Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 2 of 19
Found at i:121371 original size:32 final size:32
Alignment explanation
Indices: 121311--121656 Score: 541
Period size: 32 Copynumber: 10.8 Consensus size: 32
121301 TTCTAAAGCC
** *
121311 CACAAGTTAGTGGC-ACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
121342 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
121374 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
121406 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
121438 CACAAGTCGATGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
121470 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
121502 CATAAGTCGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
121534 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
121566 CACAAGTCGATGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
121598 CACAAGTCGGTGGCAGCCCATTTAAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
121630 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
121657 TCACCATTTT
Statistics
Matches: 290, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
31 12 0.04
32 278 0.96
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:122905 original size:4 final size:4
Alignment explanation
Indices: 122896--122946 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
122886 GTTAGGTAAA
* *
122896 AAAG AAAG AAAG -AAG ATGAAG -AAG AAAG AAAG AAAA AAAG AAAA AAAG
1 AAAG AAAG AAAG AAAG A--AAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
122944 AAA
1 AAA
122947 AAAATATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 6 0.15
4 30 0.77
6 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:122936 original size:16 final size:16
Alignment explanation
Indices: 122893--122950 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 16
122883 AGGGTTAGGT
122893 AAAAAAGAAAGAAAGA
1 AAAAAAGAAAGAAAGA
122909 AGATGAAGAAGAAAGAAAGA
1 A-A--AA-AAGAAAGAAAGA
*
122929 AAAAAAGAAAAAAAGA
1 AAAAAAGAAAGAAAGA
122945 AAAAAA
1 AAAAAA
122951 TATGAAATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 18 0.49
17 3 0.08
19 3 0.08
20 13 0.35
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAGAAAGA
Found at i:122947 original size:8 final size:8
Alignment explanation
Indices: 122893--122950 Score: 62
Period size: 8 Copynumber: 6.8 Consensus size: 8
122883 AGGGTTAGGT
122893 AAAAAAGA
1 AAAAAAGA
*
122901 AAGAAAGA
1 AAAAAAGA
122909 AGATGAAGAAGA
1 A-A--AA-AAGA
*
122921 AAGAAAGA
1 AAAAAAGA
122929 AAAAAAGA
1 AAAAAAGA
122937 AAAAAAGA
1 AAAAAAGA
122945 AAAAAA
1 AAAAAA
122951 TATGAAATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 33 0.79
9 2 0.05
11 2 0.05
12 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:123333 original size:2 final size:2
Alignment explanation
Indices: 123320--123350 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
123310 TTGTTTTATT
*
123320 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
123351 TTTGAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:125896 original size:51 final size:51
Alignment explanation
Indices: 125779--125896 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
125769 CCTAAAATAC
* * * **
125779 CAATTTTTCGCAATCAGGGATACTCCAACTCCGATTTTATTTCCAAAGCAT
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGACCTTATTTCCAAAGCAT
* * * *
125830 CGATTTTCCACAATCGGGGATACTCCAACCCCGGCCTTATTTCTAAAGCAT
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGACCTTATTTCCAAAGCAT
*
125881 CAATTTTTCATAATCG
1 CAATTTTTCACAATCG
125897 AAGATACCCC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGACCTTATTTCCAAAGCAT
Found at i:125903 original size:51 final size:51
Alignment explanation
Indices: 125797--125913 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 51
125787 CGCAATCAGG
* ** * **
125797 GATACTCCAACTCCGATTTTATTTCCAAAGCATCGATTTTCCACAATCGGG
1 GATACTCCAACCCCGACCTTATTTCCAAAGCATCAATTTTCCACAATCGAA
* * * *
125848 GATACTCCAACCCCGGCCTTATTTCTAAAGCATCAATTTTTCATAATCGAA
1 GATACTCCAACCCCGACCTTATTTCCAAAGCATCAATTTTCCACAATCGAA
* *
125899 GATACCCCAGCCCCG
1 GATACTCCAACCCCG
125914 TTGTTATCCC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (51 bp):
GATACTCCAACCCCGACCTTATTTCCAAAGCATCAATTTTCCACAATCGAA
Found at i:128523 original size:13 final size:13
Alignment explanation
Indices: 128505--128561 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
128495 CATAAAGTGT
128505 TGTATCGATACAA
1 TGTATCGATACAA
128518 TGTATCGATACATAA
1 TGTATCGATAC--AA
128533 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
128550 TATATCGATACA
1 TGTATCGATACA
128562 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:128540 original size:32 final size:32
Alignment explanation
Indices: 128485--128582 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
128475 TTCAACGATT
128485 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
128518 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
128550 TATATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
128582 T
1 T
128583 TTAAGCTACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:128542 original size:19 final size:18
Alignment explanation
Indices: 128483--128580 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
128473 ATTTCAACGA
128483 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
128502 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
128518 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
128534 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
128550 --TATATCGATACATAAG
1 TTTGTATCGATACATAAG
128566 TTTTGTATCGATACA
1 -TTTGTATCGATACA
128581 ATTTAAGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
19 23 0.36
20 12 0.19
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:128641 original size:13 final size:13
Alignment explanation
Indices: 128623--128647 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
128613 ATTACTCAAA
128623 TGTATCGATACAT
1 TGTATCGATACAT
128636 TGTATCGATACA
1 TGTATCGATACA
128648 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:128712 original size:52 final size:52
Alignment explanation
Indices: 128656--128780 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
128646 CACTGATCTT
*
128656 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
128708 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
128760 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
128781 CTTTTCATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:137915 original size:40 final size:41
Alignment explanation
Indices: 137854--138036 Score: 147
Period size: 40 Copynumber: 4.3 Consensus size: 41
137844 TAACTAGATG
* * *
137854 TATCGATACATT-ATTCAATGTATCGATACATTGCAGAATA
1 TATCGATACATTCATACAATGTATCGATACATTGAAAAATA
* * *
137894 TATCGATACATTCATAC-ATGTATTGATATATTGAAAAATG
1 TATCGATACATTCATACAATGTATCGATACATTGAAAAATA
* * *
137934 TATCGATACATCAGGGTAAAAATGACATAATGTATCGATACATTGCAGAATA
1 TATCGATACAT-----T---CAT-AC--AATGTATCGATACATTGAAAAATA
* *
137986 TATCGATACATTCATAC-ATGTATCGATATATTGAAAAATG
1 TATCGATACATTCATACAATGTATCGATACATTGAAAAATA
138026 TATCGATACAT
1 TATCGATACAT
138037 CAGGGTAAAA
Statistics
Matches: 113, Mismatches: 17, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
40 71 0.63
41 3 0.03
43 2 0.02
44 2 0.02
45 1 0.01
47 1 0.01
48 2 0.02
49 2 0.02
52 29 0.26
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (41 bp):
TATCGATACATTCATACAATGTATCGATACATTGAAAAATA
Found at i:137921 original size:20 final size:20
Alignment explanation
Indices: 137851--138036 Score: 90
Period size: 20 Copynumber: 9.7 Consensus size: 20
137841 TTTTAACTAG
*
137851 ATGTATCGATACATT-ATTC
1 ATGTATCGATACATTCATAC
*
137870 AATGTATCGATACATTGCAGA-
1 -ATGTATCGATACATT-CATAC
*
137891 ATATATCGATACATTCATAC
1 ATGTATCGATACATTCATAC
* * * * *
137911 ATGTATTGATATATTGAAAA
1 ATGTATCGATACATTCATAC
137931 ATGTATCGATACA-TC--A-
1 ATGTATCGATACATTCATAC
** * *
137947 GGGTA---A-AAATGACATA-
1 ATGTATCGATACAT-TCATAC
*
137963 ATGTATCGATACATTGCAGA-
1 ATGTATCGATACATT-CATAC
*
137983 ATATATCGATACATTCATAC
1 ATGTATCGATACATTCATAC
* * * *
138003 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTCATAC
138023 ATGTATCGATACAT
1 ATGTATCGATACAT
138037 CAGGGTAAAA
Statistics
Matches: 123, Mismatches: 30, Indels: 26
0.69 0.17 0.15
Matches are distributed among these distances:
12 2 0.02
13 1 0.01
14 1 0.01
16 7 0.06
17 1 0.01
19 8 0.07
20 102 0.83
22 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTCATAC
Found at i:138027 original size:92 final size:92
Alignment explanation
Indices: 137870--138049 Score: 351
Period size: 92 Copynumber: 2.0 Consensus size: 92
137860 TACATTATTC
*
137870 AATGTATCGATACATTGCAGAATATATCGATACATTCATACATGTATTGATATATTGAAAAATGT
1 AATGTATCGATACATTGCAGAATATATCGATACATTCATACATGTATCGATATATTGAAAAATGT
137935 ATCGATACATCAGGGTAAAAATGACAT
66 ATCGATACATCAGGGTAAAAATGACAT
137962 AATGTATCGATACATTGCAGAATATATCGATACATTCATACATGTATCGATATATTGAAAAATGT
1 AATGTATCGATACATTGCAGAATATATCGATACATTCATACATGTATCGATATATTGAAAAATGT
138027 ATCGATACATCAGGGTAAAAATG
66 ATCGATACATCAGGGTAAAAATG
138050 TGACTTTTCC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (92 bp):
AATGTATCGATACATTGCAGAATATATCGATACATTCATACATGTATCGATATATTGAAAAATGT
