Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 43
Found at i:2845437 original size:18 final size:18
Alignment explanation
Indices: 2845414--2845448 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2845404 TCTCTGCGCT
2845414 TATTTTTCAAAATCAAAA
1 TATTTTTCAAAATCAAAA
2845432 TATTTTTCAAAATCAAA
1 TATTTTTCAAAATCAAA
2845449 GATTGACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TATTTTTCAAAATCAAAA
Found at i:2845906 original size:18 final size:18
Alignment explanation
Indices: 2845865--2845902 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2845855 TTATTTTTAC
*
2845865 TTTAATTGCTTTTACTTA
1 TTTAATCGCTTTTACTTA
2845883 TTTAATCGCTTTTA-TTA
1 TTTAATCGCTTTTACTTA
2845900 TTT
1 TTT
2845903 TAATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTAATCGCTTTTACTTA
Found at i:2848853 original size:11 final size:11
Alignment explanation
Indices: 2848837--2848862 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2848827 ATCGAGCATG
2848837 TTTTATTTTTA
1 TTTTATTTTTA
2848848 TTTTATTTTTA
1 TTTTATTTTTA
2848859 TTTT
1 TTTT
2848863 GCAGGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:2851510 original size:18 final size:18
Alignment explanation
Indices: 2851469--2851506 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2851459 TTATTTTTAC
*
2851469 TTTAATTGCTTTTACTTA
1 TTTAATCGCTTTTACTTA
2851487 TTTAATCGCTTTTA-TTA
1 TTTAATCGCTTTTACTTA
2851504 TTT
1 TTT
2851507 TAATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTAATCGCTTTTACTTA
Found at i:2856245 original size:23 final size:23
Alignment explanation
Indices: 2856218--2856271 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2856208 GACTAGACAT
2856218 AAAAACATATCATAAAGGCAGAA
1 AAAAACATATCATAAAGGCAGAA
* * * * *
2856241 AAAAACTTGTCATGAAGGTAGAG
1 AAAAACATATCATAAAGGCAGAA
2856264 AAAAACAT
1 AAAAACAT
2856272 GTAATAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (23 bp):
AAAAACATATCATAAAGGCAGAA
Found at i:2856442 original size:3 final size:3
Alignment explanation
Indices: 2856436--2856534 Score: 74
Period size: 3 Copynumber: 31.3 Consensus size: 3
2856426 TTAGAAAAAC
* *
2856436 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT GGACTCT AGTT ATG ATAA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT --A-T-T A-TT ATT AT-T
** * * *
2856483 AAC ATT ATT ATT ATT TTT ATT ATT ATT ATT ATT ATA ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2856531 ATT A
1 ATT A
2856535 ACTGCGTGCC
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
2 2 0.03
3 70 0.89
4 3 0.04
5 2 0.03
6 1 0.01
7 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2857082 original size:18 final size:18
Alignment explanation
Indices: 2857040--2857084 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
2857030 ATTGATTTGA
* *
2857040 AAAATTTTATTTGGGTTT
1 AAAATATTAATTGGGTTT
2857058 -AAA-ATTAATTGGGTTT
1 AAAATATTAATTGGGTTT
2857074 AAAATATTAAT
1 AAAATATTAAT
2857085 GGATTTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.48
17 6 0.26
18 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (18 bp):
AAAATATTAATTGGGTTT
Found at i:2857167 original size:14 final size:14
Alignment explanation
Indices: 2857148--2857190 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
2857138 TGAGCTGAAT
*
2857148 ATAAATGAACGA-AC
1 ATAAATGAAC-ATAA
2857162 ATAAATGAACATAA
1 ATAAATGAACATAA
2857176 ATAAATGAACATAA
1 ATAAATGAACATAA
2857190 A
1 A
2857191 CGAACGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 1 0.04
14 26 0.96
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.19
Consensus pattern (14 bp):
ATAAATGAACATAA
Found at i:2857175 original size:24 final size:24
Alignment explanation
Indices: 2857143--2857195 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2857133 GAGATTGAGC
* *
2857143 TGAATATAAATGAACGAACATAAA
1 TGAACATAAATAAACGAACATAAA
*
2857167 TGAACATAAATAAATGAACATAAA
1 TGAACATAAATAAACGAACATAAA
*
2857191 CGAAC
1 TGAAC
2857196 GAATTATCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (24 bp):
TGAACATAAATAAACGAACATAAA
Found at i:2857283 original size:40 final size:41
Alignment explanation
Indices: 2857238--2857316 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2857228 GAACGGACAT
* *
2857238 TTGTTCGTATTCGTTCATTTGAT-TAAACGAACATAAAATA
1 TTGTTCATATTCGTTCATTTAATATAAACGAACATAAAATA
* *
2857278 TTGTTCATGTTCGTTCGTTTAATAAATAAACGAACATAA
1 TTGTTCATATTCGTTCATTTAAT--ATAAACGAACATAA
2857317 CAAACTTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 19 0.59
43 13 0.41
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (41 bp):
TTGTTCATATTCGTTCATTTAATATAAACGAACATAAAATA
Found at i:2858302 original size:21 final size:19
Alignment explanation
Indices: 2858271--2858311 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2858261 ATACTACTAG
2858271 TCGTCTTAAGTATCAATAC
1 TCGTCTTAAGTATCAATAC
*
2858290 TCGTGCTTGAAGTATCGATAC
1 TCGT-CTT-AAGTATCAATAC
2858311 T
1 T
2858312 AACTGCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (19 bp):
TCGTCTTAAGTATCAATAC
Found at i:2858485 original size:17 final size:17
Alignment explanation
Indices: 2858463--2858502 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2858453 ATATTGGTAG
2858463 CGGTACTGACAGAGTAT
1 CGGTACTGACAGAGTAT
2858480 CGGTACTGACAGAGTAT
1 CGGTACTGACAGAGTAT
*
2858497 CAGTAC
1 CGGTAC
2858503 CAAATAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (17 bp):
CGGTACTGACAGAGTAT
Found at i:2860264 original size:18 final size:16
Alignment explanation
Indices: 2860231--2860266 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
2860221 AGATATGGAA
2860231 AAGAATGAAGAACAAG
1 AAGAATGAAGAACAAG
2860247 AAGAAGTGAAGAAACAAG
1 AAGAA-TGAAG-AACAAG
2860265 AA
1 AA
2860267 AAGAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.64, C:0.06, G:0.25, T:0.06
Consensus pattern (16 bp):
AAGAATGAAGAACAAG
Found at i:2862132 original size:21 final size:20
Alignment explanation
Indices: 2862068--2862134 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
2862058 TTTGACCAAA
2862068 AGTTTCGAAACTTCTAAAAG
1 AGTTTCGAAACTTCTAAAAG
2862088 AGTTTCGAAACTTCTAAAAG
1 AGTTTCGAAACTTCTAAAAG
* * *
2862108 AGTTTTGAAACTTTCCAAAAC
1 AGTTTCGAAAC-TTCTAAAAG
2862129 AGTTTC
1 AGTTTC
2862135 CCAAAAAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 30 0.71
21 12 0.29
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (20 bp):
AGTTTCGAAACTTCTAAAAG
Found at i:2862180 original size:20 final size:19
Alignment explanation
Indices: 2862141--2862192 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
2862131 TTTCCCAAAA
* *
2862141 AGTTTCAATACTTTTCAAG
1 AGTTTCAAAACTTCTCAAG
2862160 AGTTTCAAAACTATCTCAAG
1 AGTTTCAAAACT-TCTCAAG
*
2862180 AGTTTCGAAACTT
1 AGTTTCAAAACTT
2862193 TCCTTAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (19 bp):
AGTTTCAAAACTTCTCAAG
Found at i:2863152 original size:39 final size:38
Alignment explanation
Indices: 2863103--2863177 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 38
2863093 CAATATTTAA
*
2863103 GATATTTGAAGGATGATAAGGTAAGGTTAATAATGTTG
1 GATATTTGAAGGATGATAAAGTAAGGTTAATAATGTTG
2863141 GATATTTTGAAGGATGATAAAGTAAGGTTAATAATGT
1 GATA-TTTGAAGGATGATAAAGTAAGGTTAATAATGT
2863178 CATTTCCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 4 0.11
39 31 0.89
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.35
Consensus pattern (38 bp):
GATATTTGAAGGATGATAAAGTAAGGTTAATAATGTTG
Found at i:2865115 original size:27 final size:27
Alignment explanation
Indices: 2865058--2865115 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
2865048 CTGTATATTC
* * * *
2865058 TATATGGCACTAAATGTGCAAATTGTT
1 TATATGACACTAAATGTGCAAAATATG
* *
2865085 TATATGACACTCAATGTGTAAAATATG
1 TATATGACACTAAATGTGCAAAATATG
2865112 TATA
1 TATA
2865116 CTCGTATATG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (27 bp):
TATATGACACTAAATGTGCAAAATATG
Found at i:2866283 original size:43 final size:43
Alignment explanation
Indices: 2866222--2866307 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
2866212 TTTCTCCCCT
2866222 TTTTTGTTAAATCAAAAAGTTAAAAAGTAATCAAGATATATAA
1 TTTTTGTTAAATCAAAAAGTTAAAAAGTAATCAAGATATATAA
2866265 TTTTTGTTAAATCAAAAAGTTAAAAAGTAATCAAGATATATAA
1 TTTTTGTTAAATCAAAAAGTTAAAAAGTAATCAAGATATATAA
2866308 ATATAATACG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (43 bp):
TTTTTGTTAAATCAAAAAGTTAAAAAGTAATCAAGATATATAA
Found at i:2866575 original size:14 final size:15
Alignment explanation
Indices: 2866547--2866575 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2866537 AAAGCATGTG
2866547 AAATATCCTAAAATA
1 AAATATCCTAAAATA
2866562 AAATATCC-AAAATA
1 AAATATCCTAAAATA
2866576 TCTAAATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATATCCTAAAATA
Found at i:2869279 original size:34 final size:35
Alignment explanation
Indices: 2869221--2869307 Score: 122
Period size: 34 Copynumber: 2.5 Consensus size: 35
2869211 ATTGCCCAGA
*
2869221 GGGAACAGATTCCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATT-CCCCCTAGGGGGTATCGATTCCCC
*
2869257 TGGAACAGATTCCCCCTA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
* *
2869291 GGGTACAGATCCCCCCT
1 GGGAACAGATTCCCCCT
2869308 GCATGGTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 30 0.65
35 6 0.13
36 10 0.22
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
Found at i:2869521 original size:21 final size:21
Alignment explanation
Indices: 2869488--2869527 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2869478 TTTTTGCAGA
*
2869488 AAAATCATTCCCAGACGGCTCC
1 AAAATCATCCCCA-ACGGCTCC
2869510 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2869528 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2872170 original size:20 final size:21
