Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_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: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 16
Found at i:2626076 original size:18 final size:18
Alignment explanation
Indices: 2626049--2626096 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
2626039 GCTTGAAGAG
2626049 AAAAAG-AAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
2626066 AAAAGAGAAAAAAGAAAAA
1 AAAA-AGAAAAAAGAAAAA
*
2626085 AAGAA-AAAAAAG
1 AAAAAGAAAAAAG
2626097 GGGTCAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 11 0.39
18 3 0.11
19 14 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAGAAAAA
Found at i:2627559 original size:83 final size:83
Alignment explanation
Indices: 2627459--2627774 Score: 479
Period size: 83 Copynumber: 3.7 Consensus size: 83
2627449 GAACAAATGC
*
2627459 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
2627524 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
2627542 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
2627607 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
2627625 AATGTGCTCATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-G---G-----T
*
2627690 AAAAACCAATCATTAAATTTGAAAGATG
57 -AAAACCAATCATTGAATTTGAAAGATG
* * *
2627718 AATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
2627775 TGAAACCACA
Statistics
Matches: 214, Mismatches: 9, Indels: 20
0.88 0.04 0.08
Matches are distributed among these distances:
83 133 0.62
84 2 0.01
87 1 0.00
89 1 0.00
92 2 0.01
93 75 0.35
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
CATTGAATTTGAAAGATG
Found at i:2627757 original size:93 final size:93
Alignment explanation
Indices: 2627598--2627824 Score: 330
Period size: 93 Copynumber: 2.4 Consensus size: 93
2627588 CTGGTTTGGT
* * *
2627598 AAAACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGAAAGTGTTCTTTGAGT
1 AAAACCAATCATTAAATTTGAAAGATGAATTTGCTAATAGCATCTTCTGAAAGTGTTCTTTGAGT
*
2627663 TATCTGATCTGGTTTGGTATGAACCCTA-
66 TATCTGATCTGGTTTGGTATGAAACC-AC
* *
2627691 AAAACCAATCATTAAATTTGAAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAAACCAATCATTAAATTTGAAAGATGAATTTGCTAATAGCATCTTCTGAAAGTGTTCTTTGAGT
2627756 TATCTGATCTGGTTTGGTATGAAACCAC
66 TATCTGATCTGGTTTGGTATGAAACCAC
* * * * *
2627784 AGAACCAATCGTTAGATATTGAAAAATGAATTTGCTCATAG
1 AAAACCAATCATTAAAT-TTGAAAGATGAATTTGCTAATAG
2627825 TAAAAATAAG
Statistics
Matches: 120, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
92 1 0.01
93 99 0.82
94 20 0.17
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (93 bp):
AAAACCAATCATTAAATTTGAAAGATGAATTTGCTAATAGCATCTTCTGAAAGTGTTCTTTGAGT
TATCTGATCTGGTTTGGTATGAAACCAC
Found at i:2628905 original size:113 final size:113
Alignment explanation
Indices: 2628744--2629152 Score: 709
Period size: 113 Copynumber: 3.6 Consensus size: 113
2628734 GTCAGTTAGT
2628744 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
2628809 ACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAA
2628857 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
*
2628922 ACCTTTTGCTCAAATCCATCACTTGATGGATTAGATTTGCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAA
* *
2628970 GTTCATAATGAGAATAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* * *
2629035 ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAGA
66 ACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA-A
*
2629084 GTTCATAATGAGAAGAACTCATCT---GAA-GAAGAATAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
*
2629145 ACTTTTTG
66 ACCTTTTG
2629153 GATCAGCTTT
Statistics
Matches: 285, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
110 40 0.14
111 3 0.01
113 218 0.76
114 24 0.08
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (113 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAA
Found at i:2629162 original size:90 final size:94
Alignment explanation
Indices: 2629061--2629246 Score: 317
Period size: 90 Copynumber: 2.0 Consensus size: 94
2629051 CATCACTTGA
*
2629061 TGGATCAGCTTTTCCAGAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAA-TA-AA-T
1 TGGATCAGCTTTTCCAGAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
2629122 TCATAATGAGAAGAATTTGTTCAACTTTT
66 TCATAATGAGAAGAATTTGTTCAACCTTT
2629151 TGGATCAGCTTTTCCAGAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 TGGATCAGCTTTTCCAGAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
2629216 TCATAATGAGAAGAATTTGTTTAACCTTT
66 TCATAATGAGAAGAATTTGTTCAACCTTT
2629245 TG
1 TG
2629247 CTCAAATCCA
Statistics
Matches: 89, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
90 53 0.60
91 3 0.03
92 1 0.01
93 2 0.02
94 30 0.34
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (94 bp):
TGGATCAGCTTTTCCAGAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAATTTGTTCAACCTTT
Found at i:2629244 original size:204 final size:206
Alignment explanation
Indices: 2628961--2629360 Score: 653
Period size: 204 Copynumber: 1.9 Consensus size: 206
2628951 ATTAGATTTG
* *
2628961 CCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGA
1 CCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGA
*
2629026 ATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAGAGTTCATA
66 ATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATA
* * *
2629091 ATGAGAAGAACTCATCTG-A-AG-AAGAATAAATTCATAATGAGAAGAATTTGTTCAACTTTTTG
131 ATGAGAAGAACTCATCTGAAGAGAAAGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTTTG
2629153 GATCAGCTTTT
196 GATCAGCTTTT
* *
2629164 CCAGAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
1 CCAGAAAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAG
* *
2629229 AATTTGTTTAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCTAGAAAAAAGTTCAT
65 AATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAAGTTCAT
* *
2629294 AATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAAATTGTTTAACCTTT
130 AATGAGAAGAACTCATCTGAA-GAGAAAGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTT
2629359 TG
194 TG
2629361 TTCAAATTCA
Statistics
Matches: 180, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
203 7 0.04
204 134 0.74
205 1 0.01
207 2 0.01
208 36 0.20
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (206 bp):
CCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGA
ATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATA
ATGAGAAGAACTCATCTGAAGAGAAAGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTTTG
GATCAGCTTTT
Found at i:2629310 original size:114 final size:113
Alignment explanation
Indices: 2629151--2629439 Score: 438
Period size: 114 Copynumber: 2.5 Consensus size: 113
2629141 TTCAACTTTT
*
2629151 TGGATCAGCTTTTCCAGAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 TGGATCAGCTTTT-CAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
2629216 TCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACTTGA
65 TCATAATGAGAAGAAATTGTTTAACCTTTTGCTCAAATCCATCACTTGA
* *
2629265 TGGATCAGCTTTTCTAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGT
1 TGGATCAGCTTTTC-AGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
2629330 TCATAATGAGAAGAAATTGTTTAACCTTTTGTTCAAATTCATCACTTGA
65 TCATAATGAGAAGAAATTGTTTAACCTTTTGCTCAAATCCATCACTTGA
* * * * *
2629379 TGGATCAACCTTTACAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAGGAAAG-AGAAGAA
1 TGGATC-AGCTTTTCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
2629440 TTTATTCAAC
Statistics
Matches: 160, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
112 7 0.04
113 33 0.21
114 114 0.71
115 6 0.04
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (113 bp):
TGGATCAGCTTTTCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAAATTGTTTAACCTTTTGCTCAAATCCATCACTTGA
Found at i:2629583 original size:3 final size:3
Alignment explanation
Indices: 2629575--2629644 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
2629565 TTTACCCATT
* * * *
2629575 TTA TTA TTA TTA TAA TTA TTA TCA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2629623 -TA TATA TATA TTA TTA TTA TTA
1 TTA T-TA T-TA TTA TTA TTA TTA
2629645 AAAAAATATA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.03
3 49 0.84
4 7 0.12
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2629653 original size:22 final size:22
Alignment explanation
Indices: 2629609--2629654 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2629599 TAATTATTAT
* * *
2629609 TATTATAATTATTATATATATA
1 TATTATAATTATTAAAAAAATA
*
2629631 TATTATTATTATTAAAAAAATA
1 TATTATAATTATTAAAAAAATA
2629653 TA
1 TA
2629655 ATAATAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTATAATTATTAAAAAAATA
Found at i:2630073 original size:10 final size:10
Alignment explanation
Indices: 2630058--2630085 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2630048 AAAGAAAAAG
2630058 GAGAGACCGA
1 GAGAGACCGA
2630068 GAGAGACCGA
1 GAGAGACCGA
2630078 GAGAGACC
1 GAGAGACC
2630086 AACAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (10 bp):
GAGAGACCGA
Found at i:2630115 original size:17 final size:17
Alignment explanation
Indices: 2630089--2630127 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2630079 AGAGACCAAC
* *
2630089 AAAAATAGAGAAGAAAA
1 AAAAACAGAGAACAAAA
2630106 AAAAACAGAGAACAAAA
1 AAAAACAGAGAACAAAA
2630123 AAAAA
1 AAAAA
2630128 GAAAACCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAACAGAGAACAAAA
Found at i:2631016 original size:20 final size:21
