Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 74 of 78
Found at i:15489103 original size:16 final size:17
Alignment explanation
Indices: 15489077--15489110 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
15489067 CTTTCTTCTT
*
15489077 TCATATTCTATTTTTAA
1 TCATATTCTATCTTTAA
15489094 TCAT-TTCTATCTTTAA
1 TCATATTCTATCTTTAA
15489110 T
1 T
15489111 TTTTGCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (17 bp):
TCATATTCTATCTTTAA
Found at i:15491346 original size:21 final size:18
Alignment explanation
Indices: 15491320--15491360 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
15491310 AACATTTTTG
15491320 TCCATTTCCATTATTTCAATT
1 TCCATTTCC-TT-TTTC-ATT
15491341 TCCATTTCCTTTTTCATT
1 TCCATTTCCTTTTTCATT
15491359 TC
1 TC
15491361 TTAATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 2 0.10
21 9 0.45
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56
Consensus pattern (18 bp):
TCCATTTCCTTTTTCATT
Found at i:15491818 original size:16 final size:16
Alignment explanation
Indices: 15491794--15491830 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
15491784 ATAAGTTATC
*
15491794 TTCACTTTCTTACTAT
1 TTCATTTTCTTACTAT
*
15491810 TTCATTTTCTTATTAT
1 TTCATTTTCTTACTAT
15491826 TTCAT
1 TTCAT
15491831 CATTTCCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCATTTTCTTACTAT
Found at i:15499278 original size:19 final size:20
Alignment explanation
Indices: 15499251--15499298 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
15499241 CCAAGAGCAC
*
15499251 GTATCTTCATTAAAAA-CAT
1 GTATTTTCATTAAAAATCAT
*
15499270 GTATTTTCATTAAAAATCTT
1 GTATTTTCATTAAAAATCAT
15499290 GTATTTTCA
1 GTATTTTCA
15499299 AAGGGGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (20 bp):
GTATTTTCATTAAAAATCAT
Found at i:15504325 original size:14 final size:14
Alignment explanation
Indices: 15504289--15504327 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
15504279 TGGGAGGAAG
*
15504289 GATTTATCCATGAA
1 GATTTATTCATGAA
**
15504303 GATACATTCATGAA
1 GATTTATTCATGAA
15504317 GATTTATTCAT
1 GATTTATTCAT
15504328 TAATTCATCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (14 bp):
GATTTATTCATGAA
Found at i:15515022 original size:15 final size:15
Alignment explanation
Indices: 15515004--15515033 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15514994 ATTCAGCATT
15515004 CAAAAAAAAGAAAAG
1 CAAAAAAAAGAAAAG
*
15515019 CAAAGAAAAGAAAAG
1 CAAAAAAAAGAAAAG
15515034 AAAGAAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAGAAAAG
Found at i:15522196 original size:15 final size:15
Alignment explanation
Indices: 15522176--15522205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15522166 ATTCAGCATT
*
15522176 CAAAAAGAAGAAAAG
1 CAAAAAAAAGAAAAG
15522191 CAAAAAAAAGAAAAG
1 CAAAAAAAAGAAAAG
15522206 AAATAAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAGAAAAG
Found at i:15529123 original size:15 final size:15
Alignment explanation
Indices: 15529112--15529141 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15529102 ATTCAAAAAG
15529112 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
15529127 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
15529141 A
1 A
15529142 GTTGAAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:15535289 original size:35 final size:35
Alignment explanation
Indices: 15535208--15535355 Score: 197
Period size: 35 Copynumber: 4.2 Consensus size: 35
15535198 TACTATATGT
* * *
15535208 TCATCACCATCTTCCATCACTATTTTCACACCTATA
1 TCATCACCATCTTCCATCACCA-TTGCACGCCTATA
* *
15535244 ACATCGCCATCTTCCATCACCATTGCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
**
15535279 TCATCACCATCTTATATCACCATTGCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
* * *
15535314 TCATCCCCATCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
15535349 TCATCAC
1 TCATCAC
15535356 TATTCCCTTA
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
35 80 0.81
36 19 0.19
ACGTcount: A:0.26, C:0.38, G:0.04, T:0.32
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTGCACGCCTATA
Found at i:15535315 original size:19 final size:19
Alignment explanation
Indices: 15535259--15535316 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
15535249 GCCATCTTCC
15535259 ATCACCATTGCACGCCTAT
1 ATCACCATTGCACGCCTAT
* * * *
15535278 ATCATCA--CCA-TCTTAT
1 ATCACCATTGCACGCCTAT
15535294 ATCACCATTGCACGCCTAT
1 ATCACCATTGCACGCCTAT
15535313 ATCA
1 ATCA
15535317 TCCCCATCTT
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
16 10 0.36
17 2 0.07
18 2 0.07
19 14 0.50
ACGTcount: A:0.29, C:0.34, G:0.07, T:0.29
Consensus pattern (19 bp):
ATCACCATTGCACGCCTAT
Found at i:15547611 original size:9 final size:9
Alignment explanation
Indices: 15547597--15547623 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
15547587 TCATACCATC
15547597 CCTTATAAG
1 CCTTATAAG
15547606 CCTTATAAG
1 CCTTATAAG
15547615 CCTTATAAG
1 CCTTATAAG
15547624 AAACGGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (9 bp):
CCTTATAAG
Found at i:15547763 original size:35 final size:35
Alignment explanation
Indices: 15547685--15547835 Score: 196
Period size: 35 Copynumber: 4.3 Consensus size: 35
15547675 TACTATATGT
* ** *
15547685 TCATAACCATCTTCCATCACCATTTTAACACCTATA
1 TCATCACCATCTTCCATCACCA-TTGCACGCCTATA
*
15547721 ACATCACCATCTTCCATCACCATTGCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
*
15547756 T-ATTCACCATCTTCTATCACCATTGCACGCCTATA
1 TCA-TCACCATCTTCCATCACCATTGCACGCCTATA
* * *
15547791 TCATCACCATCTTCTATCACCATTTCACTCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
15547826 TCATCACCAT
1 TCATCACCAT
15547836 TCTCTTATCA
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
34 1 0.01
35 82 0.79
36 21 0.20
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.32
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTGCACGCCTATA
Found at i:15552206 original size:35 final size:35
Alignment explanation
Indices: 15552160--15552237 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
15552150 AACCTAAAAT
*
15552160 ATCACCATCTTCCGTCACCATTGCACGCCTATATC
1 ATCACCATCTTCCATCACCATTGCACGCCTATATC
* *
15552195 ATCACCATCTTCTATCACCATTTCACGCCTATATC
1 ATCACCATCTTCCATCACCATTGCACGCCTATATC
15552230 ATCACCAT
1 ATCACCAT
15552238 TCCCTAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.26, C:0.38, G:0.05, T:0.31
Consensus pattern (35 bp):
ATCACCATCTTCCATCACCATTGCACGCCTATATC
Found at i:15552628 original size:18 final size:17
Alignment explanation
Indices: 15552602--15552638 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
15552592 TCAATTGATA
*
15552602 AAGAGAAAAAGAGAGAAG
1 AAGAAAAAAAGAGA-AAG
15552620 AAGAAAAAAAGAGAAAG
1 AAGAAAAAAAGAGAAAG
15552637 AA
1 AA
15552639 AATACTCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAGAGAAAG
Found at i:15558153 original size:35 final size:35
Alignment explanation
Indices: 15558092--15558297 Score: 313
Period size: 35 Copynumber: 5.9 Consensus size: 35
15558082 GTTCATCACC
* * *
15558092 ATCACCATTTTCACACCTATAACATCACCATCTTCC
1 ATCACCA-TTGCACACCTATATCATCACCATCTTCT
*
15558128 ATCACCATTGCACGCCTATATCATCACCATCTTCT
1 ATCACCATTGCACACCTATATCATCACCATCTTCT
15558163 ATCACCATTGCACACCTATATCATCACCATCTTCT
1 ATCACCATTGCACACCTATATCATCACCATCTTCT
* * *
15558198 ATCACCATTTCACGCCTATATCAACACCATCTTCT
1 ATCACCATTGCACACCTATATCATCACCATCTTCT
15558233 ATCACCATTGCACACCTATATCATCACCATCTTCT
