Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007994.1 Hibiscus syriacus cultivar Beakdansim tig00110444_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: 788627
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 4
Found at i:267152 original size:20 final size:20
Alignment explanation
Indices: 267118--267157 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
267108 TGTAAGTACT
* *
267118 GATACTGCTGCAGTACTATC
1 GATACTGCTACAGTAATATC
*
267138 GATACTGCTATAGTAATATC
1 GATACTGCTACAGTAATATC
267158 AAGCCCAACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (20 bp):
GATACTGCTACAGTAATATC
Found at i:269375 original size:21 final size:21
Alignment explanation
Indices: 269351--269390 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
269341 TTTTCAAAGG
269351 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
269372 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
269391 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:269487 original size:64 final size:64
Alignment explanation
Indices: 269371--269496 Score: 150
Period size: 64 Copynumber: 2.0 Consensus size: 64
269361 TGCATCAATA
*
269371 CCATGCATCGATGCATCAATGAATAAATTGAAACATCAAATGCATTCTATGCA-CTGATGCACGC
1 CCATGCATCGATGCATC-ATGAATAAATTAAAACATCAAATGCATTCTATGCATC-GATGCACGC
269435 T
64 T
* * **
269436 CCATGCATCGATGCACTC-TGATTTAATTAAAACATTTAATGCATT-TGATGCATCGATGCAC
1 CCATGCATCGATGCA-TCATGAATAAATTAAAACATCAAATGCATTCT-ATGCATCGATGCAC
269497 TAGCCATGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
63 1 0.02
64 34 0.64
65 16 0.30
66 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (64 bp):
CCATGCATCGATGCATCATGAATAAATTAAAACATCAAATGCATTCTATGCATCGATGCACGCT
Found at i:269504 original size:64 final size:64
Alignment explanation
Indices: 269371--269514 Score: 141
Period size: 64 Copynumber: 2.2 Consensus size: 64
269361 TGCATCAATA
* **
269371 CCATGCATCGATGCATCAATGAATAAATTGAAACATCAAATGCATTCTATGCACTGATGCACGCT
1 CCATGCATCGATGCATC-ATGAATAAATTAAAACATCAAATGCATTCTATGCACTGATGCACGAG
* * ** *
269436 CCATGCATCGATGCACTC-TGATTTAATTAAAACATTTAATGCATT-TGATGCA-TCGATGCACT
1 CCATGCATCGATGCA-TCATGAATAAATTAAAACATCAAATGCATTCT-ATGCACT-GATGCACG
269498 AG
63 AG
* *
269500 CCATGAATAGATGCA
1 CCATGCATCGATGCA
269515 GTCGGGCTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
63 2 0.03
64 47 0.71
65 15 0.23
66 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (64 bp):
CCATGCATCGATGCATCATGAATAAATTAAAACATCAAATGCATTCTATGCACTGATGCACGAG
Found at i:269560 original size:17 final size:19
Alignment explanation
Indices: 269538--269580 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
269528 GAAACATAGA
*
269538 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
269555 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
269574 ATGCACT
1 ATGCACT
269581 AAGTTTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:274969 original size:64 final size:63
Alignment explanation
Indices: 274833--274998 Score: 174
Period size: 64 Copynumber: 2.6 Consensus size: 63
274823 CAATGAATAA
* * * * *
274833 ATTGAAACATCGAATGCATTTTATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTT
1 ATTGAAACATCGAATGCATTTGATGCATCGATGCACTCGCCATACATCGATGCACTCGGATTT
* * *
274896 AATTAAAACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATACATTGATGCACTCGGGCTA
1 -ATTGAAACATCGAATGCATTTGATGCATCGATGCACTC-GCCATACATCGATGCACTC-GGAT-
274960 TT
62 TT
** **
274962 -TTGAAACATCGAATGCCCTTGATTAATCGATGCACTC
1 ATTGAAACATCGAATGCATTTGATGCATCGATGCACTC
274999 TTAGTGCACC
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 1 0.01
64 79 0.93
65 3 0.04
66 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (63 bp):
ATTGAAACATCGAATGCATTTGATGCATCGATGCACTCGCCATACATCGATGCACTCGGATTT
Found at i:277094 original size:20 final size:21
Alignment explanation
Indices: 277069--277117 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
277059 AGTATTGTAT
277069 TGTATGAACT-GTACCGATAC
1 TGTATGAACTAGTACCGATAC
* *
277089 TGTATG-AGTAGTATCGATAC
1 TGTATGAACTAGTACCGATAC
*
277109 TGTGTGAAC
1 TGTATGAAC
277118 ATTAATGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 20 0.87
21 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (21 bp):
TGTATGAACTAGTACCGATAC
Found at i:277188 original size:20 final size:20
Alignment explanation
Indices: 277163--277202 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
277153 TGTAAGTACT
*
277163 GATACTGCTACAGTACTATC
1 GATACTGCTACAGTAATATC
277183 GATACTGCTACAGTAATATC
1 GATACTGCTACAGTAATATC
277203 AATCCCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (20 bp):
GATACTGCTACAGTAATATC
Found at i:277459 original size:20 final size:20
Alignment explanation
Indices: 277434--277473 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
277424 AACACAAGAG
277434 AAGAGTTTTTCAATCTTATT
1 AAGAGTTTTTCAATCTTATT
277454 AAGAGTTTTTCAATCTTATT
1 AAGAGTTTTTCAATCTTATT
277474 TCATCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
AAGAGTTTTTCAATCTTATT
Found at i:281611 original size:76 final size:76
Alignment explanation
Indices: 281531--281708 Score: 250
Period size: 76 Copynumber: 2.3 Consensus size: 76
281521 GGTACCCCCT
* * **
281531 TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-CAAAACTGTTTAGGGGGGAAT
1 TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTAGGGGGG-AT
*
281595 TGATTCCTCCTA
65 CGATTCCTCCTA
* *
281607 TGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCCAAAACCATTTAGGGGGGATC
1 TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTAGGGGGGATC
*
281672 GGTTCCTCCTA
66 GATTCCTCCTA
* *
281683 TGGGGGGAATCGGTTCTCTCTGAGCA
1 TGGGGGGAATCGGTTCCCTCCGAGCA
281709 ATCTGTAATT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 75 0.82
77 16 0.18
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.25
Consensus pattern (76 bp):
TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTAGGGGGGATC
GATTCCTCCTA
Found at i:283570 original size:15 final size:15
Alignment explanation
Indices: 283550--283585 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
283540 ATCAAGATTT
283550 GGAATAGGATTTTGG
1 GGAATAGGATTTTGG
283565 GGAATAGGATTTTGG
1 GGAATAGGATTTTGG
283580 GGAATA
1 GGAATA
283586 AGAGGAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.39, T:0.31
Consensus pattern (15 bp):
GGAATAGGATTTTGG
Found at i:284359 original size:19 final size:19
Alignment explanation
Indices: 284331--284367 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
284321 CCCCTTCAAC
*
284331 GGGGGAATCGGTTCCCTCA
1 GGGGGAATCGATTCCCTCA
*
284350 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
284368 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.22
Consensus pattern (19 bp):
GGGGGAATCGATTCCCTCA
Found at i:290218 original size:76 final size:77
Alignment explanation
Indices: 290089--290296 Score: 298
Period size: 75 Copynumber: 2.8 Consensus size: 77
290079 CCGTTGTACA
* * * *
290089 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
*
290153 -CAAAACTGTTT
66 CCAAAACTATTT
* *
290164 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
290229 CCAAAACTATTT
66 CCAAAACTATTT
* * *
290241 A-GGGGG-ATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
290297 TTTGGCTTTG
Statistics
Matches: 120, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 65 0.54
76 44 0.37
77 11 0.09
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
CCAAAACTATTT
Found at i:293555 original size:24 final size:24
Alignment explanation
Indices: 293528--293597 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
293518 ATGGAGATAT
* *
293528 CAGAAATCAAAATAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * *
293552 CAGATATCAGAACAGAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
293576 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAGAACAGAATTCAG
293598 GTCATGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:293597 original size:12 final size:12
Alignment explanation
Indices: 293541--293597 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
293531 AAATCAAAAT
293541 AGAATTCAGAAC
1 AGAATTCAGAAC
293553 AG-ATATCAGAAC
1 AGAAT-TCAGAAC
* * *
293565 AGAATCCATATC
1 AGAATTCAGAAC
*
293577 AGAAATCAGAAC
1 AGAATTCAGAAC
293589 AGAATTCAG
1 AGAATTCAG
293598 GTCATGTATC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 2 0.06
12 31 0.89
13 2 0.06
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (12 bp):
AGAATTCAGAAC
Found at i:293632 original size:24 final size:24
Alignment explanation
Indices: 293557--293634 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
293547 CAGAACAGAT
* *
293557 ATCAGAACAGAATCCATA-TCAGAA
1 ATCAGAACAGAATTCA-AGTCATAA
* **
293581 ATCAGAACAGAATTCAGGTCATGT
1 ATCAGAACAGAATTCAAGTCATAA
*
293605 ATCAGAATAGAATTCAAGTCGA-AA
1 ATCAGAACAGAATTCAAGTC-ATAA
293629 ATCAGA
1 ATCAGA
293635 TAAAATAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 42 0.98
25 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (24 bp):
ATCAGAACAGAATTCAAGTCATAA
Found at i:296137 original size:23 final size:23
Alignment explanation
