Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2283
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: 183339
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
File 2 of 2
Found at i:145769 original size:19 final size:17
Alignment explanation
Indices: 145745--145838 Score: 96
Period size: 13 Copynumber: 5.8 Consensus size: 17
145735 TAGCTTAAAT
145745 TGTATCGATACAAAACTTA
1 TGTATCGATAC--AACTTA
145764 TGTATCGATAC-A--T-
1 TGTATCGATACAACTTA
145777 TGTATCGATACAACACTTA
1 TGTATCGATAC-A-ACTTA
145796 TGTATCGATAC-A--T-
1 TGTATCGATACAACTTA
145809 TGTATCGATACAACTTA
1 TGTATCGATACAACTTA
145826 TGTATCGATACAA
1 TGTATCGATACAA
145839 ATCGTTGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 22
0.75 0.00 0.25
Matches are distributed among these distances:
13 22 0.34
14 3 0.05
16 4 0.06
17 13 0.20
18 1 0.02
19 22 0.34
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (17 bp):
TGTATCGATACAACTTA
Found at i:145784 original size:32 final size:32
Alignment explanation
Indices: 145743--145837 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
145733 AGTAGCTTAA
145743 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
145775 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
145807 ATTGTATCGATAC--AACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
145837 A
1 A
145838 AATCGTTGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.28
32 44 0.72
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:147519 original size:11 final size:11
Alignment explanation
Indices: 147503--147531 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
147493 GAAAAACAAG
147503 AAATTTGCAAA
1 AAATTTGCAAA
147514 AAATTTGCAAA
1 AAATTTGCAAA
147525 AAATTTG
1 AAATTTG
147532 ATGAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (11 bp):
AAATTTGCAAA
Found at i:151762 original size:15 final size:16
Alignment explanation
Indices: 151742--151776 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
151732 GACAATCTTT
151742 TTTTCAAGA-TTTTTA
1 TTTTCAAGAGTTTTTA
*
151757 TTTTCAATAGTTTTTA
1 TTTTCAAGAGTTTTTA
151773 TTTT
1 TTTT
151777 ATTTTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTTCAAGAGTTTTTA
Found at i:153871 original size:33 final size:32
Alignment explanation
Indices: 153834--153897 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
153824 TACAAGCCAA
*
153834 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
153867 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
153898 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:153872 original size:13 final size:13
Alignment explanation
Indices: 153854--153879 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
153844 CATTTTGGGA
153854 TGTATCGATACAT
1 TGTATCGATACAT
153867 TGTATCGATACAT
1 TGTATCGATACAT
153880 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:153997 original size:13 final size:13
Alignment explanation
Indices: 153979--154003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
153969 ACATTTGGTC
153979 ATGTATCGATACA
1 ATGTATCGATACA
153992 ATGTATCGATAC
1 ATGTATCGATAC
154004 TGTGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:154723 original size:19 final size:20
Alignment explanation
Indices: 154701--154741 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
154691 AAAATTACAA
* *
154701 AAAGTTCCTTAAA-ATGTTT
1 AAAGTGCCTAAAACATGTTT
154720 AAAGTGCCTAAAACATGTTT
