Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 16
Found at i:2452737 original size:24 final size:24
Alignment explanation
Indices: 2452710--2452763 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2452700 GTATTCGAAA
2452710 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2452734 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2452758 TTTGAT
1 TTTGAT
2452764 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2453516 original size:18 final size:18
Alignment explanation
Indices: 2453493--2453528 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2453483 AAGCAAAAGG
2453493 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
2453511 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
2453529 CAACCGGCTT
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:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:2453960 original size:20 final size:20
Alignment explanation
Indices: 2453933--2453985 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2453923 CGCTTATTTT
2453933 GCGTTGCGAATTTAACTTTC
1 GCGTTGCGAATTTAACTTTC
*
2453953 GTGTTGCGAATTTAACTTTC
1 GCGTTGCGAATTTAACTTTC
*
2453973 GCGTTACGAATTT
1 GCGTTGCGAATTT
2453986 GTACCTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGTTGCGAATTTAACTTTC
Found at i:2454176 original size:61 final size:63
Alignment explanation
Indices: 2454045--2454185 Score: 189
Period size: 61 Copynumber: 2.2 Consensus size: 63
2454035 TTTTAGAAAC
2454045 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAATTCTTATTTACAAATCAAATT
2454110 A
63 A
* * **
2454111 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAATTCTTATTTCCTCATC-AATTA
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAATTCTTATTTACAAATCAAATTA
2454171 TAACAAATCAACTTT
1 -AACAAATCAACTTT
2454186 CAATGTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
60 5 0.07
61 36 0.51
62 3 0.04
66 26 0.37
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.32
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAATTCTTATTTACAAATCAAATTA
Found at i:2455624 original size:42 final size:42
Alignment explanation
Indices: 2455578--2455661 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
2455568 CAATGACAGT
* * ** * *
2455578 GGCCTCTTGAACGGTGGGAGGGGCTTCTTGGATGATGATAGG
1 GGCCTCTTGAACGATAGGAGACGCCTCTTGAATGATGATAGG
2455620 GGCCTCTTGAACGATAGGAGACGCCTCTTGAATGATGATAGG
1 GGCCTCTTGAACGATAGGAGACGCCTCTTGAATGATGATAGG
2455662 TGCATCGAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.17, G:0.37, T:0.25
Consensus pattern (42 bp):
GGCCTCTTGAACGATAGGAGACGCCTCTTGAATGATGATAGG
Found at i:2457827 original size:20 final size:19
Alignment explanation
Indices: 2457808--2457857 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
2457798 AAACTTAAAT
*
2457808 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2457827 TCACAACGCGAAAATGAAAA
1 TCGCAACGCG-AAATGAAAA
2457847 TCGCAACGCGA
1 TCGCAACGCGA
2457858 TTTTAATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2457893 original size:20 final size:20
Alignment explanation
Indices: 2457854--2457913 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
2457844 AAATCGCAAC
* *
2457854 GCGATTTT-AATTTCGAGTT
1 GCGATTTTCATTTTCGCGTT
2457873 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
2457893 GAGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
2457913 G
1 G
2457914 TGAATTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:2458227 original size:22 final size:21
Alignment explanation
Indices: 2458177--2458234 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2458167 GATGGAGATA
* *
2458177 GACGGATTTCGCCGGAAATGTG
1 GACGGATTTCGTC-GAAATGGG
*
2458199 GATGGATTTCGTCGAAGATGGG
1 GACGGATTTCGTCGAA-ATGGG
*
2458221 GACGGATGTCGTCG
1 GACGGATTTCGTCG
2458235 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.24
Consensus pattern (21 bp):
GACGGATTTCGTCGAAATGGG
Found at i:2458380 original size:20 final size:20
Alignment explanation
Indices: 2458355--2458419 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
2458345 ACGTAAAAAC
*
2458355 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
2458375 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
2458395 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
2458415 ATTTG
1 ATTTG
2458420 GAAATCGCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:2458426 original size:20 final size:20
Alignment explanation
Indices: 2458364--2458520 Score: 81
Period size: 20 Copynumber: 7.8 Consensus size: 20
2458354 CATTTGACTT
*
2458364 TCGCGTTGCGAATTT-GACTA
1 TCGCGTTGCGAATTTGGA-AA
*
2458384 TCGCGTTGCGAATTT-GACTA
1 TCGCGTTGCGAATTTGGA-AA
2458404 TCGCGTTGCGAATTTGGAAA
1 TCGCGTTGCGAATTTGGAAA
*** *
2458424 TCGCAACGCAAATTTGGAAAA
1 TCGCGTTGCGAATTTGG-AAA
** ** *
2458445 TCGCAATGCG-ATTTACATAT
1 TCGCGTTGCGAATTTGGA-AA
* *
2458465 TCGCGTTGTGAAATTGGAAA
1 TCGCGTTGCGAATTTGGAAA
* * *
2458485 -CTG-GGTGACGAAATTGGAAT
1 TC-GCGTTG-CGAATTTGGAAA
2458505 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
2458521 TTGGTCATTT
Statistics
Matches: 107, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
19 5 0.05
20 81 0.76
21 21 0.20
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGGAAA
Found at i:2458438 original size:40 final size:40
Alignment explanation
Indices: 2458355--2458439 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
2458345 ACGTAAAAAC
* * *** *
2458355 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGAATTTGACAATCGCAACGCAA
2458395 ATTTGACTATCGCGTTGCGAATTTGGA-AATCGCAACGCAA
1 ATTTGACTATCGCGTTGCGAATTT-GACAATCGCAACGCAA
2458435 ATTTG
1 ATTTG
2458440 GAAAATCGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 36 0.95
41 2 0.05
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (40 bp):
ATTTGACTATCGCGTTGCGAATTTGACAATCGCAACGCAA
Found at i:2459270 original size:112 final size:112
Alignment explanation
Indices: 2459023--2459270 Score: 265
Period size: 112 Copynumber: 2.2 Consensus size: 112
2459013 AATGCTTATT
* * * * *
2459023 CACCTACTTCTGTGATGAGTTTGAGCGAAATGTTAAATAAATTCTTCTCATTAAGAATTTTCTCT
1 CACCTTCTTCTGTGATGAATTTGAGCAAAATATTAAACAAATTCTTCTCATTAAGAATTTTCTCT
* *
2459088 CTAGACAATTTTTTCTCATTATGAACTCTTTTATTGGAAATGTTGATA
66 CTAGACAAGTTTTTCT-ATTATGAACTCTTTTATTAGAAATGTTGATA
* * * *
2459136 CACCTTCTTCTGTGATGGATTTGAG-AAAATATTAAACAAGTTCTTTTCATTATGAACTTCTTC-
1 CACCTTCTTCTGTGATGAATTTGAGCAAAATATTAAACAAATTCTTCTCATTAAGAA-TT-TTCT
*
2459199 CTCATCAGACAAGTTTTT-T-TTATGAAC-CATTTTATTAGAAATGTTGATT
64 CTC-T-AGACAAGTTTTTCTATTATGAACTC-TTTTATTAGAAATGTTGATA
* *
2459248 TATC-TCTTTCTGTGATGAATTTG
1 CACCTTC-TTCTGTGATGAATTTG
2459271 GACAGGTTGA
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
111 3 0.03
112 68 0.60
113 27 0.24
114 5 0.04
115 11 0.10
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (112 bp):
CACCTTCTTCTGTGATGAATTTGAGCAAAATATTAAACAAATTCTTCTCATTAAGAATTTTCTCT
CTAGACAAGTTTTTCTATTATGAACTCTTTTATTAGAAATGTTGATA
Found at i:2460199 original size:19 final size:20
Alignment explanation
Indices: 2460160--2460202 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2460150 GCCCGAATAT
*
2460160 CTTACAGATGGCCCAAAAGA
1 CTTACAGATGACCCAAAAGA
2460180 CTTACAGATGACCC-AAAGA
1 CTTACAGATGACCCAAAAGA
2460199 CTTA
1 CTTA
2460203 TCACCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.19
Consensus pattern (20 bp):
CTTACAGATGACCCAAAAGA
Found at i:2460327 original size:83 final size:82
Alignment explanation
Indices: 2460175--2460354 Score: 236
Period size: 83 Copynumber: 2.2 Consensus size: 82
2460165 AGATGGCCCA
* * * * *
2460175 AAAGACTTACAGATGACCCAAAGACTTATCACCATGCTCGAAATACTTATAGATAACACGAAGGA
1 AAAGACTTACTGATGACCCAAAGACTTACCACCATGCTCGAAAGACTTACAGAGAACACGAAGGA
* *
2460240 TTTAATCATCATGCTCT
66 TTTAAACATCATGCTCG
* ** *
2460257 AAAGACTTACTTATGACCCAAAGAACTTACCACTC-TGCTTTAAAGACTTACAGAGAACCCGAAG
1 AAAGACTTACTGATGACCCAAAG-ACTTACCAC-CATGCTCGAAAGACTTACAGAGAACACGAAG
2460321 GATTTAAACATCATGCTCG
64 GATTTAAACATCATGCTCG
2460340 AAAGACTTACTGATG
1 AAAGACTTACTGATG
2460355 GCCTGAATGA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 21 0.25
83 62 0.74
84 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (82 bp):
AAAGACTTACTGATGACCCAAAGACTTACCACCATGCTCGAAAGACTTACAGAGAACACGAAGGA
TTTAAACATCATGCTCG
Found at i:2461822 original size:20 final size:20
Alignment explanation
Indices: 2461799--2461836 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2461789 TTGATATTAC
2461799 TGTAGCAGTATCGATACTAT
1 TGTAGCAGTATCGATACTAT
* *
2461819 TGTAGTAGTATCGGTACT
1 TGTAGCAGTATCGATACT
2461837 CATTTTGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (20 bp):
TGTAGCAGTATCGATACTAT
Found at i:2462913 original size:20 final size:20
Alignment explanation
Indices: 2462885--2462925 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2462875 CGTTGGGCTT
*
2462885 GATATTACTGTAGCAGTATC
1 GATACTACTGTAGCAGTATC
*
2462905 GATACTACTGTAGCATTATC
1 GATACTACTGTAGCAGTATC
2462925 G
1 G
2462926 GTACCCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (20 bp):
GATACTACTGTAGCAGTATC
Found at i:2466404 original size:33 final size:33
Alignment explanation
Indices: 2466361--2466426 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2466351 TAACATTGAT
*
2466361 TCAGTGGGAAGTTACTTGGATGAAGCTTGTTTG
1 TCAGTAGGAAGTTACTTGGATGAAGCTTGTTTG
2466394 TCAGTAGGAAGTTACTTGGATGAAGCTTGTTTG
1 TCAGTAGGAAGTTACTTGGATGAAGCTTGTTTG
2466427 AGAAGCTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36
Consensus pattern (33 bp):
TCAGTAGGAAGTTACTTGGATGAAGCTTGTTTG
Found at i:2473261 original size:193 final size:196
Alignment explanation
Indices: 2472917--2473306 Score: 759
Period size: 193 Copynumber: 2.0 Consensus size: 196
2472907 ATCGATCCCA
2472917 CCACCAAATCCGATCCCTTCACACTCATATTCGCCACGGCTTCCATGACGAAACTCCTCAGCCTC
1 CCACCAAATCCGATCCCTTCACACTCATATTCGCCACGGCTTCCATGACGAAACTCCTCAGCCTC
2472982 CAATAAACTTCTCTGAAACTCTTCTCCACCTCCTGTCTAAGCTCATTGAAGGTAGTGTTTTTGTT
66 CAATAAACTTCTCTGAAACTCTTCTCCACCTCCTGTCTAAGCTCATTGAAGGTAGTGTTTTTGTT
2473047 TAAACTCACACATTTGTAT-GGGGCATCGGTTTCTTCAACCCTTCATTTATCCCTTC-TTGTTTC
131 TAAACTCACACATTTGTATGGGGGCATCGGTTTCTTCAACCCTTCATTTATCCCTTCATTGTTTC
2473110 T
196 T
2473111 CCACCAAATCCGAT-CCTTCACACTCATATTCGCCACGGCTTCCATGACGAAACTCCTCAGCCTC
1 CCACCAAATCCGATCCCTTCACACTCATATTCGCCACGGCTTCCATGACGAAACTCCTCAGCCTC
2473175 CAATAAACTTCTCTGAAACTCTTCTCCACCTCCTGTCTAAGCTCATTGAAGGTAGTGTTTTTGTT
66 CAATAAACTTCTCTGAAACTCTTCTCCACCTCCTGTCTAAGCTCATTGAAGGTAGTGTTTTTGTT
2473240 TAAACTCACACATTTGTATGGGGGCATCGGTTTCTTCAACCCTTCATTTATCCCTTCATTGTTTC
131 TAAACTCACACATTTGTATGGGGGCATCGGTTTCTTCAACCCTTCATTTATCCCTTCATTGTTTC
2473305 T
196 T
2473306 C
1 C
2473307 AATGCGACTG
Statistics
