Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2161
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: 357411
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 2
Found at i:171367 original size:33 final size:33
Alignment explanation
Indices: 171311--171377 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
171301 TTCAACGATT
*
171311 TGTATCGATACATAAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
171344 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
171377 T
1 T
171378 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:171578 original size:52 final size:52
Alignment explanation
Indices: 171449--171579 Score: 226
Period size: 52 Copynumber: 2.5 Consensus size: 52
171439 TACACTTCTT
* *
171449 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
*
171501 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
*
171553 TGTATCGATACATGCAGGTAAATTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
171580 ATATTTCGGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
Found at i:175061 original size:23 final size:22
Alignment explanation
Indices: 175030--175078 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
175020 CGTCTCTCAT
** *
175030 TTTTATGTATTTTTGTGCTTTTA
1 TTTTATGTAAATTTG-GCTGTTA
*
175053 TTTTGTGTAAATTTGGCTGTTA
1 TTTTATGTAAATTTGGCTGTTA
175075 TTTT
1 TTTT
175079 TTTTGTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.14, C:0.04, G:0.16, T:0.65
Consensus pattern (22 bp):
TTTTATGTAAATTTGGCTGTTA
Found at i:182950 original size:20 final size:20
Alignment explanation
Indices: 182925--182976 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
182915 TACAAGCCAA
**
182925 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
182945 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
182964 TGTATCGATACAA
1 TGTATCGATACAA
182977 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:183681 original size:39 final size:40
Alignment explanation
Indices: 183601--183691 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 40
183591 TTTTCTTTCT
* *
183601 CCCTTAACTAAAGTAATTTTAACAAATTCGTACATTTTCC
1 CCCTTAACTAAAGTAATTTTAACAAATTCATACATTCTCC
* * *
183641 CCCTTAA-T-AAGATAATTTTAGCAAATTTATGCATTCTCC
1 CCCTTAACTAAAG-TAATTTTAACAAATTCATACATTCTCC
* *
183680 CCTTTTACTAAA
1 CCCTTAACTAAA
183692 AAAAATCTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
38 3 0.07
39 28 0.68
40 8 0.20
41 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.38
Consensus pattern (40 bp):
CCCTTAACTAAAGTAATTTTAACAAATTCATACATTCTCC
Found at i:185080 original size:21 final size:20
Alignment explanation
Indices: 185051--185093 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
185041 GACTAGTGTG
*
185051 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTTGCGACCT
*
185072 GGGAGTGCCGGTTGCGACCT
1 GGGACTGCCGGTTGCGACCT
185092 GG
1 GG
185094 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.26, G:0.44, T:0.21
Consensus pattern (20 bp):
GGGACTGCCGGTTGCGACCT
Found at i:189477 original size:21 final size:21
Alignment explanation
Indices: 189448--189492 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
189438 AAGTTTTTAT
*
189448 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
189468 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
189490 TTT
1 TTT
189493 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:191731 original size:13 final size:13
Alignment explanation
Indices: 191713--191738 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
191703 CAATTTTTTG
191713 TGTATCGATACAT
1 TGTATCGATACAT
191726 TGTATCGATACAT
1 TGTATCGATACAT
191739 ACTTTGTGTA
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:191750 original size:32 final size:33
Alignment explanation
Indices: 191693--191756 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
191683 TACAAGCCAA
**
191693 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
191726 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
191757 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:195529 original size:10 final size:10
Alignment explanation
Indices: 195514--195543 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
195504 TTACAAATAT
195514 TTGAATTTTA
1 TTGAATTTTA
195524 TTGAATTTTA
1 TTGAATTTTA
*
195534 TTTAATTTTA
1 TTGAATTTTA
195544 ACAAGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (10 bp):
TTGAATTTTA
Found at i:195576 original size:14 final size:15
Alignment explanation
Indices: 195549--195577 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
195539 TTTTAACAAG
195549 AATAAATATATTTTT
1 AATAAATATATTTTT
195564 AATAAAT-TATTTTT
1 AATAAATATATTTTT
195578 GAGTCAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATAAATATATTTTT
Found at i:196125 original size:29 final size:26
Alignment explanation
Indices: 196072--196125 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
196062 GCAAAGTATA
*
196072 TGATTTCTTTGTTTTATTTTGAAATG
1 TGATTTCTTTGTTTTATTTTCAAATG
*
196098 TGATTTCATTTTTATTTAATTTTCAAAT
1 TGATTTC-TTTGT-TTT-ATTTTCAAAT
196126 ATGTTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 4 0.17
28 3 0.13
29 9 0.39
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (26 bp):
TGATTTCTTTGTTTTATTTTCAAATG
Found at i:199821 original size:19 final size:17
Alignment explanation
Indices: 199792--199840 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
199782 TAAAAACTTA
*
199792 ATTATATTATATTATACT
1 ATTATTTTATATTATA-T
199810 ATTATTTGTATA-TA-AT
1 ATTATTT-TATATTATAT
199826 ATTATTTT-TATTATA
1 ATTATTTTATATTATA
199841 ATAAATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 2 0.07
15 3 0.11
16 9 0.33
17 1 0.04
18 8 0.30
19 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTATTTTATATTATAT
Found at i:199849 original size:19 final size:16
Alignment explanation
Indices: 199804--199843 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
199794 TATATTATAT
* *
199804 TATACTATTATTTGTA
1 TATAATATTATTTTTA
199820 TATAATATTATTTTTA
1 TATAATATTATTTTTA
199836 TTATAATA
1 -TATAATA
199844 AATTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (16 bp):
TATAATATTATTTTTA
Found at i:204809 original size:36 final size:42
Alignment explanation
Indices: 204768--204854 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 42
204758 AATGATAATT
204768 TTAAATGG-AAT-ACCTAATTAG-CCTAGAATG-AAG-TTTG
1 TTAAATGGAAATAACCTAATTAGCCCTAGAATGAAAGTTTTG
204805 -TAAATGGGAAATAACCTAATTAGCCCTAGAATGAAAGTTTTG
1 TTAAAT-GGAAATAACCTAATTAGCCCTAGAATGAAAGTTTTG
204847 TTAAATGG
1 TTAAATGG
204855 TCCTTAAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
36 5 0.12
37 2 0.05
38 3 0.07
39 10 0.23
40 9 0.21
41 3 0.07
42 6 0.14
43 5 0.12
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (42 bp):
TTAAATGGAAATAACCTAATTAGCCCTAGAATGAAAGTTTTG
Found at i:207127 original size:20 final size:20
Alignment explanation
Indices: 207099--207136 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
207089 TAAGTGTTGG
*
207099 GTACAATGTATCGATACAAT
1 GTACAATGTATCAATACAAT
*
207119 GTACCATGTATCAATACA
1 GTACAATGTATCAATACA
207137 TTTCACTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (20 bp):
GTACAATGTATCAATACAAT
Found at i:211521 original size:20 final size:19
Alignment explanation
Indices: 211480--211531 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 19
211470 TTAATATGGT
211480 ATAAATTAA-AAATTAAAATC
1 ATAAA-TAATAAA-TAAAATC
211500 ATCAAA-AATAAATAAAATTC
1 AT-AAATAATAAATAAAA-TC
211520 ATAAATAATAAA
1 ATAAATAATAAA
211532 AAATTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 10 0.36
20 15 0.54
21 3 0.11
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAATAATAAATAAAATC
Found at i:211525 original size:27 final size:25
Alignment explanation
Indices: 211488--211550 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
211478 GTATAAATTA
* *
211488 AAAATTAAAATCATCAAAAATAAAT
1 AAAATTAAAATAATAAAAAATAAAT
