Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000551.1 Hibiscus syriacus cultivar Beakdansim tig00001075_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: 270927
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:16815 original size:24 final size:24
Alignment explanation
Indices: 16780--16843 Score: 50
Period size: 24 Copynumber: 2.8 Consensus size: 24
16770 TTTGAAAGAT
16780 ATTTT-ATAATTTTATAATATT-TA
1 ATTTTAAT-ATTTTATAATATTATA
16803 ATATTTAATATTTTAT--T-TTA-A
1 AT-TTTAATATTTTATAATATTATA
16824 ATTTTAATAATTATTATAAT
1 ATTTTAAT-ATT-TTATAAT
16844 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
20 6 0.18
21 8 0.24
22 5 0.15
23 2 0.06
24 11 0.32
25 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTAATATTTTATAATATTATA
Found at i:22462 original size:15 final size:15
Alignment explanation
Indices: 22422--22454 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
22412 AAATAATTAA
22422 AATAATATATTTTAT
1 AATAATATATTTTAT
22437 AATAATATATTTTAT
1 AATAATATATTTTAT
22452 AAT
1 AAT
22455 TATTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:23231 original size:46 final size:46
Alignment explanation
Indices: 23181--23280 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 46
23171 TGAACGCTAA
*
23181 ACGAATATATTCACGAATACTAAACAAATGTTAAACGAACATGTTC
1 ACGAATATATTCACGAACACTAAACAAATGTTAAACGAACATGTTC
* * ** ** * *
23227 ACGAACATGTTCACGAACGTTAAATGAGTGTTAAACGAATATGTTC
1 ACGAATATATTCACGAACACTAAACAAATGTTAAACGAACATGTTC
*
23273 ATGAATAT
1 ACGAATAT
23281 TAAACGAACA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (46 bp):
ACGAATATATTCACGAACACTAAACAAATGTTAAACGAACATGTTC
Found at i:23232 original size:12 final size:12
Alignment explanation
Indices: 23215--23244 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
23205 CAAATGTTAA
23215 ACGAACATGTTC
1 ACGAACATGTTC
23227 ACGAACATGTTC
1 ACGAACATGTTC
23239 ACGAAC
1 ACGAAC
23245 GTTAAATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (12 bp):
ACGAACATGTTC
Found at i:23283 original size:23 final size:23
Alignment explanation
Indices: 23257--23329 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
23247 TAAATGAGTG
* * * *
23257 TTAAACGAATATGTTCATGAATA
1 TTAAACGAACACGTTCACGAACA
23280 TTAAACGAACACGTTCACGAACA
1 TTAAACGAACACGTTCACGAACA
*
23303 TTAAACGAACACATTC-CGAACA
1 TTAAACGAACACGTTCACGAACA
23325 TTAAA
1 TTAAA
23330 TAAATGAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 11 0.24
23 34 0.76
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (23 bp):
TTAAACGAACACGTTCACGAACA
Found at i:23439 original size:35 final size:33
Alignment explanation
Indices: 23326--23439 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 33
23316 TTCCGAACAT
** * *
23326 TAAATAAATGAACACGAATA-CAT-CTAAAATA
1 TAAATAAACAAACACGAATATAATACTAAAAAA
23357 TAAATAAACAAACACGAATATAATACTAAAAAA
1 TAAATAAACAAACACGAATATAATACTAAAAAA
* *
23390 TTAAACGAACACAAAC-CGAATATAAATACCTTCAAAAA
1 -TAAA-TAA-ACAAACACGAATAT-AATA-C-TAAAAAA
23428 TAAATAAACAAA
1 TAAATAAACAAA
23440 TAAAAATACA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
31 18 0.26
32 2 0.03
33 7 0.10
34 4 0.06
35 14 0.21
36 12 0.18
37 5 0.07
38 6 0.09
ACGTcount: A:0.61, C:0.15, G:0.04, T:0.19
Consensus pattern (33 bp):
TAAATAAACAAACACGAATATAATACTAAAAAA
Found at i:30732 original size:15 final size:15
Alignment explanation
Indices: 30695--30766 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
30685 AAATAGTTAT
* *
30695 TATTTTTTATATTAA
1 TATTATTTATATAAA
*
30710 TA-TATTTATGTAAA
1 TATTATTTATATAAA
30724 TATTATTTATTATTAAAA
1 TATTATTTA-TA-T-AAA
* *
30742 TAATATTTATATAAT
1 TATTATTTATATAAA
30757 TATTATTTAT
1 TATTATTTAT
30767 TTAGAATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
14 11 0.24
15 19 0.41
16 2 0.04
17 3 0.07
18 11 0.24
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
TATTATTTATATAAA
Found at i:32516 original size:21 final size:21
Alignment explanation
Indices: 32486--32533 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
32476 GCAGGGGTAC
* *
32486 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
32507 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
32528 ATGCCA
1 ATGCCA
32534 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:32563 original size:21 final size:21
Alignment explanation
Indices: 32537--32629 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
32527 TATGCCATCT
* *
32537 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
32558 CCGCAGGGTTACATTCCTAG-
1 CCGCAGGGTTACATGCCTAGC
32578 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
32599 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
32620 CCGCAGGGTT
1 CCGCAGGGTT
32630 TTATACCATA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
20 18 0.27
21 49 0.73
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:32588 original size:41 final size:41
Alignment explanation
Indices: 32543--32620 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
32533 ATCTCCGCAG
* *
32543 GGTTACATTCCGAGCCCG-CAGGGTTACATTCCTAGCCGCCA
1 GGTTACATGCCGAGCCCGCCA-GGTTACATGCCTAGCCGCCA
*
32584 GGTTACATGCCTAGCCCGCCAGGTTACATGCCTAGCC
1 GGTTACATGCCGAGCCCGCCAGGTTACATGCCTAGCC
32621 CGCAGGGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 31 0.94
42 2 0.06
ACGTcount: A:0.19, C:0.35, G:0.24, T:0.22
Consensus pattern (41 bp):
GGTTACATGCCGAGCCCGCCAGGTTACATGCCTAGCCGCCA
Found at i:33208 original size:33 final size:34
Alignment explanation
Indices: 33149--33245 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
33139 AAATGTTTTT
*
33149 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
33183 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
33216 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
33246 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:33252 original size:34 final size:33
Alignment explanation
Indices: 33147--33252 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
33137 ATAAATGTTT
*
33147 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
33181 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
33213 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
33248 TTAAA
1 TTAAA
33253 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:33993 original size:124 final size:126
Alignment explanation
Indices: 33631--34107 Score: 895
Period size: 126 Copynumber: 3.8 Consensus size: 126
33621 TTTAAGTTAT
*
33631 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
33696 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
33757 ACCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
33822 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTATGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
33883 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATA-T-TCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
33946 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
34007 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
34072 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
34108 CCGATTATAG
Statistics
Matches: 341, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
124 121 0.35
125 2 0.01
126 218 0.64
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:34074 original size:250 final size:252
Alignment explanation
Indices: 33631--34107 Score: 913
Period size: 250 Copynumber: 1.9 Consensus size: 252
33621 TTTAAGTTAT
*
33631 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
33696 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCC
33761 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
33826 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTATGTACTGATATATCTAGTG
196 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTATGTACTGATATATCTAGTG
33883 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATA-T-TCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
33946 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCC
34011 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
34076 CCCCGGGAACGCGCCTTCACGTGAATAGTGAA
196 CCCCGGGAACGCGCCTTCACGTGAATAGTGAA
34108 CCGATTATAG
Statistics
Matches: 222, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
250 181 0.82
251 1 0.00
252 40 0.18
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (252 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCC
CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTATGTACTGATATATCTAGTG
Found at i:34185 original size:8 final size:8
Alignment explanation
Indices: 34172--34212 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
34162 TCACAATCTT
34172 TCAAATTC
1 TCAAATTC
34180 TCAAATTC
1 TCAAATTC
* *
34188 CCAAACTC
1 TCAAATTC
34196 T-AAATTC
1 TCAAATTC
34203 TCAAATTC
1 TCAAATTC
34211 TC
1 TC
34213 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:37226 original size:12 final size:13
Alignment explanation
Indices: 37193--37230 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
37183 TAAATACATA
37193 ATATATTTAATAT
1 ATATATTTAATAT
*
37206 ATTTATTTAATAT
1 ATATATTTAATAT
37219 A-ATATTTAATAT
1 ATATATTTAATAT
37231 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:37281 original size:23 final size:23
Alignment explanation
Indices: 37243--37300 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
37233 TTAGTTATAT
37243 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
37264 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
37287 TTTTACATAATATA
1 TTTTACATAATATA
37301 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:37457 original size:16 final size:16
Alignment explanation
Indices: 37436--37471 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
37426 ACCGGGTAAA
37436 GCGCGCCCCCGGAGAC
