Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001162.1 Hibiscus syriacus cultivar Beakdansim tig00002317_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: 1560963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1031185 original size:5 final size:5
Alignment explanation
Indices: 1031161--1031237 Score: 79
Period size: 5 Copynumber: 15.4 Consensus size: 5
1031151 AAAACAAAAA
* * *
1031161 ATAAT ATTAAT AACAAT ATAAT ATAAT ACAAT ATAAT ATAAT ATAAT A-AAA
1 ATAAT A-TAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1031212 AT-AT ATAAT ATATAT ATAA- ATAAT AT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT AT
1031238 GTATACTATA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
4 10 0.17
5 37 0.62
6 12 0.20
7 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:1031317 original size:36 final size:37
Alignment explanation
Indices: 1031277--1031521 Score: 183
Period size: 36 Copynumber: 6.8 Consensus size: 37
1031267 AAACCATTTT
* *
1031277 AAAAACTATACACTATATGTTTTCAAAAATATTTAAA
1 AAAAACTATATATTATATGTTTTCAAAAATATTTAAA
**
1031314 AAAAACTATATATTATATGTTTTCAAAAATACGTTTTCA
1 AAAAACTATATATTATATGTTTTCAAAAATA--TTTAAA
* * *
1031353 AAAAA-TATATTATATATACG-TTTCAAAATTATTT--T
1 AAAAACTATA-TAT-TATATGTTTTCAAAAATATTTAAA
* * *
1031388 AAAAAC--TATATTATACGTTTTCAAAATTATTT-TA
1 AAAAACTATATATTATATGTTTTCAAAAATATTTAAA
* * *
1031422 AAAAACTATATATTATATATTTTC-AAAATCGTTT--T
1 AAAAACTATATATTATATGTTTTCAAAAAT-ATTTAAA
* ***
1031457 AAAAACTATATATTATAAT-TTTT-AAAACTATTTTTT
1 AAAAACTATATATTAT-ATGTTTTCAAAAATATTTAAA
*
1031493 AAAAACTATATATTATATATTTT-AAAAAT
1 AAAAACTATATATTATATGTTTTCAAAAAT
1031522 TATATATTAT
Statistics
Matches: 177, Mismatches: 16, Indels: 31
0.79 0.07 0.14
Matches are distributed among these distances:
32 6 0.03
33 17 0.10
34 11 0.06
35 35 0.20
36 45 0.25
37 32 0.18
38 4 0.02
39 22 0.12
40 5 0.03
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (37 bp):
AAAAACTATATATTATATGTTTTCAAAAATATTTAAA
Found at i:1031517 original size:23 final size:23
Alignment explanation
Indices: 1031489--1031538 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1031479 TAAAACTATT
1031489 TTTTAAAAACTATATATTATATA
1 TTTTAAAAACTATATATTATATA
* *
1031512 TTTTAAAAATTATATATTATATG
1 TTTTAAAAACTATATATTATATA
1031535 TTTT
1 TTTT
1031539 CATGACTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTAAAAACTATATATTATATA
Found at i:1032238 original size:21 final size:21
Alignment explanation
Indices: 1032212--1032306 Score: 154
Period size: 21 Copynumber: 4.5 Consensus size: 21
1032202 GTTTCCAGAT
1032212 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
1032233 TCGCAACGCAAACATCGACTA
1 TCGCAACGCGAACATCGACTA
1032254 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
* *
1032275 TCGTAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
1032296 TCGCAATGCGA
1 TCGCAACGCGA
1032307 TTTTCCAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.33, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:1032344 original size:21 final size:20
Alignment explanation
Indices: 1032318--1032582 Score: 202
Period size: 21 Copynumber: 12.8 Consensus size: 20
1032308 TTTCCAAATT
1032318 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* *
1032338 GCGTTGCGATTTATTCCAAATT-
1 -CGTTGCGA--TAGTCCAAGTTC
1032360 CGTTGCGATAGT-CAAGTT-
1 CGTTGCGATAGTCCAAGTTC
* *
1032378 TGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* *
1032398 GCGTTGCGATTTATTCCAAATT-
1 -CGTTGCGA--TAGTCCAAGTTC
1032420 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
1032440 ACGTTGCGATAGTCAAAGTTC
1 -CGTTGCGATAGTCCAAGTTC
*
1032461 GCGTTGCGATTTATTCCAAGTT-
1 -CGTTGCGA--TAGTCCAAGTTC
* *
1032483 CGTTGCGATAATCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
1032503 GCGTTGCGATTTATTCCAAGTT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
1032525 CGTTGCGATAGTCAAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* *
1032545 GCGTTGCGATTTATTCCAAATT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
1032567 CGTTGTGATAGTCCAA
1 CGTTGCGATAGTCCAA
1032583 AATCGCAACG
Statistics
Matches: 198, Mismatches: 27, Indels: 40
0.75 0.10 0.15
Matches are distributed among these distances:
18 16 0.08
19 42 0.21
21 97 0.49
23 43 0.22
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCCAAGTTC
Found at i:1032359 original size:42 final size:42
Alignment explanation
Indices: 1032302--1032582 Score: 305
Period size: 42 Copynumber: 6.8 Consensus size: 42
1032292 ACTATCGCAA
*
1032302 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* *
1032342 TGCGATTTATTCCAAATTCGTTGCGATAGT-CAAGTT--TGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* * * *
1032381 TGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGT
1 TGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGT
* *
1032423 TGCGA--TAGTCCAAGTTCACGTTGCGATAGTCAAAGTTCGCGT
1 TGCGATTTATTCCAAGTT--CGTTGCGATAGTCCAAGTTCGCGT
* *
1032465 TGCGATTTATTCCAAGTTCGTTGCGATAATCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
*
1032507 TGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* *
1032549 TGCGATTTATTCCAAATTCGTTGTGATAGTCCAA
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1032583 AATCGCAACG
Statistics
Matches: 210, Mismatches: 20, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
37 8 0.04
39 15 0.07
40 13 0.06
41 11 0.05
42 153 0.73
44 10 0.05
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1032478 original size:63 final size:62
Alignment explanation
Indices: 1032310--1032512 Score: 304
Period size: 63 Copynumber: 3.3 Consensus size: 62
1032300 AATGCGATTT
* *
1032310 TCCAAATT-CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
* *
1032371 T-CAAGTT-TGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
* *
1032431 TCCAAGTTCACGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAA
1 TCCAAGTTC-CGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
*
1032494 TCGAAGTTCGCGTTGCGAT
1 TCCAAGTTC-CGTTGCGAT
1032513 TTATTCCAAG
Statistics
Matches: 130, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
60 57 0.44
61 7 0.05
63 66 0.51
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (62 bp):
TCCAAGTTCCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
Found at i:1033472 original size:21 final size:20
Alignment explanation
Indices: 1033446--1033562 Score: 76
Period size: 21 Copynumber: 5.7 Consensus size: 20
1033436 ATTTTGGAAT
1033446 AAATCGCAACGCAAATTTGGA
1 AAATCGCAACGC-AATTTGGA
* *
1033467 AAATCGCAACGCGAACTTCGA
1 AAATCGCAACGC-AATTTGGA
** *
1033488 CTATCGCAACG-AACTTGGA
1 AAATCGCAACGCAATTTGGA
** * *
1033507 CTATCGCAATG-AATTTGTAA
1 AAATCGCAACGCAATTTG-GA
* *
1033527 TAAATCACAACACGAATTTGGA
1 -AAATCGCAACGC-AATTTGGA
1033549 AAATCGCAACGCAA
1 AAATCGCAACGCAA
1033563 ACTTCGACTA
Statistics
Matches: 75, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
19 22 0.29
20 3 0.04
21 43 0.57
22 1 0.01
23 6 0.08
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCAATTTGGA
Found at i:1033502 original size:19 final size:19
Alignment explanation
Indices: 1033478--1033515 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1033468 AATCGCAACG
1033478 CGAACTTCGACTATCGCAA
1 CGAACTTCGACTATCGCAA
*
1033497 CGAACTTGGACTATCGCAA
1 CGAACTTCGACTATCGCAA
1033516 TGAATTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (19 bp):
CGAACTTCGACTATCGCAA
Found at i:1036218 original size:3 final size:3
Alignment explanation
Indices: 1036203--1036248 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
1036193 AAACTAAAAA
*
1036203 AAT ATT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1036249 AATTGATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1036262 original size:13 final size:14
Alignment explanation
Indices: 1036244--1036272 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1036234 TAATAATAAT
1036244 AATAAAATTGA-TA
1 AATAAAATTGAGTA
1036257 AATAAAATTGAGTA
1 AATAAAATTGAGTA
1036271 AA
1 AA
1036273 AATAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (14 bp):
AATAAAATTGAGTA
Found at i:1036282 original size:33 final size:32
Alignment explanation
Indices: 1036200--1036315 Score: 102
Period size: 33 Copynumber: 3.7 Consensus size: 32
1036190 AAAAAACTAA
*
1036200 AAAAAT-AT-TAATATAATAATAAT-AAT-AAT
1 AAAAATGATATAAAATAATAA-AATAAATAAAT
* **
1036229 AATAAT-A-ATAATAATAATAAAATTGATAAAT
1 AAAAATGATATAA-AATAATAAAATAAATAAAT
*
1036260 AAAATTGAGTA-AAAATAAATAAAATAAATAAAT
1 AAAAATGA-TATAAAAT-AATAAAATAAATAAAT
1036293 AAAAATGATATAAAATAATAAAA
1 AAAAATGATATAAAATAATAAAA
1036316 AAGGGTTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
29 12 0.17
30 9 0.13
31 7 0.10
32 13 0.19
33 28 0.40
34 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (32 bp):
AAAAATGATATAAAATAATAAAATAAATAAAT
Found at i:1036290 original size:13 final size:13
Alignment explanation
Indices: 1036272--1036296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1036262 AATTGAGTAA
1036272 AAATAAATAAAAT
1 AAATAAATAAAAT
1036285 AAATAAATAAAA
1 AAATAAATAAAA
1036297 ATGATATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:1036295 original size:23 final size:23
Alignment explanation
Indices: 1036209--1036314 Score: 69
Period size: 23 Copynumber: 4.6 Consensus size: 23
1036199 AAAAAATATT
* * *
1036209 AATATAATAAT-AATAATAATAA
1 AATAAAATAATAAATAAAAATGA
*
1036231 TAATAATAATAAT-AATAAAATTGATA
1 -AATAA-AATAATAAATAAAAATG--A
* *
1036257 AATAAAAT--TGAGTAAAAAT-A
1 AATAAAATAATAAATAAAAATGA
1036277 AATAAAATAAATAAATAAAAATGA
1 AATAAAAT-AATAAATAAAAATGA
*
1036301 TATAAAATAATAAA
1 AATAAAATAATAAA
1036315 AAAGGGTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
20 9 0.14
22 1 0.02
23 26 0.39
24 24 0.36
25 5 0.08
26 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (23 bp):
AATAAAATAATAAATAAAAATGA
Found at i:1036298 original size:19 final size:19
Alignment explanation
Indices: 1036209--1036316 Score: 56
Period size: 21 Copynumber: 5.1 Consensus size: 19
