Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009586.1 Hibiscus syriacus cultivar Beakdansim tig00116964_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: 3773412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 19
Found at i:1847154 original size:8 final size:8
Alignment explanation
Indices: 1847143--1847802 Score: 393
Period size: 8 Copynumber: 88.8 Consensus size: 8
1847133 ATTATTTAAC
1847143 TTTAATGA
1 TTTAATGA
1847151 TTTAAT-A
1 TTTAATGA
* *
1847158 -ATAATTA
1 TTTAATGA
*
1847165 TTTAA--C
1 TTTAATGA
1847171 TTTAATGA
1 TTTAATGA
1847179 TTTAAT-A
1 TTTAATGA
* *
1847186 -ATAATTA
1 TTTAATGA
1847193 CTTTAATGA
1 -TTTAATGA
*
1847202 TTTAA--C
1 TTTAATGA
1847208 TTTAATGA
1 TTTAATGA
1847216 TTTAAT-A
1 TTTAATGA
* *
1847223 -ATAATTA
1 TTTAATGA
1847230 CTTTAATGA
1 -TTTAATGA
1847239 TTTAAT--
1 TTTAATGA
1847245 TTTAATGA
1 TTTAATGA
1847253 TTTAAT-A
1 TTTAATGA
* *
1847260 -ATAATTA
1 TTTAATGA
1847267 CTTTAATGA
1 -TTTAATGA
1847276 TTTAAT--
1 TTTAATGA
1847282 TTTAATGA
1 TTTAATGA
1847290 TTTAATGA
1 TTTAATGA
*
1847298 TTTAA--C
1 TTTAATGA
1847304 TTTAATGA
1 TTTAATGA
1847312 TTTAAT-A
1 TTTAATGA
* *
1847319 -ATAATTA
1 TTTAATGA
1847326 CTTTAATGA
1 -TTTAATGA
*
1847335 TTTAA--C
1 TTTAATGA
1847341 TTTAATGA
1 TTTAATGA
1847349 TTTAAT-A
1 TTTAATGA
* *
1847356 -ATAATTA
1 TTTAATGA
1847363 CTTTAATGA
1 -TTTAATGA
1847372 TTTAATGA
1 TTTAATGA
1847380 TTTAATGA
1 TTTAATGA
1847388 TTTAAT-A
1 TTTAATGA
* *
1847395 -ATAATTA
1 TTTAATGA
1847402 TTTTAATGA
1 -TTTAATGA
1847411 TTTAATGA
1 TTTAATGA
1847419 TTTAATGA
1 TTTAATGA
*
1847427 --TAATTA
1 TTTAATGA
1847433 CTTTAATGA
1 -TTTAATGA
1847442 TTTAAT--
1 TTTAATGA
1847448 TTTAATGA
1 TTTAATGA
1847456 TTTAAT-A
1 TTTAATGA
* *
1847463 -ATAATTA
1 TTTAATGA
1847470 CTTTAATGA
1 -TTTAATGA
1847479 TTTAAT--
1 TTTAATGA
1847485 TTTAATGA
1 TTTAATGA
1847493 TTTAATGA
1 TTTAATGA
*
1847501 TTTAA--C
1 TTTAATGA
1847507 TTTAATGA
1 TTTAATGA
1847515 TTTAAT-A
1 TTTAATGA
* *
1847522 -ATAATTA
1 TTTAATGA
1847529 CTTTAATGA
1 -TTTAATGA
*
1847538 -TTAA--C
1 TTTAATGA
1847543 TTTAATGA
1 TTTAATGA
* *
1847551 -ATAATTA
1 TTTAATGA
1847558 CTTTAATGA
1 -TTTAATGA
1847567 TTTAATGA
1 TTTAATGA
1847575 TTTAATGA
1 TTTAATGA
1847583 TTTAAT-A
1 TTTAATGA
* *
1847590 -ATAATTA
1 TTTAATGA
1847597 TTTAATGA
1 TTTAATGA
1847605 TTTAATGA
1 TTTAATGA
1847613 TTTAATGA
1 TTTAATGA
1847621 TTT-A--A
1 TTTAATGA
1847626 TTTAAT-A
1 TTTAATGA
* *
1847633 -ATAATTA
1 TTTAATGA
1847640 CTTTAATGA
1 -TTTAATGA
*
1847649 TTTAA--C
1 TTTAATGA
*
1847655 TTTAATGC
1 TTTAATGA
1847663 TTTAAT-A
1 TTTAATGA
* *
1847670 -ATAATTA
1 TTTAATGA
1847677 CTTTAATGA
1 -TTTAATGA
1847686 TTTAATGA
1 TTTAATGA
1847694 TTTAATGA
1 TTTAATGA
1847702 TTTAATGA
1 TTTAATGA
1847710 TTTAATGA
1 TTTAATGA
1847718 TTTAAT-A
1 TTTAATGA
* *
1847725 -ATAATTA
1 TTTAATGA
1847732 CTTTAATGA
1 -TTTAATGA
1847741 TTTAAT--
1 TTTAATGA
*
1847747 TTTAATAA
1 TTTAATGA
1847755 TTTAAT-A
1 TTTAATGA
* *
1847762 -ATAATTA
1 TTTAATGA
*
1847769 CTTAAT--
1 TTTAATGA
1847775 TTTAATGA
1 TTTAATGA
1847783 TTTAAT--
1 TTTAATGA
1847789 TTTAATGA
1 TTTAATGA
1847797 TTTAAT
1 TTTAAT
1847803 AATAATTACT
Statistics
Matches: 516, Mismatches: 61, Indels: 150
0.71 0.08 0.21
Matches are distributed among these distances:
5 4 0.01
6 137 0.27
7 37 0.07
8 273 0.53
9 65 0.13
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.50
Consensus pattern (8 bp):
TTTAATGA
Found at i:1847457 original size:203 final size:203
Alignment explanation
Indices: 1847171--1847810 Score: 889
Period size: 203 Copynumber: 3.1 Consensus size: 203
1847161 ATTATTTAAC
*
1847171 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTACTTTAA
1 TTTAATGATTTAATAATAATTATTTTAATG-----A-TTTAATGATTTAATAATAATTACTTTAA
1847236 TGATTTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATGATTT
60 TGATTTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATGATTT
1847301 AACTTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTACTT
125 AACTTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTACTT
1847366 TAATGATTTAATGA
190 TAATGATTTAATGA
*
1847380 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATAATTACTTTAATGATTT
1 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTT
1847445 AATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATGATTTAACTTT
66 AATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATGATTTAACTTT
1847510 AATGATTTAATAATAATTACTTTAATGA-TTAACTTTAATG-------AATAATTACTTTAATGA
131 AATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGA
1847567 TTTAATGA
196 TTTAATGA
1847575 TTTAATGATTTAATAATAATTATTTAATGATTTAATGATTTAATGATTTAATTTAATAATAATTA
1 TTTAATGATTTAATAAT-A--A-TT-AT--TTTAATGATTTAATG-----ATTTAATAATAATTA
* *
1847640 CTTTAATGATTTAACTTTAATGCTTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTT
54 CTTTAATGATTTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAAT--TTTAATGATTT
* *
1847705 AATG-----A-TTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATTTAATAAT
117 AATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAAT
1847764 AATTACTTAATTTTAATGATTTAAT--
182 AATTAC-----TTTAATGATTTAATGA
1847789 TTTAATGATTTAATAATAATTA
1 TTTAATGATTTAATAATAATTA
1847811 CTTGAATTTA
Statistics
Matches: 397, Mismatches: 7, Indels: 54
0.87 0.02 0.12
Matches are distributed among these distances:
195 42 0.11
196 1 0.00
198 1 0.00
199 2 0.01
200 2 0.01
202 27 0.07
203 157 0.40
204 12 0.03
207 64 0.16
209 45 0.11
210 2 0.01
211 10 0.03
213 1 0.00
214 17 0.04
216 14 0.04
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.50
Consensus pattern (203 bp):
TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTT
AATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATGATTTAACTTT
AATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGA
TTTAATGA
Found at i:1847771 original size:37 final size:37
Alignment explanation
Indices: 1847159--1847707 Score: 470
Period size: 37 Copynumber: 14.7 Consensus size: 37
1847149 GATTTAATAA
* *
1847159 TAATTATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
*
1847196 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1847233 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
*
1847270 TAATGATTTAATTTTAATGATTTAATGAT--TTAACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATT-ACTT
** * *
1847306 TAATGATTTAATAATAATTACTTTAATGAT--TTAACTT
1 TAATGATTTAATTTTAATGA-TTTAATAATAATT-ACTT
** * * *
1847343 TAATGATTTAATAATAATTACTTTAATGATTTAATGA-TT
1 TAATGATTTAATTTTAATGA-TTTAAT-A-ATAATTACTT
** * * *
1847382 TAATGATTTAATAATAATTATTTTAATGATTTAATGA-TT
1 TAATGATTTAATTTTAATGA-TTTAAT-A-ATAATTACTT
* ** *
1847421 TAATGATAATT-ACTTTAATGATTTAATTTTAATGA-TT
1 TAATGAT--TTAATTTTAATGATTTAATAATAATTACTT
* * ** *
1847458 TAATAATAATT-ACTTTAATGATTTAATTTTAATGA-TT
1 TAATGAT--TTAATTTTAATGATTTAATAATAATTACTT
*
1847495 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
*
1847532 TAATGA-TTAACTTTAATG-------AATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1847561 TAATGATTTAATGATTTAATGATTTAATAATAATTA-TT
1 TAATGATTTAAT--TTTAATGATTTAATAATAATTACTT
1847599 TAATGATTTAATGATTTAATGATTTAATTTAATAATAATTACTT
1 TAATGATTTAAT--TTTAATG-----ATTTAATAATAATTACTT
* *
1847643 TAATGATTTAACTTTAATGCTTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1847680 TAATGATTTAATGATTTAATGATTTAAT
1 TAATGATTTAAT--TTTAATGATTTAAT
1847708 GATTTAATGA
Statistics
Matches: 459, Mismatches: 25, Indels: 54
0.85 0.05 0.10
Matches are distributed among these distances:
29 17 0.04
30 4 0.01
32 7 0.02
35 4 0.01
36 54 0.12
37 230 0.50
38 23 0.05
39 75 0.16
40 7 0.02
41 3 0.01
42 7 0.02
43 15 0.03
44 13 0.03
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (37 bp):
TAATGATTTAATTTTAATGATTTAATAATAATTACTT
Found at i:1847845 original size:42 final size:40
Alignment explanation
Indices: 1847559--1847845 Score: 165
Period size: 42 Copynumber: 6.7 Consensus size: 40
1847549 GAATAATTAC
* *
1847559 TTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTAAT
1 TTTAATGATTTAAT--TTTAAT-A-ATAATAATAATTACTTAAT
*
1847603 GATTTAATGATTTAATGATTTAAT-TTAATAATAATTACTTTAAT
1 --TTTAATGATTTAAT--TTTAATAATAATAATAATTAC-TTAAT
* * * *
1847647 GATTTAA--CTTTAATGCTTTAATAATAATTACTTTAATGATTTAAT
1 --TTTAATGATTTAAT--TTTAATAATAA-TA--ATAATTACTTAAT
* * * *
1847692 GATTTAATGATTTAATGATTTAATGAT-TTAATAA-TAATT-AC
1 --TTTAATGATTTAAT--TTTAATAATAATAATAATTACTTAAT
1847733 TTTAATGATTTAATTTTAATAATTTAATAATAATTACTTAAT
1 TTTAATGATTTAATTTTAATAA--TAATAATAATTACTTAAT
*
1847775 TTTAATGATTTAATTTTAATGATTTAATAATAATTACTTGAA-
1 TTTAATGATTTAATTTTAAT-A-ATAATAATAATTACTT-AAT
*
1847817 TTTAATGATTTATATTTGATATAATAATA
1 TTTAATGATTTA-ATTTTA-ATAATAATA
1847846 GTAAATATAT
Statistics
Matches: 202, Mismatches: 22, Indels: 38
0.77 0.08 0.15
Matches are distributed among these distances:
37 7 0.03
39 15 0.07
40 6 0.03
41 5 0.02
42 69 0.34
43 28 0.14
44 16 0.08
45 14 0.07
46 27 0.13
47 15 0.07
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (40 bp):
TTTAATGATTTAATTTTAATAATAATAATAATTACTTAAT
Found at i:1850882 original size:23 final size:23
Alignment explanation
Indices: 1850856--1850899 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1850846 AGTTGCATGC
1850856 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
1850879 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
1850900 CCTTGCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:1850955 original size:22 final size:22
Alignment explanation
Indices: 1850927--1850971 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1850917 CCCGTGATTT
*
1850927 CTGTGCTTTCTCCTTGCAGAAC
1 CTGTGCTCTCTCCTTGCAGAAC
1850949 CTGTGCTCTCTCCTTGCAGAAC
1 CTGTGCTCTCTCCTTGCAGAAC
1850971 C
1 C
1850972 CGTGATTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.36, G:0.18, T:0.33
Consensus pattern (22 bp):
CTGTGCTCTCTCCTTGCAGAAC
Found at i:1851946 original size:13 final size:13
