Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005316.1 Hibiscus syriacus cultivar Beakdansim tig00012036_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: 155458
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:3135 original size:97 final size:98
Alignment explanation
Indices: 2944--3150 Score: 346
Period size: 98 Copynumber: 2.1 Consensus size: 98
2934 TGTGTGTGTG
*
2944 TGTGTGTGTGTACTACTTGCTTCAGTTGCTTGTATGTGCGCTTATTGTATACTTCTCTGTTTTAT
1 TGTGTGTGTGTACTACTTGCTTCAGTTGCTTGTATGCGCGCTTATTGTATACTTCTC-GTTTTAT
3009 AGAATACTATCAAATTGGAGAAGGAATATATATA
65 AGAATACTATCAAATTGGAGAAGGAATATATATA
*
3043 TGTGTGTGTGTA-TACTTGCTTCAGTTGCTTGTATGCGCGCTTATTGTCTACTTCTC-TTTTATA
1 TGTGTGTGTGTACTACTTGCTTCAGTTGCTTGTATGCGCGCTTATTGTATACTTCTCGTTTTATA
* *
3106 GAAATACTATCAAATTGGAGAAGGAATATATGTG
66 G-AATACTATCAAATTGGAGAAGGAATATATATA
3140 TGTGTGTGTGT
1 TGTGTGTGTGT
3151 GTGTGTGTGT
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
96 8 0.08
97 41 0.40
98 42 0.41
99 12 0.12
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (98 bp):
TGTGTGTGTGTACTACTTGCTTCAGTTGCTTGTATGCGCGCTTATTGTATACTTCTCGTTTTATA
GAATACTATCAAATTGGAGAAGGAATATATATA
Found at i:3141 original size:2 final size:2
Alignment explanation
Indices: 3136--3164 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3126 AAGGAATATA
3136 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3165 TTGTATTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4445 original size:142 final size:142
Alignment explanation
Indices: 4189--4477 Score: 508
Period size: 142 Copynumber: 2.0 Consensus size: 142
4179 CTGTGAAATA
*
4189 AACCCAATAATCCATGAAGTATGCCAGACTACTTTGTTGGTATATCTTTTCTGTCTTAAGCACGT
1 AACCCAATAATCCATGAAGTATGCCAGACTACTTTGTTGGTATATCTTTTCTGTCCTAAGCACGT
*
4254 TTTCAAAATGCATCTTTAAACATAGATGGCAATTGGAAAATATTCATGCTTCTAACGTGTATTAG
66 TTTCAAAATGCATCTTCAAACATAGATGGCAATTGGAAAATATTCATGCTTCTAACGTGTATTAG
4319 GGGATTAAAAAC
131 GGGATTAAAAAC
* *
4331 AACCCAATAATCCGTGAAGTATGCCGGACTACTTTGTTGGTATATCTTTTCTGTCCTAAGCACGT
1 AACCCAATAATCCATGAAGTATGCCAGACTACTTTGTTGGTATATCTTTTCTGTCCTAAGCACGT
*
4396 TTTCAAAATGCATCTTCAAACATAGATGGCAATTGGCAAAA-ATTCATGCTTCTAACTTGTATTA
66 TTTCAAAATGCATCTTCAAACATAGATGGCAATTGG-AAAATATTCATGCTTCTAACGTGTATTA
*
4460 GGGGATTAAAAGC
130 GGGGATTAAAAAC
4473 AACCC
1 AACCC
4478 TTCCACCCTT
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
142 136 0.97
143 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (142 bp):
AACCCAATAATCCATGAAGTATGCCAGACTACTTTGTTGGTATATCTTTTCTGTCCTAAGCACGT
TTTCAAAATGCATCTTCAAACATAGATGGCAATTGGAAAATATTCATGCTTCTAACGTGTATTAG
GGGATTAAAAAC
Found at i:14863 original size:2 final size:2
Alignment explanation
Indices: 14851--14881 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
14841 CTCTTTGAAT
14851 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
14882 GAACCACGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18920 original size:35 final size:35
Alignment explanation
Indices: 18879--18948 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
18869 TGCAACTATA
*
18879 CTAATTAAACTTTGATTTTAATTCGATTATATCAT
1 CTAATTAAACTTTGATTTTAATTCAATTATATCAT
18914 CTAATTAAACTTTGATTTTAATTCAATTATATCAT
1 CTAATTAAACTTTGATTTTAATTCAATTATATCAT
18949 GTGCATACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (35 bp):
CTAATTAAACTTTGATTTTAATTCAATTATATCAT
Found at i:20394 original size:21 final size:21
Alignment explanation
Indices: 20369--20413 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
20359 TTTAATAAAA
*
20369 TTTATTTAAAATATTATTATT
1 TTTATTTAAAATATTAATATT
20390 TTTATTTAAAATATTAATATT
1 TTTATTTAAAATATTAATATT
20411 TTT
1 TTT
20414 TAATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTTAAAATATTAATATT
Found at i:35833 original size:17 final size:17
Alignment explanation
Indices: 35811--35860 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
35801 TGAAACGATC
*
35811 TACGTGATTGCATGCAA
1 TACGTGATTACATGCAA
*
35828 TACGTGATTACATGTAA
1 TACGTGATTACATGCAA
35845 TACGTGATTACATGCA
1 TACGTGATTACATGCA
35861 CTTGTGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (17 bp):
TACGTGATTACATGCAA
Found at i:36118 original size:32 final size:31
Alignment explanation
Indices: 36077--36180 Score: 140
Period size: 32 Copynumber: 3.3 Consensus size: 31
36067 AGTCGAGGGT
36077 TTACCTATGT-TCTTCGGGACATATGGACAATA
1 TTACCTATGTCT-TTCGGGACATATGGACAA-A
*
36109 TTACCTATGTCTTTCGAGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACA-AA
* *
36141 TTACCTATGTCTTTCGGGACATATAGAC-AG
1 TTACCTATGTCTTTCGGGACATATGGACAAA
36171 TTACCTATGT
1 TTACCTATGT
36181 TCTTAGGAGC
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
30 11 0.17
32 53 0.80
33 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACAAA
Found at i:36996 original size:20 final size:19
Alignment explanation
Indices: 36973--37012 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
36963 CACTACTTGC
36973 ACAGTATCAATACTATTCAT
1 ACAGTAT-AATACTATTCAT
* *
36993 ACAGTATAGTATTATTCAT
1 ACAGTATAATACTATTCAT
37012 A
1 A
37013 AAAAACGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (19 bp):
ACAGTATAATACTATTCAT
Found at i:47769 original size:65 final size:63
Alignment explanation
Indices: 47700--47859 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 63
47690 AATTAAATTG
*
47700 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATACACTGAGGA-T-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATACACT-AGGACTATTT-T-
47763 AA
62 AA
* * * * ** *
47765 AACATCGAATGCATTTGATGCATCGATACACCAGCCATGCATCGATGCACTCTGACTATTTTCA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATACACTAGGACTATTTTAA
*
47829 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
47860 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 31 0.38
65 45 0.55
66 5 0.06
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATACACTAGGACTATTTTAA
Found at i:57299 original size:24 final size:21
Alignment explanation
Indices: 57272--57329 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
57262 ATGTGAAATA
57272 ATGAAAGTGATCACATGTGTGTAT
1 ATGAAAGTGAT-ACATGT-T-TAT
57296 ATG-AAGTGAAATACATGTTTAT
1 ATGAAAGTG--ATACATGTTTAT
57318 ATGAAAAGTGAT
1 ATG-AAAGTGAT
57330 GAGAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (21 bp):
ATGAAAGTGATACATGTTTAT
Found at i:59595 original size:15 final size:15
Alignment explanation
Indices: 59575--59604 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
59565 AGGACTAGCG
59575 AGGATAGAGATGACC
1 AGGATAGAGATGACC
59590 AGGATAGAGATGACC
1 AGGATAGAGATGACC
59605 TAGAGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (15 bp):
AGGATAGAGATGACC
Found at i:64279 original size:24 final size:21
Alignment explanation
Indices: 64252--64309 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
64242 ATGTGAAATA
64252 ATGAAAGTGATCACATGTGTCTAT
1 ATGAAAGTGAT-ACATGT-T-TAT
64276 ATG-AAGTGAAATACATGTTTAT
1 ATGAAAGTG--ATACATGTTTAT
64298 ATGAAAAGTGAT
1 ATG-AAAGTGAT
64310 GAGAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (21 bp):
ATGAAAGTGATACATGTTTAT
Found at i:64552 original size:18 final size:20
Alignment explanation
Indices: 64507--64584 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
64497 GTTCTTAAGG
64507 AGTGGTCCTTCGGGACATATA
1 AGTGGTCCTTCGGGACA-ATA
64528 CAGTGGTCCTTCGGGAC-AT-
1 -AGTGGTCCTTCGGGACAATA
** * *
64547 AGTGGTTTTTCGGAACAATC
1 AGTGGTCCTTCGGGACAATA
* *
64567 AGTGGTCTTTCGAGACAA
1 AGTGGTCCTTCGGGACAA
64585 ATATTCAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 13 0.27
19 2 0.04
20 17 0.35
22 16 0.33
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAATA
Found at i:65312 original size:19 final size:19
Alignment explanation
Indices: 65270--65313 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
65260 AAAAACCAGA
*
65270 GAAAAATGAAAAAAAAAGC
1 GAAAAATGAAAAAAAAAAC
* *
65289 AAAAAATGAAAAAAAAAAT
1 GAAAAATGAAAAAAAAAAC
65308 GAAAAA
1 GAAAAA
65314 GATTCAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (19 bp):
GAAAAATGAAAAAAAAAAC
Found at i:66073 original size:23 final size:23
Alignment explanation
Indices: 66043--66098 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
66033 TGGCATCTAA
66043 TCAGCAGCTTCCAAAAGGCCCAG
1 TCAGCAGCTTCCAAAAGGCCCAG
*
66066 TCAGCAGCTTCCAAAAGGTCCAG
1 TCAGCAGCTTCCAAAAGGCCCAG
66089 TCAGC-GCTTC
1 TCAGCAGCTTC
66099 TAGAATGACG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.27, C:0.34, G:0.21, T:0.18
Consensus pattern (23 bp):
TCAGCAGCTTCCAAAAGGCCCAG
Found at i:69602 original size:22 final size:22
Alignment explanation
Indices: 69577--69625 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
69567 ATATATTTAT
69577 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
69599 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
*
69621 AAATA
1 TAATA
69626 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:69707 original size:19 final size:20
Alignment explanation
Indices: 69663--69762 Score: 63
Period size: 19 Copynumber: 5.2 Consensus size: 20
69653 ATTATATTTT
69663 TATT-TTAATAAT-ATTATTAA
1 TATTATTAATAATGA-TA-TAA
69683 -ATTATTAATAATGA-ATAA
1 TATTATTAATAATGATATAA
* *
69701 TATTATTTATAA--ATTTAA
1 TATTATTAATAATGATATAA
*
69719 TATTAATATAATAAT-CTAATAA
1 TATT-AT-TAATAATGAT-ATAA
*
69741 TATT-TTAATAAAGATATAA
1 TATTATTAATAATGATATAA
69760 TAT
1 TAT
69763 AACACTATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
17 1 0.02
18 10 0.16
19 29 0.45
20 15 0.23
21 2 0.03
22 7 0.11
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTATTAATAATGATATAA
Found at i:70302 original size:30 final size:30
Alignment explanation
Indices: 70263--70319 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
70253 ATTTAACGCT
* *
70263 TGAACTTTAGGTATAATATTATTTTGATCC
1 TGAACTTTAGATATAATATCATTTTGATCC
* *
70293 TGAATTTTAGATGTAATATCATTTTGA
1 TGAACTTTAGATATAATATCATTTTGA
70320 CCAGTAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TGAACTTTAGATATAATATCATTTTGATCC
Found at i:71478 original size:216 final size:213
Alignment explanation
Indices: 70918--71640 Score: 1108
Period size: 216 Copynumber: 3.4 Consensus size: 213
70908 AAATTACAAA
* * * *
70918 TTTAAGAATTAAATTGAACAAATATGAAATTACAAATTAAAATATAAATAAATTAAACAACACAT
1 TTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAAC-CAC
*
70983 ATTGATGAGGGATCAAAACGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACT
65 ATTGA-GAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACT
*
71048 AAATTATACCCATTTAAAAAGTTATGGGCCAATT-AAAAATGTAAATAAGTAATAAGTATGGGTC
129 AAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTAT-GGTC
71112 AATTTCAGATGCAAATATAAT
193 AATTTCAGATGCAAATATAAT
** * * * *
71133 TTGGAGGATTAAATTGAATAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAA-CACA
1 TTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACCACA
71197 ---A-AGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAA
66 TTGAGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAA
*
71258 ATTATACCCATTTAAAAAGTTACGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGAGTCAA
131 ATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATG-GTCAA
71323 TTTCAGATGCAAATATAAT
195 TTTCAGATGCAAATATAAT
71342 TTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACTCAC
1 TTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAAC-CAC
* * *
71407 ATTGACGAGGGATCAAATCGAAATAATTTTAAATTGCGAGGTTTAAATTAATACAAAAAAATACT
65 ATTGA-GAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACT
* * *
71472 AAATTATACTCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGAATTGGTC
129 AAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTA-TGGTC
71537 AATTTCAGATGCAAATATAAT
193 AATTTCAGATGCAAATATAAT
* * *
71558 TTTAAGGACTAAATTGAACAAATATAAAATTACAAATTTAAATTTAAATAAATTAAACTA-CACA
1 TTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACCACA
71622 ---A-AGGGATCAAATCGAAATA
66 TTGAGAGGGATCAAATCGAAATA
71641 TTGCAAAATG
Statistics
Matches: 471, Mismatches: 27, Indels: 26
0.90 0.05 0.05
Matches are distributed among these distances:
208 91 0.19
209 120 0.25
210 1 0.00
211 5 0.01
213 3 0.01
214 5 0.01
215 53 0.11
216 191 0.41
217 2 0.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (213 bp):
TTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACCACA
TTGAGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAA
ATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGTCAAT
TTCAGATGCAAATATAAT
Found at i:71729 original size:2 final size:2
Alignment explanation
Indices: 71718--71926 Score: 90
Period size: 2 Copynumber: 108.0 Consensus size: 2
71708 TTGAAACAAG
* *
71718 TA TA -A TA TA TA TA TA TA TA TA TA TA -A T- TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * *
71759 TA TA TA TA AA GTA TA TG TA T- TA TA TA TA TA AA CTA TA TA TT TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
71802 -A TA TT TA TA T- TA T- TA TA TA CTA TA TA TA AA CTA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * *
71842 TA TA TA T- TA TG TA TA -A T- TA TA AA TA -A TA TA TA T- TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
71879 TA AA T- TA TA TA GTT TA T- TA -A TA TA AA CTA TA TA GTT TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
71919 TA TA TA TA
1 TA TA TA TA
71927 GTTTAAGGTT
Statistics
Matches: 153, Mismatches: 29, Indels: 50
0.66 0.12 0.22
Matches are distributed among these distances:
1 16 0.10
2 127 0.83
3 10 0.07
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:71730 original size:9 final size:9
Alignment explanation
Indices: 71718--71874 Score: 64
Period size: 9 Copynumber: 17.3 Consensus size: 9
71708 TTGAAACAAG
71718 TATAATATA
1 TATAATATA
71727 TAT-ATATA
1 TATAATATA
71735 TAT-ATATA
1 TATAATATA
71743 -ATTAA-ACTA
1 TA-TAATA-TA
*
71752 TATAGTTTATA
1 TATA--ATATA
71763 TATAA-AGTA
1 TATAATA-TA
*
71772 TAT-GTAT-
1 TATAATATA
71779 TAT-ATATA
1 TATAATATA
71787 TA-AACTATA
1 TATAA-TATA
*
71796 TATTTAATATT
1 TA--TAATATA
*
71807 TATATTATTA
1 TATAATA-TA
*
71817 TATACTATA
1 TATAATATA
71826 TATAA-ACTA
1 TATAATA-TA
*
71835 TATATTATA
1 TATAATATA
* *
71844 TATATTATG
1 TATAATATA
71853 TATAATTATA
1 TATAA-TATA
*
71863 AATAATATA
1 TATAATATA
71872 TAT
1 TAT
71875 TGTATAAATT
Statistics
Matches: 114, Mismatches: 15, Indels: 38
0.68 0.09 0.23
Matches are distributed among these distances:
7 7 0.06
8 21 0.18
9 56 0.49
10 16 0.14
11 11 0.10
12 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (9 bp):
TATAATATA
Found at i:71909 original size:22 final size:24
Alignment explanation
Indices: 71817--71926 Score: 84
Period size: 25 Copynumber: 4.5 Consensus size: 24
71807 TATATTATTA
71817 TATACTATATATAAACTATATA-TT
1 TATA-TATATATAAACTATATAGTT
* * * *
71841 ATATATATTATGTATAATTATA-AATAA
1 -TATATA-TATATA-AACTATATAGT-T
* *
71868 TATATATTGTATAAATTATATAGTT
1 TATATA-TATATAAACTATATAGTT
71893 TAT-TA-ATATAAACTATATAGTT
1 TATATATATATAAACTATATAGTT
71915 TATATATATATA
1 TATATATATATA
71927 GTTTAAGGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
22 18 0.26
23 2 0.03
24 9 0.13
25 20 0.29
26 20 0.29
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (24 bp):
TATATATATATAAACTATATAGTT
Found at i:72055 original size:11 final size:11
Alignment explanation
Indices: 72006--72059 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
71996 TAGTAGTATT
72006 TAAACTATATA
1 TAAACTATATA
72017 TAAAC-A-ATA
1 TAAACTATATA
72026 TAAACTA-ACT-
1 TAAACTATA-TA
* *
72036 TACACTATATG
1 TAAACTATATA
72047 TAAACTATATA
1 TAAACTATATA
72058 TA
1 TA
72060 CTTTATAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 8 0.22
10 10 0.28
11 18 0.50
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (11 bp):
TAAACTATATA
Found at i:72096 original size:13 final size:13
Alignment explanation
Indices: 72073--72109 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
72063 TATAGTTTGC
*
72073 ATATGAACTATAT
1 ATATAAACTATAT
*
72086 GTATAAACTATAT
1 ATATAAACTATAT
72099 ATATAAACTAT
1 ATATAAACTAT
72110 GTAAACTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:72107 original size:55 final size:55
Alignment explanation
Indices: 72041--72364 Score: 172
Period size: 55 Copynumber: 5.9 Consensus size: 55
72031 TAACTTACAC
* * * * *
72041 TATATGTAAACTATATATACTTTATAGTTTGCATATGAACTATATGTATAAACTA
1 TATATATAAACTATATAAACTATATAGTTTACATATGAACTATATATATAAACTA
* * * * *
72096 TATATATAAACTATGTAAACTATATGGTTTACATATGACCTATATATAT--AGTT
1 TATATATAAACTATATAAACTATATAGTTTACATATGAACTATATATATAAACTA
* * * *
72149 TAT-TAGTGAACTATATAAACTATTTA-TATA-GTAT-ATACTATATATATAAA-T-
1 TATATA-TAAACTATATAAACTATATAGTTTACATATGA-ACTATATATATAAACTA
* * * * * * *
72200 TATAGTTTATA-TTTATATACTATAT-GTATT-TATAT--ACTATAT-TTTATACTA
1 TATA-TATAAACTATATAAACTATATAGT-TTACATATGAACTATATATATAAACTA
* ** * * * * *
72251 TTTATATAAACTATAGTTTATATTTATATACTATATATATGAACTATAGTTTACATATAAATTG
1 TATATATAAACTATA---TA-AACTATATAGTTTACATATGAACTATA---T--ATATAAACTA
72315 TATATATAAACTATATAAACTATATAGTTTACATATGAACTATATATATA
1 TATATATAAACTATATAAACTATATAGTTTACATATGAACTATATATATA
72365 CTATAGTTGA
Statistics
Matches: 197, Mismatches: 46, Indels: 52
0.67 0.16 0.18
Matches are distributed among these distances:
49 4 0.02
50 13 0.07
51 34 0.17
52 12 0.06
53 23 0.12
54 2 0.01
55 52 0.26
56 6 0.03
57 1 0.01
58 6 0.03
60 22 0.11
61 3 0.02
64 19 0.10
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.45
Consensus pattern (55 bp):
TATATATAAACTATATAAACTATATAGTTTACATATGAACTATATATATAAACTA
Found at i:72178 original size:2 final size:2
Alignment explanation
Indices: 72173--72290 Score: 51
Period size: 2 Copynumber: 55.5 Consensus size: 2
72163 ATAAACTATT
* * *
72173 TA TA TA GTA TA TA CTA TA TA TA TA AA T- TA TA GTT TA TA TT TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
72215 TA TA CTA TA TG TA TT TA TA TA CTA TA T- TT TA TA CTA TT TA TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
* * *
72257 TA AA CTA TA GTT TA TA TT TA TA TA CTA TA TA TA T
1 TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA T
72291 GAACTATAGT
Statistics
Matches: 86, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
1 2 0.02
2 69 0.80
3 15 0.17
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72185 original size:7 final size:6
Alignment explanation
Indices: 72173--72290 Score: 51
Period size: 7 Copynumber: 18.5 Consensus size: 6
72163 ATAAACTATT
* * *
72173 TATATA GTATATA CTATATA TATAAA T-TATA GTTTATA TTTATA TACTATA
1 TATATA -TATATA -TATATA TATATA TATATA -TATATA TATATA TA-TATA
* * * * * * *
72224 TGTATT TATATA CTATAT- TTTATA CTATTTA TATAAA CTATAGTT TATATT
1 TATATA TATATA -TATATA TATATA -TATATA TATATA -TATA-TA TATATA
72275 TATATA CTATATA TAT
1 TATATA -TATATA TAT
72291 GAACTATAGT
Statistics
Matches: 86, Mismatches: 16, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
5 7 0.08
6 35 0.41
7 44 0.51
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (6 bp):
TATATA
Found at i:72185 original size:9 final size:8
Alignment explanation
Indices: 72173--72290 Score: 51
Period size: 9 Copynumber: 13.9 Consensus size: 8
72163 ATAAACTATT
72173 TATATAGTA
1 TATATA-TA
72182 TATACTATA
1 TATA-TATA
*
72191 TATATAAA
1 TATATATA
*
72199 T-TATAGTT
1 TATATA-TA
*
72207 TATATTTA
1 TATATATA
72215 TATACTATA
1 TATA-TATA
* *
72224 TGTATTTA
1 TATATATA
72232 TATACTATA
1 TATA-TATA
*
72241 T-TTTATA
1 TATATATA
*
72248 CTATTTATA
1 -TATATATA
*
72257 TAAACTATA
1 TATA-TATA
* *
72266 GTTTATATT
1 -TATATATA
72275 TATATACTA
1 TATATA-TA
72284 TATATAT
1 TATATAT
72291 GAACTATAGT
Statistics
Matches: 81, Mismatches: 18, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
7 8 0.10
8 26 0.32
9 43 0.53
10 4 0.05
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (8 bp):
TATATATA
Found at i:72188 original size:18 final size:18
Alignment explanation
Indices: 72162--72196 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
72152 TAGTGAACTA
*
72162 TATAAACTATTTATATAG
1 TATAAACTATATATATAG
*
72180 TATATACTATATATATA
1 TATAAACTATATATATA
72197 AATTATAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
TATAAACTATATATATAG
Found at i:72220 original size:33 final size:33
Alignment explanation
Indices: 72160--72329 Score: 160
Period size: 33 Copynumber: 5.4 Consensus size: 33
72150 ATTAGTGAAC
*
72160 TATATAAAC--TA-TTTATATAGTATATACTATA
1 TATATAAACTATAGTTTATAT-TTATATACTATA
*
72191 TATATAAATTATAGTTTATATTTATATACTATA
1 TATATAAACTATAGTTTATATTTATATACTATA
* ** * *
72224 TGTATTTA-TATA--CTATATTT-TATACTATT
1 TATATAAACTATAGTTTATATTTATATACTATA
72253 TATATAAACTATAGTTTATATTTATATACTATA
1 TATATAAACTATAGTTTATATTTATATACTATA
* * * * *
72286 TATATGAACTATAGTTTACA--TATAAATTGTA
