Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008122.1 Hibiscus syriacus cultivar Beakdansim tig00110676_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: 2511854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:2265974 original size:21 final size:21
Alignment explanation
Indices: 2265932--2265981 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2265922 AAAAAACCTA
* *
2265932 AACCCT-AAATATAAACTATT
1 AACCCTAAAACATAAAATATT
*
2265952 AACCCTAAAACATAAAATGTT
1 AACCCTAAAACATAAAATATT
2265973 AACCCTAAA
1 AACCCTAAA
2265982 CCCTAAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (21 bp):
AACCCTAAAACATAAAATATT
Found at i:2266168 original size:21 final size:21
Alignment explanation
Indices: 2266144--2266183 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2266134 TTAGTGTATT
* *
2266144 ATATAGTTTATACTTTATAGC
1 ATATAGTATATAATTTATAGC
2266165 ATATAGTATATAATTTATA
1 ATATAGTATATAATTTATA
2266184 AACTATAGTT
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:0.07, T:0.47
Consensus pattern (21 bp):
ATATAGTATATAATTTATAGC
Found at i:2266294 original size:65 final size:66
Alignment explanation
Indices: 2266214--2266441 Score: 222
Period size: 65 Copynumber: 3.5 Consensus size: 66
2266204 ACTATATAGT
* * * *
2266214 TTATATTAATGTTAATTATCTTAACTATAATTTATATTAA-TATAGTATAATGTTTATAAACTAT
1 TTATATTAATATTAATTATATTAACTATAATTTATATTAACTATAATATAATATTTATAAACTAT
2266278 A
66 A
* * *
2266279 CTATATTAATATTAATTATATTAACTATAGTTTATA--AACTATACTAT-ATAATTTAT-AACAT
1 TTATATTAATATTAATTATATTAACTATAATTTATATTAACTATAATATAAT-ATTTATAAAC-T
2266340 ATA
64 ATA
* * * * *
2266343 GTTTATATTAATATTAATTTTA-TATACTATATTTTATATTAATTTTAAT-TACA-AATTATAAA
1 --TTATATTAATATTAATTATATTA-ACTATAATTTATATTAACTATAATATA-ATATTTATAAA
2266405 CTATA
62 CTATA
2266410 TTATATTAATATTAATTATATTAA-TATTAATT
1 TTATATTAATATTAATTATATTAACTA-TAATT
2266442 ATAATATATA
Statistics
Matches: 135, Mismatches: 15, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
63 7 0.05
64 18 0.13
65 58 0.43
66 32 0.24
67 10 0.07
68 9 0.07
69 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (66 bp):
TTATATTAATATTAATTATATTAACTATAATTTATATTAACTATAATATAATATTTATAAACTAT
A
Found at i:2266328 original size:14 final size:14
Alignment explanation
Indices: 2266268--2266329 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
2266258 GTATAATGTT
2266268 TATAAACTATACTA
1 TATAAACTATACTA
* *
2266282 TATTAA-TATTAATTA
1 TATAAACTA-T-ACTA
* * *
2266297 TATTAACTATAGTT
1 TATAAACTATACTA
2266311 TATAAACTATACTA
1 TATAAACTATACTA
2266325 TATAA
1 TATAA
2266330 TTTATAACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 10 0.26
16 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (14 bp):
TATAAACTATACTA
Found at i:2266342 original size:131 final size:131
Alignment explanation
Indices: 2266173--2266462 Score: 328
Period size: 131 Copynumber: 2.2 Consensus size: 131
2266163 GCATATAGTA
* * *
2266173 TATAATTTATAAACTATAGTTATATTAATGTACTATATAGTTTATATTAATGTTAATTATCT-TA
1 TATAATTTATAAACTATACTTATATTAATGAACTATATAGTTTATATTAATATTAATT-T-TATA
* **
2266237 -ACTATAATTTATATTAA-TATAGTATA-ATGTTTATAAACTATACTATATTAATATTAATTATA
64 TACTATAATTTATATTAATTATAAT-TACA-AATTATAAACTATACTATATTAATATTAATTATA
2266299 TTAAC
127 TTAAC
* *
2266304 TATAGTTTATAAACTATACTATATAATTTAT-AAC-ATATAGTTTATATTAATATTAATTTTATA
1 TATAATTTATAAACTATACT-TAT-ATTAATGAACTATATAGTTTATATTAATATTAATTTTATA
* * *
2266367 TACTATATTTTATATTAATTTTAATTACAAATTATAAACTATATTATATTAATATTAATTATATT
64 TACTATAATTTATATTAATTATAATTACAAATTATAAACTATACTATATTAATATTAATTATATT
2266432 AA-
129 AAC
* *
2266434 TATTAA-TTATAATA-TATAATTATTTTAAT
1 TA-TAATTTATAA-ACTATACTTATATTAAT
2266463 ATTAATTATA
Statistics
Matches: 136, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
128 4 0.03
129 4 0.03
130 16 0.12
131 97 0.71
132 10 0.07
133 5 0.04
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (131 bp):
TATAATTTATAAACTATACTTATATTAATGAACTATATAGTTTATATTAATATTAATTTTATATA
CTATAATTTATATTAATTATAATTACAAATTATAAACTATACTATATTAATATTAATTATATTAA
C
Found at i:2266379 original size:31 final size:31
Alignment explanation
Indices: 2266203--2266426 Score: 106
Period size: 31 Copynumber: 6.8 Consensus size: 31
2266193 TATATTAATG
*
2266203 TACTATATAGTTTATATTAATGTTAATTATCT-TA
1 TACTATAT--TTTATATTAATATTAATT-T-TATA
*
2266237 -ACTATAATTTATATTAATATAGTATAATGTTTATA
1 TACTATATTTTATATT-A-ATA-T-TAAT-TTTATA
* * *
2266272 AACTATA--CTATATTAATATTAATTATAT-
1 TACTATATTTTATATTAATATTAATTTTATA
* *
2266300 TAACTATAGTTTATAAACTATACTATATAA-TTTATA
1 T-ACTATA-TTT-TATA-T-TAATAT-TAATTTTATA
*
2266336 -ACATATAGTTTATATTAATATTAATTTTATA
1 TAC-TATATTTTATATTAATATTAATTTTATA
*
2266367 TACTATATTTTATATTAATTTTAATTACAAATTATA
1 TACTATATTTTATATTAATATTAATT-----TTATA
*
2266403 AACTATA--TTATATTAATATTAATT
1 TACTATATTTTATATTAATATTAATT
2266427 ATATTAATAT
Statistics
Matches: 150, Mismatches: 16, Indels: 48
0.70 0.07 0.22
Matches are distributed among these distances:
29 10 0.07
30 7 0.05
31 41 0.27
32 7 0.05
33 15 0.10
34 29 0.19
35 20 0.13
36 21 0.14
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (31 bp):
TACTATATTTTATATTAATATTAATTTTATA
Found at i:2266434 original size:43 final size:43
Alignment explanation
Indices: 2266387--2266472 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
2266377 TATATTAATT
2266387 TTAATTACAAATTATAA-ACTAT-ATTATATTAATATTAATTATA
1 TTAA-TACAAATTATAATA-TATAATTATATTAATATTAATTATA
** *
2266430 TTAATATTAATTATAATATATAATTATTTTAATATTAATTATA
1 TTAATACAAATTATAATATATAATTATATTAATATTAATTATA
2266473 AGTAGTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 13 0.34
43 25 0.66
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (43 bp):
TTAATACAAATTATAATATATAATTATATTAATATTAATTATA
Found at i:2266473 original size:28 final size:27
Alignment explanation
Indices: 2266396--2266472 Score: 59
Period size: 28 Copynumber: 2.7 Consensus size: 27
2266386 TTTAATTACA
*
2266396 AATTATAA-ACTATATTATATTAATATT
1 AATTATAATATTA-ATTATATTAATATT
*
2266423 AATTATATTAATATTAATTATAATATATAATT
1 AA-T-TA-TAATATTAATTATATTA-AT-ATT
*
2266455 -ATTTTAATATTAATTATA
1 AATTATAATATTAATTATA
2266473 AGTAGTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
27 2 0.05
28 15 0.37
29 3 0.07
30 12 0.29
31 6 0.15
32 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTATAATATTAATTATATTAATATT
Found at i:2269139 original size:16 final size:16
Alignment explanation
Indices: 2269120--2269158 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2269110 TGAGTCAATT
*
2269120 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
2269136 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
2269152 ACAGGTC
1 ACAGGTC
2269159 GAGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:2304852 original size:24 final size:24
Alignment explanation
Indices: 2304825--2304877 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
2304815 ATACTTTACC
*
2304825 CTAATTAATATGA-TTTTTAAATAA
1 CTAATT-ATAAGATTTTTTAAATAA
2304849 CTAAATTATAAGATTTTTTAAATAA
1 CT-AATTATAAGATTTTTTAAATAA
2304874 CTAA
1 CTAA
2304878 ATTGAGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
CTAATTATAAGATTTTTTAAATAA
Found at i:2310637 original size:40 final size:41
Alignment explanation
Indices: 2310580--2310656 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
2310570 GCCCCTAATT
2310580 TTTTTTAATCTCAC-TTTTTACCTTTAAAATTAAGGTACTA
1 TTTTTTAATCTCACTTTTTTACCTTTAAAATTAAGGTACTA
* * * *
2310620 TTTTTTAATCTCGCTTTTTTACTTTTATAATTGAGGT
1 TTTTTTAATCTCACTTTTTTACCTTTAAAATTAAGGT
2310657 CCCTAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 13 0.41
41 19 0.59
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.55
Consensus pattern (41 bp):
TTTTTTAATCTCACTTTTTTACCTTTAAAATTAAGGTACTA
Found at i:2310649 original size:85 final size:83
Alignment explanation
Indices: 2310455--2310668 Score: 231
Period size: 85 Copynumber: 2.6 Consensus size: 83
2310445 AATCCTAAGA
* * * * *
2310455 TTTTTAATCTCGTTTTGTACCTTTATAA-TTAAGTTCCTGA-TTTTTTTAATCACTTTTACCTTT
1 TTTTTAATCTCGTTTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTTAATCACTTTTACCTTT
* *
2310518 ATAATTGAAGCCTTTAAT
66 AAAATTGAAGCCTCTAAT
* * *
2310536 TTTTTCAATCTCATTTTTTACTTATATAATTTAGGCCCCTAATTTTTTTTAATCTCACTTTTTAC
1 TTTTT-AATCTCGTTTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTTAA--TCAC-TTTTAC
*
2310601 CTTTAAAATT-AAG-GTACT-AT
62 CTTTAAAATTGAAGCCT-CTAAT
*
2310621 TTTTTAATCTCGCTTTTTTACTTTTATAATTGAGGTCCCTAATTTTTT
1 TTTTTAATCTCG-TTTTTTACTTTTATAATTTAGGTCCCTAATTTTTT
2310669 CAATCATATT
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
81 5 0.05
82 19 0.17
83 8 0.07
84 15 0.14
85 40 0.36
86 8 0.07
87 15 0.14
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (83 bp):
TTTTTAATCTCGTTTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTTAATCACTTTTACCTTT
AAAATTGAAGCCTCTAAT
Found at i:2310688 original size:43 final size:42
Alignment explanation
Indices: 2310351--2310691 Score: 204
Period size: 43 Copynumber: 8.0 Consensus size: 42
2310341 TTATCTTTGC
* *
2310351 AATTGAGGTCCTTAATTTTTGTAATCCTACATTTTAT-C-TTTAT
1 AATTGAGGTCCCTAATTTTT-TAAT-CT-CATTTTTTACTTTTAT
*
2310394 AATTGAGG-CCCTTAATTTTTTTCAATCCCATTTTTTA-TATTTAT
1 AATTGAGGTCCC-TAA-TTTTTT-AATCTCATTTTTTACT-TTTAT
* ** * * * *
2310438 GATTGATAAT-CCTAAGATTTTTAATCTCGTTTTGTACCTTTAT
1 AATTGA-GGTCCCTAA-TTTTTTAATCTCATTTTTTACTTTTAT
* * * * *
2310481 AATT-AAGTTCCTGATTTTTTTAA--TCA-CTTTTACCTTTAT