Indices: 296107--296155 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
296097 GGTCAACGCT
296107 GGTCAACGGGTCGGATCGGGTCG
1 GGTCAACGGGTCGGATCGGGTCG
296130 GGTCAACGGGTCGGATCGGGTCG
1 GGTCAACGGGTCGGATCGGGTCG
296153 GGT
1 GGT
296156 TATGACCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.12, C:0.20, G:0.49, T:0.18
Consensus pattern (23 bp):
GGTCAACGGGTCGGATCGGGTCG
Found at i:298024 original size:14 final size:14
Alignment explanation
Indices: 298005--298033 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
297995 AACAAAATTC
298005 ATATCATATATCAG
1 ATATCATATATCAG
298019 ATATCATATATCAG
1 ATATCATATATCAG
298033 A
1 A
298034 ACAGAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (14 bp):
ATATCATATATCAG
Found at i:298058 original size:24 final size:24
Alignment explanation
Indices: 298031--298076 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
298021 ATCATATATC
298031 AGAACAGAATTCAAATCAGAAATT
1 AGAACAGAATTCAAATCAGAAATT
* *
298055 AGAACATATTTCAAATCAGAAA
1 AGAACAGAATTCAAATCAGAAA
298077 CCAGATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (24 bp):
AGAACAGAATTCAAATCAGAAATT
Found at i:300527 original size:18 final size:18
Alignment explanation
Indices: 300506--300569 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
300496 CTTTGGTCAA
*
300506 CGGGTCGGGTCATCGAGT
1 CGGGTCGGGTCAACGAGT
*
300524 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGAGT
* *
300542 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGAGT
*
300560 CAGGTCGGGT
1 CGGGTCGGGT
300570 TGTAACCGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.12, C:0.20, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGAGT
Found at i:300540 original size:13 final size:13
Alignment explanation
Indices: 300500--300547 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
300490 GGTCAACTTT
300500 GGTCAACGGGTCG
1 GGTCAACGGGTCG
300513 GGTCATCGAGTCGGGTCG
1 GGTCA---A--CGGGTCG
300531 GGTCAACGGGTCG
1 GGTCAACGGGTCG
300544 GGTC
1 GGTC
300548 GGGTAAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 16 0.53
15 1 0.03
16 1 0.03
18 12 0.40
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:302701 original size:104 final size:105
Alignment explanation
Indices: 302527--302734 Score: 334
Period size: 104 Copynumber: 2.0 Consensus size: 105
302517 ACAACCCCGG
302527 CACAACAGTAAGGCCCTGAGAACACAGTCGAGGAGCATTCATATATTCCTCCAACAATAACCCCC
1 CACAACAGTAAGGCCCTGAG-ACACAG-CGAGGAGCATTCATATATTCCTCCAACAATAACCCCC
302592 CAAATAAAACATTTATCAAAAACCATAGTAAATCCCCCACAA
64 CAAATAAAACATTTATCAAAAACCATAGTAAATCCCCCACAA
*
302634 CACAACAGTAAGGCCCTGAG-CACA-C-A-GAGCCTTCATATATTCTTCCTCCAACAATAACCCC
1 CACAACAGTAAGGCCCTGAGACACAGCGAGGAGCATTCATATA---TTCCTCCAACAATAACCCC
302695 CCAAATAAAACATTTATCAAAAACCATAGTAAATCCCCCA
63 CCAAATAAAACATTTATCAAAAACCATAGTAAATCCCCCA
302735 ACTGAACACA
Statistics
Matches: 97, Mismatches: 1, Indels: 9
0.91 0.01 0.08
Matches are distributed among these distances:
101 12 0.12
102 1 0.01
103 1 0.01
104 59 0.61
105 4 0.04
107 20 0.21
ACGTcount: A:0.41, C:0.31, G:0.09, T:0.19
Consensus pattern (105 bp):
CACAACAGTAAGGCCCTGAGACACAGCGAGGAGCATTCATATATTCCTCCAACAATAACCCCCCA
AATAAAACATTTATCAAAAACCATAGTAAATCCCCCACAA
Found at i:302908 original size:24 final size:24
Alignment explanation
Indices: 302883--302962 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
302873 AAATGGAGAT
* *
302883 ATCAGAAATCAAAACAGAATTCAT
1 ATCAGAAATCATAACAGAATTCAA
* *
302907 ATCATATATCATAACAGAATTCAA
1 ATCAGAAATCATAACAGAATTCAA
* *
302931 ATCAGAAATCATAACATATTTCAA
1 ATCAGAAATCATAACAGAATTCAA
302955 ATCAGAAA
1 ATCAGAAA
302963 CCAGATAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAA
Found at i:302961 original size:36 final size:37
Alignment explanation
Indices: 302883--302962 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 37
302873 AAATGGAGAT
* *
302883 ATCAGAAATCAAAACAGAATTCATATCATATATCATA
1 ATCAGAAATCAAAACAGAAATCATAACATATATCATA
* * *
302920 A-CAGAATTCAAATCAGAAATCATAACATATTTCA-A
1 ATCAGAAATCAAAACAGAAATCATAACATATATCATA
302955 ATCAGAAA
1 ATCAGAAA
302963 CCAGATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
35 2 0.06
36 33 0.92
37 1 0.03
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (37 bp):
ATCAGAAATCAAAACAGAAATCATAACATATATCATA
Found at i:309715 original size:20 final size:20
Alignment explanation
Indices: 309692--309731 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
309682 TGTAAGTACT
*
309692 GATACTGCTATAGTAGTATC
1 GATACTGCTATAGTAATATC
309712 GATACTGCTATAGTAATATC
1 GATACTGCTATAGTAATATC
309732 AAGCCCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
GATACTGCTATAGTAATATC
Found at i:312948 original size:20 final size:21
Alignment explanation
Indices: 312923--312971 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
312913 GGTATTGTAT
312923 TGTATGAACT-GTACCGATAC
1 TGTATGAACTAGTACCGATAC
*
312943 TGTATGAA-TAGTATCGATAC
1 TGTATGAACTAGTACCGATAC
*
312963 TGTGTGAAC
1 TGTATGAAC
312972 ATTAATGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (21 bp):
TGTATGAACTAGTACCGATAC
Found at i:313040 original size:20 final size:20
Alignment explanation
Indices: 313017--313076 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
313007 TGTAAGTACT
*
313017 GATACTGCTACAGTAGTATC
1 GATACTGCTATAGTAGTATC
313037 GATACTGCTATAGTAGTATC
1 GATACTGCTATAGTAGTATC
*
313057 GATACTGCTATAGTAATATC
1 GATACTGCTATAGTAGTATC
313077 AAGCCCAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (20 bp):
GATACTGCTATAGTAGTATC
Found at i:316309 original size:20 final size:20
Alignment explanation
Indices: 316268--316309 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
316258 TTATGAATAG
*
316268 TATTGTATGAACATTACCGA
1 TATTGTATGAACAGTACCGA
* *
316288 TATTGTATGAATAGTACTGA
1 TATTGTATGAACAGTACCGA
316308 TA
1 TA
316310 CTCTGTGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (20 bp):
TATTGTATGAACAGTACCGA
Found at i:317359 original size:50 final size:50
Alignment explanation
Indices: 317304--317452 Score: 298
Period size: 50 Copynumber: 3.0 Consensus size: 50
317294 AACTCGGCTA
317304 TCACATTTTGATTTTGGGTTTAAAAGTTTTAATATTAATGTCATTGAATT
1 TCACATTTTGATTTTGGGTTTAAAAGTTTTAATATTAATGTCATTGAATT
317354 TCACATTTTGATTTTGGGTTTAAAAGTTTTAATATTAATGTCATTGAATT
1 TCACATTTTGATTTTGGGTTTAAAAGTTTTAATATTAATGTCATTGAATT
317404 TCACATTTTGATTTTGGGTTTAAAAGTTTTAATATTAATGTCATTGAAT
1 TCACATTTTGATTTTGGGTTTAAAAGTTTTAATATTAATGTCATTGAAT
317453 GTAAGTGAAA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 99 1.00
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.50
Consensus pattern (50 bp):
TCACATTTTGATTTTGGGTTTAAAAGTTTTAATATTAATGTCATTGAATT
Found at i:326784 original size:7 final size:7
Alignment explanation
Indices: 326772--326800 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
326762 CTCTCATCTT
326772 AAAAATA
1 AAAAATA
326779 AAAAATA
1 AAAAATA
326786 AAAAAT-
1 AAAAATA
326792 AAAAATA
1 AAAAATA
326799 AA
1 AA
326801 TCACTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:326789 original size:13 final size:14
Alignment explanation
Indices: 326772--326800 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
326762 CTCTCATCTT
326772 AAAAATAAAAAATA
1 AAAAATAAAAAATA
326786 AAAAAT-AAAAATA
1 AAAAATAAAAAATA
326799 AA
1 AA
326801 TCACTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:340987 original size:18 final size:19
Alignment explanation
Indices: 340964--341004 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
340954 ATGTTTTGCC
*
340964 ATTTTAAATAAAA-AATTA
1 ATTTTAAATAAAATAATAA
*
340982 ATTTTAATTAAAATAATAA
1 ATTTTAAATAAAATAATAA
341001 ATTT
1 ATTT
341005 AGGTATGCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTAAATAAAATAATAA
Found at i:342901 original size:55 final size:55
Alignment explanation
Indices: 342757--343021 Score: 312
Period size: 55 Copynumber: 4.9 Consensus size: 55
342747 GATAGGACTC
* *
342757 ATCTTCAACAAACGTGTCCGCTCCCTATTTCTTCAGAGAGTATATG-AC-T---CA
1 ATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATA-GAACTTGAACA
* *
342808 ATCTTCAACAAACGTGT-TCGCTCCCTATTTCTTCAGAGAGTATATAACTTGAACA
1 ATCTTCAACAAACGTGTCT-GCTCCCTATTCCTTCAGAGAGTATAGAACTTGAACA
* * * *
342863 ACCTTTAATAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACA
1 ATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGAACTTGAACA
* * *
342918 ATCTTTAACAAACGTGTCTACTCCCTATTCCTTCAGAGAGTATA-AGACTCGAACA
1 ATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGA-ACTTGAACA
* * *
342973 AGCTTCAACAATCGTGTCTGATCCCTATTCCTTCAG-GAAGTATAGAACT
1 ATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAG-AGTATAGAACT
343022 CGAATATATC
Statistics
Matches: 186, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
51 44 0.24
52 1 0.01
54 1 0.01
55 138 0.74
56 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (55 bp):
ATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGAACTTGAACA
Found at i:343071 original size:53 final size:53
Alignment explanation
Indices: 343011--343115 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 53
343001 TCCTTCAGGA
343011 AGTATAGAACTC-GA-ATATATCTTCTAACGAGTTCGCTCCCTCTTTCTCTAAGG