ATCGATACATCAGGGTAAAAATGACAT
Found at i:141171 original size:7 final size:7
Alignment explanation
Indices: 141159--141219 Score: 74
Period size: 7 Copynumber: 9.0 Consensus size: 7
141149 ACACTCCAAA
141159 AAAAAAC
1 AAAAAAC
141166 AAAAAA-
1 AAAAAAC
*
141172 ACAAAAC
1 AAAAAAC
141179 AAAAAAAC
1 -AAAAAAC
141187 AAAAAAC
1 AAAAAAC
141194 AAAAAAC
1 AAAAAAC
141201 AAAAAA-
1 AAAAAAC
*
141207 AAAACA-
1 AAAAAAC
141213 AAAAAAC
1 AAAAAAC
141220 CAAGAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 15 0.32
7 26 0.55
8 6 0.13
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:141171 original size:8 final size:8
Alignment explanation
Indices: 141158--141243 Score: 74
Period size: 8 Copynumber: 11.1 Consensus size: 8
141148 TACACTCCAA
141158 AAAAAAAC
1 AAAAAAAC
141166 AAAAAAAC
1 AAAAAAAC
141174 ---AAAAC
1 AAAAAAAC
141179 AAAAAAAC
1 AAAAAAAC
141187 -AAAAAAC
1 AAAAAAAC
*
141194 AAAAAACAAA
1 -AAAAA-AAC
141204 AAAAAAAC
1 AAAAAAAC
141212 AAAAAAAC
1 AAAAAAAC
* *
141220 CAAGAAA-
1 AAAAAAAC
* *
141227 AAAATAGC
1 AAAAAAAC
141235 AAAAAAAC
1 AAAAAAAC
141243 A
1 A
141244 GAAAGGGGTC
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
5 5 0.08
7 10 0.16
8 35 0.57
9 9 0.15
10 2 0.03
ACGTcount: A:0.84, C:0.13, G:0.02, T:0.01
Consensus pattern (8 bp):
AAAAAAAC
Found at i:141211 original size:33 final size:35
Alignment explanation
Indices: 141156--141230 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 35
141146 TTTACACTCC
*
141156 AAAAAAAAA-CAAAAAAACAAAACAAAAAAACAAAA
1 AAAAAAAAACCAAGAAAA-AAAACAAAAAAACAAAA
* * *
141191 AACAAAAAA-CAA-AAAAAAAACAAAAAAACCAAG
1 AAAAAAAAACCAAGAAAAAAAACAAAAAAACAAAA
141224 AAAAAAA
1 AAAAAAA
141231 TAGCAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 21 0.58
34 4 0.11
35 11 0.31
ACGTcount: A:0.87, C:0.12, G:0.01, T:0.00
Consensus pattern (35 bp):
AAAAAAAAACCAAGAAAAAAAACAAAAAAACAAAA
Found at i:141217 original size:13 final size:13
Alignment explanation
Indices: 141156--141241 Score: 84
Period size: 14 Copynumber: 6.3 Consensus size: 13
141146 TTTACACTCC
141156 AAAAAAAAACAAA
1 AAAAAAAAACAAA
*
141169 AAAACAAAACAAAA
1 AAAAAAAAAC-AAA
141183 AAACAAAAAACAAA
1 AAA-AAAAAACAAA
141197 AAACAAAAAA-AAA
1 AAA-AAAAAACAAA
*
141210 ACAAAAAAACCAAGA
1 A-AAAAAAAACAA-A
* *
141225 AAAAAATAGCAAA
1 AAAAAAAAACAAA
141238 AAAA
1 AAAA
141242 CAGAAAGGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
13 23 0.37
14 32 0.51
15 8 0.13
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:141230 original size:1 final size:1
Alignment explanation
Indices: 141156--141218 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
141146 TTTACACTCC
* * * * * * *
141156 AAAAAAAAACAAAAAAACAAAACAAAAAAACAAAAAACAAAAAACAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
141219 CCAAGAAAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:141239 original size:33 final size:33
Alignment explanation
Indices: 141160--141243 Score: 75
Period size: 33 Copynumber: 2.5 Consensus size: 33
141150 CACTCCAAAA
*
141160 AAAAACAAAAAAACAAAACA-AAAAAACAAAAA
1 AAAAACAAAAAAACAAAAAACAAAAAACAAAAA
*
141192 ACAAAA-AACAAAA-AAAAAACAAAAAAACCAAGAAA
1 A-AAAACAAAAAAACAAAAAAC-AAAAAA-CAA-AAA
141227 AAAATAGCAAAAAAACA
1 AAAA-A-CAAAAAAACA
141244 GAAAGGGGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
31 5 0.12
32 7 0.17
33 10 0.25
34 6 0.15
35 5 0.12
37 6 0.15
38 1 0.03
ACGTcount: A:0.83, C:0.13, G:0.02, T:0.01
Consensus pattern (33 bp):
AAAAACAAAAAAACAAAAAACAAAAAACAAAAA
Found at i:142586 original size:28 final size:28
Alignment explanation
Indices: 142461--143491 Score: 1245
Period size: 28 Copynumber: 36.1 Consensus size: 28
142451 CATTCATCTC
*
142461 TTCAAAGCCCACAAGTCAGTGGCACCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
142489 TTCAAAGCCCATGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCTT
* *
142519 TTCAAAGCCCACAAATCAGTGGCACTATT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
142548 TTCAAAACCCACAAGTCAGTGGTACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
142576 TTCAAAGCCCATAGGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
142605 TTCAAAGCCCACAAGTTAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * *
142633 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* * *
142661 TTCAAAGCCCACAAATTAGTGGTACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
142690 TTCAAAGCCCACAAGTTAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
142718 TTCAAAGCCCACAAGTCAATGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
142746 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
142774 TTCAAAGCCCACAAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
142803 TTCAAAGCCCACAAGTCAGTAGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
142832 TT-AAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
142860 TT-AAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
142887 TCCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
142915 TTCAAAGCCCACAAGTTAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
142943 TTCAAAGCTCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
142972 TTCAAAGCCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
143000 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
143028 TCCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCT-T
*
143056 TCCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
143085 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
143113 TTCAAAGCCCACAAGTCAGCGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * *
143142 TTCAAAGCCCACAAGTTAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
143170 TTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCT-T
* *
143198 TTCAAAGCCCACAAGTCTGTGACA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCT-T
*
143226 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
143254 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * *
143283 TTCAAAGCCCAAAAGTTAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * *
143312 TTTAAAGCCCCCAAGTTAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * * *
143340 TTCAAAGCCCATAAGTTAGTGGTGA-CAT
1 TTCAAAGCCCACAAGTCAGTGG-CACCTT
143368 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
143397 TTCAAAGCCCACAAGTCAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CAC-CTT
*
143427 TTCAAAGCCCACACGAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CTT
*
143459 TTCAAAGCCCACACAAGTTAGTGGCACCATT
1 TTCAAAG-CC-CACAAGTCAGTGGCACC-TT
143490 TT
1 TT
143492 TAAAAAAAAA
Statistics
Matches: 888, Mismatches: 83, Indels: 61
0.86 0.08 0.06
Matches are distributed among these distances:
27 12 0.01
28 531 0.60
29 252 0.28
30 52 0.06
31 6 0.01
32 29 0.03
33 2 0.00
34 4 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:142664 original size:85 final size:85
Alignment explanation
Indices: 142461--143485 Score: 1337
Period size: 85 Copynumber: 12.0 Consensus size: 85
142451 CATTCATCTC
* *
142461 TTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCCCATGCAAGTCAGTGGCACCCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACCTTTTCAAAG
* *
142526 CCCACAAATCAGTGGCACTATT
64 CCCACAAGTCAGTGGCACTCTT
* * * * *
142548 TTCAAAACCCACAAGTCAGTGGTACCTTTTCAAAGCCCATAGGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGC
* *
142613 CCACAAGTTAGTGGCA-TCCT
65 CCACAAGTCAGTGGCACTCTT
* * * * *
142633 TTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAATTAGTGGTACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGC
* *
142698 CCACAAGTTAGTGGCA-TCCT
65 CCACAAGTCAGTGGCACTCTT
* * *
142718 TTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
*
142783 CACAAGTCAATGGCACTCTT
66 CACAAGTCAGTGGCACTCTT
* * *
142803 TTCAAAGCCCACAAGTCAGTAGCATCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGC
*
142867 CCACAAGTCAGTGGCAC-CCT
65 CCACAAGTCAGTGGCACTCTT
* * *
142887 TCCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
142952 CACAAGTCAGTGGCACTCTT
66 CACAAGTCAGTGGCACTCTT
* * *
142972 TTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
143037 CACAAGTCAGTGGCACTC-T
66 CACAAGTCAGTGGCACTCTT
* * * *
143056 TCCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGC
*
143121 CCACAAGTCAGCGGCACTCTT
65 CCACAAGTCAGTGGCACTCTT
* *
143142 TTCAAAGCCCACAAGTTAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGC
* *
143206 CCACAAGTCTGTGACACTC-T
65 CCACAAGTCAGTGGCACTCTT
143226 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGC
* * *
143291 CCAAAAGTTAGTGGCATTCTT
65 CCACAAGTCAGTGGCACTCTT
* * * * * * * *
143312 TTTAAAGCCCCCAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTTAGTGGTGA-CATTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG-CACCTTTTCAAAGC
143376 CCACAAGTCAGTGGCACTCTT
65 CCACAAGTCAGTGGCACTCTT
* * *
143397 TTCAAAGCCCACAAGTCAGTGGTAACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTC
1 TTCAAAGCCCACAAGTCAGTGG-CAC-CCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CTTTTC
*
143462 AAAGCCCACACAAGTTAGTGGCAC
60 AAAG-CC-CACAAGTCAGTGGCAC
143486 CATTTTTAAA
Statistics
Matches: 822, Mismatches: 95, Indels: 36
0.86 0.10 0.04
Matches are distributed among these distances:
83 6 0.01
84 170 0.21
85 461 0.56
86 100 0.12
