Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 26
Found at i:2450684 original size:3 final size:3
Alignment explanation
Indices: 2450676--2450763 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
2450666 TGTGCTAAGC
2450676 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2450724 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2450764 GTATTTTTCT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2451267 original size:15 final size:17
Alignment explanation
Indices: 2451227--2451265 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2451217 ATTTTATGAG
*
2451227 GTAAAAATATTATTATT
1 GTAAAAATATAATTATT
2451244 GTAAAAATATAATTATT
1 GTAAAAATATAATTATT
2451261 -TAAAA
1 GTAAAA
2451266 TAATATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
GTAAAAATATAATTATT
Found at i:2451363 original size:17 final size:17
Alignment explanation
Indices: 2451341--2451373 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2451331 AGAGATTACA
2451341 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
2451358 ATATTATATTTTATAT
1 ATATTATATTTTATAT
2451374 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:2461991 original size:18 final size:19
Alignment explanation
Indices: 2461954--2461991 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2461944 TCGTAAATTT
* *
2461954 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
2461973 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
2461991 T
1 T
2461992 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:2462020 original size:17 final size:16
Alignment explanation
Indices: 2461998--2462036 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2461988 AAATTATCAA
* *
2461998 TTTTATTTAAATTAAT
1 TTTTATTGAAAATAAT
2462014 TTATTATTGAAAATAAT
1 TT-TTATTGAAAATAAT
2462031 TTTTAT
1 TTTTAT
2462037 CGTGTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTATTGAAAATAAT
Found at i:2462124 original size:32 final size:33
Alignment explanation
Indices: 2462072--2462139 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
2462062 ATATGTTCGA
* * * *
2462072 GTTGTTTTCGGTTCGGGTT-AAATTCAGTTCAG
1 GTTGCTTTCGGGTCGAGTTAAAATTCAATTCAG
2462104 GTTGCTTTCGGGTCGAGTTAAAATTCAATTCAG
1 GTTGCTTTCGGGTCGAGTTAAAATTCAATTCAG
2462137 GTT
1 GTT
2462140 TATTTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.41
Consensus pattern (33 bp):
GTTGCTTTCGGGTCGAGTTAAAATTCAATTCAG
Found at i:2462200 original size:15 final size:15
Alignment explanation
Indices: 2462180--2462210 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2462170 TTAAAATTTA
*
2462180 GTTCAGGTTTCTTTC
1 GTTCAGGTTACTTTC
2462195 GTTCAGGTTACTTTC
1 GTTCAGGTTACTTTC
2462210 G
1 G
2462211 ATTCGAGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (15 bp):
GTTCAGGTTACTTTC
Found at i:2462280 original size:38 final size:38
Alignment explanation
Indices: 2462212--2462285 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
2462202 TTACTTTCGA
**
2462212 TTCGAGTTGTTTTTAGTTCGGGTTAGTTTCAGTTTTGG
1 TTCGAGTTAATTTTAGTTCGGGTTAGTTTCAGTTTTGG
* *
2462250 TTCGAGTTAATTTTGGTTCTGGTT-GATTTCAGTTTT
1 TTCGAGTTAATTTTAGTTCGGGTTAG-TTTCAGTTTT
2462286 CGCTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.03
38 30 0.97
ACGTcount: A:0.12, C:0.08, G:0.26, T:0.54
Consensus pattern (38 bp):
TTCGAGTTAATTTTAGTTCGGGTTAGTTTCAGTTTTGG
Found at i:2463081 original size:19 final size:19
Alignment explanation
Indices: 2463057--2463101 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2463047 TTGATACCAA
2463057 ATTTACATTCTGAAATTTG
1 ATTTACATTCTGAAATTTG
2463076 ATTTACATTCTGAAATTTG
1 ATTTACATTCTGAAATTTG
*
2463095 GTTTACA
1 ATTTACA
2463102 ATCCAGTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTTACATTCTGAAATTTG
Found at i:2463150 original size:20 final size:20
Alignment explanation
Indices: 2463106--2463151 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2463096 TTTACAATCC
2463106 AGTATCGATACCACCCTGTG
1 AGTATCGATACCACCCTGTG
* *
2463126 GGTATCGATACCATCCT-TG
1 AGTATCGATACCACCCTGTG
2463145 TAGTATC
1 -AGTATC
2463152 TATGCTCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (20 bp):
AGTATCGATACCACCCTGTG
Found at i:2468037 original size:103 final size:102
Alignment explanation
Indices: 2467816--2468051 Score: 248
Period size: 103 Copynumber: 2.3 Consensus size: 102
2467806 AGTAGTCAGT
* * * * *
2467816 TTTGGTATCGGTACTCAAGGGAGTATCGATATTGAGGATAAGGTACTGATACTCCCAATAAGGTA
1 TTTGGTATCGATACTCAAAGGAGTATCAATACTGAGGATAAGGTACTGATACTCCCAAGAAGGTA
* * *
2467881 TCGACACTAATGGTTTTTTTCAAACATCGAATACAAT
66 TCGACACTAATGATTTTTATCAAACATCGAATACAAA
* *
2467918 TTTGGTATC-AGTACTCAAAGGAGTATCAATACTGAGGATAATGTA-TCGATACTCTCACGAGAA
1 TTTGGTATCGA-TACTCAAAGGAGTATCAATACTGAGGATAAGGTACT-GATACTC-C-CAAGAA
* **
2467981 -GTATCGATACTAGA-GCATTTTTAT-AAACATCGAATGTAAA
62 GGTATCGACACTA-ATG-ATTTTTATCAAACATCGAATACAAA
* *
2468021 TTTGGTACCGATACTCAAAGAAGTATCAATA
1 TTTGGTATCGATACTCAAAGGAGTATCAATA
2468052 TTTTAGGAAG
Statistics
Matches: 112, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
101 1 0.01
102 46 0.41
103 53 0.47
104 12 0.11
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (102 bp):
TTTGGTATCGATACTCAAAGGAGTATCAATACTGAGGATAAGGTACTGATACTCCCAAGAAGGTA
TCGACACTAATGATTTTTATCAAACATCGAATACAAA
Found at i:2471716 original size:27 final size:26
Alignment explanation
Indices: 2471681--2471751 Score: 61
Period size: 27 Copynumber: 2.6 Consensus size: 26
2471671 GTTATTTATT
*
2471681 TTTTAATAATTTATTTTTATCTTTAAAA
1 TTTT-ATAATTTATTTTTAAC-TTAAAA
* **
2471709 TTTTATAAATTCGTTTTAACTTAAAA
1 TTTTATAATTTATTTTTAACTTAAAA
**
2471735 TTAAATTAATTTATTTT
1 TTTTA-TAATTTATTTT
2471752 AATATAAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
26 9 0.27
27 20 0.61
28 4 0.12
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (26 bp):
TTTTATAATTTATTTTTAACTTAAAA
Found at i:2477605 original size:27 final size:28
Alignment explanation
Indices: 2477575--2477630 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2477565 AAAGTTAAGT
*
2477575 AATTAAATT-AAAAATTAAACTTCAATG
1 AATTAAATTAAAAAAGTAAACTTCAATG
2477602 AATTAAATTAAAAAAGTAAACTTCAATG
1 AATTAAATTAAAAAAGTAAACTTCAATG
2477630 A
1 A
2477631 CTAAAATAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (28 bp):
AATTAAATTAAAAAAGTAAACTTCAATG
Found at i:2477637 original size:28 final size:27
Alignment explanation
Indices: 2477579--2477637 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
2477569 TTAAGTAATT
* *
2477579 AAATTAAAAATTAAACTTCAATGAATT
1 AAATTAAAAAGTAAACTTCAATGAATA
*
2477606 AAATTAAAAAAGTAAACTTCAATGACTA
1 AAATT-AAAAAGTAAACTTCAATGAATA
2477634 AAAT
1 AAAT
2477638 AGGAGTGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (27 bp):
AAATTAAAAAGTAAACTTCAATGAATA
Found at i:2478808 original size:39 final size:39
Alignment explanation
Indices: 2478707--2478809 Score: 113
Period size: 39 Copynumber: 2.6 Consensus size: 39
2478697 CATAATCCTC
*
2478707 AAATTATTTTAC-TCTAACATTTTAAAATCATAATTTCTT
1 AAATTATTTTACAT-TAACATTCTAAAATCATAATTTCTT
* * *
2478746 AAATT-TTGATACCA-TAACATTCTAAATTCTTAATTTCTT
1 AAATTATT-TTA-CATTAACATTCTAAAATCATAATTTCTT
*
2478785 AAATTATTTTACATTAACGTTCTAA
1 AAATTATTTTACATTAACATTCTAA
2478810 TTTTTTAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
38 4 0.08
39 46 0.87
40 3 0.06
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.47
Consensus pattern (39 bp):
AAATTATTTTACATTAACATTCTAAAATCATAATTTCTT
Found at i:2479159 original size:26 final size:27
Alignment explanation
Indices: 2479098--2479160 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
2479088 CATCAACTTA
*
2479098 TTAAATATATTTTATTATTAACTTTAT
1 TTAAAAATATTTTATTATTAACTTTAT
*
2479125 TTAAAAATATTTTATT-TTTA-TTTCAT
1 TTAAAAATATTTTATTATTAACTTT-AT
2479151 TTAAAAATAT
1 TTAAAAATAT
2479161 ATAATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 3 0.09
26 15 0.45
27 15 0.45
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (27 bp):
TTAAAAATATTTTATTATTAACTTTAT
Found at i:2479188 original size:26 final size:26
Alignment explanation
Indices: 2479100--2479188 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 26
2479090 TCAACTTATT
2479100 AAATATATTTTATTATTAACTTTATTTAA
1 AAATATA-TTTATT-TTAA-TTTATTTAA
*
2479129 AAATAT-TTTATTTTTATTTCATTTAAA
1 AAATATATTTATTTTAATTT-ATTT-AA
