Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 30
Found at i:2690421 original size:102 final size:102
Alignment explanation
Indices: 2690250--2690620 Score: 469
Period size: 102 Copynumber: 3.6 Consensus size: 102
2690240 GAAGATTTTA
* * * *
2690250 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
* *
2690315 ATAAACATTGAAAACATTTCCCTTGAAACGAATTTTG
66 ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
* *
2690352 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTTAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
*
2690417 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
66 ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
* *
2690454 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
** * ** ***
2690518 A-AATTATTTGAATATGTTTTATTTGAAACAAATTTCG
66 ATAAACA-TTGAAAACATTTCCCTTGAAACAAATTTCG
* ** * * * *
2690555 TCT-TCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 TCTCT-CTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
2690619 CA
65 CA
2690621 AATTTTGTCT
Statistics
Matches: 240, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
100 4 0.02
101 79 0.33
102 157 0.65
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (102 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
Found at i:2690480 original size:36 final size:36
Alignment explanation
Indices: 2690433--2690658 Score: 236
Period size: 36 Copynumber: 6.4 Consensus size: 36
2690423 ATTGAAAACA
* *
2690433 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2690469 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2690505 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** * *
2690534 TTTTATTTGAAACAAATTTCGTCT-TCCTTGAGACAA
1 TTTCCCTTGAAACAAATTTTGTCTCT-CTTGAGACAG
** * *
2690570 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
2690607 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2690643 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
2690659 ATCTTTGAAT
Statistics
Matches: 159, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 2 0.01
31 1 0.01
34 2 0.01
35 1 0.01
36 101 0.64
37 31 0.19
38 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2690607 original size:203 final size:204
Alignment explanation
Indices: 2690250--2690620 Score: 478
Period size: 203 Copynumber: 1.8 Consensus size: 204
2690240 GAAGATTTTA
* * *
2690250 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAT
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * * *
2690315 ATAAACATTGAAAACATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
66 ATAAACATTGAAAACATTTCACTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
*
2690380 AAAATTTTGTCTCCCTTTAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
131 AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
2690445 TAAATTTCG
196 TAAATTTCG
* * *
2690454 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
** * ** * * ** *
2690518 A-AATTATTTGAATATGTTTTATTTGAAACAAATTTCGTCT-TCCTTGAGACAATTTCTTTTGGA
66 ATAAACA-TTGAAAACATTTCACTTGAAACAAATTTCGTCTCT-CTTGAGACAATTTCCCTTGAA
* * *
2690581 ACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
129 ACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
2690621 AATTTTGTCT
Statistics
Matches: 140, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
202 4 0.03
203 110 0.79
204 26 0.19
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (204 bp):
TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
ATAAACATTGAAAACATTTCACTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
TAAATTTCG
Found at i:2690713 original size:138 final size:138
Alignment explanation
Indices: 2690453--2690704 Score: 396
Period size: 138 Copynumber: 1.8 Consensus size: 138
2690443 AATAAATTTC
2690453 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** * *
2690518 AAATTATTTGAATATGTTTTATTTGAAACAAATTTCGTCTTCCTTGAGACAATTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAAC
2690583 TAAGTTTT
131 TAAGTTTT
*
2690591 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * *
2690656 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGA
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGA
2690705 GTGTTTCTTG
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 102 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAAC
TAAGTTTT
Found at i:2690723 original size:65 final size:64
Alignment explanation
Indices: 2690616--2690787 Score: 211
Period size: 65 Copynumber: 2.6 Consensus size: 64
2690606 GTTTCTCTTG
* **
2690616 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTT-CCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
** *
2690681 AAACAAATTTTGTCTCCCTTGAGAGTGTTT-CTTGAAACACAAAATCTTCAAATTTATTTCCCTT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTG-AA-ACAAAATCTTCAAATTTATTTCCCCT
2690745 A
64 A
* * * *
2690746 AAACAAAATTTTGTTTCCCTTGAGACCGTTTTCATGAAACAA
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCTTGAAACAA
2690788 CAGATATCTT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
63 4 0.04
64 2 0.02
65 59 0.63
66 25 0.27
67 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (64 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:2691194 original size:17 final size:16
Alignment explanation
Indices: 2691172--2691227 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 16
2691162 TATTTTTAAT
2691172 TATATTTTTTTATTTA
1 TATATTTTTTTATTTA
2691188 CTATATTCCTTTTTATTTA
1 -TATATT--TTTTTATTTA
2691207 TATATATTTTTTA-TTA
1 TATAT-TTTTTTATTTA
2691223 TATAT
1 TATAT
2691228 CTTATATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.22
17 12 0.33
18 5 0.14
19 11 0.31
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTTTTTTATTTA
Found at i:2691212 original size:20 final size:19
Alignment explanation
Indices: 2691166--2691214 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2691156 TATATATATT
2691166 TTTAATTATATT--TTTTTA
1 TTTAA-TATATTCCTTTTTA
*
2691184 TTTACTATATTCCTTTTTA
1 TTTAATATATTCCTTTTTA
2691203 TTTATATATATT
1 TTTA-ATATATT
2691215 TTTTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 6 0.23
18 4 0.15
19 10 0.38
20 6 0.23
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAATATATTCCTTTTTA
Found at i:2691223 original size:20 final size:20
Alignment explanation
Indices: 2691172--2691223 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
2691162 TATTTTTAAT
2691172 TATA-TTTTTTTATTTACTA
1 TATATTTTTTTTATTTACTA
**
2691191 TAT-TCCTTTTTATTTA-TA
1 TATATTTTTTTTATTTACTA
2691209 TATATTTTTTATTAT
1 TATATTTTTT-TTAT
2691224 ATATCTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (20 bp):
TATATTTTTTTTATTTACTA
Found at i:2691226 original size:14 final size:15
Alignment explanation
Indices: 2691156--2691227 Score: 58
Period size: 16 Copynumber: 4.5 Consensus size: 15
2691146 GTCCCCTATA
*
2691156 TATATATATTTTTAAT
1 TATATAT-TTTTTATT
2691172 TATAT-TTTTTTATT
1 TATATATTTTTTATT
2691186 TACTATATTCCTTTTTATT
1 TA-TATA-T--TTTTTATT
2691205 TATATATATTTTT-TAT
1 TATATAT-TTTTTAT-T
2691221 TATATAT
1 TATATAT
2691228 CTTATATCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
14 9 0.19
15 5 0.10
16 18 0.38
17 2 0.04
18 4 0.08
19 10 0.21
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATATTTTTTATT
Found at i:2691335 original size:44 final size:40
Alignment explanation
Indices: 2691279--2691383 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 40
2691269 ATTTTTCTCC
* *
2691279 ATTTACTATATATATATTTTTTTCTTAATATTATATTTTA-T
1 ATTTA-TATATATATA-TATATTCTTAATATTATATTTTATT
*
2691320 ACGTTTATATATATATATATATTCTTAATATTCTATTTTATT
1 A--TTTATATATATATATATATTCTTAATATTATATTTTATT
*
2691362 ATTTATTTATATATATTATATT
1 ATTTATATATATATA-TATATT
2691384 TTACTTATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
40 13 0.23
41 27 0.48
42 12 0.21
43 4 0.07
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (40 bp):
ATTTATATATATATATATATTCTTAATATTATATTTTATT
Found at i:2691442 original size:35 final size:35
Alignment explanation
Indices: 2691402--2691483 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
2691392 TTTTTTTCTA
2691402 TTATTT-TTTT-CTTAATATCATGTATATCT-TTATTT
1 TTATTTGTTTTACTTAATAT-A--TATATCTATTATTT
* *
2691437 TTATTTGTTTTACTTAGTATATATATTTATTATTT
1 TTATTTGTTTTACTTAATATATATATCTATTATTT
2691472 TTATTTGTTTTA
1 TTATTTGTTTTA
2691484 GTAAATACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 6 0.14
35 24 0.57
36 5 0.12
37 7 0.17
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (35 bp):
TTATTTGTTTTACTTAATATATATATCTATTATTT
Found at i:2691675 original size:27 final size:25
Alignment explanation
Indices: 2691617--2691676 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
2691607 ATTTTGTTTA
* *
2691617 TTTTTATTTTTATTTTTTACGTGTT
1 TTTTTATTTTCATTTTTTACTTGTT
* *
2691642 TTGTTATTTTCCATTTTTTTCTTGTT
1 TTTTTATTTT-CATTTTTTACTTGTT
2691668 TTATTTATT
1 TT-TTTATT
2691677 ATTCTCACGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 9 0.32
26 14 0.50
27 5 0.18
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.75
Consensus pattern (25 bp):
TTTTTATTTTCATTTTTTACTTGTT
Found at i:2694642 original size:10 final size:10
Alignment explanation
Indices: 2694622--2694651 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2694612 AGATTTAATC
2694622 AGAACAAAAAG
1 AGAA-AAAAAG
2694633 AGAAAAAAAG
1 AGAAAAAAAG
2694643 AGAAAAAAA
1 AGAAAAAAA
2694652 CAAAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:2694852 original size:69 final size:69
Alignment explanation
Indices: 2694737--2694871 Score: 225
Period size: 69 Copynumber: 2.0 Consensus size: 69
2694727 TCAAACTATG
* * *
2694737 AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCAGTTCACTCGAAGATCATAGAGCATCA
1 AGATTAATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCATCA
2694802 AATT
66 AATT
* *
2694806 AGATTAATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGAGCATCA
1 AGATTAATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCATCA
2694871 A
66 A
2694872 GAGAGAGACA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (69 bp):
AGATTAATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCATCA
AATT
Found at i:2696278 original size:17 final size:17
Alignment explanation
Indices: 2696256--2696300 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
2696246 CTTAAAACAT
*
2696256 ACTTTGTTTTACTTGAG
1 ACTTTGTTTCACTTGAG
2696273 ACTTTGTTTCACTTGAG
1 ACTTTGTTTCACTTGAG
2696290 AC--TGTTTCACT
1 ACTTTGTTTCACT
2696301 CGAAAGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.33
17 18 0.67
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (17 bp):
ACTTTGTTTCACTTGAG
Found at i:2696481 original size:36 final size:35
Alignment explanation
Indices: 2696434--2696518 Score: 116
Period size: 35 Copynumber: 2.4 Consensus size: 35
2696424 ATTGAAAACA
* * *
2696434 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAAC-AAATTTGTCTCCCTTGAGACAG
*
2696470 TTTCCCTTGAAACAAATTTGTCTCCCTTTAGACAG
1 TTTCCCTTGAAACAAATTTGTCTCCCTTGAGACAG
*
2696505 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2696519 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 31 0.70
36 13 0.30
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (35 bp):
TTTCCCTTGAAACAAATTTGTCTCCCTTGAGACAG
Found at i:2696522 original size:100 final size:100