1 AGTATAGAACTCAGACATAT-TCTTC-AACGAGTTCGCTCCCTCTTTCTCTAAGG
* *
343064 AGTATAGAACTCAGACATCTTCTTCAACGGGTTCGCTCCCTCTTTCTCTAAG
1 AGTATAGAACTCAGACATATTCTTCAACGAGTTCGCTCCCTCTTTCTCTAAG
343116 TATGGAACTC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
53 38 0.79
54 7 0.15
55 3 0.06
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (53 bp):
AGTATAGAACTCAGACATATTCTTCAACGAGTTCGCTCCCTCTTTCTCTAAGG
Found at i:344504 original size:12 final size:12
Alignment explanation
Indices: 344483--344559 Score: 77
Period size: 12 Copynumber: 6.1 Consensus size: 12
344473 TGAAACTCCC
344483 TTTT-TTTTTTT
1 TTTTCTTTTTTT
344494 TTTTCTTTTTTT
1 TTTTCTTTTTTT
344506 TTTTCTTTTTTT
1 TTTTCTTTTTTT
344518 TTTT-TATTTTTCT
1 TTTTCT-TTTTT-T
*
344531 TATTTTTTCTTTTT
1 T-TTTCTT-TTTTT
344545 TTTAATCTTTTTTT
1 TTT--TCTTTTTTT
344559 T
1 T
344560 AAGCAAAATA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
11 5 0.09
12 28 0.49
13 4 0.07
14 12 0.21
15 8 0.14
ACGTcount: A:0.05, C:0.06, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:344515 original size:29 final size:29
Alignment explanation
Indices: 344482--344547 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
344472 TTGAAACTCC
*
344482 CTTTTTTTTTTTT-TTTCTT-TTTTTTTTT
1 CTTTTTTTTTTTTATTT-TTCTTATTTTTT
344510 CTTTTTTTTTTTTATTTTTCTTATTTTTT
1 CTTTTTTTTTTTTATTTTTCTTATTTTTT
344539 CTTTTTTTT
1 CTTTTTTTT
344548 AATCTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 15 0.43
29 20 0.57
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (29 bp):
CTTTTTTTTTTTTATTTTTCTTATTTTTT
Found at i:344559 original size:1 final size:1
Alignment explanation
Indices: 344483--344547 Score: 76
Period size: 1 Copynumber: 65.0 Consensus size: 1
344473 TGAAACTCCC
* * * * * *
344483 TTTTTTTTTTTTTTTCTTTTTTTTTTTCTTTTTTTTTTTTATTTTTCTTATTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
344548 AATCTTTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:356762 original size:15 final size:14
Alignment explanation
Indices: 356736--356779 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
356726 GAAAAACATG
*
356736 TAAAAT-ATAATAT
1 TAAAATAATAATAA
356749 TAAAGATAATAATAA
1 TAAA-ATAATAATAA
356764 TAAAATAATACATAA
1 TAAAATAATA-ATAA
356779 T
1 T
356780 TAATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 4 0.15
14 8 0.30
15 15 0.56
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (14 bp):
TAAAATAATAATAA
Found at i:357464 original size:44 final size:45
Alignment explanation
Indices: 357381--357484 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 45
357371 TCTATGACTT
* *
357381 GTAAGACCTTATCGTTATCACAGGCTTCCCTGCTATGTGCA-AGG
1 GTAAGACCTTACCGTTACCACAGGCTTCCCTGCTATGTGCACAGG
* * * *
357425 GTAAGACCTTACCGTTACCGCAGGC-TCCTTTGTTTTGTGCACAGG
1 GTAAGACCTTACCGTTACCACAGGCTTCC-CTGCTATGTGCACAGG
*
357470 ATAAGACCTTACCGT
1 GTAAGACCTTACCGT
357485 AGGCTCCTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 3 0.06
44 31 0.61
45 17 0.33
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (45 bp):
GTAAGACCTTACCGTTACCACAGGCTTCCCTGCTATGTGCACAGG
Found at i:357501 original size:39 final size:39
Alignment explanation
Indices: 357439--357561 Score: 174
Period size: 39 Copynumber: 3.2 Consensus size: 39
357429 GACCTTACCG
* * *
357439 TTACCGCAGGCTCCTTTGTTTTGTGCACAGGATAAGACC
1 TTACCGTAGGCTCCTCTGCTTTGTGCACAGGATAAGACC
* * *
357478 TTACCGTAGGCTCCTCAGCTTTGTGAACATGATAAGACC
1 TTACCGTAGGCTCCTCTGCTTTGTGCACAGGATAAGACC
* *
357517 TTACCGTAGGCTCCTCTTCTTTGTGCACAGGGTAAGACC
1 TTACCGTAGGCTCCTCTGCTTTGTGCACAGGATAAGACC
357556 TTACCG
1 TTACCG
357562 GGTGTACAGG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (39 bp):
TTACCGTAGGCTCCTCTGCTTTGTGCACAGGATAAGACC
Found at i:358178 original size:2 final size:2
Alignment explanation
Indices: 358173--358197 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
358163 GGTTTTTTAG
358173 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
358198 GATTTCAAAC
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:358313 original size:25 final size:25
Alignment explanation
Indices: 358284--358345 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
358274 TTCGAAAAAT
* *
358284 ATTTTTTAGAAACCTATAATATATA
1 ATTTTTAAAAAACCTATAATATATA
*
358309 ATTTTTAAAAAACGTATAATATATA
1 ATTTTTAAAAAACCTATAATATATA
*
358334 GTTTTTAAAAAA
1 ATTTTTAAAAAA
358346 TACATTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (25 bp):
ATTTTTAAAAAACCTATAATATATA
Found at i:360452 original size:16 final size:16
Alignment explanation
Indices: 360431--360465 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
360421 CTGGACCTTT
360431 TGATTGACAACAGATC
1 TGATTGACAACAGATC
360447 TGATTGACAACAGATC
1 TGATTGACAACAGATC
360463 TGA
1 TGA
360466 CAGCTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (16 bp):
TGATTGACAACAGATC
Found at i:360766 original size:12 final size:12
Alignment explanation
Indices: 360742--360776 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
360732 CTAAGGTGCC
360742 TATAATATAATA
1 TATAATATAATA
360754 TATAACTATATATA
1 TATAA-TATA-ATA
360768 TATAATATA
1 TATAATATA
360777 TTAATAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 8 0.38
14 8 0.38
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAATATAATA
Found at i:362283 original size:28 final size:29
Alignment explanation
Indices: 362247--362302 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
362237 ATTTCATATT
362247 CATAAATCAGA-TACAAAAATACAATAAC
1 CATAAATCAGATTACAAAAATACAATAAC
* * * *
362275 CATAGATCATATTATAAACATACAATAA
1 CATAAATCAGATTACAAAAATACAATAA
362303 ATCAAATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.23
Consensus pattern (29 bp):
CATAAATCAGATTACAAAAATACAATAAC
Found at i:368536 original size:20 final size:22
Alignment explanation
Indices: 368513--368593 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 22
368503 TTGGTGCAGA
*
368513 GGGAATCGAT-CCCCCCATGA-
1 GGGAACCGATACCCCCCATGAG
* **
368533 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCCATG-AG
* *
368556 GGGAACCGATCCCCCCCA-CAG
1 GGGAACCGATACCCCCCATGAG
*
368577 GGGAATCGATACCCCCC
1 GGGAACCGATACCCCCC
368594 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.18
21 24 0.49
22 1 0.02
23 15 0.31
ACGTcount: A:0.23, C:0.38, G:0.25, T:0.14
Consensus pattern (22 bp):
GGGAACCGATACCCCCCATGAG
Found at i:370854 original size:41 final size:41
Alignment explanation
Indices: 370797--370882 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
370787 TTCACGTTTA
370797 TTTGAATCTTTTTGATTTAACAAAAAGGGGGAGAAGTGTGT
1 TTTGAATCTTTTTGATTTAACAAAAAGGGGGAGAAGTGTGT
370838 TTTGAATCTTTTTGATTTAACAAAAAGGGGGAGAAGTGTGT
1 TTTGAATCTTTTTGATTTAACAAAAAGGGGGAGAAGTGTGT
370879 TTTG
1 TTTG
370883 TGTTTTAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (41 bp):
TTTGAATCTTTTTGATTTAACAAAAAGGGGGAGAAGTGTGT
Found at i:371268 original size:14 final size:14
Alignment explanation
Indices: 371249--371276 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
371239 CTCATAGGGA
371249 ACCGATTCCCCCCT
1 ACCGATTCCCCCCT
371263 ACCGATTCCCCCCT
1 ACCGATTCCCCCCT
371277 GAATGGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.57, G:0.07, T:0.21
Consensus pattern (14 bp):
ACCGATTCCCCCCT
Found at i:373498 original size:86 final size:85
Alignment explanation
Indices: 373349--373523 Score: 260
Period size: 89 Copynumber: 2.0 Consensus size: 85
373339 AGTCAATGGG
*
373349 GAATATAGATTGGACTAAGAGAAGATCAAACTTTAGTTTGAGTTTTTTCAATTTCGAAAAAAAAA
1 GAATATAGATTGGACTAAGAGAAGATCAAACTTTAGTTTGAGTTTTTTCAATTTCG-AAAAAGAA
373414 ACAAACTGAGGAGGAAAAGAA
65 ACAAACTGAGGAGGAAAAGAA
* **
373435 GAATATAGATTGGACTAAGAGAAGATCAAAGCTTTAGTTTGATTTTTTTTTTGATTTCGAAAAAA
1 GAATATAGATTGGACTAAGAGAAGATCAAA-CTTTAGTTTGA--GTTTTTTCAATTTCG-AAAAA
*
373500 GAAACAAACTGAGGAGGAAGAGAA
62 GAAACAAACTGAGGAGGAAAAGAA
373524 TATGTTTTGG
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
86 30 0.37
87 11 0.14
89 40 0.49
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (85 bp):
GAATATAGATTGGACTAAGAGAAGATCAAACTTTAGTTTGAGTTTTTTCAATTTCGAAAAAGAAA
CAAACTGAGGAGGAAAAGAA
Found at i:373524 original size:86 final size:85
Alignment explanation
Indices: 373349--373526 Score: 270
Period size: 86 Copynumber: 2.1 Consensus size: 85
373339 AGTCAATGGG
373349 GAATATAGATTGGACTAAGAGAAGATCAAACTTTAGTTTGAGTTTTTTCAATTTCGAAAAAAAAA
1 GAATATAGATTGGACTAAGAGAAGATCAAACTTTAGTTTGAGTTTTTTCAATTTCGAAAAAAAAA
373414 ACAAACTGAGGAGGAAAAGAA
66 ACAAACTGAGGAGG-AAAGAA
* **
373435 GAATATAGATTGGACTAAGAGAAGATCAAAGCTTTAGTTTGATTTTTTTTTTGATTTCGAAAAAA
1 GAATATAGATTGGACTAAGAGAAGATCAAA-CTTTAGTTTGA--GTTTTTTCAATTTCGAAAAAA
*
373500 GAAACAAACTGAGGAGG-AAG-A
63 AAAACAAACTGAGGAGGAAAGAA
373521 GAATAT
1 GAATAT
373527 GTTTTGGTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
86 37 0.44
87 14 0.16
89 34 0.40
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (85 bp):
GAATATAGATTGGACTAAGAGAAGATCAAACTTTAGTTTGAGTTTTTTCAATTTCGAAAAAAAAA
ACAAACTGAGGAGGAAAGAA
Found at i:377709 original size:31 final size:31
Alignment explanation