Alignment explanation
Indices: 2630970--2631016 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2630960 CTGCTTTTAA
*
2630970 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
2630991 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
2631010 ATATATT
1 ATATATT
2631017 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:2631086 original size:26 final size:25
Alignment explanation
Indices: 2631057--2631105 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
2631047 AAATATATAT
2631057 AATAAATAATAATTT-ATATTTTTCTC
1 AATAAAT--TAATTTAATATTTTTCTC
*
2631083 AATAAATTATTTTAATATTTTTC
1 AATAAATTAATTTAATATTTTTC
2631106 AATATCGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (25 bp):
AATAAATTAATTTAATATTTTTCTC
Found at i:2634690 original size:2 final size:2
Alignment explanation
Indices: 2634683--2634712 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2634673 CTATAATTTA
*
2634683 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2634713 GTATTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2647984 original size:80 final size:76
Alignment explanation
Indices: 2647858--2648083 Score: 250
Period size: 80 Copynumber: 2.9 Consensus size: 76
2647848 ACGATAGAAG
*
2647858 TTGACAGCAATTA-ATCGAAACCAAAATGATAAAACTATTAGATGTTAAGATCTAGTTAGTTGCA
1 TTGACAGCAATTACAT--AAACCAAAATGATAAAACTATTAGATGTTAAGATCTAGTTAGCTGCA
2647922 AAGCAGAGAATAGAGA
64 AAGC-GAG-AT-GAGA
* * *
2647938 TTGACAGCAATTACCATAAACCAAAATGATAAAACTATTAGATGTTAGGATATAGTTAACTGCAA
1 TTGACAGCAATTA-CATAAACCAAAATGATAAAACTATTAGATGTTAAGATCTAGTTAGCTGCAA
*
2648003 AGC----TGCGA
65 AGCGAGATGAGA
* * *
2648011 CTGACAACAATTACTATAAACCAAAATGATAAAACTATTACA-GTTAAGA-CATAGTTAGCTGCA
1 TTGACAGCAATTAC-ATAAACCAAAATGATAAAACTATTAGATGTTAAGATC-TAGTTAGCTGCA
2648074 AAGCTGAGAT
64 AAGC-GAGAT
2648084 TTCTTACCGT
Statistics
Matches: 126, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
72 22 0.17
73 40 0.32
74 1 0.01
77 1 0.01
80 60 0.48
82 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.25
Consensus pattern (76 bp):
TTGACAGCAATTACATAAACCAAAATGATAAAACTATTAGATGTTAAGATCTAGTTAGCTGCAAA
GCGAGATGAGA
Found at i:2649131 original size:26 final size:26
Alignment explanation
Indices: 2649102--2649160 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
2649092 TATATACTTG
2649102 TATACACATGCATTCATACATACATA
1 TATACACATGCATTCATACATACATA
2649128 TATACACATGCATTCATACATACATA
1 TATACACATGCATTCATACATACATA
2649154 TATACAC
1 TATACAC
2649161 GGAGAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.31
Consensus pattern (26 bp):
TATACACATGCATTCATACATACATA
Found at i:2650131 original size:30 final size:30
Alignment explanation
Indices: 2650097--2650160 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
2650087 AGTCGAGTTA
* *
2650097 AGCAACAAGTTTTTTAACGAGCACGAGTCG
1 AGCAACAAATTTTTTAACGAACACGAGTCG
*
2650127 AGCAACAAATTTTTTAACGAACATGAGTCG
1 AGCAACAAATTTTTTAACGAACACGAGTCG
2650157 AGCA
1 AGCA
2650161 CTACCCAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (30 bp):
AGCAACAAATTTTTTAACGAACACGAGTCG
Found at i:2661946 original size:20 final size:20
Alignment explanation
Indices: 2661917--2661955 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2661907 GAATCTAAAC
* *
2661917 TTTTAGTATTTGTTTAATGG
1 TTTTAATATTTATTTAATGG
2661937 TTTTAATATTTATTTAATG
1 TTTTAATATTTATTTAATG
2661956 AATCTAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (20 bp):
TTTTAATATTTATTTAATGG
Found at i:2662007 original size:2 final size:2
Alignment explanation
Indices: 2662000--2662031 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2661990 GTAATTAGTG
2662000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2662032 GAGGGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2663533 original size:18 final size:18
Alignment explanation
Indices: 2663510--2663552 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 18
2663500 TGGAGGCTCA
2663510 GCTTGTGATGATGATGGT
1 GCTTGTGATGATGATGGT
2663528 GC-T-TG-TGATGATGGT
1 GCTTGTGATGATGATGGT
2663543 GCTTGTGATG
1 GCTTGTGATG
2663553 TTGCAACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.55
16 3 0.14
17 3 0.14
18 4 0.18
ACGTcount: A:0.14, C:0.07, G:0.40, T:0.40
Consensus pattern (18 bp):
GCTTGTGATGATGATGGT
Found at i:2663551 original size:12 final size:15
Alignment explanation
Indices: 2663518--2663552 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2663508 CAGCTTGTGA
2663518 TGATGATGGTGCTTG
1 TGATGATGGTGCTTG
2663533 TGATGATGGTGCTTG
1 TGATGATGGTGCTTG
2663548 TGATG
1 TGATG
2663553 TTGCAACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.06, G:0.40, T:0.40
Consensus pattern (15 bp):
TGATGATGGTGCTTG
Found at i:2667857 original size:3 final size:3
Alignment explanation
Indices: 2667849--2667873 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2667839 TTATCATGAT
2667849 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2667874 CCTAAGGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2679852 original size:39 final size:39
Alignment explanation
Indices: 2679802--2679893 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 39
2679792 ATATTAGTCT
*
2679802 TTTGTATTTATATTTCATATATAAATATAATAGTAAGTG
1 TTTGTAATTATATTTCATATATAAATATAATAGTAAGTG
* * *
2679841 TTTGTAATTATATTTTATATATTAATATAATAGTAATTG
1 TTTGTAATTATATTTCATATATAAATATAATAGTAAGTG
*
2679880 TGTT-TAATAATATT
1 T-TTGTAATTATATT
2679894 AAGTGTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 45 0.96
40 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.09, T:0.52
Consensus pattern (39 bp):
TTTGTAATTATATTTCATATATAAATATAATAGTAAGTG
Found at i:2679981 original size:21 final size:21
Alignment explanation
Indices: 2679957--2680029 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
2679947 GAATGTGAAT
*
2679957 ATGAATAGATATGATGTTAAC
1 ATGAATAAATATGATGTTAAC
* * *
2679978 ATGAAGAGATATGAAGTT-AC
1 ATGAATAAATATGATGTTAAC
*
2679998 AT-AATAAATGTGATGTTAAC
1 ATGAATAAATATGATGTTAAC
*
2680018 ATGTATAAATAT
1 ATGAATAAATAT
2680030 AATCATAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 11 0.26
20 8 0.19
21 23 0.55
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (21 bp):
ATGAATAAATATGATGTTAAC
Found at i:2692486 original size:2 final size:2
Alignment explanation
Indices: 2692479--2692504 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2692469 TTGATTATGT
2692479 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
2692505 ATAACTCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2692876 original size:15 final size:15
Alignment explanation
Indices: 2692856--2692884 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2692846 ATATGTAGTC
2692856 AGTAAGTTAATGTTT
1 AGTAAGTTAATGTTT
2692871 AGTAAGTTAATGTT
1 AGTAAGTTAATGTT
2692885 CAGCTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
AGTAAGTTAATGTTT
Found at i:2708581 original size:69 final size:69
Alignment explanation
Indices: 2708505--2708644 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
2708495 CTTATAAACC
2708505 ATCACATGGCATGTACTTTTTGTGTAGGTGGGTTCATTTTAGCTCCACATTAATAAGCTTTAGGT
1 ATCACATGGCATGTACTTTTTGTGTAGGTGGGTTCATTTTAGCTCCACATTAATAAGCTTTAGGT
2708570 ATGA
66 ATGA
2708574 ATCACATGGCATGTACTTTTTGTGTAGGTGGGTTCATTTTAGCTCCACATTAATAAGCTTTAGGT
1 ATCACATGGCATGTACTTTTTGTGTAGGTGGGTTCATTTTAGCTCCACATTAATAAGCTTTAGGT
2708639 ATGA
66 ATGA
2708643 AT
1 AT
2708645 GTGTTAGTAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (69 bp):
ATCACATGGCATGTACTTTTTGTGTAGGTGGGTTCATTTTAGCTCCACATTAATAAGCTTTAGGT
ATGA
Found at i:2733140 original size:77 final size:77
Alignment explanation
Indices: 2733051--2733197 Score: 231
Period size: 77 Copynumber: 1.9 Consensus size: 77
2733041 TGTTTTAACC
* * * *
2733051 AAAAAATTTAAATACTTAAAATAAACAAAATATATAATTTAAACGCATATTTTTCAATTAACTAA
1 AAAAAATCTAAATACTTAAAATAAACAAAATATACAATATAAACACATATTTTTCAATTAACTAA
2733116 GGATATAACAAA
66 GGATATAACAAA
* * *
2733128 AAAAAATCTAAATACTTAAAATAAACAAAATGTACAATATAGACACATATTTTTCAATTAATTAA
1 AAAAAATCTAAATACTTAAAATAAACAAAATATACAATATAAACACATATTTTTCAATTAACTAA
2733193 GGATA
66 GGATA
2733198 AAAGTATAGG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (77 bp):
AAAAAATCTAAATACTTAAAATAAACAAAATATACAATATAAACACATATTTTTCAATTAACTAA
GGATATAACAAA
Found at i:2734867 original size:2 final size:2
Alignment explanation
Indices: 2734860--2734905 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2734850 CTTTCTTCCT
2734860 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
2734902 TA TA
1 TA TA
2734906 GCATTTAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2741634 original size:31 final size:31
Alignment explanation
Indices: 2741599--2741663 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2741589 AATGTACATG
*
2741599 GTCTCTAACATAATTGA-TCTGTTCGATTTTA
1 GTCTCTAACATAATCGATTC-GTTCGATTTTA
*
2741630 GTCTCTAACATTATCGATTCGTTCGATTTTA
1 GTCTCTAACATAATCGATTCGTTCGATTTTA
2741661 GTC
1 GTC
2741664 CCTCATCTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (31 bp):
GTCTCTAACATAATCGATTCGTTCGATTTTA
Found at i:2741691 original size:32 final size:33
Alignment explanation
Indices: 2741648--2741733 Score: 124
Period size: 32 Copynumber: 2.7 Consensus size: 33
2741638 CATTATCGAT
2741648 TCGTTCGATTTTAGTCCCTCA-TCTGTTAAC-CC
1 TCGTTCGATTTTAGTCCCTCAGTC-GTTAACTCC
*
2741680 TCGTTCAATTTTAGTCCCTCAGTCGTTAACTCC
