Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007925.1 Hibiscus syriacus cultivar Beakdansim tig00110331_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: 1316088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1224221 original size:20 final size:20
Alignment explanation
Indices: 1224178--1224221 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1224168 CGATAGTCAT
** * *
1224178 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCAATTTTAAG
1224198 TTTCGTGTTGCAATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
1224218 TTTC
1 TTTC
1224222 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTAAG
Found at i:1226228 original size:40 final size:40
Alignment explanation
Indices: 1226084--1226297 Score: 148
Period size: 40 Copynumber: 5.9 Consensus size: 40
1226074 AGAATAGTTT
* *
1226084 ACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
*
1226124 ACTATCGCAA--CG-AGA-GA--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
1226157 AAAATCG-AA--C-AACAA--A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAA-AATGACTATCGCAATGCGAAAATG
1226190 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* ** *
1226230 ACTATCGCAATACGAATTTGACTATTGCAA--CG-AAA-G
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
1226266 A--ATCGCAATGC-AAAATGAAAATCGCATTGCGA
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGA
1226298 TTCTCTCGTT
Statistics
Matches: 140, Mismatches: 20, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
32 15 0.11
33 31 0.22
34 21 0.15
35 2 0.01
36 7 0.05
37 7 0.05
38 5 0.04
40 52 0.37
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:1226240 original size:20 final size:20
Alignment explanation
Indices: 1226084--1226259 Score: 148
Period size: 20 Copynumber: 9.5 Consensus size: 20
1226074 AGAATAGTTT
*
1226084 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1226104 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1226124 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1226140 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
1226157 AAAATCG-AA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
1226172 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1226190 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1226210 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
1226230 ACTATCGCAATACGAATTTG
1 ACTATCGCAATGCGAAAATG
*
1226250 ACTATTGCAA
1 ACTATCGCAA
1226260 CGAAAGAATC
Statistics
Matches: 134, Mismatches: 7, Indels: 30
0.78 0.04 0.18
Matches are distributed among these distances:
13 4 0.03
14 9 0.07
15 1 0.01
16 11 0.08
17 8 0.06
18 5 0.04
19 4 0.03
20 92 0.69
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1226341 original size:20 final size:20
Alignment explanation
Indices: 1226318--1226412 Score: 120
Period size: 20 Copynumber: 4.8 Consensus size: 20
1226308 GCGATAATTG
1226318 AATTT-GCATTGCGATAGTC
1 AATTTCGCATTGCGATAGTC
* *
1226337 AAATTCGCATTACGATAGTC
1 AATTTCGCATTGCGATAGTC
*
1226357 ATTTTCGCATTGCGATAGTC
1 AATTTCGCATTGCGATAGTC
* *
1226377 ATTTTCGCGTTGCGATAGTC
1 AATTTCGCATTGCGATAGTC
* *
1226397 ATTTTCGCGTTGCGAT
1 AATTTCGCATTGCGAT
1226413 TTTAAGTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
19 4 0.06
20 65 0.94
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
AATTTCGCATTGCGATAGTC
Found at i:1226367 original size:40 final size:40
Alignment explanation
Indices: 1226323--1226412 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
1226313 AATTGAATTT
1226323 GCATTGCGATAGTCAAATTCGCATTACGATAGTCATTTTC
1 GCATTGCGATAGTCAAATTCGCATTACGATAGTCATTTTC
** * *
1226363 GCATTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTC
1 GCATTGCGATAGTCAAATTCGCATTACGATAGTCATTTTC