*
211513 AAAATTCATAAATAATAAAAAATTAAT
1 AAAATT-A-AAATAATAAAAAATAAAT
**
211540 AATTTTAAAAT
1 AAAATTAAAAT
211551 GAAAAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 10 0.32
26 2 0.06
27 19 0.61
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAATTAAAATAATAAAAAATAAAT
Found at i:217117 original size:20 final size:20
Alignment explanation
Indices: 217088--217138 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
217078 ACCCTTAAAA
*
217088 GTATCCATACACAATT-CAAT
1 GTATCGATACA-AATTGCAAT
**
217108 GTATCGATACATGTTGCAAT
1 GTATCGATACAAATTGCAAT
217128 GTATCGATACA
1 GTATCGATACA
217139 TGAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (20 bp):
GTATCGATACAAATTGCAAT
Found at i:217228 original size:13 final size:13
Alignment explanation
Indices: 217210--217235 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
217200 TACACCAAGT
217210 ATGTATCGATACA
1 ATGTATCGATACA
217223 ATGTATCGATACA
1 ATGTATCGATACA
217236 CCAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:217254 original size:34 final size:32
Alignment explanation
Indices: 217192--217256 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
217182 TTGCCAAACT
**
217192 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
217224 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
217257 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:218879 original size:12 final size:12
Alignment explanation
Indices: 218847--218880 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
218837 AACCATCAAG
*
218847 GATGAAGAAGAT
1 GATGAAGATGAT
*
218859 GATGAAGATGTT
1 GATGAAGATGAT
218871 GATGAAGATG
1 GATGAAGATG
218881 GTGACTCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:223437 original size:13 final size:13
Alignment explanation
Indices: 223419--223457 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
223409 ACATTTTTCT
223419 TTGTATCGATACA
1 TTGTATCGATACA
223432 TTGTATCGATACA
1 TTGTATCGATACA
*
223445 CTGTATCGATACA
1 TTGTATCGATACA
223458 GGAGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:223621 original size:20 final size:20
Alignment explanation
Indices: 223578--223624 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
223568 AAATCTTTTA
223578 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
223599 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
223619 CAAAAT
1 CAAAAT
223625 CAACTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:225929 original size:20 final size:20
Alignment explanation
Indices: 225904--225954 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
225894 ACCCTTAAAA
225904 GTATCGATACACAATT-CAAT
1 GTATCGATACA-AATTGCAAT
**
225924 GTATCGATACATGTTGCAAT
1 GTATCGATACAAATTGCAAT
225944 GTATCGATACA
1 GTATCGATACA
225955 TGAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATCGATACAAATTGCAAT
Found at i:226053 original size:21 final size:20
Alignment explanation
Indices: 226007--226059 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
225997 ATAGCCAAAC
**
226007 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
226027 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
226047 TTGTATCGATACA
1 TTGTATCGATACA
226060 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:228720 original size:14 final size:14
Alignment explanation
Indices: 228710--228744 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
228700 ATGAAAAATG
*
228710 AAAAAGCAAAAAAA
1 AAAAAACAAAAAAA
228724 AAAAAACAAAAACAA
1 AAAAAACAAAAA-AA
228739 AAAAAA
1 AAAAAA
228745 AATGCATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAAAAA
Found at i:230822 original size:60 final size:58
Alignment explanation
Indices: 230724--230923 Score: 204
Period size: 60 Copynumber: 3.3 Consensus size: 58
230714 GTTGACTATT
* * *
230724 TTGGTTTCACTTAAGTCATTGTTCAGGTTTCTAGTTTTATCTAGGCCTTTTCATTGAGTC
1 TTGGTTTCACTCAAGTCATTGTTTAGGTTT-TAGTTTTATCTAGGCCTTTTC-TTAAGTC
* * * *
230784 TTGGTTTCACTTAAGTCATTGTTTAGGCTTTT-GATTTTATCCAAGCCATTTTCTTTAGTC
1 TTGGTTTCACTCAAGTCATTGTTTAGG-TTTTAG-TTTTATCTAGGCC-TTTTCTTAAGTC
* * * * * *
230844 TTAGTTTCACCCAAGTCATTGTTTAGGTTCCTAGTTTTGTCTAGGCCATTTCGTTAAGAC
1 TTGGTTTCACTCAAGTCATTGTTTAGGTT-TTAGTTTTATCTAGGCCTTTTC-TTAAGTC
*
230904 TTGGTTTCGCTCAAGTCATT
1 TTGGTTTCACTCAAGTCATT
230924 TTGTAGACGT
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
59 7 0.06
60 101 0.86
61 9 0.08
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (58 bp):
TTGGTTTCACTCAAGTCATTGTTTAGGTTTTAGTTTTATCTAGGCCTTTTCTTAAGTC
Found at i:231481 original size:151 final size:152
Alignment explanation
Indices: 231298--231595 Score: 429
Period size: 151 Copynumber: 2.0 Consensus size: 152
231288 TCTTCTAACT
* * *
231298 TGTTATCAGTTTGTTTCAACTGTTAATGAAAATTTTAGAAATCACATATTCCTCATCATGTTTCT
1 TGTTATCAGTTTGTTTCAACTATTAATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCCT
* * * **
231363 TTCCTTTAGCCTATTATTAGTTTGTTTCGATTGTTGAA-AGAAATTGTAG-AACCATATATTCTT
66 TTCCTTTAGCCTATTATTAGTATATTTCGATTGTTGAAGA-AAATTGTAGAAACCACATATTCCC
231426 CATCATGTTCTTTTCTTTTAGCC
130 CATCATGTTCTTTTCTTTTAGCC
***
231449 TGTTATCAGTTTGTTTTGGCTATTAATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCCT
1 TGTTATCAGTTTGTTTCAACTATTAATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCCT
* * * * *
231514 TTCCTTTAGCCTATTATTAGTATATTTTGCTTGTTGATGAAAATTTTAGAAATCACATATTCCCC
66 TTCCTTTAGCCTATTATTAGTATATTTCGATTGTTGAAGAAAATTGTAGAAACCACATATTCCCC
231579 ATCATGTTCTTTTCTTT
131 ATCATGTTCTTTTCTTT
231596 AAGCTTGCTA
Statistics
Matches: 129, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
151 100 0.78
152 29 0.22
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (152 bp):
TGTTATCAGTTTGTTTCAACTATTAATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCCT
TTCCTTTAGCCTATTATTAGTATATTTCGATTGTTGAAGAAAATTGTAGAAACCACATATTCCCC
ATCATGTTCTTTTCTTTTAGCC
Found at i:231610 original size:76 final size:75
Alignment explanation
Indices: 231318--231596 Score: 339
Period size: 76 Copynumber: 3.7 Consensus size: 75
231308 TTGTTTCAAC
*
231318 TGTTAATGAAAATTTTAGAAATCACATATTCCTCATCATGTTTCTTTCCTTTAGCCTATTATTAG
1 TGTTAATGAAAATTTTAGAAATCACATATTCCCCATCATG-TTCTTTCCTTTAGCCTATTATTAG
* *
231383 TTTGTTTCGAT
65 TTTGTTTTGCT
* * * * ** * * *
231394 TGTTGAAAG-AAATTGTAG-AACCATATATTCTTCATCATGTTCTTTTCTTTTAGCCTGTTATCA
1 TGTT-AATGAAAATTTTAGAAATCACATATTCCCCATCATGTTC-TTTCCTTTAGCCTATTATTA
231457 GTTTGTTTTGGC-
64 GTTTGTTTT-GCT
*
231469 TATTAATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCCTTTCCTTTAGCCTATTATTAG
1 TGTTAATGAAAATTTTAGAAATCACATATTCCCCATCATGTT-CTTTCCTTTAGCCTATTATTAG
* *
231534 TATATTTTGCT
65 TTTGTTTTGCT
* *
231545 TGTTGATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTTCTTTA
1 TGTTAATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTCCTTTA
231597 AGCTTGCTAT
Statistics
Matches: 171, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
74 6 0.04
75 65 0.38
76 96 0.56
77 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (75 bp):
TGTTAATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTCCTTTAGCCTATTATTAGT
TTGTTTTGCT
Found at i:232191 original size:21 final size:21
Alignment explanation
Indices: 232158--232198 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
232148 CTAAGTAAAA
232158 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
232179 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
232199 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:232263 original size:20 final size:19
Alignment explanation
Indices: 232238--232308 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
232228 ACCCTGAAAA
232238 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
232258 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
232277 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
232298 GTATCGATACA
1 GTATCGATACA
232309 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:232404 original size:10 final size:10
