Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007776.1 Hibiscus syriacus cultivar Beakdansim tig00110057_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2207776
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:229259 original size:105 final size:103
Alignment explanation
Indices: 229032--229251 Score: 368
Period size: 105 Copynumber: 2.1 Consensus size: 103
229022 GTCGAGGGTC
229032 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
229097 TTGATTCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
229135 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTTTGGTGAGACACAT
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAAG--TCTGGTGAGACACAT
*
229200 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
64 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
229240 TATGTGGTCCTT
1 TATGTGGTCCTT
229252 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 47 0.43
105 62 0.57
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:229294 original size:23 final size:23
Alignment explanation
Indices: 229261--229335 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
229251 TATGGACATT
229261 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
229282 ATTCTATGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
** *
229305 ATTATATATGGCACTTCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
229328 ATTATATG
1 ATTATATG
229336 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.13
23 39 0.87
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGCGGCACTACGGTGCA
Found at i:232367 original size:5 final size:5
Alignment explanation
Indices: 232352--233247 Score: 1485
Period size: 5 Copynumber: 183.4 Consensus size: 5
232342 AAAATTTTAT
232352 TAATAA TAATA TAATA T-ATA T-ATA TAATA TAATAA TTAATA TAATA
1 TAAT-A TAATA TAATA TAATA TAATA TAATA TAAT-A -TAATA TAATA
232398 TAATA TAATA TAA-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232447 TAATA TAA-A TAATA TAATA TAATA TAATA TAATA T-A-A TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232494 TAATA TAATA TAATA TAATA TAATA TAATA T-ATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232543 TAATA TAATATA TAATA TAATA T-A-A TAATA TAATA TAATA TAATA TAATA
1 TAATA T-A-ATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232593 TAATA TAATA TAATA T-ATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232642 TAATA TAATA TAATA TAATA T-A-A TAATA TATATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TA-ATA TAATA TAATA TAATA
232691 TAATA T-A-A TAATA TAATA TAATA TAATA TAATA TAATA T-ATA -ATATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA-ATA
232738 TAATA TAATA TAATA TATATA TAATA TAATA TAATA TAATA TAATA TAA-A
1 TAATA TAATA TAATA TA-ATA TAATA TAATA TAATA TAATA TAATA TAATA
232788 TAATA TAATA T-ATA TAATA TAATA T-ATA -AATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232835 TAAATA TAATA TAATA TAATA TAATA TAATA T-ATA TAATA T-A-A TAATA
1 T-AATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232883 TAATA T-ATA TAATA TAATA TAATA TAATA T-ATA T-ATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232930 TAATA TAATA T-A-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
232978 TAATA TAATA TAATA TAATA TAATA T-ATA TAATA TAATA TAATA T-ATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
233026 TAATA TAATA TAATA TAATA TAATA TAATA T-ATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
233075 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
233125 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
233175 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
233225 TAATA TAATA TAATA TATATA TA
1 TAATA TAATA TAATA TA-ATA TA
233248 TTAAATACCA
Statistics
Matches: 852, Mismatches: 0, Indels: 76
0.92 0.00 0.08
Matches are distributed among these distances:
3 12 0.01
4 81 0.10
5 722 0.85
6 29 0.03
7 8 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:233723 original size:136 final size:134
Alignment explanation
Indices: 233484--233916 Score: 646
Period size: 136 Copynumber: 3.2 Consensus size: 134
233474 GACTTGAAAG
* *
233484 GAACAAGTTCTTCTCATTATGAACTT-TT-T--TCT-TTAGGACGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTGTCA-GATGAGTTCTTCTCATTATGAACT
* * * * * * *
233544 CTTC-TAGAAATGTCAATCTCTCAAGCGAGGTGTCTCTGATTCGAAATGCCATGAATCGAGTTAT
65 CTCCTTGGAAATGTCAAGCCCTTAAGCGAGATGTCACTGATTCGAAATGCCATGAATCGAGTTAT
*
233608 ATGTC
130 AGGTC
233613 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTCTGTCAGATGAGTTCTTCTCATTATGAACT
*
233678 CTCCGTTGGAAATGTCAAGCCCTTAAGCGAGATGTCACTGATTCGAAATGCCATGAATCGAGTGA
65 CTCC-TTGGAAATGTCAAGCCCTTAAGCGAGATGTCACTGATTCGAAATGCCATGAATCGAGTTA
233743 TAGGTC
129 TAGGTC
233749 GAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCTGTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTC-CTCTGTCAGATGAGTTCTTCTCATTATGAACT
* *
233814 CTCCATTGGAAATGCCAAGCCCTTAAGCGAGACGTCACTGATTCGAAATGCCATGAATCGA-TTG
65 CTCC-TTGGAAATGTCAAGCCCTTAAGCGAGATGTCACTGATTCGAAATGCCATGAATCGAGTT-
233878 ATAGGTC
128 ATAGGTC
233885 GAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTC
233917 ATTATGAACT
Statistics
Matches: 279, Mismatches: 15, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
129 26 0.09
130 2 0.01
131 1 0.00
134 29 0.10
135 4 0.01
136 217 0.78
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (134 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTGTCAGATGAGTTCTTCTCATTATGAACTC
TCCTTGGAAATGTCAAGCCCTTAAGCGAGATGTCACTGATTCGAAATGCCATGAATCGAGTTATA
GGTC
Found at i:233914 original size:17 final size:17
Alignment explanation
Indices: 233892--233933 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
233882 GTCGAACAAG
233892 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
233909 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
233926 TTCTTCTC
1 TTCTTCTC
233934 CCTCTGTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.26, G:0.05, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:234959 original size:14 final size:15
Alignment explanation
Indices: 234920--235018 Score: 73
Period size: 15 Copynumber: 6.5 Consensus size: 15
234910 TCTCGAACCC
234920 TCATTTTTCTCTTCATT
1 TCATTTTTCT-TTC-TT
*
234937 T-TTTCTTTCTTTCTT
1 TCATT-TTTCTTTCTT
*
234952 TC-TTTTTCTTTTTT
1 TCATTTTTCTTTCTT
*
234966 TCATTTTT-TTATTTT
1 TCATTTTTCTT-TCTT
*
234981 TCATTTTTCATT-TT
1 TCATTTTTCTTTCTT
234995 TCATTTTTCATTT-TT
1 TCATTTTTC-TTTCTT
235010 TCTATTTTT
1 TC-ATTTTT
235019 TTCTTTTTCT
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
14 24 0.34
15 29 0.41
16 12 0.17
17 6 0.08
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TCATTTTTCTTTCTT
Found at i:234965 original size:8 final size:8
Alignment explanation
Indices: 234935--235026 Score: 57
Period size: 7 Copynumber: 11.5 Consensus size: 8
234925 TTTCTCTTCA
234935 TTTTTTCT
1 TTTTTTCT
*
234943 TTCTTTCTT
1 TTTTTTC-T
234952 TCTTTTTCT
1 T-TTTTTCT
*
234961 TTTTTTCA
1 TTTTTTCT
234969 TTTTTT-T
1 TTTTTTCT
*
234976 ATTTTTC-
1 TTTTTTCT
*
234983 ATTTTTC-
1 TTTTTTCT
*
234990 ATTTTTC-
1 TTTTTTCT
*
234997 ATTTTTCAT
1 TTTTTTC-T
*
235006 TTTTTCTAT
1 TTTTT-TCT
235015 TTTTTTCT
1 TTTTTTCT
235023 TTTT
1 TTTT
235027 CTTCAAGCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
7 26 0.37
8 24 0.34
9 14 0.20
10 6 0.09
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:234972 original size:7 final size:7
Alignment explanation
Indices: 234962--235009 Score: 78
Period size: 7 Copynumber: 6.7 Consensus size: 7
234952 TCTTTTTCTT
234962 TTTTTCA
1 TTTTTCA
*
234969 TTTTTTTA
1 -TTTTTCA
234977 TTTTTCA
1 TTTTTCA
234984 TTTTTCA
1 TTTTTCA
234991 TTTTTCA
1 TTTTTCA
234998 TTTTTCA
1 TTTTTCA
235005 TTTTT
1 TTTTT
235010 TCTATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
7 32 0.84
8 6 0.16
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:235025 original size:7 final size:7
Alignment explanation
Indices: 234942--235029 Score: 63
Period size: 8 Copynumber: 11.9 Consensus size: 7
234932 TCATTTTTTC
234942 TTTCTTT
1 TTTCTTT
234949 CTTTC-TT
1 -TTTCTTT
234956 TTTCTTTT
1 TTTC-TTT
234964 TTTCATTT
1 TTTC-TTT
234972 TTT-TATT
1 TTTCT-TT
*
234979 TTTCATT
1 TTTCTTT
*
234986 TTTCATT
1 TTTCTTT
*
234993 TTTCATT
1 TTTCTTT
235000 TTTCATTT
1 TTTC-TTT
235008 TTTCTATT
1 TTTCT-TT
*
235016 TTTTTCTT
1 TTTCT-TT
235024 TTTCTT
1 TTTCTT
235030 CAAGCATAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
6 5 0.07
7 29 0.43
8 34 0.50
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:245439 original size:49 final size:47
Alignment explanation
Indices: 245345--245440 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 47
245335 ATTCACAAAA
245345 AAAATCCTAACCACATTTTTCTAGTTCACATCTTTTGTATGAAAATAT
1 AAAATCCTAACCACATTTTTCTAGTTCACATCTTTTGTA-GAAAATAT
* *
245393 AAAA-CCTAACCGCATGCTTTTCTAGTTCGCATACTTATTGTA-AAAATA
1 AAAATCCTAACCACAT--TTTTCTAGTTCACAT-CTT-TTGTAGAAAATA
245441 AATTCGAGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
47 10 0.24
48 4 0.10
49 20 0.48
50 3 0.07
51 5 0.12
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.36
Consensus pattern (47 bp):
AAAATCCTAACCACATTTTTCTAGTTCACATCTTTTGTAGAAAATAT
Found at i:249234 original size:23 final size:22
Alignment explanation
Indices: 249186--249234 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
249176 CTAGAATGTC
249186 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
249207 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
249230 AAGGA
1 AAGGA
249235 AAATTGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:250929 original size:103 final size:103
Alignment explanation
Indices: 250745--251065 Score: 563
Period size: 103 Copynumber: 3.1 Consensus size: 103
250735 GTCGAGGGTC
* *
250745 TATGTGGTCCTTCGAGG-CATATATGTATTCTTTGGAATAGGTGTGAAGTATGGTGAGACACATA
1 TATGTGGTCCTTCG-GGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATA
* * *
250809 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
250848 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
250913 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
250951 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
251016 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
251054 TATGTGGTCCTT
1 TATGTGGTCCTT
251066 ATGGACATTA
Statistics
Matches: 209, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
102 2 0.01
103 207 0.99
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:251172 original size:23 final size:23
Alignment explanation
Indices: 251082--251164 Score: 139
Period size: 23 Copynumber: 3.6 Consensus size: 23
251072 ATTATTATAT
*
251082 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTATGC
251105 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTATGC
*
251128 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTATGC
*
251151 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
251165 TTTATATGAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTATGC
Found at i:254464 original size:24 final size:22
Alignment explanation
Indices: 254415--254456 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
254405 CTAGAATGTC
254415 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
254436 CAGGAGGGAACCGATTCCCCC
1 AAGGAGGGAACCGATACCCCC
254457 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:256300 original size:103 final size:103