Matches: 194, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
193 134 0.69
194 51 0.26
195 9 0.05
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (196 bp):
CCACCAAATCCGATCCCTTCACACTCATATTCGCCACGGCTTCCATGACGAAACTCCTCAGCCTC
CAATAAACTTCTCTGAAACTCTTCTCCACCTCCTGTCTAAGCTCATTGAAGGTAGTGTTTTTGTT
TAAACTCACACATTTGTATGGGGGCATCGGTTTCTTCAACCCTTCATTTATCCCTTCATTGTTTC
T
Found at i:2480466 original size:3 final size:3
Alignment explanation
Indices: 2480458--2480527 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
2480448 TCATTTCGTT
* **
2480458 TTA TTA TTA TTA TTT TTA AAA TTA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
2480504 TTA TATA TTA TT- TTT TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA
2480528 AACAAATAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 2 0.04
3 49 0.86
4 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2480522 original size:25 final size:25
Alignment explanation
Indices: 2480458--2480528 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
2480448 TCATTTCGTT
* *
2480458 TTATTATTATTATTTTTA-AAATTA
1 TTATTATTATTATTATTATTAATTA
2480482 TTATTATTATTATTATTATTAATTA
1 TTATTATTATTATTATTATTAATTA
*
2480507 TATATTATT-TTTTTATTATTAA
1 T-TATTATTATTATTATTATTAA
2480529 ACAAATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 17 0.40
25 18 0.43
26 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTATTATTATTATTATTAATTA
Found at i:2482133 original size:158 final size:147
Alignment explanation
Indices: 2481971--2482331 Score: 386
Period size: 149 Copynumber: 2.4 Consensus size: 147
2481961 AAAAGGGCAT
* * *
2481971 TCTTAAAGCAACTAGATGTCTTATTCTGGTATTTTAAATAAATAAATATCTTACTTATAAAAACC
1 TCTTAAAGCACCTAGAAGTCTT-TTCTGATATTTTAAATAAATAAATATCTTACTTATAAAAACC
*
2482036 AGAAAATACATATTGTTTTATTTAAATTATTTTCT-TAGAAAAAATAATCATATT-TTAATATTT
65 A-AAAATAC-TA---ATTTATTTAAATTATTTT-TATAG---AAAT-AT--T-TTATTAATATTT
*
2482099 ATATA-TTTTTTAATATTAAGAAATGGGTTG
117 ATATATTTTTTTAATATTAAGAAATGAGTTG
* * * * *
2482129 TCTTAAAGCACCTAGAAGTCATTTTCTGATATTCTTAAATAAATAAATATCCTATTTTTATAAAT
1 TCTTAAAGCACCTAGAAGTC-TTTTCTGATATT-TTAAATAAATAAATATCTTACTTATAAAAAC
* * * * * *
2482194 TATATATACTAATTTATTTTAATTATTTTTATAGAAATGTTTTATTAATATTTATTTATTTTTTT
64 CAAAAATACTAATTTATTTAAATTATTTTTATAGAAATATTTTATTAATATTTATATATTTTTTT
2482259 AATATTAAGAAATGAGTTG
129 AATATTAAGAAATGAGTTG
*
2482278 TCTTAAAGCACCTAGAAGTCCTTTTCTGATATTTCTAAGTAAATAAATATCTTA
1 TCTTAAAGCACCTAGAAGT-CTTTTCTGATATTT-TAAATAAATAAATATCTTA
2482332 TTAATATATT
Statistics
Matches: 178, Mismatches: 18, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
147 2 0.01
148 15 0.08
149 72 0.40
150 2 0.01
151 4 0.02
153 1 0.01
154 19 0.11
157 2 0.01
158 32 0.18
159 29 0.16
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (147 bp):
TCTTAAAGCACCTAGAAGTCTTTTCTGATATTTTAAATAAATAAATATCTTACTTATAAAAACCA
AAAATACTAATTTATTTAAATTATTTTTATAGAAATATTTTATTAATATTTATATATTTTTTTAA
TATTAAGAAATGAGTTG
Found at i:2482390 original size:149 final size:147
Alignment explanation
Indices: 2482090--2482371 Score: 365
Period size: 149 Copynumber: 1.9 Consensus size: 147
2482080 TAATCATATT
* *
2482090 TTAATATTTATATATTTTTTAATATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAGTCATTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCATTTTC
** * * * *
2482155 TGATATTCTTAAATAAATAAATATCCTATTTTTATAAATTATATATACTAATTTATTTTAATTAT
66 TGATATTCTTAAATAAATAAATATCCTATTAATATAAATTATATATAC-AAATTATATTAATAAA
* *
2482220 TTTTATAGAAATGTTTTA
130 TTTGAAAGAAATGTTTTA
*
2482238 TTAATATTTATTTATTTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCCTTTT
1 TTAATATTTATTTA-TTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCATTTT
* * * * *
2482303 CTGATATT-TCTAAGTAAATAAATATCTTATTAATAT-ATTTTTCT-TA-AAATTATATTAATAA
65 CTGATATTCT-TAAATAAATAAATATCCTATTAATATAAATTATATATACAAATTATATTAATAA
2482364 ATTTGAAA
129 ATTTGAAA
2482372 TAACAGTATT
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
145 17 0.15
147 2 0.02
148 19 0.16
149 78 0.67
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (147 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCATTTTC
TGATATTCTTAAATAAATAAATATCCTATTAATATAAATTATATATACAAATTATATTAATAAAT
TTGAAAGAAATGTTTTA
Found at i:2482866 original size:28 final size:28
Alignment explanation
Indices: 2482830--2482892 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2482820 TTATAATTCT
* * *
2482830 TTATATTCAAAATTTTTATATATATTTA
1 TTATTTTCAAAATATATATATATATTTA
* *
2482858 TTATTTTCATAATATATATATATATTTT
1 TTATTTTCAAAATATATATATATATTTA
2482886 TTATTTT
1 TTATTTT
2482893 TATTTTCAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TTATTTTCAAAATATATATATATATTTA
Found at i:2488102 original size:8 final size:8
Alignment explanation
Indices: 2488089--2488142 Score: 72
Period size: 8 Copynumber: 6.5 Consensus size: 8
2488079 TGAAGAAGGA
2488089 AAAAAAAG
1 AAAAAAAG
2488097 AAAAAAAG
1 AAAAAAAG
2488105 AAAAAAAG
1 AAAAAAAG
2488113 AAAAAAAAAG
1 --AAAAAAAG
*
2488123 AAAAAAGG
1 AAAAAAAG
*
2488131 AAAAAAGG
1 AAAAAAAG
2488139 AAAA
1 AAAA
2488143 TATTGAATCA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
8 35 0.81
10 8 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2488111 original size:18 final size:18
Alignment explanation
Indices: 2488087--2488136 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
2488077 CTTGAAGAAG
*
2488087 GAAAAAAA-AGAAAAAAA
1 GAAAAAAAGAAAAAAAAA
2488104 GAAAAAAAGAAAAAAAAA
1 GAAAAAAAGAAAAAAAAA
*
2488122 GAAAAAAGGAAAAAA
1 GAAAAAAAGAAAAAA
2488137 GGAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
GAAAAAAAGAAAAAAAAA
Found at i:2488123 original size:26 final size:26
Alignment explanation
Indices: 2488088--2488142 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
2488078 TTGAAGAAGG
2488088 AAAAAAAAGAAAAAAAGAAAAAAAGA
1 AAAAAAAAGAAAAAAAGAAAAAAAGA
* *
2488114 AAAAAAAAGAAAAAAGGAAAAAAGGA
1 AAAAAAAAGAAAAAAAGAAAAAAAGA
2488140 AAA
1 AAA
2488143 TATTGAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAAGAAAAAAAGA
Found at i:2488656 original size:32 final size:32
Alignment explanation
Indices: 2488600--2488661 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2488590 TCTGGAAACA
** * *
2488600 AGAAGTATCTCTATGATATGAGCATAACAACG
1 AGAAGTATCTCTACCAGATAAGCATAACAACG
2488632 AGAAGTATCTCTACCAGATAAGCATAACAA
1 AGAAGTATCTCTACCAGATAAGCATAACAA
2488662 TCATTTCTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.23
Consensus pattern (32 bp):
AGAAGTATCTCTACCAGATAAGCATAACAACG
Found at i:2493547 original size:76 final size:76
Alignment explanation
Indices: 2493460--2493678 Score: 327
Period size: 76 Copynumber: 2.9 Consensus size: 76
2493450 CTTCAGTGCA
*
2493460 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACTTGCAGTGCAAGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACTTGCAGTGCATGATGTTTTCAAAAAGCCTT
2493525 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
2493536 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCAT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACTTGCAGTGCATGATGTTTTCAAAAAGCCTT
2493601 CGGGAGCTTTT
66 CGGGAGCTTTT
* * * ** *
2493612 TGATATTTTCAAAATCTTTGGGTCATCTGTAAGCCCTT-CAGTGCATGATGTTTTC-AAAA-CCT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAG-ACTTGCAGTGCATGATGTTTTCAAAAAGCCT
2493674 TCGGG
65 TCGGG
2493679 TCATTCATAA
Statistics
Matches: 131, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
74 7 0.05
75 4 0.03
76 118 0.90
77 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACTTGCAGTGCATGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:2493664 original size:121 final size:121
Alignment explanation
Indices: 2493536--2493922 Score: 641
Period size: 121 Copynumber: 3.2 Consensus size: 121
2493526 GGGAGCTTTT
* *
2493536 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCAT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
* *
2493601 CGGGAGCTTTTTGATATTTTCAAAATCTTTGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGCTTTTTGATATTTTCAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCA
* *
2493657 TGATGTTTTCAAAACCTTCGGGTCATTCATAAGACCTGCAGTGCAGGATGTTTTTAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
*
2493722 CGGGAGCTTTTTGATGTTTTCAAAACCTTAT-GGTCATCTGTAAGACCTTCAGTGCA
66 CGGGAGCTTTTTGATATTTTCAAAACCTT-TGGGTCATCTGTAAGACCTTCAGTGCA
2493778 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
* **
2493843 CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
66 CGGGAGCTTTTTGATATTTTCAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCA
*
2493899 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
2493923 AGCTTTTTTA
Statistics
Matches: 248, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
121 235 0.95
122 5 0.02
123 8 0.03
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTTTGATATTTTCAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:2493668 original size:45 final size:45
Alignment explanation
Indices: 2493612--2493725 Score: 122
Period size: 45 Copynumber: 2.5 Consensus size: 45
2493602 GGGAGCTTTT
* * * * * *
2493612 TGATATTTTCAAAATCTTTGGGTCA-TCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATTC-ATAAGACCTGCAGTGCA
2493657 TGATGTTTTCAAAACCTTCGGGTCATTCATAAGACCTGCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATTCATAAGACCTGCAGTGCA
* *
2493702 GGATGTTTTTAAAAAGCCTTCGGG
1 TGATG-TTTTCAAAA-CCTTCGGG
2493726 AGCTTTTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 40 0.69
46 10 0.17
47 8 0.14
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATTCATAAGACCTGCAGTGCA
Found at i:2493737 original size:76 final size:74
Alignment explanation
Indices: 2493657--2493799 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 74
2493647 CTTCAGTGCA
*
2493657 TGATGTTTTCAAAACCTTCGGGTCAT-TCATAAGACCTGCAGTGCAGGATGTTTTTAAAAAGCCT
1 TGATGTTTTCAAAACCTTAGGGTCATCT-ATAAGACCTGCAGTGCAGGATG-TTTTAAAAA-CCT
2493721 TCGGGAGCTTTT
63 TCGGGAGCTTTT
* * * * *
2493733 TGATGTTTTCAAAACCTTATGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTAGGGTCATCTATAAGACCTGCAGTGCAGGATGTTTTAAAAACCTTCG
2493798 GG
66 GG
2493800 TCATCCATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
74 8 0.13
75 8 0.13
76 43 0.72
77 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (74 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTATAAGACCTGCAGTGCAGGATGTTTTAAAAACCTTCG
GGAGCTTTT
Found at i:2493786 original size:45 final size:45
Alignment explanation
Indices: 2493733--2493836 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
2493723 GGGAGCTTTT
* ** *
2493733 TGATGTTTTCAAAACCTTATGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCCATAAGACCTGCAGTGCA
*
2493778 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCCATAAGACCTGCAGTGCA
*
2493823 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
2493837 AGCCTTCGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTAGGGTCATCCATAAGACCTGCAGTGCA
Found at i:2493865 original size:197 final size:193
Alignment explanation
Indices: 2493445--2493983 Score: 640
Period size: 197 Copynumber: 2.8 Consensus size: 193
2493435 CCACATCTAT
* *
2493445 AAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACTTGCAGTGCAAGATG
1 AAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATG
**
2493510 TTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGC
66 TTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTGC
** ** * *
2493575 AGTGCATGATGTTTTCAAAAAGCCATCGGGAGCTTTTTGATATTTTCAAAATCTTTGGGTCATCT
131 AGTGCATGATGTTTTCAAAAAGCCATCGGGAGCCATAAGATATGTGCAAAATCTTT--GTCA--T
**
2493640 GT
192 AA
*
2493642 AAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATTCATAAGACCTGCAGTGCAGGATG
1 AAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATG
* ** *
2493707 TTTTTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTATGGTCATCTGTAAGACCTTC
66 TTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTGC
* * ** *
2493772 AGTGCATGATGTTTTC-AAAA-CCTTCGGGTCATCCATAAGACCTGCA-GTGCAGGATGTTT-TC
131 AGTGCATGATGTTTTCAAAAAGCCATCGGG--AGCCATAAGA--T--ATGTGCAAAATCTTTGTC
2493833 A-AA
190 ATAA
*** * *
2493836 AAG-CCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAG
1 AAGCCCTTC---AG-TGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAG
* * *
2493900 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAAAACATTCGGGTCATCTGTAAGCC
62 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGAC
2493965 CTGCAGTGCATGATGTTTT
127 CTGCAGTGCATGATGTTTT
2493984 TAGGACCTAT
Statistics
Matches: 297, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
193 5 0.02
194 3 0.01
195 7 0.02
196 6 0.02
197 266 0.90
199 1 0.00
200 8 0.03
201 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (193 bp):
AAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATG
TTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTGC
AGTGCATGATGTTTTCAAAAAGCCATCGGGAGCCATAAGATATGTGCAAAATCTTTGTCATAA
Found at i:2493872 original size:76 final size:76
Alignment explanation
Indices: 2493778--2493983 Score: 340
Period size: 76 Copynumber: 2.7 Consensus size: 76
2493768 CTTCAGTGCA
2493778 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
2493843 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
2493854 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
2493919 CGGGAGCTTTT
66 CGGGAGCTTTT
* * ** * *
2493930 TTATGTTTTCAAAACATTCGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTT
2493984 TAGGACCTAT
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 120 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:2494146 original size:3 final size:3
Alignment explanation
Indices: 2494138--2494206 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
2494128 TCATTTCATT
**
2494138 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
2494187 TTA TATA TT- TT- TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA
2494207 AATAAATAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.83
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2495987 original size:149 final size:155
Alignment explanation
Indices: 2495635--2496035 Score: 442
Period size: 149 Copynumber: 2.6 Consensus size: 155
2495625 GATTAAATAA
* * * * * * * *
2495635 TAATATTTATTTA-TTTTTAATATCAAAGAAAAGGGCAGTCTTAAAGTAACTTGATGTCCTATTA
1 TAATATTTATTTATTTTTTAATAT-TAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTA
* *
2495699 TGATATTTTAAATAAATAAATATCTTACTTATAAAAACTAGAAAATACATATTGTTTTATTTAAA
65 TGATATTTTAAATAAATAAATATCTTATTTATAAAAACTAGAAAATACATA-T-ATTTATTTAAA
2495764 TTATTTTCTTAGAAAAAATAATCATATTT
128 TTATTTTCTTAGAAAAAATAAT-ATATTT
*
2495793 TAATATTTATATATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTAT
1 TAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTAT
* * * * * *
2495858 GATATTCTTAAATAAATAAATATCTTATTTTTATAAATTA-TATATAC-TA-ATTTATTTTAATT
66 GATATT-TTAAATAAATAAATATCTTATTTATAAAAACTAGAAAATACATATATTTATTTAAATT
* * *
2495920 ATTTT-TTA-TAGAAAT-GT-T-TTAT
130 ATTTTCTTAGAAAAAATAATATATT-T
* * * *
2495942 TAATATTTATTTATTTTTTAATATTAAGAAATGGGTTGTCTTAAAGCGCCTAGAAGTCATTTTCT
1 TAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTAT
* *
2496007 AATATTTCTAAGTAAATAAATATCTTATT
66 GATATTT-TAAATAAATAAATATCTTATT
2496036 AATATATTTT
Statistics
Matches: 212, Mismatches: 27, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
148 3 0.01
149 87 0.41
151 1 0.00
152 5 0.02
153 3 0.01
154 16 0.08
157 2 0.01
158 56 0.26
159 39 0.18
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (155 bp):
TAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTAT
GATATTTTAAATAAATAAATATCTTATTTATAAAAACTAGAAAATACATATATTTATTTAAATTA
TTTTCTTAGAAAAAATAATATATTT
Found at i:2498027 original size:35 final size:33
Alignment explanation
Indices: 2497969--2498042 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 33
2497959 TAGAATATAT
* *
2497969 TAAACAATATATGTACTAGAAATGAAAGTAAATCA
1 TAAACAATATAAGGACTAGAAATGAAA-TAAA-CA
2498004 TAAACAATATTAAGGACTA-AAATGAAATAAACA
1 TAAACAATA-TAAGGACTAGAAATGAAATAAACA
2498037 TAAACA
1 TAAACA
2498043 TAAAGGGCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
33 8 0.22
34 4 0.11
35 17 0.47
36 7 0.19
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (33 bp):
TAAACAATATAAGGACTAGAAATGAAATAAACA
Found at i:2499311 original size:74 final size:75
Alignment explanation
Indices: 2499184--2499322 Score: 194
Period size: 74 Copynumber: 1.9 Consensus size: 75
2499174 TAATAGGAAG
2499184 GGCTTCGAGAAAAAACATATTGCCCAATGGGTACCGATACCCCTCAAAGGGTACCGATACCCCTA
1 GGCTTCGAGAAAAAACATATTGCCCAATGGGTACCGATACCCCTCAAAGGGTACCGATACCCCTA
2499249 TGCAAGTTTT
66 TGCAAGTTTT
* * * * *
2499259 GGCTTCGAGAAAAATAGA-A-TGCCCTATGGGTACCGATACCTCCTTAGA-GGTACCGATACTCC
1 GGCTTCGAGAAAAA-ACATATTGCCCAATGGGTACCGATACC-CCTCAAAGGGTACCGATACCCC
2499321 TA
64 TA
2499323 GTCATTTAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
74 35 0.61
75 20 0.35
76 2 0.04
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (75 bp):
GGCTTCGAGAAAAAACATATTGCCCAATGGGTACCGATACCCCTCAAAGGGTACCGATACCCCTA
TGCAAGTTTT
Found at i:2505123 original size:20 final size:21
Alignment explanation
Indices: 2505065--2505186 Score: 92
Period size: 21 Copynumber: 5.8 Consensus size: 21
2505055 TTTGTGCTCC
*
2505065 AGGTATCGATACCCCCTTGCT
1 AGGTATCGATACCCCCTTACT
*
2505086 AGGCATCGATACCCCCTTACT
1 AGGTATCGATACCCCCTTACT
* *
2505107 AGGTATCAATA-CCCCTT-CAA
1 AGGTATCGATACCCCCTTAC-T
* *
2505127 AGTGTATCGATACCCTCTTTGAAT
1 AG-GTATCGATACCC-CCTT-ACT
2505151 -GTGTATCGATACCCCCTTA--
1 AG-GTATCGATACCCCCTTACT
*
2505170 AGGGTACCGATACCCCC
1 A-GGTATCGATACCCCC
2505187 ATCGGGTTCT
Statistics
Matches: 82, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.01
20 21 0.26
21 38 0.46
22 5 0.06
23 17 0.21
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (21 bp):
AGGTATCGATACCCCCTTACT
Found at i:2505133 original size:21 final size:22
Alignment explanation
Indices: 2505109--2505165 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
2505099 CCCTTACTAG
*
2505109 GTATCAATACCCC-TTCAAAGT
1 GTATCGATACCCCTTTCAAAGT
* *
2505130 GTATCGATACCCTCTTTGAATGT
1 GTATCGATACCC-CTTTCAAAGT
2505153 GTATCGATACCCC
1 GTATCGATACCCC
2505166 CTTAAGGGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.35
22 2 0.06
23 18 0.58
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (22 bp):
GTATCGATACCCCTTTCAAAGT
Found at i:2507155 original size:21 final size:21
Alignment explanation
Indices: 2507118--2507177 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
2507108 AATTGCTTGT
*
2507118 TTTGAATTTGTGTTTTGGATG
1 TTTGAATTTGTGTTTTGAATG
*
2507139 TTTGAA-TTGTTTGTTTGAATG
1 TTTGAATTTGTGT-TTTGAATG
*
2507160 TTT--ATTT-TGGTTTGAATG
1 TTTGAATTTGTGTTTTGAATG
2507178 ATATTTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 7 0.21
21 16 0.48
ACGTcount: A:0.17, C:0.00, G:0.25, T:0.58
Consensus pattern (21 bp):
TTTGAATTTGTGTTTTGAATG
Found at i:2509066 original size:13 final size:13
Alignment explanation
Indices: 2509050--2509074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2509040 ATATTAACAA
2509050 TAATAATTAATAG
1 TAATAATTAATAG
2509063 TAATAATTAATA
1 TAATAATTAATA
2509075 TTTTTTAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TAATAATTAATAG
Found at i:2509543 original size:131 final size:132
Alignment explanation
Indices: 2509265--2509619 Score: 437
Period size: 131 Copynumber: 2.7 Consensus size: 132
2509255 TCTAGTCATC
* * * * *
2509265 TAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGATCGGTGGATGACACAGTTCCTACGCGA
1 TAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACAATTCCTACGCGA
* * *
2509330 TGATGG-CACCATCCATCTTTAGGGAAGGTGATAACACGATTCCTACGCGAAGAGGACAATTGGT
66 TGA-GGACACAAACCATCTTTAGGGAA-GTGATAACACGATTCCTACGCGAAGAGGACAACTGGT
*
2509394 TATC
129 TATA
* * * * *
2509398 TAGGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTAGTTGGATGACACAATTCCTACGTGA
1 TAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACAATTCCTACGCGA
* * * *
2509463 TGAGGACGACAAACCATCTTTA-GGAA-TGATAACACGGTTCCTACGTGATGAGGACGACTGGTT
66 TGAGGAC-ACAAACCATCTTTAGGGAAGTGATAACACGATTCCTACGCGAAGAGGACAACTGGTT
2509526 ATA
130 ATA
* * *
2509529 TAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGATTCCTACGCAA
1 TAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACAATTCCTACGCGA
* **
2509594 TGAGGACTATATGCCATCTTTAGGGA
66 TGAGGAC-ACAAACCATCTTTAGGGA
2509620 TAATGTTTTA
Statistics
Matches: 190, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
131 109 0.57
132 5 0.03
133 64 0.34
134 12 0.06
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (132 bp):
TAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACAATTCCTACGCGA
TGAGGACACAAACCATCTTTAGGGAAGTGATAACACGATTCCTACGCGAAGAGGACAACTGGTTA
TA
Found at i:2510753 original size:30 final size:30
Alignment explanation
Indices: 2510718--2510827 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 30
2510708 TAACTCAACA
2510718 GGAAACGATCTCAAAGATTGGTGTTTCAAG
1 GGAAACGATCTCAAAGATTGGTGTTTCAAG
*
2510748 AGAAACTG-TCTCAAGAGTGACAAAATT--TGTTTCAAG
1 GGAAAC-GATCTCAA-A--G-----ATTGGTGTTTCAAG
2510784 GGAAAC-ATACTCAAAGATTGGTGTTTCAAG
1 GGAAACGAT-CTCAAAGATTGGTGTTTCAAG
*
2510814 GGAAACTATCTCAA
1 GGAAACGATCTCAA
2510828 GAGAGACAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 28
0.68 0.02 0.30
Matches are distributed among these distances:
28 3 0.05
30 31 0.48
31 4 0.06
33 2 0.03
35 2 0.03
36 19 0.30
38 3 0.05
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (30 bp):