1 TATATAAACTATAGTTTATATTTATATACTATA
72317 TATATAAACTATA
1 TATATAAACTATA
72330 TAAACTATAT
Statistics
Matches: 114, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
29 13 0.11
30 11 0.10
31 28 0.25
32 11 0.10
33 44 0.39
34 7 0.06
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (33 bp):
TATATAAACTATAGTTTATATTTATATACTATA
Found at i:72231 original size:17 final size:17
Alignment explanation
Indices: 72209--72241 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
72199 TTATAGTTTA
72209 TATTTATATACTATATG
1 TATTTATATACTATATG
72226 TATTTATATACTATAT
1 TATTTATATACTATAT
72242 TTTATACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTTATATACTATATG
Found at i:72247 original size:12 final size:13
Alignment explanation
Indices: 72207--72273 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 13
72197 AATTATAGTT
72207 TATATTTATATAC
1 TATATTTATATAC
72220 TATATGTATTTATATAC
1 --TA--TATTTATATAC
72237 TATATTT-TATAC
1 TATATTTATATAC
*
72249 TAT-TTATATAAAC
1 TATATT-TATATAC
72262 TATAGTTTATAT
1 TATA-TTTATAT
72274 TTATATACTA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 2 0.05
12 9 0.20
13 12 0.27
14 4 0.09
15 6 0.14
17 11 0.25
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:72258 original size:25 final size:28
Alignment explanation
Indices: 72207--72272 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 28
72197 AATTATAGTT
*
72207 TATATTTATATACTATATGTATTTATATAC
1 TATATTT-TATACTATATGTA-TTATAAAC
72237 TATATTTTATACTAT-T-TA-TATAAAC
1 TATATTTTATACTATATGTATTATAAAC
*
72262 TATAGTTTATA
1 TATATTTTATA
72273 TTTATATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 16 0.47
27 2 0.06
28 1 0.03
29 8 0.24
30 7 0.21
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (28 bp):
TATATTTTATACTATATGTATTATAAAC
Found at i:72277 original size:22 final size:21
Alignment explanation
Indices: 72226--72285 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
72216 ATACTATATG
*
72226 TATTTATAT-ACTATATTTTATA
1 TATTTATATAACTATA-GTT-TA
72248 CTATTTATATAAACTATAGTTTA
1 -TATTTATAT-AACTATAGTTTA
72271 TATTTATAT-ACTATA
1 TATTTATATAACTATA
72286 TATATGAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 6 0.18
22 9 0.26
23 11 0.32
24 2 0.06
25 6 0.18
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTATATAACTATAGTTTA
Found at i:72308 original size:18 final size:18
Alignment explanation
Indices: 72287--72414 Score: 50
Period size: 18 Copynumber: 6.8 Consensus size: 18
72277 TATACTATAT
*
72287 ATATGAACTATAGTTTAC
1 ATATAAACTATAGTTTAC
* *
72305 ATATAAATTGTATA-TATAAAC
1 ATATAAA--CTATAGT-T-TAC
72326 TATATAAACTATATAGTTTAC
1 -ATATAAAC--TATAGTTTAC
*
72347 ATATGAACTATA-TATATAC
1 ATATAAACTATAGT-T-TAC
** *
72366 -TAT-AGTTGATA-TTTAT
1 ATATAAACT-ATAGTTTAC
* *
72382 ATATGAACTATAGTTTGC
1 ATATAAACTATAGTTTAC
72400 ATATAAACTATAGTT
1 ATATAAACTATAGTT
72415 GATATTTACA
Statistics
Matches: 82, Mismatches: 14, Indels: 28
0.66 0.11 0.23
Matches are distributed among these distances:
16 2 0.02
17 10 0.12
18 37 0.45
19 4 0.05
20 12 0.15
21 4 0.05
22 12 0.15
23 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (18 bp):
ATATAAACTATAGTTTAC
Found at i:72319 original size:31 final size:29
Alignment explanation
Indices: 72284--72406 Score: 86
Period size: 29 Copynumber: 3.9 Consensus size: 29
72274 TTATATACTA
72284 TATATATGAACTATAGTTTACATATAAATT
1 TATATATGAACTATA-TTTACATATAAATT
* ** *
72314 GTATATATAAACTATATAAAC-TATATAGTT
1 -TATATATGAACTATATTTACATATA-AATT
* *
72344 TACATATGAACTATATATATACTATAGTTGATATT
1 TATATATGAACTATAT-T-TAC-ATA--T-AAATT
*
72379 TATATATGAACTATAGTTTGCATATAAA
1 TATATATGAACTATA-TTTACATATAAA
72407 CTATAGTTGA
Statistics
Matches: 70, Mismatches: 13, Indels: 19
0.69 0.13 0.19
Matches are distributed among these distances:
29 18 0.26
30 8 0.11
31 17 0.24
33 5 0.07
34 2 0.03
35 18 0.26
36 2 0.03
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.41
Consensus pattern (29 bp):
TATATATGAACTATATTTACATATAAATT
Found at i:72331 original size:42 final size:41
Alignment explanation
Indices: 72286--72364 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
72276 ATATACTATA
* * *
72286 TATATGAAC-TATAGTTTACATATAAATTGTATATATAAAC
1 TATATAAACATATAGTTTACATATAAACTATATATATAAAC
*
72326 TATATAAACTATATAGTTTACATATGAACTATATATATA
1 TATATAAAC-ATATAGTTTACATATAAACTATATATATA
72365 CTATAGTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 8 0.24
42 25 0.76
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.41
Consensus pattern (41 bp):
TATATAAACATATAGTTTACATATAAACTATATATATAAAC
Found at i:72426 original size:24 final size:24
Alignment explanation
Indices: 72358--72435 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
72348 TATGAACTAT
* *
72358 ATATATACTATAGTTGATATTTAT
1 ATATAAACTATAGTTGATATTTAC
* *
72382 ATATGAACTATA---G---TTTGC
1 ATATAAACTATAGTTGATATTTAC
72400 ATATAAACTATAGTTGATATTTAC
1 ATATAAACTATAGTTGATATTTAC
*
72424 ATATGAACTATA
1 ATATAAACTATA
72436 TATATAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
18 14 0.34
21 2 0.05
24 25 0.61
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (24 bp):
ATATAAACTATAGTTGATATTTAC
Found at i:72469 original size:24 final size:25
Alignment explanation
Indices: 72418--72476 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
72408 TATAGTTGAT
* *
72418 ATTTACATA-TGAACTATATATATA
1 ATTTATATAGTGAACTATATACATA
72442 ATTTAT-TAGTGAACTATATACACT-
1 ATTTATATAGTGAACTATATACA-TA
72466 ATTTATATAGT
1 ATTTATATAGT
72477 ATATACTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 2 0.07
24 23 0.77
25 5 0.17
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (25 bp):
ATTTATATAGTGAACTATATACATA
Found at i:72481 original size:7 final size:7
Alignment explanation
Indices: 72469--72742 Score: 72
Period size: 7 Copynumber: 39.9 Consensus size: 7
72459 ATACACTATT
*
72469 TATATAG
1 TATATAC
72476 TATATAC
1 TATATAC
72483 TATATA-
1 TATATAC
*
72489 TATAAAC
1 TATATAC
*
72496 TATAGT-T
1 TATA-TAC
*
72503 TATAT-T
1 TATATAC
72509 TATATAC
1 TATATAC
*
72516 TACATATAG
1 T--ATATAC
72525 TATATAC
1 TATATAC
72532 TATATA-
1 TATATAC
72538 TATATA-
1 TATATAC
72544 TA-A-AC
1 TATATAC
*
72549 TATAGT-T
1 TATA-TAC
*
72556 TATAT-T
1 TATATAC
72562 TATATAC
1 TATATAC
*
72569 TACATATAG
1 T--ATATAC
72578 TATATAC
1 TATATAC
72585 TATATA-
1 TATATAC
72591 TA-A-AC
1 TATATAC
72596 TATATAC
1 TATATAC
*
72603 TATATAG
1 TATATAC
72610 TATAATTTAC
1 TAT-A--TAC
72620 -ATATGGAC
1 TATAT--AC
72628 TATATA-
1 TATATAC
* *
72634 TAAAAACC
1 TATATA-C
*
72642 ATATAAAC
1 -TATATAC
72650 TATATAC
1 TATATAC
72657 TATAGT--
1 TATA-TAC
*
72663 TGATAT-T
1 T-ATATAC
72670 TATATAC
1 TATATAC
72677 TATATA-
1 TATATAC
*
72683 -ATATAA
1 TATATAC
*
72689 TTTATAC
1 TATATAC
72696 TATAGTA-
1 TATA-TAC
72703 TATATAAAC
1 TATAT--AC
72712 TATATA-
1 TATATAC
72718 -ATATA-
1 TATATAC
*
72723 TATAAAC
1 TATATAC
*
72730 TATATAT
1 TATATAC
72737 TATATA
1 TATATA
72743 GTTCATTAGT
Statistics
Matches: 207, Mismatches: 24, Indels: 72
0.68 0.08 0.24
Matches are distributed among these distances:
4 2 0.01
5 16 0.08
6 47 0.23
7 103 0.50
8 9 0.04
9 28 0.14
10 2 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (7 bp):
TATATAC
Found at i:72498 original size:31 final size:30
Alignment explanation
Indices: 72456--72552 Score: 86
Period size: 33 Copynumber: 3.0 Consensus size: 30
72446 ATTAGTGAAC
*
72456 TATATACACTATTTATATAGTATATACTATA
1 TATATAAACTATTTATATA-TATATACTATA
*
72487 TATATAAACTATAGTTTATATTTATATACTACATA
1 TATATAAAC--TA-TTTATATATATATACT--ATA
* * *
72522 TAGTATATACTATATATATATATAAACTATA
1 TA-TATAAACTATTTATATATATATACTATA
72553 GTTTATATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
31 11 0.20
33 23 0.43
34 9 0.17
35 5 0.09
36 6 0.11
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (30 bp):
TATATAAACTATTTATATATATATACTATA
Found at i:72513 original size:53 final size:52
Alignment explanation
Indices: 72456--72599 Score: 178
Period size: 53 Copynumber: 2.8 Consensus size: 52
72446 ATTAGTGAAC
72456 TATATACACTATTTATATAGTATATACTATATATATAAACTATAGTTTATATT
1 TATATACACTA-TTATATAGTATATACTATATATATAAACTATAGTTTATATT
72509 TATATACTAC-ATATAGTATA-TACTATA-TATATATATAAACTATAGTTTATATT
1 TATATAC-ACTAT-TA-TATAGTA-TATACTATATATATAAACTATAGTTTATATT
*
72562 TATAT--ACTA-CATATAGTATATAC--TATATATAAACTATA
1 TATATACACTATTATATAGTATATACTATATATATAAACTATA
72600 TACTATATAG
Statistics
Matches: 83, Mismatches: 1, Indels: 20
0.80 0.01 0.19
Matches are distributed among these distances:
47 15 0.18
48 8 0.10
49 3 0.04
50 2 0.02
51 1 0.01
52 1 0.01
53 43 0.52
54 10 0.12
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (52 bp):
TATATACACTATTATATAGTATATACTATATATATAAACTATAGTTTATATT
Found at i:72535 original size:29 final size:29
Alignment explanation
Indices: 72503--72589 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 29
72493 AACTATAGTT
72503 TATATTTATATACTACATATAGTATATAC
1 TATATTTATATACTACATATAGTATATAC
* *
72532 TATATATATATA-TAAACTATAG--T-T--
1 TATATTTATATACTACA-TATAGTATATAC
72556 TATATTTATATACTACATATAGTATATAC
1 TATATTTATATACTACATATAGTATATAC
72585 TATAT
1 TATAT
72590 ATAAACTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
24 16 0.34
25 3 0.06
26 2 0.04
27 2 0.04
28 3 0.06
29 21 0.45
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (29 bp):
TATATTTATATACTACATATAGTATATAC
Found at i:72715 original size:9 final size:9
Alignment explanation
Indices: 72703--72735 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
72693 TACTATAGTA
72703 TATATAAAC
1 TATATAAAC
72712 TATATAATA-
1 TATATAA-AC
72721 TATATAAAC
1 TATATAAAC
72730 TATATA
1 TATATA
72736 TTATATAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATAAAC
Found at i:72759 original size:2 final size:2
Alignment explanation
Indices: 72469--72742 Score: 83
Period size: 2 Copynumber: 127.0 Consensus size: 2
72459 ATACACTATT
* * *
72469 TA TA TA GTA TA TA CTA TA TA TA TA AA CTA TA GTT TA TA TT TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA
* * *
72513 TA CTA CA TA TA GTA TA TA CTA TA TA TA TA TA TA AA CTA TA GTT TA
1 TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA -TA TA
* * *
72558 TA TT TA TA TA CTA CA TA TA GTA TA TA CTA TA TA TA AA CTA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA
* * * * * * *