1036199 AAAAAATATT
* *
1036209 AATATAATAATAATAATAAT
1 AATAAAATAA-AATAATAAA
1036229 AATAATAATAATAATAATAAA
1 AATAA-AATAA-AATAATAAA
* *
1036250 ATTGATAAATAAAATTGAGTAAA
1 AAT-A-AAATAAAA-T-AATAAA
1036273 AAT-AAATAAAATAAATAAA
1 AATAAAATAAAAT-AATAAA
*
1036292 TAAAAATGATATAAAATAATAAA
1 -AATAA--A-ATAAAATAATAAA
1036315 AA
1 AA
1036317 AGGGTTAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
19 6 0.09
20 14 0.20
21 19 0.27
22 9 0.13
23 15 0.21
24 7 0.10
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
AATAAAATAAAATAATAAA
Found at i:1037499 original size:3 final size:3
Alignment explanation
Indices: 1037491--1037560 Score: 65
Period size: 3 Copynumber: 23.7 Consensus size: 3
1037481 AGAAAAAAGT
* * *
1037491 TAA TAA TAAA TAAA TAA TAA TAA -AA TAA T-A TAA GAA -AA AAA CAA
1 TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1037535 TAA TAG TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1037561 TATTATATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
2 6 0.10
3 45 0.78
4 7 0.12
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:1037607 original size:37 final size:37
Alignment explanation
Indices: 1037558--1037766 Score: 206
Period size: 37 Copynumber: 5.9 Consensus size: 37
1037548 AATAATAATA
* *
1037558 ATATATTATATATTTTTTCAAAAATATTTTCAAAACT
1 ATATAATATATATGTTTTCAAAAATATTTTCAAAACT
*
1037595 ATATAATATATATATTTTCAAAAATATTTT-AAAAC-
1 ATATAATATATATGTTTTCAAAAATATTTTCAAAACT
* *
1037630 -TAT-AT-TATA--TTTT-AAAAATGTTTTTAAAACT
1 ATATAATATATATGTTTTCAAAAATATTTTCAAAACT
* *
1037661 ATAT-AT-TATATGTTTTCAAAAGTGTTTTCAAAACT
1 ATATAATATATATGTTTTCAAAAATATTTTCAAAACT
* ** *
1037696 ATGTAGCATATATGTTTTCAAAAATATTTTTAAAACT
1 ATATAATATATATGTTTTCAAAAATATTTTCAAAACT
* * * *
1037733 ATATATTATATAAGTTTGC-AAAATGTTTTCAAAA
1 ATATAATATATATGTTTTCAAAAATATTTTCAAAA
1037767 ACAACAACAA
Statistics
Matches: 146, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
29 10 0.07
30 9 0.06
32 13 0.09
33 2 0.01
34 7 0.05
35 19 0.13
36 18 0.12
37 68 0.47
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATAATATATATGTTTTCAAAAATATTTTCAAAACT
Found at i:1039160 original size:37 final size:37
Alignment explanation
Indices: 1039105--1039237 Score: 216
Period size: 37 Copynumber: 3.6 Consensus size: 37
1039095 TTCAACCGGG
*
1039105 TATATTATATATTTTTTTCAAAATGTTTTCAAAAACTA
1 TATATTATATA-TATTTTCAAAATGTTTTCAAAAACTA
*
1039143 TATATTATGTA-AGTTTTCAAAATGTTTTCAAAAACTA
1 TATATTATATATA-TTTTCAAAATGTTTTCAAAAACTA
1039180 TATATTATATATATTTTCAAAATGTTTTCAAAAACTA
1 TATATTATATATATTTTCAAAATGTTTTCAAAAACTA
1039217 TATATTATATATA-TTTCAAAA
1 TATATTATATATATTTTCAAAA
1039238 ACCGATTTTT
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
36 8 0.09
37 71 0.79
38 11 0.12
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATTATATATATTTTCAAAATGTTTTCAAAAACTA
Found at i:1039647 original size:25 final size:26
Alignment explanation
Indices: 1039600--1039652 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1039590 GAATTTTTAG
*
1039600 AATTTTTTTAAAATATAT-GAAAATA
1 AATTTTTTTAAAATATATAAAAAATA
*
1039625 AATTATTTTTAAAAT-TTTAAAAAATA
1 AATT-TTTTTAAAATATATAAAAAATA
1039651 AA
1 AA
1039653 AAAATCCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AATTTTTTTAAAATATATAAAAAATA
Found at i:1049591 original size:27 final size:27
Alignment explanation
Indices: 1049549--1049612 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
1049539 CTGATTTTGT
* *
1049549 TAACAAAATCAATAAAACGTCCAATAA
1 TAACAAAACCAATAAAACGCCCAATAA
*
1049576 TAACAAAACCAGTAAAACGCCCAATAA
1 TAACAAAACCAATAAAACGCCCAATAA
*
1049603 TAATAAAACC
1 TAACAAAACC
1049613 GGTAGAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.58, C:0.22, G:0.05, T:0.16
Consensus pattern (27 bp):
TAACAAAACCAATAAAACGCCCAATAA
Found at i:1053263 original size:2 final size:2
Alignment explanation
Indices: 1053251--1053316 Score: 77
Period size: 2 Copynumber: 35.0 Consensus size: 2
1053241 GAGGCGGAGA
*
1053251 AT AT A- AT AT AT AT AT AA AT AT A- AT AT AT AT A- 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
* *
1053290 AC AT AT AT AT TT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1053317 GTTATTTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1053272 original size:17 final size:17
Alignment explanation
Indices: 1053250--1053316 Score: 84
Period size: 17 Copynumber: 3.9 Consensus size: 17
1053240 AGAGGCGGAG
1053250 AATATAATATATATATA
1 AATATAATATATATATA
1053267 AATATAATATATATAATA
1 AATATAATATATAT-ATA
* *
1053285 TATATACATATATAT-TT
1 AATATA-ATATATATATA
1053302 AATAT-ATATATATAT
1 AATATAATATATATAT
1053317 GTTATTTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.18
16 1 0.02
17 19 0.43
18 8 0.18
19 8 0.18
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATAATATATATATA
Found at i:1053278 original size:15 final size:15
Alignment explanation
Indices: 1053258--1053316 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
1053248 AGAATATAAT
1053258 ATATATATAAATATA
1 ATATATATAAATATA
1053273 ATATATAT-AATATA
1 ATATATATAAATATA
* * *
1053287 TATACATATATATTTA
1 -ATATATATAAATATA
*
1053303 ATATATATATATAT
1 ATATATATAAATAT
1053317 GTTATTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 6 0.16
15 27 0.73
16 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATATATAAATATA
Found at i:1054997 original size:2 final size:2
Alignment explanation
Indices: 1054992--1055017 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1054982 ATTATTTGAA
1054992 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
1055018 TAGCAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1057926 original size:29 final size:30
Alignment explanation
Indices: 1057855--1057914 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1057845 CAATTTAAGG
*
1057855 CAAAATGGCTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1057886 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1057915 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1058052 original size:22 final size:21
Alignment explanation
Indices: 1058004--1058046 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1057994 TTCAAGATTG
* *
1058004 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
1058025 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
1058046 C
1 C
1058047 TGCAGGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:1058120 original size:20 final size:21
Alignment explanation
Indices: 1058080--1058121 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1058070 AACAGAATGT
1058080 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
1058101 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
1058122 TTGTTCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:1058184 original size:21 final size:21
Alignment explanation
Indices: 1058158--1058200 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1058148 ATTTGAATAT
*
1058158 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1058179 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1058200 T
1 T
1058201 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1058266 original size:20 final size:22
Alignment explanation
Indices: 1058228--1058267 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1058218 TTTTAGTATA
1058228 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1058250 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1058268 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1058521 original size:34 final size:32
Alignment explanation
Indices: 1058482--1058551 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1058472 TTTTGTAAAG
*
1058482 GGGAAAGGTTATAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
1058516 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
1058548 GGGA
1 GGGA
1058552 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:1061439 original size:29 final size:30
Alignment explanation
Indices: 1061368--1061427 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1061358 CAATTTAAGG
1061368 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1061399 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1061428 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1061543 original size:22 final size:22
Alignment explanation
Indices: 1061517--1061596 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 22
1061507 TTCAAGATTG
* *
1061517 CCCAGGGGGTATAGATTCCCCC
1 CCCAGGGGGTACAGATACCCCC
1061539 CCCAGGGGGTACAGATA----C
1 CCCAGGGGGTACAGATACCCCC
*
1061557 CCC---GGGTACAGATACCTCC
1 CCCAGGGGGTACAGATACCCCC
*
1061576 CCCAAGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
1061597 TGCAGGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
15 11 0.23
18 4 0.08
19 4 0.08
22 29 0.60
ACGTcount: A:0.24, C:0.36, G:0.26, T:0.14
Consensus pattern (22 bp):
CCCAGGGGGTACAGATACCCCC
Found at i:1061564 original size:37 final size:37
Alignment explanation
Indices: 1061523--1061596 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1061513 ATTGCCCAGG
* * *
1061523 GGGTATAGATTCCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCCAAGGGGTACAGATACCCC
*
1061560 GGGTACAGATACCTCCCCCAAGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCCAAGGGGTACAGATACCCC
1061597 TGCAGGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.24, C:0.35, G:0.26, T:0.15
Consensus pattern (37 bp):
GGGTACAGATACCCCCCCCAAGGGGTACAGATACCCC
Found at i:1061732 original size:21 final size:21
Alignment explanation
Indices: 1061706--1061748 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1061696 ATTTGAATAT
*
1061706 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1061727 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1061748 T
1 T
1061749 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1061814 original size:20 final size:22
Alignment explanation
Indices: 1061776--1061815 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1061766 TTTGAGTATA
