Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 17
Found at i:3178962 original size:178 final size:170
Alignment explanation
Indices: 3178704--3179017 Score: 418
Period size: 178 Copynumber: 1.8 Consensus size: 170
3178694 TTTCTACATT
* *
3178704 TAATTGAGGCCCTAATTTTTTTAATCCTACTTTTTAACTTTATAATTGAGGCTCTTAAGTTTTTT
1 TAATTGAGGCCCTAATTTTTTTAATCCTACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTT
** * * *
3178769 CAATATCGCTTTCTACCTTTTACCTTTCAA-TGAGG-CCTCTAAGTTTTTTTAATCTCAATTTTT
66 CAATATCAATTTCTA-CATTTA----T-AATTGAGGTCC-CTAAGTTTTTTCAATCTCAA-TTAT
3178832 ACCTTTATAATTGAAGCCCCTAACTTTTTAATCCCCTTTTTAACTTTA
123 ACCTTTATAATTGAAGCCCCTAACTTTTTAATCCCCTTTTTAACTTTA
*
3178880 TAATTGAGGCCCTTAAGTTTTTTTAAT-CTCACTTTTTACCTTTATAATTGAGGCCCCTAAGTTT
1 TAATTGAGGCCC-TAA-TTTTTTTAATCCT-ACTTTTTAACTTTATAATTGAGGCCCCTAAGTTT
* *
3178944 TTTCAATCTCAATTTCTACATTTATAATTGAGGTCCCTAAGTTTTTTCAATCTCGATTATACCTT
63 TTTCAATATCAATTTCTACATTTATAATTGAGGTCCCTAAGTTTTTTCAATCTCAATTATACCTT
3179009 TATAATTGA
128 TATAATTGA
3179018 GACATCTATT
Statistics
Matches: 123, Mismatches: 10, Indels: 14
0.84 0.07 0.10
Matches are distributed among these distances:
172 19 0.15
173 24 0.20
174 2 0.02
176 12 0.10
177 10 0.08
178 56 0.46
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (170 bp):
TAATTGAGGCCCTAATTTTTTTAATCCTACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTT
CAATATCAATTTCTACATTTATAATTGAGGTCCCTAAGTTTTTTCAATCTCAATTATACCTTTAT
AATTGAAGCCCCTAACTTTTTAATCCCCTTTTTAACTTTA
Found at i:3180336 original size:22 final size:23
Alignment explanation
Indices: 3180311--3180356 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
3180301 CAATATAAAA
*
3180311 TATAATAA-ATATTATTATTTAT
1 TATAAAAATATATTATTATTTAT
3180333 TATAAAAACTTATATTATTATTTA
1 TATAAAAA--TATATTATTATTTA
3180357 AAAATATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
25 13 0.65
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATAAAAATATATTATTATTTAT
Found at i:3180521 original size:21 final size:21
Alignment explanation
Indices: 3180491--3180571 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
3180481 TGAATATCTA
*
3180491 TAAAAATATTATATTATATTT
1 TAAAATTATTATATTATATTT
*
3180512 TAAAATTATTAATAAATATATTT
1 TAAAATTATT-AT-ATTATATTT
*
3180535 TAAAGACTT-TT-TATAATATTAT
1 TAAA-A-TTATTATATTATATT-T
*
3180557 T-AAACTATTATATTA
1 TAAAATTATTATATTA
3180572 AATAAATACA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
19 1 0.02
20 3 0.06
21 21 0.45
22 5 0.11
23 12 0.26
24 3 0.06
25 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (21 bp):
TAAAATTATTATATTATATTT
Found at i:3180552 original size:23 final size:22
Alignment explanation
Indices: 3180491--3180553 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
3180481 TGAATATCTA
* *
3180491 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
3180512 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
3180535 TAAAGACTT-TTTATAATAT
1 TAAA-A-TTATTTATAATAT
3180554 TATTAAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 17 0.50
24 5 0.15
25 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:3180695 original size:26 final size:24
Alignment explanation
Indices: 3180636--3180704 Score: 59
Period size: 26 Copynumber: 2.8 Consensus size: 24
3180626 AATAATTTTA
* *
3180636 TATATTA-TAATAAAATATAATAG
1 TATATTATTATTATAATATAATAG
3180659 TATCATATATTATTATAATATAATTGAG
1 TAT-AT-TATTATTATAATATAA-T-AG
* *
3180687 TATATTATTGTAATAATA
1 TATATTATTATTATAATA
3180705 ATATTTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.08
24 2 0.05
25 2 0.05
26 22 0.59
27 3 0.08
28 5 0.14
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (24 bp):
TATATTATTATTATAATATAATAG
Found at i:3180746 original size:22 final size:24
Alignment explanation
Indices: 3180721--3180768 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
3180711 ATATTATTAA
3180721 TTAAAAATATTAATAA-T-ATATT
1 TTAAAAATATTAATAATTAATATT
* *
3180743 TTAAATATTTTAATAATTAATATT
1 TTAAAAATATTAATAATTAATATT
3180767 TT
1 TT
3180769 TCCAGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 1 0.05
24 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAAAAATATTAATAATTAATATT
Found at i:3180893 original size:70 final size:71
Alignment explanation
Indices: 3180805--3180952 Score: 259
Period size: 70 Copynumber: 2.1 Consensus size: 71
3180795 TGATCAGGAT
3180805 AATATTT--TACATTGATCAATCTGTTTTCCTCCAACC-AACACTGAAAAATGGGGAAAACA-TT
1 AATATTTACTACATTGATCAATCTGTTTTCCTCCAACCAAACACTG-AAAATGGGGAAAACATTT
3180866 TTTAAAA
65 TTTAAAA
3180873 AATATTTACTACATTGATCAATCTGTTTTCCTCCAACCAAACACTGAAAATGGGGAAAACATTTT
1 AATATTTACTACATTGATCAATCTGTTTTCCTCCAACCAAACACTGAAAATGGGGAAAACATTTT
3180938 TTAAAA
66 TTAAAA
3180944 AATATTTAC
1 AATATTTAC
3180953 GTGAAACAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
68 7 0.09
70 44 0.58
71 25 0.33
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (71 bp):
AATATTTACTACATTGATCAATCTGTTTTCCTCCAACCAAACACTGAAAATGGGGAAAACATTTT
TTAAAA
Found at i:3181128 original size:15 final size:15
Alignment explanation
Indices: 3181107--3181153 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
3181097 ATATAATTTT
3181107 AATTTAAATATATTA
1 AATTTAAATATATTA
*
3181122 TATTTAAAT-TATGTA
1 AATTTAAATATAT-TA
3181137 AATTTATAATATTATTA
1 AATTTA-AATA-TATTA
3181154 GTTATAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.12
15 15 0.58
16 3 0.12
17 2 0.08
18 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATTTAAATATATTA
Found at i:3181431 original size:11 final size:11
Alignment explanation
Indices: 3181415--3181463 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
3181405 GTTTTTCAAT
3181415 GAACCGGCTGG
1 GAACCGGCTGG
*
3181426 GAACCGG-T-A
1 GAACCGGCTGG
*
3181435 GAACCGG-TGT
1 GAACCGGCTGG
*
3181445 GAACTGGCTGG
1 GAACCGGCTGG
3181456 GAACCGGC
1 GAACCGGC
3181464 AAAATCGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 8 0.26
10 7 0.23
11 16 0.52
ACGTcount: A:0.22, C:0.24, G:0.41, T:0.12
Consensus pattern (11 bp):
GAACCGGCTGG
Found at i:3182823 original size:13 final size:13
Alignment explanation
Indices: 3182805--3182847 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
3182795 GACATTACTG
3182805 CCGCATCCGCGCC
1 CCGCATCCGCGCC
*
3182818 CCGCATCGCCCGCC
1 CCGCATC-CGCGCC
*
3182832 CCACATCCGC-CC
1 CCGCATCCGCGCC
3182844 CCGC
1 CCGC
3182848 CCAGCTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 5 0.20
13 9 0.36
14 11 0.44
ACGTcount: A:0.09, C:0.65, G:0.19, T:0.07
Consensus pattern (13 bp):
CCGCATCCGCGCC
Found at i:3186062 original size:19 final size:19
Alignment explanation
Indices: 3186038--3186085 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3186028 TGATTTGTGT
3186038 ATCGATGCACAAGT-AGTGC
1 ATCGATGCAC-AGTAAGTGC
* *
3186057 ATCGATACACTGTAGAGTGC
1 ATCGATGCACAGTA-AGTGC
3186077 ATCGATGCA
1 ATCGATGCA
3186086 TACCTTCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 9 0.38
20 13 0.54
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (19 bp):
ATCGATGCACAGTAAGTGC
Found at i:3186629 original size:18 final size:18
Alignment explanation
Indices: 3186606--3186640 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3186596 ATGGATTATC
*
3186606 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
3186624 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
3186641 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:3188923 original size:23 final size:23
Alignment explanation
Indices: 3188893--3188947 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3188883 TTATAATAAT
*
3188893 TATGTCTTTGTGATACGTT-TATC
1 TATGTCTTTGTGACACGTTCT-TC
*
3188916 TATGTCTTCGTGACACGTTCTTC
1 TATGTCTTTGTGACACGTTCTTC
*
3188939 TATGCCTTT
1 TATGTCTTT
3188948 TGGTATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.49
Consensus pattern (23 bp):
TATGTCTTTGTGACACGTTCTTC
Found at i:3189419 original size:2 final size:2
Alignment explanation
Indices: 3189412--3189488 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
3189402 GCCTTCCATA
3189412 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
3189454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3189489 AAAGAAAAGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3192298 original size:2 final size:2
Alignment explanation
Indices: 3192291--3192318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3192281 TGTAATTGTA
3192291 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
3192319 TAATGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3192800 original size:15 final size:16
Alignment explanation
Indices: 3192775--3192808 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3192765 AGTAAAGACA
*
3192775 CATACATCTTCTTTTT
1 CATACATCTTCTATTT
3192791 CATA-ATCTTCTATTT
1 CATACATCTTCTATTT
3192806 CAT
1 CAT
3192809 CTTCTACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (16 bp):
CATACATCTTCTATTT
Found at i:3196255 original size:3 final size:3
Alignment explanation
Indices: 3196249--3196273 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3196239 TTTTTTTGTA
3196249 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3196274 TAATTTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3196851 original size:166 final size:165
Alignment explanation
Indices: 3196568--3196891 Score: 639
Period size: 166 Copynumber: 2.0 Consensus size: 165
3196558 CGCCAGACGC
3196568 CGCCGGCTGCTGCATCCACAGTGACCGAAGGTCCCCCCACAGTCATCTACAGTAAACCACAGCAA
1 CGCCGGCTGCTGCATCCACAGTGACCGAAGGTCCCCCCACAGTCATCTACAGTAAACCACAGCAA
3196633 CCCCATCAATCCATATAATCCCGAAAATCTGGGATTCTATCACAAAAAAATCAGAAACCCATTCC
66 CCCCATCAATCCATATAATCCCGAAAATCTGGGATTCTATCACAAAAAAATCAGAAACCCATTCC
3196698 TAAATCTGAGACTGATCCCCTATTTTTTCCTCTGA
131 TAAATCTGAGACTGATCCCCTATTTTTTCCTCTGA
3196733 CGCCGGCTGCCTGCATCCACAGTGACCGAAGGTCCCCCCACAGTCATCTACAGTAAACCACAGCA
1 CGCCGGCTG-CTGCATCCACAGTGACCGAAGGTCCCCCCACAGTCATCTACAGTAAACCACAGCA
3196798 ACCCCATCAATCCATATAATCCCGAAAATCTGGGATTCTATCACAAAAAAATCAGAAACCCATTC
65 ACCCCATCAATCCATATAATCCCGAAAATCTGGGATTCTATCACAAAAAAATCAGAAACCCATTC
3196863 CTAAATCTGAGACTGATCCCCTATTTTTT
130 CTAAATCTGAGACTGATCCCCTATTTTTT
3196892 TCTAGACATC
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 9 0.06
166 149 0.94
ACGTcount: A:0.32, C:0.33, G:0.13, T:0.22
Consensus pattern (165 bp):
CGCCGGCTGCTGCATCCACAGTGACCGAAGGTCCCCCCACAGTCATCTACAGTAAACCACAGCAA
CCCCATCAATCCATATAATCCCGAAAATCTGGGATTCTATCACAAAAAAATCAGAAACCCATTCC
TAAATCTGAGACTGATCCCCTATTTTTTCCTCTGA
Found at i:3201536 original size:26 final size:25
Alignment explanation
Indices: 3201505--3201584 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
3201495 CCAATTTTTG
3201505 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