Indices: 377636--377709 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
377626 CAGTTACATC
*
377636 AGGGATTATATTACAAACGAACTAAATGTTG
1 AGGGATTATATTACAAACGAACTAAATATTG
** *
377667 AGGGACCATATTACAAACGGACTAAATATT-
1 AGGGATTATATTACAAACGAACTAAATATTG
377697 AGGGGATTATATT
1 A-GGGATTATATT
377710 GTAAGTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (31 bp):
AGGGATTATATTACAAACGAACTAAATATTG
Found at i:378697 original size:31 final size:31
Alignment explanation
Indices: 378621--378681 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
378611 AGTTACGTCG
378621 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
*
378652 GGGACCATATTGCAAATGGACTAAATGTTG
1 GGGACCATATTGCAAACGGACTAAATGTTG
378682 GGAGATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:379021 original size:20 final size:20
Alignment explanation
Indices: 378996--379049 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
378986 AACCAACAAA
378996 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
*
379016 TTCGCAACGCGATTTCCAAT
1 TTCGCAACGCGAATTCCAAT
379036 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
379050 ATTAAATCGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:379098 original size:21 final size:20
Alignment explanation
Indices: 379051--379102 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
379041 AACGCGAATA
379051 TTAAA-TCGCATTGCGATTT
1 TTAAATTCGCATTGCGATTT
* *
379070 TTCGAATTCGCGTTGCGATTT
1 TT-AAATTCGCATTGCGATTT
379091 TCTAAATTCGCA
1 T-TAAATTCGCA
379103 ACGCGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 21 0.81
22 1 0.04
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
TTAAATTCGCATTGCGATTT
Found at i:379141 original size:20 final size:20
Alignment explanation
Indices: 379118--379177 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
379108 AATTTGTAAA
379118 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
379138 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
379158 TCGTAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
379178 AGTTTCATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 31 0.91
21 1 0.03
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.18
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:379166 original size:40 final size:40
Alignment explanation
Indices: 379094--379177 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
379084 GCGATTTTCT
* *
379094 AAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTC
1 AAATTCGCAACGCGAATTAGTAAATCGCAACACAAAAGTC
*
379134 AAATTCGCAACGCG-A-TAGTCAAATTCGTAACACAAAAGTC
1 AAATTCGCAACGCGAATTAGT-AAA-TCGCAACACAAAAGTC
379174 AAAT
1 AAAT
379178 AGTTTCATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
38 3 0.08
39 4 0.10
40 32 0.82
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.20
Consensus pattern (40 bp):
AAATTCGCAACGCGAATTAGTAAATCGCAACACAAAAGTC
Found at i:379331 original size:22 final size:22
Alignment explanation
Indices: 379305--379352 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
379295 CTATGGCGAC
379305 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
* * *
379327 ATCCGTCCCCATTTCCGGCGAA
1 ATCCGTCCCCATCTCCGACAAA
379349 ATCC
1 ATCC
379353 ATCTATCTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:381724 original size:42 final size:42
Alignment explanation
Indices: 381677--381795 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
381667 GATGCACTTA
* * * *
381677 TCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
381719 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
* ** * *
381761 TCATCGTTCAAGTGGTCCCCGCCCGCCGTTCAAGA
1 TCATCATTCAAGAAG-CCCCTCCCACCGTTCAAGA
381796 TCCCGATTCA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.03
42 43 0.67
43 19 0.30
ACGTcount: A:0.21, C:0.38, G:0.20, T:0.21
Consensus pattern (42 bp):
TCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:381731 original size:21 final size:21
Alignment explanation
Indices: 381684--381772 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 21
381674 TTATCATCAT
* *
381684 TCAAGAGGCGCCTC-CTATCGT
1 TCAAGAGGCCCCTCTC-ATCGA
381705 TCAAGAGGCCCCTCTCATC-A
1 TCAAGAGGCCCCTCTCATCGA
* * * *
381725 TCGAAGAAGCCCCTCCCACCGT
1 TC-AAGAGGCCCCTCTCATCGA
* *
381747 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCTCATCGA
381768 TCAAG
1 TCAAG
381773 TGGTCCCCGC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
20 2 0.04
21 50 0.91
22 3 0.05
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGGCCCCTCTCATCGA
Found at i:383235 original size:13 final size:14
Alignment explanation
Indices: 383202--383239 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
383192 TTTTGATTAA
383202 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
383216 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
383230 -TGATTTGTAA
1 TTGATTTGTAA
383240 TAAGAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:383619 original size:39 final size:39
Alignment explanation
Indices: 383565--383646 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
383555 CAAGTTGTAG
383565 ATTTTGATATCCTTTTGCTTGGCACCATATGAGATTTGA
1 ATTTTGATATCCTTTTGCTTGGCACCATATGAGATTTGA
* * *
383604 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATATCCTTTTGCTTGGCACCATATGAGATTTGA
383643 ATTT
1 ATTT
383647 GATGAGCATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (39 bp):
ATTTTGATATCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:384337 original size:19 final size:20
Alignment explanation
Indices: 384275--384342 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
384265 ATACACAAGA
384275 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGCGTTGC
384295 ----TT-A-TTTCGCGTTGC
1 GAATTTGACTTTCGCGTTGC
*
384309 GAATTTGACTTTCGTGTTGC
1 GAATTTGACTTTCGCGTTGC
*
384329 GAA-TTGACTATCGC
1 GAATTTGACTTTCGC
384343 AACGCGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
14 11 0.28
15 1 0.03
16 2 0.05
18 2 0.05
19 10 0.26
20 13 0.33
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGC
Found at i:384685 original size:18 final size:18
Alignment explanation
Indices: 384662--384697 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
384652 AAGCCGGTTG
*
384662 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
384680 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
384698 CTTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:387101 original size:12 final size:12
Alignment explanation
Indices: 387080--387113 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
387070 GGTTGTGGGT
*
387080 TTTGAGATTGTG
1 TTTGATATTGTG
387092 TTTGATATTGTG
1 TTTGATATTGTG
*
387104 TTCGATATTG
1 TTTGATATTG
387114 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:387873 original size:19 final size:20
Alignment explanation
Indices: 387849--387973 Score: 107
Period size: 20 Copynumber: 6.4 Consensus size: 20
387839 ACTAAAACCT
387849 GTTGCGAAATT-AAATTCGC
1 GTTGCGAAATTGAAATTCGC
* *
387868 GTTGCGAATTTGAAATTC-A
1 GTTGCGAAATTGAAATTCGC
* * *
387887 GTTGAGAATTTG-ACTATCGC
1 GTTGCGAAATTGAAAT-TCGC
* *
387907 GTTGCGAAATTGGAAACT-GG
1 GTTGCGAAATT-GAAATTCGC
*
387927 GTTGCGAAATTGGAATTCGC
1 GTTGCGAAATTGAAATTCGC
* *
387947 GTTGCGAATTTGAGA-TCGC
1 GTTGCGAAATTGAAATTCGC
387966 GTTGCGAA
1 GTTGCGAA
387974 TTTGTTGGTC
Statistics
Matches: 84, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.02
19 39 0.46
20 40 0.48
21 2 0.02
22 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (20 bp):
GTTGCGAAATTGAAATTCGC
Found at i:387885 original size:20 final size:20
Alignment explanation
Indices: 387849--387977 Score: 115
Period size: 19 Copynumber: 6.6 Consensus size: 20
387839 ACTAAAACCT
*
387849 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
387868 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
* *
387887 GTTGAGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
* * *
387907 GTTGCGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* *
387927 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
387947 GTTGCGAATTTGAGA-TCGC
1 GTTGCGAATTTGAAATTCGC
387966 GTTGCGAATTTG
1 GTTGCGAATTTG
387978 TTGGTCATTT
Statistics
Matches: 86, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
18 2 0.02
19 46 0.53
20 31 0.36
21 6 0.07
22 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:390181 original size:27 final size:26
Alignment explanation
Indices: 390126--390177 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
390116 AACTTCAACT
*
390126 TGATCAAAATACCCTGAGCTCTCGTA
1 TGATCAAAATACCCTGAGCTCTCATA
* *
390152 TGATCGAAGTACCCTTGAGCT-TCATA
1 TGATCAAAATACCC-TGAGCTCTCATA
390178 ATGACTTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (26 bp):
TGATCAAAATACCCTGAGCTCTCATA
Found at i:390745 original size:13 final size:13
Alignment explanation
Indices: 390727--390752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
390717 TGCTCTCCTG
390727 ATATATATATATA
1 ATATATATATATA
390740 ATATATATATATA
1 ATATATATATATA
390753 TGAATACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:392805 original size:18 final size:17
Alignment explanation