*
1226403 GCGTTGCGAT
1 GCATTGCGAT
1226413 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (40 bp):
GCATTGCGATAGTCAAATTCGCATTACGATAGTCATTTTC
Found at i:1226422 original size:20 final size:20
Alignment explanation
Indices: 1226326--1226422 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
1226316 TGAATTTGCA
* *
1226326 TTGCGATAGTCAA-ATTCGCA
1 TTGCGATAGT-AAGTTTCGCG
* * * *
1226346 TTACGATAGTCATTTTCGCA
1 TTGCGATAGTAAGTTTCGCG
* *
1226366 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTAAGTTTCGCG
* *
1226386 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTAAGTTTCGCG
**
1226406 TTGCGATTTTAAGTTTC
1 TTGCGATAGTAAGTTTC
1226423 AGATTCTATT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
19 1 0.01
20 66 0.99
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTAAGTTTCGCG
Found at i:1226987 original size:21 final size:21
Alignment explanation
Indices: 1226896--1227000 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1226886 GACTCACCTG
*
1226896 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1226918 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1226938 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1226959 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1226980 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1227001 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1226993 original size:42 final size:42
Alignment explanation
Indices: 1226893--1227003 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1226883 CCCGACTCAC
* * * *
1226893 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1226935 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1226977 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1227004 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1228402 original size:14 final size:14
Alignment explanation
Indices: 1228383--1228418 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1228373 ATTGTTTAAT
1228383 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1228397 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1228411 TGATTTGT
1 TGATTTGT
1228419 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1228563 original size:14 final size:14
Alignment explanation
Indices: 1228544--1228597 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1228534 GGAAATGACT
1228544 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1228558 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1228577 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1228591 ATCGCAA
1 ATCGCAA
1228598 TGTGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1228612 original size:34 final size:33
Alignment explanation
Indices: 1228524--1228617 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
1228514 AAAACAAACT
* **
1228524 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1228558 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1228591 ATCGCAATGTGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
1228618 TGCGAAACTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1228697 original size:33 final size:33
Alignment explanation
Indices: 1228634--1228729 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
1228624 ACTAAATTCG
* *
1228634 CGTTGCGATTTTCATTTTCACATTGTGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
1228668 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
1228701 CGTTGCGATAGTCATTTCCGTATTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
1228730 AGTCAATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:1228728 original size:20 final size:19
Alignment explanation
Indices: 1228701--1228794 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 19