1061776 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1061798 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1061816 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1062069 original size:34 final size:32
Alignment explanation
Indices: 1062030--1062099 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1062020 TTTTGTAAAG
*
1062030 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1062064 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1062096 GGGA
1 GGGA
1062100 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1063869 original size:6 final size:6
Alignment explanation
Indices: 1063858--1063941 Score: 105
Period size: 6 Copynumber: 14.0 Consensus size: 6
1063848 TTATACCCAA
* * *
1063858 ATATAT ATATAT ATATAT ATATAT ATGTAT ATATAT GTATAT ATATGT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
1063906 ATATGT ATATAT GTATAT ATATGT ATATGT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1063942 GTATGTATAC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:1063888 original size:24 final size:24
Alignment explanation
Indices: 1063861--1063950 Score: 126
Period size: 24 Copynumber: 3.7 Consensus size: 24
1063851 TACCCAAATA
*
1063861 TATATATATATATATATATATATG
1 TATATATATATATATATGTATATG
1063885 TATATATATGTATATATATGTATATG
1 TATATATA--TATATATATGTATATG
*
1063911 TATATATGTATATATATGTATATG
1 TATATATATATATATATGTATATG
* *
1063935 TATATATGTATGTATA
1 TATATATATATATATA
1063951 CAATAAAGCT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
24 39 0.64
26 22 0.36
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (24 bp):
TATATATATATATATATGTATATG
Found at i:1063949 original size:4 final size:4
Alignment explanation
Indices: 1063858--1063941 Score: 105
Period size: 4 Copynumber: 21.0 Consensus size: 4
1063848 TTATACCCAA
* * *
1063858 ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATAT ATAT GTAT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
1063906 ATAT GTAT ATAT GTAT ATAT ATGT ATAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1063942 GTATGTATAC
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:1063950 original size:10 final size:10
Alignment explanation
Indices: 1063858--1063941 Score: 105
Period size: 10 Copynumber: 8.4 Consensus size: 10
1063848 TTATACCCAA
*
1063858 ATATATATAT
1 ATATATGTAT
*
1063868 ATATATATAT
1 ATATATGTAT
1063878 ATATATGTAT
1 ATATATGTAT
1063888 ATATATGTAT
1 ATATATGTAT
1063898 ATATATGTAT
1 ATATATGTAT
* *
1063908 ATGTATATAT
1 ATATATGTAT
* *
1063918 GTATATATAT
1 ATATATGTAT
*
1063928 GTATATGTAT
1 ATATATGTAT
1063938 ATAT
1 ATAT
1063942 GTATGTATAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 67 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:1065367 original size:37 final size:37
Alignment explanation
Indices: 1065326--1065826 Score: 176
Period size: 37 Copynumber: 14.4 Consensus size: 37
1065316 TTGGGTGTTG
* *
1065326 TTTCTCTTAAAACAAATTTCGTCTCACTAGATATATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
* * *
1065363 TTTCT-TCAGAACACAAA---T-T-TCA--A-AGTTGTT
1 TTTCTCTTA-AA-ACAAATTTTGTCTCACTAGAGATATT
* * *
1065393 TTTCT-TAAAAACAAATTTTGTCTCACTTGAGACATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
* * *
1065429 TTTATCTTAAAACAAATTTTGTCTCACTGGAGACA-T
1 TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
* *
1065465 TTTC-CTTCAGAACACAAA---T-T-TCA--A-AGTTGTT
1 TTTCTCTT-A-AA-ACAAATTTTGTCTCACTAGAGATATT
* *
1065496 TTTCT-TAAAAACAAATTTTGTCTCACTTGAGATATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
* * **
1065532 TTTCTCTTAAAACAAATTTCGTCTCACTGGAGA-CGT
1 TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
1065568 TTTC-CTTCAGAACACAAA---T-T-TCA--A-AG-T-TGT
1 TTTCTCTT-A-AA-ACAAATTTTGTCTCACTAGAGATAT-T
* * * *
1065598 TTT-TCTTAAAAAAAATTTTTTC-CACTTGAGACATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
** * *
1065633 TTTCTCTTAAAACAAATTTCATCTCACTTGAGACATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
* ** * *
1065670 TTCCTTCGAAAAACAAATTTTG-CATCACTTGAGACATT
1 TTTC-TCTTAAAACAAATTTTGTC-TCACTAGAGATATT
** *
1065708 TTTCTCTTAAAACAAATTTCATCTCACTTGAGATATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
* * * *
1065745 TTCCTTCTGAACACAAA---T-T-TCA--A-AGTTATT
1 TTTC-TCTTAAAACAAATTTTGTCTCACTAGAGATATT
* * *
1065775 TTT-T-TTAAAAATAAATTTTGTCTCACTTGAGACATT
1 TTTCTCTT-AAAACAAATTTTGTCTCACTAGAGATATT
*
1065811 TTTCTCTTAAATCAAA
1 TTTCTCTTAAAACAAA
1065827 CATCGTCTCG
Statistics
Matches: 344, Mismatches: 62, Indels: 116
0.66 0.12 0.22
Matches are distributed among these distances:
27 5 0.01
28 19 0.06
29 5 0.01
30 32 0.09
31 13 0.04
32 3 0.01
33 21 0.06
34 6 0.02
35 11 0.03
36 56 0.16
37 115 0.33
38 58 0.17
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (37 bp):
TTTCTCTTAAAACAAATTTTGTCTCACTAGAGATATT
Found at i:1065446 original size:65 final size:65
Alignment explanation
Indices: 1065322--1065447 Score: 161
Period size: 66 Copynumber: 1.9 Consensus size: 65
1065312 TTCCTTGGGT
*
1065322 GTTGTTTCTCTTAAAACAAATTTCGTCTCACTAGATATATTTTTCTTCAGAACACAAATTTCAAA
1 GTTGTTTCTCTTAAAACAAATTTCGTCTCACTAGACATATTTTTCTTCAGAACACAAATTTCAAA
* *
1065387 GTTGTTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACAT-TTTTATCTT-A-AA-ACAAATTT
1 GTTGTTTCTCTT-AAAACAAATTTCGTCTCAC-T-AGACATATTTT-TCTTCAGAACACAAATTT
1065448 TGTCTCACTG
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
65 19 0.35
66 20 0.37
67 6 0.11
68 9 0.17
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (65 bp):
GTTGTTTCTCTTAAAACAAATTTCGTCTCACTAGACATATTTTTCTTCAGAACACAAATTTCAAA
Found at i:1065509 original size:103 final size:103
Alignment explanation
Indices: 1065326--1065689 Score: 590
Period size: 103 Copynumber: 3.6 Consensus size: 103
1065316 TTGGGTGTTG
* * * *
1065326 TTTCTCTTAAAACAAATTTCGTCTCACTAGATATATTTTTCTTCAGAACACAAATTTCAAAGTTG
1 TTTCTCTTAAAACAAATTTCGTCTCACTGGAGACATTTTCCTTCAGAACACAAATTTCAAAGTTG
1065391 TTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATT
66 TTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATT
* *
1065429 TTTATCTTAAAACAAATTTTGTCTCACTGGAGACATTTTCCTTCAGAACACAAATTTCAAAGTTG
1 TTTCTCTTAAAACAAATTTCGTCTCACTGGAGACATTTTCCTTCAGAACACAAATTTCAAAGTTG
*
1065494 TTTTTCTTAAAAACAAATTTTGTCTCACTTGAGATATT
66 TTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATT
*
1065532 TTTCTCTTAAAACAAATTTCGTCTCACTGGAGACGTTTTCCTTCAGAACACAAATTTCAAAGTTG
1 TTTCTCTTAAAACAAATTTCGTCTCACTGGAGACATTTTCCTTCAGAACACAAATTTCAAAGTTG
*
1065597 TTTTTCTTAAAAA-AAATTTTTTC-CACTTGAGACATT
66 TTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATT
* * *
1065633 TTTCTCTTAAAACAAATTTCATCTCACTTGAGACATTTTCCTTC-GAAAAACAAATTT
1 TTTCTCTTAAAACAAATTTCGTCTCACTGGAGACATTTTCCTTCAG-AACACAAATTT
1065690 TGCATCACTT
Statistics
Matches: 244, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
100 1 0.00
101 63 0.26
102 9 0.04
103 171 0.70
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (103 bp):
TTTCTCTTAAAACAAATTTCGTCTCACTGGAGACATTTTCCTTCAGAACACAAATTTCAAAGTTG
TTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATT
Found at i:1065636 original size:65 final size:64
Alignment explanation
Indices: 1065531--1065653 Score: 144
Period size: 65 Copynumber: 1.9 Consensus size: 64
1065521 CTTGAGATAT
*
1065531 TTTTCTCTTAAAACAAATTTCGTCTCACTGGAGACGTTTTC-CTTCAGAACACAAATTTCAAAGT
1 TTTTCTCTTAAAAAAAATTTCGTCTCACTGGAGACGTTTTCTCTT-A-AA-ACAAATTTCAAAGT
1065595 TG
63 TG
** * *
1065597 TTTT-TCTTAAAAAAAATTTTTTC-CACTTGAGACATTTTTCTCTTAAAACAAATTTCA
1 TTTTCTCTTAAAAAAAATTTCGTCTCACTGGAGAC-GTTTTCTCTTAAAACAAATTTCA
1065654 TCTCACTTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
63 10 0.20
64 11 0.22
65 22 0.44
66 7 0.14
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (64 bp):
TTTTCTCTTAAAAAAAATTTCGTCTCACTGGAGACGTTTTCTCTTAAAACAAATTTCAAAGTTG
Found at i:1065703 original size:176 final size:178
Alignment explanation
Indices: 1065502--1065847 Score: 536
Period size: 176 Copynumber: 2.0 Consensus size: 178
1065492 TGTTTTTCTT
* * *
1065502 AAAAACAAATTTTGTCTCACTTGAGATATTTTTCTCTTAAAACAAATTTCGTCTCACTGGAGACG
1 AAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTGGAGACA
* *
1065567 TTTTCCTTCAGAACACAAATTTCAAAGTTGTTTTTCTTAAAAA-AAATTTTTTC-CACTTGAGAC
66 TTTTCCTTCAGAACACAAATTTCAAAGTTATTTTTCTTAAAAATAAATTTTGTCTCACTTGAGAC
**
1065630 ATTTTTCTCTTAAAACAAATTTCATCTCACTTGAGACATTTTCCTTCG
131 ATTTTTCTCTTAAAACAAACATCATCTCACTTGAGACATTTTCCTTCG
* *
1065678 AAAAACAAATTTTG-CATCACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTTGAGAT
1 AAAAACAAATTTTGTC-TCACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTGGAGAC
* *
1065742 ATTTTCCTTCTGAACACAAATTTCAAAGTTATTTTTTTTAAAAATAAATTTTGTCTCACTTGAGA
65 ATTTTCCTTCAGAACACAAATTTCAAAGTTATTTTTCTTAAAAATAAATTTTGTCTCACTTGAGA
* * *
1065807 CATTTTTCTCTTAAATCAAACATCGTCTCGCTTGAGACATT
130 CATTTTTCTCTTAAAACAAACATCATCTCACTTGAGACATT
1065848 CTCCCAAAAT
Statistics
Matches: 153, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
175 1 0.01
176 98 0.64
177 9 0.06
178 45 0.29
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (178 bp):
AAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTGGAGACA
TTTTCCTTCAGAACACAAATTTCAAAGTTATTTTTCTTAAAAATAAATTTTGTCTCACTTGAGAC
ATTTTTCTCTTAAAACAAACATCATCTCACTTGAGACATTTTCCTTCG
Found at i:1065716 original size:75 final size:75
Alignment explanation
Indices: 1065620--1065764 Score: 256
Period size: 75 Copynumber: 1.9 Consensus size: 75
1065610 AAATTTTTTC
1065620 CACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTTGAGACATTTTCCTTC-GAAAAAC
1 CACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTTGAGACATTTTCCTTCTG-AAAAC
1065684 AAATTTTGCAT
65 AAATTTTGCAT
* *
1065695 CACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTTGAGATATTTTCCTTCTGAACACA
1 CACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTTGAGACATTTTCCTTCTGAAAACA
1065760 AATTT
66 AATTT
1065765 CAAAGTTATT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