Indices: 392782--392821 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
392772 ACCGGTCATA
392782 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGA-CCG
*
392800 ACCCGACTCGTTGACCG
1 ACCCGACCCGTTGACCG
392817 ACCCG
1 ACCCG
392822 TTTGACCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.12
Consensus pattern (17 bp):
ACCCGACCCGTTGACCG
Found at i:395236 original size:23 final size:24
Alignment explanation
Indices: 395189--395279 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
395179 TTAAATTTGA
* * *
395189 ATTCTGTTATGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
395213 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
*
395236 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
395260 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
395280 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:395249 original size:47 final size:48
Alignment explanation
Indices: 395189--395279 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
395179 TTAAATTTGA
* *
395189 ATTCTGTTATGATACATGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
395236 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
395280 TTGAATTATG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 35 0.88
48 5 0.12
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:399728 original size:24 final size:24
Alignment explanation
Indices: 399701--399790 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
399691 TCAAATTTGA
* *
399701 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
399725 ATTCTGATCTGATA-TTGA-CAGG
1 ATTCTGATATGATACTTGACCTGG
* *
399747 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
399771 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
399791 TTGAATTATG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
22 17 0.30
23 6 0.11
24 33 0.59
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:399760 original size:46 final size:47
Alignment explanation
Indices: 399701--399790 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 47
399691 TCAAATTTGA
* * *
399701 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTGACAGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACAGG
*
399747 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
399791 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 34 0.87
47 5 0.13
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (47 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACAGG
Found at i:400691 original size:44 final size:44
Alignment explanation
Indices: 400574--400696 Score: 167
Period size: 46 Copynumber: 2.8 Consensus size: 44
400564 ATAAATCTCT
*
400574 TACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* *
400618 TACCATTTAAATTCCATAAGCTCATAAGCTTATTTTACCCATATAC
1 TACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* *
400664 TTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 -TACCATTTATTCCATAAGCTCGTAAGCTTATTT
400697 GTATGCTTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
44 31 0.44
46 35 0.50
47 4 0.06
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (44 bp):
TACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:400863 original size:40 final size:40
Alignment explanation
Indices: 400808--400929 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
400798 ACCGTAGTGC
*
400808 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
400848 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
400888 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
400928 TA
1 TA
400930 TAAACCTGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:405268 original size:17 final size:17
Alignment explanation
Indices: 405246--405280 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
405236 AAGATGCCTT
405246 AAGATTATGTTGGTTGA
1 AAGATTATGTTGGTTGA
405263 AAGATTATGTTGGTTGA
1 AAGATTATGTTGGTTGA
405280 A
1 A
405281 CATGGACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (17 bp):
AAGATTATGTTGGTTGA
Found at i:413306 original size:8 final size:8
Alignment explanation
Indices: 413295--413322 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
413285 GCATACCCAT
413295 GGTGCATC
1 GGTGCATC
413303 GGTGCATC
1 GGTGCATC
413311 GGTGCATC
1 GGTGCATC
413319 GGTG
1 GGTG
413323 TAAAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.21, G:0.43, T:0.25
Consensus pattern (8 bp):
GGTGCATC
Found at i:413467 original size:45 final size:45
Alignment explanation
Indices: 413418--413507 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
413408 AAAACAGCCA
* *
413418 GAGTGCATCGATGCATGGCT-GGTGCATCGATGCATCAAATGCATT
1 GAGTGCATCGATGCATGG-TAGGTGAATCGATGCATAAAATGCATT
* *
413463 GAGTGCATTGATGCATGGTATGTGAATCGATGCATAAAATGCATT
1 GAGTGCATCGATGCATGGTAGGTGAATCGATGCATAAAATGCATT
413508 CGATGTTCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTAGGTGAATCGATGCATAAAATGCATT
Found at i:414361 original size:2 final size:2
Alignment explanation
Indices: 414354--414379 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
414344 TTTACCCTAA
414354 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
414380 GCATGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:420205 original size:17 final size:18
Alignment explanation
Indices: 420183--420225 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
420173 TCTGGTCTTG
*
420183 TTGGGCCTTC-GGGTTAT
1 TTGGGCCTGCTGGGTTAT
420200 TTGGGCCTGCTGGGTTAT
1 TTGGGCCTGCTGGGTTAT
420218 TTGGGCCT
1 TTGGGCCT
420226 AGATCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.05, C:0.19, G:0.37, T:0.40
Consensus pattern (18 bp):
TTGGGCCTGCTGGGTTAT
Found at i:422644 original size:301 final size:301
Alignment explanation
Indices: 422123--422705 Score: 851
Period size: 301 Copynumber: 1.9 Consensus size: 301
422113 TAAAGCTGTT
* * * *
422123 TTATAACTAAAAATCTCACCGCAAGTCATCTAGAGTCAGGAATATTTGATAACCTTTCTAAATTG
1 TTATAACTAAAAATCTCACCGCAAGCCATCTAGAGTCAAGAATATTTGATAACATGTCTAAATTG
* *
422188 CAAGAATTAAGCTTGGAAGGGAACCAAATATCTAGTAGCATTCCCAGTAGTTTATACAAGAGCAA
66 CAAGAATTAAGCTTGGAAGGGAACCAAATATCTAGTAGCATTCCCAGCAGCTTATACAAGAGCAA
* * * *
422253 AGAGTTGAGGTATTTATCATTGTGGAACAACTCTGTGGAAGGAAGTATACCTATAGAAATCGGAA
131 AGAGTTGAGGTATATATCATTGTGGAACAACACTATGGAAGGAAATATACCTATAGAAATCGGAA
* * * *
422318 ATTTGACTATGCTCCAATATTTGTATATTGGTTACAACAATTTCAAAGGTAAAAGATTCCTCATT
196 ATTTGACTATGCTCCAATATTTGTATATTGCTCACAACAACTTCAAAGGTAAAAAATTCCTCATT
*
422383 TGCATTCCGTTCTCTTTTATTTTCATTACATAAAAGTTATC
261 TGCATTCCGTTCTCCTTTATTTTCATTACATAAAAGTTATC
* * * * *
422424 TTATAATTAACAATCTCACTGCAGGCCATCTTGAGTCAAGAATATTTGATAACATGTCTAAATTG
1 TTATAACTAAAAATCTCACCGCAAGCCATCTAGAGTCAAGAATATTTGATAACATGTCTAAATTG
** * * * * * * *
422489 CAATTATTAAGGTTGGATGGGAACCAGATTTCTGGTATCATTCCCAGCAGCTTATACAAGTGCAA
66 CAAGAATTAAGCTTGGAAGGGAACCAAATATCTAGTAGCATTCCCAGCAGCTTATACAAGAGCAA
*
422554 GGAGTTGAGGTATATATCATTGTGGAACAACACTATGGAAGGAAATATACCTATAGAAATCGGAA
131 AGAGTTGAGGTATATATCATTGTGGAACAACACTATGGAAGGAAATATACCTATAGAAATCGGAA
* * *
422619 ATTTGACTGTGCTCCAATTTTTGTATATTGCTCACAACAACTTCAGAGGTAAAAAATTCCTCATT
196 ATTTGACTATGCTCCAATATTTGTATATTGCTCACAACAACTTCAAAGGTAAAAAATTCCTCATT
* *
422684 TGTATTTCGTTCTCCTTTATTT
261 TGCATTCCGTTCTCCTTTATTT
422706 AATTAGTTGT
Statistics
Matches: 247, Mismatches: 35, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
301 247 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (301 bp):
TTATAACTAAAAATCTCACCGCAAGCCATCTAGAGTCAAGAATATTTGATAACATGTCTAAATTG
CAAGAATTAAGCTTGGAAGGGAACCAAATATCTAGTAGCATTCCCAGCAGCTTATACAAGAGCAA
AGAGTTGAGGTATATATCATTGTGGAACAACACTATGGAAGGAAATATACCTATAGAAATCGGAA
ATTTGACTATGCTCCAATATTTGTATATTGCTCACAACAACTTCAAAGGTAAAAAATTCCTCATT
TGCATTCCGTTCTCCTTTATTTTCATTACATAAAAGTTATC
Found at i:423524 original size:13 final size:13
Alignment explanation
Indices: 423491--423533 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
423481 AATTTTTTTA
423491 TTTTTAATTATATT
1 TTTTTAATT-TATT
* *
423505 GTCTTAATTTATT
1 TTTTTAATTTATT
423518 TTTTTAA-TTATT
1 TTTTTAATTTATT
423530 TTTT
1 TTTT
423534 CTATAATGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 9 0.36
13 9 0.36
14 7 0.28
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTATT
Found at i:423567 original size:15 final size:14
Alignment explanation
Indices: 423494--423568 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 14
423484 TTTTTTATTT
423494 TTAATTATATTGTC
1 TTAATTATATTGTC
* *
423508 TTAATT-TATTTTT
1 TTAATTATATTGTC
* *
423521 TTAATTATTTTTTC
1 TTAATTATATTGTC
423535 -T-A-TA-ATGTGT-
1 TTAATTATAT-TGTC
423545 TTAATTATATTGTC
1 TTAATTATATTGTC
423559 TTAATT-TATT
1 TTAATTATATT
423569 TTGTTAACTT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
10 1 0.02
11 5 0.10
12 2 0.04
13 21 0.44
14 19 0.40
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (14 bp):
TTAATTATATTGTC
Found at i:423572 original size:15 final size:14
Alignment explanation
Indices: 423494--423572 Score: 53
Period size: 15 Copynumber: 5.9 Consensus size: 14
423484 TTTTTTATTT
*
423494 TTAATTATATTGTC
1 TTAATTATTTTGTC
423508 TTAATTTATTTT-T-
1 TTAA-TTATTTTGTC
*
423521 TTAATTATTTTTTC
