Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 101 of 189
Found at i:28231167 original size:6 final size:6
Alignment explanation
Indices: 28231156--28231224 Score: 70
Period size: 6 Copynumber: 11.7 Consensus size: 6
28231146 AGTTAATTTA
** * **
28231156 GGTTAG GGTTAG GGTTAG GGTTAG GGTTTTT AGTTA- ATTTA- GGTTAG
1 GGTTAG GGTTAG GGTTAG GGTTAG GG-TTAG GGTTAG GGTTAG GGTTAG
28231203 GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTT
28231225 TTTAAGTAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
5 7 0.13
6 44 0.81
7 3 0.06
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.41
Consensus pattern (6 bp):
GGTTAG
Found at i:28231173 original size:41 final size:41
Alignment explanation
Indices: 28231128--28231386 Score: 242
Period size: 41 Copynumber: 6.1 Consensus size: 41
28231118 ATTAATTTAT
28231128 GTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGG
1 GTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGG
28231169 GTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGG
1 GTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGG
*
28231210 GTTAGGGTTAGGGTTTTTAAGTAAGATAGGTTAAGGTTAGGGTTTTTAGTTAG
1 GTTAGGGTTAGGGTTTTT-AGTTA-AT---TT-AGGTTAGGG---TTAG---G
* *
28231263 GTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGG
1 GTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGG
*** **
28231304 GTTTTTAGTTA-GG---TTAGGTTAGGGTTAGGGTTA-GGTTA-G
1 G-TTAGGGTTAGGGTTTTTA-GTTA-ATTTA-GGTTAGGGTTAGG
* *
28231343 GTTAGAGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGG
1 GTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGG
28231384 GTT
1 GTT
28231387 TTTAGTTAGG
Statistics
Matches: 182, Mismatches: 14, Indels: 44
0.76 0.06 0.18
Matches are distributed among these distances:
38 10 0.05
39 12 0.07
40 17 0.09
41 75 0.41
42 13 0.07
43 2 0.01
44 4 0.02
46 2 0.01
47 18 0.10
48 2 0.01
50 4 0.02
51 1 0.01
52 3 0.02
53 19 0.10
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (41 bp):
GTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGG
Found at i:28231242 original size:29 final size:29
Alignment explanation
Indices: 28231204--28231626 Score: 421
Period size: 29 Copynumber: 14.6 Consensus size: 29
28231194 TTAGGTTAGG
*
28231204 GTTAGGGTTAGGGTTAGGGTTTTTAAGTAA
1 GTTA-GGTTAGGGTTAGGGTTTTTAATTAA
* *
28231234 GATAGGTTAAGGTTAGGG--TTT--TT-A
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
28231258 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
* *
28231287 GTTAGGTTAGGGTTAGGGTTTTTAGTTAG
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
* *
28231316 GTTAGGTTAGGGTTAGGG---TTAGGTTAG
1 GTTAGGTTAGGGTTAGGGTTTTTA-ATTAA
28231343 GTTAGAGTTAGGGTT----TTTAATTAATT--
1 GTTAG-GTTAGGGTTAGGGTTT--TTAATTAA
* * *
28231369 T--AGGTTAGGGTTAGGGTTTTTAGTTAG
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
28231396 GTTAGGTTAGGGTTAGGGTTTTTAATTAATTTA
1 GTTAGGTTAGGGTTAGGGTTTTTAATT-A---A
*
28231429 GGTTAGGGTTAGAGTTAGGGTTTTTAATTAAGTTA
1 -GTTA-GGTTAGGGTTAGGGTTTTTAATT-A---A
28231464 GGTTAGGGTTAGGGTTAGGGTTTTTAATTAA
1 -GTTA-GGTTAGGGTTAGGGTTTTTAATTAA
* * *
28231495 GTTAGGTTAAGGTTAGGGTTTTTAGTTAG
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
28231524 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
* *
28231553 TTTAGGTTAGAGTTAGGGTTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
*
28231582 TTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
28231611 GTTAGGTTA-GGTTAGG
1 GTTAGGTTAGGGTTAGG
28231627 TTAGGTTAGG
Statistics
Matches: 341, Mismatches: 26, Indels: 54
0.81 0.06 0.13
Matches are distributed among these distances:
23 9 0.03
24 19 0.06
25 6 0.02
26 6 0.02
27 16 0.05
28 20 0.06
29 196 0.57
30 8 0.02
31 1 0.00
34 5 0.01
35 55 0.16
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (29 bp):
GTTAGGTTAGGGTTAGGGTTTTTAATTAA
Found at i:28231302 original size:6 final size:6
Alignment explanation
Indices: 28231287--28231357 Score: 62
Period size: 6 Copynumber: 12.5 Consensus size: 6
28231277 TTTTAATTAA
***
28231287 GTTA-G GTTAGG GTTAGG GTTTTTA GTTA-G GTTA-G GTTAGG GTTAGG
1 GTTAGG GTTAGG GTTAGG G-TTAGG GTTAGG GTTAGG GTTAGG GTTAGG
*
28231333 GTTA-G GTTA-G GTTAGA GTTAGG GTT
1 GTTAGG GTTAGG GTTAGG GTTAGG GTT
28231358 TTTAATTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
5 23 0.42
6 29 0.53
7 3 0.05
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (6 bp):
GTTAGG
Found at i:28231339 original size:22 final size:21
Alignment explanation
Indices: 28231311--28231357 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 21
28231301 AGGGTTTTTA
28231311 GTTAGGTTAGGTTAGGGTTAGG
1 GTTAGGTTAGGTTA-GGTTAGG
28231333 GTTAGGTTAGGTTAGAGTTAGG
1 GTTAGGTTAGGTTAG-GTTAGG
28231355 GTT
1 GTT
28231358 TTTAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (21 bp):
GTTAGGTTAGGTTAGGTTAGG
Found at i:28231462 original size:18 final size:18
Alignment explanation
Indices: 28231441--28231500 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
28231431 TTAGGGTTAG
28231441 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
****
28231459 AGTTA-GG-TTAGGGTTA
1 AGTTAGGGTTTTTAATTA
*
28231475 GGGTTAGGGTTTTTAATTA
1 -AGTTAGGGTTTTTAATTA
28231494 AGTTAGG
1 AGTTAGG
28231501 TTAAGGTTAG
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 5 0.17
17 6 0.21
18 13 0.45
19 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (18 bp):
AGTTAGGGTTTTTAATTA
Found at i:28231621 original size:5 final size:5
Alignment explanation
Indices: 28231611--28231636 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28231601 TTTTAATTAA
28231611 GTTAG GTTAG GTTAG GTTAG GTTAG G
1 GTTAG GTTAG GTTAG GTTAG GTTAG G
28231637 GTTTTCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTTAG
Found at i:28232846 original size:7 final size:7
Alignment explanation
Indices: 28232836--28232867 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
28232826 TTATATACAT
28232836 AATACTA
1 AATACTA
28232843 AATACTA
1 AATACTA
28232850 AATACTA
1 AATACTA
28232857 AATACTA
1 AATACTA
28232864 AATA
1 AATA
28232868 TCAATCGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:28233915 original size:10 final size:10
Alignment explanation
Indices: 28233896--28233943 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
28233886 CCTATTGATG
*
28233896 AAAATATAAA
1 AAAATTTAAA
28233906 AAAATTTAAA
1 AAAATTTAAA
** *
28233916 ATTATTTTAA
1 AAAATTTAAA
*
28233926 AAAATATAAA
1 AAAATTTAAA
28233936 AAAATTTA
1 AAAATTTA
28233944 TAATTATTGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:28233930 original size:30 final size:30
Alignment explanation
Indices: 28233896--28233961 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
28233886 CCTATTGATG
*
28233896 AAAATATAAAAAAATTTAAAATTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTGTAA
*
28233926 AAAATATAAAAAAATTTATAATTATTGTAA
1 AAAATATAAAAAAATTTAAAATTATTGTAA
28233956 AAAATA
1 AAAATA
28233962 AATTTGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTGTAA
Found at i:28237641 original size:21 final size:23
Alignment explanation
Indices: 28237593--28237641 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
28237583 AATTGTTGTC
* *
28237593 AGTTTTAACAAGTTTTTTATTTT
1 AGTTTTAACAAGTTTTATATGTT
*
28237616 TGTTTT-AC-AGTTTTATATGTT
1 AGTTTTAACAAGTTTTATATGTT
28237637 AGTTT
1 AGTTT
28237642 GCGCTTTGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.68
22 2 0.09
23 5 0.23
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.61
Consensus pattern (23 bp):
AGTTTTAACAAGTTTTATATGTT
Found at i:28245771 original size:17 final size:17
Alignment explanation
Indices: 28245749--28245781 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28245739 ATATTTAATA
28245749 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
28245766 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
28245782 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:28247785 original size:18 final size:20
Alignment explanation
Indices: 28247760--28247803 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28247750 GGTATCATAT
*
28247760 ATTT-ATTCAT-ATTTTTC-
1 ATTTAATTCATAATTTTACA
28247777 ATTTAATTCATAATTTTACA
1 ATTTAATTCATAATTTTACA
28247797 ATTTAAT
1 ATTTAAT
28247804 CCATTTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 6 0.26
20 7 0.30
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAATTCATAATTTTACA
Found at i:28252820 original size:17 final size:18
Alignment explanation
Indices: 28252791--28252825 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28252781 AAAAAATCAC
28252791 ATTTTTTACATTTAATAT
1 ATTTTTTACATTTAATAT
*
28252809 ATTTTTTA-ATTTCATAT
1 ATTTTTTACATTTAATAT
28252826 TACATAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTTACATTTAATAT
Found at i:28264329 original size:26 final size:25
Alignment explanation
Indices: 28264273--28264348 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 25
28264263 ATGAATTTTC
* * *
28264273 TCAAAATTTTATCAGGATAAAATCG
1 TCAAAATTTTATGAGGGTAAAATTG
*
28264298 TTAAAATTTTACTGAGGGTAAAATTG
1 TCAAAATTTTA-TGAGGGTAAAATTG
28264324 TCAAAATTTTATTG-GGGTAAAATTG
1 TCAAAATTTTA-TGAGGGTAAAATTG
28264349 GGATGAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
25 21 0.48
26 23 0.52
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (25 bp):
TCAAAATTTTATGAGGGTAAAATTG
Found at i:28264347 original size:25 final size:25
Alignment explanation
Indices: 28264273--28264348 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
28264263 ATGAATTTTC
** * *
28264273 TCAAAATTTTATCAGGATAAAATCG
1 TCAAAATTTTATTGGGGTAAAATTG
