Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008206.1 Hibiscus syriacus cultivar Beakdansim tig00110828_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: 1504526
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:133394 original size:19 final size:19
Alignment explanation
Indices: 133370--133453 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
133360 GCAACGAGAG
*
133370 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
133389 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
133408 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
133422 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
133441 AATCGCAATGCGA
1 AATCGCAACGCGA
133454 TTTTGGTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.71
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:133410 original size:52 final size:52
Alignment explanation
Indices: 133348--133453 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
133338 TCTTTTGGTT
*
133348 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
133400 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
133452 GA
1 GA
133454 TTTTGGTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:133484 original size:14 final size:14
Alignment explanation
Indices: 133465--133521 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
133455 TTTGGTTTCG
133465 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
133479 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
133498 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
133512 CGTTGCGATT
1 CGTTGCGATT
133522 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:133497 original size:33 final size:33
Alignment explanation
Indices: 133449--133529 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
133439 AAAATCGCAA
**
133449 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
133482 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
133515 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
133530 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:133532 original size:21 final size:21
Alignment explanation
Indices: 133506--133581 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
133496 CGCGTTGCGA
133506 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
133527 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
133547 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
133568 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
133582 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:133562 original size:41 final size:41
Alignment explanation
Indices: 133505--133582 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
133495 TCGCGTTGCG
*
133505 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
133546 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
133583 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:133703 original size:33 final size:33
Alignment explanation
Indices: 133661--133731 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
133651 AATACTAACT
*
133661 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
133694 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
133727 TGAAA
1 TGAAA
133732 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:134140 original size:20 final size:20
Alignment explanation
Indices: 134114--134267 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
134104 CTTTAAATAT
134114 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
134134 TGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
134156 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
134175 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
134195 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
134215 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
134235 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
134255 CGCGTTGCGATTT
1 CGCGTTGCGATTT
134268 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 93 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:134241 original size:40 final size:40
Alignment explanation
Indices: 134113--134267 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
134103 GCTTTAAATA
* *
134113 TCGCGTTGCGATTTACGGATATGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
134154 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
134194 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
134234 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
134268 TGGAAAATCG
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
40 66 0.69
41 29 0.31
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.38
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:134284 original size:21 final size:21
Alignment explanation
Indices: 134254--134336 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
134244 ATTTTCATAT
*
134254 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
134275 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
134296 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
134317 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
134337 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:134327 original size:42 final size:43
Alignment explanation
Indices: 134234--134332 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
134224 ATTTATGTGT
* *
134234 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
134275 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
134317 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
134333 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:135722 original size:20 final size:21
Alignment explanation
Indices: 135685--135723 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
135675 ATTATGTCAA
135685 TATTTTATGATAATATTGTTT
1 TATTTTATGATAATATTGTTT
135706 TATTTATATGA-AA-ATTGT
1 TATTT-TATGATAATATTGT
135724 CGTTCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TATTTTATGATAATATTGTTT
Found at i:145018 original size:12 final size:12
Alignment explanation
Indices: 145003--145070 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 12
144993 ATGTTAGATA
*
145003 AAATAAATGAAT
1 AAATAAATAAAT
145015 AAATAAATAAAT
1 AAATAAATAAAT
*
145027 -ACTAAATAAAT
1 AAATAAATAAAT
* *
145038 CAAAAGAAAGAAA-
1 --AAATAAATAAAT
*
145051 AAATAAAAAAAT
1 AAATAAATAAAT
*
145063 AAAAAAAT
1 AAATAAAT
145071 GAAAAATGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
11 19 0.44
12 17 0.40
14 7 0.16
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:145019 original size:4 final size:4
Alignment explanation
Indices: 145003--145070 Score: 50
Period size: 4 Copynumber: 17.0 Consensus size: 4
144993 ATGTTAGATA
* * * *
145003 AAAT AAAT GAAT AAAT AAAT AAAT -ACT AAAT AAAT CAAAAG AAAG AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT
* *
145051 AAAT AAAA AAAT AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT
145071 GAAAAATGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
3 5 0.10
4 43 0.84
6 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:145060 original size:9 final size:8
Alignment explanation
Indices: 145048--145111 Score: 51
Period size: 8 Copynumber: 7.5 Consensus size: 8
145038 CAAAAGAAAG
145048 AAAAAATA
1 AAAAAATA
145056 AAAAAATA
1 AAAAAATA
145064 AAAAAAT-
1 AAAAAATA
*
145071 GAAAAATGA
1 AAAAAAT-A
145080 AAATAAATCA
1 AAA-AAAT-A
145090 AAGGAAAA-A
1 AA--AAAATA
145099 AATAAAATA
1 AA-AAAATA
145108 AAAA
1 AAAA
145112 TTAATAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
7 6 0.13
8 21 0.46
9 8 0.17
10 7 0.15
11 3 0.07
12 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:145180 original size:3 final size:3
Alignment explanation
Indices: 145172--145227 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
145162 AGAAAAGAAA
* *
145172 AAT AAT AAT AAT GAG AAGT AAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T -AAT AAT AAT AAT AAT AAT AAT AAT AAT
145219 AAT AAT AAT
1 AAT AAT AAT
145228 TATATATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 44 0.94
4 1 0.02
5 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:145286 original size:14 final size:14
Alignment explanation
Indices: 145245--145291 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
145235 ATATGTATAA
145245 AAAATGATAAAAATAT
1 AAAAT-ATAAAAA-AT
*
