Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 92 of 222
Found at i:28832375 original size:41 final size:41
Alignment explanation
Indices: 28832298--28832375 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28832288 TTTGTATCTC
* * *
28832298 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28832339 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28832376 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28836614 original size:26 final size:24
Alignment explanation
Indices: 28836560--28836613 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
28836550 ACTGTTATAA
* *
28836560 AAAATTATAAAATAAAAATTAATT
1 AAAATTACAAAATAAAAAATAATT
28836584 AAAATTACATAAATGAAAAAATATATT
1 AAAATTACA-AAAT-AAAAAATA-ATT
28836611 AAA
1 AAA
28836614 TAATATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 4 0.16
26 7 0.28
27 6 0.24
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAATTACAAAATAAAAAATAATT
Found at i:28836862 original size:23 final size:23
Alignment explanation
Indices: 28836826--28836869 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28836816 AAAGCTTTTG
*
28836826 TAATACCTCAAAAATTACTACTA
1 TAATACCCCAAAAATTACTACTA
*
28836849 TAATACCCCGAAAATTACTAC
1 TAATACCCCAAAAATTACTAC
28836870 AGTAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (23 bp):
TAATACCCCAAAAATTACTACTA
Found at i:28839128 original size:21 final size:21
Alignment explanation
Indices: 28839103--28839146 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28839093 ATCTTCGAGG
28839103 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
28839124 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
28839145 AT
1 AT
28839147 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:28839152 original size:19 final size:19
Alignment explanation
Indices: 28839102--28839157 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
28839092 AATCTTCGAG
28839102 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28839121 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
28839142 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
28839158 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28839164 original size:22 final size:23
Alignment explanation
Indices: 28839115--28839180 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
28839105 ATGCAATCTT
*
28839115 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
28839136 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
28839158 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
28839181 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:28839190 original size:22 final size:23
Alignment explanation
Indices: 28839146--28839190 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28839136 AGATATGATA
*
28839146 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
28839169 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
28839191 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:28839375 original size:19 final size:21
Alignment explanation
Indices: 28839351--28839389 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
28839341 GGCTTACTGT
*
28839351 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
28839370 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
28839390 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:28839606 original size:12 final size:12
Alignment explanation
Indices: 28839583--28839616 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28839573 TTTTAGTCTA
28839583 TTTTATTAATTTT
1 TTTTATT-ATTTT
28839596 TTTTATTATTTT
1 TTTTATTATTTT
*
28839608 TATTATTAT
1 TTTTATTAT
28839617 ATTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTATTTT
Found at i:28847030 original size:88 final size:88
Alignment explanation
Indices: 28846166--28846993 Score: 1179
Period size: 88 Copynumber: 9.4 Consensus size: 88
28846156 GTGAAGATAA
* * * **
28846166 CAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATTAAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
28846231 GCAGCGGAGCATGTTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * * *
28846254 CATATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGTCACCAGCCTTGCCTCCTTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
28846319 GCAGCGGAGTAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * * *
28846342 CAGATCTTGCCTTTCTGCACTGACAGCGAAGCAGATCGAAGACATCAGCCTTACCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
28846407 GCAGCGGAGTAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * *
28846430 CAGATCTTGCCTTCCTGCACCGACAGAGAAGCAGATCGAAGACACCAACCTTGCTTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
28846495 GCAGCAGAGCAGGCTAAAAATAA
66 GCAGCGGAGCAGGCTAAAAATAG
* ** *
28846518 TAGATCTTGCCTTCCTGCACCGACAGTAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
28846583 GCAGCGGAGCAGGCTAAAAATAA
66 GCAGCGGAGCAGGCTAAAAATAG
* *
28846606 CAGACCTTGCCTTCCTGCACCGACAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
28846671 GCAGCGAAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
** * *
28846694 CAGATCTTGCCTTCCTTTACCAACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
28846759 GCAGCGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * *
28846782 CAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGTCACCAGCCTTGCTTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
28846847 GCAGCAGAGCAGGCTGAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
28846870 CAGATCTTGCCTTCCTGCACCGACAACGAAGTAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
28846935 GCAGTGGAGCAGGCTAAAAATAA
66 GCAGCGGAGCAGGCTAAAAATAG
* * * * *
28846958 CAGATCTTACCTTACTGCACCAACAGTGAAGAAGAT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGAT
28846994 TGATGACCCC
Statistics
Matches: 667, Mismatches: 73, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 667 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGCTAAAAATAG
Found at i:28847057 original size:44 final size:44
Alignment explanation
Indices: 28847007--28847338 Score: 369
Period size: 44 Copynumber: 7.7 Consensus size: 44
28846997 TGACCCCAAC
28847007 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
28847051 CCTATCTCCTTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
28847095 TCTATCTCCCT-GTGCAGCAGTGGAATAGATT-AA-A----GAAT
1 CCTATCTCCCTGGT-CAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
28847133 CCTATCTCCCTAGAT-AGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * **
28847177 CCTATCTCCCTGGTCAGCAGTGTAATTGGTTAAAAATTAAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * * * *
28847221 TCTATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGA-AT
* * *
28847265 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
28847309 CCTATCTCCCTGAG-CAGCAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
28847339 GGAAAATAGA
Statistics
Matches: 241, Mismatches: 34, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
38 29 0.12
39 2 0.01
40 2 0.01
42 1 0.00
43 7 0.03
44 198 0.82
45 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:28847232 original size:126 final size:131
Alignment explanation
Indices: 28847007--28847338 Score: 462
Period size: 126 Copynumber: 2.6 Consensus size: 131
28846997 TGACCCCAAC
*
28847007 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCTTGGTCAGCAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
* * * * *
28847072 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGTGCAGCAGTGGAATAGATT-AA-A-G-A-A
66 GGAATAGGTTAAAAATTAAGAATTCTATCTCCCTGGGCAGCAATGGAATAGATTGAAGATGTAGA
28847132 T
131 T
*
28847133 CCTATCTCCCTAGAT-AGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAG
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAG
* *
28847197 TGTAATTGGTTAAAAATTAAGAATTCTATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTGTA
65 TGGAATAGGTTAAAAATTAAGAATTCTATCTCCCTGGGCAGCAATGGAATAGATTGAAGA-TGTA
*
28847262 GGT
129 GAT
* * *
28847265 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAACCCTATCTCCCTGAG-CAGCAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTG-GTCAGCAG
*
28847329 TGGAGTAGGT
65 TGGAATAGGT
28847339 GGAAAATAGA
Statistics
Matches: 180, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
126 107 0.59
127 4 0.02
128 1 0.01
130 1 0.01
131 3 0.02
132 63 0.35
133 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (131 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
GGAATAGGTTAAAAATTAAGAATTCTATCTCCCTGGGCAGCAATGGAATAGATTGAAGATGTAGA
T
Found at i:28848206 original size:21 final size:21
Alignment explanation
Indices: 28848181--28848224 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28848171 ACCTTCGAGG
28848181 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
28848202 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
28848223 AT
1 AT
28848225 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:28848230 original size:19 final size:19
Alignment explanation
Indices: 28848180--28848235 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
28848170 AACCTTCGAG
28848180 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28848199 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
28848220 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
28848236 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28848242 original size:22 final size:23
Alignment explanation
Indices: 28848193--28848258 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
28848183 ATGCAATCTT
*
28848193 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
28848214 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
28848236 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
28848259 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:28848268 original size:22 final size:23
Alignment explanation
Indices: 28848224--28848268 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28848214 AGATATGATA
*
28848224 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
28848247 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