* *
28264298 TTAAAATTTTACTGAGGGTAAAATTG
1 TCAAAATTTTATTG-GGGTAAAATTG
28264324 TCAAAATTTTATTGGGGTAAAATTG
1 TCAAAATTTTATTGGGGTAAAATTG
28264349 GGATGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 21 0.50
26 21 0.50
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (25 bp):
TCAAAATTTTATTGGGGTAAAATTG
Found at i:28276726 original size:12 final size:12
Alignment explanation
Indices: 28276701--28276739 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28276691 ACTCGCTTCT
* *
28276701 TTACTTACTCAC
1 TTACTTGCTTAC
*
28276713 TTACTTGTTTAC
1 TTACTTGCTTAC
28276725 TTACTTGCTTAC
1 TTACTTGCTTAC
28276737 TTA
1 TTA
28276740 AATAACTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:28277055 original size:50 final size:50
Alignment explanation
Indices: 28276987--28277179 Score: 233
Period size: 50 Copynumber: 3.7 Consensus size: 50
28276977 TTTTCTGTAT
* ** **
28276987 TGCCAATGCCATATCCCAGGTATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
28277037 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
28277087 TGCCAATGCCCTGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
28277143 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
28277180 TCTCATTCCC
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 82 0.68
53 2 0.02
56 37 0.31
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:28277148 original size:56 final size:50
Alignment explanation
Indices: 28276948--28277179 Score: 227
Period size: 50 Copynumber: 4.5 Consensus size: 50
28276938 ATCCAAAGAT
* * **
28276948 ATGTCCCAGACATAGTCTTACATGGGA--TGTTTTCT-GTATTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG-A-TGCCAATGCC
* ** ** * * *
28276997 ATATCCCAGGTATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAATGCC
** *
28277047 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAATGCC
*
28277097 CTGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CTC---GATGCCAATGCC
28277153 ATGTCCCAGACATGGTCTTACATGGGA
1 ATGTCCCAGACATGGTCTTACATGGGA
28277180 TCTCATTCCC
Statistics
Matches: 150, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
49 23 0.15
50 82 0.55
51 4 0.03
52 1 0.01
53 3 0.02
56 37 0.25
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAATGCC
Found at i:28278717 original size:46 final size:47
Alignment explanation
Indices: 28278615--28278717 Score: 154
Period size: 47 Copynumber: 2.2 Consensus size: 47
28278605 ATTGTTTTCA
* *
28278615 AGTTATTGCATTGACAACCATCCTCACAATTTATCTTATTTATATCT
1 AGTTATTGCATCGACAACCATCCTCACAATTTATATTATTTATATCT
* * *
28278662 GGTTATTGCATCGATAACTATCCTCACAATTT-TATTATTTATATCT
1 AGTTATTGCATCGACAACCATCCTCACAATTTATATTATTTATATCT
28278708 AGTTATTGCA
1 AGTTATTGCA
28278718 CCAACATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
46 22 0.44
47 28 0.56
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (47 bp):
AGTTATTGCATCGACAACCATCCTCACAATTTATATTATTTATATCT
Found at i:28280857 original size:22 final size:22
Alignment explanation
Indices: 28280832--28280877 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
28280822 GGACACATTA
*
28280832 AAGCAACTGCAGATCAACACTG
1 AAGCAACTGCAAATCAACACTG
*
28280854 AAGCAACTGCAAATCAACATTG
1 AAGCAACTGCAAATCAACACTG
28280876 AA
1 AA
28280878 ACTATTCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (22 bp):
AAGCAACTGCAAATCAACACTG
Found at i:28283529 original size:31 final size:31
Alignment explanation
Indices: 28283489--28283552 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
28283479 GGTACCTTTG
*
28283489 TCGATGCATTGAAATCTTACTGTCAACGCAT
1 TCGACGCATTGAAATCTTACTGTCAACGCAT
28283520 TCGACGCATTGAAATCTTACTGTCAACGCAT
1 TCGACGCATTGAAATCTTACTGTCAACGCAT
28283551 TC
1 TC
28283553 CTTAAGTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (31 bp):
TCGACGCATTGAAATCTTACTGTCAACGCAT
Found at i:28299247 original size:27 final size:28
Alignment explanation
Indices: 28299163--28299260 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
28299153 CATGAGATTG
* * * *
28299163 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
28299192 GCATTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
28299220 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28299247 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
28299261 GACTTAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 24 0.39
28 21 0.34
29 17 0.27
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28299271 original size:27 final size:27
Alignment explanation
Indices: 28299191--28299273 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
28299181 TAAATTGTAC
* * *
28299191 AGCATTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
28299219 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
28299246 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
28299273 A
1 A
28299274 TTTTTGAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 30 0.61
28 19 0.39
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:28299274 original size:29 final size:27
Alignment explanation
Indices: 28299163--28299274 Score: 89
Period size: 28 Copynumber: 4.0 Consensus size: 27
28299153 CATGAGATTG
** * *
28299163 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* * *
28299192 GCATTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
28299220 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
28299247 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
28299275 TTTTGAATCA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
27 23 0.33
28 27 0.39
29 20 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.34
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:28307332 original size:27 final size:28
Alignment explanation
Indices: 28307248--28307345 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
28307238 CATGAGATTG
* * * *
28307248 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
28307277 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
28307305 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28307332 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
28307346 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28307356 original size:27 final size:27
Alignment explanation
Indices: 28307276--28307358 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
28307266 TAAATTGTAC
* *
28307276 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
28307304 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
28307331 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
28307358 A
1 A
28307359 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:28307359 original size:29 final size:27
Alignment explanation
Indices: 28307248--28307359 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
28307238 CATGAGATTG
** * *
28307248 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
28307277 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
28307305 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
28307332 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
28307360 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:28310295 original size:6 final size:6
Alignment explanation
Indices: 28310246--28310314 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
28310236 GACCCCCTGT
* * *
28310246 ATTAAA A-T-AA A-TAAA ATTAAC ATTAAA CTTAAA AATAAA GATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA -ATTAAA
* *
28310292 ATTAAG ATT-AA ATTGAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA
28310315 GACAAAGGTA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
4 4 0.08
5 8 0.16
6 33 0.66
7 5 0.10
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (6 bp):
ATTAAA
Found at i:28310295 original size:31 final size:30
Alignment explanation
Indices: 28310257--28310316 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
28310247 TTAAAATAAA
28310257 TAAAATTAACATTAAACTTAAAAATAAAGAT
1 TAAAATTAACATTAAA-TTAAAAATAAAGAT
* * *
28310288 TAAAATTAAGATTAAATTGAAATTAAAGA
1 TAAAATTAACATTAAATTAAAAATAAAGA
28310317 CAAAGGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (30 bp):
TAAAATTAACATTAAATTAAAAATAAAGAT
Found at i:28315753 original size:20 final size:20
Alignment explanation
Indices: 28315730--28315777 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
28315720 CATTAAAGAG
*
28315730 TGGCACAACGTATTATCTGA
1 TGGCACAACGTATTAACTGA
28315750 TGGCACAACGTATTAACTGA
1 TGGCACAACGTATTAACTGA
28315770 TGGCACAA
1 TGGCACAA
28315778 TCCCTATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (20 bp):
TGGCACAACGTATTAACTGA
Found at i:28324379 original size:39 final size:37
Alignment explanation
Indices: 28324312--28324404 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
28324302 ACCAGAATGG
* *
28324312 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
28324351 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
28324388 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
28324405 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:28324768 original size:3 final size:3
Alignment explanation
Indices: 28324760--28324807 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
28324750 ATTCCCACTC
* * * *
28324760 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28324808 CTTACCTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:28324808 original size:18 final size:18
Alignment explanation
Indices: 28324761--28324809 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
28324751 TTCCCACTCA
*
28324761 TAATAATAATAATAATAC
1 TAATAATAATACTAATAC
28324779 TAATAATAATACTAATAC
1 TAATAATAATACTAATAC