87 51 0.06
89 8 0.01
91 9 0.01
92 2 0.00
93 15 0.02
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
CACAAGTCAGTGGCACTCTT
Found at i:142742 original size:113 final size:112
Alignment explanation
Indices: 142461--143491 Score: 1262
Period size: 113 Copynumber: 9.0 Consensus size: 112
142451 CATTCATCTC
*
142461 TTCAAAGCCCACAAGTCAGTGGCA-CCATTTCAAAGCCCATGCAAGTCAGTGGCACCCTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCA--CAAGTCAGTGGCATCCTTTCAAA
* ** * *
142525 GCCCACAAATCAGTGGCACTATTTTCAAAACCCACAAGTCAGTGGTACCTT
63 GCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* * * *
142576 TTCAAAGCCCATAGGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * *
142641 CCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAATTAGTGGTACTCTT
65 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
142690 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
*
142755 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACTCTT
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * * *
142803 TTCAAAGCCCACAAGTCAGTAGCATCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* *
142868 CACAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCACCCT
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* * *
142915 TTCAAAGCCCACAAGTTAGTGGCA-CCTTTTCAAAGCTCACAAGTCAGTGGCACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAG
* *
142979 CCCACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
64 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* * *
143028 TCCAAAGCCCACAAGTCAGTGGCA-CTCTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAG
* *
143092 CCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGCGGCACTCTT
64 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * *
143142 TTCAAAGCCCACAAGTTAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGC
* * * *
143206 CCACAAGTCTGTGACACTCTTTCAAAGCCCACAAGTCAGTGGCACCCT
65 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* * * * *
143254 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCAAAAGTTAGTGGCATTCTTTTTAAAG
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAG
* * * * * * *
143319 CCCCCAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTTAGTGGTGA-CAT
64 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG-CACCTT
* * *
143368 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGTAACTCTTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGG-CA-TCCTTTCAAA
* * *
143433 GCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACCATT
63 GCCCACA--AGTCAGTGGC-AC-CCTTTCAAAG-CC-CACAAGTCAGTGGCACC-TT
143490 TT
1 TT
143492 TAAAAAAAAA
Statistics
Matches: 801, Mismatches: 93, Indels: 37
0.86 0.10 0.04
Matches are distributed among these distances:
111 2 0.00
112 72 0.09
113 433 0.54
114 203 0.25
115 41 0.05
116 12 0.01
117 9 0.01
118 1 0.00
119 9 0.01
120 3 0.00
121 13 0.02
122 3 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (112 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:143620 original size:45 final size:47
Alignment explanation
Indices: 143550--143658 Score: 123
Period size: 49 Copynumber: 2.3 Consensus size: 47
143540 CTGTCTGACA
* * *
143550 TCGCTAGCATTGAATCAACATATTGG-CACTTTT-ATTAGCCCAATG
1 TCGCTGGCCTTGAATCAACACATTGGCCACTTTTCATTAGCCCAATG
* * *
143595 TCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGTCCAATG
1 TCGCTGGCCTTGAATCAACACATTGG-CCACTTTT-CATTAGCCCAATG
*
143644 TCGCCGGCCTTGAAT
1 TCGCTGGCCTTGAAT
143659 TGGCACATGG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 22 0.42
47 7 0.13
49 24 0.45
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (47 bp):
TCGCTGGCCTTGAATCAACACATTGGCCACTTTTCATTAGCCCAATG
Found at i:144117 original size:51 final size:51
Alignment explanation
Indices: 144032--144137 Score: 176
Period size: 51 Copynumber: 2.1 Consensus size: 51
144022 TATGAAAAGG
*
144032 TACCTAGATGTATCGATACATTCTTCAATATATCGATACATTCTATCCTTT
1 TACCCAGATGTATCGATACATTCTTCAATATATCGATACATTCTATCCTTT
* * *
144083 TACCCAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTT
1 TACCCAGATGTATCGATACATTCTTCAATATATCGATACATTCTATCCTTT
144134 TACC
1 TACC
144138 TTAGCTTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (51 bp):
TACCCAGATGTATCGATACATTCTTCAATATATCGATACATTCTATCCTTT
Found at i:148330 original size:23 final size:25
Alignment explanation
Indices: 148285--148331 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
148275 CTCTACAGAT
*
148285 TTCATTTGTAAAATAATTCTATTAAC
1 TTCACTTGTAAAAT-ATTCTATTAAC
148311 TTCACTTGTAAAAT-TT-TATTA
1 TTCACTTGTAAAATATTCTATTA
148332 TTTCACATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 2 0.10
26 13 0.65
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (25 bp):
TTCACTTGTAAAATATTCTATTAAC
Found at i:150567 original size:21 final size:20
Alignment explanation
Indices: 150526--150583 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
150516 TTTTTAAATC
*
150526 TATCAATATATTATTTATAA
1 TATCAATATATAATTTATAA
150546 TATCAAATATATAAATTT-TAA
1 TATC-AATATAT-AATTTATAA
*
150567 TAT-ATTA-ATAATTTATA
1 TATCAATATATAATTTATA
150584 TTATATGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 5 0.15
18 4 0.12
19 3 0.09
20 4 0.12
21 13 0.39
22 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
TATCAATATATAATTTATAA
Found at i:151908 original size:5 final size:5
Alignment explanation
Indices: 151893--151922 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
151883 CTTAATTACA
151893 AAAAT -AAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
151923 CTCAAAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:157058 original size:13 final size:14
Alignment explanation
Indices: 157029--157061 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
157019 ATAAGAAAAA
*
157029 AAATTTAGATATTT
1 AAATTTAAATATTT
157043 AAATTTAAAT-TTT
1 AAATTTAAATATTT
157056 AAATTT
1 AAATTT
157062 GTTAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
AAATTTAAATATTT
Found at i:157328 original size:39 final size:40
Alignment explanation
Indices: 157270--157347 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
157260 ACTAAACAAA
* * *
157270 TAATAAAAGTAAATTAAATTATTT-AGTATTTTATTTTTT
1 TAATAAAAGTAAATAAAATTATTTAAATAATTTATTTTTT
157309 TAATAAAA-TAAAATAAAATTATTTAAATAATTTATTTTT
1 TAATAAAAGT-AAATAAAATTATTTAAATAATTTATTTTT
157348 AATTTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 1 0.03
39 21 0.62
40 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (40 bp):
TAATAAAAGTAAATAAAATTATTTAAATAATTTATTTTTT
Found at i:159803 original size:2 final size:2
Alignment explanation
Indices: 159796--159835 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
159786 CTTGTACCTA
159796 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
159836 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:159840 original size:2 final size:2
Alignment explanation
Indices: 159835--159875 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
159825 TCTCTCTCTC
159835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
159876 CATAGTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:160694 original size:17 final size:17
Alignment explanation
Indices: 160644--160697 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
160634 TAATTTATTA
160644 ATTTTATATTAAATATTAT
1 ATTTT-TATTAAATA-TAT
* *
160663 ACTTTTGAGTGAAATATAT
1 A-TTTTTA-TTAAATATAT
160682 ATTTTTATTAAATATA
1 ATTTTTATTAAATATA
160698 AATTATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 8 0.28
18 5 0.17
19 6 0.21
20 10 0.34
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (17 bp):
ATTTTTATTAAATATAT
Found at i:160744 original size:20 final size:21
Alignment explanation
Indices: 160719--160770 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
160709 ATATTCACTT
*
160719 AATATTAAATTATTTT-TTTA
1 AATATTAAATTATTTTGATTA
*
160739 AATATTAAA-AATTTTGATTA
1 AATATTAAATTATTTTGATTA
*
160759 AATTTTAAATTA
1 AATATTAAATTA
160771 ATTAAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.19
20 20 0.77
21 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AATATTAAATTATTTTGATTA
Found at i:166935 original size:27 final size:27
Alignment explanation
Indices: 166881--167002 Score: 147
Period size: 27 Copynumber: 4.5 Consensus size: 27
166871 CCATGATTCA
* *
166881 GTGGCATTTCTTTTAAAGTCCACCACTCC
1 GTGGCA-TCCTTTT-AAGTCCACAACTCC
* * *
166910 GTGGCACCCTTTTAAGTTCACAACTCT
1 GTGGCATCCTTTTAAGTCCACAACTCC
*
166937 GTGGCATCCTTTTAAGTCCATAACTCC
1 GTGGCATCCTTTTAAGTCCACAACTCC
* *
166964 GTGGCATCCTTTTAA-TCTACAACTTC
1 GTGGCATCCTTTTAAGTCCACAACTCC
166990 GTGGCATCCTTTT
1 GTGGCATCCTTTT
167003 GAAGCCCCCA
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
26 21 0.26
27 49 0.60
28 5 0.06
29 6 0.07
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (27 bp):
GTGGCATCCTTTTAAGTCCACAACTCC
Found at i:167129 original size:32 final size:32
Alignment explanation
Indices: 167037--167832 Score: 642
Period size: 32 Copynumber: 26.2 Consensus size: 32
167027 TTCCAAAGTC
**
167037 CACAAGTCAGTGGC-ACCCATTTTTAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* ** *
167066 CACAAGTAAGTGGC-A-TTATTTTAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