Alignment explanation
Indices: 232385--232415 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
232375 AATCTCATTT
232385 TCACTGTTCA
1 TCACTGTTCA
*
232395 TCACTATTCA
1 TCACTGTTCA
232405 TCACTGTTCA
1 TCACTGTTCA
232415 T
1 T
232416 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:232437 original size:21 final size:22
Alignment explanation
Indices: 232403--232458 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
232393 CATCACTATT
232403 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
232425 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
*
232446 CATCGCTGTTCAT
1 CATCACTGTTCAT
232459 AGGTCATTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:232513 original size:13 final size:13
Alignment explanation
Indices: 232495--232533 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
232485 TCACTATTCA
232495 TGTATCGATACAT
1 TGTATCGATACAT
*
232508 TGTATCGATACAG
1 TGTATCGATACAT
232521 TGTATCGATACAT
1 TGTATCGATACAT
232534 CATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:233066 original size:34 final size:35
Alignment explanation
Indices: 233003--233069 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
232993 CTAAGTGATT
233003 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
233039 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
233070 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:234231 original size:25 final size:24
Alignment explanation
Indices: 234203--234250 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
234193 TATTAACTTT
* *
234203 AATTTTAATTTTCTTTTAATTTTAG
1 AATTTTAATTCTATTTT-ATTTTAG
*
234228 AATTTTTATTCTATTTTATTTTA
1 AATTTTAATTCTATTTTATTTTA
234251 TTTTTTAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (24 bp):
AATTTTAATTCTATTTTATTTTAG
Found at i:235354 original size:13 final size:13
Alignment explanation
Indices: 235336--235360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
235326 CAATTCTTCA
235336 TGTATCGATACAT
1 TGTATCGATACAT
235349 TGTATCGATACA
1 TGTATCGATACA
235361 ATGTGCCATG
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:235371 original size:33 final size:32
Alignment explanation
Indices: 235316--235380 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
235306 TTTGCGACAA
*
235316 TGTATCGATACAATTCTTCATGTATCGATACAT
1 TGTATCGATACAATTC-TCATGTATCAATACAT
235349 TGTATCGATACAATGTGC-CATGTATCAATACA
1 TGTATCGATACAAT-T-CTCATGTATCAATACA
235381 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAATTCTCATGTATCAATACAT
Found at i:235454 original size:19 final size:18
Alignment explanation
Indices: 235431--235502 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 18
235421 ACATTTGTTC
235431 ATGTATCGATACAATGAA
1 ATGTATCGATACAATGAA
*
235449 CATGTATCGATACAAAGCATA
1 -ATGTATCGATACAATG-A-A
*
235470 ATGTATCGATACATCTGAA
1 ATGTATCGATACA-ATGAA
235489 AGTGTATCGATACA
1 A-TGTATCGATACA
235503 TACAAGGGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
19 17 0.37
20 27 0.59
21 2 0.04
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (18 bp):
ATGTATCGATACAATGAA
Found at i:235475 original size:20 final size:19
Alignment explanation
Indices: 235430--235482 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
235420 TACATTTGTT
*
235430 CATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
235449 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAG-A-A
235470 -ATGTATCGATACA
1 CATGTATCGATACA
235483 TCTGAAAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 16 0.52
20 14 0.45
21 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:236126 original size:33 final size:32
Alignment explanation
Indices: 236072--236135 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
236062 TTGCGACAAA
* *
236072 GTATCGATACAATTCTTCATGTCTCGATACATT
1 GTATCGATACAATTC-TCATGTATCAATACATT
236105 GTATCGATACAATGTGC-CATGTATCAATACA
1 GTATCGATACAAT-T-CTCATGTATCAATACA
236136 AATAGTGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 25 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (32 bp):
GTATCGATACAATTCTCATGTATCAATACATT
Found at i:236209 original size:19 final size:21
Alignment explanation
Indices: 236185--236237 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
236175 TACATTTGTT
*
236185 CATGTATCGATACAATG-A-A
1 CATGTATCGATACAAAGCATA
*
236204 CATGTATCGTTACAAAGCATA
1 CATGTATCGATACAAAGCATA
236225 -ATGTATCGATACA
1 CATGTATCGATACA
236238 TCTGAAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 15 0.52
20 13 0.45
21 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
CATGTATCGATACAAAGCATA
Found at i:236341 original size:755 final size:755
Alignment explanation
Indices: 234891--236406 Score: 2960
Period size: 755 Copynumber: 2.0 Consensus size: 755
234881 AGCCAAATTC
*
234891 TTGAAAAATTATAACCCAAGGTTAAATGCAACCTTACACAATTCATGGAAAATTTTACAAACGAA
1 TTGAAAAATTATAACCCAAGGTTAAATGCAACCTTACACAATTCAAGGAAAATTTTACAAACGAA
234956 AATTACCTTTGAATAGGCTGATGTTTGTGAAAGAATAAACACAAATCAAATACAAAAAGCTTTCA
66 AATTACCTTTGAATAGGCTGATGTTTGTGAAAGAATAAACACAAATCAAATACAAAAAGCTTTCA
235021 AAGAATAACAACAACGAAAATAAAAGCTCTTAAAATGAGAAAATAAGTAAAACTTTGAATGCTTT
131 AAGAATAACAACAACGAAAATAAAAGCTCTTAAAATGAGAAAATAAGTAAAACTTTGAATGCTTT
235086 GATCTCTTGGTGTTTTTTGAGGAATTCACTTGATGTTCAACTGTTGGAGACTCAAATTTATAGGC
196 GATCTCTTGGTGTTTTTTGAGGAATTCACTTGATGTTCAACTGTTGGAGACTCAAATTTATAGGC
235151 TTGAATGTTGACAAACTCGTTTGAGGTAGAATGATTGTGTTTGTAGCTGTTATTGACTTGTTTAG
261 TTGAATGTTGACAAACTCGTTTGAGGTAGAATGATTGTGTTTGTAGCTGTTATTGACTTGTTTAG
235216 TGCTTGTTTCCATGTATTCCCATTACTATGTATCGATACAATTCATAATGTATCGATACATGCAT
326 TGCTTGTTTCCATGTATTCCCATTACTATGTATCGATACAATTCATAATGTATCGATACATGCAT
*
235281 TTGAAATTATAGCCGTTTATAGCCATTTGCGACAATGTATCGATACAATTCTTCATGTATCGATA
391 TTGAAATTATAGCCGTTTATAGCCATTTGCGACAAAGTATCGATACAATTCTTCATGTATCGATA
235346 CATTGTATCGATACAATGTGCCATGTATCAATACAAATAGTGGTAAGGTAGCTACTGCCAATTTC
456 CATTGTATCGATACAATGTGCCATGTATCAATACAAATAGTGGTAAGGTAGCTACTGCCAATTTC
235411 ATGTATTGATACATTTGTTCATGTATCGATACAATGAACATGTATCGATACAAAGCATAATGTAT
521 ATGTATTGATACATTTGTTCATGTATCGATACAATGAACATGTATCGATACAAAGCATAATGTAT
235476 CGATACATCTGAAAGTGTATCGATACATACAAGGGTTTTGACCTTTGTAGCTTAAGTGAACCATA
586 CGATACATCTGAAAGTGTATCGATACATACAAGGGTTTTGACCTTTGTAGCTTAAGTGAACCATA
235541 ATGTATCGATACAAATACCCATGTATCGATACTTTAAAGTATTTTTACTTAAAAACATTCGATTT
651 ATGTATCGATACAAATACCCATGTATCGATACTTTAAAGTATTTTTACTTAAAAACATTCGATTT
235606 TAAAGCTCAAAAACATATGTTCATTACTCAAAAACACTTA
716 TAAAGCTCAAAAACATATGTTCATTACTCAAAAACACTTA
235646 TTGAAAAATTATAACCCAAGGTTAAATGCAACCTTACACAATTCAAGGAAAATTTTACAAACGAA
1 TTGAAAAATTATAACCCAAGGTTAAATGCAACCTTACACAATTCAAGGAAAATTTTACAAACGAA
235711 AATTACCTTTGAATAGGCTGATGTTTGTGAAAGAATAAACACAAATCAAATACAAAAAGCTTTCA
66 AATTACCTTTGAATAGGCTGATGTTTGTGAAAGAATAAACACAAATCAAATACAAAAAGCTTTCA
235776 AAGAATAACAACAACGAAAATAAAAGCTCTTAAAATGAGAAAATAAGTAAAACTTTGAATGCTTT
131 AAGAATAACAACAACGAAAATAAAAGCTCTTAAAATGAGAAAATAAGTAAAACTTTGAATGCTTT
235841 GATCTCTTGGTGTTTTTTGAGGAATTCACTTGATGTTCAACTGTTGGAGACTCAAATTTATAGGC
196 GATCTCTTGGTGTTTTTTGAGGAATTCACTTGATGTTCAACTGTTGGAGACTCAAATTTATAGGC
235906 TTGAATGTTGACAAACTCGTTTGAGGTAGAATGATTGTGTTTGTAGCTGTTATTGACTTGTTTAG
261 TTGAATGTTGACAAACTCGTTTGAGGTAGAATGATTGTGTTTGTAGCTGTTATTGACTTGTTTAG
235971 TGCTTGTTTCCATGTATTCCCATTACTATGTATCGATACAATTCATAATGTATCGATACATGCAT
326 TGCTTGTTTCCATGTATTCCCATTACTATGTATCGATACAATTCATAATGTATCGATACATGCAT
* *
236036 TTGAAATTATAGCTGTTTATAGCCATTTGCGACAAAGTATCGATACAATTCTTCATGTCTCGATA
391 TTGAAATTATAGCCGTTTATAGCCATTTGCGACAAAGTATCGATACAATTCTTCATGTATCGATA
*
236101 CATTGTATCGATACAATGTGCCATGTATCAATACAAATAGTGGTAGGGTAGCTACTGCCAATTTC
456 CATTGTATCGATACAATGTGCCATGTATCAATACAAATAGTGGTAAGGTAGCTACTGCCAATTTC
*
236166 ATGTATTGATACATTTGTTCATGTATCGATACAATGAACATGTATCGTTACAAAGCATAATGTAT
521 ATGTATTGATACATTTGTTCATGTATCGATACAATGAACATGTATCGATACAAAGCATAATGTAT
*
236231 CGATACATCTGAAAGTGTATTGATACATACAAGGGTTTTGACCTTTGTAGCTTAAGTGAACCATA
