATAACGGGAATCATACCCCAG
782094 GACGAGTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (47 bp):
GTTAGAAATTTACCTGGACCATAAATAACGGGAATCATACCCCAGAG
Found at i:786957 original size:5 final size:5
Alignment explanation
Indices: 786947--786988 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
786937 TTTTACAAAA
786947 ATATT ATATT ATATT ATATT AT-TT AT-TT ATTATT ATTATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT A-TATT A-TATT AT
786989 TAATAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 7 0.20
5 19 0.54
6 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
ATATT
Found at i:786979 original size:3 final size:3
Alignment explanation
Indices: 786948--787002 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
786938 TTTACAAAAA
786948 TAT TA- TAT TA- TAT TA- TAT TATT TATT TAT TAT TAT TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT T-AT
*
786993 AAT TAT TAT T
1 TAT TAT TAT T
787003 TTTTATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.13
3 30 0.67
4 9 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:786985 original size:13 final size:13
Alignment explanation
Indices: 786948--787002 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
786938 TTTACAAAAA
786948 TATTA-TATTATAT
1 TATTATTATT-TAT
786961 TA-TATTATTTATT
1 TATTATTATTTA-T
786974 TATTATTA-TTAT
1 TATTATTATTTAT
* *
786986 TATTAATAATTAT
1 TATTATTATTTAT
786999 TATT
1 TATT
787003 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
12 12 0.32
13 20 0.54
14 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:788424 original size:21 final size:20
Alignment explanation
Indices: 788358--788425 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 20
788348 TTTATTTCAA
788358 TTTAGTTATTCATTTTTTCCT
1 TTTAGTTATTCA-TTTTTCCT
* **
788379 GTTTA-TTTTTAGCATTTTTTAT
1 -TTTAGTTATT--CATTTTTCCT
788401 TTTAGTTATTCATTTTTCCCT
1 TTTAGTTATTCATTTTT-CCT
788422 TTTA
1 TTTA
788426 ATTTTAGTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
20 7 0.19
21 13 0.36
22 14 0.39
23 2 0.06
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.66
Consensus pattern (20 bp):
TTTAGTTATTCATTTTTCCT
Found at i:789175 original size:20 final size:20
Alignment explanation
Indices: 789150--789191 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
789140 GGGCATAAGG
*
789150 AAATGTATCCTCTCGAGTTT
1 AAATGTATCCTCTAGAGTTT
789170 AAATGTATCCTCTAGAGTTT
1 AAATGTATCCTCTAGAGTTT
789190 AA
1 AA
789192 CTTAGTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (20 bp):
AAATGTATCCTCTAGAGTTT
Found at i:790502 original size:23 final size:24
Alignment explanation
Indices: 790476--790526 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
790466 TTGGACTTGT
790476 TTTTTTG-AAC-TGTCTTATATTTC
1 TTTTTTGTAACTTG-CTTATATTTC
*
790499 -TTTTTGTAACTTGCTTTTATTTC
1 TTTTTTGTAACTTGCTTATATTTC
790522 TTTTT
1 TTTTT
790527 ATGAGGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.25
23 12 0.50
24 6 0.25
ACGTcount: A:0.14, C:0.12, G:0.08, T:0.67
Consensus pattern (24 bp):
TTTTTTGTAACTTGCTTATATTTC
Found at i:792361 original size:147 final size:146
Alignment explanation
Indices: 792171--792479 Score: 474
Period size: 147 Copynumber: 2.1 Consensus size: 146
792161 GATGGTGGTT
* * *
792171 GCTCAACTTCACAACGTAGGAGCGTTTGTCAACAAACAACTTTCTAGTTTCATTCAGAGTCAATT
1 GCTCAACTTCACAACGGAGGAGCGTCTGTCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATT
***
792236 TCAAATTCATTGCGAAGGATATTGAACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGA
66 TCAAATTCACAACGAAGGATATTGAACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGA
*
792301 ATGATATCCAATTCAAA
131 AGGATATCCAATTC-AA
** * *
792318 GCTCAACTTCACAGTGGAGGAGCGTCTGTCAACAAATAACTTTCCAGTTTCATTCATAGTCAATT
1 GCTCAACTTCACAACGGAGGAGCGTCTGTCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATT
* * *
792383 TCAACTTCACAACGAAGGATATTGGACTTGAAACAACACAAGATTGGATTTCAACTTCACAACGA
66 TCAAATTCACAACGAAGGATATTGAACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGA
792448 AGGATATCCAATTCAA
131 AGGATATCCAATTCAA
792464 GTCTCAACTTCACAAC
1 G-CTCAACTTCACAAC
792480 AAATGAGCCA
Statistics
Matches: 145, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
146 3 0.02
147 142 0.98
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (146 bp):
GCTCAACTTCACAACGGAGGAGCGTCTGTCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATT
TCAAATTCACAACGAAGGATATTGAACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGA
AGGATATCCAATTCAA
Found at i:792560 original size:121 final size:121
Alignment explanation
Indices: 792421--793012 Score: 907
Period size: 121 Copynumber: 4.9 Consensus size: 121
792411 TGAAACAACA
* *
792421 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGTCTCAACTTCACAACAAATGA
1 CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGA
* * *
792486 GCCATCAACGATTTCAAATTCACGAAGAAGGATATCGTGCCCACAACCAACTTACT
66 GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACTTACT
* * * * *
792542 CAAGATTAGATTTCAACTTCACGACGAAGGACATCCAATTCAAGGCTCAAATTTACAATGAAA-G
1 CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAA-CAAATG
*
792606 AGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTTCCCACAACCAACTTACT
65 AGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACTTACT
*
792663 CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGA
1 CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGA
** * *
792728 GTAATCCACGATTTTAACTTCACGACGAATGATATCGTGCCCACAACCAACTTACT
66 GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACTTACT
* * * *
792784 CAAGATTGAATTTAAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACAAAGGA
1 CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGA
* *
792849 GCCGTCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACTTACT
66 GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACTTACT
* * * *
792905 TAAGATTGGATTTCAACTTCACGAAGAAGGATATCTAATTCAAGGCTCAACTTCACAACGAATGA
1 CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGA
* * *
792970 GCCGTCTACGATTTCAACTTCACGACGAAGGATATCGTACCCA
66 GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCA
793013 AAATATTGGC
Statistics
Matches: 426, Mismatches: 43, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
120 2 0.00
121 421 0.99
122 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (121 bp):
CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGA
GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACTTACT
Found at i:792563 original size:55 final size:55
Alignment explanation
Indices: 792495--792939 Score: 196
Period size: 55 Copynumber: 7.5 Consensus size: 55
792485 AGCCATCAAC
* * *
792495 GATTTCAAATTCACGAAGAAGGATATCGTGCCCACAACCAACTTACTCAAGATTA
1 GATTTCAACTTCACGACGAAGGATATCGTACCCACAACCAACTTACTCAAGATTA
* ** ** * * * *
792550 GATTTCAACTTCACGACGAAGGACATCCAATTCA-AGGCTCAAATTTACAATGAAAGAGCCATCC
1 GATTTCAACTTCACGACGAAGGATATCGTACCCACA-AC-C-AACTTAC--T--CA-AG--AT-T
792614 A
55 A
* *
