Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 38
Found at i:2505250 original size:89 final size:89
Alignment explanation
Indices: 2505085--2505503 Score: 473
Period size: 89 Copynumber: 4.7 Consensus size: 89
2505075 ATATTTCAGA
* * ** * *
2505085 TCCTGAAGAAGCAACGAAGAAAATCAATCCTTGAGTCTGGCCTCCCCGGAAGAGTAGTGGAGCAG
1 TCCTGAAGAAGCAGCGAAGCAAATCAA-CCTTGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAG
* *
2505150 ATTTTTTTTATTTCAGATTTGGTAT
65 ATTCTTCTTATTTCAGATTTGGTAT
* *
2505175 TCCTGAAGAAGCAGCGAAGCAAATCAACCTTGAGTCTGATCTCCCTGAAAGAGTAGTGGAACATA
1 TCCTGAAGAAGCAGCGAAGCAAATCAACCTTGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGA
* *
2505240 TTATTCTTATTTCAAATTTGGTCA-
66 TTCTTCTTATTTCAGATTTGGT-AT
* * ** * *
2505264 TCCTGAATAAGTAGCGAAGCAAATCAAAATTGAGTCTGATCTCCCCGCAAGAGTAGTGGAGCAGA
1 TCCTGAAGAAGCAGCGAAGCAAATCAACCTTGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGA
* *
2505329 TTCTTTTTATTTCAGATTTGGTCT
66 TTCTTCTTATTTCAGATTTGGTAT
* * * * * *
2505353 TCTTGAAGAA-CTAACGAAGCAAATCAATCTTAAGTCTGATCTCCCCGGAAGAGTAGTGGAACGG
1 TCCTGAAGAAGC-AGCGAAGCAAATCAACCTTGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAG
*
2505417 ATTCTTCTTATTTCAGATTTGGTCT
65 ATTCTTCTTATTTCAGATTTGGTAT
* * * ** * *
2505442 TCCTAAATAAGTAGCGAAGCAAATCAATCCTCAAGTCTAATCTCCCCTGAAAGAATAGTGGA
1 TCCTGAAGAAGCAGCGAAGCAAATCAA-CCTTGAGTCTGATCTCCCC-GAAAGAGTAGTGGA
2505504 GTTGATCCAT
Statistics
Matches: 279, Mismatches: 44, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
89 225 0.81
90 42 0.15
91 12 0.04
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (89 bp):
TCCTGAAGAAGCAGCGAAGCAAATCAACCTTGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGA
TTCTTCTTATTTCAGATTTGGTAT
Found at i:2505301 original size:178 final size:178
Alignment explanation
Indices: 2505115--2505468 Score: 539
Period size: 178 Copynumber: 2.0 Consensus size: 178
2505105 AAATCAATCC
* * *
2505115 TTGAGTCTGGCCTCCCCGGAAGAGTAGTGGAGCAGATTTTTTTTATTTCAGATTTGGTATTCCTG
1 TTGAGTCTGACCTCCCCGCAAGAGTAGTGGAGCAGATTCTTTTTATTTCAGATTTGGTATTCCTG
* * * *
2505180 AAGAAGC-AGCGAAGCAAATCAACCTTGAGTCTGATCTCCCTGAAAGAGTAGTGGAACATATTAT
66 AAGAA-CTAACGAAGCAAATCAACCTTAAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTAT
*
2505244 TCTTATTTCAAATTTGGTCATCCTGAATAAGTAGCGAAGCAAATCAAAA
130 TCTTATTTCAAATTTGGTCATCCTAAATAAGTAGCGAAGCAAATCAAAA
* * *
2505293 TTGAGTCTGATCTCCCCGCAAGAGTAGTGGAGCAGATTCTTTTTATTTCAGATTTGGTCTTCTTG
1 TTGAGTCTGACCTCCCCGCAAGAGTAGTGGAGCAGATTCTTTTTATTTCAGATTTGGTATTCCTG
* * * *
2505358 AAGAACTAACGAAGCAAATCAATCTTAAGTCTGATCTCCCCGGAAGAGTAGTGGAACGGATTCTT
66 AAGAACTAACGAAGCAAATCAACCTTAAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTATT
* *
2505423 CTTATTTCAGATTTGGTCTTCCTAAATAAGTAGCGAAGCAAATCAA
131 CTTATTTCAAATTTGGTCATCCTAAATAAGTAGCGAAGCAAATCAA
2505469 TCCTCAAGTC
Statistics
Matches: 158, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
177 1 0.01
178 157 0.99
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (178 bp):
TTGAGTCTGACCTCCCCGCAAGAGTAGTGGAGCAGATTCTTTTTATTTCAGATTTGGTATTCCTG
AAGAACTAACGAAGCAAATCAACCTTAAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTATT
CTTATTTCAAATTTGGTCATCCTAAATAAGTAGCGAAGCAAATCAAAA
Found at i:2506619 original size:55 final size:55
Alignment explanation
Indices: 2505475--2506618 Score: 1111
Period size: 55 Copynumber: 20.8 Consensus size: 55
2505465 TCAATCCTCA
* * ** * * * *
2505475 AGTCTAATCTCCCCTGAAAGAATAGTGGAGTTGATCCATTTTCCAAAGATTTCTCG
1 AGTCTTATCT-CCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * *
2505531 AGTCTTATCTCCCTGAAAGAAGAGTAGAGCAGTCCCGTCTTCTAAAGATTTTTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* ** * * * *
2505586 AGTTTTATCTCATTGAAAGAAGAGAGGAGCAAACCCGTCTTCCAAATAATTTTT-T
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAA-GATTTTTCG
* * * * * **
2505641 AGTCTTGTCTCACTGAAAGAAGAGAGTAACAGACCCGTCTTCCAAAGATTTTTTT
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* *
2505696 AGTCTTATATCCCTGAAAGAA-AGTGGAGCACACCCGTCTTCCAAAGATTTTTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* *
2505750 AGTCTTATCTCCCTGAAAGAAGA-TATGAGCAGACCCGTCTTCCAAAGATTTTTCA
1 AGTCTTATCTCCCTGAAAGAAGAGT-GGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * ** *
2505805 AGTCTTATATCCCTGAAATAAGAGTGGAGAAGAGTCGTATTCCAAAGATTTTTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * * *
2505860 AGACTTATCTCTCTCAAAGAAGAGAGGAGAAGACCCGTCTTCCAAATATTTTTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * * * *
2505915 AGTCTTATATCCTTGAAAAAAGAATAGAGCAGACTCGTCTTCCAAAGATTTCTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * * *
2505970 AGTCTTATCTCCCTAAAAGAAGAGTGGAACATACTCGTCTTCTAAAGATTTATCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* *
2506025 AGTCTTATCTCCCTGAAAGAAGAGTGGAGTAGACCCATCTTCCAAAGATTTTTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * *
2506080 AGTCTTATCTCCTTGAAAGAAGTA-AGGAGTAGACCCATCTTCCAAAGATTTTTTG
1 AGTCTTATCTCCCTGAAAGAAG-AGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * *
2506135 AGTCTTATCTCCCTAAAAGAATAGAT-GAGTAGACCTGTCTTCCAAAGACTTTTCG
1 AGTCTTATCTCCCTGAAAGAAGAG-TGGAGCAGACCCGTCTTCCAAAGATTTTTCG
** * * * * ** ** * **
2506190 AGAGTTATATACTTGAAATAAGAGTGGAATAGACCTATCTTCTAAAGATTTTTTA
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * * *
2506245 AGTCTTATCTCCCTAAAAGAATAGAGGAACATA-CCGTCTTCTAAAGATTTTTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * *
2506299 AGTCTTATCTCCCTGAAAGAAGA-TAGGGGCAAACCCGTCTTCTAAAGATATTTCG
1 AGTCTTATCTCCCTGAAAGAAGAGT-GGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * *
2506354 AGTCATATATCCCTGAAAGAAGAGTGGAGCAAACTCATCTTCCAAAGATATTTT-G
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGAT-TTTTCG
* * * * * * *
2506409 AGTCTTTTCTCCCTGAAAGAATA-TATGAGCATACTCTTCTTCCAAAGATTTTTCA
1 AGTCTTATCTCCCTGAAAGAAGAGT-GGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * *
2506464 AGTCTTATCTCCCTGAAAGAATAGAGAAGCAGACCCATCTTCCAAATATTTTTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * * * * *
2506519 AGTCTTATCTCCCTGAAATAA-AGAGGAGCAGACTCGTCTTTCAAAAATTTCTCG
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
* * *
2506573 AGTTTTATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAA
1 AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAA
2506619 ATTGATCTGA
Statistics
Matches: 899, Mismatches: 172, Indels: 35
0.81 0.16 0.03
Matches are distributed among these distances:
54 150 0.17
55 728 0.81
56 21 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (55 bp):
AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCG
Found at i:2506712 original size:81 final size:80
Alignment explanation
Indices: 2506577--2506915 Score: 400
Period size: 81 Copynumber: 4.2 Consensus size: 80
2506567 TTCTCGAGTT
*
2506577 TTATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAG
1 TTATCTCCCTGAAAAAAT-GTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAG
2506642 AGGAACATATCAAGTC
65 AGGAACATATCAAGTC
* *
2506658 TTATCTCCCTGAAAAAACTGTGGAGAAGACTCGTCTTCCAAAATTGATCTGACTACTCG-AAAAG
1 TTATCTCCCTGAAAAAA-TGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAG
* * *
2506722 AAGAATAGATCAAGTC
65 AGGAACATATCAAGTC
* * * *
2506738 TTTTCTCCCCTGAAAGAATAT-TGGAGCAGACCCGTTTTCCAAAGTTGATCTGACTACCCGAAAA
1 TTATCT-CCCTGAAA-AA-ATGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAA
*
2506802 AGAGGAACATATCAAGTT
63 AGAGGAACATATCAAGTC
* * *
2506820 TTATCTCCCT-AAAAGTAGAT-TGGAGCATACTCATCTTCCAAAATTGATCTGACTA-CCTAAAA
1 TTATCTCCCTGAAAA--A-ATGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAA
*
2506882 ACGAGGAACAAATCAAGTC
63 A-GAGGAACATATCAAGTC
* *
2506901 TGATCTACCTTGAAA
1 TTATCT-CCCTGAAA
2506916 TAACAGTGGA
Statistics
Matches: 220, Mismatches: 28, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
79 1 0.00
80 33 0.15
81 153 0.70
82 29 0.13
83 4 0.02
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (80 bp):
TTATCTCCCTGAAAAAATGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGA
GGAACATATCAAGTC
Found at i:2506859 original size:162 final size:162
Alignment explanation
Indices: 2506583--2506875 Score: 466
Period size: 162 Copynumber: 1.8 Consensus size: 162
2506573 AGTTTTATCT
*
2506583 CCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAAC
1 CCCTGAAAGAATAGTGGAGCAGACCCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAAC
*
2506648 ATATCAAGTCTTATCTCCCTGAAAAAACTGTGGAGAAGACTCGTCTTCCAAAATTGATCTGACTA
66 ATATCAAGTCTTATCTCCCTGAAAAAACTGTGGAGAAGACTCATCTTCCAAAATTGATCTGACTA
2506713 CTCGAAAAGAAGAATAGATCAAGTCTTTTCTC
131 CTCGAAAAGAAGAATAGATCAAGTCTTTTCTC
* * *
2506745 CCCTGAAAGAATATTGGAGCAGACCCGTTTTCCAAAGTTGATCTGACTACCCGAAAAAGAGGAAC
1 CCCTGAAAGAATAGTGGAGCAGACCCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAAC
* * *
2506810 ATATCAAGTTTTATCTCCCT-AAAAGTAGA-T-TGGAGCATACTCATCTTCCAAAATTGATCTGA
66 ATATCAAGTCTTATCTCCCTGAAAA--A-ACTGTGGAGAAGACTCATCTTCCAAAATTGATCTGA
2506872 CTAC
128 CTAC
2506876 CTAAAAACGA
Statistics
Matches: 120, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
161 4 0.03
162 113 0.94
163 2 0.02
164 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (162 bp):
CCCTGAAAGAATAGTGGAGCAGACCCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAAC
ATATCAAGTCTTATCTCCCTGAAAAAACTGTGGAGAAGACTCATCTTCCAAAATTGATCTGACTA
CTCGAAAAGAAGAATAGATCAAGTCTTTTCTC
Found at i:2507062 original size:3 final size:3
Alignment explanation
Indices: 2507050--2507088 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
2507040 TTTCGTTCAA
2507050 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2507089 AATAATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2507162 original size:22 final size:23
Alignment explanation
Indices: 2507134--2507189 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
2507124 TACCTATTTA
* *
2507134 TAAAATTAAA-TCGGGGCCAAAT
1 TAAAATTAAACCCGGAGCCAAAT
*
2507156 TAAAATTAAACCCGGAGCCCAAT
1 TAAAATTAAACCCGGAGCCAAAT
*
2507179 TACAATTAAAC
1 TAAAATTAAAC
2507190 TCGAAGCCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.21
Consensus pattern (23 bp):
TAAAATTAAACCCGGAGCCAAAT
Found at i:2507185 original size:23 final size:23
Alignment explanation
Indices: 2507153--2507200 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2507143 ATCGGGGCCA
*
2507153 AATTAAAATTAAACCCGGAGCCC
1 AATTAAAATTAAACCCGAAGCCC
* *
2507176 AATTACAATTAAACTCGAAGCCC
1 AATTAAAATTAAACCCGAAGCCC
2507199 AA
1 AA
2507201 GTTCCAGCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19
Consensus pattern (23 bp):
AATTAAAATTAAACCCGAAGCCC
Found at i:2509094 original size:14 final size:14
Alignment explanation
Indices: 2509075--2509101 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2509065 TTTTTATCTT
2509075 TTAAAATTATTTTC
1 TTAAAATTATTTTC
2509089 TTAAAATTATTTT
1 TTAAAATTATTTT
2509102 AAAATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTC
Found at i:2511336 original size:60 final size:60
Alignment explanation
Indices: 2511226--2511350 Score: 142
Period size: 60 Copynumber: 2.1 Consensus size: 60
2511216 TGGTCTCCTT
* * * * *
2511226 ACTATAGGGTGTTATTTTGTTGAGTCTCTCGACTATTAAAGGTAACAAAATAATCCCTCA