2479156 AATATATAATTTATTTTAATTTA-TTAA
1 AA-ATAT-ATTTATTTTAATTTATTTAA
2479183 AAATAT
1 AAATAT
2479189 GACTAAATTG
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
25 3 0.06
26 11 0.21
27 14 0.26
28 6 0.11
29 7 0.13
30 12 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
AAATATATTTATTTTAATTTATTTAA
Found at i:2481521 original size:23 final size:23
Alignment explanation
Indices: 2481495--2481563 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2481485 CACCACAACT
2481495 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
2481518 CATATAATTGCACAGGAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
2481541 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
2481564 TATAATACTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:2481751 original size:103 final size:103
Alignment explanation
Indices: 2481579--2481775 Score: 367
Period size: 103 Copynumber: 1.9 Consensus size: 103
2481569 TACTGTCCAT
*
2481579 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
2481644 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2481682 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
*
2481747 GACTTCACACATGTTTCAAAGAATACATA
66 GACTTCACACATGTTCCAAAGAATACATA
2481776 CGCTAAGTCA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 91 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2482293 original size:23 final size:23
Alignment explanation
Indices: 2482266--2482334 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
2482256 CACCACAGCT
2482266 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
2482289 CATATAATTGCACAGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
2482312 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
2482335 TATAGTACTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:2482456 original size:20 final size:20
Alignment explanation
Indices: 2482419--2482458 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2482409 AGACTCACAC
* *
2482419 ATGTTCCAAAGAATACATAT
1 ATGTCCCAAAGAACACATAT
*
2482439 ATGTCCCAAAGGACACATAT
1 ATGTCCCAAAGAACACATAT
2482459 CATTCCTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (20 bp):
ATGTCCCAAAGAACACATAT
Found at i:2482508 original size:101 final size:101
Alignment explanation
Indices: 2482350--2482560 Score: 324
Period size: 102 Copynumber: 2.1 Consensus size: 101
2482340 TACTGTCTAT
* * *
2482350 AAGGACCAC--AT-ATTCCTTAAGAATCATATACATACTAGGGATCAAGTATGTGTCTCACCAGA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATACCAAGGATCAAGTATATGTCTCACCAGA
2482412 C-TCACACATGTTCCAAAGAATACATATATGTCCCA
66 CTTCACACATGTTCCAAAGAATACATATATGTCCCA
*
2482447 AAGGA-CACATATCATTCCTTAAGGATCATATACATATGCCAAGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATA--CCAAGGATCAAGTATATGTCTCACCA
*
2482511 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
64 GACTTCACACATGTTCCAAAGAATACATATATGTCCCA
2482549 AAGGACCACATA
1 AAGGACCACATA
2482561 GACCCTCGAC
Statistics
Matches: 102, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
96 3 0.03
97 5 0.05
98 2 0.02
99 22 0.22
101 26 0.25
102 38 0.37
103 6 0.06
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (101 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATACCAAGGATCAAGTATATGTCTCACCAGA
CTTCACACATGTTCCAAAGAATACATATATGTCCCA
Found at i:2488219 original size:23 final size:23
Alignment explanation
Indices: 2488193--2488261 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2488183 CACCACAGCT
2488193 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * * *
2488216 CATATAATTGCACTGGAGTACCG
1 CATATAATTGCACCGAAGTGCCA
* * *
2488239 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
2488262 TATAATACTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:2488453 original size:103 final size:103
Alignment explanation
Indices: 2488277--2488494 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
2488267 TACTGTCCAT
** *
2488277 AAGGACCACATATCATTCCTTAAGAATCATATACATATATTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2488342 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACATCACACATGTTCCAAAGAATACATATATGTCCCG
*
2488380 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
2488445 GACATCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACATCACACATGTTCCAAAGAATACATATATGTCCCG
2488483 AAGGACCACATA
1 AAGGACCACATA
2488495 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACATCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2490492 original size:51 final size:51
Alignment explanation
Indices: 2490416--2490525 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 51
2490406 GTACACTTAC
*
2490416 CTTGGAAATTGATTCTTTGTTCATATATATATATATATTTGTTTAACGTGT
1 CTTGGAAACTGATTCTTTGTTCATATATATATATATATTTGTTTAACGTGT
*
2490467 CTTGGAAACTGATTTTTTGTTCATATATATATATATATTTGTTTAACGTGT
1 CTTGGAAACTGATTCTTTGTTCATATATATATATATATTTGTTTAACGTGT
2490518 CTTAGGAA
1 CTT-GGAA
2490526 GAATAGCCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (51 bp):
CTTGGAAACTGATTCTTTGTTCATATATATATATATATTTGTTTAACGTGT
Found at i:2490593 original size:27 final size:27
Alignment explanation
Indices: 2490563--2490616 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2490553 TATAGCTTAG
2490563 TTGGA-TATATATATATATATTAAATTA
1 TTGGAGTATATATAT-TATATTAAATTA
*
2490590 TTGGAGTATATATATTATATTTAATTA
1 TTGGAGTATATATATTATATTAAATTA
2490617 GCCCATGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (27 bp):
TTGGAGTATATATATTATATTAAATTA
Found at i:2491744 original size:10 final size:10
Alignment explanation
Indices: 2491731--2491784 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
2491721 TTTATTTTTT
2491731 TTATATATAA
1 TTATATATAA
2491741 TTATATA-AA
1 TTATATATAA
*
2491750 ATATA-ATGAA
1 TTATATAT-AA
*
2491760 TTATTTAT-A
1 TTATATATAA
*
2491769 TTATATATTA
1 TTATATATAA
2491779 TTATAT
1 TTATAT
2491785 TTTGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
8 1 0.03
9 14 0.39
10 19 0.53
11 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
TTATATATAA
Found at i:2491754 original size:19 final size:19
Alignment explanation
Indices: 2491732--2491784 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
2491722 TTATTTTTTT
2491732 TATATATAATTATATAAAA
1 TATATATAATTATATAAAA
* * *
2491751 TATA-ATGAATTATTTATAT
1 TATATAT-AATTATATAAAA
*
2491770 TATATATTATTATAT
1 TATATATAATTATAT
2491785 TTTGTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.07
19 23 0.85
20 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATATAATTATATAAAA
Found at i:2494106 original size:62 final size:62
Alignment explanation
Indices: 2494009--2494132 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
2493999 GAGAGAACTT
*
2494009 GGGATTTAAGGAATCATTATATTGCTAGTTGTAAGGTACAATGCATCAGCCAACCTATATCC
1 GGGATTTAAGGAATCATTATATTGCTAGTTATAAGGTACAATGCATCAGCCAACCTATATCC
2494071 GGGATTTAAGGAATCATTATATTGCTAGTTATAAGGTACAATGCATCAGCCAACCTATATCC
1 GGGATTTAAGGAATCATTATATTGCTAGTTATAAGGTACAATGCATCAGCCAACCTATATCC
2494133 AAGCTGTTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (62 bp):
GGGATTTAAGGAATCATTATATTGCTAGTTATAAGGTACAATGCATCAGCCAACCTATATCC
Found at i:2502889 original size:15 final size:16
Alignment explanation
Indices: 2502861--2502893 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2502851 AAAATATTTC
2502861 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
2502877 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
2502892 TT
1 TT
2502894 GATCTACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:2508344 original size:4 final size:4
Alignment explanation
Indices: 2508304--2508356 Score: 54
Period size: 4 Copynumber: 12.5 Consensus size: 4
2508294 AGTAAAATAA
*
2508304 AAAT AAAT GAAAT AAAG AGAAT AAA- AGAAT AAAAT AAAT AAAT AAAT
1 AAAT AAAT -AAAT AAAT A-AAT AAAT A-AAT -AAAT AAAT AAAT AAAT
2508351 AAAT AA
1 AAAT AA
2508357 GAAAAATAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
3 1 0.02
4 30 0.71
5 10 0.24
6 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:2509847 original size:17 final size:16
Alignment explanation
Indices: 2509821--2509861 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2509811 TTAACAAAAA
*
2509821 AATATGTAATAAATAT
1 AATATATAATAAATAT
*
2509837 ATATATATAATTAATAT
1 A-ATATATAATAAATAT
2509854 AATATATA
1 AATATATA
