Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007964.1 Hibiscus syriacus cultivar Beakdansim tig00110393_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: 1737572
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 5 of 6
Found at i:1205467 original size:19 final size:19
Alignment explanation
Indices: 1205443--1205486 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1205433 TGGGTTGCAA
1205443 AATTTGA-ATTCACATTGCG
1 AATTTGAGA-TCACATTGCG
* *
1205462 AATTTGAGATCGCGTTGCG
1 AATTTGAGATCACATTGCG
1205481 AATTTG
1 AATTTG
1205487 TTAGTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (19 bp):
AATTTGAGATCACATTGCG
Found at i:1205920 original size:23 final size:23
Alignment explanation
Indices: 1205894--1205939 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1205884 ATTAGGGGCC
1205894 TTTAGGCCCCAAGTGAATTTCGT
1 TTTAGGCCCCAAGTGAATTTCGT
1205917 TTTAGGCCCCAAGTGAATTTCGT
1 TTTAGGCCCCAAGTGAATTTCGT
1205940 CTATGGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (23 bp):
TTTAGGCCCCAAGTGAATTTCGT
Found at i:1206096 original size:13 final size:13
Alignment explanation
Indices: 1206078--1206104 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1206068 TATTTGATTG
1206078 AAAAAATATTTTT
1 AAAAAATATTTTT
1206091 AAAAAATATTTTT
1 AAAAAATATTTTT
1206104 A
1 A
1206105 TTAAAACGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAAATATTTTT
Found at i:1206381 original size:35 final size:35
Alignment explanation
Indices: 1206266--1206381 Score: 112
Period size: 35 Copynumber: 3.2 Consensus size: 35
1206256 TTAACGAATT
*
1206266 TTATATTAATTATTTATTAAAGTAATAGTGTTATA
1 TTATATTAATTATTTATTAAAGTAATAATGTTATA
* *
1206301 TTA-ATT-ATT-TATATTAATAGTGAAATAAAATATTATAAA
1 TTATATTAATTATTTATTAA-AGT--AAT--AATGTTAT--A
*
1206340 TTATATTAATTATTTATTAAAGTAATACTGTTATA
1 TTATATTAATTATTTATTAAAGTAATAATGTTATA
1206375 TTATATT
1 TTATATT
1206382 TTAAAAATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
32 7 0.11
33 6 0.09
34 3 0.05
35 14 0.22
37 12 0.18
39 7 0.11
40 3 0.05
41 6 0.09
42 7 0.11
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (35 bp):
TTATATTAATTATTTATTAAAGTAATAATGTTATA
Found at i:1207059 original size:48 final size:50
Alignment explanation
Indices: 1206963--1207060 Score: 114
Period size: 48 Copynumber: 2.0 Consensus size: 50
1206953 TACAAATATT
*
1206963 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * *
1207013 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TT-ATTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
1207061 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 21 0.50
49 13 0.31
50 8 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:1207230 original size:26 final size:23
Alignment explanation
Indices: 1207189--1207244 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 23
1207179 TTTATTAAAA
1207189 TATTATTTAAATATATAAATATATTT
1 TATTA-TTAAATATATAAA-A-ATTT
1207215 TCATTATTAAATATATAAAAATTT
1 T-ATTATTAAATATATAAAAATTT
1207239 TATTAT
1 TATTAT
1207245 ATATTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 1 0.03
26 14 0.48
27 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTAAATATATAAAAATTT
Found at i:1207259 original size:27 final size:26
Alignment explanation
Indices: 1207229--1207311 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
1207219 TATTAAATAT
1207229 ATAAAAATTTTATTATATATTATTAAA
1 ATAAAAATTTTATT-TATATTATTAAA
* * *
1207256 ATAAAAATATAATCTTATATTATTATA
1 ATAAAAATTTTAT-TTATATTATTAAA
* *
1207283 AT-ATAATTTATATTTTATAATATTAAA
1 ATAAAAATTT-TA-TTTATATTATTAAA
1207310 AT
1 AT
1207312 TATAATATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 5 0.11
27 38 0.84
28 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAAAAATTTTATTTATATTATTAAA
Found at i:1207274 original size:8 final size:8
Alignment explanation
Indices: 1207272--1207332 Score: 58
Period size: 8 Copynumber: 8.1 Consensus size: 8
1207262 ATATAATCTT
*
1207272 ATATTATT
1 ATATTATA
*
1207280 ATAATATA
1 ATATTATA
1207288 AT-TTAT-
1 ATATTATA
*
1207294 ATTTTATA
1 ATATTATA
1207302 ATATTA-A
1 ATATTATA
1207309 A-ATTATA
1 ATATTATA
1207316 ATATTATA
1 ATATTATA
*
1207324 TTATTATA
1 ATATTATA
1207332 A
1 A
1207333 ATACTAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 6 0.14
7 11 0.26
8 26 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATATTATA
Found at i:1207302 original size:19 final size:21
Alignment explanation
Indices: 1207261--1207323 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
1207251 TTAAAATAAA
1207261 AATATAATCTTATATTATTAT
1 AATATAATCTTATATTATTAT
1207282 AATATAAT-TTATATT-TTAT
1 AATATAATCTTATATTATTAT
** *
1207301 AATATTAAAATTATAATATTAT
1 AATA-TAATCTTATATTATTAT
1207323 A
1 A
1207324 TTATTATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.22
20 10 0.27
21 14 0.38
22 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAATCTTATATTATTAT
Found at i:1207303 original size:14 final size:15
Alignment explanation
Indices: 1207284--1207332 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
1207274 ATTATTATAA
1207284 TATAAT-TTATATTT
1 TATAATATTATATTT
**
1207298 TATAATATTA-AAAT
1 TATAATATTATATTT
1207312 TATAATATTATATTAT
1 TATAATATTATATT-T
1207328 TATAA
1 TATAA
1207333 ATACTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 18 0.64
15 4 0.14
16 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAATATTATATTT
Found at i:1207312 original size:22 final size:22
Alignment explanation
Indices: 1207270--1207334 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
1207260 AAATATAATC
1207270 TTATATTATTATAATA-T--AAT
1 TTATATT-TTATAATATTAAAAT
1207290 TTATATTTTATAATATTAAAA-
1 TTATATTTTATAATATTAAAAT
* *
1207311 TTATAATATTATATTATTATAAAT
1 TTAT-ATTTTATAATATTA-AAAT
1207335 ACTAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 8 0.22
20 8 0.22
21 4 0.11
22 14 0.38
23 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATATTTTATAATATTAAAAT
Found at i:1207345 original size:27 final size:25
Alignment explanation
Indices: 1207244--1207345 Score: 75
Period size: 27 Copynumber: 4.0 Consensus size: 25
1207234 AATTTTATTA
* *
1207244 TATATTATTAAAATAAAAATATAATCT
1 TATATTATTAAAAT-ATAATA-AATAT
* * *
1207271 TATATTATTATAATATAATTTATATTT
1 TATATTATTAAAATATAA--TAAATAT
*
1207298 TATAATATTAAAAT-T-AT-AATAT
1 TATATTATTAAAATATAATAAATAT
1207320 TATATTATTATAAATACTAATAAATA
1 TATATTATTA-AAATA-TAATAAATA
1207346 AATAAATAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
22 12 0.20
23 5 0.08
25 2 0.03
26 6 0.10
27 32 0.54
28 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATTATTAAAATATAATAAATAT
Found at i:1208422 original size:35 final size:35
Alignment explanation
Indices: 1208353--1208424 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
1208343 TTGATGCTAT
*
1208353 TTATAATAAGTCATGCCACTTGGTAAATAGACTTA
1 TTATAATAAGTCATGCCACTTGATAAATAGACTTA
* *
1208388 TTATAATAAGTCATGTCACTTGATGAAT-GAACTTA
1 TTATAATAAGTCATGCCACTTGATAAATAG-ACTTA
1208423 TT
1 TT
1208425 TTTTAGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (35 bp):
TTATAATAAGTCATGCCACTTGATAAATAGACTTA
Found at i:1208529 original size:31 final size:31
Alignment explanation
Indices: 1208492--1208553 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1208482 CATGAAATGC
*
1208492 ATTAACTATTCATCAAAAGATTCTAATATTT
1 ATTAACTATTCATCAAAAGATTCTAACATTT
1208523 ATTAACTATTCATCAAAAGATTCTAACATTT
1 ATTAACTATTCATCAAAAGATTCTAACATTT
1208554 TGATTCATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (31 bp):
ATTAACTATTCATCAAAAGATTCTAACATTT
Found at i:1208981 original size:3 final size:3
Alignment explanation
Indices: 1208973--1209021 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1208963 GATAGAATAT
* *
1208973 TTA TTA TTA TTA ATA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1209021 T
1 T
1209022 CTCGAGTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1210522 original size:13 final size:12
Alignment explanation
Indices: 1210503--1210569 Score: 68
Period size: 13 Copynumber: 5.6 Consensus size: 12
1210493 ACAAACAATG
*
1210503 AATAAAATGATA
1 AATAAAATAATA
*
1210515 ACATAAAAAAATAA
1 A-ATAAAATAAT-A
1210529 AATAAAATAATA
1 AATAAAATAATA
1210541 AAT-AAA-AATA
1 AATAAAATAATA
1210551 AGATAAAATAA-A
1 A-ATAAAATAATA
1210563 AATAAAA
1 AATAAAA
1210570 ATCAACCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 5 0.11
11 11 0.23
12 10 0.21
13 19 0.40
14 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (12 bp):
AATAAAATAATA
Found at i:1210537 original size:10 final size:11
Alignment explanation
Indices: 1210522--1210569 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
1210512 ATAACATAAA
1210522 AAAAT-AAAAT
1 AAAATAAAAAT
1210532 AAAATAATAAAT
1 AAAATAA-AAAT
*
1210544 AAAA-ATAAGAT
1 AAAATA-AAAAT
1210555 AAAATAAAAAT
1 AAAATAAAAAT
1210566 AAAA
1 AAAA
1210570 ATCAACCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 5 0.16
11 17 0.53