75 66 0.99
76 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (75 bp):
CACTTGAGACATTTTTCTCTTAAAACAAATTTCATCTCACTTGAGACATTTTCCTTCTGAAAACA
AATTTTGCAT
Found at i:1066154 original size:15 final size:15
Alignment explanation
Indices: 1066134--1066178 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
1066124 ACAAATTTTG
1066134 TCTCCCTTGAGACAA
1 TCTCCCTTGAGACAA
*
1066149 TCTCCCTTGAGACAG
1 TCTCCCTTGAGACAA
* *
1066164 TTTCCCTTGAAACAA
1 TCTCCCTTGAGACAA
1066179 AGTTTTGTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (15 bp):
TCTCCCTTGAGACAA
Found at i:1066172 original size:88 final size:88
Alignment explanation
Indices: 1066067--1066246 Score: 238
Period size: 88 Copynumber: 2.0 Consensus size: 88
1066057 AACATAAACT
* *
1066067 TTGAGAACGTTTCCCTTGAAACAAA-TTTTATCTCACTTCAGACAATTTTTACTCAAAACAAATT
1 TTGAGAACGTTTCCCTTGAAACAAAGTTTTATCTCACTTCAGAC-AGTTTCACTCAAAACAAATT
1066131 TTGTCTCCCTTGAGACAATCTCCC
65 TTGTCTCCCTTGAGACAATCTCCC
* * * * **
1066155 TTGAG-ACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
1 TTGAGAAC-GTTTCCCTTGAAACAAAGTTTTATCTCACTTCAGACAGTTTCACTCAAAACAAATT
* *
1066219 TTGTCTCCCTTGAGACAATTTCTC
65 TTGTCTCCCTTGAGACAATCTCCC
1066243 TTGA
1 TTGA
1066247 AACAAATTTC
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
87 2 0.03
88 63 0.79
89 15 0.19
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (88 bp):
TTGAGAACGTTTCCCTTGAAACAAAGTTTTATCTCACTTCAGACAGTTTCACTCAAAACAAATTT
TGTCTCCCTTGAGACAATCTCCC
Found at i:1066229 original size:21 final size:21
Alignment explanation
Indices: 1066203--1066267 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
1066193 TGAGACAGTT
1066203 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
1066224 TCCCTTGAGAC-AA--TT-TC
1 TCCCTTGAAACAAATTTTGTC
*
1066241 T--CTTGAAACAAATTTCGTC
1 TCCCTTGAAACAAATTTTGTC
1066260 TCCCTTGA
1 TCCCTTGA
1066268 GACAGTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
15 7 0.20
16 2 0.06
17 3 0.09
18 3 0.09
19 3 0.09
20 2 0.06
21 15 0.43
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:1066231 original size:36 final size:36
Alignment explanation
Indices: 1066149--1066348 Score: 276
Period size: 36 Copynumber: 5.5 Consensus size: 36
1066139 CTTGAGACAA
*
1066149 TCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTG
1 TCTCCCTTGAGACAGTTTCTCTTGAAACAAA-TTTTG
* *
1066186 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1 TCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTG
* *
1066222 TCTCCCTTGAGACAATTTCTCTTGAAACAAATTTCG
1 TCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTG
* *
1066258 TCTCCCTTGAGACAGTTTCTCTTGAAACGAATTTTA
1 TCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTG
* *
1066294 TCTCGCC-TGAGATAGTTTCTCTTGAAACAAATTTTA
1 TCTC-CCTTGAGACAGTTTCTCTTGAAACAAATTTTG
* *
1066330 TCTCGCTTGAGATAGTTTC
1 TCTCCCTTGAGACAGTTTC
1066349 ACTCAAAACA
Statistics
Matches: 149, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
35 1 0.01
36 116 0.78
37 32 0.21
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (36 bp):
TCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTG
Found at i:1066378 original size:39 final size:39
Alignment explanation
Indices: 1066288--1066406 Score: 163
Period size: 39 Copynumber: 3.1 Consensus size: 39
1066278 CTTGAAACGA
* * **
1066288 ATTTTATCTCGCCTGAGATAGTTTCTCTTGAAAC--AA-
1 ATTTTATCTCGCTTGAGATAGTTTCACTCAAAACAAAAG
1066324 ATTTTATCTCGCTTGAGATAGTTTCACTCAAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCAAAACAAAAG
* *
1066363 ATTTTATCTTGCTTGAGATAGTTTCGCTCAAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCAAAACAAAAG
1066402 ATTTT
1 ATTTT
1066407 TAGAAACTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
36 30 0.41
38 2 0.03
39 42 0.57
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (39 bp):
ATTTTATCTCGCTTGAGATAGTTTCACTCAAAACAAAAG
Found at i:1066535 original size:52 final size:52
Alignment explanation
Indices: 1066402--1066599 Score: 191
Period size: 54 Copynumber: 3.6 Consensus size: 52
1066392 AAAACAAAAG
* *
1066402 ATTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTCGATTGTTTTCAAATGA
1 ATTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGA-TGTTTTCAAATGA
** ** * *
1066455 ATTTGAAAGAAGTTAAGCCTAATTTTTAGGGATTTCTTGATGTTTTCAAATGA
1 ATTT-TTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGA
* *
1066508 GTTTTTAGAAACTAAGCTTGATTTTTAGGGGTTTCTTGATGATGATTTTC-AATGA
1 ATTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTC-T--TGATG-TTTTCAAATGA
* *
1066563 GTTTTTAAAAGGAAACTAAGCCTAATTTTTAGGGGTT
1 ATTTTT---A-GAAACTAAGCCTGATTTTTAGGGGTT
1066600 CCTTTACAAC
Statistics
Matches: 118, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
52 24 0.20
53 21 0.18
54 27 0.23
55 16 0.14
56 5 0.04
58 1 0.01
59 24 0.20
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (52 bp):
ATTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGA
Found at i:1066988 original size:22 final size:21
Alignment explanation
Indices: 1066963--1067080 Score: 77
Period size: 21 Copynumber: 5.7 Consensus size: 21
1066953 GGGTCATCAG
1066963 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* * *
1066984 GTAAGTCCTTCGGGC-T-ATCAA
1 -TAAGTCTTTCGAGCATGAT-GA
*
1067005 TAAGTCTTT-GAGCATGATGCT
1 TAAGTCTTTCGAGCATGATG-A
* *
1067026 TAAATCCTTT-GAGTCAT-CT-A
1 TAAGT-CTTTCGAG-CATGATGA
*
1067046 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCTTTCGAGCATGATGA
*
1067067 TAAGTCATTCGAGC
1 TAAGTCTTTCGAGC
1067081 CATCCATAAG
Statistics
Matches: 73, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
19 9 0.12
20 19 0.26
21 22 0.30
22 20 0.27
23 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGA
Found at i:1066990 original size:42 final size:40
Alignment explanation
Indices: 1066942--1067072 Score: 149
Period size: 41 Copynumber: 3.2 Consensus size: 40
1066932 TCGAATTAGC
1066942 ATAAGTCCTTTGGGTCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTTGGGTCATCA-TAAGTCTTTCGAGCATGATG
*
1066983 AGTAAGTCCTTCGGG-CTATCAATAAGTCTTT-GAGCATGATG
1 A-TAAGTCCTTTGGGTC-ATC-ATAAGTCTTTCGAGCATGATG
* * * *
1067024 CTTAAATCCTTTGAGTCATCTATAAGTCTTTCGAGCAAGATG
1 -ATAAGTCCTTTGGGTCATC-ATAAGTCTTTCGAGCATGATG
1067066 ATAAGTC
1 ATAAGTC
1067073 ATTCGAGCCA
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
41 40 0.53
42 34 0.45
43 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
ATAAGTCCTTTGGGTCATCATAAGTCTTTCGAGCATGATG
Found at i:1067034 original size:41 final size:42
Alignment explanation
Indices: 1066955--1067090 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 42
1066945 AGTCCTTTGG
* *
1066955 GTCATCAGTAAGTCTTTCGAGCATGATGAGTAAGTCCTTCG-
1 GTCATCAATAAGTCTTTCGAGCATGATGAGTAAATCCTTCGA
* ** *
1066996 GGCTATCAATAAGTCTTT-GAGCATGATGCTTAAATCCTTTGA
1 GTC-ATCAATAAGTCTTTCGAGCATGATGAGTAAATCCTTCGA
* * * *
1067038 GTCATCTATAAGTCTTTCGAGCAAGATGA-TAAGTCATTCGA
1 GTCATCAATAAGTCTTTCGAGCATGATGAGTAAATCCTTCGA
* *
1067079 GCCATCCATAAG
1 GTCATCAATAAG
1067091 ACCTTTGGGC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 53 0.69
42 24 0.31
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (42 bp):
GTCATCAATAAGTCTTTCGAGCATGATGAGTAAATCCTTCGA
Found at i:1067808 original size:136 final size:135
Alignment explanation
Indices: 1067564--1067913 Score: 511
Period size: 136 Copynumber: 2.6 Consensus size: 135
1067554 AATAAACCGC
* *
1067564 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTTAT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGA-GGAGAAGAAGTTCAT
* * ** *
1067629 AATAAGAAGAACTTGTTTGACATATCACTCGATTAACAACATTTTGAATCAGTGACACCTCGCTT
65 AATGAGAAGAACTTGTTCGACATATCACTCGATTAACAACATTTCAAATCAGTGACACCTCACTT
1067694 GAGGGA
130 GAGGGA
* * * *
1067700 TCAACATTTCAAGTAGAGTGTTCATAATGAGAAGAACTCATCCGACAGAGTGAGAAAAAGTTCAT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG-GAGAAGAAGTTCAT
* * * *
1067765 AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCAAATCAGTGACATCTCACTT
65 AATGAGAAGAACTTGTTCGACATATCACTCGATTAACAACATTTCAAATCAGTGACACCTCACTT
1067830 GAGGGA
130 GAGGGA
* * *
1067836 TCAACATTTCCAGTGGAGAGTTCATAAAGAGAAGAACTCATCCGACAAAAGAAGAAGAAGTTCAT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAC-AGAGGAGAAGAAGTTCAT
1067901 AATGAGAAGAACT
65 AATGAGAAGAACT
1067914 CATCCGACAG
Statistics
Matches: 189, Mismatches: 23, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
135 1 0.01
136 185 0.98
137 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (135 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCGACATATCACTCGATTAACAACATTTCAAATCAGTGACACCTCACTTG
AGGGA
Found at i:1067909 original size:40 final size:40
Alignment explanation
Indices: 1067854--1067953 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
1067844 TCCAGTGGAG
*
1067854 AGTTCATAAAGAGAAGAACTCATCCGACAAAAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCGACAAAAGAAGAAGA
* * *
1067894 AGTTCATAATGAGAAGAACTCATCCGACAGATGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCGACAAAAGAAGAAGA
*
1067934 CGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1067954 TGTTCAACCT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATCCGACAAAAGAAGAAGA
Found at i:1067918 original size:176 final size:176
Alignment explanation
Indices: 1067719--1068092 Score: 461
Period size: 176 Copynumber: 2.1 Consensus size: 176
1067709 CAAGTAGAGT
*
1067719 GTTCATAATGAGAAGAACTCATCCGACAGA-GTGAGAAAAAGTTCATAATGAGAAGAGCTTGTTC
1 GTTCATAATGAGAAGAACTCATCCGACAGATG-GAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* *** * *
1067783 GACCTATCA-CTCGATTCA-CAACAT-T-TCAAATCAGTGACATCTCACTTGAGGGATCAACATT
65 AACCT-T-AGCTCGATTCATC-ACATATGTCAAATCAACAACACCTCACTCGAGGGATCAACATT
** * *
1067844 TCCAGTGGAGAGTTCATAAAGAGAAGAACTCATCCGACAAAAGAAGAAGAA
127 TCCAGTAAAAAGTTCATAAAGAGAAAAACTCATCCGA-AAAAGAAGAAGAA
* *
1067895 GTTCATAATGAGAAGAACTCATCCGACAGATGGAGAAGACGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCCGACAGATGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
