Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 24
Found at i:3103945 original size:46 final size:47
Alignment explanation
Indices: 3103878--3103972 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 47
3103868 TCTTCGTGAG
3103878 AATTTATTCTCCGTGTCAGGC-AGAGAAATGTATCCCCTCGAATTGA
1 AATTTATTCTCCGTGTCAGGCAAGAGAAATGTATCCCCTCGAATTGA
3103924 AATTTATTCTCCGTGTCAGGCATAGAGAAATGTATCCCCTCGAATTGA
1 AATTTATTCTCCGTGTCAGGCA-AGAGAAATGTATCCCCTCGAATTGA
3103972 A
1 A
3103973 CTCGATCCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 21 0.45
48 26 0.55
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (47 bp):
AATTTATTCTCCGTGTCAGGCAAGAGAAATGTATCCCCTCGAATTGA
Found at i:3104512 original size:23 final size:23
Alignment explanation
Indices: 3104479--3104524 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3104469 AGACAGTCTG
*
3104479 CAGGATTATTATGTATCTGACTT
1 CAGGATGATTATGTATCTGACTT
3104502 CAGGATGATTATGTATCTGACTT
1 CAGGATGATTATGTATCTGACTT
3104525 GGCCAGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (23 bp):
CAGGATGATTATGTATCTGACTT
Found at i:3106682 original size:14 final size:14
Alignment explanation
Indices: 3106663--3106692 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3106653 GATCAATACT
3106663 TTTGCATACATGCA
1 TTTGCATACATGCA
*
3106677 TTTGCATACATTCA
1 TTTGCATACATGCA
3106691 TT
1 TT
3106693 ATTCATTTCA
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:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (14 bp):
TTTGCATACATGCA
Found at i:3107072 original size:31 final size:31
Alignment explanation
Indices: 3107032--3107091 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
3107022 ATCCTGTATC
* *
3107032 TTTCGACCAAGAACCTATGTATC-CTCTAGGT
1 TTTCCACCAA-AACCAATGTATCACTCTAGGT
*
3107063 TTTCCACCAAAACCAATTTATCACTCTAG
1 TTTCCACCAAAACCAATGTATCACTCTAG
3107092 TACTACACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (31 bp):
TTTCCACCAAAACCAATGTATCACTCTAGGT
Found at i:3112763 original size:303 final size:294
Alignment explanation
Indices: 3112212--3112803 Score: 1087
Period size: 303 Copynumber: 2.0 Consensus size: 294
3112202 GAAAAATTTA
3112212 TTATCCCTTTACAGTAGACTGGAGTTCTTTTGCACCAATAACATGGCGGAATACGACTTGTGTCA
1 TTATCCCTTTACAGTAGACTGGAGTTCTTTTGCACCAATAACATGGCGGAATACGACTTGTGTCA
3112277 TGGGATTGAAAGCAGCTATAGAAAGAAAATTAAATGTCTCAAAATATATGGAGATCATCGTTAGT
66 TGGGATTGAAAGCAGCTATAGAAAGAAAATTAAATGTCTCAAAATATATGGAGATCATCGTTAGT
3112342 GGTGTATCAATTGCGAGGAGAATGGGAAACAAAAGATCCAAATTGTTGGAATACGAAATTTTACC
131 GGTGTATCAATTGCGAGGAGAATGGGAAACAAAAGATCCAAATTGTTGGAATACGAAATTTTACC
3112407 CGAATTAGTGAAAGAATTTGAGAGAGTTACCTTCAATTATCTCCCTCGAGAAGAAAATC-AATGG
196 CGAATTAGTGAAAGAATTTGAGAGAGTTACCTTCAATTATCTCCCTCGAGAAGAAAATCAAATGG
3112471 CAGATGCTTTGGCTACATTAGCTGCTATGTAATAT
261 CAGATGC-TTGGCTACATTAGCTGCTATGTAATAT
3112506 TTATCCCTTTACAAGTAGACTGGAGTTCTTTTGCACCAATAACATGGCGGAATACGAAGCTTGTG
1 TTATCCCTTTAC-AGTAGACTGGAGTTCTTTTGCACCAATAACATGGCGGAATACG-A-CTTGTG
3112571 TCATGGGATTGAAAGCAGCTATAGAAAGAAAAATTAAATGTCTCAAAATATATGGAGATTCATCG
63 TCATGGGATTGAAAGCAGCTATAGAAAG-AAAATTAAATGTCTCAAAATATATGGAGA-TCATCG
3112636 TTAGTGGTGTATCAATTGCGAGGAGAATGGGAAACAAAAGATCCCAAATTGTTGGAATACTGAAA
126 TTAGTGGTGTATCAATTGCGAGGAGAATGGGAAACAAAAGAT-CCAAATTGTTGGAATAC-GAAA
3112701 TTTTACCCTCGAATTAGTGAAAGAATTTGAGAGAGTTACCTTCAATTATCTCCCTCGAGAAGAAA
189 TTTTA-CC-CGAATTAGTGAAAGAATTTGAGAGAGTTACCTTCAATTATCTCCCTCGAGAAGAAA
3112766 ATCAAATGGCAGATGCTTGGCTACATTAGCTGCTATGT
252 ATCAAATGGCAGATGCTTGGCTACATTAGCTGCTATGT
3112804 TTCAGGCATC
Statistics
Matches: 288, Mismatches: 0, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
294 12 0.04
295 43 0.15
296 1 0.00
297 34 0.12
298 29 0.10
299 48 0.17
300 17 0.06
301 9 0.03
302 2 0.01
303 81 0.28
304 12 0.04
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (294 bp):
TTATCCCTTTACAGTAGACTGGAGTTCTTTTGCACCAATAACATGGCGGAATACGACTTGTGTCA
TGGGATTGAAAGCAGCTATAGAAAGAAAATTAAATGTCTCAAAATATATGGAGATCATCGTTAGT
GGTGTATCAATTGCGAGGAGAATGGGAAACAAAAGATCCAAATTGTTGGAATACGAAATTTTACC
CGAATTAGTGAAAGAATTTGAGAGAGTTACCTTCAATTATCTCCCTCGAGAAGAAAATCAAATGG
CAGATGCTTGGCTACATTAGCTGCTATGTAATAT
Found at i:3114147 original size:9 final size:9
Alignment explanation
Indices: 3114133--3114205 Score: 55
Period size: 9 Copynumber: 8.4 Consensus size: 9
3114123 TTGAAGAGAA
3114133 AAAGAAAAG
1 AAAGAAAAG
3114142 AAAG--AAG
1 AAAGAAAAG
*
3114149 AAAAAAAAG
1 AAAGAAAAG
*
3114158 AAAAAAAAG
1 AAAGAAAAG
*
3114167 AAAAAAAAAG
1 -AAAGAAAAG
* *
3114177 GAAGAAAAA
1 AAAGAAAAG
*
3114186 AAAGGAAA-
1 AAAGAAAAG
3114194 AAAGAAAA-
1 AAAGAAAAG
3114202 AAAG
1 AAAG
3114206 GGGTCAAGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
7 6 0.11
8 11 0.20
9 28 0.52
10 9 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:3114154 original size:20 final size:19
Alignment explanation
Indices: 3114125--3114205 Score: 83
Period size: 21 Copynumber: 4.1 Consensus size: 19
3114115 TATTATGCTT
*
3114125 GAAGAGAAAAAGAAAAGAAA
1 GAAGAAAAAAAGAAAA-AAA
3114145 GAAGAAAAAAAAGAAAAAAAA
1 GAAG-AAAAAAAG-AAAAAAA
3114166 GAA-AAAAAAAGGAAGAAAAA
1 GAAGAAAAAAA-GAA-AAAAA
* *
3114186 AAAGGAAAAAAGAAAAAAA
1 GAAGAAAAAAAGAAAAAAA
3114205 G
1 G
3114206 GGGTCAAGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
19 14 0.27
20 15 0.29
21 19 0.37
22 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
GAAGAAAAAAAGAAAAAAA
Found at i:3114157 original size:21 final size:20
Alignment explanation
Indices: 3114131--3114205 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
3114121 GCTTGAAGAG
3114131 AAAAAGAAAAGAAAGAAGAAA
1 AAAAAGAAAA-AAAGAAGAAA
3114152 AAAAAGAAAAAAAAGAA-AAA
1 AAAAAG-AAAAAAAGAAGAAA
* * *
3114172 AAAAGGAAGAAAAAAAAG-GA
1 AAAAAGAA-AAAAAGAAGAAA
3114192 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
3114206 GGGTCAAGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.15
20 23 0.50
21 12 0.26
22 4 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAAAGAAGAAA
Found at i:3114799 original size:21 final size:22
Alignment explanation
Indices: 3114767--3114812 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
3114757 ATCATGATGA
3114767 GTTTATTGCTTCCGTTAAGATT
1 GTTTATTGCTTCCGTTAAGATT
3114789 GTTTA-TGCTTCCGTTAAGATT
1 GTTTATTGCTTCCGTTAAGATT
3114810 GTT
1 GTT
3114813 ACACGGGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (22 bp):
GTTTATTGCTTCCGTTAAGATT
Found at i:3115672 original size:92 final size:92
Alignment explanation
Indices: 3115512--3115692 Score: 301
Period size: 92 Copynumber: 2.0 Consensus size: 92
3115502 AAAATCAATC
*
3115512 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* *
3115577 GGTTTGGTAT-TAACCACAGAACCAGTT
66 GGTTTGATATAAAACC-CAGAACCAGTT
* *
3115604 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
3115669 GGTTTGATATAAAACCCAGAACCA
66 GGTTTGATATAAAACCCAGAACCA
3115693 ATCATTGGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 79 0.95
93 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (92 bp):
ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGATATAAAACCCAGAACCAGTT
Found at i:3116753 original size:113 final size:113
Alignment explanation
Indices: 3116399--3117419 Score: 1461
Period size: 113 Copynumber: 9.0 Consensus size: 113
3116389 GCAAAGATTA
* *
3116399 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTG
* * * *
3116464 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTAAACCTTTTGCTT
63 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
3116515 GAATTCATCATTTGATGGATTAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTG
* *
3116580 AAGAATGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTC
63 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
3116631 AAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATACTGAGAAGAACTCATCTAAAG
1 AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
3116696 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * ** * * * **** *
3116744 GAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAAAACTCATCTGAAG
1 AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
3116809 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACATTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
3116857 AAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
3116922 AAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
3116970 AAAACCATCACTTGATGGATTAGCTTTGCCATAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
3117035 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3117083 AAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