12 10 0.31
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:1210547 original size:23 final size:23
Alignment explanation
Indices: 1210503--1210571 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 23
1210493 ACAAACAATG
*
1210503 AATAAAATGATAACATAAAAAAATAA
1 AATAAAATAATAA-AT--AAAAATAA
1210529 AATAAAATAATAAATAAAAATAA
1 AATAAAATAATAAATAAAAATAA
*
1210552 GATAAAATAA-AAATAAAAAT
1 AATAAAATAATAAATAAAAAT
1210572 CAACCATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.24
23 17 0.41
25 2 0.05
26 12 0.29
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.20
Consensus pattern (23 bp):
AATAAAATAATAAATAAAAATAA
Found at i:1210549 original size:6 final size:6
Alignment explanation
Indices: 1210521--1210571 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 6
1210511 GATAACATAA
*
1210521 AAAAAT -AAAAT -AAAAT AATAAAT AAAAAT -AAGAT -AAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT
1210566 AAAAAT
1 AAAAAT
1210572 CAACCATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 18 0.45
6 16 0.40
7 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:1210951 original size:20 final size:20
Alignment explanation
Indices: 1210928--1210970 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1210918 GAAAATTTTC
1210928 AAAAGAAAATAAAAA-TAAAA
1 AAAAG-AAATAAAAACTAAAA
*
1210948 AAAAGAACTAAAAACTAAAA
1 AAAAGAAATAAAAACTAAAA
1210968 AAA
1 AAA
1210971 CAAGGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.09
Consensus pattern (20 bp):
AAAAGAAATAAAAACTAAAA
Found at i:1213900 original size:29 final size:28
Alignment explanation
Indices: 1213858--1213941 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
1213848 TGCAACGTGG
1213858 GTAGGTCGCCAGGGAATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
1213887 GTAGGTCGCCAGGGCATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
*
1213916 GTAGGTCGCCAAGGGATCCCAACGAC
1 GTAGGTCGCC-AGGGATCCCAGCGAC
1213942 CTATGCCTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.15
Consensus pattern (28 bp):
GTAGGTCGCCAGGGATCCCAGCGACATT
Found at i:1214403 original size:27 final size:28
Alignment explanation
Indices: 1214340--1214403 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
1214330 TATATTAAAA
1214340 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAAT-ATTAATTAGTGTGTTAGTTAGTCT
* *
1214369 -AATATTAATTAGTTTG-TAGTTTGT-T
1 AAATATTAATTAGTGTGTTAGTTAGTCT
1214394 AAATAGTTAA
1 AAATA-TTAA
1214404 GTTATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
26 11 0.35
27 16 0.52
28 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (28 bp):
AAATATTAATTAGTGTGTTAGTTAGTCT
Found at i:1214555 original size:25 final size:26
Alignment explanation
Indices: 1214507--1214557 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
1214497 TAAAAGAATA
*
1214507 ATTATTTAATTAGTTTATTGTTATAATT
1 ATTAGTTAATTAGTTTA-T-TTATAATT
1214535 ATTAGTTAATTAGTTTA-TTATAA
1 ATTAGTTAATTAGTTTATTTATAA
1214558 ATTAGGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
28 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (26 bp):
ATTAGTTAATTAGTTTATTTATAATT
Found at i:1214615 original size:21 final size:21
Alignment explanation
Indices: 1214590--1214629 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1214580 GTTAATTAGT
1214590 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1214611 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1214630 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1214865 original size:30 final size:30
Alignment explanation
Indices: 1214797--1214900 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
1214787 ATTAGTTAAT
* *
1214797 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAATTAT-ATTAAAGAA
*
1214828 TCA-TTTATTAGTTTAATTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAATTATATTAAAGAA
*
1214858 TAGTTTATTAG-TTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTTAA-ATTATATTAAAGAA
1214888 TAGTTTATTAGTT
1 TAGTTTATTAGTT
1214901 GTTTAAGGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
29 11 0.17
30 42 0.66
31 10 0.16
32 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATATTAAAGAA
Found at i:1217198 original size:14 final size:14
Alignment explanation
Indices: 1217179--1217273 Score: 70
Period size: 14 Copynumber: 6.6 Consensus size: 14
1217169 TTCAAGTCGT
1217179 AAATCATTACTATC
1 AAATCATTACTATC
1217193 AAATCATTAC--T-
1 AAATCATTACTATC
*
1217204 AAATCATTAATATC
1 AAATCATTACTATC
* *
1217218 AAATCATTAAATATTA
1 AAATCATT-ACTA-TC
* *
1217234 ATAATAATTATTATTAC
1 A-AATCATTACTA-T-C
*
1217251 TAATCATTACTATC
1 AAATCATTACTATC
1217265 AAATCATTA
1 AAATCATTA
1217274 AAAATTAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
11 9 0.14
12 1 0.02
13 1 0.02
14 27 0.42
15 5 0.08
16 16 0.25
17 6 0.09
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1217320 original size:59 final size:60
Alignment explanation
Indices: 1217246--1217370 Score: 227
Period size: 59 Copynumber: 2.1 Consensus size: 60
1217236 AATAATTATT
1217246 ATTACT-AATCATTACTATCAAATCATTAAAAATTAAT-ATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
1217304 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAGTTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1217364 ATTACTA
1 ATTACTA
1217371 TCAAATCATT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
58 6 0.09
59 31 0.48
60 27 0.42
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:1217367 original size:49 final size:49
Alignment explanation
Indices: 1217304--1217920 Score: 552
Period size: 49 Copynumber: 11.3 Consensus size: 49
1217294 ATTACTAATC
*
1217304 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAGTTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1217354 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * *
1217403 ATTACTAATCA-TACTATCAAATAATTAAAAATTAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAA--T-A--ATT--TCATT
1217458 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1217508 ATTACTAATCATTACTATCAAATTATTAAAAATTAATAATAATTCATTATACTATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT-A---ATT-T-C-ATT
*
1217564 ACTAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 A-TTA-C-----TAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1217620 ATTACTAATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTAC
1 ATTACTAATCA-T--T--A-C-----TATCAAATCATTAAAAATTAATAAT-A----A-T-TT-C
*
1217685 TATC
47 -ATT
* *
1217689 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1217738 ATTACTAATCATTACCATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
1217796 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * *
1217847 ATTACTAATCATTACTATCAAATTACTATCAAATCATTAAATATTAATAATTTCATC
1 ATTACTAATCATTACTATCAAA-T-C-ATTAAA-AATT--A-A-TAATAATTTCATT
1217904 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1217921 AATCTTATAA
Statistics
Matches: 483, Mismatches: 22, Indels: 117
0.78 0.04 0.19
Matches are distributed among these distances:
48 26 0.05
49 153 0.32
50 26 0.05
51 5 0.01
52 10 0.02
53 11 0.02
54 5 0.01
55 16 0.03
56 15 0.03
57 59 0.12
58 27 0.06
59 9 0.02
60 64 0.13
61 1 0.00
62 1 0.00
63 34 0.07
64 1 0.00
65 1 0.00
66 2 0.00
67 2 0.00
68 2 0.00
69 13 0.03
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:1217461 original size:25 final size:26
Alignment explanation
Indices: 1217433--1217492 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 26
1217423 ATAATTAAAA
* *
1217433 ATTAATAATTTCATTATTA-CTAATC
1 ATTAATAATTTCATTACTATCAAATC
* *
1217458 ATTACTAA-ATCATTACTATCAAATC
1 ATTAATAATTTCATTACTATCAAATC
*
1217483 ATTAAAAATT
1 ATTAATAATT
1217493 AATAATAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTAATAATTTCATTACTATCAAATC
Found at i:1217521 original size:60 final size:59
Alignment explanation
Indices: 1217403--1217921 Score: 565
Period size: 60 Copynumber: 9.1 Consensus size: 59
1217393 TAATTTCATT
*
1217403 ATTACTAATCA-TACTATCAAATAATTAAAAA-T--TAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1217458 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
1217518 ATTACT-ATCA--A--AT----T-ATTAAAAATTAATAATAATTCATTATACTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT--TCAT--TATTACTAATC
1217571 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
1217630 ATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACT-ATC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
1217689 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * * * * * * * * * *
1217748 ATTAC-CATCA--AATCATTAAA-AATTAATAA-TAAT-TTCA-TT-ATTACTAATCATT
1 ATTACTAATCATTACT-ATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
1217800 ACTA-AA-TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
1217857 ATTACT-ATCAAATTACTATCAAATCATT--AAA-TATTAATAATTTCATCATTACTAATC
1 ATTACTAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1217914 ATTACTAA
1 ATTACTAA
1217922 ATCTTATAAA
Statistics
