Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003873.1 Hibiscus syriacus cultivar Beakdansim tig00008344_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: 73938
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1897 original size:27 final size:30
Alignment explanation
Indices: 1867--1923 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 30
1857 TGTCAATTTT
*
1867 TAAAAAATTT-GAAAT-TT-TTATTTAAAA
1 TAAAAAATTTAAAAATATTATTATTTAAAA
1894 TAAAAAATTTAAAAATATTATTATTTAAAA
1 TAAAAAATTTAAAAATATTATTATTTAAAA
1924 ATCTTAGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.38
28 4 0.15
29 2 0.08
30 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
TAAAAAATTTAAAAATATTATTATTTAAAA
Found at i:2216 original size:37 final size:37
Alignment explanation
Indices: 2136--2219 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
2126 AACAAGTTGG
* * *
2136 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAGATTTATATAATTTCTTTAAAAAATTAAAATTC
* *
2173 ATAAGATTTATATAATTT-TTTACAAAATTGAAAATAT-
1 AAAAGATTTATATAATTTCTTTAAAAAATT-AAAAT-TC
2210 AAAAGATTTA
1 AAAAGATTTA
2220 ATGAAAGGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 10 0.26
37 28 0.72
38 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAAGATTTATATAATTTCTTTAAAAAATTAAAATTC
Found at i:2630 original size:18 final size:19
Alignment explanation
Indices: 2596--2631 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2586 ATCTCTAAAC
*
2596 CTAAAAAAAACTCAAATCT
1 CTAAAAAAAACTAAAATCT
2615 CTAAAAAAAAC-AAAATC
1 CTAAAAAAAACTAAAATC
2632 CCAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17
Consensus pattern (19 bp):
CTAAAAAAAACTAAAATCT
Found at i:13317 original size:65 final size:65
Alignment explanation
Indices: 13213--13422 Score: 242
Period size: 65 Copynumber: 3.2 Consensus size: 65
13203 TCCAGAAGTT
* * *
13213 GTTTCCCTTGAAATACAAACATTTAGATTGTTTCTCTTGAAATAAGTTTTATCTCTCTTGAGACA
1 GTTTCCCTTGAAATACAAACATTGAGATTGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACA
** * *
13278 GTTTCCCTTGAAATATGAACATTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTTAGACA
1 GTTTCCCTTGAAATACAAACATTGAGATTGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACA
* * ** * * *
13343 GTTTCCCTTGTAACACAAATTTTTTAG-TCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAG
1 GTTTCCCTTGAAATACAAA-CATTGAGAT-TGTTTCTCTTGAAACAAA-TTTTATCTCTCTTGAG
*
13407 ATA
63 ACA
*
13410 GTTTCTCTTGAAA
1 GTTTCCCTTGAAA
13423 CAAATCCCTA
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
65 74 0.60
66 21 0.17
67 28 0.23
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (65 bp):
GTTTCCCTTGAAATACAAACATTGAGATTGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACA
Found at i:13935 original size:3 final size:3
Alignment explanation
Indices: 13929--14008 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
13919 ATTATTATTA
* * *
13929 TTG TTG TTG TTG TTG TTA TTA TTG TTG TTG TTG TTG TTG TTG TTG TTA
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
*
13977 TTG TTG TTG TTT TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
14009 ATTTACATGT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.04, C:0.00, G:0.28, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:13949 original size:21 final size:21
Alignment explanation
Indices: 13923--14011 Score: 133
Period size: 21 Copynumber: 4.2 Consensus size: 21
13913 AGCTGTATTA
13923 TTATTATTGTTGTTGTTGTTG
1 TTATTATTGTTGTTGTTGTTG
13944 TTATTATTGTTGTTGTTGTTG
1 TTATTATTGTTGTTGTTGTTG
* * *
13965 TTGTTGTTGTTATTGTTGTTG
1 TTATTATTGTTGTTGTTGTTG
* *
13986 TTTTTGTTGTTGTTGTTGTTG
1 TTATTATTGTTGTTGTTGTTG
14007 TTATT
1 TTATT
14012 TACATGTCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.07, C:0.00, G:0.25, T:0.69
Consensus pattern (21 bp):
TTATTATTGTTGTTGTTGTTG
Found at i:18911 original size:20 final size:20
Alignment explanation
Indices: 18876--18913 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18866 CGGGTGAACT
**
18876 TTTAGATTTTTTGGTCAATC
1 TTTAGATTTTCAGGTCAATC
18896 TTTAGATTTTCAGGTCAA
1 TTTAGATTTTCAGGTCAA
18914 CCGATGTCGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTAGATTTTCAGGTCAATC
Found at i:19743 original size:23 final size:23
Alignment explanation
Indices: 19708--19767 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
19698 ATCAAGCATA
* *
19708 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
*
19731 ATAACGTAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
19754 ATAATAAAATAGGT
1 ATAACATAATAGGT
19768 TAATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:19948 original size:23 final size:23
Alignment explanation
Indices: 19879--19938 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
19869 ACATATTAGA
19879 TAGCGCTTATATAACGTAATAGG
1 TAGCGCTTATATAACGTAATAGG
19902 TAGCGCTTATATAACGTAATAGG
1 TAGCGCTTATATAACGTAATAGG
19925 TAGCGCTTATATAA
1 TAGCGCTTATATAA
19939 TAAAATAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (23 bp):
TAGCGCTTATATAACGTAATAGG
Found at i:20024 original size:181 final size:181
Alignment explanation
Indices: 19708--20083 Score: 628