GGAAACGATCTCAAAGATTGGTGTTTCAAG
Found at i:2510826 original size:66 final size:67
Alignment explanation
Indices: 2510718--2510869 Score: 227
Period size: 66 Copynumber: 2.3 Consensus size: 67
2510708 TAACTCAACA
* *
2510718 GGAAACGAT-CTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGAGTGAC-AAAATTTGTTTC
1 GGAAAC-ATACTCAAAGATTGGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAATTTGTTTC
2510781 AAG
65 AAG
*
2510784 GGAAACATACTCAAAGATTGGTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAATTTGTTTCA
1 GGAAACATACTCAAAGATTGGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAATTTGTTTCA
2510849 AG
66 AG
* * *
2510851 AGAAATAGACTCAAAGATT
1 GGAAACATACTCAAAGATT
2510870 ATAAATTTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
65 2 0.03
66 45 0.58
67 31 0.40
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (67 bp):
GGAAACATACTCAAAGATTGGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAATTTGTTTCA
AG
Found at i:2511053 original size:36 final size:36
Alignment explanation
Indices: 2511010--2511118 Score: 146
Period size: 36 Copynumber: 3.0 Consensus size: 36
2511000 TTTGTATTCC
* *
2511010 GAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTT
1 GAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTT
* * *
2511046 GAGAGAAATTGTCTCAAGCAAGAAAAAATTTTTTTT
1 GAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTT
* *
2511082 TAGAAAAAATTGTCTCAAGCGAGACAAAATTTGTTTT
1 GAG-AGAAATTGTCTCAAGCGAGACAAAATTTGTTTT
2511119 TAAGAAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
36 33 0.53
37 29 0.47
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (36 bp):
GAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTT
Found at i:2511142 original size:37 final size:37
Alignment explanation
Indices: 2511019--2511143 Score: 139
Period size: 36 Copynumber: 3.4 Consensus size: 37
2511009 CGAGAGAAAC
* * * *
2511019 TGTCTCAAGTGAGACAAAATTTG-TTTTGAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAA
* * *
2511055 TGTCTCAAGCAAGAAAAAATTT-TTTTTTAGAAAAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAA
2511091 TTGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAA
1 -TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAA
*
2511129 TGCCTTCAA-CGAGAC
1 TGTC-TCAAGCGAGAC
2511144 GACACTTGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
36 29 0.39
37 29 0.39
38 17 0.23
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (37 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAA
Found at i:2511153 original size:37 final size:38
Alignment explanation
Indices: 2511022--2511154 Score: 105
Period size: 37 Copynumber: 3.6 Consensus size: 38
2511012 GAGAAACTGT
* * * * *
2511022 CTCAAGTGAGACAAAATTTG-TTTTGAG-AGAAATTGT
1 CTCAAGCGAGACAAAACTTGTTTTTAAGAAAAAATTGC
* * * * *
2511058 CTCAAGCAAGA-AAAAATTTTTTTTTAGAAAAAATTGT
1 CTCAAGCGAGACAAAACTTGTTTTTAAGAAAAAATTGC
*
2511095 CTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAA-TGC
1 CTCAAGCGAGACAAAACTTGTTTTTAAGAAAAAATTGC
* *
2511132 CTTCAA-CGAGACGACACTTGTTT
1 C-TCAAGCGAGACAAAACTTGTTT
2511155 CGAGAGAAAC
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
35 6 0.08
36 15 0.19
37 35 0.44
38 23 0.29
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (38 bp):
CTCAAGCGAGACAAAACTTGTTTTTAAGAAAAAATTGC
Found at i:2511500 original size:16 final size:16
Alignment explanation
Indices: 2511479--2511512 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2511469 TTCATATGTC
*
2511479 ATGTATGTATGTGTTG
1 ATGTATGTATATGTTG
2511495 ATGTATGTATATGTTG
1 ATGTATGTATATGTTG
2511511 AT
1 AT
2511513 ATGTGAGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (16 bp):
ATGTATGTATATGTTG
Found at i:2513563 original size:2 final size:2
Alignment explanation
Indices: 2513556--2513582 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2513546 TTAGATAAGT
2513556 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 T
2513583 TATTAGTGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2513872 original size:36 final size:36
Alignment explanation
Indices: 2513830--2513905 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2513820 TTATAGCTAA
*
2513830 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2513866 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2513902 AAAA
1 AAAA
2513906 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2517487 original size:15 final size:15
Alignment explanation
Indices: 2517469--2517498 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2517459 CCACGGTGCT
2517469 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2517484 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2517499 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:2517962 original size:36 final size:36
Alignment explanation
Indices: 2517920--2517995 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2517910 TTATAGCTAA
*
2517920 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2517956 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2517992 AAAA
1 AAAA
2517996 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2521577 original size:15 final size:15
Alignment explanation
Indices: 2521559--2521588 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2521549 CCACGGTGCT
2521559 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2521574 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2521589 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:2522052 original size:36 final size:36
Alignment explanation
Indices: 2522010--2522085 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2522000 TTATAGCTAA
*
2522010 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2522046 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2522082 AAAA
1 AAAA
2522086 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2525667 original size:14 final size:14
Alignment explanation
Indices: 2525648--2525676 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2525638 CCACGGTGCT
2525648 CCCGGAATCCTGCG
1 CCCGGAATCCTGCG
2525662 CCCGGAATCCTGCG
1 CCCGGAATCCTGCG
2525676 C
1 C
2525677 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.45, G:0.28, T:0.14
Consensus pattern (14 bp):
CCCGGAATCCTGCG
Found at i:2526140 original size:36 final size:36
Alignment explanation
Indices: 2526098--2526173 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2526088 TTATAGCTAA
*
2526098 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2526134 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2526170 AAAA
1 AAAA
2526174 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2529756 original size:15 final size:15
Alignment explanation
Indices: 2529738--2529767 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2529728 CCACGGTGCT
2529738 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2529753 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2529768 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:2530231 original size:35 final size:35
Alignment explanation
Indices: 2530190--2530265 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
2530180 TATAGCTAAA
*
2530190 AAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2530225 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2530260 AAAATC
1 AAAATC
2530266 CCGAAAATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (35 bp):
AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2533843 original size:15 final size:15
Alignment explanation
Indices: 2533823--2533852 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2533813 ACCACGTGCT
2533823 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2533838 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2533853 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:2534315 original size:36 final size:36
Alignment explanation
Indices: 2534273--2534348 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2534263 TTATAGCTAA
*
2534273 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2534309 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2534345 AAAA
1 AAAA
2534349 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2537928 original size:15 final size:15
Alignment explanation
Indices: 2537910--2537939 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2537900 CCACGGTGCT
2537910 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2537925 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2537940 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:2538403 original size:36 final size:36
Alignment explanation
Indices: 2538361--2538436 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2538351 TTATAGCTAA
*
2538361 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2538397 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2538433 AAAA
1 AAAA
2538437 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2553509 original size:15 final size:17
Alignment explanation
Indices: 2553478--2553512 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2553468 TTTGTTAGAA
2553478 TTAAGAGTTTAAATATT
1 TTAAGAGTTTAAATATT
2553495 TTAAGAG-TT-AATATT
1 TTAAGAGTTTAAATATT
2553510 TTA
1 TTA
2553513 TTTTCATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 2 0.11
17 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (17 bp):
TTAAGAGTTTAAATATT
Found at i:2559656 original size:7 final size:6
Alignment explanation
Indices: 2559628--2559662 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
2559618 TAACACCTCG
2559628 TGCATT TGCATT TGCATT TGCATTT TGCA-T TGCAT
1 TGCATT TGCATT TGCATT TGCA-TT TGCATT TGCAT
2559663 GTATTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
TGCATT
Found at i:2561975 original size:6 final size:6
Alignment explanation
Indices: 2561960--2562053 Score: 52
Period size: 6 Copynumber: 15.2 Consensus size: 6
2561950 AGAGAAATAT
* * *
2561960 AGAAAG AGAAAA AG-AAA AGATAAA A-AAAA TG-AAA TGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
2562006 TA-AAAA AGGAAA AGAAAG AGAAAA ATTGAAAA TGAGAAAA ATGAAAA
1 -AGAAAA AGAAAA AGAAAA AGAAAA A--GAAAA --AGAAAA A-GAAAA
2562053 A
1 A
2562054 AAGAATGAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 21
0.71 0.07 0.21
Matches are distributed among these distances:
5 14 0.20
6 34 0.49
7 11 0.16
8 10 0.14
10 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (6 bp):
AGAAAA
Found at i:2561984 original size:12 final size:11
Alignment explanation
Indices: 2561939--2562030 Score: 53
Period size: 12 Copynumber: 7.8 Consensus size: 11
2561929 TTGGCATCAT
*
2561939 AAAGAGAAAGA
1 AAAGAAAAAGA
*
2561950 AGAGAAATATAGA
1 AAAGAAA-A-AGA
2561963 AAGAGAAAAAGA
1 AA-AGAAAAAGA