1 AATTGAGGTCCCT-AATTTTTTAATCTCATTTTTTACTTTTAT
* * *
2310520 AATTGAAG-CCTTTAATTTTTTCAATCTCATTTTTTACTTATAT
1 AATTGAGGTCC-CTAATTTTTT-AATCTCATTTTTTACTTTTAT
* * * * *
2310563 AATTTAGGCCCCTAATTTTTTTTAATCTCACTTTTTACCTTTAA
1 AATTGAGGTCCCTAA--TTTTTTAATCTCATTTTTTACTTTTAT
* * *
2310607 AATTAAGGT-ACT-ATTTTTTAATCTCGCTTTTTTACTTTTAT
1 AATTGAGGTCCCTAATTTTTTAATCTC-ATTTTTTACTTTTAT
2310648 AATTGAGGTCCCTAATTTTTTCAATCAT-ATTTTTTACTTTTAT
1 AATTGAGGTCCCTAATTTTTT-AATC-TCATTTTTTACTTTTAT
2310691 A
1 A
2310692 GTTTAAGCTC
Statistics
Matches: 231, Mismatches: 42, Indels: 50
0.72 0.13 0.15
Matches are distributed among these distances:
39 23 0.10
40 20 0.09
41 21 0.09
42 26 0.11
43 76 0.33
44 56 0.24
45 9 0.04
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (42 bp):
AATTGAGGTCCCTAATTTTTTAATCTCATTTTTTACTTTTAT
Found at i:2313538 original size:120 final size:120
Alignment explanation
Indices: 2313326--2313677 Score: 632
Period size: 120 Copynumber: 2.9 Consensus size: 120
2313316 AAGTTGAGGG
* *
2313326 AAAAAATCATTATTCCAAAACAACACATGGGATCTCACAGCATCTTAAATTGCAAACATTACATT
1 AAAAAATCATTACTCCAAAACAACACATGGGATCTCACA-CATCTTAAATTGCAAACATTACATG
*
2313391 TTATAAGAAGCCATCAATAAATATGGACTCACCAATGGAAATAATACATGTTGAGA
65 TTATAAGAAGCCATCAATAAATTTGGACTCACCAATGGAAATAATACATGTTGAGA
*
2313447 AAAAAATCATTACTCCAAAACAACACATGGGATCTCACACATCTTAAATAGCAAACATTACATGT
1 AAAAAATCATTACTCCAAAACAACACATGGGATCTCACACATCTTAAATTGCAAACATTACATGT
2313512 TATAAGAAGCCATCAATAAATTTGGACTCACCAATGGAAATAATACATGTTGAGA
66 TATAAGAAGCCATCAATAAATTTGGACTCACCAATGGAAATAATACATGTTGAGA
*
2313567 AAAAAATCATTACTCCAAAACGACACATGGGATCTCACACATCTTAAATTGCAAACATTACATGT
1 AAAAAATCATTACTCCAAAACAACACATGGGATCTCACACATCTTAAATTGCAAACATTACATGT
* *
2313632 TATAAGAAGCCATCAATAAATTTGGACTCATCAATGTAAATAATAC
66 TATAAGAAGCCATCAATAAATTTGGACTCACCAATGGAAATAATAC
2313678 CTTACCATGT
Statistics
Matches: 223, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
120 185 0.83
121 38 0.17
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (120 bp):
AAAAAATCATTACTCCAAAACAACACATGGGATCTCACACATCTTAAATTGCAAACATTACATGT
TATAAGAAGCCATCAATAAATTTGGACTCACCAATGGAAATAATACATGTTGAGA
Found at i:2330993 original size:15 final size:16
Alignment explanation
Indices: 2330961--2330993 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2330951 AAAATCTTTC
2330961 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
2330977 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
2330992 TT
1 TT
2330994 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:2331766 original size:16 final size:17
Alignment explanation
Indices: 2331739--2331773 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2331729 TATCGCCGAC
2331739 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
2331756 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
2331772 CG
1 CG
2331774 TGAATAGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:2340713 original size:62 final size:62
Alignment explanation
Indices: 2340619--2340749 Score: 217
Period size: 62 Copynumber: 2.1 Consensus size: 62
2340609 AAGCAATTAC
* ** *
2340619 AGAGAAGAGCAACGACTGGAGTAAAGGGACTCACAAAGTTAACATATGTTCTTATGCATAGA
1 AGAGATGAGCAACGACTGGACCAAAGGGACTCACAAAGTTAACAGATGTTCTTATGCATAGA
*
2340681 AGAGATGAGCAACGACTGGACCAAAGTGACTCACAAAGTTAACAGATGTTCTTATGCATAGA
1 AGAGATGAGCAACGACTGGACCAAAGGGACTCACAAAGTTAACAGATGTTCTTATGCATAGA
2340743 AGAGATG
1 AGAGATG
2340750 TCAGACGGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (62 bp):
AGAGATGAGCAACGACTGGACCAAAGGGACTCACAAAGTTAACAGATGTTCTTATGCATAGA
Found at i:2344111 original size:192 final size:192
Alignment explanation
Indices: 2343783--2344143 Score: 605
Period size: 192 Copynumber: 1.9 Consensus size: 192
2343773 GAAGCTTATT
* *
2343783 TCAACACTAAATCGTTAACTCTATTACGGTATGATCCTTTTCTGGTCAAGCATCAGGAAAACTCC
1 TCAACACTAAATCGGTAACTCTATTACGGTATGATCCTTTTCCGGTCAAGCATCAGGAAAACTCC
* *
2343848 AATCATGGGCAATCTTCCATTCAAAGGCATACATAGTGCCAACCAGATAAAAAACCAGAATACCA
66 AATCATGGGCAATCTTCCATTCAAAGACATACATAGTGCCAACCAGATAAAAAACCAGAACACCA
* *
2343913 ATCGATAATGCCAGTTGATGTACTACATTATTAACATGATTAAAAACCAGACATACATAGTG
131 ATCGATAATGACAGTTGATCTACTACATTATTAACATGATTAAAAACCAGACATACATAGTG
* *
2343975 TCAACACTAAATCGGTAACTCTATTATGGTATGATCCTTTTCCGGTCAAGCATCAGGAAAACTGC
1 TCAACACTAAATCGGTAACTCTATTACGGTATGATCCTTTTCCGGTCAAGCATCAGGAAAACTCC
* * *
2344040 AATCATGGGCAATCTTCCATTCAAAGACATACATAGTGCCAACTAGATAAAAATCCAGAACACCG
66 AATCATGGGCAATCTTCCATTCAAAGACATACATAGTGCCAACCAGATAAAAAACCAGAACACCA
**
2344105 ATCGATAATGATGGTTGATCTACTACATTATTAACATGA
131 ATCGATAATGACAGTTGATCTACTACATTATTAACATGA
2344144 GATATGAGCA
Statistics
Matches: 156, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
192 156 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (192 bp):
TCAACACTAAATCGGTAACTCTATTACGGTATGATCCTTTTCCGGTCAAGCATCAGGAAAACTCC
AATCATGGGCAATCTTCCATTCAAAGACATACATAGTGCCAACCAGATAAAAAACCAGAACACCA
ATCGATAATGACAGTTGATCTACTACATTATTAACATGATTAAAAACCAGACATACATAGTG
Found at i:2350210 original size:13 final size:12
Alignment explanation
Indices: 2350169--2350215 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
2350159 TATTTGATTG
2350169 TTTTATATTTTAA
1 TTTTATATTTT-A
**
2350182 AATTATATTTTA
1 TTTTATATTTTA
2350194 TTTTATATTTTA
1 TTTTATATTTTA
2350206 TTTT-TATTTT
1 TTTTATATTTT
2350216 GATCACTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 6 0.20
12 15 0.50
13 9 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTATATTTTA
Found at i:2351177 original size:3 final size:3
Alignment explanation
Indices: 2351169--2351209 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2351159 AAATTACCAT
2351169 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2351210 CAAAAATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2352055 original size:2 final size:2
Alignment explanation
Indices: 2352048--2352073 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2352038 ATAAAATCTT
2352048 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2352074 AATTCTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2352809 original size:7 final size:7
Alignment explanation
Indices: 2352797--2352826 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2352787 GGGTAAATTA
2352797 CATCATT
1 CATCATT
2352804 CATCATT
1 CATCATT
2352811 CATCATT
1 CATCATT
2352818 CATCATT
1 CATCATT
2352825 CA
1 CA
2352827 ATTATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (7 bp):
CATCATT
Found at i:2355681 original size:22 final size:22
Alignment explanation
Indices: 2355656--2355697 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2355646 TTCTTGTAAT
*
2355656 TTGCTTT-CAAAGTTTCTCCTTG
1 TTGCTTTGC-AAGCTTCTCCTTG
2355678 TTGCTTTGCAAGCTTCTCCT
1 TTGCTTTGCAAGCTTCTCCT
2355698 CCTTCTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (22 bp):
TTGCTTTGCAAGCTTCTCCTTG
Found at i:2357299 original size:21 final size:22
Alignment explanation
Indices: 2357269--2357310 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2357259 ATTTTGAAAG
*
2357269 TTATTTTA-TTATAAAAAAAAA
1 TTATTATATTTATAAAAAAAAA
*
2357290 TTATTATATTTATAATAAAAA
1 TTATTATATTTATAAAAAAAA
2357311 GACTAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATTATATTTATAAAAAAAAA
Found at i:2357700 original size:2 final size:2
Alignment explanation
Indices: 2357695--2357737 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2357685 TTTATAAAAA
2357695 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
2357737 A
1 A
2357738 ATTTTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2359386 original size:28 final size:28
Alignment explanation
Indices: 2359333--2359386 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2359323 TGTTAGTTAA
** * *
2359333 TTAACTGTTAATATTTTTTTTTGATAAG
1 TTAACTGTTAATATTTCATATAGATAAG
2359361 TTAACTGTTAATATTTCATATAGATA
1 TTAACTGTTAATATTTCATATAGATA
2359387 TAATAAGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (28 bp):
TTAACTGTTAATATTTCATATAGATAAG
Found at i:2362720 original size:43 final size:43
Alignment explanation
Indices: 2362650--2362736 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
2362640 AAGGTCGGGC
** *
2362650 AATTGAGTTAAATTCAAGTGTAGACTACACATTTAGTATCTAA
1 AATTGAGTTAAATTCAAAAGTAAACTACACATTTAGTATCTAA
**
2362693 AATTGAGTTAAATTCAAAAGTAAACTACGTATTTAGTATCTAA
1 AATTGAGTTAAATTCAAAAGTAAACTACACATTTAGTATCTAA
2362736 A
1 A
2362737 CTATCAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (43 bp):
AATTGAGTTAAATTCAAAAGTAAACTACACATTTAGTATCTAA
Found at i:2363823 original size:7 final size:7
Alignment explanation
Indices: 2363811--2363914 Score: 61
Period size: 7 Copynumber: 14.9 Consensus size: 7
2363801 TATGTGATAA
2363811 GGTTTAG
1 GGTTTAG
2363818 GGTTTAG
1 GGTTTAG
*
2363825 GATTTAG
1 GGTTTAG
*
2363832 AGTTTA-
1 GGTTTAG
* *
2363838 TGTGATAG
1 GGT-TTAG
* *
2363846 GATTTAA
1 GGTTTAG
*
2363853 GGTTTAA
1 GGTTTAG
*
2363860 AGTTTAG
1 GGTTTAG
*
2363867 AGTTTAG
1 GGTTTAG
2363874 GGTTTA-
1 GGTTTAG
*
2363880 TGTGTTAG
1 GGT-TTAG
2363888 GGTTTAG
1 GGTTTAG
2363895 GGTTTA-
1 GGTTTAG
*
2363901 TGTGTTAG
1 GGT-TTAG
2363909 GGTTTA
1 GGTTTA
2363915 AGTTATGCCA
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
6 6 0.08
7 63 0.85
8 5 0.07
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:2363846 original size:21 final size:21
Alignment explanation
Indices: 2363821--2363918 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
2363811 GGTTTAGGGT