2509862 TGTTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AATATATAATAAATAT
Found at i:2510616 original size:98 final size:101
Alignment explanation
Indices: 2510409--2510631 Score: 274
Period size: 98 Copynumber: 2.2 Consensus size: 101
2510399 CTCAAGGTAA
* * * * *
2510409 ACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGG
1 ACAAAA-TTTGTTTAAAGGAAAACAAATTAAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGA
* * *
2510474 GAGACAAAAAATTTCCAAGAGAAACTGTCTCGAGTGAG
65 GAGAC-AAAAATTTCCAAGAGAAAATGTCTCAAGAGAG
*
2510512 ACAAAATTTGTTTAAAGGAAAACAGATTAAAAGA-TTT-TGTTTCAA-AGGAAACTGTCTCAAGA
1 ACAAAATTTGTTTAAAGGAAAACAAATTAAAAGATTTTGTGTTTCAAGA-GAAACTGTCTCAAGA
**
2510574 GAGAC-AAAATTTTTAAGAGAAAATGTCTCAAGAGAG
65 GAGACAAAAATTTCCAAGAGAAAATGTCTCAAGAGAG
*
2510610 ACAAAATTTGTTTTAAAAGAAA
1 ACAAAATTTG-TTTAAAGGAAA
2510632 TTGTCTCAAG
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
98 36 0.34
99 11 0.10
100 27 0.25
101 3 0.03
102 23 0.22
103 6 0.06
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (101 bp):
ACAAAATTTGTTTAAAGGAAAACAAATTAAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAG
AGACAAAAATTTCCAAGAGAAAATGTCTCAAGAGAG
Found at i:2510631 original size:36 final size:36
Alignment explanation
Indices: 2510547--2510660 Score: 137
Period size: 33 Copynumber: 3.2 Consensus size: 36
2510537 ATTAAAAGAT
* * *
2510547 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAAAGAAAATGTCTCAAGAGAGACAAAA
*
2510583 --T-TTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAAAGAAAATGTCTCAAGAGAGACAAAA
*
2510616 TTTGTTTTAAAAGAAATTGTCTCAAG-GAAGACAAAA
1 TTTGTTTTAAAAGAAAATGTCTCAAGAG-AGACAAAA
2510652 CTTTGTTTT
1 -TTTGTTTT
2510661 GGAAAACAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
33 28 0.42
34 1 0.01
35 2 0.03
36 28 0.42
37 8 0.12
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.31
Consensus pattern (36 bp):
TTTGTTTTAAAAGAAAATGTCTCAAGAGAGACAAAA
Found at i:2510739 original size:36 final size:35
Alignment explanation
Indices: 2510680--2510896 Score: 153
Period size: 36 Copynumber: 6.2 Consensus size: 35
2510670 ATTCAAAGAT
* *
2510680 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACATAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACA-AA
* *
2510716 TTTGTTTTAAGAGAAAATTTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGAC-AAA
* *
2510752 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGAC-AAA
* *
2510788 CTTTGTTTCAAG-GAAAACAGAT-TC-A-A-AG---AT
1 -TTTGTTTCAAGAGAAAA-TG-TCTCAAGAGAGACAAA
* *** * *
2510818 TTTGTTTCAAGGGAAACCATCTCAATAGATACAAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGAC-AAA
* * *
2510854 TTTGTTTTAAGAGAAAATGTATCAAGAAAGACAAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGAC-AAA
2510890 TTTGTTT
1 TTTGTTT
2510897 TAAGTAAATT
Statistics
Matches: 143, Mismatches: 25, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
28 1 0.01
29 13 0.09
30 6 0.04
31 1 0.01
32 1 0.01
34 2 0.01
35 1 0.01
36 103 0.72
37 14 0.10
38 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (35 bp):
TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAA
Found at i:2510842 original size:29 final size:30
Alignment explanation
Indices: 2510789--2510847 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2510779 GAGACAAAAC
*
2510789 TTTGTTTCAAGGAAAACAGATTCAA-AGAT
1 TTTGTTTCAAGGAAAACACATTCAATAGAT
*
2510818 TTTGTTTCAAGGGAAAC-CATCTCAATAGAT
1 TTTGTTTCAAGGAAAACACAT-TCAATAGAT
2510848 ACAAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 20 0.77
30 4 0.15
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (30 bp):
TTTGTTTCAAGGAAAACACATTCAATAGAT
Found at i:2510862 original size:138 final size:136
Alignment explanation
Indices: 2510449--2510900 Score: 619
Period size: 138 Copynumber: 3.3 Consensus size: 136
2510439 AAAGATTTTG
* * * ** ** *
2510449 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAAAT-TTCCAAGAGAAACTGTCTCGAGTGAGA
1 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAG-GAGA
* *
2510513 CAAAA-TTTGTTTAAAGGAAAACAGATTAAAAGATTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
65 CAAAACTTTGTTT-AAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
2510577 ACAAAA--
129 ACAAAATT
* *
2510583 T-TTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAATTGTCTCAAGGAAGA
1 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGG-AGA
*
2510647 CAAAACTTTGTTT-TGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
65 CAAAACTTTGTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
2510711 CATAATT
130 CAAAATT
* *
2510718 TGTTTTAAGAGAAAATTTCTCAAGAGAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAG-GAGA
** * *
2510783 CAAAACTTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCATCTCAATAGAT
65 CAAAACTTTGTTT-AAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
2510848 ACAAAATT
129 ACAAAATT
* *
2510856 TGTTTTAAGAGAAAATGTATCAAGAAAGACAAAATTTGTTTTAAG
1 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAG
2510901 TAAATTAGCC
Statistics
Matches: 281, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
133 83 0.30
134 26 0.09
135 8 0.03
136 70 0.25
137 1 0.00
138 93 0.33
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (136 bp):
TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGGAGAC
AAAACTTTGTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
AAAATT
Found at i:2512333 original size:83 final size:85
Alignment explanation
Indices: 2512224--2512444 Score: 229
Period size: 89 Copynumber: 2.6 Consensus size: 85
2512214 GGCTAGCTGG
* *
2512224 ATCCATAAAGTTAGGGCATTCT-ACCAATTGCTCTAGAGGGACAACTCAA-TA-TATA-AATA-A
1 ATCCATAAAG-TGGGGCGTT-TAACCAATTGCTCTAGAGGGACAACTCAATTATTATATAATATA
* *
2512284 CTTTATCAGGTTAGCTGAATCTT
64 -TTTATCAGGCTAGCTGAATATT
* * *
2512307 ATCCATAAAGCTGGGGCGTTTAACCAATTGC-CTTAGAGGGACAGCTCAAGCTTTATTGTATAGT
1 ATCCATAAAG-TGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTCAA---TTATTATATAAT
2512371 ATATTTATCAGGCTAGCTGAATATT
61 ATATTTATCAGGCTAGCTGAATATT
* * *
2512396 ATCCATAAAGTCGGGGTGTTTAACAAATTGCTCTAGAGGGATAACTCAA
1 ATCCATAAAGT-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
2512445 GCTTTATTGT
Statistics
Matches: 115, Mismatches: 12, Indels: 16
0.80 0.08 0.11
Matches are distributed among these distances:
82 2 0.02
83 41 0.36
87 2 0.02
88 4 0.03
89 64 0.56
90 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (85 bp):
ATCCATAAAGTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATTATATAATATATT
TATCAGGCTAGCTGAATATT
Found at i:2512399 original size:89 final size:89
Alignment explanation
Indices: 2512285--2512457 Score: 260
Period size: 89 Copynumber: 1.9 Consensus size: 89
2512275 TATAAATAAC
* * *
2512285 TTTATCAGGTTAGCTGAATCTTATCCATAAAG-CTGGGGCGTTTAACCAATTGC-CTTAGAGGGA
1 TTTATCAGGCTAGCTGAATATTATCCATAAAGTC-GGGGCGTTTAACAAATTGCTC-TAGAGGGA
*
2512348 CAGCTCAAGCTTTATTGTATAGTATA
64 CAACTCAAGCTTTATTGTATAGTATA
* *
2512374 TTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGTGTTTAACAAATTGCTCTAGAGGGATA
1 TTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACAAATTGCTCTAGAGGGACA
2512439 ACTCAAGCTTTATTGTATA
66 ACTCAAGCTTTATTGTATA
2512458 TAAATAATAT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
89 74 0.97
90 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (89 bp):
TTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACAAATTGCTCTAGAGGGACA
ACTCAAGCTTTATTGTATAGTATA
Found at i:2515455 original size:30 final size:29
Alignment explanation
Indices: 2515402--2515460 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2515392 TGTAAATATA
* *
2515402 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
2515432 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
2515461 ATAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:2517547 original size:64 final size:63
Alignment explanation
Indices: 2517449--2517621 Score: 188
Period size: 64 Copynumber: 2.7 Consensus size: 63
2517439 CATCGATGCA
* * * * *
2517449 TTCTTTAATATGTGCATCGATGCACTACTCATGCATCGATACACAAATTACCTTCGATG-TT-
1 TTCTTTAAAAAGTGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTTC
* * *
2517510 TTCATTTAAAAAGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTACATTTGATGTTT
1 TTC-TTTAAAAA-G-TGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTT
2517575 C
63 C
* **
2517576 TTCTTTAAAGAGTGCATCGATGCACATTCAATATGCATCGATACAC