3117148 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3117196 AAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
3117261 AAGGAAGAAGAAACTCATAATGAGAAGAATTTGTTCAACCTTTTACTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
3117309 AAATCCATCATTTGATGGATCAGCTTCT-CCAGA-AAGAGTTCATAATGAGAAAAACTCATCTGA
1 AAATCCATCATTTGATGGATTAGCTT-TGCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGA
* * * ** **
3117372 AGAAAGAAGAAGAAGTTTATAATGAGAAGAGCTTGTTCGGCCTTTTGC
64 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
3117420 ATGACTCTAT
Statistics
Matches: 821, Mismatches: 82, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
112 2 0.00
113 669 0.81
114 2 0.00
116 148 0.18
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
AAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:3117286 original size:24 final size:23
Alignment explanation
Indices: 3117243--3117287 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
3117233 GTTCATAATG
*
3117243 AGAAGAACTCATCTGAAGAAGGA
1 AGAAGAACTCATATGAAGAAGGA
3117266 AGAAGAAACTCATAATG-AGAAG
1 AGAAG-AACTCAT-ATGAAGAAG
3117288 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.11, G:0.24, T:0.13
Consensus pattern (23 bp):
AGAAGAACTCATATGAAGAAGGA
Found at i:3117777 original size:3 final size:3
Alignment explanation
Indices: 3117769--3117863 Score: 136
Period size: 3 Copynumber: 31.0 Consensus size: 3
3117759 ATTTTAAAAT
*
3117769 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
3117817 TTA TTA TTA TAA TTA TTA TAA TTA TTA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
3117864 CAAAACCCAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 76 0.93
4 6 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3119229 original size:22 final size:23
Alignment explanation
Indices: 3119187--3119234 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
3119177 ATATATATAT
3119187 ATAAATAATATTTATATTTTTCA
1 ATAAATAATATTTATATTTTTCA
* *
3119210 ATAAATTAT-TTTTTATTTTTCA
1 ATAAATAATATTTATATTTTTCA
3119232 ATA
1 ATA
3119235 TCGAAGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
ATAAATAATATTTATATTTTTCA
Found at i:3121154 original size:22 final size:22
Alignment explanation
Indices: 3121129--3121188 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
3121119 TCGAGGGTAT
3121129 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
* *
3121151 AGTGGTCCTTCGAGACGTATTC
1 AGTGGTCCTTCGGGACGTATCC
*
3121173 AGTAGTCCTTCGGGAC
1 AGTGGTCCTTCGGGAC
3121189 AAATACTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATCC
Found at i:3123545 original size:59 final size:59
Alignment explanation
Indices: 3123435--3123547 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 59
3123425 TTTTAGTTGT
* *
3123435 TGTTTTTACTATTTAACCCTTCAAGATTCTATTTTTTTAGTTTTAGTCCTTTAAATATA
1 TGTTTTTACTATTTAACCCTTCAAGATTCTATTTTTCTAGTTTTAGACCTTTAAATATA
*
3123494 TGTTTTTGCTATTTTAATCCCTT-AA-ATGTCTATTTTTACTA-TTTTA-ACCTTTAA
1 TGTTTTTACTA-TTTAA-CCCTTCAAGAT-TCTATTTTT-CTAGTTTTAGACCTTTAA
3123548 GTGTTTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
59 19 0.40
60 21 0.45
61 7 0.15
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.55
Consensus pattern (59 bp):
TGTTTTTACTATTTAACCCTTCAAGATTCTATTTTTCTAGTTTTAGACCTTTAAATATA
Found at i:3123556 original size:29 final size:30
Alignment explanation
Indices: 3123437--3123560 Score: 96
Period size: 30 Copynumber: 4.2 Consensus size: 30
3123427 TTAGTTGTTG
3123437 TTTTTACTA-TTTAA-CCCTTCAAGAT-TCTA
1 TTTTTACTATTTTAATCCCTT-AA-ATGTCTA
* * * * * *
3123466 TTTTT-TTAGTTTTAGTCCTTTAAATATATG
1 TTTTTACTA-TTTTAATCCCTTAAATGTCTA
*
3123496 TTTTTGCTATTTTAATCCCTTAAATGTCTA
1 TTTTTACTATTTTAATCCCTTAAATGTCTA
* * *
3123526 TTTTTACTATTTTAA-CCTTTAAGTGTTTA
1 TTTTTACTATTTTAATCCCTTAAATGTCTA
3123555 TTTTTA
1 TTTTTA
3123561 TTTTTTGGTC
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
28 2 0.03
29 24 0.32
30 43 0.57
31 6 0.08
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.56
Consensus pattern (30 bp):
TTTTTACTATTTTAATCCCTTAAATGTCTA
Found at i:3123573 original size:29 final size:30
Alignment explanation
Indices: 3123541--3123606 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
3123531 ACTATTTTAA
*
3123541 CCTTTAAGTGTTTATTTTTATT-TTTTGGT
1 CCTTTAAGTGTTTATATTTATTCTTTTGGT
* *
3123570 CCTTTAAGTTTTTATATTTGTTCTTTTGGT
1 CCTTTAAGTGTTTATATTTATTCTTTTGGT
3123600 CCTTTAA
1 CCTTTAA
3123607 CTTTATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.15, C:0.11, G:0.12, T:0.62
Consensus pattern (30 bp):
CCTTTAAGTGTTTATATTTATTCTTTTGGT
Found at i:3129986 original size:15 final size:16
Alignment explanation
Indices: 3129950--3129988 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3129940 AGAGCCTCTA
3129950 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
*
3129966 AATCATTCAGCGTTT-
1 AATCATTCAGCATTTG
3129981 AATCATTC
1 AATCATTC
3129989 TGAAATAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:3132476 original size:23 final size:23
Alignment explanation
Indices: 3132434--3132478 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3132424 CTCGTATAAA
*
3132434 TGCAACGAAGTGCCATGTAGAAT
1 TGCAACGAAGTGCCACGTAGAAT
* *
3132457 TGCATCGAAGTGCCGCGTAGAA
1 TGCAACGAAGTGCCACGTAGAA
3132479 ATACACCGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (23 bp):
TGCAACGAAGTGCCACGTAGAAT
Found at i:3139996 original size:23 final size:23
Alignment explanation
Indices: 3139963--3140022 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
3139953 AATCTTATAT
*
3139963 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
3139986 GGTACTTCGGTACAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
3140009 GGCACTTCAGTGCA
1 GGCACTTCGGTGCA
3140023 TTTATACGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:3146964 original size:23 final size:23
Alignment explanation
Indices: 3146938--3146997 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
3146928 AATCTTATAT
* *
3146938 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACAC
*
3146961 GGCACTTCGGTGCAATTCTACAT
1 GGCACTTCGGTGCAATTCTACAC
3146984 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3146998 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:3147745 original size:39 final size:38
Alignment explanation
Indices: 3147700--3147804 Score: 113
Period size: 39 Copynumber: 2.7 Consensus size: 38
3147690 TTTTTAAAAC
3147700 AATTTAGAATGTTAACGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAA-GTGAAATAATTTAAGAAATTAAG
* * * *
3147739 AATTTAGAATATTATGGTGTCAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTA-AGTG-AAATAATTTAAGAAATTAAG
* *
3147778 ATTTTATAATGTTAGAGTGAAATAATT
1 AATTTAGAATGTTA-AGTGAAATAATT
3147805 CGAGAATTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
38 2 0.04
39 49 0.92
40 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (38 bp):
AATTTAGAATGTTAAGTGAAATAATTTAAGAAATTAAG
Found at i:3147846 original size:2 final size:2
Alignment explanation
Indices: 3147824--3147865 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3147814 TGAATAAAAC
3147824 AT AT A- AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3147863 AT A
1 AT A
3147866 ATAAATTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3148238 original size:31 final size:31
Alignment explanation
Indices: 3148203--3148263 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3148193 TGACTACGTC
3148203 TTAATTAAATAAAAACGAAAA-TGACAATATT
1 TTAATTAAATAAAAAC-AAAAGTGACAATATT
* *
3148234 TTAATTGAATAAAAACAAAAGTGACTATAT
1 TTAATTAAATAAAAACAAAAGTGACAATAT
3148264 CTTATGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.30
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAGTGACAATATT
Found at i:3150828 original size:12 final size:13
Alignment explanation
Indices: 3150802--3150830 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3150792 GCATTGTATA
3150802 TAAACCCATAATT
1 TAAACCCATAATT
3150815 TAAACCCA-AATT
1 TAAACCCATAATT
3150827 TAAA
1 TAAA
3150831 ATCCTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAACCCATAATT
Found at i:3151953 original size:2 final size:2
Alignment explanation
Indices: 3151946--3151991 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3151936 GGATGGAAGG
3151946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3151988 AT AT
1 AT AT
3151992 GTTACTGATA
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):
AT
Found at i:3154786 original size:20 final size:19
Alignment explanation
Indices: 3154763--3154827 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