2561975 AAAGATAAAA-A
1 AAAGA-AAAAGA
*
2561986 AAATG-AAATGAA
1 AAA-GAAAAAG-A
*
2561998 AAAGAAAATAAA
1 AAAGAAAA-AGA
*
2562010 AAAGGAAAAGA
1 AAAGAAAAAGA
2562021 AAGAGAAAAA
1 AA-AGAAAAA
2562031 TTGAAAATGA
Statistics
Matches: 62, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.05
11 17 0.27
12 32 0.52
13 5 0.08
14 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:2562017 original size:24 final size:23
Alignment explanation
Indices: 2561969--2562030 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
2561959 TAGAAAGAGA
* *
2561969 AAAAG-AAAAGATAAAAAAAATG
1 AAAAGAAAAAGAAAAAAAAAAGG
*
2561991 AAATGAAAAAGAAAATAAAAAAGG
1 AAAAGAAAAAGAAAA-AAAAAAGG
*
2562015 AAAAGAAAGAGAAAAA
1 AAAAGAAAAAGAAAAA
2562031 TTGAAAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 4 0.12
23 9 0.27
24 20 0.61
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (23 bp):
AAAAGAAAAAGAAAAAAAAAAGG
Found at i:2562053 original size:16 final size:16
Alignment explanation
Indices: 2562023--2562052 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2562013 GGAAAAGAAA
2562023 GAGAAAAATTGAAAAT
1 GAGAAAAATTGAAAAT
2562039 GAGAAAAA-TGAAAA
1 GAGAAAAATTGAAAA
2562053 AAAGAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
GAGAAAAATTGAAAAT
Found at i:2563573 original size:127 final size:127
Alignment explanation
Indices: 2563309--2563618 Score: 439
Period size: 127 Copynumber: 2.4 Consensus size: 127
2563299 GTTGCGATAG
* * * **
2563309 GTTGGGGCATGACTGAACCCACATTAGGTTGAGATGATAAA-ATTCAGAAGAAGAAGAAGGCATG
1 GTTGGGGCACGACTGAACCCACATCATGTTGAGATGA-AAAGATTCAGACCAAG-AGAAGGCATG
* *
2563373 AAGAATGAGCCTTACAAACTAAGGTGATGGGGCATTTTGAAGGCCCGTACTAGTATAAGATAAT
64 AAGAATGAGCCTTACAAACTAAGGTAATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAAT
2563437 GTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAG-G-AGGCATGAA
1 GTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGAGAAGGCATGAA
** *
2563500 GAATGAGCCTTACAATTTGAGGTAATAGGGGCATTTTGAAAGGCCCGTACCAGTATAAGATAAT
66 GAATGAGCCTTACAAACTAAGGTAAT-GGGGCATTTTG-AAGGCCCGTACCAGTATAAGATAAT
* *
2563564 GTTGGGGCACGACTGAACCCACATCATGATGAGA-AAATAAGATTCAGACCAAGAG
1 GTTGGGGCACGACTGAACCCACATCATGTTGAGATGAA-AAGATTCAGACCAAGAG
2563619 GTTATTGAGA
Statistics
Matches: 165, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
125 31 0.19
126 14 0.08
127 75 0.45
128 45 0.27
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (127 bp):
GTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGAGAAGGCATGAA
GAATGAGCCTTACAAACTAAGGTAATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAAT
Found at i:2564511 original size:55 final size:55
Alignment explanation
Indices: 2564361--2565375 Score: 1424
Period size: 55 Copynumber: 18.7 Consensus size: 55
2564351 TGAAGTAAAA
* * * * *
2564361 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
*
2564416 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* *
2564469 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* * *
2564524 GAAGATTG-T-GGGTCTTATACTCTCTAAAGAAATAGGGGGCAGACACAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* * *
2564577 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* * *
2564632 GAAGATTG-T-GGGTCTTATACTCTCTGAAGATATAGGGGGCAGACGCAATAGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* *
2564685 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCCGACACAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* *
2564740 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* *
2564795 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* * * *
2564848 GAAGATTGTTCGAGTTTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
*
2564903 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* * * *
2564956 GAAGATTGTTCG-GATCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
2565011 GAAGATTGTT-G-GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* * * * *
2565064 GAAGATTGTTCGAGTCTTATACTCTTTGAAGAAATAGGGGGCAGATGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* *
2565119 GAAGATT-AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
* *
2565172 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCA-A-ACAAGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA--TCGTT
*
2565227 GAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
1 GAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
2565282 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGA--CAAGTTCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA--TCGTT
* *
2565337 GAAGA-TGATTCAAGTCTTATACCCTCTGAAGAAATAGGG
1 GAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
2565376 AGCGAACCCA
Statistics
Matches: 860, Mismatches: 76, Indels: 48
0.87 0.08 0.05
Matches are distributed among these distances:
53 336 0.39
54 21 0.02
55 497 0.58
56 3 0.00
57 3 0.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
Found at i:2564554 original size:108 final size:110
Alignment explanation
Indices: 2564361--2565375 Score: 1451
Period size: 108 Copynumber: 9.4 Consensus size: 110
2564351 TGAAGTAAAA
* * * * *
2564361 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
* *
2564425 -GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGTT
* *
2564469 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGATGAAGATTG-T
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
* * * *
2564533 -GGGTCTTATACTCTCTAAAGAAATAGGGGGCAGACACAATCGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGTT
* * *
2564577 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
* * *
2564641 -GGGTCTTATACTCTCTGAAGATATAGGGGGCAGACGCAATAGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGTT
* *
2564685 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCCGACACAATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
*
2564750 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGTT
* *
2564795 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
* * *
2564858 CGAGTTTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGTT
*
2564903 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
* * *
2564966 CG-GATCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGTT
2565011 GAAGATTGTT-G-GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
* * * *
2565074 CGAGTCTTATACTCTTTGAAGAAATAGGGGGCAGATGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGTT
* *
2565119 GAAGATT-AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
*
2565182 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCA-A-ACAAGTTTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA--TTGTT
*
2565227 GAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGT
1 GAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGT
2565291 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGA--CAAGTTCGTT
65 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA-TT-GTT
* *
2565337 GAAGA-TGATTCAAGTCTTATACCCTCTGAAGAAATAGGG
1 GAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
2565376 AGCGAACCCA
Statistics
Matches: 855, Mismatches: 39, Indels: 24
0.93 0.04 0.03
Matches are distributed among these distances:
106 2 0.00
107 5 0.01
108 662 0.77
109 8 0.01
110 177 0.21
111 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGTT
Found at i:2569984 original size:30 final size:31
Alignment explanation
Indices: 2569949--2570031 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 31
2569939 AACTTGAAGG
2569949 CTAAAATAGCTAAAACA-AAACTTTAAAAGA
1 CTAAAATAGCTAAAACAGAAACTTTAAAAGA
* * *
2569979 CTAAAATAAC-AAAACAGAAGC-TTAAAGGA
1 CTAAAATAGCTAAAACAGAAACTTTAAAAGA
*
2570008 CTAAAATAGCTAAAATAGAAACTT
1 CTAAAATAGCTAAAACAGAAACTT
2570032 AAATAGCCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 22 0.50
30 21 0.48
31 1 0.02
ACGTcount: A:0.58, C:0.13, G:0.10, T:0.19
Consensus pattern (31 bp):
CTAAAATAGCTAAAACAGAAACTTTAAAAGA
Found at i:2570003 original size:29 final size:30
Alignment explanation
Indices: 2569949--2570034 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
2569939 AACTTGAAGG
2569949 CTAAAATAGCTAAAACA-AAACTTTAAAAGA
1 CTAAAATAGCTAAAACAGAAAC-TTAAAAGA
* * *
2569979 CTAAAATAAC-AAAACAGAAGCTTAAAGGA
1 CTAAAATAGCTAAAACAGAAACTTAAAAGA
*
2570008 CTAAAATAGCTAAAATAGAAACTTAAA
1 CTAAAATAGCTAAAACAGAAACTTAAA
2570035 TAGCCAAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.46
30 26 0.54
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.19
Consensus pattern (30 bp):
CTAAAATAGCTAAAACAGAAACTTAAAAGA
Found at i:2572022 original size:134 final size:133
Alignment explanation
Indices: 2571751--2572128 Score: 494
Period size: 134 Copynumber: 2.8 Consensus size: 133
2571741 TAAGGGTGAA
*
2571751 ACGACTCCTGCGTGATGAGGAGATCTAGTCAGGGAATGACAC-TGCTCATACGTGATGAAGAGTT
1 ACGACTCCTACGTGATGAGGAGATCTAGTCAGGG-ATGACACGTGCTCATACGTGATGAAGAG-T
* * * *
2571815 TTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTATATGATGAGGATGGCTGGTTATCTGAG
64 TATGGCCATCTTTAGGAA-AGTGATAACTCGGTTCCTACATGATGAGGATGGCCGGTTATCTGAG
*
2571880 GGTAAC
128 GATAAC
*
2571886 ACGACTCCTACGTGATGAGGAGATCTAGTCAAGGGATGACACGT-CTCATACGTGATAAAGAGTT
1 ACGACTCCTACGTGATGAGGAGATCTAGTC-AGGGATGACACGTGCTCATACGTGATGAAGAGTT
* *
2571950 ATGGCCATCTTTAGGAACGATGATAACTCAGTTCCTACATGATGAGGATGGCCGGTTATCTGAGG
65 ATGGCCATCTTTAGGAAAG-TGATAACTCGGTTCCTACATGATGAGGATGGCCGGTTATCTGAGG
*
2572015 ATGAC
129 ATAAC
** * * *
2572020 ACGTTTCCTACGTGATGAAGAGGTCTGGTCAGTGGAT-A-ACGTGGCTCATACGTGATGAAGAGT
1 ACGACTCCTACGTGATGAGGAGATCTAGTCAG-GGATGACACGT-GCTCATACGTGATGAAGAGT
* * *
2572083 TCTGGCCATCTTTAGGAGAAGTGATAACACGGTTCCTACGTGATGA
64 TATGGCCATCTTTAGGA-AAGTGATAACTCGGTTCCTACATGATGA
2572129 TGACAGCTGG
Statistics
Matches: 216, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
132 4 0.02
133 4 0.02
134 148 0.69
135 55 0.25
136 5 0.02
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (133 bp):
ACGACTCCTACGTGATGAGGAGATCTAGTCAGGGATGACACGTGCTCATACGTGATGAAGAGTTA
TGGCCATCTTTAGGAAAGTGATAACTCGGTTCCTACATGATGAGGATGGCCGGTTATCTGAGGAT
AAC
Found at i:2572485 original size:33 final size:33
Alignment explanation
Indices: 2572399--2572625 Score: 102
Period size: 33 Copynumber: 6.7 Consensus size: 33
2572389 AAGGGAATGA
*
2572399 CTCAAAGATGGTT-TTGTTTCAAGAGAAAC-AT
1 CTCAAAGATGATTGTTGTTTCAAGAGAAACAAT
* **
2572430 ACTCAAAGAT--TTAAATCATTTCAAGAGAAACAAT
1 -CTCAAAGATGATT--GTTGTTTCAAGAGAAACAAT
* **
2572464 CTCAAAGATGATTGTTGTTTCATGAGAAACGGT
1 CTCAAAGATGATTGTTGTTTCAAGAGAAACAAT
* ** *
2572497 CTCAAGGAAAATAAGATATGTTTCAAGAGAAACAAT
1 CTCAAAGATGAT-TG-T-TGTTTCAAGAGAAACAAT
* * * * * * *
2572533 CTCAAAGTTTGGTTATTATTTTATGAGAAACGAT
1 CTCAAAG-ATGATTGTTGTTTCAAGAGAAACAAT
* ** * *
2572567 CTCAAGGAAAATAAGATTTGTTTCAAGGGAAACAAT
1 CTCAAAGATGAT-TG--TTGTTTCAAGAGAAACAAT