1 ATCACCATTGCACACCTATATCATCACCATCTTCT
* * *
15558268 ATCACCATTTCACGCCTATATAATCACCAT
1 ATCACCATTGCACACCTATATCATCACCAT
15558298 TCCTTATCAT
Statistics
Matches: 156, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 149 0.96
36 7 0.04
ACGTcount: A:0.29, C:0.37, G:0.03, T:0.31
Consensus pattern (35 bp):
ATCACCATTGCACACCTATATCATCACCATCTTCT
Found at i:15558188 original size:70 final size:70
Alignment explanation
Indices: 15558092--15558297 Score: 349
Period size: 70 Copynumber: 2.9 Consensus size: 70
15558082 GTTCATCACC
* * * *
15558092 ATCACCATTTTCACACCTATAACATCACCATCTTCCATCACCATTGCACGCCTATATCATCACCA
1 ATCACCA-TTGCACACCTATATCATCACCATCTTCTATCACCATTTCACGCCTATATCATCACCA
15558157 TCTTCT
65 TCTTCT
*
15558163 ATCACCATTGCACACCTATATCATCACCATCTTCTATCACCATTTCACGCCTATATCAACACCAT
1 ATCACCATTGCACACCTATATCATCACCATCTTCTATCACCATTTCACGCCTATATCATCACCAT
15558228 CTTCT
66 CTTCT
*
15558233 ATCACCATTGCACACCTATATCATCACCATCTTCTATCACCATTTCACGCCTATATAATCACCAT
1 ATCACCATTGCACACCTATATCATCACCATCTTCTATCACCATTTCACGCCTATATCATCACCAT
15558298 TCCTTATCAT
Statistics
Matches: 128, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
70 121 0.95
71 7 0.05
ACGTcount: A:0.29, C:0.37, G:0.03, T:0.31
Consensus pattern (70 bp):
ATCACCATTGCACACCTATATCATCACCATCTTCTATCACCATTTCACGCCTATATCATCACCAT
CTTCT
Found at i:15558189 original size:22 final size:23
Alignment explanation
Indices: 15558163--15558262 Score: 50
Period size: 22 Copynumber: 4.3 Consensus size: 23
15558153 ACCATCTTCT
15558163 ATCACCAT-TGC-ACACCTATATC
1 ATCACCATATGCAACACC-ATATC
* * * *
15558185 ATCACCATCTTCTATCACCATTTC
1 ATCACCATATGC-AACACCATATC
* *
15558209 A-CGCCTATAT-CAACACCATCTTC
1 ATCACC-ATATGCAACACCAT-ATC
15558232 TATCACCAT-TGC-ACACCTATATC
1 -ATCACCATATGCAACACC-ATATC
15558255 ATCACCAT
1 ATCACCAT
15558263 CTTCTATCAC
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
22 23 0.38
23 17 0.28
24 14 0.23
25 7 0.11
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.30
Consensus pattern (23 bp):
ATCACCATATGCAACACCATATC
Found at i:15558740 original size:23 final size:23
Alignment explanation
Indices: 15558714--15558771 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 23
15558704 GTTAGCTTAG
15558714 AGGAGACACATGCACGCCTAACA
1 AGGAGACACATGCACGCCTAACA
15558737 AGGAGACACATGCACGCCTAACA
1 AGGAGACACATGCACGCCTAACA
15558760 AGG-GAACACATG
1 AGGAG-ACACATG
15558772 ACCATCCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.40, C:0.28, G:0.24, T:0.09
Consensus pattern (23 bp):
AGGAGACACATGCACGCCTAACA
Found at i:15567132 original size:13 final size:13
Alignment explanation
Indices: 15567110--15567139 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
15567100 ACTAGACACA
15567110 TTTC-ACATACCT
1 TTTCAACATACCT
15567122 TTTCAACATACCT
1 TTTCAACATACCT
15567135 TTTCA
1 TTTCA
15567140 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:15571817 original size:16 final size:17
Alignment explanation
Indices: 15571785--15571818 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15571775 CACTTTGCAC
*
15571785 TTCTTTTTGTATTTTGT
1 TTCTTTTTGTATATTGT
15571802 TTCTTTTTGT-TATTGT
1 TTCTTTTTGTATATTGT
15571818 T
1 T
15571819 ACACGTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (17 bp):
TTCTTTTTGTATATTGT
Found at i:15600012 original size:15 final size:15
Alignment explanation
Indices: 15599992--15600032 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
15599982 AGAAGACGTT
15599992 GGAGTTGAAAATGAG
1 GGAGTTGAAAATGAG
*
15600007 GGAGTTAAAAATGAG
1 GGAGTTGAAAATGAG
*
15600022 AGAGTTGAAAA
1 GGAGTTGAAAA
15600033 GGATGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (15 bp):
GGAGTTGAAAATGAG
Found at i:15600194 original size:24 final size:25
Alignment explanation
Indices: 15600167--15600221 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
15600157 AAAATCATGG
*
15600167 CTTTTGGAA-AACTAAAAGAT-GTGA
1 CTTTTGGAAGAACCAAAAG-TCGTGA
15600191 CTTTT-GAAGAACCAAAAGTCGTGA
1 CTTTTGGAAGAACCAAAAGTCGTGA
15600215 CTTTTGG
1 CTTTTGG
15600222 CGATTCACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.15
24 22 0.81
25 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (25 bp):
CTTTTGGAAGAACCAAAAGTCGTGA
Found at i:15603367 original size:11 final size:12
Alignment explanation
Indices: 15603338--15603372 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
15603328 TTTGGTACTG
15603338 GAAACAAGATAA
1 GAAACAAGATAA
*
15603350 GAAACAAGATTA
1 GAAACAAGATAA
15603362 -AAACAAGATAA
1 GAAACAAGATAA
15603373 ATAAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:15614386 original size:13 final size:13
Alignment explanation
Indices: 15614368--15614436 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
15614358 CTACATATAA
*
15614368 CATCACCATCTTC
1 CATCACCATATTC
15614381 CATCACCAT-TTC
1 CATCACCATATTC
* * **
15614393 CA-C-GCTTATAA
1 CATCACCATATTC
*
15614404 CATCACCATCTTC
1 CATCACCATATTC
*
15614417 CATCACCATAGTC
1 CATCACCATATTC
15614430 CATCACC
1 CATCACC
15614437 TTCACGCCAA
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.10
12 6 0.14
13 30 0.71
ACGTcount: A:0.28, C:0.42, G:0.03, T:0.28
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:15615178 original size:17 final size:17
Alignment explanation
Indices: 15615156--15615188 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15615146 ATCCTACCCA
15615156 TATACCATAACCATTTC
1 TATACCATAACCATTTC
*
15615173 TATACCCTAACCATTT
1 TATACCATAACCATTT
15615189 TTTAAGCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTC
Found at i:15636803 original size:45 final size:45
Alignment explanation
Indices: 15636753--15636848 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
15636743 AGAGTGAAGG
*
15636753 ACAAATTTTACCTAACAAATCTTCTTCTACTATTTCTTTTTCCTA
1 ACAAATTTTACCAAACAAATCTTCTTCTACTATTTCTTTTTCCTA
* *
15636798 ACAAATTTTACCAAACAAATCTTTTTCTACTATTTCTTTTTTCTA
1 ACAAATTTTACCAAACAAATCTTCTTCTACTATTTCTTTTTCCTA
15636843 ACAAAT
1 ACAAAT
15636849 ATGTCTTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (45 bp):
ACAAATTTTACCAAACAAATCTTCTTCTACTATTTCTTTTTCCTA
Found at i:15643793 original size:14 final size:15
Alignment explanation
Indices: 15643759--15643805 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
15643749 AATTTGGAGT
15643759 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
15643774 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
15643788 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
15643805 G
1 G
15643806 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:15650475 original size:17 final size:16
Alignment explanation
Indices: 15650448--15650482 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
15650438 TAAACTATAA
*
15650448 TGCATATATAATGATG
1 TGCATATATAAAGATG
15650464 TGCATAATATAAAGATG
1 TGCAT-ATATAAAGATG
15650481 TG
1 TG
15650483 AACTATAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (16 bp):
TGCATATATAAAGATG
Found at i:15659555 original size:19 final size:20
Alignment explanation
Indices: 15659508--15659558 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
15659498 GAAACCCCTT
*
15659508 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
15659528 TTAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
15659547 TGAAGATACATG
1 TGAAAATACATG
15659559 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:15662689 original size:18 final size:18
Alignment explanation