Period size: 181 Copynumber: 2.1 Consensus size: 181
19698 ATCAAGCATA
* *
19708 ATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAACGCTTATATAATAAAATAGGTTAATT
1 ATAACGTAATAGGTAGCGCTTATATAACGTAATAGGTAACGCTTATATAATAAAATAGGTTAATT
* * *
19773 ACTTAATTTATTATTACAGCATATTAGGTAAACACCTAAAATGTTACCAAGGATAACATAACCGG
66 ACTTAATTTATTATTACAACATATTAGGTAAACACCTAAAATGTTACCAAGGATAACATAAACAG
19838 TTAATTACTGGAAACATTATCAAGCATAACAACATATTA-GATAGCGCTTAT
131 TTAATTACTGGAAACATTATCAAGCATAACAACATATTATG-TAGCGCTTAT
*
19889 ATAACGTAATAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
1 ATAACGTAATAGGTAGCGCTTATATAACGTAATAGGTAACGCTTATATAATAAAATAGGTTAATT
* * *
19954 ACTTAATTTTTTATTACAATATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAAACAG
66 ACTTAATTTATTATTACAACATATTAGGTAAACACCTAAAATGTTACCAAGGATAACATAAACAG
* *
20019 TTAATTACTGGAAACATTATCAAGCATAATAACATATTATGTAGCGCTTTT
131 TTAATTACTGGAAACATTATCAAGCATAACAACATATTATGTAGCGCTTAT
*
20070 GTAACGTAATAGGT
1 ATAACGTAATAGGT
20084 TGTGCATTAT
Statistics
Matches: 182, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
181 181 0.99
182 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (181 bp):
ATAACGTAATAGGTAGCGCTTATATAACGTAATAGGTAACGCTTATATAATAAAATAGGTTAATT
ACTTAATTTATTATTACAACATATTAGGTAAACACCTAAAATGTTACCAAGGATAACATAAACAG
TTAATTACTGGAAACATTATCAAGCATAACAACATATTATGTAGCGCTTAT
Found at i:22413 original size:21 final size:21
Alignment explanation
Indices: 22389--22430 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22379 AAATACGCCT
22389 AATTTAAAAAATATCGATACA
1 AATTTAAAAAATATCGATACA
* *
22410 AATTTAAAAAGTGTCGATACA
1 AATTTAAAAAATATCGATACA
22431 TTATGTTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (21 bp):
AATTTAAAAAATATCGATACA
Found at i:22745 original size:175 final size:177
Alignment explanation
Indices: 22400--22747 Score: 594
Period size: 175 Copynumber: 2.0 Consensus size: 177
22390 ATTTAAAAAA
* * *
22400 TATCGATACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACTGGTATA
1 TATCGACACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATA
*
22465 TTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTACGATGTTTTTGGGG
66 TTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTACGATGTTTTTGGGG
*
22530 TCGATACTTTTAATAAATGTATCGACACTTTATTGTGCACCTCATTT
131 TCGATACTTTTAATAAATGTATCGACACTTTATCGTGCACCTCATTT
*
22577 TATCGACAC-AATTTAAAAAGTATCGATACATTATGTTGACTTATTTTCTAATT-AACCGGTATA
1 TATCGACACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATA
* *
22640 TTTCTATCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGAT-TTTTTGGGG
66 TTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTACGATGTTTTTGGGG
22704 TCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTC
131 TCGATACTTTTAATAAATGTATCGACACTTTAT-CGTGCACCTC
22748 GTTTGGCATT
Statistics
Matches: 162, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
174 42 0.26
175 70 0.43
176 42 0.26
177 8 0.05
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (177 bp):
TATCGACACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATA
TTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTACGATGTTTTTGGGG
TCGATACTTTTAATAAATGTATCGACACTTTATCGTGCACCTCATTT
Found at i:22958 original size:197 final size:198
Alignment explanation
Indices: 22577--23130 Score: 860
Period size: 198 Copynumber: 2.8 Consensus size: 198
22567 CACCTCATTT
* *
22577 TATCGACACAATTTAAAAA-GTATCGATACATTATGTTGACTTATTTTCTAATTAACCGGTATAT
1 TATCGACACAATTTAAAAATGTATCGATACATTATGTTGACCTATTTTCTAATTAATCGGTATAT
* *
22641 TTCTATCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGAT-TTTTTGGGGT
66 TTCTATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGAT
* * *
22705 CGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTATAGG-CA
131 CTATACTTTTAATAAAT-TATCGACACTTTATGTGTGCACCTCGTTTGACATTCATTAT-GGACA
22769 AAAAG
194 AAAAG
22774 TATCGACACAATTTAAAAATGTATCGATACATTATGTTGACCTATTTTCTAATTAATCGGTATAT
1 TATCGACACAATTTAAAAATGTATCGATACATTATGTTGACCTATTTTCTAATTAATCGGTATAT
* *
22839 TTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGAT
66 TTCTATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGAT
*
22904 CTATACTTTTAATAAA-TATCGACACTTTATGTGTGCACCTCGTTTGACATTCATTCTGGACAAA
131 CTATACTTTTAATAAATTATCGACACTTTATGTGTGCACCTCGTTTGACATTCATTATGGACAAA
22968 AAG
196 AAG
22971 TATCGACACAATTT-AAAATGTATCG----A-TATGTTGACCTATTTTTCTAATTAAATCGGTAT
1 TATCGACACAATTTAAAAATGTATCGATACATTATGTTGACCTA-TTTTCTAATT-AATCGGTAT
*
23030 ATTTCTATCGGTTACATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
64 ATTTCTATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
* *
23095 ATCTATACAATTTTAA-AAATTATCGATACATTATGT
129 ATCTATAC--TTTTAATAAATTATCGACACTTTATGT
23131 TTACCTATTC
Statistics
Matches: 334, Mismatches: 15, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
191 12 0.04
192 11 0.03
193 79 0.24
194 3 0.01
195 20 0.06
196 13 0.04
197 78 0.23
198 94 0.28
199 24 0.07
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (198 bp):
TATCGACACAATTTAAAAATGTATCGATACATTATGTTGACCTATTTTCTAATTAATCGGTATAT
TTCTATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGAT
CTATACTTTTAATAAATTATCGACACTTTATGTGTGCACCTCGTTTGACATTCATTATGGACAAA
AAG
Found at i:24563 original size:24 final size:25
Alignment explanation
Indices: 24506--24563 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
24496 GCTGAAATTT
24506 ATATCGAAATCCAAACTCAAATTGAA
1 ATAT-GAAATCCAAACTCAAATTGAA
* * *
24532 AT-TTAAATTCAAACTCCAATT-AA
1 ATATGAAATCCAAACTCAAATTGAA
24555 ATATGAAAT
1 ATATGAAAT
24564 GAACATGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 4 0.15
24 20 0.74
25 1 0.04
26 2 0.07
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (25 bp):
ATATGAAATCCAAACTCAAATTGAA
Found at i:27088 original size:18 final size:16
Alignment explanation
Indices: 27064--27111 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
27054 GAAGAAGCAC
*
27064 TTGGTTGAGGAGAAGG
1 TTGGTTGAGAAGAAGG
27080 TTGTCGTTGAGAAG-AGG
1 TTG--GTTGAGAAGAAGG
27097 TTGGTTGAGAAGAAG
1 TTGGTTGAGAAGAAG
27112 ATTTAAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
17 6 0.21
18 8 0.29
ACGTcount: A:0.27, C:0.02, G:0.44, T:0.27
Consensus pattern (16 bp):
TTGGTTGAGAAGAAGG
Found at i:27429 original size:20 final size:20
Alignment explanation
Indices: 27406--27443 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27396 GCGTAATTCA
27406 AAAAAGTATCGATACAATTT
1 AAAAAGTATCGATACAATTT
*
27426 AAAAAGTATTGATACAAT
1 AAAAAGTATCGATACAAT
27444 ATGTTTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.29
Consensus pattern (20 bp):
AAAAAGTATCGATACAATTT
Found at i:27429 original size:21 final size:20
Alignment explanation
Indices: 27400--27443 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
27390 AAACACGCGT
27400 AATTCAAAAAAGTATCGATAC
1 AATTC-AAAAAGTATCGATAC
* *
27421 AATTTAAAAAGTATTGATAC
1 AATTCAAAAAGTATCGATAC
27441 AAT
1 AAT
27444 ATGTTTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (20 bp):
AATTCAAAAAGTATCGATAC
Found at i:27868 original size:198 final size:198
Alignment explanation
Indices: 27407--28152 Score: 965
Period size: 198 Copynumber: 3.8 Consensus size: 198
27397 CGTAATTCAA
* * *
27407 AAAAGTATCGATACAATTTAAAAAGTATTGATACAATATGTTTACCTATTCTCTAATAAAACCGG
1 AAAAGTATCGACACAATTTAAAAAGTATCGATACAATATGTTGACCTATTCTCTAATAAAACCGG
* * *
27472 TACATTTTTACCA--TACATTGTAAAATTACCTATTA-ATTATAATTATCGATTTCGATATTTTT
66 TATATTTCTACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATATTTTT
* *
27534 GGGATCGATACAATTTTAAATGTATCGACACTTTATCCGTGCACCTCGTTGGGCATTCATTCTTG
131 GGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGG
27599 ACC
196 ACC
* * * * * * * *
27602 AAAAGTATCGACACAAATTTTAAAAGTGTCGATATACTATATGGACCTATTTTCTAATTAAA-CG
1 AAAAGTATCGACAC-AATTTAAAAAGTATCGATACAATATGTTGACCTATTCTCTAATAAAACCG
* * *
27666 GTATATTTCTACCAGTTATATTGCAAATTTACCTATTACATTATAATTATCGATTTTGATATTTT
65 GTATATTTCTACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATATTTT
* * * *
27731 AGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTATG
130 TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTG
27796 GACC
195 GACC
* * * *
27800 AAAAGTATCGACACAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGG
1 AAAAGTATCGACACAATTTAAAAAGTATCGATACAATATGTTGACCTATTCTCTAATAAAACCGG
* * * * * *
27865 TATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTTTAATTATTGGTTTCGATGTTTTC
66 TATATTTCTACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATATTTTT
* * *
27930 GGGATCGATACAATTTTAAATGTATCGACACTTTATGCATGCACCTTGTTGGGCATTTATTCTGG
131 GGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGG
27995 ACC
196 ACC
* * * * * * *
27998 ---A-TATCAACACAATTTAAAAAAGTATCGACATAATATGTTCACCTATTCTGTCATAAAACTG
1 AAAAGTATCGACACAATTT-AAAAAGTATCGATACAATATGTTGACCTATTCTCTAATAAAACCG
*
28059 GTATA-TTCTTACCAGTTACATTGTAAATTTACCTATTACTTTATAATTATC-AGTTTCGATATT
65 GTATATTTC-TACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGA-TTTCGATATT
*
28122 TTTGGGATCGATAAAATTTTAAAAT-TATCGA
128 TTTGGGATCGATACAATTTT-AAATGTATCGA
28153 TACATTATTT
Statistics
Matches: 480, Mismatches: 62, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
194 16 0.03
195 139 0.29
196 41 0.09
197 61 0.13
198 223 0.46
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (198 bp):
AAAAGTATCGACACAATTTAAAAAGTATCGATACAATATGTTGACCTATTCTCTAATAAAACCGG
TATATTTCTACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATATTTTT
GGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGG
ACC
Found at i:28132 original size:393 final size:391
Alignment explanation
Indices: 27407--28152 Score: 1009
Period size: 393 Copynumber: 1.9 Consensus size: 391
27397 CGTAATTCAA
* * *
27407 AAAAGTATCGATACAATTTAAAAAGTATTGATACAATATGTTTACCTATTCTCTAATAAAACCGG
1 AAAAGTATCGACACAATTTAAAAAGTATCGATACAATATGTTGACCTATTCTCTAATAAAACCGG
* *
27472 TACATTTTTACCATACATTGTAAAATTACCTATTAATTATAATTATCGATTTCGATATTTTTGGG
66 TACATTTCTACCATACATTGTAAAATTACCTATTAATTATAATTATCGATTTCGATATTTTCGGG
* *
27537 ATCGATACAATTTTAAATGTATCGACACTTTATCCGTGCACCTCGTTGGGCATTCATTCTTGACC
131 ATCGATACAATTTTAAATGTATCGACACTTTATCCATGCACCTCGTTGGGCATTCATTCTGGACC
* * * * * * * *
27602 AAAAGTATCGACACAAATTTTAAAAGTGTCGATATACTATATGGACCTATTTTCTAATTAAACGG
