Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001399.1 Hibiscus syriacus cultivar Beakdansim tig00002732_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: 135155
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:10333 original size:1 final size:1
Alignment explanation
Indices: 10327--10431 Score: 75
Period size: 1 Copynumber: 105.0 Consensus size: 1
10317 CTTGAAGAAT
* * * * * * * * *
10327 AAAAAAAAAAAAAAAAGAAAAAAGAAAAGAAAAAAGAAAAGAAAAAGAAAAGAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
10392 AAGAAAAGAAAAAAATAGAAAAAAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10432 GAAAGGGGGT
Statistics
Matches: 74, Mismatches: 30, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (1 bp):
A
Found at i:10347 original size:12 final size:12
Alignment explanation
Indices: 10327--10435 Score: 121
Period size: 12 Copynumber: 8.8 Consensus size: 12
10317 CTTGAAGAAT
10327 AAAAA-AAAAAA
1 AAAAAGAAAAAA
10338 AAAAAGAAAAAA
1 AAAAAGAAAAAA
*
10350 GAAAAGAAAAAA
1 AAAAAGAAAAAA
*
10362 GAAAAGAAAAAGAA
1 AAAAAG-AAAA-AA
*
10376 AAGAAAGAAAAGA
1 AA-AAAGAAAAAA
10389 AAAAAGAAAAGAA
1 AAAAAGAAAA-AA
*
10402 AAAAATAGAAAAA
1 AAAAAGA-AAAAA
*
10415 AAAAAGAAAAAG
1 AAAAAGAAAAAA
10427 AAAAAGAAA
1 AAAAAGAAA
10436 GGGGGTTAAG
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
11 5 0.06
12 44 0.52
13 22 0.26
14 10 0.12
15 4 0.05
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:10372 original size:32 final size:32
Alignment explanation
Indices: 10321--10435 Score: 139
Period size: 32 Copynumber: 3.6 Consensus size: 32
10311 ATTATGCTTG
*
10321 AAGAATAAAA-AAAAAAAAAAAAGAAAAAAGAA
1 AAGAA-AAAAGAAAAGAAAAAAAGAAAAAAGAA
*
10353 AAGAAAAAAGAAAAGAAAAAGAA-AAGAAAGAA
1 AAGAAAAAAGAAAAGAAAAA-AAGAAAAAAGAA
10385 AAGAAAAAAGAAAAGAAAAAAATAGAAAAAA-AA
1 AAGAAAAAAGAAAAG-AAAAAA-AGAAAAAAGAA
10418 AAG-AAAAAGAAAAAGAAA
1 AAGAAAAAAG-AAAAGAAA
10436 GGGGGTTAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
31 4 0.05
32 47 0.64
33 18 0.24
34 5 0.07
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (32 bp):
AAGAAAAAAGAAAAGAAAAAAAGAAAAAAGAA
Found at i:11515 original size:84 final size:84
Alignment explanation
Indices: 11372--11936 Score: 1058
Period size: 84 Copynumber: 6.7 Consensus size: 84
11362 AACCTTTTAT
* **
11372 ATGTGCCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTTACAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
11437 CATTGAAGTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
*
11456 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
11521 CATTGAAGTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
*
11540 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
11605 CATTGAAGTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
*
11624 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
11689 CATTGAAGTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
11708 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
*
11773 CATTGAATTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
11792 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
*
11857 CATTGAATTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
11876 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
11937 TTATAGAACC
Statistics
Matches: 475, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 475 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (84 bp):
ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
CATTGAAGTTAGAAGATGA
Found at i:12716 original size:113 final size:113
Alignment explanation
Indices: 12548--13185 Score: 1015
Period size: 113 Copynumber: 5.6 Consensus size: 113
12538 TACAAGGTAG
*
12548 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
12613 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
*
12661 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
12726 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
*
12774 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
12839 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
12887 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *** * * * * * *
12952 AACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
* * *