Indices: 15662668--15662749 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
15662658 CTTGGCTTGC
15662668 TTTCTTTTTGAATTTCTT
1 TTTCTTTTTGAATTTCTT
* *
15662686 TTTCTTTTCTTATTTTCTT
1 TTTCTTTT-TGAATTTCTT
* *
15662705 TTT-TTTCTAAATTTTCTT
1 TTTCTTTTTGAA-TTTCTT
* *
15662723 CTTCTTTTT-ATATTT-TC
1 TTTCTTTTTGA-ATTTCTT
15662740 TTTCTTTTTG
1 TTTCTTTTTG
15662750 TACTCCAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
17 11 0.22
18 23 0.46
19 16 0.32
ACGTcount: A:0.10, C:0.13, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTCTTTTTGAATTTCTT
Found at i:15662704 original size:19 final size:20
Alignment explanation
Indices: 15662680--15662742 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 20
15662670 TCTTTTTGAA
15662680 TTTCTTTTTCTTTTCT-TAT
1 TTTCTTTTTCTTTTCTATAT
*
15662699 TTTC-TTTT-TTTTCTAAAT
1 TTTCTTTTTCTTTTCTATAT
*
15662717 TTTCTTCTTCTTTT-TATAT
1 TTTCTTTTTCTTTTCTATAT
15662736 TTTCTTT
1 TTTCTTT
15662743 CTTTTTGTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
17 6 0.16
18 10 0.27
19 17 0.46
20 4 0.11
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTCTTTTTCTTTTCTATAT
Found at i:15662744 original size:32 final size:31
Alignment explanation
Indices: 15662685--15662744 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
15662675 TTGAATTTCT
* *
15662685 TTTTCTTTTCTTATTTTCTTTTTTTTCTAAA
1 TTTTCTTTTCTTATTTTATTTTCTTTCTAAA
15662716 TTTTCTTCTTCTT-TTTATATTTTCTTTCT
1 TTTTCTT-TTCTTATTT-TATTTTCTTTCT
15662745 TTTTGTACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTCTTTTCTTATTTTATTTTCTTTCTAAA
Found at i:15663482 original size:19 final size:20
Alignment explanation
Indices: 15663441--15663491 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
15663431 GAAACCCCTT
*
15663441 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
15663461 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
15663480 TGAAGATACATG
1 TGAAAATACATG
15663492 CTATTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:15667468 original size:19 final size:18
Alignment explanation
Indices: 15667429--15667486 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
15667419 TTGGAGTGCA
* *
15667429 AAAAGAA-AGAAAAAGAT
1 AAAAGAAGAGAAAAACAG
15667446 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAA-CAG
*
15667465 AAAAGAAGA-AAAGAAAAG
1 AAAAGAAGAGAAA-AACAG
15667483 AAAA
1 AAAA
15667487 AGAAAAATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 7 0.20
18 16 0.46
19 12 0.34
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (18 bp):
AAAAGAAGAGAAAAACAG
Found at i:15667487 original size:19 final size:20
Alignment explanation
Indices: 15667432--15667490 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
15667422 GAGTGCAAAA
15667432 AGAAAGAAAAAGATAAAAGAAG
1 AGAAAG-AAAAGA-AAAAGAAG
*
15667454 AGAAA-AATCAG-AAAAGAAG
1 AGAAAGAA-AAGAAAAAGAAG
15667473 A-AAAGAAAAGAAAAAGAA
1 AGAAAGAAAAGAAAAAGAA
15667491 AAATTCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 18 0.56
20 2 0.06
21 2 0.06
22 5 0.16
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (20 bp):
AGAAAGAAAAGAAAAAGAAG
Found at i:15668155 original size:21 final size:19
Alignment explanation
Indices: 15668093--15668163 Score: 97
Period size: 19 Copynumber: 3.6 Consensus size: 19
15668083 CGGCCAAGAG
15668093 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
*
15668112 CATGTATCTTAATTAAAAT
1 CATGTATCTTCATTAAAAT
*
15668131 CATGTATTTTCATTTAAATAT
1 CATGTATCTTCA-TTAAA-AT
*
15668152 CATGTATTTTCA
1 CATGTATCTTCA
15668164 AAGGTTTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 28 0.60
20 5 0.11
21 14 0.30
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:15680283 original size:19 final size:21
Alignment explanation
Indices: 15680259--15680304 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
15680249 AAAAATCAGC
15680259 AAAGAAATTG-AAGCACTCAAA
1 AAAGAAATTGAAAGCACTC-AA
15680280 AGAAGAAATTGAAAGCACTCAA
1 A-AAGAAATTGAAAGCACTCAA
15680302 AAA
1 AAA
15680305 AAGGAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.13
22 12 0.52
23 8 0.35
ACGTcount: A:0.59, C:0.13, G:0.15, T:0.13
Consensus pattern (21 bp):
AAAGAAATTGAAAGCACTCAA
Found at i:15680287 original size:22 final size:23
Alignment explanation
Indices: 15680260--15680303 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
15680250 AAAATCAGCA
15680260 AAGAAATTG-AAGCACTCAAAAG
1 AAGAAATTGAAAGCACTCAAAAG
15680282 AAGAAATTGAAAGCACTCAAAA
1 AAGAAATTGAAAGCACTCAAAA
15680304 AAAGGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.14
Consensus pattern (23 bp):
AAGAAATTGAAAGCACTCAAAAG
Found at i:15690096 original size:22 final size:21
Alignment explanation
Indices: 15690071--15690120 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
15690061 GAAAAAAATC
*
15690071 AGAAAAGAAGCACTCGAAAAGA
1 AGAAAAGAAACACTC-AAAAGA
*
15690093 AGAAATTGAAACACTCAAAAGA
1 AGAAA-AGAAACACTCAAAAGA
15690115 AGAAAA
1 AGAAAA
15690121 AAAAGAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (21 bp):
AGAAAAGAAACACTCAAAAGA
Found at i:15698156 original size:15 final size:15
Alignment explanation
Indices: 15698121--15698149 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15698111 GTGCTTCAAC
15698121 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
15698135 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
15698150 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:15698198 original size:28 final size:27
Alignment explanation
Indices: 15698144--15698201 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
15698134 TTTCTTTGCT
* * *
15698144 TTTCTTCTTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGGAGTGCTGCAATTTC
*
15698171 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTTGGAGTGCTGCAATTTC
15698199 TTT
1 TTT
15698202 TATGATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.60
Consensus pattern (27 bp):
TTTCTTCTTTTGGAGTGCTGCAATTTC
Found at i:15701281 original size:15 final size:15
Alignment explanation
Indices: 15701261--15701297 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
15701251 AAAGGGTTCA
15701261 TTGATGTAAGGCACT
1 TTGATGTAAGGCACT
*
15701276 TTGATGTAAGGCTCT
1 TTGATGTAAGGCACT
15701291 TCTGATG
1 T-TGATG
15701298 CCTTAGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.38
Consensus pattern (15 bp):
TTGATGTAAGGCACT
Found at i:15705825 original size:13 final size:13
Alignment explanation
Indices: 15705801--15705842 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
15705791 TTTGGAGTGC
15705801 AAAAGAAAGAAAAG
1 AAAAG-AAGAAAAG
15705815 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
*
15705828 AAAA-AACAAAAG
1 AAAAGAAGAAAAG
15705840 AAA
1 AAA
15705843 GGTGAAGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 10 0.37
13 12 0.44
14 5 0.19
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:15705840 original size:12 final size:13
Alignment explanation
Indices: 15705810--15705842 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
15705800 CAAAAGAAAG
*
15705810 AAAAGAAAAGAAG
1 AAAAGAAAAGAAC
15705823 AAAAGAAAA-AAC
1 AAAAGAAAAGAAC
15705835 AAAAGAAA
1 AAAAGAAA
15705843 GGTGAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAC
Found at i:15712673 original size:19 final size:21
Alignment explanation
Indices: 15712649--15712700 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
15712639 CGGCCAAGAG
*