28848269 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:28848692 original size:15 final size:15
Alignment explanation
Indices: 28848668--28848705 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28848658 GTTTTTAGTC
28848668 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
28848682 TGTTATTATTATTTT
1 TATTATTATTAATTT
28848697 TATTATTAT
1 TATTATTAT
28848706 ATTATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:28848699 original size:12 final size:12
Alignment explanation
Indices: 28848670--28848720 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
28848660 TTTTAGTCTA
28848670 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
28848682 TGTTATTATTAT
1 TTTTATTATTAT
28848694 TTTTATTATTAT
1 TTTTATTATTAT
28848706 ATTATATATTATTAT
1 -TT-T-TATTATTAT
28848721 ACCTATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 3 0.09
12 18 0.55
13 2 0.06
14 1 0.03
15 9 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:28848715 original size:15 final size:13
Alignment explanation
Indices: 28848684--28848721 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
28848674 ATTAATTTTG
28848684 TTATTATTAT-TT
1 TTATTATTATATT
28848696 TTATTATTATATT
1 TTATTATTATATT
28848709 ATATATTATTATA
1 -T-TATTATTATA
28848722 CCTATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATATT
Found at i:28848732 original size:18 final size:15
Alignment explanation
Indices: 28848685--28848721 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
28848675 TTAATTTTGT
28848685 TATTATTAT-TT-T-
1 TATTATTATATTATA
28848697 TATTATTATATTATA
1 TATTATTATATTATA
28848712 TATTATTATA
1 TATTATTATA
28848722 CCTATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 1 0.05
15 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTATTATATTATA
Found at i:28852897 original size:22 final size:19
Alignment explanation
Indices: 28852867--28852907 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 19
28852857 AATGATTCCT
28852867 AAAAATTAATTTATTTTTTTA
1 AAAAATTAA--TATTTTTTTA
28852888 AAAAAGTTAATATTTTTTTA
1 AAAAA-TTAATATTTTTTTA
28852908 TATTTAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AAAAATTAATATTTTTTTA
Found at i:28853617 original size:18 final size:18
Alignment explanation
Indices: 28853581--28853619 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28853571 TTATTATTTT
*
28853581 TAAAATTTACTATTGAAA
1 TAAAATTTAATATTGAAA
28853599 TAAAATTTAAATATT-AAA
1 TAAAATTT-AATATTGAAA
28853617 TAA
1 TAA
28853620 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAATTTAATATTGAAA
Found at i:28853737 original size:13 final size:14
Alignment explanation
Indices: 28853714--28853746 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28853704 AATATTAAAA
28853714 ATATATAATATTTT
1 ATATATAATATTTT
28853728 ATAT-TAATATTTT
1 ATATATAATATTTT
*
28853741 AAATAT
1 ATATAT
28853747 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATATAATATTTT
Found at i:28856346 original size:27 final size:27
Alignment explanation
Indices: 28856308--28856399 Score: 145
Period size: 27 Copynumber: 3.5 Consensus size: 27
28856298 AAAGTTAAAA
28856308 AGTATATATTATATAATATTAAAACTT
1 AGTATATATTATATAATATTAAAACTT
*
28856335 AGTATAAATTATAT--TA-TAAAACTT
1 AGTATATATTATATAATATTAAAACTT
*
28856359 AGTATATATTATGTAATATTAAAACTT
1 AGTATATATTATATAATATTAAAACTT
28856386 AGTATATATTATAT
1 AGTATATATTATAT
28856400 TGTATATTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
24 20 0.34
25 2 0.03
26 2 0.03
27 34 0.59
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (27 bp):
AGTATATATTATATAATATTAAAACTT
Found at i:28857503 original size:40 final size:40
Alignment explanation
Indices: 28857382--28857521 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
28857372 GACTTCGAGT
* * * *
28857382 CGATGAGACATTGGGTGTCAATTTATTACTTTAGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATT-ATC
* * * * *
28857423 CGATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
*
28857460 CGATGAGACACTGGGTGTCAAATTATTACTTCAAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
* * *
28857500 CGATGAGGCATTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
28857522 CTGGTGTATT
Statistics
Matches: 78, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 17 0.22
38 12 0.15
39 2 0.03
40 32 0.41
41 15 0.19
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
Found at i:28859751 original size:29 final size:31
Alignment explanation
Indices: 28859719--28859779 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
28859709 AAACCTTTTT
*
28859719 ACTTTCCCCCCAATA-TTTTAC-TCCCTCCC
1 ACTTTCCCCCCAAAACTTTTACTTCCCTCCC
*
28859748 ACTTTCCCCCCAAAACTTTTACTTTCCTCCC
1 ACTTTCCCCCCAAAACTTTTACTTCCCTCCC
28859779 A
1 A
28859780 TCCCAACCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 14 0.50
30 6 0.21
31 8 0.29
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTTCCCTCCC
Found at i:28869876 original size:40 final size:40
Alignment explanation
Indices: 28869806--28870506 Score: 1214
Period size: 40 Copynumber: 17.6 Consensus size: 40
28869796 CATTTGAATG
28869806 ATATCCGGGCTAAGA---G-AGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28869842 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28869882 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28869922 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28869962 ATATCCGGGATAAGACCCGAAGGCATTTGCGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28870002 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28870042 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28870082 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28870122 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28870162 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28870202 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28870242 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28870282 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * *
28870322 ATATCCGGGATAAGACCCGAAGGCGTTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28870362 ATATCCGGGCTAAGACCCGATGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28870402 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
28870442 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28870482 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
28870507 ATTGAGCTTG
Statistics
Matches: 638, Mismatches: 21, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
36 15 0.02
39 3 0.00
40 619 0.97
41 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:28872486 original size:26 final size:26
Alignment explanation
Indices: 28872456--28872514 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
28872446 AAACTTTTCT
*
28872456 AAAAGAAGCTTAAGAGAAATTCTTAA
1 AAAAGAAGCTCAAGAGAAATTCTTAA
28872482 AAAAGAAGCTCAAGAGAAATTCTTAA
1 AAAAGAAGCTCAAGAGAAATTCTTAA
28872508 AAAAGAA
1 AAAAGAA
28872515 AACTCAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (26 bp):
AAAAGAAGCTCAAGAGAAATTCTTAA
Found at i:28872535 original size:27 final size:26
Alignment explanation
Indices: 28872456--28872527 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
28872446 AAACTTTTCT
* *
28872456 AAAAGAAGCTTAAGAGAAATTCTTAA
1 AAAAGAAACTCAAGAGAAATTCTTAA
*
28872482 AAAAGAAGCTCAAGAGAAATTCTTAA
1 AAAAGAAACTCAAGAGAAATTCTTAA
28872508 AAAAGAAAACTCAAAGAGAA
1 AAAAG-AAACTC-AAGAGAA
28872528 TTTATAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 30 0.71
27 5 0.12
28 7 0.17
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (26 bp):
AAAAGAAACTCAAGAGAAATTCTTAA
Found at i:28875626 original size:50 final size:50
Alignment explanation
Indices: 28875502--28875750 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
28875492 GATAATAACA
* * ** * *
28875502 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
28875553 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
28875603 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
28875653 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
28875708 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
28875751 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:28875680 original size:100 final size:104
Alignment explanation
Indices: 28875501--28875750 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
28875491 TGATAATAAC
**
28875501 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
28875566 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
28875603 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
28875666 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
28875708 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28875751 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:28875866 original size:13 final size:13
Alignment explanation
Indices: 28875845--28875876 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28875835 GCTTGGATCA
*
28875845 TCATCAAATAAAT
1 TCATAAAATAAAT
28875858 TCATAAAATAAAT
1 TCATAAAATAAAT
28875871 TCATAA
1 TCATAA
28875877 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:28883166 original size:51 final size:50
Alignment explanation
Indices: 28883094--28883335 Score: 263
Period size: 50 Copynumber: 4.7 Consensus size: 50
28883084 ACATGCCAAA
** *
28883094 GCCATGTCCCAGACATGGTCTTATATGGGATGTTCTCGTGAT-GGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTATATGGGA-CCTCTCGT-CTCGGTGCCCAT
* * * *
28883145 GCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTATATGGGACCTCTCGTCTCGGTGCCCAT
*
28883195 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTATATGGGACCTCTCGTCTCGGTGCCCAT
* * *
28883245 GCCATGTCCCAGACATGGTCTTACA-GGAGACCTCTCATGATCTTAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTATATGG-GACCTCTC--G-TC-T-CGG-TGCCCAT
* * *
28883301 GCCATGTCCCAGACATGATCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTATATGGGACCTCT
28883336 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
49 3 0.02
50 90 0.54
51 29 0.17
52 1 0.01
53 2 0.01
54 1 0.01
55 2 0.01
56 36 0.22
57 2 0.01
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTATATGGGACCTCTCGTCTCGGTGCCCAT