Alignment explanation
Indices: 2872133--2872173 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2872123 ATTTGAATAT
*
2872133 TATGAAGGGGTATAGATTCCC
1 TATGAAGGGGTACAGATTCCC
*
2872154 TATGAA-GGGTACCGATTCCC
1 TATGAAGGGGTACAGATTCCC
2872174 CCCCATTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACAGATTCCC
Found at i:2872236 original size:21 final size:21
Alignment explanation
Indices: 2872203--2872242 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2872193 TTTTTACAGA
*
2872203 AAAATCATTCCCAGACGGCTCC
1 AAAATCATCCCCA-ACGGCTCC
2872225 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2872243 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2874974 original size:23 final size:23
Alignment explanation
Indices: 2874948--2875074 Score: 168
Period size: 23 Copynumber: 5.6 Consensus size: 23
2874938 GGTTCTACAC
*
2874948 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGAGACAATTCTACGT
* *
2874971 GGTCCTTCGAGACATTTCTACGC
1 GGTCCTTCGAGACAATTCTACGT
*
2874994 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGAGACAATTCTACGT
* *
2875017 GGTCCTTCGAGACATTTCTACGC
1 GGTCCTTCGAGACAATTCTACGT
* *
2875040 GGTCCTTCGGGAC-A-TCTATGT
1 GGTCCTTCGAGACAATTCTACGT
2875061 GGTCCTTCGAGACA
1 GGTCCTTCGAGACA
2875075 TTTTATGTGG
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
21 17 0.19
23 72 0.81
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (23 bp):
GGTCCTTCGAGACAATTCTACGT
Found at i:2875007 original size:46 final size:46
Alignment explanation
Indices: 2874940--2875077 Score: 244
Period size: 46 Copynumber: 3.0 Consensus size: 46
2874930 GAGTCAAGGG
*
2874940 TTCTACACGGTCCTTCGGGACAATTCTACGTGGTCCTTCGAGACAT
1 TTCTACGCGGTCCTTCGGGACAATTCTACGTGGTCCTTCGAGACAT
2874986 TTCTACGCGGTCCTTCGGGACAATTCTACGTGGTCCTTCGAGACAT
1 TTCTACGCGGTCCTTCGGGACAATTCTACGTGGTCCTTCGAGACAT
*
2875032 TTCTACGCGGTCCTTCGGGAC-A-TCTATGTGGTCCTTCGAGACAT
1 TTCTACGCGGTCCTTCGGGACAATTCTACGTGGTCCTTCGAGACAT
2875076 TT
1 TT
2875078 TATGTGGCAC
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
44 23 0.26
45 1 0.01
46 66 0.73
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGGGACAATTCTACGTGGTCCTTCGAGACAT
Found at i:2888706 original size:31 final size:30
Alignment explanation
Indices: 2888671--2888758 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
2888661 ATTCAAGAGG
* *
2888671 TCAAATTAATATTTTATCTAAAGTTTAGTGA-
1 TCAAAATAATATTTTATCTAAAGTTCA-T-AC
* *
2888702 TCAAAATGATATTTCATCTAAAGTTCATAC
1 TCAAAATAATATTTTATCTAAAGTTCATAC
**
2888732 TCAAAATAATATGGTATCTAAAGTTCA
1 TCAAAATAATATTTTATCTAAAGTTCA
2888759 AGGGACATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 1 0.02
30 24 0.50
31 23 0.48
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (30 bp):
TCAAAATAATATTTTATCTAAAGTTCATAC
Found at i:2889865 original size:2 final size:2
Alignment explanation
Indices: 2889858--2889904 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2889848 CAAATGTTTA
2889858 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
2889900 AT AT A
1 AT AT A
2889905 AACATTTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2889998 original size:21 final size:21
Alignment explanation
Indices: 2889972--2890018 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2889962 ATTTTAGAAA
* *
2889972 TTTTA-TTTAAAATATATAATT
1 TTTTATTTTAAAAAAAAT-ATT
2889993 TTTTATTTTAAAAAAAATATT
1 TTTTATTTTAAAAAAAATATT
2890014 TTTTA
1 TTTTA
2890019 AATCTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTTTAAAAAAAATATT
Found at i:2901062 original size:15 final size:15
Alignment explanation
Indices: 2901042--2901070 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2901032 TTCGGACTAA
2901042 TTTCAGGCGATTAGT
1 TTTCAGGCGATTAGT
2901057 TTTCAGGCGATTAG
1 TTTCAGGCGATTAG
2901071 CACTGATCGC
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:0.21, C:0.14, G:0.28, T:0.38
Consensus pattern (15 bp):
TTTCAGGCGATTAGT
Found at i:2914363 original size:4 final size:4
Alignment explanation
Indices: 2914354--2914378 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2914344 TAATGATTAC
2914354 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
2914379 ATAGTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:2914655 original size:30 final size:30
Alignment explanation
Indices: 2914621--2914683 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
2914611 GGTTCTTCGG
2914621 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTATGGATAGTTACCGAGGATCTTTAT
*
2914651 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTATGGATAGTTACCGAGGATCTTTAT
2914681 GAC
1 GAC
2914684 ATCTGATAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTATGGATAGTTACCGAGGATCTTTAT
Found at i:2918168 original size:64 final size:63
Alignment explanation
Indices: 2918064--2918182 Score: 143
Period size: 64 Copynumber: 1.9 Consensus size: 63
2918054 TTGTTTAAGG
* **
2918064 TGCATCGATGCACAGGAAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATGTCATCGA
1 TGCATCGATGCAAAGGAAGTGCATCGATGCACCAATTTAAAAA-AAAACATCGAATGTCATCGA
* * *
2918128 TGCATCGATGCATAAGG-AGTGCATCGATGCACCCCA-TTAAATACAAACATCGAAT
1 TGCATCGATGCA-AAGGAAGTGCATCGATGCA-CCAATTTAAAAAAAAACATCGAAT
2918183 AAGATTTATG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
63 11 0.23
64 32 0.68
65 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (63 bp):
TGCATCGATGCAAAGGAAGTGCATCGATGCACCAATTTAAAAAAAAACATCGAATGTCATCGA
Found at i:2919328 original size:31 final size:30
Alignment explanation
Indices: 2919278--2919353 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
2919268 TGTCTTTCGA
* * * *
2919278 GACATATGGACAATATACCTATGTTCTAAG
1 GACATATGGATAGTTTACCTAGGTTCTAAG
**
2919308 GAACATATGGATAGTTTACCTAGGTTCTTCG
1 G-ACATATGGATAGTTTACCTAGGTTCTAAG
*
2919339 GACCTATGGATAGTT
1 GACATATGGATAGTT
2919354 ACGAGGATCT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 14 0.37
31 24 0.63
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (30 bp):
GACATATGGATAGTTTACCTAGGTTCTAAG
Found at i:2919372 original size:29 final size:30
Alignment explanation
Indices: 2919339--2919410 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
2919329 AGGTTCTTCG
*
2919339 GACCTATGGATAGTTA-CGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
2919368 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2919398 GACCTCTGGATAG
1 GACCTCTGGATAG
2919411 GTCCTTCGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:2923962 original size:13 final size:13
Alignment explanation
Indices: 2923944--2923970 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2923934 GATTTTTCAA
2923944 ACACCATGCAAGC
1 ACACCATGCAAGC
2923957 ACACCATGCAAGC
1 ACACCATGCAAGC
2923970 A
1 A
2923971 GAAATACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.37, G:0.15, T:0.07
Consensus pattern (13 bp):
ACACCATGCAAGC
Found at i:2924320 original size:6 final size:6
Alignment explanation
Indices: 2924309--2924360 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
2924299 TTAATCTCGC
2924309 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA
2924357 ATGG
1 ATGG
2924361 GCATGACGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.17
Consensus pattern (6 bp):
ATGGAA
Found at i:2930753 original size:186 final size:185
Alignment explanation
Indices: 2930430--2930807 Score: 605
Period size: 186 Copynumber: 2.0 Consensus size: 185
2930420 ATAAAATTTT
* * * *
2930430 AAATTTTAAATATATTTTATATAACATATGGGCTCAACCCAAACCATTTAAAACATAATTAATAA
1 AAATATTAAATATAATATATATAACATATGGGCTCAACCCAAACCATTTAAAACACAATTAATAA
* *
2930495 TTTAAGGTCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAGTTTATATAAAATTT
66 ATTAAGGTCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
* * *
2930560 TTATTTTATAATTATATATTATTTAAATTAATTGTAAATTGTTT-TTCTGAATTAAA
131 ATATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTATT-T-AATTAAA
* * *
2930616 AAATATTAAATATAATATATATAACATATGGGCTCAGCCCAAACTATTTAAAACCCAATTAATAA
1 AAATATTAAATATAATATATATAACATATGGGCTCAACCCAAACCATTTAAAACACAATTAATAA
*
2930681 ATTAAGTTCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 ATTAAGGTCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
2930746 ATATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTATTTAATTATA
131 ATATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTATTTAATTAAA
2930801 AAATATT
1 AAATATT
2930808 TAATTTTTAT
Statistics
Matches: 177, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
185 13 0.07
186 162 0.92
187 2 0.01
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (185 bp):
AAATATTAAATATAATATATATAACATATGGGCTCAACCCAAACCATTTAAAACACAATTAATAA
ATTAAGGTCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
ATATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTATTTAATTAAA
Found at i:2930809 original size:19 final size:19
Alignment explanation
Indices: 2930754--2930812 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2930744 TTATATTTTA
* *
2930754 TAATTATATATTATTTAAAT
1 TAATTATAAAATATTT-AAT
* * *
2930774 TAATTATAAACTGTTTATT
1 TAATTATAAAATATTTAAT
2930793 TAATTATAAAATATTTAAT
1 TAATTATAAAATATTTAAT
2930812 T
1 T
2930813 TTTATGTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATTATAAAATATTTAAT
Found at i:2932465 original size:19 final size:19
Alignment explanation
Indices: 2932441--2932494 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
2932431 TTTGGTATAA
2932441 GGGATCGATCATTTGCTAG
1 GGGATCGATCATTTGCTAG
*
2932460 GGGATCGAACATTTTGCTAG
1 GGGATCGATCA-TTTGCTAG
*
2932480 GGGATCGATCCTTTG
1 GGGATCGATCATTTG
2932495 AGCCAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.31
Consensus pattern (19 bp):
GGGATCGATCATTTGCTAG
Found at i:2933075 original size:20 final size:20
