Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold256
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: 726231
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 41294 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:520713 original size:21 final size:21
Alignment explanation
Indices: 520672--520715 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
520662 TTTTTGTACT
* * *
520672 TTTTAATAATTTTTAATATAA
1 TTTTAAAAATTTTAAAAATAA
520693 TTTTAAAAATTTTAAAAATAA
1 TTTTAAAAATTTTAAAAATAA
520714 TT
1 TT
520716 AATTGCACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAAATTTTAAAAATAA
Found at i:527778 original size:14 final size:15
Alignment explanation
Indices: 527759--527791 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
527749 AAATAAAGGG
527759 CTTTTTCTTT-TTTT
1 CTTTTTCTTTATTTT
527773 CTTTTTCTTTATTTT
1 CTTTTTCTTTATTTT
527788 -TTTT
1 CTTTT
527792 AACCTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
CTTTTTCTTTATTTT
Found at i:528481 original size:31 final size:31
Alignment explanation
Indices: 528440--528501 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
528430 AAAAAATAGA
528440 TACAAACGTATAGCTGCTTGTAGAAACTCCC
1 TACAAACGTATAGCTGCTTGTAGAAACTCCC
*
528471 TACAATCGTATAGCTGCTTGTAGAAACTCCC
1 TACAAACGTATAGCTGCTTGTAGAAACTCCC
528502 CTCAACCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (31 bp):
TACAAACGTATAGCTGCTTGTAGAAACTCCC
Found at i:530991 original size:40 final size:39
Alignment explanation
Indices: 530936--531057 Score: 217
Period size: 40 Copynumber: 3.1 Consensus size: 39
530926 TGTTGCACTT
530936 TTCTATTTCAACCCTAGTATTCTTGCTCTAAGGATTTTAC
1 TTCTATTT-AACCCTAGTATTCTTGCTCTAAGGATTTTAC
530976 TTCTATATTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
1 TTCTAT-TTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
531016 TTCTATTTTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
1 TTCTA-TTTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
531056 TT
1 TT
531058 TGCTCCATCA
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
40 77 0.96
41 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (39 bp):
TTCTATTTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
Found at i:537368 original size:53 final size:54
Alignment explanation
Indices: 537264--537369 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 54
537254 TATTCCTCTG
* *
537264 AAAGCTTGGAAGCAGGAATAAGGCCCCCCTTAACAGAAATTGCAAAACTTTCCC
1 AAAGCTTAGAAGCAGGAATAAGGCCCCCCTCAACAGAAATTGCAAAACTTTCCC
537318 AAAGCTTAGAAGCAGGAATAAGG-CCCCCTCAACAGAAATTGCAAAACTTTCC
1 AAAGCTTAGAAGCAGGAATAAGGCCCCCCTCAACAGAAATTGCAAAACTTTCC
537370 GAACTATAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 28 0.56
54 22 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (54 bp):
AAAGCTTAGAAGCAGGAATAAGGCCCCCCTCAACAGAAATTGCAAAACTTTCCC
Found at i:542293 original size:4 final size:4
Alignment explanation
Indices: 542284--542431 Score: 52
Period size: 4 Copynumber: 37.8 Consensus size: 4
542274 GGGAAAGGAG
* *
542284 AAGA AAG- AA-A AAGA AAG- AA-A AAGA AAGGA AAGGA GAGGG AAGA AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA-GA AA-GA -AAGA AAGA AAGA
*
542330 AA-A AAGA ATGA AAGAA AAGGA AAG- AAG- AAGA AA-A AAGA AAG- AA-A
1 AAGA AAGA AAGA AAG-A AA-GA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* ** *
542374 AAGA AGGA AAGAA AAGGA AAGGA GAAG- AAG- AAGA GGGA AGGAA AAGA
1 AAGA AAGA AAG-A AA-GA AA-GA -AAGA AAGA AAGA AAGA AAG-A AAGA
542421 AAGA AAGA AAG
1 AAGA AAGA AAG
542432 GTAATTTTTG
Statistics
Matches: 113, Mismatches: 12, Indels: 38
0.69 0.07 0.23
Matches are distributed among these distances:
3 31 0.27
4 50 0.44
5 27 0.24
6 5 0.04
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:542369 original size:27 final size:31
Alignment explanation
Indices: 542294--542374 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 31
542284 AAGAAAGAAA
* *
542294 AAGAAAG--AAAAAGAAAGGAAAGGAGAGGG
1 AAGAAAGAAAAAAAGAAAGAAAAGGAGAGAG
542323 AAGAAAGAAAAAGAATGAAAGAAAAGGA-A-AG
1 AAGAAAGAAAAA-AA-GAAAGAAAAGGAGAGAG
542354 AAG-AAG-AAAAAAGAAAGAAAA
1 AAGAAAGAAAAAAAGAAAGAAAA
542375 AGAAGGAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
27 9 0.20
28 2 0.04
29 11 0.24
30 3 0.07
31 7 0.15
32 3 0.07
33 11 0.24
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.01
Consensus pattern (31 bp):
AAGAAAGAAAAAAAGAAAGAAAAGGAGAGAG
Found at i:542390 original size:10 final size:11
Alignment explanation
Indices: 542284--542429 Score: 82
Period size: 10 Copynumber: 13.8 Consensus size: 11
542274 GGGAAAGGAG
542284 AAGAAAGAA-A
1 AAGAAAGAAGA
542294 AAGAAAGAA-A
1 AAGAAAGAAGA
542304 AAGAAAG--GA
1 AAGAAAGAAGA
*
542313 AAGGAGAGGGAAGA
1 AA-GA-A-AGAAGA
542327 AAGAAA-AAGA
1 AAGAAAGAAGA
*
542337 ATGAAAGAA-A
1 AAGAAAGAAGA
*
542347 AGGAAAGAAG-
1 AAGAAAGAAGA
*
542357 AAGAAAAAAGA
1 AAGAAAGAAGA
542368 AAGAAA-AAGA
1 AAGAAAGAAGA
*
542378 AGGAAAGAA-A
1 AAGAAAGAAGA
* *
542388 AGGAAAGGAG-
1 AAGAAAGAAGA
542398 AAG-AAGAAGA
1 AAGAAAGAAGA
*
542408 GGGAAGGAA-AAGA
1 ---AAGAAAGAAGA
542421 AAGAAAGAA
1 AAGAAAGAA
542430 AGGTAATTTT
Statistics
Matches: 108, Mismatches: 11, Indels: 33
0.71 0.07 0.22
Matches are distributed among these distances:
9 8 0.07
10 70 0.65
11 13 0.12
12 2 0.02
13 9 0.08
14 6 0.06
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (11 bp):
AAGAAAGAAGA
Found at i:543133 original size:309 final size:312
Alignment explanation
Indices: 542756--543389 Score: 951
Period size: 307 Copynumber: 2.0 Consensus size: 312
542746 AAAAATGGTA
* * * *
542756 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTTAAAAATCAAACTAAATTAATAAATTTCAAACATAATGCACTAAAATAATATAAAATAATA
* * *
542821 AAATTAAAAATTATGGTATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAATAAATAGCC
66 AAATTAAAAATTATGATA-TTTTTAAAGTAATAAAATGCGGAG-AAAAAATACGAACAAAGAGCC
* *
542886 GAAGTAAGAGAGTTTTACTAAATTTTTAAAAAATTCAAAAATAATTAATACAAATATTTCAAACA
129 GAAGTAAGAGACTTTTACTAAATTTTTAAAAAATTCAAAAATAATGAATACAAATATTTCAAACA
542951 AAATGTACTG-G-AA-T-AAT-ATAAAATAAT-AAAATAATATATTTTTATTGAAAGTAATAAAA
194 AAATGTACTGAGTAAGTAAATAATAAAAT-ATGAAAATAATATATTTTTATTGAAAGTAATAAAA
*
543010 TTCGAGAAAATAATACGAGCAAAAGGCAGGAATACGGG-TTTTTTTACACTAAAT
258 TTCGAGAAAATAATACGAGCAAAAGGCAGGAATAAGGGTTTTTTTTACACTAAAT
* *
543064 TAATTTAAAAATCAAACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATATAAAATTAT
1 T-ATTTAAAAATCAAACTAAATTAATAAATTTCAAACATAATGCACTAAAATAATATAAAATAAT
* * * *
543129 AAAATTAGAAATTATGATATTTTTAAAGTAATAAAATGCTGAGAAAAAATACGAACAAAGGGCTG
65 AAAATTAAAAATTATGATATTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAAGAGCCG
* * *
543194 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
130 AAGTAAGAGACTTTTACTAAATTTTTAAAAAATTCAAAAATAATGAATACAAATATTTCAAACAA
543259 AATGTACTGAAGTAATGTAAAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAA
195 AATGTACTG-AGTAA-GT-AAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAA
* * *
543324 ATTCGAGAAAATTATACGAGTAAAGGGCAGGAATAAGGGTTTTTTTTACACTAAAT
257 ATTCGAGAAAATAATACGAGCAAAAGGCAGGAATAAGGGTTTTTTTTACACTAAAT
543380 T-TTTAAAAAT
1 TATTTAAAAAT
543390 TTATATTGAA
Statistics
Matches: 293, Mismatches: 22, Indels: 16
0.89 0.07 0.05
Matches are distributed among these distances:
307 87 0.30
308 24 0.08
309 75 0.26
310 2 0.01
312 1 0.00
314 14 0.05
315 73 0.25
316 17 0.06
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (312 bp):
TATTTAAAAATCAAACTAAATTAATAAATTTCAAACATAATGCACTAAAATAATATAAAATAATA
AAATTAAAAATTATGATATTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAAGAGCCGA
AGTAAGAGACTTTTACTAAATTTTTAAAAAATTCAAAAATAATGAATACAAATATTTCAAACAAA
ATGTACTGAGTAAGTAAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAAATTC
GAGAAAATAATACGAGCAAAAGGCAGGAATAAGGGTTTTTTTTACACTAAAT
Found at i:543305 original size:156 final size:152
Alignment explanation
Indices: 542783--543334 Score: 534
Period size: 156 Copynumber: 3.5 Consensus size: 152
542773 AAATTAATAA
* * * *
542783 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAAAAATTATGGTATTTTTTAAA
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATT-AAAATTATGATA-TTTTTAAA
* **
542848 GTAATAAAATGCGGAGAAAAAAATACGAATAAATA-GCCGAAGTAAGAGAGTTTTACTAAATTTT
64 GTAATAAAATGC-GAG-AAAAAATACGAACAAA-AGGCCGAAGTAAGAGTCTTTTACTAAATTTT
*
542912 TAAAAAATTCAAAAATAATTAATACAAAT
126 TTAAAAATTC-AAAATAA-TAATACAAAT
* *
542941 ATTTCAAACAAAATGTACTGGAATAATATAAAATAATAAAA-T--AA-TAT-ATTTTTATTGAAA
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATTAAAATTATGATATTT-TT-AAA
* * * * * *
543001 GTAATAAAATTCGAGAAAATAATACGAGCAAAAGGCAGGAA-TACGGGTTTTTTTACACTAAATT
64 GTAATAAAATGCGAGAAAA-AATACGAACAAAAGGC-CGAAGTAAGAG-TCTTTT--ACTAAATT
* * *
543065 AATTTAAAAA-TCAAACTAA-ATTA-ATAA-
124 -TTTTAAAAATTCAAAATAATAATACA-AAT
* * *
543092 ATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATTAGAAATTATGATATTTTTAAAG
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATTA-AAATTATGATATTTTTAAAG
* *
543157 TAATAAAATGCTGAGAAAAAATACGAACAAAGGGCTGAAGTAAGAGTCTTTTACTAAATTTTTTA
65 TAATAAAATGC-GAGAAAAAATACGAACAAAAGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTA
543222 AAAATTCAGAAATAATGAATACAAAT
129 AAAATTCA-AAATAAT-AATACAAAT
* * *
543248 ATTTCAAACAAAATGTACTGAAGTAATGTAAAATAATAAAATATGAAAATAATAT-ATTTTTATT
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAAT-T-AAAAT--TATGATATTT-TT
*
543312 GAAAGTAATAAAATTCGAGAAAA
61 -AAAGTAATAAAATGCGAGAAAA
543335 TTATACGAGT
Statistics
Matches: 324, Mismatches: 40, Indels: 59
0.77 0.09 0.14
Matches are distributed among these distances:
151 54 0.17
152 39 0.12
153 29 0.09
154 16 0.05
155 49 0.15
156 57 0.18
157 11 0.03
158 43 0.13
159 12 0.04
160 14 0.04
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.31
Consensus pattern (152 bp):
ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATTAAAATTATGATATTTTTAAAGT
AATAAAATGCGAGAAAAAATACGAACAAAAGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTAAA
AATTCAAAATAATAATACAAAT
Found at i:545435 original size:9 final size:9
Alignment explanation
Indices: 545416--545455 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
545406 TTTGGTTAAA
*
545416 AATTAATCG
1 AATTAACCG
*
545425 AATTACCCG
1 AATTAACCG
545434 AATTAACCG
1 AATTAACCG
545443 AATTAACCG
1 AATTAACCG
545452 AATT
1 AATT
545456 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:545439 original size:18 final size:18
Alignment explanation
Indices: 545416--545460 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
545406 TTTGGTTAAA
*
545416 AATTAATCGAATTACCCG
1 AATTAATCGAATTAACCG
*
545434 AATTAACCGAATTAACCG
1 AATTAATCGAATTAACCG
545452 AATTGAATC
1 AATT-AATC
545461 ACTACATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (18 bp):
AATTAATCGAATTAACCG
Found at i:548417 original size:43 final size:42
Alignment explanation
Indices: 548311--548446 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 42
548301 TCACTAACCC
* * *
548311 TAATAACTAACACAATAGCAATAATAATAGTTTTATACTCAAAA
1 TAATAACTAAC-C-ATAACAATAATAATAGGTTTATACTAAAAA
548355 TAAT-ACTAA-CA-AACAATAATAATTAGGGTTT-TACTAAAAA
1 TAATAACTAACCATAACAATAATAA-TA-GGTTTATACTAAAAA
* * * * *
548395 TAATAACTAACCATAATAATAATACTAGTTTTTTTACTAACAA
1 TAATAACTAACCATAACAATAATAATAG-GTTTATACTAAAAA
548438 TAAT-ACTAA
1 TAATAACTAA
548447 GTAACATCTA
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
39 10 0.13
40 15 0.19
41 11 0.14
42 12 0.15
43 26 0.33