1 TTCTTTAAAAAGTGCATCGATGCAC--TCCTTATGCATCGATACAC
2517622 CTTGCCCAGA
Statistics
Matches: 93, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
61 3 0.03
62 6 0.06
63 14 0.15
64 42 0.45
65 25 0.27
66 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (63 bp):
TTCTTTAAAAAGTGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTTC
Found at i:2518086 original size:3 final size:3
Alignment explanation
Indices: 2518078--2518109 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2518068 GCTTACGGGG
2518078 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
2518110 GAAATAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2521185 original size:65 final size:64
Alignment explanation
Indices: 2521030--2521191 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 64
2521020 CTTTGACATG
* * * *
2521030 TGCATCGATGCACT-ACTCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTAAAAGGGA
1 TGCATCGATGCACTCAAT-ATGCATCGATACACCAATTACATTCGATGTTTTCATTTAAAAGAGA
** * *
2521094 TGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTC-TTT-AAAGAG
1 TGCATCGATGCACTCAATATGCATCGATACACCAATTACATTCGATG-TT-TTCATTTAAAAGAG
2521157 -
64 A
2521157 TGCATCGATGCACATTCAATATGCATCGATACACC
1 TGCATCGATGCAC--TCAATATGCATCGATACACC
2521192 TTGCCCAGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 13 0.16
64 44 0.53
65 23 0.28
66 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCACTCAATATGCATCGATACACCAATTACATTCGATGTTTTCATTTAAAAGAGA
Found at i:2521657 original size:3 final size:3
Alignment explanation
Indices: 2521649--2521680 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2521639 GCTTACGGGG
2521649 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
2521681 GAAATAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2522026 original size:20 final size:20
Alignment explanation
Indices: 2522001--2522038 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2521991 TTCCCCTTGA
2522001 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
2522021 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
2522039 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:2524050 original size:21 final size:21
Alignment explanation
Indices: 2524026--2524065 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2524016 AGTTAAAAAA
* *
2524026 ATGATAAAATAAAATAAATAT
1 ATGATAAAAGAAAAAAAATAT
*
2524047 ATGATGAAAGAAAAAAAAT
1 ATGATAAAAGAAAAAAAAT
2524066 GAAAAGTAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (21 bp):
ATGATAAAAGAAAAAAAATAT
Found at i:2525008 original size:20 final size:19
Alignment explanation
Indices: 2524959--2525008 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
2524949 TGGATTAGAT
2524959 AAAG-AATAAAAACAAAAC
1 AAAGAAATAAAAACAAAAC
*
2524977 ACAGAAAGTAAAATA-AAAAC
1 AAAGAAA-TAAAA-ACAAAAC
2524997 AAATGAAATAAA
1 AAA-GAAATAAA
2525009 GAGAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.12
19 2 0.08
20 16 0.62
21 5 0.19
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.10
Consensus pattern (19 bp):
AAAGAAATAAAAACAAAAC
Found at i:2525009 original size:25 final size:24
Alignment explanation
Indices: 2524963--2525018 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
2524953 TTAGATAAAG
*
2524963 AATAAAAACAAAACACAGAAAGTAA
1 AATAAAAACAAAACAAAGAAAG-AA
** * *
2524988 AATAAAAACAAATGAAATAAAGAG
1 AATAAAAACAAAACAAAGAAAGAA
2525012 AATAAAA
1 AATAAAA
2525019 GAATAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (24 bp):
AATAAAAACAAAACAAAGAAAGAA
Found at i:2529724 original size:16 final size:16
Alignment explanation
Indices: 2529703--2529734 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2529693 TGGGAACGGT
2529703 AATTTTTAAAATTATA
1 AATTTTTAAAATTATA
2529719 AATTTTTAAAATTATA
1 AATTTTTAAAATTATA
2529735 GGATACGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTTAAAATTATA
Found at i:2533117 original size:19 final size:19
Alignment explanation
Indices: 2533093--2533135 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2533083 ACTACATATT
2533093 GTATATATATTGTTTCCTA
1 GTATATATATTGTTTCCTA
2533112 GTATATATATTGTTTCCTA
1 GTATATATATTGTTTCCTA
2533131 GTATA
1 GTATA
2533136 ATCTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (19 bp):
GTATATATATTGTTTCCTA
Found at i:2533429 original size:131 final size:125
Alignment explanation
Indices: 2533250--2533491 Score: 349
Period size: 131 Copynumber: 1.9 Consensus size: 125
2533240 CATATTTTAA
*
2533250 ATATATATTCTTAACTTAAATAATAAACTTTGCCTACTTTAAACCAAAAAAGATACATTCGATAA
1 ATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACC--AAAA-ATACATTCGATAA
* *
2533315 ATTAAGAAAAAAAAATAAAATATATATTTTTATATTTAAGAGTTTAAATATTTTAAATATATATA
63 ATTAAG--AAAAAAATAAAATATATATTTTTATAGTTAAGAATTT-AATATTTTAAATATATATA
2533380 T
125 T
* * * * *
2533381 ATATATATTCTTACCTTAAATAATAAACTTGGGCTACTTTAAATCAAAAATATATTTGATAAATT
1 ATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAAATACATTCGATAAATT
*
2533446 AAGAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAATATT
66 AAGAAAAAAATAAAATATATATTTTTATAGTTAAGAATTTAATATT
2533492 ATACTAAGGA
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
125 6 0.06
126 34 0.33
128 17 0.17
129 4 0.04
131 41 0.40
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (125 bp):
ATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAAATACATTCGATAAATT
AAGAAAAAAATAAAATATATATTTTTATAGTTAAGAATTTAATATTTTAAATATATATAT
Found at i:2535654 original size:13 final size:13
Alignment explanation
Indices: 2535636--2535666 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2535626 TCTAAATGAA
2535636 ATTAAAAATATAC
1 ATTAAAAATATAC
2535649 ATTAAAAATATAC
1 ATTAAAAATATAC
2535662 ATTAA
1 ATTAA
2535667 TTAATGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAAATATAC
Found at i:2536584 original size:35 final size:34
Alignment explanation
Indices: 2536526--2536612 Score: 122
Period size: 35 Copynumber: 2.5 Consensus size: 34
2536516 ACCCTAAATT
*
2536526 TTAAAATATTTT-AATTTAGGGTTTAGAATGTAA
1 TTAAAGTATTTTGAATTTAGGGTTTAGAATGTAA
2536559 TTAAAGTATTTTAGAATTTAGGGTTTAGAATGTAA
1 TTAAAGTATTTT-GAATTTAGGGTTTAGAATGTAA
* *
2536594 TTGAAGTGTTTTGGAATTT
1 TTAAAGTATTTT-GAATTT
2536613 TGAACATGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 11 0.23
35 37 0.77
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (34 bp):
TTAAAGTATTTTGAATTTAGGGTTTAGAATGTAA
Found at i:2543883 original size:20 final size:20
Alignment explanation
Indices: 2543854--2543896 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2543844 ATTTCACCAC
*
2543854 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2543874 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
2543894 ATG
1 ATG
2543897 GTCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2545784 original size:16 final size:16
Alignment explanation
Indices: 2545763--2545801 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
2545753 TTGTGGGTGA
2545763 TATGTCGTGGCAATTT
1 TATGTCGTGGCAATTT
2545779 TATGTCGTGGCAATTT
1 TATGTCGTGGCAATTT
2545795 TATGTCG
1 TATGTCG
2545802 CACTCCGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.44
Consensus pattern (16 bp):
TATGTCGTGGCAATTT
Found at i:2552449 original size:20 final size:20
Alignment explanation
Indices: 2552420--2552461 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2552410 ATTTCACCAC
*
2552420 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2552440 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
2552460 AT
1 AT
2552462 AGGCTTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2559787 original size:122 final size:122
Alignment explanation
Indices: 2559568--2559811 Score: 452
Period size: 122 Copynumber: 2.0 Consensus size: 122
2559558 TGTTCCACTC
2559568 ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
1 ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
* *
2559633 GACCATCAATATCGATAACACATCAGCCATGAATGAACTGCCCATAGATTGCCATGA
66 GACCATCAATACCGATAACACATCAGCCATGAATGAACTGCCCATAGATTACCATGA
2559690 ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
1 ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
* *
2559755 GACCATCAATACCGATAACACATCAGCTATGAATGAATTGCCCATAGATTACCATGA
66 GACCATCAATACCGATAACACATCAGCCATGAATGAACTGCCCATAGATTACCATGA
2559812 CTGAGAAGCG