Alignment explanation
Indices: 2933039--2933079 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2933029 AAGTAATAAC
2933039 AAAAATTCAAATAACCAAAT
1 AAAAATTCAAATAACCAAAT
*
2933059 AAAACATTCAAGT-ACCAAAT
1 AAAA-ATTCAAATAACCAAAT
2933079 A
1 A
2933080 CCAAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.61, C:0.17, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAATTCAAATAACCAAAT
Found at i:2933131 original size:18 final size:18
Alignment explanation
Indices: 2933110--2933152 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2933100 CAAATAACAT
*
2933110 AAATGTAGCAAAATCTAA
1 AAATGCAGCAAAATCTAA
*
2933128 AAATGCATCAAAATCTAA
1 AAATGCAGCAAAATCTAA
2933146 AAATGCA
1 AAATGCA
2933153 ATAACAACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATGCAGCAAAATCTAA
Found at i:2936938 original size:29 final size:28
Alignment explanation
Indices: 2936869--2936966 Score: 106
Period size: 29 Copynumber: 3.4 Consensus size: 28
2936859 TTTAAGTATT
*
2936869 TAAAATATTTTTTAATCAAAATAAGTAC
1 TAAAATATTTTTTAGTCAAAATAAGTAC
* * *
2936897 AAAAATTACTTTTTTGGTCAAAATGAGTAC
1 TAAAA-TA-TTTTTTAGTCAAAATAAGTAC
* *
2936927 GTAAAATATTTTTTTGTTAAAATAAGTAC
1 -TAAAATATTTTTTAGTCAAAATAAGTAC
2936956 ATAAAATATTT
1 -TAAAATATTT
2936967 AATTTTTTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.07
29 30 0.52
30 20 0.34
31 4 0.07
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (28 bp):
TAAAATATTTTTTAGTCAAAATAAGTAC
Found at i:2942356 original size:35 final size:35
Alignment explanation
Indices: 2942317--2942389 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
2942307 AATAGATTTA
2942317 ATTAAAACTATCAAATCATTAGAAAGATAAAAAAT
1 ATTAAAACTATCAAATCATTAGAAAGATAAAAAAT
*
2942352 ATTAAAACTATCAAATCATTAGAAAGATAAAGAAT
1 ATTAAAACTATCAAATCATTAGAAAGATAAAAAAT
2942387 ATT
1 ATT
2942390 CGATTATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.27
Consensus pattern (35 bp):
ATTAAAACTATCAAATCATTAGAAAGATAAAAAAT
Found at i:2944981 original size:26 final size:27
Alignment explanation
Indices: 2944944--2945000 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
2944934 TCAGGCCTAC
**
2944944 ATAA-AATAATATAATTTGTATTAATA
1 ATAATAATAATATAATTAATATTAATA
*
2944970 ATAATAAT-ATATAATTAATATTTATA
1 ATAATAATAATATAATTAATATTAATA
2944996 ATAAT
1 ATAAT
2945001 TTTTAAGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATAATAATAATATAATTAATATTAATA
Found at i:2947355 original size:19 final size:20
Alignment explanation
Indices: 2947331--2947374 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2947321 CATCTTGAAG
2947331 TTTTC-TGAAATTCT-AATTT
1 TTTTCTTGAAATT-TGAATTT
2947350 TTTTCTTTGAAATTTGAATTT
1 TTTTC-TTGAAATTTGAATTT
2947371 TTTT
1 TTTT
2947375 ATTAATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
20 1 0.05
21 16 0.73
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.64
Consensus pattern (20 bp):
TTTTCTTGAAATTTGAATTT
Found at i:2948925 original size:29 final size:29
Alignment explanation
Indices: 2948855--2949088 Score: 182
Period size: 29 Copynumber: 8.1 Consensus size: 29
2948845 CAAACGGAAA
* *
2948855 CAGGACGGGAATATAATCCCATACAGAGT
1 CAGGACGGGGATATAATCCCATGCAGAGT
* * *
2948884 -AGGACGGTGATATAATCCCATGTAGAAT
1 CAGGACGGGGATATAATCCCATGCAGAGT
*
2948912 CAGGACGGGGATATAATCACATGCAGAGT
1 CAGGACGGGGATATAATCCCATGCAGAGT
* ** * * * *
2948941 CGGGACATGTATACAATACCATGTAGAGT
1 CAGGACGGGGATATAATCCCATGCAGAGT
** * *
2948970 CAATACTGAGATATAATCCCATGCAGAGT
1 CAGGACGGGGATATAATCCCATGCAGAGT
* * ** *
2948999 CAGGACAGGGATACAATTTCATGTAGAGT
1 CAGGACGGGGATATAATCCCATGCAGAGT
* * * * **
2949028 CAAGATGGAGATATAATCCTATATAGAGT
1 CAGGACGGGGATATAATCCCATGCAGAGT
* * *
2949057 CAGGAAGGGGATATAATCCCATACAGAAT
1 CAGGACGGGGATATAATCCCATGCAGAGT
2949086 CAG
1 CAG
2949089 AAATGCATCA
Statistics
Matches: 154, Mismatches: 50, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
28 23 0.15
29 131 0.85
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (29 bp):
CAGGACGGGGATATAATCCCATGCAGAGT
Found at i:2949069 original size:58 final size:58
Alignment explanation
Indices: 2948865--2949065 Score: 203
Period size: 58 Copynumber: 3.5 Consensus size: 58
2948855 CAGGACGGGA
* * * * * *
2948865 ATATAATCCCATACAGAGT-AGGAC-GGTGATATAATCCCATGTAGAATCAGGACGGGG
1 ATATAATCCCATACAGAGTCAGGACAGG-GATACAATACCATGTAGAGTCAAGACTGAG
* * * * * *
2948922 ATATAATCACATGCAGAGTCGGGACATGTATACAATACCATGTAGAGTCAATACTGAG
1 ATATAATCCCATACAGAGTCAGGACAGGGATACAATACCATGTAGAGTCAAGACTGAG
* **
2948980 ATATAATCCCATGCAGAGTCAGGACAGGGATACAATTTCATGTAGAGTCAAGA-TGGAG
1 ATATAATCCCATACAGAGTCAGGACAGGGATACAATACCATGTAGAGTCAAGACT-GAG
* *
2949038 ATATAATCCTATATAGAGTCAGGA-AGGG
1 ATATAATCCCATACAGAGTCAGGACAGGG
2949066 GATATAATCC
Statistics
Matches: 119, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
57 22 0.18
58 96 0.81
59 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (58 bp):
ATATAATCCCATACAGAGTCAGGACAGGGATACAATACCATGTAGAGTCAAGACTGAG
Found at i:2957066 original size:17 final size:17
Alignment explanation
Indices: 2957039--2957090 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2957029 ATAAAATTAT
2957039 ACTAGTAAATATATAATA
1 ACTA-TAAATATATAATA
2957057 ACTATAAATAT-TAATA
1 ACTATAAATATATAATA
**
2957073 TGTAATAAATA-ATAATA
1 ACT-ATAAATATATAATA
2957090 A
1 A
2957091 TGATATCAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 6 0.21
17 19 0.66
18 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (17 bp):
ACTATAAATATATAATA
Found at i:2957096 original size:23 final size:22
Alignment explanation
Indices: 2957070--2957141 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 22
2957060 ATAAATATTA
*
2957070 ATATGTAATAAATAATAATAAT
1 ATATGTAATATATAATAATAAT
*
2957092 GATATCAGTAAATATATAACAATAAT
1 -ATAT--GT-AATATATAATAATAAT
**
2957118 ATAAACTAATATATAATAATAAT
1 AT-ATGTAATATATAATAATAAT
2957141 A
1 A
2957142 AATCTATTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
23 20 0.50
24 1 0.03
25 4 0.10
26 15 0.38
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
ATATGTAATATATAATAATAAT
Found at i:2957105 original size:26 final size:24
Alignment explanation
Indices: 2957076--2957142 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 24
2957066 ATTAATATGT
* *
2957076 AATAAATAATAATAATGATATCAGTA
1 AATAAATAATAATAAT-ATA-AACTA
* *
2957102 AATATATAACAATAATATAAACTA
1 AATAAATAATAATAATATAAACTA
2957126 ATATATAATAATAATAA
1 A-ATA-AATAATAATAA
2957143 ATCTATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 4 0.12
25 6 0.18
26 23 0.70
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (24 bp):
AATAAATAATAATAATATAAACTA
Found at i:2957220 original size:3 final size:3
Alignment explanation
Indices: 2957075--2957211 Score: 50
Period size: 3 Copynumber: 43.7 Consensus size: 3
2957065 TATTAATATG
* * *
2957075 TAA TAAA TAA TAA TAA TGA T-A TCAG TAAA TATA TAA CAA TAA T-A TAA
1 TAA T-AA TAA TAA TAA TAA TAA T-AA T-AA TA-A TAA TAA TAA TAA TAA
* * * *
2957122 -AC TAA TATA TAA TAA TAA TAAA TCTA TTA GAA TAA CT-A TAA TATA
1 TAA TAA TA-A TAA TAA TAA T-AA T-AA TAA TAA TAA -TAA TAA TA-A
* * *
2957167 TAA -AA TAA TTA TGA TAA TAA TAT TAAA TAA TAA TAA GTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA TA
2957212 GGATAATAAC
Statistics
Matches: 102, Mismatches: 18, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
2 8 0.08
3 68 0.67
4 26 0.25
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2962700 original size:31 final size:31
Alignment explanation
Indices: 2962662--2962725 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2962652 AAAATTTAAG
2962662 ATTGTGACATGTCACTTAACGAGGTTTTATA
1 ATTGTGACATGTCACTTAACGAGGTTTTATA
2962693 ATTGTGACATGTCACTTAACGAGGTTTTATA
1 ATTGTGACATGTCACTTAACGAGGTTTTATA
2962724 AT
1 AT
2962726 GGCGGTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (31 bp):
ATTGTGACATGTCACTTAACGAGGTTTTATA
Found at i:2965085 original size:19 final size:18
Alignment explanation
Indices: 2965035--2965087 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
2965025 TTCTTCCCTT
*
2965035 TTTTTTCTTTTTTGTT-A
1 TTTTTTCTATTTTGTTCA
*
2965052 TTTTTT-TAATCTTGTTCA
1 TTTTTTCT-ATTTTGTTCA
2965070 TTTTTCTCTATTTTGTTC
1 TTTTT-TCTATTTTGTTC
2965088 CAATCCTCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 12 0.41
18 6 0.21
19 9 0.31
20 1 0.03
ACGTcount: A:0.09, C:0.11, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTTTCTATTTTGTTCA
Found at i:2965657 original size:3 final size:3
Alignment explanation
Indices: 2965649--2965746 Score: 196
Period size: 3 Copynumber: 32.7 Consensus size: 3
2965639 CAAAATGTAA
2965649 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2965697 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2965745 AA
1 AA
2965747 AGGGTCTTCG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2966320 original size:134 final size:130
Alignment explanation
Indices: 2965974--2966355 Score: 440
Period size: 131 Copynumber: 2.9 Consensus size: 130
2965964 ACTTGTTATG
* * *
2965974 CTTTTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTTATTCCACTGGTCTTCATGGAAGATT
1 CTTTTTCTTGAGGGAAAATCAGATCT-GGGATGTTGATTTATTCCACTGTTCTTCAGGGAAGATT
* * * * ** *
2966039 GAATCGAGGTTGACTTGTTCTAATGTTACTAAGATAATATCAAATCTTGAAAGAGAGGGTTCTCT
65 GAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGTTCTCC
2966104 T
130 T
** * * * *
2966105 CTACTACTTGAGGGAGAATCAGATCTGGAAATGTTGATTTTTTCCACTGTTCTTCAGGGAAGATT
1 CTTTTTCTTGAGGGAAAATCAGATCTGG-GATGTTGATTTATTCCACTGTTCTTCAGGGAAGATT
* * * * *
2966170 GAATCAAGGCAGACTTGTTCCGCTGTTACTCAGGGAACATCAAATCTTGAAAGAGAGGGATATGT
65 GAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGG-T-T-C
2966235 TCCT
127 TCCT
* * * * * *
2966239 CTTTTTCTTGAGGGAAAATCGGATATAGGGATGCTGATTCATTCCACTATTCTTTAGGGAAGATT