1 TTAATTATTTTGTC
* *
423535 -T-A-TAATGTGT-
1 TTAATTATTTTGTC
*
423545 TTAATTATATTGTC
1 TTAATTATTTTGTC
423559 TTAATTTATTTTGT
1 TTAA-TTATTTTGT
423573 TAACTTGTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
11 6 0.12
12 9 0.18
13 11 0.22
14 9 0.18
15 14 0.29
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (14 bp):
TTAATTATTTTGTC
Found at i:425351 original size:13 final size:11
Alignment explanation
Indices: 425313--425354 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
425303 CTTAAAACTT
425313 AGAAAAAGAAGA
1 AGAAAAA-AAGA
425325 AGAAAAAAAG-
1 AGAAAAAAAGA
425335 AGAATAAGAAAGA
1 AGAA-AA-AAAGA
425348 AGAAAAA
1 AGAAAAA
425355 GTCAGGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 4 0.15
11 6 0.22
12 13 0.48
13 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:428284 original size:21 final size:23
Alignment explanation
Indices: 428248--428290 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
428238 AAAATTCAAT
*
428248 TAAAATTAAAATTATTTAAATTA
1 TAAAATTAAAATTATTCAAATTA
428271 TAAAA-TAAAA-TATTCAAATT
1 TAAAATTAAAATTATTCAAATT
428291 CAATTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAATTAAAATTATTCAAATTA
Found at i:430766 original size:12 final size:12
Alignment explanation
Indices: 430749--430774 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
430739 ATAATAATAC
430749 AATATAAATAAT
1 AATATAAATAAT
430761 AATATAAATAAT
1 AATATAAATAAT
430773 AA
1 AA
430775 CGGGACGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATATAAATAAT
Found at i:431130 original size:54 final size:54
Alignment explanation
Indices: 431071--431203 Score: 230
Period size: 54 Copynumber: 2.5 Consensus size: 54
431061 GGATGACATT
431071 GTTCCTTCGTGATGAGGATGTCTAGCCATCTTTAAAGATATTTGAGATAACACA
1 GTTCCTTCGTGATGAGGATGTCTAGCCATCTTTAAAGATATTTGAGATAACACA
** * *
431125 GTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACG
1 GTTCCTTCGTGATGAGGATGTCTAGCCATCTTTAAAGATATTTGAGATAACACA
431179 GTTCCTTCGTGATGAGGATGTCTAG
1 GTTCCTTCGTGATGAGGATGTCTAG
431204 TTGTCTAAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (54 bp):
GTTCCTTCGTGATGAGGATGTCTAGCCATCTTTAAAGATATTTGAGATAACACA
Found at i:431259 original size:191 final size:189
Alignment explanation
Indices: 430934--431524 Score: 889
Period size: 191 Copynumber: 3.1 Consensus size: 189
430924 GTATGACATT
* ** *
430934 GTTCCTTCGTGATGAGGACATATAACCATCTTTAAAGATATTTGAGATAACTCGGTTCCTTCGTG
1 GTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTTCGTG
* * * * * * *** *
430999 ACGAGGACATCTGACTATCTAAGGATGATGCT-ACTCCTTTATGATGAGGAATTCTGATCAATGG
66 ATGAGGACGTCTG-TTGTCTAAGGATGATG-TGACTCCTTCATGATGAGGAGTTCTGATTGGTAG
** *
431063 ATGACATTGTTCCTTCGTGATGAGGATGTCTAGCCATCTTTAAAGATATTTGAGATAACACA
129 ATGACATTGTTCCTTCGTGATGAGGACATCT-GCCATTTTTAAAGATATTTGAGATAACACA
431125 GTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTTCGTG
1 GTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTTCGTG
*
431190 ATGAGGATGTCTAGTTGTCTAAGGATGATGTGACTCCTTCATGATGAGGAGTTCTGATTGGTAGA
66 ATGAGGACGTCT-GTTGTCTAAGGATGATGTGACTCCTTCATGATGAGGAGTTCTGATTGGTAGA
* * *
431255 TGACATTATTCCTTCGTGATGAGGCCATCTGGCCATTTTTGAAGATATTTGAGATAACACA
130 TGACATTGTTCCTTCGTGATGAGGACATCT-GCCATTTTTAAAGATATTTGAGATAACACA
*
431316 GTACCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTTCGTG
1 GTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTTCGTG
431381 ATGAGGACGTCTGGTTGTCTAAGGATGATGTGACTCCTTCATGATGAGGAGTTCTGATTGGTAGA
66 ATGAGGACGTCT-GTTGTCTAAGGATGATGTGACTCCTTCATGATGAGGAGTTCTGATTGGTAGA
*
431446 TGACATTGTTCCTTCGTGATGAGGACATCTGACCATTTTTAAAGATATTTAAGATAACAC-
130 TGACATTGTTCCTTCGTGATGAGGACATCTG-CCATTTTTAAAGATATTTGAGATAACACA
431506 GATTCCTTCGTGATGAGGA
1 G-TTCCTTCGTGATGAGGA
431525 TGTCTGGCTG
Statistics
Matches: 366, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
190 3 0.01
191 362 0.99
192 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (189 bp):
GTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTTCGTG
ATGAGGACGTCTGTTGTCTAAGGATGATGTGACTCCTTCATGATGAGGAGTTCTGATTGGTAGAT
GACATTGTTCCTTCGTGATGAGGACATCTGCCATTTTTAAAGATATTTGAGATAACACA
Found at i:431324 original size:54 final size:54
Alignment explanation
Indices: 431265--431394 Score: 206
Period size: 54 Copynumber: 2.4 Consensus size: 54
431255 TGACATTATT
* * *
431265 CCTTCGTGATGAGGCCATCTGGCCATTTTTGAAGATATTTGAGATAACACAGTA
1 CCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTA
* *
431319 CCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
1 CCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTA
*
431373 CCTTCGTGATGAGGACGTCTGG
1 CCTTCGTGATGAGGACATCTGG
431395 TTGTCTAAGG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (54 bp):
CCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTA
Found at i:433580 original size:2 final size:2
Alignment explanation
Indices: 433567--433693 Score: 238
Period size: 2 Copynumber: 64.0 Consensus size: 2
433557 ACAACTAATT
*
433567 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
433608 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
433650 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
433692 TA
1 TA
433694 CGATATAGCA
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 121 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:435923 original size:55 final size:55
Alignment explanation
Indices: 435809--436498 Score: 1039
Period size: 55 Copynumber: 12.6 Consensus size: 55
435799 ACAGGTTCAT
* * *
435809 TCCCTATTCCTTCAGAGAGTATAGGACTCG----ATCTTCAACAAACGTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* * ** *
435860 TCCCTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAAAGTGTTTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* * * *
435915 TCCCTATTCCTTCAGAGAGTATAGGACTTGAACAACCTTCAACAAACGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* *
435970 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAACAATCGTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
*
436025 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTATGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
*
436080 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* * *
436135 TCCCTATTCCTTCAAAGAGTATAAGACTCGAACAATCTTTAGCAATCGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
** *
436190 TCTTTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* *
436245 TCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTGCAACAATCGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* * * * * *
436300 TCCCTATTTCTTCAGAGAGTATAAGACTTGAACAATATTCCATAATCGTGTCTAC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
436355 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* * * *
436410 TCCCTATTTCTTCAGAGAGTGTAAGACTCGAACAATTTTCAACAATCGT-TCTAC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
436464 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAA
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAA
436499 CCTTGATGCT
Statistics
Matches: 584, Mismatches: 51, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
51 29 0.05
54 37 0.06
55 518 0.89
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (55 bp):
TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
Found at i:436060 original size:165 final size:165
Alignment explanation
Indices: 435692--436498 Score: 1042
Period size: 165 Copynumber: 4.9 Consensus size: 165
435682 CCAGAAAACA
* * * * * * * * *
435692 TGTCCGCTCCCTATTCTTTCAGGGAGTATAGGATTTGAACAATCTTCTAAAAAT-ATAT-TCGTT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTC-AACAATCGTGTCT-GCT
* * * * * *
435755 CCCTACTGCTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAACAG-GT-T-CATTCCCTAT
64 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAATC-GTGTCTGC--TCCCTAT
* *
435816 TCCTTCAGAGAGTATAGGACTCG----ATCTTCAACAAACG
125 TCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
* * ** *
435853 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAAAGTGTTTGCTCC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* * * *
435918 CTATTCCTTCAGAGAGTATAGGACTTGAACAACCTTCAACAAACGTGTCTGCTCCCTATTCCTTC
66 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTC
*
435983 AGAGAGTATAAGACTCGAACAACCTTCAACAATCG
131 AGAGAGTATAAGACTCGAACAATCTTCAACAATCG
*
436018 TGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTATGCTCC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
*
436083 CTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTC
66 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTC
* * *
436148 AAAGAGTATAAGACTCGAACAATCTTTAGCAATCG
131 AGAGAGTATAAGACTCGAACAATCTTCAACAATCG
* ** *
436183 TGTCTGCTCTTTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCCGCTCC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* * *
436248 CTATTCCTTCAGAGAGTATAAGACTCAAACAATCTGCAACAATCGTGTCTGCTCCCTATTTCTTC
66 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTC
* * * *
436313 AGAGAGTATAAGACTTGAACAATATTCCATAATCG
131 AGAGAGTATAAGACTCGAACAATCTTCAACAATCG
**
436348 TGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* * * *