15712649 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
15712668 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
15712689 CATGTATTTTCA
1 CATGTATTTTCA
15712701 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:15716500 original size:19 final size:21
Alignment explanation
Indices: 15716476--15716527 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
15716466 TGGCCAAGAG
*
15716476 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
15716495 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
15716516 CATGTATTTTCA
1 CATGTATTTTCA
15716528 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:15717441 original size:13 final size:13
Alignment explanation
Indices: 15717423--15717462 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
15717413 CATAGCTGGA
15717423 TTGAGCTAAAGAT
1 TTGAGCTAAAGAT
*
15717436 TTGAGCTGAAGAT
1 TTGAGCTAAAGAT
15717449 TTGAGCTACAAGAT
1 TTGAGCTA-AAGAT
15717463 GACCTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (13 bp):
TTGAGCTAAAGAT
Found at i:15717724 original size:51 final size:51
Alignment explanation
Indices: 15717648--15717749 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
15717638 CTCAAACATG
15717648 AAGGGACACCTTTCTCAAACATTGTGACCTTTCATGAATGTTGCTACCCAT
1 AAGGGACACCTTTCTCAAACATTGTGACCTTTCATGAATGTTGCTACCCAT
15717699 AAGGGACACCTTTCTCAAACATTGTGACCTTTCATGAATGTTGCTACCCAT
1 AAGGGACACCTTTCTCAAACATTGTGACCTTTCATGAATGTTGCTACCCAT
15717750 GAAGATGCCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
AAGGGACACCTTTCTCAAACATTGTGACCTTTCATGAATGTTGCTACCCAT
Found at i:15719497 original size:17 final size:17
Alignment explanation
Indices: 15719472--15719514 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
15719462 TATGTGAAAT
*
15719472 AATAAAGATAAAAAAAG
1 AATAGAGATAAAAAAAG
*
15719489 AATAGAGATAAAGAAAG
1 AATAGAGATAAAAAAAG
*
15719506 GATAGAGAT
1 AATAGAGAT
15719515 GGCTGTGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (17 bp):
AATAGAGATAAAAAAAG
Found at i:15719956 original size:20 final size:20
Alignment explanation
Indices: 15719931--15719986 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
15719921 GAAACCCCTT
15719931 TGAAAATACAAGATTTTTGA
1 TGAAAATACAAGATTTTTGA
15719951 TGAAAATACATA-ATTTTTGA
1 TGAAAATACA-AGATTTTTGA
*
15719971 TGAAAATACATGATTT
1 TGAAAATACAAGATTT
15719987 AAATGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (20 bp):
TGAAAATACAAGATTTTTGA
Found at i:15724093 original size:19 final size:21
Alignment explanation
Indices: 15724053--15724101 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
15724043 ACCCCTTTGG
*
15724053 AAATTCATGACTTTTAAATGA
1 AAATACATGACTTTTAAATGA
15724074 AAATACATGA-TTTT-AATGA
1 AAATACATGACTTTTAAATGA
*
15724093 AGATACATG
1 AAATACATG
15724102 TTCTTGGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.50
20 4 0.15
21 9 0.35
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
AAATACATGACTTTTAAATGA
Found at i:15728180 original size:19 final size:21
Alignment explanation
Indices: 15728137--15728188 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
15728127 GAAACCCCTT
*
15728137 TGAAAATTCATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
15728158 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
15728177 TGAAGATACATG
1 TGAAAATACATG
15728189 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:15730191 original size:24 final size:24
Alignment explanation
Indices: 15730141--15730190 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
15730131 AACACAACTC
* *
15730141 TTGGCACTTCAAATGACGTTTCTT
1 TTGGAACTTCAAATGACGTATCTT
*
15730165 TTGGAACTTCAAATGGCGTCATCTT
1 TTGGAACTTCAAATGACGT-ATCTT
15730190 T
1 T
15730191 GAAAAAGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (24 bp):
TTGGAACTTCAAATGACGTATCTT
Found at i:15731540 original size:13 final size:13
Alignment explanation
Indices: 15731503--15731540 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
15731493 CTTTTTGAAC
*
15731503 TTCTCTTTTTCTT
1 TTCTTTTTTTCTT
*
15731516 TTCTTTTATTCTT
1 TTCTTTTTTTCTT
15731529 TTCTTTTTTTCT
1 TTCTTTTTTTCT
15731541 GATTTTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:15731867 original size:19 final size:20
Alignment explanation
Indices: 15731830--15731869 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
15731820 GAATAATAAT
15731830 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
15731850 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
15731869 A
1 A
15731870 ATAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:15732325 original size:19 final size:21
Alignment explanation
Indices: 15732284--15732333 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
15732274 AACCCCTTTA
*
15732284 AAAATTCATGACTTTTAAATG
1 AAAATACATGACTTTTAAATG
15732305 AAAATACATGA-TTTT-AATG
1 AAAATACATGACTTTTAAATG
*
15732324 AAGATACATG
1 AAAATACATG
15732334 CTCTTAGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 13 0.48
20 4 0.15
21 10 0.37
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (21 bp):
AAAATACATGACTTTTAAATG
Found at i:15740260 original size:19 final size:20
Alignment explanation
Indices: 15740213--15740263 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
15740203 GAAACCTCTT
* *
15740213 TGAAAATTCATGATTTATGA
1 TGAAAATACATGATTTATAA
15740233 TGAAAATACATGATTTA-AA
1 TGAAAATACATGATTTATAA
*
15740252 TGAAGATACATG
1 TGAAAATACATG
15740264 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTATAA
Found at i:15740945 original size:13 final size:13
Alignment explanation
Indices: 15740927--15740960 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15740917 GATACTGGTC
15740927 TTGATGAAGGATG
1 TTGATGAAGGATG
*
15740940 TTGATGATGGATG
1 TTGATGAAGGATG
*
15740953 ATGATGAA
1 TTGATGAA
15740961 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:15746592 original size:17 final size:17
Alignment explanation
Indices: 15746570--15746609 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
15746560 TCCAATTATA
15746570 ATTTCAGCAATCTTGCC
1 ATTTCAGCAATCTTGCC
15746587 ATTTCAGCAATCTTGCC
1 ATTTCAGCAATCTTGCC
15746604 ATTTCA
1 ATTTCA
15746610 TGCATAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (17 bp):
ATTTCAGCAATCTTGCC
Found at i:15747152 original size:15 final size:15
Alignment explanation
Indices: 15747116--15747145 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15747106 GTGCTTCAAC
15747116 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
15747130 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
15747145 T
1 T
15747146 CTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:15747168 original size:27 final size:29
Alignment explanation
Indices: 15747138--15747199 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 29
15747128 CTTTTCTTTG
*
15747138 CTTTTC-TTCTTTTTGAA-TGC-TGAATTT
1 CTTTTCTTTC-TTTTGAAGTGCTTCAATTT
15747165 C-TTTCTTTCTTTTGAAGTGCTTCAATTT
1 CTTTTCTTTCTTTTGAAGTGCTTCAATTT
15747193 CTTTTCT
1 CTTTTCT
15747200 GATTTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 11 0.37
27 7 0.23
28 7 0.23
29 5 0.17
ACGTcount: A:0.13, C:0.18, G:0.10, T:0.60
Consensus pattern (29 bp):
CTTTTCTTTCTTTTGAAGTGCTTCAATTT
Found at i:15756236 original size:11 final size:11
Alignment explanation
Indices: 15756217--15756308 Score: 53
Period size: 11 Copynumber: 7.9 Consensus size: 11
15756207 CCTTGGCTTG
15756217 TTTTCTTTTTT
1 TTTTCTTTTTT
* *
15756228 TTTTATTTTCT