586 CGATACATCTGAAAGTGTATCGATACATACAAGGGTTTTGACCTTTGTAGCTTAAGTGAACCATA
236296 ATGTATCGATACAAATACCCATGTATCGATACTTTAAAGTATTTTTACTTAAAAACATTCGATTT
651 ATGTATCGATACAAATACCCATGTATCGATACTTTAAAGTATTTTTACTTAAAAACATTCGATTT
*
236361 TAAAGCTCAAAAACATATGTTTATTACTCAAAAACACTTA
716 TAAAGCTCAAAAACATATGTTCATTACTCAAAAACACTTA
236401 TTGAAA
1 TTGAAA
236407 TTGAAAATTA
Statistics
Matches: 753, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
755 753 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (755 bp):
TTGAAAAATTATAACCCAAGGTTAAATGCAACCTTACACAATTCAAGGAAAATTTTACAAACGAA
AATTACCTTTGAATAGGCTGATGTTTGTGAAAGAATAAACACAAATCAAATACAAAAAGCTTTCA
AAGAATAACAACAACGAAAATAAAAGCTCTTAAAATGAGAAAATAAGTAAAACTTTGAATGCTTT
GATCTCTTGGTGTTTTTTGAGGAATTCACTTGATGTTCAACTGTTGGAGACTCAAATTTATAGGC
TTGAATGTTGACAAACTCGTTTGAGGTAGAATGATTGTGTTTGTAGCTGTTATTGACTTGTTTAG
TGCTTGTTTCCATGTATTCCCATTACTATGTATCGATACAATTCATAATGTATCGATACATGCAT
TTGAAATTATAGCCGTTTATAGCCATTTGCGACAAAGTATCGATACAATTCTTCATGTATCGATA
CATTGTATCGATACAATGTGCCATGTATCAATACAAATAGTGGTAAGGTAGCTACTGCCAATTTC
ATGTATTGATACATTTGTTCATGTATCGATACAATGAACATGTATCGATACAAAGCATAATGTAT
CGATACATCTGAAAGTGTATCGATACATACAAGGGTTTTGACCTTTGTAGCTTAAGTGAACCATA
ATGTATCGATACAAATACCCATGTATCGATACTTTAAAGTATTTTTACTTAAAAACATTCGATTT
TAAAGCTCAAAAACATATGTTCATTACTCAAAAACACTTA
Found at i:237208 original size:33 final size:33
Alignment explanation
Indices: 237166--237230 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
237156 GTTAAGTAAA
237166 CTAAAGTGCTCATCCATGCGCTGCGAAAGTGAG
1 CTAAAGTGCTCATCCATGCGCTGCGAAAGTGAG
*
237199 CTAAAGTGCTCATCCATGTGCTGCGAAAGTGA
1 CTAAAGTGCTCATCCATGCGCTGCGAAAGTGA
237231 AGTGATCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (33 bp):
CTAAAGTGCTCATCCATGCGCTGCGAAAGTGAG
Found at i:244891 original size:20 final size:19
Alignment explanation
Indices: 244862--244924 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
244852 TAGCTACTGC
244862 CAAT-TTCATGTATCGATA
1 CAATGTTCATGTATCGATA
*
244880 CATTTGTTCATGTATCGATA
1 CA-ATGTTCATGTATCGATA
**
244900 CAATGAACATGTATCGATA
1 CAATGTTCATGTATCGATA
244919 CAATGT
1 CAATGT
244925 ATCGATACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
18 2 0.05
19 20 0.53
20 16 0.42
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (19 bp):
CAATGTTCATGTATCGATA
Found at i:244926 original size:13 final size:13
Alignment explanation
Indices: 244908--244934 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
244898 TACAATGAAC
244908 ATGTATCGATACA
1 ATGTATCGATACA
244921 ATGTATCGATACA
1 ATGTATCGATACA
244934 A
1 A
244935 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:246693 original size:153 final size:153
Alignment explanation
Indices: 246440--246875 Score: 513
Period size: 155 Copynumber: 2.8 Consensus size: 153
246430 CGAAATATTT
* * * * * * *
246440 TCATGTTGAAAGTATATCAAGGGTATTTTCATAATTTTTTAAAATTGAGTCTTAGGTTATCACGA
1 TCATGTCGAAAGTATACCAAGGGCATTTT-ATAATTTTTTAGAATCGAGTCTTAGGTTGTCACCA
*
246505 GGATGC-TTTATCCCAAAGGTATGCATTTAGGATAGGTTTATCCCATTTATGATCATTTTTAAGT
65 GGATGCTTTTATCCCAAAGGTATGCATTTAGGATAGGTTCATCCCATTTATGATCATTTTTAAGT
246569 TC-TTTAGGGTTATTG-GATACTA
130 TCTTTTAGGGTTATTGAGATACTA
* * * *
246591 TCATGTCGAAAGTAGACCGAAGGGCATTCTTATAATTTTTTAGAATCAAGTTTTAAGTTGTCACC
1 TCATGTCGAAAGTATACC-AAGGGCATT-TTATAATTTTTTAGAATCGAGTCTTAGGTTGTCACC
* *
246656 AAGATGCTTTTATCCCAAAGGTATGCATTTAGGATAGGTTCATCCCATTTATGATTATTTTTAAG
64 AGGATGCTTTTATCCCAAAGGTATGCATTTAGGATAGGTTCATCCCATTTATGATCATTTTTAAG
* *
246721 -TCTTTTAGGGTTATTGAGATATTT
129 TTCTTTTAGGGTTATTGAGATACTA
* * * * *
246745 TCATGTCGAAGGTATACCTAGGGGCATTTTTTGTAATTTCTTAGATTCGAGTCTTAGGTTGTCAC
1 TCATGTCGAAAGTATACC-AAGGGCA--TTTTATAATTTTTTAGAATCGAGTCTTAGGTTGTCAC
* ** * ** * * *
246810 TAGGATAATTTTATGCCAAAAATGTGCATTTGGGATTGGTTCATCCCATTTATGATCA-TTTTAA
63 CAGGATGCTTTTATCCCAAAGGTATGCATTTAGGATAGGTTCATCCCATTTATGATCATTTTTAA
246874 GT
128 GT
246876 CCTTGTCGCA
Statistics
Matches: 240, Mismatches: 37, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
151 15 0.06
152 43 0.18
153 70 0.29
154 34 0.14
155 76 0.32
156 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (153 bp):
TCATGTCGAAAGTATACCAAGGGCATTTTATAATTTTTTAGAATCGAGTCTTAGGTTGTCACCAG
GATGCTTTTATCCCAAAGGTATGCATTTAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTT
CTTTTAGGGTTATTGAGATACTA
Found at i:250158 original size:51 final size:51
Alignment explanation
Indices: 250082--250217 Score: 195
Period size: 51 Copynumber: 2.7 Consensus size: 51
250072 TTTTAACTAG
* *
250082 ATGTATCGATACATT-ATTCAATGTATCGATACATCTGGGTAAAAAGTTAGA
1 ATGTATCGATACATTCA-TAAATGTATCGATACATCTGGGTAAAAAGATAGA
* *
250133 ATGTATCGATATATTGA-AGAATGTATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTCATA-AATGTATCGATACATCTGGGTAAAAAGATAGA
*
250184 ATGTATCGATACATTCATACATGTATCGATACAT
1 ATGTATCGATACATTCATAAATGTATCGATACAT
250218 TGAAAAATAT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
51 74 0.97
52 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACATTCATAAATGTATCGATACATCTGGGTAAAAAGATAGA
Found at i:250209 original size:20 final size:20
Alignment explanation
Indices: 250183--250308 Score: 81
Period size: 20 Copynumber: 5.8 Consensus size: 20
250173 AAAAAGATAG
*
250183 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
250203 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
* *
250223 AATATATCGATACATCTGGGTAAAAAGA
1 AATGTATCGATACA--T---T--CAA-A
*
250251 CAGAATGTATCGATACATTCATA
1 -A-A-TGTATCGATACATTCAAA
* *
250274 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
250294 AATGTATCGATACAT
1 AATGTATCGATACAT
250309 CTAGGTAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 59 0.72
21 1 0.01
22 1 0.01
23 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
27 2 0.02
28 1 0.01
29 2 0.02
30 1 0.01
31 11 0.13
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:250213 original size:71 final size:71
Alignment explanation
Indices: 250133--250319 Score: 329
Period size: 71 Copynumber: 2.6 Consensus size: 71
250123 AAAAGTTAGA
* * *
250133 ATGTATCGATATATTGAAGAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
250198 TCATAC
66 TCATAC
*
250204 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
250269 TCATAC
66 TCATAC
*
250275 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
250320 TGTGACTTTT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 110 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (71 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
TCATAC
Found at i:251348 original size:153 final size:154
Alignment explanation
Indices: 250847--251661 Score: 765
Period size: 154 Copynumber: 5.3 Consensus size: 154
250837 GTGTCTACAA
* * * * ** * * *
250847 TCCTTTAAGGTTATCAAGATATTTTTATGTCGAAAG-TATAGTTAGGGGTATTTTTGTAATTTCA
1 TCCTTTAAGGTTACCAAGATACTTTCATATCG-AAGTTATACCTAGAGGTATTTTTATAATTTCT
* *
250911 TA-AAATCAAGTCTTAAGTTGTCACCAAGATGCTTTTATACCAAAGGTGTGCATTTAGGATAGGT
65 TAGAAA-CAAGTCTTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGT
* *
250975 TCATCCTATTTATGATCATTTTTAAT
129 TCATCCCATTTATGATCATTTTTAAG
** * * * * * * * * * *
251001 TTTTTTAAGGTTA-TAGGGATACTTTTATGTCGAAGGTATATCAAGCGGTATTTTCATAATTTTT
1 TCCTTTAAGGTTACCA-AGATACTTTCATATCGAAGTTATACCTAGAGGTATTTTTATAATTTCT
* *
251065 TA-AAACTGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAA-GTGTGCATTTA-GATAGGT
65 TAGAAAC-AAGTCTTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGT
* * *
251127 TAATCTCATTTATGATTATTTTTAAG
129 TCATCCCATTTATGATCATTTTTAAG
* * * * *
251153 TCTTTTAAGGTTACCAATATACTTTTATATCGAAGTTATACCTAGGGGTATTTTTGTAATTTCTT
1 TCCTTTAAGGTTACCAAGATACTTTCATATCGAAGTTATACCTAGAGGTATTTTTATAATTTCTT
* * *
251218 AGAAACAAGTCTTAGGTTGTCACCGAGATGCTTTTATGCCAAAGGTATGTATTTAGGATAGGTTC
66 AGAAACAAGTCTTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTC
* * *
251283 ATCCCATTCATAATTA-TTTTAAG
131 ATCCCATTTATGATCATTTTTAAG
*
251306 TCCTTT-AGAGTTACCGAGATACTTTCATATCGAAGTTATACCTAGAGGTATTTTTATAATTT-T