13000 GGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAGGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *** * * * * * *
13065 AACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
* *
13113 AGTTCATGAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
13178 CAACCTTT
65 CAACCTTT
13186 GTTTGATATT
Statistics
Matches: 503, Mismatches: 21, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
113 443 0.88
114 60 0.12
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
Found at i:13488 original size:3 final size:3
Alignment explanation
Indices: 13480--13586 Score: 160
Period size: 3 Copynumber: 35.7 Consensus size: 3
13470 TTTTTATCCA
* * *
13480 TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
13528 TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13576 TAT TAT TAT TA
1 TAT TAT TAT TA
13587 AATATATTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:14087 original size:18 final size:18
Alignment explanation
Indices: 14057--14091 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14047 AGAGACAGAA
14057 ACAGAAAACGAAAAAAAT
1 ACAGAAAACGAAAAAAAT
14075 ACAGAGAAA-GAAAAAAA
1 ACAGA-AAACGAAAAAAA
14092 AACAAACTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (18 bp):
ACAGAAAACGAAAAAAAT
Found at i:15034 original size:20 final size:21
Alignment explanation
Indices: 14997--15037 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
14987 GATATTTTTG
**
14997 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
15018 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
15038 ACATATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:17992 original size:19 final size:19
Alignment explanation
Indices: 17965--18020 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
17955 ACCTGATCTG
*
17965 ACCCTTTGACTTTGACCCA
1 ACCCGTTGACTTTGACCCA
**
17984 ACCCGTTGACTTTGACCTG
1 ACCCGTTGACTTTGACCCA
18003 ACCCGTTGACTATTGACC
1 ACCCGTTGACT-TTGACC
18021 GGTCTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 27 0.82
20 6 0.18
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.30
Consensus pattern (19 bp):
ACCCGTTGACTTTGACCCA
Found at i:18043 original size:22 final size:23
Alignment explanation
Indices: 18007--18064 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
17997 GACCTGACCC
18007 GTTGACTATTGACCGGTCTAAAT
1 GTTGACTATTGACCGGTCTAAAT
* *
18030 GTTGACT-TTGACCGGTCTGACT
1 GTTGACTATTGACCGGTCTAAAT
*
18052 GTTGACAATTGAC
1 GTTGACTATTGAC
18065 TTTGACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 19 0.61
23 12 0.39
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (23 bp):
GTTGACTATTGACCGGTCTAAAT
Found at i:23655 original size:35 final size:36
Alignment explanation
Indices: 23616--23697 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 36
23606 AATGGATTAT
* * *
23616 GAATTTGGA-GTTGGGCATGTAATTGAAGTATTTTG
1 GAATTTGGAGGTTGAGAATGTAACTGAAGTATTTTG
*
23651 GAATTT-GAGGTTTAGAATGTAACTGAAGTATTTTG
1 GAATTTGGAGGTTGAGAATGTAACTGAAGTATTTTG
23686 GAATTTGG-GGTT
1 GAATTTGGAGGTT
23698 TATAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 2 0.05
35 38 0.93
36 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.30, T:0.40
Consensus pattern (36 bp):
GAATTTGGAGGTTGAGAATGTAACTGAAGTATTTTG
Found at i:23698 original size:35 final size:35
Alignment explanation
Indices: 23632--23699 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
23622 GGAGTTGGGC
*
23632 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAACTGAAGTATTTTGGAATTTGAGGTTTAGA
*
23667 ATGTAACTGAAGTATTTTGGAATTTGGGGTTTA
1 ATGTAACTGAAGTATTTTGGAATTTGAGGTTTA
23700 TAATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.43
Consensus pattern (35 bp):
ATGTAACTGAAGTATTTTGGAATTTGAGGTTTAGA
Found at i:24305 original size:21 final size:21
Alignment explanation
Indices: 24281--24320 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24271 TTTATCTATC
* *
24281 ATTAAATTAGTGAAATAATAT
1 ATTAAATTAATAAAATAATAT
24302 ATTAAATTAATAAAATAAT
1 ATTAAATTAATAAAATAAT
24321 CTCATTACTT
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:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTAAATTAATAAAATAATAT
Found at i:26628 original size:42 final size:41
Alignment explanation