2363821 TTAGGATTTAGAGTTTATGTG
1 TTAGGATTTAGAGTTTATGTG
* *
2363842 ATAGGATTTA-AGGTTTAAAGT-
1 TTAGGATTTAGA-GTTT-ATGTG
*
2363863 TTA-GAGTTTAGGGTTTATGTG
1 TTAGGA-TTTAGAGTTTATGTG
* *
2363884 TTAGGGTTTAGGGTTTATGTG
1 TTAGGATTTAGAGTTTATGTG
*
2363905 TTAGGGTTTA-AGTT
1 TTAGGATTTAGAGTT
2363919 ATGCCATGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
20 9 0.14
21 51 0.80
22 4 0.06
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (21 bp):
TTAGGATTTAGAGTTTATGTG
Found at i:2363857 original size:35 final size:35
Alignment explanation
Indices: 2363800--2363872 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
2363790 TCATAACTAA
* *
2363800 TTATGTGATAAGGTTTAGGGTTT-AGGATTTAGAGT
1 TTATGTGATAAGGTTTAAGGTTTAAAG-TTTAGAGT
2363835 TTATGTGAT-AGGATTTAAGGTTTAAAGTTTAGAGT
1 TTATGTGATAAGG-TTTAAGGTTTAAAGTTTAGAGT
2363870 TTA
1 TTA
2363873 GGGTTTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 3 0.09
35 29 0.85
36 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (35 bp):
TTATGTGATAAGGTTTAAGGTTTAAAGTTTAGAGT
Found at i:2363873 original size:42 final size:42
Alignment explanation
Indices: 2363808--2363900 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
2363798 AATTATGTGA
**
2363808 TAAGGTTTAGGGTTTAGGATTTAGAGTTTATGTGATAGGATT
1 TAAGGTTTAAAGTTTAGGATTTAGAGTTTATGTGATAGGATT
* * *
2363850 TAAGGTTTAAAGTTTA-GAGTTTAGGGTTTATGTGTTAGGGTT
1 TAAGGTTTAAAGTTTAGGA-TTTAGAGTTTATGTGATAGGATT
*
2363892 TAGGGTTTA
1 TAAGGTTTA
2363901 TGTGTTAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 2 0.05
42 42 0.95
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (42 bp):
TAAGGTTTAAAGTTTAGGATTTAGAGTTTATGTGATAGGATT
Found at i:2365631 original size:26 final size:26
Alignment explanation
Indices: 2365610--2365677 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
2365600 TTTGGTTTTT
*
2365610 TGTCCCTTGTTTTTTGCTTGGTGCTC
1 TGTCCCTTGTTTTGTGCTTGGTGCTC
2365636 TGTCCCTTGTTTTGTGCTTGGTGCTC
1 TGTCCCTTGTTTTGTGCTTGGTGCTC
2365662 TGTCCCTTGTTTTGTG
1 TGTCCCTTGTTTTGTG
2365678 TGTCTGCAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.00, C:0.22, G:0.25, T:0.53
Consensus pattern (26 bp):
TGTCCCTTGTTTTGTGCTTGGTGCTC
Found at i:2366070 original size:17 final size:17
Alignment explanation
Indices: 2366048--2366084 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2366038 ATTCGAGTTT
*
2366048 GAGTTCGAGCTTTAATC
1 GAGTTCGAGCTTGAATC
2366065 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
2366082 GAG
1 GAG
2366085 CTTGAATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:2366083 original size:11 final size:11
Alignment explanation
Indices: 2366069--2366120 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
2366059 TTAATCGAGT
2366069 TCGAGCTTGAA
1 TCGAGCTTGAA
2366080 TCGAGCTTGAA
1 TCGAGCTTGAA
*
2366091 TCGAGCTTAAAA
1 TCGAGCTT-GAA
*
2366103 TCGAGCTTCAA
1 TCGAGCTTGAA
2366114 TCGAGCT
1 TCGAGCT
2366121 CTTGATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 28 0.74
12 10 0.26
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:2366108 original size:23 final size:22
Alignment explanation
Indices: 2366069--2366120 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
2366059 TTAATCGAGT
* *
2366069 TCGAGCTTGAATCGAGCTTGAA
1 TCGAGCTTAAATCGAGCTTCAA
2366091 TCGAGCTTAAAATCGAGCTTCAA
1 TCGAGCTT-AAATCGAGCTTCAA
2366114 TCGAGCT
1 TCGAGCT
2366121 CTTGATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (22 bp):
TCGAGCTTAAATCGAGCTTCAA
Found at i:2369054 original size:101 final size:101
Alignment explanation
Indices: 2368870--2369170 Score: 557
Period size: 101 Copynumber: 3.0 Consensus size: 101
2368860 TATCATGTTC
*
2368870 CCTATAGAACCCAGTTAACTTATGAAATCACAGCCAGTTATCATACCAACGTAAAAAATTCATTA
1 CCTATAGAACCCAGTTAACTTATGAAATCACAGCCAGTCATCATACCAACGTAAAAAATTCATTA
* *
2368935 TAAAAGTAAAGATATTAGACTTAAGGCTTGTACAGG
66 TAAAAGTAACGATGTTAGACTTAAGGCTTGTACAGG
*
2368971 CCTATAGAACCCAGTTAACTTATGAAATCACAGCCAGTCATCGTACCAACGTAAAAAATTCATTA
1 CCTATAGAACCCAGTTAACTTATGAAATCACAGCCAGTCATCATACCAACGTAAAAAATTCATTA
2369036 TAAAAGTAACGATGTTAGACTTAAGGCTTGTACAGG
66 TAAAAGTAACGATGTTAGACTTAAGGCTTGTACAGG
2369072 CCTATAGAACCCAGTTAACTTATGAAATCACAGCCAGTCATCATACCAACGTAAAAAATTCATTA
1 CCTATAGAACCCAGTTAACTTATGAAATCACAGCCAGTCATCATACCAACGTAAAAAATTCATTA
*
2369137 TAAAAGTAACGATGTTACACTTAAGGCTTGTACA
66 TAAAAGTAACGATGTTAGACTTAAGGCTTGTACA
2369171 AGGGGAGATG
Statistics
Matches: 194, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 194 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (101 bp):
CCTATAGAACCCAGTTAACTTATGAAATCACAGCCAGTCATCATACCAACGTAAAAAATTCATTA
TAAAAGTAACGATGTTAGACTTAAGGCTTGTACAGG
Found at i:2383274 original size:31 final size:31
Alignment explanation
Indices: 2383238--2383314 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
2383228 AAAAAATAAA
*
2383238 AGTTTAAATACTAAAATGGACCAAAATTGAT
1 AGTTTAAATACTAAAATAGACCAAAATTGAT
* * **
2383269 TGTTTAATTACTAAAATAGATTAAAATTGAT
1 AGTTTAAATACTAAAATAGACCAAAATTGAT
*
2383300 AGTTTAAGTACTAAA
1 AGTTTAAATACTAAA
2383315 TATGTATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (31 bp):
AGTTTAAATACTAAAATAGACCAAAATTGAT
Found at i:2384948 original size:20 final size:20
Alignment explanation
Indices: 2384925--2384973 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2384915 AACCAGTCCA
*
2384925 AGTCAACTCGAACCGAACTG
1 AGTCAACCCGAACCGAACTG
*
2384945 AGTCAACCCGAATCGAACTG
1 AGTCAACCCGAACCGAACTG
*
2384965 AGCCAACCC
1 AGTCAACCC
2384974 AAACTGAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.35, G:0.18, T:0.12
Consensus pattern (20 bp):
AGTCAACCCGAACCGAACTG
Found at i:2385057 original size:22 final size:22
Alignment explanation
Indices: 2385029--2385076 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2385019 ACCCGACCCG
* *
2385029 TTGATCGGTCTGATTGTTGACT
1 TTGATCGATCTGACTGTTGACT
2385051 TTGATCGATCTGACTGTTGACT
1 TTGATCGATCTGACTGTTGACT
2385073 TTGA
1 TTGA
2385077 CATTGACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.44
Consensus pattern (22 bp):
TTGATCGATCTGACTGTTGACT
Found at i:2387799 original size:21 final size:21
Alignment explanation
Indices: 2387775--2387815 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2387765 TAATCAAAAC
2387775 ATGA-AAAATTTAAAAAAATTA
1 ATGATAAAA-TTAAAAAAATTA
*
2387796 ATGATTAAATTAAAAAAATT
1 ATGATAAAATTAAAAAAATT
2387816 TAAATTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
ATGATAAAATTAAAAAAATTA
Found at i:2391724 original size:16 final size:16
Alignment explanation
Indices: 2391703--2391733 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2391693 TCTGGCTAAC
2391703 AATCGATCCTAATAAA
1 AATCGATCCTAATAAA
*
2391719 AATCGATCCTGATAA
1 AATCGATCCTAATAA
2391734 CCCTCTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (16 bp):
AATCGATCCTAATAAA
Found at i:2394074 original size:21 final size:21
Alignment explanation
Indices: 2394045--2394089 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2394035 ATTAACATCA
*
2394045 AATACCAACAGA-CTTTTAACT
1 AATACCAACA-ACCTCTTAACT
*
2394066 AATATCAACAACCTCTTAACT
1 AATACCAACAACCTCTTAACT
2394087 AAT
1 AAT
2394090 TATTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.29
Consensus pattern (21 bp):
AATACCAACAACCTCTTAACT
Found at i:2398318 original size:24 final size:24
Alignment explanation
Indices: 2398291--2398340 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2398281 ATAAAGAACC
2398291 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
2398315 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
2398339 AA
1 AA
2398341 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:2403895 original size:24 final size:24
Alignment explanation
Indices: 2403868--2403917 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2403858 ATAAAGAACC
2403868 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
2403892 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
2403916 AA
1 AA
2403918 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:2405041 original size:38 final size:38
Alignment explanation
Indices: 2404963--2405041 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
2404953 AAATTTAGTA
** *
2404963 AAACTGAAATCAACCAAAACCAAAATTAACCCGAATCG
1 AAACTGAAATCAACCAAAACCAAAAGCAACCCGAACCG
* ** **
2405001 AAACTGAAATTAACCCGAACCAAAAGCAACTTGAACCG
1 AAACTGAAATCAACCAAAACCAAAAGCAACCCGAACCG
2405039 AAA
1 AAA
2405042 GAAACCCAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.52, C:0.25, G:0.10, T:0.13
Consensus pattern (38 bp):
AAACTGAAATCAACCAAAACCAAAAGCAACCCGAACCG
Found at i:2409665 original size:44 final size:42
Alignment explanation
Indices: 2409568--2409667 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 42
2409558 AAATAAGTGT
*
2409568 GATTGAAAAAAAATAAAGGTCTCAATTATAAAGATAGAAAGTA
1 GATTG-AAAAAAATAAAGGTCTCAATTATAAAGATAGAAAATA
* * * *
2409611 AAGTTAAAAAAAATAAGAGG-CATGAATTATAACGATAGAAAATGA
1 GA-TTGAAAAAAATAA-AGGTC-TCAATTATAAAGATAGAAAAT-A
2409656 GATTGAAAAAAA
1 GATTGAAAAAAA
2409668 ATAGAAACCT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
43 12 0.26
44 32 0.70
45 2 0.04
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (42 bp):
GATTGAAAAAAATAAAGGTCTCAATTATAAAGATAGAAAATA
Found at i:2413679 original size:21 final size:21
Alignment explanation
Indices: 2413637--2413679 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2413627 TTTTCGTGCT
* * *