Alignment explanation
Indices: 255972--256292 Score: 561
Period size: 103 Copynumber: 3.1 Consensus size: 103
255962 GTCGAGGGTC
* *
255972 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
256037 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
256075 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
256140 TTGATCCCTAATATATGTGTATGATTCTTAAGGACTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
256178 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
256243 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
256281 TATGTGGTCATT
1 TATGTGGTCATT
256293 ATGGACATTA
Statistics
Matches: 205, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 205 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:256365 original size:23 final size:23
Alignment explanation
Indices: 256312--256368 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
256302 ATTATATGGC
*
256312 ACTACGGTGCAATTCTACGCGGC
1 ACTACGGTGCAATTCTACGCGGA
* *
256335 ACTACGGTGCAATTCTATGTGGA
1 ACTACGGTGCAATTCTACGCGGA
*
256358 ACTTCGGTGCA
1 ACTACGGTGCA
256369 TTTATATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (23 bp):
ACTACGGTGCAATTCTACGCGGA
Found at i:257202 original size:12 final size:12
Alignment explanation
Indices: 257185--257233 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
257175 AAAATTTTAT
257185 TAATAATAAATA
1 TAATAATAAATA
257197 TAATAATAAATA
1 TAATAATAAATA
257209 TAAT-AT-AATA
1 TAATAATAAATA
*
257219 TAATATATATATA
1 TAATA-ATAAATA
257232 TA
1 TA
257234 TATATATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 8 0.24
11 2 0.06
12 18 0.55
13 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:257221 original size:19 final size:19
Alignment explanation
Indices: 257194--257245 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
257184 TTAATAATAA
257194 ATATA-ATAATAAATATA-
1 ATATATATAATAAATATAT
*
257211 ATATAATATAATATATATAT
1 ATAT-ATATAATAAATATAT
*
257231 ATATATATATTAAAT
1 ATATATATAATAAAT
257246 CCCAATCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.14
18 1 0.03
19 20 0.69
20 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATATAATAAATATAT
Found at i:257228 original size:2 final size:2
Alignment explanation
Indices: 257194--257240 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
257184 TTAATAATAA
*
257194 AT AT A- AT A- AT AA AT AT A- AT AT A- AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
257231 AT AT AT AT AT
1 AT AT AT AT AT
257241 TAAATCCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
1 5 0.13
2 33 0.87
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:257236 original size:12 final size:11
Alignment explanation
Indices: 257194--257240 Score: 62
Period size: 10 Copynumber: 4.4 Consensus size: 11
257184 TTAATAATAA
*
257194 ATATAATAATAA
1 ATATAAT-ATAT
257206 ATATAATATA-
1 ATATAATATAT
257216 ATATAATATAT
1 ATATAATATAT
257227 ATAT-ATATAT
1 ATATAATATAT
257237 ATAT
1 ATAT
257241 TAAATCCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 20 0.59
11 7 0.21
12 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATAATATAT
Found at i:257238 original size:10 final size:10
Alignment explanation
Indices: 257194--257240 Score: 50
Period size: 9 Copynumber: 5.2 Consensus size: 10
257184 TTAATAATAA
257194 ATATA-ATA-
1 ATATATATAT
*
257202 ATAAATATA-
1 ATATATATAT
257211 ATATA-ATAT
1 ATATATATAT
257220 A-ATATATAT
1 ATATATATAT
257229 ATATATATAT
1 ATATATATAT
257239 AT
1 AT
257241 TAAATCCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 10 0.30
9 13 0.39
10 10 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATAT
Found at i:259680 original size:16 final size:18
Alignment explanation
Indices: 259655--259698 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
259645 TATAAAAGTT
*
259655 AAAAGGATAAA-GA-ATG
1 AAAAGTATAAATGATATG
*
259671 AAAAGTATAAATGATGTG
1 AAAAGTATAAATGATATG
259689 AAAAGTATAA
1 AAAAGTATAA
259699 GAAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 2 0.08
18 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.20
Consensus pattern (18 bp):
AAAAGTATAAATGATATG
Found at i:262898 original size:19 final size:20
Alignment explanation
Indices: 262859--262900 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
262849 TCCAGTATGT
262859 CCAGGGGGTATCGATTCCCC
1 CCAGGGGGTATCGATTCCCC
262879 CCAGGGGGTATCGATTCCCC
1 CCAGGGGGTATCGATTCCCC
262899 CC
1 CC
262901 TAAAGGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.19
Consensus pattern (20 bp):
CCAGGGGGTATCGATTCCCC
Found at i:269790 original size:20 final size:20
Alignment explanation
Indices: 269765--269803 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
269755 AGTATGTCCA
269765 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
269785 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
269804 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.31, G:0.33, T:0.26
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:275424 original size:36 final size:37
Alignment explanation
Indices: 275367--275467 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 37
275357 TTTCGTCCTA
275367 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
* *
275404 CTAGGATTC-AACTC-CTAAAAATATGATAGAATTTTG
1 CTAGGATTCAAACTCTC-AAAAATAGGATAGAATTATG
* * * * *
275440 CTATGTTTTAAACTCTTAAAGATAGGAT
1 CTAGGATTCAAACTCTCAAAAATAGGAT
275468 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
35 1 0.02
36 29 0.55
37 23 0.43
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
Found at i:275929 original size:11 final size:11
Alignment explanation
Indices: 275909--275993 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 11
275899 TTAATTATTT
*
275909 TTATTCTAATA
1 TTATTTTAATA
*
275920 TTATTTTAATG
1 TTATTTTAATA
*
275931 TTTTTTTAA-A
1 TTATTTTAATA
*
275941 GTTATTATATATA
1 -TTATTTTA-ATA
275954 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
275968 TTATATTTATTA
1 TTAT-TTTAATA
*
275980 TTATTTTACTA
1 TTATTTTAATA
275991 TTA
1 TTA
275994 ACGTATATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 32 0.55
12 8 0.14
13 11 0.19
14 7 0.12
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:275984 original size:15 final size:15
Alignment explanation
Indices: 275942--275984 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
275932 TTTTTTAAAG
275942 TTATTATATATATATAT
1 TTATTAT-TAT-TATAT
* *
275959 TTATAACTATTATAT
1 TTATTATTATTATAT
275974 TTATTATTATT
1 TTATTATTATT
275985 TTACTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:279545 original size:22 final size:22
Alignment explanation
Indices: 279522--279583 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
279512 CAAAAAGGGC
279522 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
279545 AAAAAGGAAAAAATAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
279566 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
279584 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:281127 original size:36 final size:36
Alignment explanation
Indices: 281080--281182 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
281070 GTGCTCACCA
*
281080 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
281116 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
* * *
281152 TTTTCTCCCTTGAGACAGTTT-CTTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
281183 TAAACATTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 9 0.14
36 54 0.86
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
Found at i:281368 original size:37 final size:37
Alignment explanation
Indices: 281301--281387 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
281291 ATTGGAAACA
** * *
281301 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
281337 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
281374 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
281388 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:281449 original size:36 final size:36
Alignment explanation
Indices: 281402--281488 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
281392 CATTGAAAAC
** * *
281402 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
281438 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* *
281474 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
281489 CAAAACCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:281524 original size:102 final size:102
Alignment explanation
Indices: 281098--281488 Score: 662
Period size: 102 Copynumber: 3.9 Consensus size: 102
281088 CTTGAGACAG
** * *
281098 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTT-TCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
281162 TGAGACAGTTTCT-TTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
281198 TTTTCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTTCTCCC
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA-TTTTGTCTCCC
*
281263 TTGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
65 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
281301 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
281366 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
281403 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
281467 TGAGACAGTTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
281489 CAAAACCTTT
Statistics
Matches: 274, Mismatches: 14, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
100 47 0.17
101 40 0.15
102 114 0.42
103 73 0.27
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:281528 original size:205 final size:202
Alignment explanation
Indices: 281097--281553 Score: 675
Period size: 205 Copynumber: 2.2 Consensus size: 202
281087 TCTTGAGACA
*
281097 GTTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTCTCCCT
1 GTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTCTCCCT
* * *
281162 TGAGACAGTTTCTTTGAAACATAAACATTGAAAACATTTTCCTTGAAATGAGTTTTGTCTCTCTT
65 TGAGACAGTTTCTCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTT
* * *
281227 GAGATAGTTTCCCTTGAAACAAAATTTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
130 GAGATAATTTCCCTTGAAACAAAATTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAACA
281292 TTGGAAAC
195 TTGGAAAC
* * *
281300 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCC
1 GTTTCCCTTGAAA-CAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTT-TCTCCC
281365 TTGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTC
64 TTGAGACAGTTTCT-CTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTC
281430 TTGAGATAATTTCCCTTGAAAC-AAA-TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
128 TTGAGATAATTTCCCTTGAAACAAAATTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAA
* * **
281493 ACCTTTGAGATT
192 ACATTGGA-AAC
* * * *
281505 GTTTCCCTCGAAACAATTTTTGTCTCCCATGAGACAGTTTCTCTTGAAA
1 GTTTCCCTTGAAACAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
281554 AACAAAATCT
Statistics
Matches: 227, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
203 86 0.38
204 33 0.15
205 108 0.48
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (202 bp):
GTTTCCCTTGAAACAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTCTCCCTT
GAGACAGTTTCTCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTG
AGATAATTTCCCTTGAAACAAAATTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAACAT
TGGAAAC
Found at i:281586 original size:67 final size:67
Alignment explanation
Indices: 281430--281588 Score: 214
Period size: 67 Copynumber: 2.4 Consensus size: 67
281420 TTTGTCTCTC
** * *
281430 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAAAACAAAAC
281495 CT
66 CT
* * *
281497 TTGAGATTGTTTCCCTCGAAACAATTTTTGTCTCCCATGAGACAGTTTCTCTTGAAAAACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAAAACAAAAC
281562 CT
66 CT
*
281564 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
281589 ATTTCGTTTC
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 75 0.94
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAAAACAAAAC
CT
Found at i:282566 original size:219 final size:213
Alignment explanation
Indices: 282168--282795 Score: 591
Period size: 219 Copynumber: 2.9 Consensus size: 213
282158 TAGCTAGAGT
*
282168 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAACAACAATTTCCCAATTTCGGAACCGA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTC-GAACCGA
* *
282233 TTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAG
65 TTTCAACTCCACGACGGAGGATATCCTGCCACCCGAGACAACACAAGTTCAACTTCACAACGAAG
* * ** * **
282298 GGACGGTTGGTTGTCAATGAACAACTTCCCAATTCCAGAACTGATTTCAACTCCAC-GAC-AGAG
130 GGACAGCTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTCCACAG-CGA-AG
*
282361 GATATCGTGCTACCCGAGAAAACA
193 GATAT--TG-GACCCGAGAAAACA
* * * * *
282385 CAAGTCCAACTTCACAACGAAGGGACGGCCTGGTTGTCAATGAACAACTTT-TCAGTTTC-ATCC
1 CAAGTTCAACTTCACAACGAAGGGACGG-CTGGTTGTCAA-CAACAA-TTTCCCAATTTCGA-AC
* * *
282448 GCGATTTCAACTCCACGATGGAGGATATCCTGCCACTCGAGACAACACAAGTTCAACTTCACAAT
62 -CGATTTCAACTCCACGACGGAGGATATCCTGCCACCCGAGACAACACAAGTTCAACTTCACAAC
** * * * *
282513 GAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTCAACTTCACAGCGA
126 GAAGGGACAGCTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTCCACAGCGA
* *
282578 AGGATATTGGACTCGAGACAACA
191 AGGATATTGGACCCGAGAAAACA
* * * * ** *
282601 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAA-GATTT--C--GTTCAGAGTCAA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTC-GAACCGA
* * * * *
282661 TTTCAACTTCAC-AGCGAAGGATAT--TAG--ACTCGAGACAACACAAGCTCAACTTCACAGCGA
65 TTTCAACTCCACGA-CGGAGGATATCCT-GCCACCCGAGACAACACAAGTTCAACTTCACAACGA
* * ** * *** * *
282721 AGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCAATTTCAACTTCACAGCGGAG
128 AGGGACAGCTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTCCACAGCGAAG
282786 GATATTGGAC
193 GATATTGGAC
282796 TCGGAACAAT
Statistics
Matches: 346, Mismatches: 54, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
206 93 0.27
207 1 0.00
208 2 0.01
209 24 0.07
211 2 0.01
212 3 0.01
213 1 0.00
214 2 0.01
215 10 0.03
216 37 0.11
217 30 0.09
218 11 0.03
219 125 0.36
220 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (213 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCGAACCGAT
TTCAACTCCACGACGGAGGATATCCTGCCACCCGAGACAACACAAGTTCAACTTCACAACGAAGG
GACAGCTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTCCACAGCGAAGGAT
ATTGGACCCGAGAAAACA
Found at i:282619 original size:106 final size:107
Alignment explanation
Indices: 282168--282798 Score: 569
Period size: 109 Copynumber: 5.9 Consensus size: 107
282158 TAGCTAGAGT
* * *
282168 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAACAACAATTTCCCAATTTCGGAACCGA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAACCAA
* * *
282233 TTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACA
66 TTTCAACTCCACAG-CGAAGGATATC-TGCGACTCGAGACAACA
* * * * **
282276 CAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAATGAACAACTTCCCAATTCCAGAACTG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTCCCAATTTCAGAACCA
* * *
282341 ATTTCAACTCCAC-GAC-AGAGGATATCGTGCTACCCGAGAAAACA
65 ATTTCAACTCCACAG-CGA-AGGATATC-TGCGACTCGAGACAACA
* * * * **
282385 CAAGTCCAACTTCACAACGAAGGGACGGCCTGGTTGTCAATGAACAACTTT-TCAGTTTCA-TCC
1 CAAGTTCAACTTCACAACGAAGGGACGG-CTGGTTGTCAA-CAACAA-TTTCCCAATTTCAGAAC
* *
282448 GCGATTTCAACTCCACGATG-G-AGGATATCCTGCCACTCGAGACAACA
63 -CAATTTCAACTCCAC-A-GCGAAGGATAT-CTGCGACTCGAGACAACA
* * * * * *
282495 CAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAACCA
*
282560 ATTTCAACTTCACAGCGAAGGATAT-TG-GACTCGAGACAACA
65 ATTTCAACTCCACAGCGAAGGATATCTGCGACTCGAGACAACA
* * * * **
282601 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAA-GATTT--C--GTTCAGAGTCAA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAACCAA
* *
282661 TTTCAACTTCACAGCGAAGGATAT-T-AGACTCGAGACAACA
66 TTTCAACTCCACAGCGAAGGATATCTGCGACTCGAGACAACA
* * * ** ** *
282701 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAACCA
* *
282766 ATTTCAACTTCACAGCGGAGGATAT-TG-GACTCG
65 ATTTCAACTCCACAGCGAAGGATATCTGCGACTCG
282799 GAACAATATT
Statistics
Matches: 448, Mismatches: 52, Indels: 48
0.82 0.09 0.09
Matches are distributed among these distances:
100 84 0.19
101 2 0.00
102 4 0.01
104 4 0.01
105 2 0.00
106 89 0.20
107 3 0.01
108 42 0.09
109 130 0.29
110 84 0.19
111 3 0.01
113 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (107 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAACCAA
TTTCAACTCCACAGCGAAGGATATCTGCGACTCGAGACAACA
Found at i:283313 original size:36 final size:37
Alignment explanation
Indices: 283256--283356 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 37
283246 TTTCGTCCTA
283256 CTAGGATTCAAACTCTAAAAAATAGGATAGAATTATG
1 CTAGGATTCAAACTCTAAAAAATAGGATAGAATTATG
* *
283293 CTAGGATTC-AACTCCT-AAAAATATGATAGAATTTTG
1 CTAGGATTCAAACT-CTAAAAAATAGGATAGAATTATG
* * * * *
283329 CTATGTTTTAAACTCTTAAATATAGGAT
1 CTAGGATTCAAACTCTAAAAAATAGGAT
283357 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
36 30 0.56
37 24 0.44
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (37 bp):
CTAGGATTCAAACTCTAAAAAATAGGATAGAATTATG
Found at i:284287 original size:23 final size:25
Alignment explanation
Indices: 284243--284288 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
284233 TTGCGTTTTT
* *
284243 TTATTTTACTACTTTATCATTATTA
1 TTATTTTACTACTTAATAATTATTA
284268 TTATTTT-C-ACTTAATAATTAT
1 TTATTTTACTACTTAATAATTAT
284289 ATGTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 1 0.05
25 7 0.37
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTTTACTACTTAATAATTATTA
Found at i:287379 original size:20 final size:20
Alignment explanation
Indices: 287326--287396 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
287316 ACAAAAAGGG
*
287326 AAAAAAGAAAAAAGAAAAGAAGC
1 AAAAAAG-AAAAA-ACAAGAA-C
287349 AAAAAAGGAAAAAACAAGAAC
1 AAAAAA-GAAAAAACAAGAAC
* * *
287370 AAAAAAGAAAGAACAAAAAT
1 AAAAAAGAAAAAACAAGAAC
287390 AAAAAAG
1 AAAAAAG
287397 GGAACAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 18 0.42
21 7 0.16
22 6 0.14
23 11 0.26
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAAGAAAAAACAAGAAC
Found at i:288904 original size:36 final size:36
Alignment explanation
Indices: 288857--289137 Score: 274
Period size: 36 Copynumber: 7.9 Consensus size: 36
288847 GTGCTCACCA
*
288857 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
288893 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATT
* * * ** *
288930 TTTTCTCCCTTGAGACAGTTTCTCTTGAAATGAGTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
*
288966 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC--AAATT
* * *
289004 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAA--
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AATT
* * * * **
289039 ---AC-AT-TGGAAACA-TTTCCCTTGAAATGAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
*
289069 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATT
*
289106 TTGTCTCCCTTGAGACAGTTTCTCC-TGAAACA
1 TTGTCTCTCTTGAGACAGTTTC-CCTTGAAACA
289138 TAAACATTGA
Statistics
Matches: 196, Mismatches: 35, Indels: 28
0.76 0.14 0.11
Matches are distributed among these distances:
28 2 0.01
29 11 0.06
30 6 0.03
32 1 0.01
33 1 0.01
34 1 0.01
35 5 0.03
36 74 0.38
37 63 0.32
38 32 0.16
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
Found at i:288986 original size:73 final size:74
Alignment explanation
Indices: 288860--289035 Score: 282
Period size: 73 Copynumber: 2.4 Consensus size: 74
288850 CTCACCATTG
* *
288860 TCTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-
1 TCTCCCTTGAGACAGTTTCTCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
288924 AAAATTTTT
66 AAAATTTTT
** ** *
288933 TCTCCCTTGAGACAGTTTCTCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TCTCCCTTGAGACAGTTTCTCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
288998 AAAATTTTT
66 AAAATTTTT
289007 TCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TCTCCCTTGAGACAGTTTCTCTTGAAACA
289036 TAAACATTGG
Statistics
Matches: 93, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 57 0.61
74 36 0.39
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (74 bp):
TCTCCCTTGAGACAGTTTCTCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
AAAATTTTT
Found at i:289089 original size:103 final size:101
Alignment explanation
Indices: 288939--289235 Score: 483
Period size: 103 Copynumber: 2.9 Consensus size: 101
288929 TTTTTCTCCC
* * *
288939 TTGAGACAGTTTCTCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAATT
1 TTGAAACA-TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAATT
*
289004 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
64 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
289042 TTGGAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTT
1 TT-GAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTT
*
289107 TGTCTCCCTTGAGACAGTTTCTCCTGAAACATAAACA
65 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
289144 TTGAAACATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA-ATT-CCTTGAAAC-AAATTTT
1 TTGAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTT
289206 GTCTCCCTTGAGACAGTTTCTCTTGAAACA
66 GTCTCCCTTGAGACAGTTTCTCTTGAAACA
289236 CAAAACCTTT
Statistics
Matches: 185, Mismatches: 8, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
98 36 0.19
99 9 0.05
100 2 0.01
101 40 0.22
102 44 0.24
103 49 0.26
104 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (101 bp):
TTGAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTT
GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:289118 original size:37 final size:37
Alignment explanation
Indices: 289051--289137 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
289041 ATTGGAAACA
** * *
289051 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
289087 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
289124 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
289138 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:289257 original size:101 final size:102
Alignment explanation
Indices: 288939--289302 Score: 457
Period size: 101 Copynumber: 3.6 Consensus size: 102
288929 TTTTTCTCCC
* * * *
288939 TTGAGACAGTTTCTCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAATT
1 TTGAAACA-TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAATT
* *
289004 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
64 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACCT
* *
289043 TGGAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTT
1 TTGAAACATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTT
* *
289108 GTCTCCCTTGAGACAGTTTCTCCTGAAACATAAA-CA
66 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACCT
*
289144 TTGAAACATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA-ATT-CCTTGAAAC-AAATTTT
1 TTGAAACATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTT
*
289206 GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCT
66 GTCTCCCTTGAGACAGTTTCTCTTGAAACA-TAAACCT
*** * ** * * * * *
289244 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTGA-AACATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACA
289303 CAAAATCTTT
Statistics
Matches: 228, Mismatches: 26, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
98 36 0.16
99 12 0.05
100 7 0.03
101 70 0.31
102 42 0.18
103 55 0.24
104 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (102 bp):
TTGAAACATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTT
GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACCT
Found at i:289333 original size:67 final size:67
Alignment explanation
Indices: 289190--289335 Score: 224
Period size: 67 Copynumber: 2.2 Consensus size: 67
289180 TGAGATAATT
*
289190 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTGTT
1 CCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTGTT
289255 TC
66 TC
* *
289257 CCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAATCTTTGA-ATT-TA
1 CCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTGT-
289320 TCTC
65 T-TC
*
289324 CCTTAAAACAAA
1 CCTTGAAACAAA
289336 ATTTCGTTTC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
65 1 0.01
66 4 0.06
67 67 0.93
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (67 bp):
CCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTGTT
TC
Found at i:290363 original size:106 final size:107
Alignment explanation
Indices: 289912--290541 Score: 590
Period size: 109 Copynumber: 5.9 Consensus size: 107
289902 TAGCTAGAGT
* * * *
289912 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAACAACAATTTCCCAATTTCGGAATCGA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAACCAA
* * *
289977 TTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGGCAACA
66 TTTCAACTCCACAG-CGGAGGATATC-TGCGACTCGAGACAACA
* * * *
290020 CAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAACCA
* * *
290085 ATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGAAAACA
65 ATTTCAACTCCACAG-CGGAGGATATC-TGCGACTCGAGACAACA
* * * * * **
290129 CAAGTCCAACTTCACAACGAAGAGACGGCTGGTTGTCAATGAACAACTTT-TCAGTTTCA-TCCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAA-TTTCCCAATTTCAGAAC-
* * *
290192 CGATTTCAACTCCAC-GATGGAGGATATCGTGCCACTCGAGACAACA
63 CAATTTCAACTCCACAG-CGGAGGATATC-TGCGACTCGAGACAACA
* * * * * *
290238 CAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAACCA
* *
290303 ATTTCAACTTCACAGCGAAGGATAT-TG-GACTCGAGACAACA
65 ATTTCAACTCCACAGCGGAGGATATCTGCGACTCGAGACAACA
* * * * **
290344 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAA-GATTT--C--GTTCAGAGTCAA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAACCAA
* * *
290404 TTTCAACTTCACAGCGAAGGATAT-T-AGACTCGAGACAACA
66 TTTCAACTCCACAGCGGAGGATATCTGCGACTCGAGACAACA
* * * ** ** *
290444 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAACCA
*
290509 ATTTCAACTTCACAGCGGAGGATAT-TG-GACTCG
65 ATTTCAACTCCACAGCGGAGGATATCTGCGACTCG
290542 GAACAATATT
Statistics
Matches: 450, Mismatches: 56, Indels: 34
0.83 0.10 0.06
Matches are distributed among these distances:
100 84 0.19
101 2 0.00
102 4 0.01
104 4 0.01
105 2 0.00
106 89 0.20
107 2 0.00
108 42 0.09
109 217 0.48
110 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (107 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAACCAA
TTTCAACTCCACAGCGGAGGATATCTGCGACTCGAGACAACA
Found at i:291055 original size:36 final size:37
Alignment explanation
Indices: 290998--291073 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
290988 TTTCGTCCTA
290998 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
* *
291035 CTAGGATTC-AACTC-CTAAAAATATGATAGAATTTTG
1 CTAGGATTCAAACTCTC-AAAAATAGGATAGAATTATG
291071 CTA
1 CTA
291074 TGTTATAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 1 0.03
36 26 0.72
37 9 0.25
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
Found at i:291557 original size:11 final size:11
Alignment explanation
Indices: 291537--291616 Score: 51
Period size: 11 Copynumber: 7.3 Consensus size: 11
291527 TATATTATTT
*
291537 TTATTCTAATA
1 TTATTTTAATA
*
291548 TTATTTTAATG
1 TTATTTTAATA
291559 TT-TTTTAA-A
1 TTATTTTAATA
*
291568 GTTATTAT-ATA
1 -TTATTTTAATA
291579 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
291593 TTA-TTTATTA
1 TTATTTTAATA
*
291603 TTATTTTACTA
1 TTATTTTAATA
291614 TTA
1 TTA
291617 ACGTATATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
10 15 0.28
11 30 0.56
12 3 0.06
13 3 0.06
14 3 0.06
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:293238 original size:80 final size:79
Alignment explanation
Indices: 292978--293242 Score: 361
Period size: 80 Copynumber: 3.3 Consensus size: 79
292968 GGGGCCTATG
* * * *
292978 GGCCTACCCAAGAATATCCTTAGATCTGTAGGGTTACCTTAAGCACACAGCAAAAAGAAAACCAA
1 GGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTATGCACACAGC--AAAGGAAACCAA
293043 CCTAAGGATATACCTT
64 CCTAAGGATATACCTT
* * * *
293059 GGGTCTACCCGAGGGTATCCTTAGATCCGTAGGGTTACCTTATGCACACAGTAAAGGAAACCAAC
1 -GGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAAC
293124 CTAAGGATATACCTT
65 CTAAGGATATACCTT
* *
293139 AGGCCTATCCAAGGGTATCCTTAGATCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAAC
1 -GGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAAC
*
293204 CTAAGGATATGCCTT
65 CTAAGGATATACCTT
*
293219 GGACCCTACCCAA-TATATCCTTAG
1 GG--CCTACCCAAGGATATCCTTAG
293243 GTCTGTAAGA
Statistics
Matches: 164, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
79 2 0.01
80 110 0.67
81 8 0.05
82 44 0.27
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (79 bp):
GGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACC
TAAGGATATACCTT
Found at i:297864 original size:2 final size:2
Alignment explanation
Indices: 297859--297899 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
297849 AGTTGAGAAA
*
297859 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
297900 GGTTTTGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:298336 original size:29 final size:29
Alignment explanation
Indices: 298304--298494 Score: 153
Period size: 29 Copynumber: 6.7 Consensus size: 29
298294 TAAAGAATGT
* *
298304 TTTTTATAAATTATATTAAAGGACAAAAC
1 TTTTTATAAATTACAATAAAGGACAAAAC
* * * *
298333 TTTTTATAAATTACAATAATGGATAGATC
1 TTTTTATAAATTACAATAAAGGACAAAAC
* *
298362 TTTTTATAAATTACAATAGA-GA-ATAACC
1 TTTTTATAAATTACAATAAAGGACA-AAAC
298390 TTATTTATAAATTACAATAGAA-GACAAATA-
1 TT-TTTATAAATTACAATA-AAGGACAAA-AC
* * *
298420 TTTTTATAAATT-CGAATAGAGAACAAATC
1 TTTTTATAAATTAC-AATAAAGGACAAAAC
* * *
298449 TTTTTATAAATTACTAT-AATGACAAGA-
1 TTTTTATAAATTACAATAAAGGACAAAAC
*
298476 TTTTTACAAATTACAATAA
1 TTTTTATAAATTACAATAA
298495 CAACTCATAT
Statistics
Matches: 129, Mismatches: 23, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
27 16 0.12
28 14 0.11
29 90 0.70
30 8 0.06
31 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (29 bp):
TTTTTATAAATTACAATAAAGGACAAAAC
Found at i:298368 original size:58 final size:58
Alignment explanation
Indices: 298304--298493 Score: 185
Period size: 58 Copynumber: 3.3 Consensus size: 58
298294 TAAAGAATGT
* * * * * *
298304 TTTTTATAAATTATATTAAAGGACAAAACTTTTTATAAATTACAATAATGGATAGATC
1 TTTTTATAAATTACAATAGAGGACAAAACTTTTTATAAATTACAATAATGGACAAATA
* *
298362 TTTTTATAAATTACAATAGA-GA-ATAACCTTATTTATAAATTACAATAGA-AGACAAATA
1 TTTTTATAAATTACAATAGAGGACA-AAACTT-TTTATAAATTACAATA-ATGGACAAATA
* * * *
298420 TTTTTATAAATT-CGAATAGAGAACAAATCTTTTTATAAATTACTATAAT-GAC-AAGA
1 TTTTTATAAATTAC-AATAGAGGACAAAACTTTTTATAAATTACAATAATGGACAAATA
*
298476 TTTTTACAAATTACAATA
1 TTTTTATAAATTACAATA
298494 ACAACTCATA
Statistics
Matches: 111, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
56 19 0.17
57 13 0.12
58 71 0.64
59 7 0.06
60 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (58 bp):
TTTTTATAAATTACAATAGAGGACAAAACTTTTTATAAATTACAATAATGGACAAATA
Found at i:298507 original size:28 final size:28
Alignment explanation
Indices: 298475--298549 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
298465 TAATGACAAG
298475 ATTTTTACAAATTACAAT-AACAACTCAT
1 ATTTTTACAAATTAC-ATGAACAACTCAT
* *
298503 ATTTTTACACATTGCATGAACAACTCAT
1 ATTTTTACAAATTACATGAACAACTCAT
298531 ATTTTTACAACCATTACAT
1 ATTTTTACAA--ATTACAT
298550 TTTGCTCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 2 0.05
28 32 0.80
30 6 0.15
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (28 bp):
ATTTTTACAAATTACATGAACAACTCAT
Found at i:300111 original size:114 final size:114
Alignment explanation
Indices: 299975--300206 Score: 324
Period size: 114 Copynumber: 2.0 Consensus size: 114
299965 ATTAAAAATG
* * * *
299975 AATGATTTAATTTTTTTTAATTACACTAAGGTGACAAT-TCAAGCTCGACACATATAGGGTTTAT
1 AATGATTTAATTTTTTTAAATTACACTAAGGT-A-AATATCAAGCTCAACACAGATAGGGTCTAT
* * * * *
300039 GTTAGGACCTACAAACGACTAGATCAAAGTCATCCATTTTTATTTTTAAAA
64 ATCAAGACATACAAACAACTAGATCAAAGTCATCCATTTTTATTTTTAAAA
* *
300090 AATGATTT-ATTTTTTTAAATTACACTAAGGTAAATAGTCAGGCTCAACACAGATAGGGTCTGTA
1 AATGATTTAATTTTTTTAAATTACACTAAGGTAAATA-TCAAGCTCAACACAGATAGGGTCTATA
300154 TCAAGACATACAAACAACTAGATCAAAGTCATCCATTTTTATTTTTAAAA
65 TCAAGACATACAAACAACTAGATCAAAGTCATCCATTTTTATTTTTAAAA
300204 AAT
1 AAT
300207 AAATAATATT
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
112 3 0.03
113 1 0.01
114 92 0.88
115 8 0.08
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (114 bp):
AATGATTTAATTTTTTTAAATTACACTAAGGTAAATATCAAGCTCAACACAGATAGGGTCTATAT
CAAGACATACAAACAACTAGATCAAAGTCATCCATTTTTATTTTTAAAA
Found at i:303567 original size:14 final size:14
Alignment explanation
Indices: 303550--303600 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
303540 TTCAAAAAAT
303550 TATTTTTATTATTA
1 TATTTTTATTATTA
**
303564 TATTTTTAAAAAATTA
1 TATTTTT--ATTATTA
303580 T-TTTTTATTATTA
1 TATTTTTATTATTA
303593 TATTTTTA
1 TATTTTTA
303601 ATTCGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 5 0.17
16 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTATTATTA
Found at i:303569 original size:28 final size:29
Alignment explanation
Indices: 303524--303598 Score: 109
Period size: 28 Copynumber: 2.6 Consensus size: 29
303514 GATAATTAAG
*
303524 TTTTTATCATTGAT-TTTTCAAAAAATTA-
1 TTTTTATTATT-ATATTTTCAAAAAATTAT
*
303552 TTTTTATTATTATATTTTTAAAAAATTAT
1 TTTTTATTATTATATTTTCAAAAAATTAT
303581 TTTTTATTATTATATTTT
1 TTTTTATTATTATATTTT
303599 TAATTCGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 2 0.05
28 23 0.53
29 18 0.42
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (29 bp):
TTTTTATTATTATATTTTCAAAAAATTAT
Found at i:303614 original size:29 final size:29
Alignment explanation
Indices: 303536--303601 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
303526 TTTATCATTG
303536 ATTTTTCAAAAAATTA-TTTTTATTATTAT
1 ATTTTT-AAAAAATTATTTTTTATTATTAT
303565 ATTTTTAAAAAATTATTTTTTATTATTAT
1 ATTTTTAAAAAATTATTTTTTATTATTAT
303594 ATTTTTAA
1 ATTTTTAA
303602 TTCGTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 9 0.25
29 27 0.75