*
28324797 TAATATTAATACT
1 TAATAATAATACT
28324810 TACCTCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAATACTAATAC
Found at i:28324809 original size:12 final size:12
Alignment explanation
Indices: 28324760--28324807 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
28324750 ATTCCCACTC
*
28324760 ATAATAATAATA
1 ATAATACTAATA
28324772 ATAATACTAATA
1 ATAATACTAATA
28324784 ATAATACTAATA
1 ATAATACTAATA
* *
28324796 CTAATATTAATA
1 ATAATACTAATA
28324808 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:28325547 original size:20 final size:20
Alignment explanation
Indices: 28325513--28325552 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28325503 TTCTATTCTG
*
28325513 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
28325533 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
28325553 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:28325719 original size:31 final size:28
Alignment explanation
Indices: 28325683--28325750 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
28325673 TTGTCTTTAT
**
28325683 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
28325713 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
28325742 TTAATTTAT
1 TTAATTTAT
28325751 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:28325767 original size:21 final size:20
Alignment explanation
Indices: 28325729--28325767 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28325719 TAATTTAATA
*
28325729 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
28325749 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
28325768 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:28330709 original size:21 final size:21
Alignment explanation
Indices: 28330667--28330709 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28330657 TTCACTATAC
*
28330667 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
28330688 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
28330709 A
1 A
28330710 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:28331820 original size:39 final size:37
Alignment explanation
Indices: 28331753--28331845 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
28331743 ACCAGAATGG
* *
28331753 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
28331792 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
28331829 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
28331846 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:28332207 original size:3 final size:3
Alignment explanation
Indices: 28332199--28332246 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
28332189 ATTCCCACTC
* * * *
28332199 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28332247 CTTACCTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:28332247 original size:18 final size:18
Alignment explanation
Indices: 28332200--28332248 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
28332190 TTCCCACTCA
*
28332200 TAATAATAATAATAATAC
1 TAATAATAATACTAATAC
28332218 TAATAATAATACTAATAC
1 TAATAATAATACTAATAC
*
28332236 TAATATTAATACT
1 TAATAATAATACT
28332249 TACCTCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAATACTAATAC
Found at i:28332248 original size:12 final size:12
Alignment explanation
Indices: 28332199--28332246 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
28332189 ATTCCCACTC
*
28332199 ATAATAATAATA
1 ATAATACTAATA
28332211 ATAATACTAATA
1 ATAATACTAATA
28332223 ATAATACTAATA
1 ATAATACTAATA
* *
28332235 CTAATATTAATA
1 ATAATACTAATA
28332247 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:28332986 original size:20 final size:20
Alignment explanation
Indices: 28332952--28332991 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28332942 TTCTATTCTG
*
28332952 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
28332972 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
28332992 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:28333158 original size:31 final size:28
Alignment explanation
Indices: 28333122--28333189 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
28333112 TTGTCTTTAT
**
28333122 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
28333152 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
28333181 TTAATTTAT
1 TTAATTTAT
28333190 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:28333206 original size:21 final size:20
Alignment explanation
Indices: 28333168--28333206 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28333158 TAATTTAATA
*
28333168 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
28333188 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
28333207 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:28333958 original size:25 final size:25
Alignment explanation
Indices: 28333924--28333995 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
28333914 ACGAATTTTC
28333924 TCAAAATTTTACTAGGATAAAATCA
1 TCAAAATTTTACTAGGATAAAATCA
* * **
28333949 TCAAAATTTTACAAAGAATAAAATTG
1 TCAAAATTTTAC-TAGGATAAAATCA
*
28333975 TCAAAAGTTTACTAGGATAAA
1 TCAAAATTTTACTAGGATAAA
28333996 GTTGGTGTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 19 0.49
26 20 0.51
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (25 bp):
TCAAAATTTTACTAGGATAAAATCA
Found at i:28335167 original size:11 final size:11
Alignment explanation
Indices: 28335153--28335191 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28335143 TTTTTTGCTG
28335153 TTATTTTGTTA
1 TTATTTTGTTA
* **
28335164 TTATATTACTA
1 TTATTTTGTTA
28335175 TTATTTTGTTA
1 TTATTTTGTTA
28335186 TTATTT
1 TTATTT
28335192 GAATATTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (11 bp):
TTATTTTGTTA
Found at i:28335190 original size:33 final size:32
Alignment explanation
Indices: 28335157--28335227 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
28335147 TTGCTGTTAT
* *
28335157 TTTGTTATTATATTACTATTATTTTGTTATTA
1 TTTGTTATTATATAACTATTATTTTATTATTA
* *
28335189 TTTGAATATTATATAACTCTTATTTTATTATTAA
1 TTTG-TTATTATATAACTATTATTTTATTATT-A
28335223 TTTGT
1 TTTGT
28335228 CTACTATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
32 4 0.12
33 23 0.72
34 5 0.16
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (32 bp):
TTTGTTATTATATAACTATTATTTTATTATTA
Found at i:28335198 original size:22 final size:22
Alignment explanation
Indices: 28335153--28335200 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28335143 TTTTTTGCTG
*
28335153 TTATTTTGTTATTATATTACTA
1 TTATTTTGTTATTATATTAATA
28335175 TTATTTTGTTATTAT-TTGAATA
1 TTATTTTGTTATTATATT-AATA
28335197 TTAT
1 TTAT
28335201 ATAACTCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (22 bp):
TTATTTTGTTATTATATTAATA
Found at i:28335306 original size:17 final size:18
Alignment explanation
Indices: 28335286--28335319 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28335276 TATTTAAGTA
28335286 TAAATACTT-TTTTAATG
1 TAAATACTTATTTTAATG
*
28335303 TAAATATTTATTTTAAT
1 TAAATACTTATTTTAAT
28335320 ATTTTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TAAATACTTATTTTAATG
Found at i:28335333 original size:23 final size:22
Alignment explanation
Indices: 28335306--28335367 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
28335296 TTTAATGTAA
*
28335306 ATATTTATTTTAATATTTTTAAT
1 ATATTTATTTTAATATATTT-AT
* * *
28335329 ATATTTAATTTATTATATTTCT
1 ATATTTATTTTAATATATTTAT
* *
28335351 AAATTTATTTTTATATA
1 ATATTTATTTTAATATA
28335368 AAAAATTAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTTATTTTAATATATTTAT
Found at i:28339897 original size:17 final size:16
Alignment explanation
Indices: 28339853--28339905 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
28339843 TTTGGTTCGC
28339853 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28339869 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28339885 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
28339902 TGTA
1 TGTA
28339906 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 22 0.61
17 14 0.39
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28340228 original size:157 final size:157
Alignment explanation
Indices: 28340028--28340344 Score: 555
Period size: 157 Copynumber: 2.0 Consensus size: 157
28340018 TAGAATACCC
*
28340028 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
28340093 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAATA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA-A
28340158 ATATATAATTTAATAAAATTCTT-ATAA
130 ATATATAATTTAATAAAATTCTTAATAA
* *
28340185 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
28340250 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
28340315 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
28340342 TTA
1 TTA
28340345 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
156 24 0.16
157 128 0.84
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:28340315 original size:16 final size:16
Alignment explanation
Indices: 28340278--28340319 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28340268 TTAATCATAT
*
28340278 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28340294 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28340309 TTAAAATATAT
1 TTAAAATATAT
28340320 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28340326 original size:14 final size:15
Alignment explanation
Indices: 28340287--28340328 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28340277 TTTAAACATA
*
28340287 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28340302 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28340316 A-TATAATTTAATA