Indices: 26564--26642 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
26554 CAATCCGTAA
* *
26564 TGATATTCAAGCTTTCATAGATCTCATTCCACCATTGGTGG
1 TGATATTCAAGCTTTCACAGATCCCATTCCACCATTGGTGG
* *
26605 TGATATTCAAAGTTTTCACAGATCCCATTTCACCATTG
1 TGATATTC-AAGCTTTCACAGATCCCATTCCACCATTG
26643 AGGATCTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 8 0.24
42 25 0.76
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (41 bp):
TGATATTCAAGCTTTCACAGATCCCATTCCACCATTGGTGG
Found at i:27819 original size:20 final size:20
Alignment explanation
Indices: 27796--27833 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27786 ATCAATACAA
*
27796 GATGCTCGGTATCGAGATTG
1 GATGCTCGATATCGAGATTG
*
27816 GATGCTCGATCTCGAGAT
1 GATGCTCGATATCGAGAT
27834 CACTTGTCTC
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:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (20 bp):
GATGCTCGATATCGAGATTG
Found at i:27885 original size:20 final size:20
Alignment explanation
Indices: 27860--27912 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
27850 GATGGACTAA
* *
27860 TCTCTATATTGAAGGATTGG
1 TCTCTATATCGAAGGACTGG
*
27880 TCTCTATACCGAAGGACTGG
1 TCTCTATATCGAAGGACTGG
27900 TCTCTATATCGAA
1 TCTCTATATCGAA
27913 TATTGAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
TCTCTATATCGAAGGACTGG
Found at i:30218 original size:18 final size:19
Alignment explanation
Indices: 30195--30233 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
30185 AAAGAAACAC
*
30195 AAAAAATTATTGTTT-TAA
1 AAAAAATCATTGTTTCTAA
*
30213 AAAAAATCATTTTTTCTAA
1 AAAAAATCATTGTTTCTAA
30232 AA
1 AA
30234 TCTTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAAATCATTGTTTCTAA
Found at i:39315 original size:35 final size:35
Alignment explanation
Indices: 39269--39343 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
39259 CGTCACGAAC
*
39269 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
*
39304 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
39339 AGTAA
1 AGTAA
39344 TCTTCCTCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.29, G:0.29, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
Found at i:39430 original size:24 final size:24
Alignment explanation
Indices: 39403--39513 Score: 82
Period size: 24 Copynumber: 4.7 Consensus size: 24
39393 TATAGCAAAA
*
39403 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
39427 ATCATATCAGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
39451 ATCAGATCAGAATCCATGTCAA-T
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
39474 ATCAGATCAGAATCCAGGTCAA-T
1 ATCAAAACAGAATTCAAGTCAAGT
*
39497 ATCATAACAGAATTCAA
1 ATCAAAACAGAATTCAA
39514 ATTTGAAATC
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
23 36 0.49
24 37 0.51
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (24 bp):
ATCAAAACAGAATTCAAGTCAAGT
Found at i:39480 original size:23 final size:23
Alignment explanation
Indices: 39420--39509 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
39410 CATAATTCAA
* *
39420 GTCAAGTATCATATCAGAATTCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
39444 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
39468 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
* *
39491 GTCAATATCATAACAGAAT
1 GTCAATATCAGATCAGAAT
39510 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 34 0.60
24 23 0.40
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:40665 original size:18 final size:18
Alignment explanation
Indices: 40642--40677 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40632 CTTCCATCCG
*
40642 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
40660 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
40678 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:41883 original size:7 final size:7
Alignment explanation
Indices: 41869--41899 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
41859 TGGTCAACGT
41869 CGGTCAA
1 CGGTCAA
*
41876 CAGTCAA
1 CGGTCAA
41883 CGGTCAA
1 CGGTCAA
41890 CGGTCAA
1 CGGTCAA
41897 CGG
1 CGG
41900 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:41909 original size:13 final size:13
Alignment explanation
Indices: 41891--41920 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41881 AACGGTCAAC