Matches: 394, Mismatches: 35, Indels: 67
0.79 0.07 0.14
Matches are distributed among these distances:
49 20 0.05
50 1 0.00
51 6 0.02
52 17 0.04
53 28 0.07
54 12 0.03
55 12 0.03
56 18 0.05
57 66 0.17
58 63 0.16
59 34 0.09
60 93 0.24
61 3 0.01
62 1 0.00
63 20 0.05
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (59 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:1217576 original size:10 final size:10
Alignment explanation
Indices: 1217561--1217587 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1217551 TCATTATACT
1217561 ATTACTAATC
1 ATTACTAATC
1217571 ATTACTAATC
1 ATTACTAATC
1217581 ATTACTA
1 ATTACTA
1217588 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:1217663 original size:24 final size:24
Alignment explanation
Indices: 1217615--1217663 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1217605 AATAATAATT
* *
1217615 TCATTATTACTAATCATTACTAAA
1 TCATTATTACAAATCATTACAAAA
1217639 TCATTATTATCAAATCATTA-AAAA
1 TCATTATTA-CAAATCATTACAAAA
1217663 T
1 T
1217664 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCATTATTACAAATCATTACAAAA
Found at i:1217849 original size:227 final size:225
Alignment explanation
Indices: 1217403--1217921 Score: 832
Period size: 227 Copynumber: 2.3 Consensus size: 225
1217393 TAATTTCATT
*
1217403 ATTACTAATCA-TACTATCAAATAATTAAAAATTAATAATTTCATTATTACTAATCATTACTAAA
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATTTCATTATTACTAATCATTACT-AA
* * *
1217467 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATT
65 TCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACCATCAAATC
*
1217532 ATTAAAAATTAATAATAATTCATTATACTATTACTAATCATTACTAATCATTACTATCAAATCAT
130 ATTAAAAATTAATAATAATT-ATCATA-TATTACTAATCATTACTAATCATTACTATCAAATCAT
1217597 TAAAAATTAATAATAATTTCATTATTACTAATC
193 TAAAAATTAATAATAATTTCATTATTACTAATC
*
1217630 ATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACT-ATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAAT-A--ATTTCATTATTACTAATCATTAC
*
1217694 TAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACCATCAA
62 TAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACCATCAA
1217759 ATCATTAAAAATTAATAATAATT-TCAT-TATTACTAATCATTACTAAATCATTACTATCAAATC
127 ATCATTAAAAATTAATAATAATTATCATATATTACTAATCATTACT-AATCATTACTATCAAATC
1217822 ATTAAAAATTAATAATAATTTCATTATTACTAATC
191 ATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
1217857 ATTACT-ATCAAATTACTATCAAATCATTAAATATTAATAATTTCATCATTACTAATCATTACTA
1 ATTACTAATC--ATTACTATCAAATCATTAAAAATTAATAATTTCATTATTACTAATCATTACTA
1217921 A
64 A
1217922 ATCTTATAAA
Statistics
Matches: 273, Mismatches: 10, Indels: 20
0.90 0.03 0.07
Matches are distributed among these distances:
224 13 0.05
225 14 0.05
226 18 0.07
227 90 0.33
228 8 0.03
229 23 0.08
230 84 0.31
231 9 0.03
232 14 0.05
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (225 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATTTCATTATTACTAATCATTACTAAT
CATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACCATCAAATCA
TTAAAAATTAATAATAATTATCATATATTACTAATCATTACTAATCATTACTATCAAATCATTAA
AAATTAATAATAATTTCATTATTACTAATC
Found at i:1221000 original size:23 final size:25
Alignment explanation
Indices: 1220949--1221005 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
1220939 TTATATAATC
1220949 TAATATATAACTTAAACTAACAAAT
1 TAATATATAACTTAAACTAACAAAT
1220974 TAATATATAACTT-AACTAACAAA-
1 TAATATATAACTTAAACTAACAAAT
*
1220997 TAATTTATA
1 TAATATATA
1221006 CTACAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 8 0.26
24 10 0.32
25 13 0.42
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (25 bp):
TAATATATAACTTAAACTAACAAAT
Found at i:1221016 original size:24 final size:24
Alignment explanation
Indices: 1220949--1221005 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1220939 TTATATAATC
1220949 TAATATATAACTTAAACTAACAAAT
1 TAATATATAAC-TAAACTAACAAAT
*
1220974 TAATATATAACTTAACTAACAAA-
1 TAATATATAACTAAACTAACAAAT
*
1220997 TAATTTATA
1 TAATATATA
1221006 CTACAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 8 0.27
24 11 0.37
25 11 0.37
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (24 bp):
TAATATATAACTAAACTAACAAAT
Found at i:1224361 original size:183 final size:185
Alignment explanation
Indices: 1224052--1224419 Score: 713
Period size: 183 Copynumber: 2.0 Consensus size: 185
1224042 ATCTTTGTAA
1224052 GCCTCATTTGGACTTGCTATCCCATCGACACCCACTACTGTCTCAGGCAGTGGTCGAAGAACACC
1 GCCTCATTTGGACTTGCTATCCCATCGACACCCACTACTGTCTCAGGCAGTGGTCGAAGAACACC
1224117 GGTTAACAGTTTCTCAAGCCAATGACTACGCACAGTGAGTAATATTTGTTGCTTCCACAATAGAA
66 GGTTAACAGTTTCTCAAGCCAATGACTACGCACAGTGAGTAATATTTGTTGCTTCCACAATAGAA
1224182 AGTTCATTTCATCAAGAAGGATATTAACCTTCTTG-TTGTGAAGTTTTTGCCATT
131 AGTTCATTTCATCAAGAAGGATATTAACCTTCTTGTTTGTGAAGTTTTTGCCATT
1224236 GCCTCATTTGGACTTGCTATCCCATCGA-ACCCACTACTGTCTCAGGCAGTGGTCGAAGAACACC
1 GCCTCATTTGGACTTGCTATCCCATCGACACCCACTACTGTCTCAGGCAGTGGTCGAAGAACACC
1224300 GGTTAACAGTTTCTCAAGCCAATGACTACGCACAGTGAGTAATATTTGTTGCTTCCACAATAGAA
66 GGTTAACAGTTTCTCAAGCCAATGACTACGCACAGTGAGTAATATTTGTTGCTTCCACAATAGAA
*
1224365 AGTTCATTTCATCAAGAATGATATTAACCTTCTTGTTTGTGAAGTTTTTGCCATT
131 AGTTCATTTCATCAAGAAGGATATTAACCTTCTTGTTTGTGAAGTTTTTGCCATT
1224420 ATTGGACGTA
Statistics
Matches: 182, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
183 135 0.74
184 47 0.26
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (185 bp):
GCCTCATTTGGACTTGCTATCCCATCGACACCCACTACTGTCTCAGGCAGTGGTCGAAGAACACC
GGTTAACAGTTTCTCAAGCCAATGACTACGCACAGTGAGTAATATTTGTTGCTTCCACAATAGAA
AGTTCATTTCATCAAGAAGGATATTAACCTTCTTGTTTGTGAAGTTTTTGCCATT
Found at i:1225288 original size:15 final size:15
Alignment explanation
Indices: 1225264--1225299 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1225254 CTTAACTCAT
*
1225264 TAATATTTTAAAATC
1 TAATAATTTAAAATC
1225279 TAATAATTTAAAATC
1 TAATAATTTAAAATC
*
1225294 AAATAA
1 TAATAA
1225300 AAATACTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAATTTAAAATC
Found at i:1231710 original size:32 final size:31
Alignment explanation
Indices: 1231668--1231734 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
1231658 CATCCAAACT
* *
1231668 CGACCCGACCTAAAAATTTTATATCCTACATC
1 CGACCCGACCTAAAAAATATATATCCTACA-C
* *
1231700 CGACCTGACCTAAAAAATATATATCCTCCAC
1 CGACCCGACCTAAAAAATATATATCCTACAC
1231731 CGAC
1 CGAC
1231735 TCCTACCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.24
Consensus pattern (31 bp):
CGACCCGACCTAAAAAATATATATCCTACAC
Found at i:1236165 original size:11 final size:11
Alignment explanation
Indices: 1236149--1236174 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1236139 ATAATATTAC
1236149 ATTTTTCATAT
1 ATTTTTCATAT
1236160 ATTTTTCATAT
1 ATTTTTCATAT
1236171 ATTT
1 ATTT
1236175 ATATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTCATAT
Found at i:1236191 original size:19 final size:19
Alignment explanation
Indices: 1236169--1236261 Score: 82
Period size: 19 Copynumber: 4.6 Consensus size: 19
1236159 TATTTTTCAT
1236169 ATATTTATATTTTAATAAA
1 ATATTTATATTTTAATAAA
1236188 ATATTT-TATTTTTAATAAA
1 ATATTTATA-TTTTAATAAA
* *
1236207 A-ATTTTAAATTTACAAATAAAAA
1 ATA-TTTATATTT--TAAT--AAA
1236230 TATATTTATATTTTAATAAA
1 -ATATTTATATTTTAATAAA
*
1236250 ATATTTAAATTT
1 ATATTTATATTT
1236262 ACAATAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
18 3 0.05
19 34 0.57
20 4 0.07
21 3 0.05
22 3 0.05
23 3 0.05
24 9 0.15
25 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTATATTTTAATAAA
Found at i:1236244 original size:43 final size:41
Alignment explanation
Indices: 1236169--1236278 Score: 147
Period size: 43 Copynumber: 2.7 Consensus size: 41
1236159 TATTTTTCAT
* *
1236169 ATATTTATATTT-TAAT-AAAATAT-TTTATTTTTAATAAA
1 ATATTTAAATTTACAATAAAAATATATTTATTTTTAATAAA
1236207 A-ATTTTAAATTTACAAATAAAAATATATTTATATTTTAATAAA
1 ATA-TTTAAATTTAC-AATAAAAATATATTTAT-TTTTAATAAA
1236250 ATATTTAAATTTACAATAAAAATATATTT
1 ATATTTAAATTTACAATAAAAATATATTT
1236279 TAGTGTTTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
37 1 0.02
38 9 0.14
40 3 0.05
41 7 0.11
42 20 0.32
43 22 0.35
44 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (41 bp):
ATATTTAAATTTACAATAAAAATATATTTATTTTTAATAAA
Found at i:1240875 original size:50 final size:51
Alignment explanation
Indices: 1240800--1240901 Score: 197
Period size: 50 Copynumber: 2.0 Consensus size: 51
1240790 CTTGGACACA
1240800 CGAACCACCTTAGTAGCTTTAGCTCCTCTCGGATGCCTAG-TCATCACTCC
1 CGAACCACCTTAGTAGCTTTAGCTCCTCTCGGATGCCTAGCTCATCACTCC
1240850 CGAACCACCTTAGTAGCTTTAGCTCCTCTCGGATGCCTAGCTCATCACTCC
1 CGAACCACCTTAGTAGCTTTAGCTCCTCTCGGATGCCTAGCTCATCACTCC
1240901 C
1 C
1240902 AAGCTTGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 40 0.78
51 11 0.22
ACGTcount: A:0.20, C:0.37, G:0.16, T:0.27
Consensus pattern (51 bp):
CGAACCACCTTAGTAGCTTTAGCTCCTCTCGGATGCCTAGCTCATCACTCC
Found at i:1244127 original size:52 final size:52
Alignment explanation