167096 CACAAGTCAGTGGCAACCCATTTGAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
167128 CACAAGTCGGTGGTAACCCATTTCAAAACCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
167160 CACAAGTCGGTGGCAACCCATTTCAAAG--CT
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * * *
167190 TACAAGTTAGTGAC-ATCC-TTCTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATT-TCAAAGCCCA
* *
167219 CACAAGTCAGTGAC-ATCC-TTCTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATT-TCAAAGCCCA
167250 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* ** * * *
167282 CACAAGTCGGTATCAACTCATTTGAAAACCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
167314 CACAAGTCGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
167346 CA-AA---AGTTGCCACCCATTTGAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
167374 CACAAGTCAATGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
167406 CATAAGTCGGTGGTAACCCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
167436 CACAAGTCAGTGGC-ATCC-TTCTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATT-TCAAAGCCCA
** *
167465 CACAAGTCAGTGGC-ATTC-TTCTGAAAGCCCA
1 CACAAGTCAGTGGCAACCCATT-TCAAAGCCCA
**
167496 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
** *
167528 CACAAGTTGGTGGCAACCCATTTCAAAGCCTA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
167560 CACAAATCGGTGGAAACCCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
167590 CGCAAGTCAGTGG-TA-TCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
**
167620 CACAAGTTGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
167650 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
167678 CATAAGTCAGTGGC-A-CCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
167706 CACAAGTCAGTGGC-ACTCTTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
167735 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * * *
167763 TACAAGCCAGTGGC-ACTCTTTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * * * * * *
167794 CACGAGTCGGTGGCATCTCTTTTCAAAGCTCG
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
167826 CACAAGT
1 CACAAGT
167833 TAATGGAACC
Statistics
Matches: 644, Mismatches: 94, Indels: 55
0.81 0.12 0.07
Matches are distributed among these distances:
27 2 0.00
28 116 0.18
29 130 0.20
30 74 0.11
31 44 0.07
32 274 0.43
33 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.21
Consensus pattern (32 bp):
CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
Found at i:167310 original size:154 final size:152
Alignment explanation
Indices: 167011--167747 Score: 674
Period size: 154 Copynumber: 4.9 Consensus size: 152
167001 TTGAAGCCCC
* * * * ** *
167011 CAAGTCGGTGG-TACCC-TTCCAAAGTCCACAAGTCAGTGGCACCCATTTTTAAGCCCACAAGTA
1 CAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTTAGTGGCACCCATTTCAAAGCCCACAAGTC
** * * *
167074 AGTGGCA-TTATTTTAAAGCCCACACAAGTCAGTGGCAACCCATTTGAAAGCCCACACAAGTCGG
66 AGTGGCACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAG
*
167138 TGGTAACCCATTTCAAAACCCACA
131 TGGT-A-TCATTTCAAAACCCACA
** * *
167162 CAAGTCGGTGGCAACCCATTTCAAAGCTTACAAGTTAGTGACATCC-TTCTCAAAGCCCACAAGT
1 CAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTTAGTGGCACCCATT-TCAAAGCCCACAAGT
* *
167226 CAGTGACATCC-TTCTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTC
65 CAGTGGCACCCATT-TCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTC
* * *
167290 GGT-ATCAACTCATTTGAAAACCCACA
129 AGTGGT--A-TCATTTCAAAACCCACA
* * * *
167316 CAAGTCGGTGGTAACCCATTTCAAAGCCCACAA--AAGTTGCCACCCATTTGAAAGCCCACACAA
1 CAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTTAG-TGGCACCCATTTCAAAG-CC-CACAA
* * * *
167379 GTCAATGGCAACCCATTTCAAAGCCCACATAAGTCGGTGGTAACCCATTTCAAAG-CC-CACAAG
63 GTCAGTGGC-ACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAG
* * *
167442 TCAGTGGCATCCTTCTC-AAAGCC-CA
127 TCAGTGGTATCATT-TCAAAACCCACA
* ** * *
167467 CAAGTCAGTGGC-ATTC-TTCTGAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACA
1 CAAGTCGGTGGCAACCCATT-TCAAAG-CC-CACAAGTTAGTGGC-ACCCATTTCAAAG-CC-CA
** * * * * *
167530 CAAGTTGGTGGCAACCCATTTCAAAGCCTACACAAATCGGTGGAAACCCATTTCAAAG-CC-CGC
60 CAAGTCAGTGGC-ACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACAC
*
167593 AAGTCAGTGGTATCATTTCAAAGCCCACA
124 AAGTCAGTGGTATCATTTCAAAACCCACA
* * * *
167622 CAAGTTGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCATAAGTC
1 CAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTTAGTGGCACCCATTTCAAAGCCCACAAGTC
* *
167686 AGTGGCA-CCATTTCAAAG-CC-CACAAGTCAGTGGC-ACTCTTTTCAAAG-CC-CACAAGTCAG
66 AGTGGCACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAG
167745 TGG
131 TGG
167748 CACCCTTTCA
Statistics
Matches: 485, Mismatches: 77, Indels: 54
0.79 0.12 0.09
Matches are distributed among these distances:
145 25 0.05
146 11 0.02
147 1 0.00
148 11 0.02
149 3 0.01
150 18 0.04
151 27 0.06
152 30 0.06
153 64 0.13
154 218 0.45
155 28 0.06
156 45 0.09
157 4 0.01
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (152 bp):
CAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTTAGTGGCACCCATTTCAAAGCCCACAAGTC
AGTGGCACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAG
TGGTATCATTTCAAAACCCACA
Found at i:167370 original size:92 final size:92
Alignment explanation
Indices: 167083--167749 Score: 431
Period size: 92 Copynumber: 7.3 Consensus size: 92
167073 AAGTGGCATT
* *
167083 ATTTTAAAGCCCACACAAGTCAGTGGCAACCCATTTGAAAGCCCACACAAGTCGGTGGTAACCCA
1 ATTTCAAAGCCCACACAAGTCAGTGGCAACTCATTTGAAAGCCCACACAAGTCGGTGGTAACCCA
* * *
167148 TTTCAAAACCCACACAAGTCGGTGGCAACCC
66 TTTCAAAGCCCACAAAAGT---T-GCCACCC
** * * * * * *
167179 ATTTCAAAG--CTTACAAGTTAGTGAC-A-TCCTTCTCAAAG-CC-CACAAGTCAGT-G-ACATC
1 ATTTCAAAGCCCACACAAGTCAGTGGCAACTCATT-TGAAAGCCCACACAAGTCGGTGGTA-ACC
* *
167236 C-TTCTCAAAGCCCACACAAGTCAGTGGCAACCC
64 CATT-TCAAAGCCCACA-AA---AGTTGCCACCC
* ** *
167269 ATTTCAAAGCCCACACAAGTCGGTATCAACTCATTTGAAAACCCACACAAGTCGGTGGTAACCCA
1 ATTTCAAAGCCCACACAAGTCAGTGGCAACTCATTTGAAAGCCCACACAAGTCGGTGGTAACCCA
167334 TTTCAAAGCCCACAAAAGTTGCCACCC
66 TTTCAAAGCCCACAAAAGTTGCCACCC
* * * * *
167361 ATTTGAAAGCCCACACAAGTCAATGGCAACCCATTTCAAAGCCCACATAAGTCGGTGGTAACCCA
1 ATTTCAAAGCCCACACAAGTCAGTGGCAACTCATTTGAAAGCCCACACAAGTCGGTGGTAACCCA
* * *
167426 TTTCAAAGCCCACAAGTCAG-TGGCATCC
66 TTTCAAAGCCCACAA--AAGTTGCCACCC
* * *
167454 -TTCTCAAAG-CC-CACAAGTCAGTGGC-ATTC-TTCTGAAAGCCCACACAAGTTGGTGGCAACC
1 ATT-TCAAAGCCCACACAAGTCAGTGGCAACTCATT-TGAAAGCCCACACAAGTCGGTGGTAACC
* *
167514 CATTTCAAAGCCCACACAAGTTGGTGGCAACCC
64 CATTTCAAAGCCCACAAAAG-T--T-GCCACCC
* * * * * * * * *
167547 ATTTCAAAGCCTACACAAATCGGTGGAAACCCATTTCAAAG-CC-CGCAAGTCAGTGGT-A-TCA
1 ATTTCAAAGCCCACACAAGTCAGTGGCAACTCATTTGAAAGCCCACACAAGTCGGTGGTAACCCA
* *
167608 TTTCAAAGCCCACACAAGTTGGTGGCAACCC
66 TTTCAAAGCCCACAAAAG-T--T-GCCACCC
* * * * *
167639 ATTTCAAAG-CC-CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC-CATAAGTCAGTGG-CA-CCA
1 ATTTCAAAGCCCACACAAGTCAGTGGCAACTCATTTGAAAGCCCACACAAGTCGGTGGTAACCCA
* * *
167696 TTTCAAAGCCCACAAGTCAG-TGGCACTC
66 TTTCAAAGCCCACAA--AAGTTGCCACCC
*
167724 TTTTCAAAG-CC-CACAAGTCAGTGGCA
1 ATTTCAAAGCCCACACAAGTCAGTGGCA
167750 CCCTTTCAAA
Statistics
Matches: 459, Mismatches: 78, Indels: 78
0.75 0.13 0.13
Matches are distributed among these distances:
85 28 0.06
86 1 0.00
88 41 0.09
89 6 0.01
90 86 0.19
91 25 0.05
92 142 0.31
93 33 0.07
94 36 0.08
95 25 0.05
96 31 0.07
97 5 0.01
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.20
Consensus pattern (92 bp):
ATTTCAAAGCCCACACAAGTCAGTGGCAACTCATTTGAAAGCCCACACAAGTCGGTGGTAACCCA
TTTCAAAGCCCACAAAAGTTGCCACCC
Found at i:167572 original size:246 final size:244
Alignment explanation
Indices: 167111--167762 Score: 856
Period size: 246 Copynumber: 2.7 Consensus size: 244
167101 GTCAGTGGCA
* *
167111 ACCCATTTGAAAGCCCACACAAGTCGGTGGTAACCCATTTCAAAACCCACACAAGTCGGTGGCAA
1 ACCCATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACA-AAGTCGGTGG-AA
** * * * *
167176 CCCATTTCAAAGCTTACAAGTTAGTGACATCCTTCTCAAAGCCCACAAGTCAGTGACATCCTTCT
64 CCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATTCTTCT
* * *
167241 CAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTATCAACTCATTTG
129 CAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTAGCAACCCATTTC
* *
167306 AAAACCCACACAAGTCGGTGGTAACCCATTTCAAAGCCCACAA-AAGTTGCC
194 AAAACCCACACAAATCGGTGGAAACCCATTTCAAAGCCCACAAGAAG-TGCC
**
167357 ACCCATTTGAAAGCCCACACAAGTCAATGGCAACCCATTTCAAAGCCCACATAAGTCGGTGGTAA
1 ACCCATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACA-AAGTCGGTGG-AA
167422 CCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATTCTTCT
64 CCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATTCTTCT
* ** * *
167487 GAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTC
129 CAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTAGCAACCCATTTC
* * * * **
167552 AAAGCCTACACAAATCGGTGGAAACCCATTTCAAAGCCCGCAAGTCAGTGGT
194 AAAACCCACACAAATCGGTGGAAACCCATTTCAAAGCCCACAAG-AAGTGCC
* * * * * *
167604 A-TCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC-AAGTCAGTGGCATC
1 ACCCATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAAGTCGGTGGAACC
* * *
167667 C-TTTCAAAGCCCATAAGTCAGTGGCA-CCATT-TCAAAGCCCACAAGTCAGTGGCACTCTTTTC