Alignment explanation
Indices: 2696347--2696721 Score: 439
Period size: 100 Copynumber: 3.7 Consensus size: 100
2696337 TAAAAAGAAG
* *
2696347 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAT-TTGTCTCCCTTGAGACAGTTTCTCT
* *
2696412 TGAAATATAAACATTGAAAACATTTCCCTTGAAACGA
64 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
*
2696449 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTGTCTCCCTTTAGACAGTTTCTCTTG
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTGTCTCCCTTGAGACAGTTTCTCTTG
*
2696514 AAACATAAACATTGAAAACATTTCCCTTGAAATAA
66 AAACATAAACATTGAAAACATTTCCCTTGAAACAA
* * * *
2696549 ATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA-TTTGTCTCCCTTGAGACAGTTTCTCTT
** * ** ***
2696614 GAAACA-AATTATTTGAATATGTTTTATTTGAAACAA
65 GAAACATAAACA-TTGAAAACATTTCCCTTGAAACAA
* * * ** * * *
2696650 ATTTCGTCT-TCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 ATTTTGTCTCT-CTTGAGATAGTTTCCCTTGAAAC-AA-ATTTGTCTCCCTTGAGACAGTTTCTC
2696714 TTGAAACA
63 TTGAAACA
2696722 AATTTTGTCT
Statistics
Matches: 242, Mismatches: 26, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
100 97 0.40
101 79 0.33
102 66 0.27
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (100 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTGTCTCCCTTGAGACAGTTTCTCTTG
AAACATAAACATTGAAAACATTTCCCTTGAAACAA
Found at i:2696581 original size:36 final size:36
Alignment explanation
Indices: 2696534--2696759 Score: 236
Period size: 36 Copynumber: 6.4 Consensus size: 36
2696524 ATTGAAAACA
* *
2696534 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2696570 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2696606 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** * *
2696635 TTTTATTTGAAACAAATTTCGTCT-TCCTTGAGACAA
1 TTTCCCTTGAAACAAATTTTGTCTCT-CTTGAGACAG
** * *
2696671 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
2696708 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2696744 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
2696760 ATCTTTGAAT
Statistics
Matches: 159, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 2 0.01
31 1 0.01
34 2 0.01
35 1 0.01
36 101 0.64
37 31 0.19
38 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2696813 original size:138 final size:138
Alignment explanation
Indices: 2696554--2696805 Score: 396
Period size: 138 Copynumber: 1.8 Consensus size: 138
2696544 AATAAATTTC
2696554 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** * *
2696619 AAATTATTTGAATATGTTTTATTTGAAACAAATTTCGTCTTCCTTGAGACAATTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAAC
2696684 TAAGTTTT
131 TAAGTTTT
*
2696692 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * *
2696757 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGA
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGA
2696806 GTGTTTCTCT
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 102 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAAC
TAAGTTTT
Found at i:2696887 original size:67 final size:67
Alignment explanation
Indices: 2696708--2696889 Score: 226
Period size: 65 Copynumber: 2.7 Consensus size: 67
2696698 CTTGAGACAG
* * * * **
2696708 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
2696771 TA
66 TA
* **
2696773 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGAGTGTTTCTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
2696838 TA
66 TA
* * *
2696840 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 TTTCCCTTAAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
2696890 ACAGATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
65 38 0.38
66 2 0.02
67 37 0.37
68 23 0.23
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:2697337 original size:23 final size:19
Alignment explanation
Indices: 2697274--2697331 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
2697264 TTTTTAATTA
*
2697274 TATTTTTTA-TTACTATAT
1 TATTTTTTATTTATTATAT
*
2697292 TCCTTTTTTATTTATTATAT
1 T-ATTTTTTATTTATTATAT
*
2697312 TATTTTTTATATATATATAT
1 TATTTTTTATTTAT-TATAT
2697332 CATTATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 18 0.55
20 14 0.42
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTTTATTTATTATAT
Found at i:2697450 original size:41 final size:41
Alignment explanation
Indices: 2697371--2697476 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 41
2697361 AATTTTTCTC
* *
2697371 CATTTACTATATATATATTTTTTTCTTAATATTATATTTTATA
1 CATTTA-TATATATATA-TATATTCTTAATATTATATTTTATA
* * *
2697414 CGTTTATATATATATATATATTCTTAATATTCTATTTTATT
1 CATTTATATATATATATATATTCTTAATATTATATTTTATA
* * *
2697455 TATTTATTTATTTATATATATT
1 CATTTATATATATATATATATT
2697477 ATATTTTTAC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 39 0.72
42 10 0.19
43 5 0.09
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (41 bp):
CATTTATATATATATATATATTCTTAATATTATATTTTATA
Found at i:2697509 original size:13 final size:13
Alignment explanation
Indices: 2697493--2697517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2697483 TTACCTTATT
2697493 TTATTTTTTTCTA
1 TTATTTTTTTCTA
2697506 TTATTTTTTTCT
1 TTATTTTTTTCT
2697518 TAATATCATG
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:2700737 original size:10 final size:10
Alignment explanation
Indices: 2700717--2700746 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2700707 AGATTTAATC
2700717 AGAACAAAAAG
1 AGAA-AAAAAG
2700728 AGAAAAAAAG
1 AGAAAAAAAG
2700738 AGAAAAAAA
1 AGAAAAAAA
2700747 CAAAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:2702313 original size:17 final size:17
Alignment explanation
Indices: 2702291--2702335 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
2702281 CTTAAAACAT
*
2702291 ACTTTGTTTTACTTGAG
1 ACTTTGTTTCACTTGAG
2702308 ACTTTGTTTCACTTGAG
1 ACTTTGTTTCACTTGAG
2702325 AC--TGTTTCACT
1 ACTTTGTTTCACT
2702336 CGAAAGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.33
17 18 0.67
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (17 bp):
ACTTTGTTTCACTTGAG
Found at i:2702513 original size:36 final size:36
Alignment explanation
Indices: 2702466--2702789 Score: 222
Period size: 36 Copynumber: 9.4 Consensus size: 36
2702456 ATTGAAAACA
* *
2702466 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2702502 TTTCCCTTGAAACAAAATTTTGTCTCCCTTTAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *** * *
2702539 TTTCTCTTGAAAC-AA---T-AAAC-ATTGAAAACA-
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTG-AGACAG
* *
2702569 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2702605 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2702641 TTTCCCTTGAAA-AAA----AT-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** * *
2702670 TTTTATTTG-AACAAATTTCGTCT-TCCTTGAGACAA
1 TTTCCCTTGAAACAAATTTTGTCTCT-CTTGAGACAG
** * * *
2702705 TTTCTTTTGGAACTAA-GTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
2702740 TTTCTCTTGAAACAAA-TTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2702775 -TT-CCTTGAAAACAAA
1 TTTCCCTTG-AAACAAA
2702790 ATCTTTGAAT
Statistics
Matches: 225, Mismatches: 41, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
28 4 0.02
29 14 0.06
30 15 0.07
31 8 0.04
32 1 0.00
33 6 0.03
34 10 0.04
35 66 0.29
36 70 0.31
37 31 0.14
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2702541 original size:37 final size:37
Alignment explanation
Indices: 2702466--2702553 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
2702456 ATTGAAAACA
* * *
2702466 TTTCCCTTGAAAC-GAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
2702502 TTTCCCTTGAAACAAAATTTTGTCTCCCTTTAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
2702539 TTTCTCTTGAAACAA
1 TTTCCCTTGAAACAA
2702554 TAAACATTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 13 0.28
37 33 0.72
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:2702611 original size:103 final size:100
Alignment explanation
Indices: 2702400--2702751 Score: 401
Period size: 100 Copynumber: 3.5 Consensus size: 100
2702390 CTCGCTTGAG
* *
2702400 AGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAATATAAATTGAAAAC
1 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAAATAAATTGAAAAC
* * *
2702465 ATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGAT
66 ATTTCCCTTGAAACAAATTTCGTCTCTCTTGAGAC
*
2702500 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTTAGACAGTTTCTCTTGAAACAATAAACATTGAA
1 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA-AAT-AA-ATTGAA
*
2702565 AACATTTCCCTTGAAATAAATTTCGTCTCTCTTGAGAC
63 AACATTTCCCTTGAAACAAATTTCGTCTCTCTTGAGAC
* *
2702603 AGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAA-AATTATTTGAA
1 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAAATAA--A-TTGAA
* ** ***
2702666 TATGTTTTATTTG-AACAAATTTCGTCT-TCCTTGAGAC
63 AACATTTCCCTTGAAACAAATTTCGTCTCT-CTTGAGAC
* ** * * * *
2702703 AATTTCTTTTGGAAC-TAA-GTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
2702752 CAAATTTGTC
Statistics
Matches: 221, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
99 32 0.14
100 84 0.38
101 16 0.07
102 34 0.15
103 55 0.25
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (100 bp):
AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAAATAAATTGAAAAC
ATTTCCCTTGAAACAAATTTCGTCTCTCTTGAGAC
Found at i:2702744 original size:35 final size:35
Alignment explanation
Indices: 2702695--2702789 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 35
2702685 TTTCGTCTTC
* * * *
2702695 CTTGAGACAATTTCTTTTGGAACTAAGTTGTCTCT
1 CTTGAGACAGTTTCTCTTGAAACAAAGTTGTCTCT
*
2702730 CTTGAGACAGTTTCTCTTGAAACAAATTTGTCTCT
1 CTTGAGACAGTTTCTCTTGAAACAAAGTTGTCTCT
2702765 CTTGAGACAG-TTC-CTTGAAAACAAA
1 CTTGAGACAGTTTCTCTTG-AAACAAA
2702790 ATCTTTGAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 4 0.07
34 10 0.19
35 40 0.74
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (35 bp):
CTTGAGACAGTTTCTCTTGAAACAAAGTTGTCTCT
Found at i:2702843 original size:134 final size:135
Alignment explanation
Indices: 2702589--2702835 Score: 347
Period size: 134 Copynumber: 1.8 Consensus size: 135
2702579 AATAAATTTC
2702589 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAA
* * * * ** *
2702654 AAATTATTTGAATATGTTTTATTTGAACAAATTTCGTCTTCCTTGAGACAATTTCTTTTGGAACT
66 AAAATATTTGAATATATTTCACTAAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACT
2702719 AAGTT
131 AAGTT
*
2702724 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAA-TTTGTCTCTCTTGAGACAG-TT-CCTTGAAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAA
* * * *
2702786 CAAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGA
66 -AAAATATTTGAATATATTT-CACTAAAACAAATTTCGTCTCCCTTGAGA
2702836 GTGTTTCTCT
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
132 9 0.09
133 17 0.17
134 41 0.42
135 31 0.32
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (135 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAA
AAAATATTTGAATATATTTCACTAAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACT
AAGTT
Found at i:2702897 original size:67 final size:66
Alignment explanation
Indices: 2702749--2702902 Score: 199
Period size: 67 Copynumber: 2.4 Consensus size: 66
2702739 GTTTCTCTTG
* ** * *