Found at i:28883264 original size:100 final size:104
Alignment explanation
Indices: 28883086--28883335 Score: 330
Period size: 100 Copynumber: 2.4 Consensus size: 104
28883076 TGATAATAAC
* **
28883086 ATGCCAAAGCCATGTCCCAGACATGGTCTTATATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* * *
28883151 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGAGACCTCTCAATCTTAAGG
* *
28883188 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
28883251 TCCCAGACATGGTCTTACAGGAGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGAGACCTCTCA--ATCTTAAGG
* * *
28883293 ATGCCAATGCCATGTCCCAGACATGATCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28883336 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGAGACCTCTCAATCTTAAGG
Found at i:28883451 original size:13 final size:13
Alignment explanation
Indices: 28883430--28883461 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28883420 GCTTGGATCA
*
28883430 TCATCAAATAAAT
1 TCATAAAATAAAT
28883443 TCATAAAATAAAT
1 TCATAAAATAAAT
28883456 TCATAA
1 TCATAA
28883462 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:28883708 original size:30 final size:30
Alignment explanation
Indices: 28883673--28883730 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28883663 CCTCGACTCT
*
28883673 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
28883703 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
28883731 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:28894169 original size:47 final size:47
Alignment explanation
Indices: 28894104--28894704 Score: 878
Period size: 47 Copynumber: 12.4 Consensus size: 47
28894094 CAGCCAAGAG
*
28894104 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28894151 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28894198 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28894247 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28894298 AGTATATGTATATATGTAATCAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AG----TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28894349 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28894396 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28894443 AGTATATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AG----TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28894494 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28894541 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28894588 AGTGTGTGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 A----GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28894639 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28894686 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
28894705 TCCCGAAAGG
Statistics
Matches: 513, Mismatches: 25, Indels: 32
0.90 0.04 0.06
Matches are distributed among these distances:
47 288 0.56
49 42 0.08
51 179 0.35
53 4 0.01
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:28894398 original size:98 final size:96
Alignment explanation
Indices: 28894106--28894704 Score: 859
Period size: 98 Copynumber: 6.2 Consensus size: 96
28894096 GCCAAGAGAG
* *
28894106 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGG
1 TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* *
28894171 CCTAATGGCCGATGTGATGAATGTGAAAGTG
66 CCTAATAGCCGATGTGATGAATGTGAAAGTT
* * *
28894202 TATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTGAT
1 TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAA--G--TGTATATATGTGAT
*
28894267 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTAT
62 AAGGCCTAATAGCCGATGTGATGAATGTGAAAGT-T
* * *
28894303 ATGTATATATGTAATCAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAG
1 -TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
*
28894368 GCCTAATAGCCGACGTGATGAATGTGAAAG--
65 GCCTAATAGCCGATGTGATGAATGTGAAAGTT
* *
28894398 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTATATGTATATATGTAAT
1 TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG----TGTATATATGTGAT
28894463 AAGGCCTAATAGCCGATGTGATGAATGTGAAAG--
62 AAGGCCTAATAGCCGATGTGATGAATGTGAAAGTT
* * *
28894496 TGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGATAAGG
1 TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
28894561 CCTAATAGCCGATGTGATGAATGTGAAAGTGT
66 CCTAATAGCCGATGTGATGAATGTGAAAGT-T
* *
28894593 GTGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAG
1 -TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
28894658 GCCTAATAGCCGATGTGATGAATGTGAAAG--
65 GCCTAATAGCCGATGTGATGAATGTGAAAGTT
* *
28894688 TGCATAAATGTGATAAG
1 TGTATATATGTGATAAG
28894705 TCCCGAAAGG
Statistics
Matches: 460, Mismatches: 29, Indels: 30
0.89 0.06 0.06
Matches are distributed among these distances:
94 103 0.22
96 42 0.09
98 226 0.49
100 48 0.10
102 41 0.09
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (96 bp):
TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATAGCCGATGTGATGAATGTGAAAGTT
Found at i:28894448 original size:145 final size:145
Alignment explanation
Indices: 28894104--28894704 Score: 1003
Period size: 145 Copynumber: 4.1 Consensus size: 145
28894094 CAGCCAAGAG
28894104 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG----TGTATATATGTA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTATATGTATATATGTA
* * *
28894165 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCC
66 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTA--TATGTGTGATAAGGCCTAATAGCC
*
28894230 GATGTGATGAATGTGAA
129 GACGTGATGAATGTGAA
* *
28894247 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATGTATATA
1 A--G--TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTATATGTATATA
*
28894312 TGTAATCAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAG
62 TGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAG
28894377 CCGACGTGATGAATGTGAA
127 CCGACGTGATGAATGTGAA
28894396 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTATATGTATATATGTA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTATATGTATATATGTA
28894461 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGA
66 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGA
28894526 CGTGATGAATGTGAA
131 CGTGATGAATGTGAA
* *
28894541 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTGTGTATATATGTA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTATATGTATATATGTA
28894606 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGA
66 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGA
*
28894671 TGTGATGAATGTGAA
131 CGTGATGAATGTGAA
* **
28894686 AGTGCATAAATGTGATAAG
1 AGTGTATATGTGTGATAAG
28894705 TCCCGAAAGG
Statistics
Matches: 434, Mismatches: 16, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
143 1 0.00
145 299 0.69
147 46 0.11
149 39 0.09
151 49 0.11
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (145 bp):
AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTATATGTATATATGTA
ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGA
CGTGATGAATGTGAA
Found at i:28894879 original size:37 final size:37
Alignment explanation
Indices: 28894823--28894901 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28894813 CCGAGCTCTA
* * *
28894823 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
28894860 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
28894897 AAGAC
1 AAGAC
28894902 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:28902263 original size:4 final size:4
Alignment explanation
Indices: 28902250--28902337 Score: 56
Period size: 4 Copynumber: 20.5 Consensus size: 4
28902240 ATTTTCCTAC
*
28902250 TTTA -TTA TTTA TTTA TTTA TTCTA -TTA TTTTA TTTTA TTTC TTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TTTA -TTTA -TTTA TTTA TTTA -TTTA
*
28902300 TTT- TATTA TTTGG TTTA TGTTTA TTTCA TTTA TTTA TT
1 TTTA T-TTA TTT-A TTTA --TTTA TTT-A TTTA TTTA TT
28902338 AACCCCAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
3 6 0.09
4 37 0.54
5 22 0.32
6 4 0.06
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:28902281 original size:13 final size:12
Alignment explanation
Indices: 28902250--28902310 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
28902240 ATTTTCCTAC
28902250 TTTATTA-TTTA
1 TTTATTATTTTA
*
28902261 TTTATTTATTCTA
1 TTTA-TTATTTTA
*
28902274 TTATTTTATTTTA
1 TT-TATTATTTTA
*
28902287 TTTCTTTATTTTA
1 TTT-ATTATTTTA
28902300 TTTTATTATTT
1 -TTTATTATTT
28902311 GGTTTATGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 4 0.10
12 4 0.10
13 29 0.71
14 4 0.10
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:28902288 original size:18 final size:17
Alignment explanation
Indices: 28902250--28902334 Score: 75
Period size: 18 Copynumber: 4.8 Consensus size: 17
28902240 ATTTTCCTAC
*
28902250 TTTATTATTTA-TTTA-
1 TTTATTCTTTATTTTAT
28902265 TTTATTCTATTATTTTAT
1 TTTATTCT-TTATTTTAT
28902283 TTTATTTCTTTATTTTAT
1 TTTA-TTCTTTATTTTAT
* **
28902301 TTTATTATTTGGTTTAT
1 TTTATTCTTTATTTTAT
28902318 GTTTATTTCATTTATTT
1 -TTTA-TTC-TTTATTT
28902335 ATTAACCCCA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
15 7 0.12
16 3 0.05
17 14 0.25
18 21 0.38
19 6 0.11
20 5 0.09
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (17 bp):
TTTATTCTTTATTTTAT
Found at i:28902322 original size:23 final size:22
Alignment explanation
Indices: 28902254--28902334 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 22
28902244 TCCTACTTTA
*
28902254 TTATTTATTTATTTATTCTATTATT
1 TTATTTATTTCTTTA-T-T-TTATT
28902279 TTATTTTATTTCTTTATTTTATT
1 TTA-TTTATTTCTTTATTTTATT
*
28902302 TTA-TTATTTGGTTTATGTTTATT
1 TTATTTATTT-CTTTAT-TTTATT
*
28902325 TCATTTATTT
1 TTATTTATTT
28902335 ATTAACCCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.12
22 5 0.10
23 16 0.33
24 7 0.14
25 4 0.08
26 11 0.22
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (22 bp):
TTATTTATTTCTTTATTTTATT
Found at i:28902337 original size:13 final size:13
Alignment explanation
Indices: 28902250--28902337 Score: 51
Period size: 13 Copynumber: 6.8 Consensus size: 13
28902240 ATTTTCCTAC
28902250 TTTA-TTATTT-A