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTTTAAAAAATTATTTTTTATTATTAT
Found at i:308737 original size:21 final size:21
Alignment explanation
Indices: 308711--308755 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
308701 GTTGCAACGT
308711 CATCGAAGACTAGACTGGTGA
1 CATCGAAGACTAGACTGGTGA
308732 CATCGAAGACTAGACTGGTGA
1 CATCGAAGACTAGACTGGTGA
308753 CAT
1 CAT
308756 TACTGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (21 bp):
CATCGAAGACTAGACTGGTGA
Found at i:311468 original size:19 final size:19
Alignment explanation
Indices: 311444--311513 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
311434 AGAATGTCCA
311444 GGGGGTA-CAGATTCCCCTG
1 GGGGGTATC-GATTCCCCTG
311463 GGGGGTATCGATTCCCC--
1 GGGGGTATCGATTCCCCTG
*
311480 --GGG-AACAGATTCCCCTG
1 GGGGGTATC-GATTCCCCTG
*
311497 GAGGGTATCGATTCCCC
1 GGGGGTATCGATTCCCC
311514 CTAAATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
14 2 0.05
15 11 0.26
19 26 0.62
20 3 0.07
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (19 bp):
GGGGGTATCGATTCCCCTG
Found at i:312501 original size:31 final size:31
Alignment explanation
Indices: 312463--312742 Score: 481
Period size: 31 Copynumber: 9.0 Consensus size: 31
312453 AGGGTCGAGG
312463 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
312494 GTTTACCTATGTTCTTCGGGATATATGGAAT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
312525 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
312556 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
312587 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
312618 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
312649 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
312680 GTTTACCTATGTTCTTCGGGACATGTGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
312711 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
312742 G
1 G
312743 GTCCTTCGGG
Statistics
Matches: 237, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 236 1.00
32 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:313248 original size:21 final size:21
Alignment explanation
Indices: 313223--313265 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
313213 AAAGAATATA
313223 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
313244 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
313265 T
1 T
313266 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:313778 original size:60 final size:60
Alignment explanation
Indices: 313685--313797 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
313675 TATATGTTAC
* * *
313685 TGCTTTATTAAGTCCCTCGATTATTAAATGTTACAAAATGATCATCCGATTATAGAGTGT
1 TGCTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAATCATCCGATTATAGAGTGT
* * * *
313745 TGCTTTATTGAGTCCCTTGACTATTAAAAGTTACAAAATAATCGTCTGATTAT
1 TGCTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAATCATCCGATTAT
313798 TCATCATGTC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (60 bp):
TGCTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAATCATCCGATTATAGAGTGT
Found at i:315248 original size:153 final size:153
Alignment explanation
Indices: 314851--315258 Score: 737
Period size: 152 Copynumber: 2.7 Consensus size: 153
314841 TATTGTTTTG
314851 GCACTATTAGGTCCCCAAATGAACTTCGATATGATGTTGTTCAACTTCGAAGCAATCACTTCTGA
1 GCACTATTAGGTCCCCAAATGAACTTCGATATGATGTTGTTCAACTTCGAAGCAATCACTTCTGA
* * *
314916 CATGTTGAAAAAAGAGAGGTATTGTACAGATTGATTAGCAAGTACTGCTTTCACTAATAATATTA
66 CATGTTGAACAAAGAGAGGTATTGTACAGGTTGATTAGCAAGGACTGCTTTCACTAATAATATTA
*
314981 TTTGATTATAATTTAAATGGTTT
131 TTTGATTACAATTTAAATGGTTT
*
315004 GTACTATTAGGT-CCCAAATGAACTTCGATATGATGTTGTTCAACTTCGAAGCAATCACTTCTGA
1 GCACTATTAGGTCCCCAAATGAACTTCGATATGATGTTGTTCAACTTCGAAGCAATCACTTCTGA
315068 CATGTTGAACAAAGAGAGGTATTGTACAGGTTGATTAGCAAGGACTGCTTTCACTAATAATATTA
66 CATGTTGAACAAAGAGAGGTATTGTACAGGTTGATTAGCAAGGACTGCTTTCACTAATAATATTA
*
315133 TTTGATTCCAATTTAAATGGTTT
131 TTTGATTACAATTTAAATGGTTT
* *
315156 GCACTATTAGGTCCCCAAATGAACTTCAATATGATGTTGTTCAACTTCGAAGCCATCACTTCTGA
1 GCACTATTAGGTCCCCAAATGAACTTCGATATGATGTTGTTCAACTTCGAAGCAATCACTTCTGA
315221 CATGTTGAACAAAGAGAGGTATTGTACAGGTTGATTAG
66 CATGTTGAACAAAGAGAGGTATTGTACAGGTTGATTAG
315259 TAGGCCTGTA
Statistics
Matches: 245, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
152 146 0.60
153 99 0.40
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (153 bp):
GCACTATTAGGTCCCCAAATGAACTTCGATATGATGTTGTTCAACTTCGAAGCAATCACTTCTGA
CATGTTGAACAAAGAGAGGTATTGTACAGGTTGATTAGCAAGGACTGCTTTCACTAATAATATTA
TTTGATTACAATTTAAATGGTTT
Found at i:315443 original size:10 final size:10
Alignment explanation
Indices: 315430--315468 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
315420 ACGTTCATGA
*
315430 ATGTTCGATT
1 ATGTTCGTTT
315440 ATGTTCGTTT
1 ATGTTCGTTT
315450 ATGTTCGTTT
1 ATGTTCGTTT
*
315460 ATGTCCGTT
1 ATGTTCGTT
315469 CATTTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.54
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:315448 original size:24 final size:22
Alignment explanation
Indices: 315421--315471 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 22
315411 CGTTCATTTA
*
315421 CGTTCATGAATGTTCGATTATGTT
1 CGTTCAT--ATGTTCGATTATGTC
*
315445 CGTT--TATGTTCGTTTATGTC
1 CGTTCATATGTTCGATTATGTC
315465 CGTTCAT
1 CGTTCAT
315472 TTATGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
20 17 0.74
22 2 0.09
24 4 0.17
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.49
Consensus pattern (22 bp):
CGTTCATATGTTCGATTATGTC
Found at i:316576 original size:16 final size:16
Alignment explanation
Indices: 316555--316612 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
316545 GTCTCCAGCG
* *
316555 TTTATGTTTGTGTTTA
1 TTTATGTTCGTGTTCA
*
316571 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
316587 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
316603 TTTATATTCG
1 TTTATGTTCG
316613 CTTATTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.10, C:0.09, G:0.21, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:318358 original size:41 final size:41
Alignment explanation
Indices: 318297--318436 Score: 165
Period size: 41 Copynumber: 3.4 Consensus size: 41
318287 GTGGCGTTTT
* * *
318297 CCGCTAAAGACTCGTACTTTAGTGGTGTTTTTGTACAAACG
1 CCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACG
* * *
318338 CCGCTAAATACTAGTTCTTTAGTGGCGGTTTTATACAAACG
1 CCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACG
* * * *
318379 TCGCTAAAGACTCA-TACTTAAGTGGCATTTTTATACGAACG
1 CCGCTAAAGACT-AGTACTTTAGTGGCGTTTTTATACAAACG
*
318420 CCGCTAAAGACTCGTAC
1 CCGCTAAAGACTAGTAC
318437 CCTATAATTT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 81 0.99
42 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (41 bp):
CCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACG
Found at i:324742 original size:191 final size:190
Alignment explanation
Indices: 324500--324908 Score: 568
Period size: 191 Copynumber: 2.1 Consensus size: 190
324490 ATTCATAGTC
** * *
324500 CTTTTGATTATTGCAAATTAAAAGATAATTTTTAATTTAAATATTAGTAGGATAATCACTCTTTT
1 CTTTTGACCATTGCAAATTAAAAGATAATATTTAATTTAAATATTAGTAGGATAATCACTCTTTG
* * *
324565 AATAAGTCAATTTAAAAAGATATTTGTTATCTTTTTAATTTTTGAATATTAAAAAATAATTATAT
66 AATAAGTCAACTTAAAAAGATATTTGTTACCTTTTTAA-CTTTGAATATT-AAAAATAATTATAT
* * *
324630 AATTTTGTATATTTCAAATTAAAATAATATTTGTTTAAGTTTGAATATTAAAAGAAGTTTAA
129 AATTTTGTATATTTCAAATTAAAATAATATCTATTTAAATTTGAATATTAAAAGAAGTTTAA
* *
324692 CTTTTGACCATTGCAAATT-AAATATAATATTTAATTTAAATATTAGTAGGATAATTACTCTTTG
1 CTTTTGACCATTGCAAATTAAAAGATAATATTTAATTTAAATATTAGTAGGATAATCACTCTTTG
* * * *
324756 AATATGTCAACTTAAAAAGGTATTTGTTACCTTTTTAACTTTGAATATTAAAGATAATTATATAC
66 AATAAGTCAACTTAAAAAGATATTTGTTACCTTTTTAACTTTGAATATTAAAAATAATTATATAA
** * * *
324821 TTTTGTATATTTCAAATTAAAATAATATCTATTTAAATTTGAATGGTAAACGGAGTTTTAT
131 TTTTGTATATTTCAAATTAAAATAATATCTATTTAAATTTGAATATTAAAAGAAG-TTTAA
** *
324882 CTTTTGAATATTTCAAATTAAAAGATA
1 CTTTTGACCATTGCAAATTAAAAGATA
324909 TTGTTATATG
Statistics
Matches: 190, Mismatches: 25, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
189 62 0.33
190 30 0.16
191 81 0.43
192 17 0.09
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (190 bp):
CTTTTGACCATTGCAAATTAAAAGATAATATTTAATTTAAATATTAGTAGGATAATCACTCTTTG
AATAAGTCAACTTAAAAAGATATTTGTTACCTTTTTAACTTTGAATATTAAAAATAATTATATAA
TTTTGTATATTTCAAATTAAAATAATATCTATTTAAATTTGAATATTAAAAGAAGTTTAA
Found at i:328854 original size:59 final size:59
Alignment explanation
Indices: 328726--328861 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 59
328716 ATAGTTGGGT
** * * *
328726 GACCATTTTGTAACTTTTAATAGTTGAGGTACTTAATAAAGCAACATCTATAGTCGAAA
1 GACCATTTTGTAACTTTTAATAGTCAAGGGACTTAATAAAACAACATCTATAATCGAAA
* * * *
328785 GACTATTTTGTAACTTTTAATAGTCAAGGGACTTAATAAAATAATATCATATAATCGAAG
1 GACCATTTTGTAACTTTTAATAGTCAAGGGACTTAATAAAACAACATC-TATAATCGAAA
328845 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
328862 ACCCTTGATA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 41 0.63
60 21 0.32
61 3 0.05
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (59 bp):
GACCATTTTGTAACTTTTAATAGTCAAGGGACTTAATAAAACAACATCTATAATCGAAA
Found at i:330522 original size:22 final size:22
Alignment explanation
Indices: 330468--330524 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
330458 GCAACGCGAT
*
330468 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
330490 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
330509 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
330525 TTGCGATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 16 0.53
20 2 0.07
21 2 0.07
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:330539 original size:22 final size:19
Alignment explanation
Indices: 330473--330539 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
330463 GCGATTTTGA
*
330473 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
330492 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
330513 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
330536 AAAA
1 AAAA
330540 ATCCAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 16 0.41
21 1 0.03
22 8 0.21
23 2 0.05
24 2 0.05
25 10 0.26
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:330687 original size:65 final size:64
Alignment explanation
Indices: 330583--330705 Score: 228
Period size: 65 Copynumber: 1.9 Consensus size: 64
330573 ATTCAAGTGG
330583 AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCCCAAGTCATTTGTAAGATCTT
1 AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCCCAAGT-ATTTGTAAGATCTT
*
330648 AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCCCAAGTGTTTGTAA
1 AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCCCAAGTATTTGTAA
330706 TGCTTAATCC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 7 0.12
65 50 0.88
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (64 bp):
AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCCCAAGTATTTGTAAGATCTT
Found at i:330842 original size:5 final size:5
Alignment explanation
Indices: 330834--330872 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
330824 CCGTCTTGTC
* *
330834 TCGGG TCGGG TCGGG TCGGG TCTGG TCGTG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG
330873 TGGTAATACG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.00, C:0.21, G:0.51, T:0.28
Consensus pattern (5 bp):
TCGGG
Found at i:331059 original size:20 final size:20
Alignment explanation
Indices: 331029--331121 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
331019 ATTTTGTATT
*
331029 ATCGCATTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* * *
331049 ATCGCGCTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * **
331069 TTCGCATTGCGATTTTCTAGA
1 ATCGCGTTGCGATAGTC-AGA
331090 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
331110 ATCGCGTTGCGA
1 ATCGCGTTGCGA
331122 ATCTGGAAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.69
21 17 0.29
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:331140 original size:61 final size:62
Alignment explanation
Indices: 331012--331203 Score: 150
Period size: 61 Copynumber: 3.2 Consensus size: 62
331002 TGGAAAATCA
* ** * * * * *
331012 CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGCTGCG-ATTTACATATTCG
1 CATTGCGATTTTCTAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAATCTACAAACTCG
**
331073 CATTGCGATTTTCTAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAATCTGGAAACT-G
1 CATTGCGATTTTCTAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAATCTACAAACTCG
* * * * * *
331134 -ATTTGCGA--TACTGGAGATCGCGTTGCGAT--TTAGAGATCGCGTTGCG-ATTTAGAGA-TCG
1 CA-TTGCGATTTTCTAGA-ATCGCGTTGCGATAGTCAGA-ATCGCGTTGCGAATCTACAAACTCG
331192 CATTGCGATTTT
1 CATTGCGATTTT
331204 GTTGGTCATT
Statistics
Matches: 106, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
57 1 0.01
58 17 0.16
59 17 0.16
60 15 0.14
61 50 0.47
62 6 0.06
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (62 bp):
CATTGCGATTTTCTAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAATCTACAAACTCG
Found at i:331171 original size:19 final size:19
Alignment explanation
Indices: 331147--331202 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
331137 TGCGATACTG
331147 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
331166 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
*
331185 GAGATCGCATTGCGATTT
1 GAGATCGCGTTGCGATTT
331203 TGTTGGTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCGTTGCGATTTA
Found at i:332477 original size:13 final size:13
Alignment explanation
Indices: 332459--332483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
332449 AGGATTTAAT
332459 AAAAAAATTATTA
1 AAAAAAATTATTA
332472 AAAAAAATTATT
1 AAAAAAATTATT
332484 TGAAGAAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAAATTATTA
Found at i:332492 original size:14 final size:14
Alignment explanation
Indices: 332459--332496 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
332449 AGGATTTAAT
332459 AAAAAAATTA-TTA
1 AAAAAAATTATTTA
*
332472 AAAAAAATTATTTG
1 AAAAAAATTATTTA
*
332486 AAGAAAATTAT
1 AAAAAAATTAT
332497 AAGTGTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (14 bp):
AAAAAAATTATTTA
Found at i:336973 original size:19 final size:20
Alignment explanation
Indices: 336949--336987 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
336939 GTACTAGTAT
336949 TTGTACTTGTTTAGC-GTTA
1 TTGTACTTGTTTAGCTGTTA
336968 TTGTACTTGTTTAGCTGTTA
1 TTGTACTTGTTTAGCTGTTA
336988 CTTTGCATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
TTGTACTTGTTTAGCTGTTA
Found at i:338235 original size:39 final size:41
Alignment explanation
Indices: 338158--338235 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
338148 AAAACTTGAA
*
338158 TCAAAAATAAAATAATAAAAATGAATTTGGTAACTAATTTT
1 TCAAAAATAAAATAATAAAAATGAATTTGGTAAATAATTTT
* *
338199 TCAAAAATAGAAATAA-ACAAAT-AA-TTGTTAAATAATT
1 TCAAAAATA-AAATAATAAAAATGAATTTGGTAAATAATT
338236 GAATTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 11 0.33
40 2 0.06
41 14 0.42
42 6 0.18
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.32
Consensus pattern (41 bp):
TCAAAAATAAAATAATAAAAATGAATTTGGTAAATAATTTT
Found at i:338861 original size:13 final size:13
Alignment explanation
Indices: 338840--338899 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
338830 ATTTTGTTAG
338840 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
338853 TATTGTA-TTATT
1 TATTTTATTTAAT
338865 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
338877 TATTTTATTTAAT
1 TATTTTATTTAAT
338890 TATTTTATTT
1 TATTTTATTT
338900 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:338865 original size:21 final size:20
Alignment explanation
Indices: 338840--338904 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
338830 ATTTTGTTAG
338840 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
338861 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
338877 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
338898 TTTTTTA
1 TATTTTA
338905 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 13 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:338875 original size:29 final size:29
Alignment explanation
Indices: 338842--338904 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
338832 TTTGTTAGTA
338842 TTTTATT-TAATTATTGT-ATTATTTAATTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTT
* *
338871 TTTTATTATTTTATTTAATTATTTTATTT
1 TTTTATTATATTATTTAATTATTTAATTT
338900 TTTTA
1 TTTTA
338905 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATTATTTAATTATTTAATTT
Found at i:338886 original size:16 final size:16
Alignment explanation
Indices: 338844--338886 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
338834 TGTTAGTATT
* *
338844 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
338860 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
338876 TTATTTTATTT
1 TTATTTAATTT
338887 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:339188 original size:20 final size:21
Alignment explanation
Indices: 339151--339194 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
339141 TTTATAACTG
339151 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAATAATTAAA
*
339172 TAAAATAATAAAA-AATTAAA
1 TAAAAAAATAAAATAATTAAA
339192 TAA
1 TAA
339195 TACAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAAAATAAAATAATTAAA
Found at i:339201 original size:20 final size:21
Alignment explanation
Indices: 339151--339202 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
339141 TTTATAACTG
*
339151 TAAAAAAATAAAATAATTAAA
1 TAAAACAATAAAATAATTAAA
*
339172 TAAAATAATAAAA-AATTAAA
1 TAAAACAATAAAATAATTAAA
*
339192 TAATACAATAA
1 TAAAACAATAA
339203 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAACAATAAAATAATTAAA
Found at i:339208 original size:16 final size:15
Alignment explanation
Indices: 339169--339210 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
339159 TAAAATAATT
*
339169 AAATAAAATAATAAA
1 AAATTAAATAATAAA
339184 AAATTAAATAATACAA
1 AAATTAAATAATA-AA
*
339200 TAATTAAATAA
1 AAATTAAATAA
339211 ATACTAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTAAATAATAAA
Found at i:339684 original size:3 final size:3
Alignment explanation
Indices: 339676--339737 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
339666 TATATTATAT
* *
339676 TTA TTA TTA TATA CTA -TA TTA TTA TTA TT- TT- TTT TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
339719 TTA TTA ATA TCA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TT
339738 TATATTTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 8 0.16
3 39 0.80
4 2 0.04
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:339687 original size:21 final size:21
Alignment explanation
Indices: 339664--339704 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
339654 GAGATTAAAA
*
339664 TATATATTATA-T-TTATTAT
1 TATATACTATATTATTATTAT
339683 TATATACTATATTATTATTAT
1 TATATACTATATTATTATTAT
339704 T
1 T
339705 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATACTATATTATTATTAT
Found at i:339688 original size:19 final size:18
Alignment explanation
Indices: 339668--339724 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 18
339658 TTAAAATATA
339668 TATTATATTTATTATTAT
1 TATTATATTTATTATTAT
*
339686 ATACTATA-TTATTATTAT
1 -TATTATATTTATTATTAT
*
339704 T-TT-TTTTTATTATTAT
1 TATTATATTTATTATTAT
339720 TATTA
1 TATTA
339725 ATATCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.03
16 12 0.38
17 3 0.09
18 10 0.31
19 6 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTATATTTATTATTAT
Found at i:339723 original size:28 final size:28
Alignment explanation
Indices: 339692--339747 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
339682 TTATATACTA
* * *
339692 TATTATTATTATTTT-TTTTTATTATTAT
1 TATTAATATCATTTTATTTATATT-TTAT
339720 TATTAATATCATTTTATTTATATTTTAT
1 TATTAATATCATTTTATTTATATTTTAT
339748 GCAGTTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (28 bp):
TATTAATATCATTTTATTTATATTTTAT
Found at i:339746 original size:34 final size:35
Alignment explanation
Indices: 339670--339747 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
339660 AAAATATATA
*
339670 TTATA-TTTATTATTATATACTATATTATTATTAT
1 TTATATTTTATTATTATATACTATATCATTATTAT
* *
339704 TT-TTTTTTATTATTAT-TATTAATATCATT-TTAT
1 TTATATTTTATTATTATATACT-ATATCATTATTAT
339737 TTATATTTTAT
1 TTATATTTTAT
339748 GCAGTTTAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
33 10 0.27
34 27 0.73
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (35 bp):
TTATATTTTATTATTATATACTATATCATTATTAT
Found at i:341484 original size:23 final size:23
Alignment explanation
Indices: 341458--341503 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
341448 CGTATTTCTG
*
341458 TTGTATTTTATTTTAGTTCTTAT
1 TTGTATTTTATTATAGTTCTTAT
* * *
341481 TTGTGTTTTGTTATAGTTTTTAT
1 TTGTATTTTATTATAGTTCTTAT
341504 GGTGTTTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.70
Consensus pattern (23 bp):
TTGTATTTTATTATAGTTCTTAT
Found at i:346854 original size:16 final size:16
Alignment explanation
Indices: 346833--346865 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
346823 ACTTCACAGA
*
346833 ACTCAAACAAGGAACC
1 ACTCAAACAAAGAACC
346849 ACTCAAACAAAGAACC
1 ACTCAAACAAAGAACC
346865 A
1 A
346866 TTCTTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.30, G:0.09, T:0.06
Consensus pattern (16 bp):
ACTCAAACAAAGAACC
Found at i:360901 original size:30 final size:29
Alignment explanation
Indices: 360743--360960 Score: 138
Period size: 30 Copynumber: 7.4 Consensus size: 29
360733 GTAATTACTG
* * * *
360743 TTTTAGTCCTTTTAGTTTCTGTTAATACCA
1 TTTTAGTCCTTTAAGTTTCTATT-TTTCCA
* * * **
360773 GTTTAGT-CTCTTAACTTTCTTTTTTTGTTA
1 TTTTAGTCCT-TTAAGTTTCTATTTTT-CCA
* * *
360803 TTTTAGTCCTGTAACTTTCTATTTTTCTA
1 TTTTAGTCCTTTAAGTTTCTATTTTTCCA
* * * *
360832 TTTT-GACCCTTAAGTTTCTATTTTTACT
1 TTTTAGTCCTTTAAGTTTCTATTTTTCCA
*
360860 TTTTA-TCCCTTTTAGTTTCTATTTGTTCCA
1 TTTTAGT-CCTTTAAGTTTCTATTT-TTCCA
* *
360890 TTTTAGTCCTTTAAGTTT-TGGTTTTTGCTA
1 TTTTAGTCCTTTAAGTTTCT-ATTTTT-CCA
* *
360920 TTTTAGCCCTTTAAGTTGCTATTTTTCTCA
1 TTTTAGTCCTTTAAGTTTCTATTTTTC-CA
*
360950 TTTTGGTCCTT
1 TTTTAGTCCTT
360961 GTAATTTTAA
Statistics
Matches: 144, Mismatches: 33, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
28 21 0.15
29 28 0.19
30 91 0.63
31 4 0.03
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.58
Consensus pattern (29 bp):
TTTTAGTCCTTTAAGTTTCTATTTTTCCA
Found at i:360942 original size:60 final size:57
Alignment explanation
Indices: 360794--360969 Score: 167