Alignment explanation
Indices: 1851928--1851953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1851918 TTATAACGAC
1851928 GTTTGTATTAGCA
1 GTTTGTATTAGCA
1851941 GTTTGTATTAGCA
1 GTTTGTATTAGCA
1851954 ATGTTTTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
GTTTGTATTAGCA
Found at i:1871321 original size:22 final size:22
Alignment explanation
Indices: 1871296--1871337 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1871286 GTGATATAAT
1871296 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAATATTTTTGG
* *
1871318 TATTTTTATTTAATTTTTTT
1 TATTTTTATTAAATATTTTT
1871338 AAATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
TATTTTTATTAAATATTTTTGG
Found at i:1873932 original size:11 final size:10
Alignment explanation
Indices: 1873912--1873936 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1873902 CTGGAAGACC
1873912 AAAGAAAAAA
1 AAAGAAAAAA
1873922 AAAGAAAAAA
1 AAAGAAAAAA
1873932 AAAGA
1 AAAGA
1873937 CAGTGAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:1875456 original size:35 final size:36
Alignment explanation
Indices: 1875389--1875456 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
1875379 ATGCTTAGCC
*
1875389 TTAAATCATAATAATAAATATAGGTTCTTACAAAAA
1 TTAAATCATAATAATAAATATAAGTTCTTACAAAAA
* *
1875425 TTAAATCATACTACTAAA-ATAAGTTCTTACAA
1 TTAAATCATAATAATAAATATAAGTTCTTACAA
1875457 TATACTCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (36 bp):
TTAAATCATAATAATAAATATAAGTTCTTACAAAAA
Found at i:1893565 original size:37 final size:36
Alignment explanation
Indices: 1893506--1893652 Score: 178
Period size: 35 Copynumber: 4.2 Consensus size: 36
1893496 ATCCCATTAT
* *
1893506 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
1893542 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
1893578 CA-TTTTCAAGGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
** *
1893613 CATTTTTTCAAAG--TTAGTTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1893647 CATTTT
1 CATTTT
1893653 AACATTATTG
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.04
34 10 0.10
35 44 0.44
36 13 0.13
37 28 0.28
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:1893581 original size:21 final size:21
Alignment explanation
Indices: 1893557--1893617 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1893547 TTCAAAGAAA
1893557 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
* *
1893578 CATTT-TC-AA----GGAAA-
1 CATTTACCAAACTTTGAAAAC
1893592 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1893613 CATTT
1 CATTT
1893618 TTTCAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 5 0.17
16 2 0.07
19 2 0.07
20 5 0.17
21 10 0.34
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1893623 original size:72 final size:68
Alignment explanation
Indices: 1893509--1893656 Score: 183
Period size: 72 Copynumber: 2.1 Consensus size: 68
1893499 CCATTATCAT
*
1893509 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAACATTTACCAAACTTTGA
1 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG--ACAGTTACCAAAC-TTGA
1893574 AAACCA
63 AAACCA
* * * **
1893580 TTTTCAAGGAAACATTTACCAAACTTTG-AAAACCATTTTTTCAAAGTTAGTTACCAAACTTGAA
1 TTTTCAA-CAAACATCTACCAAACTTTGAAAAACTA-TTTTTCAAAGACAGTTACCAAACTTGAA
1893644 AACCA
64 AACCA
1893649 TTTT-AACA
1 TTTTCAACA
1893657 TTATTGCCGT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
67 1 0.01
68 2 0.03
69 14 0.21
70 10 0.15
71 13 0.19
72 28 0.41
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.32
Consensus pattern (68 bp):
TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGACAGTTACCAAACTTGAAAA
CCA
Found at i:1896481 original size:15 final size:16
Alignment explanation
Indices: 1896461--1896490 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1896451 ACTATTCACA
1896461 TGAATAGT-AAATTTG
1 TGAATAGTGAAATTTG
1896476 TGAATAGTGAAATTT
1 TGAATAGTGAAATTT
1896491 TGTCGGCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (16 bp):
TGAATAGTGAAATTTG
Found at i:1928421 original size:2 final size:2
Alignment explanation
Indices: 1928414--1928467 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1928404 TCTCAACCAA
1928414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1928456 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1928468 CAGTGCAACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1934190 original size:13 final size:13
Alignment explanation
Indices: 1934168--1934204 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1934158 CATTTAAATG
*
1934168 ATAAACGAACATA
1 ATAAACGAACACA
*
1934181 ATAAATGAACACA
1 ATAAACGAACACA
1934194 ATAAACGAACA
1 ATAAACGAACA
1934205 ACACAAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.16, G:0.08, T:0.14
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:1934568 original size:39 final size:39
Alignment explanation
Indices: 1934524--1934602 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
1934514 CGAACGTAAA
** *
1934524 TAAACGAACG-AGCTCTCTGTTCATGTTTGTTCATTTAAT
1 TAAACGAACGAAAATCT-TGTTCATGTTCGTTCATTTAAT
1934563 TAAACGAACGCAAAATCTTGTTCATGTTCGTTCATTTAAT
1 TAAACGAACG-AAAATCTTGTTCATGTTCGTTCATTTAAT
1934603 AAATAAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 10 0.29
40 21 0.60
41 4 0.11
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (39 bp):
TAAACGAACGAAAATCTTGTTCATGTTCGTTCATTTAAT
Found at i:1942196 original size:31 final size:31
Alignment explanation
Indices: 1942158--1942225 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
1942148 TTGTGTTTGG
1942158 TTGGTTTAGCAGGAATATAATATTACCGTGA
1 TTGGTTTAGCAGGAATATAATATTACCGTGA
* * *
1942189 TTGGTTTAGTAGGAATGTAATATTACCGTGT
1 TTGGTTTAGCAGGAATATAATATTACCGTGA
1942220 TTGGTT
1 TTGGTT
1942226 AAAGGAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (31 bp):
TTGGTTTAGCAGGAATATAATATTACCGTGA
Found at i:1942242 original size:29 final size:31
Alignment explanation
Indices: 1942158--1942234 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1942148 TTGTGTTTGG
*
1942158 TTGGTTTAGCAGGAATATAATATTACCGTGA
1 TTGGTTTAGAAGGAATATAATATTACCGTGA
* * *
1942189 TTGGTTTAGTAGGAATGTAATATTACCGTGT
1 TTGGTTTAGAAGGAATATAATATTACCGTGA
1942220 TTGG-TTA-AAGGAATA
1 TTGGTTTAGAAGGAATA
1942235 AAAGATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 6 0.15
30 3 0.07
31 32 0.78
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (31 bp):
TTGGTTTAGAAGGAATATAATATTACCGTGA
Found at i:1945315 original size:106 final size:108
Alignment explanation
Indices: 1945137--1945388 Score: 303
Period size: 106 Copynumber: 2.4 Consensus size: 108
1945127 AAATCTGATG
* * * * *
1945137 ATAACAAAATAGGTTAATTACTTATTTTATTATTAATATTATCAACATATTAGGTAGCGTCTAAA
1 ATAAAAAAATAGGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAAGTAGCGCCTAAA
* * *
1945202 ATATTACCAAAGTTT-AAGTTGATGGA-CCTTAGAAATCCCACA
66 ATATTACCAAAATTTAAACTT-ATAGAGCCTTAGAAATCCCACA
* * * * *
1945244 ATAAACAAATAGGTTAATTA-ATATTTTGTTATAAATATTATCAACATATTAAGTTGTGCCTAAT
1 ATAAAAAAATAGGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAAGTAGCGCCTAAA
* * *
1945308 ATGTTACCAAAATTTAAACTTATAGAGCCTTCGAAATCCCACG
66 ATATTACCAAAATTTAAACTTATAGAGCCTTAGAAATCCCACA
* * *
1945351 ATAAAAAAATAGATTAAATACTTAGTTTGTTATAAATA
1 ATAAAAAAATAGGTTAATTACTTATTTTGTTATAAATA
1945389 AATATTAACA
Statistics
Matches: 121, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
106 53 0.44
107 53 0.44
108 15 0.12
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (108 bp):
ATAAAAAAATAGGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAAGTAGCGCCTAAA
ATATTACCAAAATTTAAACTTATAGAGCCTTAGAAATCCCACA
Found at i:1945730 original size:21 final size:21
Alignment explanation
Indices: 1945706--1945771 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1945696 TTTGTAAAAA
1945706 TATCGATACTTAGTGTAGATG
1 TATCGATACTTAGTGTAGATG
* * *
1945727 TATCGAAAC-T-CT-TACACTCCG
1 TATCGATACTTAGTGTAGA-T--G
1945748 TATCGATACTTAGTGTAGATG
1 TATCGATACTTAGTGTAGATG
1945769 TAT
1 TAT
1945772 GGAAATTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 1 0.03
21 21 0.64
22 1 0.03
23 2 0.06
24 3 0.09
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (21 bp):
TATCGATACTTAGTGTAGATG
Found at i:1946240 original size:76 final size:76
Alignment explanation
Indices: 1946140--1946306 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
1946130 AAGTTGTAAA
* * * * *
1946140 TATTTTACCGTTTACATTAATATTATACCTTAAAACAAATCGATAGGTAGTTTAACATAATAGGT
1 TATTTTACCGGTTACAATAATATTATACCTTAAAACAAACCGATAGCTAATTTAACATAATAGGT
1946205 AGCGCCTATTT
66 AGCGCCTATTT
* * * *
1946216 TATTTTACCGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTAACGTAGTAGGT
1 TATTTTACCGGTTACAATAATATTATACCTTAAAACAAACCGATAGCTAATTTAACATAATAGGT
*
1946281 TGCGCCTATTT
66 AGCGCCTATTT
1946292 TATTTTAACCGGTTA
1 TATTTT-ACCGGTTA
1946307 AGTTGTAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
76 72 0.90
77 8 0.10
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (76 bp):
TATTTTACCGGTTACAATAATATTATACCTTAAAACAAACCGATAGCTAATTTAACATAATAGGT
AGCGCCTATTT
Found at i:1946320 original size:100 final size:100
Alignment explanation
Indices: 1946216--1946398 Score: 276
Period size: 100 Copynumber: 1.8 Consensus size: 100
1946206 GCGCCTATTT
* * *
1946216 TATTTTACCGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTAACGTAGTAGGT
1 TATTTTACAGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTAACGTAATAAGT
**
1946281 TGCGCCTATTTTATTTTAACCGGTTAAGTTGTAAA
66 AACGCCTATTTTATTTTAACCGGTTAAGTTGTAAA
* * * *
1946316 TATTTTACAGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAAGT
1 TATTTTACAGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTAACGTAATAAGT
*
1946381 AACGTCTATTTTATTTTA
66 AACGCCTATTTTATTTTA
1946399 CCGTTTATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 73 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (100 bp):
TATTTTACAGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTAACGTAATAAGT
AACGCCTATTTTATTTTAACCGGTTAAGTTGTAAA
Found at i:1946334 original size:176 final size:176
Alignment explanation
Indices: 1946043--1946477 Score: 563
Period size: 176 Copynumber: 2.5 Consensus size: 176
1946033 AAGTTATAAA
* * * * *
1946043 TATTTTAACGTTTACATTATTATTATACC-TT--ATAAACCGTTAAG-TAGTTTAACATAATAGG
1 TATTTTACCGTTTACAATATTATTATACCTTTAAAAAAACCGAT-AGCTAGTTTAACGTAATAGG
* * *
1946104 TAGCGTCTATTTTATTTTAACCGGTTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACC
65 TTGCGCCTATTTTATTTTAACCGGTTAAGTTGTAAATATTTTACAGTTTACATTAATATTATACC
* * * *
1946169 TTAAAACAAATCGATAGGTAGTTTAACATAATAGGTAGCGCCTATTT
130 TTAAAACAAACCGATAGCTAGTTTAACATAATAAGTAACGCCTATTT
* * * *
1946216 TATTTTACCGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTAACGTAGTAGGT
1 TATTTTACCGTTTACAATATTATTATACCTTTAAAAAAACCGATAGCTAGTTTAACGTAATAGGT
*
1946281 TGCGCCTATTTTATTTTAACCGGTTAAGTTGTAAATATTTTACAGTTTACATTATTATTATACCT
66 TGCGCCTATTTTATTTTAACCGGTTAAGTTGTAAATATTTTACAGTTTACATTAATATTATACCT
* * * *
1946346 TTAAACAAACCGGTAGCTAGTTTAACGTAATAAGTAACGTCTATTT
131 TAAAACAAACCGATAGCTAGTTTAACATAATAAGTAACGCCTATTT
* * * * *
1946392 TATTTTACCGTTTATATTATTATTATTATACTTTTAAAAAAACAGGTAGCTAGTTTAATGTAATA
1 TATTTTACCGTTTACA--A-TATTATTATACCTTTAAAAAAACCGATAGCTAGTTTAACGTAATA
*
1946457 GGTTGTGCCTATTTTATTTTA
63 GGTTGCGCCTATTTTATTTTA
1946478 CCGTTTACAA
Statistics
Matches: 225, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
173 26 0.12
174 2 0.01
175 2 0.01
176 136 0.60
178 1 0.00
179 58 0.26
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (176 bp):
TATTTTACCGTTTACAATATTATTATACCTTTAAAAAAACCGATAGCTAGTTTAACGTAATAGGT
TGCGCCTATTTTATTTTAACCGGTTAAGTTGTAAATATTTTACAGTTTACATTAATATTATACCT
TAAAACAAACCGATAGCTAGTTTAACATAATAAGTAACGCCTATTT
Found at i:1946549 original size:77 final size:76
Alignment explanation
Indices: 1946316--1946554 Score: 275
Period size: 79 Copynumber: 3.1 Consensus size: 76
1946306 AAGTTGTAAA
* * * *
1946316 TATTTTACAGTTTACATTATTATTATACCTTTAAAC-AAACCGGTAGCTAGTTTAACGTAATAAG
1 TATTTTACCGTTTACAATATTATTATA-CTTTAAACAAAACAGGTAGCTAGTTTAACGTAATAGG
* *
1946380 TAACGTCTATTT
65 TTATGTCTATTT
* *
1946392 TATTTTACCGTTTATATTATTATTATTATACTTTTAAA-AAAACAGGTAGCTAGTTTAATGTAAT
1 TATTTTACCGTTTACA--A-TATTATTATAC-TTTAAACAAAACAGGTAGCTAGTTTAACGTAAT
* *
1946456 AGGTTGTGCCTATTT
62 AGGTTATGTCTATTT
** * *
1946471 TATTTTACCGTTTACAATATTATTATAGCTTTAAACAAAATTGGTAGTTAGTTTAACGAAATAGG
1 TATTTTACCGTTTACAATATTATTATA-CTTTAAACAAAACAGGTAGCTAGTTTAACGTAATAGG
*
1946536 TTTTGTCTATTT
65 TTATGTCTATTT
1946548 TATTTTA
1 TATTTTA
1946555 ATCGGCTAAG
Statistics
Matches: 138, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
76 30 0.22
77 43 0.31
78 1 0.01
79 64 0.46
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (76 bp):
TATTTTACCGTTTACAATATTATTATACTTTAAACAAAACAGGTAGCTAGTTTAACGTAATAGGT
TATGTCTATTT
Found at i:1946620 original size:255 final size:252
Alignment explanation
Indices: 1946140--1946653 Score: 701
Period size: 255 Copynumber: 2.0 Consensus size: 252
1946130 AAGTTGTAAA
*
1946140 TATTTTACCGTTTACATTAATATTATACCTTAAAACAAATCGATAGGTAGTTTAACATAATAGGT
1 TATTTTACCGTTTACATTAATATTATACCTTAAAACAAATCGATAGCTAGTTTAACATAATAGGT
1946205 AGCGCCTATTTTATTTTACCGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTA
66 AGCGCCTATTTTATTTTACCGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTA
* * *
1946270 ACGTAGTAGGTTGCGCCTATTTTATTTTAACCGGTTAAGTTGTAAATATTTTACAGTTTACATTA
131 ACGAAATAGGTTGCGCCTATTTTATTTTAACCGGCTAAGTTGTAAATATTTTACAGTTTACATTA
* * *
1946335 TTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAAGTAACGTCTATTT
196 TTATTATACATTTAAACAAACCGATAGCTAGTTTAACGTAATAAGTAACGTCGATTT
* * * **
1946392 TATTTTACCGTTTATATTATTATTATTATACTTTTAAAA-AAA-CAGGTAGCTAGTTTAATGTAA
1 TATTTTACCGTTTACATTA--A-TATTATAC-CTTAAAACAAATC-GATAGCTAGTTTAACATAA
* * * * ** * *
1946455 TAGGTTGTGCCTATTTTATTTTACCGTTTACAATATTATTATAGCTTTAAACAAAATTGGTAGTT
61 TAGGTAGCGCCTATTTTATTTTACCGGTTACAATATTATTATACCTTTAAAC-AAACCGATAGCT
* ** * *
1946520 AGTTTAACGAAATAGGTTTTGTCTATTTTATTTTAATCGGCTAAGTTGTAAATATTTTAC-GTTT
125 AATTTAACGAAATAGGTTGCGCCTATTTTATTTTAACCGGCTAAGTTGTAAATATTTTACAGTTT
* * *
1946584 ACATTATTATTATACATTTAAATAAACCGATAGCTAGTTTAACGTAATAGGTAGCGTCGATTT
190 ACATTATTATTATACATTTAAACAAACCGATAGCTAGTTTAACGTAATAAGTAACGTCGATTT
1946647 TATTTTA
1 TATTTTA
1946654 ACCGGTTAAG
Statistics
Matches: 228, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
252 18 0.08
254 2 0.01
255 142 0.62
256 66 0.29
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (252 bp):
TATTTTACCGTTTACATTAATATTATACCTTAAAACAAATCGATAGCTAGTTTAACATAATAGGT
AGCGCCTATTTTATTTTACCGGTTACAATATTATTATACCTTTAAACAAACCGATAGCTAATTTA
ACGAAATAGGTTGCGCCTATTTTATTTTAACCGGCTAAGTTGTAAATATTTTACAGTTTACATTA
TTATTATACATTTAAACAAACCGATAGCTAGTTTAACGTAATAAGTAACGTCGATTT
Found at i:1946649 original size:99 final size:101
Alignment explanation
Indices: 1946471--1946666 Score: 245
Period size: 99 Copynumber: 2.0 Consensus size: 101
1946461 GTGCCTATTT
** * *
1946471 TATTTTACCGTTTACAATATTATTATAGCTTTAAACAAAATTGGTAGTTAGTTTAACGAAATAGG
1 TATTTTACCGTTTACAATATTATTATAGCTTTAAACAAAACCGATAGCTAGTTTAACGAAATAGG
*** * *
1946536 TTTTGTCTATTTTATTTTAATCGGCTAAGTTGTAAA
66 TAGCGTCGATTTTATTTTAACCGGCTAAGTTGTAAA
* * *
1946572 TATTTTA-CGTTTACATTATTATTATA-CATTTAAA-TAAACCGATAGCTAGTTTAACGTAATAG
1 TATTTTACCGTTTACAATATTATTATAGC-TTTAAACAAAACCGATAGCTAGTTTAACGAAATAG
*
1946634 GTAGCGTCGATTTTATTTTAACCGGTTAAGTTG
65 GTAGCGTCGATTTTATTTTAACCGGCTAAGTTG
1946667 CAATTATTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
99 50 0.62
100 24 0.30
101 7 0.09
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (101 bp):
TATTTTACCGTTTACAATATTATTATAGCTTTAAACAAAACCGATAGCTAGTTTAACGAAATAGG
TAGCGTCGATTTTATTTTAACCGGCTAAGTTGTAAA
Found at i:1947072 original size:70 final size:69
Alignment explanation
Indices: 1946926--1947131 Score: 225
Period size: 70 Copynumber: 2.9 Consensus size: 69
1946916 ATTTTGTAGT
* *
1946926 CTTCTCATTTTCTACTTTTTTTTAAATTCGAAATTATTGATATTTGTAAAAAAAAATATTGAAAC
1 CTTCTCATTTTCTA-TTTTTTTTAAATTCGAAAATATTGATA-TT-T-AAAAAAAATATTGATAC
**
1946991 TTTGCTGC
62 TTTGCAAC
* * * * *
1946999 CTTCTTATTTTTTATTTTTTTTAAAATTTGAAAGTATTGATATTTAAAAAAAATACTGATACTTT
1 CTTCTCATTTTCTATTTTTTTT-AAATTCGAAAATATTGATATTTAAAAAAAATATTGATACTTT
1947064 GCAAC
65 GCAAC
* *
1947069 CTTCGCATTTTCTATATTATTTTAAATTCGAAAATATCT-ATATTTATAAAAAAAGTATTGATA
1 CTTCTCATTTTCTAT-TTTTTTTAAATTCGAAAATAT-TGATATTTA-AAAAAAA-TATTGATA
1947132 TTTACCTATC
Statistics
Matches: 113, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
70 52 0.46
71 15 0.13
72 17 0.15
73 29 0.26
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (69 bp):
CTTCTCATTTTCTATTTTTTTTAAATTCGAAAATATTGATATTTAAAAAAAATATTGATACTTTG
CAAC
Found at i:1951725 original size:7 final size:7
Alignment explanation
Indices: 1951713--1951743 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1951703 GTCAAAGAAA
1951713 GTCAACG
1 GTCAACG
*
1951720 GTCAACA
1 GTCAACG
1951727 GTCAACG
1 GTCAACG
1951734 GTCAACG
1 GTCAACG
1951741 GTC
1 GTC
1951744 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1951761 original size:22 final size:22
Alignment explanation
Indices: 1951733--1951775 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1951723 AACAGTCAAC
1951733 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1951755 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1951776 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1951790 original size:9 final size:9
Alignment explanation
Indices: 1951772--1951841 Score: 68
Period size: 10 Copynumber: 7.3 Consensus size: 9
1951762 GGTCGGGTCG
*
1951772 GGTCAGACC
1 GGTCAAACC
1951781 GGTCAAACC
1 GGTCAAACC
*
1951790 GGTTCAGACC
1 GG-TCAAACC
1951800 GGTCAAACC
1 GGTCAAACC
*
1951809 GGTTCGAACC
1 GG-TCAAACC
*
1951819 GGTTGAAACC
1 GG-TCAAACC
1951829 GGTCAGAACC
1 GGTCA-AACC
1951839 GGT
1 GGT
1951842 TGAAAAACGG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 20 0.39
10 31 0.61
ACGTcount: A:0.26, C:0.29, G:0.30, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1951796 original size:19 final size:20
Alignment explanation
Indices: 1951774--1951841 Score: 90
Period size: 19 Copynumber: 3.5 Consensus size: 20
1951764 TCGGGTCGGG
1951774 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
1951793 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
*
1951812 TC-GAACCGGTTGAAACCGG-
1 TCAGAACCGG-TCAAACCGGT
1951831 TCAGAACCGGT
1 TCAGAACCGGT
1951842 TGAAAAACGG
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
18 1 0.02
19 29 0.64
20 15 0.33
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.16
Consensus pattern (20 bp):
TCAGAACCGGTCAAACCGGT
Found at i:1951829 original size:20 final size:20
Alignment explanation
Indices: 1951785--1951846 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
1951775 CAGACCGGTC
*
1951785 AAACCGGTTC-AGACCGG-TC
1 AAACCGGTTCGA-ACCGGTTG
1951804 AAACCGGTTCGAACCGGTTG
1 AAACCGGTTCGAACCGGTTG
1951824 AAACCGG-TCAGAACCGGTTG
1 AAACCGGTTC-GAACCGGTTG
1951844 AAA
1 AAA
1951847 AACGGTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 17 0.44
20 22 0.56
ACGTcount: A:0.31, C:0.26, G:0.27, T:0.16
Consensus pattern (20 bp):
AAACCGGTTCGAACCGGTTG
Found at i:1951858 original size:20 final size:20
Alignment explanation
Indices: 1951814--1951862 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1951804 AAACCGGTTC
*
1951814 GAACCGGTTGAAACCGGTCA
1 GAACCGGTTGAAAACGGTCA
*
1951834 GAACCGGTTGAAAAACGGTTA
1 GAACCGGTTG-AAAACGGTCA
1951855 -AACCGGTT
1 GAACCGGTT
1951863 TCCAGCAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (20 bp):
GAACCGGTTGAAAACGGTCA
Found at i:1959059 original size:22 final size:22
Alignment explanation