1228691 GCGATTCTCT
1228701 CGTTGCGATAGTCATTTC-
1 CGTTGCGATAGTCATTTCG
1228719 CGTATTGCGATAGTCAATTTCG
1 CG--TTGCGATAGTC-ATTTCG
* *
1228741 CGTTGCGATGGTTATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1228761 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAT-TTCG
1228781 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1228795 AATGAATGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 49 0.77
21 7 0.11
22 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1228758 original size:40 final size:40
Alignment explanation
Indices: 1228701--1228794 Score: 145
Period size: 40 Copynumber: 2.4 Consensus size: 40
1228691 GCGATTCTCT
1228701 CGTTGCGATAGTCATTTCCGTATTGCGATAGTCA-ATTTCG
1 CGTTGCGATAGTCATTTCCGTATTGCGATAGTCATA-TTCG
* * *
1228741 CGTTGCGATGGTTATTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCGTATTGCGATAGTCATATTCG
1228781 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1228795 AATGAATGTC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 47 0.98
41 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGTATTGCGATAGTCATATTCG
Found at i:1231014 original size:12 final size:12
Alignment explanation
Indices: 1230999--1231025 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1230989 CTTTGGGGAT
1230999 TTCTTTTTCTTC
1 TTCTTTTTCTTC
1231011 TTCTTTTTCTTC
1 TTCTTTTTCTTC
1231023 TTC
1 TTC
1231026 AGTGTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:1231234 original size:24 final size:24
Alignment explanation
Indices: 1231200--1231253 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1231190 CTGAAAAATC
1231200 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
1231224 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
1231248 ATCAAA
1 ATCAAA
1231254 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:1232120 original size:20 final size:20
Alignment explanation
Indices: 1232095--1232161 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
1232085 AAAGTCAGTA
1232095 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
1232115 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
1232135 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
1232155 TTGCGAT
1 TTGCGAT
1232162 TTACGTATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:1232171 original size:20 final size:20
Alignment explanation
Indices: 1232148--1232278 Score: 151
Period size: 20 Copynumber: 6.7 Consensus size: 20
1232138 CGATAGTCAG
*
1232148 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1232168 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1232188 ATTCGCATTGCGATTTACG-
1 ATTCGCATTGCGATTTACGT
* *
1232207 -TTCGCAATGCGA-ATACGT
1 ATTCGCATTGCGATTTACGT
* * **
1232225 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
1232246 ATTCGCGTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
1232266 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1232279 ATTAGGAAAA
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
17 4 0.04
18 11 0.12
19 10 0.11
20 53 0.59
21 12 0.13
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1232233 original size:37 final size:39
Alignment explanation
Indices: 1232150--1232240 Score: 123
Period size: 37 Copynumber: 2.4 Consensus size: 39
1232140 ATAGTCAGAT
* * * *
1232150 TCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACG-ATTCGCAATGCGATATACGTAA
1232190 TCGCATTGCGATTTACG-TTCGCAATGCGA-ATACGTAA
1 TCGCATTGCGATTTACGATTCGCAATGCGATATACGTAA
1232227 TCGCATTGCGATTT
1 TCGCATTGCGATTT
1232241 TCCAAATTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
37 20 0.43
38 11 0.23
40 16 0.34
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (39 bp):
TCGCATTGCGATTTACGATTCGCAATGCGATATACGTAA