1 TTTATTTATTTCA
28902261 TTTATTTA-TTC-
1 TTTATTTATTTCA
*
28902272 TATTATTTTATTTTA
1 T-TTA-TTTATTTCA
* *
28902287 TTTCTTTATTTTA
1 TTTATTTATTTCA
**
28902300 TTT-TATTATTTGG
1 TTTAT-TTATTTCA
28902313 TTTATGTTTATTTCA
1 TTTA--TTTATTTCA
28902328 TTTATTTATT
1 TTTATTTATT
28902338 AACCCCAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
11 7 0.11
12 7 0.11
13 31 0.51
14 4 0.07
15 11 0.18
16 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTATTTATTTCA
Found at i:28902463 original size:8 final size:8
Alignment explanation
Indices: 28902450--28902474 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28902440 CTATTTGGTA
28902450 TATTATTT
1 TATTATTT
28902458 TATTATTT
1 TATTATTT
28902466 TATTATTT
1 TATTATTT
28902474 T
1 T
28902475 TAGTTATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:28902612 original size:36 final size:36
Alignment explanation
Indices: 28902563--28902647 Score: 134
Period size: 36 Copynumber: 2.4 Consensus size: 36
28902553 TGTTACTATT
*
28902563 TTAGTTTATTATTATAGTTACTACTATTATTCGTCC
1 TTAGTTTATTATTATAGTTACTACTATGATTCGTCC
* * *
28902599 TTAGTTTACTATTATAGTTATTATTATGATTCGTCC
1 TTAGTTTATTATTATAGTTACTACTATGATTCGTCC
28902635 TTAGTTTATTATT
1 TTAGTTTATTATT
28902648 TTGAATTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (36 bp):
TTAGTTTATTATTATAGTTACTACTATGATTCGTCC
Found at i:28904282 original size:19 final size:20
Alignment explanation
Indices: 28904260--28904301 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
28904250 TTGTTTTCTT
28904260 TTTAAT-TTTAATTTTTATG
1 TTTAATGTTTAATTTTTATG
* *
28904279 TTT-ATGTTTATTTTTTATT
1 TTTAATGTTTAATTTTTATG
28904298 TTTA
1 TTTA
28904302 GTTGTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTAATGTTTAATTTTTATG
Found at i:28904294 original size:32 final size:32
Alignment explanation
Indices: 28904258--28904324 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
28904248 ATTTGTTTTC
28904258 TTTTTAATTTTAATT-TTTATGTTTATGTTTAT
1 TTTTTAATTTTAATTGTTT-TGTTTATGTTTAT
* * * *
28904290 TTTTTATTTTTAGTTGTTTTGTTTTTTTTTAT
1 TTTTTAATTTTAATTGTTTTGTTTATGTTTAT
28904322 TTT
1 TTT
28904325 CTTGTAGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 27 0.90
33 3 0.10
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (32 bp):
TTTTTAATTTTAATTGTTTTGTTTATGTTTAT
Found at i:28904317 original size:25 final size:24
Alignment explanation
Indices: 28904244--28904324 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 24
28904234 GGATAATTGA
*
28904244 TTTTATTTGTTTTCTTTTTAATTTTAAT
1 TTTTA-TTGTTTTGTTTTT--TTTT-AT
28904272 TTTTA-TGTTTATGTTTATTTTTTAT
1 TTTTATTGTTT-TGTTT-TTTTTTAT
28904297 TTTTAGTTGTTTTGTTTTTTTTTAT
1 TTTTA-TTGTTTTGTTTTTTTTTAT
28904322 TTT
1 TTT
28904325 CTTGTAGTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
25 18 0.38
26 14 0.29
27 9 0.19
28 7 0.15
ACGTcount: A:0.14, C:0.01, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTATTGTTTTGTTTTTTTTTAT
Found at i:28906840 original size:36 final size:36
Alignment explanation
Indices: 28906750--28906857 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
28906740 AATTAGAAAG
*
28906750 AGATTTCAATTAATCAACTTAGAGTCAATTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
* *
28906786 AGATTTC-ATTAATCAACTTAAAGTGAGTTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
28906821 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
28906857 A
1 A
28906858 CTCTCGAAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 32 0.48
36 34 0.52
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (36 bp):
AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
Found at i:28909895 original size:42 final size:42
Alignment explanation
Indices: 28909836--28909920 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
28909826 TGATTACAAG
28909836 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
1 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
28909878 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
1 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
28909920 T
1 T
28909921 AAACCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (42 bp):
TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
Found at i:28918081 original size:46 final size:46
Alignment explanation
Indices: 28918009--28918129 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
28917999 TTTATCATGT
* * * * *
28918009 TTGAAGTGTTAAAGTGTTGCATATTGAAGTATTTATATGCTGTGAA
1 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
* *
28918055 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTATAAA
1 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
* *
28918101 TGGAAGTGTTTTAAA-TACTGCAAATTGAA
1 TTGAAGTG--TTAAAGTGCTGCAAATTGAA
28918130 TTGTTTAGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
46 46 0.72
47 13 0.20
48 5 0.08
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (46 bp):
TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
Found at i:28918101 original size:23 final size:23
Alignment explanation
Indices: 28918009--28918218 Score: 122
Period size: 23 Copynumber: 9.1 Consensus size: 23
28917999 TTTATCATGT
* *
28918009 TTGAAGTG-TTAAAGTGTTGCATA
1 TTGAAGTGTTTAAA-TGCTGCAAA
* * **
28918032 TTGAAGTATTTATATGCTGTGAA
1 TTGAAGTGTTTAAATGCTGCAAA
28918055 TTGAAGTG-TTAAAGTGCTGCAAA
1 TTGAAGTGTTTAAA-TGCTGCAAA
* **
28918078 TTGAAGTGTTTAAATGTTATAAA
1 TTGAAGTGTTTAAATGCTGCAAA
* *
28918101 TGGAAGTGTTTTAAATACTGCAAA
1 TTGAAGTG-TTTAAATGCTGCAAA
* ** *
28918125 TTGAATTGTTTAGTTGCTGAAAA
1 TTGAAGTGTTTAAATGCTGCAAA
* * *
28918148 TTG-AGATGTTTTATTGCTG-TAA
1 TTGAAG-TGTTTAAATGCTGCAAA
* * * * *
28918170 CTGAGGTGTATAAATGTTGTAAA
1 TTGAAGTGTTTAAATGCTGCAAA
* * *
28918193 TTGAAGTGTTTTATTGCTGAAAA
1 TTGAAGTGTTTAAATGCTGCAAA
28918216 TTG
1 TTG
28918219 GATGGTATAA
Statistics
Matches: 138, Mismatches: 42, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
22 18 0.13
23 94 0.68
24 26 0.19
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (23 bp):
TTGAAGTGTTTAAATGCTGCAAA
Found at i:28918125 original size:24 final size:24
Alignment explanation
Indices: 28918053--28918135 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
28918043 ATATGCTGTG
*
28918053 AATTGAAGTG--TTAAAGTGCTGCA
1 AATTGAAGTGTTTTAAA-TACTGCA
** **
28918076 AATTGAAGTG-TTTAAATGTTATA
1 AATTGAAGTGTTTTAAATACTGCA
*
28918099 AATGGAAGTGTTTTAAATACTGCA
1 AATTGAAGTGTTTTAAATACTGCA
*
28918123 AATTGAATTGTTT
1 AATTGAAGTGTTT
28918136 AGTTGCTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 23 0.48
24 25 0.52
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (24 bp):
AATTGAAGTGTTTTAAATACTGCA
Found at i:28918846 original size:16 final size:16
Alignment explanation
Indices: 28918825--28918864 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
28918815 TTGAATTACT
28918825 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
*
28918841 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
28918857 ATTACAGC
1 ATTACAGC
28918865 GAACCAAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:28920948 original size:20 final size:19
Alignment explanation
Indices: 28920893--28920952 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
28920883 GCCCAAATTA
28920893 TATATTAAATATATATTTT
1 TATATTAAATATATATTTT
* * *
28920912 TATTTTTAATCAAATATACTTT
1 TA-TATTAA--ATATATATTTT
28920934 T-TATTAAATATATATTTT
1 TATATTAAATATATATTTT
28920952 T
1 T
28920953 TTTGGACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 10 0.31
19 2 0.06
20 10 0.31
22 10 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTAAATATATATTTT
Found at i:28920954 original size:20 final size:20
Alignment explanation
Indices: 28920895--28920955 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
28920885 CCAAATTATA
28920895 TATTAAATATATATTTTTATT
1 TATTAAATATATATTTTT-TT
* **
28920916 T-TT-AATCAAATATACTTTT
1 TATTAAAT-ATATATTTTTTT
28920935 TATTAAATATATATTTTTTT
1 TATTAAATATATATTTTTTT
28920955 T
1 T
28920956 GGACTTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 6 0.19
20 21 0.68
21 4 0.13
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTAAATATATATTTTTTT
Found at i:28921916 original size:20 final size:20
Alignment explanation
Indices: 28921891--28921929 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28921881 TGGAGCAGGA
*
28921891 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
28921911 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
28921930 AGTATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:28923423 original size:18 final size:18
Alignment explanation
Indices: 28923383--28923430 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
28923373 ACACCAATTT
**
28923383 GTTATTTGAGCTATTCAA
1 GTTATTTGAATTATTCAA
* *
28923401 ATTATTTGAATTATTCAC
1 GTTATTTGAATTATTCAA
*
28923419 GTTATTCGAATT
1 GTTATTTGAATT
28923431 GTTAAATTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (18 bp):
GTTATTTGAATTATTCAA
Found at i:28923670 original size:14 final size:14
Alignment explanation
Indices: 28923653--28923683 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28923643 AGTAAAATAT
*
28923653 TTTCTGGAAAATGA
1 TTTCTAGAAAATGA
28923667 TTTCTAGAAAATGA
1 TTTCTAGAAAATGA
28923681 TTT
1 TTT
28923684 ACTTTTCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (14 bp):
TTTCTAGAAAATGA
Found at i:28923699 original size:19 final size:19
Alignment explanation
Indices: 28923675--28923712 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28923665 GATTTCTAGA
28923675 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
28923694 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
28923713 TGTTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:28925283 original size:43 final size:43
Alignment explanation
Indices: 28925176--28925443 Score: 281
Period size: 43 Copynumber: 6.3 Consensus size: 43
28925166 TTATTTTTAT
* * **** *
28925176 AAACGCCGCTAAAGGTTATGTTCTTTAGCGGCG-TTACGAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* * *
28925218 AAATGTCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* *