1 ACTATAGGGTGTTACTTTGTTGAGTCCCTCGACTATAAAAGATAACAAAATAATCACTCA
* * * * * * *
2511286 ACTATAGGGTGTTGCTTTGTTGAGTCCCTTGACTATAAAATATTAGAAAATGATCATTCA
1 ACTATAGGGTGTTACTTTGTTGAGTCCCTCGACTATAAAAGATAACAAAATAATCACTCA
2511346 ACTAT
1 ACTAT
2511351 TCATAAACTC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (60 bp):
ACTATAGGGTGTTACTTTGTTGAGTCCCTCGACTATAAAAGATAACAAAATAATCACTCA
Found at i:2512267 original size:31 final size:31
Alignment explanation
Indices: 2512208--2512302 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
2512198 TGGTGACATC
* * * * *
2512208 ATATATATCATGTTATTACTTTAATGATGTG
1 ATATATATCATATCATCATTTTAGTGATGTG
* * *
2512239 GTATATGTCATATCATCGTTTTAGTGATGTG
1 ATATATATCATATCATCATTTTAGTGATGTG
* *
2512270 ATATATATTATATCATCATTTTAGATTATGTG
1 ATATATATCATATCATCATTTTAG-TGATGTG
2512302 A
1 A
2512303 CGTATAGTAA
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 43 0.86
32 7 0.14
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (31 bp):
ATATATATCATATCATCATTTTAGTGATGTG
Found at i:2514869 original size:3 final size:3
Alignment explanation
Indices: 2514856--2514901 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
2514846 TTTAATAAAT
*
2514856 ATA AT- ATA ATA ATA ATA TTA A-A ATA A-A ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2514901 A
1 A
2514902 AACAAATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2514886 original size:22 final size:23
Alignment explanation
Indices: 2514851--2514894 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2514841 GATTATTTAA
*
2514851 TAAATATAATATAATAATAATAT
1 TAAATATAAAATAATAATAATAT
2514874 TAAA-ATAAAATAATAATAATA
1 TAAATATAAAATAATAATAATA
2514895 ATAATAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAATATAAAATAATAATAATAT
Found at i:2515556 original size:109 final size:110
Alignment explanation
Indices: 2515126--2515779 Score: 698
Period size: 109 Copynumber: 5.8 Consensus size: 110
2515116 GATGTAATCT
* * *
2515126 AGCAAAAAGTTGAACAAATTCTCCTCCTTATGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCAT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
2515190 TATGAACTCCT-TCTGGAAATGCTGATGATATATCTCCTTCTG--TGCTAGAGTT--
66 TATGAACT-CTACCTGGTAATGC---TG----A--TCCATC-GAATGAT-GAATTCG
* * * *
2515242 ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGCTCTTCT
1 A-GCAAAAAGTTGAACAAGTTCTTCTCATTATGAA--TCTTCTTCTTCTTCAGATGAGTTCTTCT
* * * * * * *
2515307 TATTATGAAC-CTTCTCTGGAAAAGTTGATTCATC-AAGTGATGAATTCA
63 CATTATGAACTCTAC-CTGGTAATGCTGATCCATCGAA-TGATGAATTCG
* * * *
2515355 AACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGACGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCT
* * * * * *
2515420 CATTATGAACTCTACCTGGAAAAGCTGATCTATCGAGTGATGGATTTG
63 CATTATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCG
* *
2515468 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCAT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
*
2515532 TATGAACTCTACCTGGTAATGCTGATCCATTGAATGATGAATTCG
66 TATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCG
* *
2515577 AGCAAAAAGTTGAATAAGTTCTTCTCATTATGAAT-TTCTTCTTCTTCAAATGAGTTCTTCTCAT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
* *
2515641 TATGAACTCTACCTGGTAATGTTGATCCATTGAATGATGAATTCG
66 TATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCG
*
2515686 AGCAAAAAGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCT
2515751 CATTATGAACTCTACCTGGTAATGCTGAT
63 CATTATGAACTCTACCTGGTAATGCTGAT
2515780 GACCCGAAGG
Statistics
Matches: 466, Mismatches: 53, Indels: 41
0.83 0.09 0.07
Matches are distributed among these distances:
109 198 0.42
110 5 0.01
111 9 0.02
112 44 0.09
113 131 0.28
114 4 0.01
116 1 0.00
117 30 0.06
118 2 0.00
120 42 0.09
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (110 bp):
AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCG
Found at i:2515588 original size:222 final size:219
Alignment explanation
Indices: 2515244--2515779 Score: 718
Period size: 222 Copynumber: 2.4 Consensus size: 219
2515234 CTAGAGTTAT
* * *
2515244 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGCTCTTCTTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAA--TCTTCTTCTTCTTCAGATGAGTTCTTCTCA
* * * * *
2515309 TTATGAAC-CTTCTCTGGAAAAGTTGATTCATCAAGTGATGAATTCAAACAAAAAGTTGAACAAA
64 TTATGAACTCTAC-CTGGTAATGCTGATCCATCAAGTGATGAATTCAAACAAAAAGTTGAACAAA
*
2515373 TTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTG
128 TTCTTCTCATTATGAATTTC---TT-CTTCTTCAAACGAGTTCTTCTCATTATGAACTCTACCTG
* * * *
2515438 GAAAAGCTGATCTATCGAGTGATGGATTTGA
189 GAAAAGCTGATCCATCGAATGATGAATTCGA
2515469 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCATT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
2515533 ATGAACTCTACCTGGTAATGCTGATCCATTGAA-TGATGAATTCGAGCAAAAAGTTGAATAAGTT
66 ATGAACTCTACCTGGTAATGCTGATCCA-TCAAGTGATGAATTCAAACAAAAAGTTGAACAAATT
* * *
2515597 CTTCTCATTATGAATTTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTACCTGGTAATG
130 CTTCTCATTATGAATTTCTTCTTCTTCAAACGAGTTCTTCTCATTATGAACTCTACCTGGAAAAG
* *
2515662 TTGATCCATTGAATGATGAATTCGA
195 CTGATCCATCGAATGATGAATTCGA
* * *
2515687 GCAAAAAGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTC
2515752 ATTATGAACTCTACCTGGTAATGCTGAT
63 ATTATGAACTCTACCTGGTAATGCTGAT
2515780 GACCCGAAGG
Statistics
Matches: 279, Mismatches: 26, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
218 90 0.32
219 2 0.01
221 6 0.02
222 142 0.51
223 6 0.02
225 33 0.12
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (219 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTACCTGGTAATGCTGATCCATCAAGTGATGAATTCAAACAAAAAGTTGAACAAATTC
TTCTCATTATGAATTTCTTCTTCTTCAAACGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGC
TGATCCATCGAATGATGAATTCGA
Found at i:2515903 original size:76 final size:76
Alignment explanation
Indices: 2515777--2515931 Score: 292
Period size: 76 Copynumber: 2.0 Consensus size: 76
2515767 TGGTAATGCT
*
2515777 GATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTG
2515842 TAGGACTTACA
66 TAGGACTTACA
*
2515853 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTG
2515918 TAGGACTTACA
66 TAGGACTTACA
2515929 GAT
1 GAT
2515932 ATGGGAAATA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (76 bp):
GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTG
TAGGACTTACA
Found at i:2516186 original size:37 final size:36
Alignment explanation
Indices: 2516114--2516306 Score: 172
Period size: 37 Copynumber: 5.3 Consensus size: 36
2516104 TGTCTTAAGC
* *
2516114 GAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGATAAAT-TTTGTTTCAAGAAAAACAATCTCAAGT
** ** * *
2516151 GAGATAAATTTTTGTTTCAAGTGAAACTGTTTCAAGA
1 GAGATAAA-TTTTGTTTCAAGAAAAACAATCTCAAGT
* *
2516188 GAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGATAAATTTTGTTTCAAGAAAAACAATCTCAAGT
* * ** ** **
2516224 GAGATAAAGTTCTGTTTCGAGTGAAACTGTCTCAAAC
1 GAGATAAA-TTTTGTTTCAAGAAAAACAATCTCAAGT
* *
2516261 GAGACAAA-TTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGATAAATTTTGTTTCAAGAAAAACAATCTCAAGT
2516296 GAGATAAATTT
1 GAGATAAATTT
2516307 CTGTGAAAAC
Statistics
Matches: 116, Mismatches: 37, Indels: 7
0.73 0.23 0.04
Matches are distributed among these distances:
35 25 0.22
36 30 0.26
37 60 0.52
38 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (36 bp):
GAGATAAATTTTGTTTCAAGAAAAACAATCTCAAGT
Found at i:2516309 original size:72 final size:73
Alignment explanation
Indices: 2516104--2516310 Score: 328
Period size: 73 Copynumber: 2.8 Consensus size: 73
2516094 CTGAAATAAT
* * *
2516104 TGTCTTAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGTTTC
1 TGTCTCAAACGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTC
2516169 AAGTGAAAC
65 AAGTGAAAC
* *
2516178 TGTTTCAAGA-GAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTC
1 TGTCTCAA-ACGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTC
*
2516242 GAGTGAAAC
65 AAGTGAAAC
2516251 TGTCTCAAACGAGACAAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGT
1 TGTCTCAAACGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGT
2516311 GAAAACATCC
Statistics
Matches: 123, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
72 42 0.34
73 66 0.54
74 15 0.12
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (73 bp):
TGTCTCAAACGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTCA
AGTGAAAC
Found at i:2516593 original size:165 final size:165
Alignment explanation
Indices: 2516345--2516671 Score: 539
Period size: 165 Copynumber: 2.0 Consensus size: 165
2516335 TATGGATGTG
* * * *
2516345 GGAAATAGTTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
* **
2516410 ATAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
*
2516475 TGGGTAACATGCCCCAATCTCAAGATAATGCTATT
131 TGGGTAACATGACCCAATCTCAAGATAATGCTATT
2516510 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
* **
2516575 C-GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATCTCATGTTGA
65 CAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGA
2516639 TTGGGTAACATGACCCAATCTCAAGATAATGCT
130 TTGGGTAACATGACCCAATCTCAAGATAATGCT
2516672 CATTCTTGTG
Statistics
Matches: 150, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
165 107 0.71
166 43 0.29
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (165 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
TGGGTAACATGACCCAATCTCAAGATAATGCTATT
Found at i:2517219 original size:22 final size:22
Alignment explanation
Indices: 2517185--2517283 Score: 162
Period size: 22 Copynumber: 4.5 Consensus size: 22
2517175 AATAAAGCTT
*
2517185 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * *
2517207 TTATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
2517229 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2517251 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2517273 TCATCTTTGAA
1 TCATCTTTGAA
2517284 GAGTGTAGAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2520016 original size:114 final size:113
Alignment explanation
Indices: 2519817--2520039 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 113
2519807 GATCATGCAG
* * *
2519817 TTCATCTTTCAATTCCAATAATTGGTTCTGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAA
1 TTCATCTTTCAAATCCAATAATTGGTTCTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
*
2519882 CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 CACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * * *
2519930 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAATA
1 TTCATCTTTCAAATCCAATAATTGGTTCT-GGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
2519995 ACACTTCCAAAAGATGCTATTGGGTCTCTTTATTTCTACTATGAG
65 ACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
2520040 AACGTGACAC
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 25 0.25
114 75 0.75
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (113 bp):
TTCATCTTTCAAATCCAATAATTGGTTCTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:2522268 original size:15 final size:15
Alignment explanation
Indices: 2522248--2522324 Score: 82
Period size: 15 Copynumber: 5.0 Consensus size: 15
2522238 CTTGATTCAA
*
2522248 TTTTCCTTCTTCTTT
1 TTTTCCTTTTTCTTT