196 --AAGTATCAACACAAATTTAAAAAGTATCGACATAATATATGCACCTATTCTCTAATAAAACGG
* *
27667 TATATTTCTACCAGTTATATTGCAAATTTACCTATTACATTATAATTATCGATTTTGATATTTTA
259 TATATTTCTACCAGTTACATTGCAAATTTACCTATTACATTATAATTATCGATTTCGATATTTTA
*
27732 GGGATCGATACAATTTT-AAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTATG
324 GGGATCGATAAAATTTTAAAAT-TATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTATG
27796 GACC
388 GACC
* * * *
27800 AAAAGTATCGACACAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGG
1 AAAAGTATCGACACAATTTAAAAAGTATCGATACAATATGTTGACCTATTCTCTAATAAAACCGG
* * * * * * *
27865 TATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTTTAATTATTGGTTTCGATGTTTTC
66 TACATTTCTACC--ATACATTGTAAAATTACCTATTA-ATTATAATTATCGATTTCGATATTTTC
* * *
27930 GGGATCGATACAATTTTAAATGTATCGACACTTTATGCATGCACCTTGTTGGGCATTTATTCTGG
128 GGGATCGATACAATTTTAAATGTATCGACACTTTATCCATGCACCTCGTTGGGCATTCATTCTGG
* * * *
27995 ACC-A-TATCAACAC-AATTTAAAAAAGTATCGACATAATATGTTCACCTATTCTGTCATAAAAC
193 ACCAAGTATCAACACAAATTT-AAAAAGTATCGACATAATATATGCACCTATTCTCTAATAAAAC
* *
28057 TGGTATA-TTCTTACCAGTTACATTGTAAATTTACCTATTACTTTATAATTATC-AGTTTCGATA
257 -GGTATATTTC-TACCAGTTACATTGCAAATTTACCTATTACATTATAATTATCGA-TTTCGATA
*
28120 TTTTTGGGATCGATAAAATTTTAAAATTATCGA
319 TTTTAGGGATCGATAAAATTTTAAAATTATCGA
28153 TACATTATTT
Statistics
Matches: 306, Mismatches: 39, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
391 5 0.02
392 44 0.14
393 147 0.48
394 4 0.01
395 21 0.07
396 85 0.28
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (391 bp):
AAAAGTATCGACACAATTTAAAAAGTATCGATACAATATGTTGACCTATTCTCTAATAAAACCGG
TACATTTCTACCATACATTGTAAAATTACCTATTAATTATAATTATCGATTTCGATATTTTCGGG
ATCGATACAATTTTAAATGTATCGACACTTTATCCATGCACCTCGTTGGGCATTCATTCTGGACC
AAGTATCAACACAAATTTAAAAAGTATCGACATAATATATGCACCTATTCTCTAATAAAACGGTA
TATTTCTACCAGTTACATTGCAAATTTACCTATTACATTATAATTATCGATTTCGATATTTTAGG
GATCGATAAAATTTTAAAATTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTATGGAC
C
Found at i:30686 original size:123 final size:123
Alignment explanation
Indices: 30456--30701 Score: 402
Period size: 123 Copynumber: 2.0 Consensus size: 123
30446 TTTTCCCGGG
* * *
30456 TCTTTGATTCAAAGTAGGTGGACTAATGATGCAAAGGCTTGGGCACCCAGTTTTGTTGGCTTGAA
1 TCTTTGATTCAAAGTAGGTGGACTAAGGATACAAAGGCTTGGGCACCCAGTTTTGTTGACTTGAA
* * * * *
30521 TGTGCCTCCAGAAGTAATACAAATGGCAAGGTTCGCTGCTCTACGTGCAACGTCAAGT
66 TGTGCCTCAAGAAGTAATACAAATGGAAAGGCTCACTACTCTACGTGCAACGTCAAGT
*
30579 TCTTTGATTCAAAGTAGGTGGACTAAGGATACGAAGGCTTGGGCACCCAGTTTTGTTGACTTGAA
1 TCTTTGATTCAAAGTAGGTGGACTAAGGATACAAAGGCTTGGGCACCCAGTTTTGTTGACTTGAA
*
30644 TGTGCCTCAAGAAGTAATGCAAATGGAAAGGCTCACTACTCTACGTGCAACGTCAAGT
66 TGTGCCTCAAGAAGTAATACAAATGGAAAGGCTCACTACTCTACGTGCAACGTCAAGT
30702 CAGTTATGCT
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 113 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (123 bp):
TCTTTGATTCAAAGTAGGTGGACTAAGGATACAAAGGCTTGGGCACCCAGTTTTGTTGACTTGAA
TGTGCCTCAAGAAGTAATACAAATGGAAAGGCTCACTACTCTACGTGCAACGTCAAGT
Found at i:35973 original size:18 final size:18
Alignment explanation
Indices: 35950--35997 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
35940 CTTTTGTTCT
35950 TCATATTTTTCCAATTTA
1 TCATATTTTTCCAATTTA
35968 TCATATTTTTCCAATTTA
1 TCATATTTTTCCAATTTA
35986 TCATATTTTTCC
1 TCATATTTTTCC
35998 TCTACATAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (18 bp):
TCATATTTTTCCAATTTA
Found at i:36045 original size:14 final size:16
Alignment explanation
Indices: 36017--36049 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
36007 CTCTTCATCG
36017 CATTTATTTCACCCTT
1 CATTTATTTCACCCTT
36033 CATTT-TTTC-CCCTT
1 CATTTATTTCACCCTT
36047 CAT
1 CAT
36050 CCAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (16 bp):
CATTTATTTCACCCTT
Found at i:38722 original size:183 final size:183
Alignment explanation
Indices: 38500--39151 Score: 855
Period size: 183 Copynumber: 3.6 Consensus size: 183
38490 TTAAAGTATA
* * **
38500 GACACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATGAAACTTGTTTTGTCATAT
1 GACAATTTCAACATATCCAGTAGCGCTTTACCGATTTTGTCATAATGAAACAGGTTTTGTCATAT
* * * *
38565 TTTTACCAGTTATATTATTATATATCGATACATTTTTATAAAGCATCGACACTTTATAGGCGCTA
66 TTTTACCAGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTATAGGAGCTA
* *
38630 TTACTTCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATC
131 TTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATC
* * * * * *
38683 GACAATTTCAATATATCTAGTAGCGCTTTACCCATTTTGTCATAATTATACATGTTTTGTCATAT
1 GACAATTTCAACATATCCAGTAGCGCTTTACCGATTTTGTCATAATGAAACAGGTTTTGTCATAT
** * *
38748 TTTTACTTGTTATATTGTTATAAATCGATACATTTTTATAAAGTATCGACACTTTATAGGAGTTA
66 TTTTACCAGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTATAGGAGCTA
*
38813 TTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGTATC
131 TTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATC
* * *
38866 GACACA-TTCAACATATCTAGTAGCGATTTACCGGTTTTGTCATAATGAAACAGGTTTTGTCATA
1 GACA-ATTTCAACATATCCAGTAGCGCTTTACCGATTTTGTCATAATGAAACAGGTTTTGTCATA
* ** *