* *
2572603 CTCAAAGTTTGTTTGTTGTTTCA
1 CTCAAAG-ATGATTGTTGTTTCA
2572626 TAAGAAATTG
Statistics
Matches: 137, Mismatches: 44, Indels: 26
0.66 0.21 0.13
Matches are distributed among these distances:
30 2 0.01
32 9 0.07
33 47 0.34
34 31 0.23
35 4 0.03
36 42 0.31
37 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (33 bp):
CTCAAAGATGATTGTTGTTTCAAGAGAAACAAT
Found at i:2572536 original size:36 final size:36
Alignment explanation
Indices: 2572448--2572607 Score: 107
Period size: 36 Copynumber: 4.6 Consensus size: 36
2572438 ATTTAAATCA
* ** *
2572448 TTTCAAGAGAAACAATCTCAAAGATGAT-TG-T-TG
1 TTTCAAGAGAAACAATCTCAAGGAAAATAAGATATG
* **
2572481 TTTCATGAGAAACGGTCTCAAGGAAAATAAGATATG
1 TTTCAAGAGAAACAATCTCAAGGAAAATAAGATATG
** ** * *
2572517 TTTCAAGAGAAACAATCTC-A--AAGTTTGGTTATTA
1 TTTCAAGAGAAACAATCTCAAGGAAAATAAGATA-TG
* * * *
2572551 TTTTATGAGAAACGATCTCAAGGAAAATAAGATTTG
1 TTTCAAGAGAAACAATCTCAAGGAAAATAAGATATG
*
2572587 TTTCAAGGGAAACAATCTCAA
1 TTTCAAGAGAAACAATCTCAA
2572608 AGTTTGTTTG
Statistics
Matches: 90, Mismatches: 30, Indels: 11
0.69 0.23 0.08
Matches are distributed among these distances:
33 28 0.31
34 18 0.20
35 3 0.03
36 36 0.40
37 5 0.06
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (36 bp):
TTTCAAGAGAAACAATCTCAAGGAAAATAAGATATG
Found at i:2572661 original size:70 final size:69
Alignment explanation
Indices: 2572447--2572679 Score: 265
Period size: 70 Copynumber: 3.3 Consensus size: 69
2572437 GATTTAAATC
*
2572447 ATTTCAAGAGAAACAATCTCAAAG-ATGATTGTTGTTTCATGAGAAACGGTCTCAAGGAAAATAA
1 ATTTCAAGAGAAACAATCTCAAAGTTTGATTGTTGTTTCATGAGAAAC-GTCTCAAGGAAAATAA
*
2572511 GATAT
65 GATTT
* * * * *
2572516 GTTTCAAGAGAAACAATCTCAAAGTTTGGTTATTATTTTATGAGAAACGATCTCAAGGAAAATAA
1 ATTTCAAGAGAAACAATCTCAAAGTTTGATTGTTGTTTCATGAGAAACG-TCTCAAGGAAAATAA
2572581 GATTT
65 GATTT
* * * * * * *
2572586 GTTTCAAGGGAAACAATCTCAAAGTTTGTTTGTTGTTTCATAAGAAATTGTCTCGA-GAGAGATA
1 ATTTCAAGAGAAACAATCTCAAAGTTTGATTGTTGTTTCATGAGAAA-CGTCTCAAGGA-AAATA
*
2572650 AAATTT
64 AGATTT
2572656 ATTTCAAGAGAAACAGA-CTCAAAG
1 ATTTCAAGAGAAACA-ATCTCAAAG
2572680 ATTATAAATT
Statistics
Matches: 140, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
69 26 0.19
70 112 0.80
71 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (69 bp):
ATTTCAAGAGAAACAATCTCAAAGTTTGATTGTTGTTTCATGAGAAACGTCTCAAGGAAAATAAG
ATTT
Found at i:2572849 original size:67 final size:68
Alignment explanation
Indices: 2572713--2572851 Score: 171
Period size: 67 Copynumber: 2.1 Consensus size: 68
2572703 AACAAACTTA
* * *
2572713 ATGATTTTTTTCAAAATAAATTGTCTCAAGAGAGACAAAACTTTGTTTCCAAAGAAACAGGCTCA
1 ATGATTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTCGTTTCCAAAGAAACAGGCGCA
2572778 AAG
66 AAG
*
2572781 ATGATTTTTATTTCAAAAGAAATTGTCTC-A-AGAGACAAAA-TTCGTTT-CAAGAGAAAC-GAT
1 ATGA-TTTT-TTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTCGTTTCCAA-AGAAACAG-G
2572841 CGCAAAG
62 CGCAAAG
2572848 ATGA
1 ATGA
2572852 GTGTTTCAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
66 4 0.06
67 22 0.35
68 14 0.22
69 5 0.08
70 18 0.29
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (68 bp):
ATGATTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTCGTTTCCAAAGAAACAGGCGCA
AAG
Found at i:2572914 original size:66 final size:64
Alignment explanation
Indices: 2572654--2572966 Score: 178
Period size: 64 Copynumber: 4.8 Consensus size: 64
2572644 GAGATAAAAT
* * * * * * * *
2572654 TTATTTCAAGAGAAACAGACTCAAAGATTATAAATTTTGTTTCCAATA-AAACAAACTTAATGAT
1 TTATTTCAAAAGAAACTGACTCAAAGA-GACAAAATTTGTTT-CAA-AGAAACAGACTCAAAGAT
2572718 --
63 GA
* * * * *
2572718 TTTTTTCAAAATAAATTGTCTCAAGAGAGACAAAACTTTGTTTCCAAAGAAACAGGCTCAAAGAT
1 TTATTTCAAAAGAAACTGACTCAA-AGAGACAAAA-TTTGTTT-CAAAGAAACAGACTCAAAGAT
2572783 GA
63 GA
* * * *
2572785 TTTTTATTTCAAAAGAAATTGTCTC-AAGAGACAAAATTCGTTTCAAGAGAAAC-GATCGCAAAG
1 ---TTATTTCAAAAGAAACTGACTCAAAGAGACAAAATTTGTTTCAA-AGAAACAGA-CTCAAAG
2572848 ATGA
61 ATGA
* * * * * *
2572852 GTGTTTCAAGATAAACTGACTCAAAGATTACAAAATTTGTTTCAAATGAAACAGACTTAAAGAT-
1 TTATTTCAAAAGAAACTGACTCAAAGA-GACAAAATTTGTTTCAAA-GAAACAGACTCAAAGATG
2572916 -
64 A
* * *
2572916 TT-TTTC--AAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTGAAGAGAAACA
1 TTATTTCAAAAGAAACTGACTCAA-AGAGACAAAA-TTTGTTTCAA-AGAAACA
2572967 ATTTTAAAGG
Statistics
Matches: 197, Mismatches: 35, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
61 17 0.09
62 18 0.09
63 5 0.03
64 40 0.20
65 31 0.16
66 31 0.16
67 24 0.12
68 10 0.05
69 1 0.01
70 20 0.10
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (64 bp):
TTATTTCAAAAGAAACTGACTCAAAGAGACAAAATTTGTTTCAAAGAAACAGACTCAAAGATGA
Found at i:2574499 original size:2 final size:2
Alignment explanation
Indices: 2574492--2574522 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2574482 AGCTTTATTG
2574492 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 T
2574523 TTTGTTGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2577562 original size:49 final size:48
Alignment explanation
Indices: 2577462--2577577 Score: 121
Period size: 49 Copynumber: 2.4 Consensus size: 48
2577452 GAATATAACA
* * *
2577462 CCTATCCGACATGATATCTACCCAAACATGCTTTAACTAAACAATATT
1 CCTACCCGACATGATATCTACCCAAACATGATTTAACCAAACAATATT
* * *
2577510 CCTACCCGAACATGCTATCTACCCAAA-ATGATTTATCCAAGCAAT-TGAT
1 CCTACCCG-ACATGATATCTACCCAAACATGATTTAACCAAACAATAT--T
*
2577559 CCTAACCG-CATGATATCTA
1 CCTACCCGACATGATATCTA
2577578 GTTCGCATGC
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
47 11 0.19
48 21 0.37
49 25 0.44
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (48 bp):
CCTACCCGACATGATATCTACCCAAACATGATTTAACCAAACAATATT
Found at i:2579109 original size:2 final size:2
Alignment explanation
Indices: 2579102--2579129 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2579092 AATAGAACAA
2579102 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
2579130 GTTTACAAAT
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:2579309 original size:30 final size:30
Alignment explanation
Indices: 2579270--2579362 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
2579260 ACCAAACTTG
*
2579270 AAAGGCTAAAATAGCTAAAACAGAA-CTTTA
1 AAAGACTAAAATAGCTAAAACAGAAGC-TTA
***
2579300 AAAGACTAAAATAAAAAAAAACAGAAGCTTA
1 AAAGACTAAAAT-AGCTAAAACAGAAGCTTA
* * *
2579331 AAGGACTAAAATAGCTAAAATAGAAACTTA
1 AAAGACTAAAATAGCTAAAACAGAAGCTTA
2579361 AA
1 AA
2579363 TAGCCAAAAC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
30 26 0.51
31 24 0.47
32 1 0.02
ACGTcount: A:0.60, C:0.11, G:0.12, T:0.17
Consensus pattern (30 bp):
AAAGACTAAAATAGCTAAAACAGAAGCTTA
Found at i:2582999 original size:45 final size:43
Alignment explanation
Indices: 2582944--2583208 Score: 110
Period size: 43 Copynumber: 6.2 Consensus size: 43
2582934 CCGCTAAAGT
* * * *
2582944 TAGCGACGTTTGAGAACAAAAAACGTTGCAATAGGTCAAGATCTA
1 TAGCGGCGTTTGAG-A-AAAAAACGCTGCAAAAGGTCAACATCTA
** *
2582989 TAGCGGCGTTTTTGAAACAAACGCTGCAAAAGGTCAACATCTA
1 TAGCGGCGTTTGAGAAAAAAACGCTGCAAAAGGTCAACATCTA
* ** * * * ** * *
2583032 TAGCGGAGTTTTTGGAACAAACACCACAAAAGGTCTAGATCTA
1 TAGCGGCGTTTGAGAAAAAAACGCTGCAAAAGGTCAACATCTA
* * ** * * * * *
2583075 TGGCGGCTTTTTTGGAACAAACGCCGTAAAAGGTC-AGATCTA
1 TAGCGGCGTTTGAGAAAAAAACGCTGCAAAAGGTCAACATCTA
* ** * * * *
2583117 TAGCGGCATTTTTTGATATAAACG-TCGCAAAAGGTCTAGATCTA
1 TAGCGGC-GTTTGAGAAAAAAACGCT-GCAAAAGGTCAACATCTA
* * *
2583161 TAACGGCGTTTTG-GAACAAACAC-C-GCAAAAGGTC-AGATCTA
1 TAGCGGCG-TTTGAGAA-AAAAACGCTGCAAAAGGTCAACATCTA
2583202 TAGCGGC
1 TAGCGGC
2583209 ATTTTTGGAT
Statistics
Matches: 181, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
41 13 0.07
42 23 0.13
43 113 0.62
44 21 0.12
45 11 0.06
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTGAGAAAAAAACGCTGCAAAAGGTCAACATCTA
Found at i:2583017 original size:43 final size:42
Alignment explanation
Indices: 2582971--2583227 Score: 291
Period size: 43 Copynumber: 6.0 Consensus size: 42
2582961 AAAAAACGTT
* * *
2582971 GCAATAGGTCAAGATCTATAGCGGCGTTTTTGAAACAAACGCT
1 GCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * *
2583014 GCAAAAGGTCAACATCTATAGCGGAGTTTTTGGAACAAACACC
1 GCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * *
2583057 ACAAAAGGTCTAGATCTATGGCGGCTTTTTTGGAACAAACGCC
1 GCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * * * *
2583100 GTAAAAGGTCAGATCTATAGCGGCATTTTTTGATATAAACGTC
1 GCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACGCC
* *
2583143 GCAAAAGGTCTAGATCTATAACGGCG-TTTTGGAACAAACACC
1 GCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCC
* *
2583185 GCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAGAAACGCC
1 GCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACGCC
2583228 AATAAAGTAC
Statistics
Matches: 179, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
41 13 0.07
42 43 0.24
43 110 0.61
44 13 0.07
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (42 bp):
GCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCC
Found at i:2583130 original size:86 final size:85
Alignment explanation
Indices: 2582976--2583224 Score: 304
Period size: 85 Copynumber: 2.9 Consensus size: 85
2582966 ACGTTGCAAT
* * * *
2582976 AGGTCAAGATCTATAGCGGCGTTTTTGAAACAAACGCTGCAAAAGGTCAACATCTATAGCGG-AG
1 AGGTCTAGATCTATAGCGGC-TTTTTGGAACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCA-
*
2583040 TTTTTGGA-ACAAACACCACAAA
63 TTTTTTGATACAAACACCACAAA
* *
2583062 AGGTCTAGATCTATGGCGGCTTTTTTGGAACAAACGCCGTAAAAGGTCAGATCTATAGCGGCATT
1 AGGTCTAGATCTATAGCGGC-TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATT
* ** *
2583127 TTTTGATATAAACGTCGCAAA
65 TTTTGATACAAACACCACAAA
* * *
2583148 AGGTCTAGATCTATAACGGCGTTTTGGAACAAACACCGCAAAAGGTCAGATCTATAGCGGCATTT
1 AGGTCTAGATCTATAGCGGCTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTT
* *
2583213 TTGGATAGAAAC
66 TTTGATACAAAC
2583225 GCCAATAAAG
Statistics
Matches: 142, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
85 71 0.50
86 71 0.50
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (85 bp):
AGGTCTAGATCTATAGCGGCTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTT
TTTGATACAAACACCACAAA
Found at i:2583191 original size:85 final size:85
Alignment explanation
Indices: 2582964--2583225 Score: 321
Period size: 86 Copynumber: 3.1 Consensus size: 85
2582954 TGAGAACAAA
* * * * * *
2582964 AAACGTTGCAATAGGTCAAGATCTATAGCGGCGTTTTTGAAACAAACGCTGCAAAAGGTCAACAT
1 AAACGTCGCAAAAGGTCTAGATCTATAGCGGCG-TTTTGGAACAAACGCCGCAAAAGGTC-AGAT
2583029 CTATAGCGG-AGTTTTTGGA-AC
64 CTATAGCGGCA-TTTTTGGATAC
** * * * *
2583050 AAACACCACAAAAGGTCTAGATCTATGGCGGCTTTTTTGGAACAAACGCCGTAAAAGGTCAGATC
1 AAACGTCGCAAAAGGTCTAGATCTATAGCGGC-GTTTTGGAACAAACGCCGCAAAAGGTCAGATC
* *