1 AAAGTGCCTAAAACATGTTT
154740 AA
1 AA
154742 GCATGCATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (20 bp):
AAAGTGCCTAAAACATGTTT
Found at i:157109 original size:20 final size:20
Alignment explanation
Indices: 157084--157129 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
157074 AGATATATTA
157084 ATACATTGAAAAATGTATCG
1 ATACATTGAAAAATGTATCG
****
157104 ATACATTTTTCAATGTATCG
1 ATACATTGAAAAATGTATCG
157124 ATACAT
1 ATACAT
157130 GTATGAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
ATACATTGAAAAATGTATCG
Found at i:157166 original size:20 final size:20
Alignment explanation
Indices: 157095--157172 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
157085 TACATTGAAA
*
157095 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTCTTC
* *
157115 AATGTATCGATACATGT-ATG
1 AATGTATCGATACAT-TCTTC
* *
157135 AATATATAGATACATTCTTC
1 AATGTATCGATACATTCTTC
157155 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
157173 ATCTTTTGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:160650 original size:55 final size:55
Alignment explanation
Indices: 160566--161779 Score: 1857
Period size: 55 Copynumber: 22.1 Consensus size: 55
160556 GATTCGACAT
*
160566 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* *
160621 AGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCCAGTCCTCAAAG
1 AGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
160676 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
*
160731 AGCAGGACACCTCTT-AAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
*
160785 AGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA--TTTCCAGTCCTCAAAG
1 AGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
*
160839 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* *
160894 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTC-AAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
*
160948 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* *
161003 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
*
161058 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * *
161113 AGCAAGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCCAGTCCTCAAAG
1 AGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
161168 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
*
161223 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * *
161278 AGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCACCTTTCAGTCCCCAGAG
1 AGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * *
161333 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCCCAGAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* *
161388 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTTCAGTCCCCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * *
161443 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCCCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
*
161498 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
* *
161553 AACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAG
1 AGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
*
161608 AGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAG
1 AGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
*
161663 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCATTCCTCAAAG
1 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * * * * *
161718 AGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATG
1 AGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
161773 AGCAGGA
1 AGCAGGA
161780 TACAGTTTAT
Statistics
Matches: 1085, Mismatches: 52, Indels: 44
0.92 0.04 0.04
Matches are distributed among these distances:
53 5 0.00
54 164 0.15
55 896 0.83
56 20 0.02
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.20
Consensus pattern (55 bp):
AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
Found at i:161622 original size:27 final size:27
Alignment explanation
Indices: 161592--161674 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
161582 TTGGTGGCAT
161592 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
161619 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
161647 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
161674 T
1 T
161675 CTTAAAGCCC
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:162289 original size:14 final size:14
Alignment explanation
Indices: 162272--162299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
162262 GATAAAGTGT
162272 TTGAAAAAAAAAAA
1 TTGAAAAAAAAAAA
162286 TTGAAAAAAAAAAA
1 TTGAAAAAAAAAAA
162300 AAAATTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
TTGAAAAAAAAAAA
Found at i:162405 original size:19 final size:19
Alignment explanation
Indices: 162381--162448 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
162371 AATTCAACAA
162381 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
162400 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
162415 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
162432 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
162449 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:162420 original size:13 final size:13
Alignment explanation
Indices: 162402--162426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
162392 ACATAAGTTT
162402 TGTATCGATACAA
1 TGTATCGATACAA
162415 TGTATCGATACA
1 TGTATCGATACA
162427 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:162424 original size:32 final size:32
Alignment explanation
Indices: 162383--162445 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
162373 TTCAACAATT
*
162383 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
162415 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
162446 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:162506 original size:13 final size:13
Alignment explanation
Indices: 162488--162513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
162478 CATTTTTCTG
162488 TGTATCGATACAT
1 TGTATCGATACAT
162501 TGTATCGATACAT
1 TGTATCGATACAT
162514 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:162510 original size:33 final size:33
Alignment explanation
Indices: 162468--162534 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
162458 GCCAAGGAAA
***
162468 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
162501 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
162534 T
1 T
162535 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:164933 original size:51 final size:52
Alignment explanation
Indices: 164860--164993 Score: 150
Period size: 51 Copynumber: 2.6 Consensus size: 52
164850 GTTGAGTTGC
* * *
164860 TCAA-TTCTCCACAATCGAGGATATTCCAACTCCGATTTTACTTTC-AAAACA
1 TCAATTTCTTCACAATCGGGGATATTCCAACTCCGATTTTA-TTCCAAAAACA
* * *
