Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003128.1 Hibiscus syriacus cultivar Beakdansim tig00006555_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57290
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1374 original size:15 final size:16
Alignment explanation
Indices: 1340--1379 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1330 GGGAAATGAT
* *
1340 GAAGAAAGAAGGATAA
1 GAAGAATGAAGGAAAA
1356 GAAGAATGAA-GAAAA
1 GAAGAATGAAGGAAAA
1371 GAAGAATGA
1 GAAGAATGA
1380 GGTTGACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (16 bp):
GAAGAATGAAGGAAAA
Found at i:2428 original size:3 final size:3
Alignment explanation
Indices: 2420--2488 Score: 86
Period size: 3 Copynumber: 22.3 Consensus size: 3
2410 TTTTCCGGGA
2420 TAT TAT TAT TAT TAT TAT TA- TAT TATT TAT ATAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT -TAT TAT TAT TAT TAT
* *
2466 TAT TAA TAT TATT TAT TTT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT T
2489 TTGTAGCTCC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.03
3 47 0.81
4 9 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11840 original size:125 final size:125
Alignment explanation
Indices: 11618--12004 Score: 578
Period size: 125 Copynumber: 3.1 Consensus size: 125
11608 AAGTTAGGAT
* * *
11618 ATGTTGGAGCACAACTGAACCCACATCATGTTGAGATGA-AAATATTCAGACCAAGGAGGCATGA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAA-ATTCAGACCAAGGAGGCATAA
* * *
11682 AGAATGAGCCTTACAATTTGGGGTGATGGGGCATTTTAAAGGCCCGTACCAGTATAAGACA
65 AGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
*
11743 ATGTTGGGGCACGACTGAGCCCACATCATGTTGAGATGACAAAATTCAGACCAAGGAGGCATAAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAAATTCAGACCAAGGAGGCATAAA
11808 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
* * * * * * * **
11868 ATATTGGGGCACGATTGAACCCATATCATGTTGATATGACAAGATTCAGAACAAGAAGGCATTGA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAAATTCAGACCAAGGAGGCATAAA
* * *
11933 GAATGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCTCGTACCAATATAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
*
11993 ATGTTGTGGCAC
1 ATGTTGGGGCAC
12005 TAGTGAATGT
Statistics
Matches: 239, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
125 236 0.99
126 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (125 bp):
ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAAATTCAGACCAAGGAGGCATAAA
GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
Found at i:13543 original size:215 final size:215
Alignment explanation
Indices: 13172--14107 Score: 964
Period size: 215 Copynumber: 4.3 Consensus size: 215
13162 CCAAAATTTA
* * *
13172 TAAGTCCTTCGGGCCATCAGTTAGTCTTTCGAGTATGATGCTTAAATCCTTAGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAA
* * *
13237 GCCTTTTGAGCAAGATGAAAAGTCCTTCGGGCCATCCATAAGACCTTCAGGTAGGATGTTTTCA-
66 GACTTTTGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCAGGTAGGATGTTTTCAC
13301 AAGGAATTTGAAAATGAGAAAATGATGTTTTAA-AGAGACGAAATTTTTGAAAACTAAGAATGCA
131 AA-GAATTTGAAAATGAGAAAATGATGTTTTAAGA-AGACGAAATTTTTGAAAACTAAGAATGCA
13365 ATTTCCAAAATTTCACACTTAG
194 ATTTCCAAAATTTCACACTTAG
* *
13387 TAAGTCCTTCGGGCCATCAGTAAGTCATTCGAGCATGATGATTAAATCTTTAGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAA
*
13452 GACTTTTGAGCAAGATGATAAGTCATTCGGACCATCCATAAGACCTTCAGGTAGGATGTTTTCA-
66 GACTTTTGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCAGGTAGGATGTTTTCAC
* * * *
13516 AAGGAATTTGAAAATGAGAAAATGATGTTTTAAGAAGATGAAAATTTTGAAAACTATGAATACAA
131 AA-GAATTTGAAAATGAGAAAATGATGTTTTAAGAAGACGAAATTTTTGAAAACTAAGAATGCAA
13581 TTTCCAAAATTTCACACTTAG
195 TTTCCAAAATTTCACACTTAG
* * * * * * * *
13602 TAAGTCCTTTGGGCGATCAATAAGTCTTTTGAACATGATGCTTAAATCCTTCGGGCCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAA
* * * * ** * *
13667 GCCTTTTGAGCAATATGATAAGTCCTTTGGGCCATCCATAAGACCTTTGGGCATGATGTTTTCAC
66 GACTTTTGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCAGGTAGGATGTTTTCAC
* * * * *
13732 AAG-TTTATCGAAAA-AAGAGAAA-GATTTCTCATTAA-AA-TCTGAAGA--TTTGAAAAGTAAG
131 AAGAATT-T-GAAAATGAGA-AAATGATGT-T--TTAAGAAGAC-GAA-ATTTTTGAAAACTAAG
* * * * *
13790 AAAG-ATTTCTTACCTAGTAAATTATTTCCAAAATTGG
188 AATGCA-AT-TT-CC----AAA--ATTT-CACACTTAG
* * * *
13827 TAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAACCCTTCGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAA
* * * *
13892 -ACCTTTCGAGCAAGGTGATAAGTCCTTC-TAGCCATTCATAAGACCTTCAGGTAGGATGTTTTC
66 GA-CTTTTGAGCAAGATGATAAGTCCTTCGGA-CCATCCATAAGACCTTCAGGTAGGATGTTTTC
* * ** * * * * *
13955 ACAATAAGTTGAAAAATGAGAAAGCGATATTTTAAGAAAATC-AAATATTTGAAAACTAAAAAGG
129 ACAAGAATTTG-AAAATGAGAAAATGATGTTTTAAGAAGA-CGAAATTTTTGAAAACTAAGAATG
** * * *
14019 TGATTTCTAAATTTTCGCACTTAG
192 CAATTTCCAAAATTTCACACTTAG
* * * *
14043 TAAGTCCTTCGGTCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAA
14108 CTTCACGAAA
Statistics
Matches: 599, Mismatches: 90, Indels: 63
0.80 0.12 0.08
Matches are distributed among these distances:
214 2 0.00
215 320 0.53
216 90 0.15
217 10 0.02
218 7 0.01
219 3 0.01
222 3 0.01
223 6 0.01
224 11 0.02
225 138 0.23
226 9 0.02
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (215 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAA
GACTTTTGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCAGGTAGGATGTTTTCAC
AAGAATTTGAAAATGAGAAAATGATGTTTTAAGAAGACGAAATTTTTGAAAACTAAGAATGCAAT
TTCCAAAATTTCACACTTAG
Found at i:13714 original size:42 final size:42
Alignment explanation
Indices: 13602--13714 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
13592 TCACACTTAG
* * *
13602 TAAGTCCTTTGGGCGATCAATAAGTCTTTTGAACATGATGCT
1 TAAGTCCTTTGGGCCATCAATAAGCCTTTTGAACATGATGCA
* * ** *
13644 TAAATCCTTCGGGCCATCTGTAAGCCTTTTGAGCAAT-ATG-A
1 TAAGTCCTTTGGGCCATCAATAAGCCTTTTGAAC-ATGATGCA
*
13685 TAAGTCCTTTGGGCCATCCATAAGACCTTT
1 TAAGTCCTTTGGGCCATCAATAAG-CCTTT
13715 GGGCATGATG
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
41 20 0.35
42 35 0.61
43 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (42 bp):
TAAGTCCTTTGGGCCATCAATAAGCCTTTTGAACATGATGCA
Found at i:14173 original size:22 final size:21
Alignment explanation
Indices: 14148--14213 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
14138 CAGTAAGTTT
14148 TTCGAGCATGATGATGAAATCA
1 TTCGAGCATGATGAT-AAATCA
* * * *
14170 TTCGGGACATCA-G-TAAGTCT
1 TTCGAG-CATGATGATAAATCA
14190 TTCGAGCATGATGATTAAATCA
1 TTCGAGCATGATGA-TAAATCA
14212 TT
1 TT
14214 TGGGTCATCT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
19 4 0.12
20 10 0.31
21 1 0.03
22 13 0.41
23 4 0.12
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (21 bp):
TTCGAGCATGATGATAAATCA
Found at i:14194 original size:42 final size:42
Alignment explanation
Indices: 14135--14222 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
14125 GAAGCAAATC
*
14135 CATCAGTAAGTTTTTCGAGCATGATGATGAAATCATTCGGGA
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGA
* * *
14177 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGA
14219 CATC
1 CATC
14223 TATAAGCGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGA
Found at i:14239 original size:42 final size:42
Alignment explanation
Indices: 14135--14246 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 42
14125 GAAGCAAATC
14135 CATCAGTAAGT-TTTTCGAGCATGATGATGAAATCATTCGGGA
1 CATCAGTAAGTCTTTT-GAGCATGATGATGAAATCATTCGGGA
* * * *
14177 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGT
1 CATCAGTAAGTCTTTTGAGCATGATGATGAAATCATTCGGGA
*
14219 CATCTA-TAAG-CGTTTTGAGCAAGATGAT
1 CATC-AGTAAGTC-TTTTGAGCATGATGAT
14247 AATTCCTTCG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 1 0.02
42 56 0.92
43 4 0.07
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (42 bp):
CATCAGTAAGTCTTTTGAGCATGATGATGAAATCATTCGGGA
Found at i:14303 original size:37 final size:37
Alignment explanation
Indices: 14262--14411 Score: 230
Period size: 37 Copynumber: 4.1 Consensus size: 37
14252 CTTCGGGCCG
14262 TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCA
1 TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCA
*
14299 TCTTAAGCCTTCACCAAAGAGTAGTGAAGC-AATCCA
1 TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCA
* *
14335 TTTTAAGCCTTCACCGAAGAGTAGTGAAGTAAATCCA
1 TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCA
** * *
14372 TCTTAAGCCTTCATGGAAGAGTGGTGAAGCAAATCAA
1 TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCA
14409 TCT
1 TCT
14412 CGAGTCTGAT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 33 0.32
37 69 0.68
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (37 bp):
TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCA
Found at i:14351 original size:73 final size:73
Alignment explanation
Indices: 14264--14403 Score: 235
Period size: 73 Copynumber: 1.9 Consensus size: 73
14254 TCGGGCCGTC
14264 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAGC
1 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAGC
14329 AATCCATT
66 AATCCATT
* *** *
14337 TTAAGCCTTCACCGAAGAGTAGTGAAGTAAATCCATCTTAAGCCTTCATGGAAGAGTGGTGAAGC
1 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAGC
14402 AA
66 AA
14404 ATCAATCTCG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (73 bp):
TTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAGC
AATCCATT
Found at i:14587 original size:3 final size:3
Alignment explanation
Indices: 14579--14651 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
14569 TTATCCGGGA
14579 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
14626 TAT TAT TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
14652 ATACTATTTA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18230 original size:20 final size:20
Alignment explanation
Indices: 18201--18251 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
18191 ACATACAAGA
*
18201 AGTATGGATACTGTAAGAAC
1 AGTATCGATACTGTAAGAAC
18221 AGTATCGATACTGTAAGAAC
1 AGTATCGATACTGTAAGAAC
*
18241 AATATCGATAC
1 AGTATCGATAC
18252 CTCATGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTGTAAGAAC
Found at i:18436 original size:20 final size:21
Alignment explanation
Indices: 18411--18450 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
18401 CTTTGTATAG
18411 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
18431 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
18451 CCCAACTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:18595 original size:20 final size:20
Alignment explanation
Indices: 18570--18616 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
18560 AACATCCCCA
18570 AACGGCTCCAAATAACTCCT
1 AACGGCTCCAAATAACTCCT
18590 AACGGCTCCAAATAACTCCT