3154753 TAGTATTTAG
3154763 ATAAATTTATTAATAATTTT
1 ATAAATTT-TTAATAATTTT
*
3154783 AT-AATATTTTAATAAATTTA
1 ATAAAT-TTTTAAT-AATTTT
3154803 ATAAGTATTTTT-ATAATTTT
1 ATAA--ATTTTTAATAATTTT
*
3154823 TTAAA
1 ATAAA
3154828 CTTTATTGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
18 1 0.03
19 8 0.22
20 19 0.51
21 3 0.08
22 4 0.11
23 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATAAATTTTTAATAATTTT
Found at i:3154825 original size:32 final size:31
Alignment explanation
Indices: 3154739--3154826 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
3154729 TTCGATAATA
* *
3154739 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAATAATTTTATAATATTTTA-ATAAATT
*
3154770 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAATAATTTTATAATATTTTAATAAATT
* *
3154801 TAATAAGTATTTTTATAATTTTTTAA
1 TAATAA-TAATTTTATAATATTTTAA
3154827 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
31 28 0.57
32 21 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TAATAATAATTTTATAATATTTTAATAAATT
Found at i:3154956 original size:26 final size:26
Alignment explanation
Indices: 3154899--3154958 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
3154889 AAAAATATAT
*
3154899 TAAACTTAGTAAAAAATATTATACAA
1 TAAACTTAGTAAAAAACATTATACAA
* *
3154925 TTAAACTTATTAAAAAACATTTATATAA
1 -TAAACTTAGTAAAAAACA-TTATACAA
3154953 -AAACTT
1 TAAACTT
3154959 CGAAAATCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 16 0.55
28 7 0.24
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (26 bp):
TAAACTTAGTAAAAAACATTATACAA
Found at i:3160060 original size:33 final size:33
Alignment explanation
Indices: 3160018--3160089 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
3160008 GACTCCAAAC
3160018 TCACAACCATGCGGTTATAGTTCAACTCAAATT
1 TCACAACCATGCGGTTATAGTTCAACTCAAATT
3160051 TCACAACCATGCGGTTATAGTTCAACTCAAATT
1 TCACAACCATGCGGTTATAGTTCAACTCAAATT
3160084 TCACAA
1 TCACAA
3160090 AGTTCTTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (33 bp):
TCACAACCATGCGGTTATAGTTCAACTCAAATT
Found at i:3160270 original size:29 final size:30
Alignment explanation
Indices: 3160199--3160258 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
3160189 CAATTTAAGG
3160199 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
3160230 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
3160259 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:3160373 original size:21 final size:21
Alignment explanation
Indices: 3160348--3160427 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
3160338 TTCAAGATTG
* *
3160348 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
3160369 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
3160387 CCC---GGGTACAGATAACCCC
1 CCCAGGGGGTACAGAT-ACCCC
3160406 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
3160427 C
1 C
3160428 TGCAGGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
15 10 0.20
16 1 0.02
18 4 0.08
19 4 0.08
21 21 0.42
22 10 0.20
ACGTcount: A:0.24, C:0.36, G:0.28, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:3160395 original size:15 final size:16
Alignment explanation
Indices: 3160375--3160405 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3160365 CCCCCCCAGG
3160375 GGGTACAGAT-ACCCC
1 GGGTACAGATAACCCC
3160390 GGGTACAGATAACCCC
1 GGGTACAGATAACCCC
3160406 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (16 bp):
GGGTACAGATAACCCC
Found at i:3160545 original size:21 final size:21
Alignment explanation
Indices: 3160519--3160561 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3160509 ATTTGAATAT
3160519 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
3160540 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
3160561 T
1 T
3160562 CTATTCTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:3160627 original size:20 final size:22
Alignment explanation
Indices: 3160589--3160628 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3160579 TTTGAGTATA
3160589 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
3160611 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
3160629 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:3160883 original size:34 final size:32
Alignment explanation
Indices: 3160844--3160913 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3160834 TTTTGTAAAG
*
3160844 GGGAAAGGTTATAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
3160878 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
3160910 GGGA
1 GGGA
3160914 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:3163799 original size:29 final size:30
Alignment explanation
Indices: 3163728--3163787 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
3163718 CAATTTAAGG
3163728 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
3163759 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
3163788 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:3163902 original size:21 final size:21
Alignment explanation
Indices: 3163877--3163955 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
3163867 TTCAAGATTG
* *
3163877 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
3163898 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
*
3163916 CCC---GGGTACAGATAACCC
1 CCCAGGGGGTACAGATACCCC
3163934 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
3163955 C
1 C
3163956 TGCAGGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 30 0.61
ACGTcount: A:0.24, C:0.35, G:0.28, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:3163924 original size:15 final size:16
Alignment explanation
Indices: 3163904--3163934 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3163894 CCCCCCCAGG
3163904 GGGTACAGAT-ACCCC
1 GGGTACAGATAACCCC
3163919 GGGTACAGATAACCCC
1 GGGTACAGATAACCCC
3163935 CCAGGGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (16 bp):
GGGTACAGATAACCCC
Found at i:3164029 original size:20 final size:21
Alignment explanation
Indices: 3163989--3164032 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3163979 AACAGAATGT
3163989 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
3164010 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
3164031 CC
1 CC
3164033 TGTTCAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.45, G:0.27, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:3164094 original size:21 final size:21
Alignment explanation
Indices: 3164068--3164131 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
3164058 ATTTGAATAT
3164068 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
3164089 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
*
3164110 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTATCGATTCCC
3164131 T
1 T
3164132 CTATTCTGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:3164452 original size:34 final size:32
Alignment explanation
Indices: 3164413--3164482 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3164403 TTTTGTAAAG
*
3164413 GGGAAAGGTTATAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
3164447 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
3164479 GGGA
1 GGGA
3164483 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:3165342 original size:166 final size:164
Alignment explanation
Indices: 3165070--3165406 Score: 586
Period size: 166 Copynumber: 2.0 Consensus size: 164
3165060 AATAAATACT
*
3165070 TGTTAAACATAAATGCTTAAAATTTTGTTTCGGTTTAAAAAAATACATTTTTCGCAATTTAAAGT
1 TGTTAAACATAAAAGCTTAAAATTTTGTTTCGGTTTAAAAAAATACATTTTTCGCAATTTAAAGT
* *
3165135 TTGTTTTCCTTTAGCATGCATAATAATTTATCATTACAAACAAAACTGGTTTTATGCAGCACTTG
66 TTGTTTTCCTTTAGCATGCATAATAATTTATCATTACAAACAAAACTGATTTTATGCAGCACTTA
3165200 GACAG-TTCAATGATGCTTCATATTTACATACAAC
131 GACAGTTTC-ATGATGCTTCATATTTACATACAAC
3165234 TGTTAAACATAAAAGCTTAAAATTTTGTTTCGGTTTAAAAAAAAATACATTTTTCGCAATTTAAA
1 TGTTAAACATAAAAGCTTAAAATTTTGTTTCGGTTT--AAAAAAATACATTTTTCGCAATTTAAA
* *
3165299 GTTTGTTTTCCTTTAGCATGCATAATAATTTATCGTTACAAACAAAATTGATTTTATGCAGCACT
64 GTTTGTTTTCCTTTAGCATGCATAATAATTTATCATTACAAACAAAACTGATTTTATGCAGCACT
3165364 TAGACAGTTTCATGATGCTTCATATTTACATACAAC
129 TAGACAGTTTCATGATGCTTCATATTTACATACAAC
3165400 TGCTTAA
1 TG-TTAA
3165407 TATTGTTTGT
Statistics
Matches: 164, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
164 35 0.21
166 122 0.74
167 7 0.04
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (164 bp):
TGTTAAACATAAAAGCTTAAAATTTTGTTTCGGTTTAAAAAAATACATTTTTCGCAATTTAAAGT
TTGTTTTCCTTTAGCATGCATAATAATTTATCATTACAAACAAAACTGATTTTATGCAGCACTTA
GACAGTTTCATGATGCTTCATATTTACATACAAC