1 ATTATAATTAAATA
28340329 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28340415 original size:120 final size:121
Alignment explanation
Indices: 28340281--28340573 Score: 502
Period size: 120 Copynumber: 2.4 Consensus size: 121
28340271 ATCATATTTA
28340281 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
28340346 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA-GT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAATGTG
28340401 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
28340466 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
* * *
28340522 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
28340574 TAAAATAATT
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 3 0.02
120 160 0.97
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
Found at i:28340446 original size:14 final size:15
Alignment explanation
Indices: 28340407--28340448 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28340397 AAGTAACATA
*
28340407 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28340422 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28340436 A-TATAATTTAATA
1 ATTATAATTAAATA
28340449 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28344117 original size:6 final size:6
Alignment explanation
Indices: 28344108--28344136 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28344098 TTGATGTTGG
28344108 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
28344137 TGGGGAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:28344629 original size:21 final size:21
Alignment explanation
Indices: 28344588--28344631 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
28344578 TAATAATGAT
*
28344588 AAAATTATATTTTAATCTTTTA
1 AAAATTATAATTTAA-CTTTTA
28344610 AAAATTTATAATTTAA-TTTTA
1 AAAA-TTATAATTTAACTTTTA
28344631 A
1 A
28344632 CTTCTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 10 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AAAATTATAATTTAACTTTTA
Found at i:28345539 original size:21 final size:22
Alignment explanation
Indices: 28345501--28345577 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 22
28345491 ATAAAACCAT
28345501 AAAAATAAAATAAATATTTTAA
1 AAAAATAAAATAAATATTTTAA
* * *
28345523 AAAAATTAAA-AATTATTTTTA
1 AAAAATAAAATAAATATTTTAA
*
28345544 AAAAATAAATTTAAA-ATTTATGAA
1 AAAAATAAA-ATAAATATTT-T-AA
28345568 AAAAATAAAA
1 AAAAATAAAA
28345578 ACTCCTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
21 17 0.40
22 13 0.30
23 3 0.07
24 10 0.23
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (22 bp):
AAAAATAAAATAAATATTTTAA
Found at i:28345859 original size:16 final size:17
Alignment explanation
Indices: 28345830--28345867 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28345820 CGGTTCAAAT
* *
28345830 AAAATAAATTATTTTTA
1 AAAATAAATAATTTATA
28345847 AAAATAAA-AATTTATA
1 AAAATAAATAATTTATA
28345863 AAAAT
1 AAAAT
28345868 CGATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATAAATAATTTATA
Found at i:28346114 original size:17 final size:17
Alignment explanation
Indices: 28346087--28346131 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
28346077 AAAAATCTTT
28346087 AAAA-TTCAAAAATA-A
1 AAAATTTCAAAAATATA
*
28346102 AAATATTTTAAAAATATA
1 AAA-ATTTCAAAAATATA
28346120 AAAATTTCAAAA
1 AAAATTTCAAAA
28346132 TTCAATGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.12
16 1 0.04
17 17 0.68
18 4 0.16
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTTCAAAAATATA
Found at i:28346296 original size:16 final size:16
Alignment explanation
Indices: 28346275--28346306 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28346265 AGTTGAATCA
28346275 ATTTTTATAATTTTTT
1 ATTTTTATAATTTTTT
*
28346291 ATTTTTTTAATTTTTT
1 ATTTTTATAATTTTTT
28346307 TCTGCTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTTTATAATTTTTT
Found at i:28347591 original size:21 final size:21
Alignment explanation
Indices: 28347562--28347616 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
28347552 AAGGTTTTTC
* *
28347562 TTTTCTTCTTTCCGATTCGGT
1 TTTTTTTCTTTCCGATTCCGT
*
28347583 TTTTTTTCTTT-CGATTCCTT
1 TTTTTTTCTTTCCGATTCCGT
28347603 TTTTTCTTCTTTCC
1 TTTTT-TTCTTTCC
28347617 TTTTTGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.41
21 16 0.55
22 1 0.03
ACGTcount: A:0.04, C:0.24, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTTTCTTTCCGATTCCGT
Found at i:28353869 original size:22 final size:22
Alignment explanation
Indices: 28353813--28353987 Score: 129
Period size: 22 Copynumber: 7.5 Consensus size: 22
28353803 AATTATTCAA
* *
28353813 CAAATTGGACAGCAATAATATGCT
1 CAAATTGGACAGC-ATTATAT-AT
* *
28353837 CAAAATGGACAGCATTATACAT
1 CAAATTGGACAGCATTATATAT
*
28353859 CAAATTAGACAGC-TTAAATATACT
1 CAAATTGGACAGCATT--ATATA-T
*
28353883 CAAAATTGGACAGCATTATACAT
1 C-AAATTGGACAGCATTATATAT
*
28353906 CAAATTAGACAGC-TTAAATATACT
1 CAAATTGGACAGCATT--ATATA-T
28353930 CAAAATTGGACAGCATTATATAT
1 C-AAATTGGACAGCATTATATAT
* * *
28353953 TAAAATGGACAGCATCAATATACT
1 CAAATTGGACAGCAT-TATATA-T
*
28353977 CAAAATGGACA
1 CAAATTGGACA
28353988 TCAAATTTGG
Statistics
Matches: 123, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
21 4 0.03
22 36 0.29
23 21 0.17
24 36 0.29
25 22 0.18
26 4 0.03
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.26
Consensus pattern (22 bp):
CAAATTGGACAGCATTATATAT
Found at i:28353888 original size:25 final size:24
Alignment explanation
Indices: 28353814--28353987 Score: 136
Period size: 25 Copynumber: 7.4 Consensus size: 24
28353804 ATTATTCAAC
* *
28353814 AAATTGGACAGCAATAATATGCTCA
1 AAATTGGACAGC-TTAATATACTCA
*
28353839 AAA-TGGACAGC--ATTATACATC-
1 AAATTGGACAGCTTAATATAC-TCA
*
28353860 AAATTAGACAGCTTAAATATACTCA
1 AAATTGGACAGCTT-AATATACTCA
*
28353885 AAATTGGACAGC--ATTATACATC-
1 AAATTGGACAGCTTAATATAC-TCA
*
28353907 AAATTAGACAGCTTAAATATACTCA
1 AAATTGGACAGCTT-AATATACTCA
*
28353932 AAATTGGACAGCATT-ATATA-TTA
1 AAATTGGACAGC-TTAATATACTCA
*
28353955 AAA-TGGACAGCATCAATATACTCA
1 AAATTGGACAGC-TTAATATACTCA
28353979 AAA-TGGACA
1 AAATTGGACA
28353988 TCAAATTTGG
Statistics
Matches: 123, Mismatches: 12, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
21 8 0.07
22 36 0.29
23 12 0.10
24 28 0.23
25 37 0.30
26 2 0.02
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (24 bp):
AAATTGGACAGCTTAATATACTCA
Found at i:28353910 original size:47 final size:47
Alignment explanation
Indices: 28353794--28353987 Score: 241
Period size: 47 Copynumber: 4.1 Consensus size: 47
28353784 CAACCCTGTT
* * * * * *
28353794 TTGGACAACAATTATTCAACAAATTGGACAGC-AATAATATGCTCAAAA
1 TTGGACAGC-ATTATACATCAAATTAGACAGCTTA-AATATACTCAAAA
28353842 -TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
1 TTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
28353888 TTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
1 TTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
* * * * * *
28353935 TTGGACAGCATTATATATTAAAATGGACAGCATCAATATACTCAAAA
1 TTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
28353982 -TGGACA
1 TTGGACA
28353988 TCAAATTTGG
Statistics
Matches: 132, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
46 37 0.28
47 95 0.72
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.26
Consensus pattern (47 bp):
TTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
Found at i:28355005 original size:28 final size:26
Alignment explanation
Indices: 28354973--28355070 Score: 124
Period size: 28 Copynumber: 3.6 Consensus size: 26
28354963 TTAATAAGTA
*
28354973 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT--TAATTAAACT
* *
28355001 CGCACACTTAGTACTTTACATTATACT
1 CGCACACTTAGTGCTTTA-ATTAAACT
28355028 CGCACACTTAGTGCATTTCAATTAAACT
1 CGCACACTTAGTGC-TTT-AATTAAACT
28355056 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28355071 AATCTCATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.03
27 20 0.32
28 39 0.63
29 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.32
Consensus pattern (26 bp):
CGCACACTTAGTGCTTTAATTAAACT
Found at i:28356494 original size:6 final size:6
Alignment explanation
Indices: 28356483--28356517 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
28356473 AAAGAGAAGA
* *
28356483 AAAATC AAAATC AAAATC AAAGTC AAAATA AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
28356518 ATGAAAAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.11, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:28358994 original size:22 final size:22
Alignment explanation
Indices: 28358968--28359023 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
28358958 AATGTTTTTC
28358968 TTTTCTTCTTTCCGATTCGGTT
1 TTTTCTTCTTTCCGATTCGGTT
* **
28358990 TTTTCTT-TTTTCGATTCTTTT
1 TTTTCTTCTTTCCGATTCGGTT
28359011 TTTTCTTCTTTCC
1 TTTTCTTCTTTCC
28359024 TTTTTGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.04, C:0.21, G:0.07, T:0.68
Consensus pattern (22 bp):
TTTTCTTCTTTCCGATTCGGTT
Found at i:28360554 original size:16 final size:15
Alignment explanation
Indices: 28360533--28360580 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
28360523 GATGGGAATA
28360533 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
28360549 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
28360564 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
28360580 A
1 A
28360581 ATAATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:28360556 original size:24 final size:24
Alignment explanation
Indices: 28360529--28360584 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