38930 TTTTTA-CATGTTATATTGTTATGGATCGATACATTTTTAT-TTGTATCGACACTTTATTGGTA-
65 TTTTTACCA-GTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTATAGG-AG
* * * * **
38992 CTATTACTGCTTCTCTTTTAAATTCTAAAAATGTCGATACTAATTACAATCTAATC
128 CTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATC
* * * * * * *
39048 GATACTTTCAACATATCCGGTAGCACTTTACCGGTTTTATCATAATGAAACTGGTTTTGTCATAT
1 GACAATTTCAACATATCCAGTAGCGCTTTACCGATTTTGTCATAATGAAACAGGTTTTGTCATAT
*
39113 TTTTACCTA-TTATATTGTTATGGATCGATACATTTTTAT
66 TTTTACC-AGTTATATTGTTATAGATCGATACATTTTTAT
39152 TTTTATCGAC
Statistics
Matches: 415, Mismatches: 48, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
182 156 0.38
183 257 0.62
184 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (183 bp):
GACAATTTCAACATATCCAGTAGCGCTTTACCGATTTTGTCATAATGAAACAGGTTTTGTCATAT
TTTTACCAGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTATAGGAGCTA
TTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATC
Found at i:39737 original size:13 final size:13
Alignment explanation
Indices: 39719--39749 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39709 TAAATATAGA
39719 GAGTTACTTTGTT
1 GAGTTACTTTGTT
*
39732 GAGTTATTTTGTT
1 GAGTTACTTTGTT
39745 GAGTT
1 GAGTT
39750 CCTTGACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.26, T:0.55
Consensus pattern (13 bp):
GAGTTACTTTGTT
Found at i:49734 original size:147 final size:147
Alignment explanation
Indices: 49467--49758 Score: 460
Period size: 147 Copynumber: 2.0 Consensus size: 147
49457 TAGTGTGCAA
* *
49467 TTGCGCCATTCATAGCATCGTGTCTATGTAAAGCTGCAATTCTTCTATATTTTTCTTTTTAACTT
1 TTGCGCCATTCATAGCATCATGTCTATGTAAAGATGCAATTCTTCTATATTTTTCTTTTTAACTT
* *
49532 TAATGAATTTTTTTTCTCTTTTTTCCATAATTGTTACCAAAAGAATTTCTCACATAAAACCTTGA
66 TAAAGAATTTTTTTTCTCTTTTTCCCATAATTGTTACCAAAAGAATTTCTCACATAAAACCTTGA
49597 TATTTATTTTATTTTAC
131 TATTTATTTTATTTTAC
* *
49614 TTGCGCCATTCGTAGCATCATGTCTATGTAAAGATGCAATTCTTTTATATTTTTCTTTTTTAACT
1 TTGCGCCATTCATAGCATCATGTCTATGTAAAGATGCAATTCTTCTATATTTTTC-TTTTTAACT
* *** * *
49679 TTAAAGAA-TTTTTTTCTCTTTTTCCCATAATTTTTATTTAAAGAATTTTTCACATAAAATCTTG
65 TTAAAGAATTTTTTTTCTCTTTTTCCCATAATTGTTACCAAAAGAATTTCTCACATAAAACCTTG
49743 ATATTTATTTTATTTT
130 ATATTTATTTTATTTT
49759 GCGACCACTA
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
147 116 0.88
148 16 0.12
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (147 bp):
TTGCGCCATTCATAGCATCATGTCTATGTAAAGATGCAATTCTTCTATATTTTTCTTTTTAACTT
TAAAGAATTTTTTTTCTCTTTTTCCCATAATTGTTACCAAAAGAATTTCTCACATAAAACCTTGA
TATTTATTTTATTTTAC
Found at i:50216 original size:6 final size:6
Alignment explanation
Indices: 50198--50239 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
50188 TGTAATATGT
*
50198 AAATAT AAA-AA AAATAA AAAT-A AAATAAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAAT-AA AAATAA AAATAA A
50240 TAGAATTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
5 9 0.28
6 18 0.56
7 5 0.16
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:50222 original size:11 final size:11
Alignment explanation
Indices: 50198--50239 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
50188 TGTAATATGT
50198 AAATATAAAA-A
1 AAATA-AAAATA
50209 AAATAAAAATA
1 AAATAAAAATA
50220 AAATAAAAAATAA
1 AAAT-AAAAAT-A
50233 AAATAAA
1 AAATAAA
50240 TAGAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.14
11 10 0.36
12 9 0.32
13 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:52641 original size:84 final size:82
Alignment explanation
Indices: 52522--52808 Score: 340
Period size: 84 Copynumber: 3.4 Consensus size: 82
52512 TTATTGAAAG
* * * * * * * *
52522 ATAACCATTTTTGCCTTGAGATAAGCTGCAAATGATGTGCCGTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATATGCC-TTGAGCTGAGCGTAGTCGAACTC
52587 GAAGGTCTTTTGTTGGCT
65 GAAGGTCTTTTGTTGGCT
* * * *
52605 GATAACCCTTCTGGCATTGAGTTATGTTGCAAATGATTTGCCTTGGAGCTAAGCGTAGTCGAACT
1 -ATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATATGCCTT-GAGCTGAGCGTAGTCGAACT
**
52670 CGAAGGTCTTCAGTTGGCAT
64 CGAAGGTCTTTTGTTGGC-T
* * * *
52690 ATAACCATTTTTGCCTTGAGTTATGCTGCAAATAATATGCCTTTGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATATGCC-TTGAGCTGAGCGTAGTCGAACTC
*
52755 GAAGGTCTTTTGTTGGCAA
65 GAAGGTCTTTTGTTGGC-T
*
52774 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
1 ATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGA
52809 ACACGATATC
Statistics
Matches: 171, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
83 2 0.01
84 166 0.97
85 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (82 bp):
ATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATATGCCTTGAGCTGAGCGTAGTCGAACTCG
AAGGTCTTTTGTTGGCT
Found at i:53032 original size:124 final size:124
Alignment explanation
Indices: 52859--53228 Score: 548
Period size: 123 Copynumber: 3.0 Consensus size: 124
52849 ATTGTTATTT
* * * *
52859 GTGGGCACGATAT-CCTTCATCGTGAAATTGAAATCATAGAGGGCCCCTTCGTTGTGAAGTTGAG
1 GTGGGCACGAT-TCCCTTCATCGTGAAGTTGAAAACGTAGATGGCCCCTTCGTTGTGAAGTTGAG
* * *
52923 CCTTGAATTGGACATCCTTCTTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTACTG
65 CCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTG
*
52983 GTGGGCACGATTCCCTTCATCATGAAGTTGAAAACGTAGATGGCCCCTTCGTTGTGAAGTTGAGC
1 GTGGGCACGATTCCCTTCATCGTGAAGTTGAAAACGTAGATGGCCCCTTCGTTGTGAAGTTGAGC
* * **
53048 CTTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCC-ATATAAAGATGAATGTTGTTG
66 CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTG
* * * *
53106 GTGAGCAAGATTCCCTTCGTCGTGAAGTTG-AAACTGTGGATGGCCCCTTCGTTGTGAAGTTGAG
1 GTGGGCACGATTCCCTTCATCGTGAAGTTGAAAAC-GTAGATGGCCCCTTCGTTGTGAAGTTGAG
*
53170 CCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATATTACT
65 CCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACT
53229 TCGAGTCCAA
Statistics
Matches: 221, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
122 4 0.02
123 109 0.49
124 108 0.49
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (124 bp):
GTGGGCACGATTCCCTTCATCGTGAAGTTGAAAACGTAGATGGCCCCTTCGTTGTGAAGTTGAGC
CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTG
Found at i:53585 original size:240 final size:242
Alignment explanation
Indices: 53143--53589 Score: 709
Period size: 240 Copynumber: 1.8 Consensus size: 242
53133 TTGAAACTGT
* * *
53143 GGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCC
1 GGATGGACCATTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCC
*
53208 AATCTAAAGATGAATATTACTTCGAGTCCAATATCCTTCACCGTGAAGTTGAAATTGGCTCTGAA
66 AAGCT----ATG-ATATTACTTCGAGTCCAATATCCTTCACCGTGAAGTTGAAATTGGCTCTGAA
*
53273 TGAAACTGGGAAGCCCATTCGCCGTGAAGTTGAGCTTTGAATTGGATATCCTTCATCGTGAAGTT
126 TGAAACTGGGAAGCCCATTCGCCGTGAAGTTGAGCTTTGAATTGGATATCCTTCATCGTGAAGAT
*
53338 GAAATCCAATCTAGAGTTGGTATGATATCCTTTGCTATGAATTTGAAATCGC
191 AAAATCCAATCTAGAGTTGGTATGATATCCTTTGCTATGAATTTGAAATCGC
* *
53390 GGATGGACCATTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCTTCTTCGTGAAGTTGAAATCC
1 GGATGGACCATTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCC
** * *
53455 AAGCT-TG-TATTGTTTCGAGTCCAATATCTTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAA
66 AAGCTATGATATTACTTCGAGTCCAATATCCTTCACCGTGAAGTTGAAATTGGCTCTGAATGAAA
* *
53518 CTGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGATAAAAT
131 CTGGGAAGCCCATTCGCCGTGAAGTTGAGCTTTGAATTGGATATCCTTCATCGTGAAGATAAAAT
53583 CCAATCT
196 CCAATCT
53590 TGTGTAGATG
Statistics
Matches: 186, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
240 120 0.65
242 2 0.01
247 64 0.34
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (242 bp):
GGATGGACCATTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCC
AAGCTATGATATTACTTCGAGTCCAATATCCTTCACCGTGAAGTTGAAATTGGCTCTGAATGAAA
CTGGGAAGCCCATTCGCCGTGAAGTTGAGCTTTGAATTGGATATCCTTCATCGTGAAGATAAAAT
CCAATCTAGAGTTGGTATGATATCCTTTGCTATGAATTTGAAATCGC
Found at i:55040 original size:95 final size:95
Alignment explanation
Indices: 54835--55097 Score: 321
Period size: 95 Copynumber: 2.7 Consensus size: 95
54825 GGCTAGCTAG
* * * * * *
54835 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAAAGGGACAACTTAA-TATCATTGTATAGAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTG--T--AT
* * *
54899 ATTATAATCGCCTTTATCAAGCTAGCTTAATATT
62 ATTATAATCACCTTTATCAAGCTAGATGAATATT
54933 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATATTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATATTA
*
54998 TAATCACCTTTATCAAGCTAGATGAATCTT
66 TAATCACCTTTATCAAGCTAGATGAATATT
* * * * ** *
55028 ATCCATAAAGTCGGGGTGTTTAAGCAATTGCTTTAGAGAGACAGTTCAAGCTTTATTGTATATAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATAT-T
55093 ATAAT
65 ATAAT
55098 ATTATAATCT
Statistics
Matches: 146, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
95 88 0.60
96 6 0.04
97 1 0.01
98 45 0.31
99 6 0.04
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATATTA
TAATCACCTTTATCAAGCTAGATGAATATT
Found at i:56039 original size:19 final size:19
Alignment explanation
Indices: 56015--56054 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
56005 TGTTATTATA
56015 AATAAACCTTATTGGATAC
1 AATAAACCTTATTGGATAC
56034 AATAAACCTTATTGGATAC
1 AATAAACCTTATTGGATAC
56053 AA
1 AA
56055 AAGTGTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (19 bp):
AATAAACCTTATTGGATAC
Found at i:60376 original size:60 final size:60
Alignment explanation
Indices: 60283--60418 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 60
60273 AATATGTAAT
**
60283 TAATTTCATCCCCAAACTATAACTTTCATTCTAAATTAG-TCCTAAAACTTTTGAACATTC
1 TAATTTCATCCCCAAACTATAACCCTCATTCTAAATTAGTTCC-AAAACTTTTGAACATTC
* * * * * **
60343 TAATTTCATCCCTAAACTATGACCCTCTTTCTAAATTGGTTCCCAAACTTTTGAATTTTC
1 TAATTTCATCCCCAAACTATAACCCTCATTCTAAATTAGTTCCAAAACTTTTGAACATTC
* *
60403 CAATTTCATCTCCAAA
1 TAATTTCATCCCCAAA
60419 TTCATCCAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
60 60 0.95
61 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (60 bp):
TAATTTCATCCCCAAACTATAACCCTCATTCTAAATTAGTTCCAAAACTTTTGAACATTC
Found at i:67344 original size:3 final size:3
Alignment explanation
Indices: 67336--67399 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
67326 AAAAAACATA
* *
67336 AAT AAT AAT TAT AAGA AAT AA- AAT AA- AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