145261 AAGAA-ATTAAAAAT
1 AA-AATATAAAAAAT
145275 AAAATATAAAAAAT
1 AAAATATAAAAAAT
145289 AAA
1 AAA
145292 TAAAACATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 15 0.56
15 6 0.22
16 2 0.07
17 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (14 bp):
AAAATATAAAAAAT
Found at i:145294 original size:18 final size:18
Alignment explanation
Indices: 145240--145296 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
145230 TATATATATG
*
145240 TATAAAAAAT-GATAAAAA
1 TATAAAAAATAAAT-AAAA
*
145258 TATAAGAAATTAAAAATAAAA
1 TATAA-AAA--ATAAATAAAA
145279 TATAAAAAATAAATAAAA
1 TATAAAAAATAAATAAAA
145297 CATGAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 14 0.44
19 3 0.09
20 3 0.09
21 10 0.31
22 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
TATAAAAAATAAATAAAA
Found at i:146431 original size:37 final size:38
Alignment explanation
Indices: 146377--146452 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
146367 AGTTTGGGCT
* *
146377 TGTTGGACTCTGGACTTGGTCCCT-TTCATTCGGACCC
1 TGTTGGACTCTGAACTTGGACCCTATTCATTCGGACCC
146414 TGTTGGACTCTGAACTTGGACCCTATTCATTCGGACCC
1 TGTTGGACTCTGAACTTGGACCCTATTCATTCGGACCC
146452 T
1 T
146453 AAAAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 22 0.61
38 14 0.39
ACGTcount: A:0.14, C:0.29, G:0.22, T:0.34
Consensus pattern (38 bp):
TGTTGGACTCTGAACTTGGACCCTATTCATTCGGACCC
Found at i:146518 original size:19 final size:18
Alignment explanation
Indices: 146475--146542 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 18
146465 AAAGAGAAAA
*
146475 AATAAATAAAATAAA-AT
1 AATAAATAATATAAATAT
146492 --TAAA-AATATAACATAT
1 AATAAATAATATAA-ATAT
*
146508 AATAAATAATAATAATTAT
1 AATAAATAAT-ATAAATAT
*
146527 AATAATATATTATAAA
1 AATAA-ATAATATAAA
146543 AATATTTCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
14 6 0.15
15 5 0.12
16 2 0.05
18 4 0.10
19 15 0.38
20 8 0.20
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATAATATAAATAT
Found at i:146538 original size:13 final size:13
Alignment explanation
Indices: 146513--146547 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
146503 CATATAATAA
146513 ATAATAATA-ATT
1 ATAATAATATATT
146525 ATAATAATATATT
1 ATAATAATATATT
*
146538 ATAAAAATAT
1 ATAATAATAT
146548 TTCCCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAATATATT
Found at i:146659 original size:70 final size:67
Alignment explanation
Indices: 146578--146706 Score: 161
Period size: 70 Copynumber: 1.9 Consensus size: 67
146568 ATATATGTTC
* * * *
146578 AAAAATATTTT-AAAACTTATATATTATATATATTTTTAAAAAATGCTTTTCAAAATTATATAGT
1 AAAAATATTTTAAAAAC-TATATATAATATA-AGTTTT-AAAAAT-CATTTCAAAACTATATAGT
146642 TTTCAA
62 TTTCAA
* *
146648 AAAAATGTTTTAAAAACTATATATAATATAAGTTTTCAAAATCATTTCAAAACTATATA
1 AAAAATATTTTAAAAACTATATATAATATAAGTTTTAAAAATCATTTCAAAACTATATA
146707 AGGTTTTTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
67 15 0.29
68 5 0.10
69 5 0.10
70 22 0.42
71 5 0.10
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (67 bp):
AAAAATATTTTAAAAACTATATATAATATAAGTTTTAAAAATCATTTCAAAACTATATAGTTTTC
AA
Found at i:146682 original size:39 final size:37
Alignment explanation
Indices: 146634--146897 Score: 153
Period size: 36 Copynumber: 7.1 Consensus size: 37
146624 TTTTCAAAAT
146634 TATATAGTTTTCAAAAAAATGTTTTAAAAACTATATATAA
1 TATA-AGTTTTC--AAAAATGTTTTAAAAACTATATATAA
** *
146674 TATAAGTTTTC-AAAATCATTTCAAAAC--TATATAA
1 TATAAGTTTTCAAAAATGTTTTAAAAACTATATATAA
**
146708 GGT---TTTTC-AAAATGTTTTCAAAAACTATAT-TATA
1 TATAAGTTTTCAAAAATGTTTT-AAAAACTATATATA-A
*
146742 TATACA--TTTC-AAAATGTTTTAAAAACTATATATTA
1 TATA-AGTTTTCAAAAATGTTTTAAAAACTATATATAA
* *
146777 TATATGCTTTC-AAAATGTTTTTTTAAAAACTATATATTATA
1 TATAAGTTTTCAAAAATG---TTTTAAAAACTATATA-TA-A
* * *
146818 TATACG-TTTCCAAAATGTTTCTAAAAAAT-TATATAA
1 TATAAGTTTTCAAAAATGTTT-TAAAAACTATATATAA
* * *
146854 TATATA-TATTTCCAAAAACCGTTTTCAAAACTATATATAT
1 TATA-AGT-TTT-CAAAAA-TGTTTTAAAAACTATATATAA
146894 TATA
1 TATA
146898 TGTATTTAAA
Statistics
Matches: 180, Mismatches: 21, Indels: 46
0.73 0.09 0.19
Matches are distributed among these distances:
31 13 0.07
32 5 0.03
33 2 0.01
34 13 0.07
35 16 0.09
36 43 0.24
37 2 0.01
38 10 0.06
39 41 0.23
40 23 0.13
41 12 0.07
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (37 bp):
TATAAGTTTTCAAAAATGTTTTAAAAACTATATATAA
Found at i:146689 original size:68 final size:68
Alignment explanation
Indices: 146575--146773 Score: 191
Period size: 67 Copynumber: 2.9 Consensus size: 68
146565 AATATATATG
* * * * *
146575 TTCAAAAATATTTT-AAAACTTATATATTATATATATTTTTAAAAAATGCTTTTCAAAATTATAT
1 TTCAAAAATGTTTTAAAAAC-TATATATAATATACA-TTTT-CAAAATGCTTTTCAAAACTATAT
146639 A-G-TT
63 AGGTTT
*
146643 TTCAAAAAAATGTTTTAAAAACTATATATAATATA-AGTTTTCAAAAT-CATTTCAAAACTATAT
1 TTC--AAAAATGTTTTAAAAACTATATATAATATACA-TTTTCAAAATGCTTTTCAAAACTATAT
146706 AAGGTTT
63 -AGGTTT
*
146713 TTC-AAAATGTTTTCAAAAACTATAT-TATATATACA-TTTCAAAATG-TTTTAAAAACTATATA
1 TTCAAAAATGTTTT-AAAAACTATATATA-ATATACATTTTCAAAATGCTTTTCAAAACTATATA
146774 TTATATATGC
Statistics
Matches: 113, Mismatches: 8, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
66 1 0.01
67 48 0.42
68 25 0.22
69 7 0.06
70 27 0.24
71 5 0.04
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (68 bp):
TTCAAAAATGTTTTAAAAACTATATATAATATACATTTTCAAAATGCTTTTCAAAACTATATAGG
TTT
Found at i:146717 original size:31 final size:30
Alignment explanation
Indices: 146673--146737 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
146663 ACTATATATA
146673 ATATAAGTTTTCAAAATCATTTC-AAAACT
1 ATATAAGTTTTCAAAATCATTTCAAAAACT
**
146702 ATATAAGGTTTTTCAAAATGTTTTCAAAAACT
1 ATATAA-G-TTTTCAAAATCATTTCAAAAACT
146734 ATAT
1 ATAT
146738 TATATATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 6 0.19
30 1 0.03
31 14 0.45
32 10 0.32
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (30 bp):
ATATAAGTTTTCAAAATCATTTCAAAAACT
Found at i:146774 original size:37 final size:37
Alignment explanation
Indices: 146712--146891 Score: 188
Period size: 39 Copynumber: 4.7 Consensus size: 37
146702 ATATAAGGTT
146712 TTTCAAAATGTTTTCAAAAAC--TATATTATATATACA
1 TTTCAAAATGTTTT-AAAAACTATATATTATATATACA
*
146748 TTTCAAAATGTTTTAAAAACTATATATTATATATGC-
1 TTTCAAAATGTTTTAAAAACTATATATTATATATACA
*
146784 TTTCAAAATGTTTTTTTAAAAACTATATATTATATATACG
1 TTTCAAAATG---TTTTAAAAACTATATATTATATATACA
* * *
146824 TTTCCAAAATGTTTCTAAAAAAT-TATATAATATATATA
1 TTT-CAAAATGTTT-TAAAAACTATATATTATATATACA
* *
146862 TTTCCAAAAACCGTTTTCAAAACTATATAT
1 TTT-C-AAAA-TGTTTTAAAAACTATATAT
146892 ATTATATGTA
Statistics
Matches: 124, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
35 6 0.05
36 24 0.19
37 13 0.10
38 20 0.16
39 42 0.34
40 12 0.10
41 7 0.06
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTCAAAATGTTTTAAAAACTATATATTATATATACA
Found at i:156754 original size:13 final size:13
Alignment explanation
Indices: 156736--156761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
156726 CAATAGTATT
156736 GCACTTCTGATAA
1 GCACTTCTGATAA
156749 GCACTTCTGATAA
1 GCACTTCTGATAA
156762 ATTTATCGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
GCACTTCTGATAA
Found at i:157931 original size:24 final size:24
Alignment explanation
Indices: 157910--157963 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
157900 GCATAAGGAG
157910 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
*
157934 TGCAACGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
157958 TGCATC
1 TGCATC
157964 TATACACTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAGGGA
Found at i:159081 original size:2 final size:2
Alignment explanation
Indices: 159074--159110 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
159064 AGGAAAAATG
159074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
159111 GGAAGATGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:159180 original size:2 final size:2
Alignment explanation
Indices: 159173--159208 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
159163 GAACATGTGA
159173 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
159209 GATACGACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:159635 original size:23 final size:23
Alignment explanation
Indices: 159599--159666 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
159589 AACCTTATAT
*