Found at i:1232320 original size:21 final size:21
Alignment explanation
Indices: 1232268--1232320 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1232258 ATTTACGTAT
*
1232268 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
1232289 TCGCAACGCGAATTTA-GAAAA
1 TCGCAATGCGAA-TTAGGAAAA
*
1232310 TCGTAATGCGA
1 TCGCAATGCGA
1232321 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:1238571 original size:24 final size:22
Alignment explanation
Indices: 1238543--1238588 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1238533 TATCACATCA
*
1238543 AATTAATTAATATTTACTATTTAT
1 AATTAATTAAAATTT--TATTTAT
*
1238567 AATTACTTAAAATTTTATTTAT
1 AATTAATTAAAATTTTATTTAT
1238589 TTTAAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTAATTAAAATTTTATTTAT
Found at i:1240943 original size:93 final size:92
Alignment explanation
Indices: 1240767--1240949 Score: 327
Period size: 89 Copynumber: 2.0 Consensus size: 92
1240757 CATCTTTGAT
1240767 CTTTTCTATTGCTAACAACAACATATTTTAAATGAGAAGGAAGGAAAGGGATCATCAAAAACATC
1 CTTTTCTATTGCTAACAACAACATATTTTAAAT-AGAAGGAAGGAAAGGGATCATCAAAAACATC
*
1240832 CTCTGCTAACACCCAAAAAAAAAACAAC
65 CTCTGCTAACACCAAAAAAAAAAACAAC
1240860 CTTTTCTATTGCTAACAACAACATATTTTAAAT-G-A-GAAGGAAAGGGATCATCAAAAACATCC
1 CTTTTCTATTGCTAACAACAACATATTTTAAATAGAAGGAAGGAAAGGGATCATCAAAAACATCC
1240922 TCTGCTAACACCAAAAAAAAAAACAAC
66 TCTGCTAACACCAAAAAAAAAAACAAC
1240949 C
1 C
1240950 GGTGAAAAAG
Statistics
Matches: 89, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
89 54 0.61
90 1 0.01
91 1 0.01
93 33 0.37
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.22
Consensus pattern (92 bp):
CTTTTCTATTGCTAACAACAACATATTTTAAATAGAAGGAAGGAAAGGGATCATCAAAAACATCC
TCTGCTAACACCAAAAAAAAAAACAAC
Found at i:1241989 original size:14 final size:14
Alignment explanation
Indices: 1241958--1242042 Score: 57
Period size: 14 Copynumber: 5.9 Consensus size: 14
1241948 TAAATAAAAA
1241958 TTAGCGGTT--AGTG
1 TTAGCGGTTAAAG-G
1241971 TTAGCGGTTAAAGG
1 TTAGCGGTTAAAGG
* *
1241985 TTAGCAGTTAAAAATG
1 TTAGCGGTT--AAAGG
** *
1242001 TTAGTTGTTAGGAAAG
1 TTAGCGGTTA--AAGG
1242017 TTAGCGGTTAAAGG
1 TTAGCGGTTAAAGG
*
1242031 TTAGCAGTTAAA
1 TTAGCGGTTAAA
1242043 AAAGTTAGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
13 9 0.16
14 24 0.42
15 2 0.04
16 22 0.39
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (14 bp):
TTAGCGGTTAAAGG
Found at i:1242019 original size:16 final size:16
Alignment explanation
Indices: 1242000--1242067 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 16
1241990 AGTTAAAAAT
*
1242000 GTTAGTTGTTAGGAAA
1 GTTAGCTGTTAGGAAA
* *
1242016 GTTAGCGGTTA--AAG
1 GTTAGCTGTTAGGAAA
* **
1242030 GTTAGCAGTTAAAAAA
1 GTTAGCTGTTAGGAAA
*
1242046 GTTAGTTGTTAGGAAA
1 GTTAGCTGTTAGGAAA
1242062 GTTAGC
1 GTTAGC
1242068 GATTAGTGGT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
14 12 0.30
16 28 0.70
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (16 bp):
GTTAGCTGTTAGGAAA
Found at i:1242028 original size:46 final size:46
Alignment explanation
Indices: 1241970--1242083 Score: 192
Period size: 46 Copynumber: 2.5 Consensus size: 46
1241960 AGCGGTTAGT
*
1241970 GTTAGCGGTTAAAGGTTAGCAGTTAAAAATGTTAGTTGTTAGGAAA
1 GTTAGCGGTTAAAGGTTAGCAGTTAAAAAAGTTAGTTGTTAGGAAA
1242016 GTTAGCGGTTAAAGGTTAGCAGTTAAAAAAGTTAGTTGTTAGGAAA
1 GTTAGCGGTTAAAGGTTAGCAGTTAAAAAAGTTAGTTGTTAGGAAA
* **
1242062 GTTAGCGATTAGTGGTTAGCAG
1 GTTAGCGGTTAAAGGTTAGCAG
1242084 AGTCCGAACC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (46 bp):
GTTAGCGGTTAAAGGTTAGCAGTTAAAAAAGTTAGTTGTTAGGAAA
Found at i:1242235 original size:29 final size:29
Alignment explanation
Indices: 1242187--1242251 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1242177 AGAATGAAAG