41891 GGTCAACGGGTCG
1 GGTCAACGGGTCG
41904 GGTCAACGGGTCG
1 GGTCAACGGGTCG
41917 GGTC
1 GGTC
41921 GGGTTGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:42785 original size:32 final size:32
Alignment explanation
Indices: 42727--42797 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
42717 AATCGATATG
* *
42727 ATATTGACCCGACCCAAAATATAACCGATTCA
1 ATATTGACCCGACCCAAAATACAACCGATCCA
*
42759 ATATTGACCCGACCCAAAAGT-CAACCGGTCCA
1 ATATTGACCCGACCCAAAA-TACAACCGATCCA
42791 ATATTGA
1 ATATTGA
42798 TCAAAATAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 34 0.97
33 1 0.03
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (32 bp):
ATATTGACCCGACCCAAAATACAACCGATCCA
Found at i:52008 original size:13 final size:13
Alignment explanation
Indices: 51990--52021 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
51980 GATAAAATCC
51990 TTGAAATGATTCA
1 TTGAAATGATTCA
52003 TTGAAATGATTCA
1 TTGAAATGATTCA
52016 TTGAAA
1 TTGAAA
52022 ATGGCAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGAAATGATTCA
Found at i:54798 original size:31 final size:31
Alignment explanation
Indices: 54760--54863 Score: 145
Period size: 31 Copynumber: 3.4 Consensus size: 31
54750 GTTGATTAAC
* *
54760 GGGCGCTATTACGGTCGTAGTAAATGCTATT
1 GGGCGCTATTGCGGTCGTAGTAAACGCTATT
*
54791 GGGCGCTATTGTGGTCGTAGTAAACGCTATT
1 GGGCGCTATTGCGGTCGTAGTAAACGCTATT
* *
54822 GGGCGCTATTGCAGTCGTAGCAAACGCTATT
1 GGGCGCTATTGCGGTCGTAGTAAACGCTATT
**
54853 GGATGCTATTG
1 GGGCGCTATTG
54864 TTGGAGTAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (31 bp):
GGGCGCTATTGCGGTCGTAGTAAACGCTATT
Found at i:63320 original size:26 final size:26
Alignment explanation
Indices: 63271--63320 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
63261 TGAGGGAACG
* *
63271 AATTTATAAAAGTTTAAAGGAATATA
1 AATTTATAAAAATTTAAAGAAATATA
63297 AATTTATAAAAAATTTAAA-AAATA
1 AATTTAT-AAAAATTTAAAGAAATA
63321 AAAAAGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (26 bp):
AATTTATAAAAATTTAAAGAAATATA
Found at i:63344 original size:19 final size:19
Alignment explanation
Indices: 63313--63364 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
63303 TAAAAAATTT
*
63313 AAAAAA-TAAAAAAGTATATA
1 AAAAAATTAAAATA-TAT-TA
*
63333 AAATAATTAAAATATATTA
1 AAAAAATTAAAATATATTA
*
63352 AAAAAATTGAAAT
1 AAAAAATTAAAAT
63365 TGTTAGAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.48
20 8 0.30
21 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAAATTAAAATATATTA
Found at i:67856 original size:16 final size:16
Alignment explanation
Indices: 67811--67856 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
67801 CGAAACACCA
67811 GAACCGAAAGTAACTC
1 GAACCGAAAGTAACTC
* **
67827 GAACCTAATTTAACTC
1 GAACCGAAAGTAACTC
*
67843 GATCCGAAAGTAAC
1 GAACCGAAAGTAAC
67857 CAAAACCGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (16 bp):
GAACCGAAAGTAACTC
Found at i:68105 original size:32 final size:32
Alignment explanation
Indices: 68041--68170 Score: 108
Period size: 32 Copynumber: 4.1 Consensus size: 32
68031 GATCCAAAGG
* *
68041 TTGACCTAAATCGAAAATCAA-CTGAT-TCGATA
1 TTGACCCAACTCGAAAATCAATC-GATCT-GATA
* *
68073 TTAACCCAATTCGAAAATCAATCGATCTGATA
1 TTGACCCAACTCGAAAATCAATCGATCTGATA
* *
68105 TTGACCCGACCCG-AAATCTAATCGATCTGATA
1 TTGACCCAACTCGAAAATC-AATCGATCTGATA
* *
68137 TTGACCCGAC-CTG-AAATCTAACCGATCTGATA
1 TTGACCCAACTC-GAAAATC-AATCGATCTGATA
68169 TT
1 TT
68171 AATCCGTCCC
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.07
32 78 0.91
33 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (32 bp):
TTGACCCAACTCGAAAATCAATCGATCTGATA
Found at i:69501 original size:76 final size:77
Alignment explanation
Indices: 69342--69551 Score: 291
Period size: 76 Copynumber: 2.8 Consensus size: 77
69332 CAAAGCCAAA
* * * **
69342 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
69406 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
69419 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
69484 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
69495 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
69552 TGTACAACGG
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
75 19 0.16
76 62 0.52
77 39 0.32
