Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003673.1 Hibiscus syriacus cultivar Beakdansim tig00007847_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: 93206
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2264 original size:39 final size:39
Alignment explanation
Indices: 2210--2290 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
2200 GTTGTGGGTT
2210 AATGTGTTTTGTATTTCTGCTTGCATGGTGTTTGAGAAA
1 AATGTGTTTTGTATTTCTGCTTGCATGGTGTTTGAGAAA
2249 AATGTGTTTTGTATTTCTGCTTGCATGGTGTTTGAGAAA
1 AATGTGTTTTGTATTTCTGCTTGCATGGTGTTTGAGAAA
2288 AAT
1 AAT
2291 CCTCAGTGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.22, C:0.07, G:0.25, T:0.46
Consensus pattern (39 bp):
AATGTGTTTTGTATTTCTGCTTGCATGGTGTTTGAGAAA
Found at i:6849 original size:30 final size:30
Alignment explanation
Indices: 6813--6885 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
6803 TCCGAAGGAC
6813 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGTAA
*
6843 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGTAA
*
6873 CTATCCATAGGTC
1 CTATCCAGAGGTC
6886 CTGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCATCGGTAA
Found at i:6902 original size:30 final size:29
Alignment explanation
Indices: 6838--6943 Score: 95
Period size: 31 Copynumber: 3.5 Consensus size: 29
6828 AAAGATCATC
* * * *
6838 GGTAACTATCCAGAGGTCATAAAGATCCTC
1 GGTAACTATCCATAGGTCCT-AAGAACCTA
6868 GGTAACTATCCATAGGTCCTGAAGAACCTA
1 GGTAACTATCCATAGGTCCT-AAGAACCTA
* * *
6898 GGTAAACTATCCATATGTTCCTTAGAACATA
1 GGT-AACTATCCATA-GGTCCTAAGAACCTA
*
6929 GGTATACTGTCCATA
1 GGTA-ACTATCCATA
6944 TGTCTCGAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
30 29 0.45
31 30 0.47
32 5 0.08
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (29 bp):
GGTAACTATCCATAGGTCCTAAGAACCTA
Found at i:11585 original size:30 final size:30
Alignment explanation
Indices: 11545--11617 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
11535 TCCGAAGGAC
*
11545 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
11575 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
11605 CTATCCATAGGTC
1 CTATCCAGAGGTC
11618 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:11634 original size:30 final size:30
Alignment explanation
Indices: 11553--11644 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 30
11543 ACCTATCTAG
* *
11553 AGGTCATAAAGATCCTCGGTAACTATCCAG
1 AGGTCACAAAGATCCTCGGTAACTATCCAT
*
11583 AGGTCATAAAGATCCTCGGTAACTATCCAT
1 AGGTCACAAAGATCCTCGGTAACTATCCAT
* * * *
11613 AGGTCCCGAAGAACCTAGGTAAACTATCCAT
1 AGGTCACAAAGATCCTCGGT-AACTATCCAT
11644 A
1 A
11645 TGTTCCTTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
30 44 0.80
31 11 0.20
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (30 bp):
AGGTCACAAAGATCCTCGGTAACTATCCAT
Found at i:11657 original size:31 final size:31
Alignment explanation
Indices: 11603--11695 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
11593 GATCCTCGGT
* *
11603 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
11634 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
11665 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
11696 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:33136 original size:23 final size:23
Alignment explanation
Indices: 33110--33154 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
33100 CACCACAGCT
*
33110 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
33133 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
33155 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:33399 original size:151 final size:149
Alignment explanation
Indices: 33122--33438 Score: 519
Period size: 151 Copynumber: 2.1 Consensus size: 149
33112 TATAATTGCA
*
33122 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAA
* * **
33186 TTCCTTAAGAATTATATACATATGCTAGGGATCATATATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACACATGCTAGGGATCATATATGTGTCTCACAAGACTTCACACATGTT
*
33251 CCACAGAATATATATATATATC
130 CCAAAG-A-ATATATATATATC
33273 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAAT
* * *
33338 TCCTTAAGAATCATATACACATGTTAGGGATCATATATGTGTCTCACCAGACTTCATACATGTTC
66 TCCTTAAGAATCATATACACATGCTAGGGATCATATATGTGTCTCACAAGACTTCACACATGTTC
33403 CAAAGAATATATATATATC
131 CAAAGAATATATATATATC
33422 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
33439 CCCTCGACTC
Statistics
Matches: 156, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