1 TTTTCTTTTTT
15756239 TTTTCTTTTCTT
1 TTTTCTTTT-TT
15756251 TTCTTCTTTTCTAAAT
1 TT-TTCTTTT-T---T
*
15756267 TTTTCTTCTTCT
1 TTTTCTT-TTTT
*
15756279 TTTT-TTCTTT
1 TTTTCTTTTTT
*
15756289 TTGTC-TTTTT
1 TTTTCTTTTTT
*
15756299 CTTTCTTTTT
1 TTTTCTTTTT
15756309 GCACTCCAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
10 12 0.19
11 23 0.37
12 8 0.13
13 9 0.15
15 5 0.08
16 5 0.08
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:15756288 original size:8 final size:8
Alignment explanation
Indices: 15756217--15756308 Score: 57
Period size: 8 Copynumber: 11.2 Consensus size: 8
15756207 CCTTGGCTTG
15756217 TTTTCTTT
1 TTTTCTTT
15756225 TTTT-TTT
1 TTTTCTTT
15756232 ATTTTCTTT
1 -TTTTCTTT
*
15756241 TTCTT-TTC
1 TT-TTCTTT
*
15756249 TTTTCTTC
1 TTTTCTTT
*
15756257 TTTTCTAAAT
1 TTTTCT--TT
15756267 TTTTC--T
1 TTTTCTTT
*
15756273 TCTTCTTT
1 TTTTCTTT
15756281 TTTTCTTT
1 TTTTCTTT
*
15756289 TTGTCTTTT
1 TTTTC-TTT
15756298 TCTTTCTTT
1 T-TTTCTTT
15756307 TT
1 TT
15756309 GCACTCCAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
6 5 0.07
7 5 0.07
8 36 0.54
9 13 0.19
10 8 0.12
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTTCTTT
Found at i:15756295 original size:22 final size:22
Alignment explanation
Indices: 15756266--15756307 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
15756256 CTTTTCTAAA
15756266 TTTTTCTTCTTCTTT-TTTTCT
1 TTTTTCTTCTTCTTTCTTTTCT
*
15756287 TTTTGTCTTTTTCTTTCTTTT
1 TTTT-TCTTCTTCTTTCTTTT
15756308 TGCACTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTCTTCTTCTTTCTTTTCT
Found at i:15756302 original size:14 final size:14
Alignment explanation
Indices: 15756217--15756302 Score: 54
Period size: 14 Copynumber: 6.1 Consensus size: 14
15756207 CCTTGGCTTG
*
15756217 TTTTCT-TTTTTTT
1 TTTTCTCTTTTTCT
*
15756230 TTATTTTCTTTTTC-
1 TT-TTCTCTTTTTCT
15756244 TTTTCT-TTTCTTC-
1 TTTTCTCTTT-TTCT
*
15756257 TTTTCTAAATTTTTCT
1 TTTTCT--CTTTTTCT
* *
15756273 TCTTCTTTTTTTCT
1 TTTTCTCTTTTTCT
*
15756287 TTTTGTCTTTTTCT
1 TTTTCTCTTTTTCT
15756301 TT
1 TT
15756303 CTTTTTGCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
12 3 0.05
13 14 0.24
14 25 0.43
15 8 0.14
16 8 0.14
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (14 bp):
TTTTCTCTTTTTCT
Found at i:15757571 original size:13 final size:13
Alignment explanation
Indices: 15757550--15757582 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
15757540 ACCTCTAGGT
15757550 AGCTCAAAAGTCC
1 AGCTCAAAAGTCC
*
15757563 AGTTCAAAAGTCC
1 AGCTCAAAAGTCC
15757576 AGCTCAA
1 AGCTCAA
15757583 GTTAGCTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.18
Consensus pattern (13 bp):
AGCTCAAAAGTCC
Found at i:15759569 original size:24 final size:24
Alignment explanation
Indices: 15759542--15759587 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
15759532 TGATCCTATT
* * *
15759542 CTTTGGCACTTCAAGTGATATATC
1 CTTTGGAACGTCAAGGGATATATC
15759566 CTTTGGAACGTCAAGGGATATA
1 CTTTGGAACGTCAAGGGATATA
15759588 ACTGTTGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (24 bp):
CTTTGGAACGTCAAGGGATATATC
Found at i:15759667 original size:24 final size:23
Alignment explanation
Indices: 15759592--15759667 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
15759582 GATATAACTG
15759592 TTGGTTCTTCAAAAGACATGTCT
1 TTGGTTCTTCAAAAGACATGTCT
* ** * *
15759615 TGTGGATCACCAAAAGTCATGACT
1 T-TGGTTCTTCAAAAGACATGTCT
*
15759639 ATTGGTTCTTCAAACGACATGTCT
1 -TTGGTTCTTCAAAAGACATGTCT
15759663 CTTGG
1 -TTGG
15759668 ATTATCCTAC
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
23 1 0.03
24 37 0.95
25 1 0.03
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (23 bp):
TTGGTTCTTCAAAAGACATGTCT
Found at i:15765508 original size:24 final size:25
Alignment explanation
Indices: 15765480--15765537 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
15765470 TAAGATAAGA
*
15765480 AATAAATAAGATTAATAT-GGGAAT
1 AATAAATAAGAATAATATAGGGAAT
* *
15765504 AATAAAT-GGAATAATATATGGAAT
1 AATAAATAAGAATAATATAGGGAAT
15765528 AATAAGATAA
1 AATAA-ATAA
15765538 ATAATGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 8 0.30
24 17 0.63
25 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.28
Consensus pattern (25 bp):
AATAAATAAGAATAATATAGGGAAT
Found at i:15765516 original size:12 final size:12
Alignment explanation
Indices: 15765499--15765532 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
15765489 GATTAATATG
15765499 GGAATAATAAAT
1 GGAATAATAAAT
*
15765511 GGAATAATATAT
1 GGAATAATAAAT
15765523 GGAATAATAA
1 GGAATAATAA
15765533 GATAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (12 bp):
GGAATAATAAAT
Found at i:15765540 original size:24 final size:25
Alignment explanation
Indices: 15765494--15765542 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
15765484 AATAAGATTA
*
15765494 ATATGGGAATAATAAATGGAATAAT
1 ATATGGGAATAATAAATGAAATAAT
15765519 ATAT-GGAATAATAAGAT-AAATAAT
1 ATATGGGAATAATAA-ATGAAATAAT
15765543 GAAATGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (25 bp):
ATATGGGAATAATAAATGAAATAAT
Found at i:15781150 original size:380 final size:380
Alignment explanation
Indices: 15780449--15781209 Score: 1504
Period size: 380 Copynumber: 2.0 Consensus size: 380
15780439 GGTAAATGGT
15780449 CTGATAAGAGATGGTAGTTGAAGACTTAGTTGTGATTATGATATGGAAACGAAATATGGAAGGGT
1 CTGATAAGAGATGGTAGTTGAAGACTTAGTTGTGATTATGATATGGAAACGAAATATGGAAGGGT
*
15780514 GAATTTGATAGTATCTTAGAATAACCAAGAAAGAACCAGTGTTATAACAAGCAAAGACCCAGTCT
66 GAATTTGATAGTATCTTAGAATAACCAAGAAAGAACCAGTGTTATAACAAGCAAAGACCCAGTAT
15780579 TACAAATTGTTCTAAGGGGTAGTAAATAGGACTTTGACCCGCTATCTATAAGAAGATAGGAACCA
131 TACAAATTGTTCTAAGGGGTAGTAAATAGGACTTTGACCCGCTATCTATAAGAAGATAGGAACCA
*
15780644 TAAGTATCAGGGTGAAAAAAAGACGTCACAAGCATAAGCTTGATAAGCCGGGTTTGACGCCACAA
196 TAAGTATCAAGGTGAAAAAAAGACGTCACAAGCATAAGCTTGATAAGCCGGGTTTGACGCCACAA
15780709 GTAACAAGTTACTTGATAAGTCGATAAAAGCCACAAGGACTCAATAAGAGAAAACTCTCAAGTTT
261 GTAACAAGTTACTTGATAAGTCGATAAAAGCCACAAGGACTCAATAAGAGAAAACTCTCAAGTTT
15780774 AATTTCAAATTCAAAGTTAAGTTTCTACAATGCAATATGAAGTCCATTTATAGGA
326 AATTTCAAATTCAAAGTTAAGTTTCTACAATGCAATATGAAGTCCATTTATAGGA
15780829 CTGATAAGAGATGGTAGTTGAAGACTTAGTTGTGATTATGATATGGAAACGAAATATGGAAGGGT
1 CTGATAAGAGATGGTAGTTGAAGACTTAGTTGTGATTATGATATGGAAACGAAATATGGAAGGGT
15780894 GAATTTGATAGTATCTTAGAATAACCAAGAAAGAACCAGTGTTATAACAAGCAAAGACCCAGTAT
66 GAATTTGATAGTATCTTAGAATAACCAAGAAAGAACCAGTGTTATAACAAGCAAAGACCCAGTAT
15780959 TACAAATTGTTCTAAGGGGTAGTAAATAGGACTTTGACCCGCTATCTATAAGAAGATAGGAACCA
131 TACAAATTGTTCTAAGGGGTAGTAAATAGGACTTTGACCCGCTATCTATAAGAAGATAGGAACCA
15781024 TAAGTATCAAGGTGAAAAAAAGACGTCACAAGCATAAGCTTGATAAGCCGGGTTTGACGCCACAA
196 TAAGTATCAAGGTGAAAAAAAGACGTCACAAGCATAAGCTTGATAAGCCGGGTTTGACGCCACAA
15781089 GTAACAAGTTACTTGATAAGTCGATAAAAGCCACAAGGACTCAATAAGAGAAAACTCTCAAGTTT
261 GTAACAAGTTACTTGATAAGTCGATAAAAGCCACAAGGACTCAATAAGAGAAAACTCTCAAGTTT
15781154 AATTTCAAATTCAAAGTTAAGTTTCTACAATGCAATATGAAGTCCATTTATAGGA
326 AATTTCAAATTCAAAGTTAAGTTTCTACAATGCAATATGAAGTCCATTTATAGGA
15781209 C
1 C
15781210 GTGAATCATG
Statistics
Matches: 379, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
380 379 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (380 bp):
CTGATAAGAGATGGTAGTTGAAGACTTAGTTGTGATTATGATATGGAAACGAAATATGGAAGGGT
GAATTTGATAGTATCTTAGAATAACCAAGAAAGAACCAGTGTTATAACAAGCAAAGACCCAGTAT
TACAAATTGTTCTAAGGGGTAGTAAATAGGACTTTGACCCGCTATCTATAAGAAGATAGGAACCA