436413 CTATTTCTTCAGAGAGTGTAAGACTCGAACAATTTTCAACAATCGT-TCTACTCCCTATTCCTTC
66 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTC
436477 AGAGAGTATAAGACTCGAACAA
131 AGAGAGTATAAGACTCGAACAA
436499 CCTTGATGCT
Statistics
Matches: 575, Mismatches: 61, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
160 6 0.01
161 115 0.20
162 2 0.00
163 1 0.00
164 37 0.06
165 414 0.72
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (165 bp):
TGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTC
AGAGAGTATAAGACTCGAACAATCTTCAACAATCG
Found at i:437541 original size:45 final size:44
Alignment explanation
Indices: 437458--437542 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
437448 ATTTTAAAAC
* *
437458 TCAAGCCGCCCTTTGCGGTTTTCAACTTGAGACCTCCTTTGGTT
1 TCAAGACGCCCTTTGCGGTTTTCAACTCGAGACCTCCTTTGGTT
* * *
437502 TCAAGACGCTCTTTTCGAGTTTTCATCTCGA-ACCTTCCTTT
1 TCAAGACGCCCTTTGCG-GTTTTCAACTCGAGACC-TCCTTT
437543 TTGCTTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 17 0.50
45 17 0.50
ACGTcount: A:0.15, C:0.29, G:0.16, T:0.39
Consensus pattern (44 bp):
TCAAGACGCCCTTTGCGGTTTTCAACTCGAGACCTCCTTTGGTT
Found at i:447089 original size:22 final size:22
Alignment explanation
Indices: 447061--447108 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
447051 AATTTATCTC
447061 ATTAAAGGTACTTAGATGATAA
1 ATTAAAGGTACTTAGATGATAA
447083 ATTAAAGGTACTTAGATGATAA
1 ATTAAAGGTACTTAGATGATAA
447105 ATTA
1 ATTA
447109 TAAGAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (22 bp):
ATTAAAGGTACTTAGATGATAA
Found at i:449097 original size:2 final size:2
Alignment explanation
Indices: 449090--449122 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
449080 CGGATGGGGG
449090 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 T
449123 GTTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:451016 original size:18 final size:18
Alignment explanation
Indices: 450993--451074 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
450983 ATCGGTCACA
450993 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* * *
451011 ACCCGACCTGACTCATTG
1 ACCCGACCCGACCCGTTG
** *
451029 ACTTGACCCAACCCGTTG
1 ACCCGACCCGACCCGTTG
*
451047 ACCCGACCCGATCCGTTG
1 ACCCGACCCGACCCGTTG
*
451065 ACCTGACCCG
1 ACCCGACCCG
451075 TTGACCGGCG
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:451066 original size:36 final size:36
Alignment explanation
Indices: 450997--451073 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
450987 GTCACAACCC
* * *
450997 GACCCGACCCGTTGACCCGACCTGACTCATTGACTT
1 GACCCAACCCGTTGACCCGACCCGACTCATTGACCT
*
451033 GACCCAACCCGTTGACCCGACCCGA-TCCGTTGACCT
1 GACCCAACCCGTTGACCCGACCCGACT-CATTGACCT
451069 GACCC
1 GACCC
451074 GTTGACCGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 1 0.03
36 35 0.97
ACGTcount: A:0.19, C:0.43, G:0.19, T:0.18
Consensus pattern (36 bp):
GACCCAACCCGTTGACCCGACCCGACTCATTGACCT
Found at i:453816 original size:2 final size:2
Alignment explanation
Indices: 453809--453833 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
453799 CGGATGGGGG
453809 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
453834 GTTTTAAAAA
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:459653 original size:17 final size:18
Alignment explanation
Indices: 459631--459674 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
459621 TCTGGTCCTG
*
459631 TTGGGCCTTC-AGGTTAT
1 TTGGGCCTGCTAGGTTAT
*
459648 TTGGGCCTGCTGGGTTAT
1 TTGGGCCTGCTAGGTTAT
459666 TTGGGCCTG
1 TTGGGCCTG
459675 GAACATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.07, C:0.18, G:0.36, T:0.39
Consensus pattern (18 bp):
TTGGGCCTGCTAGGTTAT
Found at i:462065 original size:301 final size:300
Alignment explanation
Indices: 461535--462125 Score: 858
Period size: 301 Copynumber: 2.0 Consensus size: 300
461525 TCAATAATTT
* * ** * *
461535 AAAGTTGTTTTATAACTAAAAATCTCACCGCAGGTCATCTAGAGTCGGGAATATTTGATAACCTT
1 AAAGTTATTTTATAACTAAAAATCTCACCGCAGGCCATCTAGAGTCAAGAATATTTGATAACATG
* * * *
461600 TCTAAATTGCAAGAATTAAGCTTGGAAGGGAACCAAATATCTGGTAGCATTCCTAGTAGTTTATA
66 TCTAAATTGCAAGAATTAAGCTTCGAAGGGAACCAAATATCTGGTAGCATTCCCAGCAGCTTATA
* *
461665 CAAGAGCAAAGAGTTGAGGTATTTATCATTGTGGAACAACTCTATGGAAGGAAGTATACCTATAG
131 CAAGAGCAAAGAGTTGAGGTATATATCATTGTGGAACAACACTATGGAAGGAAGTATACCTATAG
* * *
461730 AAATCGGAAATTTGACTATGCTCCAATATTTGTATATTGTTTACAACAATTTCAAAGGTAAAAAA
196 AAATCGGAAATTTGACTATGCTCCAATATTTGTATATTGCTCACAACAACTTCAAAGGTAAAAAA
*
461795 TTCCTCATTTGCATTCCGTTCTCTTTTATTTTCATTACATA
261 -TCCTCATTTGCATTCCGTTCTCCTTTATTTTCATTACATA
* ** * * *
461836 AAAGTTATTTTATAATTATCAATCTCACTGCAGGCCATCTTGAGTCAATAATATTTGATAACATG
1 AAAGTTATTTTATAACTAAAAATCTCACCGCAGGCCATCTAGAGTCAAGAATATTTGATAACATG
* * * * * *
461901 TCTAAATTGCAAGTATTAAGGTTCGATGGGAACCAGATTTCTGGTATCATTCCCAGCAGCTTATA
66 TCTAAATTGCAAGAATTAAGCTTCGAAGGGAACCAAATATCTGGTAGCATTCCCAGCAGCTTATA
* *
461966 CAAGTGCAAGGAGTTGAGGTATATATCATTGTGGAACAACACTATGGAAGGAAGTATACCTATAG
131 CAAGAGCAAAGAGTTGAGGTATATATCATTGTGGAACAACACTATGGAAGGAAGTATACCTATAG
* * *
462031 AAATCGGAAATTTGACTATGCTCCAATTTTTGTATCTTGCTCACAACAACTTCAGAGGTAAAAAA
196 AAATCGGAAATTTGACTATGCTCCAATATTTGTATATTGCTCACAACAACTTCAAAGGTAAAAAA
* *
462096 TCCTCATTTGTATTTCGTTCTCCTTTATTT
261 TCCTCATTTGCATTCCGTTCTCCTTTATTT
462126 AATTAGCTGT
Statistics
Matches: 255, Mismatches: 35, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
300 27 0.11
301 228 0.89
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (300 bp):
AAAGTTATTTTATAACTAAAAATCTCACCGCAGGCCATCTAGAGTCAAGAATATTTGATAACATG
TCTAAATTGCAAGAATTAAGCTTCGAAGGGAACCAAATATCTGGTAGCATTCCCAGCAGCTTATA
CAAGAGCAAAGAGTTGAGGTATATATCATTGTGGAACAACACTATGGAAGGAAGTATACCTATAG
AAATCGGAAATTTGACTATGCTCCAATATTTGTATATTGCTCACAACAACTTCAAAGGTAAAAAA
TCCTCATTTGCATTCCGTTCTCCTTTATTTTCATTACATA
Found at i:462954 original size:26 final size:26
Alignment explanation
Indices: 462914--462999 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
462904 ATAGTAATTT
462914 ATTTA-TTTTTAATTATATTGTCTTA
1 ATTTATTTTTTAATTATATTGTCTTA
* *
462939 ATTTATTTTTTAATTATTTTTTCTATA
1 ATTTATTTTTTAATTATATTGTCT-TA
* *
462966 A--T-GTGTTTAATTATATTGTCTTA
1 ATTTATTTTTTAATTATATTGTCTTA
462989 ATTTATTTTTT
1 ATTTATTTTTT
463000 TTAACTTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
23 3 0.06
24 15 0.31
25 7 0.15
26 20 0.42
27 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (26 bp):
ATTTATTTTTTAATTATATTGTCTTA
Found at i:466764 original size:3 final size:3
Alignment explanation
Indices: 466756--466803 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
466746 CTTAAAACTT
* *
466756 AGA AGA AGA AGA AGA AGAA AGA ATA AGAA AGA AGAA AGA AGA AAA AGA
1 AGA AGA AGA AGA AGA AG-A AGA AGA AG-A AGA AG-A AGA AGA AGA AGA
466804 CAGGGGTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 29 0.76
4 9 0.24
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:466798 original size:10 final size:10
Alignment explanation
Indices: 466756--466791 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
466746 CTTAAAACTT
466756 AGAAGAAG-A
1 AGAAGAAGAA
466765 AGAAGAAGAA
1 AGAAGAAGAA
*
466775 AGAATAAGAA
1 AGAAGAAGAA
466785 AGAAGAA
1 AGAAGAA
466792 AGAAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (10 bp):
AGAAGAAGAA
Found at i:470427 original size:26 final size:26
Alignment explanation
Indices: 470387--470472 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
470377 ATAGTAAATT
470387 ATTTA-TTTTTAATTATATTGTCTTA
1 ATTTATTTTTTAATTATATTGTCTTA
* *
470412 ATTTATTTTTTAATTATTTTTTCTATA
1 ATTTATTTTTTAATTATATTGTCT-TA
* *
470439 A--T-GTGTTTAATTATATTGTCTTA
1 ATTTATTTTTTAATTATATTGTCTTA
470462 ATTTATTTTTT
1 ATTTATTTTTT
470473 TAACTTGTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
23 3 0.06
24 15 0.31
25 7 0.15
26 20 0.42
27 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (26 bp):
ATTTATTTTTTAATTATATTGTCTTA
Found at i:476019 original size:70 final size:70
Alignment explanation
Indices: 475906--476046 Score: 203
Period size: 70 Copynumber: 2.0 Consensus size: 70
475896 GGATTTTTTA
** *
475906 TTCAAAGCAAAGTGTAATGGGGAAGCACTTTTACTTTGCGTCAGGTGTATT-GAGTTTAATAATT
1 TTCAAAGCAAAGTGTAATGGGGAAGCACTCGTACTTTGCGTCAGGTGT-TTCGAATTTAATAATT
475970 CCATGG
65 CCATGG
** * *
475976 TTCAAAGCATTGTGTAGTGGGGAAGCACTCGTACTTTGCGTCAGGTGTTTCGAATTTATTAATTC
1 TTCAAAGCAAAGTGTAATGGGGAAGCACTCGTACTTTGCGTCAGGTGTTTCGAATTTAATAATTC
476041 CATGG
66 CATGG
476046 T
1 T
476047 GGAGGTTAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
69 2 0.03
70 61 0.97
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (70 bp):
TTCAAAGCAAAGTGTAATGGGGAAGCACTCGTACTTTGCGTCAGGTGTTTCGAATTTAATAATTC
CATGG
Found at i:477456 original size:14 final size:13
Alignment explanation
Indices: 477422--477460 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
477412 AACTTAGAAG
477422 AAGAAGAAGAAAAA
1 AAGAAGAA-AAAAA
*
477436 AAAAAGAAAAAAGA
1 AAGAAGAAAAAA-A
477450 AAGAAGAAAAA
1 AAGAAGAAAAA
477461 GACAGGGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAAA
Found at i:482174 original size:19 final size:19
Alignment explanation