149 30 0.19
150 2 0.01
151 124 0.79
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAAT
TCCTTAAGAATCATATACACATGCTAGGGATCATATATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:34349 original size:18 final size:18
Alignment explanation
Indices: 34328--34362 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34318 TCCCATCTAG
34328 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
34346 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
34363 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:34929 original size:64 final size:63
Alignment explanation
Indices: 34831--34991 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
34821 TAATGAAGGT
* * *
34831 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
34894 GG
62 GC
*
34896 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
34960 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
34992 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:38397 original size:149 final size:149
Alignment explanation
Indices: 38156--38461 Score: 558
Period size: 149 Copynumber: 2.1 Consensus size: 149
38146 ACCGAAGTGT
38156 CGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
1 CGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
** *
38221 ATCATATACATATGCTAGGGATCATATATGTGTCTTTCAAGACTTCACACATGCTCCACAGAATA
66 ATCATATACATATGCTAGGGATCATATATGTGTCTCACAAGACTTCACACATGCTCCAAAGAATA
38286 TATATATATCCCGAAGGAC
131 TATATATATCCCGAAGGAC
38305 CGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
1 CGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
* * *
38370 ATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCATACATGTTCCAAAGAATA
66 ATCATATACATATGCTAGGGATCATATATGTGTCTCACAAGACTTCACACATGCTCCAAAGAATA
38435 TATATATATCCCGAAGGAC
131 TATATATATCCCGAAGGAC
38454 CGCGTAGA
1 CGCGTAGA
38462 CCCTCGACTC
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
ATCATATACATATGCTAGGGATCATATATGTGTCTCACAAGACTTCACACATGCTCCAAAGAATA
TATATATATCCCGAAGGAC
Found at i:39216 original size:2 final size:2
Alignment explanation
Indices: 39209--39234 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39199 ATTATTTCTT
39209 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
39235 ATCTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39381 original size:18 final size:18
Alignment explanation
Indices: 39360--39394 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39350 TCCCATCTAG
39360 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
39378 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
39395 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:39959 original size:64 final size:63
Alignment explanation
Indices: 39861--40021 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
39851 TAATAAAGGT
* * *
39861 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
39924 GG
62 GC
*
39926 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
39990 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
40022 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:44797 original size:21 final size:21
Alignment explanation
Indices: 44754--44846 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
44744 TTTTCCCAAT
** *
44754 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
*
44774 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
** *
44795 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
*
44815 TCGCAAGGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
44836 TCGCAATGCGA
1 TCGCAATGCGA
44847 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:44860 original size:20 final size:20
Alignment explanation
Indices: 44835--44969 Score: 110
Period size: 20 Copynumber: 6.7 Consensus size: 20
44825 AATTGGGAAA
44835 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
44855 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* * *
44876 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
*
44896 TTCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
44916 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
44936 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
44956 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
44970 TTTCAAAGCG
Statistics
Matches: 92, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
19 2 0.02
20 65 0.71
21 25 0.27
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:44861 original size:41 final size:41