2702749 AAACAAA-TTTGTCTCTCTTGAGACAG-TTC-CTTGAAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTTGTCTCCCTTGAGAGTGTTTCTCTTGAAAACAAAATCTTTCAAATTATTTCCCCT
2702811 A
66 A
*
2702812 AAACAAATTTTGTCTCCCTTGAGAGTGTTTCTCTTGAAACACAAAATC-TTCAAATTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGAGTGTTTCTCTTGAAA-ACAAAATCTTTCAAATTATTTCCCC
2702876 TA
65 TA
*
2702878 AAACAAAATTTTGTTTCCCTTGAGA
1 AAAC-AAATTTTGTCTCCCTTGAGA
2702903 CCGTTTTCAT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
63 7 0.09
64 16 0.20
65 3 0.04
66 26 0.33
67 27 0.34
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (66 bp):
AAACAAATTTTGTCTCCCTTGAGAGTGTTTCTCTTGAAAACAAAATCTTTCAAATTATTTCCCCT
A
Found at i:2702916 original size:66 final size:67
Alignment explanation
Indices: 2702749--2702918 Score: 199
Period size: 66 Copynumber: 2.6 Consensus size: 67
2702739 GTTTCTCTTG
* * * * *
2702749 AAACAAA-TTTGTCTCTCTTGAGACAG-TTC-CTTGAAA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACCGTTTCTCATGAAACACAAAATCTTTCAAATTATTTCCCC
2702810 TA
66 TA
** * *
2702812 AAACAAATTTTGTCTCCCTTGAGAGTGTTTCTCTTGAAACACAAAATC-TTCAAATTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACCGTTTCTCATGAAACACAAAATCTTTCAAATTATTTCCCC
2702876 TA
66 TA
*
2702878 AAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 AAAC-AAATTTTGTCTCCCTTGAGACCGTTTCTCATGAAACA
2702919 ACAGATATCT
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
63 7 0.08
64 16 0.17
65 3 0.03
66 35 0.38
67 31 0.34
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACCGTTTCTCATGAAACACAAAATCTTTCAAATTATTTCCCC
TA
Found at i:2703112 original size:18 final size:18
Alignment explanation
Indices: 2703073--2703115 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
2703063 TATATTTAAT
*
2703073 TTTTTTATTTAATATTCC
1 TTTTTTATTTAATATTCA
2703091 TTTTTTATTT-ATATT-A
1 TTTTTTATTTAATATTCA
2703107 TATTTTTAT
1 T-TTTTTAT
2703116 ATATTATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 12 0.52
18 10 0.43
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTATTTAATATTCA
Found at i:2703179 original size:11 final size:11
Alignment explanation
Indices: 2703160--2703264 Score: 72
Period size: 11 Copynumber: 9.5 Consensus size: 11
2703150 TTTTTTCTCC
2703160 TTTTATTATATA
1 TTTT-TTATATA
2703172 TTTTTTATATA
1 TTTTTTATATA
2703183 --TTTTATATA
1 TTTTTTATATA
** *
2703192 TAATATATATA
1 TTTTTTATATA
*
2703203 TTATTTTATTTA
1 TT-TTTTATATA
* *
2703215 TTTATTATTTA
1 TTTTTTATATA
* *
2703226 TATATTATAT-
1 TTTTTTATATA
* *
2703236 TTTATTATTTA
1 TTTTTTATATA
2703247 TTTTTTATATTA
1 TTTTTTATA-TA
2703259 TTTTTT
1 TTTTTT
2703265 TCTTAATTCA
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
9 9 0.12
10 8 0.11
11 38 0.51
12 20 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTTATATA
Found at i:2703180 original size:9 final size:9
Alignment explanation
Indices: 2703163--2703257 Score: 50
Period size: 9 Copynumber: 10.4 Consensus size: 9
2703153 TTTCTCCTTT
*
2703163 TATTATATA
1 TATTTTATA
*
2703172 TTTTTTATA
1 TATTTTATA
2703181 TATTTTATA
1 TATTTTATA
**
2703190 TATAATATA
1 TATTTTATA
*
2703199 TATATTAT-
1 TATTTTATA
* *
2703207 TTTATTTATT
1 TAT-TTTATA
2703217 TATTATT-TA
1 TATT-TTATA
*
2703226 TATATTATA
1 TATTTTATA
* *
2703235 TTTTATTATT
1 TATT-TTATA
*
2703245 TATTTTTTA
1 TATTTTATA
2703254 TATT
1 TATT
2703258 ATTTTTTTCT
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
8 4 0.06
9 49 0.77
10 11 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTATA
Found at i:2703206 original size:27 final size:28
Alignment explanation
Indices: 2703166--2703235 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
2703156 CTCCTTTTAT
* *
2703166 TATATATTTTTTATATATTTTATATATAA
1 TATATATATTATATATA-TTTATATATAA
* * *
2703195 TATATATATTAT-TTTATTTATTTATTA
1 TATATATATTATATATATTTATATATAA
*
2703222 TTTATATATTATAT
1 TATATATATTATAT
2703236 TTTATTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 20 0.59
28 4 0.12
29 10 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TATATATATTATATATATTTATATATAA
Found at i:2703217 original size:32 final size:31
Alignment explanation
Indices: 2703166--2703256 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
2703156 CTCCTTTTAT
*
2703166 TATATATTTTTTATATATTTTATATATAATA
1 TATATATTTTTTATTTATTTTATATATAATA
*
2703197 TATATATTATTTTATTTA-TTTAT-TATTTATA
1 TATATATT-TTTTATTTATTTTATATA-TAATA
*
2703228 TATTATATTTTATTATTTATTTTTTATAT
1 TA-TATATTTT-TTATTTATTTTATATAT
2703257 TATTTTTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
30 2 0.04
31 21 0.41
32 21 0.41
33 5 0.10
34 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TATATATTTTTTATTTATTTTATATATAATA
Found at i:2703241 original size:21 final size:21
Alignment explanation
Indices: 2703215--2703257 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2703205 ATTTTATTTA
2703215 TTTATTATTTATATATTATAT
1 TTTATTATTTATATATTATAT
* *
2703236 TTTATTATTTATTTTTTATAT
1 TTTATTATTTATATATTATAT
2703257 T
1 T
2703258 ATTTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTATTATTTATATATTATAT
Found at i:2703320 original size:7 final size:7
Alignment explanation
Indices: 2703161--2703321 Score: 53
Period size: 7 Copynumber: 21.4 Consensus size: 7
2703151 TTTTTCTCCT
2703161 TTTATTA
1 TTTATTA
* *
2703168 TATATTT
1 TTTATTA
2703175 TTTATATA
1 TTTAT-TA
2703183 TTT-TATA
1 TTTAT-TA
*
2703190 TATAATATA
1 T-TTAT-TA
*
2703199 TATATTA
1 TTTATTA
2703206 TTTTATTTA
1 -TTTA-TTA
2703215 TTTATTA
1 TTTATTA
2703222 TTTA-TA
1 TTTATTA
2703228 TATTA-TA
1 T-TTATTA
2703235 TTTTATTA
1 -TTTATTA
*
2703243 TTTATTT
1 TTTATTA
2703250 TTTA-TA
1 TTTATTA
*
2703256 -TTATTTT
1 TTTA-TTA
*
2703263 TTTCTTAA
1 TTTATT-A
*
2703271 TTCATTA
1 TTTATTA
*
2703278 CTTTATTT
1 -TTTATTA
*
2703286 TTTATTTGT
1 TTTA-TT-A
2703295 TTTATTA
1 TTTATTA
2703302 GTATTATATA
1 -T-TTAT-TA
2703312 TTTATTA
1 TTTATTA
2703319 TTT
1 TTT
2703322 TATTGTTTTA
Statistics
Matches: 118, Mismatches: 18, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
5 3 0.03
6 4 0.03
7 54 0.46
8 37 0.31
9 18 0.15
10 2 0.02
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (7 bp):
TTTATTA
Found at i:2703323 original size:8 final size:8
Alignment explanation
Indices: 2703201--2703331 Score: 69
Period size: 8 Copynumber: 16.2 Consensus size: 8
2703191 ATAATATATA
2703201 TATTATTT
1 TATTATTT
2703209 TATT-TATT
1 TATTAT-TT
2703217 TATTA-TT
1 TATTATTT
*
2703224 TA-TATAT
1 TATTATTT
2703231 TA-TATTT
1 TATTATTT
2703238 TATTA-TT
1 TATTATTT
*
2703245 TATTTTTT
1 TATTATTT
2703253 ATATTATTT
1 -TATTATTT
* *
2703262 TTTTCTTAAT
1 TATTATT--T
*
2703272 TCATTACTT
1 T-ATTATTT
2703281 TATT-TTT
1 TATTATTT
*
2703288 TATTTGTTT
1 TA-TTATTT
*
2703297 TATTAGTAT
1 TATTA-TTT
2703306 TA-TATATT
1 TATTAT-TT
2703314 TATTATTT
1 TATTATTT
*
2703322 TATTGTTT
1 TATTATTT
2703330 TA
1 TA
2703332 GTAAATACTA
Statistics
Matches: 95, Mismatches: 14, Indels: 28
0.69 0.10 0.20
Matches are distributed among these distances:
6 2 0.02
7 25 0.26
8 42 0.44
9 21 0.22
10 2 0.02
11 3 0.03
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (8 bp):
TATTATTT
Found at i:2703499 original size:25 final size:25
Alignment explanation
Indices: 2703448--2703507 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2703438 ATTTTATTCA
*
2703448 TTTGTTATTTTTATTTTTTTACGTGT
1 TTTGTTATTTTCATTTTTTTA-GTGT
*
2703474 TTTGTTATTTTCCATTTTTTT-TTGT
1 TTTGTTATTTT-CATTTTTTTAGTGT
*
2703499 TTTATTATT
1 TTTGTTATT
2703508 ATCTCACGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.37
26 11 0.37
27 8 0.27
ACGTcount: A:0.12, C:0.05, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTGTTATTTTCATTTTTTTAGTGT
Found at i:2705991 original size:11 final size:11
Alignment explanation
Indices: 2705975--2705999 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2705965 TAATCAGAAC
2705975 AAAAGAGAAAA
1 AAAAGAGAAAA
2705986 AAAAGAGAAAA
1 AAAAGAGAAAA
2705997 AAA
1 AAA
2706000 CAAAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAGAAAA
Found at i:2706199 original size:69 final size:69
Alignment explanation
Indices: 2706084--2706218 Score: 234
Period size: 69 Copynumber: 2.0 Consensus size: 69
2706074 TCAAACTATG
* *
2706084 AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCAGTTCACTCGAAGATCATAGAGCATCA
1 AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCATCA
2706149 AATT
66 AATT
* *
2706153 AGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGAGCATCA
1 AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCATCA
2706218 A
66 A
2706219 GAGAGAGACA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (69 bp):
AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCATCA
AATT
Found at i:2707630 original size:17 final size:17
Alignment explanation
Indices: 2707608--2707652 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
2707598 CTTAAAACAT
*
2707608 ACTTTGTTTTACTTGAG
1 ACTTTGTTTCACTTGAG
2707625 ACTTTGTTTCACTTGAG
1 ACTTTGTTTCACTTGAG
2707642 AC--TGTTTCACT
1 ACTTTGTTTCACT
2707653 CGAAAGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.33
17 18 0.67
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (17 bp):
ACTTTGTTTCACTTGAG
Found at i:2707861 original size:37 final size:37
Alignment explanation
Indices: 2707786--2707872 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
2707776 ATTGAAAACA
* * *
2707786 TTTCCCTTGAAAC-GAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
2707822 TTTCCCTTGAAACAAAATTTTGTCTCCCTTTAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
2707859 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2707873 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 13 0.29
37 32 0.71
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:2707876 original size:102 final size:102
Alignment explanation
Indices: 2707705--2708075 Score: 469
Period size: 102 Copynumber: 3.6 Consensus size: 102
2707695 GAAGATTTTA
* * * *
2707705 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
* *
2707770 ATAAACATTGAAAACATTTCCCTTGAAACGAATTTTG
66 ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
* *
2707807 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTTAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
*
2707872 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
66 ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
* *
2707909 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
** * ** ***
2707973 A-AATTATTTGAATATGTTTTATTTGAAACAAATTTCG
66 ATAAACA-TTGAAAACATTTCCCTTGAAACAAATTTCG
* ** * * * *
2708010 TCT-TCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 TCTCT-CTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
2708074 CA
65 CA
2708076 AATTTTGTCT
Statistics
Matches: 240, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
100 4 0.02
101 79 0.33
102 157 0.65
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (102 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
Found at i:2707935 original size:36 final size:36
Alignment explanation
Indices: 2707888--2708113 Score: 236
Period size: 36 Copynumber: 6.4 Consensus size: 36
2707878 ATTGAAAACA
* *
2707888 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2707924 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2707960 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** * *