*
2522263 TTTTCCTTTTTGTTT
1 TTTTCCTTTTTCTTT
*
2522278 TTTTCCTTTTTGTTTTT
1 TTTTCC-TTTT-TCTTT
* * *
2522295 TTTTTCTTCTTATTT
1 TTTTCCTTTTTCTTT
2522310 TTTTCCTTTTTCTTT
1 TTTTCCTTTTTCTTT
2522325 CTTTGCTGGA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
15 35 0.69
16 7 0.14
17 9 0.18
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTCCTTTTTCTTT
Found at i:2522311 original size:32 final size:32
Alignment explanation
Indices: 2522260--2522320 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2522250 TTCCTTCTTC
* *
2522260 TTTTTTTCCTTTTTGTTTTTTTCCTTTTTGTT
1 TTTTTTTCCTTCTTATTTTTTTCCTTTTTGTT
*
2522292 TTTTTTTTCTTCTTATTTTTTTCCTTTTT
1 TTTTTTTCCTTCTTATTTTTTTCCTTTTT
2522321 CTTTCTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.82
Consensus pattern (32 bp):
TTTTTTTCCTTCTTATTTTTTTCCTTTTTGTT
Found at i:2522628 original size:2 final size:2
Alignment explanation
Indices: 2522621--2522685 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2522611 GACAACAAAT
2522621 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
2522663 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2522686 TAAAAGGATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2526001 original size:28 final size:26
Alignment explanation
Indices: 2525946--2526003 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
2525936 AAATATTAAT
*
2525946 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
2525972 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
2526000 AAAA
1 AAAA
2526004 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:2528069 original size:14 final size:15
Alignment explanation
Indices: 2528049--2528083 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2528039 TTTGTTATTA
*
2528049 GGTTTGGGCCGGTCT
1 GGTTTGGGCCAGTCT
2528064 -GTTTGGGCCAGTCT
1 GGTTTGGGCCAGTCT
2528078 GGTTTG
1 GGTTTG
2528084 TAATCGGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.03, C:0.17, G:0.43, T:0.37
Consensus pattern (15 bp):
GGTTTGGGCCAGTCT
Found at i:2528156 original size:3 final size:3
Alignment explanation
Indices: 2528143--2528185 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
2528133 TTTAATAAAT
*
2528143 ATA AT- ATA ATA ATA ATA TTA A-A ATA A-A ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2528186 AACAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2528157 original size:11 final size:11
Alignment explanation
Indices: 2528135--2528181 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
2528125 ATTGATTATT
2528135 TAATA-AAT-A
1 TAATATAATAA
2528144 TAATATAATAA
1 TAATATAATAA
2528155 TAATATTAA-AA
1 TAATA-TAATAA
*
2528166 TAAAATAATAA
1 TAATATAATAA
2528177 TAATA
1 TAATA
2528182 ATAAAACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 5 0.16
10 6 0.19
11 18 0.56
12 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATATAATAA
Found at i:2528173 original size:22 final size:22
Alignment explanation
Indices: 2528135--2528187 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2528125 ATTGATTATT
*
2528135 TAATAAATATAATATAATAATAA
1 TAATAAA-ATAAAATAATAATAA
*
2528158 TATTAAAATAAAATAATAATAA
1 TAATAAAATAAAATAATAATAA
2528180 TAATAAAA
1 TAATAAAA
2528188 CAAATGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAATAAAATAAAATAATAATAA
Found at i:2532679 original size:28 final size:27
Alignment explanation
Indices: 2532646--2532700 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
2532636 TGATTTTGGG
2532646 ATTAGAG-ATTTTTAAAATAATTAAAAAA
1 ATTAGAGTATTTTTAAAA-AA-TAAAAAA
*
2532674 ATTAGAGTTTTTTTAAAAAATAAAAAA
1 ATTAGAGTATTTTTAAAAAATAAAAAA
2532701 GATCATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
28 9 0.36
29 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.36
Consensus pattern (27 bp):
ATTAGAGTATTTTTAAAAAATAAAAAA
Found at i:2534606 original size:42 final size:42
Alignment explanation
Indices: 2534544--2534659 Score: 205
Period size: 42 Copynumber: 2.8 Consensus size: 42
2534534 TTTCCCCGAA
* *
2534544 TTCCCGTGTTTGTTTTACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
2534586 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
2534628 TTCCCGTTTTTGTTTCACGTAATTCGTTTTCC
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCC
2534660 AGAATGTAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:2534897 original size:26 final size:24
Alignment explanation
Indices: 2534835--2534897 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
2534825 CATTTTCATC
2534835 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
2534859 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
2534882 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
2534898 ATTTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:2534907 original size:13 final size:13
Alignment explanation
Indices: 2534887--2534934 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
2534877 TTTATAATAA
2534887 TATAATATTATAT
1 TATAATATTATAT
* *
2534900 TTTAATATTATAA
1 TATAATATTATAT
*
2534913 AATAATCATTATAT
1 TATAAT-ATTATAT
2534927 TATAATAT
1 TATAATAT
2534935 ATTATTATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TATAATATTATAT
Found at i:2534961 original size:25 final size:25
Alignment explanation
Indices: 2534928--2535017 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 25
2534918 TCATTATATT
2534928 ATAATATATTATTATTTTTATTTTA
1 ATAATATATTATTATTTTTATTTTA
*
2534953 ATAATATATAATAAATTTTTTTTATATTTA
1 ATAATATAT--T--ATTATTTTTAT-TTTA
* * *
2534983 ATAATGAATAATATTATTATATATTTCA
1 ATAAT--ATATTATTATT-TTTATTTTA
2535011 ATAATAT
1 ATAATAT
2535018 TTTAGTAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
25 9 0.17
26 2 0.04
27 1 0.02
28 13 0.25
29 14 0.27
30 10 0.19
32 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (25 bp):
ATAATATATTATTATTTTTATTTTA
Found at i:2535261 original size:20 final size:20
Alignment explanation
Indices: 2535183--2535252 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
2535173 TTTCCAGATG
*
2535183 TTTTCAAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2535203 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
2535223 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2535243 TTTTCCAGAA
1 TTTTCCAGAA
2535253 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:2535271 original size:15 final size:15
Alignment explanation
Indices: 2535235--2535316 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
2535225 TTACAGAAAT
**
2535235 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2535250 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
2535264 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2535279 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
* *
2535294 ATAATTTAAATTCCA
1 GTAATTCAAATTCCA
2535309 GTAATTCA
1 GTAATTCA
2535317 TTTTCTGAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 12 0.21
15 44 0.79
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:2535287 original size:30 final size:30
Alignment explanation
Indices: 2535235--2535316 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
2535225 TTACAGAAAT
2535235 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
2535264 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* * **
2535294 ATAATTTAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
2535317 TTTTCTGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 16 0.33
30 32 0.67
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:2535449 original size:14 final size:14
Alignment explanation
Indices: 2535420--2535595 Score: 187
Period size: 14 Copynumber: 13.3 Consensus size: 14
2535410 TTCTCTCTCT
2535420 CTCTCCCTCCCT-C
1 CTCTCCCTCCCTCC
2535433 C-CTCCCTCCCTCTC
1 CTCTCCCTCCCTC-C
*
2535447 C-CTCCCTCCCTCT
1 CTCTCCCTCCCTCC
*
2535460 CTCTCCCTCTCTCC
1 CTCTCCCTCCCTCC
2535474 CTCTCCCTCCCTCC
1 CTCTCCCTCCCTCC
2535488 CTCTCCCT--CTCC
1 CTCTCCCTCCCTCC
2535500 CTCTCCCT-CCTCC
1 CTCTCCCTCCCTCC
* *
2535513 CTCTCTCTCCCCCC
1 CTCTCCCTCCCTCC
*
2535527 CTCTCCCTGCCTCC
1 CTCTCCCTCCCTCC
*
2535541 CTC-CCCCCCCTCC
1 CTCTCCCTCCCTCC
*
2535554 CCCT-CC-CCCTCTC
1 CTCTCCCTCCCTC-C
2535567 C-CTCCCTCCC-CC
1 CTCTCCCTCCCTCC
2535579 C-CTCCCTCCCTCC
1 CTCTCCCTCCCTCC
2535592 CTCT
1 CTCT
2535596 ATGTATGTAT
Statistics
Matches: 140, Mismatches: 12, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
12 40 0.29
13 33 0.24
14 67 0.48
ACGTcount: A:0.00, C:0.72, G:0.01, T:0.28
Consensus pattern (14 bp):
CTCTCCCTCCCTCC
Found at i:2535449 original size:18 final size:18
Alignment explanation
Indices: 2535420--2535594 Score: 179
Period size: 18 Copynumber: 9.9 Consensus size: 18
2535410 TTCTCTCTCT
2535420 CTCTCCCTCCCTCCCTCC
1 CTCTCCCTCCCTCCCTCC
2535438 CTC-CCTCTCCCTCCCTCC
1 CTCTCC-CTCCCTCCCTCC
* *
2535456 CTCTCTCTCCCTCTCTCC
1 CTCTCCCTCCCTCCCTCC
2535474 CTCTCCCTCCCTCCCTCTCC
1 CTCTCCCTCCCT-CC-CTCC
2535494 CTCTCCCT--CTCCCT-C
1 CTCTCCCTCCCTCCCTCC
* *
2535509 CTC-CCTCTCTCTCCCCCC
1 CTCTCC-CTCCCTCCCTCC
*
2535527 CTCTCCCTGCCTCCCTCC
1 CTCTCCCTCCCTCCCTCC
* *
2535545 C-CCCCCTCCC-CCTCCCC
1 CTCTCCCTCCCTCC-CTCC
2535562 CTCTCCCTCCCTCCC-CC
1 CTCTCCCTCCCTCCCTCC
2535579 C-CTCCCTCCCTCCCTC
1 CTCTCCCTCCCTCCCTC
2535595 TATGTATGTA
Statistics
Matches: 132, Mismatches: 12, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
14 2 0.02
15 6 0.05
16 17 0.13
17 24 0.18
18 65 0.49
19 6 0.05
20 12 0.09
ACGTcount: A:0.00, C:0.72, G:0.01, T:0.27
Consensus pattern (18 bp):
CTCTCCCTCCCTCCCTCC
Found at i:2535545 original size:4 final size:4
Alignment explanation
Indices: 2535422--2535594 Score: 138
Period size: 4 Copynumber: 44.8 Consensus size: 4
2535412 CTCTCTCTCT
*
2535422 CTCC CTCC CTCC CTCC CTCC CT-- CTCC CTCC CTCC CTCTC TCTCC CTCT
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC-C -CTCC CTCC
*
2535470 CTCC CT-- CTCC CTCC CTCC CT-- CTCC CTCTC C-CT CTCC CT-C CTCC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC-C CTCC CTCC CTCC CTCC
* * *
2535513 CTCTC TCTCC C-CC C-CT CTCC CTGC CTCC CTCC C-CC C-CC TCCCC CTCC
1 CTC-C -CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC -CTCC CTCC
*
2535560 C-CC TCTCC CTCC CTCC CCCC CTCC CTCC CTCC CTC
1 CTCC -CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC
2535595 TATGTATGTA
Statistics
Matches: 140, Mismatches: 11, Indels: 36
0.75 0.06 0.19
Matches are distributed among these distances:
2 6 0.04
3 16 0.11
4 102 0.73
5 10 0.07
6 6 0.04
ACGTcount: A:0.00, C:0.72, G:0.01, T:0.27
Consensus pattern (4 bp):
CTCC
Found at i:2535557 original size:6 final size:6
Alignment explanation
Indices: 2535482--2535584 Score: 66
Period size: 6 Copynumber: 16.2 Consensus size: 6
2535472 CCCTCTCCCT
* * * *
2535482 CCCTCC CTCTCC CTCTCC CTCTCC CTCCTCC CTCTCTCTC CCC-CC CTCTCC
1 CCCTCC CCCTCC CCCTCC CCCTCC C-CCTCC C-C-CTC-C CCCTCC CCCTCC
* *
2535533 CTGCCTCC CTCCCCC CCCTCC CCCTCC CCCTCT CCCTCC CTCC-CC CCCTCC
1 C--CCTCC C-CCTCC CCCTCC CCCTCC CCCTCC CCCTCC C-CCTCC CCCTCC
2535584 C
1 C
2535585 TCCCTCCCTC
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
5 5 0.06
6 49 0.61
7 15 0.19
8 9 0.11
9 2 0.03
ACGTcount: A:0.00, C:0.75, G:0.01, T:0.24
Consensus pattern (6 bp):