Alignment explanation
Indices: 44754--44846 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
44744 TTTTCCCAAT
44754 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
44795 TCGCAATGCGAATAAGTAAATCGCAAGGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
44836 TCGCAATGCGA
1 TCGCAATGCGA
44847 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:45159 original size:22 final size:22
Alignment explanation
Indices: 45131--45174 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
45121 CACTCTCTCA
45131 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
45153 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
45175 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:45405 original size:19 final size:19
Alignment explanation
Indices: 45381--45431 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
45371 ATCAACCGAG
45381 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
45400 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
45419 AATCGCAACGCGA
1 AATCGCAACGCGA
45432 TTTTAGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGCA
Found at i:45496 original size:20 final size:20
Alignment explanation
Indices: 45473--45515 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
45463 GATAGTCGAA
45473 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
45493 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
45513 TTC
1 TTC
45516 AGAAACTATT
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:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:46806 original size:18 final size:18
Alignment explanation
Indices: 46785--46829 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
46775 TCCACTTCGG
*
46785 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
46803 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
46821 GAGCCATCA
1 GAGCCATCA
46830 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:47362 original size:19 final size:20
Alignment explanation
Indices: 47311--47364 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
47301 TAGTTTACTT
* *
47311 TCGCAACACGAAAAT-GCTA
1 TCGCAACGCGGAAATGGCTA
47330 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
47350 TCGCAATGC-GAAATG
1 TCGCAACGCGGAAATG
47365 AAAATCGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:47371 original size:19 final size:19
Alignment explanation
Indices: 47349--47444 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
47339 GGAAATGGCT
47349 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
47368 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
47382 ATCGCAATGCGGAATG-AA
1 ATCGCAATGCGAAATGAAA
* *
47400 ATCGTAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
47414 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
47433 ATCGCAATGCGA
1 ATCGCAATGCGA
47445 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 6 0.10
17 2 0.03
18 10 0.17
19 21 0.36
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:47384 original size:14 final size:14
Alignment explanation
Indices: 47365--47422 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
47355 ATGCGAAATG
47365 AAAATCGCAACGAC
1 AAAATCGCAACGAC
47379 AAAATCGCAATGCGGA-
1 AAAATCGCAA--C-GAC
*
47395 ATGAAATCGTAACGAC
1 A--AAATCGCAACGAC
47411 AAAATCGCAACG
1 AAAATCGCAACG
47423 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 20 0.56
15 2 0.06
16 4 0.11
17 2 0.06
18 8 0.22
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:47386 original size:33 final size:33
Alignment explanation
Indices: 47349--47439 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
47339 GGAAATGGCT
47349 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
47382 ATCGCAATGCGGAATG-AAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
47414 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
47440 TGCGATTTGT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 29 0.56
33 23 0.44
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:47475 original size:14 final size:14
Alignment explanation
Indices: 47456--47513 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
47446 TTGTGTTTCG
47456 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
47470 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
47486 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
47502 CGTTGCGATTTT
1 CGTTGCGATTTT