67381 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
67400 CTATATTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:67509 original size:37 final size:37
Alignment explanation
Indices: 67459--67602 Score: 138
Period size: 37 Copynumber: 3.9 Consensus size: 37
67449 CGAAATGTTT
* *
67459 TTTTAAAAAACTATTTATTATACGTATTTTCAAAAACG
1 TTTT-AAAAACTATATATTATACATATTTTCAAAAACG
* * *
67497 TTTTAAAAACTATATAATATATATATTTTCAAAAATG
1 TTTTAAAAACTATATATTATACATATTTTCAAAAACG
67534 TCTTTAAAAACTATATA-T-T--ATATTTTC-AAAACG
1 T-TTTAAAAACTATATATTATACATATTTTCAAAAACG
* *
67567 TTTTTTAAAAACTATA-ATATATAAATGTTTTCAAAA
1 --TTTTAAAAACTATATAT-TATACATATTTTCAAAA
67603 CTATATATTA
Statistics
Matches: 90, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
33 6 0.07
34 21 0.23
35 2 0.02
36 2 0.02
37 30 0.33
38 26 0.29
39 3 0.03
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATACATATTTTCAAAAACG
Found at i:67561 original size:34 final size:34
Alignment explanation
Indices: 67459--67589 Score: 133
Period size: 34 Copynumber: 3.6 Consensus size: 34
67449 CGAAATGTTT
*
67459 TTTTAAAAAACTATTTATTATACGTATTTTCAAAAACG
1 TTTT-AAAAACTATATA-TATA--TATTTTCAAAAACG
*
67497 TTTTAAAAACTATATAATATATATATTTTCAAAAATG
1 TTTTAAAAAC--TAT-ATATATATATTTTCAAAAACG
67534 TCTTTAAAAACTATATAT-TATATTTTC-AAAACG
1 T-TTTAAAAACTATATATATATATTTTCAAAAACG
67567 TTTTTTAAAAACTATA-ATATATA
1 --TTTTAAAAACTATATATATATA
67590 AATGTTTTCA
Statistics
Matches: 83, Mismatches: 3, Indels: 18
0.80 0.03 0.17
Matches are distributed among these distances:
33 7 0.08
34 26 0.31
35 5 0.06
36 3 0.04
37 20 0.24
38 13 0.16
39 7 0.08
40 2 0.02
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (34 bp):
TTTTAAAAACTATATATATATATTTTCAAAAACG
Found at i:67603 original size:25 final size:25
Alignment explanation
Indices: 67569--67627 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
67559 TCAAAACGTT
*
67569 TTTTAAAAACTATA-A-TATATAAATG
1 TTTTCAAAACTATATATTATAT-AA-G
67594 TTTTCAAAACTATATATTATATAAG
1 TTTTCAAAACTATATATTATATAAG
67619 TTTTCAAAA
1 TTTTCAAAA
67628 TGTTTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 23 0.74
26 3 0.10
27 5 0.16
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (25 bp):
TTTTCAAAACTATATATTATATAAG
Found at i:67636 original size:63 final size:62
Alignment explanation
Indices: 67529--67654 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 62
67519 ATATTTTCAA
67529 AAATGTCTTTAAAAACTATATATTATATTTTCAAAACGTTTTTTAAAAACTATA-A-TATAT
1 AAATGTCTTTAAAAACTATATATTATATTTTCAAAACGTTTTTTAAAAACTATATATTATAT
* *
67589 AAATGT-TTTCAAAACTATATATTATATAAGTTTTCAAAATGTTTTTTAAAAACTATATATTATA
1 AAATGTCTTTAAAAACTATATA-T-TAT-A-TTTTCAAAACGTTTTTTAAAAACTATATATTATA
67653 T
62 T
67654 A
1 A
67655 TGTGTTTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
59 14 0.24
60 7 0.12
61 3 0.05
62 1 0.02
63 26 0.45
64 1 0.02
65 6 0.10
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (62 bp):
AAATGTCTTTAAAAACTATATATTATATTTTCAAAACGTTTTTTAAAAACTATATATTATAT
Found at i:67708 original size:2 final size:2
Alignment explanation
Indices: 67703--67749 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
67693 TATATATATA
67703 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
67745 TG TG T
1 TG TG T
67750 AAAAATATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:68453 original size:84 final size:84
Alignment explanation
Indices: 68331--68916 Score: 682
Period size: 84 Copynumber: 7.0 Consensus size: 84
68321 GCTGTGAACT
* * * * * * * * *
68331 TGATTTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCCTCGGTTGGCAGATAGCTCTTCTCG
1 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
* **
68396 ACTTAAGCTATGCTGCAGG
66 ACTTAAGTTATGCTGCAAA
* * *
68415 TGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCG
1 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
*
68480 AGTTAAGTTATGCTGCAAA
66 ACTTAAGTTATGCTGCAAA
* *
68499 TGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCG
1 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
*
68564 ACTTAAGTTATACTGCAAA
66 ACTTAAGTTATGCTGCAAA
* * * * *
68583 TGATGTG-CTGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG-TGACAGATAACCCTTCTA
1 TGATATGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
* * * *
68646 GCCTTGAGTTATGTTGTAAA
65 GACTTAAGTTATGCTGCAAA
* * * * ** *
68666 TGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTC
1 TGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
* *
68727 TACTTAAGCTATGCTGCAAA
65 GACTTAAGTTATGCTGCAAA
* * * * * * *
68747 TGATGTACCGTT-GAGCTGAGCATAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTA
1 TGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
*
68811 GACTTAAGTTGTGCTGCAAA
65 GACTTAAGTTATGCTGCAAA
68831 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
1 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
*
68896 ATTTAAGTTATGCTGCAAA
66 ACTTAAGTTATGCTGCAAA
68915 TG
1 TG
68917 TTGTTTTTTT
Statistics
Matches: 415, Mismatches: 77, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