CCCTCC
Found at i:2538640 original size:23 final size:22
Alignment explanation
Indices: 2538613--2538659 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2538603 AACCCTAAAT
*
2538613 AAGCCCAAAAATTGTATCTGCTA
1 AAGCCC-AAAATCGTATCTGCTA
* *
2538636 AAGCCCAGAATCGTATCTTCTA
1 AAGCCCAAAATCGTATCTGCTA
2538658 AA
1 AA
2538660 CTCGAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (22 bp):
AAGCCCAAAATCGTATCTGCTA
Found at i:2541263 original size:47 final size:45
Alignment explanation
Indices: 2541170--2541295 Score: 146
Period size: 47 Copynumber: 2.8 Consensus size: 45
2541160 TATAAAATCT
*
2541170 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* ** * *
2541215 CTTACCATTTAAATTCCACAAGCTCGTAAGCTTATTTTTTCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2541262 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2541296 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
44 22 0.32
45 10 0.14
46 2 0.03
47 35 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2541444 original size:40 final size:40
Alignment explanation
Indices: 2541400--2541521 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
2541390 ACCGTAGTGC
*
2541400 TACACATAAGGTCGTGCCCGCCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2541440 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
2541480 TACACATAAGGTCGTGCCCACCATATACATCGAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2541520 TA
1 TA
2541522 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2551749 original size:31 final size:30
Alignment explanation
Indices: 2551681--2551772 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 30
2551671 CAAAATCAAG
* *
2551681 ATCAAATTGATAACTTTATCTAAAGTTTAAGT
1 ATCAAATTGAT-ATTTTATCTAAA-TTTTAGT
2551713 ATCAAAATT-ATATTTTATCTAAATTTTAGT
1 ATC-AAATTGATATTTTATCTAAATTTTAGT
* * * *
2551743 GTTCAAATTGGTATTTTATCCAAAATTTAG
1 -ATCAAATTGATATTTTATCTAAATTTTAG
2551773 AGGTTGAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
30 11 0.22
31 30 0.59
32 5 0.10
33 5 0.10
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (30 bp):
ATCAAATTGATATTTTATCTAAATTTTAGT
Found at i:2558616 original size:3 final size:3
Alignment explanation
Indices: 2558608--2558674 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
2558598 TTTTGTTTAC
2558608 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2558656 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
2558675 ACGACAAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2558960 original size:77 final size:77
Alignment explanation
Indices: 2558792--2559353 Score: 655
Period size: 77 Copynumber: 7.4 Consensus size: 77
2558782 CTATGAATTT
* * *** * * * * * **
2558792 TTCTCATTATGAACTTCTTCTTTTGAAACACTGATCCAACTCCTTTTTTCATAGAATCGAGAAAA
1 TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGAT-GGAT-AAGTCAA
*
2558857 GGTTAAACAAGTTC
64 GGTTGAACAAGTTC
* *
2558871 TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCT-TTTTCTGTGATGGATAAGTCTAG
1 TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTT-TGTGATGGATAAGTCAAG
2558935 GTTGAACAAGTTC
65 GTTGAACAAGTTC
* *
2558948 TTCTCATTATGAACTTCTTCATTGAAAATGTTGATCTACCTCCTTTTGTGATGGATAAGTCAAGG
1 TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGATAAGTCAAGG
*
2559013 TTGAACAAGTTT
66 TTGAACAAGTTC
*
2559025 TTCTCATTATGAACTTCTTCATTGAAAATGTTGATCCACCTCCTTTT-T--T-GAT--G----GG
1 TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGATAAGTCAAGG
* *
2559080 TTAAACAAGTTT
66 TTGAACAAGTTC
* * * * * *
2559092 TTCTCATTATGAACTTCTTCGTTGAAAATGTTAATCCACCT-CTTTCTATGATTGATGAGTCAAG
1 TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTT-TGTGATGGATAAGTCAAG
2559156 GTTGAACAAGTTC
65 GTTGAACAAGTTC
* * * * *
2559169 TTTTCATTATGAACTTCTTTATTGGAAATGTTGATCCACCTCCTTTTGTAATGGATGAGCCAAGG
1 TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGATAAGTCAAGG
2559234 TTGAACAAGTTC
66 TTGAACAAGTTC
* * * * *
2559246 TTCTCATT-TGAACTTCTTCAATGGAAATGTTGATCCACCTCCTTCTGTGATGAACAAGTAAAGG
1 TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGATAAGTCAAGG
2559310 TTGAACAAGTTC
66 TTGAACAAGTTC
*
2559322 TTCTCATTATGAACTTCTTCATCGGAAATGTT
1 TTCTCATTATGAACTTCTTCATTGGAAATGTT
2559354 TGGTCTACCT
Statistics
Matches: 421, Mismatches: 47, Indels: 32
0.84 0.09 0.06
Matches are distributed among these distances:
66 4 0.01
67 53 0.13
68 1 0.00
70 1 0.00
71 4 0.01
73 4 0.01
74 1 0.00
76 68 0.16
77 233 0.55
78 13 0.03
79 39 0.09
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (77 bp):
TTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGATAAGTCAAGG
TTGAACAAGTTC
Found at i:2559199 original size:144 final size:149
Alignment explanation
Indices: 2558855--2559353 Score: 622
Period size: 144 Copynumber: 3.3 Consensus size: 149
2558845 GAATCGAGAA
* * *
2558855 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCT-TTTTCTG
1 AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTT-TG
2558919 TGATGGATAAGTCTAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATC
65 T-ATGGAT-AG---AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATC
* *
2558984 TACCTCCTTT-TGTGATGGATAAGTC
125 CACCT-CTTTCTGTGATTGATAAGTC
*
2559009 AAGGTTGAACAAGTT-TTTCTCATTATGAACTTCTTCATTGAAAATGTTGATCCACCTCCTTTT-
1 AAGGTTGAACAAGTTCTTT-TCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTG
* * * *
2559072 T-T-GAT-G-GGTTAAACAAGTTTTTCTCATTATGAACTTCTTCGTTGAAAATGTTAATCCACCT
65 TATGGATAGAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATCCACCT
* *
2559133 CTTTCTATGATTGATGAGTC
130 CTTTCTGTGATTGATAAGTC
*
2559153 AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTTATTGGAAATGTTGATCCACCTCCTTTTGT
1 AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGT
* *
2559218 AATGGATGAGCCAAGGTTGAACAAGTTCTTCTCATT-TGAACTTCTTCAATGGAAATGTTGATCC
66 -ATGGAT-AG---AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATCC
* * *
2559282 ACCTCCTTCTGTGA-TGAACAAGTA
126 ACCTCTTTCTGTGATTG-ATAAGTC
* *
2559306 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATCGGAAATGTT
1 AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCATTGGAAATGTT
2559354 TGGTCTACCT
Statistics
Matches: 302, Mismatches: 28, Indels: 31
0.84 0.08 0.09
Matches are distributed among these distances:
143 4 0.01
144 119 0.39
145 4 0.01
147 1 0.00
148 4 0.01
150 4 0.01
151 1 0.00
152 2 0.01
153 88 0.29
154 72 0.24
155 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (149 bp):
AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGT
ATGGATAGAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATCCACCTC
TTTCTGTGATTGATAAGTC
Found at i:2559240 original size:221 final size:220
Alignment explanation
Indices: 2558857--2559289 Score: 686
Period size: 221 Copynumber: 2.0 Consensus size: 220
2558847 ATCGAGAAAA
* * * *
2558857 GGTTAAACAAGTTCTTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTTTTTCTGTGA
1 GGTTAAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTAATCCACCTCTTTCTATGA
* *
2558922 TGGATAAGTCTAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATCTAC
66 TGGATAAGTCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATCCAC
* * * *
2558987 CTCCTTTTGTGATGGATAAGTCAAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCATTGAAA
131 CTCCTTTTGTAATGGATAAGCCAAGGTTGAACAAGTTCTTCTCATT-TGAACTTCTTCAATGAAA
2559052 ATGTTGATCCACCTCCTTTTTTGATG
195 ATGTTGATCCACCTCCTTTTTTGATG
* *
2559078 GGTTAAACAAGTTTTTCTCATTATGAACTTCTTCGTTGAAAATGTTAATCCACCTCTTTCTATGA
1 GGTTAAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTAATCCACCTCTTTCTATGA
* * * * *
2559143 TTGATGAGTCAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTTATTGGAAATGTTGATCCAC
66 TGGATAAGTCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATCCAC
* *
2559208 CTCCTTTTGTAATGGATGAGCCAAGGTTGAACAAGTTCTTCTCATTTGAACTTCTTCAATGGAAA
131 CTCCTTTTGTAATGGATAAGCCAAGGTTGAACAAGTTCTTCTCATTTGAACTTCTTCAATGAAAA
2559273 TGTTGATCCACCTCCTT
196 TGTTGATCCACCTCCTT
2559290 CTGTGATGAA
Statistics
Matches: 193, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
220 34 0.18
221 159 0.82
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (220 bp):
GGTTAAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTAATCCACCTCTTTCTATGA
TGGATAAGTCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGAAAATGTTGATCCAC
CTCCTTTTGTAATGGATAAGCCAAGGTTGAACAAGTTCTTCTCATTTGAACTTCTTCAATGAAAA
TGTTGATCCACCTCCTTTTTTGATG
Found at i:2560645 original size:24 final size:24
Alignment explanation
Indices: 2560617--2560685 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
2560607 TTCATAAAGC
*
2560617 TCGAATATTACCTCCATAGTTGCT
1 TCGAACATTACCTCCATAGTTGCT
2560641 TCGAACATTACCTCCATAGTTGCT
1 TCGAACATTACCTCCATAGTTGCT
*
2560665 TCGAACATTACCTCCAAAGTT
1 TCGAACATTACCTCCATAGTT
2560686 TAACAGCTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (24 bp):
TCGAACATTACCTCCATAGTTGCT
Found at i:2561895 original size:64 final size:63
Alignment explanation
Indices: 2561790--2561909 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 63
2561780 ATTGTTCAAG
* * *
2561790 GTGTATCGATGCACATGAAGTGCATCAATGCACTACTTTAAAATA-AAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCACCTT-AAATACAAAA-ATCGAATGCCATCA
* * * *
2561854 GTGTATCGATGCACAAGTAGTGCATCGATGGACCCCCTTAAATACAAAAATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCACCTTAAATACAAAAATCGAAT
2561910 ATGATTTATG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 12 0.25
64 36 0.75
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCAATGCACCACCTTAAATACAAAAATCGAATGCCATCA
Found at i:2562645 original size:23 final size:23
Alignment explanation
Indices: 2562593--2562653 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
2562583 CAATCTTATA
*
2562593 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * * *
2562616 CGACACTTTGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
2562639 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
2562654 TTTATACGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2565601 original size:360 final size:358
Alignment explanation
Indices: 2564938--2565637 Score: 1186
Period size: 360 Copynumber: 1.9 Consensus size: 358
2564928 ACATGAATGG
* * * *
2564938 TATTGTTCATGCACTATCGGTACTGTAAGAACAATATCGGTACTACGTACCTAGAAAACAATTTT
1 TATTGTTAATGCAATATCGGTAATGTAAGAACAATATCGGTACTACGTACCCAGAAAACAATTTT
* *
2565003 GTGCTCAAATTCTAATTTAATGGACTTTGAATTATTTTTAAAAGTTTAACAAATTCAATCAAGTC
66 GTGCTCAAATTCTAATTTAATGAACTTTGAATTATTTTTAAAAGTTTAACAAATTCAATCAACTC
* * * *
2565068 CAAAAACATTTTTGCCTTGATTTGTTATATCAAAATATTATAACACATAATTCAACAATCTTCCC
131 CAAAAACATTTTTGCATTAATTTGTTATATCAAAATATTATAAAACATAATTCAACAATCTCCCC
2565133 CTTTTTGATATAACAAAACATTTGAAAATTGTTTTTGGAAAAACTCCCCTTTAATAAAATATTTC
196 CTTTTTGATATAACAAAACATTTGAAAATTGTTTTTGGAAAAACTCCCCTTTAATAAAATATTTC
*
2565198 ACGAAAAAGATAAATATTTGGAAAATATTAAAGCTCCCATTTTTCATTATTGAAATTGAATTTTT
261 ACGAAAAAGAGAAATATTTGGAAAATATTAAAGCTCCCATTTTTCATTATTGAAATTGAATTTTT
2565263 CAAAATCATATTTCTACTAGAAAATAGTATCGA
326 CAAAATCATATTTCTACTAGAAAATAGTATCGA
* * * *
2565296 TATTGTTAATGCAATATCGGTAATGTAAGAACAGTATTGTTACTACGTACCCATAAAACAATTTT
1 TATTGTTAATGCAATATCGGTAATGTAAGAACAATATCGGTACTACGTACCCAGAAAACAATTTT