47514 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:47490 original size:32 final size:33
Alignment explanation
Indices: 47451--47529 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
47441 GCGATTTGTG
47451 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
47483 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
47516 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
47530 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:47528 original size:19 final size:19
Alignment explanation
Indices: 47470--47587 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
47460 GCGATTTTGT
47470 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
47488 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
47502 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
47521 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
47541 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
47560 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
47580 TGTTGCGA
1 CGTTGCGA
47588 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:49594 original size:19 final size:19
Alignment explanation
Indices: 49572--49620 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
49562 ATCGCAACGA
49572 GAAAATCGCAATACGAAAT
1 GAAAATCGCAATACGAAAT
* * *
49591 GAAAATCTCAATGCGAATT
1 GAAAATCGCAATACGAAAT
49610 GAAAATCGCAA
1 GAAAATCGCAA
49621 CGAGAAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (19 bp):
GAAAATCGCAATACGAAAT
Found at i:49683 original size:20 final size:20
Alignment explanation
Indices: 49658--49715 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
49648 TCGCATTGCG
*
49658 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
49678 ATTTTCGCGTTGTGATAGCC
1 ATTTTCGCGTTGCGATAGCC
49698 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
49716 TTAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:50817 original size:24 final size:24
Alignment explanation
Indices: 50771--50824 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
50761 GTATTCGAAA
* **
50771 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATAAACGGAC
*
50795 TTTGATATTGGTCAATAAACGGAT
1 TTTGATATTGGTCAATAAACGGAC
50819 TTTGAT
1 TTTGAT
50825 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATAAACGGAC
Found at i:51016 original size:12 final size:12
Alignment explanation
Indices: 50999--51023 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50989 ATATAATCCT
50999 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51011 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51023 G
1 G
51024 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:53372 original size:19 final size:19
Alignment explanation
Indices: 53319--53448 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
53309 GGAAATTACT
53319 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
53338 AT-GCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
53351 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
53370 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
53384 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
53403 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
53417 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
53436 ATCGCAACGCGAA
1 ATCGCAATGCGAA
53449 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 13, Indels: 32
0.65 0.10 0.25
Matches are distributed among these distances:
13 5 0.06
14 22 0.27
15 2 0.02
16 8 0.10
17 4 0.05
18 7 0.09
19 34 0.41
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:53389 original size:33 final size:32
Alignment explanation
Indices: 53320--53450 Score: 176
Period size: 33 Copynumber: 4.0 Consensus size: 32
53310 GAAATTACTA
* *
53320 TCGCAATGCGAAATGAAAAT-GCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-AT
*
53352 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAA-T
*
53385 TCGCAATGCGAAATGAAAATCGCAACGAGGGAA-
1 TCGCAATGCGAAATGAAAATCGCAAC--GCGAAT
53418 TCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAAT
53450 T
1 T
53451 TAATTTCGCG
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
31 4 0.05
32 22 0.25
33 59 0.67
35 3 0.03
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (32 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAAT
Found at i:53426 original size:66 final size:65
Alignment explanation
Indices: 53320--53451 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 65
53310 GAAATTACTA