Indices: 1244047--1244178 Score: 210
Period size: 52 Copynumber: 2.5 Consensus size: 52
1244037 TATCTTCATT
* * * * *
1244047 TTTTAGATTCATGAATATGATTGATGTCATCATATCATTTCCTGTTGTGTTG
1 TTTTAGATTCATGAATATGATTGGTGTCATCATATCATATCCCGCTGTGCTG
*
1244099 TTTTAGATTCATGAATATGGTTGGTGTCATCATATCATATCCCGCTGTGCTG
1 TTTTAGATTCATGAATATGATTGGTGTCATCATATCATATCCCGCTGTGCTG
1244151 TTTTAGATTCATGAATATGATTGGTGTC
1 TTTTAGATTCATGAATATGATTGGTGTC
1244179 GTTTAAATAG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.45
Consensus pattern (52 bp):
TTTTAGATTCATGAATATGATTGGTGTCATCATATCATATCCCGCTGTGCTG
Found at i:1247022 original size:29 final size:29
Alignment explanation
Indices: 1246967--1247184 Score: 246
Period size: 29 Copynumber: 7.6 Consensus size: 29
1246957 ACCCGACCAT
* * *
1246967 GTGATATTTTAGTAAATATTTTGAAAAAG
1 GTGATATTTTGGTAATTATTTTTAAAAAG
* * *
1246996 GTGATATTTTAAG-AATTAGTTTTAAAACG
1 GTGATATTTT-GGTAATTATTTTTAAAAAG
* *
1247025 ATGATATTTTGGTAATTATTTTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAAAG
1247054 GTGATATTTTGGTAATTATTTTTAAAATA-
1 GTGATATTTTGGTAATTATTTTTAAAA-AG
* * *
1247083 TTGATATTTCGGTAATT-TTTTTAAACA-
1 GTGATATTTTGGTAATTATTTTTAAAAAG
*
1247110 GTGATATTTTGGTAATTATTTTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAAAG
** *
1247139 GTGATATTTTGGTAATTATTTAAAAAAAA
1 GTGATATTTTGGTAATTATTTTTAAAAAG
*
1247168 GTGATATTTTTGTAATT
1 GTGATATTTTGGTAATT
1247185 TTCGAATGTG
Statistics
Matches: 163, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
27 16 0.10
28 17 0.10
29 128 0.79
30 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.47
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTTTAAAAAG
Found at i:1247134 original size:85 final size:85
Alignment explanation
Indices: 1247026--1247186 Score: 268
Period size: 85 Copynumber: 1.9 Consensus size: 85
1247016 TTTAAAACGA
** * *
1247026 TGATATTTTGGTAATTATTTTTAAAACGGTGATATTTTGGTAATTATTTTTAAAATATTGATATT
1 TGATATTTTGGTAATTATTTTTAAAACGGTGATATTTTGGTAATTATTTAAAAAAAAGTGATATT
1247091 TCGGTAATTTTTTTAAACAG
66 TCGGTAATTTTTTTAAACAG
1247111 TGATATTTTGGTAATTATTTTTAAAACGGTGATATTTTGGTAATTATTTAAAAAAAAGTGATATT
1 TGATATTTTGGTAATTATTTTTAAAACGGTGATATTTTGGTAATTATTTAAAAAAAAGTGATATT
**
1247176 TTTGTAATTTT
66 TCGGTAATTTT
1247187 CGAATGTGGA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.50
Consensus pattern (85 bp):
TGATATTTTGGTAATTATTTTTAAAACGGTGATATTTTGGTAATTATTTAAAAAAAAGTGATATT
TCGGTAATTTTTTTAAACAG
Found at i:1248141 original size:32 final size:32
Alignment explanation
Indices: 1248068--1248191 Score: 94
Period size: 31 Copynumber: 3.9 Consensus size: 32
1248058 CTAATGTAAC
* * *
1248068 TCTTAGGTAGGCTCTGCGGCCCTGAGAT-CAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATGTAT
*
1248099 TCTCCA-GTAGGCCCTGCGGCCCTAAGATGTAT
1 TCT-TAGGTAGGCCCTGCGGCCCTAAGATGTAT
* * * *
1248131 TCTTAGGTAGGCCTTACGGCCCCGAA-ATCTA-
1 TCTTAGGTAGGCCCTGCGG-CCCTAAGATGTAT
* * **
1248162 TCTTGGGTAGGCTCTTAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATGT
1248192 TCCCTTTAGG
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
30 5 0.07
31 41 0.57
32 21 0.29
33 5 0.07
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.28
Consensus pattern (32 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATGTAT
Found at i:1254502 original size:29 final size:29
Alignment explanation
Indices: 1254459--1254649 Score: 278
Period size: 29 Copynumber: 6.6 Consensus size: 29
1254449 ACCCGACCCA
* * *
1254459 GTGATATTTTAGTAAATATTTTGAAAAAG
1 GTGATATTTTGGTAATTATTTTTAAAAAG
*
1254488 GTGATATTTTGGTAATTATTTTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAAAG
1254517 GTGATATTTTGGTAATTATTTTTAAAATA-
1 GTGATATTTTGGTAATTATTTTTAAAA-AG
*
1254546 GTGATATTTTGGTAATTATTTTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAAAG
1254575 GTGATATTTTGGTAATTATTTTTAAAACA-
1 GTGATATTTTGGTAATTATTTTTAAAA-AG
* *
1254604 ATGATATTTTGGTAATTATTTTTAAAATG
1 GTGATATTTTGGTAATTATTTTTAAAAAG
*
1254633 GTGATATTTTTGTAATT
1 GTGATATTTTGGTAATT
1254650 TTTGAATGTG
Statistics
Matches: 147, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
29 147 1.00
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.49
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTTTAAAAAG
Found at i:1254609 original size:87 final size:87
Alignment explanation
Indices: 1254458--1254649 Score: 312
Period size: 87 Copynumber: 2.2 Consensus size: 87
1254448 GACCCGACCC
* **
1254458 AGTGATATTTTAGTAAATATTTTGAAAAAGGTGATATTTTGGTAATTATTTTTAAAACGGTGATA
1 AGTGATATTTTAGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTTAAAACAATGATA
1254523 TTTTGGTAATTATTTTTAAAAT
66 TTTTGGTAATTATTTTTAAAAT
* * *
1254545 AGTGATATTTTGGTAATTATTTTTAAAACGGTGATATTTTGGTAATTATTTTTAAAACAATGATA
1 AGTGATATTTTAGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTTAAAACAATGATA
1254610 TTTTGGTAATTATTTTTAAAAT
66 TTTTGGTAATTATTTTTAAAAT
* *
1254632 GGTGATATTTTTGTAATT
1 AGTGATATTTTAGTAATT
1254650 TTTGAATGTG
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 97 1.00
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.49
Consensus pattern (87 bp):
AGTGATATTTTAGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTTAAAACAATGATA
TTTTGGTAATTATTTTTAAAAT
Found at i:1255729 original size:26 final size:26
Alignment explanation
Indices: 1255675--1255729 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1255665 TAGGGTAACT
*
1255675 TTTTTATAGGATTTACTGCAGTATAA
1 TTTTTATAGGATTTACTGCACTATAA
* *
1255701 TTTTTAT-GAGATTTACTGGACTATGA
1 TTTTTATAG-GATTTACTGCACTATAA
1255727 TTT
1 TTT
1255730 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (26 bp):
TTTTTATAGGATTTACTGCACTATAA
Found at i:1257235 original size:17 final size:17
Alignment explanation
Indices: 1257213--1257258 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
1257203 GTTTCAGATT
*
1257213 CAGATTCTAATTCCTGA
1 CAGATTCCAATTCCTGA
1257230 CAGATTCCAATTCCTGA
1 CAGATTCCAATTCCTGA
1257247 CAGATTCCAATT
1 CAGATTCCAATT
1257259 TCCTCATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (17 bp):
CAGATTCCAATTCCTGA
Found at i:1259179 original size:28 final size:29
Alignment explanation
Indices: 1259146--1259201 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1259136 AAATTAATGT
1259146 GACCACCGAACT-TTCAATTGAATCAATA
1 GACCACCGAACTATTCAATTGAATCAATA
* * *
1259174 GACCACCTAACTATTTAATTGATTCAAT
1 GACCACCGAACTATTCAATTGAATCAAT
1259202 CAAATCACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (29 bp):
GACCACCGAACTATTCAATTGAATCAATA
Found at i:1259637 original size:16 final size:17
Alignment explanation
Indices: 1259601--1259637 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1259591 GATAAAAAAG
*
1259601 TAAACAAATTATTTGTT
1 TAAACAAATTATTTATT
1259618 TAAACAAATTA-TTATT
1 TAAACAAATTATTTATT
1259634 TAAA
1 TAAA
1259638 TTAATTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAACAAATTATTTATT
Found at i:1260914 original size:2 final size:2
Alignment explanation
Indices: 1260907--1260939 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1260897 ATTATAATAA
1260907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1260940 ATCAAATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1263348 original size:18 final size:18
Alignment explanation
Indices: 1263325--1263363 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1263315 TATCCCTTGA
1263325 AGTATGTTATTTATACCG
1 AGTATGTTATTTATACCG
*
1263343 AGTATGTTATTTATATCG
1 AGTATGTTATTTATACCG
1263361 AGT
1 AGT
1263364 GATTCTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (18 bp):
AGTATGTTATTTATACCG
Found at i:1263534 original size:19 final size:19
Alignment explanation
Indices: 1263512--1263561 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1263502 TTTGGTCACC
1263512 TAATTATTTTTTTATTACT
1 TAATTATTTTTTTATTACT
1263531 TAATTATTTTTTTATTACT
1 TAATTATTTTTTTATTACT
1263550 TAATTATTTTTT
1 TAATTATTTTTT
1263562 ATTTTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (19 bp):
TAATTATTTTTTTATTACT
Found at i:1265073 original size:23 final size:24
Alignment explanation
Indices: 1265046--1265094 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
1265036 CACGATCGAG
*
1265046 AAAGAAAACGAAAAA-GTGACACA
1 AAAGAAAAAGAAAAATGTGACACA
1265069 AAAGAAAAAGAAAAATGTGACACA
1 AAAGAAAAAGAAAAATGTGACACA
1265093 AA
1 AA
1265095 TCATAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.67, C:0.10, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAAAATGTGACACA
Found at i:1265077 original size:24 final size:23
Alignment explanation
Indices: 1265046--1265094 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
1265036 CACGATCGAG
1265046 AAAGAAAACGAAAAA-GTGACACA
1 AAAGAAAA-GAAAAATGTGACACA
1265069 AAAGAAAAAGAAAAATGTGACACA
1 AAAG-AAAAGAAAAATGTGACACA
1265093 AA
1 AA
1265095 TCATAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.67, C:0.10, G:0.16, T:0.06
Consensus pattern (23 bp):
AAAGAAAAGAAAAATGTGACACA