2413637 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2413658 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2413679 A
1 A
2413680 CGAATATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2414399 original size:149 final size:150
Alignment explanation
Indices: 2414221--2414536 Score: 564
Period size: 150 Copynumber: 2.1 Consensus size: 150
2414211 TGGTATAGGG
* * *
2414221 TCTACGCGGTCCTTCGGGATATATGTATATTCTTTGGAACATGTGTGAGGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
2414285 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
2414350 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
2414370 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
2414435 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
2414500 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
2414520 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
2414537 TGCAATTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
149 52 0.32
150 108 0.68
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:2414537 original size:23 final size:23
Alignment explanation
Indices: 2414504--2414548 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2414494 ATCATTATAT
*
2414504 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
2414527 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
2414549 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2418117 original size:27 final size:28
Alignment explanation
Indices: 2418055--2418121 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
2418045 CCTAAACCCG
2418055 AACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGAATATCACACTTAAAAA
*
2418083 AACTCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGAATATCACACTTAAAAA
2418110 AACCCGACCCGA
1 AACCCGACCCGA
2418122 CCCGAACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 15 0.41
28 22 0.59
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.13
Consensus pattern (28 bp):
AACCCGACCCGAATATCACACTTAAAAA
Found at i:2418508 original size:44 final size:44
Alignment explanation
Indices: 2418445--2418534 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
2418435 ACCCGAAATA
2418445 ATAAAAAAATACTTTTATTCAATATATGAATAAGTTACCAAAAG
1 ATAAAAAAATACTTTTATTCAATATATGAATAAGTTACCAAAAG
2418489 ATAAAAAAATACTTTTATTCAATATATGAATAAGTTACCAAAAG
1 ATAAAAAAATACTTTTATTCAATATATGAATAAGTTACCAAAAG
2418533 AT
1 AT
2418535 TGATGAGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (44 bp):
ATAAAAAAATACTTTTATTCAATATATGAATAAGTTACCAAAAG
Found at i:2420671 original size:12 final size:13
Alignment explanation
Indices: 2420638--2420670 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2420628 TGTTATGTTT
2420638 ATATTTTTAAATA
1 ATATTTTTAAATA
2420651 ATATTTTTAAATA
1 ATATTTTTAAATA
2420664 ATATTTT
1 ATATTTT
2420671 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATTTTTAAATA
Found at i:2438213 original size:37 final size:37
Alignment explanation
Indices: 2438140--2438214 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
2438130 GTTGTAAAAT
* *
2438140 ATTTATATATTTTCTTTAAAACATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAACATTGAAAATCATAAA
*
2438177 ATTTATATAATTTTTTTTATAAA-ATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAACATTGAAAATCATAAA
2438214 A
1 A
2438215 ATATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 16 0.48
39 3 0.09
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAACATTGAAAATCATAAA
Found at i:2440997 original size:122 final size:123
Alignment explanation
Indices: 2440772--2441129 Score: 492
Period size: 122 Copynumber: 2.9 Consensus size: 123
2440762 TACATTCGAA
* *
2440772 CAAAGG-AGAAGTAATCAATGT-GGAACCAATCTAGTCCACTAGCCCTATTGAATTAAACCAAAG
1 CAAAGGAAGAAGTAATCAAT-TCAGAACCAATCTAGTCCACTAGACCTATTGAATTAAACCAAAG
* * * *
2440835 AAGCTGAATTGATGCGAATGACGAAAAGAGCAACTGTAGTTAACTTACGAGTGAAG-AG
65 AAGTTGAATTGATGCAAATGAAGAAAAGAGCCACTGTAGTTAACTTACGAGTGAAGAAG
* *
2440893 CAAAGGAATAAGTAATCAATTCAGAACCAATCTAGTCCACTAGAACTATTGAATTAAACCAAAGA
1 CAAAGGAAGAAGTAATCAATTCAGAACCAATCTAGTCCACTAGACCTATTGAATTAAACCAAAGA
* * *
2440958 AGTTGAATTGGTGCAAATGAAGAAAAGAGCCACTGTAGTTAACTTACGAGTTACGAAG
66 AGTTGAATTGATGCAAATGAAGAAAAGAGCCACTGTAGTTAACTTACGAGTGAAGAAG
* * * *
2441016 -GAAGGAAGACGTAATCAATTCAGAACAAATCAAGTCCACT-GATCCTATTGAATTAAACCAAAG
1 CAAAGGAAGAAGTAATCAATTCAGAACCAATCTAGTCCACTAGA-CCTATTGAATTAAACCAAAG
* * * *
2441079 AAGTTGAATTGACGCAAATGAAGAAAAGATCCACTGCAGTTAACTTTCGAG
65 AAGTTGAATTGATGCAAATGAAGAAAAGAGCCACTGTAGTTAACTTACGAG
2441130 CTACGAGCAA
Statistics
Matches: 211, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
121 9 0.04
122 200 0.95
123 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (123 bp):
CAAAGGAAGAAGTAATCAATTCAGAACCAATCTAGTCCACTAGACCTATTGAATTAAACCAAAGA
AGTTGAATTGATGCAAATGAAGAAAAGAGCCACTGTAGTTAACTTACGAGTGAAGAAG
Found at i:2442172 original size:16 final size:14
Alignment explanation
Indices: 2442137--2442191 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
2442127 TAAAGTTGTA
2442137 TTTAATATTTAAATT
1 TTTAAT-TTTAAATT
*
2442152 ATTAATTTTAATATGT
1 TTTAATTTTAA-AT-T
2442168 TTTAATATTTAAATT
1 TTTAAT-TTTAAATT
*
2442183 TTTTATTTT
1 TTTAATTTT
2442192 TTAAATCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.24
15 13 0.38
16 8 0.24
17 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
TTTAATTTTAAATT
Found at i:2443750 original size:26 final size:26
Alignment explanation
Indices: 2443701--2443750 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2443691 GTTTTTGTGA
* *
2443701 CCTCTGAAAATTTTTAAGTTCATCGT
1 CCTCTGAAAATTTTTAAATACATCGT
2443727 CCTCT-AAAATTTTATAAATACATC
1 CCTCTGAAAATTTT-TAAATACATC
2443751 CATAGTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (26 bp):
CCTCTGAAAATTTTTAAATACATCGT
Found at i:2444753 original size:3 final size:3
Alignment explanation
Indices: 2444745--2444798 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
2444735 AAATAAAAGA
2444745 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2444790 AAA AAT AAT
1 AAT AAT AAT
2444799 TAAATAAATC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2444757 original size:18 final size:18
Alignment explanation
Indices: 2444736--2444866 Score: 75
Period size: 18 Copynumber: 7.4 Consensus size: 18
2444726 AATGAAAGGA
2444736 AATAAAAGAAATAATAAT
1 AATAAAAGAAATAATAAT
*
2444754 AATAATAA-TAATAATAAT
1 AATAA-AAGAAATAATAAT
*
2444772 AATAATA-AAATAA-AA-
1 AATAAAAGAAATAATAAT
*
2444787 AATAAAA-ATAATTA-AAT
1 AATAAAAGA-AATAATAAT
2444804 AAATCAAAAGGAAA-AATAA-
1 -AAT-AAAA-GAAATAATAAT
* *
2444823 AATAAAATAAA-AGTAAT
1 AATAAAAGAAATAATAAT
*
2444840 AAATAAATGAAATAA-AAGT
1 -AATAAAAGAAATAATAA-T
2444859 AATAAAAG
1 AATAAAAG
2444867 GACCATATGA
Statistics
Matches: 89, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
15 7 0.08
16 15 0.17
17 10 0.11
18 43 0.48
19 9 0.10
20 4 0.04
21 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (18 bp):
AATAAAAGAAATAATAAT
Found at i:2444828 original size:22 final size:23
Alignment explanation
Indices: 2444735--2444864 Score: 78
Period size: 22 Copynumber: 5.7 Consensus size: 23
2444725 AAATGAAAGG
*
2444735 AAATAAAAGAAAT-AATAATAATA
1 AAATAAAAGGAATAAATAA-AATA
*
2444758 ATAATAATAA-TAATAATAATAAAATA
1 A-AATAA-AAGGAAT-A-AATAAAATA
* *
2444784 AAA-AATAA-AAAT-AATTAAAT-
1 AAATAA-AAGGAATAAATAAAATA
2444804 AAATCAAAAGGAA-AAATAAAATA
1 AAAT-AAAAGGAATAAATAAAATA
* *
2444827 AAATAAAAGTAATAAAT-AAATG
1 AAATAAAAGGAATAAATAAAATA
*
2444849 AAATAAAAGTAATAAA
1 AAATAAAAGGAATAAA
2444865 AGGACCATAT
Statistics
Matches: 89, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.03
21 9 0.10
22 38 0.43
23 9 0.10
24 16 0.18
25 4 0.04
26 5 0.06
27 5 0.06
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (23 bp):
AAATAAAAGGAATAAATAAAATA
Found at i:2445998 original size:16 final size:15
Alignment explanation
Indices: 2445977--2446019 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2445967 TTAATAGAAT
2445977 TAATAATAATTAATAA
1 TAATAATAATTAA-AA
*
2445993 TAATAATAAAT-AAA
1 TAATAATAATTAAAA
2446007 TAAT-ATAATTAAA
1 TAATAATAATTAAA
2446020 TATTTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 8 0.33
15 1 0.04
16 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATAATAATTAAAA
Found at i:2446014 original size:13 final size:14
Alignment explanation
Indices: 2445968--2446021 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
2445958 GTAAAAAAAT
*
2445968 TAATAGAATTAATAA
1 TAATA-AATAAATAA
*
2445983 TAATTAAT-AATAA
1 TAATAAATAAATAA
2445996 TAATAAATAAATAA
1 TAATAAATAAATAA
*
2446010 T-ATAATTAAATA
1 TAATAAATAAATA
2446022 TTTTTGTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 22 0.63
14 9 0.26
15 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
TAATAAATAAATAA
Found at i:2446486 original size:84 final size:84
Alignment explanation
Indices: 2446386--2446545 Score: 250
Period size: 84 Copynumber: 1.9 Consensus size: 84
2446376 TTGTTGACAA
* **
2446386 ATAACCCTTCTTGCCTTAAGATATGCTGTGAATGATGTGCCTTGGAG-TAGAGCGTAGTCGAACT
1 ATAACCCTTCTAGCCTTAAGATATGCTGCAAATGATGTGCCTTGGAGCT-GAGCGTAGTCGAACT
2446450 CGAAGGTCTTTGGTTGGCAG
65 CGAAGGTCTTTGGTTGGCAG
* * *
2446470 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTAAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
2446535 GAAGGTCTTTG
66 GAAGGTCTTTG
2446546 TGTTTCAAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
84 68 0.99
85 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (84 bp):
ATAACCCTTCTAGCCTTAAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTTGGCAG
Found at i:2446583 original size:31 final size:34
Alignment explanation
Indices: 2446546--2446625 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 34
2446536 AAGGTCTTTG
*
2446546 TGTTTCAAGAGAAACATTTTCAAA-G-GTTTTTT
1 TGTTTCAAGAGAAACAATTTCAAATGTGTTTTTT
*
2446578 T-TTTCAAGAGAAACAATTTCAAATGTTTTTTTT
1 TGTTTCAAGAGAAACAATTTCAAATGTGTTTTTT
2446611 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
2446626 TGTCTCAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 21 0.49
32 2 0.05
33 7 0.16
34 13 0.30
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAATTTCAAATGTGTTTTTT
Found at i:2446667 original size:37 final size:36
Alignment explanation
Indices: 2446609--2446907 Score: 235
Period size: 37 Copynumber: 8.5 Consensus size: 36
2446599 AATGTTTTTT
*
2446609 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* **
2446645 CTTTGTTTCAAGGGAAATTGTCTCAATTGAGACAAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** * * *
2446682 CTTAG-TTCTAAAAGAAACTGTCTCAAGGGAGCCGAAA
1 -TTTGTTTC-AAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
2446719 TTAGTTTCAAGGAAAACATAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
2446748 TTTGTTTCAAGGGAAACTGTCTCAAGAGAG--AAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
2446782 TTTATTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
2446818 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * *
2446854 CTTAGTTCCAAAAGAAAC-GATCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
2446891 TTAGTTTCAAGGAAAAC
1 TTTGTTTCAAGGGAAAC
2446908 ATATTCAAAT
Statistics
Matches: 213, Mismatches: 36, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
34 29 0.14
35 1 0.00
36 66 0.31
37 91 0.43
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:2446772 original size:29 final size:31
Alignment explanation
Indices: 2446715--2446846 Score: 108
Period size: 34 Copynumber: 4.1 Consensus size: 31
2446705 CAAGGGAGCC
* * *
2446715 GAAATTAGTTTCAAGGAAAACATAT-TCAA-A
1 GAAATTTGTTTCAAGGGAAAC-TGTCTCAAGA
*
2446745 G-ATTTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 GAAATTTGTTTCAAGGGAAACTGTCTC-A-AGA
*
2446777 GAAAATTTATTTCAAGGGAAACTGTCTCAAGGGA
1 G-AAATTTGTTTCAAGGGAAACTGTCTCAA--GA
*
2446811 GACAAAATTTGTTTCAAGAGAAACTGTCTCAAGA
1 G---AAATTTGTTTCAAGGGAAACTGTCTCAAGA
2446845 GA
1 GA
2446847 GACAAAACTT
Statistics
Matches: 84, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.02
29 18 0.21
30 2 0.02
31 2 0.02
32 3 0.04
33 1 0.01
34 29 0.35
36 27 0.32
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATTTGTTTCAAGGGAAACTGTCTCAAGA
Found at i:2446808 original size:15 final size:15
Alignment explanation
Indices: 2446754--2446810 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
2446744 AGATTTTGTT
2446754 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
* * *
2446769 TCAAGAGAGAAAATTTATT
1 TCAAG-G-G-AAA-CTGTC
2446788 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
2446803 TCAAGGGA
1 TCAAGGGA
2446811 GACAAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 15 0.47
16 4 0.12
17 2 0.06
18 4 0.12
19 7 0.22
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (15 bp):
TCAAGGGAAACTGTC
Found at i:2446825 original size:99 final size:102
Alignment explanation
Indices: 2446646--2446833 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 102
2446636 GAGACAAAAC
*
2446646 TTTGTTTCAAGGGAAATTGTCTCAATTGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGGGAAACTGTCTCAA-TGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
* *
2446711 AGCCGAAATTAGTTTCAAG-GAAAACATATTCAAAGAT
65 AGACAAAATTAGTTTCAAGAGAAAACATATTCAAAGAT
* * * **
2446748 TTTGTTTCAAGGGAAACTGTCTCAA-GAGAGAAAATTTATTTC-AAGGGAAACTGTCTCAAGGGA
1 TTTGTTTCAAGGGAAACTGTCTCAATGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGGA
*
2446811 GACAAAATTTGTTTCAAGAGAAA
66 GACAAAATTAGTTTCAAGAGAAA
2446834 CTGTCTCAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
99 34 0.45
100 18 0.24
102 24 0.32
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAGGGAAACTGTCTCAATGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGGA
GACAAAATTAGTTTCAAGAGAAAACATATTCAAAGAT
Found at i:2446826 original size:36 final size:36
Alignment explanation
Indices: 2446748--2446907 Score: 182
Period size: 36 Copynumber: 4.5 Consensus size: 36
2446738 ATTCAAAGAT
*
2446748 TTTGTTTCAAGGGAAACTGTCTCAA--GAGAGAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
*
2446782 TTTATTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
* *
2446818 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
* * ** *
2446854 CTTAGTTCCAAAAGAAAC-GATCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAA
* *
2446891 TTAGTTTCAAGGAAAAC
1 TTTGTTTCAAGGGAAAC
2446908 ATATTCAAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
34 24 0.22
36 55 0.51
37 29 0.27
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
Found at i:2446869 original size:172 final size:173
Alignment explanation
Indices: 2446613--2446967 Score: 570
Period size: 172 Copynumber: 2.1 Consensus size: 173
2446603 TTTTTTTTTG
* * **
2446613 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATTGTCTCAATTGAGAC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
* *
2446678 AAAACTTAGTTCTAAAAGAAACTG-TCTCAAGGGAGCCGAAATTAGTTTCAAGGAAAACATATTC
66 AAAACTTAGTTCCAAAAGAAAC-GATCTCAAGGGAGACGAAATTAGTTTCAAGGAAAACATATTC
2446742 AAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTA
130 AAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTA
* *
2446786 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
2446850 AAAACTTAGTTCCAAAAGAAACGATCTCAAGGGAGACGAAATTAGTTTCAAGGAAAACATATTCA
66 AAAACTTAGTTCCAAAAGAAACGATCTCAAGGGAGACGAAATTAGTTTCAAGGAAAACATATTCA
* * * * *
2446915 AATATTTTGTTTCACGGGAAACTGTCTCAAGGGAGACAATTTG
131 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTA
2446958 TTTCAAGAGA
1 TTTCAAGAGA
2446968 GACAAAACTT
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
171 1 0.01
172 136 0.81
173 30 0.18
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (173 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
AAAACTTAGTTCCAAAAGAAACGATCTCAAGGGAGACGAAATTAGTTTCAAGGAAAACATATTCA
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTA
Found at i:2446898 original size:73 final size:69
Alignment explanation
Indices: 2446751--2446905 Score: 195
Period size: 73 Copynumber: 2.2 Consensus size: 69
2446741 CAAAGATTTT
* * **
2446751 GTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTATTTCAAGGGAAACTGTCTCAAGGGAGACAA
1 GTTTCAA-GGAAACTGTCTCAAGAGAGAAAACTTATTCCAAAAGAAACTGTCTCAAGGGAGACAA
*
2446816 AATTT
65 AATTA
2446821 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAC-GATCTCAAGGGAG
1 GTTTCAAG-GAAACTGTCTCAAGAGAG--AAAACTTA-TTCCAAAAGAAACTG-TCTCAAGGGAG
*
2446885 ACGAAATTA
61 ACAAAATTA
2446894 GTTTCAAGGAAA
1 GTTTCAAGGAAA
2446906 ACATATTCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
69 1 0.01
70 25 0.34
72 12 0.16
73 36 0.49
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (69 bp):
GTTTCAAGGAAACTGTCTCAAGAGAGAAAACTTATTCCAAAAGAAACTGTCTCAAGGGAGACAAA
ATTA
Found at i:2446972 original size:121 final size:121
Alignment explanation
Indices: 2446839--2447074 Score: 411
Period size: 121 Copynumber: 2.0 Consensus size: 121
2446829 AGAAACTGTC
*
2446839 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAAC-GATCTCAAGGGAGACGAAATTAGTTTCAAGG
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTG-TCTCAAGGGAAACGAAATTAGTTTCAAGG
* * *
2446903 AAAACATATTCAAATATTTTGTTTCACGGGAAACTGTCTCAAGGGAGACAATTTGTT
65 AAAACATAATCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTTGTT
*
2446960 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAAATGAAATTAGTTTCAAGGA
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAAACGAAATTAGTTTCAAGGA
2447025 AAACATAATCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
66 AAACATAATCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
2447075 AATTTTGTTT
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
121 108 0.99
122 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (121 bp):
TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAAACGAAATTAGTTTCAAGGA
AAACATAATCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTTGTT
Found at i:2447529 original size:96 final size:99
Alignment explanation
Indices: 2447348--2447721 Score: 369
Period size: 106 Copynumber: 3.7 Consensus size: 99
2447338 AAATCCAAGT
* * * * * * *
2447348 AAGTTGTATTGTTTCGAGTCCAATATCC-TCCTCCGTAAAGTTGAAATTGGCTCTGGAACTGAGA
1 AAGTTG-ATTGTCTCGAATCCAATATCCTTCGT-TGTGAAGTTGAAATTGGCTCTGAAACTGGGA
* * * *
2447412 AATTATTTGTTGACAACCAGCCGCCCCTTCGCTGTG
64 AGTTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTG
* * * *
2447448 AAGTT-A-T-TCTCGAGTCTAATATTCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGGGAAG
1 AAGTTGATTGTCTCGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAG
2447510 TTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTG
66 TTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTG
* *
2447544 AAGTTGAGCATGTGTTGTCTGGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
1 AAGTT--G-A----TTGTCTCGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAC
2447609 TGGGAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTG
59 TGGGAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTG
* * * **