** * *
1242187 AAAATAAAAATTAGTGGTTAATGTACGAT
1 AAAATAAAAATTAGCAGTTAATATACAAT
* *
1242216 AAAATAAAAGTTAGCAGTTAATATGCAAT
1 AAAATAAAAATTAGCAGTTAATATACAAT
1242245 AAAATAA
1 AAAATAA
1242252 CATAGTAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.28
Consensus pattern (29 bp):
AAAATAAAAATTAGCAGTTAATATACAAT
Found at i:1243601 original size:16 final size:16
Alignment explanation
Indices: 1243580--1243612 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1243570 GTTGAGGAAG
1243580 TCTGATTGTCTAAGGA
1 TCTGATTGTCTAAGGA
1243596 TCTGATTGTCTAAGGA
1 TCTGATTGTCTAAGGA
1243612 T
1 T
1243613 GACACTGCTC
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:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (16 bp):
TCTGATTGTCTAAGGA
Found at i:1243709 original size:43 final size:41
Alignment explanation
Indices: 1243603--1243764 Score: 163
Period size: 40 Copynumber: 4.0 Consensus size: 41
1243593 GGATCTGATT
*
1243603 GTCTAAGGATGACACTGCTCCTTCGCGTTGAGG-AGATCTG
1 GTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAAGATCTG
* * * * *
1243643 GTCGGTGGATGACATTGTTCCTTCGTGTTGAGGAAG-TCTGG
1 GTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAAGATCT-G
1243684 TTGTCTGAGGATGACACTGCTCCTTCGCGTTGA-GAAGATCTG
1 --GTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAAGATCTG
* * * *
1243726 GTC-GATGGACGACATTGTTCCTTCGTGTTGAGGAA-ATCT
1 GTCTGA-GGATGACACTGCTCCTTCGCGTTGAGGAAGATCT
1243765 AGCCGTTTTA
Statistics
Matches: 100, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
39 2 0.02
40 58 0.58
41 6 0.06
42 5 0.05
43 29 0.29
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (41 bp):
GTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAAGATCTG
Found at i:1243740 original size:83 final size:83
Alignment explanation
Indices: 1243596--1243760 Score: 285
Period size: 83 Copynumber: 2.0 Consensus size: 83
1243586 TGTCTAAGGA
* * *
1243596 TCTGATTGTCTAAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGGATGACATTGT
1 TCTGATTGTCTAAGGATGACACTGCTCCTTCGCGTTGAGAAGATCTGGTCGATGGACGACATTGT
1243661 TCCTTCGTGTTGAGGAAG
66 TCCTTCGTGTTGAGGAAG
* *
1243679 TCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGAAGATCTGGTCGATGGACGACATTGT
1 TCTGATTGTCTAAGGATGACACTGCTCCTTCGCGTTGAGAAGATCTGGTCGATGGACGACATTGT
1243744 TCCTTCGTGTTGAGGAA
66 TCCTTCGTGTTGAGGAA
1243761 ATCTAGCCGT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (83 bp):
TCTGATTGTCTAAGGATGACACTGCTCCTTCGCGTTGAGAAGATCTGGTCGATGGACGACATTGT
TCCTTCGTGTTGAGGAAG
Found at i:1247291 original size:21 final size:21
Alignment explanation
Indices: 1247262--1247313 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1247252 GCTTATTGTC
1247262 TTCTTTTTTTCTCATT-CTTCT
1 TTCTTTTTTTCTCATTACTT-T
* *
1247283 TTGTTTTTTTCTCTTTACTTT
1 TTCTTTTTTTCTCATTACTTT
1247304 TTCTTTTTTT
1 TTCTTTTTTT
1247314 TCTTTGCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (21 bp):
TTCTTTTTTTCTCATTACTTT
Found at i:1248210 original size:12 final size:12
Alignment explanation
Indices: 1248193--1248217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1248183 AAAAGATTAA
1248193 AAAATATTAAAG
1 AAAATATTAAAG
1248205 AAAATATTAAAG
1 AAAATATTAAAG
1248217 A
1 A
1248218 CATAACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATATTAAAG
Found at i:1249913 original size:65 final size:64
Alignment explanation
Indices: 1249859--1249994 Score: 193
Period size: 65 Copynumber: 2.1 Consensus size: 64
1249849 ATAGACTAAT
* * *
1249859 TACATTCGATGTTTCAA-ACAATCTAGGAGTGCATCGATGCATGGTCTGTGCATCGGTGCATAAA
1 TACATTCGATGTTTCAATAAAATCCA-GAGTGCATCGATGCATGG-CTGTGCATCGATGCATAAA
1249923 A
64 A
* *
1249924 TACATTCGATGTTTCAATAAAATCCAGAGTGCATCGATGCATGGCTTTGCATCGGTGCATAAAA