44 4 0.05
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.32
Consensus pattern (42 bp):
TAATAACTAACCATAACAATAATAATAGGTTTATACTAAAAA
Found at i:548638 original size:10 final size:10
Alignment explanation
Indices: 548610--548646 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
548600 AAATACATTT
548610 TTTTTCTCTTC
1 TTTTTCTC-TC
*
548621 TCTTTCTCTC
1 TTTTTCTCTC
548631 TTTTTCTCTC
1 TTTTTCTCTC
548641 TTTTTC
1 TTTTTC
548647 CGGCAGCACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:551614 original size:22 final size:22
Alignment explanation
Indices: 551589--551640 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
551579 TCAGCACGTC
* *
551589 GGTGTCTACTG-TCCAATACTTT
1 GGTGCCTACTGCT-CAACACTTT
551611 GGTGCCTACTGCTCAACACTTT
1 GGTGCCTACTGCTCAACACTTT
551633 GGTGCCTA
1 GGTGCCTA
551641 TTGGTGTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (22 bp):
GGTGCCTACTGCTCAACACTTT
Found at i:564416 original size:12 final size:12
Alignment explanation
Indices: 564401--564445 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
564391 TGAGTAAATA
*
564401 ATAATAATGATG
1 ATAATAATAATG
564413 ATAATAATAATG
1 ATAATAATAATG
564425 -TAAT-ATAAT-
1 ATAATAATAATG
564434 AGTAATAATAAT
1 A-TAATAATAAT
564446 TGGGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 5 0.17
11 8 0.28
12 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:564926 original size:83 final size:84
Alignment explanation
Indices: 564813--565311 Score: 415
Period size: 87 Copynumber: 5.8 Consensus size: 84
564803 GTTTTAATCG
** * *
564813 GCTCCACTACAACTTTAGGGAGATAGGATTGGTTTCTTCTG-TCTGCTTCACTACTGCTTAGGGA
1 GCTCCACTACTGC-TTAGGGAGATAAGATTGGTTTCTTCTGATCTGCTCCACTACTGCTTAGGGA
*
564877 GATAATACTTGGTGCGATCT
65 GATAAGACTTGGTGCGATCT
* * *
564897 GCTCCACTACTGCTTAGGGATATAAGATTGGTTTCTTTTG-TCTGCTCCATTACTGCTTAGGGAG
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTTCTGATCTGCTCCACTACTGCTTAGGGAG
* *
564961 ATAAGACTTGATGTGATCT
66 ATAAGACTTGGTGCGATCT
* * * *
564980 ACT-CACTACTGCTTAGGGAGATAAGATTTGTCATCTT-TGACCTGCTCCACTACTGCTTAGGGA
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGT-TTCTTCTGATCTGCTCCACTACTGCTTAGGGA
* *
565043 GATAGGAC-TGGTGGCTTAAATCT
65 GATAAGACTTGGT-GC---GATCT
* * **
565066 GCTTCACTACTGCTTAGGAAGATAAGATTCGCCATT-TTC-GATCTGCTCCACTACTGCTTAGGG
1 GCTCCACTACTGCTTAGGGAGATAAGATT-G-GTTTCTTCTGATCTGCTCCACTACTGCTTAGGG
* * ** *
565129 AGATAAGATCTACCGTATTTGACCT
64 AGATAAGA-CT--TG-GTGCGATCT
**** * *
565154 GCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTC-GACCTACTCCACTACTGCTTAGGGA
1 GCTCCACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTCTGATCTGCTCCACTACTGCTTAGGGA
* *
565218 GATAGGAC-TGGTGGCTTAAATCT
65 GATAAGACTTGGT-GC---GATCT
* * * * * *
565241 ACTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTC-GATCTACTCCACTACTGCTTAGGGA
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGT-TTCTTCTGATCTGCTCCACTACTGCTTAGGGA
565305 GATAAGA
65 GATAAGA
565312 TCTACCATCT
Statistics
Matches: 336, Mismatches: 57, Indels: 41
0.77 0.13 0.09
Matches are distributed among these distances:
82 31 0.09
83 98 0.29
84 12 0.04
86 7 0.02
87 122 0.36
88 63 0.19
89 1 0.00
91 1 0.00
92 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (84 bp):
GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTTCTGATCTGCTCCACTACTGCTTAGGGAG
ATAAGACTTGGTGCGATCT
Found at i:564953 original size:43 final size:42
Alignment explanation
Indices: 564813--565352 Score: 299
Period size: 44 Copynumber: 12.6 Consensus size: 42
564803 GTTTTAATCG
** *
564813 GCTCCACTACAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCT
1 GCTCCACTACTGC-TTAGGGAGATAAGATTGGTTTCTT-TGTCT
* * *
564857 GCTTCACTACTGCTTAGGGAGATAATACTTGG-TGC---GATCT
1 GCTCCACTACTGCTTAGGGAGATAAGA-TTGGTTTCTTTG-TCT
*
564897 GCTCCACTACTGCTTAGGGATATAAGATTGGTTTCTTTTGTCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTC-TTTGTCT
* * *
564940 GCTCCATTACTGCTTAGGGAGATAAGACTT-G---ATGTGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGA-TTGGTTTCTTTG-TCT
* * * *
564980 ACT-CACTACTGCTTAGGGAGATAAGATTTGTCATCTTTGACCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGT-TTCTTTG-TCT
* * ** **
565023 GCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTT-TGTCT
* * ** *
565066 GCTTCACTACTGCTTAGGAAGATAAGATTCGCCATT-TTCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGATT-G-GTTTCTTTG-TCT
**** * *
565110 GCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCT
1 GCTCCACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTTG-TCT
**** * *
565154 GCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCT
1 GCTCCACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTTG-TCT
* * * ** **
565198 ACTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTT-TGTCT
* * * * * *
565241 ACTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGT-TTCTTTG-TCT
* **** *
565285 ACTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCT
1 GCTCCACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTTG-TCT
*
565329 GCACCACTACTGCTTAGGGAGATA
1 GCTCCACTACTGCTTAGGGAGATA
565353 GGACTACTAG
Statistics
Matches: 394, Mismatches: 77, Indels: 50
0.76 0.15 0.10
Matches are distributed among these distances:
38 2 0.01
39 31 0.08
40 34 0.09
43 116 0.29
44 209 0.53
45 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (42 bp):
GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTTTGTCT
Found at i:565135 original size:44 final size:43
Alignment explanation
Indices: 564892--565352 Score: 330
Period size: 44 Copynumber: 10.7 Consensus size: 43
564882 TACTTGGTGC
* * *
564892 GATCTGCTCCACTACTGCTTAGGGATATAAGATTGGTTTC-TTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCG--CCATTTT
* *
564936 G-TCTGCTCCATTACTGCTTAGGGAGATAAGACTT-G--A-TGT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGA-TTCGCCATTTT
* * *
564975 GATCTACT-CACTACTGCTTAGGGAGATAAGATTTGTCATCTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCAT-TTT
* * * * **** *
565018 GACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTA
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCATTTT
* * *
565061 AATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCATTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCATTTT
* *
565104 CGATCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTACCGTATTT
1 -GATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCAT-TTT
* * *
565149 GACCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTACCATCTTC
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCAT-TTT
* * * * * **** *
565193 GACCTACTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTA
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCATTTT
* * * * * * *
565236 AATCTACTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTC
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCAT-TTT
* *
565280 GATCTACTCCACTACTGCTTAGGGAGATAAGA-TCTACCATCTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCAT-TTT
* *
565324 GACCTGCACCACTACTGCTTAGGGAGATA
1 GATCTGCTCCACTACTGCTTAGGGAGATA
565353 GGACTACTAG
Statistics
Matches: 337, Mismatches: 65, Indels: 30
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.01
39 26 0.08
40 5 0.01
41 1 0.00
43 107 0.32
44 192 0.57
45 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCATTTT
Found at i:565168 original size:131 final size:126
Alignment explanation
Indices: 564895--565180 Score: 349
Period size: 126 Copynumber: 2.2 Consensus size: 126
564885 TTGGTGCGAT
* * ** *** * *
564895 CTGCTCCACTACTGCTTAGGGATATAAGATTGGTTTCTTTTGTCTGCTCCATTACTGCTTAGGGA
1 CTGCTCCACTACTGCTTAGGGAGATAAGACTGGTGGCTTAAATCTGCTCCACTACTGCTTAGGAA
* ** *
564960 GATAAGACTTGATGTGATCTACTCACTACTGCTTAGGGAGATAAGATTTGTCATCTTTGAC
66 GATAAGACTTGATGTGATCTACTCACTACTGCTTAGGGAGATAAGATCTACCATATTTGAC
* *
565021 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAAGACTGGTGGCTTAAATCTGCTCCACTACTGCTTAGGAA
* * *
565086 GATAAGA-TTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTG
66 GATAAGACTT-G--A-TGT-GATCTACT-CACTACTGCTTAGGGAGATAAGATCTACCATATTTG
565150 AC
125 AC
565152 CTGCTCCACTACTGCTTAGGGAGATAAGA
1 CTGCTCCACTACTGCTTAGGGAGATAAGA
565181 TCTACCATCT
Statistics
Matches: 135, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
125 2 0.01
126 62 0.46
128 1 0.01
129 2 0.01
130 7 0.05
131 61 0.45
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (126 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGACTGGTGGCTTAAATCTGCTCCACTACTGCTTAGGAA
GATAAGACTTGATGTGATCTACTCACTACTGCTTAGGGAGATAAGATCTACCATATTTGAC
Found at i:565205 original size:175 final size:174
Alignment explanation
Indices: 564861--565352 Score: 646
Period size: 175 Copynumber: 2.9 Consensus size: 174
564851 CTGTCTGCTT
** * * * *
564861 CACTACTGCTTAGGGAGATAATACTTGGT-GC---GATCTGCTCCACTACTGCTTAGGGATATAA
1 CACTACTGCTTAGGGAGATAGGAC-TGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAA
* * * * * *
564922 GATTGGTTTCTTTT-G-TCTGCTCCATTACTGCTTAGGGAGATAAGA-CT--TG-ATGTGATCTA
65 GATTCG--TCTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTG
* ** * *
564981 CT-CACTACTGCTTAGGGAGATAAGATTTGTCATCTTTGACCTGCTC
128 CTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTACTC
565027 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAG
1 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAG
*
565092 ATTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCT
66 ATTCGTC-TTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCT
565157 CCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTACTC
130 CCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTACTC
*
565202 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAAG
1 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAG
* * * * *
565267 ATTCGTCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCTGCA
66 ATTCGTC-TTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCT
565332 CCACTACTGCTTAGGGAGATA
130 CCACTACTGCTTAGGGAGATA
565353 GGACTACTAG
Statistics
Matches: 288, Mismatches: 26, Indels: 15
0.88 0.08 0.05
Matches are distributed among these distances:
165 4 0.01
166 24 0.08
167 1 0.00
168 4 0.01
169 32 0.11
170 29 0.10
171 2 0.01
173 1 0.00
174 9 0.03
175 182 0.63
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (174 bp):
CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAG
ATTCGTCTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTACTC
Found at i:565249 original size:131 final size:130
Alignment explanation
Indices: 564976--565357 Score: 401
Period size: 131 Copynumber: 2.9 Consensus size: 130
564966 ACTTGATGTG
* *
564976 ATCTAC-TCACTACTGCTTAGGGAGATAAGATTTGTCATCTTTGACCTGCTCCACTACTGCTTAG
1 ATCTACTTCACTACTGCTTAGGGAGATAAGA-TT-CCGTCTTTGACCTGCTCCACTACTGCTTAG
* ***** * * * * * * **
565040 GGAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCATTTT
64 GGAGATAAGATCTACCATCTTAGACCTGCTCCACTACTGCTTAGGGAGATAGGACTCGCCAGCTT
**
565104 CG
129 AA
* * *
565106 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCTCCACTACTGCTTAG
1 ATCTACTTCACTACTGCTTAGGGAGATAAGAT-T-CCGTCTTTGACCTGCTCCACTACTGCTTAG
* * ***
565171 GGAGATAAGATCTACCATCTTCGACCTACTCCACTACTGCTTAGGGAGATAGGACT-GGTGGCTT
64 GGAGATAAGATCTACCATCTTAGACCTGCTCCACTACTGCTTAGGGAGATAGGACTCGCCAGCTT
565235 AA
129 AA
* * * *
565237 ATCTACTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTCGATCTACTCCACTACTGCTTAG
1 ATCTACTTCACTACTGCTTAGGGAGATAAGATTC--CGTCTTTGACCTGCTCCACTACTGCTTAG