Found at i:1273272 original size:3 final size:3
Alignment explanation
Indices: 1273261--1273298 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1273251 GATAGGGAGG
1273261 AGA AGGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1273299 AGGAATAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1273765 original size:19 final size:19
Alignment explanation
Indices: 1273741--1273845 Score: 120
Period size: 19 Copynumber: 5.2 Consensus size: 19
1273731 GCGATTTTGA
1273741 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
1273760 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
1273779 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
1273799 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
1273823 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
1273842 AAAA
1 AAAA
1273846 ATCCAAAATA
Statistics
Matches: 76, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
19 52 0.68
20 3 0.04
22 8 0.11
24 3 0.04
25 10 0.13
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:1274240 original size:14 final size:14
Alignment explanation
Indices: 1274221--1274259 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1274211 CGTTGCGATA
1274221 GTCAAAATCGCAAC
1 GTCAAAATCGCAAC
1274235 GTCAAAATCGCAAC
1 GTCAAAATCGCAAC
1274249 GTCAAAATCGC
1 GTCAAAATCGC
1274260 GTTGCGAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.15
Consensus pattern (14 bp):
GTCAAAATCGCAAC
Found at i:1274316 original size:19 final size:19
Alignment explanation
Indices: 1274292--1274328 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1274282 TGCGATACGG
1274292 GAGATCGCATTACGATTTA
1 GAGATCGCATTACGATTTA
*
1274311 GAGATCGCATTGCGATTT
1 GAGATCGCATTACGATTT
1274329 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1281685 original size:15 final size:15
Alignment explanation
Indices: 1281659--1281738 Score: 69
Period size: 15 Copynumber: 5.3 Consensus size: 15
1281649 TTCACAAAAT
*
1281659 AATAAAGTAAAAGTA
1 AATAAAGAAAAAGTA
1281674 AATAATA-AAAAAG-A
1 AATAA-AGAAAAAGTA
*
1281688 TAATAAAGTAAAAGTA
1 -AATAAAGAAAAAGTA
1281704 AATAATA-AAAAAG-A
1 AATAA-AGAAAAAGTA
*
1281718 TAATAAAGTAAAAGTA
1 -AATAAAGAAAAAGTA
1281734 AATAA
1 AATAA
1281739 GGCAAACTCG
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.08
15 45 0.85
16 4 0.08
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
AATAAAGAAAAAGTA
Found at i:1281693 original size:30 final size:30
Alignment explanation
Indices: 1281657--1281738 Score: 164
Period size: 30 Copynumber: 2.7 Consensus size: 30
1281647 AATTCACAAA
1281657 ATAATAAAGTAAAAGTAAATAATAAAAAAG
1 ATAATAAAGTAAAAGTAAATAATAAAAAAG
1281687 ATAATAAAGTAAAAGTAAATAATAAAAAAG
1 ATAATAAAGTAAAAGTAAATAATAAAAAAG
1281717 ATAATAAAGTAAAAGTAAATAA
1 ATAATAAAGTAAAAGTAAATAA
1281739 GGCAAACTCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.21
Consensus pattern (30 bp):
ATAATAAAGTAAAAGTAAATAATAAAAAAG
Found at i:1287251 original size:30 final size:31
Alignment explanation
Indices: 1287185--1287277 Score: 125
Period size: 30 Copynumber: 3.0 Consensus size: 31
1287175 GAGAAGAAAC
* *
1287185 ATGTTGAAGTGAGTGAAGATAGTGGTGAGGAAG
1 ATGTTAAAGTGAGTGAAGATGGTGGTGA-G-AG
1287218 ATGTTAAAGTGAGTGAAGATGGTGGTGAG-G
1 ATGTTAAAGTGAGTGAAGATGGTGGTGAGAG
* *
1287248 ATGTTAAAGTCAGTGAAGATGATGGTGAGA
1 ATGTTAAAGTGAGTGAAGATGGTGGTGAGA
1287278 AGCTTGAGGA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
30 28 0.51
32 1 0.02
33 26 0.47
ACGTcount: A:0.33, C:0.01, G:0.40, T:0.26
Consensus pattern (31 bp):
ATGTTAAAGTGAGTGAAGATGGTGGTGAGAG
Found at i:1294700 original size:24 final size:24
Alignment explanation
Indices: 1294673--1294745 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 24
1294663 CGTTCATTTA
1294673 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * * *
1294697 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
1294721 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
1294745 C
1 C
1294746 ATTCATTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 40 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.51
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:1294705 original size:14 final size:14
Alignment explanation
Indices: 1294683--1294739 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
1294673 CGTTCGTGAA
*
1294683 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
1294697 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
1294711 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
1294721 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
1294735 CGTTT
1 CGTTT
1294740 ATGTTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:1294755 original size:24 final size:24
Alignment explanation
Indices: 1294684--1294758 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
1294674 GTTCGTGAAC
* * * *
1294684 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCATTCGATTAT
*
1294708 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCATTCGATTAT
1294732 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCATTCGA-TTAT
1294756 GTT
1 GTT
1294759 TAACACAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCGATTAT
Found at i:1295498 original size:10 final size:10
Alignment explanation
Indices: 1295483--1295557 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1295473 GGGTCTCCAA
1295483 CGTTTATGTT
1 CGTTTATGTT
1295493 CGTTTATGTT
1 CGTTTATGTT
1295503 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1295514 ATGTTCGTGTT
1 -CGTTTATGTT
*
1295525 CGTTTATGTC
1 CGTTTATGTT
1295535 CG----TGTT
1 CGTTTATGTT
1295541 CGTTTATGTT
1 CGTTTATGTT
1295551 CGTTTAT
1 CGTTTAT
1295558 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
10 33 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.13, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1295514 original size:16 final size:16
Alignment explanation
Indices: 1295489--1295553 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1295479 CCAACGTTTA
1295489 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1295505 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1295521 TGTTCGTTTATGTCCG
1 TGTTCGTTTATGTTCG
1295537 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1295553 T
1 T
1295554 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.14, G:0.23, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1295644 original size:16 final size:16
Alignment explanation
Indices: 1295623--1295655 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1295613 AAAAAAATTT
1295623 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1295639 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1295655 T
1 T
1295656 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1305135 original size:19 final size:19
Alignment explanation
Indices: 1305089--1305135 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1305079 CCTTTTTAAT
*
1305089 AAATTTTCTGAATATTTTA
1 AAATTTTATGAATATTTTA
*
1305108 ACAACTTTAT-AATACTTTTA
1 A-AATTTTATGAATA-TTTTA
1305128 AAATTTTA
1 AAATTTTA
1305136 ATAAATTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (19 bp):
AAATTTTATGAATATTTTA
Found at i:1307867 original size:17 final size:17
Alignment explanation
Indices: 1307845--1307884 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
1307835 ACGGTCAACT
1307845 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
1307862 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
1307879 GTCAAC
1 GTCAAC
1307885 GGTCAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.17
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGG
Found at i:1316128 original size:32 final size:32
Alignment explanation
Indices: 1316087--1316157 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1316077 TTGATAGATT
* *
1316087 AAGATAAAGCGTAAGCTGCTAAGATCACAATC
1 AAGAGAAAGCATAAGCTGCTAAGATCACAATC
1316119 AAGAGAAAGCATAAGCTGCTAAGATCACAATC
1 AAGAGAAAGCATAAGCTGCTAAGATCACAATC
1316151 AAGAGAA
1 AAGAGAA
1316158 GACGTTAGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (32 bp):
AAGAGAAAGCATAAGCTGCTAAGATCACAATC
Found at i:1318002 original size:21 final size:21
Alignment explanation
Indices: 1317978--1318030 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1317968 CGTGGAGGGT
1317978 ATCGATTCCC-TAAAAGGGGAA
1 ATCGATTCCCATAAAAGGGG-A
*
1317999 ATCGATTCCCATTCAAAGGGGA
1 ATCGATTCCCA-TAAAAGGGGA
*
1318021 ATCGGTTCCC
1 ATCGATTCCC
1318031 CTTCATGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.36
22 10 0.36
23 8 0.29
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
ATCGATTCCCATAAAAGGGGA
Found at i:1318041 original size:22 final size:22
Alignment explanation
Indices: 1317978--1318051 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
1317968 CGTGGAGGGT
** *
1317978 ATCGATTCCC-TAAAAGGGGAA
1 ATCGATTCCCATTCAAGGGGGA
*
1317999 ATCGATTCCCATTCAAAGGGGA
1 ATCGATTCCCATTCAAGGGGGA
* * * *
1318021 ATCGGTTCCCCTTCATGGGGGT
1 ATCGATTCCCATTCAAGGGGGA