3201530 A-A-TATTCT-TTT-CGACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
3201551 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
3201577 ACATTCTT
1 ACATTCTT
3201585 TCCACCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.16
21 5 0.12
22 4 0.09
23 3 0.07
24 4 0.09
25 6 0.14
26 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:3202232 original size:19 final size:22
Alignment explanation
Indices: 3202208--3202252 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
3202198 ATCAAAGAGA
3202208 AAAGAGCA-A-AGAAAAAAA-C
1 AAAGAGCAGAGAGAAAAAAATC
3202227 AAAGAGCAGAGAGAAAAAAATC
1 AAAGAGCAGAGAGAAAAAAATC
3202249 AAAG
1 AAAG
3202253 CAAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 1 0.04
21 9 0.39
22 5 0.22
ACGTcount: A:0.69, C:0.09, G:0.20, T:0.02
Consensus pattern (22 bp):
AAAGAGCAGAGAGAAAAAAATC
Found at i:3202239 original size:26 final size:24
Alignment explanation
Indices: 3202194--3202246 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3202184 TCAAAAACAG
*
3202194 AAAAATCAAAGAGAAAAGAGCAAAGA
1 AAAAAACAAAGAGAAAAGAG-AAA-A
* *
3202220 AAAAAACAAAGAGCAGAGAGAAAA
1 AAAAAACAAAGAGAAAAGAGAAAA
3202244 AAA
1 AAA
3202247 TCAAAGCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 3 0.12
26 17 0.71
ACGTcount: A:0.72, C:0.08, G:0.19, T:0.02
Consensus pattern (24 bp):
AAAAAACAAAGAGAAAAGAGAAAA
Found at i:3202265 original size:18 final size:18
Alignment explanation
Indices: 3202242--3202300 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
3202232 GCAGAGAGAA
3202242 AAAAATCAAAGCAAAAAC
1 AAAAATCAAAGCAAAAAC
*
3202260 AAAAATCAAAGCAAAATC
1 AAAAATCAAAGCAAAAAC
3202278 AAAGAA--AAAGCAAAGAAC
1 AAA-AATCAAAGCAAA-AAC
3202296 AAAAA
1 AAAAA
3202301 GAGGACAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 10 0.27
18 25 0.68
19 2 0.05
ACGTcount: A:0.73, C:0.14, G:0.08, T:0.05
Consensus pattern (18 bp):
AAAAATCAAAGCAAAAAC
Found at i:3202293 original size:11 final size:11
Alignment explanation
Indices: 3202260--3202294 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3202250 AAGCAAAAAC
3202260 AAAAATCAAAG
1 AAAAATCAAAG
*
3202271 CAAAATCAAAG
1 AAAAATCAAAG
*
3202282 AAAAAGCAAAG
1 AAAAATCAAAG
3202293 AA
1 AA
3202295 CAAAAAGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.71, C:0.11, G:0.11, T:0.06
Consensus pattern (11 bp):
AAAAATCAAAG
Found at i:3203399 original size:4 final size:4
Alignment explanation
Indices: 3203390--3203471 Score: 105
Period size: 4 Copynumber: 21.0 Consensus size: 4
3203380 AAGAGTATAC
* * * *
3203390 ACAT ACAT ACAT ACGT ATAC ACAT ACAT ACAT ATAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
3203438 ACAT ACAT ATAT ACAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3203472 GATACATAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
2 2 0.03
4 64 0.97
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (4 bp):
ACAT
Found at i:3203879 original size:35 final size:36
Alignment explanation
Indices: 3203825--3203922 Score: 171
Period size: 35 Copynumber: 2.8 Consensus size: 36
3203815 GATTTTTCTA
3203825 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
3203861 AAAACAAA-TTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
**
3203896 AAAACAAATTTTGTCTCATTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
3203923 TTTTCCCTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 35 0.59
36 24 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
Found at i:3204249 original size:101 final size:96
Alignment explanation
Indices: 3204045--3204276 Score: 238
Period size: 101 Copynumber: 2.3 Consensus size: 96
3204035 TGAGAATTTT
** *
3204045 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCTTGAGATACAAATTTTGAATTTGATTCACTAA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCTTGAGATACAAATTTCGAATTTGATTCACTAA
*
3204110 AAACAAAATCTCACCTTAGATTGTTGTTTCTTTC
66 AAACAAAATCTCACCTTAGA-T-TCGTTTC-TTC
* * *
3204144 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTT-CC-TTGAGATACAAATTTCGAATTTGATTCACT
*
3204208 ATTAAACAAAGTTGATCTCA-CTTGAGA-TCGTTTC-TC
64 A-AAAACAAA----ATCTCACCTT-AGATTCGTTTCTTC
* *
3204244 AAAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 -AAAACAAATTTTGTCTCGCTTGAGACATTTTC
3204277 TCTAAAACAA
Statistics
Matches: 113, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
99 28 0.25
100 6 0.05
101 61 0.54
102 6 0.05
104 3 0.03
105 9 0.08
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (96 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCTTGAGATACAAATTTCGAATTTGATTCACTAA
AAACAAAATCTCACCTTAGATTCGTTTCTTC
Found at i:3204250 original size:35 final size:33
Alignment explanation
Indices: 3204223--3204339 Score: 135
Period size: 35 Copynumber: 3.4 Consensus size: 33
3204213 ACAAAGTTGA
3204223 TCTCACTTGAGATCGTTTCTCAAAAACAAACTTTG
1 TCTCACTTGAGA-C-TTTCTCAAAAACAAACTTTG
* * *
3204258 TCTCGCTTGAGACAATTTCTCTAAAACAAATTTTG
1 TCTCACTTGAGAC--TTTCTCAAAAACAAACTTTG
* * *
3204293 TCTCATTTGAGACTATATCAAAAACAAACTTTG
1 TCTCACTTGAGACTTTCTCAAAAACAAACTTTG
*
3204326 TCTCATTTGAGACT
1 TCTCACTTGAGACT
3204340 ATATCTTAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
33 30 0.42
34 1 0.01
35 40 0.56
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (33 bp):
TCTCACTTGAGACTTTCTCAAAAACAAACTTTG
Found at i:3204326 original size:33 final size:33
Alignment explanation
Indices: 3204242--3204344 Score: 134
Period size: 33 Copynumber: 3.1 Consensus size: 33
3204232 AGATCGTTTC
** * *
3204242 TCAAAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 TCAAAAACAAACTTTGTCTCATTTGAGAC--TATA
* *
3204277 TCTAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCAAAAACAAACTTTGTCTCATTTGAGACTATA
3204310 TCAAAAACAAACTTTGTCTCATTTGAGACTATA
1 TCAAAAACAAACTTTGTCTCATTTGAGACTATA
3204343 TC
1 TC
3204345 TTAAAGCAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 35 0.58
35 25 0.42
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (33 bp):
TCAAAAACAAACTTTGTCTCATTTGAGACTATA
Found at i:3204327 original size:68 final size:67
Alignment explanation
Indices: 3204223--3204372 Score: 183
Period size: 68 Copynumber: 2.2 Consensus size: 67
3204213 ACAAAGTTGA
* * * *
3204223 TCTCACTTGAGATCGTTTCTCAAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAAAACAAA
1 TCTCACTTGAGA-C-TATATCAAAAACAAACTTTGTCTCACTTGAGACAATATCT-TAAAACAAA
*
3204288 TTTTG
63 TTTCG
* * * *
3204293 TCTCATTTGAGACTATATCAAAAACAAACTTTGTCTCATTTGAGACTATATCTTAAAGCAAATTT
1 TCTCACTTGAGACTATATCAAAAACAAACTTTGTCTCACTTGAGACAATATCTTAAAACAAATTT
3204358 CG
66 CG
*
3204360 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
3204373 ATCATTTTCT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
67 23 0.33
68 34 0.49
69 1 0.01
70 11 0.16
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (67 bp):
TCTCACTTGAGACTATATCAAAAACAAACTTTGTCTCACTTGAGACAATATCTTAAAACAAATTT
CG
Found at i:3204659 original size:28 final size:28
Alignment explanation
Indices: 3204622--3204882 Score: 160
Period size: 29 Copynumber: 9.2 Consensus size: 28
3204612 ACAGTTTCTC
*
3204622 TTGAAAAAAATCTTTGAGTTTGTTCCTT
1 TTGAATAAAATCTTTGAGTTTGTTCCTT
* *
3204650 TAGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAT-AAAATCTTTGAGTTTGTTCCTT
* *
3204679 TTGAATAATATCTTTGAG-TTGTTTCTT
1 TTGAATAAAATCTTTGAGTTTGTTCCTT
* * **
3204706 TTG---AAAATCTTTGAGTCTATTTATT
1 TTGAATAAAATCTTTGAGTTTGTTCCTT
*** * *
3204731 TTGAA-ACAAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 TTGAATA-AAA--------TCT-TTGAGTTTGTTCCTT
*
3204768 TTGAAAAAAATCTTTGAGTTTGTTCCTT
1 TTGAATAAAATCTTTGAGTTTGTTCCTT
* *
3204796 TAGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAT-AAAATCTTTGAGTTTGTTCCTT
* *
3204825 TTGAATAATATCTTTGAG-TTGTTTCTT
1 TTGAATAAAATCTTTGAGTTTGTTCCTT
* * *
3204852 TTG-A-AAAATCTTTGAGTCTATTCATT
1 TTGAATAAAATCTTTGAGTTTGTTCCTT
3204878 TTGAA
1 TTGAA
3204883 ACAAAGTTTT
Statistics
Matches: 182, Mismatches: 33, Indels: 37
0.72 0.13 0.15
Matches are distributed among these distances:
24 11 0.06
25 20 0.11
26 9 0.05
27 24 0.13
28 41 0.23
29 55 0.30
36 3 0.02
37 18 0.10
38 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (28 bp):
TTGAATAAAATCTTTGAGTTTGTTCCTT
Found at i:3204720 original size:24 final size:24
Alignment explanation
Indices: 3204657--3204736 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 24
3204647 CTTTAGAATA
* *
3204657 AAAATCTTGGAGTTTGTTCCTTTTG
1 AAAATCTTTGAG-TTGTTTCTTTTG
3204682 AATAATATCTTTGAGTTGTTTCTTTTG
1 -A-AA-ATCTTTGAGTTGTTTCTTTTG
* *
3204709 AAAATCTTTGAGTCTATTTATTTTG
1 AAAATCTTTGAGT-TGTTTCTTTTG
3204734 AAA
1 AAA
3204737 CAAAGTTTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
24 10 0.21
25 14 0.30
26 2 0.04
27 13 0.28
28 8 0.17
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (24 bp):
AAAATCTTTGAGTTGTTTCTTTTG
Found at i:3204757 original size:146 final size:147
Alignment explanation
Indices: 3204596--3204912 Score: 609
Period size: 146 Copynumber: 2.2 Consensus size: 147
3204586 AAACGATTTT
3204596 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
3204661 TCTTGGAGTTTGTTCCTTTTGAATAATATCTTTGAGTTGTTTCTTTTG-AAAATCTTTGAGTCTA
66 TCTTGGAGTTTGTTCCTTTTGAATAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
*
3204725 TTTATTTTGAAACAAAG
131 TTCATTTTGAAACAAAG
3204742 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
3204807 TCTTGGAGTTTGTTCCTTTTGAATAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
66 TCTTGGAGTTTGTTCCTTTTGAATAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
3204872 TTCATTTTGAAACAAAG
131 TTCATTTTGAAACAAAG
*
3204889 TTTTGTCTCTCTTGAGACAATTTC
1 TTTTGTCTCTCTTGAGACAGTTTC
3204913 GTGAAAAATC
Statistics
Matches: 168, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
146 113 0.67
147 55 0.33
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (147 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
TCTTGGAGTTTGTTCCTTTTGAATAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
TTCATTTTGAAACAAAG
Found at i:3204957 original size:52 final size:53
Alignment explanation
Indices: 3204879--3204982 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
3204869 CTATTCATTT
*
3204879 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCCTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
3204931 TGAAACAAAGTTTTGTCTCTCCTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCCTGAGACAATTTCGTG-AAAAAATCTTTGAG
3204983 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 35 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCCTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:3205004 original size:30 final size:30
Alignment explanation
Indices: 3204970--3205033 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