2447650 AAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTATCTCTGAAAC
1 AAGTTGA-------TTGTCTCGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAC
*
2447715 TGTGAAG
59 TGGGAAG
2447722 CCCCTTCGTC
Statistics
Matches: 234, Mismatches: 26, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
96 77 0.33
97 4 0.02
98 1 0.00
100 6 0.03
103 1 0.00
104 1 0.00
105 1 0.00
106 143 0.61
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (99 bp):
AAGTTGATTGTCTCGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAG
TTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTG
Found at i:2447650 original size:106 final size:106
Alignment explanation
Indices: 2447465--2447721 Score: 426
Period size: 106 Copynumber: 2.4 Consensus size: 106
2447455 TCTCGAGTCT
*
2447465 AATATTCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAATCAGCC
1 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAATCAGCC
2447530 GCCCCTTCGTTGTGAAGTTGAGCATGTGTTGTCTGGAATCC
66 GCCCCTTCGTTGTGAAGTTGAGCATGTGTTGTCTGGAATCC
* *
2447571 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAATCAGCC
1 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAATCAGCC
* * *
2447636 GCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCC
66 GCCCCTTCGTTGTGAAGTTGAGCATGTGTTGTCTGGAATCC
* *
2447677 AATATCCTTCGCTGTGAAGTTGAAATT-ATCTCTGAAACTGTGAAG
1 AATATCCTTCGTTGTGAAGTTGAAATTGA-CTCTGAAACTGGGAAG
2447722 CCCCTTCGTC
Statistics
Matches: 140, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
106 140 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (106 bp):
AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAATCAGCC
GCCCCTTCGTTGTGAAGTTGAGCATGTGTTGTCTGGAATCC
Found at i:2448438 original size:32 final size:31
Alignment explanation
Indices: 2448356--2448439 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
2448346 CGTCAGGATA
* * *
2448356 TTGAATTCCCAAAGATACCCCAATATTCTATG
1 TTGAA-TCTCAAAGATGCCCCAACATTCTATG
*
2448388 TTGAATCTCAAAAAATGCCCCAACATT-TGATG
1 TTGAATCTC-AAAGATGCCCCAACATTCT-ATG
2448420 TTGAATCTTCAAAGATGCCC
1 TTGAATC-TCAAAGATGCCC
2448440 TCATTGTTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 4 0.09
32 38 0.86
33 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.30
Consensus pattern (31 bp):
TTGAATCTCAAAGATGCCCCAACATTCTATG
Found at i:2449529 original size:28 final size:29
Alignment explanation
Indices: 2449498--2449567 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
2449488 TCACTCTTTC
2449498 CTTTGTTTTTGTTTCTCTTTTTTAT-TTT
1 CTTTGTTTTTGTTTCTCTTTTTTATGTTT
* * * *
2449526 CTTTGCTTTTTCTTTGTTTTTTTTCTGTTT
1 CTTTG-TTTTTGTTTCTCTTTTTTATGTTT
*
2449556 -TTTCTTTTTGTT
1 CTTTGTTTTTGTT
2449568 CTGATTGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 12 0.35
29 19 0.56
30 3 0.09
ACGTcount: A:0.01, C:0.11, G:0.09, T:0.79
Consensus pattern (29 bp):
CTTTGTTTTTGTTTCTCTTTTTTATGTTT
Found at i:2449547 original size:22 final size:21
Alignment explanation
Indices: 2449503--2449562 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
2449493 CTTTCCTTTG
* *
2449503 TTTTTGTTTCTCTTTTTTATT
1 TTTTTGTTTTTCTTTGTTATT
2449524 TTCTTTGCTTTTTCTTTGTT-TT
1 TT-TTTG-TTTTTCTTTGTTATT
2449546 TTTTCTGTTTTTTCTTT
1 TTTT-TG-TTTTTCTTT
2449563 TTGTTCTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 4 0.12
22 19 0.58
23 10 0.30
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTGTTTTTCTTTGTTATT
Found at i:2451566 original size:5 final size:5
Alignment explanation
Indices: 2451551--2451604 Score: 99
Period size: 5 Copynumber: 10.6 Consensus size: 5
2451541 TGTATGATGT
2451551 AAATGA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
1 AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
2451602 AAA
1 AAA
2451605 GGGGAAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 44 0.92
6 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:2452647 original size:3 final size:3
Alignment explanation
Indices: 2452639--2452666 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2452629 AAATAAAAGA
2452639 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2452667 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2453840 original size:3 final size:3
Alignment explanation
Indices: 2453834--2453867 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
2453824 TTAATAGAAT
2453834 TAA TAA TAA TTAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA T
2453868 TAAATGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2453846 original size:19 final size:18
Alignment explanation
Indices: 2453822--2453870 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
2453812 CCTGTAAAAA
2453822 AATTAATAGAATTAATAAT
1 AATTAATA-AATTAATAAT
2453841 AATTAAT-AA-TAATAAT
1 AATTAATAAATTAATAAT
2453857 AA-TAATATAATTAA
1 AATTAATA-AATTAA
2453871 ATGTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 4 0.15
18 3 0.11
19 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATTAATAAATTAATAAT
Found at i:2454665 original size:87 final size:87
Alignment explanation
Indices: 2454519--2454768 Score: 455
Period size: 87 Copynumber: 2.9 Consensus size: 87
2454509 TATGTTATAT
*
2454519 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAATGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAATGCTTATATAATGTAATAGAT
2454584 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
2454606 TATTTAACGGGAAATATTATCAAATACAATAACATATTAGGTAATGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAATGCTTATATAATGTAATAGAT
2454671 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
** *
2454693 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAATGCTTATATAATGTAATAGAT
2454758 AGCGCTTATAT
66 AGCGCTTATAT
2454769 TGACCTATTT
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 157 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (87 bp):
TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAATGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:2458559 original size:120 final size:120
Alignment explanation
Indices: 2458346--2458588 Score: 387
Period size: 120 Copynumber: 2.0 Consensus size: 120
2458336 TCTTCCATTA
* * * *
2458346 TGGACATAAAGTACCGACACAATATTAAAAAGTATTGACATAGGTTGTAGATCTATTCGCTAATA
1 TGGACATAAAGTACCGACACAAAATTAAAAAGCATCGACATAGGTTGTAGACCTATTCGCTAATA
* *
2458411 AAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTATATTATAATTC
66 AAACCGATATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTC
* * *
2458466 TGGACATAAAGTACCGACACAAAATTAAAAAGCGTCGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAAAATTAAAAAGCATCGACATAGGTTGTAGACCTATTCGCTAATA
* *
2458531 AAACCGATATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTC
66 AAACCGATATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTC
2458586 TGG
1 TGG
2458589 GTTCCGATGT
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (120 bp):
TGGACATAAAGTACCGACACAAAATTAAAAAGCATCGACATAGGTTGTAGACCTATTCGCTAATA
AAACCGATATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTC
Found at i:2458724 original size:303 final size:303
Alignment explanation
Indices: 2458177--2458767 Score: 1056
Period size: 303 Copynumber: 2.0 Consensus size: 303
2458167 TTAAAATTAG
* * *
2458177 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGCGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
2458242 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
2458307 CACTTTTTGATAATGTATCGACACATTTTTCTTCCATTATGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAATGTATCGACACATTTTTCTTCCATTATGGACATAAAGTACCGACACAATATT
* * *
2458372 AAAAAGTATTGACATAGGTTGTAGATCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAGTATCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATAACGGTTATA
*
2458437 TTACAAAATTATCTAGTATATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
2458480 CGACACAAAATTAAAAAGCGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
1 CGACACAAAATTAAAAAGCGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
2458545 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
2458610 CACTTTTTGACAATGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAATGTATCGACACATTTTTCTTCCATTATGGACATAAAGTACCGACACAATATT
* * * *
2458675 AAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATAACGGTTATA
196 AAAAAGTATCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATAACGGTTATA
*
2458740 TTACAAAATTATCTATTACATTATAATT
261 TTACAAAATTATCTAGTACATTATAATT
2458768 ATGGGTTTCG
Statistics
Matches: 274, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
303 274 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGCGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAATGTATCGACACATTTTTCTTCCATTATGGACATAAAGTACCGACACAATATT
AAAAAGTATCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATAACGGTTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:2458782 original size:183 final size:183
Alignment explanation
Indices: 2458462--2459050 Score: 1020
Period size: 183 Copynumber: 3.2 Consensus size: 183
2458452 GTATATTATA
* *
2458462 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGCGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
2458527 CATAAAACCGATATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
*
2458592 CCGATGTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
2458645 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
2458710 CATAAAACCGGTATATTTATAACGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
*
2458775 TCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