28925261 AAACGCCGCTAAAGATCATGTTCCTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* * * *
28925304 AAATGTCTCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* * **
28925347 AAACGCCGCTAAAGATCATGTTCTTTAGCGGTGCTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* * *
28925390 AAACGCCACTAAAGGTCATGTTCTTTTAGCGGC-ATTTTT-ACAC
1 AAACGCCGCTAAAGATCATGTTC-TTTAGCGGCGCTTTTTCA-AC
*
28925433 AAATGCCGCTA
1 AAACGCCGCTA
28925444 TTTGTTTGGT
Statistics
Matches: 191, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
42 30 0.16
43 153 0.80
44 8 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
Found at i:28925328 original size:86 final size:86
Alignment explanation
Indices: 28925218--28925443 Score: 312
Period size: 86 Copynumber: 2.6 Consensus size: 86
28925208 GTTACGAAAA
*
28925218 AAATGTCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACAAACGCCGCTAAAGATCATGTT
1 AAATGTCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACAAACGCCGCTAAAGATCATGTT
*
28925283 CCTTAGCGGCGCTTTTTCCAC
66 CCTTAGCGGCGCTTCTTCCAC
* * *
28925304 AAATGTCTCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGTT
1 AAATGTCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACAAACGCCGCTAAAGATCATGTT
* * *
28925369 CTTTAGCGGTGCTTCTTCCGC
66 CCTTAGCGGCGCTTCTTCCAC
* * * *
28925390 AAACGCCACTAAAGGTCATGTTCTTTTAGCGGC-ATTTTT-ACACAAATGCCGCTA
1 AAATGTCACTAAAGGTCATGTTC-TTTAGCGGCGCTTTTTCA-ACAAACGCCGCTA
28925444 TTTGTTTGGT
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
86 115 0.93
87 9 0.07
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (86 bp):
AAATGTCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACAAACGCCGCTAAAGATCATGTT
CCTTAGCGGCGCTTCTTCCAC
Found at i:28930341 original size:9 final size:9
Alignment explanation
Indices: 28930327--28930703 Score: 202
Period size: 9 Copynumber: 44.4 Consensus size: 9
28930317 CATCATATAT
28930327 TTATGTAAG
1 TTATGTAAG
28930336 TTATGT-A-
1 TTATGTAAG
28930343 TTATGTAAG
1 TTATGTAAG
28930352 TTATGTAAG
1 TTATGTAAG
28930361 TTATGT-A-
1 TTATGTAAG
* *
28930368 TTAAGTAAA
1 TTATGTAAG
28930377 TTATGTAAG
1 TTATGTAAG
28930386 TTATGT-A-
1 TTATGTAAG
28930393 TTATGTAAG
1 TTATGTAAG
28930402 TTATGTAAG
1 TTATGTAAG
*
28930411 TTGTGT-A-
1 TTATGTAAG
* *
28930418 TTATGAAAC
1 TTATGTAAG
28930427 TTATGTAAG
1 TTATGTAAG
*
28930436 TTATGT--C
1 TTATGTAAG
*
28930443 TTATGTAGG
1 TTATGTAAG
28930452 TTATGTAAG
1 TTATGTAAG
28930461 TTATGT-A-
1 TTATGTAAG
28930468 TTATGTAAG
1 TTATGTAAG
28930477 TTATGT-A-
1 TTATGTAAG
* *
28930484 TTAAGTAAA
1 TTATGTAAG
28930493 TTATGTAAG
1 TTATGTAAG
*
28930502 -T-TGT--C
1 TTATGTAAG
*
28930507 TTATATAAG
1 TTATGTAAG
28930516 TTATGT-A-
1 TTATGTAAG
28930523 TTATGTAAG
1 TTATGTAAG
28930532 TTATGTAAG
1 TTATGTAAG
* ***
28930541 TTTTTGTTTT
1 -TTATGTAAG
*
28930551 TTGTGT-A-
1 TTATGTAAG
*
28930558 TTATGTAAC
1 TTATGTAAG
* *
28930567 TTATTTAAT
1 TTATGTAAG
*
28930576 TTATGTAGG
1 TTATGTAAG
28930585 TTATGTATTA-
1 TTATGTA--AG
28930595 TTATGTAAG
1 TTATGTAAG
*
28930604 TTAT-TATG
1 TTATGTAAG
*
28930612 -TA-GGATA-
1 TTATGTA-AG
28930619 TTATGTAAG
1 TTATGTAAG
28930628 TTATGTAAG
1 TTATGTAAG
* ***
28930637 TTTTTGTTTT
1 -TTATGTAAG
*
28930647 TTGTGT-A-
1 TTATGTAAG
*
28930654 TTATGTAAC
1 TTATGTAAG
* *
28930663 TTATTTAAT
1 TTATGTAAG
*
28930672 TTATGTAGG
1 TTATGTAAG
28930681 TTATGTATTA-
1 TTATGTA--AG
28930691 TTATGTAAG
1 TTATGTAAG
28930700 TTAT
1 TTAT
28930704 TATGTAGGTT
Statistics
Matches: 283, Mismatches: 48, Indels: 74
0.70 0.12 0.18
Matches are distributed among these distances:
6 1 0.00
7 62 0.22
8 25 0.09
9 171 0.60
10 24 0.08
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28930348 original size:16 final size:16
Alignment explanation
Indices: 28930327--28930538 Score: 156
Period size: 16 Copynumber: 13.0 Consensus size: 16
28930317 CATCATATAT
28930327 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
28930343 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
*
28930360 GTTATGT-A-TTAAGTAAA
1 -TTATGTAAGTTATGT--A
28930377 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
28930393 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
* *
28930410 GTTGTGT-A-TTATGAAA
1 -TTATGTAAGTTATG-TA
*
28930426 CTTATGTAAGTTATGTC
1 -TTATGTAAGTTATGTA
*
28930443 TTATGTAGGTTATGTAA
1 TTATGTAAGTTATGT-A
28930460 GTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
*
28930476 GTTATGT-A-TTAAGTAAA
1 -TTATGTAAGTTATGT--A
*
28930493 TTATGTAAG-T-TGTC
1 TTATGTAAGTTATGTA
*
28930507 TTATATAAGTTATGTA
1 TTATGTAAGTTATGTA
28930523 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
28930539 AGTTTTTGTT
Statistics
Matches: 162, Mismatches: 17, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.05
15 1 0.01
16 114 0.70
17 12 0.07
18 27 0.17
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:28930359 original size:25 final size:25
Alignment explanation
Indices: 28930327--28930638 Score: 277
Period size: 25 Copynumber: 12.4 Consensus size: 25
28930317 CATCATATAT
28930327 TTATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
* *
28930352 TTATGTAAGTTATGTATTAAGTAAA
1 TTATGTAAGTTATGTATTATGTAAG
28930377 TTATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
* * *
28930402 TTATGTAAGTTGTGTATTATGAAAC
1 TTATGTAAGTTATGTATTATGTAAG
* *
28930427 TTATGTAAGTTATGTCTTATGTAGG
1 TTATGTAAGTTATGTATTATGTAAG
28930452 TTATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
*
28930477 TTATGT-A-TTAAGTAAATTATGTAAGTTG
1 TTATGTAAGTTATGT--ATTATGTAA---G
*
28930505 TCTTATATAAGTTATGTATTATGTAAG
1 --TTATGTAAGTTATGTATTATGTAAG
* * * *
28930532 TTATGTAAGTTTTTGTTTTTTGTGTA-
1 TTATGTAAG-TTATGTATTATGT-AAG
* * *
28930558 TTATGTAACTTATTTAATTTATGTAGG
1 TTATGTAAGTTATGT-A-TTATGTAAG
28930585 TTA--T--G-TAT-TATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
* *
28930604 TTAT-TATG-TAGGATATTATGTAAG
1 TTATGTAAGTTATG-TATTATGTAAG
28930628 TTATGTAAGTT
1 TTATGTAAGTT
28930639 TTTGTTTTTT
Statistics
Matches: 233, Mismatches: 33, Indels: 41
0.76 0.11 0.13
Matches are distributed among these distances:
19 11 0.05
20 2 0.01
21 1 0.00
22 6 0.03
23 5 0.02
24 16 0.07
25 142 0.61
26 19 0.08
27 10 0.04
28 1 0.00
30 14 0.06
31 1 0.00
32 5 0.02
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.49
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTAAG
Found at i:28930621 original size:96 final size:96
Alignment explanation
Indices: 28930521--28930724 Score: 399
Period size: 96 Copynumber: 2.1 Consensus size: 96
28930511 ATAAGTTATG
28930521 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
28930586 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
28930617 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
*
28930682 TATGTATTATTATGTAAGTTATTATGTAGGT
66 TATGTATTATTATGTAAGTTATTATGTAGGA
28930713 TATTATGTAAGT
1 TATTATGTAAGT
28930725 CATCATGTTG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 107 1.00
ACGTcount: A:0.27, C:0.01, G:0.18, T:0.54
Consensus pattern (96 bp):
TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
TATGTATTATTATGTAAGTTATTATGTAGGA
Found at i:28930718 original size:24 final size:24
Alignment explanation
Indices: 28930681--28930739 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
28930671 TTTATGTAGG
*
28930681 TTATGTA--TTATTATGTAAGTTA
1 TTATGTAGGTTATTATGTAAGTCA
28930703 TTATGTAGGTTATTATGTAAGTCA
1 TTATGTAGGTTATTATGTAAGTCA
* *
28930727 TCATGTTGGTTAT
1 TTATGTAGGTTAT
28930740 GTAAGTTGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 7 0.22
24 25 0.78
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (24 bp):
TTATGTAGGTTATTATGTAAGTCA
Found at i:28930732 original size:12 final size:12
Alignment explanation
Indices: 28930327--28930724 Score: 72
Period size: 12 Copynumber: 31.8 Consensus size: 12
28930317 CATCATATAT
28930327 TTATGTAAGTTA
1 TTATGTAAGTTA
* *
28930339 TGTAT-TATGTAA
1 T-TATGTAAGTTA
28930351 GTTATGTAAGTTA
1 -TTATGTAAGTTA
*
28930364 TGTAT-TAAGTAAA
1 T-TATGTAAGT-TA
28930377 TTATGTAAGTTA
1 TTATGTAAGTTA
* *
28930389 TGTAT-TATGTAA
1 T-TATGTAAGTTA
*
28930401 GTTATGTAAGTTG
1 -TTATGTAAGTTA
* **
28930414 TGTAT-TATGAAA
1 T-TATGTAAGTTA
28930426 CTTATGTAAGTTA
1 -TTATGTAAGTTA
*
28930439 TGTCTTATGTAGGTTA
1 ----TTATGTAAGTTA
* *
28930455 TGTAAGTTA-TGTA
1 T-TATGTAAGT-TA
28930468 TTATGTAAGTTA
1 TTATGTAAGTTA
*
28930480 TGTAT-TAAGTAAA
1 T-TATGTAAGT-TA
*
28930493 TTATGTAAGTTGTC
1 TTATGTAAG-T-TA
*
28930507 TTATATAAGTTA
1 TTATGTAAGTTA
* *
28930519 TGTAT-TATGTAA
1 T-TATGTAAGTTA
*
28930531 GTTATGTAAGTTT
1 -TTATGTAAGTTA
* * **
28930544 TTGTTTTTTGTGTA
1 TT-ATGTAAGT-TA
*
28930558 TTATGTAACTTA
1 TTATGTAAGTTA
* *
28930570 TTTAATTTATG-TA
1 -TT-ATGTAAGTTA
28930583 GGTTATGT-A-TTA
1 --TTATGTAAGTTA
28930595 TTATGTAAGTTA
1 TTATGTAAGTTA
* *
28930607 TTATGTAGGATA
1 TTATGTAAGTTA
28930619 TTATGTAAG---
1 TTATGTAAGTTA
*
28930628 TTATGTAAGTTT
1 TTATGTAAGTTA
* * **
28930640 TTGTTTTTTGTGTA
1 TT-ATGTAAGT-TA
*
28930654 TTATGTAACTTA
1 TTATGTAAGTTA
* *
28930666 TTTAATTTATG-TA
1 -TT-ATGTAAGTTA
28930679 GGTTATGT-A-TTA
1 --TTATGTAAGTTA
28930691 TTATGTAAGTTA
1 TTATGTAAGTTA
*
28930703 TTATGTAGGTTA
1 TTATGTAAGTTA
28930715 TTATGTAAGT
1 TTATGTAAGT
28930725 CATCATGTTG
Statistics
Matches: 270, Mismatches: 72, Indels: 88
0.63 0.17 0.20
Matches are distributed among these distances:
9 9 0.03
10 12 0.04
11 2 0.01
12 119 0.44
13 89 0.33
14 27 0.10
16 12 0.04
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:28930764 original size:96 final size:95
Alignment explanation
Indices: 28930521--28930780 Score: 276
Period size: 96 Copynumber: 2.7 Consensus size: 95
28930511 ATAAGTTATG
* * *** * *
28930521 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGGTTATGTAAGTTGCGTATGATGTAAC-TATTTAATTTATGTAGGT
28930586 TATGTATTATTATGTAAGTTATTATGTAGGA
65 TATGTATTATTATGTAAGTTATTATGTAGGA
* * *** * *
28930617 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGGTTATGTAAGTTGCGTATGATGTAAC-TATTTAATTTATGTAGGT
*
28930682 TATGTATTATTATGTAAGTTATTATGTAGGT
65 TATGTATTATTATGTAAGTTATTATGTAGGA
* *
28930713 TATTATGTAAGTCATCATGT-TGGTTATGTAAGTTGCGATATGAT-TAA-TATTT-ATGTATGTA