164911 TTAA-TT-TTCTATAATCGGGGATACTCCAACTCCGATTTTATTCCAAAAAACA
1 TCAATTTCTTC-ACAATCGGGGATATTCCAACTCCGATTTTATTCC-AAAAACA
*
164963 TCAATTTCTTCACAATCGGGGACATTCCAAC
1 TCAATTTCTTCACAATCGGGGATATTCCAAC
164994 CCCGTTAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
50 5 0.07
51 32 0.47
52 9 0.13
53 19 0.28
54 3 0.04
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (52 bp):
TCAATTTCTTCACAATCGGGGATATTCCAACTCCGATTTTATTCCAAAAACA
Found at i:165092 original size:51 final size:51
Alignment explanation
Indices: 165034--165206 Score: 211
Period size: 52 Copynumber: 3.4 Consensus size: 51
165024 TTATTTCCGA
* ***
165034 GGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * * *
165085 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTC-ATAATC
* *
165137 GGGGATACTCCAACATCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCTCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
*
165189 GAGGATACTCCAACCTCG
1 GGGGATACTCCAACCTCG
165207 TTATTTCATC
Statistics
Matches: 100, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
51 36 0.36
52 50 0.50
53 14 0.14
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:165222 original size:28 final size:28
Alignment explanation
Indices: 165186--165267 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
165176 ATTTTTCACA
* *
165186 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
165214 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
165242 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
165268 ATCTCCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 42 0.89
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:177739 original size:14 final size:13
Alignment explanation
Indices: 177720--177780 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
177710 TCCTTCTCTC
177720 AAAAAAAAGCAAAA
1 AAAAAAAAG-AAAA
*
177734 AAAAAACA-AAAA
1 AAAAAAAAGAAAA
177746 AAAAAAAAGCAAAA
1 AAAAAAAAG-AAAA
* *
177760 CAAAGAAAGAGAAA
1 AAAAAAAAGA-AAA
177774 AAAAAAA
1 AAAAAAA
177781 TCTGCTTAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 11 0.29
13 1 0.03
14 26 0.68
ACGTcount: A:0.85, C:0.07, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:177753 original size:26 final size:28
Alignment explanation
Indices: 177720--177780 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
177710 TCCTTCTCTC
177720 AAAAAAAAGCAAAA-AAA-AAACAAAAA
1 AAAAAAAAGCAAAACAAAGAAACAAAAA
* *
177746 AAAAAAAAGCAAAACAAAGAAAGAGAAA
1 AAAAAAAAGCAAAACAAAGAAACAAAAA
177774 AAAAAAA
1 AAAAAAA
177781 TCTGCTTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 14 0.45
27 3 0.10
28 14 0.45
ACGTcount: A:0.85, C:0.07, G:0.08, T:0.00
Consensus pattern (28 bp):
AAAAAAAAGCAAAACAAAGAAACAAAAA
Found at i:177759 original size:11 final size:11
Alignment explanation
Indices: 177720--177750 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
177710 TCCTTCTCTC
*
177720 AAAAAAAAGCA
1 AAAAAAAAACA
177731 AAAAAAAAACA
1 AAAAAAAAACA
177742 AAAAAAAAA
1 AAAAAAAAA
177751 AAAGCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.90, C:0.06, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:178989 original size:56 final size:55
Alignment explanation
Indices: 178749--180831 Score: 1746
Period size: 56 Copynumber: 37.8 Consensus size: 55
178739 TCGGCTTTTT
*
178749 AGTCCTC-AAGAGCAGGACACCTCTTAAAGCCTCACACAAGTTGGTGGCA-CTTGC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCC-CACACAAGTTGGTGGCACCTTTC