**
1067960 ACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGATCAACATTT
66 ACCTTAGCTCGATTCATCACATAT---GTCAAATCAACAACACCTCACTCGAGGGATCAACATTT
* * ** *
1068025 CTAGTAAAAAGTTCATAATGAGAAAAACTCATCCGATGAAGGAGAAGAA
128 CCAGTAAAAAGTTCATAAAGAGAAAAACTCATCCGAAAAAGAAGAAGAA
1068074 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
1068093 TATTCAACCT
Statistics
Matches: 170, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
174 1 0.01
175 14 0.08
176 65 0.38
177 1 0.01
179 29 0.17
180 60 0.35
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (176 bp):
GTTCATAATGAGAAGAACTCATCCGACAGATGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTAGCTCGATTCATCACATATGTCAAATCAACAACACCTCACTCGAGGGATCAACATTTCCA
GTAAAAAGTTCATAAAGAGAAAAACTCATCCGAAAAAGAAGAAGAA
Found at i:1068144 original size:139 final size:137
Alignment explanation
Indices: 1067893--1068396 Score: 716
Period size: 139 Copynumber: 3.7 Consensus size: 137
1067883 AAAGAAGAAG
* * *
1067893 AAGTTCATAATGAGAAGAACTCATCCGACAGATGGAGAAGACGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCCGA-TGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1067958 CAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGATCAACAT
65 CAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGATCAACAT
1068023 TTCTAGTAAA
130 TTCTAGT--A
* *
1068033 AAGTTCATAATGAGAAAAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTATTC
1 AAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
1068098 AACCTTAGCTCAATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATT
66 AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGATCAACATT
*
1068163 TCCAGTGGA
131 TCTAGT--A
* *
1068172 GAGTTCATAACGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
1068237 AACCTTAGCTCGATTCTTCATATATGGAGTTGAATCATCAACACCTCACTTGAGGGATCAACATT
66 AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGATCAACATT
*
1068302 TCTAGTG
131 TCTAGTA
*
1068309 GAGTTCATAATGAGAAGAACTCATCCGAT-------AAGAAGTTCATAATGAGAAGAACTTGTTC
1 AAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
1068367 AACATTCGCTTGTTTCCATCACATAAGGAG
66 AACCTTAGCTCGATT-CATCACATATGGAG
1068397 CTGGAACAAC
Statistics
Matches: 334, Mismatches: 29, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
130 40 0.12
131 11 0.03
137 28 0.08
139 228 0.68
140 27 0.08
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGATCAACATT
TCTAGTA
Found at i:1071861 original size:25 final size:25
Alignment explanation
Indices: 1071828--1071901 Score: 139
Period size: 25 Copynumber: 3.0 Consensus size: 25
1071818 GTGAAGTTGA
*
1071828 AGAGTGAGGTAGCATTCGGGAAAAG
1 AGAGAGAGGTAGCATTCGGGAAAAG
1071853 AGAGAGAGGTAGCATTCGGGAAAAG
1 AGAGAGAGGTAGCATTCGGGAAAAG
1071878 AGAGAGAGGTAGCATTCGGGAAAA
1 AGAGAGAGGTAGCATTCGGGAAAA
1071902 ATATCAAGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.39, C:0.08, G:0.39, T:0.14
Consensus pattern (25 bp):
AGAGAGAGGTAGCATTCGGGAAAAG
Found at i:1077801 original size:37 final size:37
Alignment explanation
Indices: 1077716--1077846 Score: 124
Period size: 36 Copynumber: 3.5 Consensus size: 37
1077706 CAAAGTGTTA
* *
1077716 TCTCGCTAGAGACAATTTT-TCATAAAAAAACAAA-TTTA
1 TCTCGCTTGAGACAATTTTCTC-T--AAAAACAAATTTTG
* *
1077754 TCTCGTTTGAGACAATTTTCTGTAAAAACAAATTTTG
1 TCTCGCTTGAGACAATTTTCTCTAAAAACAAATTTTG
* * * * *
1077791 TCTCACTTGAGATAATTTT-TCTCAAAACAACTTTCG
1 TCTCGCTTGAGACAATTTTCTCTAAAAACAAATTTTG
*
1077827 TCTCGCTTGAGACATTTTTC
1 TCTCGCTTGAGACAATTTTC
1077847 CTTTGAGATG
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
36 38 0.50
37 19 0.25
38 18 0.24
39 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (37 bp):
TCTCGCTTGAGACAATTTTCTCTAAAAACAAATTTTG
Found at i:1078270 original size:30 final size:30
Alignment explanation
Indices: 1078236--1078356 Score: 84
Period size: 30 Copynumber: 3.8 Consensus size: 30
1078226 CTTGTCTCTC
1078236 TTGAGACAGTTTCTCTTGAAACAAAAATCT
1 TTGAGACAGTTTCTCTTGAAACAAAAATCT
*** **
1078266 TTGAGTTTGTTTC-CTTTGAAACAAAGTTTTGTCTCT
1 TTGAGACAGTTTCTC-TTGAAACAAA------AATCT
*
1078302 TTGAGACAGTTTCTCTTGAAACAAAAATAT
1 TTGAGACAGTTTCTCTTGAAACAAAAATCT
* *
1078332 TTGAGTA-TGTTTCCCTTGAAACAAA
1 TTGAG-ACAGTTTCTCTTGAAACAAA
1078357 GTTTTTTCTC
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
29 1 0.01
30 43 0.62
31 1 0.01
36 23 0.33
37 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (30 bp):
TTGAGACAGTTTCTCTTGAAACAAAAATCT
Found at i:1078306 original size:66 final size:68
Alignment explanation
Indices: 1078041--1078382 Score: 401
Period size: 68 Copynumber: 5.1 Consensus size: 68
1078031 TTTAGAAATT
* * * * *
1078041 GTTTCACTTGAAACATAAAACCTTTAAGATTGTTT-CTCTTGAAA-GAAGTTGTGTCTCTCTTGA
1 GTTTCTCTTGAAACATAAAATCTTTGAGATTGTTTCCT-TTGAAACAAAGTTTTGTCTCTCTTGA
*
1078104 GACG
65 GACA
* * * * *
1078108 GTTTCTCTTGAAATATAAGAAT-ATTGAGATTGTTTCCTTTGAAGCAAAATTTTGTCTCTCTTTA
1 GTTTCTCTTGAAACATAA-AATCTTTGAGATTGTTTCCTTTGAAACAAAGTTTTGTCTCTCTTGA
1078172 GACA
65 GACA
* * * * * *
1078176 ATTTTTCTTGAAACATAAAAACCTTGAGATTGTTTCCCTTGAAACAAAGTCTTGTCTCTCTTGAG
1 GTTTCTCTTGAAACATAAAATCTTTGAGATTGTTTCCTTTGAAACAAAGTTTTGTCTCTCTTGAG
1078241 ACA
66 ACA
*
1078244 GTTTCTCTTGAAACA-AAAATCTTTGAGTTTGTTTCCTTTGAAACAAAGTTTTGTCTCT-TTGAG
1 GTTTCTCTTGAAACATAAAATCTTTGAGATTGTTTCCTTTGAAACAAAGTTTTGTCTCTCTTGAG
1078307 ACA
66 ACA
* * * *
1078310 GTTTCTCTTGAAACA-AAAATATTTGAG-TATGTTTCCCTTGAAACAAAGTTTTTTCTCGCTTGA
1 GTTTCTCTTGAAACATAAAATCTTTGAGAT-TGTTTCCTTTGAAACAAAGTTTTGTCTCTCTTGA
*
1078373 GACC
65 GACA
1078377 GTTTCT
1 GTTTCT
1078383 GTAATACCCC
Statistics
Matches: 236, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.00
66 60 0.25
67 85 0.36
68 90 0.38
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (68 bp):
GTTTCTCTTGAAACATAAAATCTTTGAGATTGTTTCCTTTGAAACAAAGTTTTGTCTCTCTTGAG
ACA
Found at i:1078314 original size:36 final size:35
Alignment explanation
Indices: 1078207--1078326 Score: 108
Period size: 36 Copynumber: 3.5 Consensus size: 35
1078197 CCTTGAGATT
*
1078207 GTTTCCCTTGAAACAAAGTCTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAAGT-TTGTCTCT-TTGAGACA
** ***
1078244 GTTTCTCTTGAAACAAA-----AATCTTTGAGTTT
1 GTTTCTCTTGAAACAAAGTTTGTCTCTTTGAGACA
1078274 GTTTC-CTTTGAAACAAAGTTTTGTCTCTTTGAGACA
1 GTTTCTC-TTGAAACAAAG-TTTGTCTCTTTGAGACA
1078310 GTTTCTCTTGAAACAAA
1 GTTTCTCTTGAAACAAA
1078327 AATATTTGAG
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
29 1 0.02
30 20 0.31
31 3 0.05
36 23 0.36
37 17 0.27
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (35 bp):
GTTTCTCTTGAAACAAAGTTTGTCTCTTTGAGACA
Found at i:1079170 original size:21 final size:21
Alignment explanation
Indices: 1079117--1079232 Score: 92
Period size: 21 Copynumber: 5.4 Consensus size: 21
1079107 TGTCCCGAAT
* *
1079117 GACCACATAGATTTGTCCATAAG
1 GACCACATATATAT-TCCA-AAG
1079140 GACCACATATATATTCCAAAG
1 GACCACATATATATTCCAAAG
* * *
1079161 GATCAAATATATATCCCGAAA-
1 GACCACATATATATTCC-AAAG
* *
1079182 GACCGCATATATTTTCCAAAG
1 GACCACATATATATTCCAAAG
* * *
1079203 GATCACATATAT-GTCTCGAAG
1 GACCACATATATATTC-CAAAG
1079224 GACCACATA
1 GACCACATA
1079233 GAACCCTCGA
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.07
21 51 0.68
22 7 0.09
23 12 0.16
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (21 bp):
GACCACATATATATTCCAAAG
Found at i:1079204 original size:42 final size:42
Alignment explanation
Indices: 1079140--1079232 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
1079130 TGTCCATAAG
1079140 GACCACATATATATTCCAAAGGATCAAATATATATCCCGAAA
1 GACCACATATATATTCCAAAGGATCAAATATATATCCCGAAA
* * * * * *
1079182 GACCGCATATATTTTCCAAAGGATCACATATATGTCTCGAAG
1 GACCACATATATATTCCAAAGGATCAAATATATATCCCGAAA
1079224 GACCACATA
1 GACCACATA
1079233 GAACCCTCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (42 bp):
GACCACATATATATTCCAAAGGATCAAATATATATCCCGAAA
Found at i:1081137 original size:138 final size:137
Alignment explanation
Indices: 1080889--1081436 Score: 720
Period size: 138 Copynumber: 4.0 Consensus size: 137
1080879 TTGAAACAAA
* * * * *
1080889 TTATCCCTAAAGATAGCCAACCGTCCTCATCACGTAAGAATCGTGTCATCCACTGACCATATCTC
1 TTATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTC
* * * * *
1080954 CTCTTCACGTAGGAGCCGCGTCAACCTTAGATAACCAGTCATCCTCATTATGTAGGAACCGTGTT
66 CTCATCACGTAGGAGTCACGTCAACCTTAGATAACCAG-CGTCCTCATCATGTAGGAACCGTGTT
*
1081019 ATCACTAT
130 ATCACCAT
**
1081027 TTATCCCTAAAGATGGCCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTC
1 TTATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTC
*
1081092 CTCATCACGTAGGAGTCACGTCAACCTTAGATGACCAGCGGTCCTCATCATGTAGGAACCGTGTT
66 CTCATCACGTAGGAGTCACGTCAACCTTAGATAACCAGC-GTCCTCATCATGTAGGAACCGTGTT
1081157 ATCACCAT
130 ATCACCAT
* * *
1081165 TTATCCCTAAAGATGGCTAACCGTCCTCATCACGTAGGAACCGTGTTATCCACTGACCAGATCTC
1 TTATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTC
* * **
1081230 CTCATCACGTAGGAGTCGCGTCAACCTTAGATAACCAGCCGTCCACATCACATAGGAACCGTGTT
66 CTCATCACGTAGGAGTCACGTCAACCTTAGATAACCAG-CGTCCTCATCATGTAGGAACCGTGTT
1081295 ATCACCAT
130 ATCACCAT
* * * * * * *
1081303 TTATCCCTAAATATGACCAAGACATCCTCATCACGTAGGAACAGTGTCATCTACCGACCATATCT
1 TTATCCCTAAAGATGGCCAA-CCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * * ** *
1081368 CCTCATCACGTATGAG-CAGTGTCAACCTTAGATAACCATACTTCCTCATCACATAGAAACCGTG
65 CCTCATCACGTAGGAGTCA-CGTCAACCTTAGATAACCA-GCGTCCTCATCATGTAGGAACCGTG
1081432 TTATC
128 TTATC
1081437 TTCAAATTTA
Statistics
Matches: 364, Mismatches: 41, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
137 1 0.00
138 266 0.73
139 97 0.27
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (137 bp):
TTATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTC
CTCATCACGTAGGAGTCACGTCAACCTTAGATAACCAGCGTCCTCATCATGTAGGAACCGTGTTA
TCACCAT
Found at i:1081640 original size:3 final size:3
Alignment explanation
Indices: 1081627--1081659 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1081617 TCAAATTAAA