Found at i:3167275 original size:21 final size:21
Alignment explanation
Indices: 3167249--3167294 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
3167239 ATTCGATAGA
3167249 AATAAAATTCATACTTAAATC
1 AATAAAATTCATACTTAAATC
*
3167270 AATAAAATTGATACTTAAATC
1 AATAAAATTCATACTTAAATC
3167291 AATA
1 AATA
3167295 TAAAACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (21 bp):
AATAAAATTCATACTTAAATC
Found at i:3171718 original size:2 final size:2
Alignment explanation
Indices: 3171711--3171755 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3171701 GGGATAAATT
3171711 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
3171753 TA T
1 TA T
3171756 TGCTATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3174427 original size:26 final size:26
Alignment explanation
Indices: 3174389--3174440 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3174379 TTTCTTCAAC
* *
3174389 AATAACCTCATAAACAAGGATGGATT
1 AATAACCTAATAAACAAGGATAGATT
*
3174415 AATAACCTAATAAACATGGATAGATT
1 AATAACCTAATAAACAAGGATAGATT
3174441 TAGAGGGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.25
Consensus pattern (26 bp):
AATAACCTAATAAACAAGGATAGATT
Found at i:3176320 original size:13 final size:13
Alignment explanation
Indices: 3176302--3176330 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3176292 CATAAATGCT
3176302 CTCAATTAACAGA
1 CTCAATTAACAGA
3176315 CTCAATTAACAGA
1 CTCAATTAACAGA
3176328 CTC
1 CTC
3176331 GTAACAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (13 bp):
CTCAATTAACAGA
Found at i:3180934 original size:13 final size:13
Alignment explanation
Indices: 3180916--3180944 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3180906 CATAACTGCT
3180916 CTCAATTAACAGA
1 CTCAATTAACAGA
3180929 CTCAATTAACAGA
1 CTCAATTAACAGA
3180942 CTC
1 CTC
3180945 GTAACAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (13 bp):
CTCAATTAACAGA
Found at i:3181410 original size:39 final size:39
Alignment explanation
Indices: 3181351--3181425 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
3181341 CTTCTGCAAA
*
3181351 GCAATAGAAGTTCTATCATCCCAAACAAGCATATTATTT
1 GCAACAGAAGTTCTATCATCCCAAACAAGCATATTATTT
3181390 GCAACAGAAGTTCTATCATCCCAAACAAGCATATTA
1 GCAACAGAAGTTCTATCATCCCAAACAAGCATATTA
3181426 ACCCTGACAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.27
Consensus pattern (39 bp):
GCAACAGAAGTTCTATCATCCCAAACAAGCATATTATTT
Found at i:3183615 original size:20 final size:20
Alignment explanation
Indices: 3183521--3183889 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
3183511 GATTTTCCAT
* ** *
3183521 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3183541 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3183561 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3183581 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
3183601 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
3183621 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3183641 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3183661 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3183681 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3183701 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3183721 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3183741 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3183761 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
3183781 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3183801 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3183821 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3183841 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3183861 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3183881 AATCACAAC
1 AATCGCAAC
3183890 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3184801 original size:12 final size:12
Alignment explanation
Indices: 3184784--3184808 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3184774 ATATAATCCT
3184784 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3184796 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3184808 G
1 G
3184809 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3187135 original size:19 final size:19
Alignment explanation
Indices: 3187113--3187438 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
3187103 CGGAAAATAC
*
3187113 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3187132 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3187146 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3187166 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3187180 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3187199 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3187218 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3187232 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3187251 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3187270 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
3187284 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3187303 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
3187322 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
3187341 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3187360 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3187379 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3187393 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3187412 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3187431 AATCGCAA
1 AATCGCAA
3187439 CGAGATAATC
Statistics
Matches: 268, Mismatches: 13, Indels: 52
0.80 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 4 0.01
19 173 0.65
20 13 0.05
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3187200 original size:33 final size:34
Alignment explanation
Indices: 3187113--3187438 Score: 312
Period size: 33 Copynumber: 9.2 Consensus size: 34
3187103 CGGAAAATAC
* *
3187113 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
3187146 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
3187180 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
3187218 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
3187251 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
* *
3187284 AATCGCAATACGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
3187322 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
3187360 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
3187392 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
3187431 AATCGCAA
1 AATCGCAA
3187439 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 110 0.43
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 92 0.36
39 2 0.01
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:3187374 original size:161 final size:157
Alignment explanation
Indices: 3187141--3187460 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 157
3187131 AAATCCCAAC
*
3187141 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
3187206 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
3187271 ATCGCAACGAGAGAATCGCAATACGAA
131 ATCGCAACGAGAGAATCGCAATACGAA
*
3187298 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
3187362 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
* *
3187427 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATACGAA
3187459 AT
1 AT
3187461 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 119 0.78
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATACGAA
Found at i:3187476 original size:52 final size:52
Alignment explanation
Indices: 3187141--3187460 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
3187131 AAATCCCAAC
3187141 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3187194 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3187246 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
3187298 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
3187355 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3187407 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3187459 AT
1 AT
3187461 TATAAACGCA
Statistics
Matches: 253, Mismatches: 9, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 183 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 44 0.17
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3187576 original size:19 final size:19
Alignment explanation
Indices: 3187467--3187568 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3187457 AAATTATAAA