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (122 bp):
ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
GACCATCAATACCGATAACACATCAGCCATGAATGAACTGCCCATAGATTACCATGA
Found at i:2561158 original size:23 final size:19
Alignment explanation
Indices: 2561113--2561150 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2561103 TTGCTTTCGC
2561113 TATATATCTAAACAAACTT
1 TATATATCTAAACAAACTT
2561132 TATATATCTAAACAAACTT
1 TATATATCTAAACAAACTT
2561151 CTTGTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATATCTAAACAAACTT
Found at i:2562399 original size:90 final size:90
Alignment explanation
Indices: 2562245--2562409 Score: 262
Period size: 90 Copynumber: 1.8 Consensus size: 90
2562235 AGACGAATGA
* *
2562245 TATAATATTTAATTTTAATATTAAATAAAAATATTATTTTCTTTATTTAATAATAATGTAATATT
1 TATAATATTTAATATTAATATTAAATAAAAATATTATTTTATTTATTTAATAATAATGTAATA-T
2562310 TTTATCTTATAATATTTTCTTATTGG
65 TTTATCTTATAATATTTTCTTATTGG
* *
2562336 TATAAT-TTTGATATTAATATTAATATAAAAATATTATTTTATTTA-TTAATAATAATGTGATAT
1 TATAATATTTAATATTAATATTAA-ATAAAAATATTATTTTATTTATTTAATAATAATGTAATAT
2562399 TTTATCTTATA
65 TTTATCTTATA
2562410 TTTTCTTATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
89 12 0.17
90 31 0.45
91 26 0.38
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (90 bp):
TATAATATTTAATATTAATATTAAATAAAAATATTATTTTATTTATTTAATAATAATGTAATATT
TTATCTTATAATATTTTCTTATTGG
Found at i:2562456 original size:20 final size:19
Alignment explanation
Indices: 2562407--2562457 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
2562397 ATTTTATCTT
2562407 ATATTTTCTTATTAATTTTA
1 ATATTTT-TTATTAATTTTA
*
2562427 AGATTCTTTTACTT-ATTTCTA
1 ATATT-TTTTA-TTAATTT-TA
2562448 ATATTTTTTA
1 ATATTTTTTA
2562458 AAAACCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (19 bp):
ATATTTTTTATTAATTTTA
Found at i:2564866 original size:24 final size:24
Alignment explanation
Indices: 2564830--2564891 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
2564820 TTCTAAGGTA
*
2564830 TATTT-ATTATATTTTTATATTT-T
1 TATTTAATT-TATTTTAATATTTAT
2564853 GTATTTAATTTA-TTTAATATTTACT
1 -TATTTAATTTATTTTAATATTTA-T
2564878 TATTTAATTT-TTTT
1 TATTTAATTTATTTT
2564892 GCAGATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
23 9 0.27
24 20 0.61
25 4 0.12
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (24 bp):
TATTTAATTTATTTTAATATTTAT
Found at i:2568428 original size:13 final size:13
Alignment explanation
Indices: 2568410--2568438 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2568400 ATCTAAATGC
2568410 ATTTTGGGTAGGT
1 ATTTTGGGTAGGT
2568423 ATTTTGGGTAGGT
1 ATTTTGGGTAGGT
2568436 ATT
1 ATT
2568439 GCCATGTTAA
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:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (13 bp):
ATTTTGGGTAGGT
Found at i:2587508 original size:3 final size:3
Alignment explanation
Indices: 2587500--2587532 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2587490 TTTTCTCTCT
2587500 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2587533 GTACCAGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2588797 original size:22 final size:24
Alignment explanation
Indices: 2588750--2588799 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2588740 CTTCTTATTT
*
2588750 TATTTAATATTACATTATAGTATA
1 TATTTAATATTACATCATAGTATA
*
2588774 TATTTGATATTAC-TCAT-GTATA
1 TATTTAATATTACATCATAGTATA
2588796 TATT
1 TATT
2588800 ATTATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 3 0.12
24 12 0.50
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (24 bp):
TATTTAATATTACATCATAGTATA
Found at i:2590174 original size:16 final size:16
Alignment explanation
Indices: 2590137--2590174 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2590127 TTCTTGCCAT
*
2590137 TTTTTATTTCTATTTA
1 TTTTTATTTCTATTAA
2590153 TTTTTATTT-TATTAA
1 TTTTTATTTCTATTAA
2590168 TTGTTTA
1 TT-TTTA
2590175 CCTTTGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTATTTCTATTAA
Found at i:2593596 original size:20 final size:21
Alignment explanation
Indices: 2593573--2593619 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
2593563 ATCAAGAATA
2593573 AAAAGAA-AAGAA-ACAAAAAG
1 AAAAGAACAAGAACA-AAAAAG
2593593 AAAA-AACAAGAACAAAAAAG
1 AAAAGAACAAGAACAAAAAAG
2593613 AAAAGAA
1 AAAAGAA
2593620 GCAAAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAAGAACAAGAACAAAAAAG
Found at i:2593611 original size:15 final size:16
Alignment explanation
Indices: 2593572--2593626 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
2593562 AATCAAGAAT
*
2593572 AAAAAGAAAAGAAACA
1 AAAAAGAAAAGAAGCA
* *
2593588 AAAAGAAAAAACAAGAACA
1 AAAA-AGAAAAGAAG--CA
2593607 AAAAAGAAAAGAAGCA
1 AAAAAGAAAAGAAGCA
2593623 AAAA
1 AAAA
2593627 TCAAAGGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.32
17 7 0.23
18 8 0.26
19 6 0.19
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGAAGCA
Found at i:2594707 original size:18 final size:18
Alignment explanation
Indices: 2594684--2594719 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2594674 TCAACATCAA
*
2594684 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
2594702 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
2594720 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:2595282 original size:38 final size:36
Alignment explanation
Indices: 2595206--2595282 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
2595196 GTGCTCACCA
* * *
2595206 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAAACT
2595242 TTGTCTCTCTTGAGACAGTTTCCCTTCAAAAAAAACCT
1 TTGTCTCTCTTGAGACAGTTTCCCTT-AAAAAAAA-CT
2595280 TTG
1 TTG
2595283 AAATTGTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 25 0.69
37 6 0.17
38 5 0.14
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAAACT
Found at i:2595524 original size:37 final size:37
Alignment explanation
Indices: 2595454--2595525 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2595444 TGGAACTAAG
* * *
2595454 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
2595491 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
2595526 CAGATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:2596569 original size:106 final size:106
Alignment explanation
Indices: 2596141--2596580 Score: 641
Period size: 106 Copynumber: 4.2 Consensus size: 106
2596131 ATATCACGCC
*
2596141 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTT-C
1 ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCC
* *
2596205 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
2596247 ACTC-AAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
1 ACTCGAA-ACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
* * **
2596311 CAATTTCAGAGCCAATTTCAACTTCACAACAAAGGGCATTGG
65 CAATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
* * * * *
2596353 ACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGACAGCTGATTGTCAATAAACAATTTCCC
1 ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
2596418 AATTTCAAAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
* *
2596459 ACTCGAAACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTTAACAAACAATTTCCC
1 ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * * *
2596524 AATTCCATAACCAATTTCAACTTCACGGTAAACGATATTGG
66 AATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
* *
2596565 ACTCGGAACAATACAA
1 ACTCGAAACAACACAA
2596581 CCTACTTGGA
Statistics
Matches: 300, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
105 4 0.01
106 295 0.98
107 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (106 bp):
ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
Found at i:2598138 original size:4 final size:4
Alignment explanation
Indices: 2598131--2598198 Score: 50
Period size: 4 Copynumber: 16.8 Consensus size: 4
2598121 CCTTCGTTTG
* * * * *
2598131 TTTA TTTA TTTA -TT- TTTA TTTTC TTTA TTCA TTGA TTCA TTTT TCTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
2598179 TTTTA TTTA TTTA TTTA TTT
1 -TTTA TTTA TTTA TTTA TTT
2598199 TATTCCGTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
3 4 0.08
4 38 0.75
5 8 0.16
6 1 0.02
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:2600939 original size:36 final size:37
Alignment explanation
Indices: 2600869--2600942 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 37