1 CTTTTTCTTGAGGGAAAATCAGATCT-GGGATGTTGATTTATTCCACTGTTCTTCAGGGAAGATT
* * *
2966304 AAATCGAGGTAAACTTGTTCCACTGTTACTCAGGGAATATCAAATTTTGAAA
65 GAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAA
2966356 AGATCTGGAA
Statistics
Matches: 206, Mismatches: 40, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
130 2 0.01
131 102 0.50
132 1 0.00
133 1 0.00
134 98 0.48
135 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (130 bp):
CTTTTTCTTGAGGGAAAATCAGATCTGGGATGTTGATTTATTCCACTGTTCTTCAGGGAAGATTG
AATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGTTCTCCT
Found at i:2966530 original size:230 final size:231
Alignment explanation
Indices: 2966125--2966541 Score: 525
Period size: 230 Copynumber: 1.8 Consensus size: 231
2966115 AGGGAGAATC
** ** * *
2966125 AGATCTGGAAATGTTGATTTTTTCCACTGTTCTTCAGGGAAGATTGAATCAAGGCAGACTTGTTC
1 AGATCTGGAAACATTGATTAATTCCACTATTCTTCAAGGAAGATTGAATCAAGGCAGACTTGTTC
* * * * * * * *
2966190 CGCTGTTACTCAGGGAACATCAAATCTTGAAAGAGAGGGATATGTTCCTCTTTTTCTTGAGGGAA
66 CACTGTTACTCAGGGAACATCAAATATCGAAAGAAAGGGATATGTTCCGCTTCTTCCTAAGGGAA
* *
2966255 AATCGGATATAGGGATGCTGATTCATTCCACTATTCTTTAGGGAAGATTAAATCGAGGTAAACTT
131 AATCAGATATAGGGATGCTGATTCATTCCACTATTCTTCAGGGAAGATTAAATCGAGGTAAACTT
2966320 GTTCCACTGTTACTCAGGGAATATCAAATTTTGAAA
196 GTTCCACTGTTACTCAGGGAATATCAAATTTTGAAA
* * * *
2966356 AGATCTGGAAACATTGATTAATTCCACTATTCTTCAAGGAATATTGAATCGAGTTC-GATTTGTT
1 AGATCTGGAAACATTGATTAATTCCACTATTCTTCAAGGAAGATTGAATCAAG-GCAGACTTGTT
* * * *
2966420 CCACT-TTACTCAGGGAATATCAAATATCGAAATAAAGGGGTTTGTTCCGCTTCTTCCTAAGGGA
65 CCACTGTTACTCAGGGAACATCAAATATCGAAAGAAAGGGATATGTTCCGCTTCTTCCTAAGGGA
* * * * * *
2966484 AAATCATATATGGGGGTGTTGATTCATTCCACTGTTAC-TCAGGGAAGATTGAATCGAG
130 AAATCAGATATAGGGATGCTGATTCATTCCACTATT-CTTCAGGGAAGATTAAATCGAG
2966542 TTTGATTTGC
Statistics
Matches: 154, Mismatches: 30, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
230 96 0.62
231 57 0.37
232 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (231 bp):
AGATCTGGAAACATTGATTAATTCCACTATTCTTCAAGGAAGATTGAATCAAGGCAGACTTGTTC
CACTGTTACTCAGGGAACATCAAATATCGAAAGAAAGGGATATGTTCCGCTTCTTCCTAAGGGAA
AATCAGATATAGGGATGCTGATTCATTCCACTATTCTTCAGGGAAGATTAAATCGAGGTAAACTT
GTTCCACTGTTACTCAGGGAATATCAAATTTTGAAA
Found at i:2978487 original size:20 final size:20
Alignment explanation
Indices: 2978449--2978487 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2978439 ACGAAAAACA
*
2978449 AGTATCGATACTATCCCTAT
1 AGTATCGATACTATACCTAT
*
2978469 AGTATCGATACTTTACCTA
1 AGTATCGATACTATACCTA
2978488 CAAAAGCTAT
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:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTATACCTAT
Found at i:2980101 original size:72 final size:72
Alignment explanation
Indices: 2979984--2980129 Score: 238
Period size: 72 Copynumber: 2.0 Consensus size: 72
2979974 GTGTGCAATG
* * * * *
2979984 ATTCTATTTTTTAAATTTGGTGCTTTGATATAGTAGGTGTGGGTAAGGTGGTGTTGTGTTGTGCT
1 ATTCTATTTTATAAATTTGGTGCCTTGATAGAGTAGATGTGGGTAAGGTGGTGTTGTGTTATGCT
2980049 AATTGCC
66 AATTGCC
*
2980056 ATTCTATTTTATAAATTTGGTGCCTTGATAGAGTAGATGTGGGTAATGTGGTGTTGTGTTATGCT
1 ATTCTATTTTATAAATTTGGTGCCTTGATAGAGTAGATGTGGGTAAGGTGGTGTTGTGTTATGCT
2980121 AATTGCC
66 AATTGCC
2980128 AT
1 AT
2980130 ACGACTGTGC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.45
Consensus pattern (72 bp):
ATTCTATTTTATAAATTTGGTGCCTTGATAGAGTAGATGTGGGTAAGGTGGTGTTGTGTTATGCT
AATTGCC
Found at i:2980320 original size:2 final size:2
Alignment explanation
Indices: 2980313--2980340 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2980303 CCCCCTTTTC
2980313 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
2980341 CATAGACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2981415 original size:14 final size:14
Alignment explanation
Indices: 2981383--2981426 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2981373 ATTTTTTCAT
2981383 TTTAGG-TTTAGAG
1 TTTAGGATTTAGAG
* *
2981396 TCTAGGATTTGGAG
1 TTTAGGATTTAGAG
*
2981410 TTTAGGATTTAGGG
1 TTTAGGATTTAGAG
2981424 TTT
1 TTT
2981427 TACAATTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.45
Consensus pattern (14 bp):
TTTAGGATTTAGAG
Found at i:2982844 original size:7 final size:7
Alignment explanation
Indices: 2982834--2982865 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2982824 TAATTTCTCA
2982834 TTTCCTT
1 TTTCCTT
2982841 TTTCCTT
1 TTTCCTT
2982848 TTTCCTT
1 TTTCCTT
2982855 TTTCCTT
1 TTTCCTT
2982862 TTTC
1 TTTC
2982866 GTTTGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCCTT
Found at i:2984702 original size:32 final size:33
Alignment explanation
Indices: 2984661--2984730 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 33
2984651 TAAACCCATA
2984661 ATAGTTTAATTCT-ATTTCAATAGCTTGCCTTC
1 ATAGTTTAATTCTAATTTCAATAGCTTGCCTTC
2984693 ATAGTTTAATTCTAAAAATTTCAATAGCTTGCCTTC
1 ATAGTTTAATTCT---AATTTCAATAGCTTGCCTTC
2984729 AT
1 AT
2984731 CCCTCCATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 13 0.38
36 21 0.62
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (33 bp):
ATAGTTTAATTCTAATTTCAATAGCTTGCCTTC
Found at i:2987505 original size:29 final size:30
Alignment explanation
Indices: 2987473--2987538 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
2987463 TAATTTTAAG
* * *
2987473 AAAATATATTAAT-ATATATATATTTTCTT
1 AAAATATATAAATAAGATATATATTTACTT
*
2987502 AAAAT-TATAAATAAGATATTTATTTACTT
1 AAAATATATAAATAAGATATATATTTACTT
2987531 AGAAATAT
1 A-AAATAT
2987539 CAGAAAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 6 0.20
29 19 0.63
30 4 0.13
31 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
AAAATATATAAATAAGATATATATTTACTT
Found at i:2989717 original size:113 final size:112
Alignment explanation
Indices: 2989508--2989957 Score: 674
Period size: 113 Copynumber: 4.0 Consensus size: 112
2989498 GATAGAGTCG
* *
2989508 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTT-TATCTTTAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCT-TCTTCAGATGAGTTCTTCT
* * * * * *
2989571 TATTATGAACT-TCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCA
65 CATTATGAACTCTAC-CTGGCAATGCTGATCCATCAAGTGATGAATTCA
*
2989619 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCATTCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCT
*
2989684 CATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCG
65 CATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCA
*
2989732 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCATTCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCT
*
2989797 CATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCG
65 CATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCA
* *
2989845 AGCAAAAGGTTGAATAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCT
* * *
2989910 CATTATGAACTCTACCTGGC-ATGTTGATCCATTAAGTGATGGATTCA
65 CATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCA
2989957 A
1 A
2989958 ATCATTGCTA
Statistics
Matches: 317, Mismatches: 17, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
111 35 0.11
112 29 0.09
113 250 0.79
114 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCA
Found at i:2990363 original size:22 final size:22
Alignment explanation
Indices: 2990308--2990364 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2990298 AATAAAGCTT
*
2990308 TCATATTTGAAAAGAGAAACTA
1 TCATATTTGAAGAGAGAAACTA
2990330 TCATATTTGAAGAGA-AAATCTA
1 TCATATTTGAAGAGAGAAA-CTA
2990352 TCATATTTGAAGA
1 TCATATTTGAAGA
2990365 ATGTAGATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 3 0.09
22 30 0.91
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.32
Consensus pattern (22 bp):
TCATATTTGAAGAGAGAAACTA
Found at i:2990819 original size:54 final size:54
Alignment explanation
Indices: 2990730--2990863 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 54
2990720 ATAATCACTG
** * *
2990730 GTTCGTAAAACATGTGACAATACATTCATATTTTCTCGTGGCTTCTGCCCAGAT
1 GTTCGTAAAGTATTTGACAACACATTCATATTTTCTCGTGGCTTCTGCCCAGAT
* * * *
2990784 TTTCGTAAAGCT-TTTGATAACACATTCATCA-TTTCTTGTGGCTTCTGGCCAGAT
1 GTTCGTAAAG-TATTTGACAACACATTCAT-ATTTTCTCGTGGCTTCTGCCCAGAT
2990838 GTTCGTAAAGTATTTGACAACACATT
1 GTTCGTAAAGTATTTGACAACACATT
2990864 AATCCTTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 65 0.97
55 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAGTATTTGACAACACATTCATATTTTCTCGTGGCTTCTGCCCAGAT
Found at i:2990877 original size:54 final size:54
Alignment explanation
Indices: 2990730--2990885 Score: 163
Period size: 54 Copynumber: 2.9 Consensus size: 54
2990720 ATAATCACTG
* * * * * *
2990730 GTTCGTAAAACATGTGACAATACATTCAT-ATTTTCTCGTGGCTTCTGCCCAGAT
1 GTTCGTAAAGCTTTTGACAACACATTAATCA-TTTCTTGTGGCTTCTGCCCAGAT
* * * *
2990784 TTTCGTAAAGCTTTTGATAACACATTCATCATTTCTTGTGGCTTCTGGCCAGAT
1 GTTCGTAAAGCTTTTGACAACACATTAATCATTTCTTGTGGCTTCTGCCCAGAT
* * *
2990838 GTTCGTAAAG-TATTTGACAACACATTAATCCTTTTTTGTGGTTTCTGC
1 GTTCGTAAAGCT-TTTGACAACACATTAATCATTTCTTGTGGCTTCTGC
2990886 ACATATTTCT
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
53 1 0.01
54 83 0.98
55 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (54 bp):
GTTCGTAAAGCTTTTGACAACACATTAATCATTTCTTGTGGCTTCTGCCCAGAT
Found at i:2994916 original size:15 final size:16
Alignment explanation
Indices: 2994880--2994915 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2994870 CTTGATTCAA
2994880 TTTTTCCTTTTTTTCT
1 TTTTTCCTTTTTTTCT
*
2994896 TTTTTCTTTTTTTTCT
1 TTTTTCCTTTTTTTCT
2994912 TTTT
1 TTTT
2994916 CATTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTCCTTTTTTTCT
Found at i:2995245 original size:82 final size:86
Alignment explanation
Indices: 2995084--2995253 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 86