792615 CGATTTCAACTTCACGACGAAGGATATCGTTCCCACAACCAACTTACTCAAGATTG
1 -GATTTCAACTTCACGACGAAGGATATCGTACCCACAACCAACTTACTCAAGATTA
** ** * *
792671 GATTTCAACTTCACGACGAAGGATATCCAATTCA-AGGCTCAACTTCACAACGAATGAGTAATCC
1 GATTTCAACTTCACGACGAAGGATATCGTACCCACA-AC-CAACTT-AC-TC-AA-GA-T--T--
792735 A
55 A
* * *
792736 CGATTTTAACTTCACGACGAATGATATCGTGCCCACAACCAACTTACTCAAGATT-
1 -GATTTCAACTTCACGACGAAGGATATCGTACCCACAACCAACTTACTCAAGATTA
* * ** ** * *
792791 GAATTTAAACTTCACGACGAATGATATCCAATTCA-AGGCTCAACTTCACAACAAAGGAGCCGTC
1 G-ATTTCAACTTCACGACGAAGGATATCGTACCCACA-AC-CAACTT-AC-TC-AA-GA----T-
*
792855 CA
54 TA
* * * *
792857 CGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACTTACTTAAGATTG
1 -GATTTCAACTTCACGACGAAGGATATCGTACCCACAACCAACTTACTCAAGATTA
*
792913 GATTTCAACTTCACGAAGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
792940 TAATTCAAGG
Statistics
Matches: 286, Mismatches: 63, Indels: 82
0.66 0.15 0.19
Matches are distributed among these distances:
54 4 0.01
55 111 0.39
56 13 0.05
57 13 0.05
58 3 0.01
59 7 0.02
60 6 0.02
61 6 0.02
62 7 0.02
63 2 0.01
64 13 0.05
65 14 0.05
66 83 0.29
67 4 0.01
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (55 bp):
GATTTCAACTTCACGACGAAGGATATCGTACCCACAACCAACTTACTCAAGATTA
Found at i:794732 original size:43 final size:42
Alignment explanation
Indices: 794683--794775 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 42
794673 TTAATCCATC
794683 AATTTTA-ATTTATTTCAATTTAGTTATTCATTTTTT-CCTGTTT
1 AATTTTACATTT-TTT-AATTTAGTTATTCATTTTTTCCCT-TTT
*
794726 AATTTTAACATTTTTTATTTTAGTTATTCATTTTTTCCCTTTT
1 AATTTT-ACATTTTTTAATTTAGTTATTCATTTTTTCCCTTTT
794769 AATTTTA
1 AATTTTA
794776 GTGTATTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
42 1 0.02
43 34 0.74
44 7 0.15
45 4 0.09
ACGTcount: A:0.24, C:0.10, G:0.03, T:0.63
Consensus pattern (42 bp):
AATTTTACATTTTTTAATTTAGTTATTCATTTTTTCCCTTTT
Found at i:794768 original size:22 final size:21
Alignment explanation
Indices: 794701--794769 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
794691 TTTATTTCAA
794701 TTTAGTTATTCATTTTTTCCT
1 TTTAGTTATTCATTTTTTCCT
* *
794722 GTTTAATT-TTAACATTTTTT-AT
1 -TTTAGTTATT--CATTTTTTCCT
794744 TTTAGTTATTCATTTTTTCCCT
1 TTTAGTTATTCATTTTTT-CCT
794766 TTTA
1 TTTA
794770 ATTTTAGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
20 8 0.21
21 8 0.21
22 14 0.37
23 8 0.21
ACGTcount: A:0.19, C:0.12, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAGTTATTCATTTTTTCCT
Found at i:799665 original size:28 final size:28
Alignment explanation
Indices: 799600--799668 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
799590 TAATCTATTT
*
799600 TTTTATTTTATTTAATTTGGCCATGCAA
1 TTTTATTTTATTTAATTTGGCCATCCAA
*
799628 TTTTATTTTATTTCAATTTGGCC-TCCATG
1 TTTTATTTTATTT-AATTTGGCCATCCA-A
799657 TTTTA-TTTATTT
1 TTTTATTTTATTT
799669 TTATCTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 23 0.62
29 14 0.38
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.59
Consensus pattern (28 bp):
TTTTATTTTATTTAATTTGGCCATCCAA
Found at i:800595 original size:131 final size:129
Alignment explanation
Indices: 800268--800628 Score: 485
Period size: 130 Copynumber: 2.8 Consensus size: 129
800258 TATTGAAAAT
* *
800268 AATA-ATATCTCTTCATTTCAGTTGGAGTAATAAATGGTTGCTTTAAGGAATGAGAGGTCATTTA
1 AATAGATATCTCTTCATTTCA-TTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTA
* * * ** *
800332 TTCTAGATTGGAAATAACTAGATATTATCATTTTCTCTCGAATCAATATTGGTTTTTTAAGACGG