2600859 TGGAAAATAT
*
2600869 TTATATATTTTCTTTAAAAAAATTAAATTCATAAAAA
1 TTATATATTTTCTTTAAAAAAATTAAAATCATAAAAA
*
2600906 TTATATAATTTT-TTT-ACAAAATTAAAAAT-ATAAAAA
1 TTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAAAA
2600942 T
1 T
2600943 GTTTAATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 15 0.45
37 13 0.39
38 5 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (37 bp):
TTATATATTTTCTTTAAAAAAATTAAAATCATAAAAA
Found at i:2601404 original size:16 final size:18
Alignment explanation
Indices: 2601372--2601404 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2601362 TTATTTGACT
2601372 GAGAATTTAAGGAGAGAG
1 GAGAATTTAAGGAGAGAG
2601390 GAGAA-TTAA-GAGAGA
1 GAGAATTTAAGGAGAGA
2601405 AAGTGACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.15
Consensus pattern (18 bp):
GAGAATTTAAGGAGAGAG
Found at i:2605182 original size:48 final size:48
Alignment explanation
Indices: 2605089--2605183 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
2605079 ACATATAAAG
*
2605089 AAAAAACATAATCATTACATTAATCTTTTGATGTTTTAATAAAAAATA
1 AAAAAACATAATCATTACATTAATCTTTTGATGGTTTAATAAAAAATA
* *
2605137 AAAAAACATAATCATTACATTAATCTTTTGGTAGGTTTAGTAAAAAA
1 AAAAAACATAATCATTACATTAATCTTTTGAT-GGTTTAATAAAAAA
2605184 ATTGGTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 31 0.72
49 12 0.28
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.36
Consensus pattern (48 bp):
AAAAAACATAATCATTACATTAATCTTTTGATGGTTTAATAAAAAATA
Found at i:2607123 original size:3 final size:3
Alignment explanation
Indices: 2607117--2607212 Score: 64
Period size: 3 Copynumber: 34.0 Consensus size: 3
2607107 AATTTCGTCC
* * * *
2607117 ATT ATT ATT A-T ATAT ATA ATT A-T ATT CTT CTT ATT -TT ATT TTT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
2607160 A-T ATT -TT ATT -TT ATT -TT CTT TTT ACTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
2607202 ATT ATT -TT ATT
1 ATT ATT ATT ATT
2607213 TTGTTCTATA
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
2 16 0.21
3 53 0.71
4 6 0.08
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:2607157 original size:5 final size:5
Alignment explanation
Indices: 2607147--2607214 Score: 52
Period size: 5 Copynumber: 13.4 Consensus size: 5
2607137 TATATTCTTC
* * *
2607147 TTATT TTA-T TT-TT ATATT TTATT TTATT TTCTT TT-TAC TTATT ATTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTAT-T TTATT -TTATT
2607196 ATTATT ATTATT TTATT TT
1 -TTATT -TTATT TTATT TT
2607215 GTTCTATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 6 0.11
5 29 0.55
6 18 0.34
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:2607575 original size:19 final size:19
Alignment explanation
Indices: 2607553--2607618 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
2607543 TTTCTAAATG
*
2607553 TTTTTTATTTTTTATTTCA
1 TTTTATATTTTTTATTTCA
2607572 TTTTATA-TTTTTAGTTT-A
1 TTTTATATTTTTTA-TTTCA
*
2607590 TTTAATATTTTTTA--TCA
1 TTTTATATTTTTTATTTCA
2607607 TTTT-TATTTTTT
1 TTTTATATTTTTT
2607619 TCTAACATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 9 0.22
17 4 0.10
18 13 0.32
19 15 0.37
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATATTTTTTATTTCA
Found at i:2607582 original size:18 final size:18
Alignment explanation
Indices: 2607555--2607617 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
2607545 TCTAAATGTT
2607555 TTTTAT-TTTTTATTTCA
1 TTTTATATTTTTATTTCA
2607572 TTTTATATTTTTAGTTT-A
1 TTTTATATTTTTA-TTTCA
* *
2607590 TTTAATATTTTT-TATCA
1 TTTTATATTTTTATTTCA
2607607 TTTT-TATTTTT
1 TTTTATATTTTT
2607618 TTCTAACATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 9 0.22
17 10 0.25
18 18 0.45
19 3 0.08
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTATATTTTTATTTCA
Found at i:2607618 original size:18 final size:17
Alignment explanation
Indices: 2607554--2607619 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
2607544 TTCTAAATGT
2607554 TTTTTATTTTTTATTTCA
1 TTTTTATTTTTT-TTTCA
*
2607572 TTTTATATTTTTAGTTT-A
1 TTTT-TATTTTT-TTTTCA
* *
2607590 -TTTAATATTTTTTATCA
1 TTTTTAT-TTTTTTTTCA
2607607 TTTTTATTTTTTT
1 TTTTTATTTTTTT
2607620 CTAACATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
16 4 0.11
17 14 0.37
18 10 0.26
19 10 0.26
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTTTTTCA
Found at i:2607631 original size:28 final size:27
Alignment explanation
Indices: 2607572--2607630 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
2607562 TTTTATTTCA
*
2607572 TTTTATATTTTTAGTTTATTTAATATT
1 TTTTATATTTTTAGTTTATTTAACATT
* *
2607599 TTTTATCATTTTTATTTTTTTCTAACATT
1 TTTTAT-ATTTTTAGTTTATT-TAACATT
2607628 TTT
1 TTT
2607631 AACTTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 6 0.22
28 12 0.44
29 9 0.33
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTATATTTTTAGTTTATTTAACATT
Found at i:2608094 original size:20 final size:20
Alignment explanation
Indices: 2608068--2608116 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 20
2608058 GCTCCAACTT
2608068 TTAATATTATTTATATAC-A
1 TTAATATTATTTATATACTA
*
2608087 -T-ATAATATTTATATACTA
1 TTAATATTATTTATATACTA
2608105 TTAATATTATTT
1 TTAATATTATTT
2608117 TACTATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 1 0.04
20 8 0.32
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATATTATTTATATACTA
Found at i:2608097 original size:17 final size:17
Alignment explanation
Indices: 2608075--2608136 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
2608065 CTTTTAATAT
2608075 TATTTATATAC-ATATAA
1 TATTTATATACTAT-TAA
2608092 TATTTATATACTATTAA
1 TATTTATATACTATTAA
*
2608109 TA-TTATTTTACTATTATA
1 TATTTA-TATACTATTA-A
*
2608127 TATATATATA
1 TATTTATATA
2608137 TAACCTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.08
17 25 0.66
18 8 0.21
19 2 0.05
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTATATACTATTAA
Found at i:2608137 original size:37 final size:37
Alignment explanation
Indices: 2608068--2608138 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
2608058 GCTCCAACTT
*
2608068 TTAATATTATTTATATACATATAATATTTATATACTA
1 TTAATATTATTTATATACATATAATATATATATACTA
*
2608105 TTAATATTATTT-TACTA-TTATATATATATATATA
1 TTAATATTATTTATA-TACATATA-ATATATATATA
2608139 ACCTTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 6 0.20
37 24 0.80
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (37 bp):
TTAATATTATTTATATACATATAATATATATATACTA
Found at i:2608690 original size:13 final size:14
Alignment explanation
Indices: 2608667--2608707 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
2608657 ATTATAATGT
*
2608667 TTATAAAAATAATA
1 TTATTAAAATAATA
2608681 TT-TTAAAAT-ATA
1 TTATTAAAATAATA
*
2608693 TTATTAAAAAAATA
1 TTATTAAAATAATA
2608707 T
1 T
2608708 ACAACAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 5 0.22
13 12 0.52
14 6 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTATTAAAATAATA
Found at i:2610317 original size:16 final size:17
Alignment explanation
Indices: 2610293--2610325 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2610283 AACTTTTGTC
*
2610293 GGTTCCTTCGTTTGTTT
1 GGTTCCTTCATTTGTTT
2610310 GGTT-CTTCATTTGTTT
1 GGTTCCTTCATTTGTTT
2610326 TTTAATTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.03, C:0.15, G:0.21, T:0.61
Consensus pattern (17 bp):
GGTTCCTTCATTTGTTT
Found at i:2610743 original size:21 final size:21
Alignment explanation
Indices: 2610719--2610780 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2610709 GTTTCTCAAA
2610719 TTAATAATTTAATTTATATTT
1 TTAATAATTTAATTTATATTT
*
2610740 TTAATTATATTAATTTAT-TTT
1 TTAATAAT-TTAATTTATATTT
*
2610761 TAAATTAATTTAA-TTATATT
1 TTAA-TAATTTAATTTATATT
2610781 AATTCTATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 4 0.11
21 19 0.54
22 12 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAATAATTTAATTTATATTT
Found at i:2614905 original size:37 final size:38
Alignment explanation
Indices: 2614820--2614905 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
2614810 ATTCAACCTT
*
2614820 TTTTATATTTTTAATTTTGTAAAAAAAATTATATAAATA
1 TTTTATA-ATTTAATTTTGTAAAAAAAATTATATAAATA
* *
2614859 --TTATGAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAATTTTGTAAAAAAAATTATATAAATA
2614895 TTTTATAATTT
1 TTTTATAATTT
2614906 GTAATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
36 10 0.24