* *
565302 GGAGATAAGATCTACCATCTTTGACCTGCACCACTACTGCTTAGGGAGATAGGACT
64 GGAGATAAGATCTACCATCTTAGACCTGCTCCACTACTGCTTAGGGAGATAGGACT
565358 ACTAGCTTCA
Statistics
Matches: 210, Mismatches: 37, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
129 1 0.00
130 7 0.03
131 170 0.81
132 32 0.15
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (130 bp):
ATCTACTTCACTACTGCTTAGGGAGATAAGATTCCGTCTTTGACCTGCTCCACTACTGCTTAGGG
AGATAAGATCTACCATCTTAGACCTGCTCCACTACTGCTTAGGGAGATAGGACTCGCCAGCTTAA
Found at i:565820 original size:134 final size:133
Alignment explanation
Indices: 565661--566012 Score: 616
Period size: 134 Copynumber: 2.6 Consensus size: 133
565651 AGCATTACTA
* ** *
565661 GCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC-AGAAATTATTCGGTCTACTCCACT
1 GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTA-AAATTCTTCGGTCTACTCCACT
565725 GTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGT
65 GTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGT
565790 TCGT
130 TCGT
565794 GGCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACT
1 -GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACT
*
565859 GTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGT
65 GTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGT
*
565924 TTGT
130 TCGT
565928 GCTTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACT
1 GC-TTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACT
565993 GTAACCTCAGGGAGATAAGA
65 GTAACCTCAGGGAGATAAGA
566013 TCTGATGCGA
Statistics
Matches: 210, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
133 2 0.01
134 207 0.99
135 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (133 bp):
GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACTG
TAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTT
CGT
Found at i:565949 original size:44 final size:43
Alignment explanation
Indices: 565709--566763 Score: 243
Period size: 44 Copynumber: 23.8 Consensus size: 43
565699 TCAGAAATTA
* * * ** *
565709 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCAT-A
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG--TGC
* * * * *
565753 TTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTTCGTGGC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGT-GC
** * ** *
565797 TTCGATCTGCTCTTCTGTAA-TCTCAGGGAGATAAGATCTAAAATTC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGGT-T--TGTGC
* * * ** *
565843 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCAT-A
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG--TGC
* * *
565887 TTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTGC
** * ** *
565930 TTTCGATCTGCTCTTCTGTAA-TCTCAGGGAGATAAGATCTAAAATTC
1 -TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGGT-T--TGTGC
* * * * *
565977 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGATCTGATG-
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG-TGC
* * * * *
566020 --CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTT-TGGT
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGT-TTGT-GC
** * * * *
566062 TTTAATCCGCTCCACTGTAA-TCTCAGAGAGATAAGATCTT-TGGT
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGGT-TTGT-GC
** * * * **
566106 TTTAATCCGCTCCGCTGTAA-TCTCAGAGAGAT-AGGATTACTAGC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGG-TTTGT-GC
* * * * ** *
566150 TTCAATCTACTCCGCTGTAA-TCTCAGGGAGATAAGATCAGAAATTC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGGTTTG---TGC
* * * * ** *
566196 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGATCTAAAATTC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGT-T--TGTGC
* * * * *
566242 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGATCTGATG-
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG-TGC
* * * * *
566285 --CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTT-TGGT
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGT-TTGT-GC
** * * **
566327 TTTAATCCGCTCCACTGTAA-TCTCAGAGAGAT-AGGATTACTAGC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGG-TTTGT-GC
* * * * ** *
566371 TTCAATCTACTCCGCTGTAA-TCTCAGGGAGATAAGATCAGAAATTC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGGTTTG---TGC
* * * ** *
566417 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCAT-A
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG--TGC
* * * * *
566461 TTCAACCTGCCCCACTGTAACTTCAGGAAAATAAGGTTTGTGGC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGT-GC
** * * *
566505 TTCGATCTGCTCTTCTGTAA-TCTCAGGGAGATAAGATCTGAAATTC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGGTTTG---TGC
* * * *** *
566551 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAAACTTGCAT-A
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG--TGC
* * *
566595 TTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGCC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTG-C
** * * *
566639 TTCGATCTGCTCTTCTGTAA-TCTCAGGGAGATAAGATCTGAAATTC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGGTTTG---TGC
* * * ** *
566685 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCAT-A
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG--TGC
* * *
566729 TTCAACCTGCCCCACTGTAACTTCAGGGAGATAAG
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAG
566764 ACTTTATGCG
Statistics
Matches: 764, Mismatches: 186, Indels: 122
0.71 0.17 0.11
Matches are distributed among these distances:
40 2 0.00
41 64 0.08
42 6 0.01
43 12 0.02
44 425 0.56
45 14 0.02
46 233 0.30
47 7 0.01
49 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (43 bp):
TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTGC
Found at i:566367 original size:221 final size:218
Alignment explanation
Indices: 565945--566452 Score: 790
Period size: 221 Copynumber: 2.3 Consensus size: 218
565935 ATCTGCTCTT
565945 CTGTAATCTCAGGGAGATAAGATCTA-AAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGAT
1 CTGTAATCTCAGGGAGATAAGATC-AGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGAT
* * * * ** *
566009 AAGATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTGGTTTTAATCCGCTC
65 AAGATCTAATGCGATCTACTCCACTGTAACCTCAGAGAGATAAGATC-TTGGATGCAATCCACTC
*
566074 CACTGTAATCTCAGAGAGATAAGATCTTTGGTTTTAATCCGCTCCGCTGTAATCTCAGAGAGATA
129 CACTGTAATCTCAGAGAGATAAGATCTTTGGTTTTAATCCGCTCCACTGTAATCTCAGAGAGATA
566139 GGATTACTAGCTTCAATCTACTCCG
194 GGATTACTAGCTTCAATCTACTCCG
566164 CTGTAATCTCAGGGAGATAAGATCAGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCAGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
* * * * *
566229 AGATCTAAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGATC-T-GATGCGATCTA
66 AGATCT--AA---TGCGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTTGGATGCAATCCA
*
566292 CTCTACTGTAA-CTTCAGAGAGATAAGATCTTTGGTTTTAATCCGCTCCACTGTAATCTCAGAGA
126 CTCCACTGTAATC-TCAGAGAGATAAGATCTTTGGTTTTAATCCGCTCCACTGTAATCTCAGAGA
566356 GATAGGATTACTAGCTTCAATCTACTCCG
190 GATAGGATTACTAGCTTCAATCTACTCCG
566385 CTGTAATCTCAGGGAGATAAGATCAGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCAGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
566450 AGA
66 AGA
566453 CTTGCATATT
Statistics
Matches: 268, Mismatches: 14, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
218 1 0.00
219 69 0.26
220 1 0.00
221 163 0.61
222 1 0.00
224 33 0.12
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (218 bp):
CTGTAATCTCAGGGAGATAAGATCAGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
AGATCTAATGCGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTTGGATGCAATCCACTCCA
CTGTAATCTCAGAGAGATAAGATCTTTGGTTTTAATCCGCTCCACTGTAATCTCAGAGAGATAGG
ATTACTAGCTTCAATCTACTCCG
Found at i:566756 original size:134 final size:134
Alignment explanation
Indices: 566385--566763 Score: 713
Period size: 134 Copynumber: 2.8 Consensus size: 134
566375 ATCTACTCCG
*
566385 CTGTAATCTCAGGGAGATAAGATCAGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
* * *
566450 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGAAAATAAGGTTTGTGGCTTCGATCTGC
66 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGCCTTCGATCTGC
566515 TCTT
131 TCTT
566519 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
*
566584 AAACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGCCTTCGATCTGC
66 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGCCTTCGATCTGC
566649 TCTT
131 TCTT
566653 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
566718 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAG
66 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAG
566764 ACTTTATGCG
Statistics
Matches: 239, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 239 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (134 bp):
CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGCCTTCGATCTGC
TCTT
Found at i:566784 original size:90 final size:89
Alignment explanation
Indices: 566421--566785 Score: 212
Period size: 90 Copynumber: 4.1 Consensus size: 89
566411 AAATTCTTCG
566421 GTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCA
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCA
* * * * *
566486 GGAAAATAAG-GTTTGTG-G-CTT
66 GGGAGATAAGACTTTATGCGACCT
* ** * * ** * *
566507 CGATCTGCTCTTCTGTAATCTCAGGGAGATAAGA-TCTG-AAATTCTTCGGTCTACTCCACTGTA
1 -G-TCTACTCCACTGTAACCTCAGGGAGATAAGACT-TGCATATTCAAC---CTGCCCCACTGTA
* * * *
566570 ACCTCAGGGAGATAAAACTTGCATATTCAACCT
60 ACTTCAGGGAGATAAGACTT---TATGCGACCT
* ** **** * * * **
566603 G-C--C-CCACTGTAACTTCAGGGAGATAAGGTTTGTGCCTTCGATCTGCTCTTCTGTAA-TCTC
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACT-TC
** * ** *
566663 AGGGAGATAAGATCTGAAATTC-TTCG
65 AGGGAGATAAGA-CT-TTATGCGACCT
566689 GTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCA
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCA
566754 GGGAGATAAGACTTTATGCGACCT
66 GGGAGATAAGACTTTATGCGACCT
566778 GCTCTACT
1 G-TCTACT
566786 GTAACTTTAG
Statistics
Matches: 198, Mismatches: 57, Indels: 43
0.66 0.19 0.14
Matches are distributed among these distances:
86 2 0.01
87 13 0.07
88 56 0.28
89 7 0.04
90 106 0.54
91 8 0.04
93 1 0.01
94 2 0.01
95 1 0.01
96 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (89 bp):
GTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCA
GGGAGATAAGACTTTATGCGACCT
Found at i:566790 original size:41 final size:42
Alignment explanation
Indices: 566562--566792 Score: 124
Period size: 44 Copynumber: 5.3 Consensus size: 42
566552 TCGGTCTACT
* * *
566562 CCACTGTAACCTCAGGGAGATAAAACTTGCATATTCAACCTGCC
1 CCACTGTAACTTCAGGGAGATAAGACTT--ATATGCAACCTGCC
** * * * * * *
566606 CCACTGTAACTTCAGGGAGATAAGGTTTGTGCCTTCGATCTGCT
1 CCACTGTAACTTCAGGGAGATAAGACTTAT--ATGCAACCTGCC
** * * * ** * *
566650 CTTCTGTAA-TCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACT
1 CCACTGTAACT-TCAGGGAGATAAGA-CTTATATGCAAC---CTGCC
* *
566696 CCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCC
1 CCACTGTAACTTCAGGGAGATAAGACTT--ATATGCAACCTGCC
* *
566740 CCACTGTAACTTCAGGGAGATAAGACTT-TATGCGACCTGCT
1 CCACTGTAACTTCAGGGAGATAAGACTTATATGCAACCTGCC
*
566781 CTACTGTAACTT
1 CCACTGTAACTT
566793 TAGAGAGGTA
Statistics
Matches: 142, Mismatches: 35, Indels: 23
0.71 0.17 0.12
Matches are distributed among these distances:
41 21 0.15
42 1 0.01
43 4 0.03
44 82 0.58
45 3 0.02
46 25 0.18
47 6 0.04
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (42 bp):
CCACTGTAACTTCAGGGAGATAAGACTTATATGCAACCTGCC