28360519 TAATGATGGG
*
28360529 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
28360553 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
28360577 AATAATAA
1 AATAATAA
28360585 TTAATATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:28360563 original size:8 final size:8
Alignment explanation
Indices: 28360529--28360580 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
28360519 TAATGATGGG
*
28360529 AATAATAA
1 AATATTAA
28360537 AATATATAA
1 AATAT-TAA
28360546 AATA-TAA
1 AATATTAA
28360553 AATATTAA
1 AATATTAA
*
28360561 AATATCAA
1 AATATTAA
*
28360569 AATATTAG
1 AATATTAA
28360577 AATA
1 AATA
28360581 ATAATTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:28360756 original size:25 final size:25
Alignment explanation
Indices: 28360707--28360776 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
28360697 TGTACATATA
* * *
28360707 AAAAATAAATACATGATA-A-TATT
1 AAAAATACATACATAATATAGTGTT
**
28360730 AAAAATATGTACATAATATAGTGTT
1 AAAAATACATACATAATATAGTGTT
28360755 AAAAATACATACATAATATAGT
1 AAAAATACATACATAATATAGT
28360777 TAAGATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.38
24 1 0.03
25 23 0.59
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (25 bp):
AAAAATACATACATAATATAGTGTT
Found at i:28360791 original size:22 final size:24
Alignment explanation
Indices: 28360707--28360869 Score: 81
Period size: 23 Copynumber: 6.8 Consensus size: 24
28360697 TGTACATATA
* *
28360707 AAAAATAAATACATGATAATA--TT
1 AAAAATATATACATAAT-ATAGGTT
*
28360730 AAAAATATGTACATAATATAGTGTT
1 AAAAATATATACATAATATAG-GTT
*
28360755 AAAAATACATACATAATATA-GTT
1 AAAAATATATACATAATATAGGTT
* * **
28360778 -AAGATATATACATAAGATAACATGT
1 AAAAATATATACATAATAT-AGGT-T
* * *
28360803 AAAAAAATATATAT-ATATA-ATAT
1 AAAAATATATACATAATATAGGT-T
*
28360826 AAAAGATATATAAATAA-ATA-GTAT
1 AAAA-ATATATACATAATATAGGT-T
* *
28360850 AAATATATATACGTAATATA
1 AAAAATATATACATAATATA
28360870 AAATTTAAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
22 18 0.16
23 35 0.32
24 22 0.20
25 25 0.23
26 10 0.09
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (24 bp):
AAAAATATATACATAATATAGGTT
Found at i:28360935 original size:45 final size:44
Alignment explanation
Indices: 28360804--28360935 Score: 117
Period size: 45 Copynumber: 2.9 Consensus size: 44
28360794 ATAACATGTA
* *
28360804 AAAAAATATATAT-ATATAATATAAAAGATATATAAATAA-ATAGT
1 AAAAAATATATATAATATAATAT-TAAGAAATAT-AATAATATAGT
* * * * *
28360848 ATAAATATATATACGTAATATAAAATTTA-AAATATACCTAATATATT
1 A-AAAAATATATA--TAATATAATATTAAGAAATATA-ATAATATAGT
28360895 AAAAGAATATATATAATATAATATTAAGAAATATAATAATA
1 AAAA-AATATATATAATATAATATTAAGAAATATAATAATA
28360936 ACAAAAAAAG
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
44 1 0.01
45 28 0.41
46 18 0.26
47 14 0.20
48 8 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (44 bp):
AAAAAATATATATAATATAATATTAAGAAATATAATAATATAGT
Found at i:28361507 original size:30 final size:30
Alignment explanation
Indices: 28361414--28361588 Score: 219
Period size: 30 Copynumber: 5.8 Consensus size: 30
28361404 TAGGTACAAG
* *
28361414 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
28361444 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
*
28361474 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* * *
28361504 TGGTGGTGGAAAATGAGTAGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
28361534 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
28361564 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
28361589 TGAGAAAAGT
Statistics
Matches: 127, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
29 2 0.02
30 125 0.98
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:28362460 original size:163 final size:170
Alignment explanation
Indices: 28362279--28362781 Score: 513
Period size: 177 Copynumber: 2.9 Consensus size: 170
28362269 GTTGATTCTT
* * * ** *
28362279 TTGAAAAGCAGAAATTGAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCGCAA-A-
1 TTGAAAAGCAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAG
* * *
28362342 AG-TAGA-TTTTG-A-AAA-T-ACCT-CGACA-TGTGAACCCAAGGCTCAACTCACATCTCGCAA
66 AGTTA-ATTTTTGAAGAAATTAAACTACCACAGCGTG-ACCCAAGGCTCAACTCACATCTCGCAA
28362399 TATGAGTTGATTTTTGAAAAATATAAATTAAAAAAAACAGAAA
129 TATGAGTTGATTTTTGAAAAATATAAATT-AAAAAAACAGAAA
28362442 TTGAAAAGCAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAGCAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATA-
* * * * * *
28362507 GAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTT
65 GAGTTAATTTTTG----A-AGAAATT-AAACTACCACAGCGTGACCCAAGGCTCAACTCACATCT
*
28362572 CGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAA
124 CGCAATATGAGTTGATTTTTGAAAAATATAAATTAAAAAAACAGAAA
* * *
28362619 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATAT
1 TTGAAAAGCAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATA-
* * * *
28362684 GAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCA
65 GAGTT-A-ATTTTTG----A-AGAAATT--AAACTACCACAGCGTG--ACCCAAGGCTCAACTCA
*
28362749 CCTCTCGCAATATGAGTTGATTTTTTGAAAAAT
119 CATCTCGCAATATGAGTTGA-TTTTTGAAAAAT
28362782 TGAAATTGAA
Statistics
Matches: 291, Mismatches: 26, Indels: 26
0.85 0.08 0.08
Matches are distributed among these distances:
163 56 0.19
164 1 0.00
166 3 0.01
167 7 0.02
173 1 0.00
174 3 0.01
175 1 0.00
177 81 0.28
178 56 0.19
179 22 0.08
180 15 0.05
182 33 0.11
183 12 0.04
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (170 bp):
TTGAAAAGCAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAG
AGTTAATTTTTGAAGAAATTAAACTACCACAGCGTGACCCAAGGCTCAACTCACATCTCGCAATA
TGAGTTGATTTTTGAAAAATATAAATTAAAAAAACAGAAA
Found at i:28362463 original size:14 final size:14
Alignment explanation
Indices: 28362431--28362463 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28362421 ATAAATTAAA
*
28362431 AAAAACAGAAATTG
1 AAAAGCAGAAATTG
28362445 AAAAGCAGAAATTG
1 AAAAGCAGAAATTG
28362459 AAAAG
1 AAAAG
28362464 ACCTCAGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAAGCAGAAATTG
Found at i:28362575 original size:73 final size:73
Alignment explanation
Indices: 28362442--28362610 Score: 223
Period size: 73 Copynumber: 2.3 Consensus size: 73
28362432 AAAACAGAAA
*
28362442 TTGAAAAGCAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAA-CAGAAATTGAAAAGACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATAT
28362507 GAGTTAATTT
64 GAGTTAATTT
** * *
28362517 TTGACAAACAGAAATTGAAATTACCTCAGC-GTGTCCCGAGGCTCAACTCACCTTTCGCAATATG
1 TTGA-AAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
*
28362581 AGTTGATTT
65 AGTTAATTT
* *
28362590 TTGAAAAATATAAATTGAAAA
1 TTG-AAAACAGAAATTGAAAA
28362611 AACAGAAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
73 55 0.66
74 1 0.01
75 24 0.29
76 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (73 bp):
TTGAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTAATTT
Found at i:28362609 original size:14 final size:14
Alignment explanation
Indices: 28362590--28362639 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
28362580 GAGTTGATTT
* *
28362590 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
28362604 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
28362619 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
28362633 TT-AAAAA
1 TTGAAAAA
28362640 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:28362674 original size:177 final size:181
Alignment explanation
Indices: 28362372--28362793 Score: 683
Period size: 177 Copynumber: 2.3 Consensus size: 181
28362362 CGACATGTGA
* *
28362372 ACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTAAAAAAAAC
1 ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATT-GAAAAAAC
* * *
28362437 AGAAATTGAAAAGCAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGC
65 AGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCAC
*
28362502 AATATGAGTT-A-ATTTTTGACAAACAGAAATTG-AAATTACCTCAGCGTGT
130 AATATGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
* *
28362551 -CCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACA
1 ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACA
28362615 GAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACA
66 GAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACA
*
28362680 ATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
131 ATATGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
*
28362731 AAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAT-TGAAATTGAAAA
1 -ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAT-AAATTGAAAA
28362794 CACCTCAGCA
Statistics
Matches: 224, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
177 79 0.35
178 53 0.24
179 20 0.09
180 16 0.07
182 34 0.15
183 22 0.10
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (181 bp):
ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACA
GAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACA
ATATGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
Found at i:28362749 original size:78 final size:75
Alignment explanation
Indices: 28362619--28362860 Score: 307
Period size: 78 Copynumber: 3.2 Consensus size: 75
28362609 AAAACAGAAA
* * * *
28362619 TTGAAAAGCAGAAATT-AAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGT-AGCC-AGGCTCAACTCACCTCTCGCAATA
28362683 TGAGTTGATTTTT
64 TGAGTTGA-TTTT
* * *
28362696 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGT-AGCC-AGGCTCAACTCACCTCTCGCAATA
28362761 TGAGTTGATTTT
64 TGAGTTGATTTT