72602 CTA TA TA GTA TA -A TT TA CA TA TG GA CTA TA TA TA AA AA CCA TA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* *
72645 TA AA CTA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA -A TA TA
1 TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA
* * *
72688 -A TT TA TA CTA TA GTA TA TA TA AA CTA TA TA -A TA TA TA TA AA
1 TA TA TA TA -TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
72729 CTA TA TA T- TA TA TA
1 -TA TA TA TA TA TA TA
72743 GTTCATTAGT
Statistics
Matches: 201, Mismatches: 39, Indels: 64
0.66 0.13 0.21
Matches are distributed among these distances:
1 6 0.03
2 155 0.77
3 40 0.20
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:72762 original size:51 final size:51
Alignment explanation
Indices: 72698--73090 Score: 404
Period size: 51 Copynumber: 7.4 Consensus size: 51
72688 ATTTATACTA
72698 TAGTATATATAAACTATATAATATATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATAATATATATAAACTATATATTATATAGTTCAT
* ** * *
72749 TAGTCTATATAAACTATATGGTATATATAAACTATACATTATATAGTTTAT
1 TAGTATATATAAACTATATAATATATATAAACTATATATTATATAGTTCAT
* *
72800 TAGTATATATAAACTATATAATATATATAAACTATATGGTATATATAAACTATACAT
1 TAGTATATATAAACTATATAATATATATAAACTATA---TAT-TATATAGT-T-CAT
* *
72857 TA-TATATAGT--TC-AT-TAGTATATATAAACTATATATTATATAGTTCAT
1 TAGTATATA-TAAACTATATAATATATATAAACTATATATTATATAGTTCAT
* *
72904 TAGTATATATAACCTATATAGTATATGGTATATACAAACTATATATTATATAGTACAT
1 TAGTATATATAAACTATATA--ATA---TATAT--AAACTATATATTATATAGTTCAT
*
72962 TAGTATATATAACCTATATAGTATATGATATATACAAACTATATATTATATAGTTCAT
1 TAGTATATATAAAC--TATA-TA-AT-ATATAT--AAACTATATATTATATAGTTCAT
* *
73020 TAGTATATATAAACTATATAGTATATATAAACTATATATTGA-AAAGTTCAT
1 TAGTATATATAAACTATATAATATATATAAACTATATATT-ATATAGTTCAT
73071 TAGTATATAT-AACTTATATA
1 TAGTATATATAAAC-TATATA
73091 TTAATTTATT
Statistics
Matches: 294, Mismatches: 23, Indels: 50
0.80 0.06 0.14
Matches are distributed among these distances:
47 6 0.02
48 7 0.02
49 7 0.02
50 8 0.03
51 117 0.40
52 1 0.00
53 25 0.09
54 5 0.02
55 9 0.03
56 16 0.05
57 5 0.02
58 78 0.27
60 7 0.02
61 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (51 bp):
TAGTATATATAAACTATATAATATATATAAACTATATATTATATAGTTCAT
Found at i:72792 original size:69 final size:68
Alignment explanation
Indices: 72670--72897 Score: 221
Period size: 69 Copynumber: 3.3 Consensus size: 68
72660 AGTTGATATT
* * * * *
72670 TATATACTATATAATATAATTTATACTATA--GTATATATAAACTATATAATATATATAAACTA-
1 TATAAACTATATAATAT-ATATAAACTATATGGTATATATAAACTATACATTATATATAAACTAG
72732 TATA
65 TATA
* * * * ** *
72736 TTATATAGT-TCATTAGTCTATATAAACTATATGGTATATATAAACTATACATTATATAGTTTAT
1 -TATAAACTAT-A-TAATATATATAAACTATATGGTATATATAAACTATACATTATATA-TAAAC
72800 TAGTATA
62 TAGTATA
* *
72807 TATAAACTATATAATATATATAAACTATATGGTATATATAAACTATACATTATATATAGTTCATT
1 TATAAACTATATAATATATATAAACTATATGGTATATATAAACTATACATTATATATA---AACT
72872 AGTATA
63 AGTATA
*
72878 TATAAACTATATATTATATA
1 TATAAACTATATAATATATA
72898 GTTCATTAGT
Statistics
Matches: 134, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
66 1 0.01
67 18 0.13
68 5 0.04
69 66 0.49
70 11 0.08
71 33 0.25
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (68 bp):
TATAAACTATATAATATATATAAACTATATGGTATATATAAACTATACATTATATATAAACTAGT
ATA
Found at i:72806 original size:33 final size:33
Alignment explanation
Indices: 72769--73046 Score: 216
Period size: 33 Copynumber: 8.8 Consensus size: 33
72759 AAACTATATG
*
72769 GTATATATAAACTATACATTATATAGTTTATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
* ** *
72802 GTATATATAAACTATATAATATATATA-AACTATATG
1 GTATATATAAACTATA-CAT-TATATAGTTC-AT-TA
72838 GTATATATAAACTATACATTATATATAGTTCATTA
1 GTATATATAAACTATACA-T-TATATAGTTCATTA
*
72873 GTATATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
*
72906 GTATATAT-AAC----C--TATATAG-T-ATATG
1 GTATATATAAACTATACATTATATAGTTCAT-TA
* * *
72931 GTATATACAAACTATATATTATATAGTACATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
*
72964 GTATATAT-AAC----C--TATATAGTAT-ATGA
1 GTATATATAAACTATACATTATATAGT-TCATTA
* *
72990 -TATATACAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
* *
73022 GTATATATAAACTATATAGTATATA
1 GTATATATAAACTATACATTATATA
73047 TAAACTATAT
Statistics
Matches: 194, Mismatches: 25, Indels: 52
0.72 0.09 0.19
Matches are distributed among these distances:
24 2 0.01
25 15 0.08
26 24 0.12
31 1 0.01
32 24 0.12
33 68 0.35
34 5 0.03
35 27 0.14
36 27 0.14
37 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (33 bp):
GTATATATAAACTATACATTATATAGTTCATTA
Found at i:72944 original size:58 final size:58
Alignment explanation
Indices: 72873--73090 Score: 317
Period size: 58 Copynumber: 3.9 Consensus size: 58
72863 TAGTTCATTA
*
72873 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
*
72931 GTATATACAAACTATATATTATATAGTACATTAGTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* *
72989 ATATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAG--TA--
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* *
73043 -TATAT--AAACTATATATTGA-AAAGTTCATTAGTATATATAACTTATATA
1 GTATATACAAACTATATATT-ATATAGTTCATTAGTATATATAACCTATATA
73091 TTAATTTATT
Statistics
Matches: 151, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
51 38 0.25
52 1 0.01
53 5 0.03
56 2 0.01
58 105 0.70
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (58 bp):
GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
Found at i:72945 original size:25 final size:25
Alignment explanation
Indices: 72906--73012 Score: 79
Period size: 25 Copynumber: 4.0 Consensus size: 25
72896 TAGTTCATTA
* *
72906 GTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATAGTATATG
*
72931 GTATATACAAACTATATATTATATAG
1 GTATATACAAACTATATAGTATAT-G
* *
72957 TACATTAGTATATATAACCTATATAGTATATG
1 -------GTATATACAAACTATATAGTATATG
* *
72989 ATATATACAAACTATATATTATAT
1 GTATATACAAACTATATAGTATAT
73013 AGTTCATTAG
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
25 41 0.64
26 1 0.02
32 1 0.02
33 21 0.33
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (25 bp):
GTATATACAAACTATATAGTATATG
Found at i:73767 original size:103 final size:103
Alignment explanation
Indices: 73498--74031 Score: 730
Period size: 103 Copynumber: 5.2 Consensus size: 103
73488 TTCATCTGTG
* * * *
73498 TTCATCACTTGTTCATCCCAATTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAGACC
1 TTCATC-CGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTTAAAAACACCAAAACC
* *
73563 CAAAACAATTTCATGTTTTTTTTCGATCAAACACCAAAAAA
65 C-AAACCATTTCATG-TTTTTTTCGATCAAACACCCAAAAA
*
73604 TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAA-CCTCATTTGATCTTCAAAAACACCAAAACCC
1 TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTTAAAAACACCAAAACCC
* * *
73668 GAACCATTTCATGTTTTTTTGGATGAAACACCCAAAAA
66 AAACCATTTCATGTTTTTTTCGATCAAACACCCAAAAA
* * * * *
73706 TTCATCCGTGTTCATCCCAATACTTCCCCAAAACCCTCCTTTGATATTTGAAAACACCAAAACCC
1 TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTTAAAAACACCAAAACCC
* * *
73771 AAACCATTTCGTGTTTTTTTCGATCAAAAACCAAAAAA
66 AAACCATTTCATGTTTTTTTCGATCAAACACCCAAAAA
* * *
73809 TTCATCTGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTAATCTTTAAAAACACCAAAACTC
1 TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTTAAAAACACCAAAACCC
* * * *
73874 GAACTAATTCGTGTTTTTTTCGATCAAACACCCAAAAA
66 AAACCATTTCATGTTTTTTTCGATCAAACACCCAAAAA
* * * *
73912 CTCATTCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTTGAAAACACCAAAACCT
1 TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTTAAAAACACCAAAACCC
* *
73977 AAACCATTTCATG-TTTTCTCGATCAAACACCCACAAA
66 AAACCATTTCATGTTTTTTTCGATCAAACACCCAAAAA
* *
74014 TTCATCCATGTTCTTCCC
1 TTCATCCGTGTTCATCCC
74032 CAAACCTTTA
Statistics
Matches: 377, Mismatches: 50, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
102 89 0.24
103 227 0.60
104 30 0.08
105 25 0.07
106 6 0.02
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.31
Consensus pattern (103 bp):
TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTTAAAAACACCAAAACCC
AAACCATTTCATGTTTTTTTCGATCAAACACCCAAAAA
Found at i:74187 original size:6 final size:6
Alignment explanation
Indices: 74176--74302 Score: 96
Period size: 6 Copynumber: 21.5 Consensus size: 6
74166 ACCCTATCCA
* * *
74176 AAACCC AAACCC AATCCA AAACCC AAACCC AAACCC AAA-CC GAACCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * * * * ** * * *
74223 AAATCC AAACCC GAACCT GAACCT AAACCC AAACTT GACCCC GAACCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * *
74271 -GACCC AAACCC AAACCT AAATCC AAACCC AAA
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAA
74303 TATAAATCGA
Statistics
Matches: 94, Mismatches: 25, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
5 8 0.09
6 86 0.91
ACGTcount: A:0.46, C:0.43, G:0.05, T:0.06
Consensus pattern (6 bp):
AAACCC
Found at i:74308 original size:18 final size:18
Alignment explanation
Indices: 74274--74310 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
74264 CGAACCCGAC
*
74274 CCAAACCCAAACCTAAAT
1 CCAAACCCAAACATAAAT
*
74292 CCAAACCCAAATATAAAT
1 CCAAACCCAAACATAAAT
74310 C
1 C
74311 GAATCTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (18 bp):
CCAAACCCAAACATAAAT
Found at i:76897 original size:10 final size:10
Alignment explanation
Indices: 76882--76919 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
76872 CAATATTTGG
76882 TGTTTGATTC
1 TGTTTGATTC
76892 TGTTTGATAT-
1 TGTTTGAT-TC
*
76902 TGTTTGCTTC
1 TGTTTGATTC
76912 TGTTTGAT
1 TGTTTGAT
76920 ATTGCTTGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 1 0.04
10 22 0.92
11 1 0.04
ACGTcount: A:0.11, C:0.08, G:0.21, T:0.61
Consensus pattern (10 bp):
TGTTTGATTC
Found at i:76907 original size:20 final size:20
Alignment explanation
Indices: 76882--76942 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
76872 CAATATTTGG
*
76882 TGTTTGATTCTGTTTGATAT
1 TGTTTGCTTCTGTTTGATAT
76902 TGTTTGCTTCTGTTTGATAT
1 TGTTTGCTTCTGTTTGATAT
* **
76922 TGCTTGCTTCTACTTGATAT
1 TGTTTGCTTCTGTTTGATAT
76942 T
1 T
76943 TGTAAGGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.57
Consensus pattern (20 bp):
TGTTTGCTTCTGTTTGATAT
Found at i:77061 original size:23 final size:23
Alignment explanation
Indices: 77035--77088 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
77025 CTTAATGTAG
* *
77035 GATGCTTGCTGAATTGATGCAAT