159599 GGCACTTCGATGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
159622 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
159645 GGCACTTCAGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
159667 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:174831 original size:2 final size:2
Alignment explanation
Indices: 174820--174852 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
174810 TTGTACCAAA
174820 AT AT -T 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
174853 GTTACAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:178736 original size:46 final size:46
Alignment explanation
Indices: 178669--178765 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
178659 TTGTATACAA
* *
178669 TTTCTACTGGAAACCTAAAATGGTAAGCGTTAAGGGAGTATTTATG
1 TTTCTACTGGAAACATAAAATGGTAAACGTTAAGGGAGTATTTATG
* * * *
178715 TTTCTAGTGGAAAGATAAAATGGTAAATGTTAAGGGAGTATTTTTG
1 TTTCTACTGGAAACATAAAATGGTAAACGTTAAGGGAGTATTTATG
178761 TTTCT
1 TTTCT
178766 TTGAGCAGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (46 bp):
TTTCTACTGGAAACATAAAATGGTAAACGTTAAGGGAGTATTTATG
Found at i:180148 original size:16 final size:16
Alignment explanation
Indices: 180127--180157 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
180117 AAAAATAAAG
180127 GAACATAAACGAACAC
1 GAACATAAACGAACAC
180143 GAACATAAACGAACA
1 GAACATAAACGAACA
180158 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:180271 original size:10 final size:10
Alignment explanation
Indices: 180258--180313 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
180248 CATAAACACG
180258 AACGAACATA
1 AACGAACATA
**
180268 AACGAACACG
1 AACGAACATA
*
180278 AAC-ATAAATGA
1 AACGA-ACAT-A
180289 ACACGAACATA
1 A-ACGAACATA
180300 AACGAACATA
1 AACGAACATA
180310 AACG
1 AACG
180314 TTAGAGACCC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
9 1 0.03
10 26 0.72
11 3 0.08
12 5 0.14
13 1 0.03
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
AACGAACATA
Found at i:180306 original size:16 final size:16
Alignment explanation
Indices: 180227--180307 Score: 96
Period size: 16 Copynumber: 5.1 Consensus size: 16
180217 TAATAAATAA
*
180227 ACGAACATAAACGCGA-
1 ACGAACATAAACG-AAC
180243 ACGAACATAAAC--AC
1 ACGAACATAAACGAAC
180257 GAACGAACATAAACGAAC
1 --ACGAACATAAACGAAC
*
180275 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
180291 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
180307 A
1 A
180308 TAAACGTTAG
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.02
16 55 0.95
18 2 0.03
ACGTcount: A:0.56, C:0.23, G:0.14, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:180544 original size:24 final size:23
Alignment explanation
Indices: 180517--180573 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
180507 AAATAATTAA
180517 GAGCTCGATTAAAACTCGAGACTT
1 GAGCTCGATTAAAACTCGAGAC-T
* * **
180541 GAGCTCGATTGAAGCTCGATTCT
1 GAGCTCGATTAAAACTCGAGACT
180564 GAGCTCGATT
1 GAGCTCGATT
180574 CAAGCTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (23 bp):
GAGCTCGATTAAAACTCGAGACT
Found at i:180558 original size:11 final size:11
Alignment explanation
Indices: 180542--180605 Score: 74
Period size: 11 Copynumber: 5.6 Consensus size: 11
180532 TCGAGACTTG
*
180542 AGCTCGATTGA
1 AGCTCGATTCA
*
180553 AGCTCGATTCTG
1 AGCTCGATTC-A
180565 AGCTCGATTCA
1 AGCTCGATTCA
* *
180576 AGCTCAATTATA
1 AGCTCGATT-CA
180588 AGCTCGATTCA
1 AGCTCGATTCA
180599 AGCTCGA
1 AGCTCGA
180606 CATTGCCCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 25 0.57
12 19 0.43
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:180570 original size:12 final size:12
Alignment explanation
Indices: 180540--180597 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
180530 ACTCGAGACT
180540 TGAGCTCGA-T-
1 TGAGCTCGATTC
180550 TGAAGCTCGATTC
1 TG-AGCTCGATTC
180563 TGAGCTCGATTC
1 TGAGCTCGATTC
* * *
180575 -AAGCTCAATTA
1 TGAGCTCGATTC
*
180586 TAAGCTCGATTC
1 TGAGCTCGATTC
180598 AAGCTCGACA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 2 0.05
11 15 0.38
12 20 0.51
13 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (12 bp):
TGAGCTCGATTC
Found at i:180570 original size:23 final size:23
Alignment explanation
Indices: 180517--180605 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
180507 AAATAATTAA
* * **
180517 GAGCTCGATTAAAACTCGAGACTT
1 GAGCTCGATTCAAGCTCGATTC-T
*
180541 GAGCTCGATTGAAGCTCGATTCT
1 GAGCTCGATTCAAGCTCGATTCT
* *
180564 GAGCTCGATTCAAGCTCAATTAT
1 GAGCTCGATTCAAGCTCGATTCT
*
180587 AAGCTCGATTCAAGCTCGA
1 GAGCTCGATTCAAGCTCGA
180606 CATTGCCCCA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
23 38 0.68
24 18 0.32
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTCT
Found at i:181444 original size:24 final size:24
Alignment explanation
Indices: 181403--181478 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
181393 AGATTGAGTT
*
181403 AAACATAA-ATGAATGAACATAAAC
1 AAACATAACA-GAACGAACATAAAC
*
181427 AAACATAACCGAACGAACATAAAC
1 AAACATAACAGAACGAACATAAAC
* *
181451 GAACATAACAGAACGAACATAACC
1 AAACATAACAGAACGAACATAAAC
181475 AAAC
1 AAAC
181479 GTACACGAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.11
Consensus pattern (24 bp):
AAACATAACAGAACGAACATAAAC
Found at i:181447 original size:14 final size:14
Alignment explanation
Indices: 181428--181479 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
181418 AACATAAACA
181428 AACATAACCGAACG
1 AACATAACCGAACG
181442 AACAT-A---AACG
1 AACATAACCGAACG
*
181452 AACATAACAGAACG
1 AACATAACCGAACG
*
181466 AACATAACCAAACG
1 AACATAACCGAACG
181480 TACACGAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 9 0.28
11 1 0.03
13 1 0.03
14 21 0.66
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.08
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:181488 original size:24 final size:23
Alignment explanation
Indices: 181403--181488 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 23
181393 AGATTGAGTT
* *
181403 AAACATAAATGAATGAACATAAAC
1 AAACAT-AACGAACGAACATAAAC
181427 AAACATAACCGAACGAACATAAAC
1 AAACATAA-CGAACGAACATAAAC
* *
181451 GAACATAACAGAACGAACATAACC
1 AAACATAAC-GAACGAACATAAAC
*
181475 AAACGTACACGAAC
1 AAACATA-ACGAAC
181489 ATAAATAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.06
24 48 0.91
25 2 0.04
ACGTcount: A:0.57, C:0.22, G:0.10, T:0.10
Consensus pattern (23 bp):
AAACATAACGAACGAACATAAAC
Found at i:183181 original size:2 final size:2
Alignment explanation
Indices: 183176--183219 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
183166 TTTTTATTAT
183176 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
183218 TA
1 TA
183220 ATGAATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:183233 original size:16 final size:15
Alignment explanation
Indices: 183214--183249 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
183204 TATATATATA
183214 TATATAATGAATTATT
1 TATATAATGAATTA-T
*
183230 TATATTATGAATTAT
1 TATATAATGAATTAT
183245 TATAT
1 TATAT
183250 TTTGTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TATATAATGAATTAT
Found at i:193064 original size:20 final size:19
Alignment explanation
Indices: 193039--193091 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
193029 AACTTTAGGG
193039 AAAGTTTCGAAACTCTTGA
1 AAAGTTTCGAAACTCTTGA
* *
193058 GATAGTTTCAAAACTCTTGA
1 -AAAGTTTCGAAACTCTTGA
*
193078 AAAGTATCGAAACT
1 AAAGTTTCGAAACT
193092 TTTTGGACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (19 bp):
AAAGTTTCGAAACTCTTGA
Found at i:193280 original size:18 final size:18
Alignment explanation
Indices: 193257--193292 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
193247 TTTTAAAGTT
193257 TTGAACACATATCTTTCA
1 TTGAACACATATCTTTCA
193275 TTGAACACATATCTTTCA
1 TTGAACACATATCTTTCA
193293 AATTTAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
TTGAACACATATCTTTCA
Found at i:197468 original size:25 final size:25
Alignment explanation
Indices: 197421--197488 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
197411 AAGGGGCACA
*
197421 ATTTTTCAAAA-AC-TTCATCAAAC
1 ATTTTTCAAAATTCTTTCATCAAAC
197444 ATTTTTCAAAATTCTTTCATCAAAC
1 ATTTTTCAAAATTCTTTCATCAAAC
*
197469 ATTATTT-AAAATTATTTCAT
1 ATT-TTTCAAAATTCTTTCAT
197489 TATTTAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.28
24 1 0.03
25 25 0.62
26 3 0.08