*
1081627 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1081660 TTGTTAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1082639 original size:23 final size:23
Alignment explanation
Indices: 1082613--1082658 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1082603 AATAAGAGAA
*
1082613 GAATGATCGGTTTTGACCTTGGT
1 GAATGACCGGTTTTGACCTTGGT
*
1082636 GAATGGCCGGTTTTGACCTTGGT
1 GAATGACCGGTTTTGACCTTGGT
1082659 TTCTATCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.37
Consensus pattern (23 bp):
GAATGACCGGTTTTGACCTTGGT
Found at i:1092288 original size:28 final size:28
Alignment explanation
Indices: 1092248--1092308 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
1092238 TACTCAGGGA
1092248 CAAAGCTAGGATTCCAATTCAAGGAGAG
1 CAAAGCTAGGATTCCAATTCAAGGAGAG
1092276 CAAAGCTAGGATTCCAATTCAAGGAGAG
1 CAAAGCTAGGATTCCAATTCAAGGAGAG
1092304 CAAAG
1 CAAAG
1092309 TATAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (28 bp):
CAAAGCTAGGATTCCAATTCAAGGAGAG
Found at i:1092373 original size:32 final size:32
Alignment explanation
Indices: 1092301--1092364 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1092291 AATTCAAGGA
1092301 GAGCAAAGTATAATTAATCATAAAAAATGAGG
1 GAGCAAAGTATAATTAATCATAAAAAATGAGG
*
1092333 GAGCAAAGTATAATTAATCATAGAAAATGAGG
1 GAGCAAAGTATAATTAATCATAAAAAATGAGG
1092365 AGGTAAAGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (32 bp):
GAGCAAAGTATAATTAATCATAAAAAATGAGG
Found at i:1092530 original size:2 final size:2
Alignment explanation
Indices: 1092525--1092563 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1092515 TATTTAAATA
1092525 AT AT AT 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 AT AT AT A
1092564 GCACCATCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1092810 original size:4 final size:4
Alignment explanation
Indices: 1092803--1092829 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1092793 GTGATATATA
1092803 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
1092830 TAGTTCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1094071 original size:32 final size:32
Alignment explanation
Indices: 1093982--1094077 Score: 111
Period size: 32 Copynumber: 3.0 Consensus size: 32
1093972 ATCCGTTACA
* * **
1093982 CATTATCTAAATGTGATACTGACTCTACTGTG
1 CATTATCTAAATGTAATGCTGACTCTGTTGTG
* * *
1094014 CATTATCTTAATGCAATGATGACTCTGTTGTG
1 CATTATCTAAATGTAATGCTGACTCTGTTGTG
* *
1094046 CATTATCTGAATGTAATGCTAACTCTGTTGTG
1 CATTATCTAAATGTAATGCTGACTCTGTTGTG
1094078 ACTCATCCAC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (32 bp):
CATTATCTAAATGTAATGCTGACTCTGTTGTG
Found at i:1095916 original size:21 final size:19
Alignment explanation
Indices: 1095892--1095932 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1095882 GAGGAGGAAG
1095892 AAGAAAATGGAAAATGAGAGA
1 AAGAAAAT-G-AAATGAGAGA
1095913 AAGAAAATGAAATGAGAGA
1 AAGAAAATGAAATGAGAGA
1095932 A
1 A
1095933 TATAAAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (19 bp):
AAGAAAATGAAATGAGAGA
Found at i:1099817 original size:26 final size:24
Alignment explanation
Indices: 1099788--1099837 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
1099778 TGATCAATCC
*
1099788 CTTTTTTATTCTTTAATTTTGTTTAA
1 CTTTGTTATT-TTTAATTTT-TTTAA
*
1099814 CTTTGTTATTTTTAGTTTTTTTAA
1 CTTTGTTATTTTTAATTTTTTTAA
1099838 TAGGAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 8 0.36
26 9 0.41
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (24 bp):
CTTTGTTATTTTTAATTTTTTTAA
Found at i:1102505 original size:14 final size:15
Alignment explanation
Indices: 1102479--1102507 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1102469 CTATTTCTCT
1102479 TCAAAAAATTCATCA
1 TCAAAAAATTCATCA
1102494 TCAAAAAA-TCATCA
1 TCAAAAAATTCATCA
1102508 AAAAGCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (15 bp):
TCAAAAAATTCATCA
Found at i:1104799 original size:19 final size:18
Alignment explanation
Indices: 1104777--1104828 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
1104767 AGAACCCCAG
1104777 GGGGGTATCGATTCCCCT
1 GGGGGTATCGATTCCCCT
* *
1104795 AGGGGGAATCGGTT-CCCT
1 -GGGGGTATCGATTCCCCT
*
1104813 GAGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
1104829 TCTACACAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 10 0.37
18 6 0.22
19 11 0.41
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (18 bp):
GGGGGTATCGATTCCCCT
Found at i:1104827 original size:17 final size:18
Alignment explanation
Indices: 1104779--1104829 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1104769 AACCCCAGGG
*
1104779 GGGTATCGATTCCCCTAGG
1 GGGTATCGATT-CCCTAGA
* *
1104798 GGGAATCGGTTCCCT-GA
1 GGGTATCGATTCCCTAGA
1104815 GGGTATCGATTCCCT
1 GGGTATCGATTCCCT
1104830 CTACACAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 14 0.52
18 4 0.15
19 9 0.33
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.27
Consensus pattern (18 bp):
GGGTATCGATTCCCTAGA
Found at i:1108649 original size:22 final size:21
Alignment explanation
Indices: 1108607--1108646 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1108597 GAGTTTATTT
*
1108607 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1108628 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1108647 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1113094 original size:14 final size:14
Alignment explanation
Indices: 1113075--1113102 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1113065 GTGTTCCAAT
1113075 CAACAACAAACTTG
1 CAACAACAAACTTG
1113089 CAACAACAAACTTG
1 CAACAACAAACTTG
1113103 GAAACACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.07, T:0.14
Consensus pattern (14 bp):
CAACAACAAACTTG
Found at i:1116401 original size:31 final size:31
Alignment explanation
Indices: 1116363--1116426 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
1116353 TGATCTTTCC
*
1116363 TTAACTTACATCTTCGCCTCTAATGATGTGG
1 TTAACTTACAGCTTCGCCTCTAATGATGTGG
*
1116394 TTAACTTATAGCTTCGCCTCTAATGATGTGG
1 TTAACTTACAGCTTCGCCTCTAATGATGTGG
1116425 TT
1 TT
1116427 TGTTGCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (31 bp):
TTAACTTACAGCTTCGCCTCTAATGATGTGG
Found at i:1123093 original size:37 final size:37
Alignment explanation
Indices: 1123052--1123418 Score: 324
Period size: 37 Copynumber: 9.9 Consensus size: 37
1123042 ATATATACAT
1123052 AATATATATAATATAT-GATTTTGAAAACGTTTTTGAA
1 AATATATATAATATATAG-TTTTGAAAACGTTTTTGAA
* * * **
1123089 AATATATATAGTATATAGTTTTAAAAACATTGTTCAAA
1 AATATATATAATATATAGTTTTGAAAACGTT-TTTGAA
* * * *
1123127 AATATATACAATATGTAGTCTTGAAAACATTTTT-AA
1 AATATATATAATATATAGTTTTGAAAACGTTTTTGAA
****
1123163 AATATATATAATATATCA-TTTTGAATTTTTTTTTGAA
1 AATATATATAATATAT-AGTTTTGAAAACGTTTTTGAA
* *
1123200 AATATATATAATATATAATTTTGAAAAC-ATTTT-AA
1 AATATATATAATATATAGTTTTGAAAACGTTTTTGAA
* *
1123235 AAAATATTTAATATATAGTTTTGAAAACGTTTTT-AA
1 AATATATATAATATATAGTTTTGAAAACGTTTTTGAA
* ** *
1123271 AA-A-ATATAATATATGGTTTAAAAAAAGGTTTTTGAAAAA
1 AATATATATAATATATAGTTT-TGAAAACGTTTTTG---AA
* *
1123310 ATATATATATAATATATAGTTTTGAAATCATTTTTCGAA
1 A-ATATATATAATATATAGTTTTGAAAACGTTTTT-GAA
*
1123349 AATATATATAATATATAGTTTT-AAGACGTTTTTGGAA
1 AATATATATAATATATAGTTTTGAAAACGTTTTT-GAA
* * *
1123386 AAAATATATAATATAT--TTTAGAAAACGTGTTTG
1 AATATATATAATATATAGTTTTGAAAACGTTTTTG
1123419 GGTTTTGAAA
Statistics
Matches: 269, Mismatches: 45, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
34 14 0.05
35 42 0.16
36 49 0.18
37 80 0.30
38 52 0.19
39 6 0.02
40 1 0.00
41 9 0.03
42 16 0.06
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (37 bp):
AATATATATAATATATAGTTTTGAAAACGTTTTTGAA
Found at i:1123328 original size:76 final size:78
Alignment explanation
Indices: 1123238--1123400 Score: 199
Period size: 76 Copynumber: 2.1 Consensus size: 78
1123228 ATTTTAAAAA
* * * *
1123238 ATATTTAATATATAGTTTTGAAAACGTTTTT-AAAA-A-ATATAATATATGGTTTAAAAAAAGGT
1 ATATATAATATATAGTTTTGAAAACATTTTTCAAAATATATATAATATATAGTTT--AAAAACGT
1123300 TTTT-GAAAAAATAT
64 TTTTGGAAAAAATAT
* * *
1123314 ATATATAATATATAGTTTTGAAATCATTTTTCGAAAATATATATAATATATAGTTTTAAGACGTT
1 ATATATAATATATAGTTTTGAAAACATTTTTC-AAAATATATATAATATATAGTTTAAAAACGTT
1123379 TTTGGAAAAAATAT
65 TTTGGAAAAAATAT
1123393 ATAATATA
1 AT-ATATA
1123401 TTTTAGAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
76 28 0.38
78 13 0.18
79 13 0.18
80 20 0.27
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (78 bp):
ATATATAATATATAGTTTTGAAAACATTTTTCAAAATATATATAATATATAGTTTAAAAACGTTT
TTGGAAAAAATAT
Found at i:1123448 original size:2 final size:2
Alignment explanation
Indices: 1123443--1123469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1123433 TTTTTTCGAA
1123443 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 A
1123470 CATTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1123505 original size:6 final size:6
Alignment explanation
Indices: 1123477--1123528 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
1123467 ATACATTTTA
* * *
1123477 TTTA-T TTTATT TCTATTT ATTTATT TTTATT CTTATT TTTATT TCTATT
1 TTTATT TTTATT TTTA-TT -TTTATT TTTATT TTTATT TTTATT TTTATT
1123526 TTT
1 TTT
1123529 TGGTCCAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
5 4 0.11
6 27 0.71
7 4 0.11
8 3 0.08
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:1123509 original size:19 final size:20
Alignment explanation
Indices: 1123473--1123526 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
1123463 ATATATACAT
1123473 TTTATTTATTTTATTTC-TA
1 TTTATTTATTTTATTTCTTA
1123492 TTTATTTATTTT-TATTCTTA
1 TTTATTTATTTTAT-TTCTTA
1123512 -TT-TTTATTTCTATTT
1 TTTATTTATTT-TATTT
1123527 TTTGGTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 8 0.26
19 20 0.65
20 3 0.10
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTATTTTATTTCTTA
Found at i:1129525 original size:13 final size:13
Alignment explanation
Indices: 1129507--1129541 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1129497 TGCGTCATAA