TAAGTATCAAGGTGAAAAAAAGACGTCACAAGCATAAGCTTGATAAGCCGGGTTTGACGCCACAA
GTAACAAGTTACTTGATAAGTCGATAAAAGCCACAAGGACTCAATAAGAGAAAACTCTCAAGTTT
AATTTCAAATTCAAAGTTAAGTTTCTACAATGCAATATGAAGTCCATTTATAGGA
Found at i:15782358 original size:34 final size:33
Alignment explanation
Indices: 15782290--15782358 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
15782280 GTTGATGAAT
*
15782290 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* *
15782323 GAAGGATGATGTTATTGGCG-TGATAATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGA-AATGGTAATG
15782357 GA
1 GA
15782359 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:15790707 original size:8 final size:8
Alignment explanation
Indices: 15790670--15790706 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
15790660 TTTTTTGAGA
15790670 TTTTGGCTT
1 TTTTGG-TT
15790679 TTTTGGTT
1 TTTTGGTT
15790687 TTTTGGTT
1 TTTTGGTT
*
15790695 TTTTTGTT
1 TTTTGGTT
15790703 TTTT
1 TTTT
15790707 TAAATTAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.78
Consensus pattern (8 bp):
TTTTGGTT
Found at i:15791062 original size:11 final size:12
Alignment explanation
Indices: 15791032--15791077 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
15791022 TTGGTGCTGG
15791032 AAACAAGATAAA
1 AAACAAGATAAA
* *
15791044 AAATAAGAT-TA
1 AAACAAGATAAA
15791055 AAACAAGATAAA
1 AAACAAGATAAA
*
15791067 GAA-AAGATAAA
1 AAACAAGATAAA
15791078 GGAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:15791062 original size:23 final size:22
Alignment explanation
Indices: 15791032--15791074 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
15791022 TTGGTGCTGG
15791032 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
15791055 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
15791075 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:15806063 original size:34 final size:33
Alignment explanation
Indices: 15805995--15806063 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
15805985 GTTGATGAAT
*
15805995 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* *
15806028 GAAGGATGATGTTATTGGCG-TGATAATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGA-AATGGTAATG
15806062 GA
1 GA
15806064 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:15810051 original size:12 final size:13
Alignment explanation
Indices: 15810034--15810063 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
15810024 GTTGTAGGAG
15810034 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
15810046 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
15810059 TCTTT
1 TCTTT
15810064 CTTGTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:15810487 original size:34 final size:33
Alignment explanation
Indices: 15810419--15810487 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
15810409 GTTGATGAAT
*
15810419 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* *
15810452 GAAGGATGATGTTATTGGCG-TGATAATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGA-AATGGTAATG
15810486 GA
1 GA
15810488 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:15813846 original size:19 final size:21
Alignment explanation
Indices: 15813822--15813873 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
15813812 TGGCCAAGAG
*
15813822 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
15813841 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
15813862 CATGTATTTTCA
1 CATGTATTTTCA
15813874 AAGGGGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:15814601 original size:16 final size:16
Alignment explanation
Indices: 15814580--15814626 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
15814570 GCAAAAAGAA
15814580 AAAAAAAGACAAAAAG
1 AAAAAAAGACAAAAAG
15814596 AAAAAAA-ATCAAAATAG
1 AAAAAAAGA-CAAAA-AG
*
15814613 AAGAAAAGA-AAAAA
1 AAAAAAAGACAAAAA
15814627 AAGAAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 2 0.07
16 16 0.59
17 8 0.30
18 1 0.04
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (16 bp):
AAAAAAAGACAAAAAG
Found at i:15814609 original size:25 final size:25
Alignment explanation
Indices: 15814581--15814628 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
15814571 CAAAAAGAAA
15814581 AAAAAAGACA-AAAAGAAAAAAAATC
1 AAAAAAGA-AGAAAAGAAAAAAAATC
*
15814606 AAAATAGAAGAAAAGAAAAAAAA
1 AAAAAAGAAGAAAAGAAAAAAAA
15814629 GAAGAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.81, C:0.04, G:0.10, T:0.04
Consensus pattern (25 bp):
AAAAAAGAAGAAAAGAAAAAAAATC
Found at i:15817865 original size:19 final size:21
Alignment explanation
Indices: 15817841--15817892 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
15817831 CGGCCAAGAG
*
15817841 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
15817860 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
15817881 CATGTATTTTCA
1 CATGTATTTTCA
15817893 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:15821573 original size:11 final size:11
Alignment explanation
Indices: 15821551--15821630 Score: 65
Period size: 11 Copynumber: 6.8 Consensus size: 11
15821541 AAATGGAATT
15821551 TGGTGATGATA
1 TGGTGATGATA
15821562 TAGGTG-TGATA
1 T-GGTGATGATA
15821573 TGGTGATGGACTA
1 TGGTGAT-GA-TA
15821586 TGGTGATGATA
1 TGGTGATGATA
*
15821597 TAGGCG-TGATAA
1 T-GGTGATGAT-A
*
15821609 TGGTGATGGAAGA
1 TGGTGAT-G-ATA
15821622 TGGTGATGA
1 TGGTGATGA
15821631 ACAGATTGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
10 4 0.07
11 19 0.33
12 15 0.26
13 18 0.32
14 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.39, T:0.31
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:15821579 original size:22 final size:24
Alignment explanation
Indices: 15821551--15821597 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
15821541 AAATGGAATT
15821551 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
15821573 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
15821597 T
1 T
15821598 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:15821590 original size:35 final size:36
Alignment explanation
Indices: 15821551--15821630 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
15821541 AAATGGAATT
* **
15821551 TGGTGATGATATAGGTGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
15821586 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
15821622 TGGTGATGA
1 TGGTGATGA
15821631 ACAGATTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 20 0.49
36 21 0.51
ACGTcount: A:0.28, C:0.03, G:0.39, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
Found at i:15825220 original size:6 final size:6
Alignment explanation
Indices: 15825205--15825246 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
15825195 TGTAGGAGTA
*
15825205 TTTTTC -TTTTC TTTTTA TTTTTC TTCTTTC TTTTTC TCTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC T-TTTT
15825247 TGTTCCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 5 0.16
6 16 0.52
7 10 0.32
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:15825225 original size:17 final size:19
Alignment explanation
Indices: 15825203--15825239 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
15825193 GATGTAGGAG
15825203 TATTTTTC-T-TTTCTTTT
1 TATTTTTCTTCTTTCTTTT
15825220 TATTTTTCTTCTTTCTTTT
1 TATTTTTCTTCTTTCTTTT
15825239 T
1 T
15825240 CTCTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 9 0.50
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (19 bp):
TATTTTTCTTCTTTCTTTT