1 AACGGCTCCAAATAACTCCT
18610 AACGGCT
1 AACGGCT
18617 ATAAACGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.19
Consensus pattern (20 bp):
AACGGCTCCAAATAACTCCT
Found at i:20437 original size:2 final size:2
Alignment explanation
Indices: 20430--20468 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20420 ACTCATTTGA
20430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20469 GTATCTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22919 original size:2 final size:2
Alignment explanation
Indices: 22912--22939 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22902 ATTTTATGTT
22912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22940 AGAGAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25157 original size:2 final size:2
Alignment explanation
Indices: 25150--25175 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25140 TTGAAACTGG
25150 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
25176 AGTGATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30683 original size:12 final size:12
Alignment explanation
Indices: 30629--30683 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
30619 ATCAAAATAT
30629 AATTCAGAACAG
1 AATTCAGAACAG
*
30641 -ATATCATAACAG
1 AAT-TCAGAACAG
* *
30653 AATCCAGATCAG
1 AATTCAGAACAG
*
30665 AAATCAGAACAG
1 AATTCAGAACAG
30677 AATTCAG
1 AATTCAG
30684 GTCATATATC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
11 2 0.06
12 29 0.88
13 2 0.06
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
AATTCAGAACAG
Found at i:30694 original size:24 final size:24
Alignment explanation
Indices: 30619--30706 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 24
30609 GAAATCAAAA
* * *
30619 ATCAAAATATAATTCAGAACAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
30643 ATCATAACAGAATCCAGATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
* * *
30667 ATCAGAACAGAATTCAGGTCATAT
1 ATCAAAACAGAATTCAGATCAGAT
*
30691 ATCAAAAAAGAATTCA
1 ATCAAAACAGAATTCA
30707 AGTCGAAAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:30718 original size:24 final size:24
Alignment explanation
Indices: 30665--30718 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
30655 TCCAGATCAG
* * *
30665 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAAAAAAGAATTCAAGTCAT
*
30689 ATATCAAAAAAGAATTCAAGTCGA-
1 AAATCAAAAAAGAATTCAAGTC-AT
30713 AAATCA
1 AAATCA
30719 GATAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (24 bp):
AAATCAAAAAAGAATTCAAGTCAT
Found at i:32360 original size:35 final size:33
Alignment explanation
Indices: 32320--32564 Score: 162
Period size: 34 Copynumber: 7.0 Consensus size: 33
32310 TTTAAAAAAG
32320 ACATTTT-AGAAATATATAATATATAATTTTTAAA
1 ACATTTTGA-AAATATAT-ATATATAATTTTTAAA
*
32354 ATCATTTTGAAAACT-TATATATATAGTTTTTGAAA
1 A-CATTTTGAAAA-TATATATATATAATTTTT-AAA
* *
32389 ACATTTTTGAAAACATATATATATTATAGTTTTGAAA
1 ACA-TTTTG-AAA-ATATATATA-TATAATTTTTAAA
* *
32426 ACATTTTTTTGAAAACATATATATTATATAGTTTTAAA
1 ACA---TTTTGAAAATATATATA-TATA-ATTTTTAAA
* * *
32464 ATCATTTTG-AAATTTATATA-ATATATAGTTGAAA
1 A-CATTTTGAAAATATATATATATA-AT-TTTTAAA
* *
32498 ACATTTTTGAAAATAT-T-TATAT-ATTATATAAG
1 ACA-TTTTGAAAATATATATATATAATT-TTTAAA
*
32530 ACATTTTGAAAATATATATAATATAGTTTTTAAA
1 ACATTTTGAAAATATATAT-ATATAATTTTTAAA
32564 A
1 A
32565 AATATTTTTG
Statistics
Matches: 170, Mismatches: 19, Indels: 44
0.73 0.08 0.19
Matches are distributed among these distances:
31 12 0.07
32 9 0.05
33 10 0.06
34 38 0.22
35 37 0.22
36 11 0.06
37 26 0.15
38 19 0.11
39 8 0.05
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (33 bp):
ACATTTTGAAAATATATATATATAATTTTTAAA
Found at i:32373 original size:37 final size:37
Alignment explanation
Indices: 32331--32554 Score: 165
Period size: 35 Copynumber: 6.3 Consensus size: 37
32321 CATTTTAGAA
*
32331 ATATATAATATATAATTTTTAAAATCA-TTTTGAAAAC
1 ATATATAATATATAATTTTGAAAA-CATTTTTGAAAAC
*
32368 -T-TAT-ATATATAGTTTTTGAAAACATTTTTGAAAAC
1 ATATATAATATATA-ATTTTGAAAACATTTTTGAAAAC
*
32403 ATATAT-ATATTATAGTTTTGAAAACATTTTTTTGAAAAC
1 ATATATAATA-TATAATTTTGAAAACA--TTTTTGAAAAC
* * *
32442 ATATATATTATATAGTTTT-AAAATCA-TTTTG-AAAT
1 ATATATAATATATAATTTTGAAAA-CATTTTTGAAAAC
* *
32477 TTATATAATATAT-A-GTTGAAAACATTTTTG-AAA-
1 ATATATAATATATAATTTTGAAAACATTTTTGAAAAC
* * * * *
32510 ATAT-TTATATATTA-TAT-AAGACA-TTTTGAAAAT
1 ATATATAATATATAATTTTGAAAACATTTTTGAAAAC
32543 ATATATAATATA
1 ATATATAATATA
32555 GTTTTTAAAA
Statistics
Matches: 157, Mismatches: 15, Indels: 33
0.77 0.07 0.16
Matches are distributed among these distances:
31 5 0.03
32 15 0.10
33 13 0.08
34 27 0.17
35 35 0.22
36 7 0.04
37 17 0.11
38 8 0.05
39 28 0.18
40 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATAATATATAATTTTGAAAACATTTTTGAAAAC
Found at i:32397 original size:12 final size:12
Alignment explanation
Indices: 32380--32404 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32370 ATATATATAG
32380 TTTTTGAAAACA
1 TTTTTGAAAACA
32392 TTTTTGAAAACA
1 TTTTTGAAAACA
32404 T
1 T
32405 ATATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:32574 original size:37 final size:36
Alignment explanation
Indices: 32297--32635 Score: 185
Period size: 36 Copynumber: 9.5 Consensus size: 36
32287 GTTTTTAAAC
* * *
32297 TATATAATATAGTTTTAAAAAAGACATTTT-AGAAATA
1 TATATAATATAGTTTTTAAAAATA-TTTTTGA-AAATA