3204960 ATTTTGTGAA
*
3204970 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
*
3205000 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
3205030 AAAA
1 AAAA
3205034 TTTTGTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:3205034 original size:29 final size:29
Alignment explanation
Indices: 3204962--3205038 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 29
3204952 CTGAGACAAT
3204962 TTTGTGAAA-AAAATCTTTGAGATTGTTTC
1 TTTG-GAAACAAAATCTTTGAGATTGTTTC
* *
3204991 TTTTGAAACAAAAATCTTTGAGTTTGTTTC
1 TTTGGAAAC-AAAATCTTTGAGATTGTTTC
3205021 TTTGGAAACAAAAT-TTTG
1 TTTGGAAACAAAATCTTTG
3205039 TCTCTCTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.19
29 8 0.19
30 27 0.63
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (29 bp):
TTTGGAAACAAAATCTTTGAGATTGTTTC
Found at i:3205122 original size:64 final size:64
Alignment explanation
Indices: 3204986--3205146 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 64
3204976 CTTTGAGATT
* * *
3204986 GTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 GTTTCTTTTG-AA-AAAAATCTTTGAATTTGTTTCCTT-GAAACAAAATTTTGTATCTCTTAAGA
*
3205051 TA
63 CA
* * *
3205053 ATTTCTTTTGAAAAAAATCTTTGAATTTGTTTCGCTT-AAA-ATGAATTTTGTATCTCTTGAGAC
1 GTTTCTTTTGAAAAAAATCTTTGAATTTGTTTC-CTTGAAACA-AAATTTTGTATCTCTTAAGAC
3205116 A
64 A
* ** *
3205117 GTTTCTCTTG-AATTAATCTTTGAATATGTT
1 GTTTCTTTTGAAAAAAATCTTTGAATTTGTT
3205147 CATTTGAAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
63 18 0.22
64 29 0.36
65 20 0.25
66 4 0.05
67 9 0.11
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (64 bp):
GTTTCTTTTGAAAAAAATCTTTGAATTTGTTTCCTTGAAACAAAATTTTGTATCTCTTAAGACA
Found at i:3205392 original size:64 final size:63
Alignment explanation
Indices: 3205309--3205429 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
3205299 GGGATCCATC
* *
3205309 TTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAATTTTTT
1 TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAATTTTTT
* * **
3205373 TTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAA
1 TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAA
3205430 ATACCCACAT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 18 0.35
64 33 0.65
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (63 bp):
TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAATTTTTT
Found at i:3205485 original size:39 final size:40
Alignment explanation
Indices: 3205412--3205490 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
3205402 TTGTCTCTCG
*
3205412 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAACACCCACATTTGAGATCGTTT
* * * *
3205452 AGACAATTTCTTTT-AAAACCCCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAACACCCACATTTGAGATCGTTT
3205491 TTATTAAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 21 0.62
40 13 0.38
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAACACCCACATTTGAGATCGTTT
Found at i:3205618 original size:14 final size:15
Alignment explanation
Indices: 3205584--3205626 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
3205574 TTTTGAGTCG
*
3205584 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
3205599 TTTCTCTTGAAACA-
1 TTTCTCTTGAAACAT
*
3205613 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
3205627 GATCATCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.42
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:3205952 original size:38 final size:34
Alignment explanation
Indices: 3205910--3205997 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 34
3205900 CATTTGAATC
3205910 TGTTTTTCTTGAAACAAAACAAACAAAGTCTTTGAGTA
1 TGTTTTTCTTGAAACAAAA-AAAC--A-TCTTTGAGTA
* *
3205948 TGTTTTTCTTAAAACAAAAAAACATCTTTGAGTT
1 TGTTTTTCTTGAAACAAAAAAACATCTTTGAGTA
* *
3205982 TGTTTCTCTCGAAACA
1 TGTTTTTCTTGAAACA
3205998 CTAATCTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
34 22 0.49
35 1 0.02
37 4 0.09
38 18 0.40
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (34 bp):
TGTTTTTCTTGAAACAAAAAAACATCTTTGAGTA
Found at i:3205986 original size:34 final size:37
Alignment explanation
Indices: 3205910--3205986 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
3205900 CATTTGAATC
*
3205910 TGTTTTTCTTGAAACAAAACAAACAAAGTCTTTGAGTA
1 TGTTTTTCTTAAAACAAAACAAAC-AAGTCTTTGAGTA
*
3205948 TGTTTTTCTTAAAACAAAA-AAAC-A-TCTTTGAGTT
1 TGTTTTTCTTAAAACAAAACAAACAAGTCTTTGAGTA
3205982 TGTTT
1 TGTTT
3205987 CTCTCGAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 14 0.38
35 1 0.03
37 4 0.11
38 18 0.49
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (37 bp):
TGTTTTTCTTAAAACAAAACAAACAAGTCTTTGAGTA
Found at i:3206055 original size:36 final size:34
Alignment explanation
Indices: 3206002--3206115 Score: 98
Period size: 36 Copynumber: 3.4 Consensus size: 34
3205992 GAAACACTAA
*
3206002 TCTTTGAGATCA-ATTCCCTTTAAACGAACTTTGTC
1 TCTTTGAGA-CAGTTTCCCTTTAAACGAA-TTTGTC
*
3206037 TCATTTGAGACAGTTTCCCTTTAAACG---TCG--
1 TC-TTTGAGACAGTTTCCCTTTAAACGAATTTGTC
* *
3206067 TCTTTGAGTC-GTTTCCCTTAAAACGAATTTTGTC
1 TCTTTGAGACAGTTTCCCTTTAAACGAA-TTTGTC
3206101 TCTTTTGAGACAGTT
1 TC-TTTGAGACAGTT
3206116 GCTTTTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
28 14 0.22
29 7 0.11
30 2 0.03
32 4 0.06
34 2 0.03
35 11 0.17
36 23 0.37
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (34 bp):
TCTTTGAGACAGTTTCCCTTTAAACGAATTTGTC
Found at i:3206295 original size:46 final size:45
Alignment explanation
Indices: 3206228--3206529 Score: 161
Period size: 46 Copynumber: 7.0 Consensus size: 45
3206218 TGACTCCTAA
* * *
3206228 AGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTTATCACCTTT
1 AGATGGCCAGAAC-TCCTCATCACGTAGGAACCGTGTCATCACC-TT
* * * *
3206274 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC-C
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCA-TCACCTT
* * *
3206318 AGA---CCAGATCTCCTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
** * *
3206358 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGGCCAGAAC-TCCTCATCACGTAGGAACCGTGTCATCACC-TT
* * * ** **
3206404 AGATGGCCAGAACTCTTCATCACGTATGAGCC--GTCATTTCCCC
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
* * *
3206447 AGAT---CAGATCTCCTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
** * * * *
3206487 AGATAACCAG-TCGTCCCCATCACGTAGGAACCGAGTTATCACC
1 AGATGGCCAGAAC-TCCTCATCACGTAGGAACCGTGTCATCACC
3206530 CTTCCTAAAG
Statistics
Matches: 200, Mismatches: 36, Indels: 41
0.72 0.13 0.15
Matches are distributed among these distances:
39 2 0.01
40 31 0.16
41 29 0.14
42 7 0.04
43 55 0.28
44 9 0.05
45 6 0.03
46 57 0.28
47 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (45 bp):
AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
Found at i:3206381 original size:43 final size:44
Alignment explanation
Indices: 3206241--3206515 Score: 178
Period size: 43 Copynumber: 6.4 Consensus size: 44
3206231 TGGCCAGCCG
* * * * ** *
3206241 TCCTCATCATGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAGATC
* * * **
3206287 TCTTCATCACGTATGAGCCGTGTCATTCCCCAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGATC
*
3206328 TCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGATC
* * * ** *
3206370 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAGATC
* * * **
3206417 TCTTCATCACGTATGAGCC--GTCATTTCCCCAGAT---CAGATC
1 TCCTCATCACGTAGGAGCCGTGTCA-TACCATAGATAACCAGATC
3206457 TCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-TC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGATC
*
3206499 GTCCCCATCACGTAGGA
1 -TCCTCATCACGTAGGA
3206516 ACCGAGTTAT
Statistics
Matches: 178, Mismatches: 36, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
40 32 0.18
41 29 0.16
42 7 0.04
43 50 0.28
44 7 0.04
45 6 0.03
46 46 0.26
47 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (44 bp):
TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGATC
Found at i:3206509 original size:129 final size:129
Alignment explanation
Indices: 3206234--3206570 Score: 532
Period size: 129 Copynumber: 2.6 Consensus size: 129
3206224 CTAAAGATGG
*
3206234 CCAGCCGTCCTCATCATGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
3206299 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
66 ATGAGCCG-GTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
3206364 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
*
3206429 ATGAGCC-GTCATTTCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
66 ATGAGCCGGTCA-TTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
* * *
3206493 CCAGTCGTCCCCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGGCCAAGAACTCTTC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA-CCTT--T--AGAT-GGCC-AGAACTCTTC
*
3206558 ATCATGTATGAGC
59 ATCACGTATGAGC
3206571 AGTGTCATCC
Statistics
Matches: 193, Mismatches: 6, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
128 4 0.02
129 83 0.43
130 75 0.39
132 1 0.01
134 4 0.02
135 4 0.02
136 22 0.11
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (129 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
ATGAGCCGGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
Found at i:3212623 original size:2 final size:2
Alignment explanation
Indices: 3212618--3212658 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3212608 TCATATATTC
3212618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3212659 ATCCACGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3220218 original size:17 final size:17
Alignment explanation
Indices: 3220192--3220225 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3220182 CAAAAAACAT
3220192 AAAATATGACTTTTTGG
1 AAAATATGACTTTTTGG
*
3220209 AAAATTTGACTTTTTGG
1 AAAATATGACTTTTTGG
3220226 TCAAAGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (17 bp):
AAAATATGACTTTTTGG
Found at i:3220253 original size:23 final size:23
Alignment explanation
Indices: 3220223--3220277 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3220213 TTTGACTTTT
3220223 TGGTCAAAGTTAACAGTCAACTC
1 TGGTCAAAGTTAACAGTCAACTC
* * *
3220246 TGGTCAAAGGTAACATTCAACTT
1 TGGTCAAAGTTAACAGTCAACTC
3220269 TGG-CAAAGT
1 TGGTCAAAGT
3220278 CAACGGGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (23 bp):
TGGTCAAAGTTAACAGTCAACTC
Found at i:3220299 original size:19 final size:19
Alignment explanation
Indices: 3220272--3220328 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
3220262 TCAACTTTGG
*
3220272 CAAAGTCAACGGGTTGGGT
1 CAAAGTCAACGGGTCGGGT
* *
3220291 CAAATTCAACGTGTCGGGT
1 CAAAGTCAACGGGTCGGGT
**
3220310 CAAAGTCAATTGGTCGGGT
1 CAAAGTCAACGGGTCGGGT
3220329 TGACTCGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (19 bp):
CAAAGTCAACGGGTCGGGT
Found at i:3232842 original size:2 final size:2
Alignment explanation