1 GATGCTTGCTAAATTGATACAAT
* *
77058 GATGCTTGCTAAATTGGTACATT
1 GATGCTTGCTAAATTGATACAAT
77081 GATGCTTG
1 GATGCTTG
77089 TCGGTTGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (23 bp):
GATGCTTGCTAAATTGATACAAT
Found at i:77771 original size:18 final size:18
Alignment explanation
Indices: 77681--77771 Score: 62
Period size: 18 Copynumber: 4.9 Consensus size: 18
77671 ATAAATTTTA
*
77681 TAATATAAGAAA-TATAAA
1 TAATATAA-AAACTATAAT
*
77699 TAATATAAAGAATTGA-AAT
1 TAATATAAA-AACT-ATAAT
*
77718 TAATATAAAAACCA-AATTT
1 TAATATAAAAACTATAA--T
* *
77737 ATAATATACAAATTATAAT
1 -TAATATAAAAACTATAAT
77756 TAATATAAAAACTATA
1 TAATATAAAAACTATA
77772 TTTCAAAAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.07
18 26 0.45
19 14 0.24
20 12 0.21
21 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.32
Consensus pattern (18 bp):
TAATATAAAAACTATAAT
Found at i:81582 original size:6 final size:6
Alignment explanation
Indices: 81566--81639 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
81556 TCTCGTCTCG
81566 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
81613 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
81640 AATGGTAATA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:81774 original size:20 final size:20
Alignment explanation
Indices: 81749--82297 Score: 565
Period size: 20 Copynumber: 26.8 Consensus size: 20
81739 TCATTTTCTT
81749 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
81769 AATCGCGTTGCGATTTTCTT--
1 AATCGCGTTGCGA--TTCTTGG
81789 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
**
81809 AAGATCGCGTTGCGATT-TTCTA
1 -A-ATCGCGTTGCGATTCTT-GG
81831 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
81851 AAGATCGCGTTGCGATTTTCTT--
1 -A-ATCGCGTTGCGA--TTCTTGG
81873 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
81893 AATCGCGTTGCGATTTTCTT--
1 AATCGCGTTGCGA--TTCTTGG
81913 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
**
81933 AAGATCGCGTTGCGATT-TTCTA
1 -A-ATCGCGTTGCGATTCTT-GG
81955 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
81975 AAGATCGCGTTGCGATT-TTCTG
1 -A-ATCGCGTTGCGATTCTT-GG
81997 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
82017 AAGATCGCGTTGCGATTCTTGG
1 -A-ATCGCGTTGCGATTCTTGG
*
82039 AATCGCGTTGCGATTTTCTGG
1 AATCGCGTTGCGATTCT-TGG
82060 -ATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
**
82079 AATCGCGTTGCGATT-TTCTA
1 AATCGCGTTGCGATTCTT-GG
82099 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
82119 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
*
82139 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
*
82159 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
*
82179 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
*
82199 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
82219 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
82239 AAGATCGCGTTGCGATT-TTATG
1 -A-ATCGCGTTGCGATTCTT-GG
*
82261 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
82281 AAGATCGCGTTGCGATT
1 -A-ATCGCGTTGCGATT
82298 TTCTTTTCAA
Statistics
Matches: 467, Mismatches: 22, Indels: 78
0.82 0.04 0.14
Matches are distributed among these distances:
18 15 0.03
19 7 0.01
20 292 0.63
21 36 0.08
22 112 0.24
24 5 0.01
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTTGG
Found at i:81829 original size:42 final size:40
Alignment explanation
Indices: 81741--82358 Score: 636
Period size: 42 Copynumber: 15.1 Consensus size: 40
81731 GAATTTACTC
81741 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
81781 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
81823 ATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
81865 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
81905 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
81947 ATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
81989 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
82031 A--TTCTTGGAATCGCGTTGCGATTTTCTGG-ATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCT-TGGAATCGCGTTGCG
**
82071 A--TTCTTGGAATCGCGTTGCGATT-TTCTAAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*
82111 A--TTCTTGGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* *
82151 ATTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* *
82191 ATTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*** * *
82231 ATTCTTGGAAGATCGCGTTGCGATT-TTATGAATCGCATTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*** **** *
82273 ATTCTTGGAAGATCGCGTTGCGATT-TTCTTTTCAACGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
* * *
82315 TTTTTCTAAATCGCGTTGCGGTT-TT-GATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
82354 ATTTT
1 ATTTT
82359 GTTGGTCATT
Statistics
Matches: 533, Mismatches: 30, Indels: 31
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.00
39 12 0.02
40 248 0.47
41 12 0.02
42 257 0.48
43 3 0.01
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:82331 original size:20 final size:20
Alignment explanation
Indices: 82308--82358 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
82298 TTCTTTTCAA
* *
82308 CGTTGCGTTTTTCTAAATCG
1 CGTTGCGATTTTCTGAATCG
*
82328 CGTTGCG-GTTT-TGATATCG
1 CGTTGCGATTTTCTGA-ATCG
82347 CGTTGCGATTTT
1 CGTTGCGATTTT
82359 GTTGGTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCTGAATCG
Found at i:83353 original size:2 final size:2
Alignment explanation
Indices: 83348--83418 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
83338 ACCCTTAACC
83348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83390 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
83419 TAAAATAATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:93674 original size:23 final size:23
Alignment explanation
Indices: 93637--93701 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
93627 CAGCTCGTAT
*
93637 AAATGCACCGGAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
* * **
93660 AATTGCATCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCATGTAG
*
93683 AAATGCACCGTAGTGCCAT
1 AAATGCACCGAAGTGCCAT
93702 ATAAGATGCC
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:95305 original size:24 final size:24
Alignment explanation
Indices: 95242--95298 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
95232 TCTATAGTGT
95242 ATCGATGCATCCCTTAACATGTGC
1 ATCGATGCATCCCTTAACATGTGC
*
95266 ATCGATACATCCCTTAACATGTGC
1 ATCGATGCATCCCTTAACATGTGC
95290 ATCGATGCA
1 ATCGATGCA
95299 CTCCTTATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (24 bp):
ATCGATGCATCCCTTAACATGTGC
Found at i:98462 original size:2 final size:2
Alignment explanation
Indices: 98455--98497 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
98445 CCAAACATAA
98455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
98497 A
1 A
98498 CACCAGGTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:98831 original size:23 final size:23
Alignment explanation
Indices: 98802--98865 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
98792 CAGCTCGTAT
* *
98802 AAATGCACCGGAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGAAG
* *
98825 AATTGCACCGAAGTGCCGCGAAG
1 AAATGCACCGAAGTGCCACGAAG
* *
98848 AAATGCATCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
98866 TATAAGATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.28, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGAAG
Found at i:100440 original size:24 final size:24
Alignment explanation
Indices: 100413--100465 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
100403 TCGATGCATC
100413 CCTTAACATGTGCATCGATACACT
1 CCTTAACATGTGCATCGATACACT
*
100437 CCTTAACATGTGCATCGATGCACT
1 CCTTAACATGTGCATCGATACACT
100461 CCTTA
1 CCTTA
100466 TGGATCGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30
Consensus pattern (24 bp):
CCTTAACATGTGCATCGATACACT
Found at i:102196 original size:39 final size:39
Alignment explanation
Indices: 102125--102285 Score: 175
Period size: 39 Copynumber: 4.1 Consensus size: 39
102115 TGTACACCCA
* * * *
102125 GTAAGGGCTTACCCTGTGCAAAAAG-AAGAGGAGCCTACG
1 GTAAGGACTTACCCTGAGCACAAAGCAA-AGGAGCCTGCG
* * *
102164 GTAAGGTCTTATCCT-ATGCACAAAGCAAAGGAGCCTGCA
1 GTAAGGACTTACCCTGA-GCACAAAGCAAAGGAGCCTGCG
* * *
102203 GTAACGACTTACCCTGAGCACAAAGCCGAA-GAACCTGCG
1 GTAAGGACTTACCCTGAGCACAAAG-CAAAGGAGCCTGCG
*
102242 GTAAGGACTTACCCTGAGCACAAAGCCAAGGAGCCTGCG
1 GTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTGCG
102281 GTAAG
1 GTAAG
102286 TGGTAAGGTC
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
38 3 0.03
39 93 0.91
40 6 0.06
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.16
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTGCG
Found at i:103091 original size:25 final size:25
Alignment explanation
Indices: 103063--103117 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
103053 AAAGTCAACG
103063 GTCGGTCAACGATCAACGATAAACA
1 GTCGGTCAACGATCAACGATAAACA
* * * *
103088 GTCGGTCAATGATCAATGGTCAACA
1 GTCGGTCAACGATCAACGATAAACA
103113 GTCGG
1 GTCGG
103118 ACCTGGTCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (25 bp):
GTCGGTCAACGATCAACGATAAACA
Found at i:104114 original size:20 final size:20
Alignment explanation
Indices: 104089--104131 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
104079 TCTAAGAGCC
*
104089 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
104109 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
104129 CAT
1 CAT
104132 GTGGTAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:111735 original size:13 final size:13
Alignment explanation
Indices: 111714--111748 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
111704 CCCACTTACT
111714 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
111727 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
111740 TTTCACTTT
1 TTTCACTTT
111749 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:113406 original size:5 final size:5
Alignment explanation
Indices: 113396--113422 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
113386 CCAAGGTACC
113396 TTGCA TTGCA TTGCA TTGCA TTGCA TT
1 TTGCA TTGCA TTGCA TTGCA TTGCA TT
113423 CATAGCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTGCA
Found at i:114402 original size:20 final size:20
Alignment explanation
Indices: 114377--114419 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