Indices: 1959034--1959076 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1959024 GAAAGTCAAC
1959034 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1959056 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1959077 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1959097 original size:19 final size:19
Alignment explanation
Indices: 1959075--1959172 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
1959065 TCGGGTCGGG
*
1959075 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
1959094 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
1959113 TC-GAACCGGTTAAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
1959132 TCAAACCGGTCAGAACCGGTT
1 TCAGACCGGTCA-AACCGG-T
* *
1959153 TAAAACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1959172 T
1 T
1959173 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.04
19 40 0.59
20 14 0.21
21 11 0.16
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1959121 original size:10 final size:10
Alignment explanation
Indices: 1959079--1959172 Score: 90
Period size: 9 Copynumber: 9.7 Consensus size: 10
1959069 GTCGGGTCAG
1959079 ACCGG-TCAA
1 ACCGGTTCAA
* *
1959088 ACTGGTTCAG
1 ACCGGTTCAA
1959098 ACCGG-TCAA
1 ACCGGTTCAA
*
1959107 ACCGGTTCGA
1 ACCGGTTCAA
*
1959117 ACCGGTTAAA
1 ACCGGTTCAA
1959127 ACCGG-TCAA
1 ACCGGTTCAA
1959136 ACCGG-TCAGA
1 ACCGGTTCA-A
*
1959146 ACCGGTTTAAA
1 ACCGG-TTCAA
1959157 ACCGG-TCAA
1 ACCGGTTCAA
1959166 ACCGGTT
1 ACCGGTT
1959173 TCCAGCAGCC
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
9 31 0.45
10 30 0.43
11 6 0.09
12 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:1959133 original size:29 final size:31
Alignment explanation
Indices: 1959098--1959172 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
1959088 ACTGGTTCAG
1959098 ACCGGTCAAACCGGTTC-GAACCGG-TTAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTTAAA
1959127 ACCGGTCAAACCGG-TCAGAACCGGTTTAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTTAAA
1959157 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
1959173 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 21 0.49
30 19 0.44
31 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTTAAA
Found at i:1962458 original size:17 final size:17
Alignment explanation
Indices: 1962436--1962476 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
1962426 TCTTGTCTTC
1962436 TCTTCTTCGTCTATTTT
1 TCTTCTTCGTCTATTTT
1962453 TCTTCTTCGTCTATTTT
1 TCTTCTTCGTCTATTTT
1962470 TCTTCTT
1 TCTTCTT
1962477 TATTTCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (17 bp):
TCTTCTTCGTCTATTTT
Found at i:1963047 original size:2 final size:2
Alignment explanation
Indices: 1963040--1963067 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1963030 CAAATACTTT
1963040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1963068 GTCCTGACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1968805 original size:35 final size:35
Alignment explanation
Indices: 1968763--1968831 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
1968753 GTGATGCTTA
1968763 TTTACACTATACAGCCGCAATATGGGTACACTATT
1 TTTACACTATACAGCCGCAATATGGGTACACTATT
**
1968798 TTTACACTATACAGTTGCAATATGGGTACACTAT
1 TTTACACTATACAGCCGCAATATGGGTACACTAT
1968832 CTCATATAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (35 bp):
TTTACACTATACAGCCGCAATATGGGTACACTATT
Found at i:1970584 original size:25 final size:26
Alignment explanation
Indices: 1970531--1970584 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1970521 AAATTCAAAT
1970531 AATTAAATAAAAACATTAACAAACAA
1 AATTAAATAAAAACATTAACAAACAA
* *
1970557 AATTAAATAAAGACATT-ACAAACTA
1 AATTAAATAAAAACATTAACAAACAA
1970582 AAT
1 AAT
1970585 AACTTTATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.65, C:0.11, G:0.02, T:0.22
Consensus pattern (26 bp):
AATTAAATAAAAACATTAACAAACAA
Found at i:1973421 original size:288 final size:287
Alignment explanation
Indices: 1972906--1973477 Score: 1045
Period size: 288 Copynumber: 2.0 Consensus size: 287
1972896 AAGCCTATAT
1972906 GTTAAGGATGCAAGTTGGTCAAATCTGCTTAGACATTATGTTCTAAACAGAAAGTTTAGAAAATC
1 GTTAAGGATGCAAGTTGGTCAAATCTGCTTAGACATTATGTTCTAAACAGAAAGTTTAGAAAATC
*
1972971 ACCAGAAATTCTAAAAAATAATTGAAGAATGAATCTTATATCATTGGATTCATATATCGGTCTAG
66 ACCAGAAATTCTAAAAAATAATTGAAGAATGAATCTTATATCATTGGATTCATATATCGGTATAG
*
1973036 TTTCATTTAGAACTAACAGAAACTGATTTCGATAGGTATACAAAAAGATATGAATTTTTAATATG
131 TTTCATTTAGAACTAACAAAAACTGATTTCGATAGGTATACAAAAAGATATGAATTTTTAATATG
* * *
1973101 TGATAGGTCATAAAACAGGGCAGTAGATTATGCCTGAAACAGCTTCTTTCAGTTAACTTTGAAAA
196 TGATAGGTCAGAAAACAGGGCAGTAGATTATGCCTGAAAAAACTTCTTTCAGTTAACTTTGAAAA
1973166 TTCACTATAAATTGTACAAGTGGATAA
261 TTCACTATAAATTGTACAAGTGGATAA
* * *
1973193 GTTAAGGGTGCAAGTTGGTCAAATCTTCTTAGACATTATGTTCTCAACAGAAAGTTTAGAAAATC
1 GTTAAGGATGCAAGTTGGTCAAATCTGCTTAGACATTATGTTCTAAACAGAAAGTTTAGAAAATC
1973258 ACCAGAAATTCTAAAAAAATAATTGAAGAATGAATCTTATATCATTGGATTCATATATCGGTATA
66 ACCAGAAATTCT-AAAAAATAATTGAAGAATGAATCTTATATCATTGGATTCATATATCGGTATA
*
1973323 GTTTTATTTAGAACTAACAAAAACTGATTTCGATAGGTATACAAAAAGATATGAATTTTTAATAT
130 GTTTCATTTAGAACTAACAAAAACTGATTTCGATAGGTATACAAAAAGATATGAATTTTTAATAT
1973388 GTGATAGGTCAGAAAACAGGGCAGTAGATTATGCCTGAAAAAACTTCTTTCAGTTAACTTTGAAA
195 GTGATAGGTCAGAAAACAGGGCAGTAGATTATGCCTGAAAAAACTTCTTTCAGTTAACTTTGAAA
*
1973453 ATTCGCTATAAATTGTACAAGTGGA
260 ATTCACTATAAATTGTACAAGTGGA
1973478 ACTAGACAGA
Statistics
Matches: 274, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
287 74 0.27
288 200 0.73
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (287 bp):
GTTAAGGATGCAAGTTGGTCAAATCTGCTTAGACATTATGTTCTAAACAGAAAGTTTAGAAAATC
ACCAGAAATTCTAAAAAATAATTGAAGAATGAATCTTATATCATTGGATTCATATATCGGTATAG
TTTCATTTAGAACTAACAAAAACTGATTTCGATAGGTATACAAAAAGATATGAATTTTTAATATG
TGATAGGTCAGAAAACAGGGCAGTAGATTATGCCTGAAAAAACTTCTTTCAGTTAACTTTGAAAA
TTCACTATAAATTGTACAAGTGGATAA
Found at i:1979808 original size:29 final size:29
Alignment explanation
Indices: 1979737--1979808 Score: 67
Period size: 29 Copynumber: 2.4 Consensus size: 29
1979727 ACTGCAAAAA
1979737 ATAATAAAAAATTAGTACAATAAAATTGAAT
1 ATAAT-AAAAATTAGTACAAT-AAATTGAAT
* *
1979768 AAAATAATAAATTATTA-AAT-AATTCGAAT
1 ATAATAA-AAATTAGTACAATAAATT-GAAT
1979797 ATAATAGAAAAT
1 ATAATA-AAAAT
1979809 ATTTTATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
28 4 0.11
29 13 0.37
30 6 0.17
31 12 0.34
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (29 bp):
ATAATAAAAATTAGTACAATAAATTGAAT
Found at i:1980398 original size:3 final size:3
Alignment explanation
Indices: 1980390--1980459 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
1980380 CTTTCATATA
* *
1980390 TAT TAT TAT TAT TAT TAT CAT TAT CAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1980438 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
1980460 GCACTTCCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1995197 original size:2 final size:2
Alignment explanation
Indices: 1995190--1995219 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1995180 AGTTAAAATA
1995190 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
1995220 GTATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1997971 original size:3 final size:3
Alignment explanation
Indices: 1997963--1997992 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1997953 TTGATCCCGA
1997963 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1997993 TGTTTAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1998798 original size:21 final size:20
Alignment explanation
Indices: 1998760--1998798 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1998750 AGTTTATCAG
**
1998760 TTTATTTAAAATTGACTTTT
1 TTTATTTAAAATACACTTTT
1998780 TTTATTATAAAATACACTT
1 TTTATT-TAAAATACACTT
1998799 AAAAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTATTTAAAATACACTTTT
Found at i:1998854 original size:16 final size:16
Alignment explanation
Indices: 1998815--1998855 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1998805 ATTTGTATTT
*
1998815 ATTA-TTTTATTTATA
1 ATTATTTTTATTAATA
*
1998830 A-TATATTTATTAATA
1 ATTATTTTTATTAATA
1998845 ATTATTTTTAT
1 ATTATTTTTAT
1998856 CAATTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTATTTTTATTAATA
Found at i:2011970 original size:90 final size:89
Alignment explanation
Indices: 2011825--2011990 Score: 278
Period size: 90 Copynumber: 1.9 Consensus size: 89
2011815 CTTTTATAGC
* * * *
2011825 CAAGTTACCCGAATCATATTAGAGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1 CAAGTTACACAAATCATATTAGAATTTTATTATTTCAAATTAATTAAATCTATATTTAATCAATT
*
2011890 GAAATTTAATAATCCTCTTATATT
66 GAAATTAAATAATCCTCTTATATT
2011914 CAAGTTACACAAATCATATTAGGAATTTTATTATTTCAAATTAATTAAATCTATATTTAATCAAT
1 CAAGTTACACAAATCATATTA-GAATTTTATTATTTCAAATTAATTAAATCTATATTTAATCAAT
2011979 TGAAATTAAATA
65 TGAAATTAAATA
2011991 TTCGGGATTA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
89 19 0.27
90 52 0.73
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (89 bp):
CAAGTTACACAAATCATATTAGAATTTTATTATTTCAAATTAATTAAATCTATATTTAATCAATT
GAAATTAAATAATCCTCTTATATT
Found at i:2013814 original size:10 final size:11
Alignment explanation
Indices: 2013787--2013811 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2013777 AAATCTCCGT
2013787 TTTTAATGATG
1 TTTTAATGATG
2013798 TTTTAATGATG
1 TTTTAATGATG
2013809 TTT
1 TTT
2013812 AATTTAATTT
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTAATGATG
Found at i:2022426 original size:20 final size:20
Alignment explanation
Indices: 2022401--2022438 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2022391 TTCCCATTGA
**
2022401 AGTACATCGGTGCATTCTAC
1 AGTACATCAATGCATTCTAC
2022421 AGTACATCAATGCATTCT
1 AGTACATCAATGCATTCT
2022439 TTAACAGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (20 bp):
AGTACATCAATGCATTCTAC