Indices: 3232837--3232879 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3232827 CTACACACCA
3232837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3232878 AT
1 AT
3232880 TGTTAAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3234905 original size:20 final size:21
Alignment explanation
Indices: 3234882--3234920 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3234872 GAATCATAAT
*
3234882 ATATGCTTCAG-AATATTTGA
1 ATATACTTCAGAAATATTTGA
3234902 ATATACTTCAGAAATATTT
1 ATATACTTCAGAAATATTT
3234921 TTATTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (21 bp):
ATATACTTCAGAAATATTTGA
Found at i:3236299 original size:21 final size:21
Alignment explanation
Indices: 3236273--3236312 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3236263 ATTGTTGTAT
*
3236273 CCATCTTTATCCTGATTATGG
1 CCATCTTCATCCTGATTATGG
3236294 CCATCTTCATCCTGATTAT
1 CCATCTTCATCCTGATTAT
3236313 AAACATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (21 bp):
CCATCTTCATCCTGATTATGG
Found at i:3238713 original size:17 final size:17
Alignment explanation
Indices: 3238691--3238729 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3238681 TGAATCAAAT
3238691 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
3238708 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
3238725 -AATTA
1 TAATTA
3238730 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:3249387 original size:26 final size:26
Alignment explanation
Indices: 3249358--3249432 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 26
3249348 TAATTATAGT
*
3249358 TAATAGACTATTAATATAATAATATA
1 TAATAAACTATTAATATAATAATATA
* * * *
3249384 TAATATTACATTCTTATTTTAATAATATA
1 TAATA--A-ACTATTAATATAATAATATA
*
3249413 TAATAAAGTATTAATATAAT
1 TAATAAACTATTAATATAAT
3249433 TAATTATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
26 15 0.41
27 1 0.03
29 21 0.57
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (26 bp):
TAATAAACTATTAATATAATAATATA
Found at i:3250279 original size:2 final size:2
Alignment explanation
Indices: 3250274--3250308 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3250264 ATCATAAAAT
3250274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3250309 TAAAAAAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3265309 original size:183 final size:182
Alignment explanation
Indices: 3264997--3265665 Score: 772
Period size: 183 Copynumber: 3.7 Consensus size: 182
3264987 TTGTCAGTAC
* * * * * * * *
3264997 GTATCGATACAATTA-AAATATATATAGATACATAACAATATATCATGTAAAAATATGAGAAAAC
1 GTATCGATAC-TTTATAAACATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAAC
* * * * * * *
3265061 CGAGTTCAATATAACAAAACCGGTAAAGCGCTACTAGATATGTTGAAAGTATCGA-TTCTATTTA
65 CGATTTCAA-ATGACAAAAACAGTAAAACGCTACCAAATATGTTGAAAGTATCGATTTC-ATTTA
* * ** *
3265125 AAAAAGTATCGATACTTTTGGGGTTTAAAAGAAAAATAGTAATAGCGCCTAAAAA
128 AATAAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGCGCCTAAAAA
* * * *
3265180 GTATCGATAATTTATAAACATGTATTGATATACAACAATATAACAGGTAAAAATATGATAAAACC
1 GTATCGATACTTTATAAACATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAACC
* * * **
3265245 GATTTCATAATGATAAAAATAGTAAAATGCTACCGGATATGTTGAAAGTATCGATTTCATTTAAA
66 GATTTCA-AATGACAAAAACAGTAAAACGCTACCAAATATGTTGAAAGTATCGATTTCATTTAAA
*
3265310 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCGCCTAAAAA
130 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGCGCCTAAAAA
* *
3265363 GTATCGATACTTTATAAACATGTATCGATACACATCAATATAACAAGTAAAAATATGACAAAACC
1 GTATCGATACTTTATAAACATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAACC
* * * * * * * * **
3265428 GGTTTCATTATGACAAAACCAATAAAAAC-ATACCGAATATATTGAAAGTATCGATTCCATTGGA
66 GATTTCA-AATGACAAAAACAGT-AAAACGCTACCAAATATGTTGAAAGTATCGATTTCATTTAA
* *
3265492 ATAAGTATCGACACTTTTGAAATTTAAAAGAAAAACAGTAATAGCGCCTATAAA
129 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGCGCCTAAAAA
* * *
3265546 GTATCGATACTTTATAAA-ATTGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
1 GTATCGATACTTTATAAACA-TGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAAC
* * *
3265610 CGGTCTCGAAATGAC-AAAACAGGTAAAACGCTACCAAATATGTTGAATGTATCGAT
65 CGATTTC-AAATGACAAAAACA-GTAAAACGCTACCAAATATGTTGAAAGTATCGAT
3265666 ACTTTTATAA
Statistics
Matches: 417, Mismatches: 61, Indels: 16
0.84 0.12 0.03
Matches are distributed among these distances:
182 14 0.03
183 394 0.94
184 9 0.02
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (182 bp):
GTATCGATACTTTATAAACATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAACC
GATTTCAAATGACAAAAACAGTAAAACGCTACCAAATATGTTGAAAGTATCGATTTCATTTAAAT
AAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGCGCCTAAAAA
Found at i:3266690 original size:391 final size:388
Alignment explanation
Indices: 3266005--3266750 Score: 970
Period size: 391 Copynumber: 1.9 Consensus size: 388
3265995 AATAAAGTAA
* * *
3266005 TAGGTAAATTTACAATGTAACCGGTAAGAATATATCAGTTTAATTAGAAAATATGTCACAAATGT
1 TAGGTAAATTTACAATGTAACCAGTAAGAATATACCAGTTTAATGAGAAAATATGTCACAAATGT
* * * * * *
3266070 ATTGATACTTTTTTTATATTGTGTCAGTATTTTTTGTCCAAAATGAATGTCTACGAGGTGTACAC
66 ATCGATAC-TTGTTTATATTGTGTCAGTACTTTTTGTCCAAAATGAATGCCAACGAGGTGCACAC
* *
3266135 ATAAAATGTCGATTCATTCATAATAAGTATCGATTCCAAAAACATCGAAACCGATAATTATAATG
130 ATAAAATGTCGATTCATTCATAATAAGTATCGATCCCAAAAACATCGAAACCGATAACTATAATG
* *
3266200 TAATAGGTAAATTTACAATGTACCGGTAAGAATATACCGGTTTTATGAGAGAATAGGCCAATATA
195 TAATAGGTAAATTTACAATATACCGGTAAGAATATACCGATTTTATGAGAGAATAGGCCAATAT-
* * *
3266265 ATGTATCGATACATTTTACATTGTGTCTATACTTTTTGTCCAAAATGAATGCCCAATGAGGTGCA
259 ATGTATCGATACATTTTAAATTGTGTCGATAC-TTTTGTCCAAAATGAATG-CC-ACGAGGTGCA
* * *
3266330 CGTAT-AA-GGTTGATACATTTATAATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATG
321 CGCATAAATGGTCGATACATTCATAATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATG
3266393 TAT
386 TAT
* * * * *
3266396 TAGGTAAATTTACAATGTAATCAGTAAG-ATATACCGGTTTTATGAGAGAATATGTCAACTTAAT
1 TAGGTAAATTTACAATGTAACCAGTAAGAATATACCAGTTTAATGAGAAAATATGTC-AC-AAAT
* *
3266460 GTATCGATA-TTGTTTATATTGTGTC-GATACTTTTTGTTCAGAATGAATGGCCAACGAGGTGCA
64 GTATCGATACTTGTTTATATTGTGTCAG-TACTTTTTGTCCAAAATGAAT-GCCAACGAGGTGCA
* * * *
3266523 CGCATAAAGTGTCGA-TCTATTTATAATAAGTATCGATCCCAAAAATATCGAAACCGATAAACTA
127 CACATAAAATGTCGATTC-ATTCATAATAAGTATCGATCCCAAAAACATCGAAACCGAT-AACTA
* *
3266587 TAATGTAATAGGTAAATTTACAATATAACCGGTCA-AA-ATACCGATTTTATGAGAGAATAGGTC
190 TAATGTAATAGGTAAATTTACAATAT-ACCGGTAAGAATATACCGATTTTATGAGAGAATAGGCC
* * **
3266650 ACATAT-TGTATCGATACTTTTTTAAATTGTGTCGATACTTTTGTTCAAGCTGAATGCCACGAGG
254 A-ATATATGTATCGATAC-ATTTTAAATTGTGTCGATACTTTTGTCCAAAATGAATGCCACGAGG
*
3266714 TGCACGCATAAATTGTCGATACATTCATAATAAGTAT
317 TGCACGCATAAATGGTCGATACATTCATAATAAGTAT
3266751 TGATATTTTA
Statistics
Matches: 307, Mismatches: 37, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
388 13 0.04
389 5 0.02
390 105 0.34
391 131 0.43
392 46 0.15
393 7 0.02
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (388 bp):
TAGGTAAATTTACAATGTAACCAGTAAGAATATACCAGTTTAATGAGAAAATATGTCACAAATGT
ATCGATACTTGTTTATATTGTGTCAGTACTTTTTGTCCAAAATGAATGCCAACGAGGTGCACACA
TAAAATGTCGATTCATTCATAATAAGTATCGATCCCAAAAACATCGAAACCGATAACTATAATGT
AATAGGTAAATTTACAATATACCGGTAAGAATATACCGATTTTATGAGAGAATAGGCCAATATAT
GTATCGATACATTTTAAATTGTGTCGATACTTTTGTCCAAAATGAATGCCACGAGGTGCACGCAT
AAATGGTCGATACATTCATAATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATGTAT
Found at i:3266714 original size:195 final size:198
Alignment explanation
Indices: 3265992--3266750 Score: 901
Period size: 193 Copynumber: 3.9 Consensus size: 198
3265982 TATTGAAATT
* * * *
3265992 GATAATA-AA-GTAATAGGTAAATTTACAATGTAACCGGTAAGAATATATC-AGTTTAATTAGAA
1 GATAATATAATGTAATAGGTAAATTTACAATGTAACCGGTAAGAATATACCGA-TTTTATGAGAG
* * *
3266054 AATATGTCACA-AATGTATTGATACTTTTTTTATATTGTGTC-AGTATTTTTTGTCCAAAATGAA
65 AATAGGTCACATAATGTATCGATAC-TTTTTTATATTGTGTCGA-TACTTTTTGTCCAAAATGAA
* * * * * * *
3266117 TG-TCTACGAGGTGTACACATAAAATGTCGATTCATTCATAATAAGTATCGATTCCAAAAACATC
128 TGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCATAATAAGTATCGATCCCAAAAACATC
3266181 GAAACC
193 GAAACC
*
3266187 GATAATTATAATGTAATAGGTAAATTTACAATGT-ACCGGTAAGAATATACCGGTTTTATGAGAG
1 GATAA-TATAATGTAATAGGTAAATTTACAATGTAACCGGTAAGAATATACCGATTTTATGAGAG
* * * * *
3266251 AATAGGCCAATATAATGTATCGATAC-ATTTTACATTGTGTCTATACTTTTTGTCCAAAATGAAT
65 AATAGGTC-ACATAATGTATCGATACTTTTTTATATTGTGTCGATACTTTTTGTCCAAAATGAAT
* * * *
3266315 GCCCAATGAGGTGCACGTAT-AAG-GTTGATACATTTATAATAAGTATCGATCCCAAAAACATCG
129 GCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCATAATAAGTATCGATCCCAAAAACATCG
3266378 AAACC
194 AAACC
* * * *
3266383 GATAAT-T-ATGTATTAGGTAAATTTACAATGTAATCAGTAAG-ATATACCGGTTTTATGAGAGA
1 GATAATATAATGTAATAGGTAAATTTACAATGTAACCGGTAAGAATATACCGATTTTATGAGAGA
* * * * *
3266445 ATATGTCAACTTAATGTATCGATA-TTGTTTATATTGTGTCGATACTTTTTGTTCAGAATGAATG
66 ATAGGTC-ACATAATGTATCGATACTTTTTTATATTGTGTCGATACTTTTTGTCCAAAATGAATG
* * *
3266509 GCCAACGAGGTGCACGCATAAAGTGTCGAT-CTATTTATAATAAGTATCGATCCCAAAAATATCG
130 CCCAACGAGGTGCACGCATAAAGTGTCGATAC-ATTCATAATAAGTATCGATCCCAAAAACATCG
3266573 AAACC
194 AAACC
* *
3266578 GATAAACTATAATGTAATAGGTAAATTTACAATATAACCGGTCA-AA-ATACCGATTTTATGAGA
1 GAT-AA-TATAATGTAATAGGTAAATTTACAATGTAACCGGTAAGAATATACCGATTTTATGAGA
* * * **
3266641 GAATAGGTCACATATTGTATCGATACTTTTTTAAATTGTGTCGATAC-TTTTGTTCAAGCTGAAT
64 GAATAGGTCACATAATGTATCGATACTTTTTTATATTGTGTCGATACTTTTTGTCCAAAATGAAT
*
3266705 G-CC-ACGAGGTGCACGCATAAATTGTCGATACATTCATAATAAGTAT
129 GCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCATAATAAGTAT
3266751 TGATATTTTA
Statistics
Matches: 487, Mismatches: 57, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
193 113 0.23
194 12 0.02
195 89 0.18
196 53 0.11
197 98 0.20
198 81 0.17
199 41 0.08
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (198 bp):
GATAATATAATGTAATAGGTAAATTTACAATGTAACCGGTAAGAATATACCGATTTTATGAGAGA
ATAGGTCACATAATGTATCGATACTTTTTTATATTGTGTCGATACTTTTTGTCCAAAATGAATGC
CCAACGAGGTGCACGCATAAAGTGTCGATACATTCATAATAAGTATCGATCCCAAAAACATCGAA
ACC
Found at i:3270542 original size:20 final size:19
Alignment explanation
Indices: 3270493--3270548 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
3270483 AGGGATTATC
3270493 AGTGGTCCTTCGGGAC-AT
1 AGTGGTCCTTCGGGACAAT
** *
3270511 AGTGGTTATTCGGAACAATT
1 AGTGGTCCTTCGGGACAA-T
3270531 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
3270549 ATATTCAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 13 0.43
19 1 0.03
20 16 0.53
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAAT
Found at i:3273097 original size:16 final size:17
Alignment explanation
Indices: 3273076--3273110 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3273066 GGATGTGAGC