2995074 TTCATGAAGA
2995084 TTTGCCTTTGTAATTGACAATCTTTATTCCTGTGAGCAAATATCCTTCACCTTGCCTAGGGGTGT
1 TTTGCCTTTGTAATTGACAATCTTTATTCCTGTGAGCAAATATCCTTCACCTTGCCTAGGGGTGT
2995149 TCAAATAACCGAACTAATTCG
66 TCAAATAACCGAACTAATTCG
2995170 TTTGCCTTTGTAATTGACAAT-TTT-TTCCTGTGAGCAAA-ATCCTTCACCTTGCCTA-GGGTGT
1 TTTGCCTTTGTAATTGACAATCTTTATTCCTGTGAGCAAATATCCTTCACCTTGCCTAGGGGTGT
2995231 TCAAATAACCGAACTAATTCG
66 TCAAATAACCGAACTAATTCG
2995252 TT
1 TT
2995254 AACCGACCGA
Statistics
Matches: 84, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
82 29 0.35
83 17 0.20
84 14 0.17
85 3 0.04
86 21 0.25
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (86 bp):
TTTGCCTTTGTAATTGACAATCTTTATTCCTGTGAGCAAATATCCTTCACCTTGCCTAGGGGTGT
TCAAATAACCGAACTAATTCG
Found at i:2995767 original size:170 final size:166
Alignment explanation
Indices: 2995403--2995767 Score: 488
Period size: 173 Copynumber: 2.2 Consensus size: 166
2995393 AACCGAAATA
* * * *
2995403 AATTTTAATATTAAATATATATATAACATATGGGCTCAACCCAATCATTTAAACTCAATTAATAA
1 AATTTAAATATTAAATATTTATATAACATATGGGCTCAACCCAACCATTTAAACCCAATTAATAA
*
2995468 TTTAAGATCCATAACTTTTAAACTTAAAAATATTATTAATTAAAAATTATATAAATTTTTTATTT
66 TTTAAGATCCATAACTTTTAAACTTAAAAATATTATTAATTAAAAATTATATAAATTTTATATTT
* *
2995533 ATAATTATATATTTAAATTATTTGTAAACTGTTTTT
131 ATAATTATATATTTAAATTAATTATAAACTGTTTTT
*
2995569 AATTAAAAAATATTAAATATTATATATAACATATGGGCT-AAGCCCAACCATTTAAAACCCAATT
1 AATT--TAAATATTAAATATT-TATATAACATATGGGCTCAA-CCCAACCATTT-AAACCCAATT
*
2995633 AATAATTTAAGATCCAATAAC-TTTAAACTTAAATCAATATTAATT-ATTAAAAATTTATCTAAA
61 AATAATTTAAGATCC-ATAACTTTTAAACTTAAA--AATATT-ATTAATTAAAAA-TTATAT-AA
*
2995696 ATTTTAT-TTTATAATTATATATTTAAATTAATTATAAACTTTTTTT
120 ATTTTATATTTATAATTATATATTTAAATTAATTATAAACTGTTTTT
*
2995742 GAATTTAAATATTTAAT-TTTATATAA
1 -AATTTAAATATTAAATATTTATATAA
2995768 ATTAGAAAAT
Statistics
Matches: 175, Mismatches: 12, Indels: 20
0.85 0.06 0.10
Matches are distributed among these distances:
166 4 0.02
168 14 0.08
169 27 0.15
170 43 0.25
171 7 0.04
172 24 0.14
173 44 0.25
174 12 0.07
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (166 bp):
AATTTAAATATTAAATATTTATATAACATATGGGCTCAACCCAACCATTTAAACCCAATTAATAA
TTTAAGATCCATAACTTTTAAACTTAAAAATATTATTAATTAAAAATTATATAAATTTTATATTT
ATAATTATATATTTAAATTAATTATAAACTGTTTTT
Found at i:2995883 original size:30 final size:30
Alignment explanation
Indices: 2995826--2995885 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2995816 ACCGAAATTT
* **
2995826 TTCGGTTCGGTTAATATGTTCGAAAAAAAA
1 TTCGGTTCGGTTAATAGGTTAAAAAAAAAA
2995856 TTCGGTTCGGTTAAT-GGTTAAAGAAAAAAA
1 TTCGGTTCGGTTAATAGGTTAAA-AAAAAAA
2995886 AAGTTTGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (30 bp):
TTCGGTTCGGTTAATAGGTTAAAAAAAAAA
Found at i:2995911 original size:15 final size:15
Alignment explanation
Indices: 2995891--2995919 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2995881 AAAAAAAGTT
2995891 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
2995906 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
2995920 CGGTCGGCTA
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:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:2999004 original size:12 final size:14
Alignment explanation
Indices: 2998977--2999015 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
2998967 CAAACATAAA
2998977 AAATGAAAAGATGC
1 AAATGAAAAGATGC
2998991 AAATG-AAA-ATGC
1 AAATGAAAAGATGC
*
2999003 AAATGCAAAGATG
1 AAATGAAAAGATG
2999016 TGAATATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 6 0.26
14 8 0.35
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (14 bp):
AAATGAAAAGATGC
Found at i:2999105 original size:7 final size:7
Alignment explanation
Indices: 2999070--2999110 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
2999060 AGCAAATAAC
*
2999070 AAATACA
1 AAATGCA
2999077 AAATG-A
1 AAATGCA
2999083 AAATGCA
1 AAATGCA
2999090 AAGATGCA
1 AA-ATGCA
2999098 AAATGC-
1 AAATGCA
2999104 AAATGCA
1 AAATGCA
2999111 TGTACGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
6 12 0.40
7 11 0.37
8 7 0.23
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:3009488 original size:2 final size:2
Alignment explanation
Indices: 3009481--3009534 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3009471 TACTTTTGTG
3009481 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
3009523 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3009535 GTGTAAGCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3017173 original size:29 final size:29
Alignment explanation
Indices: 3017140--3017211 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
3017130 GTTGGGAGCG
* *
3017140 TCAGTGCATCGATGCATACCCATGGTGCA
1 TCAGTGCATCAATGCATACCCATGGTACA
3017169 TCAGTGCATCAATGCATACCCATGGTACA
1 TCAGTGCATCAATGCATACCCATGGTACA
*
3017198 TCGGTGCATCAATG
1 TCAGTGCATCAATG
3017212 TAAAATTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (29 bp):
TCAGTGCATCAATGCATACCCATGGTACA
Found at i:3017298 original size:18 final size:17
Alignment explanation
Indices: 3017244--3017292 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3017234 TTGGACCCTT
* *
3017244 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3017262 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3017280 AGTGCATTCGATG
1 AGTGCA-TCGATG
3017293 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3017332 original size:64 final size:65
Alignment explanation
Indices: 3017264--3017388 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 65
3017254 TGCACTAAGA
* *
3017264 GTGCATCGATGCATCAAGTGCATTCGA-TGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATTGTTTCATAAA-AGCCACAGTGCATCGATGCATGGCT
3017327 G
65 G
* * *
3017328 GTGCATCGATGCATCAAATGCATTCGATTTTTTCATAAAATCCTCAGTGCATCGATGCATG
1 GTGCATCGATGCATCAAATGCATTCGATTGTTTCATAAAAGCCACAGTGCATCGATGCATG
3017389 AAATTCATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 26 0.48
65 25 0.46
66 3 0.06
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATTGTTTCATAAAAGCCACAGTGCATCGATGCATGGCTG
Found at i:3018146 original size:14 final size:15
Alignment explanation
Indices: 3018127--3018155 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3018117 TCAAGCATTT
3018127 AACAATCCA-AAACA
1 AACAATCCAGAAACA
3018141 AACAATCCAGAAACA
1 AACAATCCAGAAACA
3018156 TAAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:3026096 original size:65 final size:63
Alignment explanation
Indices: 3025898--3026107 Score: 207
Period size: 65 Copynumber: 3.3 Consensus size: 63
3025888 TGCACTAAGA
* *
3025898 GTGCATCGATGCATCAAGTGCATTTGATGTTTCAA-AATT-ACTAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTTGATGTTTCAATAATTCA-T-G-GTGCATCGATGCATGGTT
3025961 G
63 G
* * * *
3025962 GTGTATCGATGCATTAAATGCATTCGATGTTTTCATAAAATCCTCA--GTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTTGATG-TTTCA-ATAAT--TCATGGTGCATCGATGCATGGT
3026025 AT-
62 -TG
*
3026027 GTGCATCGATGCATGAAATGCATTTGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTTGATGTTTCAA--TAATTCATGGTGCATCGATGCATGG-TT
3026091 G
63 G
*
3026092 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
3026108 CTTTGATAAA
Statistics
Matches: 122, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
62 4 0.03
63 4 0.03
64 45 0.37
65 62 0.51
66 2 0.02
67 3 0.02
69 1 0.01
70 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTTGATGTTTCAATAATTCATGGTGCATCGATGCATGGTTG
Found at i:3026494 original size:19 final size:18
Alignment explanation
Indices: 3026443--3026491 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
3026433 AATCTCTTTA
3026443 ATTTATTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
3026462 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
3026481 ATTTTTTATTT
1 ATTTTTTATTT
3026492 TAAAAATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:3028988 original size:11 final size:11
Alignment explanation
Indices: 3028972--3029020 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
3028962 TTTGTGTTTC
3028972 TATTTTCATTT
1 TATTTTCATTT
*
3028983 TATTTTCGTTT
1 TATTTTCATTT
*
3028994 TATTTT-GTTT
1 TATTTTCATTT
*
3029004 TATTTTTATTT
1 TATTTTCATTT
3029015 TATTTT
1 TATTTT
3029021 TTTAGCAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 10 0.29
11 25 0.71
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (11 bp):
TATTTTCATTT
Found at i:3028999 original size:5 final size:5
Alignment explanation
Indices: 3028972--3029020 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
3028962 TTTGTGTTTC
* *
3028972 TATTT TCATTT TATTT TCGTTT TATTT TGTTT TATTTT TATTT TATTT
1 TATTT T-ATTT TATTT T-ATTT TATTT TATTT TA-TTT TATTT TATTT
3029020 T
1 T
3029021 TTTAGCAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 23 0.62
6 14 0.38
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:3029006 original size:21 final size:21
Alignment explanation
Indices: 3028980--3029020 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3028970 TCTATTTTCA
*
3028980 TTTTATTTTCGTTTTATTTTG
1 TTTTATTTTCATTTTATTTTG
*
3029001 TTTTATTTTTATTTTATTTT
1 TTTTATTTTCATTTTATTTT
3029021 TTTAGCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTATTTTCATTTTATTTTG
Found at i:3030883 original size:18 final size:18
Alignment explanation
Indices: 3030837--3030885 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3030827 AATCTATTTA
3030837 ATTTGTTTATTTAAATATT
1 ATTT-TTTATTTAAATATT
* * *
3030856 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAAATATT
3030875 ATTTTTTATTT
1 ATTTTTTATTT
3030886 CAAAAACAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 8 0.32
19 16 0.64
20 1 0.04
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTATTTAAATATT
Found at i:3035669 original size:30 final size:30
Alignment explanation
Indices: 3035631--3035758 Score: 193
Period size: 30 Copynumber: 4.3 Consensus size: 30
3035621 AATCATAAAT
** *
3035631 TGGTCACTAACGTTATTATTTGTTACAAAA
1 TGGTCACTAACGTTATCGTTTGGTACAAAA
* *
3035661 TAGTCACTAACGTTATCGTTTGGTATAAAA
1 TGGTCACTAACGTTATCGTTTGGTACAAAA
*
3035691 TGGTCACTAACGTTATCGTTTGATACAAAA
1 TGGTCACTAACGTTATCGTTTGGTACAAAA
*
3035721 TGGTCACTAACGTTATTGTTTGGTACAAAA
1 TGGTCACTAACGTTATCGTTTGGTACAAAA
3035751 TGGTCACT
1 TGGTCACT
3035759 CAATGTTAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 88 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (30 bp):
TGGTCACTAACGTTATCGTTTGGTACAAAA
Found at i:3037280 original size:28 final size:28
Alignment explanation
Indices: 3037249--3037335 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
3037239 TAATAACACT
3037249 TGGAAAACAACAAATCAATAAAGTTTCA
1 TGGAAAACAACAAATCAATAAAGTTTCA
*
3037277 TGGAGAAA-AACAAAGCAATAAA-TTTCCA
1 TGGA-AAACAACAAATCAATAAAGTTT-CA
* * * *
3037305 TTGTAAACAATAAAGT-AATAAAGTCTCA
1 TGGAAAACAACAAA-TCAATAAAGTTTCA
3037333 TGG
1 TGG
3037336 TCCTGAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
27 6 0.13
28 36 0.77
29 5 0.11
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.23
Consensus pattern (28 bp):
TGGAAAACAACAAATCAATAAAGTTTCA
Found at i:3043366 original size:22 final size:22
Alignment explanation
Indices: 3043327--3043371 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3043317 AAGATTAAGG
**
3043327 TAAAAGTTTAAAGTTGAA-ATA
1 TAAAAGTTTAAAAATGAACATA
3043348 TAAAATGTTTAAAAATGAACATA
1 TAAAA-GTTTAAAAATGAACATA
3043371 T
1 T
3043372 TTTTAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.33
Consensus pattern (22 bp):
TAAAAGTTTAAAAATGAACATA
Found at i:3045863 original size:30 final size:27
Alignment explanation
Indices: 3045800--3045870 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 27
3045790 ACTAAGCCTA
* *
3045800 AAACCCAATTAAAACCCAAACCAACCT
1 AAACCCAAATAAAACCCAAACCAACCG
3045827 AAACCCAAATAAAACCCCAAAACCCAACCG
1 AAACCCAAATAAAA-CCC-AAA-CCAACCG
* *
3045857 AGACCCAACTAAAA
1 AAACCCAAATAAAA
3045871 AAACCCATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 13 0.35
28 3 0.08
29 3 0.08
30 18 0.49
ACGTcount: A:0.54, C:0.37, G:0.03, T:0.07
Consensus pattern (27 bp):
AAACCCAAATAAAACCCAAACCAACCG
Found at i:3047358 original size:5 final size:5
Alignment explanation
Indices: 3047340--3047396 Score: 64
Period size: 5 Copynumber: 11.4 Consensus size: 5
3047330 AATTAGGTCC
* *
3047340 TTATT TTATGT TTATT TTATTT TTATT TTATG TTATT TT-TT TTACT TT-TT
1 TTATT TTAT-T TTATT TTA-TT TTATT TTATT TTATT TTATT TTATT TTATT
3047390 TTATT TT
1 TTATT TT
3047397 TTAGTTGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 7 0.16
5 27 0.61
6 10 0.23
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:3047359 original size:16 final size:15
Alignment explanation
Indices: 3047340--3047396 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 15
3047330 AATTAGGTCC
*
3047340 TTATTTTATGTTTATT
1 TTATTTTAT-TTTATG
3047356 TTATTTTTATTTTATG
1 TTA-TTTTATTTTATG
3047372 TTATTTT-TTTTACT-
1 TTATTTTATTTTA-TG
3047386 TT-TTTTATTTT
1 TTATTTTATTTT
3047397 TTAGTTGTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
13 4 0.11
14 11 0.30
15 5 0.14
16 11 0.30
17 6 0.16
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.79
Consensus pattern (15 bp):
TTATTTTATTTTATG
Found at i:3047379 original size:11 final size:11
Alignment explanation
Indices: 3047340--3047378 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
3047330 AATTAGGTCC
3047340 TTATTTTATGT
1 TTATTTTATGT
*
3047351 TTATTTTATTT
1 TTATTTTATGT
3047362 TTATTTTATG-
1 TTATTTTATGT
3047372 TTATTTT
1 TTATTTT
3047379 TTTTACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (11 bp):
TTATTTTATGT
Found at i:3047390 original size:22 final size:22
Alignment explanation
Indices: 3047340--3047382 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3047330 AATTAGGTCC
3047340 TTATTTTATGTTTATTTTATTT
1 TTATTTTATGTTTATTTTATTT
3047362 TTATTTTATG-TTATTTT-TTT
1 TTATTTTATGTTTATTTTATTT
3047382 T
1 T
3047383 ACTTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 7 0.33
22 10 0.48
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (22 bp):
TTATTTTATGTTTATTTTATTT
Found at i:3047393 original size:18 final size:19
Alignment explanation
Indices: 3047340--3047398 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 19
3047330 AATTAGGTCC
3047340 TTATTTTATGTTTATTTTATTT
1 TTATTTTATG-TTA-TTT-TTT
3047362 TTATTTTATGTTATTTTTT
1 TTATTTTATGTTATTTTTT
3047381 TTACTTTT-T-TTATTTTTT
1 TTA-TTTTATGTTATTTTTT
3047399 AGTTGTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.25
19 7 0.19
20 7 0.19
21 3 0.08
22 10 0.28
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (19 bp):
TTATTTTATGTTATTTTTT
Found at i:3051627 original size:20 final size:21
Alignment explanation
Indices: 3051604--3051642 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3051594 TTAGAAGCTC
3051604 AGAATCAGAA-ATTAGGGAAA
1 AGAATCAGAATATTAGGGAAA
**
3051624 AGAATTGGAATATTAGGGA
1 AGAATCAGAATATTAGGGA
3051643 GCCAGGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.28, T:0.21
Consensus pattern (21 bp):
AGAATCAGAATATTAGGGAAA
Found at i:3052169 original size:39 final size:39
Alignment explanation
Indices: 3052110--3052294 Score: 250
Period size: 39 Copynumber: 4.8 Consensus size: 39
3052100 AATTTCATCT
3052110 CAGAAGA-TTTATCTCGCTTGAGATAGTTTTACTCGAAA
1 CAGAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAA
* *
3052148 CAGAAGATTTTATCTCTCTTGAGATAGTTTCACTCGAAA
1 CAGAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAA
* * *
3052187 TAGAAGATTTCATCTCGATTGAGATAGTTTCT-CTCGAAA
1 CAGAAGATTTTATCTCGCTTGAGATAGTTT-TACTCGAAA
* * *
3052226 AAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAA
1 CAGAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAA
* *
3052265 CAGAAGA-TTTATCTCACTTGAGATTGTTTT
1 CAGAAGATTTTATCTCGCTTGAGATAGTTTT
3052295 TCTTAAAACA
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
38 27 0.21
39 100 0.79
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (39 bp):
CAGAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAA
Found at i:3052223 original size:19 final size:19
Alignment explanation
Indices: 3052166--3052223 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
3052156 TTTATCTCTC
*
3052166 TTGAGATAGTTTCACTCGAA
1 TTGAGATAGTTTCTCTCG-A
*
3052186 AT-AGA-AGATTTCATCTCGA
1 TTGAGATAG-TTTC-TCTCGA
3052205 TTGAGATAGTTTCTCTCGA
1 TTGAGATAGTTTCTCTCGA
3052224 AAAAAAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
18 2 0.06
19 15 0.48
20 12 0.39
21 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGAGATAGTTTCTCTCGA
Found at i:3052786 original size:59 final size:59
Alignment explanation
Indices: 3052309--3052777 Score: 584
Period size: 59 Copynumber: 7.9 Consensus size: 59
3052299 AAAACAAACT
*
3052309 ACGCCCCACCAGAGGGGTTAACATTTCTTTTGCTCGATTCACAACACTTCGAATCAGCA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
* * * **
3052368 ACGCACCACCA-ATGGGGTTAACATTT-CTTATGTTCGATTCACAACATTTCGAATCAATA
1 ACGCCCCACCAGA-GGGGTTAACATTTCCTT-TGCTCGATTCACAACACTTCGAATCAGCA
* * * * *
3052427 ATGCCCCACCAAAGGGGTTAATATTT-CTTCTGCTCAATTCACAATACTTCGAATCAGCA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTT-TGCTCGATTCACAACACTTCGAATCAGCA
* * * * *
3052486 ATGCCCCATCAGAGGGATTAACATTTCCTTTGCTTGATTCACAACACTTCGAATCAACA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
* * * * *
3052545 ACGCCCCACCAGAAGGGTTAACATTTTCTTTGCTGGATTCACAACACTTCGAAGCAGTA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
* * * * *
3052604 ACACACCACCAGAGGGGTTAACATTTCTTTTGCTCGATTCATAACACTTCAAATCAGCA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
* * * * *
3052663 ACGCCCCACTAGAGGGGTTAACATTTCCTTTGCTTGATTTACAACACTTTGAATCAGTA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
* * *
3052722 ACGCTCCACCATAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCAAATCA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCA
3052778 ATAACGCTCA
Statistics
Matches: 346, Mismatches: 60, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
58 3 0.01
59 339 0.98
60 4 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (59 bp):
ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
Found at i:3059792 original size:2 final size:2
Alignment explanation
Indices: 3059781--3060194 Score: 57
Period size: 2 Copynumber: 200.0 Consensus size: 2
3059771 TTAAAACAAT
*
3059781 TA TA -A TA TA TA TA AA GTA TA TA -A TA -A TA TA -A 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
* * * * *
3059820 AA CTT TA TA GTT TA TA TA TA AA CTA TA TA TA AA GTA TA TA TGA TA
1 TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA T-A TA
* ** * * *
3059865 TA CA TA TA -A CC TA TA TA CTT TA TA TT TA TA TA CTA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
3059908 CTA TA TA GTG TA TA TA TGA -A CA -A TA TA TA AA CTA TA TA GTT TA
1 -TA TA TA -TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * *
3059951 T- TA CTA TA AA CTA TA TG TA TA AA CTA TA TA CA CTA TA -A CTA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
* * * * * *
3059994 TA TG TA TA AA CTA TA TG TA TA TA TA TA AA CTA TA TA TT TA TA AA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * * *
3060038 T- TA CA TA TT TA AA CTA TA TA GTT TA TA TA AA CTC 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
* * * * *
3060080 AA CTA TA TG TA -A TA TA TA TA CTA TA TA AA T- TA TA -A AA TA TG
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