1 TCCTTTAAG-GTTACCAAGATACTTTCATATCGAAGTTATACCTAGAGGTATTTTTATAATTTCT
* * * * * * * * *
251369 CTAGAACCGAGTCTTAAGTCGTCACCAGGATGCTTTTATACCAAAAGTATGCATTGAGGATAGGT
65 -TAGAAACAAGTCTTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGT
*
251434 TCATCCCATTTATGATCATTTTTAAA
129 TCATCCCATTTATGATCATTTTTAAG
* * * ** ** *
251460 TCCTTTAAGGTTATCAAGATATTTTCATATTGAA-TGTATATTTAGAGACATTTTCATAATTTCT
1 TCCTTTAAGGTTACCAAGATACTTTCATATCGAAGT-TATACCTAGAGGTATTTTTATAATTTCT
** * * * *
251524 TAG-AACTGAA-TCCTT-GGTTGTCACCGGGACGCTTTTATGCTAAAGGTGTGTATTTAAGATAG
65 TAGAAAC--AAGT-CTTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAG
* *
251586 GTTCATTCCATTTATGATCATTTTTTAG
127 GTTCATCCCATTTATGATCATTTTTAAG
* ** * * * *
251614 TCCTTTAGGGTTGTCAACATACTTTAATGTCGAAGCTATACCCTAGAG
1 TCCTTTAAGGTTACCAAGATACTTTCATATCGAAGTTATA-CCTAGAG
251662 ACATTTTGGT
Statistics
Matches: 545, Mismatches: 98, Indels: 35
0.80 0.14 0.05
Matches are distributed among these distances:
152 117 0.21
153 162 0.30
154 254 0.47
155 12 0.02
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (154 bp):
TCCTTTAAGGTTACCAAGATACTTTCATATCGAAGTTATACCTAGAGGTATTTTTATAATTTCTT
AGAAACAAGTCTTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTC
ATCCCATTTATGATCATTTTTAAG
Found at i:260700 original size:13 final size:13
Alignment explanation
Indices: 260682--260706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260672 ATATTGCTTA
260682 GTATCGATACATT
1 GTATCGATACATT
260695 GTATCGATACAT
1 GTATCGATACAT
260707 GTTTTTTGTA
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):
GTATCGATACATT
Found at i:261408 original size:31 final size:33
Alignment explanation
Indices: 261296--261430 Score: 134
Period size: 34 Copynumber: 4.1 Consensus size: 33
261286 TTGAAGTGAT
* *
261296 TGAGAGGCTCTATCTTAGCCTT-TAAAAAAGATAG
1 TGAGAGGTTCTATCTTAG-CTTGT-GAAAAGATAG
* *
261330 GGAGAAAGGTTCTATTTTAGCTTGTGAAAAGATAG
1 TGAG--AGGTTCTATCTTAGCTTGTGAAAAGATAG
*
261365 TGAATAGGTTCTATCTTAGCTTGTGAAAAGATAG
1 TG-AGAGGTTCTATCTTAGCTTGTGAAAAGATAG
* *
261399 -G-GAGGTTCTATCTTAGCCT-TCAAAAGATAG
1 TGAGAGGTTCTATCTTAGCTTGTGAAAAGATAG
261429 TG
1 TG
261431 TTGTAAGGTT
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
30 10 0.12
31 17 0.20
33 1 0.01
34 31 0.36
35 13 0.15
36 14 0.16
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (33 bp):
TGAGAGGTTCTATCTTAGCTTGTGAAAAGATAG
Found at i:263944 original size:20 final size:21
Alignment explanation
Indices: 263915--263953 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
263905 TCTTGATCCT
*
263915 ATGTTTTGTG-TTAATTGTTG
1 ATGTTATGTGCTTAATTGTTG
263935 ATGTTATGTGCTTAATTGT
1 ATGTTATGTGCTTAATTGT
263954 ACATGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.03, G:0.23, T:0.56
Consensus pattern (21 bp):
ATGTTATGTGCTTAATTGTTG
Found at i:263959 original size:21 final size:20
Alignment explanation
Indices: 263915--263959 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
263905 TCTTGATCCT
* **
263915 ATGTTTTGTGTTAATTGTTG
1 ATGTTATGTGTTAATTGTAC
263935 ATGTTATGTGCTTAATTGTAC
1 ATGTTATGTG-TTAATTGTAC
263956 ATGT
1 ATGT
263960 ATTTGATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.53
Consensus pattern (20 bp):
ATGTTATGTGTTAATTGTAC
Found at i:266736 original size:33 final size:32
Alignment explanation
Indices: 266694--266757 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
266684 CACACCTAGA
266694 TGTATCGATACATA-TTGCTTAGTATCGATACAT
1 TGTATCGATACA-AGTT-CTTAGTATCGATACAT
*
266727 TGTATCGATACAAGTTCTTTGTATCGATACA
1 TGTATCGATACAAGTTCTTAGTATCGATACA
266758 CCATAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACAAGTTCTTAGTATCGATACAT
Found at i:267408 original size:31 final size:30
Alignment explanation
Indices: 267370--267430 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
267360 ATAGGGAGAA
267370 AGGTTCTATCTCAG-CTTGTGAAAAGATAGTG
1 AGGTTCTATCTCAGCCTT-T-AAAAGATAGTG
*
267401 AGGTTCTATCTTAGCCTTTAAAAGATAGTG
1 AGGTTCTATCTCAGCCTTTAAAAGATAGTG
267431 TTGTAAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.39
31 14 0.50
32 3 0.11
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (30 bp):
AGGTTCTATCTCAGCCTTTAAAAGATAGTG
Found at i:270682 original size:9 final size:9
Alignment explanation
Indices: 270670--270694 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
270660 TATTTCTAAT
270670 TCATTTTAG
1 TCATTTTAG
270679 TCATTTTAG
1 TCATTTTAG
270688 TCATTTT
1 TCATTTT
270695 CCATAAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (9 bp):
TCATTTTAG
Found at i:270902 original size:28 final size:29
Alignment explanation
Indices: 270870--270953 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 29
270860 CCTTAAGGAT
*
270870 TTTTTGTCATTTCATGCATTTTTATGTTC
1 TTTTTGTCATTTCATGCATTTTTATGTAC
* * * *
270899 TTTTAGTCATTTC-T-CATGATTTAAGAAC
1 TTTTTGTCATTTCATGCAT-TTTTATGTAC
*
270927 TTTTTGTCATTTCATGTATTTTTATGT
1 TTTTTGTCATTTCATGCATTTTTATGT
270954 CATTTTATAT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
27 3 0.07
28 19 0.45
29 18 0.43
30 2 0.05
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.58
Consensus pattern (29 bp):
TTTTTGTCATTTCATGCATTTTTATGTAC
Found at i:270912 original size:57 final size:57
Alignment explanation
Indices: 270832--270958 Score: 168
Period size: 57 Copynumber: 2.2 Consensus size: 57
270822 AATTTTTTCA
* *
270832 TTTTATGTTATTTAGTCATTTTCT-ATGACCTTAAGGATTTTTTGTCATTTCATGCAT
1 TTTTATGTTATTTAGTCATTTTCTCATGA-CTTAAGAACTTTTTGTCATTTCATGCAT
* * *
270889 TTTTATGTTCTTTTAGTCA-TTTCTCATGATTTAAGAACTTTTTGTCATTTCATGTAT
1 TTTTATGTT-ATTTAGTCATTTTCTCATGACTTAAGAACTTTTTGTCATTTCATGCAT
*
270946 TTTTATGTCATTT
1 TTTTATGTTATTT
270959 TATATGAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
56 3 0.05
57 46 0.75
58 12 0.20
ACGTcount: A:0.20, C:0.12, G:0.11, T:0.57
Consensus pattern (57 bp):
TTTTATGTTATTTAGTCATTTTCTCATGACTTAAGAACTTTTTGTCATTTCATGCAT
Found at i:271158 original size:58 final size:58
Alignment explanation
Indices: 271036--271230 Score: 200
Period size: 58 Copynumber: 3.4 Consensus size: 58
271026 GAGGGATTTT
* * * * * *
271036 TATGTCATTTCATACATTTTTATATCATTTTAGTAATTTTTCATGATTT-G-GG-AAC
1 TATGTAATTTCATGCATTTTAAAATCATTTTAGTCATTTTTCATGATTTAGAGGTTAC
*
271091 TATTTTGTAATTTCATGCATTTTAAAATCATTTTTGTCATTTTTCATGATTTAGAGGTTAC
1 TA---TGTAATTTCATGCATTTTAAAATCATTTTAGTCATTTTTCATGATTTAGAGGTTAC
** * * * * *
271152 TATGTAATTTCATGCATTTTAGCATCATCTTAATCA-TTTTCAATGATTTAAAAGTTAT
1 TATGTAATTTCATGCATTTTAAAATCATTTTAGTCATTTTTC-ATGATTTAGAGGTTAC
271210 TATGTAATTTCATGCATTTTA
1 TATGTAATTTCATGCATTTTA
271231 GTCATTTGTC
Statistics
Matches: 118, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
55 2 0.02
57 5 0.04
58 104 0.88
59 1 0.01
60 2 0.02
61 4 0.03
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (58 bp):
TATGTAATTTCATGCATTTTAAAATCATTTTAGTCATTTTTCATGATTTAGAGGTTAC
Found at i:271695 original size:21 final size:22
Alignment explanation
Indices: 271654--271697 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
271644 GACATATTTA
271654 AATGTTTTTCAAGCAATAAATT
1 AATGTTTTTCAAGCAATAAATT
* *
271676 AATGTTTTTTAAGTAA-AAATT
1 AATGTTTTTCAAGCAATAAATT
271697 A
1 A
271698 TTCAAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (22 bp):
AATGTTTTTCAAGCAATAAATT
Found at i:272126 original size:35 final size:34
Alignment explanation
Indices: 272087--272152 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
272077 CAAGTGATTG
*
272087 AGAGGTTCTATCTTAGCCTTTTTAAAAGATAGGGA
1 AGAGGTTCTATCTTAGCC-TTTGAAAAGATAGGGA
*
272122 AGAGGTTCTATCTTGGCCTTTGAAAAGATAG
1 AGAGGTTCTATCTTAGCCTTTGAAAAGATAG
272153 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 12 0.41
35 17 0.59
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTTGAAAAGATAGGGA
Found at i:273283 original size:3 final size:3
Alignment explanation
Indices: 273268--273299 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