Found at i:2025410 original size:30 final size:30
Alignment explanation
Indices: 2025350--2025417 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
2025340 TATATAGATA
*
2025350 AATTCAAATCATCCAAAAACAATATCAAAC
1 AATTCAAATCATCCAAAAACAATATAAAAC
*
2025380 AATTCAAA-CATCCAACAACCAA-AGTAAAAC
1 AATTCAAATCATCCAA-AAACAATA-TAAAAC
*
2025410 AATCCAAA
1 AATTCAAA
2025418 AGCATTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.57, C:0.25, G:0.01, T:0.16
Consensus pattern (30 bp):
AATTCAAATCATCCAAAAACAATATAAAAC
Found at i:2028892 original size:83 final size:83
Alignment explanation
Indices: 2028726--2028888 Score: 319
Period size: 83 Copynumber: 2.0 Consensus size: 83
2028716 GCTCATCTCG
2028726 AATTCACTTTGCATTAGCTTAGAAAATTATTGGCAAAGAACATCATTAGTAGAACCAAATATTAT
1 AATTCACTTTGCATTAGCTTAGAAAATTATTGGCAAAGAACATCATTAGTAGAACCAAATATTAT
2028791 ATCATCAACATAAATTGA
66 ATCATCAACATAAATTGA
2028809 AATTCACTTTGCATTAGCTTAGAAAATTATTGGCAAAGAACATCATTAGTAGAACCAAATA-TAT
1 AATTCACTTTGCATTAGCTTAGAAAATTATTGGCAAAGAACATCATTAGTAGAACCAAATATTAT
2028873 ATCATCAACATAAATT
66 ATCATCAACATAAATT
2028889 TGAACTACTA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 19 0.24
83 61 0.76
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (83 bp):
AATTCACTTTGCATTAGCTTAGAAAATTATTGGCAAAGAACATCATTAGTAGAACCAAATATTAT
ATCATCAACATAAATTGA
Found at i:2040637 original size:34 final size:32
Alignment explanation
Indices: 2040584--2040653 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
2040574 CCTTGCAAAC
*
2040584 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTTACGGGCTAAACTAGAACATT
*
2040616 TCCCTAGCTTTTATACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTT-TACGGGCTAAACTAGAACATT
2040650 TCCC
1 TCCC
2040654 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 23 0.68
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGCTAAACTAGAACATT
Found at i:2041011 original size:21 final size:21
Alignment explanation
Indices: 2040986--2041028 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2040976 CCGTATGACA
*
2040986 GGGGGAAT-TGGTACCCCTTGG
1 GGGGGAATCT-GTACCCCCTGG
2041007 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
2041028 G
1 G
2041029 CAATCTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.14, C:0.23, G:0.42, T:0.21
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:2043079 original size:34 final size:34
Alignment explanation
Indices: 2043039--2043128 Score: 162
Period size: 34 Copynumber: 2.6 Consensus size: 34
2043029 TAGTTTTTTG
2043039 GGGCTAAACTAGAACCTTTCCCTAGCTTTTACAC
1 GGGCTAAACTAGAACCTTTCCCTAGCTTTTACAC
2043073 GGGCTAAACTAGAACCTTTCCCTAGCTTTTACAC
1 GGGCTAAACTAGAACCTTTCCCTAGCTTTTACAC
* *
2043107 GGGCTAAGCTAGAACATTTCCC
1 GGGCTAAACTAGAACCTTTCCC
2043129 CTTTACAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (34 bp):
GGGCTAAACTAGAACCTTTCCCTAGCTTTTACAC
Found at i:2043499 original size:21 final size:21
Alignment explanation
Indices: 2043474--2043580 Score: 144
Period size: 22 Copynumber: 5.0 Consensus size: 21
2043464 CCGTTAGACA
*
2043474 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
*
2043495 GGGGGAATCTGTTCCCCCT-G
1 GGGGGAATCTGTACCCCCTGG
*
2043515 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
* *
2043536 GAGGGGAATCTATACCCTCTGG
1 G-GGGGAATCTGTACCCCCTGG
2043558 GGTGGGAATCTGTACCCCCTGG
1 GG-GGGAATCTGTACCCCCTGG
2043580 G
1 G
2043581 TAATCTGATT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.24
21 20 0.27
22 36 0.49
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:2043521 original size:41 final size:43
Alignment explanation
Indices: 2043474--2043580 Score: 155
Period size: 41 Copynumber: 2.5 Consensus size: 43
2043464 CCGTTAGACA
* *
2043474 GGGGGAATCGGTACCCCCTGGG-GGGGAATCTGTTCCCCCT-G
1 GGGGGAATCGGTACCCCCTGGGAGGGGAATCTATACCCCCTGG
*
2043515 GGGGGAATCGGTACCCCCTGGGAGGGGAATCTATACCCTCTGG
1 GGGGGAATCGGTACCCCCTGGGAGGGGAATCTATACCCCCTGG
*
2043558 GGTGGGAATCTGTACCCCCTGGG
1 GG-GGGAATCGGTACCCCCTGGG
2043581 TAATCTGATT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
41 22 0.37
42 15 0.25
43 3 0.05
44 19 0.32
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.20
Consensus pattern (43 bp):
GGGGGAATCGGTACCCCCTGGGAGGGGAATCTATACCCCCTGG
Found at i:2044447 original size:18 final size:18
Alignment explanation
Indices: 2044424--2044460 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2044414 CATTATTCAC
*
2044424 CTTTCGTAATGTTTCATT
1 CTTTCGTAAAGTTTCATT
2044442 CTTTCGTAAAGTTTCATT
1 CTTTCGTAAAGTTTCATT
2044460 C
1 C
2044461 AGATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (18 bp):
CTTTCGTAAAGTTTCATT
Found at i:2046270 original size:3 final size:3
Alignment explanation
Indices: 2046262--2046291 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2046252 ATTGTTTTAA
2046262 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2046292 TAAATTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2053909 original size:80 final size:80
Alignment explanation
Indices: 2053811--2054038 Score: 384
Period size: 80 Copynumber: 2.9 Consensus size: 80
2053801 TAGTGGCATA
*
2053811 TATGTTCAGAAACAAAGGTCCCCTGTGCATTTCACTTTGATGATGTTTGAATAGGTGAATGCAAC
1 TATGTTCAGAAACAAAGGTCCCCTGTGCATTTCACTTTGATGATGTTTGAATTGGTGAATGCAAC
2053876 AAGCCAACAAGTCCT
66 AAGCCAACAAGTCCT
*
2053891 TATGTTCAGAAACTAAGGTCCCCTGTGCATTTCACTTTGATGATGTTTGAATTGGTGAATGCAAC
1 TATGTTCAGAAACAAAGGTCCCCTGTGCATTTCACTTTGATGATGTTTGAATTGGTGAATGCAAC
*
2053956 AAGCTAACAAGTCCT
66 AAGCCAACAAGTCCT
* * * * *
2053971 TGTCTTCAGAAACAAAGGTCCCCTGTGCATTCCATTTTGATGATATTTGAATTGGTGAATGCAAC
1 TATGTTCAGAAACAAAGGTCCCCTGTGCATTTCACTTTGATGATGTTTGAATTGGTGAATGCAAC
2054036 AAG
66 AAG
2054039 TCCTTAATTG
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 139 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (80 bp):
TATGTTCAGAAACAAAGGTCCCCTGTGCATTTCACTTTGATGATGTTTGAATTGGTGAATGCAAC
AAGCCAACAAGTCCT
Found at i:2054478 original size:29 final size:29
Alignment explanation
Indices: 2054436--2054494 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2054426 TAATTTTGCA
*
2054436 ATATCAGAAGAACTGTAGCAGAACAATAC
1 ATATCAGAAGAACTATAGCAGAACAATAC
*
2054465 ATATCAGAAGAACTATAGTAGAACAATAC
1 ATATCAGAAGAACTATAGCAGAACAATAC
2054494 A
1 A
2054495 AACTCTAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (29 bp):
ATATCAGAAGAACTATAGCAGAACAATAC
Found at i:2055715 original size:22 final size:22
Alignment explanation
Indices: 2055685--2055731 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2055675 CTACGGCGAC
* *
2055685 ATCTGTCCCCATCTCCGACAAA
1 ATCTATCCCCATCTCCAACAAA
*
2055707 ATCTATCCCCATCTCCAACGAA
1 ATCTATCCCCATCTCCAACAAA
2055729 ATC
1 ATC
2055732 CGTCTATCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.40, G:0.06, T:0.23
Consensus pattern (22 bp):
ATCTATCCCCATCTCCAACAAA
Found at i:2056120 original size:19 final size:19
Alignment explanation
Indices: 2056098--2056176 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 19
2056088 AAATCGCAAC
2056098 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
2056117 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
2056136 GTGATTTTC---T--CGTT
1 GCGATTTTCATTTCGCGTT
* *
2056150 GCAATTTTCATTTCGTGTT
1 GCGATTTTCATTTCGCGTT
2056169 GCGATTTT
1 GCGATTTT
2056177 AAGTTTCAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.22
16 1 0.02
17 1 0.02
19 35 0.71
20 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:2056157 original size:33 final size:33
Alignment explanation
Indices: 2056108--2056176 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
2056098 GCGATTTTAG
* *
2056108 TTTCGCGTTGCGATTTTCATTTCGCGTTGTGAT
1 TTTCGCGTTGCAATTTTCATTTCGCGTTGCGAT
* *
2056141 TTTCTCGTTGCAATTTTCATTTCGTGTTGCGAT
1 TTTCGCGTTGCAATTTTCATTTCGCGTTGCGAT
2056174 TTT
1 TTT
2056177 AAGTTTCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.52
Consensus pattern (33 bp):
TTTCGCGTTGCAATTTTCATTTCGCGTTGCGAT
Found at i:2057880 original size:21 final size:21
Alignment explanation
Indices: 2057830--2057882 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2057820 GTTAGAGGAG
*
2057830 TTACGTGATGAGGTCAATGAT
1 TTACGTGAAGAGGTCAATGAT
* * *
2057851 TTGCATGAAGAGGTCAGT-ACT
1 TTACGTGAAGAGGTCAATGA-T
2057872 TTACGTGAAGA
1 TTACGTGAAGA
2057883 CAATGATGCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.30
Consensus pattern (21 bp):
TTACGTGAAGAGGTCAATGAT
Found at i:2058005 original size:21 final size:21
Alignment explanation
Indices: 2057957--2058005 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2057947 AATGATGCTT
* * * *
2057957 TACGTGGTGAGGTATCTACTT
1 TACGTGATGAGGTAGCCACTC
*
2057978 TATGTGATGAGGTAGCCACTC
1 TACGTGATGAGGTAGCCACTC
2057999 TACGTGA
1 TACGTGA
2058006 GATTGTTTCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (21 bp):
TACGTGATGAGGTAGCCACTC
Found at i:2058313 original size:21 final size:21
Alignment explanation
Indices: 2058287--2058391 Score: 93
Period size: 21 Copynumber: 5.0 Consensus size: 21
2058277 GATTCACCTG
*
2058287 TTATCGTTCAAGAGGCCTCTC
1 TTATCGTTCAAGAGGCCCCTC
* * *
2058308 TTATCGTTCAAAAGGCCCTTA
1 TTATCGTTCAAGAGGCCCCTC
* *
2058329 TCATCTTTCAAGAGGCCCCTC
1 TTATCGTTCAAGAGGCCCCTC
** * *
2058350 CCACCGTTCAAGAGGCCCCTG
1 TTATCGTTCAAGAGGCCCCTC
* * *
2058371 TCATCGTTCAAGGGGTCCCTC
1 TTATCGTTCAAGAGGCCCCTC
2058392 CCACCGTTCG
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.20, C:0.33, G:0.19, T:0.28
Consensus pattern (21 bp):
TTATCGTTCAAGAGGCCCCTC
Found at i:2058339 original size:42 final size:42
Alignment explanation
Indices: 2058289--2058400 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 42
2058279 TTCACCTGTT
* ** * *
2058289 ATCGTTCAAGAGGCCTCTCTTATCGTTCAAAAGGCCCTTATC
1 ATCGTTCAAGAGGCCCCTCCCACCGTTCAAAAGGCCCCTATC
* * *
2058331 ATCTTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTGTC
1 ATCGTTCAAGAGGCCCCTCCCACCGTTCAAAAGGCCCCTATC
* *
2058373 ATCGTTCAAGGGGTCCCTCCCACCGTTC
1 ATCGTTCAAGAGGCCCCTCCCACCGTTC
2058401 GAGAGCCCGA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.26
Consensus pattern (42 bp):
ATCGTTCAAGAGGCCCCTCCCACCGTTCAAAAGGCCCCTATC
Found at i:2058399 original size:21 final size:21
Alignment explanation
Indices: 2058335--2058405 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
2058325 CTTATCATCT
2058335 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
** *
2058356 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCCCACCG
* *
2058377 TTCAAGGGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
*
2058398 TTCGAGAG
1 TTCAAGAG
2058406 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.20
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:2059829 original size:14 final size:14
Alignment explanation
Indices: 2059810--2059846 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2059800 GCTTGTTTAA
2059810 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
2059824 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
2059838 TTGATTTGT
1 TTGATTTGT
2059847 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2059838 original size:78 final size:78
Alignment explanation
Indices: 2059749--2059910 Score: 270
Period size: 78 Copynumber: 2.1 Consensus size: 78
2059739 AAATTGATGT
*
2059749 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGA
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAATTGA
2059814 TTTGTAAAAGTTG
66 TTTGTAAAAGTTG
* * ***
2059827 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTACTTGTTTAATTGA
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAATTGA
2059892 TTTGTAAAAGTTG
66 TTTGTAAAAGTTG
2059905 ATTTGT
1 ATTTGT
2059911 TGTTTTAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (78 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAATTGA
TTTGTAAAAGTTG
Found at i:2059999 original size:20 final size:20
Alignment explanation
Indices: 2059974--2060012 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2059964 CACACTTTTG
2059974 CAACGCGAAAATCAAATTCA
1 CAACGCGAAAATCAAATTCA
*
2059994 CAACGCGAAAGTCAAATTC
1 CAACGCGAAAATCAAATTC
2060013 GTGTTGCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAATCAAATTCA
Found at i:2060053 original size:49 final size:49
Alignment explanation
Indices: 2059978--2060071 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
2059968 CTTTTGCAAC
*
2059978 GCGAAAATCAAATTCACAACGCGAAAGTCAAATTCGTGTTGCGATGGTT
1 GCGAAAATCAAATTCACAACGCGAAAGTCAAATTCGCGTTGCGATGGTT
* * *
2060027 GCGAAAGTCAAATTCGCAACGTGAAAGTCAAATTCGCGTTGCGAT
1 GCGAAAATCAAATTCACAACGCGAAAGTCAAATTCGCGTTGCGAT
2060072 AGTCAAATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (49 bp):
GCGAAAATCAAATTCACAACGCGAAAGTCAAATTCGCGTTGCGATGGTT
Found at i:2060054 original size:20 final size:20
Alignment explanation
Indices: 2060029--2060122 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 20
2060019 CGATGGTTGC
2060029 GAAAGTCAAATTCGCAACGT
1 GAAAGTCAAATTCGCAACGT
*** *
2060049 GAAAGTCAAATTCGCGTTGC
1 GAAAGTCAAATTCGCAACGT
* *
2060069 GATAGTCAAATTCGCAAAGCT
1 GAAAGTCAAATTCGCAACG-T
* *
2060090 -CAAGT-AAATTCGCAACAT
1 GAAAGTCAAATTCGCAACGT
2060108 GAAAGTCAAATTCGC
1 GAAAGTCAAATTCGC
2060123 GTTGCGATTT
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
18 1 0.02
19 14 0.25
20 42 0.74
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGT
Found at i:2062134 original size:18 final size:18
Alignment explanation
Indices: 2062111--2062147 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2062101 CGAAATTTAT
2062111 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2062129 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2062147 A
1 A
2062148 CTCCAATCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2062554 original size:25 final size:25
Alignment explanation
Indices: 2062526--2062575 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2062516 CATTATTTTC
*
2062526 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2062551 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2062576 TAATTGATTT
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:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2062746 original size:29 final size:29
Alignment explanation
Indices: 2062704--2062762 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
2062694 GCGATTTTCT
* * *
2062704 CGTTGTGATTGTTGTGATAGTCAAATTCG
1 CGTTGCGATTGTTGCGAAAGTCAAATTCG
2062733 CGTTGCGATTGTTGCGAAAGTCAAATTCG
1 CGTTGCGATTGTTGCGAAAGTCAAATTCG
2062762 C
1 C
2062763 AAACACTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (29 bp):
CGTTGCGATTGTTGCGAAAGTCAAATTCG
Found at i:2070031 original size:22 final size:22
Alignment explanation
Indices: 2070003--2070073 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
2069993 GAAAGTCAAC
* *
2070003 GGTCAACAGTCGTGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
* *
2070025 GGTCAACGGTTGGGTCGGGTTG
1 GGTCAACGGTCGGGTCGGGTCG
*
2070047 GGTCAACGGTCGGGTCGGG-CC
1 GGTCAACGGTCGGGTCGGGTCG
2070068 GGTCAA
1 GGTCAA
2070074 ACCGGTTCAG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 6 0.14
22 36 0.86
ACGTcount: A:0.13, C:0.21, G:0.45, T:0.21
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:2070106 original size:10 final size:10
Alignment explanation
Indices: 2070074--2070125 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
2070064 GGCCGGTCAA
2070074 ACCGGTTCAG
1 ACCGGTTCAG
* *
2070084 ACC-GATCAA
1 ACCGGTTCAG
2070093 ACCGGTTCAG
1 ACCGGTTCAG
* *
2070103 ACC-GATCAA
1 ACCGGTTCAG
2070112 ACCGGTTCAG
1 ACCGGTTCAG
2070122 ACCG
1 ACCG
2070126 ATCAAATCGG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
9 14 0.44
10 18 0.56
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (10 bp):
ACCGGTTCAG
Found at i:2070144 original size:19 final size:19
Alignment explanation
Indices: 2070070--2070138 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
2070060 GTCGGGCCGG
2070070 TCAAACCGGTTCAGACCGA
1 TCAAACCGGTTCAGACCGA
2070089 TCAAACCGGTTCAGACCGA
1 TCAAACCGGTTCAGACCGA
2070108 TCAAACCGGTTCAGACCGA
1 TCAAACCGGTTCAGACCGA
*
2070127 TCAAATCGGTTC
1 TCAAACCGGTTC
2070139 GAACCGGTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (19 bp):
TCAAACCGGTTCAGACCGA
Found at i:2077294 original size:17 final size:17
Alignment explanation
Indices: 2077272--2077310 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2077262 AACGATCAAC
2077272 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2077289 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2077306 GGTCA
1 GGTCA
2077311 GACCGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2077324 original size:9 final size:9
Alignment explanation
Indices: 2077306--2077335 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2077296 GGTCGGGTCG
*
2077306 GGTCAGACC
1 GGTCAAACC
2077315 GGTCAAACC
1 GGTCAAACC
2077324 GGTCAAACC
1 GGTCAAACC
2077333 GGT
1 GGT
2077336 TTCCAGCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2083619 original size:20 final size:20
Alignment explanation
Indices: 2083594--2083633 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2083584 TAAAGAAAAT
*
2083594 CAGTAAGATCATAAATAATC
1 CAGTAAAATCATAAATAATC
2083614 CAGTAAAATCATAAATAATC
1 CAGTAAAATCATAAATAATC
2083634 GTCATACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (20 bp):
CAGTAAAATCATAAATAATC
Found at i:2083975 original size:19 final size:19
Alignment explanation
Indices: 2083953--2083990 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2083943 TAAAAAATAG
2083953 AAAAATATTA-AATTACAAT
1 AAAAAT-TTACAATTACAAT
*
2083972 AAAAATTTACCATTACAAT
1 AAAAATTTACAATTACAAT
2083991 CAACTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTTACAATTACAAT
Found at i:2084052 original size:147 final size:150
Alignment explanation
Indices: 2083871--2084169 Score: 568
Period size: 147 Copynumber: 2.0 Consensus size: 150
2083861 GTAGCTAGAG
2083871 AAAAATAGAGGAAAACCTAAAAATGATTCAAAAGTTAAAAACTGAGATTTTTTTTGAGAAGATAA
1 AAAAATAGAGGAAAACCTAAAAATGATTCAAAAGTTAAAAACTGAGATTTTTTTTGAGAAGATAA
2083936 AAGATTTTAAAAAATAGAAAAATATTAAATTACAATAAAAATTTACCATTAC-A-ATCAACTAAA
66 AAGATTTTAAAAAATAGAAAAATATTAAATTACAATAAAAATTTACCATTACAACATCAACTAAA
2083999 CACATAATAAAGATATTTCT
131 CACATAATAAAGATATTTCT
2084019 AAAAATA-AGGAAAACCTAAAAATGATTCAAAAGTTAAAAACTGAGATTTTTTTTGAGAAGATAA
1 AAAAATAGAGGAAAACCTAAAAATGATTCAAAAGTTAAAAACTGAGATTTTTTTTGAGAAGATAA
2084083 AAGATTTTAAAAAATAGAAAAATATTAAATTACAATAAAAATTTACCATTACAATCATCAACTAA
66 AAGATTTTAAAAAATAGAAAAATATTAAATTACAATAAAAATTTACCATTACAA-CATCAACTAA
2084148 ACACATAATAAAGATATTTCT
130 ACACATAATAAAGATATTTCT
2084169 A
1 A
2084170 TATAATCATT
Statistics
Matches: 148, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
147 109 0.74
148 8 0.05
150 31 0.21
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.28
Consensus pattern (150 bp):
AAAAATAGAGGAAAACCTAAAAATGATTCAAAAGTTAAAAACTGAGATTTTTTTTGAGAAGATAA
AAGATTTTAAAAAATAGAAAAATATTAAATTACAATAAAAATTTACCATTACAACATCAACTAAA
CACATAATAAAGATATTTCT
Found at i:2084122 original size:19 final size:19
Alignment explanation
Indices: 2084100--2084137 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2084090 TAAAAAATAG
2084100 AAAAATATTA-AATTACAAT
1 AAAAAT-TTACAATTACAAT
*
2084119 AAAAATTTACCATTACAAT
1 AAAAATTTACAATTACAAT
2084138 CATCAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTTACAATTACAAT
Found at i:2085342 original size:15 final size:14
Alignment explanation
Indices: 2085324--2085369 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
2085314 TTTTAAGACT
2085324 TATTTTTTTATAAAA
1 TATTTTTTT-TAAAA
*
2085339 TATTTATTTT-AAA
1 TATTTTTTTTAAAA
2085352 TATTATTTTTTAAAA
1 TATT-TTTTTTAAAA
2085367 TAT
1 TAT
2085370 AAATAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.26