3060121 TG TA TA AA CTA TA TA TA TA CTA TA TG TG TA AA T- TG 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
* *
3060164 -A TC TA TA TA TA TA AA CTA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
3060195 GTTTACATAT
Statistics
Matches: 287, Mismatches: 81, Indels: 88
0.63 0.18 0.19
Matches are distributed among these distances:
1 15 0.05
2 239 0.83
3 33 0.11
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:3059793 original size:9 final size:9
Alignment explanation
Indices: 3059781--3059820 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
3059771 TTAAAACAAT
3059781 TATAATATA
1 TATAATATA
3059790 TATAA-AGTA
1 TATAATA-TA
3059799 TATAATA-A
1 TATAATATA
3059807 TATAATATA
1 TATAATATA
3059816 TATAA
1 TATAA
3059821 ACTTTATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 9 0.32
9 18 0.64
10 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (9 bp):
TATAATATA
Found at i:3059846 original size:11 final size:11
Alignment explanation
Indices: 3059832--3060312 Score: 84
Period size: 11 Copynumber: 44.6 Consensus size: 11
3059822 CTTTATAGTT
3059832 TATATATAAAC
1 TATATATAAAC
*
3059843 TATATATAAAG
1 TATATATAAAC
*
3059854 TATATATGATA-
1 TATATAT-AAAC
* *
3059865 TACATATAACC
1 TATATATAAAC
**
3059876 TATATACTTTA-
1 TATATA-TAAAC
* *
3059887 TATTTATATAC
1 TATATATAAAC
3059898 TATATATAAAC
1 TATATATAAAC
*
3059909 TATATAGT---G
1 TATATA-TAAAC
*
3059918 TATATATGAAC
1 TATATATAAAC
*
3059929 AATATATAAAC
1 TATATATAAAC
**
3059940 TATATAGTTTA-
1 TATATA-TAAAC
3059951 T-TACTATAAAC
1 TATA-TATAAAC
3059962 TATATGTATAAAC
1 TATA--TATAAAC
*
3059975 --TATATACAC
1 TATATATAAAC
*
3059984 TATA-ACTATA-
1 TATATA-TAAAC
*
3059994 TATGTATAAAC
1 TATATATAAAC
*
3060005 TATATGT--A-
1 TATATATAAAC
3060013 TATATATAAAC
1 TATATATAAAC
*
3060024 TATATAT---T
1 TATATATAAAC
* *
3060032 TATAAAT-TAC
1 TATATATAAAC
*
3060042 -ATATTTAAAC
1 TATATATAAAC
3060052 TATATAGT----
1 TATATA-TAAAC
3060060 T-TATATAAACTC
1 TATATATAAA--C
3060072 TATATATAAAC
1 TATATATAAAC
*
3060083 TATATGTAATA-
1 TATATATAA-AC
*
3060094 TATATACTATA-
1 TATATA-TAAAC
* *
3060105 TAAATTATAAAA
1 TATA-TATAAAC
*
3060117 TATGTGTATAAAC
1 TA--TATATAAAC
*
3060130 TATATATATAC
1 TATATATAAAC
* *
3060141 TATATGTGTAAATTG
1 TATA--TATAAA--C
*
3060156 TATATATAATC
1 TATATATAAAC
3060167 TATATATATAAAC
1 --TATATATAAAC
3060180 TATATAT--AC
1 TATATATAAAC
*
3060189 TATATAGT---T
1 TATATA-TAAAC
* *
3060198 TACATATGAAC
1 TATATATAAAC
*
3060209 CATATATAAAC
1 TATATATAAAC
*
3060220 TCTATATAAACC
1 TATATATAAA-C
3060232 ATATATATAAAC
1 -TATATATAAAC
***
3060244 TATATATATGT
1 TATATATAAAC
3060255 TCATTAATATAAAC
1 T-A-T-ATATAAAC
*
3060269 T-T-TATGAAC
1 TATATATAAAC
3060278 TATATAT--A-
1 TATATATAAAC
*
3060286 TATATATATAC
1 TATATATAAAC
3060297 --TATATAAAC
1 TATATATAAAC
3060306 TATATAT
1 TATATAT
3060313 TATATAGTTC
Statistics
Matches: 338, Mismatches: 71, Indels: 122
0.64 0.13 0.23
Matches are distributed among these distances:
6 1 0.00
7 4 0.01
8 22 0.07
9 46 0.14
10 21 0.06
11 163 0.48
12 20 0.06
13 51 0.15
14 6 0.02
15 4 0.01
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (11 bp):
TATATATAAAC
Found at i:3059894 original size:15 final size:15
Alignment explanation
Indices: 3059876--3060066 Score: 51
Period size: 15 Copynumber: 12.4 Consensus size: 15
3059866 ACATATAACC
*
3059876 TATATACTTTATATT
1 TATATACTATATATT
3059891 TATATACTATATA--
1 TATATACTATATATT
*
3059904 TA-A-ACTATATAGTG
1 TATATACTATATA-TT
* *
3059918 TATATA-TGA-ACAATA
1 TATATACT-ATA-TATT
*
3059933 TATAAACTATATAGTT
1 TATATACTATATA-TT
3059949 TAT-TACTATAAACTATAT
1 TATATACTAT--A-TAT-T
* **
3059967 GTATAAACTATATACAC
1 -TATATACTATATA-TT
*
3059984 TATA-ACTATATATG
1 TATATACTATATATT
*
3059998 TATAAACTATATGTATAT
1 TATATACTATA--TAT-T
*
3060016 ATATAAACTATATATT
1 -TATATACTATATATT
* * *
3060032 TATAAATTACATATT
1 TATATACTATATATT
3060047 TA-A-ACTATATAGTT
1 TATATACTATATA-TT
3060061 TATATA
1 TATATA
3060067 AACTCTATAT
Statistics
Matches: 134, Mismatches: 17, Indels: 49
0.67 0.09 0.25
Matches are distributed among these distances:
11 8 0.06
12 1 0.01
13 8 0.06
14 11 0.08
15 58 0.43
16 15 0.11
17 10 0.07
18 4 0.03
19 14 0.10
20 5 0.04
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (15 bp):
TATATACTATATATT
Found at i:3059913 original size:64 final size:64
Alignment explanation
Indices: 3059832--3059980 Score: 158
Period size: 64 Copynumber: 2.3 Consensus size: 64
3059822 CTTTATAGTT
* * *
3059832 TATATATAAACTATATATAAAGTATATATGATA-TACATATAACCTATATACTTTA-TATTTATA
1 TATATATAAAC--TATATAAAGTATATATGA-ACAACATATAAACTATATACTTTATTA-CTATA
*
3059895 TAC
62 AAC
** * *
3059898 TATATATAAACTATATAGTGTATATATGAACAATATATAAACTATATAGTTTATTACTATAAAC
1 TATATATAAACTATATAAAGTATATATGAACAACATATAAACTATATACTTTATTACTATAAAC
3059962 TATATGTATAAACTATATA
1 TATA--TATAAACTATATA
3059981 CACTATAACT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 44 0.62
65 2 0.03
66 24 0.34
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (64 bp):
TATATATAAACTATATAAAGTATATATGAACAACATATAAACTATATACTTTATTACTATAAAC
Found at i:3059959 original size:86 final size:86
Alignment explanation
Indices: 3059806--3059966 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 86
3059796 GTATATAATA
* * * *
3059806 ATATAATATATATAAACTTTATAGTTTATATATAAACTATATATAAAGTATATATGATATACATA
1 ATATAATATATATAAACTATATAGTGTATATATAAACAATATATAAACTATATATGATATACATA
*
3059871 TAACCTATATACTTTATATTT
66 TAAACTATATACTTTATATTT
* * *
3059892 ATATACTATATATAAACTATATAGTGTATATATGAACAATATATAAACTATATA-GTTTATTAC-
1 ATATAATATATATAAACTATATAGTGTATATATAAACAATATATAAACTATATATG-ATA-TACA
3059955 TATAAACTATAT
64 TATAAACTATAT
3059967 GTATAAACTA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
85 1 0.02
86 61 0.94
87 3 0.05
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (86 bp):
ATATAATATATATAAACTATATAGTGTATATATAAACAATATATAAACTATATATGATATACATA
TAAACTATATACTTTATATTT
Found at i:3059986 original size:86 final size:86
Alignment explanation
Indices: 3059812--3059987 Score: 196
Period size: 86 Copynumber: 2.0 Consensus size: 86
3059802 AATAATATAA
* * * * *
3059812 TATATATAAACTTTATAGTTTATATATAAACTATATATAAAGTATATATGATATACATATAACCT
1 TATATATAAACTATATAGTGTATATATAAACAATATATAAACTATATATGATATACATATAAACT
* * * *
3059877 ATATACTTTATATTTATATAC
66 ATATACTATAAATATATACAC
* *
3059898 TATATATAAACTATATAGTGTATATATGAACAATATATAAACTATATA-GTTTATTAC-TATAAA
1 TATATATAAACTATATAGTGTATATATAAACAATATATAAACTATATATG-ATA-TACATATAAA
*
3059961 CTATAT-GTATAAACTATATACAC
64 CTATATACTATAAA-TATATACAC
3059984 TATA
1 TATA
3059988 ACTATATATG
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
85 5 0.07
86 67 0.89
87 3 0.04
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (86 bp):
TATATATAAACTATATAGTGTATATATAAACAATATATAAACTATATATGATATACATATAAACT
ATATACTATAAATATATACAC
Found at i:3060027 original size:13 final size:13
Alignment explanation
Indices: 3059955--3060252 Score: 113
Period size: 13 Copynumber: 21.2 Consensus size: 13
3059945 AGTTTATTAC
*
3059955 TATAAACTATATG
1 TATAAACTATATA
3059968 TATAAACTATATA
1 TATAAACTATATA
*
3059981 CACTATAACTATATA
1 TA-TA-AACTATATA
3059996 TGTATAAACTATATGTATATA
1 --TATAAAC------TATATA
3060017 TATAAACTATATA
1 TATAAACTATATA
* *
3060030 TTTATAAATTACATA
1 --TATAAACTATATA
*
3060045 TTTAAACTATATAGTTTA
1 TATAAAC--TATA---TA
*
3060063 TATAAACTCTATA
1 TATAAACTATATA
3060076 TATAAACTATATGTAA
1 TATAAACTATA--T-A
3060092 TATATATACTATATAAA
1 TATA-A-ACTATAT--A
* * *
3060109 TTATAAAATATGTG
1 -TATAAACTATATA
3060123 TATAAACTATATA
1 TATAAACTATATA
*
3060136 TAT--ACTATATG
1 TATAAACTATATA
* * *
3060147 TGTAAATTGTATA
1 TATAAACTATATA
*
3060160 TATAATCTATATA
1 TATAAACTATATA
3060173 TATAAACTATATA
1 TATAAACTATATA
* * *
3060186 TACTATATAGTTTACA
1 TA-TA-A-ACTATATA
* *
3060202 TATGAAC--CATA
1 TATAAACTATATA
*
3060213 TATAAAC--TCTA
1 TATAAACTATATA
*
3060224 TATAAACCATATA
1 TATAAACTATATA
3060237 TATAAACTATATA
1 TATAAACTATATA
3060250 TAT
1 TAT
3060253 GTTCATTAAT
Statistics
Matches: 215, Mismatches: 39, Indels: 62
0.68 0.12 0.20
Matches are distributed among these distances:
11 26 0.12
13 96 0.45
14 5 0.02
15 29 0.13
16 23 0.11
17 5 0.02
18 18 0.08
19 7 0.03
21 6 0.03
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.41
Consensus pattern (13 bp):
TATAAACTATATA
Found at i:3060302 original size:13 final size:13
Alignment explanation
Indices: 3059832--3060302 Score: 66
Period size: 13 Copynumber: 36.3 Consensus size: 13
3059822 CTTTATAGTT
*
3059832 TATATATAAACTA
1 TATATATATACTA
*
3059845 TATATA-A-AGTA
1 TATATATATACTA
3059856 TATATGATATAC-A
1 TATAT-ATATACTA
3059869 TATAACCTATATACTTTA
1 TAT-A--TATATAC--TA
*
3059887 TATTTATATACTA
1 TATATATATACTA
3059900 TATATA-A-ACTA
1 TATATATATACTA
*
3059911 TATAGTGTATA-TA
1 TATA-TATATACTA
*
3059924 TGA-ACA-ATA-TA
1 T-ATATATATACTA
* * *
3059935 TAAACTATATAGTT
1 TATA-TATATACTA
*
3059949 TATTACTATAAACTA
1 TA-TA-TATATACTA
* *
3059964 TATGTATAAACTA
1 TATATATATACTA
*
3059977 TATACACTATAACTA
1 TATATA-TAT-ACTA
*
3059992 TATATGTATAAACTA
1 TATA--TATATACTA
*
3060007 TATGTATATA-TA
1 TATATATATACTA
* *
3060019 TAAACTATATA-TT
1 TATA-TATATACTA
*
3060032 TATAAAT-TACATA
1 TATATATATAC-TA
* *
3060045 TTTAAACTATA-TA
1 TATATA-TATACTA
* * *
3060058 GTTTATATAAACTC
1 -TATATATATACTA
*
3060072 TATATATAAACTA
1 TATATATATACTA
*
3060085 TATGTA-ATA-TA
1 TATATATATACTA
3060096 TATACTATATA--A
1 TATA-TATATACTA
* *
3060108 -AT-TATAAAATA
1 TATATATATACTA
* * *
3060119 TGTGTATAAAC--
1 TATATATATACTA
3060130 TATATATATACTA
1 TATATATATACTA
* * * * *
3060143 TATGTGTAAATTG
1 TATATATATACTA
3060156 TATATATA-ATCTA
1 TATATATATA-CTA
*
3060169 TATATATAAACTA
1 TATATATATACTA
3060182 TATATACTATA-TA
1 TATATA-TATACTA
* * *
3060195 GTTTACATATGAACCA
1 -TATATATAT--ACTA
*
3060211 TATATA-A-ACTC