**
1129507 ATTTATGATGCGC
1 ATTTATGACACGC
1129520 ATTTATGACACGC
1 ATTTATGACACGC
1129533 ATTTATGAC
1 ATTTATGAC
1129542 GCTTATTGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:1129675 original size:85 final size:84
Alignment explanation
Indices: 1129520--1129685 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 84
1129510 TATGATGCGC
* * *
1129520 ATTTATGACACGCATTTATGACGCTTATTGCGCATCATTGAAGCCCCCGTCATAAATGAAGACGA
1 ATTTATGACACACATTTATGACGCTTATTGCGCATCATTGAAGCACACGTCATAAA-GAAGACGA
*
1129585 CACACATTTGTGTGTCATAA
65 CACACATTCGTGTGTCATAA
* ** *
1129605 ATTTATGACACACATTTATGAC-TTATATTGCGTGTCATTGAAGCACACGTCATTAGAA-AAGAT
1 ATTTATGACACACATTTATGACGCT-TATTGCGCATCATTGAAGCACACGTCA-TA-AAGAAGAC
*
1129668 GATACACATTCGTGTGTC
63 GACACACATTCGTGTGTC
1129686 TTGATTGTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 64 0.93
86 2 0.03
87 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (84 bp):
ATTTATGACACACATTTATGACGCTTATTGCGCATCATTGAAGCACACGTCATAAAGAAGACGAC
ACACATTCGTGTGTCATAA
Found at i:1135250 original size:22 final size:23
Alignment explanation
Indices: 1135225--1135275 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
1135215 CTTCAAATCA
*
1135225 GGTTTGAGAACCAATTCAG-TCG
1 GGTTTGAGAACCAATTCAGAACG
* *
1135247 GGTTCGAGAGCCAATTCAGAACG
1 GGTTTGAGAACCAATTCAGAACG
1135270 GGTTTG
1 GGTTTG
1135276 GCTTAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (23 bp):
GGTTTGAGAACCAATTCAGAACG
Found at i:1136363 original size:35 final size:37
Alignment explanation
Indices: 1136319--1136644 Score: 394
Period size: 37 Copynumber: 8.7 Consensus size: 37
1136309 ATATATACAT
*
1136319 AATATATATAATATATGGTTTTGAAAACATTTTTGAAAA
1 AATATATATAATATATAGTTTTGAAAACATTTTTG--AA
*
1136358 AATATATATATAGTATATAGTTTTGAAAACATTGTTCGAA
1 AATATATATA-A-TATATAGTTTTGAAAACATT-TTTGAA
*
1136398 AATATATA-AATATGTAGTTTTGAAAACATTTTT-AA
1 AATATATATAATATATAGTTTTGAAAACATTTTTGAA
* *
1136433 AATATATATAATATATAATTTTAAAAACATTTTTGAA
1 AATATATATAATATATAGTTTTGAAAACATTTTTGAA
*
1136470 AATATATATAATATATAATTTTGAAAACATTTTTGAA
1 AATATATATAATATATAGTTTTGAAAACATTTTTGAA
* *
1136507 AATATATATAACATATAATTTTGAAAACA-TTTT-AA
1 AATATATATAATATATAGTTTTGAAAACATTTTTGAA
*
1136542 AAAATATATAATATATAGTTTTGAAAACATTTTTTTTGAA
1 AATATATATAATATATAGTTTTGAAAACA---TTTTTGAA
* * * **
1136582 AATATGTATAATATATA-TTTTTAAGATGTTTTTGGAA
1 AATATATATAATATATAGTTTTGAAAACATTTTT-GAA
*
1136619 AATATATATAATAT-TATTTTTGAAAA
1 AATATATATAATATATAGTTTTGAAAA
1136645 TGTGTTTGGG
Statistics
Matches: 254, Mismatches: 21, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
35 38 0.15
36 35 0.14
37 108 0.43
38 1 0.00
39 22 0.09
40 28 0.11
41 19 0.07
42 3 0.01
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (37 bp):
AATATATATAATATATAGTTTTGAAAACATTTTTGAA
Found at i:1136530 original size:110 final size:108
Alignment explanation
Indices: 1136319--1136644 Score: 404
Period size: 112 Copynumber: 2.9 Consensus size: 108
1136309 ATATATACAT
* *
1136319 AATATATATAATATATGGTTTTGAAAACATTTTTGAAAAAATATATATATAGTATATAGTTTTGA
1 AATATATATAATATATAGTTTTGAAAACATTTTTG--AAAATATATATA-A-TATATAATTTTGA
* *
1136384 AAACATTGTTCGAAAATATATA-AATATGTAGTTTTGAAAACATTTTTAA
62 AAACATT-TTTGAAAATATATATAATAT-TAATTTTGAAAACA-TTTTAA
* *
1136433 AATATATATAATATATAATTTTAAAAACATTTTTGAAAATATATATAATATATAATTTTGAAAAC
1 AATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAATTTTGAAAAC
*
1136498 ATTTTTGAAAATATATATAACATATAATTTTGAAAACATTTTAA
66 ATTTTTGAAAATATATATAATAT-TAATTTTGAAAACATTTTAA
* * *
1136542 AAAATATATAATATATAGTTTTGAAAACATTTTTTTTGAAAATATGTATAATATAT-ATTTTTAA
1 AATATATATAATATATAGTTTTGAAAACA---TTTTTGAAAATATATATAATATATAATTTTGAA
* ** *
1136606 GATGTTTTTGGAAAATATATATAATATTATTTTTGAAAA
63 AACATTTTT-GAAAATATATATAATATTAATTTTGAAAA
1136645 TGTGTTTGGG
Statistics
Matches: 189, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
109 45 0.24
110 36 0.19
111 25 0.13
112 51 0.27
114 32 0.17
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (108 bp):
AATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAATTTTGAAAAC
ATTTTTGAAAATATATATAATATTAATTTTGAAAACATTTTAA
Found at i:1136681 original size:2 final size:2
Alignment explanation
Indices: 1136676--1136707 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1136666 TTTTTTTGAA
1136676 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
1136708 TATTTATTTG
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:1136743 original size:20 final size:19
Alignment explanation
Indices: 1136708--1136751 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1136698 ATATATATAT
1136708 TATTTATTTGTTTTATTTC
1 TATTTATTTGTTTTATTTC
*
1136727 TATTTATTTATTTTTATTTC
1 TATTTATTT-GTTTTATTTC
*
1136747 CATTT
1 TATTT
1136752 TTAGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (19 bp):
TATTTATTTGTTTTATTTC
Found at i:1140610 original size:18 final size:19
Alignment explanation
Indices: 1140576--1140622 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
1140566 ACCCGGATAA
*
1140576 AGTTAAACTATTTTTAAAT
1 AGTTAAAATATTTTTAAAT
1140595 AGTTAAAATA-TTTTAAAT
1 AGTTAAAATATTTTTAAAT
*
1140613 AGTTGAAATA
1 AGTTAAAATA
1140623 ATATTTGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (19 bp):
AGTTAAAATATTTTTAAAT
Found at i:1140736 original size:18 final size:19
Alignment explanation
Indices: 1140702--1140748 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
1140692 ACTCGGATCG
*
1140702 AGTTAAACTATTTTTAAAT
1 AGTTAAAATATTTTTAAAT
1140721 AGTTAAAATA-TTTTAAAT
1 AGTTAAAATATTTTTAAAT
*
1140739 AGTTGAAATA
1 AGTTAAAATA
1140749 ATATTCGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (19 bp):
AGTTAAAATATTTTTAAAT
Found at i:1140802 original size:9 final size:9
Alignment explanation
Indices: 1140778--1140838 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
1140768 TTAAACTATT
1140778 TTTAAATAG
1 TTTAAATAG
* *
1140787 TTAAAATAA
1 TTTAAATAG
1140796 TTTAAATAG
1 TTTAAATAG
* *
1140805 TTGAAATAA
1 TTTAAATAG
*
1140814 TATTCAAATAT
1 T-TT-AAATAG
1140825 TTTAAATAG
1 TTTAAATAG
1140834 TTTAA
1 TTTAA
1140839 CTCGATCCGG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
9 32 0.78
10 3 0.07
11 6 0.15
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.43
Consensus pattern (9 bp):
TTTAAATAG
Found at i:1140818 original size:64 final size:64
Alignment explanation
Indices: 1140536--1140818 Score: 346
Period size: 64 Copynumber: 4.4 Consensus size: 64
1140526 CAAATAAATT
* **
1140536 AATATTTTAAAATAGTTGAAATAATATTAGACCCGGATAAAGTTAAACTATTTTTAAATAGTTAA
1 AATATTTT-AAATAGTTGAAATAATATTCGACCCGGATCGAGTTAAACTATTTTTAAATAGTTAA
* * ** ** *
1140601 AATATTTTAAATAGTTGAAATAATATTTGA--C---T--ATTTAATTTATTCAATCCAGATCGAG
1 AATATTTTAAATAGTTGAAATAATATTCGACCCGGATCGAGTTAAACTATT---TTTAAAT--AG
1140659 TTAA
61 TTAA
* *
1140663 AATATTTTAAATAGTTGAAATAATATTGGACTCGGATCGAGTTAAACTATTTTTAAATAGTTAA
1 AATATTTTAAATAGTTGAAATAATATTCGACCCGGATCGAGTTAAACTATTTTTAAATAGTTAA
1140727 AATATTTTAAATAGTTGAAATAATATTCGACCCGGATCGAGTTAAACTATTTTTAAATAGTTAA
1 AATATTTTAAATAGTTGAAATAATATTCGACCCGGATCGAGTTAAACTATTTTTAAATAGTTAA
*
1140791 AATAATTTAAATAGTTGAAATAATATTC
1 AATATTTTAAATAGTTGAAATAATATTC
1140819 AAATATTTTA
Statistics
Matches: 189, Mismatches: 17, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
57 9 0.05
59 1 0.01
60 4 0.02
62 36 0.19
64 117 0.62
65 8 0.04
66 4 0.02
67 1 0.01
69 9 0.05
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (64 bp):
AATATTTTAAATAGTTGAAATAATATTCGACCCGGATCGAGTTAAACTATTTTTAAATAGTTAA
Found at i:1140831 original size:20 final size:18
Alignment explanation
Indices: 1140778--1140838 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
1140768 TTAAACTATT
*
1140778 TTTAAATAGTTAAAATAA
1 TTTAAATAGTTGAAATAA
1140796 TTTAAATAGTTGAAATAA
1 TTTAAATAGTTGAAATAA
* * *
1140814 TATTCAAATATTTTAAATAG
1 T-TT-AAATAGTTGAAATAA
1140834 TTTAA
1 TTTAA
1140839 CTCGATCCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 20 0.54
19 4 0.11
20 13 0.35
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.43
Consensus pattern (18 bp):
TTTAAATAGTTGAAATAA
Found at i:1142453 original size:3 final size:3
Alignment explanation
Indices: 1142445--1142469 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1142435 TTAACCCCCA
1142445 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
1142470 ATTCTCCCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1144316 original size:17 final size:17
Alignment explanation
Indices: 1144287--1144336 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
1144277 TAAGAGTTAA
*
1144287 TTTAATAAATGAACTAG
1 TTTAATGAATGAACTAG
*
1144304 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
1144321 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
1144337 CTTCCCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:1145253 original size:3 final size:3
Alignment explanation
Indices: 1145245--1145376 Score: 167
Period size: 3 Copynumber: 42.7 Consensus size: 3
1145235 TTATGCAAAT
1145245 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
1145292 AGA AGA AGA AGA AGA GAGA AGA AGA AGA AGA GAGA AGAA AGG AGA AGA
1 AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA -AGA AG-A AGA AGA AGA
* * * *
1145340 GGA AGA AGA AAA AGAA AGA TGAA AGA ACA AGA AGA AG
1 AGA AGA AGA AGA AG-A AGA AG-A AGA AGA AGA AGA AG
1145377 GTTGAGGGAT
Statistics
Matches: 113, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.02
3 97 0.86
4 14 0.12
ACGTcount: A:0.64, C:0.01, G:0.34, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:1149542 original size:21 final size:20
Alignment explanation
Indices: 1149515--1149613 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1149505 AATCAGTTTC
1149515 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1149536 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1149557 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1149577 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1149598 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1149614 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1149606 original size:20 final size:20