*
53320 TCGCAATGCGAAATGAAAATGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
53385 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAAT-GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
53450 T
65 T
53451 T
1 T
53452 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 20 0.31
66 44 0.69
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (65 bp):
TCGCAATGCGAAATGAAAATGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:53466 original size:19 final size:20
Alignment explanation
Indices: 53444--53486 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
53434 AAATCGCAAC
53444 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
53463 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
53483 GCGA
1 GCGA
53487 TTCCCTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:53646 original size:14 final size:14
Alignment explanation
Indices: 53627--53663 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
53617 CATCAATTAA
53627 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
53641 ACAAATCACCTTTT
1 ACAAATCAACTTTT
53655 ACAAATCAA
1 ACAAATCAA
53664 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:57173 original size:20 final size:19
Alignment explanation
Indices: 57142--57283 Score: 70
Period size: 20 Copynumber: 7.8 Consensus size: 19
57132 TCTTTTGGTT
57142 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
57161 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
57182 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
57201 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
57215 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
57231 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
57248 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
*
57268 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
57284 TGCGATTTTT
Statistics
Matches: 93, Mismatches: 17, Indels: 25
0.69 0.13 0.19
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 17 0.18
20 47 0.51
21 2 0.02
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:57224 original size:33 final size:33
Alignment explanation
Indices: 57167--57265 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
57157 ACGAGATAAT
*
57167 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
57201 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
57234 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
57266 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:57320 original size:19 final size:19
Alignment explanation
Indices: 57284--57364 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
57274 AAAATCGCAA
*
57284 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
57303 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
57322 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
57336 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
57356 TGCGATTTT
1 TGCGATTTT
57365 CATTCTCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 22 0.45
20 11 0.22
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:57904 original size:20 final size:20
Alignment explanation
Indices: 57879--57931 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
57869 GCGCTATGTA
57879 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
57899 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
57919 TATCTCGTTGCGA
1 AATCGCGTTGCGA
57932 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:59912 original size:21 final size:21
Alignment explanation
Indices: 59874--59932 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
59864 AAAGTTTGGG
* *
59874 TTTTTTTAAGATTTAAAAAATA
1 TTTTTTTAA-AATAAAAAAATA
*
59896 TTTTTTTAAAATAAAAAATTA
1 TTTTTTTAAAATAAAAAAATA
*
59917 TATATTTT-AAATAAAA
1 T-TTTTTTAAAATAAAA
59933 TTTCTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTTTTTAAAATAAAAAAATA
Found at i:61175 original size:30 final size:30
Alignment explanation
Indices: 61121--61196 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
61111 TAATGTCCCT
* *
61121 TGAACTTTAGATACCATATTATTTTGAGT-A-
1 TGAACTTTAGATA-AATATCATTTTGA-TCAC
61151 TGAACTTTAGATGAAATATCATTTTGATCAC
1 TGAACTTTAGAT-AAATATCATTTTGATCAC
*
61182 TAAACTTTAGATAAA
1 TGAACTTTAGATAAA
61197 ATATTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.03
30 27 0.68
31 12 0.30
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (30 bp):
TGAACTTTAGATAAATATCATTTTGATCAC