1 TCGTTCGATTTTAGTCCCTCAGTCGTTAACTCC
*
2741713 T-ATTCGATTTTAGTCCCTCAG
1 TCGTTCGATTTTAGTCCCTCAG
2741734 CTATGTCATA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 44 0.90
33 5 0.10
ACGTcount: A:0.17, C:0.29, G:0.13, T:0.41
Consensus pattern (33 bp):
TCGTTCGATTTTAGTCCCTCAGTCGTTAACTCC
Found at i:2743913 original size:60 final size:59
Alignment explanation
Indices: 2743834--2743970 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 59
2743824 TAAAGTACAC
* * * *
2743834 AAATGGTC-TCTCGATTATAATATGTTATTTTATTGAGTTAC-TCAATTATTAAAAGTTAT
1 AAATGGTCATC-CGACTATAAGAAGTTATTTTATTGAG-TACATCAACTATTAAAAGTTAT
* * * * ** *
2743893 AAAATGGTCATCCTACTATAAGAAGTTGTTTTGTTGAGTCCATCGGCTATTAAAAGTTGT
1 -AAATGGTCATCCGACTATAAGAAGTTATTTTATTGAGTACATCAACTATTAAAAGTTAT
2743953 AAATGGTCATCCGACTAT
1 AAATGGTCATCCGACTAT
2743971 TCATTATGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
59 19 0.30
60 42 0.67
61 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (59 bp):
AAATGGTCATCCGACTATAAGAAGTTATTTTATTGAGTACATCAACTATTAAAAGTTAT
Found at i:2744417 original size:22 final size:19
Alignment explanation
Indices: 2744372--2744421 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
2744362 TTTAAATATC
2744372 ATTT-ATAATTTTTTAATA
1 ATTTAATAATTTTTTAATA
2744390 AGTTTAATAATTATTTTATACTA
1 A-TTTAATAATT-TTTTA-A-TA
2744413 ATTTAATAA
1 ATTTAATAA
2744422 AATTTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 6 0.22
21 5 0.19
22 9 0.33
23 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTAATAATTTTTTAATA
Found at i:2744434 original size:22 final size:22
Alignment explanation
Indices: 2744392--2744448 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
2744382 TTTTAATAAG
** *
2744392 TTTAATAATTATTTTATACTAA
1 TTTAATAACAATTTAATACTAA
*
2744414 TTTAATAA-AATTTAATAACTAT
1 TTTAATAACAATTTAAT-ACTAA
*
2744436 TTTTATAACAATT
1 TTTAATAACAATT
2744449 CAATCATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.21
22 19 0.66
23 4 0.14
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAATAACAATTTAATACTAA
Found at i:2750405 original size:66 final size:66
Alignment explanation
Indices: 2750289--2750471 Score: 241
Period size: 66 Copynumber: 2.8 Consensus size: 66
2750279 AGGCTGAGCA
* * *
2750289 CCAGATGGGAAAACTTCATTCGAG-T-G-TTTTGCACTTGACCATCAGAGCTTTCTGACTGAAC-
1 CCAGATGGGAAAACTTCATTTGAGCTCGCTTTTTCACTTGACCATCAGAGCTTTCAGACTGAACA
2750350 T
66 T
*
2750351 CCAGATGGGAAAACTTCATTTGAGCTCGGCTTTTTCACTTGACCATCAGAGCTTTCAGACTGAGC
1 CCAGATGGGAAAACTTCATTTGAGCTC-GCTTTTTCACTTGACCATCAGAGCTTTCAGACTGAAC
2750416 AT
65 AT
* * * *
2750418 -CAGATGGAAAAACTTCATCTGAGCTCTTCTTTTTCACCTGACCATCAGAGCTTT
1 CCAGATGGGAAAACTTCATTTGAGCTC-GCTTTTTCACTTGACCATCAGAGCTTT
2750472 TAGTCAGCAT
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
62 23 0.21
63 1 0.01
65 1 0.01
66 81 0.76
67 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (66 bp):
CCAGATGGGAAAACTTCATTTGAGCTCGCTTTTTCACTTGACCATCAGAGCTTTCAGACTGAACA
T
Found at i:2751411 original size:2 final size:2
Alignment explanation
Indices: 2751404--2751429 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2751394 TATTCATTTG
2751404 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2751430 TTGATTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2752839 original size:84 final size:84
Alignment explanation
Indices: 2752688--2752845 Score: 253
Period size: 84 Copynumber: 1.9 Consensus size: 84
2752678 AAATTCAATC
* *
2752688 GGTGCCCCTCAATCTGTTTCTCCAGCACTTATGCGATCAAATTCTGCTATTCTGGGATCTCAGGG
1 GGTGCCCCTCAATCTGGTTCTCCAGCACTTATGCGATCAAATTCTGCTATTCTGGGATCTCAAGG
2752753 TGGTTCAATACCTTCTTTT
66 TGGTTCAATACCTTCTTTT
* * * * *
2752772 GGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCAAGTTCTGCTATTTTGGGATCTTAAGG
1 GGTGCCCCTCAATCTGGTTCTCCAGCACTTATGCGATCAAATTCTGCTATTCTGGGATCTCAAGG
2752837 TGGTTCAAT
66 TGGTTCAAT
2752846 GCCTCCACAG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (84 bp):
GGTGCCCCTCAATCTGGTTCTCCAGCACTTATGCGATCAAATTCTGCTATTCTGGGATCTCAAGG
TGGTTCAATACCTTCTTTT
Found at i:2764290 original size:41 final size:41
Alignment explanation
Indices: 2764242--2764325 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
2764232 AAGTTAGATG
2764242 ATTGGTGATTGTAAGGTAGTAAGTCTATTTTCTTAGATTCC
1 ATTGGTGATTGTAAGGTAGTAAGTCTATTTTCTTAGATTCC
2764283 ATTGGTGATTGTAAGGTAGTAAGTCTATTTTCTTAGATTCC
1 ATTGGTGATTGTAAGGTAGTAAGTCTATTTTCTTAGATTCC
2764324 AT
1 AT
2764326 GAAAATGGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (41 bp):
ATTGGTGATTGTAAGGTAGTAAGTCTATTTTCTTAGATTCC
Found at i:2765796 original size:17 final size:17
Alignment explanation
Indices: 2765774--2765807 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2765764 GATAGGCTTA
2765774 AATATCTTTTACTGCCT
1 AATATCTTTTACTGCCT
2765791 AATATCTTTTACTGCCT
1 AATATCTTTTACTGCCT
2765808 GGACCTAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (17 bp):
AATATCTTTTACTGCCT
Found at i:2772925 original size:60 final size:60
Alignment explanation
Indices: 2772851--2772986 Score: 227
Period size: 60 Copynumber: 2.3 Consensus size: 60
2772841 TTTTTGTCCA
*
2772851 TCTATTTATTATAAAAGTCGTTAAGTTTTTAATGAATCTAAGATCAAATTTTTGTCGATT
1 TCTATTTATTATAAAAGTCGTTAAGTTTTTAATGAATCTAAGATCAAATTTTTGTCGATC
* * * *
2772911 TCTATTTATTATAAAAGTCGTTGAGTTTTTAATGAATCTATGGTCAATTTTTTGTCGATC
1 TCTATTTATTATAAAAGTCGTTAAGTTTTTAATGAATCTAAGATCAAATTTTTGTCGATC
2772971 TCTATTTATTATAAAA
1 TCTATTTATTATAAAA
2772987 CCGTTGAATT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.48
Consensus pattern (60 bp):
TCTATTTATTATAAAAGTCGTTAAGTTTTTAATGAATCTAAGATCAAATTTTTGTCGATC
Found at i:2773024 original size:60 final size:58
Alignment explanation
Indices: 2772828--2773085 Score: 213
Period size: 60 Copynumber: 4.3 Consensus size: 58
2772818 ATATTTCCTG
* * * *
2772828 CTATGATCAATTTTTTTTGTCCA-TCTATTTATTATAAAAGTCGTT-AAGTTTTTAATGAAT
1 CTATGAT-AA-TTCTTTTGTCGATTCTATTTATTATAAAA-CCGTTGAA-TTTTTAGTGAAT
* * * * *
2772888 CTAAGATCAAAT-TTTTGTCGATTTCTATTTATTATAAAAGTCGTTGAGTTTTTAATGAAT
1 CTATGAT-AATTCTTTTGTCGA-TTCTATTTATTATAAAA-CCGTTGAATTTTTAGTGAAT
* *
2772948 CTATGGTCAATT-TTTTGTCGATCTCTATTTATTATAAAACCGTTGAATTTTCT-GTGAAC
1 CTATGAT-AATTCTTTTGTCGAT-TCTATTTATTATAAAACCGTTGAATTTT-TAGTGAAT
* * * * *
2773007 CTATGATGAATTCTTTTGTCGATTCCTATTAATCAGAACACCATTGAATTTTTAGTGAAT
1 CTATGAT-AATTCTTTTGTCGATT-CTATTTATTATAAAACCGTTGAATTTTTAGTGAAT
*
2773067 CTATGA-ATTTCTTTTGTCG
1 CTATGATAATTCTTTTGTCG
2773086 GTTTCGATTT
Statistics
Matches: 170, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
58 20 0.12
59 28 0.16
60 121 0.71
61 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (58 bp):
CTATGATAATTCTTTTGTCGATTCTATTTATTATAAAACCGTTGAATTTTTAGTGAAT
Found at i:2774402 original size:53 final size:53
Alignment explanation
Indices: 2774344--2774471 Score: 256
Period size: 53 Copynumber: 2.4 Consensus size: 53
2774334 GTATTTACGG
2774344 AATATGTAAAACTTTAAAATTTAACTGTATAAACACAGTTCTAATTATACGAA
1 AATATGTAAAACTTTAAAATTTAACTGTATAAACACAGTTCTAATTATACGAA
2774397 AATATGTAAAACTTTAAAATTTAACTGTATAAACACAGTTCTAATTATACGAA
1 AATATGTAAAACTTTAAAATTTAACTGTATAAACACAGTTCTAATTATACGAA
2774450 AATATGTAAAACTTTAAAATTT
1 AATATGTAAAACTTTAAAATTT
2774472 TAATTATCTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 75 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (53 bp):
AATATGTAAAACTTTAAAATTTAACTGTATAAACACAGTTCTAATTATACGAA
Found at i:2774543 original size:16 final size:16
Alignment explanation
Indices: 2774515--2774547 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2774505 TTATCAACAA
2774515 AGATATAACAAAAATT
1 AGATATAACAAAAATT
2774531 AGATAATAA-AAAAATT
1 AGAT-ATAACAAAAATT
2774547 A
1 A
2774548 AATCGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (16 bp):
AGATATAACAAAAATT
Found at i:2776387 original size:160 final size:161
Alignment explanation
Indices: 2776110--2776412 Score: 475
Period size: 160 Copynumber: 1.9 Consensus size: 161
2776100 CACTGAAACG
*
2776110 GTAAAACTGTGGTATATTAGAGTTGATACGGGTGCTTTCTTTTTGCTATCTATAAATACAATGCT
1 GTAAAAC-GTGGTATATCAGAGTTGATACGGGTGCTTTCTTTTTGCTATCTATAAATACAATGCT
* *
2776175 ATCATCTGGCATCTGAACTTTGCAAGTATAATAACCCTTTTTTCATGGGATTTTGTTCTTGTAAA
65 ATCATCTGGCATCTGAACTTTGCAAGTATAATAACCCTTTTCTCAAGGGATTTTGTTCTTGTAAA
* *
2776240 GCTATAGTTAAAAATTGAAAGAAAAAAAGGAA
130 GATATAGTGAAAAATTGAAAGAAAAAAAGGAA
* * *
2776272 GTAAAAC-TGGTATATCAGATTTGATATGGGTTCTTTCTTTTTGCTATCTATAAATACAATGCTA
1 GTAAAACGTGGTATATCAGAGTTGATACGGGTGCTTTCTTTTTGCTATCTATAAATACAATGCTA
* * *
2776336 TCATCTGGTAT-TCGAATTTTGCAAGTATAATAACTCTTTTCTCAAGGGATTTTGTTCTTGTAAA
66 TCATCTGGCATCT-GAACTTTGCAAGTATAATAACCCTTTTCTCAAGGGATTTTGTTCTTGTAAA
2776400 GATATAGTGAAAA
130 GATATAGTGAAAA
2776413 CTTGCTTGGA
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
159 1 0.01
160 121 0.94
162 7 0.05
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (161 bp):
GTAAAACGTGGTATATCAGAGTTGATACGGGTGCTTTCTTTTTGCTATCTATAAATACAATGCTA
TCATCTGGCATCTGAACTTTGCAAGTATAATAACCCTTTTCTCAAGGGATTTTGTTCTTGTAAAG
ATATAGTGAAAAATTGAAAGAAAAAAAGGAA
Found at i:2777197 original size:34 final size:34
Alignment explanation
Indices: 2777133--2777200 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
2777123 TAATAGACCA
* * *
2777133 GAATTACATAAGATACACATTACCTTCTAACCCT
1 GAATAACATAAGATACACATAACCTACTAACCCT
*
2777167 GAATAACATAAGATAGACATAACAC-ACTAACCCT