Alignment explanation
Indices: 1149581--1149773 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
1149571 GATTTTCCAG
* ** *
1149581 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1149601 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1149621 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1149641 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1149661 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1149681 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1149701 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1149721 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
1149742 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1149762 AATCGCAACGCG
1 AATCGCAACGCG
1149774 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1150185 original size:33 final size:33
Alignment explanation
Indices: 1150146--1150216 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1150136 TTCACTTAGA
1150146 TTTCATTTCGCGTTGCGATACTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATACTCTCGTTGCGAT
** *
1150179 TTTCATTTCGCGTTGTTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATACTCTCGTTGCGAT
1150212 TTTCA
1 TTTCA
1150217 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATACTCTCGTTGCGAT
Found at i:1150322 original size:21 final size:21
Alignment explanation
Indices: 1150296--1150372 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1150286 TGCAGAAGAG
1150296 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
1150317 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
1150337 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
1150359 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1150373 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1150395 original size:19 final size:19
Alignment explanation
Indices: 1150307--1150415 Score: 84
Period size: 19 Copynumber: 5.8 Consensus size: 19
1150297 CGCAACGAGA
*
1150307 GAAATGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGC
** *
1150326 GAAAATGACTATCTGCAACGA
1 G-AAATGAAAATC-GCAACGC
1150347 GAAAAATGAAAATCGCAA--C
1 G--AAATGAAAATCGCAACGC
*
1150366 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1150382 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
1150401 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1150416 TTGCGATTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
18 1 0.01
19 28 0.39
20 9 0.12
21 11 0.15
22 10 0.14
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1150451 original size:14 final size:14
Alignment explanation
Indices: 1150432--1150488 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1150422 TTTTCATTCG
1150432 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1150446 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1150465 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1150479 CGTTGCGATT
1 CGTTGCGATT
1150489 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1150470 original size:33 final size:33
Alignment explanation
Indices: 1150416--1150496 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
1150406 CAAAATCGCA
1150416 TTGCGATTTTCA-TTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1150448 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1150481 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1150497 TCTCGTTGCG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 12 0.25
33 36 0.75
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1150499 original size:21 final size:21
Alignment explanation
Indices: 1150473--1150537 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1150463 CGCGTTGCGA
1150473 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1150494 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
1150514 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1150535 TTC
1 TTC
1150538 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1150534 original size:20 final size:20
Alignment explanation
Indices: 1150439--1150535 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
1150429 TCGCGTTGCG
1150439 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1150459 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
1150472 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
1150492 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
*
1150513 ATTCTCTCGTTACGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1150533 ATT
1 ATT
1150536 TCAACCAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
13 3 0.05
14 9 0.15
19 9 0.15
20 22 0.37
21 17 0.28
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1152276 original size:17 final size:17
Alignment explanation
Indices: 1152246--1152278 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1152236 GTTGCTGCCA
1152246 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
1152263 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
1152279 AAATAGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:1152483 original size:14 final size:14
Alignment explanation
Indices: 1152464--1152520 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1152454 CGAAACTTAA
1152464 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1152478 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1152497 AATCGCAACGACAG
1 AATCGCAACGAGAG
1152511 AATCGCAACG
1 AATCGCAACG
1152521 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1152504 original size:33 final size:33
Alignment explanation
Indices: 1152446--1152569 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
1152436 TAGTTTACTT
* * *
1152446 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
1152480 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
1152513 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
1152546 TTGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
1152570 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.85
34 12 0.15
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:1152546 original size:14 final size:14
Alignment explanation
Indices: 1152495--1152553 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1152485 ACGCGAAATG
1152495 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1152509 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
1152528 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1152542 AAAATTGCAACG
1 AAAATCGCAACG
1152554 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1152565 original size:19 final size:19
Alignment explanation
Indices: 1152478--1152569 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
1152468 GCAACGAGAG
**
1152478 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
*
1152497 AATCGCAA--CG--A-CAG
1 AATCGCAACGCGAAACCAA
1152511 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1152530 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
*
1152544 AATTGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1152563 AATCGCA
1 AATCGCA
1152570 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 19 0.33
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 27 0.47
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1152587 original size:19 final size:19
Alignment explanation
Indices: 1152565--1152702 Score: 107
Period size: 19 Copynumber: 7.8 Consensus size: 19
1152555 GAAACCAAAA
*
1152565 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1152584 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1152598 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1152617 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
1152633 T--CGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1152650 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1152669 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1152688 TTGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1152703 AAGTTTCGTG
Statistics
Matches: 89, Mismatches: 20, Indels: 20
0.69 0.16 0.16
Matches are distributed among these distances:
14 15 0.17
16 8 0.09
17 8 0.09
19 58 0.65
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1152612 original size:33 final size:33
Alignment explanation
Indices: 1152570--1152700 Score: 154
Period size: 33 Copynumber: 3.8 Consensus size: 33
1152560 CAAAATCGCA
*
1152570 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1152603 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1152636 TTGTGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA---T--TCTCTCG
* *
1152674 TTGCGATTCTCATTTTGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1152701 TTAAGTTTCG
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
33 54 0.65
35 1 0.01
36 1 0.01
38 27 0.33
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1154631 original size:14 final size:14
Alignment explanation
Indices: 1154612--1154650 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1154602 ATTGTTTAAT
1154612 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1154626 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1154640 TGATTGTGTAA
1 TGATT-TGTAA
1154651 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1154783 original size:19 final size:19
Alignment explanation
Indices: 1154753--1154847 Score: 121
Period size: 19 Copynumber: 5.2 Consensus size: 19
1154743 AAATGCTATT
1154753 GCAATGCGGAAATGAAAATC
1 GCAATGC-GAAATGAAAATC
1154773 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
1154792 GCAA--CG--A-GAGAATC
1 GCAATGCGAAATGAAAATC
1154806 GCAATGCGAAATG-AAATC
1 GCAATGCGAAATGAAAATC
1154824 GCAATGCGGAAATGAAAATC
1 GCAATGC-GAAATGAAAATC
1154844 GCAA
1 GCAA
1154848 CGAGAGATCG
Statistics
Matches: 66, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 12 0.18
19 23 0.35
20 16 0.24
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Done.