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTTTTCAAAATTCTTTCATCAAAC
Found at i:197926 original size:31 final size:30
Alignment explanation
Indices: 197837--197965 Score: 168
Period size: 30 Copynumber: 4.2 Consensus size: 30
197827 GCTAAGCACT
*
197837 AAATAGTATAGGGACTTGACCACTAAGGTC
1 AAATAGTATAGGGACTTGACCACCAAGGTC
* *
197867 AAATAGTATAAGGACTTAACCACCAAGGTC
1 AAATAGTATAGGGACTTGACCACCAAGGTC
*
197897 AAATAGTATAGGGACTTGACCAACCAAGGTT
1 AAATAGTATAGGGACTTGACC-ACCAAGGTC
* * * *
197928 AAATAGTATAGGGGCGTGACCAACCAATGTT
1 AAATAGTATAGGGACTTGACC-ACCAAGGTC
197959 AAATAGT
1 AAATAGT
197966 GCATGGACCA
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 46 0.52
31 43 0.48
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (30 bp):
AAATAGTATAGGGACTTGACCACCAAGGTC
Found at i:199013 original size:214 final size:214
Alignment explanation
Indices: 198628--199049 Score: 551
Period size: 214 Copynumber: 2.0 Consensus size: 214
198618 TTCAAATAAT
** * * * *
198628 ACTAGACATCCTCAACATGAAGGAACAATGTCGTCCACTGACTAGACCTCCTCAATATGAAGGAG
1 ACTAGACATCCTCAACACAAAGGAACAATGTCATACACTGACTAGACATCCTCAACATGAAGGAG
* * ** *
198693 CATTGTCATCGTCAAATTTGACATCGAGCAAATCACCCAAAGCGACCAAATCTCCTCATCACGTA
66 CAATGTCATCATCAAATTTGACATAAAGCAAATCACCCAAAGCAACCAAATCTCCTCATCACGTA
* * * * * *
198758 GAAACTGTGTTGTTTCCAAAACCAAGTTATCTCCAGACAATCATACTTTCTCAACGTGAAGGAAC
131 GAAACCGGGTTGTTTCCAAAACCAAATTATCTCCAGACAATCAGAATTCCTCAACGTGAAGGAAC
198823 AATGTTGTCTTCAAATTTG
196 AATGTTGTCTTCAAATTTG
* *
198842 ACTAGACATTCTCAACACAAAGGAACAATGTCATACACAT-ACTAGACATCCTCAACATGAATGA
1 ACTAGACATCCTCAACACAAAGGAACAATGTCATACAC-TGACTAGACATCCTCAACATGAAGGA
* * * *
198906 GCAATGTCATCATCAGATTTGACATAAATCAAGTCACCCAAAGTAACCAAATCTCCTCATCACGT
65 GCAATGTCATCATCAAATTTGACATAAAGCAAATCACCCAAAGCAACCAAATCTCCTCATCACGT
* * * * * *
198971 AGGATCCGGGTTGTTTTCAAAATCAAATTATCTTTC-GACAATCAGAATTCCTCAATGTGAAGGA
130 AGAAACCGGGTTGTTTCCAAAACCAAATTATC-TCCAGACAATCAGAATTCCTCAACGTGAAGGA
199035 ACAATGTTGTCTTCA
194 ACAATGTTGTCTTCA
199050 GATGCACAGT
Statistics
Matches: 177, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
214 174 0.98
215 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.26
Consensus pattern (214 bp):
ACTAGACATCCTCAACACAAAGGAACAATGTCATACACTGACTAGACATCCTCAACATGAAGGAG
CAATGTCATCATCAAATTTGACATAAAGCAAATCACCCAAAGCAACCAAATCTCCTCATCACGTA
GAAACCGGGTTGTTTCCAAAACCAAATTATCTCCAGACAATCAGAATTCCTCAACGTGAAGGAAC
AATGTTGTCTTCAAATTTG
Found at i:200861 original size:4 final size:4
Alignment explanation
Indices: 200847--200903 Score: 105
Period size: 4 Copynumber: 14.0 Consensus size: 4
200837 TAAATATTCA
200847 TTAT GTTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
200896 TTAT TTAT
1 TTAT TTAT
200904 CATTGCTTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 48 0.92
5 4 0.08
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:204003 original size:25 final size:24
Alignment explanation
Indices: 203959--204021 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
203949 TATTTATTCG
* *
203959 ATTTTAAAAA-AATATAAATTTTT
1 ATTTTAAAAATAAAATAAATTTTC
203982 ATGCTTTAAAAATAAAAT-AATTTTC
1 AT--TTTAAAAATAAAATAAATTTTC
204007 ATTTTGAAAAATAAA
1 ATTTT-AAAAATAAA
204022 TGTTATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 5 0.15
24 9 0.26
25 16 0.47
26 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (24 bp):
ATTTTAAAAATAAAATAAATTTTC
Found at i:204005 original size:24 final size:22
Alignment explanation
Indices: 203966--204021 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
203956 TCGATTTTAA
203966 AAAAATATAAATTTTT-ATGCTTT-
1 AAAAATA-AAATTTTTCAT--TTTG
203989 AAAAATAAAATAATTTTCATTTTG
1 AAAAATAAAAT--TTTTCATTTTG
204013 AAAAATAAA
1 AAAAATAAA
204022 TGTTATGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 4 0.14
23 10 0.34
24 13 0.45
25 2 0.07
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (22 bp):
AAAAATAAAATTTTTCATTTTG
Found at i:215855 original size:16 final size:16
Alignment explanation
Indices: 215834--215864 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
215824 GATAAAGAAC
*
215834 ATGAGAATAACTCATA
1 ATGAGAAGAACTCATA
215850 ATGAGAAGAACTCAT
1 ATGAGAAGAACTCAT
215865 TCGATTAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (16 bp):
ATGAGAAGAACTCATA
Found at i:216540 original size:23 final size:23
Alignment explanation
Indices: 216514--216582 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
216504 CACCACAGCT
* *
216514 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
216537 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
*
216560 CATAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
216583 TATAAGATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCA
Found at i:217376 original size:64 final size:63
Alignment explanation
Indices: 217266--217385 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
217256 CATAAATCTT
** * * *
217266 ATTCGATGTTTGTATTTAAGGGGGTGCATTGATGCACTACTTGTGCATCAATACACTGATGGC
1 ATTCGATGTTTGTATTTAAAAGAGTGCATCGATGCACTACATGTGCATCAATACACTGATGGC
* * *
217329 ATTCGATGTTTTTATTTTAAAAGAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 ATTCGATGTTTGTA-TTTAAAAGAGTGCATCGATGCACTACATGTGCATCAATACAC
217386 CTTGAACAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 13 0.27
64 35 0.73
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (63 bp):
ATTCGATGTTTGTATTTAAAAGAGTGCATCGATGCACTACATGTGCATCAATACACTGATGGC
Found at i:237434 original size:17 final size:17
Alignment explanation
Indices: 237412--237454 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
237402 TTCTCATTGC
237412 CTCAACATTTCACCATA
1 CTCAACATTTCACCATA
237429 CTCAACATTTCACCATA
1 CTCAACATTTCACCATA
237446 CTCAACATT
1 CTCAACATT
237455 AAACATCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (17 bp):
CTCAACATTTCACCATA
Found at i:239213 original size:3 final size:3
Alignment explanation
Indices: 239205--239235 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
239195 TTTATAGTGG
239205 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
239236 AAATGATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:239452 original size:72 final size:72
Alignment explanation
Indices: 239321--239665 Score: 347
Period size: 72 Copynumber: 4.7 Consensus size: 72
239311 ATCACTATTG
* * ** * * *
239321 AGTTATTCTCATTATGAAC-TCTTC-CATTGGAAATATTGACCCGAC-CTCTTTTGTGATGGAAT
1 AGTTCTTCTCATTATGAACTTCTTCTC-TGGGAAATGCTGATCCAACTC-CTTCTGTGATGGAAT
239383 CGAGCAACA
64 CGAGCAACA
** *
239392 AGTTCTTCTCATTATGAACTTCTTCTCTGGGAAATTTTGATCCAACTCCTTCTGTTATGGAATCG
1 AGTTCTTCTCATTATGAACTTCTTCTCTGGGAAATGCTGATCCAACTCCTTCTGTGATGGAATCG
239457 AGCAACA
66 AGCAACA
* * * * * *
239464 AGTTATTCTTATTATGAACTTCTTCTCTAGGAAATGCTAATTCAACTCATTCTGTGATGGAATCG
1 AGTTCTTCTCATTATGAACTTCTTCTCTGGGAAATGCTGATCCAACTCCTTCTGTGATGGAATCG
*
239529 ATCAACA
66 AGCAACA
* * * * * *
239536 AGTTCTTATCATTATGAACTTGTTCTTTGGGAAATGCTAAACCAACTCCTTCTGTGATGGATTCA
1 AGTTCTTCTCATTATGAACTTCTTCTCTGGGAAATGCTGATCCAACTCCTTCTGTGATGGAATC-
239601 AGCAAAGACTGAACA
65 -G---AG-C--AACA
* *
239616 AGTTCTTCTCATTATGAACTTCTTATCT-TGAAATGCTGATCCAACTCCTT
1 AGTTCTTCTCATTATGAACTTCTTCTCTGGGAAATGCTGATCCAACTCCTT
239666 ATGTAACATC
Statistics
Matches: 228, Mismatches: 35, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
71 18 0.08
72 158 0.69
73 2 0.01
74 1 0.00
77 1 0.00
78 1 0.00
79 19 0.08
80 28 0.12
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (72 bp):
AGTTCTTCTCATTATGAACTTCTTCTCTGGGAAATGCTGATCCAACTCCTTCTGTGATGGAATCG
AGCAACA
Found at i:241610 original size:30 final size:29
Alignment explanation
Indices: 241571--241629 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
241561 GAGAATTTAC
* *
241571 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
241600 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
241630 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:241894 original size:23 final size:23
Alignment explanation
Indices: 241860--241927 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
241850 CATCTTATAT
*
241860 GGCACTTCGGTGTATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * **
241883 GGCACTTAGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACGC
*
241906 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
241928 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:242365 original size:2 final size:2