*
32334 TATA-ATATATAATTTTT-AAAATCA-TTTTGAAAACT-
1 TATATA-ATATAGTTTTTAAAAAT-ATTTTTGAAAA-TA
* *
32369 TATAT-ATATAGTTTTTGAAAACATTTTTGAAAACATA
1 TATATAATATAGTTTTTAAAAATATTTTTG-AAA-ATA
* * *
32406 TATATATTATAGTTTTGAAAACATTTTTTTGAAAACATA
1 TATATAATATAGTTTTTAAAA-ATATTTTTG-AAA-ATA
* *
32445 TATATTATATAG-TTTT-AAAATCA-TTTTG-AAATT
1 TATATAATATAGTTTTTAAAAAT-ATTTTTGAAAATA
** * *
32478 TATATAATATA-TAGTTGAAAACATTTTTGAAAATA
1 TATATAATATAGTTTTTAAAAATATTTTTGAAAATA
* * *
32513 T-T-T-ATATA--TTATATAAGACA-TTTTGAAAATA
1 TATATAATATAGTTTTTA-AAAATATTTTTGAAAATA
* *
32544 TATATAATATAGTTTTTAAAAAATATTTTTG-AAGTT
1 TATATAATATAGTTTTT-AAAAATATTTTTGAAAATA
** *
32580 TATATTGTATATGTTTTTAAAAATGTTTTTGAAAATA
1 TATATAATATA-GTTTTTAAAAATATTTTTGAAAATA
32617 CGTATA-ATATATAGTTTTT
1 --TATATA-ATATAGTTTTT
32636 TTTTTTAAAA
Statistics
Matches: 235, Mismatches: 37, Indels: 59
0.71 0.11 0.18
Matches are distributed among these distances:
31 13 0.06
32 11 0.05
33 17 0.07
34 28 0.12
35 25 0.11
36 49 0.21
37 38 0.16
38 21 0.09
39 33 0.14
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (36 bp):
TATATAATATAGTTTTTAAAAATATTTTTGAAAATA
Found at i:32681 original size:23 final size:24
Alignment explanation
Indices: 32655--32700 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
32645 AAAAAAAGCA
32655 TTTTGAAAA-GTTATATATTATGT
1 TTTTGAAAATGTTATATATTATGT
*
32678 TTTTGAAAATTTTTATATATTAT
1 TTTTGAAAA-TGTTATATATTAT
32701 TATTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTGAAAATGTTATATATTATGT
Found at i:32703 original size:3 final size:3
Alignment explanation
Indices: 32690--32747 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
32680 TTGAAAATTT
32690 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32736 TTA TTA TTA TTA
1 TTA TTA TTA TTA
32748 GTTCCTATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:35869 original size:19 final size:19
Alignment explanation
Indices: 35845--35890 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
35835 ATTTAGACAT
35845 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
35864 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
35883 TTTACATT
1 TTTGCATT
35891 CACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:39550 original size:80 final size:81
Alignment explanation
Indices: 39283--40112 Score: 888
Period size: 80 Copynumber: 10.0 Consensus size: 81
39273 TAAACAAACT
* *
39283 ATTTGCATG-ATAACTTAAGTCGAGAAGGGTTATTTGCCGACCAAAGACCCCCGAGTTCGATTAC
1 ATTTGCA-GCATAACTTAAGTCGAGAAGGGTTA--T-CTGACCAAAGA-CCCTGAGTTCGATTAC
39347 ACTCAGCTTCGAGGGCACATC
61 ACTCAGCTTCGAGGGCACATC
* * *
39368 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACC-CTGAGTTCGATTACA
* *
39433 CTCAGC-TCCAAGGCACATC
62 CTCAGCTTCGAGGGCACATC
* * * *
39452 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAGGACCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTGAGTTCGATTACACTCA
39516 GCTTCGAGGGCACATC
66 GCTTCGAGGGCACATC
* * *
39532 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACC-CTGAGTTCGATTACA
* *
39597 CTCAGC-TCCAAGGCACATC
62 CTCAGCTTCGAGGGCACATC
* * * *
39616 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAGGACCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTGAGTTCGATTACACTCA
39680 GCTTCGAGGGCACATC
66 GCTTCGAGGGCACATC
* * *
39696 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACC-CTGAGTTCGATTACA
* *
39761 CTCAGC-TCCAAGGCACATC
62 CTCAGCTTCGAGGGCACATC
* * * *
39780 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAGGACCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTGAGTTCGATTACACTCA
*
39844 GCTTCGAGGGTACATC
66 GCTTCGAGGGCACATC
* *
39860 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAAGACCTTTGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACC-AAAGACC-CTGAGTTCGATTAC
* * *
39925 GCTCAGC-TCCAAGGCACATC
61 ACTCAGCTTCGAGGGCACATC
* * * * * *
39945 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATATG-CCAAAGACCCTTAAGTTCGATTACACTC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCC-TGAGTTCGATTACACTC
*
40009 AGCTTTGAGGGCACATC
65 AGCTTCGAGGGCACATC
* * * * * * *
40026 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC--TGACC-AAAGACCCT-GAGTTCGATTACA
* *
40091 CTCAGC-TCTAAGGCACATC
62 CTCAGCTTCGAGGGCACATC
40110 ATT
1 ATT
40113 CAAGGCTAGA
Statistics
Matches: 623, Mismatches: 91, Indels: 63
0.80 0.12 0.08
Matches are distributed among these distances:
79 51 0.08
80 182 0.29
81 37 0.06
82 2 0.00
83 3 0.00
84 172 0.28
85 159 0.26
86 17 0.03
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (81 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTGAGTTCGATTACACTCA
GCTTCGAGGGCACATC
Found at i:39559 original size:164 final size:164
Alignment explanation
Indices: 39331--40112 Score: 1386
Period size: 164 Copynumber: 4.8 Consensus size: 164
39321 GACCAAAGAC
39331 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
1 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
39396 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
66 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
39461 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGA
131 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGA
39495 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
1 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