2707989 TTTTATTTGAAACAAATTTCGTCT-TCCTTGAGACAA
1 TTTCCCTTGAAACAAATTTTGTCTCT-CTTGAGACAG
** * *
2708025 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
2708062 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2708098 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
2708114 ATCTTTGAAT
Statistics
Matches: 159, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 2 0.01
31 1 0.01
34 2 0.01
35 1 0.01
36 101 0.64
37 31 0.19
38 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2708062 original size:203 final size:204
Alignment explanation
Indices: 2707705--2708075 Score: 478
Period size: 203 Copynumber: 1.8 Consensus size: 204
2707695 GAAGATTTTA
* * *
2707705 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAT
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * * *
2707770 ATAAACATTGAAAACATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
66 ATAAACATTGAAAACATTTCACTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
*
2707835 AAAATTTTGTCTCCCTTTAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
131 AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
2707900 TAAATTTCG
196 TAAATTTCG
* * *
2707909 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
** * ** * * ** *
2707973 A-AATTATTTGAATATGTTTTATTTGAAACAAATTTCGTCT-TCCTTGAGACAATTTCTTTTGGA
66 ATAAACA-TTGAAAACATTTCACTTGAAACAAATTTCGTCTCT-CTTGAGACAATTTCCCTTGAA
* * *
2708036 ACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
129 ACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
2708076 AATTTTGTCT
Statistics
Matches: 140, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
202 4 0.03
203 110 0.79
204 26 0.19
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (204 bp):
TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
ATAAACATTGAAAACATTTCACTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
TAAATTTCG
Found at i:2708167 original size:138 final size:138
Alignment explanation
Indices: 2707908--2708159 Score: 396
Period size: 138 Copynumber: 1.8 Consensus size: 138
2707898 AATAAATTTC
2707908 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** * *
2707973 AAATTATTTGAATATGTTTTATTTGAAACAAATTTCGTCTTCCTTGAGACAATTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAAC
2708038 TAAGTTTT
131 TAAGTTTT
*
2708046 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * *
2708111 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGA
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGA
2708160 GTGTTTCTCT
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 102 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAAC
TAAGTTTT
Found at i:2708241 original size:67 final size:67
Alignment explanation
Indices: 2708062--2708243 Score: 226
Period size: 65 Copynumber: 2.7 Consensus size: 67
2708052 CTTGAGACAG
* * * * **
2708062 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
2708125 TA
66 TA
* **
2708127 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGAGTGTTTCTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
2708192 TA
66 TA
* * *
2708194 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 TTTCCCTTAAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
2708244 ACAGATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
65 38 0.38
66 2 0.02
67 37 0.37
68 23 0.23
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:2708969 original size:106 final size:106
Alignment explanation
Indices: 2708844--2709260 Score: 486
Period size: 106 Copynumber: 4.0 Consensus size: 106
2708834 ATATCGTGCC
* * * *
2708844 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGGTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCC
* * **
2708909 AGTTTCATAATCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
2708950 ATTCGAGACAACACAAGTTCAACTTCACAACGAAGAGAC-GCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCC
2709014 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2709055 ACTCAAGACAGCACAAGCTCAACTTCACAGA-GAAGGGACGGCTGACTGTCAACAAACAACTTT-
1 ACTCAAGACAACACAAGCTCAACTTCACA-ACGAAGGGACGGCTGATTGTCAACAAACAA-TTTC
*
2709118 CCAATTTCAGGGCCAATTTCAACTTC-CGAGCGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCAC-AGCGAAGGATATTGG
* * * *
2709161 ACCCAAGGCAACATAAGCTCAACTTCACGACGAAGGGGA-GGCTGATTGTCAAC-AA-AATTT--
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAA-GGGACGGCTGATTGTCAACAAACAATTTCC
*
2709221 C-----CAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
2709258 ACT
1 ACT
2709261 TGGAACAATA
Statistics
Matches: 277, Mismatches: 26, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
96 1 0.00
97 32 0.12
98 1 0.00
102 1 0.00
103 3 0.01
104 2 0.01
105 96 0.35
106 135 0.49
107 6 0.02
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (106 bp):
ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2709029 original size:105 final size:106
Alignment explanation
Indices: 2708844--2709216 Score: 493
Period size: 106 Copynumber: 3.5 Consensus size: 106
2708834 ATATCGTGCC
* * * * *
2708844 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGGTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAACTTCCC
* * **
2708909 AGTTTCATAATCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
2708950 ATTCGAGACAACACAAGTTCAACTTCACAACGAAGAGAC-GCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAACTTCCC
2709014 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2709055 ACTCAAGACAGCACAAGCTCAACTTCACAGA-GAAGGGACGGCTGACTGTCAACAAACAACTTTC
1 ACTCAAGACAACACAAGCTCAACTTCACA-ACGAAGGGACGGCTGATTGTCAACAAACAACTTCC
*
2709119 CAATTTCAGGGCCAATTTCAACTTC-CGAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCAC-AGCGAAGGATATTGG
* * * *
2709161 ACCCAAGGCAACATAAGCTCAACTTCACGACGAAGGGGA-GGCTGATTGTCAACAAA
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAA-GGGACGGCTGATTGTCAACAAA
2709217 ATTTCCAGAG
Statistics
Matches: 239, Mismatches: 23, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
105 94 0.39
106 141 0.59
107 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (106 bp):
ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2710580 original size:2 final size:2
Alignment explanation
Indices: 2710573--2710731 Score: 145
Period size: 2 Copynumber: 83.0 Consensus size: 2
2710563 TAATTTCATC
* * * *
2710573 AT AT AT AT AT AT AT AT AT AT TT TT A- AT -T AT AT AT -T TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
2710612 AT TT AT TT ACT AT AT -T TT TT AT TT AT AT -T AT AT -T AT TT TT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2710652 AT AT AT AT -T AT TT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2710692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2710732 GTATGTATGT
Statistics
Matches: 134, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
1 8 0.06
2 124 0.93
3 2 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (2 bp):
AT
Found at i:2710600 original size:33 final size:32
Alignment explanation
Indices: 2710562--2710721 Score: 141
Period size: 33 Copynumber: 5.0 Consensus size: 32
2710552 TACTTTTATA
2710562 TTAATTTCATCATATATATATATATATATAT-TT
1 TTAATTT-AT-ATATATATATATATATATATATT
* * * *
2710595 TTAA-TTATATATTTTTTATTTATTTACTATATTT
1 TTAATTTATATA-TATATATATATATA-TATA-TT
* * * *
2710629 TTTATTTATAT-TATAT-TATTTTTATATATA
1 TTAATTTATATATATATATATATATATATATT
2710659 TT-ATTTATATATATATATATATATATATATT
1 TTAATTTATATATATATATATATATATATATT
* *
2710690 ATATATATATATATATATATATATATATATAT
1 TTA-ATTTATATATATATATATATATATATAT
2710722 ATATATATAT
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
29 8 0.08
30 11 0.11
31 28 0.27
32 11 0.11
33 34 0.33
34 5 0.05
35 6 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (32 bp):
TTAATTTATATATATATATATATATATATATT
Found at i:2710887 original size:31 final size:30
Alignment explanation
Indices: 2710832--2710981 Score: 81
Period size: 31 Copynumber: 4.8 Consensus size: 30
2710822 TTTTTTCTTA
* * *
2710832 ATATTCTATTTTTGTTTTTATTTATTTATAT
1 ATATTATATTTTTATTTAT-TTTATTTATAT
* *
2710863 ATATTATATTTTTACTTTATTTTATTTTTTT
1 ATATTATATTTTTA-TTTATTTTATTTATAT
* * * * *
2710894 CTATTAT-TTTTTTTCTTAATATCATGTATAT
1 ATATTATATTTTTAT-TT-ATTTTATTTATAT
* *
2710925 CT-TTAT-TTTTTATTTGTTTTACTTAGTATTAT
1 ATATTATATTTTTATTTATTTTA-TT--TA-TAT
2710957 ATATTTATTATTTTTATTTATTTTA
1 ATA-TTA-TATTTTTATTTATTTTA
2710982 GTAAATACTA
Statistics
Matches: 89, Mismatches: 19, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
28 3 0.03
29 4 0.04
30 17 0.19
31 39 0.44
32 8 0.09
34 3 0.03
35 1 0.01
36 14 0.16
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (30 bp):
ATATTATATTTTTATTTATTTTATTTATAT
Found at i:2710892 original size:18 final size:18
Alignment explanation
Indices: 2710847--2710907 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
2710837 CTATTTTTGT
* *
2710847 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
2710864 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
2710882 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
2710900 TTTT-TTTT
1 TTTTATTTT
2710908 CTTAATATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 16 0.44
18 20 0.56
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:2711118 original size:19 final size:18
Alignment explanation
Indices: 2711096--2711131 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2711086 TTTTTTAACA
2711096 TTTTATTCATTTTGTTTAT
1 TTTTATT-ATTTTGTTTAT
*
2711115 TTTTATTATTTTTTTTA
1 TTTTATTATTTTGTTTA
2711132 CTTGTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTATTATTTTGTTTAT
Found at i:2711170 original size:26 final size:27
Alignment explanation
Indices: 2711125--2711176 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2711115 TTTTATTATT
2711125 TTTTTTACTTGTTTTGTTATT-TTCTA
1 TTTTTTACTTGTTTTGTTATTATTCTA
*
2711151 TTTTTT-CTTGTTTTATTTATTATTCT
1 TTTTTTACTTGTTTT-GTTATTATTCT
2711177 CAAGTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 11 0.48
27 4 0.17
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.75
Consensus pattern (27 bp):
TTTTTTACTTGTTTTGTTATTATTCTA
Found at i:2712416 original size:2 final size:2
Alignment explanation
Indices: 2712409--2712448 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2712399 GTATATTTAA
2712409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2712449 TAACACAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2715293 original size:54 final size:54
Alignment explanation
Indices: 2715221--2715439 Score: 206
Period size: 54 Copynumber: 4.0 Consensus size: 54
2715211 TAAAGGAGTG
* * * * * *
2715221 AAGAAAACAGTCACTAGTGAATTTGAACCAAGACCGAGCATCACATCTTATGGC
1 AAGAAATCATTCACTAGTGAATTTGAATCAAGACCAAGCACCACTTCTTATGGC
* * *
2715275 AAGAAATCATTCACTAGTGATTTTGAAGT-GAGACCAAGAACCACTTCTTATGGCAAC
1 AAGAAATCATTCACTAGTGAATTTGAA-TCAAGACCAAGCACCACTTCTTATGG---C
* * * * * * *
2715332 AATAAATCAATCACTAGTGAAATTTTAATCAAGACCGAGCATCACGTCTTATGGT
1 AAGAAATCATTCACTAGTG-AATTTGAATCAAGACCAAGCACCACTTCTTATGGC
* * * *
2715387 TAGAAATCATTCACTAGTGATTTTGAGTCGAGACCAAGCACCACTTCTTATGG
1 AAGAAATCATTCACTAGTGAATTTGAATCAAGACCAAGCACCACTTCTTATGG
2715440 TGGCAATGAC
Statistics
Matches: 130, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
54 70 0.54
55 16 0.12
57 19 0.15
58 25 0.19
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (54 bp):