1 GCGCGCCCCCGGAGAC
*
37452 GCGCGCCCCCGGGGAC
1 GCGCGCCCCCGGAGAC
37468 GCGC
1 GCGC
37472 CTTTGCCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.50, G:0.42, T:0.00
Consensus pattern (16 bp):
GCGCGCCCCCGGAGAC
Found at i:38245 original size:42 final size:42
Alignment explanation
Indices: 38185--38267 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
38175 ATCTGCTCCG
* *
38185 GCTTCTTCTCCTCTGGCTGCTACTCCAGTGAGTTCGGCACCT
1 GCTTCTTCTCCTCCGGCTGCTACTCCAGTGAGTTCGCCACCT
*
38227 GCTTCTTCTCCTCCGGCTGCTCCTCCAGTGAGTTCGCCACC
1 GCTTCTTCTCCTCCGGCTGCTACTCCAGTGAGTTCGCCACC
38268 GCCTCCGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.08, C:0.40, G:0.20, T:0.31
Consensus pattern (42 bp):
GCTTCTTCTCCTCCGGCTGCTACTCCAGTGAGTTCGCCACCT
Found at i:46177 original size:23 final size:21
Alignment explanation
Indices: 46130--46177 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
46120 CTATAGACAC
*
46130 AACTGTTCAAACAAAATTAAA
1 AACTGTTCAAACAAAATCAAA
* *
46151 AACTGTTCGAACCTAAAATCAAT
1 AACTGTTC-AAAC-AAAATCAAA
46174 AACT
1 AACT
46178 ATATTCTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 3 0.14
23 11 0.50
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (21 bp):
AACTGTTCAAACAAAATCAAA
Found at i:51356 original size:3 final size:3
Alignment explanation
Indices: 51332--51384 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
51322 TCTACAAAAA
51332 TAT T-T TAT TA- TAT TA- TATT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
51375 TAT TAT TAT T
1 TAT TAT TAT T
51385 TAGGCCCCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 38 0.83
4 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:51475 original size:33 final size:33
Alignment explanation
Indices: 51438--51500 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
51428 ATAAATCAAC
51438 GTATTTGAGTCCTATTAAAACACTAAAACCAAT
1 GTATTTGAGTCCTATTAAAACACTAAAACCAAT
* *
51471 GTATTTGAGTCTTATTGAAACACTAAAACC
1 GTATTTGAGTCCTATTAAAACACTAAAACC
51501 GAATCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (33 bp):
GTATTTGAGTCCTATTAAAACACTAAAACCAAT
Found at i:53086 original size:110 final size:110
Alignment explanation
Indices: 52890--53405 Score: 817
Period size: 110 Copynumber: 4.7 Consensus size: 110
52880 TGATGGTAGT
* * ** * *
52890 AGCTCAACTTCATAGCGTAGGGGCGGTTGATTGTCAACAAACAAATTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
*
52955 CAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
53000 AGCTCAACTTCATAGTGAAGGGGCGACGGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
*
53065 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
*
53110 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAATTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
53175 CAAATTT-AACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
66 C-AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * *
53220 ATCTCAACTCCACAGCGAAGGGGCGACTGACTGTCAATAAACAACTTTTCAGTTTCATTCAGAGG
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
53285 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
53330 AGCTCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAGCTTTCCAG--T--TTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
53391 CAATTTCAACTTCAC
66 CAATTTCAACTTCAC
53406 GACGAAGAGA
Statistics
Matches: 378, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
106 22 0.06
108 1 0.00
109 5 0.01
110 345 0.91
111 5 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (110 bp):
AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
Found at i:53762 original size:84 final size:83
Alignment explanation
Indices: 53610--53897 Score: 287
Period size: 84 Copynumber: 3.5 Consensus size: 83
53600 TTCAAGGTCG
* * * * *
53610 GAGAAGGGCTATCTGCCACCCAAAAGGCATTCGAGTTCGACTACGCTCAACTCCAAGACATATCA
1 GAGAAGGGCTATCTGCCA-CC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
53675 TTTGCAGCATAACTTAAGTC
64 TTTGCAGCATAACTTAAGTC
* * *
53695 GAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGAGTACGCTCAGCTCCAAGGCACATTAT
1 GAGAAGGGCTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* *
53760 TTGTAGCATAGCTTAAGTC
65 TTGCAGCATAACTTAAGTC
* ** * * * * *
53779 TAGAAAAGCTATCTG---CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 GAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* *
53841 TTACAGCATAACTCAA-TGC
65 TTGCAGCATAACTTAAGT-C
* * * *
53860 TAGAAGGGTTATCTGTCACCAAAGATCTTCGAGTTCGA
1 GAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGA
53898 TTCCATTCAG
Statistics
Matches: 168, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
80 29 0.17
81 37 0.22
84 83 0.49
85 18 0.11
86 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (83 bp):
GAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTC
Found at i:54254 original size:5 final size:5
Alignment explanation
Indices: 54244--54311 Score: 68
Period size: 5 Copynumber: 13.2 Consensus size: 5
54234 AAAAACATTT
* *
54244 TATTA TATTA TATTA TATTA TATTA TTTTA TTTTA TATTTTA TATT- TATT-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA--TTA TATTA TATTA
54294 TATTA TTATTA TTATTA T
1 TATTA -TATTA -TATTA T
54312 TATTTTATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
4 8 0.14
5 33 0.58
6 11 0.19
7 5 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (5 bp):
TATTA
Found at i:54301 original size:3 final size:3
Alignment explanation
Indices: 54243--54320 Score: 68
Period size: 3 Copynumber: 28.7 Consensus size: 3
54233 CAAAAACATT
54243 TTA TTA -TA TTA -TA TTA -TA TTA -TA TTA TT- TTA TT- TTA -TA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54283 TTA -TA TTTA TTTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54321 TTTTAGGCCT
Statistics
Matches: 64, Mismatches: 0, Indels: 22
0.74 0.00 0.26
Matches are distributed among these distances:
2 20 0.31
3 38 0.59
4 6 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54312 original size:15 final size:15
Alignment explanation
Indices: 54243--54320 Score: 68
Period size: 13 Copynumber: 5.7 Consensus size: 15
54233 CAAAAACATT
54243 TTATTA-TATTA-TA
1 TTATTATTATTATTA
54256 TTA-TATTA-TATTA
1 TTATTATTATTATTA
54269 TT-TTATT-TTA-TA
1 TTATTATTATTATTA
54281 TT-TTA-TATTTATTTA
1 TTATTATTA-TTA-TTA
54296 TTATTATTATTATTA
1 TTATTATTATTATTA
54311 TTATT-TTATT
1 TTATTATTATT
54321 TTTTAGGCCT
Statistics
Matches: 55, Mismatches: 0, Indels: 19
0.74 0.00 0.26
Matches are distributed among these distances:
11 1 0.02
12 11 0.20
13 18 0.33
14 5 0.09
15 12 0.22
16 6 0.11
17 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATTATTATTA
Found at i:54321 original size:5 final size:5
Alignment explanation
Indices: 54246--54322 Score: 57
Period size: 5 Copynumber: 14.4 Consensus size: 5
54236 AAACATTTTA
* * * *
54246 TTATA TTATA TTATA TTATA TTATT TTATTT TATATT TTATAT TTA-T
1 TTATT TTATT TTATT TTATT TTATT TTA-TT T-TATT TTAT-T TTATT
54293 TTATT ATTATT ATTATT ATTATT TTATT TT
1 TTATT -TTATT -TTATT -TTATT TTATT TT
54323 TTAGGCCTCA
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
4 4 0.06
5 33 0.50
6 27 0.41
7 2 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (5 bp):
TTATT
Found at i:54446 original size:30 final size:32
Alignment explanation
Indices: 54379--54451 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 32
54369 AAATTAACGT
* *
54379 ATTTGAGTCCTATTGAAACACTAAAAGCAACAT
1 ATTTGAGTCCTATTG-AACACTAAAAGCAAAAC
* *
54412 ATTTGAGTCCTATTG-A-GCTAAAATCAAAAC
1 ATTTGAGTCCTATTGAACACTAAAAGCAAAAC
54442 ATTTGAGTCC
1 ATTTGAGTCC
54452 AAGGAATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 20 0.56
31 1 0.03
33 15 0.42
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (32 bp):
ATTTGAGTCCTATTGAACACTAAAAGCAAAAC
Found at i:58690 original size:110 final size:110
Alignment explanation
Indices: 58494--59037 Score: 740
Period size: 110 Copynumber: 5.0 Consensus size: 110
58484 TGATGGTAGT
* * * *** *
58494 AGCTCAACTTCATAGCGTAGGGGTGGTTGACTGTCAACAAACAAATTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACGGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * *
58559 CAATTTTAACTTCACAGCGAAGGATATTGGACTTGAGACAACATA
66 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
* *
58604 AGCTCAACTTCACAGTGAAGGGGCGACGGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACGGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
*
58669 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATACA
66 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
* *
58714 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAAG-TTCATTCAGAG
1 AGCTCAACTTCACAGCGAAGGGGCGACGGACTGTCAACAAACAACTTTTC-AGTTTCATTCAGAG
*
58778 TCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
65 TCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
* * * * * * * *
58824 ATCTCAATTTCACAGCGAAGGGGCGGCTGACTTTCAATAAACAACTTTTCAGTTTTATTCAGAGG
1 AGCTCAACTTCACAGCGAAGGGGCGACGGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
58889 CAATTTCAACTTCACATCGAATGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
*
58934 AGCTCAACTTCACAGCGAAGGGGCGACTGG-CTGTCAACAAACAACTTTCCAG--T--TTCAGAG
1 AGCTCAACTTCACAGCGAAGGGGCGAC-GGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAG
* * * *
58994 TCAATTTCAACTTCACGACGAATGATATTGGCCTCGAAACAACA
65 TCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACA
59038 TAAATGTTTG
Statistics
Matches: 389, Mismatches: 42, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
106 46 0.12
108 1 0.00
109 2 0.01
110 337 0.87
111 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (110 bp):
AGCTCAACTTCACAGCGAAGGGGCGACGGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
Found at i:59367 original size:84 final size:84
Alignment explanation
Indices: 59142--59669 Score: 672