178803 AGTCCTC-AA-AGCAGGACACCTCTTTAAAGCCCACACAAGTT-GTGGC-CCTTTC
1 AGTCCTCAAAGAGCAGGACACCTC-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * **
178855 AGTCCCCAAAGAGCAGGACA-C-CTTCAAGCCCAC-CCAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
178907 TAGTCCT-AAAG-GCAGGACCCCTCTTAAAGCCC-CACAAGTTGGTGGAAACCTTTC
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG-CACCTTTC
* *
178961 AGTTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACCAGTTGGTGGCAACTTTC
1 AG-TCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
179017 AAGTCCCCAAGGAGAGCA-GACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCC
1 -AGTCCTCAA--AGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
179074 AGTCCTTCAAAAAGAGCAGGACACCTCTTAAATGCCCACACAAGTTGGTGGCACGCTTTC
1 AGTCC-TC--AAAGAGCAGGACACCTCTTAAA-GCCCACACAAGTTGGTGGCAC-CTTTC
*
179134 AGTCCCTC-AAGAGGCAGGACACCTCTTAAAG-CCAGCACAAGTTGGTGGC-CCTTCC
1 AGT-CCTCAAAGA-GCAGGACACCTCTTAAAGCCCA-CACAAGTTGGTGGCACCTTTC
*
179189 AGTCCCTCAAAGAGCAGGAC-CCT-TT-AAGCCCACCCAAGTTGGTGGC-CCATTTGCC
1 AGT-CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTT--C
* *
179244 AGTCCGC-AAG-GCAGGGACACCTCGTAAAGCCCACACAAGTTGGTGGCGACC-TTC
1 AGTCCTCAAAGAGCA-GGACACCTCTTAAAGCCCACACAAGTTGGTGGC-ACCTTTC
* *
179298 CGTCCTCCAAAGAGCAGGACACCTCTTAAAG-CCA-ACAA-TT-GTGGCACCTTCACC
1 AGTCCT-CAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT--TC
* * *
179352 TAGTCCTC-CAGAGCAGGACACCGCTT-AAGCACCACAC-AGTTGGTGGCA-TTTTC
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGC-CCACACAAGTTGGTGGCACCTTTC
* * * *
179405 AGTCCTCAAAGA-CAGAACACCTC-TAAGAGCCCACACAAGTTGGTGTCAGCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAA-AGCCCACACAAGTTGGTGGCACCTTTC
*
179459 AGTCCCTCAAGGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGGCACC-TTC
1 AGT-CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGT-GGCACCTTTC
* * * **
179515 AGTCGCCCAAAGAGCAGAGACACCT-TCAAAG-CCACCCAAGTTGGTGGCATTTTTTTTTTTTCC
1 AGTC-CTCAAAGAGCAG-GACACCTCTTAAAGCCCACACAAGTTGGTGGCA-------CCTTT-C
*
179578 AGTCCTC-AAGAGCAGGACACCTCTTAAAGGCCCA-ACAAGTTGGTGGC-CATTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAA-GCCCACACAAGTTGGTGGCACCTTTC
* * * * * *
179631 AGTCCCCCAAATGAGTA-GAC-CATCTTAAAG-CCACACAAGTTGGTGGCGCCGTCC
1 AGT-CCTCAAA-GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
179685 AGTCCTC-AAGATCAGGACACCTCTTAAAGCCCACACAAGGTTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAA-G-TTGGTGGCACCTTTC
* * *
179741 -GTCC-CAAAGAGCAAGGACACCTCTTTAAATCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGC-AGGACACCTC-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
179796 AGTCCTCCAAAGAGCAGGACACCTCTTAAAAGCACACACAAGTTGGTGGCA-TTTGTCC
1 AGTCCT-CAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-C
* * * * * **
179854 AATCCGC-AAGAACAGGACACCT-TTCAAGCCCACACAAGTTGGGGGCATTTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
179908 AGGCCTC-AA-AGCAGGACAGCCTCTT-AAGCCCACAC-AGTTGGTGGCA--TTTC
1 AGTCCTCAAAGAGCAGGACA-CCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
179958 ATTCCCCAAAGAGCAGGACA-CTTTTCAAGCCCCACACAAGTTGGTGGCACCCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAG-CCCACACAAGTTGGTGGCA-CCTTTC
* * *
180014 AGTACC-CAAAGAGCAGGACACCTC-TAAAGCCCACACAAGTTGGTGGCGCCGTCC
1 AGT-CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