*
2565361 GTTCTCAAATTCTAATTTAATGAACTTTGAATTATTTTTGAAAAGTTTGAACAAATTCAATCAAC
66 GTGCTCAAATTCTAATTTAATGAACTTTGAATTATTTTT-AAAAGTTT-AACAAATTCAATCAAC
2565426 TCCAAAAACATTTTT-CATTAATTTGTTATATCAAAATATTATAAAACATAATTCAACAATCTCC
129 TCCAAAAACATTTTTGCATTAATTTGTTATATCAAAATATTATAAAACATAATTCAACAATCTCC
* *
2565490 CCCTTTTTGATATAACATAACATTTGAAAATTTGTTTTTGGAAAAACTCTCCTTTAATAAAATAT
194 CCCTTTTTGATATAACAAAACATTTGAAAA-TTGTTTTTGGAAAAACTCCCCTTTAATAAAATAT
*
2565555 TTCACGAAAAAGAGAAATATTTGGAAAATATTAAAGCTCTCATTTTTCATTATTGAAATTGAATT
258 TTCACGAAAAAGAGAAATATTTGGAAAATATTAAAGCTCCCATTTTTCATTATTGAAATTGAATT
*
2565620 TTTCAAACTCATATTTCT
323 TTTCAAAATCATATTTCT
2565638 CCTCATCTTT
Statistics
Matches: 319, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
358 94 0.29
359 82 0.26
360 143 0.45
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (358 bp):
TATTGTTAATGCAATATCGGTAATGTAAGAACAATATCGGTACTACGTACCCAGAAAACAATTTT
GTGCTCAAATTCTAATTTAATGAACTTTGAATTATTTTTAAAAGTTTAACAAATTCAATCAACTC
CAAAAACATTTTTGCATTAATTTGTTATATCAAAATATTATAAAACATAATTCAACAATCTCCCC
CTTTTTGATATAACAAAACATTTGAAAATTGTTTTTGGAAAAACTCCCCTTTAATAAAATATTTC
ACGAAAAAGAGAAATATTTGGAAAATATTAAAGCTCCCATTTTTCATTATTGAAATTGAATTTTT
CAAAATCATATTTCTACTAGAAAATAGTATCGA
Found at i:2566938 original size:35 final size:35
Alignment explanation
Indices: 2566899--2566966 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
2566889 TTCAATTTAA
*
2566899 GGTTTAGAATATATTTGAAGTATTTTGGAATTTGG
1 GGTTTAGAATATAATTGAAGTATTTTGGAATTTGG
* *
2566934 GGTTTAGAATGTAATTGAAGTGTTTTGGAATTT
1 GGTTTAGAATATAATTGAAGTATTTTGGAATTT
2566967 TGAACATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (35 bp):
GGTTTAGAATATAATTGAAGTATTTTGGAATTTGG
Found at i:2573346 original size:5 final size:5
Alignment explanation
Indices: 2573338--2573401 Score: 53
Period size: 5 Copynumber: 12.8 Consensus size: 5
2573328 GAAAAGAGAA
* * *
2573338 AAAAT AAAAT AAAAT AAAATT AAGAA- AATAT TAAA- AAAAT AAAA- ATAAT
1 AAAAT AAAAT AAAAT AAAA-T AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
2573387 AAAAAT AAAAT AAAA
1 -AAAAT AAAAT AAAA
2573402 AGACATTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
4 7 0.15
5 31 0.66
6 7 0.15
7 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:2573382 original size:26 final size:26
Alignment explanation
Indices: 2573334--2573401 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 26
2573324 AAAAGAAAAG
2573334 AGAAAAAATAAAATAAAATAAAATTA
1 AGAAAAAATAAAATAAAATAAAATTA
* * *
2573360 AGAAAATATTAAA-AAAATAAAAATA
1 AGAAAAAATAAAATAAAATAAAATTA
*
2573385 A-TAAAAATAAAATAAAA
1 AGAAAAAATAAAATAAAA
2573402 AGACATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 8 0.23
25 16 0.46
26 11 0.31
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (26 bp):
AGAAAAAATAAAATAAAATAAAATTA
Found at i:2573400 original size:11 final size:11
Alignment explanation
Indices: 2573337--2573402 Score: 54
Period size: 9 Copynumber: 6.5 Consensus size: 11
2573327 AGAAAAGAGA
2573337 AAAAATAAAAT
1 AAAAATAAAAT
2573348 -AAAATAAAAT
1 AAAAATAAAAT
* *
2573358 --TAAGAAAAT
1 AAAAATAAAAT
*
2573367 ATTAAA-AAAAT
1 A-AAAATAAAAT
2573378 AAAAAT--AAT
1 AAAAATAAAAT
2573387 AAAAATAAAAT
1 AAAAATAAAAT
2573398 AAAAA
1 AAAAA
2573403 GACATTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
9 16 0.36
10 13 0.29
11 14 0.31
12 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2573412 original size:20 final size:18
Alignment explanation
Indices: 2573343--2573412 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 18
2573333 GAGAAAAAAT
*
2573343 AAAATAAAATAAAATTAAGA
1 AAAATTAAATAAAA-TAA-A
2573363 AAATATTAAA-AAAATAAA
1 AAA-ATTAAATAAAATAAA
*
2573381 AATAATAAAAATAAAATAAA
1 AA-AAT-TAAATAAAATAAA
2573401 AAGACATTAAAT
1 AA-A-ATTAAAT
2573413 TTTGAAAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 5 0.12
19 7 0.17
20 22 0.54
21 7 0.17
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAATTAAATAAAATAAA
Found at i:2574664 original size:28 final size:28
Alignment explanation
Indices: 2574633--2574714 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
2574623 ATAAAATGAA
2574633 AAATAATATTAATAAATATATAATAAAT
1 AAATAATATTAATAAATATATAATAAAT
* * *
2574661 AAATACTAATAATATA-ATATAATAAAT
1 AAATAATATTAATAAATATATAATAAAT
*
2574688 AAA-ATATATATAATATAGTATATAATA
1 AAATA-ATAT-TAATA-AATATATAATA
2574715 TACCATATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
26 1 0.02
27 16 0.37
28 18 0.42
30 8 0.19
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (28 bp):
AAATAATATTAATAAATATATAATAAAT
Found at i:2574679 original size:5 final size:5
Alignment explanation
Indices: 2574635--2574980 Score: 126
Period size: 5 Copynumber: 68.6 Consensus size: 5
2574625 AAAATGAAAA
*
2574635 ATAAT ATTAAT A-AAT AT-AT AATAA- ATAA- ATACT AATAAT ATAAT
1 ATAAT A-TAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT
*
2574679 ATAAT A-AAT AAAAT AT-AT ATAAT ATAGTAT ATAAT ATACCAT ATAA-
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATA--AT ATAAT
* * * *
2574725 ATGTAT ATAAT ATGAT ATAAT ATAAC ATATAT ATAAT ATAAAT ATAAC
1 AT-AAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT AT-AAT ATAAT
* * *
2574773 ATTAT ATAAT ATATTGT ATAAT ATAA- ATATTT ATAAT AT-AT ATAAT
1 ATAAT ATAAT ATA--AT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT
* *
2574819 AT-AT AATTTAT ACTATT ATAAT ATCTAAT ATCTAAT ACATAAT AT-AT
1 ATAAT -A-TAAT A-TAAT ATAAT A--TAAT A--TAAT --ATAAT ATAAT
* * * *
2574866 ATAAT TTATT AT-AT ATACT AT-AT GAT-AT ATAAT AT-GT A-ATAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT ATAAT
* *
2574913 AT-AT ATTAT ATGAT AT-AT A-ATAT ATAAT AT-AT A-ATAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATA-AT ATAAT ATAAT
* *
2574960 ATAA- AAAAT AT-AT ATACT ATA
1 ATAAT ATAAT ATAAT ATAAT ATA
2574981 TACTATCCCG
Statistics
Matches: 264, Mismatches: 33, Indels: 88
0.69 0.09 0.23
Matches are distributed among these distances:
4 61 0.23
5 139 0.53
6 32 0.12
7 31 0.12
9 1 0.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:2574688 original size:23 final size:23
Alignment explanation
Indices: 2574648--2574704 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
2574638 ATATTAATAA
*
2574648 ATATATAATA-AATAAATACTAAT
1 ATATATAATATAATAAATA-AAAT
2574671 A-ATATAATATAATAAATAAAAT
1 ATATATAATATAATAAATAAAAT
2574693 ATATATAATATA
1 ATATATAATATA
2574705 GTATATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATATAATATAATAAATAAAAT
Found at i:2574698 original size:2 final size:2
Alignment explanation
Indices: 2574691--2574982 Score: 142
Period size: 2 Copynumber: 157.5 Consensus size: 2
2574681 AATAAATAAA
* * *
2574691 AT AT AT AT A- AT AT AGT AT AT A- AT AT ACC AT AT AA AT GT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
2574733 A- AT AT GAT AT A- AT AT A- AC AT AT AT AT A- AT AT AA AT AT A-
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2574771 AC AT -T AT AT A- AT AT AT -T GT AT A- AT AT AA AT AT TT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2574808 AT AT AT AT A- AT AT AT A- AT TT AT ACT AT -T AT A- AT AT CT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
2574846 AT AT CT A- AT AC AT A- AT AT AT AT A- AT TT AT -T AT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
2574885 AT AT GAT AT AT A- AT AT GT A- AT AT AT A- AT AT AT AT -T AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2574924 GAT AT AT A- AT AT AT A- AT AT AT A- AT AT AT A- AT AT A- AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2574962 A- AA AA AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT A-T AT AT A
2574983 CTATCCCGGA
Statistics
Matches: 223, Mismatches: 28, Indels: 78
0.68 0.09 0.24
Matches are distributed among these distances:
1 31 0.14
2 177 0.79
3 15 0.07
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2574703 original size:7 final size:7
Alignment explanation
Indices: 2574647--2574957 Score: 220
Period size: 7 Copynumber: 44.9 Consensus size: 7
2574637 AATATTAATA
2574647 AATATAT
1 AATATAT
*
2574654 AATAAAT
1 AATATAT
2574661 AA-ATACT
1 AATATA-T
2574668 AATAATAT
1 AAT-ATAT
2574676 AATATAAT
1 AATAT-AT
*
2574684 AA-ATAA
1 AATATAT
2574690 AATATAT
1 AATATAT
2574697 -ATAATAT
1 AAT-ATAT
*
2574704 AGTATAT
1 AATATAT
*
2574711 AATATAC
1 AATATAT
*
2574718 CATATA-
1 AATATAT
*
2574724 AATGTAT
1 AATATAT
2574731 -ATA-AT
1 AATATAT
2574736 -ATGATAT
1 AAT-ATAT
*
2574743 AATATAAC
1 AATAT-AT
2574751 ATATATAT
1 A-ATATAT
2574759 AATATA-
1 AATATAT
2574765 AATATA-
1 AATATAT
2574771 ACATTATAT
1 A-A-TATAT
2574780 AATATAT
1 AATATAT
*
2574787 --TGTAT
1 AATATAT
2574792 AATATA-
1 AATATAT
2574798 AATAT-T
1 AATATAT
*
2574804 TATA-AT
1 AATATAT
2574810 -ATATAT
1 AATATAT
2574816 AATATAT
1 AATATAT
*
2574823 AATTTAT
1 AATATAT
*
2574830 ACTATTAT
1 AATA-TAT
*
2574838 AATATCT
1 AATATAT
*
2574845 AATATCT
1 AATATAT
*
2574852 AATACAT
1 AATATAT
2574859 AATATATAT
1 -A-ATATAT
*
2574868 AATTTAT
1 AATATAT
*
2574875 TATATAT
1 AATATAT
*
2574882 ACTATAT
1 AATATAT
*
2574889 GATATAT
1 AATATAT
*
2574896 AATATGT
1 AATATAT
2574903 AATATAT
1 AATATAT
2574910 AATATAT
1 AATATAT
*
2574917 ATTATAT
1 AATATAT
*
2574924 GATATAT
1 AATATAT
2574931 AATATAT
1 AATATAT
2574938 AATATAT
1 AATATAT
2574945 AATATAT
1 AATATAT
2574952 AATATA
1 AATATA
2574958 ATATAAAAAA
Statistics
Matches: 241, Mismatches: 38, Indels: 50
0.73 0.12 0.15
Matches are distributed among these distances:
5 11 0.05
6 32 0.13
7 157 0.65
8 28 0.12
9 13 0.05
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (7 bp):
AATATAT
Found at i:2574785 original size:62 final size:61
Alignment explanation
Indices: 2574669--2574962 Score: 158
Period size: 62 Copynumber: 4.7 Consensus size: 61
2574659 ATAAATACTA
* *
2574669 ATAATATAATATAATAAATAAAATATATATAATATAGTATATAATATACCATATAAATGTAT
1 ATAATATAATATAAT-AATAAAATATATATAATATAATATATAATATACAATATAAATGTAT
* * * *
2574731 ATAATATGATATAAT-ATAACATATATATAATATAA-ATATAACATTATATAATAT--AT-TGT
1 ATAATATAATATAATAATAAAATATATATAATATAATATAT-A-A-TATACAATATAAATGTAT
* * * *
2574790 ATAATATAAATATTTATAATATATATAATATATAATTTATACTATTATAATAT-CTAATATCTAA
1 ATAATAT-AATA-TAATAATA-AAAT-ATATATAA--TATAATA-TATAATATAC-AATAT-AAA
**
2574854 TACAT
57 TGTAT
* * * * * * *
2574859 AATATATATAATTTATTATATATACTATATGAT-ATATAATATGTAATATATAATATATAT-TAT
1 -ATA-ATATAATATAATA-ATAAAATATAT-ATAATATAATATATAATATACAATATAAATGTAT
*
2574922 ATGATATATAATAT-ATAAT-ATATAATATATAATATAATATA
1 AT-A-ATATAATATAATAATAAAAT-ATATATAATATAATATA
2574963 AAAAATATAT
Statistics
Matches: 176, Mismatches: 31, Indels: 51
0.68 0.12 0.20
Matches are distributed among these distances:
59 13 0.07
60 27 0.15
61 19 0.11
62 29 0.16
63 15 0.09
64 10 0.06
65 20 0.11
66 11 0.06
67 2 0.01
68 10 0.06
69 7 0.04
70 9 0.05
71 4 0.02
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (61 bp):
ATAATATAATATAATAATAAAATATATATAATATAATATATAATATACAATATAAATGTAT
Found at i:2578046 original size:3 final size:3
Alignment explanation
Indices: 2578038--2578070 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2578028 TACATAATGC