Period size: 60 Copynumber: 3.0 Consensus size: 57
360784 TAACTTTCTT
* * * * * * *
360794 TTTTTGTTATTTTAGTCCTGTAACTTTCTATTTTTCTATTTTGACCCTTAAGTTTCTA
1 TTTTTGCTATTTTAGCCCTTTAAGTTTCTATTTTTCCATTTTGTCCTTTAAGTTT-TA
* * * *
360852 TTTTTACT-TTTTATCCCTTTTAGTTTCTATTTGTTCCATTTTAGTCCTTTAAGTTTTGG
1 TTTTTGCTATTTTAGCCCTTTAAGTTTCTATTT-TTCCATTTT-GTCCTTTAAGTTTT-A
*
360911 TTTTTGCTATTTTAGCCCTTTAAGTTGCTATTTTTCTCATTTTGGTCCTTGTAA-TTTTA
1 TTTTTGCTATTTTAGCCCTTTAAGTTTCTATTTTTC-CATTTT-GTCCTT-TAAGTTTTA
360970 AATATTTACT
Statistics
Matches: 95, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
57 19 0.20
58 15 0.16
59 21 0.22
60 37 0.39
61 3 0.03
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.59
Consensus pattern (57 bp):
TTTTTGCTATTTTAGCCCTTTAAGTTTCTATTTTTCCATTTTGTCCTTTAAGTTTTA
Found at i:362205 original size:29 final size:29
Alignment explanation
Indices: 362132--362274 Score: 96
Period size: 30 Copynumber: 4.9 Consensus size: 29
362122 GTTTAGTCTT
* * * *
362132 TTAACTTTCTTTTTTTGTTATTTT-AGTCC
1 TTAAGTTTCTGTTTTTGCTATTTTGA-CCC
*
362161 TGTAACTTTCTGTTTTT-CTATTTTGACCC
1 T-TAAGTTTCTGTTTTTGCTATTTTGACCC
* *
362190 TTAAGTTTCTGTTTTTACTGTTTT-ATCCC
1 TTAAGTTTCTGTTTTTGCTATTTTGA-CCC
* * * *
362219 TTTTAA-TTTCTGTTTGTGCCATTTTAGTCCT
1 --TTAAGTTTCTGTTTTTGCTATTTT-GACCC
*
362250 TTAAGTTTCGGTTTTTGCTATTTTG
1 TTAAGTTTCTGTTTTTGCTATTTTG
362275 GTCCTTTAAG
Statistics
Matches: 91, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
28 15 0.16
29 24 0.26
30 46 0.51
31 6 0.07
ACGTcount: A:0.13, C:0.15, G:0.12, T:0.59
Consensus pattern (29 bp):
TTAAGTTTCTGTTTTTGCTATTTTGACCC
Found at i:362231 original size:30 final size:28
Alignment explanation
Indices: 362167--362304 Score: 91
Period size: 30 Copynumber: 4.7 Consensus size: 28
362157 GTCCTGTAAC
362167 TTTCTGTTTTTCTATTTTGACCCTTAAG
1 TTTCTGTTTTTCTATTTTGACCCTTAAG
*
362195 TTTCTGTTTTTACTGTTTT-ATCCCTTTTAA-
1 TTTCTGTTTTT-CTATTTTGA-CCC--TTAAG
* * * *
362225 TTTCTGTTTGTGCCATTTTAGTCCTTTAAG
1 TTTCTGTTT-TTCTATTTT-GACCCTTAAG
* * *
362255 TTTCGGTTTTTGCTATTTTGGTCCTTTAAG
1 TTTCTGTTTTT-CTATTTT-GACCCTTAAG
* *
362285 TTGCTATTTTTCTCATTTTG
1 TTTCTGTTTTTCT-ATTTTG
362305 GTCCTTGTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
28 12 0.14
29 17 0.20
30 51 0.59
31 7 0.08
ACGTcount: A:0.12, C:0.16, G:0.13, T:0.59
Consensus pattern (28 bp):
TTTCTGTTTTTCTATTTTGACCCTTAAG
Found at i:362305 original size:30 final size:31
Alignment explanation
Indices: 362238--362310 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
362228 CTGTTTGTGC
* * *
362238 CATTTTAGTCCTTTAAGTTTCGGTTTTTGCT
1 CATTTTGGTCCTTTAAGTTGCGATTTTTGCT
*
362269 -ATTTTGGTCCTTTAAGTTGCTATTTTT-CT
1 CATTTTGGTCCTTTAAGTTGCGATTTTTGCT
362298 CATTTTGGTCCTT
1 CATTTTGGTCCTT
362311 GTAATTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.12, C:0.16, G:0.15, T:0.56
Consensus pattern (31 bp):
CATTTTGGTCCTTTAAGTTGCGATTTTTGCT
Found at i:383156 original size:19 final size:21
Alignment explanation
Indices: 383119--383161 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
383109 TAACTTTTTC
*
383119 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
383139 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
383159 TTT
1 TTT
383162 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:383161 original size:20 final size:20
Alignment explanation
Indices: 383119--383225 Score: 62
Period size: 20 Copynumber: 5.2 Consensus size: 20
383109 TAACTTTTTC
*
383119 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATT-TTAACT
383139 TTTTCTCTTTCATTTTAACT
1 TTTTCTCTTTCATTTTAACT
* *
383159 TTTACTTTTTC-TCTTT--CT
1 TTTTCTCTTTCAT-TTTAACT
*
383177 TTTACTCATCTTCTTCCCTTATTAA-T
1 TTT--TC-TC-T-TT-CATT-TTAACT
383203 TTTTCTCTTTCATTTTAACT
1 TTTTCTCTTTCATTTTAACT
383223 TTT
1 TTT
383226 ACTTTTTCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
18 5 0.07
19 9 0.13
20 34 0.50
21 3 0.04
22 2 0.03
23 4 0.06
24 4 0.06
25 3 0.04
26 4 0.06
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTCTCTTTCATTTTAACT
Found at i:383204 original size:64 final size:64
Alignment explanation
Indices: 383131--383263 Score: 266
Period size: 64 Copynumber: 2.1 Consensus size: 64
383121 TTCTCTTTCT
383131 TTATTAATTTTTCTCTTTCATTTTAACTTTTACTTTTTCTCTTTCTTTTACTCATCTTCTTCCC
1 TTATTAATTTTTCTCTTTCATTTTAACTTTTACTTTTTCTCTTTCTTTTACTCATCTTCTTCCC
383195 TTATTAATTTTTCTCTTTCATTTTAACTTTTACTTTTTCTCTTTCTTTTACTCATCTTCTTCCC
1 TTATTAATTTTTCTCTTTCATTTTAACTTTTACTTTTTCTCTTTCTTTTACTCATCTTCTTCCC
383259 TTATT
1 TTATT
383264 CTCTCCATAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (64 bp):
TTATTAATTTTTCTCTTTCATTTTAACTTTTACTTTTTCTCTTTCTTTTACTCATCTTCTTCCC
Found at i:386538 original size:24 final size:24
Alignment explanation
Indices: 386511--386560 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
386501 TGGTGGTTGA
386511 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
386535 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
386559 TT
1 TT
386561 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:390165 original size:24 final size:24
Alignment explanation
Indices: 390129--390174 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
390119 CCGAAGCATA
* * *
390129 TGAAGATGCTCACCATCCAGCCAC
1 TGAAGAGGATCACCAGCCAGCCAC
390153 TGAAGAGGATCACCAGCCAGCC
1 TGAAGAGGATCACCAGCCAGCC
390175 GATGAGGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.13
Consensus pattern (24 bp):
TGAAGAGGATCACCAGCCAGCCAC
Found at i:394124 original size:31 final size:31
Alignment explanation
Indices: 394072--394158 Score: 133
Period size: 31 Copynumber: 2.8 Consensus size: 31
394062 AGTCAAGGGC
394072 TACCTATGTCCTTT-GGACATATGGACA-GTT
1 TACCTATGTCCTTTGGGACATATGGACATG-T
394102 TACCTATGTCCTTTGGGACATATGGACATGT
1 TACCTATGTCCTTTGGGACATATGGACATGT
* *
394133 TACCTATGTTCTTTGGAACATATGGA
1 TACCTATGTCCTTTGGGACATATGGA
394159 TAGGTCTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
30 14 0.26
31 38 0.72
32 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (31 bp):
TACCTATGTCCTTTGGGACATATGGACATGT
Found at i:394195 original size:22 final size:21
Alignment explanation
Indices: 394142--394196 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
394132 TTACCTATGT
* * *
394142 TCTTTGGAACATATGGATAGG
1 TCTTTGGGACACATGCATAGG
*
394163 TCTTTCAGGACACATGCATAGG
1 TCTTT-GGGACACATGCATAGG
394185 TCCTTTGGGACA
1 T-CTTTGGGACA
394197 TATTTCAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 5 0.19
22 18 0.67
23 4 0.15
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (21 bp):
TCTTTGGGACACATGCATAGG
Found at i:403943 original size:43 final size:43
Alignment explanation
Indices: 403895--403979 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
403885 TTTTAATAAA
403895 ATATTAATTAAATCTCTATTTTTTACACC-CACTTAAATCTACG
1 ATATTAATTAAATCTCTATTTTTTAC-CCTCACTTAAATCTACG
*
403938 ATATTAATTAAATCTCTATTTTTTACCCTCACTTAAGTCTAC
1 ATATTAATTAAATCTCTATTTTTTACCCTCACTTAAATCTAC
403980 ACACAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 2 0.05
43 38 0.95
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (43 bp):
ATATTAATTAAATCTCTATTTTTTACCCTCACTTAAATCTACG
Found at i:410107 original size:80 final size:80
Alignment explanation
Indices: 409958--410109 Score: 180
Period size: 80 Copynumber: 1.9 Consensus size: 80
409948 AACATTTCCG
* * * * * * *
409958 GTAAAATGCCCAATATTAATATTTCTGGTAGAAAAAATAATGTTTTAGGTAGCGTTTTATCGGAT
1 GTAAAACGCCCAATAATAATATTTCCGATAGAAAAAATAATGTTTTAGGTAACGTTTTACCGGAA
410023 ATGTTAACAAACCCA
66 ATGTTAACAAACCCA
* ** **
410038 GTAAAACGCCCAATAATAATATTTCCGATAGAAATAATAAAT-TTTTAGGTAATTTTTTACCTTA
1 GTAAAACGCCCAATAATAATATTTCCGATAGAAAAAAT-AATGTTTTAGGTAACGTTTTACCGGA
410102 AATGTTAA
65 AATGTTAA
410110 AAAAATAATA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
80 56 0.95
81 3 0.05
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (80 bp):
GTAAAACGCCCAATAATAATATTTCCGATAGAAAAAATAATGTTTTAGGTAACGTTTTACCGGAA
ATGTTAACAAACCCA
Found at i:410476 original size:176 final size:171
Alignment explanation
Indices: 410152--410965 Score: 865
Period size: 176 Copynumber: 4.9 Consensus size: 171
410142 TTAATTGTAT
* * * * *
410152 ATTAAGCTGTCGCACGTGAGATTTCAACGTTTAAATAAGCTGAATGGGAAATAAAGCATTTAAAA
1 ATTAGGCTGCCGCACGTAAGATTTC-CCATTTAAATAAGCTGAAT-GGAAATAAAGCATTT--AA
410217 AAACTAAAAAGAAAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCGTGAATTAA
62 AAA-T-AAAAG-AAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCGTGAATTAA
* * * *
410282 ACCTATCTCAAAATCAATGGCAAGATCATTAGGAATGATAATCAAGAA
124 ACCCATCTCAAAATCAATGGCAAGATCATCAGGAAGGATCATCAAGAA
*
410330 ATTAGGCTGCCACACGTAAGATTTCCCATTTAAATAAGCTGAATGGGAAATAAAGCATTTAAAAA
1 ATTAGGCTGCCGCACGTAAGATTTCCCATTTAAATAAGCTGAAT-GGAAATAAAGCATTT--AAA
* *
410395 AACTAAAAAGAAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCATAAATTAAAC
63 AA-T-AAAAGAAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCGTGAATTAAAC
*
410460 CCAACTCAAAATCAATGGCAAGATCATCAGGAAGGATCATCAAGAA
126 CCATCTCAAAATCAATGGCAAGATCATCAGGAAGGATCATCAAGAA
* *
410506 ATTAGGCTGCCGCACATAAGATTTCCCATTTAAATAAGCTAAATAGGAAATAAAGCA-TT-----
1 ATTAGGCTGCCGCACGTAAGATTTCCCATTTAAATAAGCTGAAT-GGAAATAAAGCATTTAAAAA
* * *
410565 T-----AAAAAAAAGATTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAATCCAT
65 TAAAAGAAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCGTGAATTAAACCCAT
* * * * *
410625 CTCAATATCAATGGTAAGATCATCGGGAAGGATCATAAAAAA
130 CTCAAAATCAATGGCAAGATCATCAGGAAGGATCATCAAGAA
* * * * *
410667 ATTAAGTTGACGCACGTAAGATTTTTCCATTTAAATAAGCTGAATGGAAATAAAACA-TT-----
1 ATTAGGCTGCCGCACGTAAGA-TTTCCCATTTAAATAAGCTGAATGGAAATAAAGCATTTAAAAA
*
410726 TAAAAGAAAAAAAA-A-TTTAACCACGTTTCTA-TTTTTATCCAGAATTCGTGAATTAAACCTAT
65 TAAAAGAAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCGTGAATTAAACCCAT
410788 CTCAAAATCAAT-----G---A-C---AA-GATCATCAAGAA
130 CTCAAAATCAATGGCAAGATCATCAGGAAGGATCATCAAGAA
* * * * ** * * *
410817 ATTAGGATGCCGCAAGTGAGATTTATCTGTTTAAATAAGCTAAATGAAAATAAAACATTTAAAAA
1 ATTAGGCTGCCGCACGTAAGATTT-CCCATTTAAATAAGCTGAATGGAAATAAAGCATTTAAAAA
* * *
410882 T--AAG-AAAAAAA-TTTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAACCCAT
65 TAAAAGAAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCGTGAATTAAACCCAT
410943 CTCAAAATCAATGGCAAGATCAT
130 CTCAAAATCAATGGCAAGATCAT
410966 GGATCATCAA
Statistics
Matches: 557, Mismatches: 55, Indels: 62
0.83 0.08 0.09
Matches are distributed among these distances:
149 3 0.01
150 54 0.10
151 4 0.01
153 7 0.01
154 20 0.04
155 41 0.07
156 1 0.00
158 1 0.00
160 1 0.00
161 121 0.22
162 21 0.04
163 39 0.07
164 16 0.03
165 1 0.00
166 8 0.01
167 1 0.00
175 2 0.00
176 147 0.26
177 48 0.09
178 21 0.04
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (171 bp):
ATTAGGCTGCCGCACGTAAGATTTCCCATTTAAATAAGCTGAATGGAAATAAAGCATTTAAAAAT
AAAAGAAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCGTGAATTAAACCCATC
TCAAAATCAATGGCAAGATCATCAGGAAGGATCATCAAGAA
Found at i:410576 original size:161 final size:160
Alignment explanation
Indices: 410405--410965 Score: 648
Period size: 161 Copynumber: 3.5 Consensus size: 160
410395 AACTAAAAAG
* * * * * *
410405 AAAAAAAAGATTTTAACCACGTTTCTATTTTTTATCCAGAATTCATAAATTAAACCCAACTCAAA
1 AAAAAAAAAATTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAACCCATCTCAAA
* *