273258 CCAAGAGGAA
*
273268 GAT GAT AAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
273300 AGAACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:279337 original size:13 final size:13
Alignment explanation
Indices: 279319--279343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
279309 ATATTTCTTG
279319 GTATCGATACATT
1 GTATCGATACATT
279332 GTATCGATACAT
1 GTATCGATACAT
279344 ATTCCATGTA
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):
GTATCGATACATT
Found at i:279529 original size:63 final size:63
Alignment explanation
Indices: 279411--279584 Score: 219
Period size: 63 Copynumber: 2.7 Consensus size: 63
279401 CCTACCATTG
* * * * * *
279411 TTCATATTGAATTATATCAATACATGGT-AAGTTGTATCAATACATTGAGCCCAATGG-CTATAA
1 TTCA-ATTGCATTGTATCGATACATAGTGAA-TTGTATCGATACATTGAGCCCAATGGCCT-GAA
279474 T
63 T
279475 TTCAATTGCATTGTATCGATACATAGTGAATTGTATCGATACATTGAGCCCAATGGCCTGAAT
1 TTCAATTGCATTGTATCGATACATAGTGAATTGTATCGATACATTGAGCCCAATGGCCTGAAT
* *
279538 TTCAAATGCATTGTATCGATACATTA-TGAATCGTATCGATACATTGA
1 TTCAATTGCATTGTATCGATACA-TAGTGAATTGTATCGATACATTGA
279585 AGCGTGTATG
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
63 89 0.90
64 10 0.10
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (63 bp):
TTCAATTGCATTGTATCGATACATAGTGAATTGTATCGATACATTGAGCCCAATGGCCTGAAT
Found at i:280055 original size:41 final size:41
Alignment explanation
Indices: 280010--280091 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
280000 CTTTGAAAAG
280010 ATAGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAACAAT
1 ATAGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAACAAT
280051 ATAGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAACAAT
1 ATAGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAACAAT
280092 TCAAGTAGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (41 bp):
ATAGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAACAAT
Found at i:281153 original size:20 final size:20
Alignment explanation
Indices: 281128--281178 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
281118 CCCTTAAAAA
281128 TATCGATACATATC-CAGA-TG
1 TATCGATACATA-CACA-ATTG
281148 TATCGATACATACACAATTG
1 TATCGATACATACACAATTG
281168 TATCGATACAT
1 TATCGATACAT
281179 GAAATTGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (20 bp):
TATCGATACATACACAATTG
Found at i:282878 original size:15 final size:15
Alignment explanation
Indices: 282858--282892 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
282848 AACCATCAAA
282858 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
282873 GATGATGATGATAAT
1 GATGATGAAGATAAT
282888 GATGA
1 GATGA
282893 AGTTGACTTG
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:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:289975 original size:19 final size:20
Alignment explanation
Indices: 289951--290004 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
289941 TATCGATACG
* **
289951 TTGTATCGATTCATGTTC-A
1 TTGTATCGATACATGCACAA
289970 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCACAA
289990 TTGTATCGATACATG
1 TTGTATCGATACATG
290005 AAACTGGCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:290070 original size:13 final size:13
Alignment explanation
Indices: 290049--290078 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
290039 CGATACATGG
*
290049 TACATTGTATCGA
1 TACAATGTATCGA
290062 TACAATGTATCGA
1 TACAATGTATCGA
290075 TACA
1 TACA
290079 TGAATAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:290076 original size:33 final size:33
Alignment explanation
Indices: 290034--290098 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
290024 TACCACTATT
*
290034 TGTATCGATACATG-GTACATTGTATCGATACAA
1 TGTATCGATACATGAATA-ATTGTATCGATACAA
290067 TGTATCGATACATGAATAATTGTATCGATACA
1 TGTATCGATACATGAATAATTGTATCGATACA
290099 TTGTCCCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGAATAATTGTATCGATACAA
Found at i:292393 original size:22 final size:22
Alignment explanation
Indices: 292366--292408 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
292356 GACAAGTTTA
292366 AATGTTTGTT-AAGTAATAAATC
1 AATGTTTGTTAAAGTAA-AAATC
*
292388 AATGTTTTTTAAAGTAAAAAT
1 AATGTTTGTTAAAGTAAAAAT
292409 ACTTAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (22 bp):
AATGTTTGTTAAAGTAAAAATC
Found at i:297612 original size:32 final size:32
Alignment explanation
Indices: 297571--297637 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
297561 GGATCAAGCG
297571 AAACCATGCTCTACACCTATGAGTACTTTAAC
1 AAACCATGCTCTACACCTATGAGTACTTTAAC
297603 AAACCATGCTCTACACCTATGAGTACTTTAAC
1 AAACCATGCTCTACACCTATGAGTACTTTAAC
297635 AAA
1 AAA
297638 ATCCAACCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.27, G:0.09, T:0.27
Consensus pattern (32 bp):
AAACCATGCTCTACACCTATGAGTACTTTAAC
Found at i:299247 original size:52 final size:52
Alignment explanation
Indices: 299178--299290 Score: 181
Period size: 52 Copynumber: 2.2 Consensus size: 52
299168 ATTACCTTAT
*
299178 AACATAAAAGGGGGAGAGCTTGCATAAATTTAAGGTATATTCGGTCAAATGAA
1 AACA-AAAAAGGGGAGAGCTTGCATAAATTTAAGGTATATTCGGTCAAATGAA
** *
299231 AACAAAAAAGGGGAGAGCTTGCATAAATTTGGGGTATATTCGGTTAAATGAA
1 AACAAAAAAGGGGAGAGCTTGCATAAATTTAAGGTATATTCGGTCAAATGAA
299283 AACAAAAA
1 AACAAAAA
299291 GGAGGAAAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
52 52 0.93
53 4 0.07
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (52 bp):
AACAAAAAAGGGGAGAGCTTGCATAAATTTAAGGTATATTCGGTCAAATGAA
Found at i:300530 original size:34 final size:35
Alignment explanation
Indices: 300464--300531 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
300454 CAAGTAATTG
* *
300464 AGAGGTTCTATCTTAGCCTTTATAAAAGATAGGGA
1 AGAGGTTCTATCTTAGCCATTAGAAAAGATAGGGA
300499 AGAGGTTCTATCTTAGCCATT-GAAAAGATAGGG
1 AGAGGTTCTATCTTAGCCATTAGAAAAGATAGGG
300532 TTGTAAGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.35
35 20 0.65
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (35 bp):
AGAGGTTCTATCTTAGCCATTAGAAAAGATAGGGA
Found at i:301972 original size:20 final size:20
Alignment explanation
Indices: 301927--301983 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
301917 TTGTATTGAT
301927 ACAA-TGTATCGATACAT-G
1 ACAATTGTATCGATACATGG
**
301945 TTAATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
301965 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
301984 AAACTGGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 2 0.06
19 13 0.39
20 18 0.55
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:302049 original size:13 final size:13
Alignment explanation
Indices: 302028--302057 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
302018 CGATACATGG
*
302028 TACATTGTATCGA
1 TACAGTGTATCGA
302041 TACAGTGTATCGA
1 TACAGTGTATCGA
302054 TACA
1 TACA
302058 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TACAGTGTATCGA
Found at i:302055 original size:33 final size:33
Alignment explanation
Indices: 302013--302077 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
302003 TACCACTGTT
* *
302013 TGTATCGATACATGGT-ACATTGTATCGATACAG
1 TGTATCGATACATGATGA-ATTGTATCAATACAG
302046 TGTATCGATACATGATGAATTGTATCAATACA
1 TGTATCGATACATGATGAATTGTATCAATACA
302078 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCAATACAG
Found at i:303965 original size:429 final size:429
Alignment explanation
Indices: 303132--303992 Score: 1361
Period size: 429 Copynumber: 2.0 Consensus size: 429
303122 AAACTATTGT
* *
303132 ATTTGTTTTGATCTCACCTTTCCACAAACACCAGCCTACTTAGAGGCAATTTTTGTTTGTATAAT
1 ATTTGTTTTGAGCTCACCTTTCCACAAACACCAGCCTACTTAGAGGCAATTCTTGTTTGTATAAT
* * * * *
303197 TTCTTTGTTTAGATAGGGTTGTGTTCAACCTTGAGTGATAATCTCTTAGGAACTTGGGGTATAGT
66 TTCTTTGTCTACATAAGGTTGTGTTCAACCTTGAGTGATAATCTCCTAGAAACTTGGGGTATAGT
*
303262 TCTTGAAGAGATTGAGAGGTTATTATCTTAGCCTTTAAAAGATAAGGTTTGTAAGGTTATACTTT
131 TCTTGAAGAGATTGAGAGGATATTATCTTAGCCTTTAAAAGATAAGGTTTGTAAGGTTATACTTT