66 CATTTCAAAGCCCACAAGTCAGTGGCATCC-TTCTCAAAGCCCACAAGTCAGTGGCATTCTTCTC
167729 AAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAGCC
130 AAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCC
167763 TACAAGCCAG
Statistics
Matches: 361, Mismatches: 42, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
237 10 0.03
238 4 0.01
239 12 0.03
240 2 0.01
241 34 0.09
242 26 0.07
243 3 0.01
244 9 0.02
246 256 0.71
247 3 0.01
248 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (244 bp):
ACCCATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAAGTCGGTGGAACC
CATTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATTCTTCTCA
AAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTAGCAACCCATTTCAA
AACCCACACAAATCGGTGGAAACCCATTTCAAAGCCCACAAGAAGTGCC
Found at i:175962 original size:22 final size:22
Alignment explanation
Indices: 175934--175977 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
175924 AGAAAGGCTT
175934 CATTCTTTTAA-TTCAAACCAAA
1 CATTCTTTTAACTT-AAACCAAA
175956 CATTCTTTTAACTTAAACCAAA
1 CATTCTTTTAACTTAAACCAAA
175978 ACGGAACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (22 bp):
CATTCTTTTAACTTAAACCAAA
Found at i:187523 original size:27 final size:28
Alignment explanation
Indices: 187485--187538 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
187475 AACTTCAATC
* *
187485 AAAATATTTTTATCATTATTTAATTATA
1 AAAATATTTTTACCAATATTTAATTATA
*
187513 AAAATA-TTTTACCAATATTTCATTAT
1 AAAATATTTTTACCAATATTTAATTAT
187539 CTTTTCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (28 bp):
AAAATATTTTTACCAATATTTAATTATA
Found at i:187855 original size:21 final size:21
Alignment explanation
Indices: 187829--187868 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
187819 AATATTAAAT
187829 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-ATTTATATA
187850 TTTTATAATTAAATTTATA
1 TTTTATAATTAAATTTATA
187869 AAATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAATTAAATTTATATA
Found at i:187877 original size:21 final size:22
Alignment explanation
Indices: 187835--187877 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
187825 AAATTTTTAT
* * *
187835 ATTAATATTTATATATTTTATA
1 ATTAATATTTATAAAATATATA
187857 ATTAA-ATTTATAAAATATATA
1 ATTAATATTTATAAAATATATA
187878 TTTATTGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTAATATTTATAAAATATATA
Found at i:187946 original size:25 final size:25
Alignment explanation
Indices: 187905--187952 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
187895 ATTTAAATTA
187905 ATTTAATTTAAATTATA-AAATTTT
1 ATTTAATTTAAATTATATAAATTTT
*
187929 ATTTAATATTTAATTATATAAATT
1 ATTTAAT-TTAAATTATATAAATT
187953 AAAATTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTAATTTAAATTATATAAATTTT
Found at i:191678 original size:2 final size:2
Alignment explanation
Indices: 191673--191723 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
191663 AAGCTTGTTC
191673 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
191715 TA TG TA TA T
1 TA TA TA TA T
191724 GTGTGTGTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:191728 original size:2 final size:2
Alignment explanation
Indices: 191723--191753 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
191713 TATATGTATA
191723 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
191754 ACGCATGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:192713 original size:21 final size:21
Alignment explanation
Indices: 192672--192713 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
192662 TATTAGCTCA
*
192672 TTAAATTTAAAAATTAAAATT
1 TTAAATTTAAAAATCAAAATT
*
192693 TTAAATTTTAAAA-CAACAATT
1 TTAAATTTAAAAATCAA-AATT
192714 ATCTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATTTAAAAATCAAAATT
Found at i:192921 original size:24 final size:24
Alignment explanation
Indices: 192877--192922 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
192867 CTTACCAAAT
**
192877 TAATTATCCATTTAAATTAAACAA
1 TAATTATCCATCGAAATTAAACAA
192901 TAATTATCCTATCGAAA-TAAAC
1 TAATTATCC-ATCGAAATTAAAC
192923 TATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (24 bp):
TAATTATCCATCGAAATTAAACAA
Found at i:194780 original size:17 final size:18
Alignment explanation
Indices: 194752--194785 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
194742 ATAAATAAAT
194752 AAATAAATAATATAATTG
1 AAATAAATAATATAATTG
194770 AAATAAA-AATATAATT
1 AAATAAATAATATAATT
194786 ACATCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAATAAATAATATAATTG
Found at i:195429 original size:20 final size:20
Alignment explanation
Indices: 195390--195432 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
195380 CAATAATGCC
*
195390 ATTTTTATTATCTTTTAAAT
1 ATTTTTATTATCTTTCAAAT
195410 ATTTTTATTAT-TTCTCAAAT
1 ATTTTTATTATCTT-TCAAAT
195430 ATT
1 ATT
195433 ATTAAGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTATTATCTTTCAAAT
Found at i:195614 original size:21 final size:19
Alignment explanation
Indices: 195575--195617 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
195565 TTAATATATA
*
195575 TAATAATTTAAATTTAAAT
1 TAATAATTTAAATTAAAAT
195594 TAATAATTTTAAAATTAAAAT
1 TAATAA-TTT-AAATTAAAAT
195615 TAA
1 TAA
195618 ATTATTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAATTTAAATTAAAAT
Found at i:195618 original size:26 final size:26
Alignment explanation
Indices: 195530--195621 Score: 71
Period size: 26 Copynumber: 3.5 Consensus size: 26
195520 TACGCTTTGA
* *
195530 AAAATTAAATTAA-AGTTTTAAATATG
1 AAAATTAAATTAATAATTTTAAA-ATT
* * * *
195556 ATATTTATATTAAT-ATATATAATAATTT
1 AAAATTAAATTAATAAT-TTTAA-AA-TT
*
195584 AAATTTAAATTAATAATTTTAAAATT
1 AAAATTAAATTAATAATTTTAAAATT
195610 AAAATTAAATTA
1 AAAATTAAATTA
195622 TTATGATAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
26 24 0.47
27 7 0.14
28 18 0.35
29 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AAAATTAAATTAATAATTTTAAAATT
Found at i:196987 original size:3 final size:3
Alignment explanation
Indices: 196979--197010 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
196969 ACTTATTCTT
196979 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
197011 TTGAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:197144 original size:20 final size:20
Alignment explanation
Indices: 197109--197147 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
197099 TATAATTATT
**
197109 TATTATTATATTTAATATAA
1 TATTATTATAAATAATATAA
197129 TATTATTATAAATAATATA
1 TATTATTATAAATAATATA
197148 TTAATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATTATAAATAATATAA
Found at i:197669 original size:15 final size:16
Alignment explanation
Indices: 197645--197677 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
197635 TAATAATGTA
197645 AATATAAATTATA-AT
1 AATATAAATTATATAT
*
197660 AATATTAATTATATAT
1 AATATAAATTATATAT
197676 AA
1 AA
197678 AAATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAAATTATATAT
Found at i:198123 original size:16 final size:17
Alignment explanation
Indices: 198099--198145 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
198089 ATATAATATA
*
198099 AAAATTAATTTAAAAAT
1 AAAATTAATATAAAAAT
198116 AAAA-TAATATAAAAAT
1 AAAATTAATATAAAAAT
*
198132 AATATTAATATAAA
1 AAAATTAATATAAA
198146 TTAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTAATATAAAAAT
Found at i:198169 original size:38 final size:39
Alignment explanation
Indices: 198127--198215 Score: 89
Period size: 38 Copynumber: 2.3 Consensus size: 39
198117 AAATAATATA
198127 AAAATA-ATATTAATATAAATTA-AATAT-TTAAATATTTT
1 AAAATATATA-TAATATAAATTATAATATGTTAAA-ATTTT
* *
198165 AAAATTTATATGATATAAATTATTAATATGTTAAAA-TTT
1 AAAATATATATAATATAAATTA-TAATATGTTAAAATTTT
*
198204 -AAATAAATATAA
1 AAAATATATATAA
198216 AATATTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
38 25 0.60
39 6 0.14
40 6 0.14
41 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (39 bp):
AAAATATATATAATATAAATTATAATATGTTAAAATTTT
Found at i:198214 original size:33 final size:33
Alignment explanation
Indices: 198136--198221 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 33
198126 AAAAATAATA
*
198136 TTAATATAAAT-TAAATATTTAAATATTTTAAAAT
1 TTAA-ATAAATATAAATA-TTAAATATGTTAAAAT
* *
198170 TTATAT-GATATAAATTATT-AATATGTTAAAAT
1 TTAAATAAATATAAA-TATTAAATATGTTAAAAT
198202 TTAAATAAATATAAAATATT
1 TTAAATAAATAT-AAATATT
198222 TTAAATATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
32 19 0.44
33 16 0.37
34 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (33 bp):
TTAAATAAATATAAATATTAAATATGTTAAAAT
Found at i:198224 original size:20 final size:20
Alignment explanation
Indices: 198201--198240 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
198191 TATGTTAAAA
198201 TTTAAATA-AATATAAAATAT
1 TTTAAATATAAT-TAAAATAT
198221 TTTAAATATAATTAAAATAT
1 TTTAAATATAATTAAAATAT
198241 AATAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAATATAATTAAAATAT
Found at i:198246 original size:20 final size:20
Alignment explanation
Indices: 198203--198246 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
198193 TGTTAAAATT
**
198203 TAAATAAATATAAAATATTT
1 TAAATAAATATAAAATATAA
198223 TAAATATAAT-TAAAATATAA
1 TAAATA-AATATAAAATATAA
198243 TAAA