180068 AGTCCTCAAAGAGGCA-GACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGA-GCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
180123 AGTCCCCAAAGAGCAGGACACCTGTCAAAGCCCACCCAAGTTTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAG--TTGGTGGCACCTTTC
180179 AGTCC-CAAAGGAGCAGGACACCTCTT--AG-CCACACAAGTT-GT-GCACCTTTC
1 AGTCCTCAAA-GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
180229 AGGCATCAAAGAGC--GAC-CTTCTTAAAGCCCACAGACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCAC--ACAAGTTGGTGGCACCTTTC
* * *
180283 AGTCCCCAAAGAGCAGGAC-CCT-TTCAAAGCCCAC-CAAG-GGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* * *
180335 AGTCCTCAAAGAGCA-GACAAGCCT-TTAAAAGCCACAAAAAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGAC-A-CCTCTT-AAAGCC-CACACAAGTTGGTGGCACCTTTC
* * * * *
180392 ATTCC-CCAAGAGCAGGACACATCTT-AAGCCCA-ACAAGTTGGTGGCCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG-CACCTTTC
180445 AGTCCTCAAAGAGCA-GACA-CTCTTAAAAAAGCCCACAC-AGTTTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT---AAAGCCCACACAAG-TT-GGTGGCACCTTTC
* * *
180502 AGTCCCCAAAAGAGCAGGACACCTCTTAAAAGCCCACACAAGTT-GTGGCGCCTTCC
1 AGTCCTC-AAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* **
180558 AGT-CTCAAAAGAGCAGGACCAACTCTT-AAGCCC-CACAAGTTGGTGGCAATTTTCCCAC
1 AGTCCTC-AAAGAGCAGGA-CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT----C
* ** *
180616 AGTCCTCAAAGAACAGGAACACCT-TGCAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGG-ACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
180671 AGT-C-CAAAGAGCAGGACACCTATTAAAGAAAGCCTCACAGCAAGTTGGT-GCGACCTTTA
1 AGTCCTCAAAGAGCAGGACACCTCTT----AAAGCC-CACA-CAAGTTGGTGGC-ACCTTTC
* * *
180730 AGTCGCCCAAAGAGCATGACA-CTTTTCAAAGCCCACACAAGTTGGTGGGCA-CTTTC
1 AGTC-CTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGT-GGCACCTTTC
* * * *
180786 AGTCCTCAAAGAGCATGACGCCT-TTCAAGCCCGACACGAGTTGGTG
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCC-ACACAAGTTGGTG
180832 CACGTTTTAC
Statistics
Matches: 1684, Mismatches: 168, Indels: 354
0.76 0.08 0.16
Matches are distributed among these distances:
47 5 0.00
48 3 0.00
49 5 0.00
50 31 0.02
51 49 0.03
52 153 0.09
53 210 0.12
54 231 0.14
55 235 0.14
56 314 0.19
57 186 0.11
58 120 0.07
59 61 0.04
60 21 0.01
61 22 0.01
62 30 0.02
63 8 0.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:179604 original size:117 final size:117
Alignment explanation
Indices: 179455--179677 Score: 319
Period size: 117 Copynumber: 1.9 Consensus size: 117
179445 TGGTGTCAGC
*
179455 TTCCAGTCCCTCAAGGAGCAGGACACCTCTTAAA-GCCCACACAAGTTGGTGGGCACCTTCAGTC
1 TTCCAGTCCCTCAAGGAGCAGGACACCTCTTAAAGGCCCA-ACAAGTTGGTGGCCA-CTTCAGTC
* *
179519 GCCCAAA-GAGCAGAGACACCTTCAAAGCCACCCAAGTTGGTGGCATTTTTTTTTT
64 CCCCAAATGAGCAGA-ACACCTT-AAAGCCACACAAGTTGGTGGCATTTTTTTTTT
*
179574 TTCCAGT-CCTCAA-GAGCAGGACACCTCTTAAAGGCCCAACAAGTTGGTGGCCATTTCAGTCCC
1 TTCCAGTCCCTCAAGGAGCAGGACACCTCTTAAAGGCCCAACAAGTTGGTGGCCACTTCAGTCCC
* * *
179637 CCAAATGAGTAGACCATCTTAAAGCCACACAAGTTGGTGGC
66 CCAAATGAGCAGAACACCTTAAAGCCACACAAGTTGGTGGC
179678 GCCGTCCAGT
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
115 20 0.21
116 18 0.19
117 39 0.41
118 11 0.12
119 7 0.07
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (117 bp):
TTCCAGTCCCTCAAGGAGCAGGACACCTCTTAAAGGCCCAACAAGTTGGTGGCCACTTCAGTCCC
CCAAATGAGCAGAACACCTTAAAGCCACACAAGTTGGTGGCATTTTTTTTTT