37 26 0.63
38 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTTATAATTTAATTTTGTAAAAAAAATTATATAAATA
Found at i:2618830 original size:48 final size:48
Alignment explanation
Indices: 2618737--2618831 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
2618727 ACATATAAAG
*
2618737 AAAAAACATAATCATTACATTAATCTTTTGATGTTTTAATAAAAAATT
1 AAAAAACATAATCATTACATTAATCTTTTGATGGTTTAATAAAAAATT
* *
2618785 AAAAAACATAATCATTACATTAATCTTTTGGTAGGTTTAGTAAAAAA
1 AAAAAACATAATCATTACATTAATCTTTTGAT-GGTTTAATAAAAAA
2618832 ATTGGTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 31 0.72
49 12 0.28
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (48 bp):
AAAAAACATAATCATTACATTAATCTTTTGATGGTTTAATAAAAAATT
Found at i:2627156 original size:17 final size:17
Alignment explanation
Indices: 2627125--2627158 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2627115 ACGTGTATTT
**
2627125 TATTGTTAATGTGATAA
1 TATTGTTAACATGATAA
2627142 TATTGTTAACATGATAA
1 TATTGTTAACATGATAA
2627159 CTTACACGGT
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:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
TATTGTTAACATGATAA
Found at i:2627366 original size:2 final size:2
Alignment explanation
Indices: 2627359--2627385 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2627349 CTTATTATTA
2627359 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2627386 ATGGTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2636402 original size:2 final size:2
Alignment explanation
Indices: 2636395--2636431 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2636385 AAGTTATTTG
2636395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2636432 GGCTGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2643369 original size:13 final size:13
Alignment explanation
Indices: 2643353--2643382 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2643343 TATAAAAATT
2643353 ATATATTATTTAA
1 ATATATTATTTAA
*
2643366 ATATATTATTTTA
1 ATATATTATTTAA
2643379 ATAT
1 ATAT
2643383 TAATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATATTATTTAA
Found at i:2643798 original size:240 final size:240
Alignment explanation
Indices: 2643376--2643857 Score: 853
Period size: 240 Copynumber: 2.0 Consensus size: 240
2643366 ATATATTATT
2643376 TTAATATTAATAATTTAGTTTATATTTTTTAATTATATTAATTTTATTCTTTGACTAACATTGAT
1 TTAATATTAATAATTTAGTTTATATTTTTTAATTATATTAATTTTATTCTTTGACTAACATTGAT
*
2643441 TATTATATTACTTATATAACGATTAAGAATATTGACATGATAATTTATTATATTATCGTGATAGT
66 TATTATATTACTTATATAACGATTAAGAATATTGACATGATAATTTATTATATAATCGTGATAGT
2643506 TTACTGTATTGACGTATTAATGAGTGAATTATATATACAAAAGTTAAATTAAAATTTGTACCAAC
131 TTACTGTATTGACGTATTAATGAGTGAATTATATATACAAAAGTTAAATTAAAATTTGTACCAAC
2643571 TTTGAAATTGTAATTGA-CTTTTAATCTAATTTAAGGACAATTTA
196 TTTGAAATTGTAATTGATCTTTTAATCTAATTTAAGGACAATTTA
* *
2643615 TTAATATTAATAATTTAGTTTATATTTTTTAAATT-TTTTAAATTTTATTCTTTGACTTACATTG
1 TTAATATTAATAATTTAGTTTATATTTTTT-AATTATATT-AATTTTATTCTTTGACTAACATTG
*
2643679 ATTATTATATTACTTATATAACGATTTAGAATATTGACATGATAATTTATTATATAATCGTGATA
64 ATTATTATATTACTTATATAACGATTAAGAATATTGACATGATAATTTATTATATAATCGTGATA
* *
2643744 GTTTA-TAGTATTGACGTATTGATGAGTGAATTATATATACAAAAGTTAAATTAAAATTTTTACC
129 GTTTACT-GTATTGACGTATTAATGAGTGAATTATATATACAAAAGTTAAATTAAAATTTGTACC
*
2643808 AACTTTGAAATTGTAATTGATTTTTTAATCTAATTTAAGGACAATTTA
193 AACTTTGAAATTGTAATTGATCTTTTAATCTAATTTAAGGACAATTTA
2643856 TT
1 TT
2643858 TTAATTAAAA
Statistics
Matches: 232, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
239 34 0.15
240 170 0.73
241 28 0.12
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (240 bp):
TTAATATTAATAATTTAGTTTATATTTTTTAATTATATTAATTTTATTCTTTGACTAACATTGAT
TATTATATTACTTATATAACGATTAAGAATATTGACATGATAATTTATTATATAATCGTGATAGT
TTACTGTATTGACGTATTAATGAGTGAATTATATATACAAAAGTTAAATTAAAATTTGTACCAAC
TTTGAAATTGTAATTGATCTTTTAATCTAATTTAAGGACAATTTA
Found at i:2646235 original size:22 final size:21
Alignment explanation
Indices: 2646183--2646236 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
2646173 GGCATGTGAA
*
2646183 ATCTATGTCCCGAAGGACGTC
1 ATCTATGTCCCGAAGGACCTC
2646204 ATCTATGTCCCGAAGGACCT-
1 ATCTATGTCCCGAAGGACCTC
2646224 ATTCATATGTCCC
1 A-TC-TATGTCCC
2646237 CAATGACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.03
21 21 0.70
22 8 0.27
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (21 bp):
ATCTATGTCCCGAAGGACCTC
Found at i:2646563 original size:20 final size:18
Alignment explanation
Indices: 2646524--2646563 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
2646514 TGCATACCTC
*
2646524 ATGTTCATATAATCTCTT
1 ATGTTCATATAATATCTT
2646542 ATGTTCATATCACATATCTT
1 ATGTTCATAT-A-ATATCTT
2646562 AT
1 AT
2646564 AACATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.47
Consensus pattern (18 bp):
ATGTTCATATAATATCTT
Found at i:2647621 original size:17 final size:18
Alignment explanation
Indices: 2647599--2647632 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2647589 CCATAACTTA
2647599 TCATT-CTTTAAGTTTCT
1 TCATTCCTTTAAGTTTCT
2647616 TCATTCCTTTAAGTTTC
1 TCATTCCTTTAAGTTTC
2647633 AATAGTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (18 bp):
TCATTCCTTTAAGTTTCT
Found at i:2649679 original size:64 final size:63
Alignment explanation
Indices: 2649610--2649746 Score: 156
Period size: 64 Copynumber: 2.1 Consensus size: 63
2649600 TACACTGATA
*
2649610 GTGCATCGATGCATAAATATGC-TTCGATGTTTTGAAAAAT-CCT-GAGTGCATCGATGCA-TGT
1 GTGCATCG-TGCATAAA-AT-CATTCGATGTTTT-AAAAATACATGGAGTGCATCGATGCATTGT
*
2649671 CTT
62 -AT
*
2649674 GTGCATCTGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATTGTAT
1 GTGCATC-GTGCATAAAATC-ATTCGATGTTTTAAAAATACATGGAGTGCATCGATGCATTGTAT
2649739 GTGCATCG
1 GTGCATCG
2649747 GTACACTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
62 1 0.02
63 7 0.11
64 29 0.45
65 24 0.38
66 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (63 bp):
GTGCATCGTGCATAAAATCATTCGATGTTTTAAAAATACATGGAGTGCATCGATGCATTGTAT
Found at i:2649764 original size:65 final size:65
Alignment explanation
Indices: 2649632--2649818 Score: 186
Period size: 65 Copynumber: 2.9 Consensus size: 65
2649622 ATAAATATGC
* * * * *
2649632 TTCGATGTTTTGAAAAAT-CCTGAGTGCATCGATGCA-TGTCTTGTGCATCTGTGCA-TAAAATC
1 TTCGATGTTTT-AATAATACATGAGTGCATCGATGCATTGT-TTGTGCATCGGTACACTAAAAGC
2649694 AA
64 AA
* *
2649696 TTCGATGTTTTAATAATACATGGAGTGCATCGATGCATTGTATGTGCATCGGTACACT-AAAGCT
1 TTCGATGTTTTAATAATACAT-GAGTGCATCGATGCATTGTTTGTGCATCGGTACACTAAAAGCA
2649760 A
65 A
* * * * *
2649761 TTCGATG-TTCAATTAAAACAAGAGTGCATCGTTGCATTGATTTATGCATCGGTACACT
1 TTCGATGTTTTAA-TAATACATGAGTGCATCGATGCATTG-TTTGTGCATCGGTACACT
2649819 TACCTGGAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
63 5 0.05
64 34 0.33
65 61 0.59
66 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (65 bp):
TTCGATGTTTTAATAATACATGAGTGCATCGATGCATTGTTTGTGCATCGGTACACTAAAAGCAA
Found at i:2657686 original size:65 final size:65
Alignment explanation
Indices: 2657527--2657692 Score: 196
Period size: 65 Copynumber: 2.6 Consensus size: 65
2657517 GAAAAAGCCT
* *
2657527 GGGTGCATCGATGCA-TGTCTTGTGCATCGGTGCA-TAAAATCAATTTGATGTTTCAATAATACA
1 GGGTGCATCGATGCATTGT-TTGTGCATCGGTACACTAAAATCAATTTGATGTTTCAATAAAACA
*
2657590 T
65 A
* * *
2657591 GGAGTGCATCGATGCATTGTATGTGCATCGGTACACTAAAGT-TATTTGATG-TTCAATTAAAAC
1 GG-GTGCATCGATGCATTGTTTGTGCATCGGTACACTAAAATCAATTTGATGTTTCAA-TAAAAC
2657654 AA
64 AA
* *
2657656 GGGTGCATCGATGCATTGATTTATGAATCGGTACACT
1 GGGTGCATCGATGCATTG-TTTGTGCATCGGTACACT
2657693 TACCTGAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
64 23 0.26
65 57 0.65
66 8 0.09
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (65 bp):
GGGTGCATCGATGCATTGTTTGTGCATCGGTACACTAAAATCAATTTGATGTTTCAATAAAACAA
Found at i:2658489 original size:22 final size:22
Alignment explanation
Indices: 2658462--2658509 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
2658452 GAAAGATTGA
2658462 CCCTTTTTAATAAAAGATCAAT
1 CCCTTTTTAATAAAAGATCAAT
* *
2658484 CCC-TTTTAATAAAGGATCGAT
1 CCCTTTTTAATAAAAGATCAAT
2658505 CCCTT
1 CCCTT
2658510 ATGCATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.35
Consensus pattern (22 bp):
CCCTTTTTAATAAAAGATCAAT
Found at i:2659925 original size:20 final size:20
Alignment explanation
Indices: 2659900--2659946 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