2578038 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2578071 AACGACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2583194 original size:29 final size:31
Alignment explanation
Indices: 2583113--2583197 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
2583103 TGCATTCAAC
* *
2583113 ATTTGAAAATATTAGATCCTTATTTCAACTT
1 ATTTGAAAAGATTAGATCTTTATTTCAACTT
* *
2583144 ATTTGAAAAGGTTAGA-CTTTTATTTGAACTT
1 ATTTGAAAAGATTAGATC-TTTATTTCAACTT
2583175 -TTT-AAAAGATTAGATCTTTATTT
1 ATTTGAAAAGATTAGATCTTTATTT
2583198 AAACATTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 17 0.36
30 5 0.11
31 25 0.53
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTTGAAAAGATTAGATCTTTATTTCAACTT
Found at i:2583370 original size:52 final size:52
Alignment explanation
Indices: 2583309--2583414 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
2583299 ATACATATGG
2583309 ATGTATATTTGATCTTTATCCGATGAGTTTCAACCCGATTCTATAAGGTCGA
1 ATGTATATTTGATCTTTATCCGATGAGTTTCAACCCGATTCTATAAGGTCGA
2583361 ATGTATATTTGATCTTTATCCGATGAGTTTCAACCCGATTCTATAAGGTCGA
1 ATGTATATTTGATCTTTATCCGATGAGTTTCAACCCGATTCTATAAGGTCGA
2583413 AT
1 AT
2583415 TCAAGTTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (52 bp):
ATGTATATTTGATCTTTATCCGATGAGTTTCAACCCGATTCTATAAGGTCGA
Found at i:2584621 original size:31 final size:31
Alignment explanation
Indices: 2584582--2584673 Score: 136
Period size: 31 Copynumber: 3.1 Consensus size: 31
2584572 TTAAGTATCT
2584582 AAAGTATTTTTTTTGTCAAAATAGGTACCTA
1 AAAGTATTTTTTTTGTCAAAATAGGTACCTA
* *
2584613 AAATTATTTTTTTGGTCAAAATAGGTACCT-
1 AAAGTATTTTTTTTGTCAAAATAGGTACCTA
*
2584643 AAAGTA--TTTTATGTCAAAATAGGTACCTA
1 AAAGTATTTTTTTTGTCAAAATAGGTACCTA
2584672 AA
1 AA
2584674 CTACCCAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 20 0.36
29 2 0.04
30 5 0.09
31 28 0.51
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (31 bp):
AAAGTATTTTTTTTGTCAAAATAGGTACCTA
Found at i:2587411 original size:801 final size:799
Alignment explanation
Indices: 2585870--2587466 Score: 2734
Period size: 801 Copynumber: 2.0 Consensus size: 799
2585860 TATGAATTAG
*
2585870 AAATTTCTTAGGCAAACGAGTGAGGCTCTTTGAGGTCTGATGTGTTTGAATATGGCTCAAATTAA
1 AAATTTCTTAGGCAAACAAGTGAGGCTCTTTGAGGTCTGATGTGTTTGAATATGGCTCAAATTAA
* * *
2585935 TGTGCAACAAGGCTTATTCCAATTTGTCCCCTTTGTGTACCCTAGCAAACCAAGTTCAAGAATGA
66 TGTGCAACAAGGCTTATTCCAATTTGTCCCCTTTGTGTACCCTAGCAAAACAAATTCAAGAATCA
*
2586000 ATAAATGGGTATAACAACATATAATCTAATAAGTAATAACTATGTTGCTTGAGCTTTTATTTTCT
131 ATAAATGGGTATAACAACATATAATCTAATAAGTAATAACTATGTTGCTTGAGATTTTATTTTCT
*
2586065 TGAATAAATTACCCGTTTAATACCTAAACTATCAAATTTGGTGTGTTTTAATACTTAAACTTTTA
196 TGAATAAATTACACGTTTAATACCTAAACTATCAAATTTGGTGTGTTTTAATACTTAAACTTTTA
*
2586130 ATTTTTCCAAAATCATACCTAACGTTTAGTTTTTGTTTCATTTTAGTATCTCGTCATTAAAAACT
261 ATTTTTCCAAAATCATACATAACGTTTAGTTTTTGTTTCATTTTAGTATCTCGTCATTAAAAACT
* *
2586195 TAACGGGTGATTTTTATGTGGCACCTTTTTTATAGATAAATTGTATCATTCATCACTCAATTATC
326 TAACGGGTGATTTTTATGTGGAACCTTTTTTATAGATAAATTGCATCATTCATCACTCAATTATC
*
2586260 TTCTCACTCCTAATTTGGTCACTAAAGTTTAATTTTTTTTAATTTAATTACTTAACTTTCAAAAT
391 TTCCCACTCCTAATTTGGTCACTAAAGTTTAATTTTTTTTAATTTAATTACTTAACTTTCAAAAT
*
2586325 ACTCCTAATTTAATGACTCTAACTTTCAAATTTATTTTTTATTTTTAATTATATTTTAATAAAAT
456 ACTCCTAATTTAATGACTCTAACTTTCAAATTTATTTTTTATTTTTAATTATATATTAATAAAAT
* * * *
2586390 AATATCATGTCACAAAAATTATTAATAAAATAAATTAGAGTTATTAAAATAAGAGCAATTTGAAA
521 AATATAATGTCACAAAAAATATTAATAAAATAAATTAGAGTGATTAAAATAAGAACAATTTGAAA
2586455 GTTGAGTAGTTAAATTGAAAATTTTCAACTTTAGTACCAAAATAGGAATAAGAATATAGTTAAAT
586 GTTGAGTAGTTAAATTGAAAATTTTCAACTTTAGTACCAAAATAGGAATAAGAATATAGTTAAAT
*
2586520 GATGAATGATGTAATTTACCCATAAAAAAACAATACCGTTAAGTTTTTAGTGGAGAGATACTAAA
651 GATGAATGATGTAATTTACCCATAAAAAAACAATACCGTTAAGTTTTTAGTGGAGAGATAATAAA
* *
2586585 ATGAAAAAAAAAACTAAATGTTAGGTATGGTTTTAAAAAAAATGAA-AGTTCAAGTACTAAAACG
716 ATGAAAAAAAAAACTAAACGTTAGGTATGATTTT--AAAAAATGAAGAGTTCAAGTACTAAAACG
* *
2586649 AACCAAAATTGATAGTTTACCA
779 AA-CAAAACTAATAGTTTACCA
*
2586671 AAATTTCTTAGGTAAACAAGTGAGGCTCTTTGAGGTCTGATGTGTTTGAATATGGCTCAAATTAA
1 AAATTTCTTAGGCAAACAAGTGAGGCTCTTTGAGGTCTGATGTGTTTGAATATGGCTCAAATTAA
*
2586736 TGTGCAACAAGGCTTATTCCAATTTGTCCCCTTTGTGTACCTTAGCAAAACAAATTCAAGAATCA
66 TGTGCAACAAGGCTTATTCCAATTTGTCCCCTTTGTGTACCCTAGCAAAACAAATTCAAGAATCA
2586801 ATAAATGGGTATAACAACATATAATCTAATAAGTAATAACTATGTTGCTTGAGATTTTATTTTCT
131 ATAAATGGGTATAACAACATATAATCTAATAAGTAATAACTATGTTGCTTGAGATTTTATTTTCT
* ** * *
2586866 TGAATAAATTACACGTTTAATACTTAAACTATCAGTTTTGGTGTGTTTTAGTACTTAAATTTTTA
196 TGAATAAATTACACGTTTAATACCTAAACTATCAAATTTGGTGTGTTTTAATACTTAAACTTTTA
*
2586931 ATTTTTCCAAAATCATACATAACGTTTAGTTTTTGTTTCATTTTAGTA-CATCGTCGTTAAAAAC
261 ATTTTTCCAAAATCATACATAACGTTTAGTTTTTGTTTCATTTTAGTATC-TCGTCATTAAAAAC
* *
2586995 TTAATGGGTGATTTTTATGTGGAACCTTTTTTAT-GCGTAAATTGCATCATTCATCACTCAATTA
325 TTAACGGGTGATTTTTATGTGGAACCTTTTTTATAG-ATAAATTGCATCATTCATCACTCAATTA
2587059 TCTTCCCACTCCTAATTTGGTCACTAAAGTTTAATTTTTTTTAATTTAATTACTTAACTTTCAAA
389 TCTTCCCACTCCTAATTTGGTCACTAAAGTTTAATTTTTTTTAATTTAATTACTTAACTTTCAAA
*
2587124 ATACTCTTAATTTAATGACTCTAACTTTCAAATTTATTTTTTATTTTTAATTATATATTAATAAA
454 ATACTCCTAATTTAATGACTCTAACTTTCAAATTTATTTTTTATTTTTAATTATATATTAATAAA
*
2587189 ATAATATAATTTCACAAAAAATATTAATAAAATAAATTAGAGTGATTAAAATAAGAACAATTTGA
519 ATAATATAATGTCACAAAAAATATTAATAAAATAAATTAGAGTGATTAAAATAAGAACAATTTGA
*
2587254 AAGTTGAGTAGTTAAATTGAAAATTTTCAACTTTAGTACCAAAATAGGAATGAGAATATAGTTAA
584 AAGTTGAGTAGTTAAATTGAAAATTTTCAACTTTAGTACCAAAATAGGAATAAGAATATAGTTAA
* * ** ***
2587319 GTGATTAATGATGTAATTTACCCATAAAAATGCAATGTTGTTAAGTTTTTAGT-GACGAGATAAT
649 ATGATGAATGATGTAATTTACCCATAAAAAAACAATACCGTTAAGTTTTTAGTGGA-GAGATAAT
* *
2587383 AAAATGAAACAAAAAACTAAACGTTAGGTATGATTTTAAAAAATTAAGAGTTCAAGTACTAAAAC
713 AAAATGAAAAAAAAAACTAAACGTTAGGTATGATTTTAAAAAATGAAGAGTTCAAGTACTAAAAC
2587448 GAACAAAACTAATAGTTTA
778 GAACAAAACTAATAGTTTA
2587467 AGTACTAAAC
Statistics
Matches: 750, Mismatches: 42, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
799 23 0.03
800 24 0.03
801 703 0.94
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (799 bp):
AAATTTCTTAGGCAAACAAGTGAGGCTCTTTGAGGTCTGATGTGTTTGAATATGGCTCAAATTAA
TGTGCAACAAGGCTTATTCCAATTTGTCCCCTTTGTGTACCCTAGCAAAACAAATTCAAGAATCA
ATAAATGGGTATAACAACATATAATCTAATAAGTAATAACTATGTTGCTTGAGATTTTATTTTCT
TGAATAAATTACACGTTTAATACCTAAACTATCAAATTTGGTGTGTTTTAATACTTAAACTTTTA
ATTTTTCCAAAATCATACATAACGTTTAGTTTTTGTTTCATTTTAGTATCTCGTCATTAAAAACT
TAACGGGTGATTTTTATGTGGAACCTTTTTTATAGATAAATTGCATCATTCATCACTCAATTATC
TTCCCACTCCTAATTTGGTCACTAAAGTTTAATTTTTTTTAATTTAATTACTTAACTTTCAAAAT
ACTCCTAATTTAATGACTCTAACTTTCAAATTTATTTTTTATTTTTAATTATATATTAATAAAAT
AATATAATGTCACAAAAAATATTAATAAAATAAATTAGAGTGATTAAAATAAGAACAATTTGAAA
GTTGAGTAGTTAAATTGAAAATTTTCAACTTTAGTACCAAAATAGGAATAAGAATATAGTTAAAT
GATGAATGATGTAATTTACCCATAAAAAAACAATACCGTTAAGTTTTTAGTGGAGAGATAATAAA
ATGAAAAAAAAAACTAAACGTTAGGTATGATTTTAAAAAATGAAGAGTTCAAGTACTAAAACGAA
CAAAACTAATAGTTTACCA
Found at i:2596814 original size:17 final size:17
Alignment explanation
Indices: 2596792--2596826 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2596782 AACGGTCAAC
2596792 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2596809 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2596826 G
1 G
2596827 TCGGGTCGGG
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:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2596819 original size:7 final size:7
Alignment explanation
Indices: 2596778--2596802 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2596768 GGTCAAAGGA
2596778 GGTCAAC
1 GGTCAAC
2596785 GGTCAAC
1 GGTCAAC
2596792 GGTCAAC
1 GGTCAAC
2596799 GGTC
1 GGTC
2596803 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:2598270 original size:11 final size:11
Alignment explanation
Indices: 2598254--2598284 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2598244 GATTAAAAAT
*
2598254 AAGATAATGAA
1 AAGATAAAGAA
2598265 AAGATAAAGAA
1 AAGATAAAGAA
2598276 AAGATAAAG
1 AAGATAAAG
2598285 GAATTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (11 bp):
AAGATAAAGAA
Found at i:2602603 original size:20 final size:20
Alignment explanation
Indices: 2602580--2602623 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2602570 TTTTTTGAAA
*
2602580 TTTTGGCTTTTTTTGTTTTT
1 TTTTGCCTTTTTTTGTTTTT
2602600 TTTTGCCTTTTTTTGTTTTT
1 TTTTGCCTTTTTTTGTTTTT
2602620 TTTT
1 TTTT
2602624 AAATAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (20 bp):
TTTTGCCTTTTTTTGTTTTT
Found at i:2602620 original size:10 final size:10
Alignment explanation
Indices: 2602587--2602623 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
2602577 AAATTTTGGC
2602587 TTTTTTTGTT
1 TTTTTTTGTT
**
2602597 TTTTTTTGCC
1 TTTTTTTGTT
2602607 TTTTTTTGTT
1 TTTTTTTGTT
2602617 TTTTTTT
1 TTTTTTT
2602624 AAATAGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:2609123 original size:26 final size:26
Alignment explanation
Indices: 2609094--2609145 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2609084 CTTTGTTGGT
*
2609094 TCTTCATCTTCATTAGCATTTGAGTA
1 TCTTCATCATCATTAGCATTTGAGTA
2609120 TCTTCATCATCATTAGCATTTGAGTA
1 TCTTCATCATCATTAGCATTTGAGTA
2609146 GCCATTCTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (26 bp):
TCTTCATCATCATTAGCATTTGAGTA
Found at i:2611844 original size:26 final size:26
Alignment explanation
Indices: 2611814--2611866 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2611804 TTGGTTCTTG
2611814 ATCTTCATCTTCATTAGCATTTGAGT
1 ATCTTCATCTTCATTAGCATTTGAGT
*
2611840 ATCTTCATCTTTATTAGCATTTGAGT
1 ATCTTCATCTTCATTAGCATTTGAGT
2611866 A
1 A
2611867 GCCATTCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (26 bp):
ATCTTCATCTTCATTAGCATTTGAGT
Found at i:2613904 original size:67 final size:66
Alignment explanation
Indices: 2613745--2613957 Score: 313
Period size: 67 Copynumber: 3.2 Consensus size: 66
2613735 AAAAAAATTT
** * **
2613745 GAAACAATCTCAAAGGTTTACATTTCAAGAGAAACTGTCTCAAGCGAGATGAAATTT-TTTTTAG
1 GAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACGAAATTTGTTTCAAG
2613809 A
66 A
* * *
2613810 GAAA-AATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCAATACGAAACTTTGTTTCGA
1 GAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACGAAA-TTTGTTTCAA
2613874 GA
65 GA
* *
2613876 GAAACAATCTTAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAG
1 GAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACGAAATTTGTTTCAAG
2613941 A
66 A
2613942 GAAACAATCTCAAAGG
1 GAAACAATCTCAAAGG
2613958 AGACAGATAA
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
64 44 0.33
65 7 0.05
66 36 0.27
67 45 0.34
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (66 bp):
GAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACGAAATTTGTTTCAAG
A
Found at i:2618900 original size:14 final size:14
Alignment explanation
Indices: 2618883--2618912 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2618873 AAAATGCAAT
2618883 AATTAAAGGACTAA
1 AATTAAAGGACTAA
*
2618897 AATTAAAGTACTAA
1 AATTAAAGGACTAA
2618911 AA
1 AA
2618913 AATAAAGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (14 bp):
AATTAAAGGACTAA
Found at i:2619219 original size:30 final size:30