Alignment explanation
Indices: 242358--242382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
242348 AAGGAAATGG
242358 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 T
242383 GTTTGGATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:245567 original size:20 final size:21
Alignment explanation
Indices: 245542--245585 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
245532 TAGGGGTTTT
*
245542 TTATTCTGAATTT-TTATTTA
1 TTATTCTGAATTTCATATTTA
245562 TTATTCTGAATTTCATATTTA
1 TTATTCTGAATTTCATATTTA
245583 TTA
1 TTA
245586 AAAGAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (21 bp):
TTATTCTGAATTTCATATTTA
Found at i:245740 original size:2 final size:2
Alignment explanation
Indices: 245659--245726 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
245649 TTACACACAC
245659 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
245701 AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
245727 ACTTTAATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249016 original size:2 final size:2
Alignment explanation
Indices: 249003--249035 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
248993 AAAATTTTAG
*
249003 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
249036 CTTTGAGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:249687 original size:20 final size:20
Alignment explanation
Indices: 249662--249703 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
249652 CTAAATATGC
*
249662 TGTACAAATGCATGTATGTA
1 TGTACAAATGCATGAATGTA
*
249682 TGTACATATGCATGAATGTA
1 TGTACAAATGCATGAATGTA
249702 TG
1 TG
249704 AAAACTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
TGTACAAATGCATGAATGTA
Found at i:251658 original size:30 final size:30
Alignment explanation
Indices: 251624--251689 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
251614 AGAACCGAAA
* *
251624 GAATCGGCTGAAAATTGAGAAAATCGGGGT
1 GAATCGGCTGAAAATCGACAAAATCGGGGT
**
251654 GAATCGGCTGAAAATCGACAAAATCGGTTT
1 GAATCGGCTGAAAATCGACAAAATCGGGGT
251684 GAATCG
1 GAATCG
251690 CCGGTTCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (30 bp):
GAATCGGCTGAAAATCGACAAAATCGGGGT
Found at i:254901 original size:23 final size:23
Alignment explanation
Indices: 254871--254916 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
254861 AAAATGTAAC
254871 TGCTACTGATGTTGATGATGATG
1 TGCTACTGATGTTGATGATGATG
254894 TGCTACTGATGTTGATGATGATG
1 TGCTACTGATGTTGATGATGATG
254917 ATGAGAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.30, T:0.39
Consensus pattern (23 bp):
TGCTACTGATGTTGATGATGATG
Found at i:255170 original size:14 final size:14
Alignment explanation
Indices: 255125--255170 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
255115 ATGTTCGTAT
255125 TATTTAATTGTTTG
1 TATTTAATTGTTTG
*
255139 AATTGT-ATTGTTTG
1 TATT-TAATTGTTTG
*
255153 TATTTAATTGTTTT
1 TATTTAATTGTTTG
255167 TATT
1 TATT
255171 ATTTAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.65
Consensus pattern (14 bp):
TATTTAATTGTTTG
Found at i:258551 original size:13 final size:13
Alignment explanation
Indices: 258533--258557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
258523 AATCAAAAAC
258533 ATCAAATTTAGAA
1 ATCAAATTTAGAA
258546 ATCAAATTTAGA
1 ATCAAATTTAGA
258558 TTTTTGAATT
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
ATCAAATTTAGAA
Found at i:259071 original size:44 final size:44
Alignment explanation
Indices: 258983--259079 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
258973 GGCCTTGTGC
* * *
258983 ATCGATGCACATTCAAGGCATGTATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATAGTGT
* *
259027 ATCGATGCACATTCAAAGGGATGCATCGATGCA-CTGTTA-AGTGT
1 ATCGATGCACATTC-AAGGCATGCATCGATGCACCT-TCATAGTGT
259071 ATCGATGCA
1 ATCGATGCA
259080 TGAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 29 0.63
45 17 0.37
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATAGTGT
Found at i:267846 original size:29 final size:30
Alignment explanation
Indices: 267778--267835 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
267768 AATTTAAGGA
*
267778 AAAATATTTTTGGACTTGAATTGAATTTAC
1 AAAATGTTTTTGGACTTGAATTGAATTTAC
267808 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
267836 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:269332 original size:19 final size:20
Alignment explanation
Indices: 269308--269355 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
269298 AATGATTTTC
*
269308 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
269327 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
269347 TTTTGAAAA
1 TTTTGAAAA
269356 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:270690 original size:29 final size:30
Alignment explanation
Indices: 270621--270679 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
270611 CAATTTAAGG
*
270621 CAAAATATTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
270651 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
270680 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:270995 original size:20 final size:22
Alignment explanation
Indices: 270957--270996 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
270947 TTTGAGTAGA
270957 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
270979 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
270997 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:271278 original size:32 final size:34
Alignment explanation
Indices: 271211--271280 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
271201 TTTTGTAAAG
*
271211 GGGAAAAGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCGTGTAAAAGCTA
* *
271245 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCGTGTAAAAGCTA
271277 GGGA
1 GGGA
271281 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (34 bp):
GGGAAAAGTTCTAGCTTAGCCCGTGTAAAAGCTA
Found at i:273330 original size:22 final size:25
Alignment explanation
Indices: 273275--273324 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
273265 ATTTTATACA
273275 TTTAAAATTTTGTAATATAATATTT
1 TTTAAAATTTTGTAATATAATATTT
**
273300 TTTTTAATTTT-TAATATAAT-TTT
1 TTTAAAATTTTGTAATATAATATTT
273323 TT
1 TT
273325 AGAATTCGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 9 0.39
25 9 0.39
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTAAAATTTTGTAATATAATATTT
Found at i:273751 original size:21 final size:22
Alignment explanation
Indices: 273727--273770 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
273717 TAATTTTGTA
273727 TTTAGATTATTCG-ATTTAAAT
1 TTTAGATTATTCGAATTTAAAT
**
273748 TTTATCTTATTCGTAATTTAAAT
1 TTTAGATTATTCG-AATTTAAAT
273771 AAGTAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTAGATTATTCGAATTTAAAT
Found at i:273971 original size:60 final size:60
Alignment explanation
Indices: 273899--274050 Score: 182
Period size: 60 Copynumber: 2.5 Consensus size: 60
273889 AAATTAGAAT
* * * *
273899 CCTCATTTTAAATTAGTCCTTAAATTTTTTAATATTCTACTTTCATC-CTCAAACTATGAC
1 CCTCATTCTAAATTAGTCCTTAAATTTTTAAATATTCCAATTTCATCTCT-AAACTATGAC
* * **
273959 TCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTCCAATTTTGTCTCTAAACTATGAC
1 CCTCATTCTAAATTAGTCCTTAAATTTTTAAATATTCCAATTTCATCTCTAAACTATGAC
* *
274019 CCTC-TCTCTAAATTAGCCCCTAAATTTTTAAA
1 CCTCAT-TCTAAATTAGTCCTTAAATTTTTAAA
274051 AATAGAGTCA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.01
60 75 0.96
61 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (60 bp):
CCTCATTCTAAATTAGTCCTTAAATTTTTAAATATTCCAATTTCATCTCTAAACTATGAC
Found at i:276378 original size:31 final size:31
Alignment explanation
Indices: 276319--276378 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
276309 TGGTAAAGGA
*
276319 TTTATTTGCAGATTTATTAATTTGTAATTAT
1 TTTATTTGAAGATTTATTAATTTGTAATTAT
* *
276350 TTTATTTGAATATTATATT-ATTTTTAATT
1 TTTATTTGAAGATT-TATTAATTTGTAATT
276379 CATTGAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.62
Consensus pattern (31 bp):
TTTATTTGAAGATTTATTAATTTGTAATTAT
Found at i:281567 original size:18 final size:19
Alignment explanation
Indices: 281538--281579 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
281528 ATCATGATCG
*
281538 AAATTCTAAAAATTTAAAA
1 AAATTCTAAAAACTTAAAA
281557 AAATT-TAAAAACTTAAAA
1 AAATTCTAAAAACTTAAAA
*
281575 TAATT