2458828 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCAATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
2458893 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
* * *
2458958 CCGATGTTTTTTCAA--TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
2459012 ATTATGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
2459051 GAAAACTTTG
Statistics
Matches: 388, Mismatches: 15, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
183 308 0.79
184 76 0.20
186 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:2460268 original size:3 final size:3
Alignment explanation
Indices: 2460260--2460313 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
2460250 ACTTGTTTGG
* *
2460260 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
2460308 TTC ATC
1 ATC ATC
2460314 GTCAGCTTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.28, C:0.33, G:0.02, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:2460314 original size:12 final size:12
Alignment explanation
Indices: 2460261--2460330 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
2460251 CTTGTTTGGA
*
2460261 TCATCATCATCA
1 TCATCATCATCT
*
2460273 TCATCATCATCA
1 TCATCATCATCT
2460285 TCATCATCATCT
1 TCATCATCATCT
*
2460297 TCATCGTCATCT
1 TCATCATCATCT
* *
2460309 TCATCGTCAGCT
1 TCATCATCATCT
*
2460321 TCATCTTCAT
1 TCATCATCAT
2460331 TGACCGCTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.24, C:0.33, G:0.04, T:0.39
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:2462107 original size:33 final size:33
Alignment explanation
Indices: 2462070--2462135 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2462060 CATCTTAATA
* *
2462070 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCATCAACACCCCAACTTCTTTCACCACT
* *
2462103 TCACCCATCAACACCTCTACTTCTTTCACCACT
1 TCACCCATCAACACCCCAACTTCTTTCACCACT
2462136 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCATCAACACCCCAACTTCTTTCACCACT
Found at i:2462194 original size:21 final size:21
Alignment explanation
Indices: 2462169--2462233 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2462159 CCCCTTATGC
* *
2462169 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2462190 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
2462211 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2462232 CT
1 CT
2462234 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:2464755 original size:161 final size:162
Alignment explanation
Indices: 2464490--2464827 Score: 527
Period size: 161 Copynumber: 2.1 Consensus size: 162
2464480 ATCATTTTGA
* *
2464490 TACCGGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATATATATTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATATTTTTAAAGTATCG
2464555 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
* * * *
2464619 TATCGACACTTTCAATATATCTGGTAACGTTT
131 TACCGACACTTTAAATATATCCGGTAACGCTT
*
2464651 TACCGGTTTTATCATATTTTTACATGGTATATCGTTTTGGATCGATACAT-TTTTTAAAAGTATC
1 TACCGGTTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATATTTTT-AAAGTATC
* ** *
2464715 GACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAA
65 GACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAA
* * *
2464780 GTACCGACACTTTAAATGTGTCCGGTAGCGCTT
130 GTACCGACACTTTAAATATATCCGGTAACGCTT
2464813 TACCGGTTTTATCAT
1 TACCGGTTTTATCAT
2464828 TTCAATACCG
Statistics
Matches: 161, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
160 5 0.03
161 111 0.69
162 45 0.28
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (162 bp):
TACCGGTTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATATTTTTAAAGTATCG
ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
TACCGACACTTTAAATATATCCGGTAACGCTT
Found at i:2465819 original size:15 final size:15
Alignment explanation
Indices: 2465801--2465838 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2465791 TGTCGGTTGG
*
2465801 TTTGGATTGGGTTAA
1 TTTGGATTGGATTAA
*
2465816 TTTGCATTGGATTAA
1 TTTGGATTGGATTAA
2465831 TTTGGATT
1 TTTGGATT
2465839 TTAAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.50
Consensus pattern (15 bp):
TTTGGATTGGATTAA
Found at i:2467126 original size:20 final size:20
Alignment explanation
Indices: 2467101--2467138 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2467091 ACGATGGACA
*
2467101 GCACAGCACTGCACAGAACG
1 GCACAGCACAGCACAGAACG
*
2467121 GCACAGCGCAGCACAGAA
1 GCACAGCACAGCACAGAA
2467139 ATGAATGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.34, G:0.26, T:0.03
Consensus pattern (20 bp):
GCACAGCACAGCACAGAACG
Found at i:2473662 original size:18 final size:18
Alignment explanation
Indices: 2473639--2473679 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2473629 AGCGATCTCT
* *
2473639 TTCTCTTTCTCTCTCCCG
1 TTCTCTATCCCTCTCCCG
*
2473657 TTCTCTATCCCTTTCCCG
1 TTCTCTATCCCTCTCCCG
2473675 TTCTC
1 TTCTC
2473680 GATTTCGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.44, G:0.05, T:0.49
Consensus pattern (18 bp):
TTCTCTATCCCTCTCCCG
Found at i:2475994 original size:13 final size:13
Alignment explanation
Indices: 2475976--2476010 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
2475966 GCCATTTTCC
2475976 CTCTCTCTCTGCG
1 CTCTCTCTCTGCG
2475989 CTCTCTCTCTGCG
1 CTCTCTCTCTGCG
2476002 CTCTCTCTC
1 CTCTCTCTC
2476011 GTCTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.49, G:0.11, T:0.40
Consensus pattern (13 bp):
CTCTCTCTCTGCG
Found at i:2476897 original size:3 final size:3
Alignment explanation
Indices: 2476889--2476927 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2476879 ATAAATAGGA
2476889 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2476928 CTATATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2477077 original size:81 final size:81
Alignment explanation
Indices: 2476956--2477114 Score: 205
Period size: 81 Copynumber: 2.0 Consensus size: 81
2476946 AAAACGTATA
* ** * **
2476956 ATATATAACTTTTCAAAATGTTTTTTTTTAAAACTATATATTATACGTATTTTCAGAAACGTTTT
1 ATATATAAC-TTTCAAAATATTTTTTTAAAAAACTATATATTATACATATTTTCA-AAACGACTT
2477021 TTAAAAAC-ATATACAAC
64 TTAAAAACTATATACAAC
* *
2477038 ATATATAAC-TTCAAAAATATTTTTTTAAAAAACTATATATTATATATATTTTCAAAATGACTTT
1 ATATATAACTTTC-AAAATATTTTTTTAAAAAACTATATATTATACATATTTTCAAAACGACTTT
2477102 TAAAAACTATATA
65 TAAAAACTATATA
2477115 ATATATAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
80 17 0.25
81 41 0.61
82 9 0.13
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (81 bp):
ATATATAACTTTCAAAATATTTTTTTAAAAAACTATATATTATACATATTTTCAAAACGACTTTT
AAAAACTATATACAAC
Found at i:2477095 original size:40 final size:39
Alignment explanation
Indices: 2476952--2477121 Score: 132
Period size: 40 Copynumber: 4.3 Consensus size: 39
2476942 TTCAAAAACG
* *
2476952 TATAATATATA-ACTTTTCAAAATGTTTTTTTTTAAAACTA
1 TATAATATATATA-TTTTCAAAAT-ATTTTTTTAAAAACTA
* ** **
2476992 TATATTATACGTATTTTCAGAAA-CGTTTTTTAAAAACATA
1 TATAATATATATATTTTCA-AAATATTTTTTTAAAAAC-TA
* * **
2477032 TACAACATATATAACTTCAAAAATATTTTTTTAAAAAACTA
1 TATAATATATATATTTTC-AAAATATTTTTTT-AAAAACTA
* *
2477073 TATATTATATATATTTTCAAAATGA--CTTTTAAAAACTA
1 TATAATATATATATTTTCAAAAT-ATTTTTTTAAAAACTA
2477111 TATAATATATA
1 TATAATATATA
2477122 AATGTTTTCG
Statistics
Matches: 101, Mismatches: 22, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
38 18 0.18
39 15 0.15
40 35 0.35
41 27 0.27
42 6 0.06
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (39 bp):
TATAATATATATATTTTCAAAATATTTTTTTAAAAACTA
Found at i:2477244 original size:2 final size:2
Alignment explanation
Indices: 2477239--2477273 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2477229 GAAAAAAGAC
2477239 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2477274 ATAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2477277 original size:10 final size:11
Alignment explanation
Indices: 2477239--2477277 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
2477229 GAAAAAAGAC
2477239 TATATAT-ATA
1 TATATATAATA
2477249 TATATAT-ATA
1 TATATATAATA
2477259 TATATATAATA
1 TATATATAATA
2477270 TATA-ATAA
1 TATATATAA
2477278 AAAGAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 21 0.75
11 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATATATAATA
Found at i:2479438 original size:17 final size:17
Alignment explanation
Indices: 2479418--2479450 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2479408 AATTTTTTTT
2479418 TAAAA-AAATAATTAAAA
1 TAAAACAAA-AATTAAAA
2479435 TAAAACAAAAATTAAA
1 TAAAACAAAAATTAAA
2479451 CTTTAAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAACAAAAATTAAAA
Found at i:2488705 original size:2 final size:2
Alignment explanation
Indices: 2488698--2488722 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2488688 CCTGAATTCC
2488698 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2488723 GTCTAGAACT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2493007 original size:64 final size:64
Alignment explanation
Indices: 2492939--2493158 Score: 207
Period size: 64 Copynumber: 3.5 Consensus size: 64
2492929 TTGAAGGTGT
* ** *
2492939 ATCGATGCACAGGAAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCAAAGGAAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCAAATGCAATTCGTG
2493002 C
64 C
* *
2493003 ATCGATGCATAAGTAA-TGCATCGATGCATCCCATTAATAATGAAACATCAAATGCAATTCGTGC
1 ATCGATGCA-AAGGAAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
* * * * * * * **