Found at i:64888 original size:171 final size:167
Alignment explanation
Indices: 64549--64890 Score: 582
Period size: 171 Copynumber: 2.0 Consensus size: 167
64539 ATACTGTGAA
*
64549 CAATATTCATATAGTTTCATGTGGTGTTAATGCCTTATCGATGCTAATAACTTTAAACACATAAA
1 CAATATTCA-ATAGTTTCATGTGGTGTTAATGCATTATCGATGCTAATAACTTTAAACACATAAA
64614 TACCAAATACTGTTCAAGCAGTACCAGTACTCCTTAGTTTTGCACAATTCAGTAAGCATTTGGTA
65 TACCAAATACTGTTCAAGCAGTACCAGTACTCCTTAGTTTTGCACAATTCAGTAAGCATTTGGTA
64679 TTGATACTCTATCATTATCGATACTAGTATCGATACTT
130 TTGATACTCTATCATTATCGATACTAGTATCGATACTT
64717 CAATATTC-ATAG-TTCATGTGGTGTTAATGCATTATCGATGCTAATAACTTTAAAACACACATA
1 CAATATTCAATAGTTTCATGTGGTGTTAATGCATTATCGATGCTAATAACTTT--AA-ACACATA
64780 AATACC-AATACTGTTCATAGCAGTACCAGTACTCCTTATGTTTTGCACAATTCAGTAAGCTATT
63 AATACCAAATACTGTTCA-AGCAGTACCAGTACTCCTTA-GTTTTGCACAATTCAGTAAGC-A-T
64844 TTGGTATTGATACTCTATCATTATCGATACTAGTATCGATACTT
124 TTGGTATTGATACTCTATCATTATCGATACTAGTATCGATACTT
64888 CAA
1 CAA
64891 GTGGTAGTAT
Statistics
Matches: 166, Mismatches: 1, Indels: 11
0.93 0.01 0.06
Matches are distributed among these distances:
165 38 0.23
166 4 0.02
167 13 0.08
168 41 0.25
169 21 0.13
170 1 0.01
171 48 0.29
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (167 bp):
CAATATTCAATAGTTTCATGTGGTGTTAATGCATTATCGATGCTAATAACTTTAAACACATAAAT
ACCAAATACTGTTCAAGCAGTACCAGTACTCCTTAGTTTTGCACAATTCAGTAAGCATTTGGTAT
TGATACTCTATCATTATCGATACTAGTATCGATACTT
Found at i:74713 original size:44 final size:46
Alignment explanation
Indices: 74664--74755 Score: 152
Period size: 44 Copynumber: 2.0 Consensus size: 46
74654 GTGCCACATA
74664 AAATGTCTCGAAGGACCACATAG-A-TGTCCCGAAGGACCGCGTAG
1 AAATGTCTCGAAGGACCACATAGAATTGTCCCGAAGGACCGCGTAG
* *
74708 AAATGTCTCGAAGGACCACGTAGAATTGTCCCGAAGGACCGTGTAG
1 AAATGTCTCGAAGGACCACATAGAATTGTCCCGAAGGACCGCGTAG
74754 AA
1 AA
74756 CCCTTGACTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 22 0.50
45 1 0.02
46 21 0.48
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (46 bp):
AAATGTCTCGAAGGACCACATAGAATTGTCCCGAAGGACCGCGTAG
Found at i:74719 original size:23 final size:23
Alignment explanation
Indices: 74664--74747 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
74654 GTGCCACATA
* *
74664 AAATGTCTCGAAGGACCACATAG
1 AAATGTCCCGAAGGACCACGTAG
*
74687 --ATGTCCCGAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCACGTAG
*
74708 AAATGTCTCGAAGGACCACGTAG
1 AAATGTCCCGAAGGACCACGTAG
*
74731 AATTGTCCCGAAGGACC
1 AAATGTCCCGAAGGACC
74748 GTGTAGAACC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.35
23 34 0.65
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (23 bp):
AAATGTCCCGAAGGACCACGTAG
Found at i:77542 original size:20 final size:21
Alignment explanation
Indices: 77517--77557 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
77507 CTAGAATGGG
*
77517 GGGAATCGGTA-CCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
77537 GGGAATCTATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
77558 ATATTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:80462 original size:34 final size:35
Alignment explanation
Indices: 80423--80499 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 35
80413 CAAACCATGC
*
80423 AGGGGGGATCTGTACCCGGGGAATCGATA-CCCCT
1 AGGGGGGATCTGTACCAGGGGAATCGATACCCCCT
* *
80457 AGGGGGAATCTGTTCCAGGGGAATCGATACCCCCT
1 AGGGGGGATCTGTACCAGGGGAATCGATACCCCCT
*
80492 GGGGGGGA
1 AGGGGGGA
80500 ATCTATTCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 26 0.70
35 11 0.30
ACGTcount: A:0.21, C:0.23, G:0.39, T:0.17
Consensus pattern (35 bp):
AGGGGGGATCTGTACCAGGGGAATCGATACCCCCT
Found at i:83163 original size:14 final size:15
Alignment explanation
Indices: 83144--83172 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
83134 TGCATTTAGA
83144 TATTTT-GGATATTT
1 TATTTTAGGATATTT
83158 TATTTTAGGATATTT
1 TATTTTAGGATATTT
83173 CACATGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (15 bp):
TATTTTAGGATATTT
Found at i:86508 original size:39 final size:38
Alignment explanation
Indices: 86454--86528 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 38
86444 TATGGAAATG
*
86454 ACATTATTAACCTTACTTTATCATCCTTCAAAATATCCA
1 ACATTATTAACCTTACCTTATCATCCTTC-AAATATCCA
86493 ACATTATTAACCTTACCTTATCATCCTTCAAATATC
1 ACATTATTAACCTTACCTTATCATCCTTCAAATATC
86529 TTAAATATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 7 0.20
39 28 0.80
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.39