114367 TCTAAGAGCC
*
114377 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
114397 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
114417 CAT
1 CAT
114420 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:119904 original size:42 final size:42
Alignment explanation
Indices: 119857--119947 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 42
119847 CGTTCGATAA
* * * * *
119857 TATGTTTGTTCGTTCGTTTATGTTTGTTTATTTATGTTTATT
1 TATGTTTGTTCGTTCATGTATGTTCGTTTATGTATGTTCATT
* * *
119899 TATGTTTGTTTGTTTATGTATGTTCGTTTATGTGTGTTCATT
1 TATGTTTGTTCGTTCATGTATGTTCGTTTATGTATGTTCATT
119941 TATGTTT
1 TATGTTT
119948 ATCACAATCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.12, C:0.04, G:0.19, T:0.65
Consensus pattern (42 bp):
TATGTTTGTTCGTTCATGTATGTTCGTTTATGTATGTTCATT
Found at i:119909 original size:28 final size:28
Alignment explanation
Indices: 119877--119945 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
119867 CGTTCGTTTA
* * *
119877 TGTTTGTTTATTTATGTTTATTTATGTT
1 TGTTTGTTTATGTATGTTCATTTATGTG
*
119905 TGTTTGTTTATGTATGTTCGTTTATGTG
1 TGTTTGTTTATGTATGTTCATTTATGTG
**
119933 TGTTCATTTATGT
1 TGTTTGTTTATGT
119946 TTATCACAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.13, C:0.03, G:0.19, T:0.65
Consensus pattern (28 bp):
TGTTTGTTTATGTATGTTCATTTATGTG
Found at i:119914 original size:18 final size:18
Alignment explanation
Indices: 119857--119927 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
119847 CGTTCGATAA
* *
119857 TATGTTTGTTCGTTCGTT
1 TATGTATGTTCGTTTGTT
* **
119875 TATGTTTGTTTATTTATGTT
1 TATGTATG-TTCGTT-TGTT
* *
119895 TATTTATGTTTGTTTGTT
1 TATGTATGTTCGTTTGTT
119913 TATGTATGTTCGTTT
1 TATGTATGTTCGTTT
119928 ATGTGTGTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
18 25 0.60
19 8 0.19
20 9 0.21
ACGTcount: A:0.11, C:0.04, G:0.18, T:0.66
Consensus pattern (18 bp):
TATGTATGTTCGTTTGTT
Found at i:119930 original size:14 final size:14
Alignment explanation
Indices: 119875--119936 Score: 79
Period size: 14 Copynumber: 4.4 Consensus size: 14
119865 TTCGTTCGTT
*
119875 TATGTTTGTTTATT
1 TATGTTTGTTTATG
*
119889 TATGTTTATTTATG
1 TATGTTTGTTTATG
*
119903 TTTGTTTGTTTATG
1 TATGTTTGTTTATG
*
119917 TATGTTCGTTTATG
1 TATGTTTGTTTATG
*
119931 TGTGTT
1 TATGTT
119937 CATTTATGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.13, C:0.02, G:0.19, T:0.66
Consensus pattern (14 bp):
TATGTTTGTTTATG
Found at i:119937 original size:14 final size:14
Alignment explanation
Indices: 119875--119945 Score: 70
Period size: 14 Copynumber: 5.1 Consensus size: 14
119865 TTCGTTCGTT
* *
119875 TATGTTTGTTTATT
1 TATGTTCGTTTATG
**
119889 TATGTTTATTTATG
1 TATGTTCGTTTATG
* *
119903 TTTGTTTGTTTATG
1 TATGTTCGTTTATG
119917 TATGTTCGTTTATG
1 TATGTTCGTTTATG
* *
119931 TGTGTTCATTTATG
1 TATGTTCGTTTATG
119945 T
1 T
119946 TTATCACAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.14, C:0.03, G:0.18, T:0.65
Consensus pattern (14 bp):
TATGTTCGTTTATG
Found at i:120154 original size:13 final size:13
Alignment explanation
Indices: 120136--120161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
120126 TTTCGTTCGT
120136 TTATGTTCATTTA
1 TTATGTTCATTTA
120149 TTATGTTCATTTA
1 TTATGTTCATTTA
120162 CGTTCGTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TTATGTTCATTTA
Found at i:120180 original size:10 final size:10
Alignment explanation
Indices: 120167--120218 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
120157 ATTTACGTTC
120167 GTTCGTTTGT
1 GTTCGTTTGT
120177 GTTCGTTTACGTT
1 GTTCGTTT--G-T
120190 CGTTCGTTTGT
1 -GTTCGTTTGT
* *
120201 GTTCATTTAT
1 GTTCGTTTGT
120211 GTTCGTTT
1 GTTCGTTT
120219 ACAACAGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 23 0.66
11 1 0.03
12 2 0.06
13 1 0.03
14 8 0.23
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (10 bp):
GTTCGTTTGT
Found at i:120185 original size:24 final size:24
Alignment explanation
Indices: 120152--120217 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
120142 TCATTTATTA
120152 TGTTCATTTACGTTCGTTCGTTTG
1 TGTTCATTTACGTTCGTTCGTTTG
*
120176 TGTTCGTTTACGTTCGTTCGTTTG
1 TGTTCATTTACGTTCGTTCGTTTG
*
120200 TGTTCATTTATGTTCGTT
1 TGTTCATTTACGTTCGTT
120218 TACAACAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.08, C:0.15, G:0.21, T:0.56
Consensus pattern (24 bp):
TGTTCATTTACGTTCGTTCGTTTG
Found at i:120194 original size:14 final size:14
Alignment explanation
Indices: 120153--120198 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
120143 CATTTATTAT
*
120153 GTTCATTTACGTTC
1 GTTCGTTTACGTTC
120167 GTTCGTTT--G-T-
1 GTTCGTTTACGTTC
120177 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
120191 GTTCGTTT
1 GTTCGTTT
120199 GTGTTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
10 8 0.30
11 1 0.04
12 2 0.07
13 1 0.04
14 15 0.56
ACGTcount: A:0.07, C:0.17, G:0.22, T:0.54
Consensus pattern (14 bp):
GTTCGTTTACGTTC
Found at i:120448 original size:2 final size:2
Alignment explanation
Indices: 120441--120477 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
120431 ACAATAAATT
120441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
120478 CAGAAAACCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:122073 original size:61 final size:60
Alignment explanation
Indices: 121895--122079 Score: 289
Period size: 60 Copynumber: 3.1 Consensus size: 60
121885 CTCTAAAAGA
* * *
121895 AAAAGTTAAATGCATAACGGTGCATTTTGGTATAAAGGTGCCACTAATGCAAGTTAGATG
1 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATG
*
121955 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATT
1 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATG
* * * *
122015 AAAAGTTAAATGCCGAACGGTGTATTTTTGCCAGAAAGTTGCCACTAATGCAAGTTAGATG
1 AAAAGTTAAATGCCTAACGGTGCA-TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATG
122076 AAAA
1 AAAA
122080 CAATACATTT
Statistics
Matches: 115, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
60 78 0.68
61 37 0.32
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (60 bp):
AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATG
Found at i:122917 original size:39 final size:39
Alignment explanation
Indices: 122862--123021 Score: 171
Period size: 39 Copynumber: 4.1 Consensus size: 39
122852 TGTACACCCA
* * *
122862 GTAAGGGCTTACCCTGTGCACAAAGTAGAGGAGCCTACG
1 GTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACG
* * *
122901 GTAAGGTCTTATCCTGTA-CACAAAGCATAGGAGCCTAC-
1 GTAAGGACTTACCCTG-AGCACAAAGCAGAGGAGCCTACG
* * * * *
122939 ATAGGGACTTACCATGAGCACAAAGCCGAGGAACCTACG
1 GTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACG
* * *
122978 GTAAGGACTTACCCTGAGCATAAAGCCGAGGAGCCTGCG
1 GTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACG
123017 GTAAG
1 GTAAG
123022 TGGTAAGGTC
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 1 0.01
38 28 0.28
39 70 0.71
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACG
Found at i:123003 original size:77 final size:76
Alignment explanation
Indices: 122865--123013 Score: 183
Period size: 77 Copynumber: 1.9 Consensus size: 76
122855 ACACCCAGTA
* * * * * * *
122865 AGGGCTTACCCTGTGCACAAAGTAGAGGAGCCTACGGTAAGGTCTTATCCTGTACACAAAGCATA
1 AGGGCTTACCATGAGCACAAAGCAGAGGAACCTACGGTAAGGACTTACCCTGTACACAAAGCAGA
122930 GGAGCCTACAT
66 GGAGCCTACAT
* * *
122941 AGGGACTTACCATGAGCACAAAGCCGAGGAACCTACGGTAAGGACTTACCCTG-AGCATAAAGCC
1 AGGG-CTTACCATGAGCACAAAGCAGAGGAACCTACGGTAAGGACTTACCCTGTA-CACAAAGCA
123005 GAGGAGCCT
64 GAGGAGCCT
123014 GCGGTAAGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
76 5 0.08
77 56 0.92
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (76 bp):
AGGGCTTACCATGAGCACAAAGCAGAGGAACCTACGGTAAGGACTTACCCTGTACACAAAGCAGA
GGAGCCTACAT
Found at i:125127 original size:19 final size:20
Alignment explanation
Indices: 125094--125142 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
125084 CTCTATATCA
*
125094 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATTTCAATTTG
*
125114 TTTTTTAAAA-TTCAATTTG
1 TTTTTCAAAATTTCAATTTG
*
125133 TCTTTCAAAA
1 TTTTTCAAAA
125143 CAAAATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTCAAAATTTCAATTTG
Found at i:128625 original size:20 final size:20
Alignment explanation
Indices: 128600--128646 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
128590 CATTTTTCAT
128600 ATTTTAAA-AGCTTTAAACAC
1 ATTTTAAACA-CTTTAAACAC
*
128620 ATTTTAAACACTTTAAACAT
1 ATTTTAAACACTTTAAACAC
128640 ATTTTAA
1 ATTTTAA
128647 TTAACTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTTAAACACTTTAAACAC
Found at i:129672 original size:21 final size:21
Alignment explanation
Indices: 129557--129694 Score: 72
Period size: 20 Copynumber: 6.7 Consensus size: 21
129547 GCGAAATAAA
*
129557 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTATCCAG
** *
129577 AATCGCAAATC-AGTT-CCCAG
1 AATCGCAACGCGA-TTATCCAG
**
129597 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGATTATCCAG
* *
129618 AATCGCAATGCGA-TAGTACA-
1 AATCGCAACGCGATTA-TCCAG
* ** *
129638 AATTAGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTATCCAG
* **
129660 AATCGCAACGCGAATATATA-
1 AATCGCAACGCGATTATCCAG
129680 AATCGCAACGCGATT
1 AATCGCAACGCGATT
129695 CTGACTATCG
Statistics
Matches: 87, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.01
20 42 0.48
21 41 0.47
22 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTATCCAG
Found at i:129685 original size:20 final size:20
Alignment explanation
Indices: 129660--129915 Score: 80
Period size: 20 Copynumber: 12.7 Consensus size: 20
129650 GATTTTCCAG
129660 AATCGCAACGCGAATATATA
1 AATCGCAACGCGAATATATA
*
129680 AATCGCAACGCG-AT-TCTGA
1 AATCGCAACGCGAATATAT-A
* * * *
129699 CTATCGCAACGAGTATCCGTA-A
1 -AATCGCAACGCGAAT--ATATA
* * ***
129721 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATATATA
129741 AATCGCAACGAC-AATACGTA-A
1 AATCGCAACG-CGAATA--TATA
129762 AATCGCAACGC--ATATACGTA
1 AATCGCAACGCGAATATA--TA
** * *
129782 AATTACAACGAGAATACATA
1 AATCGCAACGCGAATATATA
* * *
129802 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATATA
* **
129822 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATATA
* * ***
129842 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATATATA
129862 AATCGCAACGAC-AATACGTA-A
1 AATCGCAACG-CGAATA--TATA
* ***