Alignment explanation
Indices: 2619160--2619220 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2619150 AATAAATATA
** * *
2619160 ACAGTGGCTAAATTGGAATAAAAATAAAAC
1 ACAGTGGCTAAATTAAAACAAAAACAAAAC
*
2619190 ACAGTGGCTAAATTAAAACCAAAACAAAAC
1 ACAGTGGCTAAATTAAAACAAAAACAAAAC
2619220 A
1 A
2619221 GAGAGAATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.16
Consensus pattern (30 bp):
ACAGTGGCTAAATTAAAACAAAAACAAAAC
Found at i:2621058 original size:20 final size:20
Alignment explanation
Indices: 2621033--2621083 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
2621023 ATCTTATTCC
2621033 CTGGTAATCTT-ACATTCCCA
1 CTGGTAATCTTCA-ATTCCCA
2621053 CTGGTAATCTTCAATTCCCA
1 CTGGTAATCTTCAATTCCCA
2621073 CTGGTAATCTT
1 CTGGTAATCTT
2621084 TCATCCCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTCAATTCCCA
Found at i:2624355 original size:29 final size:29
Alignment explanation
Indices: 2624313--2624371 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2624303 TGAGTATCTC
2624313 ATCGTTAAAAACTTAAGAT-ATTAGTACCT
1 ATCGTTAAAAACTTAAG-TGATTAGTACCT
* *
2624342 ATCGTTTAAAACTTAAGTGTTTAGTACCT
1 ATCGTTAAAAACTTAAGTGATTAGTACCT
2624371 A
1 A
2624372 ACTATCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (29 bp):
ATCGTTAAAAACTTAAGTGATTAGTACCT
Found at i:2624877 original size:87 final size:92
Alignment explanation
Indices: 2624744--2624924 Score: 232
Period size: 93 Copynumber: 2.0 Consensus size: 92
2624734 TAATCAATGA
* * *
2624744 AATAAGAGTATTTTTTTCACCAACATTTCAAAAGATACAAATTAATCAC-ACCTTA-TT-TT-TA
1 AATAAGAGTAATTTTTTCACCAACATTCCAAAAGATACAAAATAATCACAACCTTATTTATTATA
2624805 TTACAAACCG-GTCACTCAATCATATTT
66 TTACAAACCGAG-CACTCAATCATATTT
* *
2624832 AATAAGAGTAATTTTTTCA-CAACATTCCAAAA-ATTGCAAAATAATCACAGACTTTATTTTATT
1 AATAAGAGTAATTTTTTCACCAACATTCCAAAAGA-TACAAAATAATCACA-ACCTTA-TTTATT
2624895 ATATTACAAACCGAGCACTCAATCATATTT
63 ATATTACAAACCGAGCACTCAATCATATTT
2624925 GACTTAGATA
Statistics
Matches: 80, Mismatches: 5, Indels: 11
0.83 0.05 0.11
Matches are distributed among these distances:
86 1 0.01
87 24 0.30
88 18 0.22
89 5 0.06
91 2 0.03
92 2 0.03
93 27 0.34
94 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.35
Consensus pattern (92 bp):
AATAAGAGTAATTTTTTCACCAACATTCCAAAAGATACAAAATAATCACAACCTTATTTATTATA
TTACAAACCGAGCACTCAATCATATTT
Found at i:2625882 original size:33 final size:33
Alignment explanation
Indices: 2625811--2625882 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2625801 TATCAACCGA
* *
2625811 TCCAACCTAGAAATATATATCATCTACCTGAAC
1 TCCAACCTAAAAATATATATCATCCACCTGAAC
* *
2625844 T-CAACCTAAAAATTTTATATCCTCCACCT-AAC
1 TCCAACCTAAAAA-TATATATCATCCACCTGAAC
2625876 TCCAACC
1 TCCAACC
2625883 CAACTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.28
Consensus pattern (33 bp):
TCCAACCTAAAAATATATATCATCCACCTGAAC
Found at i:2627514 original size:21 final size:21
Alignment explanation
Indices: 2627490--2627543 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
2627480 CACCGTAACT
2627490 TCCATAGCCACCACCTCCACG
1 TCCATAGCCACCACCTCCACG
*
2627511 TCCATAGCTACCACCTCCACG
1 TCCATAGCCACCACCTCCACG
*
2627532 TCCATATCCACC
1 TCCATAGCCACC
2627544 TATACCACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.50, G:0.07, T:0.19
Consensus pattern (21 bp):
TCCATAGCCACCACCTCCACG
Found at i:2627771 original size:18 final size:18
Alignment explanation
Indices: 2627745--2627799 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
2627735 AAGGAGGAGG
* * *
2627745 ACCATAACCGCCATCACC
1 ACCAAAACCACCATAACC
*
2627763 ACCAAAACCACCATAATC
1 ACCAAAACCACCATAACC
* *
2627781 ACCAAATCCACCAAAACC
1 ACCAAAACCACCATAACC
2627799 A
1 A
2627800 TCATTGTATG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.45, C:0.44, G:0.02, T:0.09
Consensus pattern (18 bp):
ACCAAAACCACCATAACC
Found at i:2627772 original size:9 final size:9
Alignment explanation
Indices: 2627760--2627799 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
2627750 AACCGCCATC
2627760 ACCACCAAA
1 ACCACCAAA
*
2627769 ACCACCATA
1 ACCACCAAA
*
2627778 ATCACCAAA
1 ACCACCAAA
*
2627787 TCCACCAAA
1 ACCACCAAA
2627796 ACCA
1 ACCA
2627800 TCATTGTATG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.50, C:0.42, G:0.00, T:0.07
Consensus pattern (9 bp):
ACCACCAAA
Found at i:2631805 original size:31 final size:31
Alignment explanation
Indices: 2631767--2631840 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
2631757 TTCGTACCAA
2631767 ATTAACCATTAACCAAACTTTTAAAAAAATC
1 ATTAACCATTAACCAAACTTTTAAAAAAATC
2631798 ATTAACCATTAACCAAACTTTTAAAAAAATC
1 ATTAACCATTAACCAAACTTTTAAAAAAATC
2631829 ATTAACCATTAA
1 ATTAACCATTAA
2631841 ATGACCAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (31 bp):
ATTAACCATTAACCAAACTTTTAAAAAAATC
Found at i:2639893 original size:19 final size:20
Alignment explanation
Indices: 2639855--2639894 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2639845 ATATCGGTAT
*
2639855 TGACCCCTAAGTATCGATAC
1 TGACCCCTAAGTATCAATAC
*
2639875 TGACCCCT-GGTATCAATAC
1 TGACCCCTAAGTATCAATAC
2639894 T
1 T
2639895 ATTTTTAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (20 bp):
TGACCCCTAAGTATCAATAC
Found at i:2660056 original size:24 final size:24
Alignment explanation
Indices: 2660014--2660060 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2660004 TGGTTGGTTG
*
2660014 AATGGTTGTTTAAACTTTATTTTT
1 AATGGTTATTTAAACTTTATTTTT
2660038 AATGGTATATTTAAA-TTTATTTT
1 AATGGT-TATTTAAACTTTATTTT
2660061 GGTTCTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (24 bp):
AATGGTTATTTAAACTTTATTTTT
Found at i:2666949 original size:19 final size:21
Alignment explanation
Indices: 2666912--2666954 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2666902 TAACTTTTTC
2666912 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
2666932 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
2666952 TTT
1 TTT
2666955 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:2666960 original size:19 final size:20
Alignment explanation
Indices: 2666911--2666960 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2666901 TTAACTTTTT
*
2666911 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
2666931 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
2666950 CTTTTACCTTT
1 CTTTTACCTTT
2666961 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:2671314 original size:59 final size:59
Alignment explanation
Indices: 2671237--2671354 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 59
2671227 CATGGGTATC
* *
2671237 GATGTCGACCCTTCAATATCGATACTTCATGAATGAGTATCGATACTTCCTGTTGAATT
1 GATGTCGACCCTTCAATATCGATACTTCATAAATGAGTATCGATACTCCCTGTTGAATT
* *
2671296 GATGTCGA-CCTTGTAATATCGATACTTCATAAATGGGTATCGATACTCCCTGTTGAATT
1 GATGTCGACCCTT-CAATATCGATACTTCATAAATGAGTATCGATACTCCCTGTTGAATT
2671355 TACTATTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 4 0.07
59 50 0.93
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (59 bp):
GATGTCGACCCTTCAATATCGATACTTCATAAATGAGTATCGATACTCCCTGTTGAATT
Found at i:2693138 original size:19 final size:19
Alignment explanation
Indices: 2693114--2693175 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
2693104 AACCATATTT
2693114 TTTTTATATAGAAACTAGA
1 TTTTTATATAGAAACTAGA
** * *
2693133 TTTTTAGGTTGCAACCT-GA
1 TTTTTATATAG-AAACTAGA
2693152 TTTTTCATATAGAAACTAGA
1 TTTTT-ATATAGAAACTAGA
2693172 TTTT
1 TTTT
2693176 AGGTTGCAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (19 bp):
TTTTTATATAGAAACTAGA
Found at i:2693176 original size:38 final size:38
Alignment explanation
Indices: 2693113--2693232 Score: 186
Period size: 38 Copynumber: 3.1 Consensus size: 38
2693103 GAACCATATT
*
2693113 TTTTTTATATAGAAACTAGATTTTTAGGTTGCAACCTGA
1 TTTTTCATATAGAAACTAGA-TTTTAGGTTGCAACCTGA
*
2693152 TTTTTCATATAGAAACTAGATTTTAGGTTGCAACTTGA
1 TTTTTCATATAGAAACTAGATTTTAGGTTGCAACCTGA
* * *
2693190 TTTTTCATATAGAAACCAAATTTTAGGTTGCAACCTTA
1 TTTTTCATATAGAAACTAGATTTTAGGTTGCAACCTGA
2693228 TTTTT
1 TTTTT
2693233 GTATTGGAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
38 56 0.75
39 19 0.25
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (38 bp):
TTTTTCATATAGAAACTAGATTTTAGGTTGCAACCTGA
Found at i:2693194 original size:19 final size:19
Alignment explanation
Indices: 2693126--2693194 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
2693116 TTTATATAGA
2693126 AACTAGATTTTTAGGTTGC
1 AACTAGATTTTTAGGTTGC
** * *
2693145 AACCT-GATTTTTCATATAGA
1 AA-CTAGATTTTT-AGGTTGC
2693165 AACTAGA-TTTTAGGTTGC
1 AACTAGATTTTTAGGTTGC
*
2693183 AACTTGATTTTT
1 AACTAGATTTTT
2693195 CATATAGAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
18 9 0.24
19 19 0.51
20 9 0.24
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (19 bp):
AACTAGATTTTTAGGTTGC
Found at i:2695807 original size:20 final size:20
Alignment explanation
Indices: 2695782--2695820 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2695772 AAAGCTCATA
2695782 TAGGATCATATAGATGTATT
1 TAGGATCATATAGATGTATT
*
2695802 TAGGATCATATAGTTGTAT
1 TAGGATCATATAGATGTAT
2695821 GTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (20 bp):
TAGGATCATATAGATGTATT
Found at i:2699594 original size:43 final size:42
Alignment explanation
Indices: 2699546--2699630 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
2699536 CAGCTCGTAA
2699546 TTTGCACCGAAGTAC-CATATAATTGTCCCCAAGGACCACATAG
1 TTTGCACCGAAGTACGCATAT--TTGTCCCCAAGGACCACATAG
* *
2699589 TTTGCACCGAAGTGCTGCATATTTGTCCCGAAGGACCACATA
1 TTTGCACCGAAGTAC-GCATATTTGTCCCCAAGGACCACATA
2699631 ATTATCCTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 33 0.87
45 5 0.13
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (42 bp):
TTTGCACCGAAGTACGCATATTTGTCCCCAAGGACCACATAG
Found at i:2699630 original size:21 final size:21
Alignment explanation
Indices: 2699552--2699652 Score: 80
Period size: 21 Copynumber: 4.8 Consensus size: 21
2699542 GTAATTTGCA
* *
2699552 CCGAAGTACCATATAATTGTC
1 CCGAAGGACCACATAATTGTC
* *
2699573 CCCAAGGACCACATAGTT-TGC
1 CCGAAGGACCACATAATTGT-C
** *
2699594 ACCGAAGTG-CTGCATATTTGTC
1 -CCGAAG-GACCACATAATTGTC
*
2699616 CCGAAGGACCACATAATTATC
1 CCGAAGGACCACATAATTGTC
*
2699637 CTGAAGGACCACATAA
1 CCGAAGGACCACATAA
2699653 AACCCTCGAC
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.03
21 45 0.73
22 13 0.21
23 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (21 bp):
CCGAAGGACCACATAATTGTC
Found at i:2700280 original size:54 final size:54
Alignment explanation
Indices: 2700214--2700344 Score: 165
Period size: 54 Copynumber: 2.4 Consensus size: 54
2700204 GATACTTCCC
* *
2700214 TTCAAGGGTATCGATACCTCCTCATGGTACCGATACCGATAT-AGCATTCAATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATGA-CATTCAATGT
* * * * *
2700268 TTCAAGGTTATCGATACCTTCTCAAGGTACCGATACCAATCTGACTTTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATGACATTCAATGT
*
2700322 TTAAAGGGTATCGATACCATCCT
1 TTCAAGGGTATCGATACC-TCCT
2700345 TCAGGTATCC
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
54 61 0.94
55 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATGACATTCAATGT
Found at i:2700353 original size:20 final size:21