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:71494 original size:21 final size:21
Alignment explanation
Indices: 71468--71507 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
71458 GAGAAATTGT
71468 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
71489 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
71508 AAACAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:75381 original size:21 final size:21
Alignment explanation
Indices: 75355--75394 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
75345 CCCCCTTTGA
*
75355 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
75376 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
75395 TGGGGTTATG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:77347 original size:17 final size:17
Alignment explanation
Indices: 77325--77372 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
77315 TTTCAACATT
77325 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
77342 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
77359 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
77373 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:77667 original size:29 final size:29
Alignment explanation
Indices: 77631--77689 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
77621 TACATAATAA
77631 ATTGAAGAAGTGTTAAAGTAAGGGGGAGT
1 ATTGAAGAAGTGTTAAAGTAAGGGGGAGT
77660 ATTGAAGAAGTGTTAAAGTAAGGGGGAGT
1 ATTGAAGAAGTGTTAAAGTAAGGGGGAGT
77689 A
1 A
77690 ATTTCAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (29 bp):
ATTGAAGAAGTGTTAAAGTAAGGGGGAGT
Found at i:78129 original size:76 final size:75
Alignment explanation
Indices: 77981--78192 Score: 255
Period size: 75 Copynumber: 2.8 Consensus size: 75
77971 CAATTCAAAG
* * *
77981 CCAAAAATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAA
1 CCAAAAATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAA
**
78046 ATGGTTTTGGCC
65 ACAGTTTT-GCC
* * * *
78058 CCGAGATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCTATAGGAGGAACCGATTCCCCCTAAA
1 CCAAAAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAA
*
78123 CAGTTTTGCT
66 CAGTTTTGCC
* * * * * *
78133 CTAAAAATTCTAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 CCAAAAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
78193 CTTGTACAAC
Statistics
Matches: 115, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
74 17 0.15
75 35 0.30
76 35 0.30
77 28 0.24
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.21
Consensus pattern (75 bp):
CCAAAAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAA
CAGTTTTGCC
Found at i:80852 original size:2 final size:2
Alignment explanation
Indices: 80845--80878 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
80835 ATAACGGATA
80845 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
80879 CAAAATGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80956 original size:24 final size:24
Alignment explanation
Indices: 80918--80987 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
80908 CAAATCAGAG
* *
80918 TCCATGTCAAGTATCACATAAAAA
1 TCCAGGTCAAATATCACATAAAAA
* * * *
80942 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCACATAAAAA
* *
80966 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCACATAAA
80988 CTATTTATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (24 bp):
TCCAGGTCAAATATCACATAAAAA
Found at i:80987 original size:48 final size:47
Alignment explanation
Indices: 80893--80987 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 47
80883 ATGAAAACAT
* * * **
80893 AATTCAGGTCAAGTACAAATCAGAGTCCATGTCAAGTATCACATAAA
1 AATTCAGGTCAAATACAAATCAGAATCCAGGTCAAAAATCACATAAA
* *
80940 AATTCAGGTCAAATATCATATCAGAATCCAGGTCAAAAATCAGATAAA
1 AATTCAGGTCAAATA-CAAATCAGAATCCAGGTCAAAAATCACATAAA
80988 CTATTTATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 14 0.35
48 26 0.65
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (47 bp):
AATTCAGGTCAAATACAAATCAGAATCCAGGTCAAAAATCACATAAA
Found at i:81685 original size:18 final size:18
Alignment explanation
Indices: 81662--81704 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
81652 GGAAGTCAAC
*
81662 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGAGTCG
81680 GGTCAACGGGTCGAGTCG