1 TAAA
198247 ATTTATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATAAATATAAAATATAA
Found at i:198267 original size:19 final size:18
Alignment explanation
Indices: 198235--198280 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
198225 AATATAATTA
*
198235 AAATATAATAAAATTTAT
1 AAATATTATAAAATTTAT
198253 AAATATTATATAAATTTAT
1 AAATATTATA-AAATTTAT
198272 AAATGATTA
1 AAAT-ATTA
198281 CGGTTACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.36
19 12 0.48
20 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AAATATTATAAAATTTAT
Found at i:198267 original size:29 final size:30
Alignment explanation
Indices: 198206--198275 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
198196 TAAAATTTAA
198206 ATAAATAT-A-AAATATTTTAAATATAATT
1 ATAAATATAATAAATATTTTAAATATAATT
*
198234 A-AAATATAATAAA-ATTTATAAATATTA-T
1 ATAAATATAATAAATATTT-TAAATATAATT
*
198262 ATAAAT-TTATAAAT
1 ATAAATATAATAAAT
198276 GATTACGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 6 0.17
28 14 0.40
29 15 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATAAATATAATAAATATTTTAAATATAATT
Found at i:198613 original size:19 final size:19
Alignment explanation
Indices: 198589--198626 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
198579 TACCTCAACA
198589 AATAATTGTTTATAATGAG
1 AATAATTGTTTATAATGAG
198608 AATAATTGTTTATAATGAG
1 AATAATTGTTTATAATGAG
198627 GTCATGCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
AATAATTGTTTATAATGAG
Found at i:198816 original size:18 final size:18
Alignment explanation
Indices: 198793--198828 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
198783 AAATTTTCAC
*
198793 ATATTTTATATATTCATT
1 ATATTTTATACATTCATT
198811 ATATTTTATACATTCATT
1 ATATTTTATACATTCATT
198829 TCATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTTATACATTCATT
Found at i:201665 original size:16 final size:16
Alignment explanation
Indices: 201616--201668 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
201606 GTTAAATTTA
*
201616 TTTAATAAATAAATAT
1 TTTAATAAATAAAAAT
201632 TTTAAATAGAA-AATAAAT
1 TTT-AATA-AATAA-AAAT
201650 TTTAATAAATAAAAAT
1 TTTAATAAATAAAAAT
201666 TTT
1 TTT
201669 TATTAATCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 12 0.38
17 12 0.38
18 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAATAAATAAAAAT
Found at i:201669 original size:17 final size:17
Alignment explanation
Indices: 201616--201670 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
201606 GTTAAATTTA
*
201616 TTTAATAAATAAATATT
1 TTTAATAAATAAAAATT
*
201633 TTAAATAGAA-AATAAA-T
1 TTTAATA-AATAA-AAATT
201650 TTTAATAAATAAAAATT
1 TTTAATAAATAAAAATT
201667 TTTA
1 TTTA
201671 TTAATCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 5 0.16
17 22 0.71
18 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAATAAATAAAAATT
Found at i:201932 original size:61 final size:61
Alignment explanation
Indices: 201853--201977 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
201843 TAATTGTTTT
201853 TTTTTTTGGAGGGTTTGTAATTTTATTTATATAAAAGTTATAAAATTGTTTACAAAGAAAG
1 TTTTTTTGGAGGGTTTGTAATTTTATTTATATAAAAGTTATAAAATTGTTTACAAAGAAAG
201914 TTTTTTTGGAGGGTTTGTAATTTTATTTATATAAAAGTTATAAAATTGTTTACAAAGAAAG
1 TTTTTTTGGAGGGTTTGTAATTTTATTTATATAAAAGTTATAAAATTGTTTACAAAGAAAG
201975 TTT
1 TTT
201978 ATAACATAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (61 bp):
TTTTTTTGGAGGGTTTGTAATTTTATTTATATAAAAGTTATAAAATTGTTTACAAAGAAAG
Found at i:203644 original size:15 final size:15
Alignment explanation
Indices: 203624--203654 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
203614 TTAAGATTCA
*
203624 TGTTTATTATTATAT
1 TGTTTATTATAATAT
203639 TGTTTATTATAATAT
1 TGTTTATTATAATAT
203654 T
1 T
203655 TACTAATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TGTTTATTATAATAT
Found at i:206994 original size:27 final size:27
Alignment explanation
Indices: 206952--207008 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
206942 ACTGTGCAAC
*
206952 ATTAATTATTTTAAATTGAATTTCAAA
1 ATTAATTATTTCAAATTGAATTTCAAA
*
206979 ATTAATTATTTCAAATTGAATTTTAAA
1 ATTAATTATTTCAAATTGAATTTCAAA
207006 ATT
1 ATT
207009 GATTGATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (27 bp):
ATTAATTATTTCAAATTGAATTTCAAA
Found at i:207009 original size:13 final size:13
Alignment explanation
Indices: 206959--207010 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
206949 AACATTAATT
206959 ATTTT-AAATTGA
1 ATTTTAAAATTGA
*
206971 ATTTCAAAATT-A
1 ATTTTAAAATTGA
*
206983 ATTATTTCAAATTGA
1 A-T-TTTAAAATTGA
206998 ATTTTAAAATTGA
1 ATTTTAAAATTGA
207011 TTGATAACAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 6 0.19
13 16 0.50
14 8 0.25
15 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (13 bp):
ATTTTAAAATTGA
Found at i:209313 original size:2 final size:2
Alignment explanation
Indices: 209306--209352 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
209296 AGCTTTTGTT
209306 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
209348 TC TC T
1 TC TC T
209353 AATTATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:209471 original size:27 final size:25
Alignment explanation
Indices: 209432--209482 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
209422 AACACAGAAT
**
209432 AATAAAATTTTTTAATTTTATAAATAA
1 AATAAAAAATTTT-ATTTT-TAAATAA
209459 AATAAAAAATTTTATTTTTAAATA
1 AATAAAAAATTTTATTTTTAAATA
209483 TATTTTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 5 0.23
27 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATAAAAAATTTTATTTTTAAATAA
Found at i:210252 original size:6 final size:6
Alignment explanation
Indices: 210241--210269 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
210231 TAAAACTCAA
210241 TCTTTT TCTTTT TCTTTT TCTTTT T-TTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
210270 ACATGGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TCTTTT
Found at i:212120 original size:17 final size:18
Alignment explanation
Indices: 212098--212136 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
212088 TTAAATATTA
*
212098 AATTTTATGTTT-AAAAT
1 AATTTTATATTTAAAAAT
*
212115 AATTTTTTATTTAAAAAT
1 AATTTTATATTTAAAAAT
212133 AATT
1 AATT
212137 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTTTATATTTAAAAAT
Found at i:212131 original size:18 final size:19
Alignment explanation
Indices: 212100--212136 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
212090 AAATATTAAA
*
212100 TTTTATGTTTAAAATAATT
1 TTTTATGTTAAAAATAATT
212119 TTTTAT-TTAAAAATAATT
1 TTTTATGTTAAAAATAATT
212137 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTTATGTTAAAAATAATT
Found at i:212170 original size:23 final size:24
Alignment explanation
Indices: 212144--212197 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
212134 ATTATAAAAA
212144 TATATAAATATTAAT-ATAATTTT
1 TATATAAATATTAATAATAATTTT
* *
212167 TATA-ATATTTTAATAATAATTTT
1 TATATAAATATTAATAATAATTTT
212190 TAT-TAAAT
1 TATATAAAT
212198 TAAATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATAAATATTAATAATAATTTT
Found at i:213166 original size:13 final size:13
Alignment explanation
Indices: 213150--213175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
213140 TAAATTAATT
213150 AAATTAATTTTAA
1 AAATTAATTTTAA
213163 AAATTAATTTTAA
1 AAATTAATTTTAA
213176 TTCGAATTAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTAATTTTAA
Found at i:213490 original size:3 final size:3
Alignment explanation
Indices: 213482--213512 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
213472 TGCCAAACCC
213482 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
213513 AAATAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:213781 original size:21 final size:19
Alignment explanation
Indices: 213747--213785 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
213737 AATTATAAAA
213747 TTTAAATATATAAATAATT
1 TTTAAATATATAAATAATT
213766 TTTAATATATTATAAATAAT
1 TTTAA-ATA-TATAAATAAT
213786 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAATATATAAATAATT
Found at i:220713 original size:53 final size:56
Alignment explanation
Indices: 220602--220719 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 56
220592 TTAGAATTCA
* * * ** *
220602 AATTTAAAATTTGTTAATACTAAATTAAAAGATAAATTTTATAAGTCAATGGAGTTT
1 AATTTAAAATTTGTTAATAC-AAATTAAAAAATAAATTATATAAATCAATAAAATTT
*
220659 AATTTAAAATTT-TTTATA-AAATTAAAAAAT-AATTATATAAATCAATAAAATTT
1 AATTTAAAATTTGTTAATACAAATTAAAAAATAAATTATATAAATCAATAAAATTT
220712 AATTTAAA
1 AATTTAAA
220720 TTTATCTAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 26 0.48
54 11 0.20
56 5 0.09
57 12 0.22
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (56 bp):
AATTTAAAATTTGTTAATACAAATTAAAAAATAAATTATATAAATCAATAAAATTT
Found at i:222436 original size:20 final size:20
Alignment explanation
Indices: 222389--222436 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
222379 AATTTTAAAG
* * *
222389 TAATTATTGTACATTAATAT
1 TAATTAATGTAAATTAAAAT
222409 T-ATATAATGTAAATTAAAAT
1 TAAT-TAATGTAAATTAAAAT
222429 TAATTAAT
1 TAATTAAT
222437 CGTGATTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (20 bp):
TAATTAATGTAAATTAAAAT
Found at i:233556 original size:33 final size:34