14 6 0.22
15 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTTTTTTAAAA
Found at i:2093842 original size:10 final size:9
Alignment explanation
Indices: 2093799--2093841 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
2093789 AATCATAAGA
*
2093799 TAAAAAATA
1 TAAAAAATT
*
2093808 TATAAAATT
1 TAAAAAATT
* *
2093817 CAGAAAATT
1 TAAAAAATT
2093826 TAAAAAATT
1 TAAAAAATT
2093835 TAAAAAA
1 TAAAAAA
2093842 AAACATAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (9 bp):
TAAAAAATT
Found at i:2094190 original size:178 final size:175
Alignment explanation
Indices: 2093860--2094203 Score: 575
Period size: 178 Copynumber: 1.9 Consensus size: 175
2093850 TTCATATATA
2093860 TATTTTTGAATAACTATGTTTAATTTATTTCTAAAAGTTCATAAAAAAAATTAAAATGAAATCAC
1 TATTTTTGAATAACTATGTTTAATTTATTTCTAAAAGTTCAT-AAAAAAATTAAAATGAAATCAC
*
2093925 ATGAGAAAAAAATCTAAAAAAAAAACCATGTTCTTTTTAATTAAAATATTTTTATTTTTTAATAT
65 ATGAGAAAAAAATCT-AAAAAAAAACCATGTTCTTTTTAATTAAAATATTTTTATTTTTAAATAT
*
2093990 TTTATGTTTGGGTTTGGATTTTTTATTTTAAAGTTTCAAAAATATTT
129 TTTATGTTTGGATTTGGATTTTTTATTTTAAAGTTTCAAAAATATTT
2094037 TATTTTTGAATAACTATGTTTAATTTATTTCTAAAAGTTCAT-AAAAAATTAAAATGAAATCACA
1 TATTTTTGAATAACTATGTTTAATTTATTTCTAAAAGTTCATAAAAAAATTAAAATGAAATCACA
*
2094101 TGAGAAATAAAAAAAATCT-AAACAAAACCATGTTCTTTTTAATTAAAATATTTTTATTTTTAAA
66 TGAG-----AAAAAAATCTAAAAAAAAACCATGTTCTTTTTAATTAAAATATTTTTATTTTTAAA
*
2094165 TATTTTATGTTTGGATTTTGATTTTTTATTTTAAAGTTT
126 TATTTTATGTTTGGATTTGGATTTTTTATTTTAAAGTTT
2094204 TCGAATACCC
Statistics
Matches: 158, Mismatches: 4, Indels: 9
0.92 0.02 0.05
Matches are distributed among these distances:
175 26 0.16
177 42 0.27
178 80 0.51
180 10 0.06
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.46
Consensus pattern (175 bp):
TATTTTTGAATAACTATGTTTAATTTATTTCTAAAAGTTCATAAAAAAATTAAAATGAAATCACA
TGAGAAAAAAATCTAAAAAAAAACCATGTTCTTTTTAATTAAAATATTTTTATTTTTAAATATTT
TATGTTTGGATTTGGATTTTTTATTTTAAAGTTTCAAAAATATTT
Found at i:2094798 original size:15 final size:16
Alignment explanation
Indices: 2094774--2094805 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2094764 AAACGCAGAG
2094774 TTATTAAAAATATTTT
1 TTATTAAAAATATTTT
2094790 TTATT-AAAATATTTT
1 TTATTAAAAATATTTT
2094805 T
1 T
2094806 AATTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTAAAAATATTTT
Found at i:2094835 original size:15 final size:15
Alignment explanation
Indices: 2094797--2094841 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2094787 TTTTTATTAA
2094797 AATATTTTTAATTTTT
1 AATA-TTTTAATTTTT
*
2094813 AATTTTTTAATTTTT
1 AATATTTTAATTTTT
*
2094828 AGTATTTTATATTT
1 AATATTTTA-ATTT
2094842 ATATTTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
AATATTTTAATTTTT
Found at i:2096144 original size:246 final size:248
Alignment explanation
Indices: 2095705--2096203 Score: 975
Period size: 246 Copynumber: 2.0 Consensus size: 248
2095695 ATTTCATTAT
2095705 TTCATCATTCTCTTTATTTAAAAGAGAAAACCTAGATTGGATTTTTGTTGCACAAAAAAGGAAAA
1 TTCATCATTCTCTTTATTTAAAAGAGAAAACCTAGATTGGATTTTTGTTGCACAAAAAAGGAAAA
2095770 AGTTTGCAGATCTAAACCCGGGTTTGTACATATTCTGTTTCTATCTCGTTATTATCTCTCTCTTG
66 AGTTTGCAGATCTAAACCCGGGTTTGTACATATTCTGTTTCTATCTCGTTATTATCTCTCTCTTG
2095835 TGCTCATCATTTATTTTTGATGATTCGTGCTTATTTTAAGCTAAACATGAAATTGAAATTTCTCA
131 TGCTCATCATTTATTTTTGATGATTCGTGCTTATTTTAAGCTAAACATGAAATTGAAATTTCTCA
*
2095900 TGTCTGTTTTATTTTATTTTTTTAATTTTGAGGTTGTAACTTGTAAA-TAAGA
196 TGTCTGTTTTATTTTAATTTTTTAATTTTGAGGTTGTAACTTGTAAATTAAGA
2095952 TTCA-CATTCTCTTTATTTAAAAGAGAAAACCTAGATTGGATTTTTGTTGCACAAAAAAGGAAAA
1 TTCATCATTCTCTTTATTTAAAAGAGAAAACCTAGATTGGATTTTTGTTGCACAAAAAAGGAAAA
2096016 AGTTTGCAGATCTAAACCCGGGTTTGTACATATTCTGTTTCTATCTCGTTATTATCTCTCTCTTG
66 AGTTTGCAGATCTAAACCCGGGTTTGTACATATTCTGTTTCTATCTCGTTATTATCTCTCTCTTG
2096081 TGCTCATCATTTATTTTTGATGATTCGTGCTTATTTTAAGCTAAACATGAAATTGAAATTTCTCA
131 TGCTCATCATTTATTTTTGATGATTCGTGCTTATTTTAAGCTAAACATGAAATTGAAATTTCTCA
2096146 TGTCTGTTTTATTTTAATTTTTTAATTTTGAGGTTGTAACTTGTAAATTAAGA
196 TGTCTGTTTTATTTTAATTTTTTAATTTTGAGGTTGTAACTTGTAAATTAAGA
2096199 TTCAT
1 TTCAT
2096204 AATTTTATTC
Statistics
Matches: 249, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
246 236 0.95
247 13 0.05
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.44
Consensus pattern (248 bp):
TTCATCATTCTCTTTATTTAAAAGAGAAAACCTAGATTGGATTTTTGTTGCACAAAAAAGGAAAA
AGTTTGCAGATCTAAACCCGGGTTTGTACATATTCTGTTTCTATCTCGTTATTATCTCTCTCTTG
TGCTCATCATTTATTTTTGATGATTCGTGCTTATTTTAAGCTAAACATGAAATTGAAATTTCTCA
TGTCTGTTTTATTTTAATTTTTTAATTTTGAGGTTGTAACTTGTAAATTAAGA
Found at i:2102741 original size:33 final size:34
Alignment explanation
Indices: 2102704--2102767 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
2102694 TTTTATATTT
2102704 TTAATTTTGTAAAAAAAAT-TATAAATATTAGAA
1 TTAATTTTGTAAAAAAAATATATAAATATTAGAA
* *
2102737 TTAATTTTTTAAAGAAAATATATAAATATTA
1 TTAATTTTGTAAAAAAAATATATAAATATTA
2102768 TACAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (34 bp):
TTAATTTTGTAAAAAAAATATATAAATATTAGAA
Found at i:2102956 original size:20 final size:20
Alignment explanation
Indices: 2102920--2102957 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2102910 AATCTTATTC
**
2102920 CTGATAATCTTTTATTCCTA
1 CTGATAATCTTACATTCCTA
2102940 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
2102958 GTTAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (20 bp):
CTGATAATCTTACATTCCTA
Found at i:2117056 original size:11 final size:11
Alignment explanation
Indices: 2117040--2117069 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2117030 TAATATATAA
2117040 TATATAGTATG
1 TATATAGTATG
2117051 TATATAGTATG
1 TATATAGTATG
2117062 TATATAGT
1 TATATAGT
2117070 TTGTGTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (11 bp):
TATATAGTATG
Found at i:2118269 original size:12 final size:12
Alignment explanation
Indices: 2118254--2118293 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
2118244 ATTTGGTTTT
2118254 TTATATTTATTA
1 TTATATTTATTA
2118266 TTATA-TTATTA
1 TTATATTTATTA
2118277 TTATATTTATTA
1 TTATATTTATTA
2118289 TTATA
1 TTATA
2118294 ATTACAAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATATTTATTA
Found at i:2118797 original size:191 final size:185
Alignment explanation
Indices: 2118438--2118815 Score: 668
Period size: 191 Copynumber: 2.0 Consensus size: 185
2118428 CCGCCGCCGC
2118438 CTCATGTTTCCAGAAGATCCCAGCTGCCACCTCAGTGTTCCACCCCGCTGTAGCCACGACACCGC
1 CTCATGTTTCCAGAAGATCCCAGCTGCCA-C-CAGTGTTCCACCCCGCTGTAGCCACGACACCGC
2118503 CTCTTCGAAGACTCCAGAACATCACGCCGGCCGTCCACGTCTCAGCTATGGGGTGAGTCACACAT
64 CTCTTCGAAGACTCCAGAACATCACGCCGGCCGTCCACGTCTCAGCTATGGGGTGAGTCACACAT
2118568 AGTTTGGTGACTCACCGAAGTTTCCACTCTTTAACCAGTCCGAGAGGAGCGTCGTGG
129 AGTTTGGTGACTCACCGAAGTTTCCACTCTTTAACCAGTCCGAGAGGAGCGTCGTGG
2118625 CTCATGTTTCCAGAAGATCCCAGCTGCCA-CAGGTGTTCCACCCCGCTGTAGCCACGACACCCAC
1 CTCATGTTTCCAGAAGATCCCAGCTGCCACCA-GTGTTCCACCCCGCTGTAGCCACG--A--CAC
2118689 CGCCTCTTCGAAGACTCCAGAAACATCACGCCGGCCGTCCACGTCTCAGCTATGGGGTGAGTCAC
61 CGCCTCTTCGAAGACTCCAG-AACATCACGCCGGCCGTCCACGTCTCAGCTATGGGGTGAGTCA-
2118754 CACATAGTTTGGTGACTCACCGAAGTTTCCACTCTTTAACCAGTCCGAGAGGAGCGTCGTGG
124 CACATAGTTTGGTGACTCACCGAAGTTTCCACTCTTTAACCAGTCCGAGAGGAGCGTCGTGG
2118816 TGGCTTATAA
Statistics
Matches: 184, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
184 2 0.01
185 24 0.13
187 30 0.16
189 23 0.12
190 43 0.23
191 62 0.34
ACGTcount: A:0.22, C:0.34, G:0.23, T:0.21
Consensus pattern (185 bp):
CTCATGTTTCCAGAAGATCCCAGCTGCCACCAGTGTTCCACCCCGCTGTAGCCACGACACCGCCT
CTTCGAAGACTCCAGAACATCACGCCGGCCGTCCACGTCTCAGCTATGGGGTGAGTCACACATAG
TTTGGTGACTCACCGAAGTTTCCACTCTTTAACCAGTCCGAGAGGAGCGTCGTGG
Found at i:2120319 original size:31 final size:31
Alignment explanation
Indices: 2120284--2120371 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
2120274 AAAAAAAAAA
2120284 ATCATTAAATTTATCAAAATATTACAAAATG
1 ATCATTAAATTTATCAAAATATTACAAAATG
* * * *
2120315 ATCATTATATTTATCAAATTGTTATAAAATG
1 ATCATTAAATTTATCAAAATATTACAAAATG
* *
2120346 ATCATTAAATTTATTAAAAAATTACA
1 ATCATTAAATTTATCAAAATATTACA
2120372 CTTATTAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (31 bp):
ATCATTAAATTTATCAAAATATTACAAAATG
Found at i:2125566 original size:22 final size:25
Alignment explanation
Indices: 2125528--2125577 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
2125518 ATAATATTAC
2125528 TTTTATGACACGTTTTCCT-T-TAT
1 TTTTATGACACGTTTTCCTCTCTAT
*
2125551 TTTTATGACATG-TTTCCTCTCTAT
1 TTTTATGACACGTTTTCCTCTCTAT
2125575 TTT
1 TTT
2125578 GACACATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 12 0.50
24 6 0.25
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.58
Consensus pattern (25 bp):
TTTTATGACACGTTTTCCTCTCTAT
Found at i:2138882 original size:23 final size:23
Alignment explanation
Indices: 2138834--2138885 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2138824 AGGTGTCAAA
* *
2138834 TAGATTTGTCCCGAAGGACCATG
1 TAGAATTGTCCCGAAGGACCACG
* *
2138857 TAGAATTGTTCCGAAGGACCGCG
1 TAGAATTGTCCCGAAGGACCACG
2138880 TAGAAT
1 TAGAAT
2138886 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCACG
Found at i:2144919 original size:41 final size:41
Alignment explanation
Indices: 2144871--2144994 Score: 239
Period size: 41 Copynumber: 3.0 Consensus size: 41
2144861 TTATCTCCAC
2144871 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
1 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
2144912 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
1 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
*
2144953 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCTAGGTA
1 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
2144994 A
1 A
2144995 TGAATTGTAG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (41 bp):
AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