Found at i:15825684 original size:35 final size:36
Alignment explanation
Indices: 15825638--15825717 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
15825628 AAATGAAATT
* **
15825638 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
15825673 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
15825709 TGGTGATGA
1 TGGTGATGA
15825718 ACATATTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 20 0.49
36 21 0.51
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
Found at i:15828778 original size:11 final size:10
Alignment explanation
Indices: 15828762--15828814 Score: 61
Period size: 11 Copynumber: 4.9 Consensus size: 10
15828752 ATTGGAGTGC
15828762 AAAAAGAAAA
1 AAAAAGAAAA
15828772 GAAAAAGACAAA
1 -AAAAAGA-AAA
*
15828784 AAGAAGAAAA
1 AAAAAGAAAA
15828794 AAAAACGAAAAA
1 AAAAA-G-AAAA
15828806 AAAAAGAAA
1 AAAAAGAAA
15828815 TTCAAAAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 10 0.27
11 15 0.41
12 12 0.32
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:15828783 original size:19 final size:19
Alignment explanation
Indices: 15828761--15828814 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
15828751 AATTGGAGTG
*
15828761 CAAAAAGAAAAGAAAAAGA
1 CAAAAAGAAAAGAAAAAAA
15828780 CAAAAAGAAGAA-AAAAAAA
1 CAAAAAGAA-AAGAAAAAAA
*
15828799 CGAAAAAAAAAAGAAA
1 C-AAAAAGAAAAGAAA
15828815 TTCAAAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (19 bp):
CAAAAAGAAAAGAAAAAAA
Found at i:15828785 original size:14 final size:12
Alignment explanation
Indices: 15828762--15828814 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
15828752 ATTGGAGTGC
*
15828762 AAAAAGAAAAGA
1 AAAAAAAAAAGA
15828774 AAAAGACAAAAAGA
1 AAAA-A-AAAAAGA
15828788 AGAAAAAAAAACG-
1 A-AAAAAAAAA-GA
15828801 AAAAAAAAAAGA
1 AAAAAAAAAAGA
15828813 AA
1 AA
15828815 TTCAAAAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
11 1 0.03
12 15 0.43
13 7 0.20
14 9 0.26
15 3 0.09
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:15828793 original size:22 final size:22
Alignment explanation
Indices: 15828762--15828814 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
15828752 ATTGGAGTGC
*
15828762 AAAAAGAAAAGAAAAA-GACAAA
1 AAAAAGAAAA-AAAAACGAAAAA
*
15828784 AAGAAGAAAAAAAAACGAAAAA
1 AAAAAGAAAAAAAAACGAAAAA
15828806 AAAAAGAAA
1 AAAAAGAAA
15828815 TTCAAAAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAACGAAAAA
Found at i:15835217 original size:13 final size:12
Alignment explanation
Indices: 15835191--15835249 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
15835181 CTTATTGAAT
15835191 TTTTC-TTTTTC
1 TTTTCTTTTTTC
15835202 TTTTCTTTTATTC
1 TTTTCTTTT-TTC
15835215 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
15835229 TCTTCTTTTGTC
1 TTTTCTTTTTTC
15835241 TTTTTCTTT
1 -TTTTCTTT
15835250 CTTTTGACAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:15835550 original size:19 final size:20
Alignment explanation
Indices: 15835522--15835561 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
15835512 GGATAATAAT
15835522 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
15835542 ATAAG-AATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
15835561 A
1 A
15835562 GGATGGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:15836016 original size:19 final size:20
Alignment explanation
Indices: 15835975--15836025 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
15835965 GAAACCCCTT
*
15835975 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
15835995 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
15836014 TGAAGATACATG
1 TGAAAATACATG
15836026 CTCTTGTCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:15836941 original size:30 final size:31
Alignment explanation
Indices: 15836902--15836961 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
15836892 ACATGCTGCC
**
15836902 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
15836933 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
15836962 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:15848601 original size:19 final size:19
Alignment explanation
Indices: 15848550--15848593 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
15848540 AAGAAATGGA
15848550 AAGGTAGAAGAAAGGTTTT
1 AAGGTAGAAGAAAGGTTTT
15848569 AAGGTAGAAGAAAGGTTTT
1 AAGGTAGAAGAAAGGTTTT
15848588 AAGGTA
1 AAGGTA
15848594 TTTAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (19 bp):
AAGGTAGAAGAAAGGTTTT
Found at i:15848819 original size:8 final size:8
Alignment explanation
Indices: 15848789--15848830 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
15848779 TCTTTTTGAA
15848789 CTTCTCTTT
1 CTTCT-TTT
15848798 -TTCTTTT
1 CTTCTTTT
15848805 CTTTTCTTTT
1 C--TTCTTTT
15848815 CTTCTTTT
1 CTTCTTTT
15848823 CTTCTTTT
1 CTTCTTTT
15848831 ATGATTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.10
8 19 0.63
10 8 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
CTTCTTTT
Found at i:15853113 original size:24 final size:21
Alignment explanation
Indices: 15853078--15853120 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
15853068 GGCTCATTCT
*
15853078 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
15853101 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
15853121 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:15860108 original size:18 final size:17
Alignment explanation
Indices: 15860087--15860166 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 17
15860077 CCTTGGATTG
15860087 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG-ATTTTT
15860105 CTTT-TTCTTT--TCTTTT
1 CTTTCTT-TTTGAT-TTTT
15860121 C-TTCTTTTCTGATTTTT
1 CTTTCTTTT-TGATTTTT
*
15860138 CTCTTC-TTTTGTCTTTTT
1 CT-TTCTTTTTG-ATTTTT
*
15860156 CTTTCATTTTG
1 CTTTCTTTTTG
15860167 CACTCCAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 20
0.71 0.01 0.28
Matches are distributed among these distances:
15 5 0.10
16 8 0.16
17 12 0.24
18 23 0.45
19 3 0.06
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.72
Consensus pattern (17 bp):
CTTTCTTTTTGATTTTT
Found at i:15860125 original size:13 final size:12
Alignment explanation
Indices: 15860101--15860159 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
15860091 CTTTTTGAAT
15860101 TTTTC-TTTTTC
1 TTTTCTTTTTTC
15860112 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
15860125 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
15860139 TCTTCTTTTGTC
1 TTTTCTTTTTTC
15860151 TTTTTCTTT
1 -TTTTCTTT
15860160 CATTTTGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:15860125 original size:19 final size:19
Alignment explanation
Indices: 15860103--15860159 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
15860093 TTTTGAATTT
15860103 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
*
15860122 TTC-TTTTCTGATTT-TTCTC
1 TTCTTTTTCT--TTTCTTTTC
15860141 TTCTTTTGTCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
15860160 CATTTTGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 9 0.30
21 4 0.13
22 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:15860460 original size:19 final size:20
Alignment explanation
Indices: 15860432--15860471 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
15860422 GGATAATAAT
15860432 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
15860452 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
15860471 A
1 A