3273076 AAAAGA-AAAGGGATAT
1 AAAAGAGAAAGGGATAT
3273092 AAAAGAGAAAGGGATAT
1 AAAAGAGAAAGGGATAT
3273109 AA
1 AA
3273111 GAAATTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
AAAAGAGAAAGGGATAT
Found at i:3277444 original size:18 final size:19
Alignment explanation
Indices: 3277421--3277475 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
3277411 AGGGATTATC
3277421 AGTGGTCCTTCGGGACA-T
1 AGTGGTCCTTCGGGACATT
** *
3277439 AGTGGTTATTCGGAACAATT
1 AGTGGTCCTTCGGGAC-ATT
*
3277459 AGTGGTCCTTCAGGACA
1 AGTGGTCCTTCGGGACA
3277476 AATATTTAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 13 0.46
19 2 0.07
20 13 0.46
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACATT
Found at i:3277476 original size:20 final size:18
Alignment explanation
Indices: 3277421--3277476 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
3277411 AGGGATTATC
3277421 AGTGGTCCTTCGGGAC-AT
1 AGTGGTCCTTC-GGACAAT
**
3277439 AGTGGTTATTCGGAACAATT
1 AGTGGTCCTTCGG-ACAA-T
3277459 AGTGGTCCTTCAGGACAA
1 AGTGGTCCTTC-GGACAA
3277477 ATATTTAGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.07
18 11 0.37
19 1 0.03
20 14 0.47
21 2 0.07
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGACAAT
Found at i:3278992 original size:30 final size:30
Alignment explanation
Indices: 3278958--3279015 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3278948 TTTAATGTTC
3278958 ATTTCATATTT-AATTGGAGTTTGAATTTAA
1 ATTTCA-ATTTGAATTGGAGTTTGAATTTAA
* *
3278988 ATTTCAATTTGAGTTTGAGTTTGAATTT
1 ATTTCAATTTGAATTGGAGTTTGAATTT
3279016 CAATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (30 bp):
ATTTCAATTTGAATTGGAGTTTGAATTTAA
Found at i:3278996 original size:24 final size:24
Alignment explanation
Indices: 3278965--3279019 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
3278955 TTCATTTCAT
3278965 ATTT-AATTGGAGTTTGAATTTAA
1 ATTTCAATTGGAGTTTGAATTTAA
* * *
3278988 ATTTCAATTTGAGTTTGAGTTTGA
1 ATTTCAATTGGAGTTTGAATTTAA
3279012 ATTTCAAT
1 ATTTCAAT
3279020 ATAAATTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (24 bp):
ATTTCAATTGGAGTTTGAATTTAA
Found at i:3281618 original size:200 final size:199
Alignment explanation
Indices: 3280759--3281765 Score: 1563
Period size: 199 Copynumber: 5.0 Consensus size: 199
3280749 TTTTAAATTT
*
3280759 GTATCGATCCCCAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
* * *
3280824 ATAAGAATATACCGGTTTTATGACAAAATAGGTCAACATAATGTATCGATACTTTTTTAAATTGT
66 GTAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATAC-TTTTTAATTTGT
* * *
3280889 GTCGATACTTTTTGTCCACAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTAT
130 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAT
3280954 TGTAA
195 TGTAA
3280959 GTATCGATCCCAAAAACATCGAAA-CGAATAATTATAAAGTAATAGGTAAATTTACAATGTAACC
1 GTATCGATCCCAAAAACATCGAAACCG-ATAATTATAAAGTAATAGGTAAATTTACAATGTAACC
* * *
3281023 GGTAAGAATATGCCAGTTTTATGACAGAATAGGTCAACATAATGTATCGATAC-CTTTACATTTG
65 GGTAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATACTTTTTA-ATTTG
* *
3281087 TGTCGATACTTTTGGTCCAGAATGAATGCCCAATGAGGTGCACACATAAAGTGTCGATACATTTA
129 TGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA
3281152 TTGTAA
194 TTGTAA
* * *
3281158 GTATCGATCTCAAAAATATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGCAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
* * * * *
3281223 GTAAGAATATATCGGTTTTATAACATAGTAGGTCAACATAATGTATCGATACTTTTTTTTAAATT
66 GTAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATAC---TTTTTAATTT
* * *
3281288 GTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGA-GTGCACGCATAATGTGTCGATATATTT
128 GTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTT
*
3281352 ATTATAA
193 ATTGTAA
* * * *
3281359 GTATCAATCCAAAAAATAGCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
* *
3281424 GTAAGAATATACCGATTTTATGACAGAATAGGTCAACATAATGTATCGATACGTTTTACATTTGT
66 GTAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATACTTTTTA-ATTTGT
*
3281489 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTTGATACATTTAT
130 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAT
3281554 TGTAA
195 TGTAA
*
3281559 G-AGTCGATCCCAAAAACATCAAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACC
1 GTA-TCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACC
* * * * *
3281623 GATAAAAATATACTGGTTTTATGACAGAGTAGGTCAACATAATGTATCGATACTTTTTAATTTAT
65 GGTAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATACTTTTTAATTTGT
* *
3281688 GTCGATATTTTTGGTCCAGAATGAATGCCTAACGAGGTGCACGCATAAAGTGTCGATACATTTAT
130 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAT
3281753 TGTAA
195 TGTAA
3281758 GTATCGAT
1 GTATCGAT
3281766 ACATAATGAT
Statistics
Matches: 737, Mismatches: 59, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
198 9 0.01
199 297 0.40
200 252 0.34
201 137 0.19
202 38 0.05
203 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
GTAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATACTTTTTAATTTGTG
TCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
GTAA
Found at i:3281826 original size:401 final size:396
Alignment explanation
Indices: 3280759--3281765 Score: 1571
Period size: 401 Copynumber: 2.5 Consensus size: 396
3280749 TTTTAAATTT
*
3280759 GTATCGATCCCCAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
* *
3280824 ATAAGAATATACCGGTTTTATGACAAAATAGGTCAACATAATGTATCGATACTTTTTTAAATTGT
66 ATAAGAATATACTGGTTTTATGACAAAGTAGGTCAACATAATGTATCGATACTTTTTTAAATTGT
* *
3280889 GTCGATACTTTTTGTCCACAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTAT
131 GTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAT
* *
3280954 TGTAAGTATCGATCCCAAAAACATCGAAACGAATAATTATAAAGTAATAGGTAAATTTACAATGT
196 TGTAAGTATCGAT-CCAAAAATAT-AAAACGAATAATTATAAAG-AATAGGTAAATTTACAATGT
*
3281019 AACCGGTAAGAATATGCC-AGTTTTATGACAGAATAGGTCAACATAATGTATCGATACCTTTACA
258 AACCGGTAAGAATATACCGA-TTTTATGACAGAATAGGTCAACATAATGTATCGATACCTTTACA
*
3281083 TTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAATGAGGTGCACACATAAAGTGTCGATACA
322 TTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACA
3281148 TTTATTGTAA
387 TTTATTGTAA
* * *
3281158 GTATCGATCTCAAAAATATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGCAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
* * *
3281223 GTAAGAATATA-TCGGTTTTATAACATAGTAGGTCAACATAATGTATCGATACTTTTTTTTAAAT
66 ATAAGAATATACT-GGTTTTATGACAAAGTAGGTCAACATAATGTATCGATAC--TTTTTTAAAT
* *
3281287 TGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGA-GTGCACGCATAATGTGTCGATATATT
128 TGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATT
* *
3281351 TATTATAAGTATCAATCCAAAAA-ATAGCGAAACCG-ATAATTATAAAGTAATAGGTAAATTTAC
193 TATTGTAAGTATCGATCCAAAAATATA---AAA-CGAATAATTATAAAG-AATAGGTAAATTTAC
*
3281414 AATGTAACCGGTAAGAATATACCGATTTTATGACAGAATAGGTCAACATAATGTATCGATACGTT
253 AATGTAACCGGTAAGAATATACCGATTTTATGACAGAATAGGTCAACATAATGTATCGATAC-CT
* *
3281479 TTACATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTTG
317 TTACATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCG
3281544 ATACATTTATTGTAA
382 ATACATTTATTGTAA
*
3281559 G-AGTCGATCCCAAAAACATCAAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACC
1 GTA-TCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACC
* * * *
3281623 GATAAAAATATACTGGTTTTATGACAGAGTAGGTCAACATAATGTATCGATAC-TTTTTAATTTA
65 GATAAGAATATACTGGTTTTATGACAAAGTAGGTCAACATAATGTATCGATACTTTTTTAAATTG
*
3281687 TGTCGATA-TTTTTGGTCCAGAATGAATGCCTAACGAGGTGCACGCATAAAGTGTCGATACATTT
130 TGTCGATACTTTTT-GTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTT
3281751 ATTGTAAGTATCGAT
194 ATTGTAAGTATCGAT
3281766 ACATAATGAT
Statistics
Matches: 559, Mismatches: 36, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
397 5 0.01
398 40 0.07
399 152 0.27
400 128 0.23
401 233 0.42
402 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (396 bp):
GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
ATAAGAATATACTGGTTTTATGACAAAGTAGGTCAACATAATGTATCGATACTTTTTTAAATTGT
GTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAT
TGTAAGTATCGATCCAAAAATATAAAACGAATAATTATAAAGAATAGGTAAATTTACAATGTAAC
CGGTAAGAATATACCGATTTTATGACAGAATAGGTCAACATAATGTATCGATACCTTTACATTTG
TGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTA
TTGTAA
Found at i:3283580 original size:20 final size:21
Alignment explanation
Indices: 3283557--3283596 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3283547 TAAACTTTTA
3283557 TATAT-GTATCAATACTTTGT
1 TATATCGTATCAATACTTTGT
*
3283577 TATATCGGTCTCAATACTTT
1 TATATC-GTATCAATACTTT
3283597 AATTCCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
TATATCGTATCAATACTTTGT
Found at i:3284171 original size:23 final size:24
Alignment explanation
Indices: 3284126--3284171 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
3284116 ATCAACTTTA
*
3284126 ATAATGCGCAACCTATTACGTTAC
1 ATAATGCGCAACCTAATACGTTAC
* *
3284150 ATAA-GCGCTACCTAATATGTTA
1 ATAATGCGCAACCTAATACGTTA
3284172 TTATGCTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (24 bp):
ATAATGCGCAACCTAATACGTTAC
Found at i:3284329 original size:23 final size:23
Alignment explanation
Indices: 3284278--3284329 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
3284268 TTAATCAATT
* *
3284278 TATTATATAAGTTCTACCTATTA
1 TATTATATAAGTGCTACCTAATA
**
3284301 CGTTATATAAGTGCTACCTAATA
1 TATTATATAAGTGCTACCTAATA
3284324 TATTAT
1 TATTAT
3284330 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (23 bp):
TATTATATAAGTGCTACCTAATA
Found at i:3284391 original size:135 final size:136
Alignment explanation
Indices: 3284224--3284485 Score: 368
Period size: 136 Copynumber: 1.9 Consensus size: 136
3284214 CCTTGGTAAC
* * * *
3284224 ATTTTAGGTGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAATC-AATTTATTATAT-A
1 ATTTTAGGCGTTTACCTAATATGATATAATAACAAATTAAGTAATTAACCTAATTTATTATATGA
* * * * *
3284287 A-GTTCTACCTATTACGTTATATAAGTGCTACCTAATATATTATTGTGCTTGATAATGTTTCTAG
66 ACG--CTACCTACTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTCTAG
3284351 TAATTAAT
129 TAATTAAT
*
3284359 ATTTTAGGCGTTTACCTAATATGATATAATAACAAATTAAGTAATTAACCTATTTTATTATATGA
1 ATTTTAGGCGTTTACCTAATATGATATAATAACAAATTAAGTAATTAACCTAATTTATTATATGA
* * *
3284424 ACGCTACTTACTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTTCTA
66 ACGCTACCTACTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTCTA
3284486 ATTAAATAAT
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
135 46 0.41
136 62 0.56
137 2 0.02
138 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.43
Consensus pattern (136 bp):
ATTTTAGGCGTTTACCTAATATGATATAATAACAAATTAAGTAATTAACCTAATTTATTATATGA
ACGCTACCTACTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTCTAGTA
ATTAAT
Found at i:3284537 original size:16 final size:16
Alignment explanation
Indices: 3284516--3284567 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
3284506 TGATTTAGAT
*
3284516 TTTAACCGATCACTTA
1 TTTAACCAATCACTTA
*
3284532 TTTAACTAATCACTTA
1 TTTAACCAATCACTTA
3284548 TTTAACCAATCACATTA
1 TTTAACCAATCAC-TTA
3284565 TTT
1 TTT
3284568 TTTAACCGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 26 0.81
17 6 0.19
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAACCAATCACTTA
Found at i:3287168 original size:76 final size:76
Alignment explanation
Indices: 3287042--3287194 Score: 245
Period size: 76 Copynumber: 2.0 Consensus size: 76
3287032 ACAGAAATAT
*
3287042 TAAAAATTACTTGTATATCAGTTATGAAAGCAAGGATGTGATTAAATTGTTCGCGTATAAGTAAA
1 TAAAAATTACTTGTATATCAGTTACGAAAGCAAGGATGTGATTAAATTGTTCGCGTATAAGTAAA
*
3287107 TGAATAGCACC
66 CGAATAGCACC
* * *
3287118 TAAAAATTACTTGTATA-CAAGTTACGGAAGCAAGGATGTGATTATATTGTTCGCGTATAAGTAC
1 TAAAAATTACTTGTATATC-AGTTACGAAAGCAAGGATGTGATTAAATTGTTCGCGTATAAGTAA
3287182 ACGAATAGCACC
65 ACGAATAGCACC
3287194 T
1 T
3287195 TTTATAGGTT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 1 0.01
76 70 0.99
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (76 bp):
TAAAAATTACTTGTATATCAGTTACGAAAGCAAGGATGTGATTAAATTGTTCGCGTATAAGTAAA
CGAATAGCACC
Found at i:3289538 original size:20 final size:20
Alignment explanation
Indices: 3289510--3289586 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 20
3289500 TTCCCTTTGA
3289510 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
* *
3289530 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATACATTC--T-AC
* *
3289553 ATGTGCATCGATGCACTACT-C
1 A-GTGCATCGATACA-TTCTAC
3289574 A-TGCATCGATACA
1 AGTGCATCGATACA
3289587 CCAATCACCT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
19 11 0.23
20 15 0.32
21 2 0.04
22 1 0.02
23 4 0.09
24 12 0.26
25 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:3289567 original size:24 final size:20
Alignment explanation
Indices: 3289510--3289567 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
3289500 TTCCCTTTGA
*
3289510 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
3289530 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
3289553 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3289568 CTACTCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:3289642 original size:64 final size:64
Alignment explanation
Indices: 3289555--3289712 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
3289545 TCTTTAACAT
* * *
3289555 GTGCATCGATGCACTACTCATGCATCGATACACCAA-T-CACCTTCGATGTTTTCA-TTTTAAGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACCAACTGCA--TTCGATGTTTCCATTTTTAA-G
3289617 GG
63 GG
* * *
3289619 GTGCATCGATGCACTCCTTATGCATCGATGCACTAACTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACCAACTGCATTCGATGTTTCCATTTTTAAGGG
** *
3289683 GTGCATAAATGCACTTCC-TGTGCATCGATA
1 GTGCATCGATGCAC-TCCTTATGCATCGATA
3289713 AACACTGAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
64 68 0.85
65 10 0.12
66 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACCAACTGCATTCGATGTTTCCATTTTTAAGGG
Found at i:3305201 original size:21 final size:21
Alignment explanation
Indices: 3305162--3305201 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3305152 AATATTTTCA
* *
3305162 ATTATTAAATTTTTTAAAAGT
1 ATTATTAAATTTATGAAAAGT
3305183 ATTATTAAATTTATGAAAA
1 ATTATTAAATTTATGAAAA
3305202 TGTTATAAAA
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:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTATTAAATTTATGAAAAGT
Found at i:3305287 original size:32 final size:32
Alignment explanation
Indices: 3305244--3305334 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 32
3305234 ATTGATAAGT
* *
3305244 TTTAGTAAATTTTAA-AAATATTTTATAACAA
1 TTTAATAAAATTTAATAAATATTTTATAACAA
* **
3305275 TTTAATAAAATTTAATAATTATTTTATATTAA
1 TTTAATAAAATTTAATAAATATTTTATAACAA
** * *
3305307 TTTAATGGAATTTAATGACTATTTTATA
1 TTTAATAAAATTTAATAAATATTTTATA
3305335 GTAACTTGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 13 0.26
32 37 0.74
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (32 bp):
TTTAATAAAATTTAATAAATATTTTATAACAA
Found at i:3307270 original size:2 final size:2
Alignment explanation
Indices: 3307263--3307302 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3307253 TGGATTTTTA
3307263 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
3307303 TATTTTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3307989 original size:34 final size:34
Alignment explanation
Indices: 3307930--3307996 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
3307920 TTCTTGAGAG
*
3307930 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTCA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTCA
3307964 TTGTTTTCTCCTTATTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
3307997 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTCA
Found at i:3310873 original size:2 final size:2
Alignment explanation
Indices: 3310866--3310898 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3310856 TTTTGGATTT
3310866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3310899 TATTTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3314239 original size:41 final size:41
Alignment explanation
Indices: 3314193--3314316 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 41
3314183 ATAAATGTAA
* *
3314193 TATTTTAATTATAACTAAGATAAATAAACTTTATTTGTTAT
1 TATTTTAATTATAAATAAGATAAGTAAACTTTATTTGTTAT
3314234 TATTTTCAATCT-TACAATAAG--AAGTAAACTTTA-----TAT
1 TATTTT-AAT-TATA-AATAAGATAAGTAAACTTTATTTGTTAT
* * * *
3314270 TATTTTTATTACAAGTAAGATAAGTAAACTTTATTTGTTAC
1 TATTTTAATTATAAATAAGATAAGTAAACTTTATTTGTTAT
3314311 TATTTT
1 TATTTT
3314317 CAATCTTACA
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
34 6 0.09
35 3 0.05
36 21 0.32
41 25 0.38
42 5 0.08
43 6 0.09
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (41 bp):
TATTTTAATTATAAATAAGATAAGTAAACTTTATTTGTTAT
Found at i:3314421 original size:33 final size:33
Alignment explanation
Indices: 3314363--3314435 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
3314353 TAATTTCCGT
** *
3314363 TCGGGTT-AAATTCGGTTCAAGTTTCTTTCGGA
1 TCGGGTTAAAATTCGACTCAAATTTCTTTCGGA
*
3314395 TCGGGTTAAAATTCGACTCAAATTTCTTTCGGT
1 TCGGGTTAAAATTCGACTCAAATTTCTTTCGGA
*
3314428 TCGAGTTA
1 TCGGGTTA
3314436 CTTTCGGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (33 bp):
TCGGGTTAAAATTCGACTCAAATTTCTTTCGGA
Found at i:3315138 original size:16 final size:15
Alignment explanation
Indices: 3315094--3315141 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3315084 TATGAATAAC
*
3315094 AATATTATTTTTTAA
1 AATAATATTTTTTAA
3315109 AATAA-ATTATTTTAA
1 AATAATATT-TTTTAA
*
3315124 ATTAATATTTCTTTAA
1 AATAATATTT-TTTAA
3315140 AA
1 AA
3315142 GTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 3 0.11
15 15 0.56
16 9 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AATAATATTTTTTAA
Found at i:3324781 original size:2 final size:2
Alignment explanation
Indices: 3324774--3324809 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3324764 CGTACAAGTG
3324774 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
3324810 GATCCAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3329875 original size:37 final size:37
Alignment explanation
Indices: 3329834--3329937 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 37
3329824 GTGCTTATGG
* * *
3329834 ATCCTATCTTTAAGAGTTTAAATCATAGTAGAAA-TCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAAATTCT
**
3329871 ATCCTATTTTAGGAGTTTGAATCCTAACA-AAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGTAGAAATTCT
*
3329907 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
3329938 GACGAAAAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
35 3 0.05
36 25 0.45
37 28 0.50
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAAATTCT
Found at i:3330815 original size:106 final size:106
Alignment explanation
Indices: 3330631--3332006 Score: 2200
Period size: 106 Copynumber: 13.0 Consensus size: 106
3330621 GCATTGTTCC
* * ** *
3330631 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * *
3330695 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3330737 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
3330802 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3330843 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
3330908 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3330949 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
3331014 TCAACGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3331055 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
3331120 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3331161 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
3331226 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3331267 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
3331332 CCAGCGGTCCCTTCGTAGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3331373 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
3331437 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3331478 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
3331543 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3331584 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
3331649 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3331690 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTTAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
3331755 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3331796 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * * * * * *
3331861 TCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTATCTT
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTG
*
3331902 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
3331967 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
3332007 AGAGAGAAAC
Statistics
Matches: 1183, Mismatches: 83, Indels: 8
0.93 0.07 0.01
Matches are distributed among these distances:
105 98 0.08
106 1083 0.92
107 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3332062 original size:36 final size:36
Alignment explanation
Indices: 3332015--3332148 Score: 144
Period size: 37 Copynumber: 3.7 Consensus size: 36
3332005 CTAGAGAGAA
*
3332015 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAG
1 ACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGAAG
* * * *
3332051 ACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAA
1 ACTGTCTCAAGCGAGACAAAATTTGTTTC-AAGGAAG
* * * *
3332088 ACTATCTCAAGCGAGATAAAATCTTGTTTTAAATG-AG
1 ACTGTCTCAAGCGAGACAAAAT-TTG-TTTCAAGGAAG