2493067 ATCGATGCATA-GTAGTGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCAAAGGAAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
* * *
2493130 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCA-AAGGAAGTGCATCGATGCAT
2493159 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
62 1 0.01
63 49 0.37
64 72 0.55
65 10 0.08
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCAAAGGAAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
Found at i:2493114 original size:63 final size:64
Alignment explanation
Indices: 2492983--2493158 Score: 248
Period size: 63 Copynumber: 2.8 Consensus size: 64
2492973 TAAAATAAAT
* *
2492983 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATGAA
1 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATGAA
*
2493047 ACATCAAATGCAATTCGTGCATCGATGCAT-AGTAGTGCATCGATGCATCCCAGTAATAAT-ACA
1 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATGA-A
* * ** * *
2493110 ACATCGAATACATTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCAT
2493159 ACCTTCATTA
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
62 1 0.01
63 53 0.52
64 47 0.47
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (64 bp):
ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATGAA
Found at i:2493866 original size:30 final size:31
Alignment explanation
Indices: 2493812--2493965 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
2493802 AGGGTCGAGG
* *
2493812 GTTTACCTATGTTCTTCAGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2493843 GTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2493873 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2493904 GTTTACCTATGTTCTTCGGGAC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2493934 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2493965 G
1 G
2493966 GTTCTTCGGG
Statistics
Matches: 117, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
30 56 0.48
31 61 0.52
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2493907 original size:61 final size:61
Alignment explanation
Indices: 2493812--2493965 Score: 240
Period size: 61 Copynumber: 2.5 Consensus size: 61
2493802 AGGGTCGAGG
* *
2493812 GTTTACCTATGTTCTTCAGGACATATGAACTGTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGAC-TATGGACT
*
2493873 GTTTACCTATGTTCTTCGGGACATATGGATTGTTTACCTATGTTCTTCGGGACTATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACTATGGACT
*
2493934 GTTTACCTAGGTTCTTCGGGATC-TATGGACTG
1 GTTTACCTATGTTCTTCGGGA-CATATGGACTG
2493966 GTTCTTCGGG
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
61 81 0.94
62 5 0.06
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (61 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACTATGGACT
Found at i:2494269 original size:6 final size:6
Alignment explanation
Indices: 2494258--2494299 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
2494248 AGTAGTAATG
2494258 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
2494300 ATGCATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:2497842 original size:31 final size:31
Alignment explanation
Indices: 2497797--2497859 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2497787 AAGGTCGAGG
*
2497797 GTTTACATATGTTCTTC-GGAACATATGGACT
1 GTTTACATAGGTTCTTCGGGAAC-TATGGACT
* *
2497828 GTTTACCTAGGTTCTTCGGGATCTATGGACT
1 GTTTACATAGGTTCTTCGGGAACTATGGACT
2497859 G
1 G
2497860 GTCCTTCGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACATAGGTTCTTCGGGAACTATGGACT
Found at i:2498918 original size:18 final size:18
Alignment explanation
Indices: 2498895--2498931 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2498885 CAAAATTTAT
2498895 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2498913 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2498931 A
1 A
2498932 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2498948 original size:24 final size:25
Alignment explanation
Indices: 2498893--2498950 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
2498883 GCCAAAATTT
2498893 ATATTGAAATTCAAACTCAAATTGAA
1 ATATT-AAATTCAAACTCAAATTGAA
* *
2498919 AT-TTAAATTCAAACTCCAATT-AC
1 ATATTAAATTCAAACTCAAATTGAA
2498942 ATATTAAAT
1 ATATTAAAT
2498951 GAATTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 3 0.10
24 22 0.76
25 2 0.07
26 2 0.07
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.34
Consensus pattern (25 bp):
ATATTAAATTCAAACTCAAATTGAA
Found at i:2499366 original size:25 final size:25
Alignment explanation
Indices: 2499307--2499356 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2499297 CATTATTTTC
* *
2499307 CAAATAATGTACCCATAACAATGTT
1 CAAATAATTTACCCACAACAATGTT
2499332 CAAATAATTTACCCACAACAATGTT
1 CAAATAATTTACCCACAACAATGTT
2499357 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (25 bp):
CAAATAATTTACCCACAACAATGTT
Found at i:2502136 original size:24 final size:23
Alignment explanation
Indices: 2502073--2502124 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
2502063 AACATCATCA
2502073 AAATTCGAGTATTGACCAAGATC
1 AAATTCGAGTATTGACCAAGATC
* *
2502096 AAAGTCTGGGTATTGACCAAGATC
1 AAATTC-GAGTATTGACCAAGATC
2502120 AAATT
1 AAATT
2502125 TCGAATACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (23 bp):
AAATTCGAGTATTGACCAAGATC
Found at i:2503092 original size:20 final size:19
Alignment explanation
Indices: 2503049--2503155 Score: 69
Period size: 20 Copynumber: 5.4 Consensus size: 19
2503039 AAAACATTTG
* *
2503049 TGTTGCGAAAATAAAA-CC
1 TGTTGCGAAATTAAAATCA
2503067 TGTTGCGAAATTAAAATTCA
1 TGTTGCGAAATTAAAA-TCA
2503087 TGTTGCG-AATTCGAAAATCGA
1 TGTTGCGAAATT--AAAATC-A
*
2503108 -GTTGCGAAATCGAAAATCGA
1 TGTTGCGAAAT-TAAAATC-A
* *
2503128 -GTTGCGAATTTGAAATTCA
1 TGTTGCGAAATT-AAAATCA
2503147 GTGTTGCGA
1 -TGTTGCGA
2503156 TTTAGAGATT
Statistics
Matches: 73, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
18 15 0.21
19 5 0.07
20 38 0.52
21 15 0.21
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (19 bp):
TGTTGCGAAATTAAAATCA
Found at i:2503166 original size:21 final size:20
Alignment explanation
Indices: 2503128--2503297 Score: 101
Period size: 20 Copynumber: 8.3 Consensus size: 20
2503118 CGAAAATCGA
*
2503128 GTTGCGAATTT-GAAATTCAGT
1 GTTGCG-ATTTAGAAATTC-GC
*
2503149 GTTGCGATTTAGAGATTCGC
1 GTTGCGATTTAGAAATTCGC
* * **
2503169 GTTACGATTTACATTTTCGC
1 GTTGCGATTTAGAAATTCGC
*
2503189 GTTGCGAATTTAGAAAATCGC
1 GTTGCG-ATTTAGAAATTCGC
** * * *
2503210 AATGCGATTTACATATTCAC
1 GTTGCGATTTAGAAATTCGC
* *
2503230 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTAGAAATTCGC
** * *
2503251 AATGCGATTTACATATTCGC
1 GTTGCGATTTAGAAATTCGC
* *
2503271 GTTGCGAATTTGGAAATT-GG
1 GTTGCG-ATTTAGAAATTCGC
2503291 GTTGCGA
1 GTTGCGA
2503298 AATTGGAGTT
Statistics
Matches: 109, Mismatches: 36, Indels: 10
0.70 0.23 0.06
Matches are distributed among these distances:
19 1 0.01
20 61 0.56
21 47 0.43
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTAGAAATTCGC
Found at i:2503218 original size:41 final size:41
Alignment explanation
Indices: 2503173--2503286 Score: 201
Period size: 41 Copynumber: 2.8 Consensus size: 41
2503163 ATTCGCGTTA
* *
2503173 CGATTTACATTTTCGCGTTGCGAATTTAGAAAATCGCAATG
1 CGATTTACATATTCGCGTTGCGAATTTGGAAAATCGCAATG
*
2503214 CGATTTACATATTCACGTTGCGAATTTGGAAAATCGCAATG
1 CGATTTACATATTCGCGTTGCGAATTTGGAAAATCGCAATG
2503255 CGATTTACATATTCGCGTTGCGAATTTGGAAA
1 CGATTTACATATTCGCGTTGCGAATTTGGAAA
2503287 TTGGGTTGCG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (41 bp):
CGATTTACATATTCGCGTTGCGAATTTGGAAAATCGCAATG
Found at i:2503294 original size:20 final size:20
Alignment explanation
Indices: 2503128--2503322 Score: 85
Period size: 20 Copynumber: 9.6 Consensus size: 20
2503118 CGAAAATCGA
* *
2503128 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGGAATTC-GC
*
2503149 GTTGCG-ATTTAGAGATTCGC
1 GTTGCGAATTTGGA-ATTCGC
* ** *
2503169 GTTACG-ATTTACATTTTCGC
1 GTTGCGAATTTGGA-ATTCGC
* *
2503189 GTTGCGAATTTAGAAAATCGC
1 GTTGCGAATTT-GGAATTCGC
** ** *
2503210 AATGCG-ATTTACATATTCAC
1 GTTGCGAATTTGGA-ATTCGC
*
2503230 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTTGG-AATTCGC
** **
2503251 AATGCG-ATTTACATATTCGC
1 GTTGCGAATTTGGA-ATTCGC
*
2503271 GTTGCGAATTTGGAAATT-GG
1 GTTGCGAATTTGG-AATTCGC
* *
2503291 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAATTTGGAATTCGC
2503311 GTTGCGAATTTG
1 GTTGCGAATTTG
2503323 TTGATCATTT
Statistics
Matches: 126, Mismatches: 38, Indels: 21
0.68 0.21 0.11
Matches are distributed among these distances:
19 5 0.04
20 77 0.61
21 41 0.33
22 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGGAATTCGC
Found at i:2507509 original size:14 final size:14
Alignment explanation
Indices: 2507490--2507535 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
2507480 AGATTGGACT
2507490 AAATATAAACAAAC
1 AAATATAAACAAAC
**
2507504 AAATATAAATGAAC
1 AAATATAAACAAAC
* *
2507518 GAACATAAACAAAC
1 AAATATAAACAAAC
2507532 AAAT
1 AAAT
2507536 TATTAAACGC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.67, C:0.13, G:0.04, T:0.15
Consensus pattern (14 bp):
AAATATAAACAAAC
Found at i:2507997 original size:21 final size:20
Alignment explanation
Indices: 2507963--2508003 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2507953 CATAATTATT
2507963 TAAAAAATTAAATAAAAATA
1 TAAAAAATTAAATAAAAATA
*
2507983 TAAAAATATTTAATAAAAATA
1 TAAAAA-ATTAAATAAAAATA
2508004 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAATTAAATAAAAATA
Done.