410470 ATCAATGGCAAGATCATCAGGAAGGATCATCAAGAAATTAGGCTGCCGCACATAAGATTTCCCAT
66 ATCAATGGCAAGATCATC-GGAAGGATCATCAAGAAATTAGGATGCCGCACATAAGATTTTCCAT
*
410535 TTAAATAAGCTAAATAGGAAATAAAGCATTT-
130 TTAAATAAGCTAAAT-GGAAATAAAACATTTA
* * *
410566 AAAAAAAAGATTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAATCCATCTCAAT
1 AAAAAAAAAATTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAACCCATCTCAAA
* * * * * * *
410631 ATCAATGGTAAGATCATCGGGAAGGATCATAAAAAAATTAAGTTGACGCACGTAAGATTTTTCCA
66 ATCAATGGCAAGATCATC-GGAAGGATCATCAAGAAATTAGGATGCCGCACATAAGA-TTTTCCA
*
410696 TTTAAATAAGCTGAATGGAAATAAAACATTTAA
129 TTTAAATAAGCTAAATGGAAATAAAACATTT-A
* * *
410729 AAGAAAAAAAAATTTAACCACGTTTCTATTT-TTATCCAGAATTCGTGAATTAAACCTATCTCAA
1 AA-AAAAAAAATTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAACCCATCTCAA
* *
410793 AATCAAT-----G---A-C--AA-GATCATCAAGAAATTAGGATGCCGCA-AGTGAGATTTATCT
65 AATCAATGGCAAGATCATCGGAAGGATCATCAAGAAATTAGGATGCCGCACA-TAAGATTT-TCC
* *
410845 GTTTAAATAAGCTAAATGAAAATAAAACATTTAAAA
128 ATTTAAATAAGCTAAATGGAAATAAAACATTT---A
410881 ATAAGAAAAAAATTTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAACCCATCTC
1 A-AA-AAAAAAA-TTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAACCCATCTC
410946 AAAATCAATGGCAAGATCAT
63 AAAATCAATGGCAAGATCAT
410966 GGATCATCAA
Statistics
Matches: 341, Mismatches: 38, Indels: 39
0.82 0.09 0.09
Matches are distributed among these distances:
149 3 0.01
150 56 0.16
151 2 0.01
152 4 0.01
153 8 0.02
154 20 0.06
155 39 0.11
158 1 0.00
160 1 0.00
161 121 0.35
162 21 0.06
163 39 0.11
164 26 0.08
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (160 bp):
AAAAAAAAAATTTTAACCACGTTTCTATTTCTTACCCAGAATTCGTGAATTAAACCCATCTCAAA
ATCAATGGCAAGATCATCGGAAGGATCATCAAGAAATTAGGATGCCGCACATAAGATTTTCCATT
TAAATAAGCTAAATGGAAATAAAACATTTA
Found at i:418240 original size:14 final size:14
Alignment explanation
Indices: 418202--418240 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
418192 ATTTTAAATA
*
418202 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
418216 TTTTACATTTGCAT
1 ATTTACATTTGCAT
418230 ATTTACATTTG
1 ATTTACATTTG
418241 GCATCTCTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:426298 original size:22 final size:22
Alignment explanation
Indices: 426272--426348 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
426262 ATCTACACTC
426272 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
426294 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
426316 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
426338 TTCAAAGATGA
1 TTCAAAGATGA
426349 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:427131 original size:76 final size:76
Alignment explanation
Indices: 427005--427176 Score: 281
Period size: 76 Copynumber: 2.3 Consensus size: 76
426995 CTATTTCCCA
427005 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
427070 AGCCTTAGGGT
66 AACCTTAGAGT
* *
427081 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
427146 AACCTTCGAGT
66 AACCTTAGAGT
* *
427157 CAGCTGTAAGCCCTACAGTG
1 CATCTGTAAGTCCTACAGTG
427177 TAGAATGTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 88 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGAGT
Found at i:427447 original size:112 final size:113
Alignment explanation
Indices: 427198--427692 Score: 745
Period size: 112 Copynumber: 4.4 Consensus size: 113
427188 TTTTTCTTAA
*
427198 AACATTTCCAG-GTAGAGTTCATAATGA-AAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAA
1 AACATTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* *
427261 TGAGAAGAACTTGTTTAACCTTTTG-TTCGAATCCATCACTTGATGGATC
65 TGAGAAGAACTTGTTCAACCTTTTGCTT-GAATTCATCACTTGATGGATC
427310 AACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
1 AACATTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
*
427374 TGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCA-TTCGATGGATC
65 TGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTT-GATGGATC
* *
427423 ATCATTTTCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-AAGAAGTTCATAAT
1 AACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
427486 GAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATC
66 GAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATC
* * *
427534 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAAT
1 AACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
427598 GAGAAGAATTTGTTCAACCATTTGCCTGAATTCATCACTTGATGGATT
66 GAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATC
* *
427646 AACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 AACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
427693 ACGTTCATAA
Statistics
Matches: 353, Mismatches: 22, Indels: 15
0.91 0.06 0.04
Matches are distributed among these distances:
111 71 0.20
112 194 0.55
113 86 0.24
114 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
AACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATC
Found at i:427708 original size:17 final size:17
Alignment explanation
Indices: 427662--427710 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
427652 TCCAGAGAAA
427662 GTTCATAATGAGAAGAAC
1 GTTCATAATGAGAAG-AC
*
427680 --TCAT-CTGAAGAAGAC
1 GTTCATAATG-AGAAGAC
427695 GTTCATAATGAGAAGA
1 GTTCATAATGAGAAGA
427711 GCTTGTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 10 0.40
18 2 0.08
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.22
Consensus pattern (17 bp):
GTTCATAATGAGAAGAC
Found at i:427852 original size:301 final size:302
Alignment explanation
Indices: 427472--428033 Score: 878
Period size: 301 Copynumber: 1.8 Consensus size: 302
427462 GAAGAAGGAA
* * *
427472 AAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATCAAC
1 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAAC
*
427537 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAG
66 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
* * * *
427601 AAGAATTTGTTCAACCATTTGC-CTGAATTCATCACTTGATGGATTAACTTTTCCAGAGAAAGTT
131 AAGAACTTGTTCAACC-TTTGCTC-AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTT
* *
427665 CATAATGAGAAGAACTCATCT-GAAGAAGACGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTT
194 CATAATGAGAAGAACTCATCTAGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTGTT
427729 TGATGCTATCACAGAAGGAAATAGATCAGTATCAACATTTCCAG
259 TGATGCTATCACAGAAGGAAATAGATCAGTATCAACATTTCCAG
*
427773 AAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAAC
1 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAAC
* * *
427838 TTTTCCATAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
66 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
* * *
427903 AAGAGCTTGTTCAATCTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCA
131 AAGAACTTGTTCAACCTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCA
427968 TAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTT
196 TAATGAGAAGAACTCATCT-----A-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTT
428033 T
255 T
428034 TGCTCAAATC
Statistics
Matches: 235, Mismatches: 17, Indels: 11
0.89 0.06 0.04
Matches are distributed among these distances:
301 161 0.69
302 36 0.15
308 38 0.16
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (302 bp):
AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAAC
ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAACTTGTTCAACCTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCA
TAATGAGAAGAACTCATCTAGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTGTTTG
ATGCTATCACAGAAGGAAATAGATCAGTATCAACATTTCCAG
Found at i:427969 original size:112 final size:113
Alignment explanation
Indices: 427771--428131 Score: 618
Period size: 113 Copynumber: 3.2 Consensus size: 113
427761 CAACATTTCC
427771 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
* *
427836 ACTTTTCCATAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
427884 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAATC-TTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
*
427948 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
66 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
427996 AGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
* * *
428061 GCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 GCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
428109 AGAAGAAATTCATAATGAGAAGA
1 AGAAGAAGTTCATAATGAGAAGA
428132 ACTCATCTGA
Statistics
Matches: 235, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
112 108 0.46
113 127 0.54
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (113 bp):
AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:428112 original size:20 final size:20
Alignment explanation
Indices: 428087--428152 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
428077 TTCATAATGA
428087 GAAGAACTCATCTGAAGAAG
1 GAAGAACTCATCTGAAGAAG
***
428107 GAAGAAGAAATTCAT-AATG-A-
1 GAAGAACTCA-TC-TGAA-GAAG
428127 GAAGAACTCATCTGAAGAAG
1 GAAGAACTCATCTGAAGAAG
428147 GAAGAA
1 GAAGAA
428153 GAAATTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 20 0.59
21 5 0.15
22 2 0.06
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.15
Consensus pattern (20 bp):
GAAGAACTCATCTGAAGAAG
Found at i:428185 original size:39 final size:40
Alignment explanation
Indices: 428077--428251 Score: 277
Period size: 40 Copynumber: 4.5 Consensus size: 40
428067 CCAGGTAGAG
428077 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
428117 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
* * *
428157 TTCATAATGAGAA-AACTCATCTAAAGAA-GAAGAATAAG
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
*
428195 TTCATAATGAGAAGAACTCATCTTG-AG-AGGAAGAAGAAG
1 TTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAA
428234 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
428252 TGTTCGACCT
Statistics
Matches: 127, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
38 22 0.17
39 51 0.40
40 54 0.43
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (40 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
Found at i:429968 original size:149 final size:146
Alignment explanation
Indices: 429807--430081 Score: 412
Period size: 149 Copynumber: 1.9 Consensus size: 146
429797 AAAATAATCA
* * *
429807 TATTTTAATATTTATTTATTTTTTAATATTAAGAAATGGGATGTCTTAA-AGTACCTAGAAGTCC
1 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGATGTCTTAAGA-CACCTAGAAGTCC
* *
429871 TTTTCTGATA-TTCTTAAATAAATAAATATCATATT-TTTATAAATTATATATATATTAATTTAT
65 TTTTCTGATATTTC-TAAATAAATAAATAT--T-TTATTTATAAA-TATATATAAATTAATATAT
429934 TTAATTATTTTTAGAAAGATTT
125 TTAATTATTTTTAGAAAGATTT
* *
429956 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAGACACCTAGAAGTTCT
1 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGATGTCTTAAGACACCTAGAAGTCCT
430021 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAATATATTT
66 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAATATATTT
430082 TCTTAAAAAT
Statistics
Matches: 116, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
146 21 0.18
147 9 0.08
149 82 0.71
150 4 0.03
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.49
Consensus pattern (146 bp):
TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGATGTCTTAAGACACCTAGAAGTCCT
TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAATATATTTAATT
ATTTTTAGAAAGATTT
Done.