1 GAATAACATAAGATACACATAAC-CTACTAACCCT
2777201 CGATAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (34 bp):
GAATAACATAAGATACACATAACCTACTAACCCT
Found at i:2789699 original size:2 final size:2
Alignment explanation
Indices: 2789624--2789683 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
2789614 CGTTTGGGTT
2789624 TA TA TA T- TA TA T- TA T- TA T- TA -A 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
2789661 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
2789684 TCACTTATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
1 5 0.09
2 48 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2793066 original size:21 final size:21
Alignment explanation
Indices: 2793024--2793069 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2793014 TAAGACATTG
* *
2793024 TTTTAATAAAATTAAAATTAT
1 TTTTAATAAAATGAAAACTAT
* *
2793045 TTTTATTAAAATGACAACTAT
1 TTTTAATAAAATGAAAACTAT
2793066 TTTT
1 TTTT
2793070 TGTGCCCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTAATAAAATGAAAACTAT
Found at i:2794321 original size:24 final size:24
Alignment explanation
Indices: 2794294--2794384 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
2794284 CATAAATCAG
* *
2794294 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2794318 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
2794342 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
2794366 GTCAAGTATCAGATTAGAA
1 GTCAAGTATCAGATCAGAA
2794385 ATCAAATCGA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
23 2 0.03
24 56 0.93
25 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2795507 original size:18 final size:18
Alignment explanation
Indices: 2795486--2795521 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2795476 CTTCCATCCG
*
2795486 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2795504 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2795522 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2796853 original size:15 final size:15
Alignment explanation
Indices: 2796833--2796864 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2796823 TCAACGTCGA
2796833 TCAACGGTCAACGGG
1 TCAACGGTCAACGGG
2796848 TCAACGGTCAACGGG
1 TCAACGGTCAACGGG
2796863 TC
1 TC
2796865 GGGTCAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.31, T:0.16
Consensus pattern (15 bp):
TCAACGGTCAACGGG
Found at i:2796882 original size:18 final size:18
Alignment explanation
Indices: 2796859--2796904 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2796849 CAACGGTCAA
2796859 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
2796877 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
2796895 CGGGTCGGGT
1 CGGGTCGGGT
2796905 TGTGACCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:2796900 original size:13 final size:13
Alignment explanation
Indices: 2796838--2796882 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
2796828 GTCGATCAAC
*
2796838 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
2796853 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
2796866 GGTCAACAGGTCG
1 GGTCAACGGGTCG
2796879 GGTC
1 GGTC
2796883 GGGTCAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 16 0.57
15 12 0.43
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2799041 original size:24 final size:24
Alignment explanation
Indices: 2799014--2799104 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
2799004 CATAAATCAG
* * *
2799014 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2799038 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
2799062 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
2799086 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
2799105 ATCAAATCGA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
23 2 0.03
24 58 0.94
25 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2799121 original size:48 final size:48
Alignment explanation
Indices: 2799026--2799121 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
2799016 CAAGTAACAT
** *
2799026 ATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATATCAG
1 ATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAATCAG
*
2799074 ATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC-GAAAATCAG
1 ATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAAATCAG-AAATCAG
2799122 GTAAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 1 0.02
48 38 0.90
49 3 0.07
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (48 bp):
ATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAATCAG
Found at i:2800234 original size:18 final size:18
Alignment explanation
Indices: 2800213--2800248 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2800203 CTTCCATCCG
*
2800213 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2800231 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2800249 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2801579 original size:8 final size:8
Alignment explanation
Indices: 2801561--2801593 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
2801551 TCAACGTCGT
2801561 TCAAC-GG
1 TCAACGGG
2801568 TCAACGGG
1 TCAACGGG
2801576 TCAACGGG
1 TCAACGGG
2801584 TCAACGGG
1 TCAACGGG
2801592 TC
1 TC
2801594 GGGTCAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.15
Consensus pattern (8 bp):
TCAACGGG
Found at i:2801598 original size:13 final size:13
Alignment explanation
Indices: 2801566--2801629 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 13
2801556 GTCGTTCAAC
2801566 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
2801582 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2801595 GGTCAACATGTCGGGTCG
1 GGTC-A-A---CGGGTCG
2801613 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2801626 GGTC
1 GGTC
2801630 GGGTTGTGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 17 0.40
14 1 0.02
15 1 0.02
16 12 0.28
17 1 0.02
18 11 0.26
ACGTcount: A:0.17, C:0.23, G:0.42, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2801611 original size:18 final size:18
Alignment explanation
Indices: 2801588--2801633 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2801578 AACGGGTCAA
*
2801588 CGGGTCGGGTCAACATGT
1 CGGGTCGGGTCAACAGGT
*
2801606 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
2801624 CGGGTCGGGT
1 CGGGTCGGGT
2801634 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.22, G:0.48, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:2809656 original size:31 final size:31
Alignment explanation
Indices: 2809596--2809678 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
2809586 ATTAAACGAC
* * *
2809596 TACAAAATGATCATTAAATTTTATCAAATTAT
1 TACAAAATAATTATCAAA-TTTATCAAATTAT
* * *
2809628 TATAAAATAGTTATCAAATTTATTAAATTAT
1 TACAAAATAATTATCAAATTTATCAAATTAT
*
2809659 TACAAAATAATTATTAAATT
1 TACAAAATAATTATCAAATT
2809679 GACAAATCTC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 29 0.69
32 13 0.31
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (31 bp):
TACAAAATAATTATCAAATTTATCAAATTAT
Found at i:2809863 original size:31 final size:28
Alignment explanation
Indices: 2809797--2809868 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 28
2809787 ATGATTGTTC
2809797 TTATCATTAAATTTTATAAAGTTATAAAA
1 TTATCATTAAA-TTTATAAAGTTATAAAA
* *
2809826 TGATCATTAAATTTATCGAATAGTTATAGAA
1 TTATCATTAAATTTAT--AA-AGTTATAAAA
2809857 TTATCATTAAAT
1 TTATCATTAAAT
2809869 GATACAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 5 0.14
29 10 0.27
30 2 0.05
31 20 0.54
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (28 bp):
TTATCATTAAATTTATAAAGTTATAAAA
Found at i:2816249 original size:31 final size:31
Alignment explanation
Indices: 2816206--2816297 Score: 157
Period size: 31 Copynumber: 3.0 Consensus size: 31
2816196 ACAGTCTCTT
* *
2816206 AACATTTTGTCCGTTTGTAATATGGTCCCCC
1 AACATTTAGTCCGTTTGCAATATGGTCCCCC
2816237 AACATTTAGTCCGTTTGCAATATGGTCCCCC
1 AACATTTAGTCCGTTTGCAATATGGTCCCCC
*
2816268 AACATTTAGTCTGTTTGCAATATGGTCCCC
1 AACATTTAGTCCGTTTGCAATATGGTCCCC
2816298 GATCGTTTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (31 bp):
AACATTTAGTCCGTTTGCAATATGGTCCCCC
Found at i:2818276 original size:30 final size:30
Alignment explanation
Indices: 2818242--2818300 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2818232 AACGGTCGGG
2818242 GACCATATTGCAAACAGACTAAACGTTGGA
1 GACCATATTGCAAACAGACTAAACGTTGGA
** *
2818272 GACCATATTGCAAATGGACTAAATGTTGG
1 GACCATATTGCAAACAGACTAAACGTTGG
2818301 GGGATTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (30 bp):
GACCATATTGCAAACAGACTAAACGTTGGA
Found at i:2821255 original size:21 final size:21
Alignment explanation
Indices: 2821216--2821259 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2821206 TTATGTCAAA
*
2821216 TTTAAAAATTAATATATTAATT
1 TTTAAAAATTAATAAATT-ATT
*
2821238 TTTAAAAATT-TTAAATTATT
1 TTTAAAAATTAATAAATTATT
2821258 TT
1 TT
2821260 ATAGTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAAAATTAATAAATTATT
Found at i:2832612 original size:18 final size:19
Alignment explanation
Indices: 2832589--2832627 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2832579 ATTTTAGACA
*
2832589 TTTTAACCTAA-ATATATT
1 TTTTAAACTAACATATATT
*
2832607 TTTTAAATTAACATATATT
1 TTTTAAACTAACATATATT
2832626 TT
1 TT
2832628 CATTAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAAACTAACATATATT
Found at i:2833312 original size:20 final size:20
Alignment explanation
Indices: 2833269--2833314 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2833259 TCTGGCAATG
* *
2833269 AACCGGCTGAAAACTGGTAG
1 AACCGGCTGAAAACTGATAA
2833289 AACCGGCTGAAAA-TCGATAA
1 AACCGGCTGAAAACT-GATAA
2833309 AACCGG
1 AACCGG
2833315 GATGAACCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (20 bp):
AACCGGCTGAAAACTGATAA
Found at i:2834002 original size:64 final size:64
Alignment explanation
Indices: 2833894--2834098 Score: 236
Period size: 64 Copynumber: 3.2 Consensus size: 64
2833884 TAATGAAGGT
* * * * **
2833894 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGCTGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCATTATTAATGAG
* * ** *
2833958 ATGCATCGATGCATTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
* * *
2834022 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATG-TTTCATTATTAATGAG
2834085 AGTGCATCGATGCA
1 A-TGCATCGATGCA
2834099 TGAATTGCAT
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
63 3 0.03
64 111 0.93
65 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
Found at i:2834092 original size:45 final size:45
Alignment explanation
Indices: 2834042--2834143 Score: 204
Period size: 45 Copynumber: 2.3 Consensus size: 45
2834032 GCACTACTTA
2834042 TGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAGAG
1 TGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAGAG
2834087 TGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAGAG
1 TGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAGAG
2834132 TGCATCGATGCA
1 TGCATCGATGCA
2834144 CTTCCTGTGC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (45 bp):
TGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAGAG
Found at i:2836793 original size:218 final size:215
Alignment explanation
Indices: 2836418--2836815 Score: 568
Period size: 218 Copynumber: 1.8 Consensus size: 215
2836408 TTGAATTGTA
* * *
2836418 TGTCCAGCTCAGTTGGTAGAGCACAAGACTCTTAACTTTGGGGTCGTGGGATCGAGTCCTACGGT
1 TGTCCAGCTCAGTTGGTAGAGCACAAGACTCATAACCTTGGGGTCGAGGGATCGAGTCCTACGGT
* * * *
2836483 GGCAATTCATAATTCGAAGGTCTCCCACGGAAGCTACACTCAACCTGGCGTTGGGGGCAGCCTAC
66 GGCAATTCATAATTCGAAGGTCTCCCACGGAAGCTACACTCAACCTGACATTGAGGCCAGCCTAC
2836548 TATCCTACCTCCCCTTACCTCATTACATATGGGAATAAGGGTCAGCTAATAATTATTTAAATGAA
131 TATCCTACCTCCCCTTACCTCATTACATATGGGAATAAGGGTCAGCTAATAATTATTTAAATGAA
2836613 TGATCAGTTACTTAGTTGCC
196 TGATCAGTTACTTAGTTGCC
* *
2836633 TGTCCAGCTCAGTTGGTAGAGCACAAGGCTCATAATCCTTGTGGTCGAGGGATCGAGT-CTCACG
1 TGTCCAGCTCAGTTGGTAGAGCACAAGACTCATAA-CCTTGGGGTCGAGGGATCGAGTCCT-ACG
* * * *** *
2836697 GTGGGCAATTCATAATTC-AGATGTCTTCCACGGAAGTTGTTCTTAACCTGACATTAGAGGCCAG
64 GT-GGCAATTCATAATTCGA-AGGTCTCCCACGGAAGCTACACTCAACCTGACATT-GAGGCCAG
*
2836761 CCTACTATCCTACCTCCCCTTACC-CTATTACATATGGGAGTAAGGGTCAGCTAAT
126 CCTACTATCCTACCTCCCCTTACCTC-ATTACATATGGGAATAAGGGTCAGCTAAT
2836816 TTTTAATGAT
Statistics
Matches: 160, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
215 35 0.22
216 25 0.16
217 42 0.26
218 58 0.36
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (215 bp):
TGTCCAGCTCAGTTGGTAGAGCACAAGACTCATAACCTTGGGGTCGAGGGATCGAGTCCTACGGT
GGCAATTCATAATTCGAAGGTCTCCCACGGAAGCTACACTCAACCTGACATTGAGGCCAGCCTAC
TATCCTACCTCCCCTTACCTCATTACATATGGGAATAAGGGTCAGCTAATAATTATTTAAATGAA
TGATCAGTTACTTAGTTGCC
Found at i:2837946 original size:36 final size:36
Alignment explanation
Indices: 2837899--2838012 Score: 107
Period size: 36 Copynumber: 3.3 Consensus size: 36
2837889 AAGAAAGTGC
2837899 TCCTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGG
1 TCCTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGG
* * * * *
2837935 TCCTTCATCAGGAG-ATGATCAA-GA--AGCT--T-C
1 TCCTTCATCAGGGGAAGGA-GAAGGAGGTGCTGATGG
* *
2837965 TTCTTCATCAGGGGAAGGAGAAGGAGGTGTTGATGG
1 TCCTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGG
2838001 TCCTTCATCAGG
1 TCCTTCATCAGG
2838013 AGATAATCAA
Statistics
Matches: 57, Mismatches: 13, Indels: 16
0.66 0.15 0.19
Matches are distributed among these distances:
30 14 0.25
31 6 0.11
33 5 0.09
35 6 0.11
36 26 0.46
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (36 bp):
TCCTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGG
Found at i:2838103 original size:30 final size:28
Alignment explanation
Indices: 2838072--2838165 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 28
2838062 GATGGTCCTT
*
2838072 CATCAGGAGATAATCAAGAAGCTTCTTCTT
1 CATCAGGAGATAA--AAGAAGCTTCTTCTC
* *
2838102 CATCAGGTGATGAAAAGGAAGCTTTTTCTC
1 CATCAGGAGAT-AAAA-GAAGCTTCTTCTC
2838132 CATCAGGGGACGA-AAAAGAAGCTTCTTCTC
1 CATCA--GGA-GATAAAAGAAGCTTCTTCTC
2838162 CATC
1 CATC
2838166 TGAGGATGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
29 2 0.04
30 42 0.78
31 6 0.11
32 2 0.04
33 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (28 bp):
CATCAGGAGATAAAAGAAGCTTCTTCTC
Found at i:2838111 original size:66 final size:66
Alignment explanation
Indices: 2837901--2838108 Score: 371
Period size: 66 Copynumber: 3.2 Consensus size: 66
2837891 GAAAGTGCTC
*
2837901 CTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGGTCCTTCATCAGGAGATGATCAAGAAGCTTCT
1 CTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGGTCCTTCATCAGGAGATAATCAAGAAGCTTCT
2837966 T
66 T
*
2837967 CTTCATCAGGGGAAGGAGAAGGAGGTGTTGATGGTCCTTCATCAGGAGATAATCAAGAAGCTTCT
1 CTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGGTCCTTCATCAGGAGATAATCAAGAAGCTTCT
2838032 T
66 T
* * *
2838033 CTCCATCAGGTGAAGGGGAAGGAGGTGCTGATGGTCCTTCATCAGGAGATAATCAAGAAGCTTCT
1 CTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGGTCCTTCATCAGGAGATAATCAAGAAGCTTCT
2838098 T
66 T
2838099 CTTCATCAGG
1 CTTCATCAGG
2838109 TGATGAAAAG
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 135 1.00
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.25
Consensus pattern (66 bp):
CTTCATCAGGGGAAGGAGAAGGAGGTGCTGATGGTCCTTCATCAGGAGATAATCAAGAAGCTTCT
T
Found at i:2838194 original size:54 final size:54
Alignment explanation
Indices: 2838132--2838248 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
2838122 GCTTTTTCTC
*
2838132 CATCAGGGGACGAAAAAGAAGCTTCTTCTCCATC-TGAGGATGGCGATGCTCCTT
1 CATCAGGGGACGAAAAAGAAGCTTCTTCTCCATCAAG-GGATGGCGATGCTCCTT
* ** * * *
2838186 CATCAGGGGATGGTAAATAAGCTTCTTCTTCATCAAGGGATGGCGGTGCTCCTT
1 CATCAGGGGACGAAAAAGAAGCTTCTTCTCCATCAAGGGATGGCGATGCTCCTT
2838240 CATCAGGGG
1 CATCAGGGG
2838249 GTAGTGAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 54 0.98
55 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (54 bp):
CATCAGGGGACGAAAAAGAAGCTTCTTCTCCATCAAGGGATGGCGATGCTCCTT
Found at i:2838217 original size:30 final size:30
Alignment explanation
Indices: 2838087--2838228 Score: 109
Period size: 30 Copynumber: 4.9 Consensus size: 30
2838077 GGAGATAATC
*
2838087 AAGAAGCTTCTTCTTCATCAGGTGAT-GAA
1 AAGAAGCTTCTTCTTCATCAGGGGATGGAA
* * * *
2838116 AAGGAAGCTTTTTCTCCATCAGGGGACGAAA
1 AA-GAAGCTTCTTCTTCATCAGGGGATGGAA
* * *
2838147 AAGAAGCTTCTTCTCCATCTGAGGATGG--
1 AAGAAGCTTCTTCTTCATCAGGGGATGGAA
* * *
2838175 -CGATGC-TC--CTTCATCAGGGGATGGTA
1 AAGAAGCTTCTTCTTCATCAGGGGATGGAA
* *
2838201 AATAAGCTTCTTCTTCATCAAGGGATGG
1 AAGAAGCTTCTTCTTCATCAGGGGATGG
2838229 CGGTGCTCCT
Statistics
Matches: 86, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
24 13 0.15
26 2 0.02
27 7 0.08
28 2 0.02
29 2 0.02
30 56 0.65
31 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (30 bp):
AAGAAGCTTCTTCTTCATCAGGGGATGGAA
Found at i:2839429 original size:54 final size:54
Alignment explanation
Indices: 2839339--2839497 Score: 210
Period size: 54 Copynumber: 2.9 Consensus size: 54
2839329 CTCCATCACT
* * * *
2839339 GGATGATAAAGAAGCTTCTTCTTCATTAGTGCACGGCGGTGCTCCTTTATCAAG
1 GGATGATAAAGAAGCTTCTTCTTCATCAGAGGACGGCGGTGCTCCTTCATCAAG
*
2839393 GGATGATAAAGAAGCTTCTTCTTCATCAGAGGACGGCGGTGCTCCTTCATCAGG
1 GGATGATAAAGAAGCTTCTTCTTCATCAGAGGACGGCGGTGCTCCTTCATCAAG
* * * * * * *
2839447 GGATAATAAAGAAACTTATTCTTCATCAGGGGACGACAGTACTCCTTCATC
1 GGATGATAAAGAAGCTTCTTCTTCATCAGAGGACGGCGGTGCTCCTTCATC
2839498 GGGAGATGGT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (54 bp):
GGATGATAAAGAAGCTTCTTCTTCATCAGAGGACGGCGGTGCTCCTTCATCAAG
Found at i:2855106 original size:143 final size:145
Alignment explanation
Indices: 2854805--2855147 Score: 543
Period size: 143 Copynumber: 2.4 Consensus size: 145
2854795 CCCATAAAAG
***
2854805 TTTTATACTATAT-TTTTTTTATAATTTTTTAAAATTAGGAGTTTATTTCTTTTATATATTTTTG
1 TTTTATACTATATATTTTTTTATAATTTTTTAAAATTAGG-GGCCATTTCTTTTATATATTTTTG
* * **
2854869 TGTGCTTTAATATTTTTTTTACATTTTTTGAGATGATAATGACTTACTATTTGTTTATTTTAATA
65 TGTGCTTTAATATTTTTTTGACATTTTTTGAGATGATAATGAATTACTATTAATTTATTTTAATA
2854934 AAAAAATTAATATCAA
130 AAAAAATTAATATCAA
2854950 TTTTATACTATATATTTTTTTATAA-TTTTTAAAATTAGGGGCCCATTTCTTTTATATATTTTTG
1 TTTTATACTATATATTTTTTTATAATTTTTTAAAATTAGGGG-CCATTTCTTTTATATATTTTTG
* *
2855014 TGTGCTTTAATA-TTTTTTGACA-TTTTTGGGATGATAATTAATTACTATTAATTTATTTTAATA
65 TGTGCTTTAATATTTTTTTGACATTTTTTGAGATGATAATGAATTACTATTAATTTATTTTAATA
2855077 AAAAAATTAATATCAA
130 AAAAAATTAATATCAA
2855093 TTTTATACTATATA-TTTTTTATAATTTTTTAAAATTAGGGGCCATTTTCTTTTAT
1 TTTTATACTATATATTTTTTTATAATTTTTTAAAATTAGGGGCCA-TTTCTTTTAT
2855148 TTCGCCCCGA
Statistics
Matches: 185, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
142 13 0.07
143 92 0.50
144 10 0.05
145 59 0.32
146 11 0.06