Period size: 84 Copynumber: 6.3 Consensus size: 84
59132 AAGAGAATTG
* * * * * * **
59142 TGCCTACCAAAGACCTTCGAGTTCAACTACACTCAGCTCAAAGACACAACATTTGCAGCATAGTT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
59207 TAAGTCGAGAAGGGCTATC
66 TAAGTCGAGAAGGGCTATC
* *
59226 TGTCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAAC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
*
59291 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGCTATC
* * *
59311 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTTAGCTTCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
59376 TAAGTCGAGAAGGGCTATC
66 TAAGTCGAGAAGGGCTATC
* * *
59395 TGCCAACCAAAAGACATTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTGCAGCATAAC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
*
59460 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGCTATC
* * * * *
59480 TGCCAACCAAATACCTTCGAATTCGAGTACGCTCAGCTCCAAGGCACATTATTTGTAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
59545 TAAGTCGAGAAGGGCTATC
66 TAAGTCGAGAAGGGCTATC
* * * * * *
59564 TG----CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAAC
* * *
59625 TCAA-TGCTAGAAGGGTTATC
65 TTAAGT-CGAGAAGGGCTATC
* *
59645 TGTC-ACCAAAGACATTCGAGTTCGA
1 TGCCAACCAAAGACCTTCGAGTTCGA
59670 TTCCATTCAG
Statistics
Matches: 389, Mismatches: 48, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
80 27 0.07
81 39 0.10
84 172 0.44
85 151 0.39
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
TAAGTCGAGAAGGGCTATC
Found at i:59426 original size:169 final size:168
Alignment explanation
Indices: 59142--59669 Score: 719
Period size: 169 Copynumber: 3.2 Consensus size: 168
59132 AAGAGAATTG
* * * * * *
59142 TGCCTACCAAAGACCTTCGAGTTCAACTACACTCAGC-TCAAAGACACAACATTTGCAGCATAGT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTTGCAGCATAGC
59206 TTAAGTCGAGAAGGGCTATCTGTCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
65 TTAAGTCGAGAAGGGCTATCTG-CAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
59271 CATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
129 CATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
*
59311 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTTAGCTTCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
* *
59376 TAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACATTCGAGTTCGACTACGCTCAACTCCAAGGC
66 TAAGTCGAGAAGGGCTATCTG-CAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
59441 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
130 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* * * * * * *
59480 TGCCAACCAAATACCTTCGAATTCGAGTACGCTCAGCTCCAAGGCACATTATTTGTAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
* * * * *
59545 TAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
66 TAAGTCGAGAAGGGCTATCTGCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGC
* * * *
59606 ACATCATTTACAGCATAACTCAA-TGCTAGAAGGGTTATC
130 ATATCATTTGCAGCATAACTTAAGT-CGAGAAGGGTTATC
* *
59645 TGTC-ACCAAAGACATTCGAGTTCGA
1 TGCCAACCAAAGACCTTCGAGTTCGA
59670 TTCCATTCAG
Statistics
Matches: 323, Mismatches: 33, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
164 43 0.13
165 44 0.14
169 234 0.72
170 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (168 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
TAAGTCGAGAAGGGCTATCTGCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
TATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
Found at i:60020 original size:5 final size:5
Alignment explanation
Indices: 60010--60066 Score: 57
Period size: 5 Copynumber: 11.2 Consensus size: 5
60000 TCTACAAAAA
60010 TATTT TATTT TA--T TATTT TATTT TATATT TA-TT TATTTAT TATTAT
1 TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT TA-TT-T TATT-T
60056 TATTT TATTT T
1 TATTT TATTT T
60067 TTAGGCCCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
3 3 0.07
4 4 0.09
5 23 0.50
6 13 0.28
7 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:60027 original size:8 final size:8
Alignment explanation
Indices: 60014--60069 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
60004 CAAAAATATT
60014 TTATTTTA
1 TTATTTTA
60022 TTATTTTA
1 TTATTTTA
*
60030 TT-TTATA
1 TTATTTTA
60037 TT-TATTTA
1 TTAT-TTTA
60045 TTTATTATTA
1 -TTATT-TTA
60055 TTATTTTA
1 TTATTTTA
60063 TT-TTTTA
1 TTATTTTA
60070 GGCCCCACAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 12 0.29
8 18 0.43
9 8 0.19
10 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Found at i:60618 original size:45 final size:43
Alignment explanation
Indices: 60529--60629 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 43
60519 TCTCCTAATT
60529 TTATTATTTTTATTTCTTTTTACATTGTTATATATATATATATA
1 TTATTATTTTT-TTTCTTTTTACATTGTTATATATATATATATA
*
60573 TTATTTATTTTTTTTCATTTTT-CATT-TTTTA-ATAATATTATTATA
1 TTA-TTATTTTTTTTC-TTTTTACATTGTTATATAT-ATA-TA-TATA
*
60618 TTAATATTTTTT
1 TTATTATTTTTT
60630 ATTATTCTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
42 2 0.04
43 7 0.14
44 21 0.42
45 20 0.40
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (43 bp):
TTATTATTTTTTTTCTTTTTACATTGTTATATATATATATATA
Found at i:66056 original size:3 final size:3
Alignment explanation
Indices: 66048--66081 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
66038 CATATTAATC
66048 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
66082 CCGTAGCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:74264 original size:15 final size:15
Alignment explanation
Indices: 74244--74280 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
74234 ATATTATTCT
74244 TTCGAAAATGTATGC
1 TTCGAAAATGTATGC
74259 TTCGAAAATGTATGC
1 TTCGAAAATGTATGC
*
74274 TGCGAAA
1 TTCGAAA
74281 GGCAATTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (15 bp):
TTCGAAAATGTATGC
Found at i:81281 original size:33 final size:34
Alignment explanation
Indices: 81230--81295 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
81220 CATTAATTAA
* *
81230 TTAACAGTTTCTATCTAACT--GGAGTATTTTACT
1 TTAACAATTTCTAACTAACTAGGGA-TATTTTACT
*
81263 TTAACAATTTTTAACTAACTAGGGATATTTTAC
1 TTAACAATTTCTAACTAACTAGGGATATTTTAC
81296 CCCAAAGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.61
34 8 0.29
35 3 0.11
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (34 bp):
TTAACAATTTCTAACTAACTAGGGATATTTTACT
Found at i:88966 original size:49 final size:49
Alignment explanation
Indices: 88894--88992 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
88884 TTTTATTGAA
88894 AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
1 AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
88943 AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
1 AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
88992 A
1 A
88993 GGGGGGGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.22
Consensus pattern (49 bp):
AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
Found at i:90205 original size:7 final size:6
Alignment explanation
Indices: 90174--90204 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
90164 TTATGATCGA
90174 AATTTT AAATTTT AATTTT AATTTT AATTTT
1 AATTTT -AATTTT AATTTT AATTTT AATTTT
90205 TGCAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:100074 original size:15 final size:15
Alignment explanation
Indices: 100045--100091 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
100035 TTAAATTAAT
**
100045 TTATAAAATGTTAAA
1 TTATAAAATAATAAA
100060 TTATAAAATAATAAA
1 TTATAAAATAATAAA
* *
100075 -TATATAATTATAAA
1 TTATAAAATAATAAA
100089 TTA
1 TTA
100092 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
TTATAAAATAATAAA
Found at i:100109 original size:23 final size:23
Alignment explanation
Indices: 100048--100122 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
100038 AATTAATTTA
* *
100048 TAAAATGTTAAATTATAAAATAA-
1 TAAAATTTTAAA-TATAAATTAAT
* *
100071 T-AAATATATAATTATAAATTAAT
1 TAAAAT-TTTAAATATAAATTAAT
*
100094 TAAAATTTTAAATATAATTTAAT
1 TAAAATTTTAAATATAAATTAAT
*
100117 TTAAAT
1 TAAAAT
100123 ATATTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
22 13 0.32
23 24 0.59
24 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
TAAAATTTTAAATATAAATTAAT
Found at i:100117 original size:17 final size:18
Alignment explanation
Indices: 100077--100125 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
100067 ATAATAAATA
*
100077 TATAATTATAAAT-TAAT
1 TATAATTTTAAATATAAT
*
100094 TAAAATTTTAAATATAAT
1 TATAATTTTAAATATAAT
100112 T-TAA-TTTAAATATA
1 TATAATTTTAAATATA
100126 TTTTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 10 0.36
17 13 0.46
18 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAATTTTAAATATAAT
Found at i:112494 original size:6 final size:6
Alignment explanation
Indices: 112483--112508 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
112473 TTTTTTTTCA
112483 CAGTTT CAGTTT CAGTTT CAGTTT CA
1 CAGTTT CAGTTT CAGTTT CAGTTT CA
112509 AAAATATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (6 bp):
CAGTTT
Found at i:113020 original size:44 final size:45
Alignment explanation
Indices: 112964--113051 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
112954 TGATAGAGTA
*
112964 TTATTTAAAATGTTATTTTTTATTA-AAAATATTAATATC-GAAAG
1 TTATCTAAAATGTTATTTTTTA-TAGAAAATATTAATATCAGAAAG
*
113008 TTATCTAAAATGTTATTTTTTATAGAAAATGTTAATATCAGAAA
1 TTATCTAAAATGTTATTTTTTATAGAAAATATTAATATCAGAAA
113052 TATTTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 2 0.05
44 34 0.85
45 4 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (45 bp):
TTATCTAAAATGTTATTTTTTATAGAAAATATTAATATCAGAAAG
Found at i:113345 original size:46 final size:46
Alignment explanation