2583115 TATAGCGGCATTTTTTGATAT
65 TATAGCGGCATTTTTGGATAC
* *
2583136 AAACGTCGCAAAAGGTCTAGATCTATAACGGCGTTTTGGAACAAACACCGCAAAAGGTCAGATCT
1 AAACGTCGCAAAAGGTCTAGATCTATAGCGGCGTTTTGGAACAAACGCCGCAAAAGGTCAGATCT
*
2583201 ATAGCGGCATTTTTGGATAG
66 ATAGCGGCATTTTTGGATAC
2583221 AAACG
1 AAACG
2583226 CCAATAAAGT
Statistics
Matches: 149, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
85 72 0.48
86 77 0.52
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (85 bp):
AAACGTCGCAAAAGGTCTAGATCTATAGCGGCGTTTTGGAACAAACGCCGCAAAAGGTCAGATCT
ATAGCGGCATTTTTGGATAC
Found at i:2583296 original size:41 final size:41
Alignment explanation
Indices: 2583198--2583301 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
2583188 AAAGGTCAGA
* * * *
2583198 TCTATAGCGGCATTTTTGGATAGAAACGCCAATAAAGTACAAG
1 TCTATAGCGGC--GTTTGTATAAAAACGCCAATAAAATACAAG
* * *
2583241 TCTATAGCGTCGTTTGTATAAAAACGCCACTAAAATGCAAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCAATAAAATACAAG
* *
2583282 TCTATAGTGGCGTTTTTATA
1 TCTATAGCGGCGTTTGTATA
2583302 GCGTTGTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 41 0.80
43 10 0.20
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (41 bp):
TCTATAGCGGCGTTTGTATAAAAACGCCAATAAAATACAAG
Found at i:2583440 original size:81 final size:81
Alignment explanation
Indices: 2583343--2583493 Score: 234
Period size: 81 Copynumber: 1.9 Consensus size: 81
2583333 AAGTCTAAAA
* * *
2583343 CGGCGTTTGTATAAAAACGCCACTATACATGACCCCTATTGCGGCG-TTTTATAAAAACGTCGCT
1 CGGCGTTTGTATAAAAACACCACTATACATGA-CCCTATTACGGCGTTTTTATAAAAACGCCGCT
*
2583407 ACAGTATTACTCTTTAG
65 AAAGTATTACTCTTTAG
2583424 CGGCGTTTGTCA-AAAAACACCACTATACATGACCCTATTACGGCGTTTTTATAAAAACGCCGCT
1 CGGCGTTTGT-ATAAAAACACCACTATACATGACCCTATTACGGCGTTTTTATAAAAACGCCGCT
2583488 AAAGTA
65 AAAGTA
2583494 CAACTCTGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
80 12 0.19
81 51 0.80
82 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (81 bp):
CGGCGTTTGTATAAAAACACCACTATACATGACCCTATTACGGCGTTTTTATAAAAACGCCGCTA
AAGTATTACTCTTTAG
Found at i:2583480 original size:41 final size:40
Alignment explanation
Indices: 2583307--2583484 Score: 150
Period size: 40 Copynumber: 4.4 Consensus size: 40
2583297 TTATAGCGTT
** **
2583307 GTTTGTATAAAAACGCCACTTATTACA--AGTCTAAAACGGC
1 GTTTGTATAAAAACGCCAC-TA-TACATGACCCTATTACGGC
*
2583347 GTTTGTATAAAAACGCCACTATACATGACCCCTATTGCGGC
1 GTTTGTATAAAAACGCCACTATACATGA-CCCTATTACGGC
* * * * * *
2583388 GTTT-TATAAAAACGTCGCTACAGTATTACTCT-TTAGCGGC
1 GTTTGTATAAAAACGCCACTATA-CATGACCCTATTA-CGGC
*
2583428 GTTTGTCA-AAAAACACCACTATACATGACCCTATTACGGC
1 GTTTGT-ATAAAAACGCCACTATACATGACCCTATTACGGC
*
2583468 GTTTTTATAAAAACGCC
1 GTTTGTATAAAAACGCC
2583485 GCTAAAGTAC
Statistics
Matches: 108, Mismatches: 21, Indels: 18
0.73 0.14 0.12
Matches are distributed among these distances:
38 4 0.04
39 5 0.05
40 69 0.64
41 29 0.27
42 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (40 bp):
GTTTGTATAAAAACGCCACTATACATGACCCTATTACGGC
Found at i:2583521 original size:81 final size:82
Alignment explanation
Indices: 2583345--2583521 Score: 211
Period size: 81 Copynumber: 2.2 Consensus size: 82
2583335 GTCTAAAACG
* * * *
2583345 GCGTTTGT-ATAAAAACGCCACTATACATGACCCCTATTGCGGCGTTTTATAAAAACGTCGCTAC
1 GCGTTTGTAATAAAAACACCACTATACATGACCCCTATTACGGCGTTTTATAAAAACGCCGCTAA
** * *
2583409 AGTATTACTCTTTAGCG
66 AGTACAACTCTATAGCA
*
2583426 GCGTTTGTCA-AAAAACACCACTATACATGA-CCCTATTACGGCGTTTTTATAAAAACGCCGCTA
1 GCGTTTGTAATAAAAACACCACTATACATGACCCCTATTACGGCG-TTTTATAAAAACGCCGCTA
2583489 AAGTACAACTCTGAT-GCA
65 AAGTACAACTCT-ATAGCA
*
2583507 GC-TTTTTAATAAAAA
1 GCGTTTGTAATAAAAA
2583522 ACGCCATTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
80 17 0.21
81 63 0.77
82 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (82 bp):
GCGTTTGTAATAAAAACACCACTATACATGACCCCTATTACGGCGTTTTATAAAAACGCCGCTAA
AGTACAACTCTATAGCA
Found at i:2584909 original size:12 final size:12
Alignment explanation
Indices: 2584870--2584909 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
2584860 TAAAGTAAAA
2584870 TAAATTATTTAT
1 TAAATTATTTAT
2584882 T-AATTGATTCTAT
1 TAAATT-ATT-TAT
2584895 TAAATTATTTAT
1 TAAATTATTTAT
2584907 TAA
1 TAA
2584910 TTGATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.16
12 10 0.40
13 7 0.28
14 4 0.16
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (12 bp):
TAAATTATTTAT
Found at i:2585955 original size:147 final size:147
Alignment explanation
Indices: 2585688--2585978 Score: 438
Period size: 147 Copynumber: 2.0 Consensus size: 147
2585678 TTATTATGAG
* * *
2585688 ATACATTACTATCTAGAACAAATATATTTAGCAGGTTGATCAAATCGCTTATCTTTATTCTTTTA
1 ATACATTACTATCTAGAACAAATATATTTAGCAAGTTGATCAAACCGCTTATCTTTATTCTCTTA
* * **
2585753 TATTCCCTTAGGTTATGAGTAGAGTTATCTCGGATATTTTCAAGGTCATGAGCGAAACTAAAAAA
66 TATTCCCTTAGGTTATGAGTAGAGTTATCTCAGATATTTTCAAGATCACAAGCGAAACTAAAAAA
2585818 TATATCCTTATACAACA
131 TATATCCTTATACAACA
* * *
2585835 ATACATTACTATCTAGAACAAGTATATTTAGCAAGTTGGTCAACCCGCTTATCTTTATTCTCTTA
1 ATACATTACTATCTAGAACAAATATATTTAGCAAGTTGATCAAACCGCTTATCTTTATTCTCTTA
* * ** *
2585900 TATTCCCTTAGGTTATTAGTAGAGTTGTCTCAGATATTTTTGAGATCCCAAGCGAAACTAAAAAA
66 TATTCCCTTAGGTTATGAGTAGAGTTATCTCAGATATTTTCAAGATCACAAGCGAAACTAAAAAA
*
2585965 TATATTCTTATACA
131 TATATCCTTATACA
2585979 GAAAAAGTAT
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
147 128 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (147 bp):
ATACATTACTATCTAGAACAAATATATTTAGCAAGTTGATCAAACCGCTTATCTTTATTCTCTTA
TATTCCCTTAGGTTATGAGTAGAGTTATCTCAGATATTTTCAAGATCACAAGCGAAACTAAAAAA
TATATCCTTATACAACA
Found at i:2586122 original size:43 final size:43
Alignment explanation
Indices: 2586074--2586322 Score: 227
Period size: 43 Copynumber: 5.8 Consensus size: 43
2586064 TTATAGAAGC
** *
2586074 GAGATTAAAACTATTAAGGGCCTCAATTATAAAGGTAAAAAGT
1 GAGATTAAAAAAATTAAGAGCCTCAATTATAAAGGTAAAAAGT
* *
2586117 GAGATTAAAAAAATTAAGAACCTCAATTGTAAAGGTAAAAAGT
1 GAGATTAAAAAAATTAAGAGCCTCAATTATAAAGGTAAAAAGT
* * * * * *
2586160 GAGATTGAGAAAATTATGAGCCTCAAATATAAAAGGCAAAAACT
1 GAGATTAAAAAAATTAAGAGCCTCAATTAT-AAAGGTAAAAAGT
* * **
2586204 GAGATTAAAAAAATTATG-GCATTCAATTATAAATTTAAAAAGT
1 GAGATTAAAAAAATTAAGAGC-CTCAATTATAAAGGTAAAAAGT
* * * *
2586247 GAGATTAAACAAATT-AGAAACATCAATTATAAATGTCAAAAA-T
1 GAGATTAAAAAAATTAAG-AGCCTCAATTATAAAGGT-AAAAAGT
* * * *
2586290 GAGATCACAAAAATTAA-AACCTCAATTACAAAG
1 GAGATTAAAAAAATTAAGAGCCTCAATTATAAAG
2586323 AGAAAATTTA
Statistics
Matches: 168, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
42 14 0.08
43 113 0.67
44 41 0.24
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (43 bp):
GAGATTAAAAAAATTAAGAGCCTCAATTATAAAGGTAAAAAGT
Found at i:2586210 original size:87 final size:86
Alignment explanation
Indices: 2586093--2586322 Score: 236
Period size: 87 Copynumber: 2.7 Consensus size: 86
2586083 ACTATTAAGG
* *
2586093 GCCTCAATTAT-AAAGGTAAAAAGTGAGATTAAAAAAATTAAGAACCTCAATTGTAAAGGTAAAA
1 GCCTCAATTATAAAAGGCAAAAA-TGAGATTAAAAAAATTAAGAACCTCAATTATAAAGGTAAAA
*
2586157 AGTGAGATTGAGA-AAATTATG-A
65 AGTGAGATT-AAACAAATTA-GAA
* * * * **
2586179 GCCTCAAATATAAAAGGCAAAAACTGAGATTAAAAAAATTATG-GCATTCAATTATAAATTTAAA
1 GCCTCAATTATAAAAGGCAAAAA-TGAGATTAAAAAAATTAAGAAC-CTCAATTATAAAGGTAAA
2586243 AAGTGAGATTAAACAAATTAGAA
64 AAGTGAGATTAAACAAATTAGAA
* * * * * * *
2586266 ACATCAATTATAAATGTCAAAAATGAGATCACAAAAATTAA-AACCTCAATTACAAAG
1 GCCTCAATTATAAAAGGCAAAAATGAGATTAAAAAAATTAAGAACCTCAATTATAAAG
2586323 AGAAAATTTA
Statistics
Matches: 117, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
85 10 0.09
86 30 0.26
87 77 0.66
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.24
Consensus pattern (86 bp):
GCCTCAATTATAAAAGGCAAAAATGAGATTAAAAAAATTAAGAACCTCAATTATAAAGGTAAAAA
GTGAGATTAAACAAATTAGAA
Found at i:2595535 original size:12 final size:11
Alignment explanation
Indices: 2595518--2595560 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2595508 TCCATCTCTA
2595518 TTTTCTCTTTAT
1 TTTTCTCTTT-T
2595530 TTTTCTCTTTT
1 TTTTCTCTTTT
* *
2595541 TGTTCACTTTT
1 TTTTCTCTTTT
*
2595552 CTTTCTCTT
1 TTTTCTCTT
2595561 ATTTCTCCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:2596081 original size:20 final size:21
Alignment explanation
Indices: 2596043--2596082 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2596033 TTTGGGTTTA
*
2596043 AATATCGATACTGGGATGAAC
1 AATATCAATACTGGGATGAAC
2596064 AATATCAATACT-GGATGAA
1 AATATCAATACTGGGATGAA
2596083 TTGGAGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
AATATCAATACTGGGATGAAC
Found at i:2597500 original size:2 final size:2
Alignment explanation
Indices: 2597493--2597530 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2597483 GGCATTGCCA
2597493 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2597531 ATTATGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2599288 original size:63 final size:63
Alignment explanation
Indices: 2599210--2599337 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
2599200 AATTATTGAA
2599210 TTGTTCATTTCTCTATCAATGAGATAGCTACAATATTTAACAATTTTCAACTATTAGACCAGT
1 TTGTTCATTTCTCTATCAATGAGATAGCTACAATATTTAACAATTTTCAACTATTAGACCAGT
2599273 TTGTTCATTTCTCTATCAATGAGATAGCTACAATATTTAACAATTTTCAACTATTAGACCAGT
1 TTGTTCATTTCTCTATCAATGAGATAGCTACAATATTTAACAATTTTCAACTATTAGACCAGT
2599336 TT
1 TT
2599338 TTTAGTTTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (63 bp):
TTGTTCATTTCTCTATCAATGAGATAGCTACAATATTTAACAATTTTCAACTATTAGACCAGT
Found at i:2603403 original size:27 final size:27
Alignment explanation
Indices: 2603373--2603427 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2603363 TGTGAATGTG
2603373 TGTGTGTATTCCTCCCATTTTGCTTCC
1 TGTGTGTATTCCTCCCATTTTGCTTCC
2603400 TGTGTGTATTCCTCCCATTTTGCTTCC
1 TGTGTGTATTCCTCCCATTTTGCTTCC
2603427 T
1 T
2603428 CATTTATGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.07, C:0.29, G:0.15, T:0.49
Consensus pattern (27 bp):
TGTGTGTATTCCTCCCATTTTGCTTCC
Found at i:2604852 original size:9 final size:9
Alignment explanation
Indices: 2604838--2604862 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2604828 TTAAAATGTA
2604838 AAATAATTT
1 AAATAATTT
2604847 AAATAATTT
1 AAATAATTT
2604856 AAATAAT
1 AAATAAT
2604863 ATTTTTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATAATTT
Found at i:2619761 original size:2 final size:2
Alignment explanation
Indices: 2619754--2619812 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
2619744 AATACTCAAC
2619754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2619795 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2619813 TCCCAATCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2622374 original size:9 final size:9
Alignment explanation