AAGAAATCATTCACTAGTGAATTTGAATCAAGACCAAGCACCACTTCTTATGGC
Found at i:2715318 original size:136 final size:135
Alignment explanation
Indices: 2715060--2715327 Score: 378
Period size: 136 Copynumber: 2.0 Consensus size: 135
2715050 CTTGTGGGGA
* * * *
2715060 CAATGATGTTGATTTTAAACGACTGAAGAAATCAATCACTAGTGAATTTGAACCGAGACCGAGCG
1 CAATGATGTTGATCTTAAACGACTGAAGAAAACAATCACTAGTGAATTTGAACCAAGACCGAGCA
* ** * **
2715125 TCACGTCTTATGGTTAGAAATCATTCACTAGTGATTTTAAGTCGGAACTAATCACCACTTCTATA
66 TCACATCTTATGGCAAGAAATCATTCACTAGTGATTTTAAGTCGGAACCAAGAACCACTTCT-TA
2715190 TGGTGG
130 TGGTGG
* * *
2715196 CAATGATGTTGATCTTAAAGGAGTGAAGAAAACAGTCACTAGTGAATTTGAACCAAGACCGAGCA
1 CAATGATGTTGATCTTAAACGACTGAAGAAAACAATCACTAGTGAATTTGAACCAAGACCGAGCA
2715261 TCACATCTTATGGCAAGAAATCATTCACTAGTGATTTTGAAGT--GAGACCAAGAACCACTTCTT
66 TCACATCTTATGGCAAGAAATCATTCACTAGTGATTTT-AAGTCGGA-ACCAAGAACCACTTCTT
2715324 ATGG
129 ATGG
2715328 CAACAATAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
135 7 0.06
136 106 0.91
137 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (135 bp):
CAATGATGTTGATCTTAAACGACTGAAGAAAACAATCACTAGTGAATTTGAACCAAGACCGAGCA
TCACATCTTATGGCAAGAAATCATTCACTAGTGATTTTAAGTCGGAACCAAGAACCACTTCTTAT
GGTGG
Found at i:2715405 original size:112 final size:111
Alignment explanation
Indices: 2715231--2715439 Score: 339
Period size: 112 Copynumber: 1.9 Consensus size: 111
2715221 AAGAAAACAG
2715231 TCACTAGTGAATTTGAACCAAGACCGAGCATCACATCTTATGGCAAGAAATCATTCACTAGTGAT
1 TCACTAGTGAATTTGAACCAAGACCGAGCATCACATCTTATGGCAAGAAATCATTCACTAGTGAT
2715296 TTTGAAGT-GAGACCAAGAACCACTTCTTATGGCAACAATAAATCAA
66 TTTG-AGTCGAGACCAAGAACCACTTCTTATGGCAACAATAAATCAA
* * * **
2715342 TCACTAGTGAAATTTTAATCAAGACCGAGCATCACGTCTTATGGTTAGAAATCATTCACTAGTGA
1 TCACTAGTG-AATTTGAACCAAGACCGAGCATCACATCTTATGGCAAGAAATCATTCACTAGTGA
*
2715407 TTTTGAGTCGAGACCAAGCACCACTTCTTATGG
65 TTTTGAGTCGAGACCAAGAACCACTTCTTATGG
2715440 TGGCAATGAC
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
111 12 0.13
112 78 0.87
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (111 bp):
TCACTAGTGAATTTGAACCAAGACCGAGCATCACATCTTATGGCAAGAAATCATTCACTAGTGAT
TTTGAGTCGAGACCAAGAACCACTTCTTATGGCAACAATAAATCAA
Found at i:2715524 original size:247 final size:247
Alignment explanation
Indices: 2715088--2715571 Score: 747
Period size: 247 Copynumber: 2.0 Consensus size: 247
2715078 ACGACTGAAG
* *
2715088 AAATCAATCACTAGTGAATTTGAACCGAGACCGAGCGTCACGTCTTATGGTTAGAAATCATTCAC
1 AAATCAATCACTAGTGAATTTGAACCAAGACCGAGCATCACGTCTTATGGTTAGAAATCATTCAC
* * * *
2715153 TAGTGATTTTAAGTCGGAACTAATCACCACTTCTATATGGTGGCAATGATGTTGATCTTAAAGGA
66 TAGTGATTTTAAGTCGGAACCAAGCACCACTTCTATATGGTGGCAATGACGTTGATCATAAAGGA
* *
2715218 GTGAAGAAAACAGTCACTAGTGAATTTGAACCAAGACCGAGCATCACATCTTATGGCAAGAAATC
131 GTGAAAAAAACAGTCACTAGTGAATTTGAACCAAGACCGAACATCACATCTTATGGCAAGAAATC
* **
2715283 ATTCACTAGTGATTTTGAAGTGAGACCAAGAACCACTTCTTATGGCAACAAT
196 ATTCACTAGTGATTTCGAACCGAGACCAAGAACCACTTCTTATGGCAACAAT
* *
2715335 AAATCAATCACTAGTGAAATTTTAATCAAGACCGAGCATCACGTCTTATGGTTAGAAATCATTCA
1 AAATCAATCACTAGTG-AATTTGAACCAAGACCGAGCATCACGTCTTATGGTTAGAAATCATTCA
*
2715400 CTAGTGATTTTGAGTC-GAGACCAAGCACCACTTCT-TATGGTGGCAATGACGTTGATCATAAAG
65 CTAGTGATTTTAAGTCGGA-ACCAAGCACCACTTCTATATGGTGGCAATGACGTTGATCATAAAG
* * **
2715463 GATTGAAAAAAACATTCACTAGTGAATTTGAACTGAGACCGAACATCACATCTTATGGCAAGAAA
129 GAGTGAAAAAAACAGTCACTAGTGAATTTGAACCAAGACCGAACATCACATCTTATGGCAAGAAA
* * *
2715528 TCATTCACTAGTGATTTCGAACCGAGACCGAGCACTACTTCTTA
194 TCATTCACTAGTGATTTCGAACCGAGACCAAGAACCACTTCTTA
2715572 CGGTGGCAAT
Statistics
Matches: 214, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
247 141 0.66
248 73 0.34
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (247 bp):
AAATCAATCACTAGTGAATTTGAACCAAGACCGAGCATCACGTCTTATGGTTAGAAATCATTCAC
TAGTGATTTTAAGTCGGAACCAAGCACCACTTCTATATGGTGGCAATGACGTTGATCATAAAGGA
GTGAAAAAAACAGTCACTAGTGAATTTGAACCAAGACCGAACATCACATCTTATGGCAAGAAATC
ATTCACTAGTGATTTCGAACCGAGACCAAGAACCACTTCTTATGGCAACAAT
Found at i:2716579 original size:28 final size:27
Alignment explanation
Indices: 2716548--2716604 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
2716538 TTTATACTTT
* *
2716548 TATTAACAATAAAATTTAAATAATAAAA
1 TATTAACAATAAAAATT-AATAAAAAAA
* *
2716576 TATTATCATTAAAAATTAATAAAAAAA
1 TATTAACAATAAAAATTAATAAAAAAA
2716603 TA
1 TA
2716605 ATTCTCAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (27 bp):
TATTAACAATAAAAATTAATAAAAAAA
Found at i:2716807 original size:22 final size:23
Alignment explanation
Indices: 2716768--2716810 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2716758 TTCTAATAAT
2716768 TTTATTTTTATAACATATTTTTC
1 TTTATTTTTATAACATATTTTTC
*
2716791 TTTATTTTTAT-AGATATTTT
1 TTTATTTTTATAACATATTTT
2716811 ATTTCTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTTTTATAACATATTTTTC
Found at i:2717038 original size:6 final size:6
Alignment explanation
Indices: 2717027--2717053 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2717017 CAACTCTGGT
2717027 TTGTGA TTGTGA TTGTGA TTGTGA TTG
1 TTGTGA TTGTGA TTGTGA TTGTGA TTG
2717054 ATCTCTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (6 bp):
TTGTGA
Found at i:2718099 original size:28 final size:28
Alignment explanation
Indices: 2718068--2718131 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
2718058 TCACTTTGAT
2718068 CAAC-TACAAAATATAATATTTATAAAAG
1 CAACATAC-AAATATAATATTTATAAAAG
* *
2718096 CAACATACTAATATGATATTTATAAAAG
1 CAACATACAAATATAATATTTATAAAAG
2718124 CAACATAC
1 CAACATAC
2718132 TAAACTATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (28 bp):
CAACATACAAATATAATATTTATAAAAG
Found at i:2718132 original size:28 final size:28
Alignment explanation
Indices: 2718077--2718134 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2718067 TCAACTACAA
2718077 AATATAATATTTATAAAAGCAACATACT
1 AATATAATATTTATAAAAGCAACATACT
*
2718105 AATATGATATTTATAAAAGCAACATACT
1 AATATAATATTTATAAAAGCAACATACT
2718133 AA
1 AA
2718135 ACTATCACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.31
Consensus pattern (28 bp):
AATATAATATTTATAAAAGCAACATACT
Found at i:2718953 original size:29 final size:29
Alignment explanation
Indices: 2718911--2718997 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
2718901 TCCATTATTA
*
2718911 TTTTACTCAACAGTGTTTAACCGTTCCTC
1 TTTTACTCAACAGTGTTTAACCGTTCATC
* * *
2718940 TTTTACTCAGCAGTGTTTGACCTTTCATC
1 TTTTACTCAACAGTGTTTAACCGTTCATC
2718969 TTTTACTCAACAGTGTTTAACCGTTCATC
1 TTTTACTCAACAGTGTTTAACCGTTCATC
2718998 AAACTGGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (29 bp):
TTTTACTCAACAGTGTTTAACCGTTCATC
Found at i:2725503 original size:55 final size:55
Alignment explanation
Indices: 2725302--2725941 Score: 343
Period size: 53 Copynumber: 12.0 Consensus size: 55
2725292 ATACAATTTT
*** ** * **
2725302 TTTTAAAGAAAACTAAGTCCAATTTTTGGAAGTTTCTTGATTATTTTTAAATGAAA
1 TTTTAAAG-AAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* * * *
2725358 TTTCAAAGAAACTAAGTCTGATTTTCAGAAATTTCCTT-ATGA-GTTTAAATGAGC
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTT-CTTGATGATTTTTAAATGAGC
* * * *
2725412 TTTTAGA-AAACTAAGTCCT-ATTTTCAGAAGTTTCTTGATAATTTTTAAATGAGG
1 TTTTAAAGAAACTAAGT-TTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* * * * *
2725466 TTTTAAAGAAACGAAGTTTGATTTTTACAAGTTTCTTGACGATTTTCAAATGAGC
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* * * *
2725521 TTTTAAAAAAACTAAGTTTGATTTTCATAAGTTTCTTAATGATTTTTAAATGATC
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* * * * ** *
2725576 TTTCAAAGAAATTAAGTTTGATTTTCAGAGGTTTCTTGA-CA-TAATAAAT---T
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* ** * ** * *
2725626 TTTTAAAGAACCTAAGCCT-ATTTTTAGGGGTTTCTTGAT-ATTTTCAAATGA-A
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* * ** ** * *
2725678 TTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-A
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* * ** ** * * * * *
2725731 TTTGAAATATGCTAAGCCTAATTTTTAGGAA-TCTCTTGATG-TTTTCAAATGA-A
1 TTTTAAAGAAACTAAGTTTGATTTTCA-GAAGTTTCTTGATGATTTTTAAATGAGC
* * * ** * * *
2725784 TTTGAAAGAACCTAAGCTTGATTTTCAGGGGTTTCTTGATG-TTTTCAAAAGA-A
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* * ** * * * * *
2725837 TTTGAAAGAAGCTAAGCCTAATTTTCAGAGGTTTATTGAT-ATTTTCAAATGA-A
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
* * * * ** *
2725890 TTTGAAATAAGCTAAGTCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA
1 TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGA
2725942 ATTTGAAAGA
Statistics
Matches: 483, Mismatches: 85, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
49 18 0.04
50 19 0.04
52 21 0.04
53 239 0.49
54 35 0.07
55 141 0.29
56 10 0.02
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (55 bp):
TTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGC
Found at i:2725566 original size:110 final size:108
Alignment explanation
Indices: 2725310--2725928 Score: 380
Period size: 106 Copynumber: 5.8 Consensus size: 108
2725300 TTTTTTAAAG
* ** *
2725310 AAAACTAAGTCCAATTTTTGGAAGTTTCTTGATTATTTTTAAATGAAATTTCAAAGAAACTAAGT
1 AAAACTAAGTCCTATTTTCAGAAGTTTCTTGATAATTTTTAAATGAAATTTCAAAGAAACTAAGT
* * * *
2725375 CTGATTTTCAGAAATTTCCTT-ATGAGTTTAAATGAGCTTTTAG
66 TTGATTTTCAGAAGTTT-CTTGACGAGTTTAAATGAGCTTTTAA
** * *
2725418 AAAACTAAGTCCTATTTTCAGAAGTTTCTTGATAATTTTTAAATGAGGTTTTAAAGAAACGAAGT
1 AAAACTAAGTCCTATTTTCAGAAGTTTCTTGATAATTTTTAAATGAAATTTCAAAGAAACTAAGT
* * *
2725483 TTGATTTTTACAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
66 TTGATTTTCAGAAGTTTCTTGACGAGTTT-AAATGAGCTTTT-AA
* * * * ** *
2725528 AAAACTAAGT-TTGATTTTCATAAGTTTCTTAATGATTTTTAAATGATCTTTCAAAGAAATTAAG
1 AAAACTAAGTCCT-ATTTTCAGAAGTTTCTTGATAATTTTTAAATGAAATTTCAAAGAAACTAAG
* * *
2725592 TTTGATTTTCAGAGGTTTCTTGAC-A-TAATAAAT---TTTTTAA
65 TTTGATTTTCAGAAGTTTCTTGACGAGT-TTAAATGAGCTTTTAA
* * ** * * *
2725632 AGAACCTAAG-CCTATTTTTAGGGGTTTCTTGAT-ATTTTCAAATG-AATTTGAAAGAAGCTAAG
1 A-AAACTAAGTCCTATTTTCAGAAGTTTCTTGATAATTTTTAAATGAAATTTCAAAGAAACTAAG
** ** * * * *
2725694 CCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
65 TTTGATTTTCAGAAGTTTCTTGACGAGTTT-AAATGAGCTTTTAA
** * * * * * *
2725737 ATATGCTAAG-CCTAATTTTTAGGAA-TCTCTTGAT-GTTTTCAAATG-AATTTGAAAGAACCTA
1 A-AAACTAAGTCCT-ATTTTCA-GAAGTTTCTTGATAATTTTTAAATGAAATTTCAAAGAAACTA
* ** * * * * *
2725798 AGCTTGATTTTCAGGGGTTTCTTGATG-TTTTCAAAAGA-ATTTGAA
63 AGTTTGATTTTCAGAAGTTTCTTGACGAGTTT-AAATGAGCTTTTAA
* * * * * * *
2725843 AGAAGCTAAG-CCTAATTTTCAGAGGTTTATTGAT-ATTTTCAAATG-AATTTGAAATAAGCTAA
1 A-AAACTAAGTCCT-ATTTTCAGAAGTTTCTTGATAATTTTTAAATGAAATTTCAAAGAAACTAA
* **
2725905 GTCTGATTTTCAGGGGTTTCTTGA
64 GTTTGATTTTCAGAAGTTTCTTGA
2725929 TGTTTTCAAA
Statistics
Matches: 426, Mismatches: 70, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
102 34 0.08
103 15 0.04
104 18 0.04
105 29 0.07
106 155 0.36
107 4 0.01
108 81 0.19
109 15 0.04
110 75 0.18
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (108 bp):
AAAACTAAGTCCTATTTTCAGAAGTTTCTTGATAATTTTTAAATGAAATTTCAAAGAAACTAAGT
TTGATTTTCAGAAGTTTCTTGACGAGTTTAAATGAGCTTTTAA
Found at i:2725712 original size:53 final size:53
Alignment explanation
Indices: 2725630--2726199 Score: 734
Period size: 53 Copynumber: 10.7 Consensus size: 53
2725620 TAAATTTTTT