Indices: 113295--113382 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
113285 TTGGTAGAGC
*
113295 GCTACCTAAAATGTTATT-TTTTCTACCGAAAATATTAATATCAATA
1 GCTACCTAAAATGTTATTCCTTT-TACCGAAAATATTAATATCAATA
* *
113341 GCTACTTAAAATGTTATTCCTTTTACCGAAAATGTTAATATC
1 GCTACCTAAAATGTTATTCCTTTTACCGAAAATATTAATATC
113383 GGAAATATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
46 35 0.92
47 3 0.08
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (46 bp):
GCTACCTAAAATGTTATTCCTTTTACCGAAAATATTAATATCAATA
Found at i:113859 original size:3 final size:3
Alignment explanation
Indices: 113851--113905 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
113841 TCCTGGTCTT
113851 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
113899 TTA TTA T
1 TTA TTA T
113906 CTGCATCTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:124856 original size:18 final size:19
Alignment explanation
Indices: 124835--124875 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
124825 TAAACATATT
* *
124835 ATATTAAATATTTTA-GAA
1 ATATTAAATAATTCATGAA
124853 ATA-TAAATAATTCATGAA
1 ATATTAAATAATTCATGAA
124871 ATATT
1 ATATT
124876 TTATCAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 9 0.47
18 9 0.47
19 1 0.05
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (19 bp):
ATATTAAATAATTCATGAA
Found at i:126626 original size:4 final size:4
Alignment explanation
Indices: 126619--126680 Score: 70
Period size: 4 Copynumber: 15.5 Consensus size: 4
126609 TGATACATAC
* * * * *
126619 ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATGT ATAT ATGT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
126667 ATAT ATGT ATAT AT
1 ATAT ATAT ATAT AT
126681 GTATGTATGT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:126687 original size:4 final size:4
Alignment explanation
Indices: 126638--126695 Score: 80
Period size: 4 Copynumber: 14.5 Consensus size: 4
126628 TATATATATA
* * * *
126638 TATG TATG TATG TATA TATG TATA TATG TATA TATG TATA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126686 TATG TATG TA
1 TATG TATG TA
126696 CAACAATGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:126695 original size:8 final size:8
Alignment explanation
Indices: 126619--126692 Score: 112
Period size: 8 Copynumber: 9.2 Consensus size: 8
126609 TGATACATAC
*
126619 ATATATAT
1 ATATATGT
*
126627 ATATATAT
1 ATATATGT
126635 ATATATGT
1 ATATATGT
*
126643 ATGTATGT
1 ATATATGT
126651 ATATATGT
1 ATATATGT
126659 ATATATGT
1 ATATATGT
126667 ATATATGT
1 ATATATGT
126675 ATATATGT
1 ATATATGT
*
126683 ATGTATGT
1 ATATATGT
126691 AT
1 AT
126693 GTACAACAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 62 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
ATATATGT
Found at i:128140 original size:14 final size:14
Alignment explanation
Indices: 128121--128155 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
128111 GCTCGATGAA
* *
128121 GAAGAAGCTAAGGT
1 GAAGAAGCCAAGCT
128135 GAAGAAGCCAAGCT
1 GAAGAAGCCAAGCT
128149 GAAGAAG
1 GAAGAAG
128156 AAGAAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.34, T:0.09
Consensus pattern (14 bp):
GAAGAAGCCAAGCT
Found at i:130935 original size:9 final size:9
Alignment explanation
Indices: 130921--130966 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
130911 AACTTAAATC
130921 AAAATAATT
1 AAAATAATT
130930 AAAATAATAT
1 AAAATAAT-T
130940 AAAAT-ATT
1 AAAATAATT
130948 AATAAT-ATAT
1 AA-AATAAT-T
130958 AAAATAATT
1 AAAATAATT
130967 TATATGATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 3 0.09
9 19 0.58
10 11 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATAATT
Found at i:130957 original size:18 final size:20
Alignment explanation
Indices: 130921--130981 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
130911 AACTTAAATC
130921 AAAATAATTAA-AATAATAT
1 AAAATAATTAATAATAATAT
130940 AAAAT-ATTAATAAT-ATAT
1 AAAATAATTAATAATAATAT
* *
130958 AAAATAATTTAT-ATGATAT
1 AAAATAATTAATAATAATAT
130977 AAAAT
1 AAAAT
130982 TAAATATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
18 16 0.42
19 22 0.58
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATAATTAATAATAATAT
Found at i:131077 original size:41 final size:41
Alignment explanation
Indices: 131032--131115 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 41
131022 TTAATATAGA
* *
131032 TAATATTAA-ATATTAATTTTTAATATTATATATA-TTAATTT
1 TAATATTAATATATTAA-TATT-ATATTATAGATATTTAATTT
* *
131073 TAATATTAATTTTTTAATATTATATTATAGATATTTAATTT
1 TAATATTAATATATTAATATTATATTATAGATATTTAATTT
131114 TA
1 TA
131116 TATCATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 11 0.30
41 21 0.57
42 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (41 bp):
TAATATTAATATATTAATATTATATTATAGATATTTAATTT
Found at i:131107 original size:40 final size:47
Alignment explanation
Indices: 131054--131179 Score: 124
Period size: 37 Copynumber: 3.0 Consensus size: 47
131044 TTAATTTTTA
*
131054 ATATTATATATA-TTAATTTTA-AT-AT-T-AATT-TTTTA-ATATT
1 ATATTATAGATATTTAATTTTATATCATATAAATTATTTTATATATT
131094 ATATTATAGATATTTAATTTTATATCATATAAATTATTTTATATA-T
1 ATATTATAGATATTTAATTTTATATCATATAAATTATTTTATATATT
131140 -TA-T-T--A-A--T-ATTTTATATCATATAAATTATTTTATATATT
1 ATATTATAGATATTTAATTTTATATCATATAAATTATTTTATATATT
131178 AT
1 AT
131180 TAATATATAT
Statistics
Matches: 76, Mismatches: 1, Indels: 19
0.79 0.01 0.20
Matches are distributed among these distances:
37 29 0.38
38 2 0.03
39 1 0.01
40 12 0.16
41 10 0.13
42 2 0.03
43 3 0.04
44 2 0.03
45 6 0.08
46 6 0.08
47 3 0.04
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (47 bp):
ATATTATAGATATTTAATTTTATATCATATAAATTATTTTATATATT
Found at i:131110 original size:35 final size:35
Alignment explanation
Indices: 131032--131111 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 35
131022 TTAATATAGA
*
131032 TAATATTAAATATTAATTTTTAATATTATATATAT
1 TAATATTTAATATTAATTTTTAATATTATATATAT
131067 TAAT-TTTAATATTAATTTTTTAATATTATAT-TA-
1 TAATATTTAATATTAA-TTTTTAATATTATATATAT
131100 TAGATATTTAAT
1 TA-ATATTTAAT
131112 TTTATATCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
33 2 0.05
34 14 0.34
35 25 0.61
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (35 bp):
TAATATTTAATATTAATTTTTAATATTATATATAT
Found at i:131130 original size:35 final size:37
Alignment explanation
Indices: 131091--131185 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
131081 ATTTTTTAAT
* *
131091 ATTATATTATAGA-TATTTA-ATTTTATATCATATAA
1 ATTATTTTATAGATTATTAATATTTTATATCATATAA
*
131126 ATTATTTTATATATTATTAATATTTTATATCATATAA
1 ATTATTTTATAGATTATTAATATTTTATATCATATAA
*
131163 ATTATTTTATATATTATTAATAT
1 ATTATTTTATAGATTATTAATAT
131186 ATATAATATA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 11 0.20
36 5 0.09
37 39 0.71
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (37 bp):
ATTATTTTATAGATTATTAATATTTTATATCATATAA
Found at i:131134 original size:19 final size:19
Alignment explanation
Indices: 131110--131174 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
131100 TAGATATTTA
131110 ATTTTATATCATATAAATT
1 ATTTTATATCATATAAATT
*
131129 ATTTTATAT-ATTATTAA-T
1 ATTTTATATCA-TATAAATT
131147 ATTTTATATCATATAAATT
1 ATTTTATATCATATAAATT
131166 ATTTTATAT
1 ATTTTATAT
131175 ATTATTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 16 0.39
19 25 0.61
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTATATCATATAAATT
Found at i:131136 original size:12 final size:12
Alignment explanation
Indices: 131055--131180 Score: 55
Period size: 12 Copynumber: 10.3 Consensus size: 12
131045 TAATTTTTAA
*
131055 TATTATATATAT
1 TATTTTATATAT
131067 TAATTTTA-ATAT
1 T-ATTTTATATAT
*
131079 TAATTTTTTAATAT
1 T-ATTTTAT-ATAT
* *
131093 TATATTATAGA-
1 TATTTTATATAT
*
131104 TA-TTTA-ATTT
1 TATTTTATATAT
* *
131114 TATATCATATAAAT
1 TAT-T-TTATATAT
131128 TATTTTATATAT
1 TATTTTATATAT
* *
131140 TA-TTAATATTT
1 TATTTTATATAT
* *
131151 TATATCATATAAAT
1 TAT-T-TTATATAT
131165 TATTTTATATAT
1 TATTTTATATAT
131177 TATT
1 TATT
131181 AATATATATA
Statistics
Matches: 82, Mismatches: 21, Indels: 22
0.66 0.17 0.18
Matches are distributed among these distances:
9 1 0.01
10 5 0.06
11 11 0.13
12 33 0.40
13 15 0.18
14 17 0.21
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (12 bp):
TATTTTATATAT
Found at i:131160 original size:37 final size:37
Alignment explanation
Indices: 131110--131185 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
131100 TAGATATTTA
131110 ATTTTATATCATATAAATTATTTTATATATTATTAAT
1 ATTTTATATCATATAAATTATTTTATATATTATTAAT
131147 ATTTTATATCATATAAATTATTTTATATATTATTAAT
1 ATTTTATATCATATAAATTATTTTATATATTATTAAT
131184 AT
1 AT
131186 ATATAATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (37 bp):
ATTTTATATCATATAAATTATTTTATATATTATTAAT
Found at i:137733 original size:36 final size:36
Alignment explanation
Indices: 137682--137753 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
137672 TACGAATTTG
137682 AGTTTCCCCCCATAGGTAATGACAAAGACCCTGATGA
1 AGTTTCCCCCCATAGGTAATGACAAAGA-CCTGATGA
137719 AGTTT-CCCCCATAGGTAATGACAAAGACCTGATGA
1 AGTTTCCCCCCATAGGTAATGACAAAGACCTGATGA
137754 GGTTCAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 8 0.23
36 22 0.63
37 5 0.14
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (36 bp):
AGTTTCCCCCCATAGGTAATGACAAAGACCTGATGA
Found at i:140148 original size:107 final size:108
Alignment explanation
Indices: 139825--140150 Score: 550
Period size: 106 Copynumber: 3.0 Consensus size: 108
139815 ATAATTACAA
*
139825 ATTAATTTTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
1 ATTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
* *
139890 AAATTAAAACGTTAAAATATTATCGTATCAGTAAAGTGTCGAGAT
66 AAATT-AAACGTT-AAATATTACCGTATCAGCAAAGTGTCGAGAT