* *
303327 GCCTTAAAAGCAATCAATTCTTGTAGTGAATTGGATAATCACTCGACGAGAAAGTGCCAAGGAGA
196 GCCTTAAAAGCAATCAATTCTTGTAGTGAATTAGATAACCACTCGACGAGAAAGTGCCAAGGAGA
* * * *
303392 GAGGACGTAGGTACTGGATTGGACCGAACCTCTATAAACTCTTGTGTCGATCATTTCTTCCGTAA
261 GAGGACGTAGGCACCGGATTGGACCGAACCTCTATAAACTCTTGTGTCCAACATTTCTTCCGTAA
* * * *
303457 TCTTTTTATCTTTCAAAATGTTTTGCACTAAATCCTTCAAAACACTCAAAATTTGAAAAGAACCA
326 TCTTTTTATCTTTCAAAATGTTTTGCACCAAACCCTTCAAAACACTAAAAATTCGAAAAGAACCA
*
303522 ATTCACCTCCCTCTTGGTTCATTATTCCTTAAGCTTTCA
391 ATTCACCTCCCTCTTGGTTCATTAATCCTTAAGCTTTCA
303561 ATTTGTTTTGAGCTCA-CTCTTCCACAAACACCAGCCTACTTAGAGGCAATTCTTGTTTGTATAA
1 ATTTGTTTTGAGCTCACCT-TTCCACAAACACCAGCCTACTTAGAGGCAATTCTTGTTTGTATAA
* *
303625 TTTCTTTGTCTACATAAGGTTGTGTTCAACCTTGAGTTATAATCTCCTAGAAATTTGGGGTATAG
65 TTTCTTTGTCTACATAAGGTTGTGTTCAACCTTGAGTGATAATCTCCTAGAAACTTGGGGTATAG
*
303690 TT-TTAGAAGAGATTGAGAGGATGTTATCTTAGCCTTTAAAAGATAAGGTTTGTAAGGTTATACC
130 TTCTT-GAAGAGATTGAGAGGATATTATCTTAGCCTTTAAAAGATAAGGTTTGTAAGGTTATA-C
* * * *
303754 TTTGCCTTAAAGGTAATCAATTCTTGTAGTGAATTAGATAACCACTCGACGAGAAAGTGTCGAGG
193 TTTGCCTTAAAAGCAATCAATTCTTGTAGTGAATTAGATAACCACTCGACGAGAAAGTGCCAAGG
*
303819 AGAGAGGACGTAGGCACCGGATTGGACCGAACCTCTATAAACTTTTGTGTCCAACATTTCTTCC-
258 AGAGAGGACGTAGGCACCGGATTGGACCGAACCTCTATAAACTCTTGTGTCCAACATTTCTTCCG
* * **
303883 TCAATCTTTTTATCTTTCGAATTGTTTTGCACCAAACCCTTCAAAATTCTAAAAATTCGAAAAGA
323 T-AATCTTTTTATCTTTCAAAATGTTTTGCACCAAACCCTTCAAAACACTAAAAATTCGAAAAGA
* *
303948 ACCAATTCACC-CCCTCTTGGTTTATTAATCCTTGAGCTTTCA
387 ACCAATTCACCTCCCTCTTGGTTCATTAATCCTTAAGCTTTCA
303990 ATT
1 ATT
303993 GGTATCAAAG
Statistics
Matches: 395, Mismatches: 33, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
428 4 0.01
429 206 0.52
430 185 0.47
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (429 bp):
ATTTGTTTTGAGCTCACCTTTCCACAAACACCAGCCTACTTAGAGGCAATTCTTGTTTGTATAAT
TTCTTTGTCTACATAAGGTTGTGTTCAACCTTGAGTGATAATCTCCTAGAAACTTGGGGTATAGT
TCTTGAAGAGATTGAGAGGATATTATCTTAGCCTTTAAAAGATAAGGTTTGTAAGGTTATACTTT
GCCTTAAAAGCAATCAATTCTTGTAGTGAATTAGATAACCACTCGACGAGAAAGTGCCAAGGAGA
GAGGACGTAGGCACCGGATTGGACCGAACCTCTATAAACTCTTGTGTCCAACATTTCTTCCGTAA
TCTTTTTATCTTTCAAAATGTTTTGCACCAAACCCTTCAAAACACTAAAAATTCGAAAAGAACCA
ATTCACCTCCCTCTTGGTTCATTAATCCTTAAGCTTTCA
Found at i:311196 original size:20 final size:18
Alignment explanation
Indices: 311171--311218 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
311161 TTTTGAAAAT
*
311171 AAATTTTTATCAAGGGGGA
1 AAATTTTTATCAA-AGGGA
311190 GAAATTTGTTTATCAAAGGGA
1 -AAA-TT-TTTATCAAAGGGA
311211 AAATTTTT
1 AAATTTTT
311219 TTTCTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 3 0.12
19 2 0.08
20 6 0.24
21 6 0.24
22 8 0.32
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (18 bp):
AAATTTTTATCAAAGGGA
Found at i:311954 original size:13 final size:13
Alignment explanation
Indices: 311936--311992 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
311926 TTCAATAATT
311936 TGTATCGATACAA
1 TGTATCGATACAA
311949 TGTATCGATACATAA
1 TGTATCGATAC--AA
311964 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
311981 TGTATCGATACA
1 TGTATCGATACA
311993 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:311973 original size:19 final size:18
Alignment explanation
Indices: 311949--312011 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
311939 ATCGATACAA
311949 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
311968 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
311981 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
*
312000 TGTATCCATACA
1 TGTATCGATACA
312012 ATGTATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:311976 original size:32 final size:32
Alignment explanation
Indices: 311935--312019 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
311925 TTTCAATAAT
311935 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
311967 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
311999 TTGTATCCATACAATGTATCG
1 TTGTATCGATACAATGTATCG
312020 CTATGAAGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:315313 original size:13 final size:13
Alignment explanation
Indices: 315295--315319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315285 CATTATGCTT
315295 TGTATCGATACAA
1 TGTATCGATACAA
315308 TGTATCGATACA
1 TGTATCGATACA
315320 TGTTCATTGT
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:315319 original size:33 final size:32
Alignment explanation
Indices: 315273--315339 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
315263 TACATACCCA
*
315273 AATGTATCAATACAT-TATGCTTTGTATCGATAC
1 AATGTATCAATACATGT-T-CATTGTATCGATAC
*
315306 AATGTATCGATACATGTTCATTGTATCGATAC
1 AATGTATCAATACATGTTCATTGTATCGATAC
315338 AA
1 AA
315340 GGACAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 15 0.48
33 15 0.48
34 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (32 bp):
AATGTATCAATACATGTTCATTGTATCGATAC
Found at i:315332 original size:19 final size:20
Alignment explanation
Indices: 315304--315360 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
315294 TTGTATCGAT
*
315304 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
315323 TC-ATTGTATCGATACAAGG
1 ACAATTGTATCGATACATGG
315342 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
315361 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:315432 original size:19 final size:20
Alignment explanation
Indices: 315389--315441 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
315379 CTACCACTGT
* *
315389 TTGTATCGACACATGGTACA
1 TTGTATCGATACATGATACA
315409 TTGTATCGATACATGATA-A
1 TTGTATCGATACATGATACA
315428 TTGTATCGATACAT
1 TTGTATCGATACAT
315442 TGCTTCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGTATCGATACATGATACA
Found at i:316423 original size:13 final size:13
Alignment explanation
Indices: 316405--316430 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
316395 CAATTTTTTG
316405 TGTATCGATACAT
1 TGTATCGATACAT
316418 TGTATCGATACAT
1 TGTATCGATACAT
316431 ACTTGCTGTA
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:316495 original size:21 final size:21
Alignment explanation
Indices: 316469--316544 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
316459 CTGCCAAGAA
*
316469 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
316490 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
316510 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
316531 ATGTATCGATACAT
1 ATGTATCGATACAT
316545 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:316515 original size:20 final size:20
Alignment explanation
Indices: 316490--316562 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
316480 CATCTTTTTT
316490 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
316510 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
316531 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
316551 ATGTATCGATAC
1 ATGTATCGATAC
316563 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:316526 original size:41 final size:41
Alignment explanation
Indices: 316469--316562 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
316459 CTGCCAAGAA
*
316469 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
316510 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
316551 ATGTATCGATAC
1 ATGTATCGATAC
316563 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:317191 original size:36 final size:36
Alignment explanation
Indices: 317148--317218 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
317138 ATAAGGTAAT
317148 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
1 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
317184 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTA
1 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTA
317219 GGCCAAGTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.37, G:0.06, T:0.42
Consensus pattern (36 bp):
TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