1 TATTATGTAAGT--T-ATGTAAGGTTATGTAAGTTGCG-TATGATGTAACTATTTAATTTATGTA
*
28930774 AGTTATG
62 GGTTATG
28930781 ATATGATTGA
Statistics
Matches: 149, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
95 14 0.09
96 112 0.75
98 14 0.09
99 9 0.06
ACGTcount: A:0.27, C:0.02, G:0.18, T:0.52
Consensus pattern (95 bp):
TATTATGTAAGTTATGTAAGGTTATGTAAGTTGCGTATGATGTAACTATTTAATTTATGTAGGTT
ATGTATTATTATGTAAGTTATTATGTAGGA
Found at i:28930904 original size:21 final size:20
Alignment explanation
Indices: 28930865--28930903 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
28930855 GTAATGTATC
*
28930865 AATTTTTAAAAATATATATA
1 AATTTTAAAAAATATATATA
28930885 AATTTT-AAAAATATATATA
1 AATTTTAAAAAATATATATA
28930904 TTAAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTTAAAAAATATATATA
Found at i:28930941 original size:9 final size:9
Alignment explanation
Indices: 28930927--28931007 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 9
28930917 TAAATATTAA
28930927 TAAGTTATG
1 TAAGTTATG
28930936 TAAGTTATG
1 TAAGTTATG
* *
28930945 TATTA-TAAATT
1 TA--AGT-TATG
*
28930956 TAAATTATG
1 TAAGTTATG
28930965 TAAGTTATG
1 TAAGTTATG
28930974 -AA-TTATG
1 TAAGTTATG
28930981 TAAGTTATG
1 TAAGTTATG
* *
28930990 TAAATTACG
1 TAAGTTATG
*
28930999 TCAGTTATG
1 TAAGTTATG
28931008 AAATTTGAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
7 5 0.09
8 4 0.07
9 40 0.71
10 2 0.04
11 5 0.09
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:28930979 original size:16 final size:16
Alignment explanation
Indices: 28930931--28931009 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
28930921 TATTAATAAG
*
28930931 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGAA
* *
28930947 TTA--TAAATT-TAAA
1 TTATGTAAGTTATGAA
28930960 TTATGTAAGTTATGAA
1 TTATGTAAGTTATGAA
28930976 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATG--AA
* *
28930994 TTACGTCAGTTATGAA
1 TTATGTAAGTTATGAA
28931010 ATTTGAACTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 22 0.43
18 14 0.27
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
TTATGTAAGTTATGAA
Found at i:28931800 original size:14 final size:14
Alignment explanation
Indices: 28931781--28931810 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28931771 CTCGAACAAC
28931781 AAGATGATTAACTA
1 AAGATGATTAACTA
28931795 AAGATGATTAACTA
1 AAGATGATTAACTA
28931809 AA
1 AA
28931811 AAACCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
AAGATGATTAACTA
Found at i:28934153 original size:18 final size:20
Alignment explanation
Indices: 28934122--28934158 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
28934112 TAAAATTATA
28934122 ATTTTTAGTGTTTTTATTTC
1 ATTTTTAGTGTTTTTATTTC
28934142 ATTTTTA-T-TTTTTATTT
1 ATTTTTAGTGTTTTTATTT
28934159 TAATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (20 bp):
ATTTTTAGTGTTTTTATTTC
Found at i:28934767 original size:14 final size:14
Alignment explanation
Indices: 28934746--28934787 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
28934736 CTTAATTAAA
28934746 CCATAATCCCTAAT
1 CCATAATCCCTAAT
*
28934760 CTATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
28934775 CCATACTCCCTAA
1 CCATAATCCCTAA
28934788 ACCTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:28934784 original size:15 final size:15
Alignment explanation
Indices: 28934742--28934788 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
28934732 AACCCTTAAT
28934742 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
28934756 T-AATCTATAATCCC
1 TAAATCCATAATCCC
*
28934770 TAAATCCATACTCCC
1 TAAATCCATAATCCC
28934785 TAAA
1 TAAA
28934789 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:28935056 original size:14 final size:14
Alignment explanation
Indices: 28935037--28935085 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
28935027 AAATCCCAAC
28935037 CCCTAATCCATAAT
1 CCCTAATCCATAAT
28935051 CCCTAATCCATAAT
1 CCCTAATCCATAAT
* *
28935065 CCCTAAACCCATACT
1 CCCT-AATCCATAAT
28935080 CCCTAA
1 CCCTAA
28935086 ATCTTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAATCCATAAT
Found at i:28935082 original size:15 final size:15
Alignment explanation
Indices: 28935044--28935086 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
28935034 AACCCCTAAT
*
28935044 CCATAATCCCT-AAT
1 CCATAATCCCTAAAC
28935058 CCATAATCCCTAAAC
1 CCATAATCCCTAAAC
*
28935073 CCATACTCCCTAAA
1 CCATAATCCCTAAA
28935087 TCTTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (15 bp):
CCATAATCCCTAAAC
Found at i:28935117 original size:298 final size:296
Alignment explanation
Indices: 28934579--28935188 Score: 865
Period size: 298 Copynumber: 2.0 Consensus size: 296
28934569 AATTATACAT
28934579 TTTTACAATTATATAAGAAAATATTTAAAATATAAATAAAAAATTAATCTAAACCCAAAACCCTA
1 TTTTACAATTATATAAGAAAATATTTAAAATATAAATAAAAAATTAATCTAAACCCAAAACCCTA
* *
28934644 ACTCGACCCTTGAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCTAAACTCCTAA
66 ACTCGACCCCTGAAACCCTAAATCCCTAACTCTTAACCACTAACACCTAACCCCTAAACTCCTAA
* *
28934709 CCCCTAAACCTTAAATCCTAGCCAACCCTTAATTAAACCATAATCCCTAATCTATAATCCCTAAA
131 CCCCTAAACCTTAAATCC-A-CCAACCCCTAATT--ACCATAATCCCTAATCCATAATCCCTAAA
* ** *
28934774 TCCATACTCCCTAAACCTTAAAATATAAACTCCTAAATTGGCCTTAAATCTTAAATTAATCATAT
192 CCCATACTCCCTAAACCTTAAAATATAAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATAT
*
28934839 ACCCTAAACTAAAAACCCTAAACAAATTTATTATTATCTC
257 ACCCTAAACCAAAAACCCTAAACAAATTTATTATTATCTC
* *
28934879 TTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTAATCTAAACCCAAAAT
1 TTTTACAATTATATAAGAAAATATTTAAAATATAAA-T--AAAA-AATTAATCTAAACCCAAAAC
* ** * * *
28934944 CCTAACTCGACCCCT-AAATCCCTAACT-TTTAACTCTTAGCACATCTAACCCCTAAACCTCT-A
62 CCTAACTCGACCCCTGAAA-CCCTAAATCCCTAACTCTTAAC-CA-CTAACACCT-AACCCCTAA
*
28935006 ACCCTCTAACCCCTAAACCTTAAAT-C-CCAACCCCTAA-T-CCATAATCCCTAATCCATAATCC
123 ACTC-CTAACCCCTAAACCTTAAATCCACCAACCCCTAATTACCATAATCCCTAATCCATAATCC
* *
28935067 CTAAACCCATACTCCCTAAATCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAAT
187 CTAAACCCATACTCCCTAAACCTTAAAATATAAACTCCTAAACCGGCCTTAAATCTTAAATAAAT
*
28935132 CATATACCCTAAACCAAAAACTCTAAACAAATTTATTATTATCTC
252 CATATACCCTAAACCAAAAACCCTAAACAAATTTATTATTATCTC
28935177 TTTTACAATTAT
1 TTTTACAATTAT
28935189 TTTAAATAAT
Statistics
Matches: 280, Mismatches: 21, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
298 136 0.49
300 35 0.12
301 2 0.01
302 10 0.04
303 17 0.06
304 42 0.15
305 12 0.04
306 26 0.09
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (296 bp):
TTTTACAATTATATAAGAAAATATTTAAAATATAAATAAAAAATTAATCTAAACCCAAAACCCTA
ACTCGACCCCTGAAACCCTAAATCCCTAACTCTTAACCACTAACACCTAACCCCTAAACTCCTAA
CCCCTAAACCTTAAATCCACCAACCCCTAATTACCATAATCCCTAATCCATAATCCCTAAACCCA
TACTCCCTAAACCTTAAAATATAAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATATACCC
TAAACCAAAAACCCTAAACAAATTTATTATTATCTC
Found at i:28935396 original size:41 final size:41
Alignment explanation
Indices: 28935336--28935414 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
28935326 TAAAATATTT
* *
28935336 TTAGCGACGCTTTTCCAAAAACGCCGCTAAAGCTCCCAACA
1 TTAGCGACGCTTTTCCAAAAACGCCGCCAAAGCCCCCAACA
*
28935377 TTAGCGACGCTTTTTCAAAAACGCCGCCAAAGCCCCCA
1 TTAGCGACGCTTTTCCAAAAACGCCGCCAAAGCCCCCA
28935415 GATTTTTGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.19
Consensus pattern (41 bp):
TTAGCGACGCTTTTCCAAAAACGCCGCCAAAGCCCCCAACA
Found at i:28935625 original size:114 final size:114
Alignment explanation
Indices: 28935425--28935845 Score: 605
Period size: 114 Copynumber: 3.7 Consensus size: 114
28935415 GATTTTTGGC
* * * *
28935425 CGCTAAATCCCCGAAAGCTCAGAAAATGGTGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTA
1 CGCTAAATCCCCGAAAGCTCACAAAACGGAGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTC
* * **
28935490 AAAAACGCCGTTAAAGCCCTGAGCGTTAGCGGCATTTTCTTAAAAACGT
66 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
* ** *
28935539 CGCTAAATCCCTCGAAAGCTCAGAAAACGGAGTCGTTATGCTTA-GTTTTTTTGTGGCGCTTTCT
1 CGCTAAATCCC-CGAAAGCTCACAAAACGGAGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
28935603 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
65 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
* * * *
28935653 CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGTTTTCTC
1 CGCTAAATCCCCGAAAGCTCACAAAACGGAGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTC
* * *
28935718 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGGTTTCCTAAAAACGC
66 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
* * *
28935767 CGTTAAATCCCCGAAAGCTCACAAAAC-GACGTCGTTGGGCTTA-TTTTTTTTGCGGCACTTTCT
1 CGCTAAATCCCCGAAAGCTCACAAAACGGA-GTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
28935830 CAAAAACGCCGCTAAA
65 CAAAAACGCCGCTAAA
28935846 TCCCCGAAAG
Statistics
Matches: 279, Mismatches: 25, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
113 61 0.22
114 190 0.68
115 28 0.10
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (114 bp):
CGCTAAATCCCCGAAAGCTCACAAAACGGAGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTC
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
Found at i:28935839 original size:72 final size:73
Alignment explanation
Indices: 28935759--28935918 Score: 225
Period size: 72 Copynumber: 2.2 Consensus size: 73
28935749 GCGGTTTCCT
* *
28935759 AAAAACGCCGTTAAATCCCCGAAAGCTCACAAAA-CGACGTCGTTGGGCTTAT-TTTTTTTGCGG
1 AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAATCG-CGTCGTTGGGCTTATGTTTTTTTGCGA
28935822 CACTTTCTC
65 CACTTTCTC
* * *
28935831 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATTGTGTCGTTGGGCTTATGTTTTTTTGCGAC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAATCGCGTCGTTGGGCTTATGTTTTTTTGCGAC
**
28935896 GTTTTCTC
66 ACTTTCTC
*
28935904 AAAAACGCCACTAAA
1 AAAAACGCCGCTAAA
28935919 GCACTGAGCA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
72 46 0.59
73 32 0.41
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (73 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAATCGCGTCGTTGGGCTTATGTTTTTTTGCGAC
ACTTTCTC