139935 ATTTAATTCTTAATCTAATAATCATGCATTAAAT-AATCAACTAATTATTACTAATAATTTAAAT
1 A-TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAAT
139999 TAAATTAAACGTTAAA-ATTACCGTATCAGCAAAGTGTCGAGAT
65 TAAATTAAACGTTAAATATTACCGTATCAGCAAAGTGTCGAGAT
*
140042 ATTAATTCTTAATCTAATAATCATGCATTAAATAAATC-ACTAATTATTTCTAATAATTTAAATT
1 ATTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
* *
140106 AAATTAAACGTTAAATGTTACCGTATCAGCAAAGTGTAGAGAT
66 AAATTAAACGTTAAATATTACCGTATCAGCAAAGTGTCGAGAT
140149 AT
1 AT
140151 ATGATTTCCA
Statistics
Matches: 207, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
106 72 0.35
107 57 0.28
108 3 0.01
109 7 0.03
110 37 0.18
111 31 0.15
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (108 bp):
ATTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
AAATTAAACGTTAAATATTACCGTATCAGCAAAGTGTCGAGAT
Found at i:140295 original size:20 final size:20
Alignment explanation
Indices: 140267--140308 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
140257 ATATACTTAA
*
140267 AAAGATAGAGTATTTGAGAG
1 AAAGATAGAGAATTTGAGAG
*
140287 AAAGTTAGAGAATTTGAGAG
1 AAAGATAGAGAATTTGAGAG
140307 AA
1 AA
140309 TTTGGTGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.24
Consensus pattern (20 bp):
AAAGATAGAGAATTTGAGAG
Found at i:140487 original size:50 final size:50
Alignment explanation
Indices: 140433--140558 Score: 164
Period size: 50 Copynumber: 2.5 Consensus size: 50
140423 AGATACCCAG
* *
140433 GTATAGCGCGGATCAGGGGGCGTGCTATACCCACGTGGCGCCAAATCACC
1 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* ** * * *
140483 GTATATCGCGGGGCAGGGGGTGCGTTATACCCACGTGGCGCCAAATCAGC
1 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
140533 GTATAACGC-GATTCAGGGGGCGCGCT
1 GTATAACGCGGA-TCAGGGGGCGCGCT
140559 TTACTGCTAC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
49 1 0.02
50 62 0.98
ACGTcount: A:0.21, C:0.27, G:0.35, T:0.17
Consensus pattern (50 bp):
GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:140632 original size:30 final size:29
Alignment explanation
Indices: 140570--140632 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
140560 TACTGCTACG
* *
140570 GGTGTTAGATCGGGAAATATAATCTGACC
1 GGTGTTAGATCGGGAAATATAATATCACC
* *
140599 GGTGTTAGATCGGTAAATATACTGATCACC
1 GGTGTTAGATCGGGAAATATAAT-ATCACC
140629 GGTG
1 GGTG
140633 ATTTATTGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAATATCACC
Found at i:141328 original size:28 final size:28
Alignment explanation
Indices: 141295--141351 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
141285 TCACTATTGC
* * *
141295 TTTCAAGCATTGGCTTGACAATATAATG
1 TTTCAAGCATTGACTCGACAACATAATG
141323 TTTCAAGCATTGACTCGACAACATAATG
1 TTTCAAGCATTGACTCGACAACATAATG
141351 T
1 T
141352 AAACAGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (28 bp):
TTTCAAGCATTGACTCGACAACATAATG
Found at i:143333 original size:2 final size:2
Alignment explanation
Indices: 143326--143355 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
143316 CATCATGTAT
143326 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
143356 AGCCTGAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:143554 original size:271 final size:253
Alignment explanation
Indices: 143344--144099 Score: 1491
Period size: 253 Copynumber: 3.0 Consensus size: 253
143334 TGTGTGTGTG
143344 TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
1 TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
143409 TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
66 TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
143474 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
131 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
143539 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTA-
196 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTAT
143596 T-TGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
1 TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
143660 TTGTATCATG-ATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
66 TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
143724 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
131 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
143789 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTAT
196 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTAT
143847 TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
1 TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
143912 TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
66 TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
143977 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
131 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
144042 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTAT
196 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTAT
144100 GATTAATTAT
Statistics
Matches: 501, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
250 176 0.35
251 74 0.15
252 74 0.15
253 177 0.35
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (253 bp):
TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTAT
Found at i:143788 original size:250 final size:252
Alignment explanation
Indices: 143344--144100 Score: 1491
Period size: 250 Copynumber: 3.0 Consensus size: 252
143334 TGTGTGTGTG
143344 TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
1 TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
143409 TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
66 TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
143474 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
131 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
143539 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTA
196 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTA
143596 T-TGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
1 TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
143660 TTGTATCATG-ATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
66 TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
143724 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
131 TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
143789 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTA
196 AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTA
143846 TTGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATA
1 -TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATA
143911 ATTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCA
65 ATTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCA
143976 TTGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACT
130 TTGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACT
144041 CAATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTA
195 CAATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTA
144099 TG
1 TG
144101 ATTAATTATT
Statistics
Matches: 502, Mismatches: 0, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
250 176 0.35
251 74 0.15
252 76 0.15
253 176 0.35
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (252 bp):
TGTGTGTGTGTGAGCCTGAGTAATGAGAACATATACATTTGCTTACCGTTTATTTGTTATTATAA
TTGTATCATGAATATGTGCGGATTACCGATATACATCGTTATGAAATTCATCATGTATGTTGCAT
TGGGTTTGTGAAGAGGAAGAATAATCGAAATACAGGTTGGTGCATCCTTACCGGATGATAAACTC
AATTATTGATTTATAGACTGGTGCATCCTTATCGGATGATAAACCATTCATCATGTA
Found at i:144716 original size:60 final size:59
Alignment explanation
Indices: 144643--144788 Score: 143
Period size: 59 Copynumber: 2.5 Consensus size: 59
144633 AAATAAGGAT
* * * *
144643 AAAG-TACATAAATGGTCATCCGATTATAAGATATTGTTTTGTTGAGT-TCTCTAACTATTA
1 AAAGTTACA-AAATGGTCACCCAACTATAAGA-ATTGTTTTGTTGAGTCCCT-TAACTATTA
* * * * *
144703 AAAGTTACAAAATGGTCCCCCAACTATACGAGTTGTTTTTTTGAGTCCCTTGACTATTA
1 AAAGTTACAAAATGGTCACCCAACTATAAGAATTGTTTTGTTGAGTCCCTTAACTATTA
* * *
144762 AAAGTTATAAAATGGTTACCTAACTAT
1 AAAGTTACAAAATGGTCACCCAACTAT
144789 TTATTATGTT
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
59 44 0.62
60 23 0.32
61 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCACCCAACTATAAGAATTGTTTTGTTGAGTCCCTTAACTATTA
Found at i:147443 original size:7 final size:7
Alignment explanation
Indices: 147431--147491 Score: 122
Period size: 7 Copynumber: 8.7 Consensus size: 7
147421 AGAGAAAGAG
147431 GTTGCCT
1 GTTGCCT
147438 GTTGCCT
1 GTTGCCT
147445 GTTGCCT
1 GTTGCCT
147452 GTTGCCT
1 GTTGCCT
147459 GTTGCCT
1 GTTGCCT
147466 GTTGCCT
1 GTTGCCT
147473 GTTGCCT
1 GTTGCCT
147480 GTTGCCT
1 GTTGCCT
147487 GTTGC
1 GTTGC
147492 TAATTAACCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.00, C:0.28, G:0.30, T:0.43
Consensus pattern (7 bp):
GTTGCCT
Found at i:147828 original size:28 final size:26
Alignment explanation
Indices: 147768--147829 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
147758 CATAAATATT
147768 TAAAATA-ATATTTTTATATATTTAA
1 TAAAATATATATTTTTATATATTTAA
*
147793 TATTAATATATA-TTTTAGTATCATTTAA
1 TA-AAATATATATTTTTA-TAT-ATTTAA
147821 TGAAAATAT
1 T-AAAATAT
147830 TAATTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 2 0.07
26 9 0.30
27 6 0.20
28 12 0.40
29 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (26 bp):
TAAAATATATATTTTTATATATTTAA
Found at i:148289 original size:24 final size:24
Alignment explanation
Indices: 148261--148312 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
148251 ATTATTTCAA
148261 TATTTTAAAA-ATAATAATATTAAT
1 TATTTTAAAATA-AATAATATTAAT
** *
148285 TATTTTCTAATAAATAATATTACT
1 TATTTTAAAATAAATAATATTAAT
148309 TATT
1 TATT
148313 ATACTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTTTAAAATAAATAATATTAAT
Found at i:152010 original size:31 final size:30
Alignment explanation