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (145 bp):
TTTTATACTATATATTTTTTTATAATTTTTTAAAATTAGGGGCCATTTCTTTTATATATTTTTGT
GTGCTTTAATATTTTTTTGACATTTTTTGAGATGATAATGAATTACTATTAATTTATTTTAATAA
AAAAATTAATATCAA
Found at i:2856244 original size:2 final size:2
Alignment explanation
Indices: 2856237--2856268 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2856227 ATGTTAAAGT
2856237 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
2856269 AATAAATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2861586 original size:27 final size:27
Alignment explanation
Indices: 2861556--2861621 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
2861546 CTTTTTCTTT
* * *
2861556 TAAAAATTTATAAATTTGACTCTAACA
1 TAAAATTTTACAAATTTGACTATAACA
2861583 TAAAATTTTACAAATTTGACTATAACA
1 TAAAATTTTACAAATTTGACTATAACA
2861610 TAAAATTTTACA
1 TAAAATTTTACA
2861622 TTTATCTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (27 bp):
TAAAATTTTACAAATTTGACTATAACA
Found at i:2866515 original size:24 final size:24
Alignment explanation
Indices: 2866488--2866542 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
2866478 ATTATTTTTA
2866488 ATATATATACTTTTAATAAAATTTAT
1 ATATATATA-TTTTAATAAAA-TTAT
*
2866514 ATATATATATTTTTATAAAATTAT
1 ATATATATATTTTAATAAAATTAT
2866538 ATATA
1 ATATA
2866543 AATTGGTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 9 0.32
25 10 0.36
26 9 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATATATATTTTAATAAAATTAT
Found at i:2866527 original size:26 final size:25
Alignment explanation
Indices: 2866484--2866542 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 25
2866474 CTTTATTATT
2866484 TTTA-ATATATATACTTTTAATAAAA
1 TTTATATATATATACTTTT-ATAAAA
*
2866509 TTTATATATATATATTTTTATAAAA
1 TTTATATATATATACTTTTATAAAA
2866534 -TTATATATA
1 TTTATATATA
2866543 AATTGGTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 9 0.28
25 10 0.31
26 13 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTATATATATATACTTTTATAAAA
Found at i:2867043 original size:21 final size:20
Alignment explanation
Indices: 2867019--2867070 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
2867009 CGCGAACTCC
2867019 AATTTCGCAACTCAATTTCTA
1 AATTTCGCAACTCAATTTC-A
*
2867040 AA-TTCGCAACACTGAATTTCA
1 AATTTCGC-A-ACTCAATTTCA
2867061 AATTT-GCAAC
1 AATTTCGCAAC
2867071 GCGAATTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
19 2 0.07
20 6 0.22
21 8 0.30
22 11 0.41
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.33
Consensus pattern (20 bp):
AATTTCGCAACTCAATTTCA
Found at i:2867078 original size:20 final size:20
Alignment explanation
Indices: 2866998--2867078 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
2866988 AAATGACCAA
* *
2866998 CAAATTTACAACGCGAA-CT
1 CAAATTTGCAACGCGAATTT
* *
2867017 CCAATTTCGCAACTC-AATTT
1 CAAATTT-GCAACGCGAATTT
* *
2867037 CTAAATTCGCAACACTGAATTT
1 C-AAATTTGCAACGC-GAATTT
2867059 CAAATTTGCAACGCGAATTT
1 CAAATTTGCAACGCGAATTT
2867079 TGTTTTAGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
19 8 0.17
20 19 0.40
21 15 0.31
22 6 0.12
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (20 bp):
CAAATTTGCAACGCGAATTT
Found at i:2867109 original size:20 final size:21
Alignment explanation
Indices: 2867019--2867109 Score: 82
Period size: 20 Copynumber: 4.5 Consensus size: 21
2867009 CGCGAACTCC
*
2867019 AATTTCGCAACTC-AATTTCT
1 AATTTCGCAACACGAATTTCT
* *
2867039 AAATTCGCAACACTGAATTTCA
1 AATTTCGCAACAC-GAATTTCT
*
2867061 AATTT-GCAACGCGAATTT-T
1 AATTTCGCAACACGAATTTCT
** *
2867080 GTTTTAGCAACACGAATTT-T
1 AATTTCGCAACACGAATTTCT
2867100 AATTTCGCAA
1 AATTTCGCAA
2867110 TAGGTTTTAG
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.05
20 37 0.66
21 6 0.11
22 10 0.18
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (21 bp):
AATTTCGCAACACGAATTTCT
Found at i:2870567 original size:20 final size:20
Alignment explanation
Indices: 2870542--2870580 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2870532 TGTTGCGATT
2870542 GTTGCGAAAGTCAAATTCGC
1 GTTGCGAAAGTCAAATTCGC
2870562 GTTGCGAAAGTCAAATTCG
1 GTTGCGAAAGTCAAATTCG
2870581 AAACGCGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (20 bp):
GTTGCGAAAGTCAAATTCGC
Found at i:2870588 original size:20 final size:20
Alignment explanation
Indices: 2870545--2870590 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2870535 TGCGATTGTT
****
2870545 GCGAAAGTCAAATTCGCGTT
1 GCGAAAGTCAAATTCGAAAC
2870565 GCGAAAGTCAAATTCGAAAC
1 GCGAAAGTCAAATTCGAAAC
2870585 GCGAAA
1 GCGAAA
2870591 TCGCAATGCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGAAAC
Found at i:2870614 original size:20 final size:20
Alignment explanation
Indices: 2870591--2870636 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2870581 AAACGCGAAA
*
2870591 TCGCAATGCGAATTTGACTT
1 TCGCAATGCGAATTTGAATT
**
2870611 TCGCGTTGCGAATTTGAATT
1 TCGCAATGCGAATTTGAATT
2870631 TCGCAA
1 TCGCAA
2870637 CCATCAGAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
TCGCAATGCGAATTTGAATT
Found at i:2870831 original size:64 final size:64
Alignment explanation
Indices: 2870730--2870878 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
2870720 AATTTAAAAT
2870730 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTA
* * *** * *
2870794 AACAAATCAACTTTTACAAATCACTTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTA
2870858 AACAAATCAACTTTTACAAAT
1 AACAAATCAACTTTTACAAAT
2870879 ACATCAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.52, C:0.18, G:0.01, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTA
Found at i:2872212 original size:21 final size:21
Alignment explanation
Indices: 2872183--2872321 Score: 127
Period size: 21 Copynumber: 6.6 Consensus size: 21
2872173 ATGAATCGGG
* * *
2872183 CTCTCGAACGATGGGAGAGAC
1 CTCTTGAACGATGGGAGGGGC
**
2872204 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
2872225 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
2872246 CTCTTTAAC-AGTGGGAGGGGC
1 CTCTTGAACGA-TGGGAGGGGC
* * *
2872267 CTCTTGAAGGATTGTAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* * * *
2872288 CTCTTGAAAGATAGGAGAGAC
1 CTCTTGAACGATGGGAGGGGC
*
2872309 CTATTGAACGATG
1 CTCTTGAACGATG
2872322 ACAGGTGAAT
Statistics
Matches: 94, Mismatches: 22, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
21 93 0.99
22 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:2874673 original size:24 final size:24
Alignment explanation
Indices: 2874646--2874695 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2874636 CAAAATTTTC
2874646 AAAATAAAAATAATTAAAAAAACT
1 AAAATAAAAATAATTAAAAAAACT
2874670 AAAATAAAAATAATTAAAAAAACT
1 AAAATAAAAATAATTAAAAAAACT
2874694 AA
1 AA
2874696 CACTCGGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (24 bp):
AAAATAAAAATAATTAAAAAAACT
Found at i:2874819 original size:22 final size:22
Alignment explanation
Indices: 2874764--2874821 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
2874754 GATGGAGATA
* *
2874764 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCGAAGATGGG
*
2874786 GACAGATTTCGTCGAAGATGGG
1 GACGGATTTCGTCGAAGATGGG
*
2874808 GACGGATGTCGTCG
1 GACGGATTTCGTCG
2874822 TAAAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.41, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCGAAGATGGG
Found at i:2875009 original size:20 final size:20
Alignment explanation
Indices: 2874988--2875097 Score: 157
Period size: 20 Copynumber: 5.5 Consensus size: 20
2874978 TGACTTTTGT
* * *
2874988 GTTGCGAATTACAAATTCGT
1 GTTGCGATTTACAGATTCGC
*
2875008 GTTGCGAATTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
2875028 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
2875048 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCGC
* *
2875068 GTTGCGATTTATATATTCGC
1 GTTGCGATTTACAGATTCGC
2875088 GTTGCGATTT
1 GTTGCGATTT
2875098 TGGAAACTGA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:2875112 original size:40 final size:40
Alignment explanation
Indices: 2874988--2875114 Score: 112
Period size: 40 Copynumber: 3.2 Consensus size: 40
2874978 TGACTTTTGT
* * * * * * *
2874988 GTTGCGAATTACAAATTCGTGTTGCGAATTACAGATTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACAAACTCGA
* * *
2875028 GTTGCGATTTACAGATTCGCGTTGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACAAACTCGA
* * **
2875068 GTTGCGATTTATATATTCGCGTTGCGATTTTGGAAACT-GA
1 GTTGCGATTTACAGATTCGCGTTGCGA-TTTACAAACTCGA
2875108 GTTGCGA
1 GTTGCGA
2875115 AATTGGAGTT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 68 0.92
41 6 0.08
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACAAACTCGA
Found at i:2875112 original size:60 final size:60
Alignment explanation
Indices: 2874988--2875137 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
2874978 TGACTTTTGT
* * * *
2874988 GTTGCGAATTACAAATTCGTGTTGCGAATTACAGATTCGCGTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAAATTCGCGTTGCGAATTACAGATTCGCGTTGCGATTTACAAACTCGA
* * * * * **
2875048 GTTGCGATTTACATATTCGCGTTGCGATTTATATATTCGCGTTGCGATTTTGGAAACT-GA
1 GTTGCGAATTACAAATTCGCGTTGCGAATTACAGATTCGCGTTGCGA-TTTACAAACTCGA
** *
2875108 GTTGCGAAATT-GGAGTTCGCGTTGCGAATT
1 GTTGCG-AATTACAAATTCGCGTTGCGAATT
2875138 TGTTGGTCAT
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
60 62 0.87
61 9 0.13
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (60 bp):