1 AAATT
281580 AAATTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTCTAAAAACTTAAAA
Found at i:295994 original size:60 final size:61
Alignment explanation
Indices: 295920--296045 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
295910 ATTGTCTACC
* * *
295920 ACTATAGGATGTTACTTTGTTGAG-TCTCTCAACTATTTAAAATTATAAAATAATCACTTG
1 ACTATAGGATGTTACTTTGTTGAGTTCCCTCAACTATTAAAAATTACAAAATAATCACTTG
** *
295980 ACTATA-GAGTGTTACTTTGTTGAGTTCCCTCAACTATTAAAAATTACAAAATGGTCATTTG
1 ACTATAGGA-TGTTACTTTGTTGAGTTCCCTCAACTATTAAAAATTACAAAATAATCACTTG
296041 ACTAT
1 ACTAT
296046 TCATATGTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.03
60 21 0.36
61 35 0.60
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (61 bp):
ACTATAGGATGTTACTTTGTTGAGTTCCCTCAACTATTAAAAATTACAAAATAATCACTTG
Found at i:296370 original size:60 final size:60
Alignment explanation
Indices: 296243--296370 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
296233 ATAGTTGGAT
* * *
296243 GACCATTTTGTAACTTTTAAAAGTCGAAGGATTCAACAAAGAAACACACTGTAGTCGATG
1 GACCATTTTGTAACTTTTAAAAGTCGAAGGACTCAACAAAGAAACACACTATAGTCGAGG
* * * * * ** *
296303 GATCATTTTGTAACTTTTAATAGTTGGAGGACTCAACAAAGTAACATTCTATAGTTGAGG
1 GACCATTTTGTAACTTTTAAAAGTCGAAGGACTCAACAAAGAAACACACTATAGTCGAGG
*
296363 GGCCATTT
1 GACCATTT
296371 GTTTACTTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAAAAGTCGAAGGACTCAACAAAGAAACACACTATAGTCGAGG
Found at i:297647 original size:20 final size:20
Alignment explanation
Indices: 297624--297662 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
297614 TGAAACATCT
* *
297624 TAGAACGTTTTAGAATGTTC
1 TAGAACATTTTAAAATGTTC
297644 TAGAACATTTTAAAATGTT
1 TAGAACATTTTAAAATGTT
297663 TTAAAATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (20 bp):
TAGAACATTTTAAAATGTTC
Found at i:299017 original size:126 final size:127
Alignment explanation
Indices: 298848--299101 Score: 442
Period size: 126 Copynumber: 2.0 Consensus size: 127
298838 TGAGAAGGAA
298848 TTTGACTTGTCATCAATCTAATTAAGGAATATGGAGTGTTAGAATTAGATTTAAAACATGTTAAA
1 TTTGACTTGTCATCAATCTAATTAAGGAATATGGAGTGTTAGAATTAGATTTAAAACATGTTAAA
* * *
298913 AATCTGGTATGATTCTTGAAGTTAATAAAGAGGAGAGGA-ATTAA-GGTTAAAGACAAGATAAT
66 AATCTGGTATGATTCTTGAAGTTAATAAAG-GGAAAAGATAATAAGGGTT-AAGACAAGATAAT
298975 TTTGACTTGTCATCAATCTAA-TAAGGAATATGGAGTGTTAGAATTAGATTTAAAACATGTTAAA
1 TTTGACTTGTCATCAATCTAATTAAGGAATATGGAGTGTTAGAATTAGATTTAAAACATGTTAAA
299039 AATCTGGTATGATTCTTGAAGTTAATAAAGGGAAAAGATAATAAGGGTTAAGACAAGATAAT
66 AATCTGGTATGATTCTTGAAGTTAATAAAGGGAAAAGATAATAAGGGTTAAGACAAGATAAT
299101 T
1 T
299102 GATTATAAAT
Statistics
Matches: 122, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
125 6 0.05
126 91 0.75
127 25 0.20
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.32
Consensus pattern (127 bp):
TTTGACTTGTCATCAATCTAATTAAGGAATATGGAGTGTTAGAATTAGATTTAAAACATGTTAAA
AATCTGGTATGATTCTTGAAGTTAATAAAGGGAAAAGATAATAAGGGTTAAGACAAGATAAT
Found at i:299357 original size:64 final size:64
Alignment explanation
Indices: 299288--299444 Score: 192
Period size: 64 Copynumber: 2.5 Consensus size: 64
299278 TTGAAGGTGT
** ***
299288 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCAGTAATAAT-AAAACATCGAATGCAATTCATG
299351 C
64 C
* * *
299352 ATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCAATTCATGC
* *
299416 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
299445 ACTTTCATTG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 77 0.95
65 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCAATTCATGC
Found at i:300134 original size:31 final size:31
Alignment explanation
Indices: 300096--300178 Score: 148
Period size: 31 Copynumber: 2.7 Consensus size: 31
300086 AGGGTCGAGG
300096 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGAACT
300127 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGAACT
* *
300158 ATTTACCTAGGTTCTTCGGGA
1 GTTTACCTATGTTCTTCGGGA
300179 TCTATGGACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGAACT
Found at i:303543 original size:3 final size:3
Alignment explanation
Indices: 303529--303563 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
303519 AGAGATATTC
*
303529 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
303564 ATGTACGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:305001 original size:31 final size:31
Alignment explanation
Indices: 304912--305005 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
304902 AGGGTCGAGG
*
304912 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
304943 GTTTAACTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
304974 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
305005 G
1 G
305006 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:307972 original size:15 final size:15
Alignment explanation
Indices: 307952--307980 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
307942 CCCAGGGTAT
307952 TTTAGTGAATGCGTA
1 TTTAGTGAATGCGTA
307967 TTTAGTGAATGCGT
1 TTTAGTGAATGCGT
307981 GTAGTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (15 bp):
TTTAGTGAATGCGTA
Found at i:309609 original size:54 final size:55
Alignment explanation
Indices: 309373--309807 Score: 304
Period size: 54 Copynumber: 8.0 Consensus size: 55
309363 AACCATTCCT
* ** *
309373 GATTTTTGGCTTATGTTATTCGGGATTTAGGTTAGAGTGTCAAATA-ATAGTATGT
1 GATTTTTGGCGTATGTTATTC-GGATTTAGGTGCGAGTGTCAAATAGATAGTATGA
* ** * * * * * * *
309428 GGTTTTTGGAATGTGTTATTTGGATTTAGCTGTGGGTGTCAAATAG-TAATATGT
1 GATTTTTGGCGTATGTTATTCGGATTTAGGTGCGAGTGTCAAATAGATAGTATGA
* * *
309482 GATTTTTGAC-TATGTTATTCGGATTTAGGT--GAGTGACACGTAGTAGTAGTAGTATGA
1 GATTTTTGGCGTATGTTATTCGGATTTAGGTGCGAGTGTCA---AATAG-A-TAGTATGA
* *
309539 GATCTTTGGTGTATGTTATTCGGATTTAGGTGCGAGTGTCAAATAGAT-GTATGA
1 GATTTTTGGCGTATGTTATTCGGATTTAGGTGCGAGTGTCAAATAGATAGTATGA
* *
309593 GATTTTTGGCGTATGTTACTCGTATTTAGGTGCGAGTGTCAAATAG-TAGTATGA
1 GATTTTTGGCGTATGTTATTCGGATTTAGGTGCGAGTGTCAAATAGATAGTATGA
* ** * * * *
309647 GTTTTTTGTTGTATGTTATTTGGATTTAGGTGCGAGTGTCCAATAG-TAATA-CA
1 GATTTTTGGCGTATGTTATTCGGATTTAGGTGCGAGTGTCAAATAGATAGTATGA
* * * * * * *
309700 TGATTTTTCGCGTATGCTGTTCAGATTTAGATAC-AGGTTTCAAATAG-TAGTAT-A
1 -GATTTTTGGCGTATGTTATTCGGATTTAGGTGCGA-GTGTCAAATAGATAGTATGA
* * * * * * *
309754 TGATTTTTAGC-TAGTCTTACTCTGATTTAGATGTGAGTGACAAATAG-TAGTATG
1 -GATTTTTGGCGTA-TGTTATTCGGATTTAGGTGCGAGTGTCAAATAGATAGTATG
309808 TTTAATTTTA
Statistics
Matches: 301, Mismatches: 62, Indels: 34
0.76 0.16 0.09
Matches are distributed among these distances:
51 6 0.02
53 22 0.07
54 210 0.70
55 18 0.06
56 1 0.00
57 17 0.06
58 20 0.07
60 7 0.02
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (55 bp):
GATTTTTGGCGTATGTTATTCGGATTTAGGTGCGAGTGTCAAATAGATAGTATGA
Found at i:309705 original size:108 final size:106
Alignment explanation
Indices: 309372--309761 Score: 347
Period size: 108 Copynumber: 3.6 Consensus size: 106
309362 TAACCATTCC
* * * *
309372 TGATTTTTGGCTTATGTTATTCGGGATTTAGGTTAGAGTGTCAAATAATAGTATGTGGTTTTTGG
1 TGATTTTTGGCGTATGTTATTC-GGATTTAGG-T-GAGTGTCAAATAGTAGTATGAGATTTTTGG
** * * * * *
309437 AATGTGTTATTTGGATTTAGCTGTGGGTGTCAAATAGTAATATG
63 TGTATGTTATTTGGATTTAGGTGCGAGTGTCAAATAGTAATATA
* * *
309481 TGATTTTTGAC-TATGTTATTCGGATTTAGGTGAGTGACACGTAGTAGTAGTAGTATGAGATCTT
1 TGATTTTTGGCGTATGTTATTCGGATTTAGGTGAGTGTCA---A--A-TAGTAGTATGAGATTTT
* *
309545 TGGTGTATGTTATTCGGATTTAGGTGCGAGTGTCAAATAG--ATGTA
60 TGGTGTATGTTATTTGGATTTAGGTGCGAGTGTCAAATAGTAATATA
* * *
309590 TGAGATTTTTGGCGTATGTTACTCGTATTTAGGTGCGAGTGTCAAATAGTAGTATGAGTTTTTTG
1 T--GATTTTTGGCGTATGTTATTCGGATTTAGGT--GAGTGTCAAATAGTAGTATGAGATTTTTG
* * *
309655 TTGTATGTTATTTGGATTTAGGTGCGAGTGTCCAATAGTAATACA
62 GTGTATGTTATTTGGATTTAGGTGCGAGTGTCAAATAGTAATATA
* * * * * * *
309700 TGATTTTTCGCGTATGCTGTTCAGATTTAGATACAGGTTTCAAATAGTAGTAT-ATGATTTTT
1 TGATTTTTGGCGTATGTTATTCGGATTTAGGT-GA-GTGTCAAATAGTAGTATGA-GATTTTT
309762 AGCTAGTCTT
Statistics
Matches: 229, Mismatches: 37, Indels: 31
0.77 0.12 0.10
Matches are distributed among these distances:
105 7 0.03
106 1 0.00
107 11 0.05
108 109 0.48
109 15 0.07
110 5 0.02
111 56 0.24
112 18 0.08
114 7 0.03
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.42
Consensus pattern (106 bp):
TGATTTTTGGCGTATGTTATTCGGATTTAGGTGAGTGTCAAATAGTAGTATGAGATTTTTGGTGT
ATGTTATTTGGATTTAGGTGCGAGTGTCAAATAGTAATATA