* * *
2725630 AAAGAACCTAAGCCT-ATTTTTAGGGGTTTCTTGATATTTTCAAATGAATTTG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
*
2725682 AAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
* * * ** *
2725735 AAATATGCTAAGCCTAATTTTTAGGAATCTCTTGATGTTTTCAAATGAATTTG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
* * * *
2725788 AAAGAACCTAAGCTTGATTTTCAGGGGTTTCTTGATGTTTTCAAAAGAATTTG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
* * *
2725841 AAAGAAGCTAAGCCTAATTTTCAGAGGTTTATTGATATTTTCAAATGAATTTG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
* * *
2725894 AAATAAGCTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
* * * *
2725947 AAAG-AGCCTAAGCCTGCCTGATTTTTAGGGGTTTTTTTATGTTTTCAAATGAATTTG
1 AAAGAAG-CTAA----GCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
*
2726004 AAAG-AGCTAAGCCTAATTTTCAGGGCTTTCTTGATGTTTTCAAATGAATTTG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
* * *
2726056 AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATAAATTTA
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
* * * *
2726109 AAAAAATCTAAGCCTGAA-TTTCAGGGGTTTCTTGATGTTTTCAAATCAATTTTT
1 AAAGAAGCTAAGCCT-AATTTTCAGGGGTTTCTTGATGTTTTCAAATGAA-TTTG
* * *
2726163 AAAGAAGTTAAGCCTAATTTTTAGGGGTTTATTGATG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATG
2726200 ATAATTGTAA
Statistics
Matches: 451, Mismatches: 57, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
52 57 0.13
53 312 0.69
54 34 0.08
56 4 0.01
57 44 0.10
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (53 bp):
AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTG
Found at i:2727415 original size:139 final size:139
Alignment explanation
Indices: 2726894--2727418 Score: 802
Period size: 139 Copynumber: 3.8 Consensus size: 139
2726884 GGATAAACCA
* *
2726894 ATCAACATTTACAGTGGAGAGTTCATAA-CAAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAA-AAGAACTCATCCGATGAGGGAGAAGAAGTTCA
* * *
2726958 TAATGATAAGAATTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACATCT
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCT
*
2727023 CACTCGAGGG
130 CACTTGAGGG
* * * * *
2727033 ATCAACATTTCTAGTTGAGAGTTTATAATGAAAATAACTCATCCGATGAGGGAGAAGAAGTTCAA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAAAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * ** *
2727098 AATGAGAATAACTTGTTCAACCTTAGCTCGATTCAGCATATATGGAGTTGAATCAACAACACTTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTC
2727163 ACTTGAGGG
131 ACTTGAGGG
* *
2727172 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGACGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAAAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
*
2727237 AATGAGAAGAACTTGTTCAACCTTAGCTCCATTCATCGCATATGGAGTTGAATCAACAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTC
2727302 ACTTGAGGG
131 ACTTGAGGG
* * *
2727311 ATCAACATTTCCAATGGGAGAGTTCATAATGAAAAGAACTCATCTGGTGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGT-GGAGAGTTCATAATGAAAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
* *
2727376 TAATGAGAAGAACTTGGTCAATCTTAGCTC-ATTCATCGCATAT
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATAT
2727419 AGATTTGGAA
Statistics
Matches: 348, Mismatches: 36, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
139 273 0.78
140 75 0.22
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (139 bp):
ATCAACATTTCCAGTGGAGAGTTCATAATGAAAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTC
ACTTGAGGG
Found at i:2727801 original size:214 final size:214
Alignment explanation
Indices: 2727489--2727914 Score: 739
Period size: 214 Copynumber: 2.0 Consensus size: 214
2727479 TCAACATTGT
* *
2727489 CATTCTTGCTCGATTCGATCACAGAAGGAGGTGGATTATCGTTTCCAATGGAAAAGTTCATAATG
1 CATTCTTGCTAGATTCGATCACAGAAGGAGGTGGATCATCGTTTCCAATGGAAAAGTTCATAATG
*
2727554 AGAAGAACTCGTCCGAACAGAAGAGTGAAAAGTTCATAATAAGAATAACTTGGAGCTCAGAGATA
66 AGAAGAACTCATCCGAACAGAAGAGTGAAAAGTTCATAATAAGAATAACTTGGAGCTCAGAGATA
* *
2727619 TCAGACAACCAAGAT-GGGTAAAATTGGTTCTTTATGTCTTCGCTCCATTCCCGTTTCACAGCAA
131 TCAGAC-ACCAAGATGGGGTAAAATTGGTTCTTTATGTCTTCGCTACATT-CCGTTTCACAACAA
2727683 TGAGCGAATAGGGGCAGTTTG
194 TGAGCGAATAGGGGCAGTTTG
2727704 CATTCTTGCTAGATTCGATCACAGAAGGAGGTGGATCATCGTTTCCAATGGAAAAG-TCATAATG
1 CATTCTTGCTAGATTCGATCACAGAAGGAGGTGGATCATCGTTTCCAATGGAAAAGTTCATAATG
* * *
2727768 AGAAGAACTCATCCTAACAGAAGAGTGAAAAGTTTATAATGAGAATAACTTGGAGCTCAGAGATA
66 AGAAGAACTCATCCGAACAGAAGAGTGAAAAGTTCATAATAAGAATAACTTGGAGCTCAGAGATA
*
2727833 TCAGACACCAAGCTGGGGTAAAATTGGTTCTTTATGTCTTCGCTACATTCCGTTTCACAACAATG
131 TCAGACACCAAGATGGGGTAAAATTGGTTCTTTATGTCTTCGCTACATTCCGTTTCACAACAATG
2727898 AGCGAATAGGGGCAGTT
196 AGCGAATAGGGGCAGTT
2727915 GTAATCACCA
Statistics
Matches: 201, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
213 39 0.19
214 108 0.54
215 54 0.27
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (214 bp):
CATTCTTGCTAGATTCGATCACAGAAGGAGGTGGATCATCGTTTCCAATGGAAAAGTTCATAATG
AGAAGAACTCATCCGAACAGAAGAGTGAAAAGTTCATAATAAGAATAACTTGGAGCTCAGAGATA
TCAGACACCAAGATGGGGTAAAATTGGTTCTTTATGTCTTCGCTACATTCCGTTTCACAACAATG
AGCGAATAGGGGCAGTTTG
Found at i:2729198 original size:20 final size:19
Alignment explanation
Indices: 2729136--2729199 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
2729126 CCAGTGGAGA
2729136 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
2729155 CATCCGATGATGGAGAAGAA--
1 -GTTC-ATAAT-GAGAAGAACT
2729175 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
2729195 GTTCA
1 GTTCA
2729200 ACTTTAGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
20 7 0.21
21 4 0.12
22 8 0.24
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:2729369 original size:139 final size:139
Alignment explanation
Indices: 2729081--2729369 Score: 474
Period size: 140 Copynumber: 2.1 Consensus size: 139
2729071 ATCCTAGCAT
* *
2729081 ATATAGAGTTGAATCAACAACACTTCACTTGAGGGATCAACATTTCCAGTGGAGAGTTCATAATG
1 ATATAGAGTTGAATCAACAACACCTCACTTGAGGGATCAACATTTCCAATGGAGAGTTCATAATG
* * *
2729146 AGAAGAACTCATCCGATGATGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTAGCTCG
66 AAAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGGTCAACTTTAGCTCG
*
2729211 ATTCATCGC
131 ATCCATCGC
*
2729220 ATATGGAGTTGAATCAACAACACCTCACTTGAGGGATCAACATTTCCAATGGGAGAGTTCATAAT
1 ATATAGAGTTGAATCAACAACACCTCACTTGAGGGATCAACATTTCCAAT-GGAGAGTTCATAAT
*
2729285 GAAAAGAACTCATCCGATGAGGGAGAAGAAGTTTATAATGAGAAGAACTTGGTCAA-TCTTAGCT
65 GAAAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGGTCAACT-TTAGCT
2729349 C-ATCCATCGC
129 CGATCCATCGC
2729359 ATATAGAGTTG
1 ATATAGAGTTG
2729370 GAAATGCACC
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
139 66 0.47
140 73 0.53
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (139 bp):
ATATAGAGTTGAATCAACAACACCTCACTTGAGGGATCAACATTTCCAATGGAGAGTTCATAATG
AAAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGGTCAACTTTAGCTCG
ATCCATCGC
Found at i:2730378 original size:20 final size:21
Alignment explanation
Indices: 2730325--2730383 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
2730315 ATCGGTTTCT
2730325 GGAGA-AGTGAAG-AGAGAAG
1 GGAGAGAGTGAAGAAGAGAAG
* *
2730344 GGGGAGGATTG-AGAAG-GAAG
1 GGAGA-GAGTGAAGAAGAGAAG
2730364 GGAGAGAGTGAAGAAGAGAA
1 GGAGAGAGTGAAGAAGAGAA
2730384 AATAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 8 0.26
20 15 0.48
21 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.49, T:0.07
Consensus pattern (21 bp):
GGAGAGAGTGAAGAAGAGAAG
Found at i:2730653 original size:59 final size:59
Alignment explanation
Indices: 2730581--2730701 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 59
2730571 AATAGATGGA
2730581 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCAATAATATGGCTC
1 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCAATAATATGGCTC
* *
2730640 TAAGTGTCCTATCGAACCCTCCTAGTCGTAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCAATAATATGGCTC
2730699 TAA
1 TAA
2730702 CCAACCCTCC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCAATAATATGGCTC
Found at i:2732922 original size:25 final size:28
Alignment explanation
Indices: 2732867--2732928 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
2732857 CTGCATGTAA
*
2732867 TTATTATTTTCTCTATTGAGAATTAATT
1 TTATTATTTTCTCTAATGAGAATTAATT
2732895 TTATTATTTTCT-TAATG-GTAA-TAA-T
1 TTATTATTTTCTCTAATGAG-AATTAATT
2732920 TTATTATTT
1 TTATTATTT
2732929 AAAAATTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 10 0.31
26 4 0.12
27 6 0.19
28 12 0.38
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (28 bp):
TTATTATTTTCTCTAATGAGAATTAATT
Found at i:2734318 original size:22 final size:22
Alignment explanation
Indices: 2734293--2734371 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
2734283 CTTATCACGG
*
2734293 AAGTGTCTTAGCACTAATACTA
1 AAGTGCCTTAGCACTAATACTA
* *
2734315 AAGTGCCTCAGCACTAATACAA
1 AAGTGCCTTAGCACTAATACTA
* *
2734337 AAGTG-CATATGCACTGATACTA
1 AAGTGCCTTA-GCACTAATACTA
*
2734359 AAGTACCTTAGCA
1 AAGTGCCTTAGCA
2734372 GTGAGATATG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 2 0.04
22 41 0.89
23 3 0.07
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (22 bp):
AAGTGCCTTAGCACTAATACTA
Found at i:2737555 original size:14 final size:15
Alignment explanation
Indices: 2737527--2737556 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2737517 CCCATTTCGT
2737527 TTTATTTTCATTTTA
1 TTTATTTTCATTTTA
2737542 TTTATTTT-ATTTTA
1 TTTATTTTCATTTTA
2737556 T
1 T
2737557 CAGATGCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTCATTTTA
Found at i:2741928 original size:19 final size:20
Alignment explanation
Indices: 2741891--2741929 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2741881 AGGCCAAGGG
**
2741891 TTTCGAGGGAAACTGATATT
1 TTTCGAGGGAAACAAATATT
2741911 TTTCGA-GGAAACAAATATT
1 TTTCGAGGGAAACAAATATT
2741930 ATATTCGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (20 bp):
TTTCGAGGGAAACAAATATT
Found at i:2742197 original size:31 final size:31
Alignment explanation
Indices: 2742156--2742222 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2742146 CTCAAGGACC
*
2742156 AAAATGTTATATA-TCGATAACGTAAGTAACTA
1 AAAATGTTATAAACT-GATAACGTAAGTAAC-A
*
2742188 AAAAT-TTATAAACTGATAACGTAAGTGACA
1 AAAATGTTATAAACTGATAACGTAAGTAACA
2742218 AAAAT
1 AAAAT
2742223 ATTACTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.19
31 20 0.62
32 6 0.19
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (31 bp):
AAAATGTTATAAACTGATAACGTAAGTAACA
Found at i:2743469 original size:16 final size:16
Alignment explanation
Indices: 2743450--2743480 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2743440 ATATACTAAT
*
2743450 TAAATTAATTTTTTAA
1 TAAATTAATATTTTAA
2743466 TAAATTAATATTTTA
1 TAAATTAATATTTTA
2743481 GTATTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATTAATATTTTAA
Found at i:2749995 original size:23 final size:23
Alignment explanation
Indices: 2749930--2750022 Score: 120
Period size: 23 Copynumber: 4.1 Consensus size: 23
2749920 GCTCACATAA
*
2749930 TTTTCACCGAAGTGCCACATA-A
1 TTTTCACCGAAGTGCCACATAGG
*
2749952 TTATC-CCGAA-TGACCACATAGG
1 TTTTCACCGAAGTG-CCACATAGG
*
2749974 TTTTCACCAAAGTGCCACATAGG
1 TTTTCACCGAAGTGCCACATAGG
*
2749997 TTTGCACCGAAGTGCCACATAGG
1 TTTTCACCGAAGTGCCACATAGG