Alignment explanation
Indices: 2700328--2700379 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
2700318 ATGTTTAAAG
2700328 GGTATCGATACCATCC-TT-CA
1 GGTATCGATACCA-CCTTTACA
* *
2700348 GGTATCCATACTACCTTTACA
1 GGTATCGATACCACCTTTACA
2700369 -GTATCGATACC
1 GGTATCGATACC
2700380 TCTTCAACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCACCTTTACA
Found at i:2706707 original size:21 final size:21
Alignment explanation
Indices: 2706677--2706775 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
2706667 AATTTGCACT
*
2706677 GAAGTACCACATAATTGTCCC
1 GAAGGACCACATAATTGTCCC
* *
2706698 CAAGGACCACATAGTT-TGCACC
1 GAAGGACCACATAATTGT-C-CC
* *
2706720 GAAGTG-CCGCATATTTGTCCC
1 GAAG-GACCACATAATTGTCCC
* * *
2706741 GAATGACAACATAATTATCCC
1 GAAGGACCACATAATTGTCCC
2706762 GAAGGACCACATAA
1 GAAGGACCACATAA
2706776 AACCCTCGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.03
21 42 0.70
22 14 0.23
23 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.21
Consensus pattern (21 bp):
GAAGGACCACATAATTGTCCC
Found at i:2706753 original size:43 final size:43
Alignment explanation
Indices: 2706669--2706775 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 43
2706659 CAACTCGTAA
* *
2706669 TTTGCACTGAAGTACCACATAATTGTCCCCAAGGACCACATAG
1 TTTGCACCGAAGTACCACATAATTGTCCCCAAGGACAACATAG
* * * * * *
2706712 TTTGCACCGAAGTGCCGCATATTTGTCCCGAATGACAACATAA
1 TTTGCACCGAAGTACCACATAATTGTCCCCAAGGACAACATAG
*
2706755 TTAT-C-CCGAAGGACCACATAA
1 TT-TGCACCGAAGTACCACATAA
2706776 AACCCTCGAA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 12 0.24
43 38 0.75
44 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
TTTGCACCGAAGTACCACATAATTGTCCCCAAGGACAACATAG
Found at i:2707437 original size:54 final size:54
Alignment explanation
Indices: 2707339--2707480 Score: 160
Period size: 54 Copynumber: 2.6 Consensus size: 54
2707329 ACTTCCCTTC
* * * * * *
2707339 AAGGGTATCAATACCTCCTCATGGTACCGATATCGATATAGCATTCGGTGTTTT
1 AAGGGTATCGATACCTCCTCAAGGTATCGATACCAATATAGCATTCGATGTTTT
* * *
2707393 AAGGTTATCGATACCTCCTCAAGGTATCGATACCAATCTGGCATTCGATGTTTT
1 AAGGGTATCGATACCTCCTCAAGGTATCGATACCAATATAGCATTCGATGTTTT
* *
2707447 AAGGGTATCGATTCCATCCTTC-ATGTATCGATAC
1 AAGGGTATCGATACC-TCC-TCAAGGTATCGATAC
2707481 TACCCTTACA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
54 58 0.78
55 14 0.19
56 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (54 bp):
AAGGGTATCGATACCTCCTCAAGGTATCGATACCAATATAGCATTCGATGTTTT
Found at i:2707487 original size:20 final size:20
Alignment explanation
Indices: 2707471--2707528 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
2707461 CATCCTTCAT
2707471 GTATCGATACTACCCTTACA
1 GTATCGATACTACCCTTACA
2707491 GTATCGATACTACCCTTACA
1 GTATCGATACTACCCTTACA
2707511 GTATCGATACTACCCTTA
1 GTATCGATACTACCCTTA
2707529 ATAATTTCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.31
Consensus pattern (20 bp):
GTATCGATACTACCCTTACA
Found at i:2707495 original size:40 final size:40
Alignment explanation
Indices: 2707451--2707528 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
2707441 TGTTTTAAGG
* *
2707451 GTATCGATTCCATCCTT-CATGTATCGATACTACCCTTACA
1 GTATCGATACCACCCTTACA-GTATCGATACTACCCTTACA
*
2707491 GTATCGATACTACCCTTACAGTATCGATACTACCCTTA
1 GTATCGATACCACCCTTACAGTATCGATACTACCCTTA
2707529 ATAATTTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (40 bp):
GTATCGATACCACCCTTACAGTATCGATACTACCCTTACA
Found at i:2712709 original size:32 final size:32
Alignment explanation
Indices: 2712590--2712714 Score: 123
Period size: 31 Copynumber: 4.0 Consensus size: 32
2712580 AACCTCGACA
* * *
2712590 ACTGTCCATAGGTCCCAAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCATAGAACATAGGTAAT
* *
2712621 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTCCCATAGAACATAGGTAAT
*
2712652 ACTGTTCATATGTCCCGGA-AG-ACATAGGTAAT
1 ACTGTCCATATGTCCC--ATAGAACATAGGTAAT
** *
2712684 TTTGTCCATATGTTCCATAGAACATAGGTAA
1 ACTGTCCATATGTCCCATAGAACATAGGTAA
2712715 ACCCTCGACT
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
30 2 0.03
31 48 0.63
32 26 0.34
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTCCCATAGAACATAGGTAAT
Found at i:2723176 original size:41 final size:41
Alignment explanation
Indices: 2723007--2723217 Score: 139
Period size: 41 Copynumber: 5.1 Consensus size: 41
2722997 ATATTGCAGT
* * *
2723007 GTTTGTTTCAAAAACGCCACTAAAGAACGATTCTTTTGCGGT
1 GTTTGTTT-AAAAATGCCACTAAAGTACGATTCTTTTGCGGC
* * * * * * *
2723049 GCTTGTTTAGAAATGCCACTATAGTACTAGGT-TGTAGCTGG-
1 GTTTGTTTAAAAATGCCACTAAAGTACGA-TTCTTTTGC-GGC
* * * * *
2723090 GTTTGTCTAAAAATGCCACAATATATGTACG---CTATTGTGGT
1 GTTTGTTTAAAAATGCCAC--TA-AAGTACGATTCTTTTGCGGC
*
2723131 GTTTGTTTAAAAATGCCACTAAAGAACGATTCTTTTGCGGC
1 GTTTGTTTAAAAATGCCACTAAAGTACGATTCTTTTGCGGC
* * *
2723172 GTTTGTTTAGAAA--CACACTAAAGTAGGATTCTTTGGCGGC
1 GTTTGTTTAAAAATGC-CACTAAAGTACGATTCTTTTGCGGC
2723212 GTTTGT
1 GTTTGT
2723218 AAAATAAACA
Statistics
Matches: 130, Mismatches: 28, Indels: 24
0.71 0.15 0.13
Matches are distributed among these distances:
38 5 0.04
39 3 0.02
40 30 0.23
41 76 0.58
42 10 0.08
43 2 0.02
44 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (41 bp):
GTTTGTTTAAAAATGCCACTAAAGTACGATTCTTTTGCGGC
Found at i:2723722 original size:24 final size:24
Alignment explanation
Indices: 2723690--2723738 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2723680 ATAGAACACC
2723690 GAGTAGGAAATTTTGAAATCTTAT
1 GAGTAGGAAATTTTGAAATCTTAT
2723714 GAGTAGGAAATTTTGAAATCTTAT
1 GAGTAGGAAATTTTGAAATCTTAT
2723738 G
1 G
2723739 TGATCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (24 bp):
GAGTAGGAAATTTTGAAATCTTAT
Found at i:2732639 original size:34 final size:34
Alignment explanation
Indices: 2732600--2732667 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
2732590 TGACCAACAA
* *
2732600 GCATAATCATTTTGGATACAATGTCAACAATTTT
1 GCATAATCATTTTGGAGACAATATCAACAATTTT
*
2732634 GCATAATCATTTTGGAGGCAATATCAACAATTTT
1 GCATAATCATTTTGGAGACAATATCAACAATTTT
2732668 ACAACCATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (34 bp):
GCATAATCATTTTGGAGACAATATCAACAATTTT
Found at i:2734960 original size:25 final size:25
Alignment explanation
Indices: 2734932--2734994 Score: 101
Period size: 25 Copynumber: 2.5 Consensus size: 25
2734922 AGTGCTTTAG
*
2734932 GTTCTTTTG-TTTTTTCCTTTTTATT
1 GTTCTTTTGCATTTTT-CTTTTTATT
2734957 GTTCTTTTGCATTTTTCTTTTTATT
1 GTTCTTTTGCATTTTTCTTTTTATT
2734982 GTTCTTTTGCATT
1 GTTCTTTTGCATT
2734995 ATCTAACACA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 31 0.86
26 5 0.14
ACGTcount: A:0.06, C:0.13, G:0.10, T:0.71
Consensus pattern (25 bp):
GTTCTTTTGCATTTTTCTTTTTATT
Found at i:2734976 original size:13 final size:13
Alignment explanation
Indices: 2734954--2734994 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2734944 TTTCCTTTTT
2734954 ATTGTTCTTTTGC
1 ATTGTTCTTTTGC
* *
2734967 ATTTTTCTTTT-T
1 ATTGTTCTTTTGC
2734979 ATTGTTCTTTTGC
1 ATTGTTCTTTTGC
2734992 ATT
1 ATT
2734995 ATCTAACACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.10, C:0.12, G:0.10, T:0.68
Consensus pattern (13 bp):
ATTGTTCTTTTGC
Found at i:2734988 original size:12 final size:12
Alignment explanation
Indices: 2734948--2734989 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
2734938 TTGTTTTTTC
2734948 CTTTTTATTGTT
1 CTTTTTATTGTT
* *
2734960 CTTTTGCATTTTT
1 CTTTT-TATTGTT
2734973 CTTTTTATTGTT
1 CTTTTTATTGTT
2734985 CTTTT
1 CTTTT
2734990 GCATTATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.74
Consensus pattern (12 bp):
CTTTTTATTGTT
Found at i:2742175 original size:18 final size:19
Alignment explanation
Indices: 2742140--2742176 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2742130 TATGGAATGT
2742140 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2742160 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2742177 GGATTATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2742857 original size:15 final size:15
Alignment explanation
Indices: 2742837--2742870 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2742827 AATTTTCATT
*
2742837 AAATAAGTTTACATG
1 AAATAAGTTTACACG
2742852 AAATAAGTTTACACG
1 AAATAAGTTTACACG
2742867 AAAT
1 AAAT
2742871 GAAGAGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (15 bp):
AAATAAGTTTACACG
Found at i:2745250 original size:37 final size:37
Alignment explanation
Indices: 2745177--2745251 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
2745167 GTTGGAAAAT
*
2745177 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
2745214 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
2745251 A
1 A
2745252 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:2746011 original size:48 final size:48
Alignment explanation
Indices: 2745948--2746048 Score: 143
Period size: 48 Copynumber: 2.1 Consensus size: 48
2745938 ATATGGGACT
* * *
2745948 AATTTAAAATAAAATTCATAATTTGA-GAATAGAATTAAAATATTTAAA
1 AATTTAAAATAAAATTCATAATTT-ACAAATAAAATTAAAATATTCAAA
2745996 AATTTAAAACT-AAATTCATAATTTACAAATAAAATTAAAATATTCAAA
1 AATTTAAAA-TAAAATTCATAATTTACAAATAAAATTAAAATATTCAAA
2746044 AATTT
1 AATTT
2746049 GAGGTCAGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
47 1 0.02
48 46 0.96
49 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (48 bp):
AATTTAAAATAAAATTCATAATTTACAAATAAAATTAAAATATTCAAA
Found at i:2756094 original size:21 final size:21
Alignment explanation
Indices: 2756046--2756098 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2756036 ATTAATCACA
2756046 TCAATTTTATATATTAAAAAAT
1 TCAATTTTA-ATATTAAAAAAT
*
2756068 TCAATTTTAAT-TTAAATTAAT
1 TCAATTTTAATATTAAA-AAAT
*
2756089 TTAATTTTAA
1 TCAATTTTAA
2756099 AATAATGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 9 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
TCAATTTTAATATTAAAAAAT
Found at i:2756097 original size:16 final size:16
Alignment explanation
Indices: 2756073--2756110 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2756063 AAAATTCAAT
*
2756073 TTTAA-TTTAAATTAA
1 TTTAATTTTAAAATAA
2756088 TTTAATTTTAAAATAA
1 TTTAATTTTAAAATAA
2756104 TGTTAAT
1 T-TTAAT
2756111 AAATAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 10 0.50
17 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAATTTTAAAATAA
Found at i:2760606 original size:20 final size:20
Alignment explanation
Indices: 2760553--2760609 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
2760543 ATGAATTGGA
*
2760553 TGAACAGTATCGATACTGAT
1 TGAAGAGTATCGATACTGAT
*
2760573 TGAAGTACTATCGATACTGAT
1 TGAAG-AGTATCGATACTGAT
2760594 GTGAAG-GTATCGATAC
1 -TGAAGAGTATCGATAC
2760610 CAAGAGGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.41
21 14 0.44
22 5 0.16
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (20 bp):
TGAAGAGTATCGATACTGAT
Found at i:2762197 original size:8 final size:10
Alignment explanation
Indices: 2762173--2762197 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2762163 ATGTGACCAT
2762173 AATATATGAG
1 AATATATGAG
2762183 AATATATGAG
1 AATATATGAG
2762193 AATAT
1 AATAT
2762198 TATATGATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (10 bp):
AATATATGAG
Done.