3187467 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3187486 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3187506 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3187522 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3187539 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3187558 CGCATTGCGAT
1 CGCATTGCGAT
3187569 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3187694 original size:14 final size:14
Alignment explanation
Indices: 3187675--3187711 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3187665 CATCAATTAC
3187675 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3187689 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3187703 ACAAATCAA
1 ACAAATCAA
3187712 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3187723 original size:12 final size:12
Alignment explanation
Indices: 3187706--3187778 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
3187696 ATCTTTTACA
3187706 AATCAATTAAAC
1 AATCAATTAAAC
*
3187718 AATCAA--AAATTG
1 AATCAATTAAA--C
**
3187730 AATCAACTTTTAC
1 AATCAA-TTAAAC
3187743 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
3187756 AATCAA-AAAAC
1 AATCAATTAAAC
3187767 AATCAATTAAAC
1 AATCAATTAAAC
3187779 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:3187740 original size:38 final size:38
Alignment explanation
Indices: 3187692--3187764 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
3187682 AACTTTTACA
*
3187692 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
3187730 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
3187765 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:3189622 original size:19 final size:19
Alignment explanation
Indices: 3189582--3189716 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
3189572 TAGTTTACTT
* *
3189582 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3189602 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3189621 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3189640 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
3189654 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3189673 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3189687 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3189706 TCGCAATGCGA
1 TCGCAACGCGA
3189717 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3189657 original size:14 final size:14
Alignment explanation
Indices: 3189638--3189694 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3189628 GCGAAATGAA
*
3189638 AATCGCAACGACAG
1 AATCGCAACGAAAG
3189652 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
3189669 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3189685 AATCGCAACG
1 AATCGCAACG
3189695 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3189661 original size:33 final size:33
Alignment explanation
Indices: 3189619--3189711 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
3189609 GCGAAACCAA
*
3189619 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3189652 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3189685 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3189712 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3189708 original size:52 final size:54
Alignment explanation
Indices: 3189582--3189716 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
3189572 TAGTTTACTT
*
3189582 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
3189640 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
3189687 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
3189717 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:3189734 original size:19 final size:19
Alignment explanation
Indices: 3189712--3189840 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3189702 AAAATCGCAA
3189712 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3189731 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3189745 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3189764 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3189778 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3189797 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3189816 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3189836 TGCGA
1 TGCGA
3189841 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3189754 original size:33 final size:33
Alignment explanation
Indices: 3189712--3189803 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3189702 AAAATCGCAA
3189712 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3189745 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3189778 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3189804 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3190043 original size:93 final size:93
Alignment explanation
Indices: 3189884--3190263 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
3189874 TTGAATGGAT
3189884 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3189949 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3189977 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3190042 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3190070 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3190134 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3190162 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3190227 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3190255 AAATTTACT
1 AAATTTACT
3190264 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3190197 original size:185 final size:186
Alignment explanation
Indices: 3189884--3190263 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
3189874 TTGAATGGAT
3189884 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3189949 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3190014 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
3190070 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3190134 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
3190199 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
3190255 AAATTTACT
1 AAATTTACT
3190264 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3191987 original size:14 final size:14
Alignment explanation
Indices: 3191968--3192057 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3191958 TTGAAATGAA
3191968 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3191982 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
3191999 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
3192015 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3192034 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3192048 AATCGCAACG
1 AATCGCAACG
3192058 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3192005 original size:33 final size:33
Alignment explanation
Indices: 3191960--3192074 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3191950 TCTTTTGGTT
3191960 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3191993 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3192026 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3192059 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3192075 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3192006 original size:19 final size:18
Alignment explanation
Indices: 3191967--3192079 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
3191957 GTTGAAATGA
3191967 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
3191982 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
3191999 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
3192015 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
3192032 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
3192048 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
3192065 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
3192080 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:3192110 original size:14 final size:14
Alignment explanation
Indices: 3192091--3192145 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3192081 TTTGGTTTCG
3192091 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3192105 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
3192124 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3192138 CGTTGCGA
1 CGTTGCGA
3192146 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3192308 original size:33 final size:33
Alignment explanation
Indices: 3192266--3192336 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3192256 AATACTAACT
*
3192266 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3192299 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3192332 TGAAA