Found at i:28935878 original size:186 final size:186
Alignment explanation
Indices: 28935632--28936096 Score: 657
Period size: 186 Copynumber: 2.5 Consensus size: 186
28935622 CTGAGCATTA
* * *
28935632 GCGGCGCTTTCTTAAAAACGTCGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTAT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAT
* * *
28935697 GTTTTTTTGCGGCGTTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGGTTTCCTAAA
66 GTTTTTTTGCGGCGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGCGGCGCTTTCCTAAA
** * *
28935762 AACGCCGTTAAATCCCCGAAAGCTCACAAAAC-GACGTCGTTGGGCTTAT-TTTTTTT
131 AACGCCGCAAAATCCCCAAAAGCTCACAAAACAG-CAT-GTTGGGCTTATGTTTTTTT
* ** *
28935818 GCGGCACTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATTGTGTCGTTGGGCTTAT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAT
* * *
28935883 GTTTTTTTGCGACGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGTGGCGCTTTCTTAAA
66 GTTTTTTTGCGGCGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGCGGCGCTTTCCTAAA
* *
28935948 AACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCATGTTGGGCTTATGTTTTTTT
131 AACGCCGCAAAATCCCCAAAAGCTCACAAAACAGCATGTTGGGCTTATGTTTTTTT
** *
28936004 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCTTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAT
* * **
28936068 GGTTTTTTGCGGCGCTTTCTGGAAAACGC
66 GTTTTTTTGCGGCGTTTTCTCAAAAACGC
28936097 TGCGAAAAAT
Statistics
Matches: 247, Mismatches: 30, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
185 35 0.14
186 211 0.85
187 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (186 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAT
GTTTTTTTGCGGCGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGCGGCGCTTTCCTAAA
AACGCCGCAAAATCCCCAAAAGCTCACAAAACAGCATGTTGGGCTTATGTTTTTTT
Found at i:28936031 original size:113 final size:114
Alignment explanation
Indices: 28935824--28936031 Score: 310
Period size: 113 Copynumber: 1.8 Consensus size: 114
28935814 TTTTGCGGCA
* * ** **
28935824 CTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATTGTGTCGTTGGGCTTATGTTTTT
1 CTTTCTCAAAAACGCCGCAAAATCCCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTATGTTTTT
*
28935889 TTGCGACGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGTGGCG
66 TTGCGACGCTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGTGGCG
* *
28935938 CTTTCTTAAAAACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCAT-GTTGGGCTTATGTTTTT
1 CTTTCTCAAAAACGCCGCAAAATCCCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTATGTTTTT
* *
28936002 TTGCGGCGCTTTCTCAAAAACGCCGCTAAA
66 TTGCGACGCTTTCTCAAAAACGCCACTAAA
28936032 TCCTTGAAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
113 44 0.53
114 39 0.47
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (114 bp):
CTTTCTCAAAAACGCCGCAAAATCCCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTATGTTTTT
TTGCGACGCTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGTGGCG
Found at i:28936051 original size:72 final size:72
Alignment explanation
Indices: 28935934--28936096 Score: 213
Period size: 72 Copynumber: 2.3 Consensus size: 72
28935924 GAGCATTAGT
* *
28935934 GGCGCTTTCTTAAAAACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCAT-GTTGGGCTTATGT
1 GGCGCTTTCTCAAAAACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTA-GG
28935998 TTTTTTGC
65 TTTTTTGC
* ** * *
28936006 GGCGCTTTCTCAAAAACGCCGCTAAATC-CTTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
1 GGCGCTTTCTCAAAAACGCCGCAAAATCTC-CAAAAGCTCAGAAAACAGCATCGTTGGGCTTAGG
28936070 TTTTTTGC
65 TTTTTTGC
**
28936078 GGCGCTTTCTGGAAAACGC
1 GGCGCTTTCTCAAAAACGC
28936097 TGCGAAAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
71 1 0.01
72 69 0.86
73 10 0.12
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (72 bp):
GGCGCTTTCTCAAAAACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTAGGT
TTTTTGC
Found at i:28937872 original size:4 final size:4
Alignment explanation
Indices: 28937856--28937897 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
28937846 CAGTTCGCTT
28937856 TGTC TGT- TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
28937898 TTGTTTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.00, C:0.21, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:28938388 original size:16 final size:18
Alignment explanation
Indices: 28938357--28938395 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
28938347 GATTATGTGA
28938357 TTGTGTCAACATTTATGC
1 TTGTGTCAACATTTATGC
*
28938375 TTGTG-CAA-ATTTATGT
1 TTGTGTCAACATTTATGC
28938391 TTGTG
1 TTGTG
28938396 GAGAATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (18 bp):
TTGTGTCAACATTTATGC
Found at i:28940544 original size:26 final size:26
Alignment explanation
Indices: 28940515--28940566 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
28940505 TTTAGTTTCC
**
28940515 TTAATTATAGTTTCTTTTTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
*
28940541 TTAATTTTAGTTTCTTAGTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
28940567 AATAAAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.52
Consensus pattern (26 bp):
TTAATTATAGTTTCTTAGTCTACAAG
Found at i:28949035 original size:15 final size:14
Alignment explanation
Indices: 28949008--28949034 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28948998 TTTGACTATC
28949008 AACTTTTTAAAAAT
1 AACTTTTTAAAAAT
28949022 AACTTTTTAAAAA
1 AACTTTTTAAAAA
28949035 AAAGTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AACTTTTTAAAAAT
Found at i:28957123 original size:8 final size:8
Alignment explanation
Indices: 28957110--28957136 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
28957100 TTAACTAGTT
28957110 TAATTAAC
1 TAATTAAC
28957118 TAATTAAC
1 TAATTAAC
28957126 TAATTAAC
1 TAATTAAC
28957134 TAA
1 TAA
28957137 CTAGACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
TAATTAAC
Found at i:28962098 original size:13 final size:13
Alignment explanation
Indices: 28962069--28962145 Score: 73
Period size: 13 Copynumber: 5.9 Consensus size: 13
28962059 CAAGTATGGA
**
28962069 GCTAAGTGATATG
1 GCTAAGTGATACC
*
28962082 GCTAAGTGGTACC
1 GCTAAGTGATACC
* * *
28962095 GCTAAGGGGTGCC
1 GCTAAGTGATACC
*
28962108 ACTAAGTGATACC
1 GCTAAGTGATACC
*
28962121 GCTAAGTGACACC
1 GCTAAGTGATACC
*
28962134 GCTAAGTAATAC
1 GCTAAGTGATAC
28962146 TGCGAAATGG
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (13 bp):
GCTAAGTGATACC
Found at i:28969205 original size:23 final size:23
Alignment explanation
Indices: 28969199--28969290 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 23
28969189 TTTATAATAC
28969199 TATTTTTTAAAATTTTAAATATA
1 TATTTTTTAAAATTTTAAATATA
* * *
28969222 TATTTTTAAAATTATTTTTAAAAATT
1 TATTTTTTAAA--A-TTTTAAATATA
*
28969248 TAATTTTTTTTAAATTTTAAATATA
1 T-A-TTTTTTAAAATTTTAAATATA
* *
28969273 -ATTTTTTAATATTATAAA
1 TATTTTTTAAAATTTTAAA
28969291 ACATTTAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
22 14 0.26
23 11 0.20
25 10 0.19
26 11 0.20
27 1 0.02
28 7 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTTTTTAAAATTTTAAATATA
Found at i:28969219 original size:22 final size:23
Alignment explanation
Indices: 28969179--28969234 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 23
28969169 GAAATGTACA
*
28969179 TTTTAAATGTTTTATAATACTAT-T
1 TTTTAAA-ATTTTATAATA-TATAT
28969203 TTTTAAAATTTTA-AATATATAT
1 TTTTAAAATTTTATAATATATAT
28969225 TTTTAAAATT
1 TTTTAAAATT
28969235 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 3 0.10
22 15 0.50
23 5 0.17
24 7 0.23
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAAAATTTTATAATATATAT
Found at i:28969239 original size:12 final size:13
Alignment explanation
Indices: 28969211--28969244 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
28969201 TTTTTTAAAA
28969211 TTTTAAATATATAT
1 TTTTAAA-ATATAT
28969225 TTTTAAAAT-TAT
1 TTTTAAAATATAT
28969237 TTTTAAAA
1 TTTTAAAA
28969245 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
13 2 0.10
14 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAAATATAT
Found at i:28975433 original size:21 final size:21
Alignment explanation
Indices: 28975407--28975460 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
28975397 TGACCAGTTA
28975407 TAATATATATTTTTAATTTTC
1 TAATATATATTTTTAATTTTC
* * *
28975428 TAATATAAATTTTTACTTTTT
1 TAATATATATTTTTAATTTTC
28975449 TAATATATATTT
1 TAATATATATTT
28975461 AAAAAAAGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TAATATATATTTTTAATTTTC
Found at i:28975499 original size:18 final size:19
Alignment explanation
Indices: 28975476--28975519 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
28975466 AAGCCATAAT
28975476 TTTTTTAACAAATAAAT-A
1 TTTTTTAACAAATAAATCA
*
28975494 TTTTTTAATAAATAAATCA
1 TTTTTTAACAAATAAATCA
28975513 TTTTTTA
1 TTTTTTA
28975520 TTTTTTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTTTAACAAATAAATCA
Found at i:28975555 original size:24 final size:23
Alignment explanation
Indices: 28975502--28975557 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
28975492 TATTTTTTAA
* * *
28975502 TAAATAAATCATTTTTTATTTTT
1 TAAATAAATCAATTTTCACTTTT
*
28975525 TCCAATAAACTCAATTTTCACTTTT
1 T-AAATAAA-TCAATTTTCACTTTT
28975550 TAAATAAA
1 TAAATAAA
28975558 ATATTATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 12 0.46
25 13 0.50
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATAAATCAATTTTCACTTTT
Found at i:28975640 original size:15 final size:15
Alignment explanation
Indices: 28975615--28975655 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
28975605 ATCTTTAAAA
28975615 ATAATTTTAAAAAATC
1 ATAA-TTTAAAAAATC
*
28975631 ATAATTTAAAAAATT
1 ATAATTTAAAAAATC
28975646 AT-ATTTAAAA
1 ATAATTTAAAA
28975656 TTAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.33
15 12 0.50
16 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATTTAAAAAATC
Found at i:28975677 original size:22 final size:20
Alignment explanation
Indices: 28975636--28975677 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
28975626 AAATCATAAT