65 TTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCAAATCAATATTGGAATTTTAAGACGA
* ** * *
800397 ACTAGATATCTCTTCATTTCAATAAGAGTAATAAATGATTGCTTTAACGCAAGAGAGGTCATTTA
1 AATAGATATCTCTTCATTTC-ATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTA
** * *
800462 TTCTCGATTGGAAATAATTAGATATTATTGTTTTCTTTCAAATCAATATT-GAATTTTAAGGCGA
65 TTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCAAATCAATATTGGAATTTTAAGACGA
* *
800526 AATAGTGATATCTCCTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCGTT
1 AATA--GATATCTCTTCATTTC-ATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATT
800591 TATTCTCGATT-GAAATAATTAGATATTATCATTTTCTC
63 TATTCTCGATTGGAAATAATTAGATATTATCATTTTCTC
800629 CCTTAAAATT
Statistics
Matches: 200, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
129 16 0.08
130 120 0.60
131 64 0.32
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (129 bp):
AATAGATATCTCTTCATTTCATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
TCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCAAATCAATATTGGAATTTTAAGACGA
Found at i:802559 original size:60 final size:60
Alignment explanation
Indices: 802466--802586 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
802456 TGGTGATGGG
802466 TCTAGATTGATTAGAACATAGTATGATTTCACGTGAAATATGTGCCTTCTAGATATGAAT
1 TCTAGATTGATTAGAACATAGTATGATTTCACGTGAAATATGTGCCTTCTAGATATGAAT
* ** *
802526 TCTAGATTGATTATAGTATAGTGTGATTTCACGTGAAATATGTGCCTTCTAGATATGAAT
1 TCTAGATTGATTAGAACATAGTATGATTTCACGTGAAATATGTGCCTTCTAGATATGAAT
802586 T
1 T
802587 GGATGTAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (60 bp):
TCTAGATTGATTAGAACATAGTATGATTTCACGTGAAATATGTGCCTTCTAGATATGAAT
Found at i:803093 original size:20 final size:19
Alignment explanation
Indices: 803068--803116 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 19
803058 CTTGGAAAAC
803068 CGTTTTCTCCAGGGAATAA
1 CGTTTTCTCCAGGGAATAA
803087 TCGTTTTCTCCAGGGAATAA
1 -CGTTTTCTCCAGGGAATAA
803107 CTGTTTTCTC
1 C-GTTTTCTC
803117 TCTCGATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.39
Consensus pattern (19 bp):
CGTTTTCTCCAGGGAATAA
Found at i:811151 original size:2 final size:2
Alignment explanation
Indices: 811146--811176 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
811136 TTAAAAAATA
811146 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 A
811177 AATGGTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:813291 original size:2 final size:2
Alignment explanation
Indices: 813284--813309 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
813274 TAATACATAC
813284 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
813310 GTTGGTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:817995 original size:14 final size:14
Alignment explanation
Indices: 817978--818008 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
817968 TGGAACGGAG
817978 GAGATGGAGGAGCA
1 GAGATGGAGGAGCA
817992 GAGATGGAGGAGCA
1 GAGATGGAGGAGCA
818006 GAG
1 GAG
818009 GGTGAAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.52, T:0.06
Consensus pattern (14 bp):
GAGATGGAGGAGCA
Found at i:825555 original size:22 final size:23
Alignment explanation
Indices: 825524--825567 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
825514 TTTATTTATT
825524 TATTAGTATTTATAATAATATAA
1 TATTAGTATTTATAATAATATAA
* *
825547 TATTA-TATTTTTAATATTATA
1 TATTAGTATTTATAATAATATA
825568 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATTAGTATTTATAATAATATAA
Done.