**
28362773 TTGAAAAATTGAAATTG-AAAACACCTCAGCATGT-G--AGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGTAGCCAGGCTCAACTCACCTCTCGCAATATG
28362834 AGTTGA-TTT
66 AGTTGATTTT
*
28362843 TTGAAAAACATAAATTGA
1 TTGAAAAACAGAAATTGA
28362861 GCAGAAATTG
Statistics
Matches: 147, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
70 17 0.12
71 32 0.22
74 1 0.01
76 15 0.10
77 32 0.22
78 50 0.34
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAAACACCTCAGCATGTAGCCAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTT
Found at i:28362812 original size:71 final size:71
Alignment explanation
Indices: 28362629--28363003 Score: 292
Period size: 71 Copynumber: 4.9 Consensus size: 71
28362619 TTGAAAAGCA
* * *
28362629 GAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTT
1 GAAATTGAAAATACCTCAGCATGTGA---G-G-CTCAACTCACCTCTCGCAATATGAGTTGA-TT
* **
28362694 TTTTGACAAACA
60 TTTTGAAAAATT
*
28362706 GAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 GAAATTG-AAAATACCTCAGCATGT--G---AGGCTCAACTCACCTCTCGCAATATGAGTTGATT
28362771 TTTTGAAAAATT
60 TTTTGAAAAATT
*
28362783 GAAATTGAAAACACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGA
1 GAAATTGAAAATACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-
28362847 AAAACATAAATT
65 ---A-A-AAATT
** * *
28362859 GAGCAGAAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGA
1 -----GAAATTGAAAATACCTC-A-GCAT-GTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
**
28362924 TTTTTTG-ATGA-T
58 TTTTTTGAAAAATT
* * *
28362936 -AAATTGAAAATACCTCAATGTGACT-TGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTT
1 GAAATTGAAAATACCTC-A-G-CA-TGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
28362999 TTGAA
62 TTGAA
28363004 TTAAAACAGA
Statistics
Matches: 255, Mismatches: 19, Indels: 53
0.78 0.06 0.16
Matches are distributed among these distances:
70 6 0.02
71 91 0.36
72 2 0.01
73 1 0.00
74 2 0.01
75 1 0.00
76 20 0.08
77 25 0.10
78 44 0.17
79 2 0.01
80 2 0.01
81 16 0.06
82 1 0.00
83 3 0.01
84 33 0.13
85 6 0.02
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (71 bp):
GAAATTGAAAATACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA
AAAATT
Found at i:28362965 original size:155 final size:157
Alignment explanation
Indices: 28362741--28363093 Score: 452
Period size: 155 Copynumber: 2.2 Consensus size: 157
28362731 AAGCCAAGGC
28362741 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAACACCTCAGCATG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAACACCTCAGCATG
* * *
28362806 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-A-AAAACATAAATTG-AGCAGAA
66 TGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATAAAACAGAAATTGAAACAGAA
* * *
28362867 ATTGAAAATACCTCAACGGGTCTTGAGGT
131 ATGGAAAACACCTC-A-GCGTCTTGAGGT
** * *
28362896 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-ATGA-T-AAATTGAAAATACCTCAATGTG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAACACCTC-A-G-C
*
28362958 ACT-TGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAA
63 A-TGTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAA-TAAAACAGAAATTG-AA
*
28363022 ATAGAAATGGAAAACACCTCAGCGTCTTGAGGT
125 ACAGAAATGGAAAACACCTCAGCGTCTTGAGGT
*
28363055 TCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAA
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA
28363094 CACATAAATT
Statistics
Matches: 172, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
152 15 0.09
153 2 0.01
154 3 0.02
155 68 0.40
156 7 0.04
157 1 0.01
159 50 0.29
160 8 0.05
161 18 0.10
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (157 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAACACCTCAGCATG
TGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATAAAACAGAAATTGAAACAGAA
ATGGAAAACACCTCAGCGTCTTGAGGT
Found at i:28363319 original size:77 final size:75
Alignment explanation
Indices: 28363159--28363574 Score: 391
Period size: 77 Copynumber: 5.4 Consensus size: 75
28363149 TGGCCCGAGA
*
28363159 CTCAACTCACCTCTCGCAATATGAGTTGATTCTTTT-AAAAAGAAAAAATTGAAAATACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA-AAAAAATTGAAAATACCTCAGC
**
28363223 GTGTCCCAAGG
65 GTGTCCTGAGG
* * * * *
28363234 TTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGATAAAAATAGAATTTGAAAATATCTCAG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAAAA-AAAAATTGAAAATACCTCAG
28363299 CGTGTCCTGAGG
64 CGTGTCCTGAGG
* * * * *
28363311 CTCAACTCACCTTTCGCAATATGAATTGA--TTTTTGACAAACAAAAATTGAAATTACCTCAGC-
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAAAAATTGAAAATACCTCAGCG
*
28363373 -GTCTTGAGG
66 TGTCCTGAGG
* * *
28363382 CTTAACTCACTTCTCGTAATATGAGTTGATTTTTTTTGAAACATAAATTAAAAAACGAAAATTGA
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTG--------A--AAAAAA--AAAATTGA
*
28363447 AAATACCTCAGTGTGTCCTGAGG
53 AAATACCTCAGCGTGTCCTGAGG
** *
28363470 CTCAACTCACCTCTCGCAATATGAGTTGA---AATT-AAAACACAAAAATTGAAAATACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA-AAAAAAATTGAAAATACCTCAGC
* *
28363531 GTGCCCCGAGG
65 GTGTCCTGAGG
* *
28363542 CTCAACTCACCTCTTGCAATATGAGCTGATTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
28363575 GAAAAAGTAG
Statistics
Matches: 276, Mismatches: 41, Indels: 48
0.76 0.11 0.13
Matches are distributed among these distances:
71 32 0.12
72 55 0.20
73 20 0.07
74 11 0.04
75 41 0.15
76 2 0.01
77 56 0.20
82 1 0.00
84 6 0.02
86 18 0.07
88 34 0.12
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (75 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAAAAATTGAAAATACCTCAGCG
TGTCCTGAGG
Found at i:28363381 original size:416 final size:415
Alignment explanation
Indices: 28362740--28363494 Score: 940
Period size: 416 Copynumber: 1.8 Consensus size: 415
28362730 TAAGCCAAGG
***
28362740 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAACACCTCAGCAT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAAAATTGAAAACACCTCAGCAT
* *
28362805 GTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAGCAGAAATT
66 GTAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATT--G-AGAAATT
* * * **
28362870 GAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGA
128 GAAAATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTGAACA
* *
28362935 TAAATTGAAAATACCTCAATGTGACTTGAGG-TTCAACTCACCTCTCACAATATGAGTTGATTTT
193 AAAATTGAAAATACCTCAATGCGACTTGAGGCTT-AACTCACCTCTCACAATATGAGTTGATTTT
* * *
28362999 TTGAATTAAAACAGAAATTGAAAATA-G-AAATGGAAAACACCTCA-GCGTCTTGAGGTTCAACT
257 TT---TTAAAACAGAAATT-AAAAAACGAAAATGGAAAACACCTCAGGCGTCCTGAGGCTCAACT
28363061 CACCTCTCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAGAAATTCAAAATA
318 CACCTCTCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAGAAATTCAAAATA
28363126 GAATTTGAAAGGACCTCGACGTGTGGCCCGAGA
383 GAATTTGAAAGGACCTCGACGTGTGGCCCGAGA
*
28363159 CTCAACTCACCTCTCGCAATATGAGTTGATTCTTTT-AAAAAGAAAAAATTGAAAATACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATT-TTTTGAAAAA-AAAAAATTGAAAACACCTCAGC
* * *** * *
28363223 GTGTCCCAAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGATA-A-AAA-T-AGAAT
64 ATGT---AAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATTGAGAAA
* * * *
28363284 TTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTTTCGCAATATGAATTGA-TTTTTGAC
126 TTGAAAATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTG--
* * * **
28363348 AAACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGCTTAACTCACTTCTCGTAATATGAGTTGA
189 -AACAAAAATTGAAAATACCTCAATGCGACTTGAGGCTTAACTCACCTCTCACAATATGAGTTGA
* * * * *
28363411 TTTTTTTTGAAACATAAATTAAAAAACGAAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAAC
253 TTTTTTTTAAAACAGAAATTAAAAAACGAAAATGGAAAACACCTCAG-GCGTCCTGAGGCTCAAC
28363476 TCACCTCTCGCAATATGAG
317 TCACCTCTCGCAATATGAG
28363495 TTGAAATTAA
Statistics
Matches: 286, Mismatches: 37, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
412 5 0.02
413 13 0.05
414 15 0.05
415 6 0.02
416 124 0.43
417 3 0.01
418 17 0.06
419 36 0.13
420 26 0.09
421 3 0.01
422 1 0.00
423 37 0.13
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (415 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAAAATTGAAAACACCTCAGCAT
GTAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATTGAGAAATTGAA
AATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTGAACAAAA
ATTGAAAATACCTCAATGCGACTTGAGGCTTAACTCACCTCTCACAATATGAGTTGATTTTTTTT
AAAACAGAAATTAAAAAACGAAAATGGAAAACACCTCAGGCGTCCTGAGGCTCAACTCACCTCTC
GCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAGAAATTCAAAATAGAATTTGA
AAGGACCTCGACGTGTGGCCCGAGA
Found at i:28363542 original size:72 final size:72
Alignment explanation
Indices: 28363426--28363566 Score: 228
Period size: 72 Copynumber: 2.0 Consensus size: 72
28363416 TTTGAAACAT
* * * *
28363426 AAATTAAAAAACGAAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
1 AAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
28363491 TGAGTTG
66 TGAGTTG
* *
28363498 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATA
1 AAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
28363563 TGAG
66 TGAG
28363567 CTGATTTTGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (72 bp):
AAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
TGAGTTG
Found at i:28363589 original size:159 final size:154
Alignment explanation
Indices: 28363108--28363593 Score: 454
Period size: 159 Copynumber: 3.1 Consensus size: 154
28363098 TAAATTAAAA
* * * ** * *
28363108 AAAAAGAAATTCAAAATAGAATTTGAAAGGACCTC-GACGTGTGGCCCGAGACTCAACTCACCTC
1 AAAATGAAATTAAAAATAGAAATTGAAAATACCTCAG-CGTGT--CCTGAGGCTCAACTCACCTC
* * *
28363172 TCGCAATATGAGTTGATTCTTTTAAAAAGAAAAAATTGAAAATACCTCAGCGTGTCCCAAGGTTC