80 23 0.06
81 35 0.08
82 2 0.00
83 40 0.10
84 313 0.75
85 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (84 bp):
TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
ACTTAAGTTATGCTGCAAA
Found at i:68530 original size:168 final size:167
Alignment explanation
Indices: 68331--68916 Score: 759
Period size: 168 Copynumber: 3.5 Consensus size: 167
68321 GCTGTGAACT
* * * * *
68331 TGATTTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCCTCGGTTGGCAGATAGCTCTTCTCG
1 TGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCCTTGGTTGGCAGATAGCCCTTCTCG
** * *
68396 ACTTAAGCTATGCTGCAGGTGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
* *
68461 TAGCAGATAACCCTTCTCGAGTTAAGTTATGCTGCAAA
130 TAGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAA
* *
68499 TGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCG
1 TGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCCTTGGTTGGCAGATAGCCCTTCTCG
* * *
68564 ACTTAAGTTATACTGCAAATGATGTGCTGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGC-CTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
* * * * *
68629 GA-CAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAA
130 TAGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAA
* * **
68666 TGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGT-C-T--TTGGCAGATAGCCCTTCTC
1 TGATATG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCCTTGGTTGGCAGATAGCCCTTCTC
* * * *
68727 TACTTAAGCTATGCTGCAAATGATGTACCGTTGAGCTGAGCATAGTCGAACTCAAAGGTCTTTTG
65 GACTTAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* * *
68792 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAA
129 TTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAA
* * * *
68831 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
1 TGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCCTTGGTTGGCAGATAGCCCTTCTCG
* *
68896 ATTTAAGTTATGCTGCAAATG
66 ACTTAAGCTATGCTGCAAATG
68917 TTGTTTTTTT
Statistics
Matches: 357, Mismatches: 53, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
164 103 0.29
165 36 0.10
166 2 0.01
167 36 0.10
168 178 0.50
169 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (167 bp):
TGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCCTTGGTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTT
AGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAA
Found at i:68765 original size:332 final size:335
Alignment explanation
Indices: 68291--68916 Score: 920
Period size: 332 Copynumber: 1.9 Consensus size: 335
68281 GAAAATTTAT
* * * * * *
68291 TGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTGAACTTGATTTGCCTTTGAGCTGAGTGTAA
1 TGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTGAACATGATATGCCCTCGAGCTGAGTGTAA
* **
68356 TCGAACTCAAAGGTCCTCGGTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAGGTGATGT
66 TCGAACTCAAAGGTCCT--GTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * * * * *
68421 GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGAGTTAA
129 ACCTTGGAGCTGAGCATAGTCAAACTCAAAGGTCTTTGGTTAGCAGACAACCCTTCTAGACTTAA
*
68486 GTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
194 GTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
*
68551 ATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCTGTTGAGCTGAGCGTAGTCGAACTC
259 ATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCTGTTGAGCTGAGCGTAGTCGAACTC
68616 AAAGGTCTTTGG
324 AAAGGTCTTTGG
* *
68628 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGT-AA-ATGATATGCCCTCGAAGCTGAGTGTA
1 TGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTGAACATGATATGCCCTCG-AGCTGAGTGTA
*** *
68691 ATCGAACTCGGGGGT-CT-TTGGCAGATAGCCCTTCTCTACTTAAGCTATGCTGCAAATGATGTA
65 ATCGAACTCAAAGGTCCTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTA
* * *
68754 CCGTT-GAGCTGAGCATAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAA
130 CC-TTGGAGCTGAGCATAGTCAAACTCAAAGGTCTTTGGTTAGCAGACAACCCTTCTAGACTTAA
*
68818 GTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
194 GTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
* *
68883 ATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
259 ATAACCCTTCTCGACTTAAGTTATACTGCAAATG
68917 TTGTTTTTTT
Statistics
Matches: 258, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
332 188 0.73
333 2 0.01
335 12 0.05
336 25 0.10
337 31 0.12
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (335 bp):
TGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTGAACATGATATGCCCTCGAGCTGAGTGTAA
TCGAACTCAAAGGTCCTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTAC
CTTGGAGCTGAGCATAGTCAAACTCAAAGGTCTTTGGTTAGCAGACAACCCTTCTAGACTTAAGT
TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
AACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCTGTTGAGCTGAGCGTAGTCGAACTCAA
AGGTCTTTGG
Found at i:73656 original size:6 final size:6
Alignment explanation
Indices: 73645--73670 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
73635 ATCGAATAAA
73645 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
73671 TAACTTTCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Done.