Found at i:568183 original size:7 final size:7
Alignment explanation
Indices: 568168--568223 Score: 71
Period size: 7 Copynumber: 8.3 Consensus size: 7
568158 TTAGCCTCTC
568168 CATTTTT
1 CATTTTT
*
568175 CAATTTT
1 CATTTTT
568182 CA-TTTT
1 CATTTTT
*
568188 CTTTTTT
1 CATTTTT
*
568195 TATTTTT
1 CATTTTT
568202 CA-TTTT
1 CATTTTT
568208 CATTTTT
1 CATTTTT
568215 CATTTTT
1 CATTTTT
568222 CA
1 CA
568224 GAGTGCCCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 11 0.26
7 31 0.74
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:568201 original size:20 final size:20
Alignment explanation
Indices: 568168--568223 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
568158 TTAGCCTCTC
*
568168 CATTTTTCAATTTTCATTTT
1 CATTTTTCATTTTTCATTTT
* *
568188 CTTTTTTTATTTTTCATTTT
1 CATTTTTCATTTTTCATTTT
568208 CATTTTTCATTTTTCA
1 CATTTTTCATTTTTCA
568224 GAGTGCCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (20 bp):
CATTTTTCATTTTTCATTTT
Found at i:569236 original size:39 final size:40
Alignment explanation
Indices: 569142--569254 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 40
569132 TTTTTCTCAG
* * *
569142 TTTCATTTTCATTTTGATCTTGATTTTGATTTTTTTCTTC
1 TTTCATTTTCATTTTAATTTTGATTTTGATTTTTTTCCTC
* * *
569182 TTTC-TTCTT-TTTTTTATTTTTATTTTTGATTTTTTTCCT-
1 TTTCATT-TTCATTTTAATTTTGA-TTTTGATTTTTTTCCTC
*
569221 TTTCATTTTCATTTTAACTTTGATTTTGATTTTT
1 TTTCATTTTCATTTTAATTTTGATTTTGATTTTT
569255 ATTTTTCTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
39 28 0.47
40 32 0.53
ACGTcount: A:0.12, C:0.11, G:0.05, T:0.72
Consensus pattern (40 bp):
TTTCATTTTCATTTTAATTTTGATTTTGATTTTTTTCCTC
Found at i:569937 original size:26 final size:28
Alignment explanation
Indices: 569908--569963 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 28
569898 TGAAATAATC
*
569908 AGAAATAATTATTCAAAAA-GAATG-AA
1 AGAAATAATTACTCAAAAAGGAATGCAA
* *
569934 AG-AATATTTGCTCAAAAAGGAATGCAA
1 AGAAATAATTACTCAAAAAGGAATGCAA
569961 AGA
1 AGA
569964 TGTATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
25 13 0.54
26 7 0.29
27 4 0.17
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.21
Consensus pattern (28 bp):
AGAAATAATTACTCAAAAAGGAATGCAA
Found at i:577528 original size:83 final size:84
Alignment explanation
Indices: 577368--577785 Score: 245
Period size: 86 Copynumber: 4.9 Consensus size: 84
577358 CTTAACTAAA
* * *
577368 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTTCGCTAAGTTAATAGCAAAATCATTGTTGAC
1 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTCCGCTAAGTTAATAGCAAAATCATTGCTAAC
*
577433 CTTTTAAGGCACTTAGCGG
66 CTCTTAAGGCACTTAGCGG
* * * **
577452 TTTATTTGA-GCACACACCTTTT-AAGGGTATTGTCCGCTAAGTTAATAGTAGAATTTTTGCTAA
1 TTTATTTCAGGCACACA-CTTTTCAAGGGTATTGTCCGCTAAGTTAATAGCAAAATCATTGCTAA
* **
577515 CCTCTTAATGCACTTAGCCAAA
65 CCTCTTAAGGCACTTAG-C-GG
* * * * * * * * * * * *
577537 TTTATTTGAAGCACAC-CCTAT-GAGAGTATTGTTCACTAAGTTGATAGCAGAACCACTGCTAAC
1 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTCCGCTAAGTTAATAGCAAAATCATTGCTAAC
* * **
577600 CTCTCAATGCACTTAGTCAAA
66 CTCTTAAGGCACTTAG-C-GG
* * ** * * * * * * *
577621 TTTATTTAAGGCGCACACCCTACAAGGGTA-TGACTTGCTAAGTCAATAGTAGAATCATTGCTAG
1 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTC-CGCTAAGTTAATAGCAAAATCATTGCTAA
* * *
577685 CCTCCTAAGACACTTAGCGAAA
65 CCTCTTAAGGCACTTAGCG--G
* * * * * * * * * *
577707 TTTATTTAAGGCACACACCTTACGAGGGTGTTG-CTAGTTAAGTTAATAGCAAAAACGTTGCTAG
1 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTC-CGCTAAGTTAATAGCAAAATCATTGCTAA
577771 CCTCTTAAGGCACTT
65 CCTCTTAAGGCACTT
577786 GGCTAAGTTT
Statistics
Matches: 262, Mismatches: 62, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
83 56 0.21
84 81 0.31
85 14 0.05
86 109 0.42
87 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (84 bp):
TTTATTTCAGGCACACACTTTTCAAGGGTATTGTCCGCTAAGTTAATAGCAAAATCATTGCTAAC
CTCTTAAGGCACTTAGCGG
Found at i:577699 original size:86 final size:85
Alignment explanation
Indices: 577609--577904 Score: 263
Period size: 86 Copynumber: 3.5 Consensus size: 85
577599 CCTCTCAATG
* * * * *
577609 CACTTAGTC-AAATTTATTTAAGGCGCACACCCTACAAGGGTATGACTTGCTAAGTCAATAGTAG
1 CACTTAG-CGAAATTTATTTAAGGCACACACCCTACGAGGGTATG-CTAGCTAAGTCAATAGCAA
*
577673 AATCATTGCTAGCCTCCTAAGA
64 AAACATTGCTAGCCTCCTAAGA
* * * *
577695 CACTTAGCGAAATTTATTTAAGGCACACACCTTACGAGGGTGTTGCTAGTTAAGTTAATAGCAAA
1 CACTTAGCGAAATTTATTTAAGGCACACACCCTACGAGGGT-ATGCTAGCTAAGTCAATAGCAAA
* * *
577760 AACGTTGCTAGCCTCTTAAGG
65 AACATTGCTAGCCTCCTAAGA
* * * * * * * *
577781 CACTTGGCTAAGTTTATTTAAAGCACAAACCCTACGAGGGTATTGCCA-CTAAGCCAATAACAAA
1 CACTTAGCGAAATTTATTTAAGGCACACACCCTACGAGGGTA-TGCTAGCTAAGTCAATAGCAAA
* ** * * * *
577845 ATCGCTACTAGCTTTCTAAGC
65 AACATTGCTAGCCTCCTAAGA
* * *
577866 CATTTAGCGATATTTATTTAAGGCACACACCCTATGAGG
1 CACTTAGCGAAATTTATTTAAGGCACACACCCTACGAGG
577905 ATATTACCCT
Statistics
Matches: 167, Mismatches: 40, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
85 58 0.35
86 107 0.64
87 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (85 bp):
CACTTAGCGAAATTTATTTAAGGCACACACCCTACGAGGGTATGCTAGCTAAGTCAATAGCAAAA
ACATTGCTAGCCTCCTAAGA
Found at i:586368 original size:18 final size:19
Alignment explanation
Indices: 586347--586387 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
586337 GGAGAATACC
*
586347 AAAAGAATGAAAAATA-GA
1 AAAAGAAAGAAAAATATGA
*
586365 AAAAGAAAGGAAAATATGA
1 AAAAGAAAGAAAAATATGA
586384 AAAA
1 AAAA
586388 AAATAGCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAAGAAAGAAAAATATGA
Found at i:587704 original size:22 final size:22
Alignment explanation
Indices: 587677--587722 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
587667 ATAAAATTAT
*
587677 TAAATA-TGAAAATAATATAATA
1 TAAATATTGAAAAGAA-ATAATA
*
587699 TAAATATTTAAAAGAAATAATA
1 TAAATATTGAAAAGAAATAATA
587721 TA
1 TA
587723 GACGAGCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
TAAATATTGAAAAGAAATAATA
Found at i:594567 original size:17 final size:15
Alignment explanation
Indices: 594536--594565 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
594526 TAGGTATACT
594536 TAAATATTAAAAAAA
1 TAAATATTAAAAAAA
594551 TAAATATTAAAAAAA
1 TAAATATTAAAAAAA
594566 AAGAGAGACA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATATTAAAAAAA
Found at i:597212 original size:3 final size:3
Alignment explanation
Indices: 597204--597229 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
597194 CTAATATCTT
597204 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
597230 CACATTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:603120 original size:21 final size:20
Alignment explanation
Indices: 603092--603130 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
603082 ATTTTTTTTG
603092 AATTGAGTCGAGTAAAATGA
1 AATTGAGTCGAGTAAAATGA
*
603112 AATTCGAGTCGAGTTAAAT
1 AATT-GAGTCGAGTAAAAT
603131 TGAATGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (20 bp):
AATTGAGTCGAGTAAAATGA
Found at i:603385 original size:9 final size:9
Alignment explanation
Indices: 603339--603402 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
603329 CTATTATTTC
603339 ATATTTTTA
1 ATATTTTTA
*
603348 A-ATTTTTTT
1 ATA-TTTTTA
603357 ATATTCTTT-
1 ATATT-TTTA
603366 ATATTTTTTA
1 ATA-TTTTTA
603376 ATATTTTTA
1 ATATTTTTA
* *
603385 AAATTTATA
1 ATATTTTTA
603394 AT-TTTTTA
1 ATATTTTTA
603402 A
1 A
603403 AAAAATATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
8 7 0.16
9 29 0.64
10 9 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
ATATTTTTA
Found at i:603395 original size:18 final size:18
Alignment explanation
Indices: 603339--603404 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
603329 CTATTATTTC
* *
603339 ATATTTTTAAATTTTTTT
1 ATATTTTTAAAATTTTTA
* *
603357 ATATTCTTTATATTTTTTA
1 ATATT-TTTAAAATTTTTA
*
603376 ATATTTTTAAAATTTATA
1 ATATTTTTAAAATTTTTA
603394 AT-TTTTTAAAA
1 ATATTTTTAAAA
603405 AAATATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
17 9 0.21
18 17 0.40
19 16 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTTAAAATTTTTA
Found at i:603443 original size:19 final size:19
Alignment explanation
Indices: 603408--603464 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
603398 TTTAAAAAAA
*
603408 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
603426 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
603445 TGA-AAATTATTTTG-ATTTT
1 T-ATAAA-TATTTTGAATTTT
603464 T
1 T
603465 TTTTTTGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 7 0.20
19 20 0.57
20 8 0.23
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:603492 original size:137 final size:136
Alignment explanation
Indices: 603351--603621 Score: 463
Period size: 137 Copynumber: 2.0 Consensus size: 136
603341 ATTTTTAAAT
*
603351 TTTTTTATATTCTTTATATTTTTTAATATTTTTAAAATTTATAATTTTTTAAAAAAATATAAATT
1 TTTTTTATATTCTTTATATTTTTTAATATTTTTAAAATTTATAATTTTTTAAAAAAATATAAAAT
** * *
603416 TTAGAATTTTTATAAATATTTTGAATTTT-TGAAAATTATTTTGATTTTTTTTTTTGTAATTTTT
66 TTAGAATTTTTATAAATATTTTGAATTTTAAAAAAATAATTTT-A-GTTTTTTTTTGTAATTTTT
*
603480 GTTGAGTG
129 GCTGAGTG
603488 TTTTTTATATTCTTTATATTTTTTAATATTTTTAAAATTTATAATTTTTTAAAAAAATATAAAAT
1 TTTTTTATATTCTTTATATTTTTTAATATTTTTAAAATTTATAATTTTTTAAAAAAATATAAAAT
603553 TTAGAATTTTTATAAATATTTTGAATTTTAAAAAAATAATTTTAGTTTTTTTTTGTAATTTTTGC
66 TTAGAATTTTTATAAATATTTTGAATTTTAAAAAAATAATTTTAGTTTTTTTTTGTAATTTTTGC
603618 TGAG
131 TGAG
603622 AGCGACTAAT
Statistics
Matches: 127, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
136 23 0.18
137 94 0.74
138 10 0.08
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (136 bp):
TTTTTTATATTCTTTATATTTTTTAATATTTTTAAAATTTATAATTTTTTAAAAAAATATAAAAT
TTAGAATTTTTATAAATATTTTGAATTTTAAAAAAATAATTTTAGTTTTTTTTTGTAATTTTTGC
TGAGTG
Found at i:603536 original size:27 final size:27
Alignment explanation
Indices: 603505--603574 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
603495 TATTCTTTAT
*
603505 ATTTTTT-AATATTTTTAAAATTTATA
1 ATTTTTTAAATATTTTTAAAATTTAGA
* ** *
603531 ATTTTTTAAAAAAATATAAAATTTAGA
1 ATTTTTTAAATATTTTTAAAATTTAGA
603558 ATTTTTATAAATATTTT
1 ATTTTT-TAAATATTTT
603575 GAATTTTAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
26 7 0.21
27 20 0.61
28 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
ATTTTTTAAATATTTTTAAAATTTAGA
Found at i:603566 original size:18 final size:19
Alignment explanation
Indices: 603545--603581 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
603535 TTTAAAAAAA
603545 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
603563 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
603582 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:605108 original size:166 final size:170
Alignment explanation
Indices: 604788--605168 Score: 450
Period size: 168 Copynumber: 2.2 Consensus size: 170
604778 GGTCAGTTGG
* * *
604788 CTGATTTTGAAACATCTAGAGCTAAATTCAATTGGTTTTTGTAAAGATTTCAATCTTACTCTTTG
1 CTGATTTTGAAACATCTAGAGCTAAATTGAAATGGTTTTTGTAAAGATTCCAATCTTACTCTTTG
* * * * * *
604853 TTTCTATAAATATTTGAAGCTGAATTCAACTACAATTTTCTAAATAATTCCTGGATAATGACAAC
66 TTTCTATAAAGAATTGAAGCTGAATTCAACTACAATTCTCTAAAGAATTCATCG--AATGACAAC
604918 ATTTGCAGAATGATACCTCATAAGACT-TGT-TCTATTTTGAA
129 ATTTGCAGAATGATACCTCATAAGACTATGTCT-TATTTTGAA
* * * * * * *
604959 CTGGTTTTGAAACATCTAGGGCTAAATTGAACTGGCTTTTGTAAATATTCCTATCTT-TTCTTT-
1 CTGATTTTGAAACATCTAGAGCTAAATTGAAATGGTTTTTGTAAAGATTCCAATCTTACTCTTTG