Found at i:318173 original size:13 final size:13
Alignment explanation
Indices: 318155--318179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
318145 ACTGAAGCAA
318155 TGTATCGATACAT
1 TGTATCGATACAT
318168 TGTATCGATACA
1 TGTATCGATACA
318180 ATCTGGAAAA
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:321800 original size:13 final size:13
Alignment explanation
Indices: 321782--321807 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
321772 CAATTTTTTG
321782 TGTATCGATACAT
1 TGTATCGATACAT
321795 TGTATCGATACAT
1 TGTATCGATACAT
321808 ACTTGCTGTA
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:321872 original size:21 final size:21
Alignment explanation
Indices: 321846--321921 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
321836 CTGCCAAGAA
*
321846 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
321867 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
321887 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
321908 ATGTATCGATACAT
1 ATGTATCGATACAT
321922 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:321892 original size:20 final size:20
Alignment explanation
Indices: 321867--321939 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
321857 CATCTTTTTT
321867 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
321887 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
321908 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
321928 ATGTATCGATAC
1 ATGTATCGATAC
321940 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:321903 original size:41 final size:41
Alignment explanation
Indices: 321846--321939 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
321836 CTGCCAAGAA
*
321846 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
321887 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
321928 ATGTATCGATAC
1 ATGTATCGATAC
321940 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:330474 original size:13 final size:13
Alignment explanation
Indices: 330456--330482 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
330446 ACAATTGTCC
330456 ATGTATCGATACA
1 ATGTATCGATACA
330469 ATGTATCGATACA
1 ATGTATCGATACA
330482 A
1 A
330483 AGCAAGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:332667 original size:20 final size:19
Alignment explanation
Indices: 332623--332675 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
332613 ATAGTAACCC
332623 ATGTATCGATACATCCCAG
1 ATGTATCGATACATCCCAG
*
332642 ATGTATCGATACATCTTTCA-
1 ATGTATCGATACATC--CCAG
332662 ATGTATCGATACAT
1 ATGTATCGATACAT
332676 TTTAGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 15 0.48
20 14 0.45
21 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACATCCCAG
Found at i:338907 original size:19 final size:19
Alignment explanation
Indices: 338863--338918 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
338853 CTGCCAGCTT
* **
338863 CATGTATCGATACAATTGTG
1 CATGTATTGATACAA-TGAA
338883 CATGTATTGATACAATGAA
1 CATGTATTGATACAATGAA
338902 CATGTATTGATACAATG
1 CATGTATTGATACAATG
338919 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATTGATACAATGAA
Found at i:341680 original size:20 final size:20
Alignment explanation
Indices: 341655--341706 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
341645 TTACAAGCCA
*
341655 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
341675 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
*
341695 -TGGATCGATACA
1 ATGTATCGATACA
341707 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:343182 original size:20 final size:19
Alignment explanation
Indices: 343157--343198 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
343147 ATTTTAAATC
343157 AAATCAAAATAAAAATAAAA
1 AAATCAAAA-AAAAATAAAA
**
343177 AAATCATTAAAAAATAAAA
1 AAATCAAAAAAAAATAAAA
343196 AAA
1 AAA
343199 ATCGTGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATCAAAAAAAAATAAAA
Found at i:347815 original size:13 final size:13
Alignment explanation
Indices: 347797--347824 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
347787 TACAAAAGAT
347797 CAATGTATCGATA
1 CAATGTATCGATA
347810 CAATGTATCGATA
1 CAATGTATCGATA
347823 CA
1 CA
347825 TTTAAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:347919 original size:32 final size:32
Alignment explanation
Indices: 347863--347952 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
347853 GCAGTAGCTT
* *
347863 TGTAGCGATACATTCTATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
* *
347895 TGTATCGATACATTGTATCAATACAACACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
* *
347927 TGCATCGATACACTGTATCGATACAA
1 TGTATCGATACATTGTATCGATACAA
347953 GTTGTTGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAACTTA
Found at i:348592 original size:33 final size:33
Alignment explanation
Indices: 348527--348593 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
348517 CGTTAGGCAT
* *
348527 AATGTATCAATACAATTCTTCATATATTGATAC
1 AATGTATCAATACAATTCCTCATATATCGATAC
* *
348560 AATGTATCGATACAATCTCCT-ATGTATCGATAC
1 AATGTATCAATACAAT-TCCTCATATATCGATAC
348593 A
1 A
348594 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (33 bp):
AATGTATCAATACAATTCCTCATATATCGATAC
Found at i:348665 original size:19 final size:19
Alignment explanation
Indices: 348622--348677 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
348612 CTACCAGTTT
*
348622 CATGTATCGATACAATTGAG
1 CATGTATTGATACAA-TGAG
*
348642 TATGTATTGATACAATGAG
1 CATGTATTGATACAATGAG
348661 CATGTATTGATACAATG
1 CATGTATTGATACAATG
348678 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (19 bp):
CATGTATTGATACAATGAG
Found at i:348838 original size:22 final size:21
Alignment explanation
Indices: 348812--348867 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
348802 AATTATTTTT
348812 ACTCAAAAACATTCGATTTA-A
1 ACTCAAAAACATT-GATTTATA
* *
348833 AGCTCAAAAATATTTATTTATA
1 A-CTCAAAAACATTGATTTATA
*
348855 ACTCTAAAACATT
1 ACTCAAAAACATT
348868 TTAGATATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (21 bp):
ACTCAAAAACATTGATTTATA
Found at i:348870 original size:22 final size:21
Alignment explanation
Indices: 348804--348870 Score: 50
Period size: 21 Copynumber: 3.1 Consensus size: 21
348794 ATACTTTGAA
*
348804 TTATTT-TTACTCAAAAACATT
1 TTATTTATAACTC-AAAACATT
**
348825 CGATTTA-AAGCTCAAAA-ATAT
1 TTATTTATAA-CTCAAAACAT-T
348846 TTATTTATAACTCTAAAACATT
1 TTATTTATAACTC-AAAACATT
348868 TTA
1 TTA
348871 GATATTGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
20 2 0.06
21 18 0.51
22 13 0.37
23 2 0.06
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (21 bp):
TTATTTATAACTCAAAACATT
Found at i:349710 original size:20 final size:20
Alignment explanation
Indices: 349687--349761 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
349677 AAATACCCAG
349687 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
349707 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
349727 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
349747 ATGTATCGATACATT
1 ATGTATCGATACATT
349762 CTGTCTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:351444 original size:10 final size:11
Alignment explanation
Indices: 351429--351457 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
351419 CTACTAGACG
351429 ATTTTTCAAA-
1 ATTTTTCAAAC
351439 ATTTTTCAAAC
1 ATTTTTCAAAC
351450 ATTTTTCA
1 ATTTTTCA
351458 TAAAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTTCAAAC
Found at i:352192 original size:32 final size:32
Alignment explanation
Indices: 352151--352215 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
352141 AATCAATTAA
*
352151 TCCAGACACGTCTCCAATATTGTCAATGTGGT
1 TCCAAACACGTCTCCAATATTGTCAATGTGGT
352183 TCCAAACACGTCTCCAATATTGTCAATGTGGT
1 TCCAAACACGTCTCCAATATTGTCAATGTGGT
352215 T
1 T
352216 ATTTTTTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (32 bp):
TCCAAACACGTCTCCAATATTGTCAATGTGGT
Done.