129883 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATATA
129903 AATCGCAACGCGA
1 AATCGCAACGCGA
129916 TTTTTAAAAC
Statistics
Matches: 172, Mismatches: 44, Indels: 40
0.67 0.17 0.16
Matches are distributed among these distances:
17 2 0.01
18 2 0.01
19 6 0.03
20 116 0.67
21 40 0.23
22 5 0.03
24 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATATATA
Found at i:129812 original size:81 final size:81
Alignment explanation
Indices: 129718--129912 Score: 284
Period size: 81 Copynumber: 2.4 Consensus size: 81
129708 CGAGTATCCG
*
129718 TAAAATCGTAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCATATACGTAA
1 TAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT-AAATCGCAACGCATATACGTAA
* *
129783 ATTACAACGAGAATACA
65 ATCACAACGACAATACA
* * * * *
129800 T-AAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAA
1 TAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAATCGCAACGCATATACGTAAA
* *
129864 TCGCAACGACAATACG
66 TCACAACGACAATACA
129880 TAAAATCGCAACGCGTATCCGTAAATCGCAACG
1 TAAAATCGCAACGCGTATCCGTAAATCGCAACG
129913 CGATTTTTAA
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
80 33 0.33
81 67 0.66
82 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (81 bp):
TAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAATCGCAACGCATATACGTAAA
TCACAACGACAATACA
Found at i:129823 original size:40 final size:41
Alignment explanation
Indices: 129701--129912 Score: 293
Period size: 41 Copynumber: 5.2 Consensus size: 41
129691 GATTCTGACT
** * *
129701 ATCGCAACGAGTATCCGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
129742 ATCGCAACGACAATACGTAAAATCGCAACGCATATACGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
** * * *
129783 ATTACAACGAGAATACAT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
129823 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
129863 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
129904 ATCGCAACG
1 ATCGCAACG
129913 CGATTTTTAA
Statistics
Matches: 150, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 71 0.47
41 79 0.53
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.19
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:130511 original size:20 final size:19
Alignment explanation
Indices: 130472--130579 Score: 100
Period size: 19 Copynumber: 5.9 Consensus size: 19
130462 TTCTAAACTT
*
130472 AAAATCGCAACATGAAATG
1 AAAATCGCAACACGAAATG
*
130491 AAAACCGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
** *
130511 ACTATCGCAACGCGAAATG
1 AAAATCGCAACACGAAATG
130530 AAAATCGC-A-ACG--A-G
1 AAAATCGCAACACGAAATG
* *
130544 AGAATCGCAACGCGAAATG
1 AAAATCGCAACACGAAATG
*
130563 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
130580 CCAAAATCGT
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
14 8 0.11
15 2 0.03
16 2 0.03
17 2 0.03
18 2 0.03
19 40 0.56
20 15 0.21
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:130529 original size:39 final size:36
Alignment explanation
Indices: 130474--130579 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 36
130464 CTAAACTTAA
** *
130474 AATCGCAACATGAAATGAAAACCGCAACACGAAAATG
1 AATCGCAACGCGAAATGAAAATCGCAACACGAAAA-G
*
130511 ACTATCGCAACGCGAAATGAAAATCGC-A-ACG-AGAG
1 A--ATCGCAACGCGAAATGAAAATCGCAACACGAAAAG
*
130546 AATCGCAACGCGAAATGAAAATCGCAACGCGAAA
1 AATCGCAACGCGAAATGAAAATCGCAACACGAAA
130580 CCAAAATCGT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
33 24 0.41
34 1 0.02
35 4 0.07
36 3 0.05
37 4 0.07
38 1 0.02
39 21 0.36
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (36 bp):
AATCGCAACGCGAAATGAAAATCGCAACACGAAAAG
Found at i:130585 original size:19 final size:19
Alignment explanation
Indices: 130546--130588 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
130536 GCAACGAGAG
**
130546 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
130565 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
130584 AATCG
1 AATCG
130589 TATTGTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:130619 original size:19 final size:19
Alignment explanation
Indices: 130595--130717 Score: 130
Period size: 19 Copynumber: 6.6 Consensus size: 19
130585 ATCGTATTGT
130595 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
130614 GATTTTAATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
130633 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
130647 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
**
130666 GATAGTCATTTCCGCGTTGC
1 GATTTTCATTT-CGCGTTGC
** *
130686 GATAGTCATTCTCTCGTTGC
1 GATTTTCATT-TCGCGTTGC
130706 GATTTTCATTTC
1 GATTTTCATTTC
130718 AACCAAAAGA
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.11
16 3 0.03
17 2 0.02
19 39 0.44
20 33 0.38
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:130683 original size:20 final size:20
Alignment explanation
Indices: 130641--130708 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
130631 GCGATTCTCT
**
130641 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
130660 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
130680 CGTTGCGATAGTCA-TTCTCT
1 CGTTGCGATAGTCATTTC-CG
130700 CGTTGCGAT
1 CGTTGCGAT
130709 TTTCATTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.41
20 26 0.59
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:132574 original size:94 final size:94
Alignment explanation
Indices: 132413--132792 Score: 633
Period size: 94 Copynumber: 4.1 Consensus size: 94
132403 TAGATTGCTT
* * *
132413 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
132478 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
132507 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
132572 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
132601 AGTAAATTTGTTCT-GTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
1 AGTAAATTTATT-TGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
*
132665 TATTTTTCTTTGTTTTGTCTTTTGGTTGAA
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
132695 AGTAAATTT-TTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAG
1 AGTAAATTTATTT-GGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
132759 TATTTGTCTTTGTTTTGTCTTTTGGTTG-A
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
132788 AGTAA
1 AGTAA
132793 TGCAATCTAT
Statistics
Matches: 272, Mismatches: 10, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
92 1 0.00
93 28 0.10
94 242 0.89
95 1 0.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:132951 original size:19 final size:19
Alignment explanation
Indices: 132929--133016 Score: 69
Period size: 19 Copynumber: 4.8 Consensus size: 19
132919 GAAACTATAA
132929 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
132948 TCGCATTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
132962 TCTCGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
132981 TCGCATTGCGATTTTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
133002 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
133017 AAGTTCCAGA
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
14 7 0.14
16 3 0.06
17 3 0.06
19 23 0.45
21 15 0.29
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:133010 original size:21 final size:19
Alignment explanation
Indices: 132965--133016 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
132955 ACGATTCTCT
* *
132965 CGTTGCAATTTTCATTTCG
1 CGTTGCGATTTTCATTTCA
*
132984 CATTGCGATTTTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCA
133005 CGTTGCGATTTT
1 CGTTGCGATTTT
133017 AAGTTCCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
21 15 0.56
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.50
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCA
Found at i:133493 original size:21 final size:21
Alignment explanation
Indices: 133469--133535 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
133459 TCATTCCTCG
133469 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
133490 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
133511 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
133532 AGAG
1 AGAG
133536 CTCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:133493 original size:42 final size:42
Alignment explanation
Indices: 133417--133535 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
133407 AACTCGCCTG
* * * * * * *
133417 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
133459 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
133501 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
133536 CTCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:134906 original size:14 final size:14
Alignment explanation
Indices: 134887--134922 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
134877 ATTGTTTAAT
134887 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
134901 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
134915 TGATTTGT
1 TGATTTGT
134923 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:135045 original size:19 final size:17
Alignment explanation
Indices: 135029--135079 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
135019 AAAAATGACT
135029 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
135048 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
135062 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
135079 A
1 A
135080 AATCGCAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:135071 original size:33 final size:33
Alignment explanation
Indices: 135029--135122 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
135019 AAAAATGACT
* *
135029 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
135062 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
135095 ATCGCAACGGGAAACT-AAAATCGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
135123 CGAAACTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:135085 original size:19 final size:19
Alignment explanation
Indices: 135029--135087 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
135019 AAAAATGACT
135029 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
135048 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
135062 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
135081 ATCGCAA
1 ATCGCAA
135088 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:135116 original size:19 final size:19