1 TGAAA
3192337 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3192570 original size:22 final size:22
Alignment explanation
Indices: 3192518--3192572 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3192508 TGGTTGTGAG
**
3192518 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3192540 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3192562 GGATTTCTTCG
1 GGATTTCTTCG
3192573 CCGTAGAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3192743 original size:20 final size:20
Alignment explanation
Indices: 3192718--3192911 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3192708 CTTTAAATAT
3192718 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3192738 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3192760 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3192779 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3192799 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3192819 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3192839 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3192859 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3192879 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3192899 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3192912 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3192905 original size:60 final size:60
Alignment explanation
Indices: 3192718--3192911 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3192708 CTTTAAATAT
**
3192718 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3192779 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3192839 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3192899 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3192912 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3192928 original size:21 final size:20
Alignment explanation
Indices: 3192904--3192980 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
3192894 ATATTCGCGT
3192904 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
3192925 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
3192945 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
3192967 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
3192981 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:3192991 original size:20 final size:20
Alignment explanation
Indices: 3192966--3193017 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3192956 AAGAATCGCG
*
3192966 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3192986 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3193006 TTGCGATTCTGG
1 TTGCGATTCTGG
3193018 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:3193242 original size:9 final size:9
Alignment explanation
Indices: 3193210--3193244 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3193200 TTGAAGGATG
*
3193210 TTTTATTAA
1 TTTTATTTA
*
3193219 TTTTAATTA
1 TTTTATTTA
3193228 TTTTATTTA
1 TTTTATTTA
3193237 TTTTATTT
1 TTTTATTT
3193245 TATATCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:3193871 original size:18 final size:19
Alignment explanation
Indices: 3193836--3193873 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3193826 ATATATATAT
3193836 AATTATTAAATAAAATTAA
1 AATTATTAAATAAAATTAA
*
3193855 AATTATT-AATTAAATTAA
1 AATTATTAAATAAAATTAA
3193873 A
1 A
3193874 GATGATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTATTAAATAAAATTAA
Found at i:3193897 original size:2 final size:2
Alignment explanation
Indices: 3193890--3193921 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3193880 TTAATAATTT
3193890 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
3193922 AAATAAAGGT
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:3195775 original size:36 final size:36
Alignment explanation
Indices: 3195726--3195817 Score: 157
Period size: 36 Copynumber: 2.6 Consensus size: 36
3195716 CAGAGGGCTC
* *
3195726 GTTCATTCATTTACGTTTGTGAACGTTCGGTAATAT
1 GTTCGTTCATTTACGTTCGTGAACGTTCGGTAATAT
3195762 GTTCGTTCATTTACGTTCGTGAACGTTCGGTAATAT
1 GTTCGTTCATTTACGTTCGTGAACGTTCGGTAATAT
*
3195798 GTTCGTTCATTTATGTTCGT
1 GTTCGTTCATTTACGTTCGT
3195818 TCGTTCGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.46
Consensus pattern (36 bp):
GTTCGTTCATTTACGTTCGTGAACGTTCGGTAATAT
Found at i:3196164 original size:24 final size:23
Alignment explanation
Indices: 3196121--3196169 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
3196111 CCGTTTGTTA
*
3196121 ATGTTTGTTTATTGTGTTCGTTT
1 ATGTTTGTTCATTGTGTTCGTTT
3196144 ATGTTTGTTCATTTGTGTTCGTTT
1 ATGTTTGTTCA-TTGTGTTCGTTT
3196168 AT
1 AT
3196170 CATTTAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.10, C:0.06, G:0.20, T:0.63
Consensus pattern (23 bp):
ATGTTTGTTCATTGTGTTCGTTT
Found at i:3196168 original size:37 final size:39
Alignment explanation
Indices: 3196075--3196169 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 39
3196065 TGTTCGTTTG
** *
3196075 TGTTCATTTACGTTCGTTTATTGTGTTTGTTTACATCCGTT
1 TGTTCATTTGTGTTCGTTTATTGTGTTCGTTTA-AT-CGTT
*
3196116 TGTT-A-ATGT-TT-GTTTATTGTGTTCGTTT-AT-GTT
1 TGTTCATTTGTGTTCGTTTATTGTGTTCGTTTAATCGTT
3196149 TGTTCATTTGTGTTCGTTTAT
1 TGTTCATTTGTGTTCGTTTAT
3196170 CATTTAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
33 7 0.16
34 1 0.02
35 5 0.11
36 2 0.04
37 22 0.49
38 2 0.04
39 1 0.02
40 1 0.02
41 4 0.09
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.60
Consensus pattern (39 bp):
TGTTCATTTGTGTTCGTTTATTGTGTTCGTTTAATCGTT
Found at i:3209715 original size:2 final size:2
Alignment explanation
Indices: 3209708--3209757 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3209698 TGTTTATAAA
3209708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3209750 AT AT AT AT
1 AT AT AT AT
3209758 TTAAATCCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3209851 original size:2 final size:2
Alignment explanation
Indices: 3209844--3209873 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3209834 ATAATGCAGC
3209844 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
3209874 AACATTGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3210673 original size:27 final size:27
Alignment explanation
Indices: 3210642--3210705 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
3210632 GATTTCGAGT
3210642 ATTTATTTTCAAAATATGCTTTTGATG
1 ATTTATTTTCAAAATATGCTTTTGATG
*
3210669 ATTTAATTTCAAAATATGCTTTTGATG
1 ATTTATTTTCAAAATATGCTTTTGATG
3210696 ATTTATTTTC
1 ATTTATTTTC
3210706 TTTTGTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (27 bp):
ATTTATTTTCAAAATATGCTTTTGATG
Found at i:3210939 original size:81 final size:82
Alignment explanation
Indices: 3210728--3211041 Score: 531
Period size: 81 Copynumber: 3.8 Consensus size: 82
3210718 TGTATCCATC
* * * *
3210728 AAAATTATTTGATAGTAATTTATTATTTTTATTTGTTTTCACTGTTATGGGTATACTGTTGTTTA
1 AAAACTATTAGATAGTAATTTATTATTTTTATTTGTTTTCACTGTTCTGGGTATATTGTTGTTTA
3210793 AATGTCGTATACATAAAA
66 AATGTCGTATACAT-AAA
3210811 AAAACTATTAGATAGTAATTTATTATTTTTATTTGTTTTCACTGTTCTGGGTATATTGTTGTTTA
1 AAAACTATTAGATAGTAATTTATTATTTTTATTTGTTTTCACTGTTCTGGGTATATTGTTGTTTA
3210876 AATGTCGTATACAT-AA
66 AATGTCGTATACATAAA
* *
3210892 AAAACTATTACATAGTAATTTATTATTTTTATTTGTTTTCACTGTTCTGGGTAAATTGTTGTTTA
1 AAAACTATTAGATAGTAATTTATTATTTTTATTTGTTTTCACTGTTCTGGGTATATTGTTGTTTA
*
3210957 AATGTCGTGTACATAAA
66 AATGTCGTATACATAAA
**
3210974 AAAACTATTAGATAGTAATTTATTATTTTTATTTGTTTTCGTTGTTCTGGGTATATTGTTGTTTA
1 AAAACTATTAGATAGTAATTTATTATTTTTATTTGTTTTCACTGTTCTGGGTATATTGTTGTTTA
3211039 AAT
66 AAT
3211042 TTCTAAACTG
Statistics
Matches: 219, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
81 78 0.36
82 66 0.30
83 75 0.34
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.50
Consensus pattern (82 bp):
AAAACTATTAGATAGTAATTTATTATTTTTATTTGTTTTCACTGTTCTGGGTATATTGTTGTTTA
AATGTCGTATACATAAA
Found at i:3221738 original size:14 final size:13
Alignment explanation
Indices: 3221710--3221769 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
3221700 GTTCATTTAC
*
3221710 GTTCATTTATTGT
1 GTTCGTTTATTGT
3221723 GTTCGTTTACTTGT
1 GTTCGTTTA-TTGT
3221737 GTTCG--T-TTGT
1 GTTCGTTTATTGT
3221747 GTTCGTTTATTGT
1 GTTCGTTTATTGT
*
3221760 GTTCATTTAT
1 GTTCGTTTAT
3221770 GTTTGTTACA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 9 0.22
12 2 0.05
13 21 0.51
14 9 0.22
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.60
Consensus pattern (13 bp):
GTTCGTTTATTGT
Found at i:3224513 original size:24 final size:24
Alignment explanation