63 TCGCAATATGAGTTGA-T-TTTTAAAAA-CAAAAATTGAAAATACCTCAGCGTG-CCCGAGGCTC
*
28363237 AACTCACCTCTCACAATATGAGTTGATTTT-
124 AACTCACCTCTCGCAATATGAGTTGATTTTG
** * * *
28363267 --TTTG--A-TAAAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTTTCG
1 AAAATGAAATTAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
* * * ** *
28363327 CAATATGAATTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGT-CTTGAGGCTTAACTCA
66 CAATATGAGTTGATTTTT-AAAAACAAAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCA
* *
28363391 CTTCTCGTAATATGAGTTGATTTTTTTTG
130 CCTCTCGCAATATGAGTTGA----TTTTG
*
28363420 AAACAT-AAATTAAAAA-ACGAAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTC
1 AAA-ATGAAATTAAAAATA-G-AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
**
28363483 TCGCAATATGAGTTGA-AATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAA
63 TCGCAATATGAGTTGATTTTTAAAA-ACAAAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAA
* *
28363547 CTCACCTCTTGCAATATGAGCTGATTTTG
126 CTCACCTCTCGCAATATGAGTTGATTTTG
28363576 AAAAAGTAGAAATTAAAA
1 -AAAA-T-GAAATTAAAA
28363594 GGTTCAACCC
Statistics
Matches: 265, Mismatches: 40, Indels: 44
0.76 0.11 0.13
Matches are distributed among these distances:
148 28 0.11
150 26 0.10
151 5 0.02
152 36 0.14
154 26 0.10
155 2 0.01
156 7 0.03
157 10 0.04
158 33 0.12
159 63 0.24
160 29 0.11
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (154 bp):
AAAATGAAATTAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
CAATATGAGTTGATTTTTAAAAACAAAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCAC
CTCTCGCAATATGAGTTGATTTTG
Found at i:28363956 original size:72 final size:73
Alignment explanation
Indices: 28363720--28364083 Score: 333
Period size: 72 Copynumber: 4.8 Consensus size: 73
28363710 AGTGTGTAAT
* * * * *
28363720 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAAAATAGAAATTGAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA----TATTTT--GAAAACAGAAATTGAAAA
*
28363785 TACCTCAGCATGTGAAC
60 TACCTCAGC--GTG-TC
*
28363802 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-----TATTTTGAAAACAGAAATTGAAAAT
*
28363866 ACCTCAACGTGTC
61 ACCTCAGCGTGTC
* ** *
28363879 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTGAAAACAGAAATTGAAAATACCTC
*
28363943 AGTGTGTC
66 AGCGTGTC
** * * * *
28363951 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TATTTTGAA-AACAGAAATTGAAAATAC
28364016 CTCAGCGTGTC
63 CTCAGCGTGTC
* * *
28364027 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG--ATTTTGAAAAACAAAAATT-AAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTG-AAAACAGAAATTGAAAA
28364084 GGCTTAACTC
Statistics
Matches: 250, Mismatches: 25, Indels: 25
0.83 0.08 0.08
Matches are distributed among these distances:
71 3 0.01
72 79 0.32
73 2 0.01
75 6 0.02
76 59 0.24
77 1 0.00
78 34 0.14
80 24 0.10
81 31 0.12
82 11 0.04
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (73 bp):
CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTGAAAACAGAAATTGAAAATACCTC
AGCGTGTC
Found at i:28364031 original size:76 final size:76
Alignment explanation
Indices: 28363720--28364065 Score: 414
Period size: 76 Copynumber: 4.5 Consensus size: 76
28363710 AGTGTGTAAT
* *
28363720 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAAAATAGAAATTGAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTT--AAAAACAGAAATTGAAAA
*
28363785 TACCTCAGCATGTGAAC
63 TACCTCAGC--GTG-TC
* *
28363802 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTTAAAAACAGAAATTGAAAAT
*
28363866 ACCTCAACGTGTC
64 ACCTCAGCGTGTC
* ** * * * *
28363879 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA----ATTTTGAAAACAGAAATTGAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATAC
*
28363940 CTCAGTGTGTC
66 CTCAGCGTGTC
** * *
28363951 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATAC
28364016 CTCAGCGTGTC
66 CTCAGCGTGTC
*
28364027 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
28364066 GAAAAACAAA
Statistics
Matches: 236, Mismatches: 22, Indels: 18
0.86 0.08 0.07
Matches are distributed among these distances:
72 66 0.28
76 69 0.29
77 1 0.00
78 34 0.14
80 24 0.10
81 31 0.13
82 11 0.05
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (76 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATAC
CTCAGCGTGTC
Found at i:28364052 original size:148 final size:150
Alignment explanation
Indices: 28363767--28364083 Score: 421
Period size: 148 Copynumber: 2.1 Consensus size: 150
28363757 TTTTTTTTAA
*
28363767 AAAAATAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAG-ATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAG
* **
28363832 TTGATTTTTTTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTT
65 TTGA-TTTTTTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCT
*
28363897 CTCGCAATATAAGTTGAATTTTG
129 CTAGCAATATAAGTTG-ATTTTG
* * ** *
28363920 -AAAACAGAAATTGAAATTACCTCAG-TGTG-TCCTGAGGCTCAACTCATTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGATGTGAACC-GAGGCTCAACTCACCTCTCGCAATATAAG
* *
28363982 TTGA-TTTTTTTTT-AACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
65 TTGATTTTTTTTTTGAA-AACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCT
*
28364045 CTAGCAATATGAGTTGATTTTG
129 CTAGCAATATAAGTTGATTTTG
*
28364067 AAAAACAAAAATT-AAAA
1 AAAAACAGAAATTGAAAA
28364084 GGCTTAACTC
Statistics
Matches: 146, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
147 11 0.08
148 76 0.52
149 2 0.01
150 34 0.23
152 23 0.16
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (150 bp):
AAAAACAGAAATTGAAAATACCTCAGATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGT
TGATTTTTTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
AGCAATATAAGTTGATTTTG
Found at i:28369523 original size:12 final size:12
Alignment explanation
Indices: 28369506--28369532 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28369496 TCGACTGTGA
28369506 CCAAACAGCCAT
1 CCAAACAGCCAT
28369518 CCAAACAGCCAT
1 CCAAACAGCCAT
28369530 CCA
1 CCA
28369533 TGATGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.44, G:0.07, T:0.07
Consensus pattern (12 bp):
CCAAACAGCCAT
Found at i:28372584 original size:4 final size:4
Alignment explanation
Indices: 28372538--28372573 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
28372528 TGGGATATGC
* *
28372538 AATG TATG AATG AATG CATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG
28372574 TCAAATGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (4 bp):
AATG
Found at i:28374172 original size:21 final size:22
Alignment explanation
Indices: 28374148--28374192 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28374138 TGATGGGAAT
28374148 AATA-AAATATATC-AAATATCA
1 AATATAAA-ATATCAAAATATCA
*
28374169 AATATCAAATATCAAAATATCA
1 AATATAAAATATCAAAATATCA
28374191 AA
1 AA
28374193 ATATTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (22 bp):
AATATAAAATATCAAAATATCA
Found at i:28374196 original size:8 final size:7
Alignment explanation
Indices: 28374156--28374192 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
28374146 ATAATAAAAT
28374156 ATATCAA
1 ATATCAA
28374163 ATATCAA
1 ATATCAA
28374170 ATATCAA
1 ATATCAA
28374177 ATATCAAA
1 ATATC-AA
28374185 ATATCAA
1 ATATCAA
28374192 A
1 A
28374193 ATATTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (7 bp):
ATATCAA
Found at i:28374369 original size:23 final size:22
Alignment explanation
Indices: 28374318--28374371 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
28374308 ATACTACATC
28374318 AATATGTACATAT-ATA--AAA
1 AATATGTACATATAATATTAAA
**
28374337 AATAAATACATGATAATATTAAA
1 AATATGTACAT-ATAATATTAAA
28374360 AATATGTACATA
1 AATATGTACATA
28374372 ATATAGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 3 0.11
22 1 0.04
23 12 0.44
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AATATGTACATATAATATTAAA
Found at i:28374418 original size:22 final size:24
Alignment explanation
Indices: 28374334--28374419 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
28374324 TACATATATA
* *
28374334 AAAAATAAATACATGATAATA--TT
1 AAAAATATATACATAAT-ATAGGTT
*
28374357 AAAAATATGTACATAATATAGTGTT
1 AAAAATATATACATAATATAG-GTT
*
28374382 AAAAATACATACATAATATA-GTT
1 AAAAATATATACATAATATAGGTT
*
28374405 -AAGATATATACATAA
1 AAAAATATATACATAA
28374420 GATAACATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
22 16 0.30
23 17 0.32
25 20 0.38
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAATATATACATAATATAGGTT
Found at i:28374444 original size:30 final size:29
Alignment explanation
Indices: 28374408--28374474 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
28374398 TATAGTTAAG
*
28374408 ATATATACATAAGATAACATGTAAAAATAT
1 ATATATAAATAAGATAACAT-TAAAAATAT
* * *
28374438 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAAATAT
28374467 ATA-ATAAA
1 ATATATAAA
28374475 ATAGTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 5 0.15
29 11 0.33
30 17 0.52
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAAATAT
Found at i:28374466 original size:29 final size:30
Alignment explanation
Indices: 28374408--28374483 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
28374398 TATAGTTAAG
* *
28374408 ATATATACATAAGATAACATGTAAAAATAT
1 ATATATAAATAATATAACATGTAAAAATAT
* *
28374438 ATATATAAATAATATAATAT-TAAAGATAT
1 ATATATAAATAATATAACATGTAAAAATAT
*
28374467 ATA-ATAAAATAGTATAA
1 ATATAT-AAATAATATAA
28374484 ATATATATAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 2 0.05
29 21 0.52
30 17 0.43
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (30 bp):
ATATATAAATAATATAACATGTAAAAATAT