Indices: 482150--482188 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
482140 ATTCTTTAGA
482150 ACCAAATCATTTAAAGACT
1 ACCAAATCATTTAAAGACT
482169 ACCAAATCATTTAAAGACT
1 ACCAAATCATTTAAAGACT
482188 A
1 A
482189 TCGAACTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (19 bp):
ACCAAATCATTTAAAGACT
Found at i:482845 original size:72 final size:72
Alignment explanation
Indices: 482766--482908 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 72
482756 GGCAATTTGT
* ** ** * *
482766 CAAAACTAGAAACGTTGAGCTTGGGCAACAACAACCTTGAAGGTTAAATCCCCATGACTGTGGGA
1 CAAAACTAGAAACGTTGACCTTGACCAACAACAACCTCAAAGGGTAAATCCCCATGACTATGGGA
*
482831 AGCCTTC
66 AACCTTC
* * * *
482838 CAAAACTAGAAGCGTTGACCTTGACCAACAACAATCTCAAAGGGTCAATCCCCGTGACTATGGGA
1 CAAAACTAGAAACGTTGACCTTGACCAACAACAACCTCAAAGGGTAAATCCCCATGACTATGGGA
482903 AACCTT
66 AACCTT
482909 TCACATTTGA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (72 bp):
CAAAACTAGAAACGTTGACCTTGACCAACAACAACCTCAAAGGGTAAATCCCCATGACTATGGGA
AACCTTC
Found at i:484568 original size:24 final size:23
Alignment explanation
Indices: 484519--484568 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
484509 CCGACCCGTT
* *
484519 GACCCGACTCGTTTGACCAACTC
1 GACCCGACCCGTTTGACCAACCC
* *
484542 GACCCGACCCGGTTTGCCCGACCC
1 GACCCGACCC-GTTTGACCAACCC
484566 GAC
1 GAC
484569 TGCCCGACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.18, C:0.44, G:0.22, T:0.16
Consensus pattern (23 bp):
GACCCGACCCGTTTGACCAACCC
Found at i:485573 original size:30 final size:32
Alignment explanation
Indices: 485537--485606 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
485527 TAAGGTGACC
* * *
485537 CTTGGGTATG-CTTTGTGGCCCTGAG-ATTTT
1 CTTGGGTAAGCCTTTGTGGCCCCGAGAATTAT
485567 CTTGGGTAAGCCTTTGTGGCCCCGAGAATTAT
1 CTTGGGTAAGCCTTTGTGGCCCCGAGAATTAT
485599 CTTGGGTA
1 CTTGGGTA
485607 GGTTCGCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 9 0.26
31 14 0.40
32 12 0.34
ACGTcount: A:0.14, C:0.19, G:0.30, T:0.37
Consensus pattern (32 bp):
CTTGGGTAAGCCTTTGTGGCCCCGAGAATTAT
Found at i:493152 original size:137 final size:136
Alignment explanation
Indices: 492899--493145 Score: 377
Period size: 136 Copynumber: 1.8 Consensus size: 136
492889 TGATTGCTCG
*
492899 ACCCGTTGACCGTTGACTTTGACCAAAAAGTCAAATTTTTTGAAAAGTCATATTTTATGATTTTC
1 ACCCGTTGACCGTTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTCATATTTTATGATTTTC
* **
492964 GACGTCCTGAGTCCGATTCCTAAGTCCGTTTTGCCAAATTTGAACCTGAAAGTCTCCAAATTGTC
66 GACGTCCTGAGTCCGATTCCGAAGTCCGTTTTGCCAAATTCAAACCTGAAAGTCTCCAAATTGTC
493029 AGTCAA
131 AGTCAA
* * * * **
493035 ACCCGTTGACTGTTGAGTTTGACCAAAAATTCAAAATTTTTGAAAAGTCGTATTTTATTTTTTTT
1 ACCCGTTGACCGTTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTCATATTTTA-TGATTTT
* *
493100 CGACGTCCTGAGTTCGATTCCGAAGTCCGTTTTGCTAAATTCAAAC
65 CGACGTCCTGAGTCCGATTCCGAAGTCCGTTTTGCCAAATTCAAAC
493146 TCGAAAGCCT
Statistics
Matches: 98, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
136 52 0.53
137 46 0.47
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (136 bp):
ACCCGTTGACCGTTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTCATATTTTATGATTTTC
GACGTCCTGAGTCCGATTCCGAAGTCCGTTTTGCCAAATTCAAACCTGAAAGTCTCCAAATTGTC
AGTCAA
Found at i:495857 original size:31 final size:31
Alignment explanation
Indices: 495822--495880 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
495812 ATTAATTTAA
**
495822 ACATTTAATATTATGATGATTTATTTATAAT
1 ACATTTAATATTAAAATGATTTATTTATAAT
* *
495853 ACATTTTATATTAAAATTATTTATTTAT
1 ACATTTAATATTAAAATGATTTATTTAT
495881 TTTTACATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (31 bp):
ACATTTAATATTAAAATGATTTATTTATAAT
Found at i:496008 original size:19 final size:20
Alignment explanation
Indices: 495984--496034 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
495974 TCATTTAAAT
495984 ATGACTTGCTTTCCA-CACA
1 ATGACTTGCTTTCCACCACA
496003 ATGACTTGCTTTCCACCACA
1 ATGACTTGCTTTCCACCACA
496023 ATGACTTGCTTT
1 ATGACTTGCTTT
496035 TTCCACTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGACTTGCTTTCCACCACA
Found at i:500270 original size:26 final size:26
Alignment explanation
Indices: 500241--500329 Score: 114
Period size: 26 Copynumber: 3.5 Consensus size: 26
500231 ATAGTAATTT
500241 ATTTATTTTTTAATTATATTGTCTTA
1 ATTTATTTTTTAATTATATTGTCTTA
500267 ATTTATTTTTTAATTAT-TT-T-TTCA
1 ATTTATTTTTTAATTATATTGTCTT-A
* *
500291 A-TAATGTGTTTAATTATATTGTCTTA
1 ATTTAT-TTTTTAATTATATTGTCTTA
500317 ATTTATTTTTTAA
1 ATTTATTTTTTAA
500330 CTTGTGCAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
23 5 0.09
24 13 0.25
25 4 0.08
26 26 0.49
27 5 0.09
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.64
Consensus pattern (26 bp):
ATTTATTTTTTAATTATATTGTCTTA
Found at i:500271 original size:50 final size:51
Alignment explanation
Indices: 500216--500330 Score: 146
Period size: 50 Copynumber: 2.3 Consensus size: 51
500206 TTAGCTTTTC
* * *
500216 AATTTATTTTTTAACATAGTAATTT-ATTTAT-TTTTTAATTATATTGTCTT
1 AATTTATTTTTTAACATA-TAATTTCAATAATGTGTTTAATTATATTGTCTT
* **
500266 AATTTATTTTTTAA-TTATTTTTTCAATAATGTGTTTAATTATATTGTCTT
1 AATTTATTTTTTAACATATAATTTCAATAATGTGTTTAATTATATTGTCTT
500316 AATTTATTTTTTAAC
1 AATTTATTTTTTAAC
500331 TTGTGCAACA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
48 4 0.07
49 6 0.11
50 46 0.82
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (51 bp):
AATTTATTTTTTAACATATAATTTCAATAATGTGTTTAATTATATTGTCTT
Found at i:500275 original size:24 final size:24
Alignment explanation
Indices: 500248--500325 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
500238 TTTATTTATT
500248 TTTTAATTATATTGTCTTAATTTA
1 TTTTAATTATATTGTCTTAATTTA
* * * *
500272 TTTTTTAATTATTTTTTCAATAATGT-
1 --TTTTAATTATATTGTC-TTAATTTA
*
500298 GTTTAATTATATTGTCTTAATTTA
1 TTTTAATTATATTGTCTTAATTTA
500322 TTTT
1 TTTT
500326 TTAACTTGTG
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
23 5 0.12
24 16 0.40
26 14 0.35
27 5 0.12
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (24 bp):
TTTTAATTATATTGTCTTAATTTA
Found at i:507412 original size:15 final size:16
Alignment explanation
Indices: 507392--507422 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
507382 GACTTTGACC
507392 GAAAAGTCA-ATTTTA
1 GAAAAGTCATATTTTA
507407 GAAAAGTCATATTTTA
1 GAAAAGTCATATTTTA
507423 TGTTTTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (16 bp):
GAAAAGTCATATTTTA
Found at i:510249 original size:44 final size:44
Alignment explanation
Indices: 510159--510494 Score: 493
Period size: 43 Copynumber: 7.7 Consensus size: 44
510149 GTTCCTTTAC
* *
510159 TGTGTGCAAGAGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGT
* *
510202 TGTGTGCAAGGGTAAGCTTTATAGTTTCCCCCAGGTCCCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGT
* *
510246 TGTGTGCAAGGGTAAGCCTTACAGTTTTCCTCAGGTCCCTTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCC-TTTGT
*
510291 TGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTCCCTTTGC
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGT
* *
510334 TGTGTGCAAGGGTAAGCC-TACAGTTTCCCTCAGGTCCCTTTGC
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGT
* ** *
510377 TATGTGCAAGGGTAAGCCTTACAGTTTCCCCCATTTCCCTTTGC
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGT
*
510421 TGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTT-T
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGT
510463 CTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 -TGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
510495 GGCTCTTTTG
Statistics
Matches: 267, Mismatches: 20, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
42 8 0.03
43 116 0.43
44 111 0.42
45 32 0.12
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.34
Consensus pattern (44 bp):
TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGT
Found at i:510416 original size:87 final size:87
Alignment explanation
Indices: 510146--510494 Score: 522
Period size: 87 Copynumber: 4.0 Consensus size: 87
510136 ACCATTACAA
* * * * *
510146 CAGGTTCCTTTACTGTGTGCAAGAGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAA
* *
510211 GGGTAAGCTTTATAGTTTCCCC
66 GGGTAAGCCTTACAGTTTCCCC
* * *
510233 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTTCCTCAGGTCCCTTTTGTTGTGTGC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGTCCC-TTTGCTGTGTGC
510298 AAGGGTAAGCCTTACAGTTT-CCC
64 AAGGGTAAGCCTTACAGTTTCCCC
*
510321 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC-TACAGTTTCCCTCAGGTCCCTTTGCTATGTGCA
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC-CAGGTCCCTTTGCTGTGTGCA
510385 AGGGTAAGCCTTACAGTTTCCCC
65 AGGGTAAGCCTTACAGTTTCCCC
** * *
510408 CATTTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTTCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAA
510473 GGGTAAGCCTTACAGTTTCCCC
66 GGGTAAGCCTTACAGTTTCCCC
510495 GGCTCTTTTG
Statistics
Matches: 240, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
86 35 0.15
87 119 0.50
88 56 0.23
89 30 0.12
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (87 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAA
GGGTAAGCCTTACAGTTTCCCC
Done.