Alignment explanation
Indices: 233500--233633 Score: 132
Period size: 32 Copynumber: 3.8 Consensus size: 34
233490 ATAAAATATG
233500 ATATT-AAATATAATAAAAAATATAAATATATTAAT
1 ATATTAAAAT-TAAT-AAAAATATAAATATATTAAT
* *
233535 ACTA-TAAAATTTAT-ATAATATAAAT-TATTAAT
1 A-TATTAAAATTAATAAAAATATAAATATATTAAT
*
233567 ATATTAAAATTAATAAAAATATAAAATATTTTAATT
1 ATATTAAAATTAATAAAAATAT-AAATATATTAA-T
*
233603 AATATTAAAATATAATAAAATATATGAATAT
1 -ATATTAAAAT-TAATAAAA-ATATAAATAT
233634 GATATATTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
31 2 0.02
32 17 0.20
33 16 0.19
34 4 0.05
35 10 0.12
36 7 0.08
37 10 0.12
38 13 0.16
39 4 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (34 bp):
ATATTAAAATTAATAAAAATATAAATATATTAAT
Found at i:233580 original size:27 final size:27
Alignment explanation
Indices: 233501--233607 Score: 69
Period size: 25 Copynumber: 3.9 Consensus size: 27
233491 TAAAATATGA
*
233501 TATTAAATATAATAAAA--AATATAAAT
1 TATT-AATATATTAAAATTAATATAAAT
*
233527 ATATTAATACTATAAAATTTATATAATATAAAT
1 -TATTAATA-TATTAAA---AT-TAATATAAAT
*
233560 TATTAATATATTAAAATTAATA-AAAA
1 TATTAATATATTAAAATTAATATAAAT
* **
233586 TA-TAAAATATTTTAATTAATAT
1 TATTAATATATTAAAATTAATAT
233608 TAAAATATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
25 16 0.25
26 9 0.14
27 14 0.22
28 2 0.03
30 1 0.02
31 6 0.09
32 8 0.12
33 9 0.14
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
TATTAATATATTAAAATTAATATAAAT
Found at i:233595 original size:25 final size:26
Alignment explanation
Indices: 233550--233617 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
233540 AAAATTTATA
* *
233550 TAATATAAATTATTAATATATTAAAAT
1 TAATATAAAATA-TAAAATATTAAAAT
**
233577 TAATA-AAAATATAAAATATTTTAAT
1 TAATATAAAATATAAAATATTAAAAT
233602 TAATATTAAAATATAA
1 TAATA-TAAAATATAA
233618 TAAAATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 16 0.46
26 5 0.14
27 14 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAATATAAAATATAAAATATTAAAAT
Found at i:237087 original size:2 final size:2
Alignment explanation
Indices: 237080--237108 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
237070 CTACAAGAAT
237080 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
237109 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:237113 original size:2 final size:2
Alignment explanation
Indices: 237108--237161 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
237098 TCTCTCTCTC
237108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
237150 TA TA TA TA TA TA
1 TA TA TA TA TA TA
237162 GAAAGAATCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:239501 original size:17 final size:17
Alignment explanation
Indices: 239479--239517 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
239469 ATAAATATAT
239479 ATAAAT-TAAGAAATGAA
1 ATAAATATAA-AAATGAA
*
239496 ATAAATATAAAAATTAA
1 ATAAATATAAAAATGAA
239513 ATAAA
1 ATAAA
239518 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAAATATAAAAATGAA
Found at i:239550 original size:15 final size:16
Alignment explanation
Indices: 239530--239561 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
239520 TATTTTAACT
239530 TTTAAAATCAAA-TTA
1 TTTAAAATCAAACTTA
239545 TTTAAAATCAAACTTA
1 TTTAAAATCAAACTTA
239561 T
1 T
239562 AAATAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAATCAAACTTA
Found at i:243908 original size:15 final size:15
Alignment explanation
Indices: 243888--243926 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
243878 TATTTATATT
243888 TAAATTTAAATAACA
1 TAAATTTAAATAACA
*
243903 TAAATTTGAATAACA
1 TAAATTTAAATAACA
243918 -AAAGTTTAA
1 TAAA-TTTAA
243927 CGATAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (15 bp):
TAAATTTAAATAACA
Found at i:247457 original size:29 final size:29
Alignment explanation
Indices: 247424--247497 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 29
247414 ATTTATATTT
247424 AAAATATTTTATAATTTATATAAA-TTTA
1 AAAATATTTTATAATTTATATAAATTTTA
*
247452 AGAAATATTCGTT-TCATTTATATAAATTTTA
1 A-AAATATT--TTATAATTTATATAAATTTTA
247483 AAATATATATTTATA
1 AAA-ATAT-TTTATA
247498 TCGTATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
28 1 0.03
29 7 0.19
30 16 0.43
31 12 0.32
32 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (29 bp):
AAAATATTTTATAATTTATATAAATTTTA
Found at i:247507 original size:18 final size:19
Alignment explanation
Indices: 247486--247523 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
247476 AATTTTAAAA
247486 TATATATTT-ATATCGTAT
1 TATATATTTAATATCGTAT
*
247504 TATATATTTAATATTGTAT
1 TATATATTTAATATCGTAT
247523 T
1 T
247524 CAAATCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
TATATATTTAATATCGTAT
Found at i:247708 original size:32 final size:32
Alignment explanation
Indices: 247672--247737 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
247662 CAGATTTATG
* *
247672 TTATTTTAGTTTT-GAGTCATTTTGGATTCAAA
1 TTATTTCAGTTTTGGA-TCATTTTAGATTCAAA
247704 TTATTTCAGTTTTGGATCATTTTAGATTCAAA
1 TTATTTCAGTTTTGGATCATTTTAGATTCAAA
247736 TT
1 TT
247738 TAATACATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.53
Consensus pattern (32 bp):
TTATTTCAGTTTTGGATCATTTTAGATTCAAA
Found at i:248128 original size:21 final size:23
Alignment explanation
Indices: 248104--248147 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
248094 AAATAAAATT
*
248104 ATTAGCATTAAA-AAA-TATTTA
1 ATTAGCAATAAATAAATTATTTA
*
248125 ATTATCAATAAATAAATTATTTA
1 ATTAGCAATAAATAAATTATTTA
248148 TAAAAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (23 bp):
ATTAGCAATAAATAAATTATTTA
Found at i:253842 original size:14 final size:14
Alignment explanation
Indices: 253823--253874 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
253813 AAAATAAATA
253823 TAATATAAATATAT
1 TAATATAAATATAT
*
253837 TAATATTATAAAATAT
1 TAATA-TA-AATATAT
253853 ATAATATAAAT-TAT
1 -TAATATAAATATAT
253867 TAATATAA
1 TAATATAA
253875 TAAAATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 8 0.24
14 8 0.24
15 4 0.12
16 8 0.24
17 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATATAAATATAT
Found at i:253870 original size:30 final size:31
Alignment explanation
Indices: 253820--253927 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 31
253810 AAAAAAATAA
*
253820 ATATAATATAAATATATTAATATTATAAAAT
1 ATATAATATAAATATATTAATATAATAAAAT
253851 ATATAATATAAAT-TATTAATATAATAAAATTT
1 ATATAATATAAATATATTAATATAATAAAA--T
* *
253883 ATAAAAATATAAAATATTTTAA-ATAATATTAAA-
1 AT-ATAATAT-AAATATATTAATATAATA--AAAT
253916 ATATAATATAAA
1 ATATAATATAAA
253928 AGATAATATG
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
30 15 0.23
31 16 0.24
32 9 0.14
33 8 0.12
34 10 0.15
35 5 0.08
36 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
ATATAATATAAATATATTAATATAATAAAAT
Found at i:253905 original size:10 final size:10
Alignment explanation
Indices: 253818--253920 Score: 58
Period size: 9 Copynumber: 10.7 Consensus size: 10
253808 GTAAAAAAAT
*
253818 AAATATAATA
1 AAATATATTA
253828 TAAATATATTA
1 -AAATATATTA
*
253839 ATAT-TA-TA
1 AAATATATTA
253847 AAATATA-TA
1 AAATATATTA
* *
253856 ATATAAATTA
1 AAATATATTA
* *
253866 TTAATATAATA
1 -AAATATATTA
*
253877 AAATTTA-TA
1 AAATATATTA
253886 AAA-ATA-TA
1 AAATATATTA
*
253894 AAATAT-TTT
1 AAATATATTA
253903 AAATAATATTA
1 AAAT-ATATTA
253914 AAATATA
1 AAATATA
253921 ATATAAAAGA
Statistics
Matches: 71, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
8 12 0.17
9 23 0.32
10 15 0.21
11 21 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATATATTA
Found at i:253919 original size:47 final size:49
Alignment explanation
Indices: 253816--253927 Score: 133
Period size: 47 Copynumber: 2.3 Consensus size: 49
253806 AAGTAAAAAA
* *
253816 ATAAATATAATATAAATATATTAATATTATAAAATATATAATATAAATT
1 ATAAATATAATATAAATATATTAAAAATATAAAATATATAATATAAATT
* * *
253865 ATTAATATAATA-AAATTTA-TAAAAATATAAAATATTTTAA-ATAATATT
1 ATAAATATAATATAAATATATTAAAAATATAAAATA-TATAATATAA-ATT
253913 A-AAATATAATATAAA
1 ATAAATATAATATAAA
253928 AGATAATATG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
47 26 0.48
48 17 0.31
49 11 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (49 bp):
ATAAATATAATATAAATATATTAAAAATATAAAATATATAATATAAATT
Found at i:253927 original size:22 final size:18
Alignment explanation
Indices: 253809--253933 Score: 74
Period size: 20 Copynumber: 6.6 Consensus size: 18
253799 ATAATAAAAG
* *
253809 TAAAAAAAT-AAATATAA
1 TAAAAATATAAAATATTA
* *
253826 TATAAATATATTAATATTA
1 TAAAAATATA-AAATATTA
*
253845 TAAAATATATAATATAAATTA
1 TAAAA-ATATAA-A-ATATTA
* *
253866 TTAATATAATAAAAT-TTA
1 TAAAAAT-ATAAAATATTA
*
253884 TAAAAATATAAAATATTT
1 TAAAAATATAAAATATTA
*
253902 TAAATAATATTAAAATATAA
1 TAAA-AATA-TAAAATATTA
*
253922 TATAAAAGATAA
1 TA-AAAATATAA
253934 TATGTAAATA
Statistics
Matches: 82, Mismatches: 16, Indels: 18
0.71 0.14 0.16
Matches are distributed among these distances:
17 14 0.17
18 14 0.17
19 18 0.22
20 22 0.27
21 14 0.17
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (18 bp):
TAAAAATATAAAATATTA
Found at i:254357 original size:4 final size:4
Alignment explanation
Indices: 254348--254376 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
254338 TTACAAAGTC