1 GGTCAACGGGTCGAGTCG
81698 GGTCAAC
1 GGTCAAC
81705 CCGGTTCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.23, G:0.44, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGAGTCG
Found at i:88070 original size:24 final size:24
Alignment explanation
Indices: 87996--88079 Score: 64
Period size: 24 Copynumber: 3.6 Consensus size: 24
87986 AAACATAATT
* *
87996 CAGGTCAAGTA-CAAATCAGAGTC
1 CAGGTCAAATATCAAATCAGAATC
* * * * * *
88019 CATGTCAAGTATCACATAAAAATT
1 CAGGTCAAATATCAAATCAGAATC
*
88043 CAGGTCAAATATCATATCAGAATC
1 CAGGTCAAATATCAAATCAGAATC
*
88067 CAGGT-AAAAATCA
1 CAGGTCAAATATCA
88080 GATAAACTAT
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
23 17 0.36
24 30 0.64
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (24 bp):
CAGGTCAAATATCAAATCAGAATC
Found at i:88085 original size:47 final size:47
Alignment explanation
Indices: 87992--88085 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 47
87982 ATTAAAACAT
* * * **
87992 AATTCAGGTCAAGTACAAATCAGAGTCCATGTCAAGTATCACATAAA
1 AATTCAGGTCAAATACAAATCAGAATCCAGGTCAAAAATCACATAAA
* *
88039 AATTCAGGTCAAATATCATATCAGAATCCAGGT-AAAAATCAGATAAA
1 AATTCAGGTCAAATA-CAAATCAGAATCCAGGTCAAAAATCACATAAA
88086 CTATTTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 25 0.64
48 14 0.36
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (47 bp):
AATTCAGGTCAAATACAAATCAGAATCCAGGTCAAAAATCACATAAA
Found at i:88790 original size:18 final size:18
Alignment explanation
Indices: 88767--88808 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
88757 CAACGATCAA
88767 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
88785 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
88803 CGGGTC
1 CGGGTC
88809 AACCCAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:88810 original size:13 final size:13
Alignment explanation
Indices: 88763--88790 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
88753 AAGTCAACGA
88763 TCAACGGGTCGGG
1 TCAACGGGTCGGG
88776 TCAACGGGTCGGG
1 TCAACGGGTCGGG
88789 TC
1 TC
88791 GGGTCAACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:88811 original size:13 final size:13
Alignment explanation
Indices: 88785--88811 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88775 GTCAACGGGT
88785 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
88798 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
88811 C
1 C
88812 CCAGTTCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.26, G:0.44, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:89410 original size:2 final size:2
Alignment explanation
Indices: 89398--89429 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
89388 GAAAACCACG
*
89398 TA TA CA 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
89430 AACCAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:96749 original size:2 final size:2
Alignment explanation
Indices: 96742--96771 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
96732 CCTAAACCAA
96742 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
96772 GATTCAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98779 original size:18 final size:19
Alignment explanation
Indices: 98756--98799 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
98746 CCAGTAATCC
98756 TATTCC-CTAATAATCTTA
1 TATTCCACTAATAATCTTA
* *
98774 TATTCCCACTAGTAATTTTA
1 TATT-CCACTAATAATCTTA
98794 TATTCC
1 TATTCC
98800 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.45
Consensus pattern (19 bp):
TATTCCACTAATAATCTTA
Found at i:99412 original size:17 final size:17
Alignment explanation
Indices: 99376--99409 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
99366 CTGTAAGAGT
99376 TTTAAATTTTTATATAA
1 TTTAAATTTTTATATAA
*
99393 TTTAAATATTTTTTATA
1 TTTAAAT-TTTTATATA
99410 TTTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATTTTTATATAA
Found at i:104152 original size:15 final size:15
Alignment explanation
Indices: 104132--104160 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
104122 TTTGCTTTGT
104132 TAAATTAAAATAAAA
1 TAAATTAAAATAAAA
104147 TAAATTAAAATAAA
1 TAAATTAAAATAAA
104161 GTTACTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATTAAAATAAAA
Found at i:104525 original size:14 final size:15