Found at i:28374565 original size:23 final size:24
Alignment explanation
Indices: 28374349--28374567 Score: 87
Period size: 23 Copynumber: 9.0 Consensus size: 24
28374339 TAAATACATG
28374349 ATAATATTAA-AAATATGTACATAAT
1 ATAATATTAAGAAATA--TACATAAT
* *
28374374 ATAGTGTTAA-AAATACATACATAAT
1 ATAATATTAAGAAAT--ATACATAAT
* * *
28374399 AT-A-GTTAAGATATATACATAAG
1 ATAATATTAAGAAATATACATAAT
* * *
28374421 ATAACATGTAAAAATATATATATAAATAAT
1 ATAATAT-T---AAGA-A-ATATACATAAT
* *
28374451 ATAATATTAAAGATATATA-ATAAA
1 ATAATATT-AAGAAATATACATAAT
* * * * *
28374475 ATAGTATAAATATATATACGTAAT
1 ATAATATTAAGAAATATACATAAT
* * *
28374499 ATAAAATTTA-AAATATACCTAAT
1 ATAATATTAAGAAATATACATAAT
* * *
28374522 ATATTA-AAAG-AATATATATAAT
1 ATAATATTAAGAAATATACATAAT
28374544 ATAATATTAAGAAATATA-ATAAT
1 ATAATATTAAGAAATATACATAAT
28374567 A
1 A
28374568 ACAAAAAAAG
Statistics
Matches: 146, Mismatches: 33, Indels: 32
0.69 0.16 0.15
Matches are distributed among these distances:
22 26 0.18
23 39 0.27
24 29 0.20
25 28 0.19
27 5 0.03
28 3 0.02
29 1 0.01
30 15 0.10
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (24 bp):
ATAATATTAAGAAATATACATAAT
Found at i:28375140 original size:30 final size:29
Alignment explanation
Indices: 28375047--28375191 Score: 173
Period size: 30 Copynumber: 4.8 Consensus size: 29
28375037 TAGGTACAAG
*
28375047 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAG-AAGTGTGGCTAGTGGAGT
* ** *
28375077 AGGTAATGGAGCAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAG-AAGTGTGGCTAGTGGAGT
28375107 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGAA-GTGTGGCTAGTGGAGT
* *
28375137 TGGTGGTGGAAAATGAGTGGCTAGTGGAGT
1 TGGTGGTGGAGAA-GTGTGGCTAGTGGAGT
*
28375167 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAGAA-GTGTGGCTAGT
28375192 TGAGAAAAGT
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 2 0.02
30 98 0.98
ACGTcount: A:0.21, C:0.04, G:0.48, T:0.28
Consensus pattern (29 bp):
TGGTGGTGGAGAAGTGTGGCTAGTGGAGT
Found at i:28376962 original size:27 final size:28
Alignment explanation
Indices: 28376932--28376990 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
28376922 CATCCTAAGA
**
28376932 TAGTCT-GACGGGACGTTAAACACGAGG
1 TAGTCTCGACGGGACACTAAACACGAGG
**
28376959 TAGT-TCGACGGGACACTAAACGTGAGG
1 TAGTCTCGACGGGACACTAAACACGAGG
28376986 TAGTC
1 TAGTC
28376991 CATCTTGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.20
Consensus pattern (28 bp):
TAGTCTCGACGGGACACTAAACACGAGG
Found at i:28380167 original size:17 final size:18
Alignment explanation
Indices: 28380137--28380181 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
28380127 GGTTTTTGGA
*
28380137 TTTTAGGG--TTTAAGGT
1 TTTTAGGGTTTTTAAGAT
28380153 TTTT-GGGTTTTTAAGAT
1 TTTTAGGGTTTTTAAGAT
28380170 TTTTAGGGTTTT
1 TTTTAGGGTTTT
28380182 GGAGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 4 0.16
17 11 0.44
18 7 0.28
ACGTcount: A:0.16, C:0.00, G:0.27, T:0.58
Consensus pattern (18 bp):
TTTTAGGGTTTTTAAGAT
Found at i:28381224 original size:31 final size:30
Alignment explanation
Indices: 28381188--28381259 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
28381178 ATTATATACG
28381188 AATTTTAATTTAATGTGCAATATCACACAT-A
1 AATTTTAATTTAATGT--AATATCACACATGA
* * * * *
28381219 AATTTTGATTTTATGTAATTTTATACATGA
1 AATTTTAATTTAATGTAATATCACACATGA
28381249 AATTTTAATTT
1 AATTTTAATTT
28381260 GATTTAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 9 0.26
30 11 0.32
31 14 0.41
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (30 bp):
AATTTTAATTTAATGTAATATCACACATGA
Found at i:28381253 original size:30 final size:29
Alignment explanation
Indices: 28381214--28381270 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
28381204 GCAATATCAC
* *
28381214 ACATAAATTTTGATTTTATGTAATTTTAT
1 ACATAAATTTTAATTTGATGTAATTTTAT
*
28381243 ACATGAAATTTTAATTTGATTTAATTTT
1 ACAT-AAATTTTAATTTGATGTAATTTT
28381271 CAAAAATCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (29 bp):
ACATAAATTTTAATTTGATGTAATTTTAT
Found at i:28387705 original size:21 final size:21
Alignment explanation
Indices: 28387690--28387738 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
28387680 TTTATTTATT
28387690 AAAATAATAATTTTATAAATA
1 AAAATAATAATTTTATAAATA
*
28387711 AAAATAATAGTTTTATAAAT-
1 AAAATAATAATTTTATAAATA
28387731 AAAATAAT
1 AAAATAAT
28387739 TTAAGGGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAATAATAATTTTATAAATA
Found at i:28388264 original size:16 final size:15
Alignment explanation
Indices: 28388228--28388271 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
28388218 TGTTTGTGAG
*
28388228 TTTTTTATAAAAATAT
1 TTTTTTAT-AAATTAT
28388244 TTTTTTATAAATTAT
1 TTTTTTATAAATTAT
*
28388259 TATTTTAATAAAT
1 T-TTTTTATAAAT
28388272 AAATTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTTATAAATTAT
Found at i:28388766 original size:15 final size:15
Alignment explanation
Indices: 28388730--28388772 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28388720 AATCCTTACT
28388730 TTTTTTATTTAATTTA
1 TTTTTTATTT-ATTTA
*
28388746 -TATTTATTTATTTA
1 TTTTTTATTTATTTA
*
28388760 TTTTTTATCTATT
1 TTTTTTATTTATT
28388773 AAACAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTATTTATTTA
Found at i:28388772 original size:19 final size:19
Alignment explanation
Indices: 28388733--28388772 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28388723 CCTTACTTTT
*
28388733 TTTATTTAATTTATATTTA
1 TTTATTTAATTTATATCTA
* *
28388752 TTTATTTATTTTTTATCTA
1 TTTATTTAATTTATATCTA
28388771 TT
1 TT
28388773 AAACAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTAATTTATATCTA
Found at i:28389672 original size:26 final size:26
Alignment explanation
Indices: 28389640--28389693 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
28389630 CAAGTTGTTT
* * *
28389640 AAAATATTATAATGGATTCTTTAAAA
1 AAAATATTAGAATGAATTATTTAAAA
*
28389666 AAAATATTAGAATTAATTATTTAAAA
1 AAAATATTAGAATGAATTATTTAAAA
28389692 AA
1 AA
28389694 TCAAGATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
AAAATATTAGAATGAATTATTTAAAA
Found at i:28391667 original size:23 final size:22
Alignment explanation
Indices: 28391607--28391667 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
28391597 ATCAGTATAT
28391607 GACACAT-AAGTGCCT-AAAAC
1 GACACATAAAGTGCCTGAAAAC
* * * *
28391627 AACACACAAGGTGTCTGAAATAC
1 GACACATAAAGTGCCTGAAA-AC
28391650 GACACATAAAGTGCCTGA
1 GACACATAAAGTGCCTGA
28391668 TCGGCAAAGC
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 5 0.17
21 6 0.20
22 3 0.10
23 16 0.53
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (22 bp):
GACACATAAAGTGCCTGAAAAC
Found at i:28392775 original size:18 final size:19
Alignment explanation
Indices: 28392754--28392789 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
28392744 ATTATTTATC
28392754 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
28392772 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
28392790 TATACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:28392798 original size:19 final size:18
Alignment explanation
Indices: 28392758--28392800 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
28392748 TTTATCTAAT
*
28392758 AAATATCTTTTAAATAAT
1 AAATATCTTTTAAATAAC
28392776 AAATATCTATTT-AATATAC
1 AAATATCT-TTTAAATA-AC
28392795 AAATAT
1 AAATAT
28392801 AAATATTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATCTTTTAAATAAC
Found at i:28403204 original size:19 final size:19
Alignment explanation
Indices: 28403177--28403232 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
28403167 GGAAAGTTCA
28403177 ATATTATTATTTTTAATAT
1 ATATTATTATTTTTAATAT
* *
28403196 ATATAATTATATATTAA-AT
1 ATATTATTAT-TTTTAATAT
*
28403215 ATATTATTATATTTAATA
1 ATATTATTATTTTTAATA
28403233 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.13
19 21 0.70
20 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTATTATTTTTAATAT
Found at i:28409425 original size:16 final size:16
Alignment explanation
Indices: 28409404--28409442 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28409394 AATAATAGAA
28409404 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
28409420 ATATATGAAAGTATGT
1 ATATATAAAAACATGT
28409436 ATATATA
1 ATATATA
28409443 TATAAATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:28410411 original size:17 final size:17
Alignment explanation
Indices: 28410371--28410412 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
28410361 TCAGAAAAGG
28410371 TTTTTTTTTCTCTCTTT
1 TTTTTTTTTCTCTCTTT
* * *
28410388 ATATTTTTTCTTTCTTT
1 TTTTTTTTTCTCTCTTT
28410405 TTTTTTTT
1 TTTTTTTT
28410413 GCAAATGTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTCTCTCTTT
Found at i:28414045 original size:23 final size:22
Alignment explanation
Indices: 28414004--28414051 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 22
28413994 TAAACTTATT
*
28414004 TTTTTATTATCTAAATTTAATA
1 TTTTTATTATCTAAATTTAAAA
28414026 TTTTT-TTATCTAAACCTTTAAAA
1 TTTTTATTATCTAAA--TTTAAAA
28414049 TTT
1 TTT
28414052 CGAGCAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 5 0.22
23 9 0.39
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTATTATCTAAATTTAAAA
Found at i:28419211 original size:23 final size:23
Alignment explanation
Indices: 28419176--28419220 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28419166 TGGAGTATAA
* *
28419176 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
28419199 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
28419221 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Done.