39560 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
66 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
39625 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGA
131 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGA
39659 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
1 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
39724 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
66 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
39789 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGA
131 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGA
*
39823 CCCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTGCAGCATAACTTAAGTCGAGAAGG
1 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
39888 GTTATCTGCCAACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
66 GTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
* * * *
39953 TATAGCTTAAGTCGAGAAGAGCTATATGCCAAAGA
130 CATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGA
** * * * * *
39988 CCCTTAAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
1 CCC-CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
** * *
40053 GGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
65 GGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
40113 CAAGGCTAGA
Statistics
Matches: 599, Mismatches: 17, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
164 406 0.68
165 131 0.22
166 62 0.10
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (164 bp):
CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGA
Found at i:40904 original size:74 final size:70
Alignment explanation
Indices: 40798--41118 Score: 275
Period size: 74 Copynumber: 4.5 Consensus size: 70
40788 ATATATACAT
* *
40798 ATTTTGAAACTACGTATATAATATATAGTTTTTAATAGTTTTT-AAAACTATATAATATATAGTT
1 ATTTTGAAAATA--TATATAATATATAGTTTTTAACA-TTTTTGAAAACTATAT-ATATATAGTT
*
40862 TTAAAAAAGAC
62 TT-TAAAA-AC
* *
40873 ATTTTAGAAAATATATATAATATATAATTTTTAAAATCATTTTGAAAACT-TATATATATAGTTT
1 ATTTT-GAAAATATATATAATATATAGTTTTTAACAT--TTTTGAAAACTATATATATATAGTTT
*
40937 TTGAAAAC
63 TTAAAAAC
* *
40945 ATTTTTGAAAACATATAT-ATATTATAGTTTTGAAAACATTTTTTTGAAAACATATATATTATAT
1 A-TTTTGAAAATATATATAATA-TATAGTTTT--TAACA--TTTTTGAAAAC-TATATA-TATAT
*
41009 AG-TTTTAAAATC
58 AGTTTTTAAAAAC
* *** *
41021 ATTTTG-AAATTTATATAATATATAGTTGAAAACATTTTTGAAAA-TAT-T-TATATA--TTATA
1 ATTTTGAAAATATATATAATATATAGTTTTTAACATTTTTGAAAACTATATATATATAGTTTTTA
*
41080 TAAGAC
66 -AAAAC
41086 ATTTTGAAAATATATATAATATATAGTTTTTAA
1 ATTTTGAAAATATATATAATATATAGTTTTTAA
41119 AAAAATATTT
Statistics
Matches: 208, Mismatches: 22, Indels: 41
0.77 0.08 0.15
Matches are distributed among these distances:
64 4 0.02
65 15 0.07
66 22 0.11
67 1 0.00
68 3 0.01
70 10 0.05
71 3 0.01
72 27 0.13
73 8 0.04
74 61 0.29
75 21 0.10
76 26 0.12
77 7 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (70 bp):
ATTTTGAAAATATATATAATATATAGTTTTTAACATTTTTGAAAACTATATATATATAGTTTTTA
AAAAC
Found at i:40951 original size:12 final size:12
Alignment explanation
Indices: 40934--40958 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40924 ATATATATAG
40934 TTTTTGAAAACA
1 TTTTTGAAAACA
40946 TTTTTGAAAACA
1 TTTTTGAAAACA
40958 T
1 T
40959 ATATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:40962 original size:35 final size:34
Alignment explanation
Indices: 40836--41109 Score: 161
Period size: 35 Copynumber: 7.7 Consensus size: 34
40826 TTTTTAATAG
**
40836 TTTTT-AAAACTATATAATATATAGTTTTAAAAAAGACA
1 TTTTTGAAAAC-ATAT-ATATATA-TTTT-TGAAA-ACA
* * *
40874 TTTTAGAAAATATATATAATATATAATTTTTAAAATCA
1 TTTTTGAAAACATATAT-ATATAT--TTTTGAAAA-CA
*
40912 -TTTTGAAAACTTATATATATAGTTTTTGAAAACA
1 TTTTTGAAAACATATATATATA-TTTTTGAAAACA
40946 TTTTTGAAAACATATATATATTATAGTTTTGAAAACA
1 TTTTTGAAAACATATATATA-TAT--TTTTGAAAACA
40983 TTTTTTTGAAAACATATATATTATATAGTTTT-AAAATCA
1 --TTTTTGAAAACATATATA-TATAT--TTTTGAAAA-CA
** **
41022 -TTTTG-AAATTTATATAATATATAGTTGAAAACA
1 TTTTTGAAAACATATAT-ATATATTTTTGAAAACA
* * *
41055 TTTTTG-AAA-ATATTTATATATTATAT-AAGACA
1 TTTTTGAAAACATATATATATATT-TTTGAAAACA
*
41087 -TTTTGAAAATATATATAATATAT
1 TTTTTGAAAACATATAT-ATATAT
41110 AGTTTTTAAA
Statistics
Matches: 195, Mismatches: 20, Indels: 46
0.75 0.08 0.18
Matches are distributed among these distances:
31 5 0.03
32 14 0.07
33 14 0.07
34 20 0.10
35 40 0.21
36 13 0.07
37 29 0.15
38 22 0.11
39 36 0.18
40 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
TTTTTGAAAACATATATATATATTTTTGAAAACA
Found at i:40964 original size:37 final size:36
Alignment explanation
Indices: 40794--41120 Score: 238
Period size: 34 Copynumber: 9.0 Consensus size: 36
40784 TTATATATAT
* *
40794 ACATATTTTGAAACTACGTATATAATATATAGTTTTTAAT
1 ACAT-TTTTGAAA--ACATATAT-ATATATAGTTTTTAAA
* *
40834 A-GTTTTT-AAAACTATATA-ATATATAGTTTTAAAAAA
1 ACATTTTTGAAAAC-ATATATATATATAGTTTT--TAAA
* * *
40870 GACATTTTAGAAAATATATATAATATATAATTTTTAAA
1 -ACATTTTTGAAAACATATAT-ATATATAGTTTTTAAA
40908 ATCA-TTTTGAAAAC-T-TATATATATAGTTTTTGAAA
1 A-CATTTTTGAAAACATATATATATATAGTTTTT-AAA
*
40943 ACATTTTTGAAAACATATATATATTATAGTTTTGAAA
1 ACATTTTTGAAAACATATATATA-TATAGTTTTTAAA
40980 ACATTTTTTTGAAAACATATATATTATATAG-TTTTAAA
1 ACA--TTTTTGAAAACATATATA-TATATAGTTTTTAAA
** *
41018 ATCA-TTTTG-AAATTTATATAATATATAG--TTGAAA