GTTGCGAATTACAAATTCGCGTTGCGAATTACAGATTCGCGTTGCGATTTACAAACTCGA
Found at i:2880597 original size:23 final size:23
Alignment explanation
Indices: 2880557--2880622 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
2880547 TAAGAATAAT
*
2880557 TATGCATTTGTGACACGTTTATC
1 TATGCATTTATGACACGTTTATC
** * *
2880580 TATGTTTTTATGATACGTTTATT
1 TATGCATTTATGACACGTTTATC
2880603 TATGCATTTATGACACGTTT
1 TATGCATTTATGACACGTTT
2880623 TTCGGTCGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (23 bp):
TATGCATTTATGACACGTTTATC
Found at i:2881420 original size:15 final size:15
Alignment explanation
Indices: 2881400--2881429 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2881390 TAATAAGGTT
*
2881400 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
2881415 ATTTATTATAAAATA
1 ATTTATTATAAAATA
2881430 TGAATTGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:2881477 original size:22 final size:22
Alignment explanation
Indices: 2881461--2881503 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2881451 AATTTATTAG
2881461 TATGGATTAATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
*
2881483 TATGGATTGATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
2881504 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:2881528 original size:32 final size:31
Alignment explanation
Indices: 2881487--2881589 Score: 116
Period size: 32 Copynumber: 3.5 Consensus size: 31
2881477 TTAAAATATG
2881487 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
2881518 GAATTGATTTATTTT-AA-AA--TA-T-G---
1 G-ATTGATTTATTTTAAATAATTTATTAGTAT
2881541 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
*
2881572 GAATTAATTTATTTTAAA
1 G-ATTGATTTATTTTAAA
2881590 ATATGGATTG
Statistics
Matches: 60, Mismatches: 1, Indels: 21
0.73 0.01 0.26
Matches are distributed among these distances:
22 13 0.22
23 3 0.05
24 2 0.03
26 3 0.05
27 2 0.03
28 3 0.05
30 2 0.03
31 4 0.07
32 28 0.47
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (31 bp):
GATTGATTTATTTTAAATAATTTATTAGTAT
Found at i:2881529 original size:54 final size:54
Alignment explanation
Indices: 2881415--2881978 Score: 453
Period size: 54 Copynumber: 10.2 Consensus size: 54
2881405 TTTTAAAATA
* * *
2881415 ATTTATTATAAAATATGAATTGATTTATTTTAAAATAATTTATTAGTATGGATTA
1 ATTTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAGTATGGATTG
*
2881470 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
* *
2881524 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
*
2881578 ATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTG
** ** * ** * * * *
2881626 ATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATAGATTG
1 ATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
** * * ** * * *
2881680 ATTTATTTT-AAATAATTTATTAGTATTGA-TTGATTTATTTTA-AAATATGGATTG
1 ATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
*
2881734 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTT-AA-AA--TA-T-G----GATTGATTTATTTTAAATAATTTATTAGTATGGATTG
2881798 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
*
2881852 ATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTT-AA-AA--TA-T-G----GATTGATTTATTTTAAATAATTTATTAGTATGGATTG
* *
2881916 ATTTATTTTAAAATATGAATTGATTTATTATT--AT--TGTAGTT-GTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATT-TTAAATAATTTA-TTAGTATGGATTG
2881967 ATTTATTTTAAA
1 ATTTATTTTAAA
2881979 TAATTTATTA
Statistics
Matches: 440, Mismatches: 34, Indels: 74
0.80 0.06 0.14
Matches are distributed among these distances:
47 4 0.01
48 25 0.06
49 3 0.01
50 5 0.01
51 26 0.06
52 4 0.01
53 3 0.01
54 226 0.51
55 36 0.08
56 3 0.01
57 2 0.00
58 5 0.01
59 5 0.01
60 5 0.01
62 8 0.02
63 14 0.03
64 66 0.15
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:2881540 original size:22 final size:22
Alignment explanation
Indices: 2881515--2881557 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2881505 AATTTATTAG
2881515 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
2881537 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
2881558 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:2881657 original size:32 final size:32
Alignment explanation
Indices: 2881616--2881927 Score: 369
Period size: 32 Copynumber: 10.7 Consensus size: 32
2881606 TATTGTAGTT
2881616 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2881648 GTATGGATTGATTTATTTT--A-AA---A-TA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2881673 -TA--GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
2881702 GTATTGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2881725 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
2881756 GTATAGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2881788 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2881811 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2881842 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
2881874 GTATTGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2881906 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2881928 ATATGAATTG
Statistics
Matches: 242, Mismatches: 8, Indels: 60
0.78 0.03 0.19
Matches are distributed among these distances:
22 41 0.17
23 7 0.03
24 3 0.01
25 6 0.02
26 7 0.03
28 7 0.03
29 6 0.02
30 3 0.01
31 8 0.03
32 154 0.64
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:2881678 original size:22 final size:22
Alignment explanation
Indices: 2881653--2881745 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
2881643 TATTAGTATG
2881653 GATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAAATATA
2881675 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTT-AA-AA--TA-TA
*
2881702 GTATTGATTGATTTATTTTAAAATATG
1 G-ATTGA-T---TTATTTTAAAATATA
2881729 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
2881746 TAATTTATTA
Statistics
Matches: 60, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
22 24 0.40
23 2 0.03
24 2 0.03
25 1 0.02
26 7 0.12
27 5 0.08
28 7 0.12
29 1 0.02
30 2 0.03
31 2 0.03
32 7 0.12
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:2881753 original size:14 final size:14
Alignment explanation
Indices: 2881734--2881787 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2881724 ATATGGATTG
2881734 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
2881748 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
2881766 ATTTATTTTAAATA
1 ATTTATTTTAAATA
2881780 ATTTATTT
1 ATTTATTT
2881788 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:2881814 original size:22 final size:22
Alignment explanation
Indices: 2881789--2881831 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2881779 AATTTATTTG
2881789 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2881811 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2881832 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2881847 original size:118 final size:115
Alignment explanation
Indices: 2881725--2882010 Score: 486
Period size: 118 Copynumber: 2.5 Consensus size: 115
2881715 TATTTTAAAA
*
2881725 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAATAATTTATTTGT
* *
2881790 ATGGATTGATTTATTTTAAAATATGGATTGATTTATT-TTAAATAATTTA-TTAG
66 ATGGATTGATTTATTTTAAAATATGAATTGATTTATTATT--AT--TGTAGTT-G
2881843 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAATAATTTATTTGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAATAATTTATTTGT
2881908 ATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTATTGTAGTTG
66 ATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTATTGTAGTTG
2881958 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAA
2882011 ATATGGATTG
Statistics
Matches: 163, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
115 57 0.35
116 2 0.01
117 2 0.01
118 100 0.61
119 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (115 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAATAATTTATTTGT
ATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTATTGTAGTTG
Found at i:2881938 original size:86 final size:86
Alignment explanation
Indices: 2881537--2882042 Score: 509
Period size: 86 Copynumber: 6.0 Consensus size: 86
2881527 TATTTTAAAA
2881537 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTAATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTAATTTATTTTAAAATATGGATTGAT
*
2881602 TTA--TT--AT--TGTAGTT-G
66 TTATTTTAAATAATTTA-TTAG
* * *
2881617 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTAATTTATTTTAAAATATGGATTGAT
2881682 TTATTTTAAATAATTTATTAG
66 TTATTTTAAATAATTTATTAG
* * * * * * *
2881703 TATTGATTGATTTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTA--TT--AGTATAGA
1 TATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATGAATTAATTTATTTTAAAATATGGA
*
2881763 TTGATTTATTTTAAATAATTTATTTG
61 TTGATTTATTTTAAATAATTTATTAG
* * * * *
2881789 TATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTA--TT--AGTATGGA
1 TATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATGAATTAATTTATTTTAAAATATGGA
2881849 TTGATTTATTTTAAATAATTTATTAG
61 TTGATTTATTTTAAATAATTTATTAG
* * * * *
2881875 TATTGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTAATTTATTTTAAAATATGGATTGAT
*
2881940 TTATTATT--AT--TGTAGTT-G
66 TTATT-TTAAATAATTTA-TTAG
*
2881958 TATGGATTGATTTATTTTAAATAATTTATTAGTATTG-ATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTA-TGAATTAATTTATTTTAAAATATGGATTGA
2882022 TTTATTTTAAATAATTTATTA