2659890 AAAACAATAG
2659900 ATTAAATAAATAATATACTA
1 ATTAAATAAATAATATACTA
2659920 ATTAAATAAATAATATACTA
1 ATTAAATAAATAATATACTA
2659940 AGTTAAA
1 A-TTAAA
2659947 AATAAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATTAAATAAATAATATACTA
Found at i:2660150 original size:18 final size:16
Alignment explanation
Indices: 2660108--2660153 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
2660098 AATATTGGTC
*
2660108 AAATAATTA-AATATA
1 AAATAAATATAATATA
2660123 AAATAAATATAATATA
1 AAATAAATATAATATA
2660139 ATAATAAAATATAAT
1 A-AAT-AAATATAAT
2660154 TAGCTTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
17 3 0.11
18 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAAATATAATATA
Found at i:2660413 original size:21 final size:20
Alignment explanation
Indices: 2660396--2660433 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2660386 GTTAGATTAA
2660396 TAAAATTT-GATTTAAGATT
1 TAAAATTTAGATTTAAGATT
2660415 TAAAATTTAAGATTTAAGA
1 TAAAATTT-AGATTTAAGA
2660434 CCATGTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAATTTAGATTTAAGATT
Found at i:2660416 original size:7 final size:7
Alignment explanation
Indices: 2660404--2660433 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2660394 AATAAAATTT
2660404 GATTTAA
1 GATTTAA
2660411 GATTTAA
1 GATTTAA
*
2660418 AATTTAA
1 GATTTAA
2660425 GATTTAA
1 GATTTAA
2660432 GA
1 GA
2660434 CCATGTGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (7 bp):
GATTTAA
Found at i:2662161 original size:14 final size:15
Alignment explanation
Indices: 2662142--2662170 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2662132 TGCGTTTTCC
2662142 AAAATGTCT-TCTTA
1 AAAATGTCTATCTTA
2662156 AAAATGTCTATCTTA
1 AAAATGTCTATCTTA
2662171 TCCGATGTAC
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:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (15 bp):
AAAATGTCTATCTTA
Found at i:2663544 original size:16 final size:16
Alignment explanation
Indices: 2663523--2663553 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2663513 ATAATTGAGG
2663523 ATATTTAGAATAAATT
1 ATATTTAGAATAAATT
*
2663539 ATATTTTGAATAAAT
1 ATATTTAGAATAAAT
2663554 AGATCGTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATATTTAGAATAAATT
Found at i:2663733 original size:18 final size:19
Alignment explanation
Indices: 2663710--2663749 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2663700 CTGTTGGTAG
2663710 AATTATAAGAATAATC-AT
1 AATTATAAGAATAATCAAT
**
2663728 AATTATAATTATAATCAAT
1 AATTATAAGAATAATCAAT
2663747 AAT
1 AAT
2663750 CATACATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTATAAGAATAATCAAT
Found at i:2667101 original size:24 final size:23
Alignment explanation
Indices: 2667074--2667122 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2667064 CTTTTTAGGT
*
2667074 AAAATGAATTAATTATTTTTCATG
1 AAAA-GAATTAACTATTTTTCATG
*
2667098 AAAAGACTTAACTATTTTTCATG
1 AAAAGAATTAACTATTTTTCATG
2667121 AA
1 AA
2667123 TAAAGATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (23 bp):
AAAAGAATTAACTATTTTTCATG
Found at i:2679901 original size:2 final size:2
Alignment explanation
Indices: 2679894--2679921 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2679884 AGCAACAAAC
2679894 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
2679922 CACAGATACA
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:2685551 original size:12 final size:12
Alignment explanation
Indices: 2685536--2685564 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2685526 CTCATCATCT
2685536 CCCACATCTTCA
1 CCCACATCTTCA
2685548 CCCACATCTTCA
1 CCCACATCTTCA
2685560 CCCAC
1 CCCAC
2685565 CACCCGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.55, G:0.00, T:0.21
Consensus pattern (12 bp):
CCCACATCTTCA
Found at i:2687023 original size:27 final size:27
Alignment explanation
Indices: 2686981--2687048 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
2686971 CTGTAGGAAT
2686981 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
2687006 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
2687033 TATAGAGATATGATTT
1 TATAGAGATATGATTT
2687049 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:2687412 original size:19 final size:19
Alignment explanation
Indices: 2687388--2687424 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2687378 ATAATGCGGT
2687388 CTGATGCGATCCGATGCGA
1 CTGATGCGATCCGATGCGA
* *
2687407 CTGATGCGGTCTGATGCG
1 CTGATGCGATCCGATGCG
2687425 GGCCGATGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.24, G:0.35, T:0.24
Consensus pattern (19 bp):
CTGATGCGATCCGATGCGA
Found at i:2687846 original size:16 final size:16
Alignment explanation
Indices: 2687821--2687859 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2687811 TAGATAAGTT
* *
2687821 CTTTTTGTTGCAATAG
1 CTTTTAGTTGCAAAAG
2687837 CTTTTAGTTGCAAAAG
1 CTTTTAGTTGCAAAAG
2687853 CTTTTAG
1 CTTTTAG
2687860 CTTTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (16 bp):
CTTTTAGTTGCAAAAG
Found at i:2687958 original size:16 final size:16
Alignment explanation
Indices: 2687933--2687987 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
2687923 TAGATAAGTT
*
2687933 CTTTTTGTTGCAATAG
1 CTTTTAGTTGCAATAG
2687949 CTTTTAGTTGCAATAG
1 CTTTTAGTTGCAATAG
*
2687965 CTTTTAGTTGCAAAAG
1 CTTTTAGTTGCAATAG
2687981 CTTTTAG
1 CTTTTAG
2687988 CTTTTAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (16 bp):
CTTTTAGTTGCAATAG
Found at i:2687958 original size:112 final size:112
Alignment explanation
Indices: 2687761--2687971 Score: 404
Period size: 112 Copynumber: 1.9 Consensus size: 112
2687751 ATGTGTACTA
*
2687761 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTATGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
2687826 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
66 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
2687873 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
*
2687938 TGTTGCAATAGCTTTTAGTTGCAATAGCTTTTAG
66 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAG
2687972 TTGCAAAAGC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 97 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (112 bp):
AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
Found at i:2694132 original size:14 final size:14
Alignment explanation
Indices: 2694113--2694166 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
2694103 TTTGATTAAT
*
2694113 TTTATGTTTGTTCG
1 TTTATATTTGTTCG
* *
2694127 TTTATGTTTGTTTG
1 TTTATATTTGTTCG
* *
2694141 TTTACATTTGTTCA
1 TTTATATTTGTTCG
2694155 TTTATATTTGTT
1 TTTATATTTGTT
2694167 TATCATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.13, C:0.06, G:0.15, T:0.67
Consensus pattern (14 bp):
TTTATATTTGTTCG
Found at i:2700540 original size:12 final size:12
Alignment explanation
Indices: 2700516--2700548 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2700506 AATAAGTATA
2700516 ATAA-AAAAATT
1 ATAACAAAAATT
*
2700527 ATAACAAAATTT
1 ATAACAAAAATT
2700539 ATAACAAAAA
1 ATAACAAAAA
2700549 ATCGCACGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACAAAAATT
Found at i:2700892 original size:51 final size:51
Alignment explanation
Indices: 2700813--2700924 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 51
2700803 CTACGTGGCG
* * * **
2700813 TATAGCGCGGATCAGGGGGCGCGCTATAC-TCACGTATAAGCCATGTCAGCA
1 TATAGCGCGGATCAGGGGGCACGCTATACACCACGT-GAAGCCAAATCAGCA
* * *
2700864 TATAGCGCGGTAT-AGGGGGCATGTTATACACCACGTGACGCCAAATCAGCA
1 TATAGCGCGG-ATCAGGGGGCACGCTATACACCACGTGAAGCCAAATCAGCA
2700915 TATAGCGCGG
1 TATAGCGCGG
2700925 GACAGAGAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 44 0.86
52 7 0.14
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (51 bp):
TATAGCGCGGATCAGGGGGCACGCTATACACCACGTGAAGCCAAATCAGCA
Found at i:2701026 original size:29 final size:29
Alignment explanation
Indices: 2700956--2701029 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
2700946 CAACGAGTGT
* * *
2700956 TAGATCGGGAAATATAATCTGACCGGTGT
1 TAGATCGGAAAATATAATCTGACCGATGC
**
2700985 TAGATCAAAAAATATAATCTGACCGATGC
1 TAGATCGGAAAATATAATCTGACCGATGC
*
2701014 TAGATCGGTAAATATA
1 TAGATCGGAAAATATA
2701030 CCGATCACCG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (29 bp):
TAGATCGGAAAATATAATCTGACCGATGC
Done.