1 A-CATTTTTGAAAACATATAT-ATATATAGTTTTTAAA
* *
41052 ACATTTTTG-AAA-ATAT-T-TATATA-TTATATAAG
1 ACATTTTTGAAAACATATATATATATAGTT-TTTAAA
*
41084 ACA-TTTTGAAAATATATATAATATATAGTTTTTAAA
1 ACATTTTTGAAAACATATAT-ATATATAGTTTTTAAA
41120 A
1 A
41121 AAATATTTTT
Statistics
Matches: 235, Mismatches: 23, Indels: 62
0.73 0.07 0.19
Matches are distributed among these distances:
30 6 0.03
31 5 0.02
32 10 0.04
33 9 0.04
34 41 0.17
35 34 0.14
36 25 0.11
37 27 0.11
38 34 0.14
39 30 0.13
40 14 0.06
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ACATTTTTGAAAACATATATATATATAGTTTTTAAA
Found at i:41160 original size:38 final size:39
Alignment explanation
Indices: 40931--41193 Score: 93
Period size: 37 Copynumber: 7.2 Consensus size: 39
40921 CTTATATATA
* * *
40931 TAGTTTTT-GAAAACATTTTTGAAAACATATAT-ATATTA
1 TAGTTTTTAAAAAATATTTTTGAAAATATATATAATA-TA
* * * * *
40969 TAGTTTTGAAAACATTTTTTTGAAAACATATATATTATA
1 TAGTTTTTAAAAAATATTTTTGAAAATATATATAATATA
*
41008 TAG-TTTT--AAAATCA-TTTTG-AAATTTATATAATATA
1 TAGTTTTTAAAAAAT-ATTTTTGAAAATATATATAATATA
* *
41043 TAG---TT-GAAAACATTTTTGAAAATAT-T-T-ATATA
1 TAGTTTTTAAAAAATATTTTTGAAAATATATATAATATA
* * * * *** *
41075 T--TATATAAGACAT-TTTGAAAATATATATAAT-ATATA
1 TAGTTTTTAAAAAATATTTTTGAAAATATAT-ATAATATA
* ** **
41111 GT--TTTTAAAAAAATATTTTTGAAGTTATATATTGTATA
1 -TAGTTTTTAAAAAATATTTTTGAAAATATATATAATATA
* **
41149 T-GTTTTT-AAAAATGTTTTTGAAAATACGTATAATATA
1 TAGTTTTTAAAAAATATTTTTGAAAATATATATAATATA
41186 TAGTTTTT
1 TAGTTTTT
41194 TTTTTAAAAA
Statistics
Matches: 165, Mismatches: 42, Indels: 36
0.68 0.17 0.15
Matches are distributed among these distances:
32 6 0.04
33 14 0.08
34 13 0.08
35 21 0.13
36 15 0.09
37 35 0.21
38 34 0.21
39 25 0.15
40 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (39 bp):
TAGTTTTTAAAAAATATTTTTGAAAATATATATAATATA
Found at i:41268 original size:3 final size:3
Alignment explanation
Indices: 41260--41315 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
41250 TTTTATATAG
41260 ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41306 ATT ATT ATT A
1 ATT ATT ATT A
41316 GTTCCTATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44128 original size:30 final size:30
Alignment explanation
Indices: 44092--44155 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
44082 GTTGTGACCG
44092 GTCAAAACAGTTCCAAAACCGATCAAACCA
1 GTCAAAACAGTTCCAAAACCGATCAAACCA
* *
44122 GTCAAAACAGTTCCAAAACCGGTCAAACCG
1 GTCAAAACAGTTCCAAAACCGATCAAACCA
44152 GTCA
1 GTCA
44156 CTTTTTCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.30, G:0.14, T:0.14
Consensus pattern (30 bp):
GTCAAAACAGTTCCAAAACCGATCAAACCA
Found at i:46199 original size:12 final size:12
Alignment explanation
Indices: 46174--46243 Score: 88
Period size: 12 Copynumber: 5.8 Consensus size: 12
46164 ACGAAGATAT
* *
46174 CAGAAATCAAAA
1 CAGAATTCAGAA
46186 CAGAATTCAGAA
1 CAGAATTCAGAA
46198 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
*
46210 CAGAATTCAGAT
1 CAGAATTCAGAA
*
46222 CAGAAATCAGAA
1 CAGAATTCAGAA
46234 CAGAATTCAG
1 CAGAATTCAG
46244 GTCATATATC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
11 2 0.04
12 46 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:46201 original size:24 final size:24
Alignment explanation
Indices: 46172--46280 Score: 130
Period size: 24 Copynumber: 4.5 Consensus size: 24
46162 AAACGAAGAT
*
46172 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
46196 AACAGATATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
46220 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
46244 GTCATATATCATAACAGAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
*
46267 ATTCGGAAATCAGA
1 A-TCAGAAATCAGA
46281 TAAAATATTT
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:46239 original size:48 final size:47
Alignment explanation
Indices: 46172--46280 Score: 146
Period size: 48 Copynumber: 2.3 Consensus size: 47
46162 AAACGAAGAT
*
46172 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATTCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATTCA
** * *
46219 GATCAGAAATCAGAACAGAATTCAGGTCATATATCATAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATTCA
*
46267 ATTCGGAAATCAGA
1 A-TCAGAAATCAGA
46281 TAAAATATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 1 0.02
48 53 0.98
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATTCA
Found at i:48823 original size:18 final size:18
Alignment explanation
Indices: 48775--48833 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
48765 CAACGGTCAA
*
48775 CGGGTCGGGTC-ATCGGAT
1 CGGGTCGGGTCAAT-GGGT
***
48793 CGGGTCAAATCAATGGGT
1 CGGGTCGGGTCAATGGGT
*
48811 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAATGGGT
48829 CGGGT
1 CGGGT
48834 TAGGTTGTGA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 30 0.94
19 2 0.06
ACGTcount: A:0.15, C:0.20, G:0.44, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAATGGGT
Found at i:48857 original size:9 final size:10
Alignment explanation
Indices: 48843--48919 Score: 70
Period size: 9 Copynumber: 7.8 Consensus size: 10
48833 TTAGGTTGTG
48843 ACCGGTC-AA
1 ACCGGTCAAA
48852 ACCGGTCAAA
1 ACCGGTCAAA
* *
48862 ACAGTTCCAAA
1 ACCGGT-CAAA
*
48873 ACTGGTC-AA
1 ACCGGTCAAA
48882 ACCGGTCAAA
1 ACCGGTCAAA
* *
48892 ACAGTTCCAAA
1 ACCGGT-CAAA
48903 ACCGGTC-AA
1 ACCGGTCAAA
48912 ACCGGTCA