254348 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
254377 GGAATCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:254832 original size:20 final size:20
Alignment explanation
Indices: 254794--254832 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
254784 TTTTTTAAAT
* *
254794 ATTTTTTAAATATAAATATA
1 ATTTTTAAAAAATAAATATA
*
254814 ATTTTTAAAAAATATATAT
1 ATTTTTAAAAAATAAATAT
254833 TTATATTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTTAAAAAATAAATATA
Found at i:254847 original size:13 final size:13
Alignment explanation
Indices: 254829--254853 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
254819 TAAAAAATAT
254829 ATATTTATATTTG
1 ATATTTATATTTG
254842 ATATTTATATTT
1 ATATTTATATTT
254854 AAATTCAAAT
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:258726 original size:2 final size:2
Alignment explanation
Indices: 258721--258750 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
258711 GTGTGTGTGT
*
258721 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
258751 ATCAACACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:259976 original size:5 final size:6
Alignment explanation
Indices: 259950--259978 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
259940 AAACTTGTAC
259950 AAATTT AAATTT AAATTT AAA-TT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
259979 TTTTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:262045 original size:3 final size:3
Alignment explanation
Indices: 262037--262070 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
262027 TGTCTGTGTT
262037 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
262071 ACTCTTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:264930 original size:13 final size:13
Alignment explanation
Indices: 264909--264946 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
264899 TTTGATTTTT
264909 TATTT-TTTTTAA
1 TATTTATTTTTAA
264921 TATTTATTTTTAA
1 TATTTATTTTTAA
264934 TATTTATATTTTA
1 TATTTAT-TTTTA
264947 TACATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTATTTTTAA
Found at i:265078 original size:6 final size:6
Alignment explanation
Indices: 265067--265119 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
265057 AATTTAAAAA
* * *
265067 ATATTT ATATTT ATATTT ATA-TT AAATAT ATATTT ATATTAA ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATT-T ATATTT
265115 ATATT
1 ATATT
265120 CGAATTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 4 0.10
6 30 0.77
7 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
ATATTT
Found at i:265098 original size:17 final size:17
Alignment explanation
Indices: 265078--265112 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
265068 TATTTATATT
265078 TATATTTATATTAAATA
1 TATATTTATATTAAATA
265095 TATATTTATATTAAATA
1 TATATTTATATTAAATA
265112 T
1 T
265113 TTATATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTTATATTAAATA
Found at i:265173 original size:19 final size:19
Alignment explanation
Indices: 265137--265173 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
265127 AAATAACATA
*
265137 AAATTTAGCAATGTACCTC
1 AAATTTAGCAATGGACCTC
*
265156 AAATTTAGCGATGGACCT
1 AAATTTAGCAATGGACCT
265174 GAATTTTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (19 bp):
AAATTTAGCAATGGACCTC
Found at i:268060 original size:21 final size:21
Alignment explanation
Indices: 268034--268082 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
268024 AGCTCTGATC
*
268034 AGCCACTATAGCATTAATATT
1 AGCCACCATAGCATTAATATT
268055 AGCCACCATAGCATTAATATT
1 AGCCACCATAGCATTAATATT
268076 AGCCACC
1 AGCCACC
268083 CTACTCTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (21 bp):
AGCCACCATAGCATTAATATT
Found at i:275607 original size:15 final size:15
Alignment explanation
Indices: 275587--275621 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
275577 TAAAGCTTTA
275587 AAATCCTAACAACCC
1 AAATCCTAACAACCC
*
275602 AAATCCTAACAACTC
1 AAATCCTAACAACCC
275617 AAATC
1 AAATC
275622 GTGATTCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATCCTAACAACCC
Found at i:276393 original size:121 final size:121
Alignment explanation
Indices: 276242--276481 Score: 365
Period size: 121 Copynumber: 2.0 Consensus size: 121
276232 AAAACCTTTT
** * *
276242 TTAACCATAAAACTTGATTTACTGTTGCTATTGCTATTATAAATTCTACTTATGCT-GTGGATTG
1 TTAACCATAAAACTTGATTTACTACTGCTATTGCTACTATAAATTCTACTT-TGATAGTGGATTG
*
276306 TGATGCAATCTCTACTTTTATAAAAACCATGAGAAAACTTTTGAACCAAGGTTGATA
65 TGATGCAATCTCTACTTTTATAAAAACCATGAGAAAACTCTTGAACCAAGGTTGATA
*
276363 TTAACCATAAAACTTGATTTACTACTGCTATTGCTACTATAAATTCTACTTTTATAGTGGATTGT
1 TTAACCATAAAACTTGATTTACTACTGCTATTGCTACTATAAATTCTACTTTGATAGTGGATTGT
* * * * *
276428 GATGCAATCTTTGCTTTTTTAAACATCATGAGAAAACTCTTGAACCAAGGTTGA
66 GATGCAATCTCTACTTTTATAAAAACCATGAGAAAACTCTTGAACCAAGGTTGA
276482 AATAATATCT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
120 2 0.02
121 105 0.98
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (121 bp):
TTAACCATAAAACTTGATTTACTACTGCTATTGCTACTATAAATTCTACTTTGATAGTGGATTGT
GATGCAATCTCTACTTTTATAAAAACCATGAGAAAACTCTTGAACCAAGGTTGATA
Found at i:278151 original size:18 final size:18
Alignment explanation
Indices: 278128--278211 Score: 72
Period size: 17 Copynumber: 4.9 Consensus size: 18
278118 ATATAACACG
*
278128 AATATATTAATATTATAA
1 AATATATTAATAATATAA
278146 AATATA-T-ATAATA-AA
1 AATATATTAATAATATAA
278161 AAT-TATTAAT-ATATTAA
1 AATATATTAATAATA-TAA
* *
278178 AATTTA-TAAAAATATAA
1 AATATATTAATAATATAA
*
278195 AATATTTTAAATAATAT
1 AATATATT-AATAATAT
278212 TTAAACATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
14 2 0.04
15 9 0.17
16 7 0.13
17 16 0.30
18 12 0.23
19 7 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATATTAATAATATAA
Found at i:281789 original size:2 final size:2
Alignment explanation
Indices: 281782--281816 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
281772 CTTAGATACC
281782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
281817 TAATAAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:282819 original size:21 final size:21
Alignment explanation
Indices: 282776--282819 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
282766 TTATAAATTT
***
282776 ATCTAATTTTCAAAAATCTAA
1 ATCTAATTTTCAAAAAAAAAA
*
282797 ATCTTATTTTCAAAAAAAAAA
1 ATCTAATTTTCAAAAAAAAAA
282818 AT
1 AT
282820 GGCTTGAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
ATCTAATTTTCAAAAAAAAAA
Found at i:283619 original size:2 final size:2
Alignment explanation
Indices: 283612--283637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
283602 TTAATAAATT
283612 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
283638 AGTCAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:285003 original size:20 final size:18
Alignment explanation
Indices: 284962--285007 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
284952 AGATTTGATC
*
284962 TTAAATATAATTTTTTATT
1 TTAAAT-TAATTTTTTAAT
284981 TTAAATTAATTTAATTTAAT
1 TTAAATTAATTT--TTTAAT
285001 TTAAATT
1 TTAAATT
285008 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 12 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATTAATTTTTTAAT
Found at i:285209 original size:27 final size:27
Alignment explanation
Indices: 285179--285326 Score: 64
Period size: 26 Copynumber: 5.6 Consensus size: 27
285169 TATTTAATAA
285179 TTTAATAATTTATATTATATTTATATT
1 TTTAATAATTTATATTATATTTATATT
* * *
285206 TTT-ATTATATTATAATAATATTTAAAATAT
1 TTTAATAAT-TTAT-ATTATATTT-ATAT-T
* *
285236 TTT-AT-ATTTATA-TAAATTT-TAATAA
1 TTTAATAATTTATATTATATTTAT-AT-T
* *
285261 ATTAATAATTTATA-T-TATTTAAATT
1 TTTAATAATTTATATTATATTTATATT
** * *
285286 TAAAAT-ATATATTTTATATATTATA-T
1 TTTAATAATTTATATTATAT-TTATATT
285312 TTTAATAA-TTATATT
1 TTTAATAATTTATATT
285327 TAATATTATG
Statistics
Matches: 88, Mismatches: 21, Indels: 25
0.66 0.16 0.19
Matches are distributed among these distances:
24 5 0.06
25 9 0.10
26 30 0.34
27 21 0.24
28 12 0.14
29 5 0.06
30 6 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAATAATTTATATTATATTTATATT
Found at i:285213 original size:22 final size:22
Alignment explanation
Indices: 285188--285248 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
285178 ATTTAATAAT
**
285188 TTATATTATATTTATATTTTTA
1 TTATATTATATTTATATTTAAA
* *
285210 TTATATTATAATAATATTTAAA
1 TTATATTATATTTATATTTAAA
* *
285232 ATATTTTATATTTATAT
1 TTATATTATATTTATAT
285249 AAATTTTAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATATTATATTTATATTTAAA
Found at i:285282 original size:17 final size:17
Alignment explanation
Indices: 285178--285282 Score: 51
Period size: 17 Copynumber: 6.4 Consensus size: 17
285168 GTATTTAATA
285178 ATTTAATAATTTATATT
1 ATTTAATAATTTATATT
* *
285195 ATATTTAT-ATTTTTATT
1 AT-TTAATAATTTATATT
*
285212 ATATT-ATAA-TAATATT
1 AT-TTAATAATTTATATT
** *
285228 -TAAAATATTTTATATTT
1 ATTTAATAATTTATA-TT
* * *
285245 ATATAA-ATTTTA-ATA
1 ATTTAATAATTTATATT
*
285260 AATTAATAATTTATATT
1 ATTTAATAATTTATATT
285277 ATTTAA
1 ATTTAA
285283 ATTTAAAATA
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
15 9 0.14
16 17 0.26
17 31 0.48
18 8 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAATAATTTATATT
Done.