* * * * *
605022 TTTCTATATAGAATTGAAGTTGAA-TCTAACTGCAATTCTGTAAAGATTTCATCG-ATGACAACA
66 TTTCTATAAAGAATTGAAGCTGAATTC-AACTACAATTCTCTAAAGAATTCATCGAATGACAACA
* *
605085 TTTGCAGAATGATGCCTCATAAGACTAATGTCTTATTTTTAA
130 TTTGCAGAATGATACCTCATAAGACT-ATGTCTTATTTTGAA
* *
605127 CTGATGTTGAAACAACTAGAGCTAAATTGAAATGGTTTTTGT
1 CTGATTTTGAAACATCTAGAGCTAAATTGAAATGGTTTTTGT
605169 TTCTGTAAAG
Statistics
Matches: 178, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
166 34 0.19
168 49 0.28
169 41 0.23
170 5 0.03
171 49 0.28
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (170 bp):
CTGATTTTGAAACATCTAGAGCTAAATTGAAATGGTTTTTGTAAAGATTCCAATCTTACTCTTTG
TTTCTATAAAGAATTGAAGCTGAATTCAACTACAATTCTCTAAAGAATTCATCGAATGACAACAT
TTGCAGAATGATACCTCATAAGACTATGTCTTATTTTGAA
Found at i:608631 original size:109 final size:109
Alignment explanation
Indices: 608440--608650 Score: 386
Period size: 109 Copynumber: 1.9 Consensus size: 109
608430 GACTTCAATA
* *
608440 GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGATTTACTCCTCTCTTCTTATCTTTATCA
1 GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGACTTACTCCTCTCTTCTTATCGTTATCA
608505 TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATCACGTTG
66 TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATCACGTTG
* *
608549 GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGGCTTACTCCTCTCTTCTTATCGTTGTCA
1 GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGACTTACTCCTCTCTTCTTATCGTTATCA
608614 TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAAT
66 TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAAT
608651 TACATTTTTC
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 98 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (109 bp):
GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGACTTACTCCTCTCTTCTTATCGTTATCA
TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATCACGTTG
Found at i:615381 original size:19 final size:20
Alignment explanation
Indices: 615347--615385 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
615337 AAGAAATTTG
*
615347 TCTAATATGATTAAAAATAT
1 TCTAAAATGATTAAAAATAT
615367 TCTAAAATG-TTAAAAATAT
1 TCTAAAATGATTAAAAATAT
615386 ATATGTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TCTAAAATGATTAAAAATAT
Found at i:621789 original size:33 final size:33
Alignment explanation
Indices: 621748--621868 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 33
621738 CTATATCAAC
621748 TTGTTATAAGCATGATATTTCTACCATATTGAT
1 TTGTTATAAGCATGATATTTCTACCATATTGAT
* ** ** *
621781 TTGTTATAAGCATGTTATGTTGCATTGCATGGGGTGACAAC
1 TTGTTATAAGCATGATAT-TT-C-TACCAT--ATTG---AT
621822 TTGTTATAAGCATGATATTTCTACCATATTGAT
1 TTGTTATAAGCATGATATTTCTACCATATTGAT
621855 TTGTTATAAGCATG
1 TTGTTATAAGCATG
621869 TTATGTTGCA
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
33 32 0.47
34 2 0.03
35 1 0.01
36 6 0.09
38 6 0.09
39 1 0.01
40 2 0.03
41 18 0.26
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (33 bp):
TTGTTATAAGCATGATATTTCTACCATATTGAT
Found at i:621827 original size:74 final size:74
Alignment explanation
Indices: 621744--621891 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
621734 GCTACTATAT
621744 CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
1 CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
*
621809 ATGGGGTGA
66 ATGGAGTGA
621818 CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
1 CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
621883 ATGGAGTGA
66 ATGGAGTGA
621892 GACGATATGA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.41
Consensus pattern (74 bp):
CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
ATGGAGTGA
Found at i:624183 original size:64 final size:64
Alignment explanation
Indices: 624108--624279 Score: 308
Period size: 64 Copynumber: 2.7 Consensus size: 64
624098 TCATATGAAA
* *
624108 CTTTATGGTACAATAACTCATATTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
1 CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
* *
624172 CTTTATAGTACAATGACCCATACTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
1 CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
624236 CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGG
1 CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGG
624280 TAATAATTCA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 102 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (64 bp):
CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
Found at i:627832 original size:16 final size:17
Alignment explanation
Indices: 627811--627844 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
627801 GAGATATAGT
627811 TAAATA-TTAAAAAAAA
1 TAAATATTTAAAAAAAA
627827 TAAATATTTTAAAAAAAA
1 TAAATA-TTTAAAAAAAA
627845 ATACATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATATTTAAAAAAAA
Found at i:630851 original size:16 final size:17
Alignment explanation
Indices: 630811--630851 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
630801 TTCAAAATTT
630811 AAATTTTAAAATTATAA
1 AAATTTTAAAATTATAA
*
630828 AAAGTTTAAAA-TA-AA
1 AAATTTTAAAATTATAA
630843 AAATATTTA
1 AAAT-TTTA
630852 GAAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTTTAAAATTATAA
Found at i:630922 original size:15 final size:15
Alignment explanation
Indices: 630890--630922 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
630880 ATTAAATTAC
*
630890 AAATATTTTTTAATA
1 AAATATTTTTTAAAA
630905 AAATATTTTTTAAAA
1 AAATATTTTTTAAAA
630920 AAA
1 AAA
630923 AGTAGCGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATTTTTTAAAA
Found at i:638952 original size:19 final size:20
Alignment explanation
Indices: 638928--638967 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
638918 GTTGGTAAAT
638928 ACATGTGTA-ATAATAATAA
1 ACATGTGTATATAATAATAA
*
638947 ACATGTGTATTTAATAATAA
1 ACATGTGTATATAATAATAA
638967 A
1 A
638968 ATATGTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
ACATGTGTATATAATAATAA
Found at i:638963 original size:20 final size:20
Alignment explanation
Indices: 638928--638976 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
638918 GTTGGTAAAT
*
638928 ACATGTGTA-ATAATAATAA
1 ACATGTGTATTTAATAATAA
638947 ACATGTGTATTTAATAATAA
1 ACATGTGTATTTAATAATAA
*
638967 A-ATATGTATT
1 ACATGTGTATT
638977 GCTTATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (20 bp):
ACATGTGTATTTAATAATAA
Found at i:638974 original size:19 final size:20
Alignment explanation
Indices: 638938--638976 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
638928 ACATGTGTAA
*
638938 TAATAATAAACATGTGTATT
1 TAATAATAAACATATGTATT
638958 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
638977 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:639113 original size:16 final size:15
Alignment explanation
Indices: 639087--639119 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
639077 CAAAACAGGG
639087 AGAAAAAAGAAAGAA
1 AGAAAAAAGAAAGAA
639102 AGAAAAAGAGAAAGAA
1 AGAAAAA-AGAAAGAA
639118 AG
1 AG
639120 GAGGAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGAAAGAA
Found at i:639799 original size:24 final size:24
Alignment explanation
Indices: 639772--639818 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
639762 ATTGAAATGG
639772 ATTG-ATTTAATATGTGA-TGAATTT
1 ATTGAATTT-ATAT-TGATTGAATTT
639796 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
639819 GATATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:641354 original size:24 final size:24
Alignment explanation
Indices: 641307--641354 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
641297 GATGAATTAT
* *
641307 AATTTAAAGTATATTGGTTGAATA
1 AATTTAAAGTATAATGATTGAATA
641331 AATTTAAAGTATGAATGATT-AATA
1 AATTTAAAGTAT-AATGATTGAATA
641355 TACTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (24 bp):
AATTTAAAGTATAATGATTGAATA
Found at i:641865 original size:76 final size:74
Alignment explanation
Indices: 641722--641868 Score: 168
Period size: 76 Copynumber: 2.0 Consensus size: 74
641712 ATATGTCATT
* * * **
641722 ATATAAGTATATGAGGTTCGATTATATATATATATACATGTATAAGATCTAGTTTTGAAGTTTAG
1 ATATAAGTATATGAGGTTCGAATATATATATATATACATGTATAAGATCTAGTATTGAAATCAAG
641787 TATGAATTG
66 TATGAATTG
* * * * ** *
641796 ATATATGTATATGTTAGTTTCGAATATGTATATATTTACATGTATAATTTCTTGTATTGAAATCA
1 ATATAAGTATATG--AGGTTCGAATATATATATATATACATGTATAAGATCTAGTATTGAAATCA
641861 AGTATGAA
64 AGTATGAA
641869 ATTATAATAC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
74 12 0.20
76 47 0.80
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (74 bp):
ATATAAGTATATGAGGTTCGAATATATATATATATACATGTATAAGATCTAGTATTGAAATCAAG
TATGAATTG
Found at i:644570 original size:23 final size:22
Alignment explanation
Indices: 644516--644571 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
644506 AAGGTTTAGA
644516 TAGGGTTTAGGAAAAATTAAAT
1 TAGGGTTTAGGAAAAATTAAAT
644538 TAGGGTTTAGGAAAAATTAAAT
1 TAGGGTTTAGGAAAAATTAAAT
644560 TAGGGTATTAGG
1 TAGGGT-TTAGG
644572 TTTTTTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (22 bp):
TAGGGTTTAGGAAAAATTAAAT
Found at i:646914 original size:19 final size:18
Alignment explanation
Indices: 646892--646976 Score: 59
Period size: 19 Copynumber: 4.6 Consensus size: 18
646882 TTCAAAACTT
646892 AAAAATTCAGAAATTATAA
1 AAAAATTCA-AAATTATAA
*
646911 AAAATATT-AATAATTATTTA
1 AAAA-ATTCAA-AATTA-TAA
*
646931 AAAAATCTAAAAAATTAT-A
1 AAAAAT-T-CAAAATTATAA
* *
646950 AAAAATTGAAAATT-GAA
1 AAAAATTCAAAATTATAA
646967 AAAAATTCAA
1 AAAAATTCAA
646977 GTTTTTATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
17 16 0.29
18 2 0.04
19 19 0.35
20 11 0.20
21 5 0.09
22 2 0.04
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAAATTCAAAATTATAA
Found at i:646946 original size:21 final size:19
Alignment explanation
Indices: 646902--646955 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
646892 AAAAATTCAG
*
646902 AAATTATAAAAAATATTAA
1 AAATTATAAAAAATATAAA
* *
646921 TAATTATTTAAAAAATCTAAA
1 AAATTA--TAAAAAATATAAA
646942 AAATTATAAAAAAT
1 AAATTATAAAAAAT
646956 TGAAAATTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 13 0.45
21 16 0.55
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTATAAAAAATATAAA
Found at i:646955 original size:10 final size:10
Alignment explanation
Indices: 646902--646956 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
646892 AAAAATTCAG
646902 AAATTATAAA
1 AAATTATAAA
*
646912 AAA-TATTAA
1 AAATTATAAA
*
646921 TAATTATTTAAA
1 AAATTA--TAAA
*
646933 AAA-TCTAAA
1 AAATTATAAA
646942 AAATTATAAA
1 AAATTATAAA
646952 AAATT
1 AAATT
646957 GAAAATTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 14 0.40
10 15 0.43
11 1 0.03
12 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATTATAAA
Found at i:647615 original size:326 final size:327
Alignment explanation
Indices: 647010--647663 Score: 1301
Period size: 326 Copynumber: 2.0 Consensus size: 327
647000 TTAATATTTA
647010 TTTATATAATCAGATATGTATTTACTTTTAAAAAAATAATGTTTTAAAATTAGTAAATTAAAAAT
1 TTTATATAATCAGATATGTATTTACTTTTAAAAAAATAATGTTTTAAAATTAGTAAATTAAAAAT
647075 TATTAACCTATTATTCTATAAAAAGAATTATCAACCTATTAAAATTTATTTAAAATAATTACTAA
66 TATTAACCTATTATTCTATAAAAAGAATTATCAACCTATTAAAATTTATTTAAAATAATTACTAA
647140 TAATGACACTGGTACATAAATTACCGAATCTACATCCGATGCAGCAGTGGACCCAATTCTTTGCA
131 TAATGACACTGGTACATAAATTACCGAATCTACATCCGATGCAGCAGTGGACCCAATTCTTTGCA