1318043 ATCGATTCC
1 ATCGATTCC
1318052 TCCTACTCTA
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 10 0.24
22 32 0.76
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (22 bp):
ATCGATTCCCATTCAAGGGGGA
Found at i:1320054 original size:18 final size:18
Alignment explanation
Indices: 1320031--1320066 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1320021 GTTCTCCAAC
1320031 GTCATGTCTAACGTCATT
1 GTCATGTCTAACGTCATT
1320049 GTCATGTCTAACGTCATT
1 GTCATGTCTAACGTCATT
1320067 TGCTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (18 bp):
GTCATGTCTAACGTCATT
Found at i:1323579 original size:34 final size:32
Alignment explanation
Indices: 1323517--1323586 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1323507 ACCTTACAAC
* *
1323517 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
1323549 TCCCTAGATTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
1323583 TCCC
1 TCCC
1323587 CTTTACAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:1324044 original size:18 final size:19
Alignment explanation
Indices: 1324017--1324080 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1324007 GCCTCGGGGC
* *
1324017 ACTGTGCAAACAGTGA-TT
1 ACTGTTCAAACAGTAATTT
*
1324035 ACTGTTCAAATAGTAATTT
1 ACTGTTCAAACAGTAATTT
* *
1324054 ACTGTTCAAATAGTAAATT
1 ACTGTTCAAACAGTAATTT
*
1324073 ACTATTCA
1 ACTGTTCA
1324081 TAAAATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 13 0.32
19 27 0.68
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (19 bp):
ACTGTTCAAACAGTAATTT
Found at i:1324057 original size:19 final size:19
Alignment explanation
Indices: 1324032--1324080 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1324022 GCAAACAGTG
1324032 ATTACTGTTCAAATAGTAA
1 ATTACTGTTCAAATAGTAA
*
1324051 TTTACTGTTCAAATAGTAA
1 ATTACTGTTCAAATAGTAA
*
1324070 ATTACTATTCA
1 ATTACTGTTCA
1324081 TAAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (19 bp):
ATTACTGTTCAAATAGTAA
Found at i:1324176 original size:29 final size:31
Alignment explanation
Indices: 1324144--1324203 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1324134 AAATTTTGAA
*
1324144 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1324173 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1324204 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1326321 original size:42 final size:41
Alignment explanation
Indices: 1326124--1326428 Score: 298
Period size: 42 Copynumber: 7.4 Consensus size: 41
1326114 AAAATGATGT
* * *
1326124 AATAGTCATGCACTTTAGCGGCGTTTTT-TATAAACGCCGG
1 AATAGTCATGCACTTTAGTGGCATTTTTGTATAAACGCCGC
* * * **
1326164 AATAATAATGCATTTTAGTGGCA-TTTTGTAATAAACAACGC
1 AATAGTCATGCACTTTAGTGGCATTTTTGT-ATAAACGCCGC
* **
1326205 AATAGTCATGCACTTTAGCGGTGTTTTTG-ATAAACGCCGC
1 AATAGTCATGCACTTTAGTGGCATTTTTGTATAAACGCCGC
* * *
1326245 AATAGTCATG--CTTTAGTGACCA-TTTTGTAATAAACGTCAC
1 AATAGTCATGCACTTTAGTG-GCATTTTTGT-ATAAACGCCGC
* **
1326285 AATAGTCATGCACTTTAGTGGCATTTTTGCAGTAAACATCGC
1 AATAGTCATGCACTTTAGTGGCATTTTTGTA-TAAACGCCGC
* * *
1326327 AATAGTCATGTACTTTAGTGGCGTTTTTGCAGTAAACGCCGC
1 AATAGTCATGCACTTTAGTGGCATTTTTGTA-TAAACGCCGC
*
1326369 AATAGTCATGCACTTTAGTGGCATTTTTGTAATAAATGCCGC
1 AATAGTCATGCACTTTAGTGGCATTTTTGT-ATAAACGCCGC
** *
1326411 TGTAGTCATGAACTTTAG
1 AATAGTCATGCACTTTAG
1326429 CAACATTTTT
Statistics
Matches: 217, Mismatches: 37, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
38 12 0.06
39 4 0.02
40 57 0.26
41 28 0.13
42 115 0.53
43 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (41 bp):
AATAGTCATGCACTTTAGTGGCATTTTTGTATAAACGCCGC
Found at i:1327036 original size:85 final size:85
Alignment explanation
Indices: 1326893--1327062 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
1326883 CATTCCTCGG
1326893 CACAAATTTTAGTATTATTTTCATAGCTGTTTCGATACTCACATTGTCAATCTTGGGGTTTTGCT
1 CACAAATTTTAGTATTATTTTCATAGCTGTTTCGATACTCACATTGTCAATCTTGGGGTTTTGCT
1326958 TTGGTTTATTTGTCTGTACA
66 TTGGTTTATTTGTCTGTACA
1326978 CACAAATTTTAGTATTATTTTCATAGCTGTTTCGATACTCACATTGTCAATCTTGGGGTTTTGCT
1 CACAAATTTTAGTATTATTTTCATAGCTGTTTCGATACTCACATTGTCAATCTTGGGGTTTTGCT
1327043 TTGGTTTATTTGTCTGTACA
66 TTGGTTTATTTGTCTGTACA
1327063 GCTAATAAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.47
Consensus pattern (85 bp):
CACAAATTTTAGTATTATTTTCATAGCTGTTTCGATACTCACATTGTCAATCTTGGGGTTTTGCT
TTGGTTTATTTGTCTGTACA
Found at i:1337160 original size:18 final size:18
Alignment explanation
Indices: 1337139--1337179 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1337129 CGCGCTATCT
*
1337139 TACGCCAGAAAGTCCTCG
1 TACGCCAAAAAGTCCTCG
1337157 TACGCCAAAAAGTCCTCG
1 TACGCCAAAAAGTCCTCG
1337175 TACGC
1 TACGC
1337180 ATCATTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TACGCCAAAAAGTCCTCG
Found at i:1350914 original size:2 final size:2
Alignment explanation
Indices: 1350907--1350938 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1350897 CTTATTTTCA
1350907 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
1350939 TGAATAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1351014 original size:38 final size:38
Alignment explanation
Indices: 1350972--1351062 Score: 157
Period size: 38 Copynumber: 2.4 Consensus size: 38
1350962 GCTGGCTCCT
*
1350972 ACATTAGTTTTAGGAAATCAAATAAGTTGGAATCTTC-A
1 ACATTAGTTTTAGGAAATCAAATAAGTTAGAATC-TCAA
1351010 ACATTAGTTTTAGGAAATCAAATAAGTTAGAATCTCAA
1 ACATTAGTTTTAGGAAATCAAATAAGTTAGAATCTCAA
1351048 ACATTAGTTTTAGGA
1 ACATTAGTTTTAGGA
1351063 TGATTGCTAC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 2 0.04
38 49 0.96
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (38 bp):
ACATTAGTTTTAGGAAATCAAATAAGTTAGAATCTCAA
Found at i:1351037 original size:19 final size:19
Alignment explanation
Indices: 1350977--1351037 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
1350967 CTCCTACATT
1350977 AGTTTTAGGAAATCAAATA
1 AGTTTTAGGAAATCAAATA
* *
1350996 AG--TT-GGAATCTTCAACATT
1 AGTTTTAGGAA--ATCAA-ATA
1351015 AGTTTTAGGAAATCAAATA
1 AGTTTTAGGAAATCAAATA
1351034 AGTT
1 AGTT
1351038 AGAATCTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 4 0.12
17 2 0.06
18 4 0.12
19 12 0.38
20 4 0.12
21 2 0.06
22 4 0.12
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (19 bp):
AGTTTTAGGAAATCAAATA
Found at i:1354660 original size:163 final size:166
Alignment explanation
Indices: 1354471--1354797 Score: 590
Period size: 163 Copynumber: 2.0 Consensus size: 166
1354461 CATCATAGAT
* *
1354471 TAATAAAAAATATATATAAAACTTGGCAAAAAGGCGTCAGAGGCCCTCAAACTTTAAAAAAAAAA
1 TAATAAAAAATATATATAAAACTTGGCAAAAAGGCGTCAAAGGCCCTCAAACTTAAAAAAAAAAA
1354536 AACAATGTGGTCCATATCGTGTTTTGGATCAA-ATGGCCCTCCAACTCAAAAAAAAAACTCAATG
66 AACAATGTGGTCCATATCGTGTTTTGGATCAATATGGCCCTCCAACTC-AAAAAAAAACTCAATG
1354600 TGA-TTTTTGACCAACGTTTTATGTTTTTGACCAATG
130 TGACTTTTTGACCAACGTTTTATGTTTTTGACCAATG
1354636 TAAT-AAAAA-ATATATAAAACTTGGCAAAAAGGCGTCAAAGGCCCTCAAACTTAAAAAAAAAAA
1 TAATAAAAAATATATATAAAACTTGGCAAAAAGGCGTCAAAGGCCCTCAAACTTAAAAAAAAAAA
1354699 AACAATGTGGTCCATATCGTGTTTTGGATCAATATGGCCCTCCAACTCAAAAAAAAACTCAATGT
66 AACAATGTGGTCCATATCGTGTTTTGGATCAATATGGCCCTCCAACTCAAAAAAAAACTCAATGT
*
1354764 GACTTTTTGATCAACGTTTTATGTTTTTGACCAA
131 GACTTTTTGACCAACGTTTTATGTTTTTGACCAA
1354798 CGACGCCGTT
Statistics
Matches: 157, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
163 103 0.66
164 50 0.32
165 4 0.03
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (166 bp):
TAATAAAAAATATATATAAAACTTGGCAAAAAGGCGTCAAAGGCCCTCAAACTTAAAAAAAAAAA
AACAATGTGGTCCATATCGTGTTTTGGATCAATATGGCCCTCCAACTCAAAAAAAAACTCAATGT
GACTTTTTGACCAACGTTTTATGTTTTTGACCAATG
Found at i:1357165 original size:18 final size:18
Alignment explanation
Indices: 1357125--1357179 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
1357115 GGGGATTTTT
*
1357125 TAAAATAAAAAATAA-GAA
1 TAAAATAAAAAA-AATTAA
*
1357143 TTAAATAAAAGAAAATTAA
1 TAAAATAAAA-AAAATTAA
1357162 TAAAATAAAAAAAATTAA
1 TAAAATAAAAAAAATTAA
1357180 ATAGAGTGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
TAAAATAAAAAAAATTAA
Found at i:1357182 original size:19 final size:19
Alignment explanation
Indices: 1357131--1357182 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1357121 TTTTTAAAAT
* *
1357131 AAAAAATAAGAATTAAATAA
1 AAAAAATTA-AATAAAATAA
1357151 AAGAAAATT-AATAAAATAA
1 AA-AAAATTAAATAAAATAA
1357170 AAAAAATTAAATA
1 AAAAAATTAAATA
1357183 GAGTGAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 15 0.54
20 2 0.07
21 5 0.18
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAAAATTAAATAAAATAA
Found at i:1358107 original size:19 final size:20
Alignment explanation
Indices: 1358073--1358113 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
1358063 AGTAAAAATT
1358073 AACTAAAATAAGCGCTTATC
1 AACTAAAATAAGCGCTTATC
1358093 AACTAAAAT-AGCGCTTATC
1 AACTAAAATAAGCGCTTATC
1358112 AA
1 AA
1358114 TTCCCCCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (20 bp):
AACTAAAATAAGCGCTTATC