2750020 TTT
1 TTT
2750023 GCCTCAAAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
20 2 0.03
21 12 0.20
22 8 0.13
23 37 0.61
24 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (23 bp):
TTTTCACCGAAGTGCCACATAGG
Found at i:2750037 original size:23 final size:24
Alignment explanation
Indices: 2749962--2750038 Score: 99
Period size: 23 Copynumber: 3.3 Consensus size: 24
2749952 TTATCCCGAA
*
2749962 TGACCACATAGGTTTTCACCAAAG
1 TGACCACATAGGTTTGCACCAAAG
*
2749986 TG-CCACATAGGTTTGCACCGAAG
1 TGACCACATAGGTTTGCACCAAAG
2750009 TG-CCACATAGGTTTGC-CTCAAAG
1 TGACCACATAGGTTTGCAC-CAAAG
2750032 -GACCACA
1 TGACCACA
2750039 CAGATTATCC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.04
23 44 0.92
24 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (24 bp):
TGACCACATAGGTTTGCACCAAAG
Found at i:2750457 original size:17 final size:17
Alignment explanation
Indices: 2750427--2750460 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2750417 TCAATTTAAT
*
2750427 CATATAACGCATATTCA
1 CATATAACACATATTCA
*
2750444 CATATAACATATATTCA
1 CATATAACACATATTCA
2750461 TAACATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (17 bp):
CATATAACACATATTCA
Found at i:2754358 original size:21 final size:21
Alignment explanation
Indices: 2754334--2754384 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2754324 CTGTTATGTC
*
2754334 AGCATCGTAAACTGCCACGGT
1 AGCATCGTAAACTACCACGGT
* *
2754355 AGCATTGT-AACTACCACGTT
1 AGCATCGTAAACTACCACGGT
*
2754375 AGCACCGTAA
1 AGCATCGTAA
2754385 TTGTCAATGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
AGCATCGTAAACTACCACGGT
Found at i:2754626 original size:23 final size:22
Alignment explanation
Indices: 2754585--2754632 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
2754575 ATAATTATTT
2754585 ATATTATTAAATATATAAATAC
1 ATATTATTAAATATATAAATAC
*
2754607 ATATTATTTAAAT-TATTAAATCC
1 ATATTA-TTAAATATA-TAAATAC
2754630 ATA
1 ATA
2754633 ACAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATTATTAAATATATAAATAC
Found at i:2754834 original size:21 final size:21
Alignment explanation
Indices: 2754810--2754863 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2754800 TTCATGGCAC
* *
2754810 TGATGTGGTAGTTTACGGTAT
1 TGATATGGTAGTTTACAGTAT
* *
2754831 TGATTTGG-AGATTTACAGTGT
1 TGATATGGTAG-TTTACAGTAT
2754852 TGATATGGTAGT
1 TGATATGGTAGT
2754864 CTGCGATGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.22, C:0.04, G:0.31, T:0.43
Consensus pattern (21 bp):
TGATATGGTAGTTTACAGTAT
Found at i:2755590 original size:16 final size:16
Alignment explanation
Indices: 2755571--2755604 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2755561 CAATATACGA
2755571 ATAAACATATATTTAT
1 ATAAACATATATTTAT
**
2755587 ATAAATGTATATTTAT
1 ATAAACATATATTTAT
2755603 AT
1 AT
2755605 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAACATATATTTAT
Found at i:2755678 original size:16 final size:18
Alignment explanation
Indices: 2755646--2755679 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2755636 TATTAATGTA
2755646 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
2755664 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
2755680 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:2757199 original size:21 final size:20
Alignment explanation
Indices: 2757137--2757201 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 20
2757127 ATAGTTTTAG
* *
2757137 TATTTTTTAATATTTATATTC
1 TATTTTTT-ATATTTATTTTT
*
2757158 AATTTTTTAGTAATTTATTTTT
1 TATTTTTTA-T-ATTTATTTTT
2757180 TATTTTTTATATTTACTTTTT
1 TATTTTTTATATTTA-TTTTT
2757201 T
1 T
2757202 GAATATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 6 0.16
21 15 0.41
22 16 0.43
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTTTTTATATTTATTTTT
Found at i:2761257 original size:25 final size:25
Alignment explanation
Indices: 2761225--2761274 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2761215 TTCGTTTTCC
*
2761225 TTTTTCCAGAGTTTAAGATTTTGGA
1 TTTTTCCAGAGCTTAAGATTTTGGA
2761250 TTTTTCCAGAGCTTAAGATTTTGGA
1 TTTTTCCAGAGCTTAAGATTTTGGA
2761275 CTTAGAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (25 bp):
TTTTTCCAGAGCTTAAGATTTTGGA
Found at i:2762529 original size:3 final size:3
Alignment explanation
Indices: 2762516--2762552 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2762506 AAATATTATA
*
2762516 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2762553 TATTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2762559 original size:3 final size:3
Alignment explanation
Indices: 2762553--2762591 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
2762543 AATAATAATA
2762553 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
2762592 CAAATTACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2778887 original size:38 final size:37
Alignment explanation
Indices: 2778841--2778914 Score: 130
Period size: 38 Copynumber: 2.0 Consensus size: 37
2778831 CCGGGCCATC
*
2778841 TTAAGCCTTCAGCAAAGAGTAGTGAAGCAAAATCAATT
1 TTAAGCCTTCACCAAAGAGTAGTGAAGC-AAATCAATT
2778879 TTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAAT
1 TTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAAT
2778915 CTAGAGTCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 8 0.23
38 27 0.77
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (37 bp):
TTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATT
Found at i:2779101 original size:3 final size:3
Alignment explanation
Indices: 2779093--2779133 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2779083 GCTTGAAAAA
2779093 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2779134 ATACAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2788757 original size:16 final size:16
Alignment explanation
Indices: 2788736--2788774 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2788726 AAACTATATA
* * *
2788736 ATATATTTTCAGAATT
1 ATATATTTTAAAAAAT
2788752 ATATATTTTAAAAAAT
1 ATATATTTTAAAAAAT
2788768 ATATATT
1 ATATATT
2788775 ATATACATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (16 bp):
ATATATTTTAAAAAAT
Found at i:2789649 original size:134 final size:134
Alignment explanation
Indices: 2789408--2789894 Score: 592
Period size: 134 Copynumber: 3.6 Consensus size: 134
2789398 GGAGAGCTAT
*
2789408 TTTGAACCGAGACCGAGCACCACTTCTTATGGCCAGAAATCATTCACTAGTGATTTTAAACCGAG
1 TTTGAACCGAGACCGAGCATCACTTCTTATGGCCAGAAATCATTCACTAGTGATTTTAAACCGAG
* * * * *
2789473 ATCGAGTACCACATCTTATGGCGGCGATGATGTTGATCTTAAAGGAGTGAAGAAATCAATTACTA
66 ACCAAGCACCACTTCTTATGGTGGCGATGATGTTGATCTTAAAGGAGTGAAGAAA-CAATTACTA
2789538 GTAAA
130 GTAAA
* * * *
2789543 TTTGAACCGAGACCGAGCATCACGTT-TTATGGTCA-AAATCATTCACTATTGATTTTGAGCCGA
1 TTTGAACCGAGACCGAGCATCAC-TTCTTATGGCCAGAAATCATTCACTAGTGATTTTAAACCGA
*
2789606 GACCAAGCACCACTTCTTATGGTGGCAATGATGTTGATCTTAAAAGGAGTGAAG-AA-AATTAAC
65 GACCAAGCACCACTTCTTATGGTGGCGATGATGTTGATCTT-AAAGGAGTGAAGAAACAATT-AC
*
2789669 TAGTGAA
128 TAGTAAA
* * ** *
2789676 TTTGAACTGAGACCGAGCATCACATCTTATGGTAAGAAATCATTCACTAGTGATTTCAAACCGAG
1 TTTGAACCGAGACCGAGCATCACTTCTTATGGCCAGAAATCATTCACTAGTGATTTTAAACCGAG
* ** *
2789741 ACCAAGCACCACTTCTTATGGAGGCGATGATGTTGATCTTAAAGGAGTGAAGAAAACTTTTCCTA
66 ACCAAGCACCACTTCTTATGGTGGCGATGATGTTGATCTTAAAGGAGTGAAG-AAACAATTACTA
* *
2789806 GCAAT
130 GTAAA
* * ** * * *
2789811 TTTGAACCGAGACTGAG---CACTTCTTATGGCCAAAAATCATTCACCGGTGATTTTGAACCCAT
1 TTTGAACCGAGACCGAGCATCACTTCTTATGGCCAGAAATCATTCACTAGTGATTTTAAACCGAG
* *
2789873 ACCGAGCATCACTTCTTATGGT
66 ACCAAGCACCACTTCTTATGGT
2789895 AAGAATCATT
Statistics
Matches: 302, Mismatches: 42, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
132 59 0.20
133 50 0.17
134 125 0.41
135 64 0.21
136 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (134 bp):
TTTGAACCGAGACCGAGCATCACTTCTTATGGCCAGAAATCATTCACTAGTGATTTTAAACCGAG
ACCAAGCACCACTTCTTATGGTGGCGATGATGTTGATCTTAAAGGAGTGAAGAAACAATTACTAG
TAAA
Found at i:2789869 original size:51 final size:51
Alignment explanation
Indices: 2789809--2789946 Score: 143
Period size: 53 Copynumber: 2.6 Consensus size: 51
2789799 TTTCCTAGCA
* *
2789809 ATTTTGAACCGAGACTGAG-CACTTCTTATGGCCAAAAATCATTCACCGGTG
1 ATTTTGAACCGAGACCGAGACACTTCTTATGG-CAAAAATCATTCACCAGTG
* * * * *
2789860 ATTTTGAACCCATACCGAGCATCACTTCTTATGGTAAGAATCATTCACTAGTG
1 ATTTTGAACCGAGACCGAG-A-CACTTCTTATGGCAAAAATCATTCACCAGTG
* *
2789913 ATTTTGAACCGATACCGAGTATCACATCTTATGG
1 ATTTTGAACCGAGACCGAG-A-CACTTCTTATGG
2789947 TGGCAATGAT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 16 0.22
53 46 0.62
54 12 0.16
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (51 bp):
ATTTTGAACCGAGACCGAGACACTTCTTATGGCAAAAATCATTCACCAGTG
Found at i:2789914 original size:53 final size:53
Alignment explanation
Indices: 2789828--2789947 Score: 168
Period size: 53 Copynumber: 2.2 Consensus size: 53
2789818 CGAGACTGAG
* *
2789828 CACTTCTTATGGCCAAAAATCATTCACCGGTGATTTTGAACCCATACCGAGCAT
1 CACTTCTTATGG-TAAAAATCATTCACCAGTGATTTTGAACCCATACCGAGCAT
* * * *
2789882 CACTTCTTATGGTAAGAATCATTCACTAGTGATTTTGAACCGATACCGAGTAT
1 CACTTCTTATGGTAAAAATCATTCACCAGTGATTTTGAACCCATACCGAGCAT
*
2789935 CACATCTTATGGT
1 CACTTCTTATGGT
2789948 GGCAATGATG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 47 0.80
54 12 0.20
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (53 bp):
CACTTCTTATGGTAAAAATCATTCACCAGTGATTTTGAACCCATACCGAGCAT
Found at i:2793133 original size:82 final size:82
Alignment explanation
Indices: 2792996--2793159 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
2792986 AACACCTGTC
2792996 ACTCAGACGCCATTATGCATTAATTTTTCTAGTTGCAGGACTCCGTTTCAATTAAAGATGGGACT
1 ACTCAGACGCCATTATGCATTAATTTTTCTAGTTGCAGGACTCCGTTTCAATTAAAGATGGGACT
2793061 CATTCATCTTCTTCCCA
66 CATTCATCTTCTTCCCA
2793078 ACTCAGACGCCATTATGCATTAATTTTTCTAGTTGCAGGACTCCGTTTCAATTAAAGATGGGACT
1 ACTCAGACGCCATTATGCATTAATTTTTCTAGTTGCAGGACTCCGTTTCAATTAAAGATGGGACT
2793143 CATTCATCTTCTTCCCA
66 CATTCATCTTCTTCCCA
2793160 CCTTCCACGG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (82 bp):
ACTCAGACGCCATTATGCATTAATTTTTCTAGTTGCAGGACTCCGTTTCAATTAAAGATGGGACT
CATTCATCTTCTTCCCA
Found at i:2797281 original size:23 final size:23
Alignment explanation
Indices: 2797228--2797283 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2797218 CCCGTTGTCC
*
2797228 GCTGCCGCCAACCGCCGTATGCT
1 GCTGCCGTCAACCGCCGTATGCT
* *
2797251 GCTGCCGTCGACCGCCGTTTGCT
1 GCTGCCGTCAACCGCCGTATGCT
2797274 GCTGCCGTCA
1 GCTGCCGTCA
2797284 GCCGTCCACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.09, C:0.41, G:0.29, T:0.21
Consensus pattern (23 bp):
GCTGCCGTCAACCGCCGTATGCT
Found at i:2797736 original size:128 final size:129
Alignment explanation
Indices: 2797579--2797833 Score: 503
Period size: 128 Copynumber: 2.0 Consensus size: 129
2797569 CCAAACTTTC
2797579 TTTTTTTTTTACCGTAACTCCTTATTCCAGCTACCCAGATCTCACCATGGAACCCATACGCCCGT
1 TTTTTTTTTTACCGTAACTCCTTATTCCAGCTACCCAGATCTCACCATGGAACCCATACGCCCGT
2797644 CTCAACACAGGCGAACTAGTGGGTTAGCTGCAACAGCCGTGGTAGGTGCAGCCGCTGTGAACTT
66 CTCAACACAGGCGAACTAGTGGGTTAGCTGCAACAGCCGTGGTAGGTGCAGCCGCTGTGAACTT
2797708 TTTTTTTTTTACCGTAACT-CTTATTCCAGCTACCCAGATCTCACCATGGAACCCATACGCCCGT
1 TTTTTTTTTTACCGTAACTCCTTATTCCAGCTACCCAGATCTCACCATGGAACCCATACGCCCGT