1 ACCGGTCA
48920 CTTTTTCCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
9 24 0.44
10 14 0.26
11 16 0.30
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:48880 original size:30 final size:30
Alignment explanation
Indices: 48843--48919 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
48833 TTAGGTTGTG
48843 ACCGGTCAAACCGGTCAAAACAGTTCCAAA
1 ACCGGTCAAACCGGTCAAAACAGTTCCAAA
*
48873 ACTGGTCAAACCGGTCAAAACAGTTCCAAA
1 ACCGGTCAAACCGGTCAAAACAGTTCCAAA
48903 ACCGGTCAAACCGGTCA
1 ACCGGTCAAACCGGTCA
48920 CTTTTTCCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.14
Consensus pattern (30 bp):
ACCGGTCAAACCGGTCAAAACAGTTCCAAA
Found at i:53480 original size:16 final size:18
Alignment explanation
Indices: 53448--53482 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
53438 AATATAAAAC
53448 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
53466 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
53482 A
1 A
53483 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:53644 original size:22 final size:23
Alignment explanation
Indices: 53603--53646 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
53593 AAATATATAT
53603 ATATATAACACTAATAATAAAAC
1 ATATATAACACTAATAATAAAAC
53626 ATATAT-ACA-TATATAATAAAA
1 ATATATAACACTA-ATAATAAAA
53647 TTAATAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.10
22 12 0.60
23 6 0.30
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
ATATATAACACTAATAATAAAAC
Found at i:53652 original size:31 final size:29
Alignment explanation
Indices: 53585--53686 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 29
53575 TGCAAATAGG
* *
53585 AAAT-ATATAAATATATATATATATAACA
1 AAATAATAAAAATATATACATATATAACA
* *
53613 CTAATAATAAAACATATATACATATATAATA
1 -AAATAATAAAA-ATATATACATATATAACA
* *
53644 AAATTAATAGAAAGTAATATGCATATATAACA
1 AAA-TAATA-AAAAT-ATATACATATATAACA
53676 AGAATAATAAA
1 A-AATAATAAA
53687 GTAGGAAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
29 3 0.05
30 7 0.12
31 24 0.41
32 23 0.39
33 2 0.03
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (29 bp):
AAATAATAAAAATATATACATATATAACA
Found at i:54066 original size:37 final size:36
Alignment explanation
Indices: 54016--54153 Score: 163
Period size: 37 Copynumber: 3.8 Consensus size: 36
54006 GTGCTTGTGG
* * * * * *
54016 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATAT
* *
54053 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-AT
*
54090 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATAT
54124 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
54154 GGACGAAAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATAT
Found at i:54127 original size:34 final size:34
Alignment explanation
Indices: 54052--54150 Score: 155
Period size: 34 Copynumber: 2.8 Consensus size: 34
54042 AGTAGAACTC
54052 TATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGT
1 TATCCTATTTTTAGGAGTTTGAATCCT---AAAATGT
54089 TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-T
1 TATCCTATTTTTAGGAGTTTGAATCCTAAAATGT
54122 ATATCCTATTTTTAGGAGTTTGAATCCTA
1 -TATCCTATTTTTAGGAGTTTGAATCCTA
54151 GTAGGACGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
33 1 0.02
34 33 0.54
37 27 0.44
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (34 bp):
TATCCTATTTTTAGGAGTTTGAATCCTAAAATGT
Found at i:55083 original size:204 final size:205
Alignment explanation
Indices: 54694--55651 Score: 1391
Period size: 204 Copynumber: 4.7 Consensus size: 205
54684 CATTGTTCCA
* * ** *
54694 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * ** * *
54758 CCAGC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 ACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAA
**
54822 GTTGAAATTGAATCTGAATGAAA-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
129 GTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
54886 TGCGTTGTCTGG
194 TGCGTTGTCTGG
* *
54898 AGTCCAATATCTTTCGTTGTGAAGTTGAAA-TGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAAC
54962 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
55027 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
55092 CGTTGTCTGG
196 CGTTGTCTGG
* *
55102 AGTCC-ATATCC-TCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAATTGTTGTTGAC--A-
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAAC
*
55162 AGCAGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
55227 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCA-CGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
55291 CGTTGTCTGG
196 CGTTGTCTGG
* * *
55301 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGACTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAAC
*
55366 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
* *
55431 TGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAACCAGCGG-CCCTTCGTCGTGAAGTT
131 TGAAATTGGCTCTG-AA-T--G-AAA-T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
55495 GAACTTGCGTTGTCTGG
189 GAACTTGCGTTGTCTGG
* * * *
55512 AGTCCACTATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAA
* * ** * *
55577 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTGCCACGATATCCTCCG-TCGT
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT-CCA--ATATCCTTCGCT-GT
*
55641 GGAGTTGAAAT
126 GAAGTTGAAAT
55652 CGCGGATGGC
Statistics