Indices: 151975--152053 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
151965 CAAGTATTAT
151975 ATTAGATATTTTATTAAAATATATATAT-AAG
1 ATTAGATATTTTA--AAAATATATATATCAAG
* * *
152006 ATTAGACATTTTAAAAATATATTTATCATG
1 ATTAGATATTTTAAAAATATATATATCAAG
152036 -TTAGATATTTTAAAAATA
1 ATTAGATATTTTAAAAATA
152054 CACGCACTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 29 0.67
30 2 0.05
31 12 0.28
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (30 bp):
ATTAGATATTTTAAAAATATATATATCAAG
Found at i:156134 original size:21 final size:21
Alignment explanation
Indices: 156091--156134 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
156081 AAAGGTAAAG
* * *
156091 AAAAACGTATCATCAAGACAT
1 AAAAACATATCATAAAAACAT
*
156112 AAAAACATATCATAAAAATAT
1 AAAAACATATCATAAAAACAT
156133 AA
1 AA
156135 TTATTGTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.14, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAACATATCATAAAAACAT
Found at i:163851 original size:26 final size:26
Alignment explanation
Indices: 163817--163874 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
163807 TAACTAACAA
*
163817 TTCTCTTTCCTTTTACGAAACATCTT
1 TTCTTTTTCCTTTTACGAAACATCTT
*
163843 TTCTTTTTCCTTTTCCGAAACATCTT
1 TTCTTTTTCCTTTTACGAAACATCTT
*
163869 TCCTTT
1 TTCTTT
163875 ATCCCTTCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.16, C:0.28, G:0.03, T:0.53
Consensus pattern (26 bp):
TTCTTTTTCCTTTTACGAAACATCTT
Found at i:163883 original size:25 final size:26
Alignment explanation
Indices: 163832--163883 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
163822 TTTCCTTTTA
* * *
163832 CGAAACATCTTTTCTTTTTCCTTTTC
1 CGAAACATCTTTCCTTTATCCTCTTC
163858 CGAAACATCTTTCCTTTATCC-CTTC
1 CGAAACATCTTTCCTTTATCCTCTTC
163883 C
1 C
163884 CTCATTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.17, C:0.33, G:0.04, T:0.46
Consensus pattern (26 bp):
CGAAACATCTTTCCTTTATCCTCTTC
Found at i:173567 original size:18 final size:19
Alignment explanation
Indices: 173526--173567 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
173516 CCTCCTTTGA
* *
173526 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCAT
*
173545 AGGGGAATCGATACCCCAT
1 AGGGGAACCGATACCCCAT
173564 -GGGG
1 AGGGG
173568 TTCTGGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.24, C:0.29, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCAT
Found at i:176449 original size:29 final size:29
Alignment explanation
Indices: 176404--176467 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
176394 AAAAAATTTG
*
176404 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
*
176433 TTAATTGGGTTCAGTTAATAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
*
176462 TAAATT
1 TTAATT
176468 TTAGTTCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.45
Consensus pattern (29 bp):
TTAATTCGGTTCAGTTAATAATTTTCAAA
Found at i:177691 original size:2 final size:2
Alignment explanation
Indices: 177684--177732 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
177674 GCCTGCTGCA
177684 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
177725 AT AT AT AT
1 AT AT AT AT
177733 TAGAATATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:188059 original size:15 final size:15
Alignment explanation
Indices: 188039--188074 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
188029 CAGTTGAGTC
188039 TGGTATACAAGCTGT
1 TGGTATACAAGCTGT
*
188054 TGGTATACAGGCTGT
1 TGGTATACAAGCTGT
188069 T-GTATA
1 TGGTATA
188075 AAAGGGCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (15 bp):
TGGTATACAAGCTGT
Found at i:191331 original size:25 final size:24
Alignment explanation
Indices: 191277--191332 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
191267 CCTTTAATCC
*
191277 TTTTT-ATAAATTTAATTTTTAAA
1 TTTTTAATAAATTTAATATTTAAA
* *
191300 TAATTTAATAAATTTAACTATTTATA
1 T-TTTTAATAAATTTAA-TATTTAAA
191326 TTTTTAA
1 TTTTTAA
191333 AATTCATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.04
24 3 0.12
25 15 0.58
26 7 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTTAATAAATTTAATATTTAAA
Found at i:196476 original size:33 final size:33
Alignment explanation
Indices: 196431--196503 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
196421 GCACCACCAA
* * *
196431 CAGCAGCCTACTGTAGGAGTCTCTAATCAGTTG
1 CAGCAGCCTACTGTAGGAATCCCTAATCAGTCG
*
196464 CAGCAGCTTACTGTAGGAATCCCTAATCAGTCG
1 CAGCAGCCTACTGTAGGAATCCCTAATCAGTCG
196497 CAGCAGC
1 CAGCAGC
196504 AGAATATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (33 bp):
CAGCAGCCTACTGTAGGAATCCCTAATCAGTCG
Found at i:199090 original size:418 final size:417
Alignment explanation
Indices: 198294--199121 Score: 1462
Period size: 418 Copynumber: 2.0 Consensus size: 417
198284 GTTGTGGTGA
198294 GTTGAACGATGATGTGACAGTCTATAGATAATATGACAGTCTATAATTATTTTAAGGGTAAACTA
1 GTTGAACGATGATGTGACAGTCTATAGATAATATGACAGTCTATAATTATTTTAAGGGTAAACTA
* *
198359 CGTAAATGATCACTAATATTTATTAAATTTTTGTTTTCATCACTGATGTTTCAAAAATCACATAT
66 CGCAAATGATCACTAATATTTATTAAATTTTTGTTTTCACCACTGATGTTTCAAAAATCACATAT
*
198424 CGGTCATTAACATTATCGTTTGTCACAAATTGATCACTTGACGTTAACAATCGTTAACAGGAGTG
131 CGGTCATTAACATTATCGTTTGTCACAAATTGATCACTTGACGTTAACAATCGTTAACAGGAGCG
198489 ACGAAAAACACAGCGGACGTATTAACTGCTTACATGGACTAGGTTTATTGGGTTGACTGCTACGT
196 ACGAAAAACACAGCGGACGTATTAACTGCTTACATGGACTAGGTTTATTGGGTTGACTGCTACGT
198554 TGGAGACCCAAAAGCCTTCAACGATCACTTATTCTCCTTTAAAAAACCAATCTCTAAATTTAGGG
261 TGGAGACCCAAAAGCCTTCAACGATCACTTATTCTCCTTTAAAAAACCAATCTCTAAATTTAGGG
* * *
198619 TTTTCATTCCTATCTCTATTCTTTAAAAAAATTGAAAATTGT-AAGAGAAGAGAAATTTTGTGAA
326 TTTTCATTCCTATCTATATTCTTTAAAAAAATTGAAAATTGTAAAGAG-A-AGATATCTTGTGAA
198683 GATGGAAGACTCCATTATGGTGACTTTTG
389 GATGGAAGACTCCATTATGGTGACTTTTG
*
198712 GTTGAACGATGATGTGACAGTCTATAGATAATATGATAGTCTATAATTATTTTAAGGGTAAACTA
1 GTTGAACGATGATGTGACAGTCTATAGATAATATGACAGTCTATAATTATTTTAAGGGTAAACTA
198777 CGCAAATGATCACTAATATTTATTAAATTTTTGTTTTCACCACTGATGTTTCAAAAATCACATAT
66 CGCAAATGATCACTAATATTTATTAAATTTTTGTTTTCACCACTGATGTTTCAAAAATCACATAT
*
198842 CGGTCATTAACATTATCGTTTGTCACAAATTGATCACTTGACGTTAACAATCGTTACCAGGAGCG
131 CGGTCATTAACATTATCGTTTGTCACAAATTGATCACTTGACGTTAACAATCGTTAACAGGAGCG
*
198907 ACGAAAAACACAGCTGACGTATTAACTGCTTACATGGACTAGGTTTATTGGGTTGACTGCTACGT
196 ACGAAAAACACAGCGGACGTATTAACTGCTTACATGGACTAGGTTTATTGGGTTGACTGCTACGT
* *
198972 TGGAGACCCAAAATCCTTCAACGATCACTTATTCTCCTTTAAAAAACCAATCCCTAAACTTAATT
261 TGGAGACCCAAAAGCCTTCAACGATCACTTATTCTCCTTTAAAAAACCAAT--CT---CTAAATT
199037 TAGGGTTTTCATTCCTATCTATATTCTTTAAAAAAATTGAAAATTGT-AAGAGAAGATAAATCTT
321 TAGGGTTTTCATTCCTATCTATATTCTTTAAAAAAATTGAAAATTGTAAAGAGAAGAT--ATCTT
199101 GTGAAGATGGAAGACTCCATT
384 GTGAAGATGGAAGACTCCATT
199122 GATGTTATTC
Statistics
Matches: 392, Mismatches: 11, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
418 304 0.78
420 2 0.01
421 3 0.01
422 1 0.00
423 82 0.21
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (417 bp):
GTTGAACGATGATGTGACAGTCTATAGATAATATGACAGTCTATAATTATTTTAAGGGTAAACTA
CGCAAATGATCACTAATATTTATTAAATTTTTGTTTTCACCACTGATGTTTCAAAAATCACATAT
CGGTCATTAACATTATCGTTTGTCACAAATTGATCACTTGACGTTAACAATCGTTAACAGGAGCG
ACGAAAAACACAGCGGACGTATTAACTGCTTACATGGACTAGGTTTATTGGGTTGACTGCTACGT
TGGAGACCCAAAAGCCTTCAACGATCACTTATTCTCCTTTAAAAAACCAATCTCTAAATTTAGGG
TTTTCATTCCTATCTATATTCTTTAAAAAAATTGAAAATTGTAAAGAGAAGATATCTTGTGAAGA
TGGAAGACTCCATTATGGTGACTTTTG
Found at i:199317 original size:23 final size:22
Alignment explanation
Indices: 199287--199482 Score: 130
Period size: 23 Copynumber: 8.5 Consensus size: 22
199277 TCTCAGACTA
*
199287 ATGGAAGAAGAATAAATTGATTT
1 ATGGAAGAAGAAGAAATTG-TTT
*
199310 ATGGAAGAAGAAGAAACATGTTT
1 ATGGAAGAAGAAGAAA-TTGTTT
* * *
199333 ATGGAAGAAAAATAAATGGGTTT
1 ATGGAAGAAGAAGAAAT-TGTTT
* *
199356 ATGAAAGAAGAAAAAATGTGTTT
1 ATGGAAGAAGAAGAAAT-TGTTT
**
199379 ATGGAAGAAGAAGAAGGTGTTT
1 ATGGAAGAAGAAGAAATTGTTT
* *
199401 ATGGAAGAATAAGGAACA-AGTTT
1 ATGGAAGAAGAA-GAA-ATTGTTT
* *
199424 ATGTATAAGAA-AA-AAATGGGTTTT
1 ATG--GAAGAAGAAGAAAT-TG-TTT
*
199448 ATGGAAGAAGAA-ACAATGAGTTT
1 ATGGAAGAAGAAGA-AAT-TGTTT
199471 ATGGAAGAAGAA
1 ATGGAAGAAGAA
199483 TTATTATTAA
Statistics
Matches: 141, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
21 1 0.01
22 23 0.16
23 97 0.69
24 15 0.11
25 5 0.04
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.24
Consensus pattern (22 bp):
ATGGAAGAAGAAGAAATTGTTT
Found at i:199357 original size:46 final size:45
Alignment explanation
Indices: 199287--199459 Score: 161
Period size: 46 Copynumber: 3.8 Consensus size: 45
199277 TCTCAGACTA
* * *
199287 ATGGAAGAAGAATAAATTGATTTATGGAAGAAGAAGAAACATGTTT
1 ATGGAAGAA-AAAAAATGGGTTTATGGAAGAAGAAGAAACATGTTT
* * **
199333 ATGGAAGAAAAATAAATGGGTTTATGAAAGAAGAAAAAATGTGTTT
1 ATGGAAGAAAAA-AAATGGGTTTATGGAAGAAGAAGAAACATGTTT
* * * * *
199379 ATGGAAGAAGAAGAA-GGTGTTTATGGAAGAATAAGGAACAAGTTT
1 ATGGAAGAAAAAAAATGG-GTTTATGGAAGAAGAAGAAACATGTTT
*
199424 ATGTATA-AGAAAAAAATGGGTTTTATGGAAGAAGAA
1 ATGGA-AGA-AAAAAAATGGG-TTTATGGAAGAAGAA
199460 ACAATGAGTT
Statistics
Matches: 101, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
44 2 0.02
45 29 0.29
46 54 0.53
47 16 0.16
ACGTcount: A:0.48, C:0.01, G:0.26, T:0.25
Consensus pattern (45 bp):
ATGGAAGAAAAAAAATGGGTTTATGGAAGAAGAAGAAACATGTTT
Found at i:199449 original size:69 final size:68
Alignment explanation
Indices: 199291--199479 Score: 184
Period size: 69 Copynumber: 2.7 Consensus size: 68
199281 AGACTAATGG
* * * * * ***
199291 AAGAAGAATAAATTGATTTATGGAAGAAGAAGAAACATGTTTATGGAAGAAAAATAAATGGGTTT
1 AAGAAGAAAAAATGGGTTTATGGAAGAAGAAG-AACGTGTTTATGGAAGAAAAAGAAACAAGTTT
199356 ATGA
65 ATGA
* * * *
199360 AAGAAGAAAAAATGTGTTTATGGAAGAAGAAGAAGGTGTTTATGGAAGAATAAGGAACAAGTTTA
1 AAGAAGAAAAAATGGGTTTATGGAAGAAGAAGAACGTGTTTATGGAAGAAAAAGAAACAAGTTTA