Found at i:179777 original size:498 final size:488
Alignment explanation
Indices: 178749--180605 Score: 1603
Period size: 498 Copynumber: 3.8 Consensus size: 488
178739 TCGGCTTTTT
* *
178749 AGTCCTCAAGAGC-AGGACACCTCTTAAAGCCTCACACAAGTTGGTGGC-A-CTTGCAGTCCT-C
1 AGTCCGCAAGAGCAAGGACACCTCTTAAAGCC-CACACAAGTTGGTGGCGACCTT-CCGTCCTCC
*
178810 -AA-AGCAGGACACCTCTTTAAAGCCCACACAAGTTGTGGC-CCTTTCAGTCCCCAAAGAGCAGG
64 AAAGAGCAGGACACCTC-TTAAAG-CCACACAAGTTGTGGCACCTTCCAGTCCCC--AGAGCAGG
* *
178872 ACA-CCTTCAAGCCCACCCAGTTGGTGGCATTTTTCTAGTCCT-AAAGGCAGGACCCCTCTTAAA
125 ACACCCTTCAAGCCCACACAGTTGGTGGCATTTTTC-AGTCCTCAAA-GCAGGACACCTC-TAAA
* *
178935 GCCC-CACAAGTTGGTGGAAACCTTTCAGTTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACAC
187 GCCCACACAAGTTGGT-GACA-CTTTCAGTCCCTCAAAGAGCAGGACACCTCTTAAAGCCCACAC
* * *
178999 CAGTTGGTGGCAACTTTCAAGTCCCCAAGGAG-AGCAGACACCTTTCAAAGCCCACCCAAGTTGG
250 AAGTTGGTGGC-ACCTTC-AGTCCCCAAAGAGCAG-AGACACC-TTCAAAGCCCACCCAAGTTGG
*
179063 TGGCATTTTCCAGTCCTTCAAAAAGAGCAGGACACCTCTTAAATGCCCACACAAGTTGGTGGCAC
311 TGGCATTTTCCAGTCCTTC--AAAGAGCAGGACACCTCTTAAAGGCCCACACAAGTTGGTGGCAC
* * *
179128 GCTTTCAGTCCCTCAAGAGGCAGGACACCTCTTAAAGCCAGCACAAGTTGGTGGCCCTTCCAGTC
374 GATTTCAGTCCCCCAAGAGGCAGGACACCTCTTAAAGCCAGCACAAGTTGGTGGCCCGTCCAGTC
*
179193 CCTCAAAGAGCAGGACCCTTTAAGCCCACCCAAGTTGGTGGCCCATTTGCC
439 CCTCAAAGAGCAGGACCCTTTAAGCCCACACAAGTTGGTGGCCCATTT-CC
* *
179244 AGTCCGCAAG-GCAGGGACACCTCGTAAAGCCCACACAAGTTGGTGGCGACCTTCCGTCCTCCAA
1 AGTCCGCAAGAGCAAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGACCTTCCGTCCTCCAA
179308 AGAGCAGGACACCTCTTAAAGCCA-ACAA-TTGTGGCACCTTCACCTAGTCCTCCAGAGCAGGAC
66 AGAGCAGGACACCTCTTAAAGCCACACAAGTTGTGGCACCTT--CC-AGTCC-CCAGAGCAGGAC
*
179371 ACCGCTT-AAGCACCACACAGTTGGTGGCA-TTTTCAGTCCTCAAAGACAGAACACCTCTAAGAG
127 ACC-CTTCAAGC-CCACACAGTTGGTGGCATTTTTCAGTCCTCAAAG-CAGGACACCTCTAA-AG
* * *
179434 CCCACACAAGTTGGTGTCAGCTTCCAGTCCCTCAAGGAGCAGGACACCTCTTAAAGCCCACACAA
188 CCCACACAAGTTGGTGACA-CTTTCAGTCCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAA
179499 GTTGGTGGGCACCTTCAGTCGCCCAAAGAGCAGAGACACCTTCAAAG-CCACCCAAGTTGGTGGC
252 GTTGGT-GGCACCTTCAGTC-CCCAAAGAGCAGAGACACCTTCAAAGCCCACCCAAGTTGGTGGC
179563 ATTTTTTTTTTTTCCAGTCC-TC-AAGAGCAGGACACCTCTTAAAGGCCCA-ACAAGTTGGTGGC
315 A--------TTTTCCAGTCCTTCAAAGAGCAGGACACCTCTTAAAGGCCCACACAAGTTGGTGGC
* * *
179625 -C-ATTTCAGTCCCCCAA-ATG-AGTAGACCATCTTAAAGCCA-CACAAGTTGGTGGCGCCGTCC
372 ACGATTTCAGTCCCCCAAGAGGCAGGACACC-TCTTAAAGCCAGCACAAGTTGGTGGC-CCGTCC
*
179685 AGT-CCTC-AAGATCAGGACACCTCTTAAAGCCCACACAAGGTTTGGTGGCACC-TTT-C
435 AGTCCCTCAAAGAGCAGGAC-CCT-TT-AAGCCCACACAA-G-TTGGTGGC-CCATTTCC
*
179741 -GTCC-CAAAGAGCAAGGACACCTCTTTAAATCCCACACAAGTTGGTGGCG-CCTTCCAGTCCTC
1 AGTCCGC-AAGAGCAAGGACACCTC-TTAAAGCCCACACAAGTTGGTGGCGACCTTCC-GTCCTC
** * * *
179803 CAAAGAGCAGGACACCTCTTAAAAGCACACACAAGTTGGTGGCATTTGTCCAATCCGCAAGAACA
63 CAAAGAGCAGGACACCTCTT-AAAGC-CACACAAGTT-GTGGCACCT-TCCAGTCC-CCAGAGCA
* * * *
179868 GGACACCTTTCAAGCCCACACAAGTTGGGGGCATTTTTCCAGGCCTCAAAGCAGGACAGCCTCTT
123 GGACACCCTTCAAGCCCACAC-AGTTGGTGGCATTTTT-CAGTCCTCAAAGCAGGACA-CCTCTA
* * * *
179933 AAGCCCACAC-AGTTGGTGGCA-TTTCATTCCC-CAAAGAGCAGGACA-CTTTTCAAGCCCCACA
185 AAGCCCACACAAGTTGGTGACACTTTCAGTCCCTCAAAGAGCAGGACACCTCTTAAAG-CCCACA
* *
179994 CAAGTTGGTGGCACCCTTTCAGTACCCAAAGAGCAG-GACACC-TCTAAAGCCCACACAAGTTGG
249 CAAGTTGGTGGCA-CC-TTCAGTCCCCAAAGAGCAGAGACACCTTC-AAAGCCCACCCAAGTTGG