Found at i:312875 original size:32 final size:32
Alignment explanation
Indices: 312829--312919 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
312819 TAAATTTAAT
* *
312829 TAAACAAGCGGATTACCGAATGTAAATGAACA
1 TAAACAAACAGATTACCGAATGTAAATGAACA
** *
312861 TAAATGAGCAGATTACCGAATGTAAATGAACA
1 TAAACAAACAGATTACCGAATGTAAATGAACA
*
312893 TAAACAAACAGATTACCGAACGTAAAT
1 TAAACAAACAGATTACCGAATGTAAAT
312920 AAATGAAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.20
Consensus pattern (32 bp):
TAAACAAACAGATTACCGAATGTAAATGAACA
Found at i:313689 original size:21 final size:21
Alignment explanation
Indices: 313665--313707 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
313655 ATAGTTCCTA
313665 TGGGATGCCGTAGAAAGTATT
1 TGGGATGCCGTAGAAAGTATT
* **
313686 TGGGGTGTTGTAGAAAGTATT
1 TGGGATGCCGTAGAAAGTATT
313707 T
1 T
313708 TTTCCAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.35, T:0.35
Consensus pattern (21 bp):
TGGGATGCCGTAGAAAGTATT
Found at i:316560 original size:11 final size:11
Alignment explanation
Indices: 316536--316577 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
316526 GCACTAAAAC
* *
316536 AACACTAAACG
1 AACATTAAATG
316547 AACATTAAATG
1 AACATTAAATG
316558 AACATTAAATG
1 AACATTAAATG
*
316569 GACATTAAA
1 AACATTAAA
316578 CGAATATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (11 bp):
AACATTAAATG
Found at i:319290 original size:30 final size:30
Alignment explanation
Indices: 319276--319484 Score: 343
Period size: 30 Copynumber: 6.9 Consensus size: 30
319266 TAAGTAATCA
319276 TCCATATGTCCCG-AAACATAGGTAAACAG
1 TCCATATGTCCCGAAAACATAGGTAAACAG
319305 TCCATATGTCCC-AAAGACATAGGTAAACAG
1 TCCATATGTCCCGAAA-ACATAGGTAAACAG
319335 TCCATATGTCCCGAAAACATAGGTAAACAG
1 TCCATATGTCCCGAAAACATAGGTAAACAG
*
319365 TCCATATGTCCC-AAAACAAAGGTAAACAG
1 TCCATATGTCCCGAAAACATAGGTAAACAG
*
319394 TCCATATGTCCCAAAGAACATAGGTTAAACAG
1 TCCATATGTCCCGAA-AACATAGG-TAAACAG
319426 TCCATATGTCCCGAAAACATAGGTAAACAG
1 TCCATATGTCCCGAAAACATAGGTAAACAG
319456 TCCATATGTCCCGAAGAACATAGGTAAAC
1 TCCATATGTCCCGAA-AACATAGGTAAAC
319485 CTCGACCCTT
Statistics
Matches: 170, Mismatches: 3, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
29 42 0.25
30 76 0.45
31 31 0.18
32 21 0.12
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (30 bp):
TCCATATGTCCCGAAAACATAGGTAAACAG
Found at i:319462 original size:91 final size:89
Alignment explanation
Indices: 319276--319484 Score: 364
Period size: 91 Copynumber: 2.3 Consensus size: 89
319266 TAAGTAATCA
*
319276 TCCATATGTCCCGAAACATAGGTAAACAGTCCATATGTCCCAAAGACATAGGTAAACAGTCCATA
1 TCCATATGTCCCAAAACATAGGTAAACAGTCCATATGTCCCAAAGACATAGGTAAACAGTCCATA
319341 TGTCCCGAAAACATAGGTAAACAG
66 TGTCCCGAAAACATAGGTAAACAG
*
319365 TCCATATGTCCCAAAACAAAGGTAAACAGTCCATATGTCCCAAAGAACATAGGTTAAACAGTCCA
1 TCCATATGTCCCAAAACATAGGTAAACAGTCCATATGTCCCAAAG-ACATAGG-TAAACAGTCCA
319430 TATGTCCCGAAAACATAGGTAAACAG
64 TATGTCCCGAAAACATAGGTAAACAG
319456 TCCATATGTCCCGAAGAACATAGGTAAAC
1 TCCATATGTCCC-AA-AACATAGGTAAAC
319485 CTCGACCCTT
Statistics
Matches: 113, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
89 43 0.38
90 7 0.06
91 49 0.43
92 2 0.02
93 12 0.11
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (89 bp):
TCCATATGTCCCAAAACATAGGTAAACAGTCCATATGTCCCAAAGACATAGGTAAACAGTCCATA
TGTCCCGAAAACATAGGTAAACAG
Found at i:323403 original size:31 final size:31
Alignment explanation
Indices: 323365--323520 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
323355 CCCGAAGGAC
* * *
323365 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
323396 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
323427 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
323458 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
323489 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
323520 C
1 C
323521 CCTCGACCCT
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 120 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:326248 original size:18 final size:20
Alignment explanation
Indices: 326217--326253 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
326207 AAAACATGTA
326217 AAATCATAAAACAA-TTTAT
1 AAATCATAAAACAAGTTTAT
*
326236 AAAT-ATAATACAAGTTTA
1 AAATCATAAAACAAGTTTA
326254 GAAAATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATCATAAAACAAGTTTAT
Found at i:333471 original size:57 final size:57
Alignment explanation
Indices: 333351--333478 Score: 138
Period size: 57 Copynumber: 2.2 Consensus size: 57
333341 TAAATAGTCA
* * *
333351 AATGATTAATTTATAACTTTTAATAGTCAAGTGATTCAACAAAGTAACTCTATAATTG
1 AATGA-TAATTTGTAACTTTTAATAGTCAAGTGATTCAACAAAATAACTCTATAATCG
*
333409 AATGATAATTTGTAACTTTTAATAGTCGAA-TGACTT-AATAAAATAA-TACTTATAATCG
1 AATGATAATTTGTAACTTTTAATAGTC-AAGTGA-TTCAACAAAATAACT-C-TATAATCG
*
333467 -ATGATCATTTGT
1 AATGATAATTTGT
333479 GTATTTAACC
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
56 1 0.02
57 44 0.72
58 16 0.26
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (57 bp):
AATGATAATTTGTAACTTTTAATAGTCAAGTGATTCAACAAAATAACTCTATAATCG
Found at i:334427 original size:42 final size:42
Alignment explanation
Indices: 334381--334481 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
334371 TATATATATA
334381 TATTATTTTAATAATTTAATATTAACATC-CTTAAAAATAATT
1 TATTA-TTTAATAATTTAATATTAACATCACTTAAAAATAATT
* *
334423 TATTACTTAATAATTTAATATTAACATCATTTAAAAATAATT
1 TATTATTTAATAATTTAATATTAACATCACTTAAAAATAATT
334465 TATTATTTAATAATTTA
1 TATTATTTAATAATTTA
334482 TTACCTAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 22 0.40
42 33 0.60
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (42 bp):
TATTATTTAATAATTTAATATTAACATCACTTAAAAATAATT
Found at i:334436 original size:15 final size:14
Alignment explanation
Indices: 334416--334519 Score: 71
Period size: 15 Copynumber: 7.6 Consensus size: 14
334406 CATCCTTAAA
334416 AATAATTTATTACTT
1 AATAATTTATTA-TT
*
334431 AATAATTTAATATT
1 AATAATTTATTATT
* *
334445 AACATCATTTA--A-A
1 -A-ATAATTTATTATT
334458 AATAATTTATTATTT
1 AATAATTTATTA-TT
*
334473 AATAATTTATTACCT
1 AATAATTTATTA-TT
334488 AATAATTTATT-TT
1 AATAATTTATTATT
334501 -AT-ATTT-TTATT
1 AATAATTTATTATT
334512 -ATAATTTA
1 AATAATTTA
334520 AGTGATATAT
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
10 2 0.03
11 15 0.21
12 7 0.10
13 2 0.03
14 3 0.04
15 36 0.50
16 7 0.10
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (14 bp):
AATAATTTATTATT
Found at i:342943 original size:25 final size:26
Alignment explanation
Indices: 342856--342962 Score: 135
Period size: 26 Copynumber: 4.1 Consensus size: 26
342846 TACTTGTTTG
*
342856 TTAATAGTTATAAAATGATTTTATTA
1 TTAAAAGTTATAAAATGATTTTATTA
*
342882 TTAAAATTTATAAAATGATTTTATTA
1 TTAAAAGTTATAAAATGATTTTATTA
* *
342908 TTAAAATTTATAAAATGATTTT-TAA
1 TTAAAAGTTATAAAATGATTTTATTA
* * *
342933 GTAAAAGTTATAGAATGATATTTTTTA
1 TTAAAAGTTATAAAATGAT-TTTATTA
342960 TTA
1 TTA
342963 TTAAAAATTG
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
25 18 0.25
26 49 0.69
27 4 0.06
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (26 bp):
TTAAAAGTTATAAAATGATTTTATTA
Found at i:348173 original size:26 final size:26
Alignment explanation
Indices: 348144--348197 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
348134 TATTATTTAC
348144 ATGTGAACCTACATAATAACATCATA
1 ATGTGAACCTACATAATAACATCATA
*
348170 ATGTGAGCCTACATAATAACATCATA
1 ATGTGAACCTACATAATAACATCATA
348196 AT
1 AT
348198 AATCAAACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (26 bp):
ATGTGAACCTACATAATAACATCATA
Found at i:348969 original size:3 final size:3
Alignment explanation
Indices: 348961--349011 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
348951 TTATATATAT
348961 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
349006 ATA TTA
1 TTA TTA
349012 CATTTTACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:349514 original size:12 final size:12
Alignment explanation
Indices: 349497--349526 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
349487 CAGGGAGAGA
*
349497 AAAAAAAACCAG
1 AAAAAAAACAAG
349509 AAAAAAAACAAG
1 AAAAAAAACAAG
349521 AAAAAA
1 AAAAAA
349527 GAGAACTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAG
Found at i:355328 original size:26 final size:25
Alignment explanation
Indices: 355299--355376 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