*
3332125 ACTGCCTCAAGCGAGACAAAATTT
1 ACTGTCTCAAGCGAGACAAAATTT
3332149 ATATTGGAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
36 30 0.37
37 43 0.53
38 5 0.06
39 3 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (36 bp):
ACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGAAG
Found at i:3332921 original size:22 final size:22
Alignment explanation
Indices: 3332895--3332971 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
3332885 TTGTGTTTGG
3332895 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* * *
3332917 TCAAATGTTTGGTATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
* *
3332939 TCAAATGTTTGTCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3332961 TCAAAGGTTTG
1 TCAAAGGTTTG
3332972 ATGGGGTAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3333582 original size:19 final size:18
Alignment explanation
Indices: 3333556--3333603 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
3333546 TTTTTGTCCC
3333556 TTTTTCTTTTTGATTTTG
1 TTTTTCTTTTTGATTTTG
**
3333574 TTCTTTCTTTTTTCTTTTG
1 TT-TTTCTTTTTGATTTTG
*
3333593 TTTCTCTTTTT
1 TTTTTCTTTTT
3333604 TCTTTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTTGATTTTG
Found at i:3333609 original size:17 final size:18
Alignment explanation
Indices: 3333569--3333612 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3333559 TTCTTTTTGA
*
3333569 TTTTGTTCTTTCTTTTTTC
1 TTTTGTT-TCTCTTTTTTC
3333588 TTTTGTTTCTCTTTTTTC
1 TTTTGTTTCTCTTTTTTC
3333606 -TTTGTTT
1 TTTTGTTT
3333613 TTGATTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 7 0.29
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTGTTTCTCTTTTTTC
Found at i:3336845 original size:37 final size:37
Alignment explanation
Indices: 3336802--3336904 Score: 106
Period size: 37 Copynumber: 2.8 Consensus size: 37
3336792 TAGGATAAAG
*
3336802 ATAAAAAGAAAATAGATAAATAAATGAGTAAAAT-AT-
1 ATAAAAAGAAAA-AGATAAATAAATAAGTAAAATAATA
* * *
3336838 ATAAAAAAGTAAAAGCATATATATATAAGTAAAATAATA
1 AT-AAAAAGAAAAAG-ATAAATAAATAAGTAAAATAATA
*
3336877 ATAAAAAGAAAAAGA-AAATCAA-AAGTAA
1 ATAAAAAGAAAAAGATAAATAAATAAGTAA
3336905 TATACGTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
35 6 0.11
36 8 0.15
37 26 0.47
38 13 0.24
39 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (37 bp):
ATAAAAAGAAAAAGATAAATAAATAAGTAAAATAATA
Found at i:3336859 original size:20 final size:20
Alignment explanation
Indices: 3336834--3336871 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3336824 AATGAGTAAA
3336834 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
3336854 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
3336872 TAATAATAAA
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:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:3337406 original size:37 final size:36
Alignment explanation
Indices: 3337365--3337468 Score: 118
Period size: 36 Copynumber: 2.8 Consensus size: 36
3337355 GTGCTTGTGG
* *
3337365 ATCCTATCTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTGAATCATAGTAGAACTCT
* ** * *
3337402 ATCCTATTTTAGGAGTTTGAATCTTAACAAAATTCT
1 ATCCTATTTTAGGAGTTTGAATCATAGTAGAACTCT
*
3337438 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCATAGTAG
3337469 GACGAAAAGG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 28 0.51
37 27 0.49
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:3339914 original size:64 final size:64
Alignment explanation
Indices: 3339824--3339963 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 64
3339814 ATCCCTTGAC
* *
3339824 GGGTACATCGATGCACAATCTATGCATCGGTACA-TAAATCCCATTCGATGTTTGTATTTTAAAG
1 GGGTGCATCGATGCACAATCTATGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAAG
* * ** *
3339888 GGGTGCATCGATGCACTA-CTTGTGCATCGATACACTAATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACAATC-TATGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
*
3339952 GAGTGCATCGAT
1 GGGTGCATCGAT
3339964 ACACCTTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.02
64 64 0.97
65 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
GGGTGCATCGATGCACAATCTATGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
Found at i:3343440 original size:15 final size:15
Alignment explanation
Indices: 3343422--3343456 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3343412 CGAGGGTTCT
3343422 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3343437 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3343452 GTAGT
1 GTAGT
3343457 GGTAGTGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:3350221 original size:15 final size:15
Alignment explanation
Indices: 3350203--3350237 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3350193 CGAGGGTTCT
3350203 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3350218 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3350233 GTAGT
1 GTAGT
3350238 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:3354990 original size:18 final size:18
Alignment explanation
Indices: 3354967--3355039 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
3354957 ACTGAATATT
3354967 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3354985 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
3355004 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
3355023 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3355040 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3355014 original size:38 final size:38
Alignment explanation
Indices: 3354966--3355042 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
3354956 CACTGAATAT
*
3354966 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
* *
3355004 TTGTTCCGAAGAACCACTATGTCTCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
3355042 T
1 T
3355043 AATCCCTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
Found at i:3357477 original size:18 final size:18
Alignment explanation
Indices: 3357454--3357489 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3357444 ATATTTTCTA
3357454 AATAAGATCAATAGTCTT
1 AATAAGATCAATAGTCTT
3357472 AATAAGATCAATAGTCTT
1 AATAAGATCAATAGTCTT
3357490 TTGTTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
AATAAGATCAATAGTCTT
Found at i:3367973 original size:37 final size:37
Alignment explanation
Indices: 3367940--3368065 Score: 162
Period size: 37 Copynumber: 3.4 Consensus size: 37
3367930 CTTTGAGATT
* *
3367940 GTTTCTCTCGAAACAAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTCGAAACAAAGTTTTGTCTCTCTTGAGACA
* * **
3367977 GTTTCTCTCAAAACAATGTTTCATCTCTCTTGAGACA
1 GTTTCTCTCGAAACAAAGTTTTGTCTCTCTTGAGACA
* * *
3368014 GTTTCTATTGAAACAAAGTTTTGTCTCTATTGAGACA
1 GTTTCTCTCGAAACAAAGTTTTGTCTCTCTTGAGACA
*
3368051 GTTTCTCTTGAAACA
1 GTTTCTCTCGAAACA
3368066 TAAACAATTG
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (37 bp):
GTTTCTCTCGAAACAAAGTTTTGTCTCTCTTGAGACA
Found at i:3368123 original size:37 final size:36
Alignment explanation
Indices: 3368082--3368168 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
3368072 ATTGAGATTC
*
3368082 TTTCTCTTGAAACAAAGTTTTGTCT-TATTTGAGACAG
1 TTTCTCTTGAAACAAAG-TTTGTCTCT-CTTGAGACAG
3368119 TTTCTCTTGAAACAAAGTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTGTCTCTCTTGAGACAG
3368155 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
3368169 TAAACAATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 30 0.62
37 18 0.38
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAAGTTTGTCTCTCTTGAGACAG
Found at i:3368194 original size:103 final size:100
Alignment explanation
Indices: 3368006--3368267 Score: 344
Period size: 103 Copynumber: 2.6 Consensus size: 100
3367996 TTCATCTCTC
*
3368006 TTGAGACAGTTTCTATTGAAACAAAGTTTTGTCTCTATTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGAGACAGTTTCTCTTGAAACAAAG-TTTGTCTCTATTGAGACAGTTTCTCTTGAAACATAAAC
* * * * *
3368071 AATTGAGATTCTTTCTCTTGAAACAAAGTTTTGTCTTA
65 AATTGAGATTCTTTCCCTTGAAA-AAAATTATCTC-GA
*
3368109 TTTGAGACAGTTTCTCTTGAAACAAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAC
1 -TTGAGACAGTTTCTCTTGAAACAAAGTTTGTCTCTATTGAGACAGTTTCTCTTGAAACATAAAC
* *
3368174 AATTGATATTGTTTCCCTTGAAAAAAATTATCTCGA
65 AATTGAGATTCTTTCCCTTGAAAAAAATTATCTCGA
* * * * * *
3368210 TTGAGACAGTTTCTCTCGAAATAAAATTTTGTCTCAATTAACACAGTTTCTCTTGAAA
1 TTGAGACAGTTTCTCTTGAAA-CAAAGTTTGTCTCTATTGAGACAGTTTCTCTTGAAA
3368268 AAAAGTTTAT
Statistics
Matches: 141, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
100 20 0.14
101 31 0.22
102 8 0.06
103 57 0.40
104 25 0.18
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (100 bp):
TTGAGACAGTTTCTCTTGAAACAAAGTTTGTCTCTATTGAGACAGTTTCTCTTGAAACATAAACA
ATTGAGATTCTTTCCCTTGAAAAAAATTATCTCGA
Found at i:3368257 original size:137 final size:134
Alignment explanation
Indices: 3368082--3368499 Score: 507
Period size: 137 Copynumber: 3.1 Consensus size: 134
3368072 ATTGAGATTC
* * *
3368082 TTTCTCTTGAAACAAAGTTTTGTCTTATTTGAGACAGTTTCTCTTGAAACAAAGTTTGTCTCTCT
1 TTTCTCTTGAAA-AAAATTTTGTCTCAATTGAGACAGTTTCTCTTGAAACAAAGTTTGTCTCTCT
*
3368147 TGAGACAGTTTCTCTTGAAACATAAACAATTGATATTGTTTCCCTTGAAAAAAATTATCTCGATT
65 TGAGACAGTTTCTCTTGAAACATAAACAATTGAGATTGTTTCCCTTGAAAAAAATT-TCTCG-TT
3368212 GAGACAG
128 GAGACAG
* * * * *
3368219 TTTCTCTCGAAATAAAATTTTGTCTCAATTAACACAGTTTCTCTTGAAAAAAAGTTTATCTCTCT
1 TTTCTCTTGAAA-AAAATTTTGTCTCAATTGAGACAGTTTCTCTTGAAACAAAGTTTGTCTCTCT
* *
3368284 TGAGACAGTTTCTCTTGAAACTTAAACAATTGAGATTGTTTCCCTTGAAACAAATTT-T-G-T--
65 TGAGACAGTTTCTCTTGAAACATAAACAATTGAGATTGTTTCCCTTGAAAAAAATTTCTCGTTGA
3368344 --C--
130 GACAG
* * **
3368345 --TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAAAAAATTTTGTCTCAATTGAGACAGTTTCTCTTGAAACAAAG-TTTGTCTCTCT
* * *
3368408 TGAGACAGTTTCCCTTGAAACATAAAGAATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGC
65 TGAGACAGTTTCTCTTGAAACATAAACAATTGAGATTGTTTCCCTTGAAA-AAA-ATT-TCTCG-
3368473 TTGAGACAG
126 TTGAGACAG
*
3368482 TTTCTCTTGAAACAAATT
1 TTTCTCTTGAAAAAAATT
3368500 ATCCCTAAAG
Statistics
Matches: 238, Mismatches: 27, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
123 35 0.15
124 65 0.27
125 2 0.01
126 2 0.01
127 1 0.00
128 2 0.01
129 1 0.00
131 1 0.00
132 1 0.00
134 1 0.00
135 2 0.01
136 1 0.00
137 109 0.46
139 15 0.06
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (134 bp):
TTTCTCTTGAAAAAAATTTTGTCTCAATTGAGACAGTTTCTCTTGAAACAAAGTTTGTCTCTCTT
GAGACAGTTTCTCTTGAAACATAAACAATTGAGATTGTTTCCCTTGAAAAAAATTTCTCGTTGAG
ACAG
Found at i:3368298 original size:36 final size:37
Alignment explanation
Indices: 3368184--3368303 Score: 131
Period size: 36 Copynumber: 3.4 Consensus size: 37
3368174 AATTGATATT
* *
3368184 GTTTCCCTTGAAA-AAAA--TTATCTCGATTGAGACA
1 GTTTCTCTTGAAATAAAAGTTTATCTCAATTGAGACA
* * * * *