199425 TGTA
66 TG-A
* * *
199429 TAAG-A-AAAAAATGGGTTTTATGGAAGAAGAAACAATGAGTTTATGGAAGAA
1 -AAGAAGAAAAAATGGG-TTTATGGAAGAAG-AAGAACGTGTTTATGGAAGAA
199480 GAATTATTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
68 36 0.36
69 43 0.43
70 21 0.21
ACGTcount: A:0.48, C:0.02, G:0.25, T:0.25
Consensus pattern (68 bp):
AAGAAGAAAAAATGGGTTTATGGAAGAAGAAGAACGTGTTTATGGAAGAAAAAGAAACAAGTTTA
TGA
Found at i:199471 original size:92 final size:92
Alignment explanation
Indices: 199287--199482 Score: 254
Period size: 92 Copynumber: 2.1 Consensus size: 92
199277 TCTCAGACTA
* * *
199287 ATGGAAGAAGAATAAATTGATTTATGGAAGAAGAAGAAACATGTTTATGGAAGAAAAATAAATGG
1 ATGGAAGAAGAAGAAAGTGATTTATGGAAGAAGAAGAAACAAGTTTATGGAAGAAAAATAAATGG
*
199352 GTTTATGAAAGAAGAAAAAATGTGTTT
66 GTTTATGAAAGAAGAAAAAATGAGTTT
* * * *
199379 ATGGAAGAAGAAGAAGGTG-TTTATGGAAGAATAAGGAACAAGTTTATGTATA-AGAAAA-AAAT
1 ATGGAAGAAGAAGAAAGTGATTTATGGAAGAAGAAGAAACAAGTTTATGGA-AGA-AAAATAAAT
* *
199441 GGGTTTTATGGAAGAAGAAACAATGAGTTT
64 GGG-TTTATGAAAGAAGAAAAAATGAGTTT
199471 ATGGAAGAAGAA
1 ATGGAAGAAGAA
199483 TTATTATTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
91 35 0.38
92 56 0.62
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.24
Consensus pattern (92 bp):
ATGGAAGAAGAAGAAAGTGATTTATGGAAGAAGAAGAAACAAGTTTATGGAAGAAAAATAAATGG
GTTTATGAAAGAAGAAAAAATGAGTTT
Found at i:200350 original size:21 final size:21
Alignment explanation
Indices: 200326--200365 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
200316 AAAACAATTA
* *
200326 AATTTATTTATTTTGAAATCC
1 AATTTAATTATTATGAAATCC
200347 AATTTAATTATTATGAAAT
1 AATTTAATTATTATGAAAT
200366 TTACATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
AATTTAATTATTATGAAATCC
Found at i:203237 original size:2 final size:2
Alignment explanation
Indices: 203232--203283 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
203222 GTTATTACCC
203232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
203274 AT AT AT AT AT
1 AT AT AT AT AT
203284 TTATTTTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:203359 original size:24 final size:23
Alignment explanation
Indices: 203297--203369 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
203287 TTTTCTTTGC
203297 ATTTTTATTATTACTATTATATTT
1 ATTTTTATTA-TACTATTATATTT
* *
203321 ATTATTATTTTTACTATTATATTT
1 ATTTTTA-TTATACTATTATATTT
203345 -TCCTTTTATTATACTTATTTATATT
1 AT--TTTTATTATAC-TA-TTATATT
203370 ATATATGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.03
24 24 0.60
25 8 0.20
26 7 0.17
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTTTATTATACTATTATATTT
Found at i:203388 original size:22 final size:22
Alignment explanation
Indices: 203351--203410 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
203341 ATTTTCCTTT
*
203351 TATTATACTTATTTATA-TTATA
1 TATTATA-TTTTTTATATTTATA
*
203373 TATGTATATTTTTTATATTTTATT
1 TAT-TATATTTTTTATA-TTTATA
203397 TATTATATTTTTTA
1 TATTATATTTTTTA
203411 CTTTCTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 11 0.33
23 15 0.45
24 7 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATATTTTTTATATTTATA
Found at i:203408 original size:15 final size:15
Alignment explanation
Indices: 203297--203408 Score: 74
Period size: 15 Copynumber: 7.4 Consensus size: 15
203287 TTTTCTTTGC
203297 ATTTTTA-TTATTACT
1 ATTTTTATTTATTA-T
*
203312 A-TTATATTTATTATT
1 ATTTTTATTTATTA-T
*
203327 ATTTTTA-CTATTAT
1 ATTTTTATTTATTAT
203341 ATTTTCCT-TTTATTAT
1 ATTTT--TATTTATTAT
203357 ACTTATTTATATTA-TAT
1 A-TT-TTTAT-TTATTAT
* * *
203374 ATGTATATTTTTTAT
1 ATTTTTATTTATTAT
203389 A-TTTTATTTATTAT
1 ATTTTTATTTATTAT
203403 ATTTTT
1 ATTTTT
203409 TACTTTCTCT
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
14 23 0.31
15 26 0.35
16 14 0.19
17 7 0.09
18 5 0.07
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (15 bp):
ATTTTTATTTATTAT
Found at i:203448 original size:12 final size:11
Alignment explanation
Indices: 203426--203466 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
203416 TCTTTCTTTT
203426 TATTATTCTTG
1 TATTATTCTTG
203437 TATTATTACTTG
1 TATTATT-CTTG
* *
203449 TATTATTTTTA
1 TATTATTCTTG
203460 TATTATT
1 TATTATT
203467 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:203644 original size:32 final size:34
Alignment explanation
Indices: 203590--203652 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
203580 TATATTTTTC
203590 TATTAATTTTCTATATTTTTATT-ATCATTATATA
1 TATTAATTTTCTATATTTTTATTGAT-ATTATATA
*
203624 TATTTATTTTCT-T-TTTTTATTGATATTAT
1 TATTAATTTTCTATATTTTTATTGATATTAT
203653 TGTTGTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 13 0.48
33 3 0.11
34 11 0.41
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (34 bp):
TATTAATTTTCTATATTTTTATTGATATTATATA
Found at i:203855 original size:2 final size:2
Alignment explanation
Indices: 203848--203872 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
203838 GTATTGTTAC
203848 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
203873 TGTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:204054 original size:24 final size:23
Alignment explanation
Indices: 204018--204068 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
204008 TGTTTATTTG
* *
204018 TTTTATTTATTTTCTT-TTTCTT
1 TTTTATTTATTTTATTATTTATT
204040 TTTTATATATATTTTATTATTTATT
1 TTTTAT-T-TATTTTATTATTTATT
204065 TTTT
1 TTTT
204069 TACTTACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
24 8 0.33
25 9 0.38
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTATTTATTTTATTATTTATT
Found at i:208757 original size:16 final size:16
Alignment explanation
Indices: 208701--208777 Score: 52
Period size: 17 Copynumber: 4.7 Consensus size: 16
208691 TCCAATCAAG
208701 AACAA-AAAAGAAAAGA
1 AACAAGAAAA-AAAAGA
* *
208717 AGCAA-AAAAGCAAAAAA
1 AACAAGAAAA--AAAAGA
208734 AACAAAGAAAAAAAAGA
1 AAC-AAGAAAAAAAAGA
**
208751 AACAAGAACAAAAATCA
1 AACAAGAA-AAAAAAGA
208768 AA-AAGAAAAA
1 AACAAGAAAAA
208778 GGGACAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
15 3 0.06
16 18 0.36
17 23 0.46
18 2 0.04
19 4 0.08
ACGTcount: A:0.79, C:0.09, G:0.10, T:0.01
Consensus pattern (16 bp):
AACAAGAAAAAAAAGA
Found at i:208760 original size:23 final size:22
Alignment explanation
Indices: 208720--208777 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
208710 GAAAAGAAGC
208720 AAAAAAGCAAAAAAAACAAAGAA-
1 AAAAAAG-AAAAAAAACAAA-AAT
*
208743 AAAAAAGAAACAAGAACAAAAAT
1 AAAAAAGAAA-AAAAACAAAAAT
*
208766 CAAAAAGAAAAA
1 AAAAAAGAAAAA
208778 GGGACAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAAAAACAAAAAT
Found at i:209625 original size:22 final size:22
Alignment explanation
Indices: 209551--209627 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
209541 GCTACCCCAT
*
209551 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
209573 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
209595 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
209617 CAAACCTTTGA
1 CAAACCTTTGA
209628 CCAAACATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:210633 original size:106 final size:106
Alignment explanation
Indices: 210443--212136 Score: 2569
Period size: 106 Copynumber: 16.0 Consensus size: 106
210433 ATATCATGCC
* * * *
210443 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
210508 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
210549 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGTACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
210614 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
210655 ACTCCAGACAACGCAAGGTCAACTTCACAACGAAGGGAGCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
210720 AATTTCAGAGCCACTTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
210761 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
210826 AATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
210867 ACTCAAGACAATGCAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
210932 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
210973 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAGCAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
211038 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
211079 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
211144 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
211185 ACTCAAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAAAAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
211250 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
211291 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
211356 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
211397 ACTCCAGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
211462 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
211503 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
211568 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
211609 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
211674 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
211715 ACTCCAGACAATGCAAGTTCAACTTCACGACAAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
211780 AATTTCAGAGCCAATTTCAACTTCACAGC-ATAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGA-AGGATATTGG
* * * * * * *
211821 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGTTGTTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
211886 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
211927 AC-CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT-T
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT
*
211987 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
212027 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * *
212092 AGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
212133 ACTC
1 ACTC
212137 AGAACAATGC
Statistics
Matches: 1453, Mismatches: 124, Indels: 22
0.91 0.08 0.01
Matches are distributed among these distances:
100 81 0.06
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 5 0.00
106 1352 0.93
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:212969 original size:37 final size:36
Alignment explanation
Indices: 212867--212971 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 36
212857 CCTTTTCGTC
212867 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCT-AAAATAGGATAGAATT
* * * *
212904 TTGCTAGGATTCAGACTCCTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCC-TAAAATAGGATAGAATT
* * *
212941 CTACTATGATTTAAACTTCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAA-ATAGGAT
212972 CCACAAGCAT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
36 4 0.07
37 51 0.91
38 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
Found at i:214090 original size:2 final size:2
Alignment explanation
Indices: 214083--214119 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
214073 GTATTGTTAC
214083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
214120 TGTAATTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:214249 original size:33 final size:31
Alignment explanation
Indices: 214180--214251 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 31
214170 TCGTCATTTA
* *
214180 ATTTATTA-ATTTATATATATTTACTTTTTT
1 ATTTATTATATATATATATATTTACTTTGTT
214210 ATTTATTATATATATATATTATTCGTACTTTGTT
1 ATTTATTATATATATATA-TATT--TACTTTGTT
214244 A-TTATTAT
1 ATTTATTAT
214252 TTTGTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 8 0.22
31 8 0.22
32 4 0.11
33 7 0.19
34 9 0.25
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (31 bp):
ATTTATTATATATATATATATTTACTTTGTT
Found at i:218076 original size:9 final size:9
Alignment explanation
Indices: 218062--218099 Score: 67
Period size: 9 Copynumber: 4.1 Consensus size: 9
218052 TTGGTTGGAA
218062 AATTGGAGC
1 AATTGGAGC
218071 AATTGGAGC
1 AATTGGAGC
218080 AATTGGAGC
1 AATTGGAGC
218089 AATTGGCAGC
1 AATTGG-AGC
218099 A
1 A
218100 TGATTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (9 bp):
AATTGGAGC
Found at i:221142 original size:60 final size:60
Alignment explanation
Indices: 221053--221179 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
221043 TAAAGTATGC
* * *
221053 AAATGAT-TCTCCGACTATATGATGATACTTTGTTGAATACAT-TGACTATTAAAAGTTACA
1 AAATGATCTCTCCGACTATAGGATGATACTTTATTGAAT-CATCTAACTATTAAAA-TTACA
* **
221113 AAATGATCTCT-CGACTATAGGAT-ATTACTTTATTGAGTCATCTAACTATTAAAATTTTA
1 AAATGATCTCTCCGACTATAGGATGA-TACTTTATTGAATCATCTAACTATTAAAATTACA
221172 AAATGATC
1 AAATGATC
221180 ACCTGACTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
59 15 0.26
60 40 0.69
61 3 0.05
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (60 bp):
AAATGATCTCTCCGACTATAGGATGATACTTTATTGAATCATCTAACTATTAAAATTACA
Found at i:221975 original size:41 final size:41
Alignment explanation
Indices: 221923--222001 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
221913 TATATTTATG
221923 CATTTTATGTGTATTTTCAATCAATAATATATTTTCGTCTC
1 CATTTTATGTGTATTTTCAATCAATAATATATTTTCGTCTC
* *
221964 CATTTTATGTGTATTTTCTATCAATAATCTATTTTCGT
1 CATTTTATGTGTATTTTCAATCAATAATATATTTTCGT
222002 ATCCTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (41 bp):
CATTTTATGTGTATTTTCAATCAATAATATATTTTCGTCTC
Found at i:222285 original size:70 final size:71
Alignment explanation
Indices: 222172--222313 Score: 268
Period size: 70 Copynumber: 2.0 Consensus size: 71
222162 TCATAGGTTC
222172 ACATGCTTTATTGCCCTTGTCATTCCAAAATGTATTCAAAGTCTTTAGTTTCTTTGAATTTTTT-
1 ACATGCTTTATTGCCCTTGTCATTCCAAAATGTATTCAAAGTCTTTAGTTTCTTTGAATTTTTTC
222236 CCACAA
66 CCACAA
*
222242 ACATGCTTTATTGCCCTTGTCATTCCAAAATGTATTCAAAGTCTTTAGTTTCTTTTAATTTTTTC
1 ACATGCTTTATTGCCCTTGTCATTCCAAAATGTATTCAAAGTCTTTAGTTTCTTTGAATTTTTTC
222307 CCACAA
66 CCACAA
222313 A
1 A
222314 AAGACGTATT
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 63 0.90
71 7 0.10
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.44
Consensus pattern (71 bp):
ACATGCTTTATTGCCCTTGTCATTCCAAAATGTATTCAAAGTCTTTAGTTTCTTTGAATTTTTTC
CCACAA
Found at i:235428 original size:18 final size:18
Alignment explanation
Indices: 235394--235429 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
235384 ATTTAATATA
*
235394 ATTACATATTTGATCTAT
1 ATTACATATATGATCTAT
*
235412 ATTACATATATGTTCTAT
1 ATTACATATATGATCTAT
235430 CAATAGATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTACATATATGATCTAT
Found at i:235990 original size:13 final size:13
Alignment explanation
Indices: 235974--235998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
235964 GTTAATGTTA
235974 TAAAATAATAATT
1 TAAAATAATAATT
235987 TAAAATAATAAT
1 TAAAATAATAAT
235999 AAATCATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAATAATAATT
Found at i:236620 original size:14 final size:14
Alignment explanation
Indices: 236597--236665 Score: 50
Period size: 15 Copynumber: 4.8 Consensus size: 14
236587 TATTTATACA
*
236597 TATAAAAAATAATC
1 TATAATAAATAATC
*
236611 TATAATAAATACAGAC
1 TATAATAAATA-A-TC
* * *
236627 -ATCATAAAAAATA
1 TATAATAAATAATC
*
236640 TAAATATAAATAATC
1 TATA-ATAAATAATC
236655 TATAATAAATA
1 TATAATAAATA
236666 CAGACGATGT
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
14 19 0.47
15 20 0.50
16 1 0.03
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.29
Consensus pattern (14 bp):
TATAATAAATAATC
Found at i:238994 original size:58 final size:58
Alignment explanation
Indices: 238900--239014 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 58
238890 TGTTAAACCC
* * *
238900 CGACTATAAGGTGTTGCTCTTTTGAGCTCCTAACTATTAAAAGTTACAAAAGGATCAT
1 CGACTATAAGATATTGCTCTTTTGAGCTCCTAACTATTAAAAATTACAAAAGGATCAT
* *
238958 CGACTATAAGATATTGCT-TTGTTGAG-TCACTGACTATTAAAAATTACAAAATGATCA
1 CGACTATAAGATATTGCTCTT-TTGAGCTC-CTAACTATTAAAAATTACAAAAGGATCA
239015 CTCCACTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 4 0.08
58 46 0.92
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (58 bp):
CGACTATAAGATATTGCTCTTTTGAGCTCCTAACTATTAAAAATTACAAAAGGATCAT
Found at i:241707 original size:18 final size:20
Alignment explanation
Indices: 241666--241709 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
241656 TTGTTTATTT
*
241666 TAATATTTAATAATTATTTTA
1 TAATATTTAATAA-TATTTGA
241687 TAATATTTAA-AA-ATTTGA
1 TAATATTTAATAATATTTGA
241705 TAATA
1 TAATA
241710 AAAATATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
20 2 0.09
21 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TAATATTTAATAATATTTGA
Found at i:243933 original size:20 final size:20
Alignment explanation
Indices: 243908--243948 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
243898 ATTCACTCGA
243908 TATGAATGTGGTAGAAATTC
1 TATGAATGTGGTAGAAATTC
243928 TATGAATGTGGTAGAAATTC
1 TATGAATGTGGTAGAAATTC
243948 T
1 T
243949 GTAACTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (20 bp):
TATGAATGTGGTAGAAATTC
Found at i:244677 original size:18 final size:18
Alignment explanation
Indices: 244651--244685 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
244641 TCGAAAGGAC
*
244651 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
244669 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
244686 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:257058 original size:62 final size:64
Alignment explanation
Indices: 256988--257140 Score: 177
Period size: 66 Copynumber: 2.4 Consensus size: 64
256978 GTTAGTCCTT
* * * *
256988 CAAATTCAATGATAAATAAGATTATGTT-TATA-TAATTATGTTTGTTTGTAGTGTTATT-TCTC
1 CAAATTCAATGATAAATAAGATTATATTATATATTAATTATGGTTATATGTAGTGTTATTCT-TC
* *
257050 CAAATTCAATGATAAACAAGATTAATATTAATATATTAATTATGGTTATATGTATTGTTATTCTT
1 CAAATTCAATGATAAATAAGATT-ATATT-ATATATTAATTATGGTTATATGTAGTGTTATTCTT
*
257115 T
64 C
* *
257116 TAAATTCAATGATAAATATGATTAT
1 CAAATTCAATGATAAATAAGATTAT
257141 TAATATGTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
62 22 0.29
63 4 0.05
65 6 0.08
66 43 0.57
67 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (64 bp):
CAAATTCAATGATAAATAAGATTATATTATATATTAATTATGGTTATATGTAGTGTTATTCTTC
Found at i:257407 original size:33 final size:33
Alignment explanation
Indices: 257370--257447 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 33
257360 TAATAAGTAA
* * **
257370 TGAGTTTTTAGTGGGTTTTTATTTAATAGATAG
1 TGAGTTTTTAGTAGATGATTATTTAATAGATAG
* * *
257403 TGAGTTTTCAGTAGATGATTATTTAATAGGTAT
1 TGAGTTTTTAGTAGATGATTATTTAATAGATAG
*
257436 TGAGTCTTTAGT
1 TGAGTTTTTAGT
257448 TTATGTAATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (33 bp):
TGAGTTTTTAGTAGATGATTATTTAATAGATAG
Found at i:263674 original size:27 final size:27
Alignment explanation
Indices: 263643--263697 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
263633 TTTAAGCATC
263643 GATTATTATTGGAAATATTAATAATTA
1 GATTATTATTGGAAATATTAATAATTA
263670 GATTATTATTGGAAATATTAATAATTA
1 GATTATTATTGGAAATATTAATAATTA
263697 G
1 G
263698 TTAGTCTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (27 bp):
GATTATTATTGGAAATATTAATAATTA
Found at i:264654 original size:21 final size:23
Alignment explanation
Indices: 264616--264663 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
264606 ATGTTCAACA
264616 TTTTTATGAGTTATGAAATCA-CT
1 TTTTTATGAGTTATGAAAT-AGCT
*
264639 TTTTTATTA-TTA-GAAATAGCT
1 TTTTTATGAGTTATGAAATAGCT
264660 TTTT
1 TTTT
264664 GAATTTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 1 0.04
21 11 0.48
22 3 0.13
23 8 0.35
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.54
Consensus pattern (23 bp):
TTTTTATGAGTTATGAAATAGCT
Done.