65 TTTATTTTAAATAATTTATTA
2882043 TTGTAGTTGT
Statistics
Matches: 370, Mismatches: 31, Indels: 44
0.83 0.07 0.10
Matches are distributed among these distances:
80 65 0.18
81 2 0.01
82 17 0.05
83 68 0.18
84 10 0.03
85 11 0.03
86 172 0.46
87 7 0.02
88 2 0.01
90 13 0.04
91 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (86 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTAATTTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTATTAG
Found at i:2882029 original size:54 final size:55
Alignment explanation
Indices: 2881617--2882042 Score: 408
Period size: 54 Copynumber: 7.6 Consensus size: 55
2881607 ATTGTAGTTG
*
2881617 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTATAAA
*
2881671 TATAGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTA-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTATAAA
*
2881725 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTT--ATAA---A
** * * ** * * *
2881785 TTTGTATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 ----TATGGATTGATTTATTTTAAATA-ATTTATTAGTATTGA-TTGATTTATTTTATAAA
2881843 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAATAATTTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTT--ATAA---A
** * * **
2881903 TTTGTATGGATTGATTTATTTTAAA-ATATGAATT-G-ATTTATT-A-TTATTGTAGT-TG
1 ----TATGGATTGATTTATTTTAAATA-ATTTATTAGTATTGATTGATTTATTTTA-TAAA
2881958 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTA-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTATAAA
2882012 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
2882043 TTGTAGTTGT
Statistics
Matches: 305, Mismatches: 35, Indels: 64
0.75 0.09 0.16
Matches are distributed among these distances:
51 26 0.09
52 2 0.01
53 6 0.02
54 158 0.52
55 17 0.06
56 5 0.02
57 5 0.02
58 1 0.00
59 1 0.00
60 7 0.02
61 4 0.01
62 9 0.03
63 12 0.04
64 52 0.17
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (55 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTATAAA
Found at i:2882114 original size:31 final size:31
Alignment explanation
Indices: 2882057--2882115 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2882047 AGTTGTATGG
* *
2882057 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATATCAGTATTACAAAACTAAA
*
2882088 ATTATTTAAATATCAGTATTGCAAAACT
1 ATTATTTAAATATCAGTATTACAAAACT
2882116 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATATCAGTATTACAAAACTAAA
Found at i:2884594 original size:4 final size:4
Alignment explanation
Indices: 2884585--2884615 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2884575 AGTTTTTTCC
2884585 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
2884616 TTAACAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:2899201 original size:2 final size:2
Alignment explanation
Indices: 2899194--2899222 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2899184 AAAGTACCAA
2899194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2899223 AACGTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2900005 original size:23 final size:23
Alignment explanation
Indices: 2899976--2900026 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
2899966 CCAAATGAAA
*
2899976 AAAAATGTG-TCATAAAGACAGAG
1 AAAAATGTGCT-ATAAAAACAGAG
2899999 AAAAATGTGCTATAAAAACAGAG
1 AAAAATGTGCTATAAAAACAGAG
2900022 AAAAA
1 AAAAA
2900027 CATATAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.16
Consensus pattern (23 bp):
AAAAATGTGCTATAAAAACAGAG
Found at i:2900460 original size:20 final size:19
Alignment explanation
Indices: 2900392--2900483 Score: 76
Period size: 20 Copynumber: 4.7 Consensus size: 19
2900382 ATAACTAACG
* *
2900392 AATTCGCAACGCGATTTCA
1 AATTCGCAACACAATTTCA
* * *
2900411 AATTCGTAACACGAACTCCA
1 AATTCGCAACAC-AATTTCA
* *
2900431 ATTTCACAACACAATTTTCA
1 AATTCGCAACACAA-TTTCA
* *
2900451 AATTCGCAACTCAAATTTAA
1 AATTCGCAACAC-AATTTCA
2900471 AATTCGCAACACA
1 AATTCGCAACACA
2900484 TAATTAAAAT
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
19 13 0.24
20 40 0.73
21 2 0.04
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (19 bp):
AATTCGCAACACAATTTCA
Found at i:2900490 original size:20 final size:20
Alignment explanation
Indices: 2900437--2900494 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2900427 TCCAATTTCA
* *
2900437 CAACACAATTTTCAAATTCG
1 CAACACAAATTTAAAATTCG
*
2900457 CAACTCAAATTTAAAATTCG
1 CAACACAAATTTAAAATTCG
2900477 CAACACATAA-TTAAAATT
1 CAACACA-AATTTAAAATT
2900495 TACGTTGCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (20 bp):
CAACACAAATTTAAAATTCG
Found at i:2902813 original size:29 final size:29
Alignment explanation
Indices: 2902781--2902862 Score: 164
Period size: 29 Copynumber: 2.8 Consensus size: 29
2902771 GCACCCATTT
2902781 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
2902810 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
2902839 CGAATTAATTCCCAGAATAGCACC
1 CGAATTAATTCCCAGAATAGCACC
2902863 GGTCAACGGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (29 bp):
CGAATTAATTCCCAGAATAGCACCAAAAC
Found at i:2902895 original size:20 final size:19
Alignment explanation
Indices: 2902870--2902965 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 19
2902860 ACCGGTCAAC
2902870 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGT-AACGGGTCG
2902890 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGT-AACGGGTCG
2902910 GGTCAACGGT--CGGGTCG
1 GGTCAACGGTAACGGGTCG
*
2902927 GGTAAACTGGT--CGGGTCG
1 GGTCAAC-GGTAACGGGTCG
*
2902945 GGTAAACGGGTAAACGGGTCG
1 GGTCAAC-GGT-AACGGGTCG
2902966 TGACCGGTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
17 13 0.19
18 20 0.29
20 30 0.43
21 7 0.10
ACGTcount: A:0.20, C:0.21, G:0.43, T:0.17
Consensus pattern (19 bp):
GGTCAACGGTAACGGGTCG
Found at i:2902920 original size:7 final size:7
Alignment explanation
Indices: 2902862--2902905 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
2902852 AGAATAGCAC
2902862 CGGTCAA
1 CGGTCAA
2902869 CGGTCAA
1 CGGTCAA
2902876 CGGTCAA
1 CGGTCAA
2902883 CGGGTC--
1 C-GGTCAA
*
2902889 GGGTCAA
1 CGGTCAA
2902896 CGGTCAA
1 CGGTCAA
2902903 CGG
1 CGG
2902906 GTCGGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
7 24 0.75
8 4 0.12
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (7 bp):
CGGTCAA
Found at i:2902922 original size:12 final size:13
Alignment explanation
Indices: 2902897--2902925 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2902887 TCGGGTCAAC
2902897 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2902910 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
2902922 GGTC
1 GGTC
2902926 GGGTAAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2902940 original size:18 final size:17
Alignment explanation
Indices: 2902883--2902953 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 17
2902873 CAACGGTCAA
*
2902883 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
*
2902900 CAACGGGTCGGGTCAACGGT
1 ---CGGGTCGGGTAAACGGT
2902920 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
2902938 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
2902954 GTAAACGGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
17 15 0.31
18 17 0.35
20 17 0.35
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:2902998 original size:11 final size:10
Alignment explanation
Indices: 2902968--2903019 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
2902958 ACGGGTCGTG
2902968 ACCGGTC-AA
1 ACCGGTCAAA
2902977 ACCGGTCAAA
1 ACCGGTCAAA
2902987 ACCGGTTCAAA
1 ACCGG-TCAAA
*
2902998 ACCGGT-TAA
1 ACCGGTCAAA
2903007 ACCGGTCAAA
1 ACCGGTCAAA
2903017 ACC
1 ACC
2903020 AGTTTCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:2910161 original size:29 final size:29
Alignment explanation
Indices: 2910143--2910224 Score: 164
Period size: 29 Copynumber: 2.8 Consensus size: 29
2910133 GCACCCATTT
2910143 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
2910172 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
2910201 CGAATTAATTCCCAGAATAGCACC
1 CGAATTAATTCCCAGAATAGCACC
2910225 GGTCAACGGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (29 bp):
CGAATTAATTCCCAGAATAGCACCAAAAC
Found at i:2910257 original size:20 final size:19
Alignment explanation
Indices: 2910232--2910327 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 19
2910222 ACCGGTCAAC
2910232 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGT-AACGGGTCG
2910252 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGT-AACGGGTCG
2910272 GGTCAACGGT--CGGGTCG
1 GGTCAACGGTAACGGGTCG
*
2910289 GGTAAACTGGT--CGGGTCG
1 GGTCAAC-GGTAACGGGTCG
*
2910307 GGTAAACGGGTAAACGGGTCG
1 GGTCAAC-GGT-AACGGGTCG
2910328 TGACCGGTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
17 13 0.19
18 20 0.29
20 30 0.43
21 7 0.10
ACGTcount: A:0.20, C:0.21, G:0.43, T:0.17
Consensus pattern (19 bp):
GGTCAACGGTAACGGGTCG
Found at i:2910282 original size:7 final size:7
Alignment explanation
Indices: 2910224--2910267 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
2910214 AGAATAGCAC
2910224 CGGTCAA
1 CGGTCAA
2910231 CGGTCAA
1 CGGTCAA
2910238 CGGTCAA
1 CGGTCAA
2910245 CGGGTC--
1 C-GGTCAA
*
2910251 GGGTCAA
1 CGGTCAA
2910258 CGGTCAA
1 CGGTCAA
2910265 CGG
1 CGG
2910268 GTCGGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
7 24 0.75
8 4 0.12
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (7 bp):
CGGTCAA
Done.