Found at i:2148979 original size:2 final size:2
Alignment explanation
Indices: 2148974--2149001 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2148964 ACACACGCAC
2148974 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
2149002 CAATGATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2153322 original size:23 final size:23
Alignment explanation
Indices: 2153296--2153385 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
2153286 CACCACAGCT
*
2153296 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2153319 CGTAGAATTGCACCGTAGTACCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2153342 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
2153365 CGTAGAAATACACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
2153386 TATATAAGGT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2159240 original size:22 final size:20
Alignment explanation
Indices: 2159215--2159262 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
2159205 CATTTTAATA
*
2159215 TATATAATATTAATTATTATTT
1 TATATAAT-TTAATTA-AATTT
2159237 TATAATAATTTAATTAAATTT
1 TAT-ATAATTTAATTAAATTT
2159258 TATAT
1 TATAT
2159263 GACTTCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.08
21 7 0.29
22 10 0.42
23 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATAATTTAATTAAATTT
Found at i:2159250 original size:28 final size:29
Alignment explanation
Indices: 2159193--2159260 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
2159183 TATTATTGGA
*
2159193 ATTAATTTTATTCATTTTAATATATATAAT
1 ATTAATTTTATT-ATTATAATATATATAAT
*
2159223 ATTAATTATTATT-TTATAATA-ATTTAAT
1 ATTAATT-TTATTATTATAATATATATAAT
*
2159251 -TAAATTTTAT
1 ATTAATTTTAT
2159261 ATGACTTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.12
27 5 0.15
28 6 0.18
29 7 0.21
30 7 0.21
31 5 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTAATTTTATTATTATAATATATATAAT
Found at i:2159566 original size:21 final size:21
Alignment explanation
Indices: 2159524--2159566 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2159514 AATTACATTT
* ** *
2159524 AAAAACTACTCATTTTTGAAG
1 AAAAACTAATCATAATTAAAG
2159545 AAAAACTAATCATAATTAAAG
1 AAAAACTAATCATAATTAAAG
2159566 A
1 A
2159567 TTAAATGTCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (21 bp):
AAAAACTAATCATAATTAAAG
Found at i:2160521 original size:42 final size:42
Alignment explanation
Indices: 2160474--2160563 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
2160464 TTAAATAGTG
** *
2160474 ACAAAAATAATTATTGTTGCAAACCACCAACTAAGACTAATA
1 ACAAAAATAATTATCATTACAAACCACCAACTAAGACTAATA
* * * *
2160516 ACAAAAATAATTGTCATTATAAACCACCAACTAAGACTAGTG
1 ACAAAAATAATTATCATTACAAACCACCAACTAAGACTAATA
2160558 ACAAAA
1 ACAAAA
2160564 TATTTTCGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (42 bp):
ACAAAAATAATTATCATTACAAACCACCAACTAAGACTAATA
Found at i:2171987 original size:33 final size:33
Alignment explanation
Indices: 2171926--2172018 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
2171916 CGAGAATGAA
** *
2171926 AATCGCAACGCGGAAATGACTATTGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
* *
2171960 AATCGCAACACGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
2171993 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
2172019 TTGTGATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 41 0.80
34 10 0.20
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2172046 original size:20 final size:19
Alignment explanation
Indices: 2172026--2172127 Score: 115
Period size: 20 Copynumber: 5.5 Consensus size: 19
2172016 GCATTGTGAT
2172026 TTTTCATTTCGCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
*
2172045 --TTC---TCTCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
2172059 TTTTCATTTCGCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
**
2172078 TAGTCATTTCCGCGTTGCGA
1 TTTTCATTT-CGCGTTGCGA
*
2172098 TTTTCATTATCTCGTTGCGA
1 TTTTCATT-TCGCGTTGCGA
2172118 TTTTCATTTC
1 TTTTCATTTC
2172128 AACCAAAAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 19 0.28
20 33 0.48
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.47
Consensus pattern (19 bp):
TTTTCATTTCGCGTTGCGA
Found at i:2172066 original size:33 final size:35
Alignment explanation
Indices: 2172026--2172119 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 35
2172016 GCATTGTGAT
*
2172026 TTTTCATTTCGCGTTGCGATTC-T-CTCGTTGCGA
1 TTTTCATTTCGCGTTGCGATTCTTCCGCGTTGCGA
2172059 TTTTCATTTCGCGTTGCGATAGTCATTTCCGCGTTGCGA
1 TTTTCATTTCGCGTTGCGAT--TC--TTCCGCGTTGCGA
*
2172098 TTTTCATTATCTCGTTGCGATT
1 TTTTCATT-TCGCGTTGCGATT
2172120 TTCATTTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
33 20 0.38
35 2 0.04
38 2 0.04
39 17 0.33
40 11 0.21
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (35 bp):
TTTTCATTTCGCGTTGCGATTCTTCCGCGTTGCGA
Found at i:2174001 original size:94 final size:93
Alignment explanation
Indices: 2173814--2174189 Score: 598
Period size: 94 Copynumber: 4.1 Consensus size: 93
2173804 TAGATTGCTT
* * *
2173814 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2173875 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
2173904 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2173969 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
2173998 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2174063 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
2174092 AGTAAATTTGTTTGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2174157 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
2174185 AGTAA
1 AGTAA
2174190 TGCAATCCAT
Statistics
Matches: 269, Mismatches: 12, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
90 33 0.12
92 3 0.01
93 27 0.10
94 206 0.77
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:2174361 original size:19 final size:19
Alignment explanation
Indices: 2174288--2174377 Score: 73
Period size: 19 Copynumber: 4.9 Consensus size: 19
2174278 TATCTTTTGG
2174288 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
2174307 TTTCGCGTTACGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* *
2174323 --TCTCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTTTCA
**
2174340 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
2174359 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
2174378 AAGTTCCAGA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 9 0.17
16 2 0.04
17 3 0.06
19 25 0.47
21 14 0.26
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:2174896 original size:21 final size:20
Alignment explanation
Indices: 2174837--2174897 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
2174827 CTCGAGAATC
2174837 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
2174857 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
2174878 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
2174898 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:2176268 original size:14 final size:14
Alignment explanation
Indices: 2176249--2176284 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2176239 ATTGTTTAAT
2176249 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2176263 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2176277 TGATTTGT
1 TGATTTGT
2176285 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2176413 original size:19 final size:18
Alignment explanation
Indices: 2176391--2176522 Score: 83
Period size: 19 Copynumber: 7.7 Consensus size: 18
2176381 AAAAATGACT
2176391 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
2176410 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
2176424 ATCTCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
2176443 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
2176457 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
2176476 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
2176490 ATCGCAACGCGAAACT-AAA
1 ATCGCAA-GCGAAA-TGAAA
2176509 ATCGCAAAGCGAAA
1 ATCGC-AAGCGAAA
2176523 CTAAATTCGC
Statistics
Matches: 89, Mismatches: 7, Indels: 34
0.68 0.05 0.26
Matches are distributed among these distances:
14 29 0.33
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 40 0.45
20 2 0.02
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:2176441 original size:33 final size:33
Alignment explanation
Indices: 2176391--2176515 Score: 198
Period size: 33 Copynumber: 3.8 Consensus size: 33
2176381 AAAAATGACT
*
2176391 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
2176424 ATCTCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
2176457 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2176490 ATCGCAACGCGAAACT-AAAATCGCAA
1 ATCGCAACGCGAAA-TGAAAATCGCAA
2176516 AGCGAAACTA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2176461 original size:14 final size:14
Alignment explanation
Indices: 2176409--2176465 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2176399 GCGAAATGAA
2176409 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
2176423 AATCTCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2176442 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2176456 AATCGCAACG
1 AATCGCAACG
2176466 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2176539 original size:19 final size:19
Alignment explanation
Indices: 2176456--2176532 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
2176446 GCAACGAGAG
*
2176456 AATCGCAACGCGAAA-TGAA
1 AATCGCAAAGCGAAACT-AA
2176475 AATCGC-AA-CG--AC-AA
1 AATCGCAAAGCGAAACTAA
*
2176489 AATCGCAACGCGAAACTAA
1 AATCGCAAAGCGAAACTAA
2176508 AATCGCAAAGCGAAACTAA
1 AATCGCAAAGCGAAACTAA
*
2176527 ATTCGC
1 AATCGC
2176533 GTTGCGATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.17
15 2 0.04
16 2 0.04
17 2 0.04
18 3 0.06
19 31 0.65
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.12
Consensus pattern (19 bp):
AATCGCAAAGCGAAACTAA
Done.