647205 GCAGTGTTAATTAGCAGCAATGGCAATGAAACTCAATTCTTGTTTCATTCTTTGCCTGCTACTAA
196 GCAGTGTTAATTAGCAGCAATGGCAATGAAACTCAATTCTTGTTTCATTCTTTGCCTGCTACTAA
647270 TTTTCATTTTCATGGCGGCCCACATCCTGGTCATCACCTTGGCCCTGCCCTTCCGCCATTTCCGA
261 TTTTCATTTTCATGGCGGCCCACATCCTGGTCATCACCTTGGCCCTGCCCTTCCGCCATTTCCGA
647335 AG
326 AG
647337 TTTATATAATC-GATATGTATTTACTTTTAAAAAAATAATGTTTTAAAATTAGTAAATTAAAAAT
1 TTTATATAATCAGATATGTATTTACTTTTAAAAAAATAATGTTTTAAAATTAGTAAATTAAAAAT
647401 TATTAACCTATTATTCTATAAAAAGAATTATCAACCTATTAAAATTTATTTAAAATAATTACTAA
66 TATTAACCTATTATTCTATAAAAAGAATTATCAACCTATTAAAATTTATTTAAAATAATTACTAA
647466 TAATGACACTGGTACATAAATTACCGAATCTACATCCGATGCAGCAGTGGACCCAATTCTTTGCA
131 TAATGACACTGGTACATAAATTACCGAATCTACATCCGATGCAGCAGTGGACCCAATTCTTTGCA
647531 GCAGTGTTAATTAGCAGCAATGGCAATGAAACTCAATTCTTGTTTCATTCTTTGCCTGCTACTAA
196 GCAGTGTTAATTAGCAGCAATGGCAATGAAACTCAATTCTTGTTTCATTCTTTGCCTGCTACTAA
647596 TTTTCATTTTCATGGCGGCCCACATCCTGGTCATCACCTTGGCCCTGCCCTTCCGCCATTTCCGA
261 TTTTCATTTTCATGGCGGCCCACATCCTGGTCATCACCTTGGCCCTGCCCTTCCGCCATTTCCGA
647661 AG
326 AG
647663 T
1 T
647664 GGTGACTATG
Statistics
Matches: 327, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
326 316 0.97
327 11 0.03
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (327 bp):
TTTATATAATCAGATATGTATTTACTTTTAAAAAAATAATGTTTTAAAATTAGTAAATTAAAAAT
TATTAACCTATTATTCTATAAAAAGAATTATCAACCTATTAAAATTTATTTAAAATAATTACTAA
TAATGACACTGGTACATAAATTACCGAATCTACATCCGATGCAGCAGTGGACCCAATTCTTTGCA
GCAGTGTTAATTAGCAGCAATGGCAATGAAACTCAATTCTTGTTTCATTCTTTGCCTGCTACTAA
TTTTCATTTTCATGGCGGCCCACATCCTGGTCATCACCTTGGCCCTGCCCTTCCGCCATTTCCGA
AG
Found at i:648081 original size:21 final size:20
Alignment explanation
Indices: 648051--648089 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
648041 TTAATTAATT
648051 TTTATTTTTTTTAAAAAATA
1 TTTATTTTTTTTAAAAAATA
648071 TTTATTTTTTTTAAAAAAT
1 TTTATTTTTTTTAAAAAAT
648090 CAAACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTTTTTAAAAAATA
Found at i:653309 original size:22 final size:22
Alignment explanation
Indices: 653266--653329 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
653256 TTATTTAAAA
653266 TTAAATATTAAATATAAT-TATATT
1 TTAAATA--AAATATAATATA-ATT
*
653290 ATTTAATAAAATATAATATAATT
1 -TTAAATAAAATATAATATAATT
*
653313 TTAAATAAAATAAAATA
1 TTAAATAAAATATAATA
653330 AAATAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 15 0.43
23 12 0.34
24 2 0.06
25 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAATAAAATATAATATAATT
Found at i:655395 original size:11 final size:11
Alignment explanation
Indices: 655379--655403 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
655369 CTTCATGTAT
655379 GTTTGTATGAA
1 GTTTGTATGAA
655390 GTTTGTATGAA
1 GTTTGTATGAA
655401 GTT
1 GTT
655404 CGTGTTAAGT
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:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (11 bp):
GTTTGTATGAA
Found at i:666814 original size:18 final size:18
Alignment explanation
Indices: 666791--666830 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
666781 TAATTTTTTA
*
666791 AAAAATA-TATAATACATT
1 AAAAATACTA-AAAACATT
666809 AAAAATACTAAAAACATT
1 AAAAATACTAAAAACATT
666827 AAAA
1 AAAA
666831 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATACTAAAAACATT
Found at i:668290 original size:17 final size:17
Alignment explanation
Indices: 668270--668344 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
668260 ATTAAACAAA
668270 TAAAATAAATAGATATT
1 TAAAATAAATAGATATT
668287 TAAAA-AAATTA-A-ATT
1 TAAAATAAA-TAGATATT
*
668302 TAAATTAAAATAGAT-TT
1 TAAAAT-AAATAGATATT
*
668319 TATAAGTAAATAG-TAATT
1 TA-AAATAAATAGAT-ATT
668337 T-AAATAAA
1 TAAAATAAA
668345 ATTTAGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 17
0.70 0.04 0.25
Matches are distributed among these distances:
15 7 0.15
16 13 0.28
17 21 0.45
18 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
TAAAATAAATAGATATT
Found at i:672171 original size:42 final size:43
Alignment explanation
Indices: 672015--672295 Score: 243
Period size: 42 Copynumber: 6.6 Consensus size: 43
672005 GTTTTTGTAC
* * ** *
672015 AAAAGCGCCGCTAAAGACCATGTTCTGTAGCGATG-TTTG-TAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAT-A
** * * * **
672057 AAAAAGCGCCGCTAAAGATTATGATCTCTAGCGGCGTTTTTATA
1 AAAAA-CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
* * * * * * *
672101 CAAAGCGCTGTTAAAGAACATGCTCTTTAGCGACGCTTA-ATA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
** * *
672143 AAAAACGCAACTAGAGATCATGTTCTTTAGCGGCGCTT--ATGA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAT-A
* * * *
672185 AAAAACACCGCTAAAGAACATGTTATTCAGCGGCGCTTAGA-A
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
672227 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAT-
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
672269 AAAAACGCCGCTAAAGACCATGTTCTT
1 AAAAACGCCGCTAAAGACCATGTTCTT
672296 CAGTGACGTT
Statistics
Matches: 193, Mismatches: 39, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.01
42 133 0.69
43 49 0.25
44 8 0.04
45 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
Found at i:672320 original size:42 final size:42
Alignment explanation
Indices: 672274--672392 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 42
672264 TAGATAAAAA
* *
672274 CGCCGCTAAAGACCATGTTCTTCAGTGACGTTTTTCTCTAAG
1 CGCCGCTAAAGAACATGTTCTTCAGCGACGTTTTTCTCTAAG
* * * *
672316 CGCCGCCAAAAAACATGTTCTTTAGCGGCGTTTTTCTCTAAG
1 CGCCGCTAAAGAACATGTTCTTCAGCGACGTTTTTCTCTAAG
* * *
672358 CGCCGCTAAAGAACATGATCTTTAACGACGTTTTT
1 CGCCGCTAAAGAACATGTTCTTCAGCGACGTTTTT
672393 GGTTGTAAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTCAGCGACGTTTTTCTCTAAG
Found at i:672320 original size:84 final size:84
Alignment explanation
Indices: 672112--672345 Score: 211
Period size: 84 Copynumber: 2.8 Consensus size: 84
672102 AAAGCGCTGT
* * * ** * * * *
672112 TAAAGAACATGCTCTTTAGCGACGCTTA-ATAAAAAACGCAACTAGAGATCATGTTCTTTAGCGG
1 TAAAGAACATGTTATTCAGCGACGCTTAGA-AAAAAACGCCGCCAAAAAACATGTTCTTTAGCGG
672176 CGCTTATGAAAAAACACCGC
65 CGCTTATGAAAAAACACCGC
* * * *
672196 TAAAGAACATGTTATTCAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
1 TAAAGAACATGTTATTCAGCGACGCTTAGAAAAAAACGCCGCCAAAAAACATGTTCTTTAGCGGC
*
672261 GCTTA-GATAAAAACGCCGC
66 GCTTATGA-AAAAACACCGC
* * * * ****** *
672280 TAAAGACCATGTTCTTCAGTGACGTTTTTCTCTAAGCGCCGCCAAAAAACATGTTCTTTAGCGGC
1 TAAAGAACATGTTATTCAGCGACGCTTAGAAAAAAACGCCGCCAAAAAACATGTTCTTTAGCGGC
672345 G
66 G
672346 TTTTTCTCTA
Statistics
Matches: 124, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
83 2 0.02
84 121 0.98
85 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (84 bp):
TAAAGAACATGTTATTCAGCGACGCTTAGAAAAAAACGCCGCCAAAAAACATGTTCTTTAGCGGC
GCTTATGAAAAAACACCGC
Found at i:692810 original size:21 final size:21
Alignment explanation
Indices: 692784--692845 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
692774 NNNNNNCTTA
**
692784 AAGCAGAGGCGACAGCGAGGG
1 AAGCAGAGGCGACAGCGAGAC
* *
692805 AAGCAGAGGCTACAGCAAGAC
1 AAGCAGAGGCGACAGCGAGAC
692826 AAGCAGAGGCCG-CAGCGAGA
1 AAGCAGAGG-CGACAGCGAGA
692846 GAAACAACGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.39, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGACAGCGAGAC
Found at i:693351 original size:42 final size:42
Alignment explanation
Indices: 693296--693588 Score: 396
Period size: 42 Copynumber: 7.0 Consensus size: 42
693286 GTTTGTGAAA
**
693296 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TTC
*
693339 -AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * *
693380 TATGCGTCGCTAAAGAACATGATCTTTAGCGGCGTTTGTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * *
693422 TATGCGTCGCTAAAGAACATGATCTTTAGGGGCGTTTTTTT-
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
693463 TAAGCGCCGCTAAAGAACATGATTTTTAGGGGCGTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTTC
* * *
693506 AAAGCGCTGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
693548 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
693589 ATGTAAGCGC
Statistics
Matches: 228, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
41 33 0.14
42 164 0.72
43 31 0.14
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:693709 original size:22 final size:22
Alignment explanation
Indices: 693678--693720 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
693668 TAGTGGCGTT
* *
693678 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
693700 AAAAAACGCCGCTAAAAACCT
1 AAAAAACGCCGCTAAAAACCT
693721 GTTCTGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:694974 original size:8 final size:8
Alignment explanation
Indices: 694961--694986 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
694951 ATATATATAT
694961 TTTAATTA
1 TTTAATTA
694969 TTTAATTA
1 TTTAATTA
694977 TTTAATTA
1 TTTAATTA
694985 TT
1 TT
694987 ATATCTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTAATTA
Found at i:695715 original size:11 final size:10
Alignment explanation
Indices: 695700--695799 Score: 79
Period size: 11 Copynumber: 10.1 Consensus size: 10
695690 ATTTTTTTAA
695700 ATTTTAAAAT
1 ATTTTAAAAT
695710 ACTTTTAAAAT
1 A-TTTTAAAAT
695721 ACTTTTTTAAAAT
1 A---TTTTAAAAT
*
695734 -TTTT--TA-
1 ATTTTAAAAT
695740 ATTTTAAAAT
1 ATTTTAAAAT
695750 ATTTTTAAAAT
1 A-TTTTAAAAT
695761 ATTTTAAAAT
1 ATTTTAAAAT
*
695771 ATTTT--TA-
1 ATTTTAAAAT
695778 ATTTTAAAAT
1 ATTTTAAAAT
695788 ATTTTTAAAAT
1 A-TTTTAAAAT
695799 A
1 A
695800 AATATTTTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
7 10 0.14
8 1 0.01
9 6 0.08
10 17 0.23
11 30 0.41
13 9 0.12
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:695727 original size:38 final size:37
Alignment explanation
Indices: 695684--695832 Score: 145
Period size: 38 Copynumber: 3.7 Consensus size: 37
695674 TTTTTTTTAT
*
695684 TTTTTTATTTTTTTAAATTTTAAAATACTTTTAAAATA
1 TTTTTTATTTTTTT-AATTTTAAAATATTTTTAAAATA
*
695722 CTTTTTTAAAATTTTTTAATTTTAAAATATTTTTAAAATA
1 -TTTTTT--ATTTTTTTAATTTTAAAATATTTTTAAAATA
** *
695762 TTTTAAAATATTTTTAATTTTAAAATATTTTTAAAATAAA
1 TTTT-TTATTTTTTTAATTTTAAAATATTTTTAAAAT--A
695802 TATTTTTATTTTTGTTTTAATTTTTAAAATA
1 T-TTTTTA--TTT-TTTTAA-TTTTAAAATA
695833 AATTTTTGGT
Statistics
Matches: 91, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
38 28 0.31
39 10 0.11
40 25 0.27
41 10 0.11
42 2 0.02
43 6 0.07
44 10 0.11
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (37 bp):
TTTTTTATTTTTTTAATTTTAAAATATTTTTAAAATA
Found at i:695745 original size:29 final size:27
Alignment explanation
Indices: 695712--695767 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
695702 TTTAAAATAC
*
695712 TTTTAAAATACTTTTTTAAAATTTTTTAA
1 TTTTAAAATA--TTTTTAAAATATTTTAA
695741 TTTTAAAATATTTTTAAAATATTTTAA
1 TTTTAAAATATTTTTAAAATATTTTAA
695768 AATATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 16 0.62
29 10 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAAAATATTTTTAAAATATTTTAA
Found at i:696664 original size:29 final size:30
Alignment explanation
Indices: 696599--696677 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
696589 ATTAATAACA
696599 AAGGATTAAAATGTCAACTTTTCAAACATAC
1 AAGGATTAAAATGT-AACTTTTCAAACATAC
* *
696630 AAGGATTAAAATGT-TCTTTTCAATA-ATAG
1 AAGGATTAAAATGTAACTTTTCAA-ACATAC
*
696659 AGGGATTAAAATG-AACTTT
1 AAGGATTAAAATGTAACTTT
696678 ATGATATAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 27 0.64
30 1 0.02
31 14 0.33