355289 AATTTTTGAC
355299 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
355325 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
355345 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
355371 ATTCTT
1 ATTCTT
355377 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:355337 original size:20 final size:20
Alignment explanation
Indices: 355314--355388 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
355304 ATCTCTTTGA
355314 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
355334 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
355360 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
355379 CACCTTGAAA
1 GACCTTGAAA
355389 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:356010 original size:18 final size:17
Alignment explanation
Indices: 355966--356012 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
355956 GAGTGCAAAG
*
355966 ATCAAACCAAAGAAAAA
1 ATCAAAGCAAAGAAAAA
355983 A-CAAAGAGCAAAGAGAAAA
1 ATC-AA-AGCAAAGA-AAAA
356002 ATCAAAGCAAA
1 ATCAAAGCAAA
356013 AATCAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 13 0.52
19 7 0.28
20 1 0.04
ACGTcount: A:0.68, C:0.15, G:0.13, T:0.04
Consensus pattern (17 bp):
ATCAAAGCAAAGAAAAA
Found at i:356012 original size:25 final size:23
Alignment explanation
Indices: 355984--356040 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
355974 AAAGAAAAAA
*
355984 CAAAGAGCAAAGAGAAAAATCAAAG
1 CAAAAAGCAAAGA-AAAAA-CAAAG
*
356009 CAAAAATCAAAGAAAAAACAAAG
1 CAAAAAGCAAAGAAAAAACAAAG
356032 AACAAAAAG
1 --CAAAAAG
356041 AGGACAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 17 0.63
ACGTcount: A:0.70, C:0.12, G:0.14, T:0.04
Consensus pattern (23 bp):
CAAAAAGCAAAGAAAAAACAAAG
Found at i:356015 original size:12 final size:11
Alignment explanation
Indices: 355996--356033 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
355986 AAGAGCAAAG
355996 AGAAAAATCAA
1 AGAAAAATCAA
356007 AGCAAAAATCAA
1 AG-AAAAATCAA
*
356019 AGAAAAAACAA
1 AGAAAAATCAA
356030 AGAA
1 AGAA
356034 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:356037 original size:18 final size:18
Alignment explanation
Indices: 355973--356037 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 18
355963 AAGATCAAAC
*
355973 CAAAGAAAAAACAAAGAG
1 CAAAGAAAAAACAAAGAA
355991 CAAAGAGAAAAATCAAAGCAAAAA
1 CAAAGA-AAAAA-CAAAG----AA
356015 TCAAAGAAAAAACAAAGAA
1 -CAAAGAAAAAACAAAGAA
356034 CAAA
1 CAAA
356038 AAGAGGACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
18 10 0.26
19 7 0.18
20 5 0.13
23 5 0.13
24 6 0.15
25 6 0.15
ACGTcount: A:0.72, C:0.12, G:0.12, T:0.03
Consensus pattern (18 bp):
CAAAGAAAAAACAAAGAA
Found at i:356038 original size:12 final size:11
Alignment explanation
Indices: 355973--356038 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
355963 AAGATCAAAC
355973 CAAAGAAAAAA
1 CAAAGAAAAAA
**
355984 CAAAG-AGCAA
1 CAAAGAAAAAA
* *
355994 -AGAGAAAAAT
1 CAAAGAAAAAA
*
356004 CAAAGCAAAAAT
1 CAAAG-AAAAAA
356016 CAAAGAAAAAA
1 CAAAGAAAAAA
356027 CAAAGAACAAAA
1 CAAAGAA-AAAA
356039 AGAGGACAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
9 3 0.07
10 5 0.12
11 20 0.47
12 15 0.35
ACGTcount: A:0.73, C:0.12, G:0.12, T:0.03
Consensus pattern (11 bp):
CAAAGAAAAAA
Found at i:356910 original size:23 final size:24
Alignment explanation
Indices: 356884--356928 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
356874 TGAAAGGAGC
*
356884 AACATTTTT-AAAACTTTTGATTA
1 AACATTTTTCAAAACTATTGATTA
356907 AACATTTTTCAAAACTATTGAT
1 AACATTTTTCAAAACTATTGAT
356929 ATTTTCAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (24 bp):
AACATTTTTCAAAACTATTGATTA
Found at i:357214 original size:4 final size:4
Alignment explanation
Indices: 357205--357254 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
357195 GATCGAGAAA
*
357205 ACAT ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT A-AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
357250 ACAT A
1 ACAT A
357255 AAATTTGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 36 0.88
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:357840 original size:105 final size:102
Alignment explanation
Indices: 357713--357951 Score: 272
Period size: 105 Copynumber: 2.3 Consensus size: 102
357703 TGAGAATTTT
* * *
357713 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATAC-AAATTTTGAATCTGATTCAC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGAT-CTAAATTTCGAATCTGATTCAC
*
357777 -TAAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
65 AT-AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
357818 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCTAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCTAAATTTCGAATCTGATTCACA
* * *
357883 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
357920 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
357952 TCTAAAAACA
Statistics
Matches: 117, Mismatches: 12, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 7 0.06
104 5 0.04
105 76 0.65
106 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCTAAATTTCGAATCTGATTCACA
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:357925 original size:36 final size:36
Alignment explanation
Indices: 357897--358016 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
357887 ACAAAGTTGA
**
357897 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
357933 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * * *
357969 TCTCATTTGAGACTATATCT-T-AAAGCAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
358003 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
358017 TCATTTTCTC
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
34 23 0.32
35 8 0.11
36 40 0.56
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:358003 original size:34 final size:36
Alignment explanation
Indices: 357915--358016 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
357905 GAGATCGTTT
* *
357915 TCTC-AAAAACAAACTTTGTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
** *
357950 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
*
357986 TCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
358017 TCATTTTCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.40
35 5 0.09
36 29 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
Found at i:358310 original size:29 final size:29
Alignment explanation
Indices: 358268--358513 Score: 147
Period size: 29 Copynumber: 8.5 Consensus size: 29
358258 TTTCTCTTGA
358268 AAAAATCTTTGAGTTTGTTCATTTTGAAT
1 AAAAATCTTTGAGTTTGTTCATTTTGAAT
* *
358297 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCATTTTGAAT
*
358326 AAATATCTTTGAG-TTGTTTC-TTTTGAA-
1 AAAAATCTTTGAGTTTG-TTCATTTTGAAT
* * *
358353 AAAAATCTTTGAGTCTATTTATTTTGAA-
1 AAAAATCTTTGAGTTTGTTCATTTTGAAT
* ** **
358381 ACAAAGT-TTTGTCTCTCTTGAGACAGTTTCTCTTG-A-
1 A-AAAATCTTTG--AGT-TTG-TTCA---T-T-TTGAAT
* *
358417 AAAAATCTTTGAGTTTGTTCCTTTGGAAT
1 AAAAATCTTTGAGTTTGTTCATTTTGAAT
* * *
358446 AAAAATCTTGGAGTTTGTTCCTTTTAAAT
1 AAAAATCTTTGAGTTTGTTCATTTTGAAT
*
358475 AAATATCTTTGAG-TTGTTTC-TTTTG---
1 AAAAATCTTTGAGTTTG-TTCATTTTGAAT
358500 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
358514 CTATTTATTT
Statistics
Matches: 169, Mismatches: 30, Indels: 39
0.71 0.13 0.16
Matches are distributed among these distances:
25 12 0.07
27 16 0.09
28 32 0.19
29 86 0.51
30 1 0.01
31 1 0.01
32 2 0.01
33 3 0.02
34 1 0.01
35 5 0.03
36 7 0.04
37 3 0.02
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCATTTTGAAT
Found at i:358351 original size:28 final size:26
Alignment explanation
Indices: 358257--358381 Score: 117
Period size: 28 Copynumber: 4.5 Consensus size: 26
358247 TCTTGAGACA
*
358257 GTTTCTCTTGAAAAAATCTTTGAGTT
1 GTTTCTTTTGAAAAAATCTTTGAGTT
*
358283 -TGTTCATTTTGAATAAAAATCTTGGAGTTT
1 GT-TTC-TTTTG-A-AAAAATCTTTGAG-TT
*
358313 GTTCCTTTTGAATAAATATCTTTGAGTT
1 GTTTCTTTTGAA-AAA-ATCTTTGAGTT
358341 GTTTCTTTTGAAAAAAATCTTTGAGTCT
1 GTTTCTTTTG-AAAAAATCTTTGAGT-T
* *
358369 ATTTATTTTGAAA
1 GTTTCTTTTGAAA
358382 CAAAGTTTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
25 1 0.01
26 3 0.04
27 18 0.22
28 28 0.34
29 27 0.33
30 4 0.05
31 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (26 bp):
GTTTCTTTTGAAAAAATCTTTGAGTT
Done.