Alignment explanation
Indices: 135061--135137 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
135051 GCAACGAGAG
*
135061 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
135080 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
135094 AATCGCAACGGGAAACTAA
1 AATCGCAACGCGAAACTAA
135113 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
135132 ATTCGC
1 AATCGC
135138 GTTGCGATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 1 0.02
17 2 0.04
18 2 0.04
19 33 0.67
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:135161 original size:19 final size:19
Alignment explanation
Indices: 135133--135257 Score: 125
Period size: 19 Copynumber: 6.7 Consensus size: 19
135123 CGAAACTAAA
135133 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
135152 TTCACTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
135167 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
135185 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
135204 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATTTTCAT
135224 ATTCGCGTTGCGATTTTCAT
1 -TTCGCGTTGCGATTTTCAT
*
135244 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
135258 CTCTCGTTGC
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
14 9 0.10
16 3 0.03
17 3 0.03
19 39 0.45
20 31 0.36
21 2 0.02
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:135216 original size:20 final size:19
Alignment explanation
Indices: 135170--135297 Score: 104
Period size: 20 Copynumber: 6.8 Consensus size: 19
135160 GCGATTCTCT
**
135170 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
135189 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
135209 CGTTGCGATATTCATATTCG
1 CGTTGCGATAGTCAT-TTCG
**
135229 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
135248 CATTGCGAT--TC---TCT
1 CGTTGCGATAGTCATTTCG
*
135262 CGTTGCGATAGTAATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
135282 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
135298 AAGATGATTG
Statistics
Matches: 88, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.11
16 1 0.01
17 2 0.02
19 27 0.31
20 46 0.52
21 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:135289 original size:53 final size:56
Alignment explanation
Indices: 135170--135290 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 56
135160 GCGATTCTCT
* *
135170 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATATTCATATTCG
1 CGTTGCGATTTTCATTTCGCATTGCGATA-TC--TTCCGCGTTGCGATAGTAATATTCG
*
135229 CGTTGCGATTTTCATTTCGCATTGCGAT-TC-T-CTCGTTGCGATAGTAAT-TTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGATATCTTCCGCGTTGCGATAGTAATATT-CG
135282 CGTTGCGAT
1 CGTTGCGAT
135291 AGACATTAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
52 2 0.03
53 25 0.43
54 1 0.02
57 2 0.03
59 28 0.48
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40
Consensus pattern (56 bp):
CGTTGCGATTTTCATTTCGCATTGCGATATCTTCCGCGTTGCGATAGTAATATTCG
Found at i:137828 original size:24 final size:24
Alignment explanation
Indices: 137777--137828 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
137767 ATCTGAGTAT
** *
137777 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
137801 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
137825 TGAC
1 TGAC
137829 TAATACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:138689 original size:20 final size:20
Alignment explanation
Indices: 138666--139147 Score: 115
Period size: 20 Copynumber: 23.9 Consensus size: 20
138656 TTGCGATAGT
*
138666 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
* *
138686 CAGATTCGCATTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
*
138706 CAGATTCGCGTTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
* *
138726 C-GTATTTGCGTTGCGATTTA
1 CAG-AATCGCGTTGCGATTTA
* * *
138746 C-GTATTCGCATTGCGAATTA
1 CAG-AATCGCGTTGCGATTTA
* * ***
138766 GAAAAATCGCAACGCGAATTT-
1 -CAGAATCGCGTTGCG-ATTTA
** ** *
138787 GGGAAATCGCAATGCGATAGT-
1 CAG-AATCGCGTTGCGAT-TTA
*
138808 CAGAATCGCGTTGCGA-AT-
1 CAGAATCGCGTTGCGATTTA
* * ** *
138826 CTGGAAACTGATTTGCGA-TTC
1 C-AGAATC-GCGTTGCGATTTA
* *
138847 CGGAGATCGCGTTGCGAATTA
1 CAGA-ATCGCGTTGCGATTTA
138868 TC-G-ATCGCGTTGCGATTTA
1 -CAGAATCGCGTTGCGATTTA
* *
138887 C-GGATACACGTTGCGATTTTA
1 CAGAAT-CGCGTTGCGA-TTTA
* **
138908 C-GTATTATCGTTGCGATTTA
1 CAG-AATCGCGTTGCGATTTA
* *
138928 C-GGATACGCATTGCGATTTA
1 CAGAAT-CGCGTTGCGATTTA
* *
138948 C-GTATTCTCGTTGCGATTTA
1 CAG-AATCGCGTTGCGATTTA
138968 CAG-ATACGCGTTGCGATTTA
1 CAGAAT-CGCGTTGCGATTTA
* * *
138988 C-GTATTCTCGTTGTGATTTA
1 CAG-AATCGCGTTGCGATTTA
*
139008 C-GGATACGCGTTGCGATTTTA
1 CAGAAT-CGCGTTGCGA-TTTA
* * *
139029 C-GTATTGTCGTTGCAATTTA
1 CAGAATCG-CGTTGCGATTTA
* *
139049 C-GGATACGCGTTGTGATTTTA
1 CAGAAT-CGCGTTGCGA-TTTA
* * *
139070 C-GGATACTCGTTGCGATAGT-
1 CAGAAT-CGCGTTGCGAT-TTA
139090 CAGAATCGCGTTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
* * *
139110 TATG-TTCGCGTTGCGATTTT
1 CA-GAATCGCGTTGCGATTTA
* *
139130 CATATTCGCGTTGCGATT
1 CAGAATCGCGTTGCGATT
139148 CTGGAAAATC
Statistics
Matches: 355, Mismatches: 75, Indels: 64
0.72 0.15 0.13
Matches are distributed among these distances:
18 4 0.01
19 27 0.08
20 235 0.66
21 84 0.24
22 5 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
CAGAATCGCGTTGCGATTTA
Found at i:138740 original size:40 final size:40
Alignment explanation
Indices: 138674--139147 Score: 196
Period size: 40 Copynumber: 11.8 Consensus size: 40
138664 GTCAGAATCT
138674 CGTTGCGATTTACAGATTCGCATTGCGATTTACAG-ATTCG
1 CGTTGCGATTTACAGATTCGCATTGCGATTTAC-GTATTCG
* *
138714 CGTTGCGATTTAC-GTATTTGCGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
* * * * * ** ** * *
138754 CATTGCGAATTAGAAAAATCGCAACGCGAATTTGGGAAATCG
1 CGTTGCGATTTA-CAGATTCGCATTGCG-ATTTACGTATTCG
** * * * * * **
138796 CAATGCGATAGT-CAGAATCGCGTTGCGA-AT-CTGGAAACTG
1 CGTTGCGAT-TTACAGATTCGCATTGCGATTTAC-GTATTC-G
** * * *
138836 ATTTGCGA-TTCCGGAGA-TCGCGTTGCGAATTATCG-AT-CG
1 CGTTGCGATTTAC--AGATTCGCATTGCGATTTA-CGTATTCG
* * * * **
138875 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTAT
1 CGTTGCGATTTACAGATTCGCATTGCGA-TTTACGTATTCG
* * *
138916 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCG
* * *
138956 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCG
* * * *
138996 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATT-G
1 CGTTGCGATTTACAGATTCGCATTGCGA-TTTACGTATTCG
* * * * * * * *
139036 TCGTTGCAATTTACGGATACGCGTTGTGATTTTACGGATACT
1 -CGTTGCGATTTACAGATTCGCATTGCGA-TTTACGTATTCG
* * * ** *
139078 CGTTGCGATAGT-CAGAATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACAGATTCGCATTGCGATTTACGTATTCG
* * *
139118 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATTCGCATTGCGATT
139148 CTGGAAAATC
Statistics
Matches: 339, Mismatches: 71, Indels: 48
0.74 0.16 0.10
Matches are distributed among these distances:
38 3 0.01
39 27 0.08
40 177 0.52
41 112 0.33
42 18 0.05
43 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (40 bp):
CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCG
Found at i:138782 original size:21 final size:21
Alignment explanation
Indices: 138758--138803 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
138748 TATTCGCATT
138758 GCGAATTAGAAAAATCGCAAC
1 GCGAATTAGAAAAATCGCAAC
* ** *
138779 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGAAAAATCGCAAC
138800 GCGA
1 GCGA
138804 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGAAAAATCGCAAC
Found at i:138923 original size:41 final size:41
Alignment explanation
Indices: 138875--139086 Score: 304
Period size: 41 Copynumber: 5.2 Consensus size: 41
138865 TTATCGATCG
*
138875 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTAT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTAT
* *
138916 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTAT
* *
138956 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTAT
* *
138996 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTAT
* * *
139037 CGTTGCAATTTACGGATACGCGTTGTGATTTTACGGA-TACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTA-T
139078 CGTTGCGAT
1 CGTTGCGAT
139087 AGTCAGAATC
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 76 0.49
41 79 0.51
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTAT
Found at i:139165 original size:21 final size:21
Alignment explanation
Indices: 139141--139193 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
139131 ATATTCGCGT
139141 TGCGATTCTGGAAAATCGCAA
1 TGCGATTCTGGAAAATCGCAA
* ** *
139162 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGGAAAATCGCAA
139183 TGCGATTCTGG
1 TGCGATTCTGG
139194 GAACTGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCGATTCTGGAAAATCGCAA
Found at i:139225 original size:20 final size:20
Alignment explanation
Indices: 139135--139229 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
139125 ATTTTCATAT
* *
139135 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGG-AGA
* * *
139156 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGA-GA
139177 TCGCATTGCGATTCTGG-GA
1 TCGCATTGCGATTCTGGAGA
*
139196 ACTG-ATTTGCGATTCTGGAGA
1 TC-GCA-TTGCGATTCTGGAGA
*
139217 TCGCGTTGCGATT
1 TCGCATTGCGATT
139230 TTTATTTCGC
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.05
20 26 0.46
21 25 0.44
22 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATTCTGGAGA
Found at i:145529 original size:9 final size:9
Alignment explanation
Indices: 145515--145569 Score: 69
Period size: 9 Copynumber: 6.1 Consensus size: 9
145505 CACTTACAGA
145515 TCAAACTTG
1 TCAAACTTG
145524 TCAAACTTG
1 TCAAACTTG
*
145533 TTAAA-TTGG
1 TCAAACTT-G
145542 TCAAACTTG
1 TCAAACTTG
145551 TCAAA-TTG
1 TCAAACTTG
145559 ATCAAACTTG
1 -TCAAACTTG
145569 T
1 T
145570 TAGAATGTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 5 0.12
9 30 0.75
10 5 0.12
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (9 bp):
TCAAACTTG
Found at i:145546 original size:18 final size:18
Alignment explanation
Indices: 145523--145571 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
145513 GATCAAACTT
145523 GTCAAACTTGTTAAATTG
1 GTCAAACTTGTTAAATTG
*
145541 GTCAAACTTGTCAAATTG
1 GTCAAACTTGTTAAATTG
*
145559 ATCAAACTTGTTA
1 GTCAAACTTGTTA
145572 GAATGTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (18 bp):
GTCAAACTTGTTAAATTG
Done.