Indices: 3224424--3224515 Score: 62
Period size: 24 Copynumber: 3.8 Consensus size: 24
3224414 CAATCTTATA
* *
3224424 TGGCACTACGGTGC-AATTCTACG
1 TGGCACTTCAGTGCAAATTCTACG
* *
3224447 TGACACTTCGGTGCAAATTTCTAACG
1 TGGCACTTCAGTGCAAA-TTCT-ACG
* * * **
3224473 CAGTC-GTTCAGAACAAATTCTACG
1 -TGGCACTTCAGTGCAAATTCTACG
3224497 TGGCACTTCAGTGCAAATT
1 TGGCACTTCAGTGCAAATT
3224516 TATATGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
23 14 0.27
24 16 0.31
25 8 0.16
26 11 0.22
27 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (24 bp):
TGGCACTTCAGTGCAAATTCTACG
Found at i:3225081 original size:21 final size:21
Alignment explanation
Indices: 3225056--3225104 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3225046 TACTGTAGTG
3225056 GTGCATCAGTACACTATAGCA
1 GTGCATCAGTACACTATAGCA
* * *
3225077 GTGCATCGGTATACTGTAGCA
1 GTGCATCAGTACACTATAGCA
3225098 GTGCATC
1 GTGCATC
3225105 TATACACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
GTGCATCAGTACACTATAGCA
Found at i:3225165 original size:55 final size:55
Alignment explanation
Indices: 3225078--3225221 Score: 243
Period size: 55 Copynumber: 2.6 Consensus size: 55
3225068 ACTATAGCAG
* *
3225078 TGCATCGGTATACTGTAGCAGTGCATCTATACACAATTTATATTCGATGTATTTA
1 TGCATCGGTACACTGTAGCAGTGCATCGATACACAATTTATATTCGATGTATTTA
*
3225133 TGCATCGGTACACTGTAGCAGTGCATCGATACACAATTTATATTCGATGTATTTG
1 TGCATCGGTACACTGTAGCAGTGCATCGATACACAATTTATATTCGATGTATTTA
* *
3225188 TGCATCGGTACACTATAGCAGTGCATCGGTACAC
1 TGCATCGGTACACTGTAGCAGTGCATCGATACAC
3225222 TGTATCACTA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 84 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (55 bp):
TGCATCGGTACACTGTAGCAGTGCATCGATACACAATTTATATTCGATGTATTTA
Found at i:3225811 original size:305 final size:305
Alignment explanation
Indices: 3225260--3225868 Score: 1182
Period size: 305 Copynumber: 2.0 Consensus size: 305
3225250 ACTGTTCATG
*
3225260 ACAATGTTCGTACTGTATAGTACTGTTCATAAATACATTTTTACCTTAAATTTTTATAATGAAAC
1 ACAATGTTCGTACCGTATAGTACTGTTCATAAATACATTTTTACCTTAAATTTTTATAATGAAAC
3225325 ATAATTTAATAGTATATTATTGTATTTTCTTAATATGAGTTCAAATATTTTGTTATTTTGTAAGA
66 ATAATTTAATAGTATATTATTGTATTTTCTTAATATGAGTTCAAATATTTTGTTATTTTGTAAGA
3225390 ATACTGTTTTAAAAAGTCAATGTGACATCTCGGACTCGTATCCGGGTCGGGTACAGGTTGGGGGT
131 ATACTGTTTTAAAAAGTCAATGTGACATCTCGGACTCGTATCCGGGTCGGGTACAGGTTGGGGGT
3225455 GTTACATTTAATGGAATCAGAGCTACGGTTTAGTCGATTCTCGGCATAAACCAAAGTCTAGATTG
196 GTTACATTTAATGGAATCAGAGCTACGGTTTAGTCGATTCTCGGCATAAACCAAAGTCTAGATTG
3225520 TTTTATAATGTATACATGCCAACAAAATAGTGAAAACTTCTGATA
261 TTTTATAATGTATACATGCCAACAAAATAGTGAAAACTTCTGATA
3225565 ACAATGTTCGTACCGTATAGTACTGTTCATAAATACATTTTTACCTTAAATTTTTATAATGAAAC
1 ACAATGTTCGTACCGTATAGTACTGTTCATAAATACATTTTTACCTTAAATTTTTATAATGAAAC
*
3225630 ATAATTTAATAGTATATTATTGTATTTTCTTAATATGATTTCAAATATTTTGTTATTTTGTAAGA
66 ATAATTTAATAGTATATTATTGTATTTTCTTAATATGAGTTCAAATATTTTGTTATTTTGTAAGA
*
3225695 ATACTGTTTTAAAAAGTCAATGTGACATCTCGGACTCGTATCCGGGTCGGGTACGGGTTGGGGGT
131 ATACTGTTTTAAAAAGTCAATGTGACATCTCGGACTCGTATCCGGGTCGGGTACAGGTTGGGGGT
*
3225760 GTTACATTTAATGGAATCAGAGCTACGGTTTAGTCGATTCTCGGCATAAACCGAAGTCTAGATTG
196 GTTACATTTAATGGAATCAGAGCTACGGTTTAGTCGATTCTCGGCATAAACCAAAGTCTAGATTG
3225825 TTTTATAATGTATACATGCCAACAAAATAGTGAAAACTTCTGAT
261 TTTTATAATGTATACATGCCAACAAAATAGTGAAAACTTCTGAT
3225869 CTGATGGAAT
Statistics
Matches: 300, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 300 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (305 bp):
ACAATGTTCGTACCGTATAGTACTGTTCATAAATACATTTTTACCTTAAATTTTTATAATGAAAC
ATAATTTAATAGTATATTATTGTATTTTCTTAATATGAGTTCAAATATTTTGTTATTTTGTAAGA
ATACTGTTTTAAAAAGTCAATGTGACATCTCGGACTCGTATCCGGGTCGGGTACAGGTTGGGGGT
GTTACATTTAATGGAATCAGAGCTACGGTTTAGTCGATTCTCGGCATAAACCAAAGTCTAGATTG
TTTTATAATGTATACATGCCAACAAAATAGTGAAAACTTCTGATA
Found at i:3226569 original size:2 final size:2
Alignment explanation
Indices: 3226562--3226587 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3226552 GATATAACAT
3226562 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
3226588 ACATATACAT
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:3229613 original size:33 final size:33
Alignment explanation
Indices: 3229567--3229632 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3229557 AACCAGGACA
*
3229567 TAACCAAACAACCCACAAAGGGATAATTGAAGG
1 TAACCAAACAACCCACAAAGGGATAATTAAAGG
*
3229600 TAACCAAAGAACCCACAAAGGGATAATTAAAGG
1 TAACCAAACAACCCACAAAGGGATAATTAAAGG
3229633 CAACATGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (33 bp):
TAACCAAACAACCCACAAAGGGATAATTAAAGG
Found at i:3235680 original size:23 final size:25
Alignment explanation
Indices: 3235632--3235678 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3235622 TATTTTTGTT
*
3235632 AATTTAATATTATATATATTATTTA
1 AATTTAATACTATATATATTATTTA
3235657 AATTTAATACTATATAT-TTATT
1 AATTTAATACTATATATATTATT
3235679 AATAGTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AATTTAATACTATATATATTATTTA
Found at i:3235724 original size:18 final size:18
Alignment explanation
Indices: 3235701--3235743 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3235691 TATAATAAAC
*
3235701 TATAATTTAATGGAACAA
1 TATAATTTAATAGAACAA
*
3235719 TATAATTTAATAGATCAA
1 TATAATTTAATAGAACAA
3235737 -ATAATTT
1 TATAATTT
3235744 TTAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (18 bp):
TATAATTTAATAGAACAA
Found at i:3235800 original size:21 final size:22
Alignment explanation
Indices: 3235746--3235830 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 22
3235736 AATAATTTTT
* *
3235746 AATATATAAATTATTAATATAATTT
1 AATATATAAA-TAATAAT-TAA-TA
**
3235771 AATA-A-AAATAATTCTTAATA
1 AATATATAAATAATAATTAATA
*
3235791 AATAT-TAAATTATAATTAATA
1 AATATATAAATAATAATTAATA
3235812 AATATATAAATAAT-ATTAA
1 AATATATAAATAATAATTAA
3235831 ATTATAATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.10
21 25 0.51
22 11 0.22
23 3 0.06
24 1 0.02
25 4 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATATAAATAATAATTAATA
Found at i:3235845 original size:15 final size:15
Alignment explanation
Indices: 3235795--3235845 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
3235785 TTAATAAATA
3235795 TTAAATTATAATTAA-
1 TTAAATTATAA-TAAT
3235810 -TAAATATATAAATAAT
1 TTAAAT-TAT-AATAAT
3235826 ATTAAATTATAATAAT
1 -TTAAATTATAATAAT
3235842 TTAA
1 TTAA
3235846 TCAAATAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.16
15 10 0.32
16 8 0.26
17 3 0.10
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAATTATAATAAT
Found at i:3235874 original size:135 final size:137
Alignment explanation
Indices: 3235702--3235975 Score: 412
Period size: 143 Copynumber: 2.0 Consensus size: 137
3235692 ATAATAAACT
**
3235702 ATAATTTAATGGAACAATATAATTTAATAGATCAAAT-A-A-TTTTTAATATATAAATTATTAAT
1 ATAATTTAATCAAACAATATAATTTAATAGATCAAATAATAGTTTTTAATATATAAATTATTAAT
*
3235764 ATAATTTAAT-AAAAATAATTCTTAATAAATATTAAATTATAATTAATAAATATATAAATAATAT
66 ATAATTTAATGAAAAATAATTCTTAAGAAATATTAAATTATAATTAATAAATATAT--ATAATAT
3235828 TAAATTATA
129 TAAATTATA
* * *
3235837 ATAATTTAATCAAATAATGTAATTTAATAGATGAAATAATTCTTAGTTTTTAATATATAAATTAT
1 ATAATTTAATCAAACAATATAATTTAATAGATCAAATAA----TAGTTTTTAATATATAAATTAT
3235902 TAATATAATTTAATGAAAAATAATTCTTAAGAAATATTAAATTATAATTAATAAATATATATAAT
62 TAATATAATTTAATGAAAAATAATTCTTAAGAAATATTAAATTATAATTAATAAATATATATAAT
3235967 ATTAAATTA
127 ATTAAATTA
3235976 ACAAAAGATA
Statistics
Matches: 125, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
135 32 0.26
136 1 0.01
141 15 0.12
142 33 0.26
143 44 0.35
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (137 bp):
ATAATTTAATCAAACAATATAATTTAATAGATCAAATAATAGTTTTTAATATATAAATTATTAAT
ATAATTTAATGAAAAATAATTCTTAAGAAATATTAAATTATAATTAATAAATATATATAATATTA
AATTATA
Found at i:3235991 original size:24 final size:24
Alignment explanation
Indices: 3235942--3235997 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
3235932 GAAATATTAA
* *
3235942 ATTATAATTAATAAATATATATAAT
1 ATTA-AATTAACAAATAGATATAAT
3235967 ATTAAATTAACAAA-AGATATGAAT
1 ATTAAATTAACAAATAGATAT-AAT
3235991 ATATAAA
1 AT-TAAA
3235998 ATATACTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
24 14 0.52
25 8 0.30
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATTAAATTAACAAATAGATATAAT
Found at i:3236187 original size:29 final size:29
Alignment explanation
Indices: 3236153--3236245 Score: 116
Period size: 29 Copynumber: 3.2 Consensus size: 29
3236143 AAATTTTGAC
* ** *
3236153 TAGTGACTAAAATGTAAGTTTTGAAAGTT
1 TAGTGACTAAAATATAAACTTTAAAAGTT
*