1 TATATATATACTA
*
3060222 TATATA-A-ACCA
1 TATATATATACTA
*
3060233 TATATATAAACTA
1 TATATATATACTA
* *
3060246 TATATATGTTC-A
1 TATATATATACTA
* *
3060258 T-TAATATAAACTT
1 TAT-ATATATACTA
3060271 TATGAACTATATA-TA
1 TAT--A-TATATACTA
3060286 TATATATATACTA
1 TATATATATACTA
3060299 TATA
1 TATA
3060303 AACTATATAT
Statistics
Matches: 335, Mismatches: 71, Indels: 104
0.66 0.14 0.20
Matches are distributed among these distances:
9 5 0.01
10 1 0.00
11 59 0.18
12 32 0.10
13 146 0.44
14 27 0.08
15 51 0.15
16 9 0.03
17 1 0.00
18 4 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.41
Consensus pattern (13 bp):
TATATATATACTA
Found at i:3060318 original size:9 final size:9
Alignment explanation
Indices: 3060280--3060312 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3060270 TTATGAACTA
3060280 TATATATA-
1 TATATATAC
3060288 TATATATAC
1 TATATATAC
*
3060297 TATATAAAC
1 TATATATAC
3060306 TATATAT
1 TATATAT
3060313 TATATAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (9 bp):
TATATATAC
Found at i:3060388 original size:31 final size:29
Alignment explanation
Indices: 3060275--3060395 Score: 105
Period size: 31 Copynumber: 4.3 Consensus size: 29
3060265 AAACTTTATG
*
3060275 AACTATATATA-TATATATATACT-ATATA
1 AACTATATATATTATATAT-TATTAATATA
3060303 AAC--TATATATTATATAGTTCATTAATATA
1 AACTATATATATTATATA-TT-ATTAATATA
* *
3060332 AA--AAATGTATTA-AT-TTATTAATATA
1 AACTATATATATTATATATTATTAATATA
*
3060357 AACTATATATATTATATAGTTCATTAGTATA
1 AACTATATATATTATATA-TT-ATTAATATA
3060388 AACTATAT
1 AACTATAT
3060396 GAACAATAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
25 11 0.14
26 8 0.11
27 15 0.20
28 10 0.13
29 14 0.18
30 2 0.03
31 16 0.21
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (29 bp):
AACTATATATATTATATATTATTAATATA
Found at i:3060461 original size:22 final size:23
Alignment explanation
Indices: 3060422--3060466 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3060412 ATATTAATTT
**
3060422 TATAGTTTATTGAGATAA-AGTA
1 TATAGTTTATACAGATAATAGTA
*
3060444 TATAGTTTATACATATAATAGTA
1 TATAGTTTATACAGATAATAGTA
3060467 ATTGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (23 bp):
TATAGTTTATACAGATAATAGTA
Found at i:3060982 original size:100 final size:99
Alignment explanation
Indices: 3060797--3060986 Score: 224
Period size: 100 Copynumber: 1.9 Consensus size: 99
3060787 TCTTTTGATT
* * *
3060797 TTTTTCGATCCAACACCCTAAATCCATACCTTATTCATCCATGTTCATCCCAAAAACCGTCCTTT
1 TTTTTCGATCAAACACCCCAAATCCATACCTTATTCATCCATGTTCATCCC-AAAACCCTCCTTT
* *
3060862 GATTTTCACAAACACTAAAACCAAACCCTATCTTA
65 GATCTTCACAAACACCAAAACCAAACCCTATCTTA
* * * * *
3060897 TTTTTCGATCAAACACCCCAAATTCAT-CTCTTGTTCATTCGTGTTCATCCTC-AAACCCTTCTT
1 TTTTTCGATCAAACACCCCAAATCCATAC-CTTATTCATCCATGTTCATCC-CAAAACCCTCCTT
3060960 TGATCCTT-ACAAACACCCAAAACCAAA
64 TGAT-CTTCACAAACA-CCAAAACCAAA
3060987 GTCCAACATA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
99 21 0.28
100 54 0.71
101 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (99 bp):
TTTTTCGATCAAACACCCCAAATCCATACCTTATTCATCCATGTTCATCCCAAAACCCTCCTTTG
ATCTTCACAAACACCAAAACCAAACCCTATCTTA
Found at i:3061259 original size:53 final size:52
Alignment explanation
Indices: 3061186--3061335 Score: 160
Period size: 53 Copynumber: 2.8 Consensus size: 52
3061176 TCTTCATATG
* * * *
3061186 TTCATATTTTCTAAGCCTAAACCCTAACTAAGCCTTTTTATCTTTTGTATCTAT-
1 TTCATCTTCTCTAA-CCTAAACCCTAACTAAGCCTCTTCATC-TTT-TATCTATC
* * *
3061240 TT-ATTTTCTCTAACACTAAACCCTAACTAAGACTCTTCATCTTTTATCTTTC
1 TTCATCTTCTCTAAC-CTAAACCCTAACTAAGCCTCTTCATCTTTTATCTATC
* *
3061292 TTCATCTTCTCTAACCTTAAACCCTAACCAAGCCTCTTCTTCTT
1 TTCATCTTCTCTAACC-TAAACCCTAACTAAGCCTCTTCATCTT
3061336 CTCTTTATTC
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
51 6 0.07
52 7 0.09
53 67 0.82
54 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.03, T:0.43
Consensus pattern (52 bp):
TTCATCTTCTCTAACCTAAACCCTAACTAAGCCTCTTCATCTTTTATCTATC
Found at i:3063977 original size:30 final size:31
Alignment explanation
Indices: 3063926--3063983 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
3063916 GTAACTTCTG
3063926 TTTATTTATATTTATTAAATTAATTTTTATA
1 TTTATTTATATTTATTAAATTAATTTTTATA
* *
3063957 TTTA-TTATGTTTATTTAATTAATTTTT
1 TTTATTTATATTTATTAAATTAATTTTT
3063984 CGATATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTATTTATATTTATTAAATTAATTTTTATA
Found at i:3063995 original size:34 final size:32
Alignment explanation
Indices: 3063924--3063997 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 32
3063914 AGGTAACTTC
3063924 TGTTTATTTATATTTATTAAATTAATTTTTATA
1 TGTTTA-TTATATTTATTAAATTAATTTTTATA
* *
3063957 --TTTATTATGTTTATTTAATTAATTTTTCGATA
1 TGTTTATTATATTTATTAAATTAATTTTT--ATA
3063989 TGTTTATTA
1 TGTTTATTA
3063998 ATGCTTCTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
30 21 0.60
31 4 0.11
32 3 0.09
34 7 0.20
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (32 bp):
TGTTTATTATATTTATTAAATTAATTTTTATA
Found at i:3064874 original size:14 final size:14
Alignment explanation
Indices: 3064835--3064874 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3064825 GATTATATTG
* *
3064835 AAGATTTATAACAT
1 AAGAATTATAATAT
*
3064849 AAGAATCATAATAT
1 AAGAATTATAATAT
3064863 AAGAATTATAAT
1 AAGAATTATAAT
3064875 TAATATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (14 bp):
AAGAATTATAATAT
Found at i:3065046 original size:16 final size:16
Alignment explanation
Indices: 3065017--3065059 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
3065007 TTTCATCAAT
*
3065017 GGTAATATAT-AAGTTA
1 GGTAA-ATATCAAGTCA
3065033 GGTAAATATCAAGTCA
1 GGTAAATATCAAGTCA
3065049 GGTAAATATCA
1 GGTAAATATCA
3065060 TATTAGTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (16 bp):
GGTAAATATCAAGTCA
Found at i:3075162 original size:215 final size:215
Alignment explanation
Indices: 3074752--3075349 Score: 936
Period size: 215 Copynumber: 2.8 Consensus size: 215
3074742 AAAAATTACT
* *
3074752 CGAAGGATTTAAGCATCATGCTCGAAATACTTATTGATGGCCCGAAGGACTTATAAATTGTGAAA
1 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAA
* *
3074817 TTTTGAAAATCA-CATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAAATCA-TTTTTCATTTT
66 TTTTGAAAAT-AGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACACCATTTTTTCATTTT
*
3074880 CAAATT-TATGTGAAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTG
130 CAAATTCT-TGTGAAAATATCCTACCCGAAGATTTTATGGATGGCCCGAAGGACTTATCATCTTG
3074944 CTCTAAAGGCTTACAGATGACC
194 CTCTAAAGGCTTACAGATGACC
* * *
3074966 CGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGGCCGAAGAACTTATAAATTGTGAAA
1 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAA
* * * *
3075031 TTTTGAAAATAGAATTCTTAGTTTTAAAAAAATT-CATCTTCTTAAAACGCCATTTTTTCATTTT
66 TTTTGAAAATAGCATTCTTCGTTTT-CAAAAATTCCATCTTCTTAAAACACCATTTTTTCATTTT
* * *
3075095 CAAATTCTTGTGAAAACATCCTACCTGAAGATTTTATGGATGGCCCGAAGGATTTATCATCTTGC
130 CAAATTCTTGTGAAAATATCCTACCCGAAGATTTTATGGATGGCCCGAAGGACTTATCATCTTGC
*
3075160 TCTAAAGGCTTATAGATGACC
195 TCTAAAGGCTTACAGATGACC
* *
3075181 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTATAAATCGTGAAA
1 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAA
* *
3075246 TTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACACTATTTTTTCATTTTC
66 TTTTGAAAATAGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACACCATTTTTTCATTTTC
*
3075311 AAATTCATGTGAAAATATCCTACCCGAA-AGTTTTATGGA
131 AAATTCTTGTGAAAATATCCTACCCGAAGA-TTTTATGGA
3075350 CGGATTTGCT
Statistics
Matches: 348, Mismatches: 30, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
213 1 0.00
214 104 0.30
215 242 0.70
216 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (215 bp):
CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAA
TTTTGAAAATAGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACACCATTTTTTCATTTTC
AAATTCTTGTGAAAATATCCTACCCGAAGATTTTATGGATGGCCCGAAGGACTTATCATCTTGCT
CTAAAGGCTTACAGATGACC
Found at i:3075226 original size:42 final size:40
Alignment explanation
Indices: 3075128--3075229 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 40
3075118 CCTGAAGATT
* * * * *
3075128 TTATGGATGGCCCGAAGGATTTATCATCTTGCTCTAAAGGC
1 TTATAGAT-GCCCGAAGGATTTAGCATCATGCTCGAAAGAC
3075169 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTATAGATG-CCCGAAGGATTT-AGCATCATGCTCGAAAGAC
3075211 TTACT-GATAGCCCGAAGGA
1 TTA-TAGAT-GCCCGAAGGA
3075230 CTTATAAATC
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
40 1 0.02
41 19 0.37
42 30 0.58
43 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (40 bp):
TTATAGATGCCCGAAGGATTTAGCATCATGCTCGAAAGAC
Found at i:3075449 original size:37 final size:37
Alignment explanation
Indices: 3075352--3075470 Score: 152
Period size: 37 Copynumber: 3.2 Consensus size: 37
3075342 TTTATGGACG
3075352 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA-T
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
* * *
3075388 GGTTTACTTCACTGCTCCTT-GGTGAAGGCTTAAGATT
1 GATTTGCTTCACTACT-CTTCGGTGAAGGCTTAAGATT
* * *
3075425 GATTTGCTTCACTCCTTTTCGGTGAAGGCTTAAAATT
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
3075462 GACTTTGCT
1 GA-TTTGCT
3075471 CCAATTCTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
36 30 0.42
37 35 0.49
38 6 0.08
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (37 bp):
GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
Found at i:3076876 original size:6 final size:6
Alignment explanation
Indices: 3076865--3076890 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3076855 TCATTATAAG
3076865 AATGCA AATGCA AATGCA AATGCA AA
1 AATGCA AATGCA AATGCA AATGCA AA
3076891 AGGTGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AATGCA
Done.