Found at i:1359486 original size:13 final size:13
Alignment explanation
Indices: 1359463--1359499 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1359453 CTGTTCAGAA
1359463 AAAAAATATAAAAT
1 AAAAAA-ATAAAAT
1359477 AAAAAAATAAAAT
1 AAAAAAATAAAAT
*
1359490 AATAAAATAA
1 AAAAAAATAA
1359500 TGAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:1359505 original size:16 final size:16
Alignment explanation
Indices: 1359462--1359496 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1359452 TCTGTTCAGA
*
1359462 AAAAAAATATAA-AAT
1 AAAAAAATAAAATAAT
1359477 AAAAAAATAAAATAAT
1 AAAAAAATAAAATAAT
1359493 AAAA
1 AAAA
1359497 TAATGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAAAATAAAATAAT
Found at i:1359506 original size:5 final size:5
Alignment explanation
Indices: 1359498--1359531 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
1359488 ATAATAAAAT
1359498 AATGA AATGAAA AATGA AATGA AATGA AATGA AA
1 AATGA AATG--A AATGA AATGA AATGA AATGA AA
1359532 CAAAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 22 0.81
7 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (5 bp):
AATGA
Found at i:1364440 original size:2 final size:2
Alignment explanation
Indices: 1364435--1364494 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1364425 ATACTGAATA
1364435 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
1364477 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1364495 TGATAAATTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1379359 original size:97 final size:98
Alignment explanation
Indices: 1379193--1379387 Score: 383
Period size: 97 Copynumber: 2.0 Consensus size: 98
1379183 TGCTGGGTGC
1379193 GGAGGGTGGCACCGGTGTTCCCTTTGGAAGCTGATGAGGATCATTGGTCCGTACTTTCCGGCGTG
1 GGAGGGTGGCACCGGTGTTCCCTTTGGAAGCTGATGAGGATCATTGGTCCGTACTTTCCGGCGTG
1379258 TCTTTGAGTCGGAGACCCCACATGTGA-CTCCT
66 TCTTTGAGTCGGAGACCCCACATGTGACCTCCT
1379290 GGAGGGTGGCACCGGTGTTCCCTTTGGAAGCTGATGAGGATCATTGGTCCGTACTTTCCGGCGTG
1 GGAGGGTGGCACCGGTGTTCCCTTTGGAAGCTGATGAGGATCATTGGTCCGTACTTTCCGGCGTG
1379355 TCTTTGAGTCGGAGACCCCACATGTGACCTCCT
66 TCTTTGAGTCGGAGACCCCACATGTGACCTCCT
1379388 CATACGGTGG
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 92 0.95
98 5 0.05
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (98 bp):
GGAGGGTGGCACCGGTGTTCCCTTTGGAAGCTGATGAGGATCATTGGTCCGTACTTTCCGGCGTG
TCTTTGAGTCGGAGACCCCACATGTGACCTCCT
Found at i:1382574 original size:107 final size:104
Alignment explanation
Indices: 1382377--1382584 Score: 389
Period size: 107 Copynumber: 2.0 Consensus size: 104
1382367 AAAATGAAAA
1382377 ATCTACAAATTATAGTTTTTGCTGTTGGTTGAAATATCTTTTCCACCATAATTTTTTTCTCATCT
1 ATCTACAAATTATAGTTTTTGCTGTTGGTTGAAATATCTTTTCCACCATAATTTTTTTCTCATCT
1382442 TTACCTGTTTGACATTGATTTTACGGTCAAAATGGATTT
66 TTACCTGTTTGACATTGATTTTACGGTCAAAATGGATTT
1382481 ATCTACAAATTATAGTTTTTGCTGTTGGTTTGAAATTATCTTTTCCACCATAATTTTTTTCTCAT
1 ATCTACAAATTATAGTTTTTGCTGTTGG-TTGAAA-TATCTTTTCCACCATAATTTTTTTCTCA-
1382546 TCTTTACCTGTTTGACATTGATTTTACGGTCAAAATGGA
63 TCTTTACCTGTTTGACATTGATTTTACGGTCAAAATGGA
1382585 CTTTTTAACT
Statistics
Matches: 101, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
104 28 0.28
105 6 0.06
106 28 0.28
107 39 0.39
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (104 bp):
ATCTACAAATTATAGTTTTTGCTGTTGGTTGAAATATCTTTTCCACCATAATTTTTTTCTCATCT
TTACCTGTTTGACATTGATTTTACGGTCAAAATGGATTT
Found at i:1387619 original size:19 final size:19
Alignment explanation
Indices: 1387595--1387640 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1387585 AAATTTAGTT
1387595 TTTATATTAATTACAATTC
1 TTTATATTAATTACAATTC
** *
1387614 TTTATATTTTTTATAATTC
1 TTTATATTAATTACAATTC
1387633 -TTATATTA
1 TTTATATTA
1387641 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:1387643 original size:14 final size:14
Alignment explanation
Indices: 1387624--1387671 Score: 80
Period size: 14 Copynumber: 3.4 Consensus size: 14
1387614 TTTATATTTT
1387624 TTATAATTCTTATA
1 TTATAATTCTTATA
1387638 TTATAATTCTTATA
1 TTATAATTCTTATA
1387652 TTATAATT-TGTATA
1 TTATAATTCT-TATA
1387666 TTATAA
1 TTATAA
1387672 ATTTAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 1 0.03
14 32 0.97
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (14 bp):
TTATAATTCTTATA
Found at i:1387683 original size:85 final size:84
Alignment explanation
Indices: 1387584--1387742 Score: 250
Period size: 85 Copynumber: 1.9 Consensus size: 84
1387574 TTATCATAAT
* *
1387584 TAAATTTAGTTTTTATATTAATT-ACAATTCTTTATATTTTTTATAATTCTTATATTAT-AATTC
1 TAAATTTAATTTTTATATTAATTCA-AATTCTTTATATTATTTATAATTCTTATATTATAAATT-
1387647 TTATATTATAATTTGTATATTA
64 TTAT-TTATAATTTGTATATTA
*
1387669 TAAATTTAATTTTTATATTAATTCAAATTTTTTATATTATTTATAATTCTTATATTATAAATTTT
1 TAAATTTAATTTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTTT
1387734 ATTTATAAT
66 ATTTATAAT
1387743 CACTAAATTA
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
84 7 0.10
85 57 0.83
86 5 0.07
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (84 bp):
TAAATTTAATTTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTTT
ATTTATAATTTGTATATTA
Found at i:1387699 original size:18 final size:19
Alignment explanation
Indices: 1387675--1387725 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1387665 ATTATAAATT
1387675 TAATTTTTATATTAATTCA
1 TAATTTTTATATTAATTCA
*
1387694 -AATTTTTTATATT-ATTTA
1 TAA-TTTTTATATTAATTCA
*
1387712 TAATTCTTATATTA
1 TAATTTTTATATTA
1387726 TAAATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATTTTTATATTAATTCA
Found at i:1387739 original size:13 final size:14
Alignment explanation
Indices: 1387705--1387741 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1387695 ATTTTTTATA
1387705 TTATTTAT-AATTC
1 TTATTTATAAATTC
1387718 TTATATTATAAATT-
1 TTAT-TTATAAATTC
1387732 TTATTTATAA
1 TTATTTATAA
1387742 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:1388010 original size:15 final size:15
Alignment explanation
Indices: 1387987--1388017 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1387977 TGCTCTAAGA
*
1387987 TCTTGTAATTAAGGT
1 TCTTATAATTAAGGT
1388002 TCTTATAATTAAGGT
1 TCTTATAATTAAGGT
1388017 T
1 T
1388018 TTACAAGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (15 bp):
TCTTATAATTAAGGT
Found at i:1390806 original size:60 final size:61
Alignment explanation
Indices: 1390717--1390857 Score: 196
Period size: 60 Copynumber: 2.3 Consensus size: 61
1390707 TTGTCCCTTA
* * *
1390717 ATTTTAAATTTATTCAATTTAGTCTAAATTTAATGATT-TAATATATTAATTTAAGCTTCAT
1 ATTTAAAATTTGTTCAATTTAGTCCAAATTTAATG-TTATAATATATTAATTTAAGCTTCAT
* * * *
1390778 ATTTCAACTTT-TTCAATTTATTCCAAATTTAATGTTATAATTTATTAATTTAAGCTTCAT
1 ATTTAAAATTTGTTCAATTTAGTCCAAATTTAATGTTATAATATATTAATTTAAGCTTCAT
1390838 ATTTAAAATTTGTTCAATTT
1 ATTTAAAATTTGTTCAATTT
1390858 GATCCTTATA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
59 2 0.03
60 52 0.73
61 17 0.24
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (61 bp):
ATTTAAAATTTGTTCAATTTAGTCCAAATTTAATGTTATAATATATTAATTTAAGCTTCAT
Found at i:1390943 original size:16 final size:16
Alignment explanation
Indices: 1390914--1390947 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1390904 ATTAATAAAT
1390914 TATATATAGTTTTATA
1 TATATATAGTTTTATA
1390930 TATACTATAG-TTTATA
1 TATA-TATAGTTTTATA
1390946 TA
1 TA
1390948 CTAATGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TATATATAGTTTTATA
Found at i:1391003 original size:18 final size:18
Alignment explanation
Indices: 1390980--1391142 Score: 130
Period size: 18 Copynumber: 9.4 Consensus size: 18
1390970 TGTATCTACC
*
1390980 ATATACTATATAGGTTAT
1 ATATACTATATAGTTTAT
*
1390998 ATATACTA-AT-G--AACT
1 ATATACTATATAGTTTA-T
*
1391013 ATATAATATATAGTTTAT
1 ATATACTATATAGTTTAT
*
1391031 ATATACTA-AT-G--AACT
1 ATATACTATATAGTTTA-T
*
1391046 ATATAATATATAGTTTAT
1 ATATACTATATAGTTTAT
**
1391064 ATATACTA-AT-GAACTAT
1 ATATACTATATAG-TTTAT
* *
1391081 ATATAATGTATAGTTTAT
1 ATATACTATATAGTTTAT
*
1391099 ATATACCATATAGTTTAT
1 ATATACTATATAGTTTAT
*
1391117 ATATATTATATAGTTTAT
1 ATATACTATATAGTTTAT
1391135 ATATACTA
1 ATATACTA
1391143 ATAAACTATA
Statistics
Matches: 112, Mismatches: 20, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
14 2 0.02
15 16 0.14
16 7 0.06
17 17 0.15
18 67 0.60
19 3 0.03
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (18 bp):
ATATACTATATAGTTTAT
Found at i:1391023 original size:33 final size:33
Alignment explanation
Indices: 1390980--1391166 Score: 241
Period size: 33 Copynumber: 5.5 Consensus size: 33
1390970 TGTATCTACC
* *
1390980 ATATACTATATAGGTTATATATACTAATGAACT
1 ATATAATATATAGTTTATATATACTAATGAACT
1391013 ATATAATATATAGTTTATATATACTAATGAACT
1 ATATAATATATAGTTTATATATACTAATGAACT
1391046 ATATAATATATAGTTTATATATACTAATGAACTAT
1 ATATAATATATAGTTTATATATACTAATGAAC--T
* **
1391081 ATATAATGTATAGTTTATATATACCATATAGTTTA-T
1 ATATAATATATAGTTTATATATA-C-TA-A-TGAACT
* *
1391117 ATATATTATATAGTTTATATATACTAATAAACT