2797772 CTCAACACAGGCGAACTAGTGGGTTAGCTGCAACAGCCGTGGTAGGTGCAGCCGCTGTGAAC
66 CTCAACACAGGCGAACTAGTGGGTTAGCTGCAACAGCCGTGGTAGGTGCAGCCGCTGTGAAC
2797834 CGTACTAGTA
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 107 0.85
129 19 0.15
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (129 bp):
TTTTTTTTTTACCGTAACTCCTTATTCCAGCTACCCAGATCTCACCATGGAACCCATACGCCCGT
CTCAACACAGGCGAACTAGTGGGTTAGCTGCAACAGCCGTGGTAGGTGCAGCCGCTGTGAACTT
Found at i:2802627 original size:19 final size:19
Alignment explanation
Indices: 2802600--2802665 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
2802590 AAAATCGAAA
*
2802600 TCGGTTTTTTCGGTTCGGT
1 TCGGATTTTTCGGTTCGGT
**
2802619 TCGGATTTTTC--AACGGT
1 TCGGATTTTTCGGTTCGGT
* *
2802636 TCGAATTTTTCGGTTCAGT
1 TCGGATTTTTCGGTTCGGT
2802655 TC-GATTTTTCG
1 TCGGATTTTTCG
2802666 ATTTTTCAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
17 14 0.38
18 8 0.22
19 15 0.41
ACGTcount: A:0.11, C:0.17, G:0.24, T:0.48
Consensus pattern (19 bp):
TCGGATTTTTCGGTTCGGT
Found at i:2804390 original size:22 final size:22
Alignment explanation
Indices: 2804346--2804410 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
2804336 ATATGAAATT
*
2804346 TGTCCCGAAGGACCTCATGTATA
1 TGTCCCGAAAGACCT-ATGTATA
*
2804369 TGTCCCGAATGACCTATGTATA
1 TGTCCCGAAAGACCTATGTATA
2804391 TGTCCCGAAAGACCTATGTA
1 TGTCCCGAAAGACCTATGTA
2804411 ACCCTCGGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 26 0.65
23 14 0.35
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (22 bp):
TGTCCCGAAAGACCTATGTATA
Found at i:2805841 original size:19 final size:19
Alignment explanation
Indices: 2805817--2805868 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
2805807 CATGCTTGTA
*
2805817 GTATCGATACCCTTCCACG
1 GTATCGATACCCATCCACG
2805836 GTATCGATACCCATCCACG
1 GTATCGATACCCATCCACG
2805855 GTATCGATACCCAT
1 GTATCGATACCCAT
2805869 TTTCGATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (19 bp):
GTATCGATACCCATCCACG
Found at i:2808230 original size:59 final size:61
Alignment explanation
Indices: 2808164--2808310 Score: 171
Period size: 59 Copynumber: 2.5 Consensus size: 61
2808154 ATTAAAAGTA
* * * * *
2808164 TTTATTTTTATTTTAAATTATTAAATCTATTTTATTATTGTCTTAA-TCT-AAAA-ATATAT
1 TTTATTTTTATTTTAACTTATTAAATATATTTTAATATTATCATAACT-TAAAAATATATAT
*
2808223 TTTATTTTTATTTTAACTTA--AAATATATTTTAATCTTATCATAACTTAAAAATATATAT
1 TTTATTTTTATTTTAACTTATTAAATATATTTTAATATTATCATAACTTAAAAATATATAT
* *
2808282 TTTATTTTTATCTTAACTT-TTAAAAATAT
1 TTTATTTTTATTTTAACTTATTAAATATAT
2808311 ATCTTATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
57 20 0.27
58 5 0.07
59 43 0.57
60 7 0.09
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (61 bp):
TTTATTTTTATTTTAACTTATTAAATATATTTTAATATTATCATAACTTAAAAATATATAT
Found at i:2808283 original size:31 final size:30
Alignment explanation
Indices: 2808164--2808538 Score: 179
Period size: 30 Copynumber: 12.5 Consensus size: 30
2808154 ATTAAAAGTA
* * ** *
2808164 TTTATTTTTATTTTAAATTATTAAATCTAT
1 TTTATTTTTATCTTAACTTAAAAAATATAT
* *
2808194 TTTATTATTGTCTTAA-TCT-AAAAATATAT
1 TTTATTTTTATCTTAACT-TAAAAAATATAT
*
2808223 TTTATTTTTATTTTAACTT--AAAATATAT
1 TTTATTTTTATCTTAACTTAAAAAATATAT
* * *
2808251 TTTAATCTTATCATAACTTAAAAATATATAT
1 TTTATTTTTATCTTAACTTAAAAA-ATATAT
*
2808282 TTTATTTTTATCTTAACTTTTAAAAATATAT
1 TTTATTTTTATCTTAAC-TTAAAAAATATAT
* ** *
2808313 CTTATTTTTAT-TTGAACTTATTACATATAT
1 TTTATTTTTATCTT-AACTTAAAAAATATAT
* * * * **
2808343 TATATTCTTAACTTAAGTTATTAAATATAT
1 TTTATTTTTATCTTAACTTAAAAAATATAT
* * * * ** *
2808373 TTTA-GTCTACCTTAAATTATTAAATATAA
1 TTTATTTTTATCTTAACTTAAAAAATATAT
* ** * * **
2808402 TTCATCCTTATTTTAACATAAAGTATATAT
1 TTTATTTTTATCTTAACTTAAAAAATATAT
* * * **
2808432 TTTATTCTTATTTTTAACTTAACATGTATAT
1 TTTATTTTTA-TCTTAACTTAAAAAATATAT
* * * *
2808463 TTTATTTATATTTTAATTTAAAAATATTTAT
1 TTTATTTTTATCTTAACTTAAAAA-ATATAT
** * * * * *
2808494 GCTAATTTTGTTTTGA-TTTAAAAATATAT
1 TTTATTTTTATCTTAACTTAAAAAATATAT
2808523 TTTATTTTTATCTTAA
1 TTTATTTTTATCTTAA
2808539 TTTTAAAATA
Statistics
Matches: 259, Mismatches: 75, Indels: 23
0.73 0.21 0.06
Matches are distributed among these distances:
28 24 0.09
29 59 0.23
30 91 0.35
31 79 0.31
32 6 0.02
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (30 bp):
TTTATTTTTATCTTAACTTAAAAAATATAT
Found at i:2808310 original size:33 final size:31
Alignment explanation
Indices: 2808213--2808312 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 31
2808203 GTCTTAATCT
* * **
2808213 AAAA-ATATATTTTATTTTTATTTTAACTT-
1 AAAATATATATTTTAATCTTATCATAACTTA
2808242 -AAA-ATATATTTTAATCTTATCATAACTTA
1 AAAATATATATTTTAATCTTATCATAACTTA
* * *
2808271 AAAATATATATTTTATTTTTATCTTAACTTTTA
1 AAAATATATATTTTAATCTTATCATAAC--TTA
2808304 AAAATATAT
1 AAAATATAT
2808313 CTTATTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 24 0.41
30 3 0.05
31 20 0.34
33 12 0.20
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (31 bp):
AAAATATATATTTTAATCTTATCATAACTTA
Found at i:2808387 original size:90 final size:91
Alignment explanation
Indices: 2808212--2808396 Score: 205
Period size: 90 Copynumber: 2.0 Consensus size: 91
2808202 TGTCTTAATC
* * * *
2808212 TAAAAATATATTTTATTTTTATTTTAACTTAAAATATATTTTAATCTTATCATAACTTAAAAATA
1 TAAAAATATATCTTATTTTTATTTGAACTTAAAATATATTATAATCTTAACATAACTTAAAAATA
* * * *
2808277 TATATTTTATTTTTATCTTAACTT-T
66 TATATTTTATGTCTACCTTAAATTAT
* * * * **
2808302 TAAAAATATATCTTATTTTTATTTGAACTTATTACATATATTATATTCTTAACTTAAGTTATTAA
1 TAAAAATATATCTTATTTTTATTTGAACTTA--AAATATATTATAATCTTAACATAACTTAAAAA
2808367 -ATATATTTTA-GTCTACCTTAAATTAT
64 TATATATTTTATGTCTACCTTAAATTAT
2808393 TAAA
1 TAAA
2808397 TATAATTCAT
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
90 39 0.50
91 15 0.19
92 24 0.31
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (91 bp):
TAAAAATATATCTTATTTTTATTTGAACTTAAAATATATTATAATCTTAACATAACTTAAAAATA
TATATTTTATGTCTACCTTAAATTAT
Found at i:2808395 original size:29 final size:30
Alignment explanation
Indices: 2808330--2808400 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
2808320 TTATTTGAAC
* * *
2808330 TTATTACATATATTATATTCTTAACTTAAG
1 TTATTAAATATATTATAGTCTTAACTTAAA
* *
2808360 TTATTAAATATATTTTAGTC-TACCTTAAA
1 TTATTAAATATATTATAGTCTTAACTTAAA
2808389 TTATTAAATATA
1 TTATTAAATATA
2808401 ATTCATCCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 19 0.53
30 17 0.47
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (30 bp):
TTATTAAATATATTATAGTCTTAACTTAAA
Found at i:2808546 original size:30 final size:29
Alignment explanation
Indices: 2808164--2808549 Score: 186
Period size: 31 Copynumber: 12.9 Consensus size: 29
2808154 ATTAAAAGTA
* * * *
2808164 TTTATTTTTATTTTAAATTATTAAATCTAT
1 TTTATTTTTATCTTAATTTA-AAAATATAT
* * *
2808194 TTTATTATTGTCTTAATCTAAAAATATAT
1 TTTATTTTTATCTTAATTTAAAAATATAT
* *
2808223 TTTATTTTTATTTTAACTT-AAAATATAT
1 TTTATTTTTATCTTAATTTAAAAATATAT
* * * *
2808251 TTTAATCTTATCATAACTTAAAAATATATAT
1 TTTATTTTTATCTTAA-TTTAAAA-ATATAT
2808282 TTTATTTTTATCTTAACTTTTAAAAATATAT
1 TTTATTTTTATCTTAA--TTTAAAAATATAT
* * * *
2808313 CTTATTTTTAT-TTGAACTTATTACATATAT
1 TTTATTTTTATCTT-AATTTA-AAAATATAT
* * * * *
2808343 TATATTCTTAACTTAAGTTATTAAATATAT
1 TTTATTTTTATCTTAATTTA-AAAATATAT
* * * * * *
2808373 TTTA-GTCTACCTTAAATTATTAAATATAA
1 TTTATTTTTATCTTAATTTA-AAAATATAT
* ** * ** *
2808402 TTCATCCTTATTTTAACATAAAGTATATAT
1 TTTATTTTTATCTTAATTTAAA-AATATAT
* * * **
2808432 TTTATTCTTATTTTTAACTTAACATGTATAT
1 TTTATTTTTA-TCTTAATTTAA-AAATATAT
* *
2808463 TTTATTTATATTTTAATTTAAAAATAT-T
1 TTTATTTTTATCTTAATTTAAAAATATAT
* * * *
2808491 TATGCTAATTTTGTTTTGATTTAAAAATATAT
1 T-T--TATTTTTATCTTAATTTAAAAATATAT
*
2808523 TTTATTTTTATCTTAATTTTAAAATAT
1 TTTATTTTTATCTTAATTTAAAAATAT
2808550 TATAAGAATA
Statistics
Matches: 272, Mismatches: 69, Indels: 31
0.73 0.19 0.08
Matches are distributed among these distances:
28 23 0.08
29 73 0.27
30 82 0.30
31 85 0.31
32 9 0.03
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTATTTTTATCTTAATTTAAAAATATAT
Found at i:2808627 original size:29 final size:27
Alignment explanation
Indices: 2808597--2808697 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 27
2808587 AACAAATTAT
*
2808597 TTTTTAAGTTAATAAAAATTAAAATGTA
1 TTTTTAAGTTAATAAAAA-TAAAATATA
*
2808625 TTTTTAAGTTAAAATAAGAATAAAATATA
1 TTTTTAAGTT--AATAAAAATAAAATATA
*
2808654 TTTCTAAGTTAAGATAAAAATAAAATATACA
1 TTTTTAAGTT-A-ATAAAAATAAAATAT--A
2808685 TTTTTAATGTTAA
1 TTTTTAA-GTTAA
2808698 GATGTTAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
28 12 0.19
29 31 0.50
30 8 0.13
31 8 0.13
32 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (27 bp):
TTTTTAAGTTAATAAAAATAAAATATA
Found at i:2808720 original size:18 final size:18
Alignment explanation
Indices: 2808687--2808733 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2808677 AATATACATT
*
2808687 TTTAATGTTAAGATGTTAA
1 TTTAAT-TTAAGATGTGAA
*
2808706 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGTGAA
*
2808724 TTTAAGTTAA
1 TTTAATTTAA
2808734 AATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTAATTTAAGATGTGAA
Found at i:2809561 original size:69 final size:69
Alignment explanation
Indices: 2809450--2809584 Score: 261
Period size: 69 Copynumber: 2.0 Consensus size: 69
2809440 TTGTTGTTAT
2809450 TGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
1 TGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
2809515 AAGC
66 AAGC
*
2809519 TGTCGGAACCGTCTTTCGGTTGGGCTCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
1 TGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
2809584 A
66 A
2809585 CCGACCACTT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (69 bp):
TGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
AAGC
Found at i:2809979 original size:25 final size:26
Alignment explanation
Indices: 2809908--2809980 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
2809898 TGAAAGAAAG
*
2809908 AAATAATAAAATAATAATAAAAGGTTA
1 AAATAA-AAAATAATAATAAAAAGTTA
* *
2809935 AATTAAAAAA-AATATTTAAAAAG-TA
1 AAATAAAAAATAATA-ATAAAAAGTTA
2809960 AAATAAAAAATAA-AGATAAAA
1 AAATAAAAAATAATA-ATAAAA
2809981 CTTAGGATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 21 0.55
26 12 0.32
27 5 0.13
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (26 bp):
AAATAAAAAATAATAATAAAAAGTTA
Found at i:2811215 original size:6 final size:5
Alignment explanation
Indices: 2811202--2811261 Score: 50
Period size: 6 Copynumber: 10.8 Consensus size: 5
2811192 TTGGACCTGG
2811202 AAAA- AAAAGT AAAAT AAAAT AAGTAAT AAAAT AATAAT AATAAT AATAAT
1 AAAAT AAAA-T AAAAT AAAAT AA--AAT AAAAT AA-AAT AA-AAT AA-AAT
2811252 AAATAT AAAA
1 AAA-AT AAAA
2811262 AACTATATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.08
5 15 0.30
6 26 0.52
7 5 0.10
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:2811229 original size:12 final size:11
Alignment explanation
Indices: 2811214--2811259 Score: 65
Period size: 12 Copynumber: 3.9 Consensus size: 11
2811204 AAAAAAGTAA
2811214 AATAAAATAAGT
1 AATAAAATAA-T
2811226 AATAAAATAAT
1 AATAAAATAAT
2811237 AATAATAATAAT
1 AATAA-AATAAT
2811249 AATAAATATAA
1 AATAAA-ATAA
2811260 AAAACTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 7 0.22
12 25 0.78
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Done.