15860472 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:15860926 original size:19 final size:20
Alignment explanation
Indices: 15860885--15860935 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
15860875 GAATCCCCTT
*
15860885 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
15860905 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
15860924 TGAAGATACATG
1 TGAAAATACATG
15860936 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:15861097 original size:22 final size:22
Alignment explanation
Indices: 15861066--15861107 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
15861056 GTGTTTTGGC
*
15861066 GCCTATTTG-ATGTCACATGGAA
1 GCCTACTTGAATG-CACATGGAA
15861088 GCCTACTTGAATGCACATGG
1 GCCTACTTGAATGCACATGG
15861108 GTGTTCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
GCCTACTTGAATGCACATGGAA
Found at i:15861843 original size:30 final size:31
Alignment explanation
Indices: 15861804--15861863 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
15861794 ACATGCTGCC
**
15861804 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
15861835 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
15861864 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:15863834 original size:16 final size:16
Alignment explanation
Indices: 15863813--15863845 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15863803 TAGTTAGCTC
15863813 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
15863829 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
15863845 A
1 A
15863846 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:15866415 original size:36 final size:36
Alignment explanation
Indices: 15866363--15866475 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
15866353 GATACTATTT
*
15866363 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
15866399 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
15866435 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
15866470 ACATCA
1 TCATCA
15866476 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:15866418 original size:13 final size:11
Alignment explanation
Indices: 15866363--15866461 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
15866353 GATACTATTT
15866363 TCATCACCATAA
1 TCATCACCAT-A
*
15866375 TCCATCTCCATTA
1 T-CATCACCA-TA
*
15866388 TCA-CGCCTATA
1 TCATCACC-ATA
15866399 TCATCACCATA
1 TCATCACCATA
15866410 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
15866424 TCA-CGCCTATA
1 TCATCACC-ATA
15866435 TCATCACCATA
1 TCATCACCATA
15866446 TTCCATCACCATA
1 -T-CATCACCATA
15866459 TCA
1 TCA
15866462 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:15866490 original size:33 final size:33
Alignment explanation
Indices: 15866375--15866514 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
15866365 ATCACCATAA
* * *
15866375 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
15866409 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
15866447 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
15866480 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
15866513 TC
1 TC
15866515 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:15872118 original size:36 final size:36
Alignment explanation
Indices: 15872066--15872178 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
15872056 GATACTATTT
*
15872066 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
15872102 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
15872138 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
15872173 ACATCA
1 TCATCA
15872179 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:15872121 original size:13 final size:11
Alignment explanation
Indices: 15872066--15872164 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
15872056 GATACTATTT
15872066 TCATCACCATAA
1 TCATCACCAT-A
*
15872078 TCCATCTCCATTA
1 T-CATCACCA-TA
*
15872091 TCA-CGCCTATA
1 TCATCACC-ATA
15872102 TCATCACCATA
1 TCATCACCATA
15872113 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
15872127 TCA-CGCCTATA
1 TCATCACC-ATA
15872138 TCATCACCATA
1 TCATCACCATA
15872149 TTCCATCACCATA
1 -T-CATCACCATA
15872162 TCA
1 TCA
15872165 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:15872193 original size:33 final size:33
Alignment explanation
Indices: 15872078--15872217 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
15872068 ATCACCATAA
* * *
15872078 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
15872112 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
15872150 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
15872183 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
15872216 TC
1 TC
15872218 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:15874214 original size:16 final size:16
Alignment explanation
Indices: 15874193--15874225 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15874183 TAGTTAGCTC
15874193 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
15874209 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
15874225 A
1 A
15874226 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:15875756 original size:19 final size:20
Alignment explanation
Indices: 15875732--15875785 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
15875722 TATCCTTTCT
15875732 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
15875751 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
*
15875771 -TATTATTATTCCATT
1 TTATT-TTATTTCATT
15875786 TATTAATTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.13
19 12 0.40
20 11 0.37
21 3 0.10
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:15876039 original size:12 final size:12
Alignment explanation
Indices: 15876024--15876048 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15876014 GTTTCTCTCT
15876024 TTAGTTCTTAAG
1 TTAGTTCTTAAG
15876036 TTAGTTCTTAAG
1 TTAGTTCTTAAG
15876048 T
1 T
15876049 GAACTTTATC
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:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TTAGTTCTTAAG
Found at i:15882369 original size:35 final size:37
Alignment explanation
Indices: 15882300--15882369 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
15882290 ATAAGATACA
* *
15882300 ATATGTCCATCACCATTATCACGACTATATCATCACC
1 ATATGTCCATCACCATTATCACGACAATAACATCACC
*
15882337 ATAT-TCCATCACCA-TATCACGCCAATAACATCA
1 ATATGTCCATCACCATTATCACGACAATAACATCA
15882370 TCCTTCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 16 0.53
36 10 0.33
37 4 0.13
ACGTcount: A:0.36, C:0.33, G:0.04, T:0.27
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGACAATAACATCACC
Found at i:15882384 original size:33 final size:33
Alignment explanation
Indices: 15882340--15882408 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
15882330 CATCACCATA
*
15882340 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
15882373 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
15882406 TTC
1 TTC
15882409 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:15890000 original size:15 final size:15
Alignment explanation
Indices: 15889965--15889993 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15889955 CTGCTTCAAC
15889965 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
15889979 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
15889994 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Done.