****
180057 TGGCGCCGTCCAGTCC-TCAAAGAGGCA-GACACCTCTTAAA-GCCCACACAAGTTGGTGGCAC-
311 TGGCATTTTCCAGTCCTTCAAAGA-GCAGGACACCTCTTAAAGGCCCACACAAGTTGGTGGCACG
* * * * * *** *
180118 CTTTCAGTCCCCAAAGA-GCAGGACACCTGTCAAAGCCCA-CCCAAGTTTTGGTGGCATTTTCAG
375 ATTTCAGTCCCCCAAGAGGCAGGACACCTCTTAAAG-CCAGCACAAG--TTGGTGGCCCGTCCAG
180181 T-CC-CAAAGGAGCAGGACACCTCTT-AG-CCACACAAGTT-GT-GCACC-TTT-C
437 TCCCTCAAA-GAGCAGGAC-CCT-TTAAGCCCACACAAGTTGGTGGC-CCATTTCC
* ** * *
180229 AGGCATCAA-AG--AGCGAC-CTTCTTAAAGCCCACAGACAAGTTGGTGGC-ACCTTTCAGTCC-
1 AGTCCGCAAGAGCAAG-GACACCTCTTAAAGCCCAC--ACAAGTTGGTGGCGACC-TTCCGTCCT
** ** *
180288 CCAAAGAGCAGGAC-CCT-TTCAAAGCC-CACCAAGGGGTGGCATTTTCCAGTCCTCAAAGAGCA
62 CCAAAGAGCAGGACACCTCTT-AAAGCCACA-CAAGTTGTGGCACCTTCCAGTCC-C-CAGAGCA
* * * * * * * *
180350 -GACAAGCCTTTAAAAGCCACAAAAAAGTTGGTGGCACTTTTCATTCCCCAAGAGCAGGACACAT
123 GGAC-A-CCCTT-CAAGCC-C-ACACAGTTGGTGGCATTTTTCAGTCCTCAA-AGCAGGACACCT
* * * *
180414 CTTAAGCCCA-ACAAGTTGGTGGCCGCCTTCCAGT-CCTCAAAGAGCA-GACA-CTCTTAAAAAA
182 CTAAAGCCCACACAAGTTGGT-GAC-ACTTTCAGTCCCTCAAAGAGCAGGACACCTCTT---AAA
*
180475 GCCCACAC-AGTTTGGGTGGCACCTTTCAGTCCCCAAAAGAGCAG-GACACCTCTTAAAAGCCCA
242 GCCCACACAAG-TT-GGTGGCACC-TTCAGTCCCC-AAAGAGCAGAGACA-C-CTTCAAAGCCCA
* *** *
180538 CACAAGTT-GTGGCGCCTTCCAGT-C-TCAAAAGAGCAGGACCAACTCTT-AA-GCCC-CACAAG
301 CCCAAGTTGGTGGCATTTTCCAGTCCTTC-AAAGAGCAGGA-CACCTCTTAAAGGCCCACACAAG
180597 TTGGTGGCA
364 TTGGTGGCA
180606 ATTTTCCCAC
Statistics
Matches: 1168, Mismatches: 94, Indels: 206
0.80 0.06 0.14
Matches are distributed among these distances:
481 11 0.01
482 18 0.02
483 12 0.01
484 38 0.03
485 39 0.03
486 31 0.03
487 38 0.03
488 35 0.03
489 50 0.04
490 46 0.04
491 55 0.05
492 33 0.03
493 18 0.02
494 44 0.04
495 91 0.08
496 57 0.05
497 105 0.09
498 223 0.19
499 80 0.07
500 38 0.03
501 45 0.04
502 23 0.02
503 26 0.02
504 12 0.01
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (488 bp):
AGTCCGCAAGAGCAAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGACCTTCCGTCCTCCAA
AGAGCAGGACACCTCTTAAAGCCACACAAGTTGTGGCACCTTCCAGTCCCCAGAGCAGGACACCC
TTCAAGCCCACACAGTTGGTGGCATTTTTCAGTCCTCAAAGCAGGACACCTCTAAAGCCCACACA
AGTTGGTGACACTTTCAGTCCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGC
ACCTTCAGTCCCCAAAGAGCAGAGACACCTTCAAAGCCCACCCAAGTTGGTGGCATTTTCCAGTC
CTTCAAAGAGCAGGACACCTCTTAAAGGCCCACACAAGTTGGTGGCACGATTTCAGTCCCCCAAG
AGGCAGGACACCTCTTAAAGCCAGCACAAGTTGGTGGCCCGTCCAGTCCCTCAAAGAGCAGGACC
CTTTAAGCCCACACAAGTTGGTGGCCCATTTCC
Found at i:181468 original size:31 final size:31
Alignment explanation
Indices: 181411--181470 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
181401 TTCAACAAGT
181411 TGTATCGATACATAAGTTTTAGCGATACAGA
1 TGTATCGATACATAAGTTTTAGCGATACAGA
*
181442 TGTATC-ATACATAAGTATTTATCGATACA
1 TGTATCGATACATAAGT-TTTAGCGATACA
181471 TAATTAGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (31 bp):
TGTATCGATACATAAGTTTTAGCGATACAGA
Found at i:181621 original size:21 final size:19
Alignment explanation
Indices: 181578--181625 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
181568 CCCAGAGGTA
*
181578 CGATACATTTTACATGTAT
1 CGATACATTTTACATGTAG
181597 CGATACATTTTAACAATGTAG
1 CGATACATTTT-AC-ATGTAG
181618 CGAT-CATT
1 CGATACATT
181626 CAGGCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 6 0.23
21 9 0.35
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (19 bp):
CGATACATTTTACATGTAG
Done.