3236182 TAGTGACTAAAGTATAAACTTTAAAAGTT
1 TAGTGACTAAAATATAAACTTTAAAAGTT
* *
3236211 TAGTGACTAAAGTATAAACTTTAAAAATT
1 TAGTGACTAAAATATAAACTTTAAAAGTT
3236240 TA-TGAC
1 TAGTGAC
3236246 CCGAAATTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 4 0.07
29 54 0.93
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.35
Consensus pattern (29 bp):
TAGTGACTAAAATATAAACTTTAAAAGTT
Found at i:3238756 original size:31 final size:31
Alignment explanation
Indices: 3238719--3238779 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
3238709 TTAATCGTGG
*
3238719 TCACTTTCATTTCGTTTTAATTAATATGTGA
1 TCACTTTCATTTCATTTTAATTAATATGTGA
*
3238750 TCACTTTCGTTTCATTTTAATTAATATGTG
1 TCACTTTCATTTCATTTTAATTAATATGTG
3238780 GTCATTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (31 bp):
TCACTTTCATTTCATTTTAATTAATATGTGA
Found at i:3240509 original size:39 final size:39
Alignment explanation
Indices: 3240466--3240545 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
3240456 CCATCTCAAA
3240466 TTGCGTTACACTTTTAAGAATCGAGAACATGGTTTTACC
1 TTGCGTTACACTTTTAAGAATCGAGAACATGGTTTTACC
3240505 TTGCGTTACACTTTTAAGAATCGAGAACATGGTTTTACC
1 TTGCGTTACACTTTTAAGAATCGAGAACATGGTTTTACC
3240544 TT
1 TT
3240546 CTTATTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (39 bp):
TTGCGTTACACTTTTAAGAATCGAGAACATGGTTTTACC
Found at i:3247934 original size:23 final size:23
Alignment explanation
Indices: 3247908--3247953 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3247898 CGAAGGACCG
3247908 CGTAGAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACTGAAGTGCCA
* *
3247931 CGTAGAATTGCACTGTAGTGCCA
1 CGTAGAAATGCACTGAAGTGCCA
3247954 TATAAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACTGAAGTGCCA
Found at i:3247962 original size:23 final size:23
Alignment explanation
Indices: 3247916--3247963 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3247906 CGCGTAGAAA
* *
3247916 TGCACTGAAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACATAAAAT
* *
3247939 TGCACTGTAGTGCCATATAAAAT
1 TGCACTGAAGTGCCACATAAAAT
3247962 TG
1 TG
3247964 TCCATAAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (23 bp):
TGCACTGAAGTGCCACATAAAAT
Found at i:3251446 original size:2 final size:2
Alignment explanation
Indices: 3251441--3251475 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3251431 AAAAGTAAGA
3251441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3251476 CTATGGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3254051 original size:2 final size:2
Alignment explanation
Indices: 3254044--3254076 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3254034 GTTCATTTCT
3254044 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3254077 GTTTCTGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3255386 original size:61 final size:61
Alignment explanation
Indices: 3255284--3255405 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
3255274 ACAAATGGTC
*
3255284 GTTTTTATCGAAATATAATTCTTACATTGTCAGCACATTTTCTTCTAATATTACTGATCTA
1 GTTTTTATCAAAATATAATTCTTACATTGTCAGCACATTTTCTTCTAATATTACTGATCTA
* * *
3255345 GTTTTTATCAAAATATCATT-TGTACATTGTCAGTACCTTTTCTTCTAATATTACTGATCTA
1 GTTTTTATCAAAATATAATTCT-TACATTGTCAGCACATTTTCTTCTAATATTACTGATCTA
3255406 ACACCATTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
60 1 0.02
61 55 0.98
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (61 bp):
GTTTTTATCAAAATATAATTCTTACATTGTCAGCACATTTTCTTCTAATATTACTGATCTA
Found at i:3256830 original size:32 final size:32
Alignment explanation
Indices: 3256793--3256883 Score: 123
Period size: 32 Copynumber: 2.9 Consensus size: 32
3256783 GAAGGACCTA
* *
3256793 TCCATATGTTTCAAAGAACATAGGTAACATTG
1 TCCATATGTCTCAAAGAACATAGGTAACACTG
*
3256825 TCCATATGTCTCGAAGAACATAGGTAA-ACTG
1 TCCATATGTCTCAAAGAACATAGGTAACACTG
*
3256856 TCCATATGTCTCGAAAG-ACATAAGTAAC
1 TCCATATGTCTC-AAAGAACATAGGTAAC
3256884 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
31 24 0.46
32 28 0.54
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (32 bp):
TCCATATGTCTCAAAGAACATAGGTAACACTG
Found at i:3256861 original size:31 final size:32
Alignment explanation
Indices: 3256793--3256883 Score: 123
Period size: 31 Copynumber: 2.9 Consensus size: 32
3256783 GAAGGACCTA
* * *
3256793 TCCATATGTTTCAAAGAACATAGGTAACATTG
1 TCCATATGTCTCGAAGAACATAGGTAACACTG
3256825 TCCATATGTCTCGAAGAACATAGGTAA-ACTG
1 TCCATATGTCTCGAAGAACATAGGTAACACTG
*
3256856 TCCATATGTCTCGAA-AGACATAAGTAAC
1 TCCATATGTCTCGAAGA-ACATAGGTAAC
3256884 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 27 0.51
32 25 0.47
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (32 bp):
TCCATATGTCTCGAAGAACATAGGTAACACTG
Found at i:3261063 original size:18 final size:18
Alignment explanation
Indices: 3261042--3261077 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3261032 ATTCGAATTA
3261042 TTTTTA-TTATTTAGTTG
1 TTTTTATTTATTTAGTTG
*
3261059 TTTTTATTTTTTTAGTTG
1 TTTTTATTTATTTAGTTG
3261077 T
1 T
3261078 ATCGTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (18 bp):
TTTTTATTTATTTAGTTG
Found at i:3263940 original size:23 final size:23
Alignment explanation
Indices: 3263910--3263962 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
3263900 ATTGCAGGAA
3263910 AATCTTCTAGTACTTCCAACATG
1 AATCTTCTAGTACTTCCAACATG
3263933 AATCTTCTAGTACTTCCAACATG
1 AATCTTCTAGTACTTCCAACATG
3263956 AATCTTC
1 AATCTTC
3263963 CTTGAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (23 bp):
AATCTTCTAGTACTTCCAACATG
Found at i:3269162 original size:17 final size:17
Alignment explanation
Indices: 3269140--3269173 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3269130 AGACTTGTAA
*
3269140 GAAAAACTTGTCACGGT
1 GAAAAACTTCTCACGGT
*
3269157 GAAAAATTTCTCACGGT
1 GAAAAACTTCTCACGGT
3269174 CATCACCATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (17 bp):
GAAAAACTTCTCACGGT
Found at i:3270358 original size:20 final size:21
Alignment explanation
Indices: 3270333--3270376 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
3270323 GGCGAGAGTG
3270333 GGTCTGTT-TGTACAAGACAT
1 GGTCTGTTATGTACAAGACAT
3270353 GGTCTGTTGATGTACAAGACAT
1 GGTCTGTT-ATGTACAAGACAT
3270375 GG
1 GG
3270377 AGCAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.32
Consensus pattern (21 bp):
GGTCTGTTATGTACAAGACAT
Found at i:3271640 original size:17 final size:17
Alignment explanation
Indices: 3271606--3271659 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
3271596 ACCGGACAAA
* *
3271606 TTTATTATTTTAGAGAG
1 TTTATTAATTTAAAGAG
**
3271623 TTTATTAATTTACCGAG
1 TTTATTAATTTAAAGAG
3271640 --TATTAATTTAAAGAG
1 TTTATTAATTTAAAGAG
3271655 TTTAT
1 TTTAT
3271660 ACTGTACAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTAAAGAG
Found at i:3273795 original size:33 final size:33
Alignment explanation
Indices: 3273750--3273816 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
3273740 AGTTACATGT
3273750 ATATTTGAAAGTGATTTAAAAAATATGTGATTTA
1 ATATTTGAAAGTGATTTAAAAAA-ATGTGATTTA
*
3273784 ATATTT-AAAGTGATTTGAAAAAATGTGATTTA
1 ATATTTGAAAGTGATTTAAAAAAATGTGATTTA
3273816 A
1 A
3273817 AATAGAGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 11 0.34
33 15 0.47
34 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (33 bp):
ATATTTGAAAGTGATTTAAAAAAATGTGATTTA
Found at i:3280021 original size:38 final size:38
Alignment explanation
Indices: 3279969--3280054 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 38
3279959 GAGTCGATCA
* * * *
3279969 CGAGTTCGAGTCTAATATCTACCGGCCTTTGACTGAGT
1 CGAGTTCGAATCTAATATCCACCGACCTTTGACCGAGT
* *
3280007 CGAGTTCGAATCTAATTTCCATCGACCTTTGACCGAGT
1 CGAGTTCGAATCTAATATCCACCGACCTTTGACCGAGT
*
3280045 CTAGTTCGAA
1 CGAGTTCGAA
3280055 CTGCTCAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (38 bp):
CGAGTTCGAATCTAATATCCACCGACCTTTGACCGAGT
Found at i:3284616 original size:18 final size:18
Alignment explanation
Indices: 3284593--3284627 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3284583 CTAGGAGATT
3284593 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
3284611 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
3284628 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:3284713 original size:21 final size:22
Alignment explanation
Indices: 3284684--3284727 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3284674 GTTGTATGAT
3284684 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
3284705 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
3284727 A
1 A
3284728 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Done.