3368218 GTTTCTCTCGAAATAAAATTTTGTCTCAATTAACACA
1 GTTTCTCTTGAAATAAAAGTTTATCTCAATTGAGACA
**
3368255 GTTTCTCTTGAAA-AAAAGTTTATCTCTCTTGAGACA
1 GTTTCTCTTGAAATAAAAGTTTATCTCAATTGAGACA
3368291 GTTTCTCTTGAAA
1 GTTTCTCTTGAAA
3368304 CTTAAACAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
34 11 0.16
35 4 0.06
36 30 0.43
37 25 0.36
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (37 bp):
GTTTCTCTTGAAATAAAAGTTTATCTCAATTGAGACA
Found at i:3368348 original size:21 final size:21
Alignment explanation
Indices: 3368319--3368373 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3368309 ACAATTGAGA
*
3368319 TTGTTTCCCTTGAAACAAATT
1 TTGTCTCCCTTGAAACAAATT
3368340 TTGTCTCCCTTGAAACAAATT
1 TTGTCTCCCTTGAAACAAATT
3368361 TTGTCTCCCTTGA
1 TTGTCTCCCTTGA
3368374 GACAGTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (21 bp):
TTGTCTCCCTTGAAACAAATT
Found at i:3368410 original size:37 final size:37
Alignment explanation
Indices: 3368210--3368429 Score: 165
Period size: 37 Copynumber: 5.6 Consensus size: 37
3368200 ATTATCTCGA
* * **
3368210 TTGAGACAGTTTCTCTCGAAATAAAATTTTGTCTCAA
1 TTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
* * * * *
3368247 TTAACACAGTTTCTCTTGAAA-AAAAGTTTATCTCTC
1 TTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
*
3368283 TTGAGACAGTTTCTCTTGAAACTTAAACAATTGAGATTGTTTCCC
1 TTGAGACAGTTTCTCTTGAAAC---AA-AATT----TTGTCTCCC
* *
3368328 TTGAAACAAATTTTGTCTCCCTTGAAAC-AAATTTTGTCTCCC
1 TTGAGAC--A-GTT-TCT--CTTGAAACAAAATTTTGTCTCCC
* *
3368370 TTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
*
3368407 TTGAGACAGTTTCCCTTGAAACA
1 TTGAGACAGTTTCTCTTGAAACA
3368430 TAAAGAATTG
Statistics
Matches: 146, Mismatches: 21, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
36 38 0.26
37 52 0.36
38 3 0.02
39 2 0.01
40 3 0.02
41 3 0.02
42 14 0.10
45 12 0.08
46 4 0.03
47 2 0.01
48 2 0.01
49 3 0.02
51 8 0.05
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (37 bp):
TTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
Found at i:3368452 original size:124 final size:123
Alignment explanation
Indices: 3368233--3368476 Score: 389
Period size: 124 Copynumber: 2.0 Consensus size: 123
3368223 TCTCGAAATA
*
3368233 AAATTTTGTCTCAATTAACACAGTTTCTCTTGAAAAAAAGTTTATCTCTCTTGAGACAGTTTCTC
1 AAATTTTGTCTCAATTAACACAGTTTCTCTTGAAAAAAAGTTTATCTCTCTTGAGACAGTTTCCC
*
3368298 TTGAAACTTAAACAATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAAAC
66 TTGAAACATAAACAATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAAAC
** * * * *
3368356 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCC
1 AAATTTTGTCTCAATTAACACAGTTTCTCTTGAAAAAAAG-TTTATCTCTCTTGAGACAGTTTCC
* *
3368421 CTTGAAACATAAAGAATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGA
65 CTTGAAACATAAACAATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGA
3368477 GACAGTTTCT
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
123 35 0.32
124 75 0.68
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (123 bp):
AAATTTTGTCTCAATTAACACAGTTTCTCTTGAAAAAAAGTTTATCTCTCTTGAGACAGTTTCCC
TTGAAACATAAACAATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAAAC
Found at i:3368752 original size:139 final size:138
Alignment explanation
Indices: 3368494--3368914 Score: 466
Period size: 139 Copynumber: 3.0 Consensus size: 138
3368484 TCTCTTGAAA
* * * ** * *
3368494 CAAATTATCCCTAAAGACGACTAGTTGTCTTCATCACATAGGAATAATGTCGTCCATCGACCAGA
1 CAAATTATCCCAAAAAATGACTAGACGTCCTCATCACGTAGGAATAATGTCGTCCA-CGACCAGA
* ** * * * *
3368559 TCTCCTCATCATGTAGAAATAACGTCAACCTCAAATAACCATACTTCCTCATCACGTAGGAACCG
65 TCTCCTAATCATGTAGAAGCAGCGTCATCCTCAGATAACCAAACTTCCTCATCACGTAGGAACCG
3368624 TGTTGTCTC
130 TGTTGTCTC
* * *
3368633 CAAATTATCCCAAAAAATGACTAGACTTCCTCATCACGTAGGAATAATATCGTCCACATACCAGA
1 CAAATTATCCCAAAAAATGACTAGACGTCCTCATCACGTAGGAATAATGTCGTCCAC-GACCAGA
* * * * * ** * *
3368698 TATCATAATCACGTAGAAGCAGCATCATCCTCAGATAACCAGACTTTTTTATCACGTAAGAACCG
65 TCTCCTAATCATGTAGAAGCAGCGTCATCCTCAGATAACCAAACTTCCTCATCACGTAGGAACCG
3368763 TGTTGTCTC
130 TGTTGTCTC
* * * * * *
3368772 CAAATTATCCCTAAAGATGGCTAGACGTCCTCACCACGTAGGAACAATGTCGTCCACCGACCACA
1 CAAATTATCCCAAAAAATGACTAGACGTCCTCATCACGTAGGAATAATGTCGTCCA-CGACCAGA
* * * *
3368837 TCTCCTCAA-CATGCAGGAGCAGCGTCATCCTTAGATAGCCAAACTTCCTCATCACGTAGGAACC
65 TCTCCT-AATCATGTAGAAGCAGCGTCATCCTCAGATAACCAAACTTCCTCATCACGTAGGAACC
*
3368901 GTGTTGTCAC
129 GTGTTGTCTC
3368911 CAAA
1 CAAA
3368915 ATCATCTCCA
Statistics
Matches: 231, Mismatches: 48, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
138 1 0.00
139 227 0.98
140 3 0.01
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (138 bp):
CAAATTATCCCAAAAAATGACTAGACGTCCTCATCACGTAGGAATAATGTCGTCCACGACCAGAT
CTCCTAATCATGTAGAAGCAGCGTCATCCTCAGATAACCAAACTTCCTCATCACGTAGGAACCGT
GTTGTCTC
Found at i:3369164 original size:3 final size:3
Alignment explanation
Indices: 3369158--3369221 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
3369148 GGGTTCTAAT
* *
3369158 TTA TTA TTA AT- TTA GTTA TTAA CTTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA
* *
3369205 TTA CTA ATA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
3369222 TATTTTCATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 1 0.02
3 42 0.84
4 5 0.10
5 2 0.04
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3369203 original size:15 final size:15
Alignment explanation
Indices: 3369183--3369234 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3369173 TTATTAACTT
3369183 ATTATTATTATTATC
1 ATTATTATTATTATC
*
3369198 ATTATTATTACTAAT-
1 ATTATTATTA-TTATC
*
3369213 ATTATTATTTATTTTC
1 ATTATTA-TTATTATC
3369229 A-TATTA
1 ATTATTA
3369235 CAGTTGGCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 24 0.77
16 7 0.23
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTATTATTATC
Found at i:3371866 original size:20 final size:20
Alignment explanation
Indices: 3371841--3371883 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3371831 TGTTGTTATT
3371841 GTGGTCCTTTAAATAACCAA
1 GTGGTCCTTTAAATAACCAA
*
3371861 GTGGTCCTTTGAATAACCAA
1 GTGGTCCTTTAAATAACCAA
3371881 GTG
1 GTG
3371884 AACCTAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (20 bp):
GTGGTCCTTTAAATAACCAA
Found at i:3373992 original size:36 final size:36
Alignment explanation
Indices: 3373950--3374025 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3373940 TATAGCTAAA
*
3373950 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3373986 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3374022 AAAA
1 AAAA
3374026 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:3378517 original size:15 final size:15
Alignment explanation
Indices: 3378499--3378528 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3378489 CCACGGTGCT
3378499 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
3378514 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
3378529 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:3378994 original size:36 final size:36
Alignment explanation
Indices: 3378952--3379027 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3378942 TATAGCTAAA
*
3378952 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3378988 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3379024 AAAA
1 AAAA
3379028 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:3380724 original size:37 final size:38
Alignment explanation
Indices: 3380674--3380749 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
3380664 TAGCAGATTC
3380674 GAGTGCAAACAAAG-GATGGTGAGTGGTTAAGGCGTGT
1 GAGTGCAAACAAAGTGATGGTGAGTGGTTAAGGCGTGT
3380711 GAGTGCAAACAAAGTGATGGTGAGTGGTTAAGGCGTGT
1 GAGTGCAAACAAAGTGATGGTGAGTGGTTAAGGCGTGT
3380749 G
1 G
3380750 CCTGTTAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 14 0.37
38 24 0.63
ACGTcount: A:0.29, C:0.08, G:0.41, T:0.22
Consensus pattern (38 bp):
GAGTGCAAACAAAGTGATGGTGAGTGGTTAAGGCGTGT
Found at i:3385185 original size:60 final size:60
Alignment explanation
Indices: 3385108--3385228 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
3385098 AAATTAAAAC
*
3385108 CAACTAATCATAGCTTCACATCTAAAAGGTATCTAAAAATCAACTATAACAAATCAGATA
1 CAACTAATCATAGCTTCACATCTAAAAGGTATCTAAAAATCAACTATAACAAATCAAATA
* * * * * * * *
3385168 CAACTAATTATGGCTTCACGTCTAAATGGTGTCTGAAAATCAATTATAATAAATCAAATA
1 CAACTAATCATAGCTTCACATCTAAAAGGTATCTAAAAATCAACTATAACAAATCAAATA
3385228 C
1 C
3385229 GTAAAGCAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (60 bp):
CAACTAATCATAGCTTCACATCTAAAAGGTATCTAAAAATCAACTATAACAAATCAAATA
Found at i:3385731 original size:57 final size:57
Alignment explanation
Indices: 3385643--3385763 Score: 235
Period size: 57 Copynumber: 2.1 Consensus size: 57
3385633 GAAGGGGGCA
3385643 TAAATTTATATAGGAGTCTTCCGAAAAAACATTATCTTATTAATTTATCAAAATTAT
1 TAAATTTATATAGGAGTCTTCCGAAAAAACATTATCTTATTAATTTATCAAAATTAT
3385700 TAAATTTATATAGGAGTCTTCCGAAAAAACATTATCTTATTAATTTATCAAAATTAT
1 TAAATTTATATAGGAGTCTTCCGAAAAAACATTATCTTATTAATTTATCAAAATTAT
3385757 T-AATTTA
1 TAAATTTA
3385764 GATCTTGGGC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 6 0.09
57 58 0.91
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (57 bp):
TAAATTTATATAGGAGTCTTCCGAAAAAACATTATCTTATTAATTTATCAAAATTAT
Found at i:3386739 original size:2 final size:2
Alignment explanation
Indices: 3386732--3386796 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
3386722 TTCGAAGTAC
3386732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3386774 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3386797 TGTATTCAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3387586 original size:88 final size:88
Alignment explanation
Indices: 3387477--3387637 Score: 243
Period size: 88 Copynumber: 1.8 Consensus size: 88
3387467 ACTGACATCT
* * * *
3387477 AATATAGAGAAATTTGGATTCGAGGAAATTTCGGATTTCAGGTAAACATTAATCCTAGATATGTT
1 AATATAGAGAAATTTGAATTCGAGGAAAATTCGAATTTCAGGTAAACATTAACCCTAGATATGTT
3387542 TTGCATCGCATCGAGTGGGCACA
66 TTGCATCGCATCGAGTGGGCACA
* * *
3387565 AATATTAGAG-AATTTTAATTCGAGGAAAATTCGAATTTCAGGTAAACATTTACCCTAGTTATGT
1 AATA-TAGAGAAATTTGAATTCGAGGAAAATTCGAATTTCAGGTAAACATTAACCCTAGATATGT
3387629 TTTGCATCG
65 TTTGCATCG
3387638 AGTGGGGACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
88 60 0.92
89 5 0.08
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (88 bp):
AATATAGAGAAATTTGAATTCGAGGAAAATTCGAATTTCAGGTAAACATTAACCCTAGATATGTT
TTGCATCGCATCGAGTGGGCACA
Found at i:3390537 original size:3 final size:3
Alignment explanation
Indices: 3390529--3390557 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3390519 ACAAAAAATG
3390529 TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3390558 AAACGAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Done.