Alignment explanation
Indices: 104486--104527 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
104476 AAACTAAAGT
*
104486 AAATAAATCAA-TGA
1 AAATAAATAAAGTGA
*
104500 AACTAAATAAAGTGA
1 AAATAAATAAAGTGA
104515 AAATAAA-AAAGTG
1 AAATAAATAAAGTG
104528 TAACACCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (15 bp):
AAATAAATAAAGTGA
Found at i:108765 original size:26 final size:22
Alignment explanation
Indices: 108713--108764 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
108703 GCGATGCTAA
*
108713 CCACCCACTAACGGCTCTAACC
1 CCACCCACTAACGACTCTAACC
*
108735 CCACCCACTAACGACTCTAACT
1 CCACCCACTAACGACTCTAACC
108757 CCACCCAC
1 CCACCCAC
108765 CATTGAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.52, G:0.06, T:0.13
Consensus pattern (22 bp):
CCACCCACTAACGACTCTAACC
Found at i:110511 original size:3 final size:3
Alignment explanation
Indices: 110505--110542 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
110495 CCACCAATGG
110505 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
110543 ACAACAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:113986 original size:29 final size:29
Alignment explanation
Indices: 113952--114032 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
113942 TTATGGTTGC
113952 CATTTTAGGTTGTAACATATTTCCAACCA
1 CATTTTAGGTTGTAACATATTTCCAACCA
* * * *
113981 TATTTTAGGTTGTAATACATTTCCAATCA
1 CATTTTAGGTTGTAACATATTTCCAACCA
* *
114010 CATTTTAGGTTGCATCATATTTC
1 CATTTTAGGTTGTAACATATTTC
114033 TAATATGCTC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (29 bp):
CATTTTAGGTTGTAACATATTTCCAACCA
Found at i:117708 original size:20 final size:19
Alignment explanation
Indices: 117685--117724 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
117675 TAGTCACCAA
*
117685 AATTAGGTTTTATATATTTT
1 AATTAGGTTTT-CATATTTT
*
117705 AATTTGGTTTTCATATTTT
1 AATTAGGTTTTCATATTTT
117724 A
1 A
117725 TTTACTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.60
Consensus pattern (19 bp):
AATTAGGTTTTCATATTTT
Found at i:120244 original size:18 final size:18
Alignment explanation
Indices: 120221--120263 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
120211 TGAATTACAT
120221 CATTCATACATGCATTTA
1 CATTCATACATGCATTTA
** *
120239 CATTCATATTTGTATTTA
1 CATTCATACATGCATTTA
120257 CATTCAT
1 CATTCAT
120264 GTTTCACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (18 bp):
CATTCATACATGCATTTA
Found at i:122424 original size:3 final size:3
Alignment explanation
Indices: 122416--122440 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
122406 GACATCACAT
122416 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
122441 AATAATTTAA
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):
TTA
Found at i:122882 original size:33 final size:34
Alignment explanation
Indices: 122827--122904 Score: 140
Period size: 33 Copynumber: 2.3 Consensus size: 34
122817 TTAATTAAAT
122827 AATAATAATAATAAAAATTGTCAACTCATATAGA
1 AATAATAATAATAAAAATTGTCAACTCATATAGA
*
122861 AATAATAATAAT-AAAATTGTCAAGTCATATAGA
1 AATAATAATAATAAAAATTGTCAACTCATATAGA
122894 AATAATAATAA
1 AATAATAATAA
122905 AATAATTTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 31 0.72
34 12 0.28
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (34 bp):
AATAATAATAATAAAAATTGTCAACTCATATAGA
Found at i:123213 original size:26 final size:30
Alignment explanation
Indices: 123157--123215 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
123147 TTATTTTTTC
*
123157 ACCCGACCCGACCCGATAGATAGTTTAAAAA
1 ACCCGACCCGACCCGATAGATAG-ATAAAAA
123188 ACCCGACCCGACCCGA-A-ATA-ATAAAAA
1 ACCCGACCCGACCCGATAGATAGATAAAAA
123215 A
1 A
123216 AAATTTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 7 0.26
29 3 0.11
30 1 0.04
31 16 0.59
ACGTcount: A:0.44, C:0.31, G:0.14, T:0.12
Consensus pattern (30 bp):
ACCCGACCCGACCCGATAGATAGATAAAAA
Found at i:134609 original size:21 final size:21
Alignment explanation
Indices: 134583--134623 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
134573 CGAAATTTAG
*
134583 TGCATCGGTGCATTGTAGCAA
1 TGCATCGATGCATTGTAGCAA
134604 TGCATCGATGCATTGTAGCA
1 TGCATCGATGCATTGTAGCA
134624 CTGTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATTGTAGCAA
Done.