28975636 TTAAAAAATTATATTTAAAA
1 TTAAAAAATTATATTTAAAA
*
28975656 TTAAATAAATATATTTTTAAAA
1 TTAAA-AAAT-TATATTTAAAA
28975678 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAAAAATTATATTTAAAA
Found at i:28975718 original size:21 final size:21
Alignment explanation
Indices: 28975672--28975713 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
28975662 AAATATATTT
*
28975672 TTAAAAATTTTAAAATATACA
1 TTAAAAATTTTAAAAAATACA
28975693 TTAAAAATATTATAAAAAATA
1 TTAAAAAT-TT-TAAAAAATA
28975714 ATAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 2 0.11
23 8 0.44
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAAAATTTTAAAAAATACA
Found at i:28975824 original size:15 final size:14
Alignment explanation
Indices: 28975804--28975862 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 14
28975794 TAAAACCAAT
28975804 AATAAAAAATAAATA
1 AATAAAAAA-AAATA
28975819 AATAAAAGAAAAATA
1 AATAAAA-AAAAATA
28975834 AA-AAACTTAAAAAATA
1 AATAAA---AAAAAATA
28975850 AATAAAGAAAAAA
1 AATAAA-AAAAAA
28975863 CTTAAAAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 3 0.08
15 20 0.53
16 11 0.29
17 4 0.11
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (14 bp):
AATAAAAAAAAATA
Found at i:28975844 original size:24 final size:22
Alignment explanation
Indices: 28975817--28975878 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 22
28975807 AAAAAATAAA
28975817 TAAATAAAAGAAAAATAAAAAACT
1 TAAA-AAAA-AAAAATAAAAAACT
*
28975841 TAAAAAATAAATAAAGAAAAAACT
1 TAAAAAA-AAA-AAATAAAAAACT
28975865 TAAAAAGAAAAAAA
1 TAAAAA-AAAAAAA
28975879 ATGAAAAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
23 8 0.24
24 25 0.74
25 1 0.03
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (22 bp):
TAAAAAAAAAAAATAAAAAACT
Found at i:28975885 original size:24 final size:24
Alignment explanation
Indices: 28975827--28975886 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
28975817 TAAATAAAAG
*
28975827 AAAAATAAAAAACTTAAAAAATAA
1 AAAAATGAAAAACTTAAAAAATAA
*
28975851 ATAAA-GAAAAAACTTAAAAAGA-AA
1 AAAAATG-AAAAACTTAAAAA-ATAA
28975875 AAAAATGAAAAA
1 AAAAATGAAAAA
28975887 GGACAAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 28 0.93
25 2 0.07
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.13
Consensus pattern (24 bp):
AAAAATGAAAAACTTAAAAAATAA
Found at i:28975887 original size:16 final size:15
Alignment explanation
Indices: 28975801--28975878 Score: 52
Period size: 15 Copynumber: 5.1 Consensus size: 15
28975791 TTATAAAACC
* *
28975801 AATAATAAA-AAATA
1 AATAAAAAAGAAAAA
*
28975815 AATAAATAAA-AGAAA
1 AATAAA-AAAGAAAAA
**
28975830 AATAAAAAACTTAAAA
1 AATAAAAAA-GAAAAA
28975846 AATAAATAAAGAAAAA
1 AATAAA-AAAGAAAAA
* *
28975862 ACTTAAAAAGAAAAA
1 AATAAAAAAGAAAAA
28975877 AA
1 AA
28975879 ATGAAAAAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
14 8 0.16
15 22 0.44
16 17 0.34
17 3 0.06
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (15 bp):
AATAAAAAAGAAAAA
Found at i:28977469 original size:31 final size:31
Alignment explanation
Indices: 28977427--28977497 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
28977417 TTAAAATCTT
* * *
28977427 TCTTAACAATAATTCTAAAAAAATAAAAAAA
1 TCTTAAAAATAAATATAAAAAAATAAAAAAA
* *
28977458 TCTTAAAAATAAATATAAAATAATAAAAATA
1 TCTTAAAAATAAATATAAAAAAATAAAAAAA
*
28977489 TATTAAAAA
1 TCTTAAAAA
28977498 GTATGTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (31 bp):
TCTTAAAAATAAATATAAAAAAATAAAAAAA
Found at i:28983758 original size:17 final size:17
Alignment explanation
Indices: 28983736--28983799 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
28983726 AATCTTAGAG
28983736 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
28983753 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
28983772 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
28983789 TTTTAATTGTA
1 TTCTAATTGTA
28983800 GCCCTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.55
18 4 0.11
19 11 0.29
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:28983775 original size:36 final size:36
Alignment explanation
Indices: 28983728--28983798 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
28983718 GATTATGTAA
28983728 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
*
28983764 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
28983799 AGCCCTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:28983777 original size:19 final size:19
Alignment explanation
Indices: 28983727--28983783 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
28983717 TGATTATGTA
28983727 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
28983746 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
28983763 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
28983782 AT
1 AT
28983784 ACAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:28984080 original size:48 final size:48
Alignment explanation
Indices: 28984003--28984098 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
28983993 TGAGGGAATT
* *
28984003 CTGTTGAATCCTTTATCGAGCGAGATTAGGCTGACTTAGGTGTTTTTA
1 CTGTTGAATCCATTATCGAGCGAGATTAGGCTGACTTAGGCGTTTTTA
* *
28984051 CTGTTGAATCCATTATC-ATTGCGTG-TTAGGTTGACTTAGGCGTTTTTA
1 CTGTTGAATCCATTATCGA--GCGAGATTAGGCTGACTTAGGCGTTTTTA
28984099 AGCAAAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 1 0.02
48 37 0.88
49 4 0.10
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCCATTATCGAGCGAGATTAGGCTGACTTAGGCGTTTTTA
Found at i:28985102 original size:6 final size:6
Alignment explanation
Indices: 28985091--28985119 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28985081 ATAGTTCCCT
28985091 CACCCC CACCCC CA-CCC CACCCC CACCCC
1 CACCCC CACCCC CACCCC CACCCC CACCCC
28985120 ACCGCAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCCC
Found at i:28985110 original size:11 final size:11
Alignment explanation
Indices: 28985094--28985122 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
28985084 GTTCCCTCAC
28985094 CCCCACCCCCA
1 CCCCACCCCCA
28985105 CCCCACCCCCA
1 CCCCACCCCCA
28985116 CCCCACC
1 CCCCACC
28985123 GCAAATACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (11 bp):
CCCCACCCCCA
Found at i:28988412 original size:20 final size:20
Alignment explanation
Indices: 28988387--28988426 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28988377 GATTAATTTT
28988387 TTTTATGAACTTTTTAAAAA
1 TTTTATGAACTTTTTAAAAA
** *
28988407 TTTTATTTATTTTTTAAAAA
1 TTTTATGAACTTTTTAAAAA
28988427 AAGTTTGAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATGAACTTTTTAAAAA
Found at i:28988727 original size:25 final size:25
Alignment explanation
Indices: 28988693--28988743 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28988683 AGACCAGCGA
28988693 ATCGTTATTGACTATTAAAGGACCT
1 ATCGTTATTGACTATTAAAGGACCT
28988718 ATCGTTATTGACTATTAAAGGACCT
1 ATCGTTATTGACTATTAAAGGACCT
28988743 A
1 A
28988744 AATTGATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (25 bp):
ATCGTTATTGACTATTAAAGGACCT
Found at i:28988752 original size:25 final size:25
Alignment explanation
Indices: 28988697--28988752 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
28988687 CAGCGAATCG
**
28988697 TTATTGACTATTAAAGGACCTATCG
1 TTATTGACTATTAAAGGACCTATAA
28988722 TTATTGACTATTAAAGGACCTA-AA
1 TTATTGACTATTAAAGGACCTATAA
28988746 TTGATTG
1 TT-ATTG
28988753 GTTAACAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (25 bp):
TTATTGACTATTAAAGGACCTATAA
Found at i:28993966 original size:39 final size:40
Alignment explanation
Indices: 28993868--28994089 Score: 249
Period size: 40 Copynumber: 5.6 Consensus size: 40
28993858 AATGATGTCT
* * *
28993868 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCC
* *
28993908 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
28993948 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* * *
28993987 GGGTTAAGTCCCGGAGGCATTTGTGCGAGTTACTAAATT-T
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AATTCC
* *
28994027 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
*
28994067 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
28994090 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 35 0.22
40 107 0.68
41 13 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:28994069 original size:80 final size:80
Alignment explanation
Indices: 28993865--28994089 Score: 280
Period size: 80 Copynumber: 2.8 Consensus size: 80
28993855 TTGAATGATG
* * * * *
28993865 TCTGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCTGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
28993928 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAT
* * *
28993945 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGGAGGCATT
1 TCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
28994008 TGTGCGAGTTACTAAAT
65 TGTGCGAGATACT-AAT
* *
28994025 T-TGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
28994089 G
66 G
28994090 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 2 0.02
79 52 0.42
80 69 0.55
81 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAT
Found at i:29014384 original size:11 final size:11
Alignment explanation
Indices: 29014368--29014414 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
29014358 GACCACGGAA
29014368 GAAAGGAAAAT
1 GAAAGGAAAAT
*
29014379 GAAAGGAAACT
1 GAAAGGAAAAT
*
29014390 AGAAAGGAAAAA
1 -GAAAGGAAAAT
*
29014402 GAGA-GAAAAT
1 GAAAGGAAAAT
29014412 GAA
1 GAA
29014415 TGAGAGAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
10 7 0.24
11 13 0.45
12 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.28, T:0.06
Consensus pattern (11 bp):
GAAAGGAAAAT
Found at i:29014396 original size:12 final size:12
Alignment explanation
Indices: 29014367--29014400 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
29014357 AGACCACGGA
29014367 AGAAAGGAAAAT
1 AGAAAGGAAAAT
*
29014379 -GAAAGGAAACT
1 AGAAAGGAAAAT
29014390 AGAAAGGAAAA
1 AGAAAGGAAAA
29014401 AGAGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.65, C:0.03, G:0.26, T:0.06
Consensus pattern (12 bp):
AGAAAGGAAAAT
Done.