Matches: 693, Mismatches: 39, Indels: 33
0.91 0.05 0.04
Matches are distributed among these distances:
199 43 0.06
200 106 0.15
201 47 0.07
202 31 0.04
203 124 0.18
204 163 0.24
205 2 0.00
206 1 0.00
208 1 0.00
209 3 0.00
210 1 0.00
211 94 0.14
212 52 0.08
213 3 0.00
214 1 0.00
215 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (205 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAAC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGG
Found at i:55445 original size:105 final size:102
Alignment explanation
Indices: 54694--55651 Score: 1309
Period size: 99 Copynumber: 9.3 Consensus size: 102
54684 CATTGTTCCA
* * * *
54694 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA--TGGAAATTG-TTGTTGACAAG
* * *
54759 CAGC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
62 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
54799 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAAT-GAAA-T-TTGTTGACAAGCAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGGAAATTGTTGTTGACAAGCAGC
54861 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
54898 AGTCCAATATCTTTCGTTGTGAAGTTGAAA-TGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT--GAAT-GGAAATTGTTGTTGACAAGC
*
54962 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
63 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55002 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAT-GAAATT-TTGTTGACAAGCAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGGAAATTGTTGTTGACAAGCAGC
55065 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
55102 AGTCC-ATATCC-TCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAATTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-A-TGG-AAATTGTTGTTGACAAGC
*
55165 A---GTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
63 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55202 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAT-GAAATT-TTGTTGACAAGCA-C
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGGAAATTGTTGTTGACAAGCAGC
55264 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
55301 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGACTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-A-TGGAAA-TTGTTGTTGACAAGC
*
55366 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
63 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55406 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AA-T-GG-AAATTG-TTGTTGACAA
*
55471 CCAGCGG-CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
61 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
55512 AGTCCACTATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AA-TG-GAAATTG-TTGTTGACAAG
* * * *
55577 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
62 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
55618 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
55652 CGCGGATGGC
Statistics
Matches: 778, Mismatches: 43, Indels: 60
0.88 0.05 0.07
Matches are distributed among these distances:
97 13 0.02
98 50 0.06
99 144 0.19
100 102 0.13
101 18 0.02
102 38 0.05
103 19 0.02
104 94 0.12
105 141 0.18
106 117 0.15
107 21 0.03
109 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (102 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGGAAATTGTTGTTGACAAGCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:56345 original size:68 final size:67
Alignment explanation
Indices: 56242--56403 Score: 193
Period size: 68 Copynumber: 2.4 Consensus size: 67
56232 GGAAACGATC
* *
56242 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTATTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACGGTCTCAAGGGAAACAAAATT-TGTATTAAGGGAAA
56307 TAAAT
63 TAAAT
** * * * * *
56312 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACGGTCTCAAGGGAAACAAAATTTGTATTAAGGGAAATAA
56377 AT
66 AT
*
56379 TCAAAGA-TTT-TGTTTCAAGGGAAAC
1 TCAAAGATTTTGTGTTTCAAGAGAAAC
56404 TGACGAAAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
65 13 0.16
66 3 0.04
67 22 0.28
68 32 0.41
69 3 0.04
70 6 0.08
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACGGTCTCAAGGGAAACAAAATTTGTATTAAGGGAAATAA
AT
Found at i:56551 original size:36 final size:36
Alignment explanation
Indices: 56501--56570 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
56491 TCAATGTTTA
*
56501 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
56537 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
56571 CTCTTCTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:56620 original size:35 final size:35
Alignment explanation
Indices: 56501--56620 Score: 102
Period size: 35 Copynumber: 3.4 Consensus size: 35
56491 TCAATGTTTA
*
56501 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT-T
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATCT
* *
56537 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC-
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATCT
* * * *
56572 T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATCT
1 TGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATCT
*
56608 TGTTTTAAGAAAA
1 TGTTTCAAGAAAA
56621 ACAATCATGA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
34 3 0.05
35 32 0.48
36 28 0.42
37 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (35 bp):
TGTTTCAAGAAAACTGTCTCAAGAGAGACAAATCT
Done.