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (30 bp):
AAGGATTAAAATGTAACTTTTCAAACATAC
Found at i:699848 original size:197 final size:197
Alignment explanation
Indices: 699513--699906 Score: 788
Period size: 197 Copynumber: 2.0 Consensus size: 197
699503 TTTTGTGATT
699513 TATATACCTTACCTATACATGCATACATACAAAGATTAGAAACTTTCAAGTTATAGGTACTGCTT
1 TATATACCTTACCTATACATGCATACATACAAAGATTAGAAACTTTCAAGTTATAGGTACTGCTT
699578 TTCTAGCTGTTATATGTTCTAGGAACAGTTGTTCTTTTACCTTCTATGAACTGTACAACATTCCT
66 TTCTAGCTGTTATATGTTCTAGGAACAGTTGTTCTTTTACCTTCTATGAACTGTACAACATTCCT
699643 TTTCCTATTTCAGACCGTCTTGTGCCGGAACTTTAGCTTTGATTCAGTTCTGAGTTCCAGGAACA
131 TTTCCTATTTCAGACCGTCTTGTGCCGGAACTTTAGCTTTGATTCAGTTCTGAGTTCCAGGAACA
699708 TG
196 TG
699710 TATATACCTTACCTATACATGCATACATACAAAGATTAGAAACTTTCAAGTTATAGGTACTGCTT
1 TATATACCTTACCTATACATGCATACATACAAAGATTAGAAACTTTCAAGTTATAGGTACTGCTT
699775 TTCTAGCTGTTATATGTTCTAGGAACAGTTGTTCTTTTACCTTCTATGAACTGTACAACATTCCT
66 TTCTAGCTGTTATATGTTCTAGGAACAGTTGTTCTTTTACCTTCTATGAACTGTACAACATTCCT
699840 TTTCCTATTTCAGACCGTCTTGTGCCGGAACTTTAGCTTTGATTCAGTTCTGAGTTCCAGGAACA
131 TTTCCTATTTCAGACCGTCTTGTGCCGGAACTTTAGCTTTGATTCAGTTCTGAGTTCCAGGAACA
699905 TG
196 TG
699907 GTTCGGGTCT
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 197 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (197 bp):
TATATACCTTACCTATACATGCATACATACAAAGATTAGAAACTTTCAAGTTATAGGTACTGCTT
TTCTAGCTGTTATATGTTCTAGGAACAGTTGTTCTTTTACCTTCTATGAACTGTACAACATTCCT
TTTCCTATTTCAGACCGTCTTGTGCCGGAACTTTAGCTTTGATTCAGTTCTGAGTTCCAGGAACA
TG
Found at i:706223 original size:51 final size:51
Alignment explanation
Indices: 706100--706235 Score: 132
Period size: 51 Copynumber: 2.7 Consensus size: 51
706090 TATCGATGAA
* * *
706100 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGCATCGATAAGTAATGGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGCACCAAGAAGTAATGGT
* * ** * * *
706151 CACATGAGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCT-TTGAG-
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGCACCAAGAAG-TAATG-GT
* *
706202 CACGTGTGTAGTACTGTGTGAATGTTACTACGTG
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTG
706236 TCTCGATAAA
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
51 64 0.97
52 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGCACCAAGAAGTAATGGT
Found at i:706276 original size:102 final size:102
Alignment explanation
Indices: 706100--706288 Score: 283
Period size: 102 Copynumber: 1.9 Consensus size: 102
706090 TATCGATGAA
* *
706100 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGCATCGATAAGTAATGGTCACATGAGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGCATCGATAACTAACGGTCACATGAGTAGTAC
*
706165 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
66 TAAGTGAAGGCTACTACGTGTACCAAGAAGCTTTGAG
* * * *
706202 CACGTGTGTAGTACTGTGTGAATGTTACTACGTGTC-TCGATAAACT-ACGGTTACATGTGTAGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTG-CATCGAT-AACTAACGGTCACATGAGTAGT
706265 ACTAAGTGAAGGCTACTACGTGTA
64 ACTAAGTGAAGGCTACTACGTGTA
706289 TTGAATGATA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
102 74 0.95
103 4 0.05
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGCATCGATAACTAACGGTCACATGAGTAGTAC
TAAGTGAAGGCTACTACGTGTACCAAGAAGCTTTGAG
Found at i:710659 original size:89 final size:89
Alignment explanation
Indices: 710485--710751 Score: 304
Period size: 89 Copynumber: 3.0 Consensus size: 89
710475 AAAAGCTCTT
* * * * * *
710485 AAACTTTTTCAAAAAAAGTAATTAAGCCTTTACTCTTTTTTTTTATACTCATTTGGGTACTTGAG
1 AAACTTTTTCAAAAAAAGCAATTAAGCC---CCTATTTTTTTTTACACTCAATTGGGTACTTGAA
* * *
710550 CTTTTAAAATGCATCAAAAAGGCCCTC
63 CTGTCAAAATGCATAAAAAAGGCCCTC
* * * *
710577 AAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTATTTTGCACTCAATTGGGTATTTAAACTG
1 AAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTTACACTCAATTGGGTACTTGAACTG
* **
710642 TCAAAATGCATAAAAAAGACTTTC
66 TCAAAATGCATAAAAAAGGCCCTC
*
710666 AAAC-TTTT-AAAAAAATGCAATTAAGCCCCTACTTTTTTTTTTCACTCAATTAGGGTACTTGAA
1 AAACTTTTTCAAAAAAA-GCAATTAAGCCCCTA-TTTTTTTTTACACTCAATT-GGGTACTTGAA
*
710729 CTGCCAAAATGCATAAAAAAGGC
63 CTGTCAAAATGCATAAAAAAGGC
710752 TAGGGGCGGA
Statistics
Matches: 150, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
87 7 0.05
88 19 0.13
89 67 0.45
90 30 0.20
92 27 0.18
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (89 bp):
AAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTTACACTCAATTGGGTACTTGAACTG
TCAAAATGCATAAAAAAGGCCCTC
Found at i:711310 original size:29 final size:30
Alignment explanation
Indices: 711250--711334 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 30
711240 AAAAAGTTGT
* *
711250 AAAATTTTATAAAAATCAT-AAAATATTATAG
1 AAAATTATA-AAAAAT-ATAAAAAAATTATAG
* *
711281 AATA-TATAGAAATATATAAAAAAATT-TAG
1 AAAATTATA-AAAAATATAAAAAAATTATAG
*
711310 AAAATTATAAAAAATGTAAAAAAAT
1 AAAATTATAAAAAATATAAAAAAAT
711335 ATAAAATCCG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 22 0.50
30 19 0.43
31 3 0.07
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.31
Consensus pattern (30 bp):
AAAATTATAAAAAATATAAAAAAATTATAG
Found at i:711322 original size:9 final size:9
Alignment explanation
Indices: 711185--711340 Score: 54
Period size: 9 Copynumber: 16.3 Consensus size: 9
711175 TTTTAATAAC
711185 AAAATATATA
1 AAAAT-TATA
711195 AAAGATT-TA
1 AAA-ATTATA
* *
711204 AAACTTGTTA
1 AAAATT-ATA
*
711214 AAAATTAGA
1 AAAATTATA
711223 AAAA-TATA
1 AAAATTATA
711231 AAAATCGTA-A
1 AAAAT--TATA
*
711241 AAAAGTTGTA
1 AAAA-TTATA
*
711251 AAATTTTATA
1 AAA-ATTATA
*
711261 AAAATCATA
1 AAAATTATA
711270 AAATATTAT-
1 AAA-ATTATA
*
711279 AGAATATATA
1 AAAAT-TATA
*
711289 GAAATATATAAA
1 -AAA-AT-TATA
711301 AAAATT-TA
1 AAAATTATA
711309 GAAAATTATAA
1 -AAAATTAT-A
711320 AAAATGTA-A
1 AAAAT-TATA
*
711329 AAAAATATA
1 AAAATTATA
711338 AAA
1 AAA
711341 TCCGTAAAAA
Statistics
Matches: 111, Mismatches: 16, Indels: 39
0.67 0.10 0.23
Matches are distributed among these distances:
8 14 0.13
9 39 0.35
10 39 0.35
11 13 0.12
12 6 0.05
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:711323 original size:19 final size:19
Alignment explanation
Indices: 711294--711340 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
711284 ATATAGAAAT
* *
711294 ATATAAAAAAATTTAGAAAA
1 ATAT-AAAAAATGTAAAAAA
*
711314 TTATAAAAAATGTAAAAAA
1 ATATAAAAAATGTAAAAAA
711333 ATATAAAA
1 ATATAAAA
711341 TCCGTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (19 bp):
ATATAAAAAATGTAAAAAA
Found at i:712314 original size:29 final size:30
Alignment explanation
Indices: 712254--712338 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 30
712244 AAAAAGTTGT
* *
712254 AAAATTTTATAAAAATCAT-AAAATATTATAG
1 AAAATTATA-AAAAAT-ATAAAAAAATTATAG
* *
712285 AATA-TATAGAAATATATAAAAAAATT-TAG
1 AAAATTATA-AAAAATATAAAAAAATTATAG
*
712314 AAAATTATAAAAAATGTAAAAAAAT
1 AAAATTATAAAAAATATAAAAAAAT
712339 ATAAAATCCG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 22 0.50
30 19 0.43
31 3 0.07
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.31
Consensus pattern (30 bp):
AAAATTATAAAAAATATAAAAAAATTATAG
Found at i:712326 original size:9 final size:9
Alignment explanation
Indices: 712189--712344 Score: 54
Period size: 9 Copynumber: 16.3 Consensus size: 9
712179 TTTTAATAAC
712189 AAAATATATA
1 AAAAT-TATA
712199 AAAGATT-TA
1 AAA-ATTATA
* *
712208 AAACTTGTTA
1 AAAATT-ATA
*
712218 AAAATTAGA
1 AAAATTATA
712227 AAAA-TATA
1 AAAATTATA
712235 AAAATCGTA-A
1 AAAAT--TATA
*
712245 AAAAGTTGTA
1 AAAA-TTATA
*
712255 AAATTTTATA
1 AAA-ATTATA
*
712265 AAAATCATA
1 AAAATTATA
712274 AAATATTAT-
1 AAA-ATTATA
*
712283 AGAATATATA
1 AAAAT-TATA
*
712293 GAAATATATAAA
1 -AAA-AT-TATA
712305 AAAATT-TA
1 AAAATTATA
712313 GAAAATTATAA
1 -AAAATTAT-A
712324 AAAATGTA-A
1 AAAAT-TATA
*
712333 AAAAATATA
1 AAAATTATA
712342 AAA
1 AAA
712345 TCCGTAAAAA
Statistics
Matches: 111, Mismatches: 16, Indels: 39
0.67 0.10 0.23
Matches are distributed among these distances:
8 14 0.13
9 39 0.35
10 39 0.35
11 13 0.12
12 6 0.05
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:712327 original size:19 final size:19
Alignment explanation
Indices: 712298--712344 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
712288 ATATAGAAAT
* *
712298 ATATAAAAAAATTTAGAAAA
1 ATAT-AAAAAATGTAAAAAA
*
712318 TTATAAAAAATGTAAAAAA
1 ATATAAAAAATGTAAAAAA
712337 ATATAAAA
1 ATATAAAA
712345 TCCGTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (19 bp):
ATATAAAAAATGTAAAAAA
Found at i:712959 original size:90 final size:94
Alignment explanation
Indices: 712772--712965 Score: 225
Period size: 90 Copynumber: 2.1 Consensus size: 94
712762 TAATTGAGTG
* * ** *
712772 AAAAAAAAAGCAGGGGATTAATTGCTTGTTTTTGAAAAAGTTTGAGGGCATTTTTTTTATGAATT
1 AAAAAAAAAACAAGGGATTAATTGCTTGTTTTTGAAAAAGTTTGA-GGCA-TTAATTAATGAATT
** * * *
712837 TTGGCAGTTTAAGTACCCAATTGAGTGCAAA
64 TTGAAAGTTCAAATACCCAATTGAATGCAAA
* *
712868 AAAAAAAAAACAAGGGCTTAATTGCTT-TTTTTGAAAAAGTTTGA-G-A-TAATTAATGCATTTT
1 AAAAAAAAAACAAGGGATTAATTGCTTGTTTTTGAAAAAGTTTGAGGCATTAATTAATGAATTTT
*
712929 GAAAGTTCAAATACCCAATTGAATGTAAA
66 GAAAGTTCAAATACCCAATTGAATGCAAA
712958 AAAAAAAA
1 AAAAAAAA
712966 GTAGACTTAA
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
90 42 0.49
92 1 0.01
93 1 0.01
95 17 0.20
96 24 0.28
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (94 bp):
AAAAAAAAAACAAGGGATTAATTGCTTGTTTTTGAAAAAGTTTGAGGCATTAATTAATGAATTTT
GAAAGTTCAAATACCCAATTGAATGCAAA
Found at i:715786 original size:254 final size:248
Alignment explanation
Indices: 714965--715830 Score: 1247
Period size: 251 Copynumber: 3.5 Consensus size: 248
714955 GTCAGAAATC
** * * * *
714965 GCTCAAGGTAATGATGATCCAAGATGAATACCCTA-TCGTTTACCAGTGCCTGCCATATAGTGTT
1 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTT-CCATTGCCTGCCATATAGTGTT
* * * *
715029 GTGTATGTATTCATAAAGTAATTAATTTGAAAGGAAAAGAAATACATAAGCTTGTTTTTCCTTTT
65 ATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTG-TTTTCTTTTT
* * * ** * * * *
715094 TACCTTAAAAAAATC-TCGCCATTGC-GGCTGGTTATACTGCTTTTCCTGTTGAACCTGCAAACG
129 TACCTTAAACAAATCTTC-CCATT-CTTGCGGGTTCGACTTCATTTCCTGTAGAACCAGC-AACG
*
715157 TTTAAAATATTGGATTCTAAGCTCAAACATTATATGTTAT-AACCTAGGAAAGAGATT
191 TTTAAAATATTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
*
715214 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTTCCTGCCATATAGTGTTA
1 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTA
*
715279 TGTACGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTTTTA
66 TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTTTTA
* * * *
715344 CCTTAAGCAAATATTCTTTCCGTT-TCTGTGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGT
131 CCTTAAAC-AA-A-TCTTCCCATTCT-TGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGT
* *
715408 TTAAAATATTGGATTGTAAGCTCGAACATTATATGTTATAAACCTAGGAAATAGATT
192 TTAAAATATTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
* *
715465 GCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATATTGTTA
1 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTA
* *
715530 TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAATGAAAAACATAAACTTGTTTTCTTTTTTA
66 TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTTTTA
715595 CCGGCTTAAACAAATCTTCCCATTCTTGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGTT
131 -C--CTTAAACAAATCTTCCCATTCTTGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGTT
715660 TAAAATATTGGATTAATGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
193 TAAAATATTGGA-T--TGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
*
715719 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTTCCTGCCATATAGTGTTA
1 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTA
* *
715784 TGTATGTATTCATAAAGTTGTTAATTTGAAAGGAAAAGAGATACATA
66 TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATA
715831 TCTCTGCAAA
Statistics
Matches: 555, Mismatches: 47, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
248 17 0.03
249 104 0.19
250 47 0.08
251 228 0.41
252 5 0.01
253 2 0.00
254 152 0.27
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (248 bp):
GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTA
TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTTTTA
CCTTAAACAAATCTTCCCATTCTTGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGTTTAA
AATATTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
Found at i:720252 original size:21 final size:21
Alignment explanation
Indices: 720226--720300 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
720216 TTAAAAATAG
*
720226 CGGTGGCGGTGAGATTAGTTA
1 CGGTAGCGGTGAGATTAGTTA
* *
720247 CGGTGGCGGTGAGATTAGTTT
1 CGGTAGCGGTGAGATTAGTTA
* * *
720268 CTGTAACGGTGAGATTAGATA
1 CGGTAGCGGTGAGATTAGTTA
*
720289 CTGTAGCGGTGA
1 CGGTAGCGGTGA
720301 TGTAATCATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.21, C:0.11, G:0.39, T:0.29
Consensus pattern (21 bp):
CGGTAGCGGTGAGATTAGTTA
Found at i:720527 original size:30 final size:30
Alignment explanation
Indices: 720373--720520 Score: 149
Period size: 30 Copynumber: 5.0 Consensus size: 30
720363 AATTTTTTTG
*
720373 CATTTTGACCCCTGAAATTTTC-CAAAATTA
1 CATTTTGACCCCT-AAACTTTCTCAAAATTA
* * *
720403 CATTTTGACCCTTAAACTTTCCCAAAACTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
** * *
720433 CATTTCAACCCCTAAA-TTTTTTAAAA-TA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* * *
720461 CATTTTGGCCCCTAAACTTTATCTAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* *
720491 TATTTTGACCCATAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
720521 TGTTTTGCCC
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
28 15 0.16
29 21 0.22
30 59 0.62
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTCAAAATTA
Found at i:720867 original size:7 final size:7
Alignment explanation
Indices: 720855--720948 Score: 75
Period size: 7 Copynumber: 13.3 Consensus size: 7
720845 CCGAACGGAG
720855 AAGAAAA
1 AAGAAAA
*
720862 AAGAAAG
1 AAGAAAA
**
720869 AAGAAGG
1 AAGAAAA
*
720876 AAG-AAG
1 AAGAAAA
*
720882 AAGAAGA
1 AAGAAAA
720889 AAGAAAGA
1 AAGAAA-A
720897 AAG-AAA
1 AAGAAAA
720903 AAGAGAAA
1 AAGA-AAA
720911 AAGAGAAA
1 AAGA-AAA
*
720919 AAGAGAA
1 AAGAAAA
720926 AAGAAAA
1 AAGAAAA
*
720933 AGGAAAA
1 AAGAAAA
*
720940 AGGAAAA
1 AAGAAAA
720947 AA
1 AA
720949 AAATTTGACA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
6 9 0.12
7 45 0.62
8 19 0.26
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:720872 original size:14 final size:14
Alignment explanation
Indices: 720853--720948 Score: 83
Period size: 14 Copynumber: 6.8 Consensus size: 14
720843 GGCCGAACGG
720853 AGAAGAAAAAAGAA
1 AGAAGAAAAAAGAA
**
720867 AGAAGAAGGAAG-A
1 AGAAGAAAAAAGAA
*
720880 AGAAGAAGAAAGAA
1 AGAAGAAAAAAGAA
720894 AGAAAGAAAAAGAGAA
1 AG-AAGAAAAA-AGAA
720910 A-AAGAGAAAAAGAGA
1 AGAAGA-AAAAAGA-A
*
720925 A-AAGAAAAAGGAA
1 AGAAGAAAAAAGAA
720938 A-AAGGAAAAAA
1 AGAA-GAAAAAA
720949 AAATTTGACA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
13 16 0.23
14 32 0.46
15 17 0.24
16 5 0.07
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAAGAA
Found at i:720892 original size:10 final size:9
Alignment explanation
Indices: 720853--720927 Score: 57
Period size: 8 Copynumber: 8.0 Consensus size: 9
720843 GGCCGAACGG
720853 AGAAGAAAAA
1 AGAAG-AAAA
720863 AGAAAGAAGAA
1 AG-AAGAA-AA
* *
720874 GGAAGAAGA
1 AGAAGAAAA
720883 AGAAGAAAGAA
1 AGAAG-AA-AA
720894 AGAAAGAAAA
1 AG-AAGAAAA
720904 AG-AGAAAA
1 AGAAGAAAA
720912 AG-AGAAAA
1 AGAAGAAAA
720920 AG-AGAAAA
1 AGAAGAAAA
720928 GAAAAAGGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
8 22 0.39
9 5 0.09
10 15 0.27
11 11 0.20
12 3 0.05
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:721240 original size:8 final size:8
Alignment explanation
Indices: 721229--721258 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
721219 CCAGCAGAAA
721229 AAAAAGAG
1 AAAAAGAG
721237 AAAAAGAAG
1 AAAAAG-AG
721246 AAAAAGAG
1 AAAAAGAG
721254 AAAAA
1 AAAAA
721259 AAAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:721249 original size:17 final size:18
Alignment explanation
Indices: 721224--721268 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
721214 GCAGCCCAGC
*
721224 AGAAAAAAAAGAG-AAAA
1 AGAAGAAAAAGAGAAAAA
721241 AGAAGAAAAAGAGAAAAA
1 AGAAGAAAAAGAGAAAAA
*
721259 AAAAGAAAAA
1 AGAAGAAAAA
721269 AGAGGTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AGAAGAAAAAGAGAAAAA
Found at i:721269 original size:19 final size:18
Alignment explanation
Indices: 721228--721272 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
721218 CCCAGCAGAA
*
721228 AAAAAAGAGAAAAAGAAG
1 AAAAAAGAGAAAAAAAAG
721246 -AAAAAGAGAAAAAAAAAG
1 AAAAAAGAG-AAAAAAAAG
721264 AAAAAAGAG
1 AAAAAAGAG
721273 GTTCAATTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAAAG
Found at i:721639 original size:22 final size:21
Alignment explanation
Indices: 721609--721649 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
721599 GTGTTTTAAG
*
721609 AATTTTCGTGTTTCTAAAAAAA
1 AATTCTCGTGTTTC-AAAAAAA
721631 AATTCTCGTGTTTCAAAAA
1 AATTCTCGTGTTTCAAAAA
721650 TTGTCGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
AATTCTCGTGTTTCAAAAAAA
Found at i:721657 original size:39 final size:36
Alignment explanation
Indices: 721590--721666 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 36
721580 GAAAATATTC
* * *
721590 AAAAAATTTGTGTTTTAAGAATTTTCGTGTTTCTAAA
1 AAAAAATTTGTGTTTCAAAAATTGTCGTGTTT-TAAA
721627 AAAAAATTCTCGTGTTTCAAAAATTGTCGTGTTTTAAA
1 AAAAAATT-T-GTGTTTCAAAAATTGTCGTGTTTTAAA
721665 AA
1 AA
721667 TTTTCATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
37 8 0.23
38 7 0.20
39 20 0.57
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (36 bp):
AAAAAATTTGTGTTTCAAAAATTGTCGTGTTTTAAA
Found at i:721666 original size:18 final size:18
Alignment explanation
Indices: 721587--721893 Score: 248
Period size: 17 Copynumber: 17.4 Consensus size: 18
721577 ATCGAAAATA
*
721587 TTCAAAAAATTT-GTGTT
1 TTCAAAAATTTTCGTGTT
*
721604 TT-AAGAATTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
* *
721621 TCTAAAAAAAAATTCTCGTG-T
1 T-T---CAAAAATTTTCGTGTT
*
721642 TTCAAAAATTGTCGTGTT
1 TTCAAAAATTTTCGTGTT
*
721660 TT-AAAAATTTTCATG-T
1 TTCAAAAATTTTCGTGTT
* *
721676 TTC-TAAATTTTCGT-AT
1 TTCAAAAATTTTCGTGTT
721692 TTCAAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
*
721710 TTC-AAAGTTTTGCGTG-T
1 TTCAAAAATTTT-CGTGTT
*
721727 TTCAAAAATCTTCGTGTT
1 TTCAAAAATTTTCGTGTT
721745 TTCAAAAA-TTTCG-GTGT
1 TTCAAAAATTTTCGTGT-T
** **
721762 TTCAAAAAAATTCCCGTT
1 TTCAAAAATTTTCGTGTT
721780 TT-AAAAATTTTCAG-GTT
1 TTCAAAAATTTTC-GTGTT
*
721797 TTCAAAATTTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
* *
721815 TTCAAAAAATTCTCTTG-T
1 TTC-AAAAATTTTCGTGTT
**
721833 TTCAAAAATCCTCGTGTT
1 TTCAAAAATTTTCGTGTT
*
721851 TTCAAAAATTTTGGTGTT
1 TTCAAAAATTTTCGTGTT
*
721869 TT-GAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
721886 TTCAAAAA
1 TTCAAAAA
721894 AAATCTCGTG
Statistics
Matches: 234, Mismatches: 33, Indels: 45
0.75 0.11 0.14
Matches are distributed among these distances:
16 25 0.11
17 109 0.47
18 74 0.32
19 12 0.05
20 1 0.00
21 2 0.01
22 11 0.05
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (18 bp):
TTCAAAAATTTTCGTGTT
Found at i:721741 original size:35 final size:34
Alignment explanation
Indices: 721587--721919 Score: 244
Period size: 35 Copynumber: 9.4 Consensus size: 34
721577 ATCGAAAATA
*
721587 TTCAAAAAATTT-GTGTTTT-AAGAATTTTCGTGT
1 TTCAAAAATTTTCGTGTTTTCAA-AATTTTCGTGT
* *
721620 TTCTAAAAAAAAATTCTCGTG-TTTCAAAAATTGTCGTGT
1 TTC-----AAAAATTTTCGTGTTTTC-AAAATTTTCGTGT
* * * *
721659 TTTAAAAATTTTCATG-TTTCTAAATTTTCGTAT
1 TTCAAAAATTTTCGTGTTTTCAAAATTTTCGTGT
*
721692 TTCAAAAATTTTCGTGTTTTCAAAGTTTTGCGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAATTTT-CGTGT
* *
721727 TTCAAAAATCTTCGTGTTTTCAAAAATTTCGGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAATTTTC-GTGT
** ** *
721762 TTCAAAAAAATTCCCGTTTTAAAAATTTTCAG-GTT
1 TTCAAAAATTTTCGTGTTTTCAAAATTTTC-GTG-T
* * *
721797 TTCAAAATTTTTCGTGTTTTCAAAAAATTCTCTTGT
1 TTCAAAAATTTTCGTGTTTTC--AAAATTTTCGTGT
** *
721833 TTCAAAAATCCTCGTGTTTTCAAAAATTTTGGTGT
1 TTCAAAAATTTTCGTGTTTTC-AAAATTTTCGTGT
** * *
721868 TTTGAAAATTTTCGTGTTTTCAAAAAAAATCTCGTGT
1 TTCAAAAATTTTCGTGTTTTC---AAAATTTTCGTGT
*
721905 TTCATAAATTTTCGT
1 TTCAAAAATTTTCGT
721920 TTTAAAAAAA
Statistics
Matches: 235, Mismatches: 48, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
33 27 0.11
34 27 0.11
35 103 0.44
36 19 0.08
37 32 0.14
38 10 0.04
39 15 0.06
40 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (34 bp):
TTCAAAAATTTTCGTGTTTTCAAAATTTTCGTGT
Found at i:721954 original size:17 final size:17
Alignment explanation
Indices: 721587--721954 Score: 239
Period size: 17 Copynumber: 21.1 Consensus size: 17
721577 ATCGAAAATA
*
721587 TTCAAAAAATTT-GTGT
1 TTCAAAAATTTTCGTGT
* *
721603 TTTAAGAATTTTCGTGT
1 TTCAAAAATTTTCGTGT
*
721620 TTCTAAAAAAAAATTCTCGTGT
1 TTC-----AAAAATTTTCGTGT
*
721642 TTCAAAAATTGTCGTGT
1 TTCAAAAATTTTCGTGT
* *
721659 TTTAAAAATTTTCATGT
1 TTCAAAAATTTTCGTGT
* *
721676 TTC-TAAATTTTCGTAT
1 TTCAAAAATTTTCGTGT
721692 TTCAAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
*
721710 TTC-AAAGTTTTGCGTGT
1 TTCAAAAATTTT-CGTGT
*
721727 TTCAAAAATCTTCGTGTT
1 TTCAAAAATTTTCGTG-T
721745 TTCAAAAA-TTTCGGTGT
1 TTCAAAAATTTTC-GTGT
** **
721762 TTCAAAAAAATTCCCGT
1 TTCAAAAATTTTCGTGT
*
721779 TTTAAAAATTTTCAG-GTT
1 TTCAAAAATTTTC-GTG-T
*
721797 TTCAAAATTTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
* *
721815 TTCAAAAAATTCTCTTGT
1 TTC-AAAAATTTTCGTGT
**
721833 TTCAAAAATCCTCGTGTT
1 TTCAAAAATTTTCGTG-T
*
721851 TTCAAAAATTTTGGTGT
1 TTCAAAAATTTTCGTGT
**
721868 TTTGAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
* *
721886 TTCAAAAAAAATCTCGTGT
1 TTC--AAAAATTTTCGTGT
*
721905 TTCATAAATTTTCGT-T
1 TTCAAAAATTTTCGTGT
* **
721921 TTAAAAAAATAAT--TGT
1 TT-CAAAAATTTTCGTGT
*
721937 TTCAAAAATCTTCGTGT
1 TTCAAAAATTTTCGTGT
721954 T
1 T
721955 AAAAAAAATT
Statistics
Matches: 273, Mismatches: 54, Indels: 49
0.73 0.14 0.13
Matches are distributed among these distances:
15 8 0.03
16 28 0.10
17 130 0.48
18 68 0.25
19 14 0.05
20 10 0.04
22 15 0.05
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTCAAAAATTTTCGTGT
Found at i:725441 original size:7 final size:7
Alignment explanation
Indices: 725429--725480 Score: 86
Period size: 7 Copynumber: 7.1 Consensus size: 7
725419 TCTTGAAATC
725429 AACCCTA
1 AACCCTA
725436 AACCCTA
1 AACCCTA
725443 AACCCTA
1 AACCCTA
725450 AACCCTA
1 AACCCTA
725457 AACCCTA
1 AACCCTA
725464 AACCCCCTA
1 AA--CCCTA
725473 AACCCTA
1 AACCCTA
725480 A
1 A
725481 CCATTCACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
7 36 0.84
9 7 0.16
ACGTcount: A:0.42, C:0.44, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCCTA
Done.