1 ATATAATATATAGTTTATATATACTAATGAACT
*
1391150 ATATAATGTATAGTTTA
1 ATATAATATATAGTTTA
1391167 GGGTTTAGAA
Statistics
Matches: 136, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
32 2 0.01
33 80 0.59
34 2 0.01
35 24 0.18
36 23 0.17
37 2 0.01
38 1 0.01
39 2 0.01
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (33 bp):
ATATAATATATAGTTTATATATACTAATGAACT
Found at i:1391055 original size:55 final size:52
Alignment explanation
Indices: 1390942--1391057 Score: 119
Period size: 55 Copynumber: 2.1 Consensus size: 52
1390932 TACTATAGTT
* * *
1390942 TATATACTAATGAACTATATAAATAGTTTGTATCTACCATATACTATATAGGTTA
1 TATATACTAATGAACTATATAAATAGTTTATATATACAATATACTATATA-G--A
1390997 TATATACTAATGAACTATATAATATATAGTTTATATATACTAATGA-ACTATATA-A
1 TATATACTAATGAACTATAT-A-A-ATAGTTTATATATAC-AAT-ATACTATATAGA
1391052 TATATA
1 TATATA
1391058 GTTTATATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
55 27 0.51
56 1 0.02
57 1 0.02
58 13 0.25
59 10 0.19
60 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.41
Consensus pattern (52 bp):
TATATACTAATGAACTATATAAATAGTTTATATATACAATATACTATATAGA
Found at i:1391220 original size:2 final size:2
Alignment explanation
Indices: 1391203--1391332 Score: 66
Period size: 2 Copynumber: 60.0 Consensus size: 2
1391193 ATATGTAAAT
*
1391203 TA TA CTA TA TA GTA TA TA TA GTT TA TA TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * ** * *
1391246 TA TA AA TA TA AA CTA TA GTA TA TA TA TA GG TCA TA TG TA AA CTA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA T-A TA TA TA TA -TA
*
1391290 TA TA GTA TA TA AA TA TCA -A CTA TA GTA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA T-A TA -TA TA -TA TA TA TA TA TA TA TA TA
1391333 GGTCATATGT
Statistics
Matches: 98, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
1 2 0.02
2 78 0.80
3 18 0.18
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1391222 original size:9 final size:9
Alignment explanation
Indices: 1391208--1391271 Score: 51
Period size: 9 Copynumber: 6.7 Consensus size: 9
1391198 TAAATTATAC
1391208 TATATAGTA
1 TATATAGTA
1391217 TATATAGTTTA
1 TATATAG--TA
1391228 TATATA-TAA
1 TATATAGT-A
1391237 TATATAGTA
1 TATATAGTA
1391246 TATAAATA-TA
1 TAT--ATAGTA
*
1391256 AACTATAGTA
1 TA-TATAGTA
1391266 TATATA
1 TATATA
1391272 TAGGTCATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
8 1 0.02
9 25 0.56
10 7 0.16
11 12 0.27
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (9 bp):
TATATAGTA
Found at i:1391262 original size:29 final size:29
Alignment explanation
Indices: 1391198--1391274 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
1391188 AGTTCATATG
* * *
1391198 TAAAT-TATACTATATAGTATATATAGTT
1 TAAATATATAATATATAGTATATATAATA
*
1391226 TATATATATAATATATAGTATATA-AATA
1 TAAATATATAATATATAGTATATATAATA
1391254 TAAACTATAGTATATATATAG
1 TAAA-TATA-TA-ATATATAG
1391275 GTCATATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 9 0.22
29 21 0.52
30 2 0.05
31 8 0.20
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (29 bp):
TAAATATATAATATATAGTATATATAATA
Found at i:1391292 original size:51 final size:51
Alignment explanation
Indices: 1391198--1391324 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
1391188 AGTTCATATG
* * *
1391198 TAAAT-TATACTATA-TAGTATATATAGTTTATATATATAATATATAGTATA
1 TAAATATAAACTATAGTA-TATATATAGGTCATATATATAATATATAGTATA
*
1391248 TAAATATAAACTATAGTATATATATAGGTCATATGTA-AACTATATAGTATA
1 TAAATATAAACTATAGTATATATATAGGTCATATATATAA-TATATAGTATA
*
1391299 TAAATATCAACTATAGTATATATATA
1 TAAATATAAACTATAGTATATATATA
1391325 TATATATAGG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
50 7 0.10
51 60 0.87
52 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (51 bp):
TAAATATAAACTATAGTATATATATAGGTCATATATATAATATATAGTATA
Found at i:1391293 original size:20 final size:19
Alignment explanation
Indices: 1391268--1391363 Score: 56
Period size: 20 Copynumber: 4.8 Consensus size: 19
1391258 CTATAGTATA
*
1391268 TATATAGGTCATATGTAAAC
1 TATATAGGT-ATATATAAAC
1391288 TATATA-GTATATAAATATCAAC
1 TATATAGGTATAT--ATA--AAC
*
1391310 TATAGTA--TATATATATA-
1 TATA-TAGGTATATATAAAC
*
1391327 TATATAGGTCATATGTAAAC
1 TATATAGGT-ATATATAAAC
*
1391347 TATATAGTTTATATATA
1 TATATAG-GTATATATA
1391364 TAGTTCATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
16 2 0.03
17 4 0.07
18 6 0.10
19 9 0.15
20 24 0.40
21 1 0.02
22 12 0.20
23 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (19 bp):
TATATAGGTATATATAAAC
Found at i:1391334 original size:59 final size:58
Alignment explanation
Indices: 1391259--1391472 Score: 197
Period size: 59 Copynumber: 3.6 Consensus size: 58
1391249 AAATATAAAC
1391259 TATAGTATATATATAGGTCATATGTAAACTATATAGTATATAAATATCAACTATAGTATA
1 TATA-TATATATATAGGTCATATGTAAACTATATAGTATATAAATAT-AACTATAGTATA
* * **
1391319 TATATATATATATAGGTCATATGTAAACTATATAGTTTATATATATAGTTCATATGTA-A
1 TATATATATATATAGGTCATATGTAAACTATATAGTATATAAATATAACT-ATA-GTATA
* *
1391378 -ATAT-TA-ACTATAGTTTATATGTAAACTATAGTTCA-TATATAAATATAAACCT-TAGTATA
1 TATATATATA-TATAGGTCATATGTAAACTATA--T-AGTATATAAATAT-AA-CTATAGTATA
*
1391437 TATATATTTTTATATATAGTTCATATGTAAACTATA
1 TATATA----TATATATAGGTCATATGTAAACTATA
1391473 GTTCATATAT
Statistics
Matches: 127, Mismatches: 11, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
56 1 0.01
57 22 0.17
58 9 0.07
59 57 0.45
60 13 0.10
61 1 0.01
65 23 0.18
66 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (58 bp):
TATATATATATATAGGTCATATGTAAACTATATAGTATATAAATATAACTATAGTATA
Found at i:1391365 original size:33 final size:32
Alignment explanation
Indices: 1391259--1391378 Score: 128
Period size: 33 Copynumber: 3.9 Consensus size: 32
1391249 AAATATAAAC
1391259 TATAG-TATATATATAGGTCATATGTAAACTA
1 TATAGTTATATATATAGGTCATATGTAAACTA
* * * *
1391290 TATAG-TATATAAATA--TCA-A-CTATAGTA
1 TATAGTTATATATATAGGTCATATGTAAACTA
1391317 TATA-TATATATATATAGGTCATATGTAAACTA
1 TATAGT-TATATATATAGGTCATATGTAAACTA
*
1391349 TATAGTTTATATATATAGTTCATATGTAAA
1 TATAG-TTATATATATAGGTCATATGTAAA
1391379 TATTAACTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
27 9 0.12
28 10 0.14
29 3 0.04
30 3 0.04
31 15 0.21
32 9 0.12
33 22 0.31
34 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (32 bp):
TATAGTTATATATATAGGTCATATGTAAACTA
Found at i:1391406 original size:18 final size:18
Alignment explanation
Indices: 1391378--1391424 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1391368 TCATATGTAA
* *
1391378 ATATTAACTATAGTTTAT
1 ATATAAACTATAGTTCAT
*
1391396 ATGTAAACTATAGTTCAT
1 ATATAAACTATAGTTCAT
1391414 ATATAAA-TATA
1 ATATAAACTATA
1391425 AACCTTAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
ATATAAACTATAGTTCAT
Found at i:1391426 original size:24 final size:24
Alignment explanation
Indices: 1391362--1391427 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
1391352 AGTTTATATA
* *
1391362 TATAGTTCATATGTAAATATTAAC
1 TATAGTTCATATATAAATATAAAC
*
1391386 TATAG-T--T-TAT--ATGTAAAC
1 TATAGTTCATATATAAATATAAAC
1391404 TATAGTTCATATATAAATATAAAC
1 TATAGTTCATATATAAATATAAAC
1391428 CTTAGTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
18 11 0.34
19 1 0.03
20 2 0.06
21 2 0.06
22 3 0.09
23 1 0.03
24 12 0.38
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (24 bp):
TATAGTTCATATATAAATATAAAC
Found at i:1391490 original size:18 final size:17
Alignment explanation
Indices: 1391447--1391490 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1391437 TATATATTTT
*
1391447 TATATATAGTTCATATG
1 TATATATAGTTCATATA
*
1391464 TAAACTATAGTTCATATA
1 TATA-TATAGTTCATATA
1391482 TATAGTATA
1 TATA-TATA
1391491 AAATAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATAGTTCATATA
Found at i:1391552 original size:19 final size:18
Alignment explanation
Indices: 1391528--1391565 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
1391518 TATATATATA
1391528 AACTATATAATTTATTAAT
1 AACTATATAATTTA-TAAT
1391547 AACTATATAATTTATAAT
1 AACTATATAATTTATAAT
1391565 A
1 A
1391566 TATTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
AACTATATAATTTATAAT
Found at i:1391573 original size:14 final size:14
Alignment explanation
Indices: 1391539--1391578 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1391529 ACTATATAAT
*
1391539 TTATTAATAACTATA
1 TTATTTATAA-TATA
*
1391554 TAATTTATAATATA
1 TTATTTATAATATA
1391568 TTATTTATAAT
1 TTATTTATAAT
1391579 TATACATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATTTATAATATA
Found at i:1392743 original size:31 final size:31
Alignment explanation
Indices: 1392705--1392777 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
1392695 ACATAAATTA
1392705 TCCTCAACTATAGGGTGATGCTTAGTATGGT
1 TCCTCAACTATAGGGTGATGCTTAGTATGGT
1392736 TCCTCAACTATAGGGTGATGCTTAGTATGGT
1 TCCTCAACTATAGGGTGATGCTTAGTATGGT
1392767 TCCTCAACTAT
1 TCCTCAACTAT
1392778 TAAATGTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (31 bp):
TCCTCAACTATAGGGTGATGCTTAGTATGGT
Done.