Indices: 2622360--2622427 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
2622350 CTTCTAGTTG
*
2622360 TTACTATTT
1 TTACTATTA
2622369 TTACTATTA
1 TTACTATTA
*
2622378 TGA-TATTAA
1 TTACTATT-A
*
2622387 TTACTATTC
1 TTACTATTA
2622396 TTACTATTA
1 TTACTATTA
*
2622405 TGA-TATTAA
1 TTACTATT-A
*
2622414 TTACTATTC
1 TTACTATTA
2622423 TTACT
1 TTACT
2622428 TGTAGTTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 8 0.17
9 31 0.66
10 8 0.17
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (9 bp):
TTACTATTA
Found at i:2622391 original size:27 final size:27
Alignment explanation
Indices: 2622360--2622427 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
2622350 CTTCTAGTTG
*
2622360 TTACTATTTTTACTATTATGATATTAA
1 TTACTATTCTTACTATTATGATATTAA
2622387 TTACTATTCTTACTATTATGATATTAA
1 TTACTATTCTTACTATTATGATATTAA
2622414 TTACTATTCTTACT
1 TTACTATTCTTACT
2622428 TGTAGTTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (27 bp):
TTACTATTCTTACTATTATGATATTAA
Found at i:2627850 original size:22 final size:22
Alignment explanation
Indices: 2627825--2627870 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2627815 ATTAATATAA
*
2627825 AATTAAAAAATTATAGAAATTT
1 AATTAAAAAATTATAGAAAATT
*
2627847 AATTAAAAAATTATATAAAATT
1 AATTAAAAAATTATAGAAAATT
2627869 AA
1 AA
2627871 AGAAGAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AATTAAAAAATTATAGAAAATT
Found at i:2627870 original size:18 final size:18
Alignment explanation
Indices: 2627819--2627871 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 18
2627809 AAATCGATTA
2627819 ATATAAAATTAAAAAATT
1 ATATAAAATTAAAAAATT
*
2627837 ATAGAAATTTAATTAAAAAATT
1 ATA-TAA---AATTAAAAAATT
2627859 ATATAAAATTAAA
1 ATATAAAATTAAA
2627872 GAAGAGACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 10 0.34
19 2 0.07
21 2 0.07
22 15 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
ATATAAAATTAAAAAATT
Found at i:2630772 original size:29 final size:29
Alignment explanation
Indices: 2630734--2630836 Score: 172
Period size: 29 Copynumber: 3.6 Consensus size: 29
2630724 ATGTAAAAGA
2630734 TATATATATATATATATATATATATATAT
1 TATATATATATATATATATATATATATAT
2630763 TATATATATATATATATATATATATATAT
1 TATATATATATATATATATATATATATAT
2630792 TATATATATATATATATATATATATAT-T
1 TATATATATATATATATATATATATATAT
* *
2630820 TCATATGTATCTATATA
1 T-ATATATATATATATA
2630837 CGTATGCGAG
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
28 2 0.03
29 69 0.97
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (29 bp):
TATATATATATATATATATATATATATAT
Found at i:2630836 original size:2 final size:2
Alignment explanation
Indices: 2630733--2630818 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
2630723 CATGTAAAAG
2630733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
2630774 AT AT AT AT AT AT AT AT AT -T 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
2630815 AT AT
1 AT AT
2630819 TTCATATGTA
Statistics
Matches: 82, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.02
2 80 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2639324 original size:2 final size:2
Alignment explanation
Indices: 2639319--2639347 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2639309 AAATAGATAA
2639319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2639348 AAAGTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2639612 original size:13 final size:14
Alignment explanation
Indices: 2639568--2639614 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
2639558 AATAATAATA
*
2639568 ATAATAATTAAATAT
1 ATAA-AATTAAACAT
*
2639583 ATTAAAAATAAACAT
1 A-TAAAATTAAACAT
2639598 ATAAAATTAAA-AT
1 ATAAAATTAAACAT
2639611 ATAA
1 ATAA
2639615 CTAAACAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 6 0.21
14 9 0.32
15 10 0.36
16 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAAAATTAAACAT
Found at i:2639621 original size:25 final size:25
Alignment explanation
Indices: 2639591--2639638 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
2639581 ATATTAAAAA
2639591 TAAACATATAAAATTAAAA-TATAAC
1 TAAACA-ATAAAATTAAAACTATAAC
*
2639616 TAAACAATGAAATTAAAACTATA
1 TAAACAATAAAATTAAAACTATA
2639639 TATTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.27
Consensus pattern (25 bp):
TAAACAATAAAATTAAAACTATAAC
Found at i:2639693 original size:30 final size:30
Alignment explanation
Indices: 2639625--2639696 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
2639615 CTAAACAATG
* *
2639625 AAATTAAAACTATATATTTAAAATATATAA
1 AAATTAAAACTATATAATTAAAATAAATAA
*
2639655 AAAATAAAACT-TATAATT-AAATAAATGAA
1 AAATTAAAACTATATAATTAAAATAAAT-AA
2639684 AATATTAAAACTA
1 AA-ATTAAAACTA
2639697 GTGACTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.20
29 10 0.29
30 18 0.51
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (30 bp):
AAATTAAAACTATATAATTAAAATAAATAA
Found at i:2641086 original size:3 final size:3
Alignment explanation
Indices: 2641078--2641161 Score: 120
Period size: 3 Copynumber: 29.0 Consensus size: 3
2641068 GGGCCTTTAG
*
2641078 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG T-A TAA -AA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2641123 TAA TAA TAA TAT TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2641162 CAACAAATGG
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 5 0.07
3 69 0.93
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2641645 original size:123 final size:119
Alignment explanation
Indices: 2641494--2642069 Score: 512
Period size: 123 Copynumber: 4.9 Consensus size: 119
2641484 TCAATCTCCA
* * *
2641494 TATGTGATGAATCAAG-ATAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCATTCTTCA
1 TATGTGATGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC-TTCTTCA
* *
2641558 GATGAGTTCTTCTCATTATAAACTTTATCTGGAAATGTTGATGATGATCTATCTCC
65 GATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATGATGATCTATCT-C
* * * *
2641614 TTCTGTGATAGAGTCAAGCAAAAGGTTGAACAAG-CCATTCTCATTATGAACTTCTTATTCCTCT
1 -TATGTGAT-GAGTCAAGCAAAAGGTTGAACAAGTTC-TTCTCATTATGAACTTCTT-CTCTTCT
* * * *
2641678 TCAGATAAGTTATTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTTC
62 TCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATGATGATCTATC-TC
* * *
2641737 TTTTGTGATAGAGTCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTT
1 -TATGTGAT-GAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCTTCTT
* * * * *
2641802 CAGATAAGTTCTTCTCATTATGAATTTTCTCT-GAAAA----A-GTTGATCCA--TC
63 CAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATGATGATCTATCTC
* * * *
2641851 -AAGTGATGAATTCGAA-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTTCT
1 TATGTGATG-AGTC-AAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT--CTTCT
* * * * * *
2641914 TCAGATGAGTTTTTCTCATTATGAACTCTACCTGG-CAA--TGCTAAT--TC-A--TC
62 TCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATGATGATCTATCTC
* * * * * *
2641964 GA-GTGATGAATTAAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGATCTTCTTTTTCTTCTTC
1 TATGTGATG-AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TTCTCTTCTTC
*
2642028 AGATGAGTTCTTCTCATTATGAACTCT-TCTGGAAAAGTTGAT
64 AGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGAT
2642070 CCATCAAGTG
Statistics
Matches: 387, Mismatches: 47, Indels: 49
0.80 0.10 0.10
Matches are distributed among these distances:
111 6 0.02
112 81 0.21
113 80 0.21
114 12 0.03
116 1 0.00
117 7 0.02
118 1 0.00
121 7 0.02
122 13 0.03
123 175 0.45
124 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (119 bp):
TATGTGATGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATGATGATCTATCTC
Found at i:2641975 original size:113 final size:113
Alignment explanation
Indices: 2641752--2642090 Score: 452
Period size: 113 Copynumber: 3.0 Consensus size: 113
2641742 TGATAGAGTC
* *
2641752 AAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTC
1 AAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
2641816 TCATTATGAATTTTCTCTGAAAAAGTTGATCCATCAAGTGATGAATTCG
66 TCATTATGAACTCTC-CTGGAAAAGTTGATCCATCAAGTGATGAATTCG
* * * *
2641865 AA-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTTCTTCAGATGAGTTTTTC
1 AAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * * * *
2641929 TCATTATGAACTCTACCTGGCAATGCTAATTCATCGAGTGATGAATT-A
66 TCATTATGAACTCT-CCTGGAAAAGTTGATCCATCAAGTGATGAATTCG
* * *
2641977 AAGCAAAAGGTTAAACAAGTTCTTCTCATTATGATCTTCTT-TTTCTTCTTCAGATGAGTTCTTC
1 AAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
2642041 TCATTATGAACTCTTCTGGAAAAGTTGATCCATCAAGTGATGAATTCG
66 TCATTATGAACTCTCCTGGAAAAGTTGATCCATCAAGTGATGAATTCG
2642089 AA
1 AA
2642091 TCTTTGTTAA
Statistics
Matches: 191, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
111 25 0.13
112 77 0.40
113 88 0.46
114 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTCTCCTGGAAAAGTTGATCCATCAAGTGATGAATTCG
Found at i:2643051 original size:34 final size:32
Alignment explanation
Indices: 2642989--2643058 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2642979 ACCTTACAAC
* *
2642989 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
2643021 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
2643055 TCCC
1 TCCC
2643059 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:2643467 original size:21 final size:21
Alignment explanation
Indices: 2643423--2643498 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
2643413 TTGCAGCCTT
*
2643423 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
2643443 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
2643464 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
*
2643485 GGTGCATCGATGCA
1 GATGCATCGATGCA
2643499 CTAATTGCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 17 0.32
21 36 0.68
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:2643713 original size:30 final size:30
Alignment explanation
Indices: 2643679--2643738 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2643669 AACTTTGAAT
2643679 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
* *
2643709 AAATTCAATTCCAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
2643739 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:2643934 original size:45 final size:45
Alignment explanation
Indices: 2643870--2643960 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
2643860 ATTGTTACCA
2643870 ATTGTTGGAAAATATATGAAAATGTTAAGCTCCCCCTTTTCCATT
1 ATTGTTGGAAAATATATGAAAATGTTAAGCTCCCCCTTTTCCATT
*
2643915 ATTGTTGGAAAATATATGAAAATGTTAAGCTCCCCCTTTTTCATT
1 ATTGTTGGAAAATATATGAAAATGTTAAGCTCCCCCTTTTCCATT
2643960 A
1 A
2643961 AGAAATAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (45 bp):
ATTGTTGGAAAATATATGAAAATGTTAAGCTCCCCCTTTTCCATT
Done.