Consensus pattern (38 bp):
ACATTATTAACCTTACCTTATCATCCTTCAAATATCCA
Found at i:87486 original size:19 final size:20
Alignment explanation
Indices: 87435--87488 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
87425 AAACTTTAAG
87435 GAAAGT-TTCGAAACTCTTGA
1 GAAAGTATT-GAAACTCTTGA
* *
87455 GATAGTTTTGAAACTCTTGA
1 GAAAGTATTGAAACTCTTGA
87475 -AAAGTATTGAAACT
1 GAAAGTATTGAAACT
87489 TTTTGGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.40
20 16 0.53
21 2 0.07
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
GAAAGTATTGAAACTCTTGA
Found at i:87534 original size:20 final size:20
Alignment explanation
Indices: 87495--87561 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
87485 AACTTTTTGG
* *
87495 GAAACTGTTTTGGAAAGTTTC
1 GAAACTCTTTTAG-AAGTTTC
*
87516 AAAACTCTTTTAGAAGTTTC
1 GAAACTCTTTTAGAAGTTTC
87536 GAAACTCTTTTAGAAGTTTC
1 GAAACTCTTTTAGAAGTTTC
87556 GAAACT
1 GAAACT
87562 TTTGGTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 32 0.76
21 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (20 bp):
GAAACTCTTTTAGAAGTTTC
Found at i:89387 original size:18 final size:16
Alignment explanation
Indices: 89364--89399 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 16
89354 TTTCTTTCTT
89364 TTCTTGTTTCTTCACTTC
1 TTCTTG-TTCTTCA-TTC
89382 TTCTTGTTCTTCATTC
1 TTCTTGTTCTTCATTC
89398 TT
1 TT
89400 TTCCATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.06, C:0.25, G:0.06, T:0.64
Consensus pattern (16 bp):
TTCTTGTTCTTCATTC
Found at i:91152 original size:17 final size:17
Alignment explanation
Indices: 91127--91166 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
91117 AGCTTATTTG
*
91127 GTACTGATACTCTGTCA
1 GTACCGATACTCTGTCA
91144 GTACCGATACTCTGTCA
1 GTACCGATACTCTGTCA
91161 GTACCG
1 GTACCG
91167 CTACCAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (17 bp):
GTACCGATACTCTGTCA
Found at i:91348 original size:21 final size:19
Alignment explanation
Indices: 91318--91358 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
91308 TAATGCAGTT
91318 AGTATCGATACTTCAAGCACG
1 AGTATCGATACTT-AAG-ACG
*
91339 AGTATTGATACTTAAGACG
1 AGTATCGATACTTAAGACG
91358 A
1 A
91359 CTAGTAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (19 bp):
AGTATCGATACTTAAGACG
Found at i:92453 original size:14 final size:14
Alignment explanation
Indices: 92434--92476 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
92424 AATTCGTTCG
92434 TTTATGTTCATTTA
1 TTTATGTTCATTTA
92448 TTTATGTTCATTTA
1 TTTATGTTCATTTA
*
92462 TGTT-CGTTCATTTA
1 T-TTATGTTCATTTA
92476 T
1 T
92477 ATTCAGCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (14 bp):
TTTATGTTCATTTA
Found at i:92461 original size:24 final size:24
Alignment explanation
Indices: 92429--92481 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
92419 TCGATAATTC
* *
92429 GTTCGTTTATGTTCATTTATTTAT
1 GTTCATTTATGTTCATTCATTTAT
*
92453 GTTCATTTATGTTCGTTCATTTAT
1 GTTCATTTATGTTCATTCATTTAT
*
92477 ATTCA
1 GTTCA
92482 GCTCAATCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.58
Consensus pattern (24 bp):
GTTCATTTATGTTCATTCATTTAT
Found at i:92583 original size:17 final size:16
Alignment explanation
Indices: 92532--92583 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
92522 AATTTTAACC
* *
92532 TTAAATCCATTAATATT
1 TTAAACCCAATAA-ATT
*
92549 TTAAACCCAATTAATT
1 TTAAACCCAATAAATT
92565 TTAAACCCAAATAAATT
1 TTAAACCC-AATAAATT
92582 TT
1 TT
92584 TCAAATCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 11 0.37
17 19 0.63
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAACCCAATAAATT
Found at i:93091 original size:3 final size:3
Alignment explanation
Indices: 93085--93140 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
93075 GGCACGCAGT
* * *
93085 TAA TAA TAA TAA T-A TTA TTA TAA TAA TAA TAA TAA TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
93131 TAA TAA TAA T
1 TAA TAA TAA T
93141 GTTTTATCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:93115 original size:23 final size:23
Alignment explanation
Indices: 93085--93140 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
93075 GGCACGCAGT
** * *
93085 TAATAATAATAATATTATTATAA
1 TAATAATAATAATAAAAATAAAA
93108 TAATAATAATAATAAAAATAAAA
1 TAATAATAATAATAAAAATAAAA
93131 TAATAATAAT
1 TAATAATAAT
93141 GTTTTATCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATAATAATAATAAAAATAAAA
Done.