1 TACATTCGATGTTTCAATAAAATCCAGAGTGCATCGATGCATGGCTGTGCATCGATGCATAAAA
*
1249988 TGCATTC
1 TACATTC
1249995 AAAATGGGGT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
64 25 0.38
65 35 0.53
66 6 0.09
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (64 bp):
TACATTCGATGTTTCAATAAAATCCAGAGTGCATCGATGCATGGCTGTGCATCGATGCATAAAA
Found at i:1250709 original size:16 final size:16
Alignment explanation
Indices: 1250690--1250727 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1250680 CATCAAATTC
1250690 AAACATA-ACAATCCAA
1 AAACATATA-AATCCAA
1250706 AAACATATAAATCCAA
1 AAACATATAAATCCAA
1250722 AAACAT
1 AAACAT
1250728 GCAAAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.63, C:0.21, G:0.00, T:0.16
Consensus pattern (16 bp):
AAACATATAAATCCAA
Found at i:1253508 original size:2 final size:2
Alignment explanation
Indices: 1253501--1253534 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1253491 CATGCATAAG
1253501 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
1253535 GTTCATGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1253556 original size:12 final size:12
Alignment explanation
Indices: 1253538--1253573 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1253528 TATATATGTT
1253538 CATGTGATATGA
1 CATGTGATATGA
*
1253550 TATGTGATATGA
1 CATGTGATATGA
*
1253562 CCTGTGATATGA
1 CATGTGATATGA
1253574 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:1253736 original size:15 final size:15
Alignment explanation
Indices: 1253718--1253750 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1253708 GAGGGTATAA
1253718 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
1253733 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
1253748 TAG
1 TAG
1253751 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:1260236 original size:65 final size:64
Alignment explanation
Indices: 1260167--1260296 Score: 174
Period size: 65 Copynumber: 2.0 Consensus size: 64
1260157 GTACACTAAT
* * *
1260167 TACATTCGATGTTTCAA-ACA-AGCTAGGAGTGCATCGATGCATGGCCTGTGCATAGGTGCATAA
1 TACATTCAATGTTTCAATA-ATAGCCA-GAGTGCATCGATGCATGG-ATGTGCATAGGTGCATAA
1260230 AA
63 AA
* *
1260232 TACATTCAATGTTTCAATAATATCCAGAGTGCATCGATGCATGGATGTGCATCGGTGCATAAAA
1 TACATTCAATGTTTCAATAATAGCCAGAGTGCATCGATGCATGGATGTGCATAGGTGCATAAAA
1260296 T
1 T
1260297 GTATTCAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
64 19 0.33
65 35 0.60
66 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (64 bp):
TACATTCAATGTTTCAATAATAGCCAGAGTGCATCGATGCATGGATGTGCATAGGTGCATAAAA
Found at i:1262546 original size:21 final size:22
Alignment explanation
Indices: 1262521--1262574 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1262511 AGAATAAAAA
*
1262521 ATAAAATAAAAAT-AGAATGAG
1 ATAAAATAAAAATAAGAATAAG
*
1262542 ATAAAATAAAAATAATAATAAG
1 ATAAAATAAAAATAAGAATAAG
1262564 ATAAAAATAAA
1 AT-AAAATAAA
1262575 GCAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 13 0.45
22 8 0.28
23 8 0.28
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (22 bp):
ATAAAATAAAAATAAGAATAAG
Found at i:1263429 original size:29 final size:29
Alignment explanation
Indices: 1263396--1263460 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1263386 AGAATGAAAG
* ** * *
1263396 AAAATAAAATTTAGTGGTTAATGTGCGAT
1 AAAATAAAAGTTAGCAGTTAATATGCAAT
1263425 AAAATAAAAGTTAGCAGTTAATATGCAAT
1 AAAATAAAAGTTAGCAGTTAATATGCAAT
1263454 AAAATAA
1 AAAATAA
1263461 CATAGTAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (29 bp):
AAAATAAAAGTTAGCAGTTAATATGCAAT
Found at i:1264701 original size:31 final size:31
Alignment explanation
Indices: 1264634--1264693 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1264624 CAATTTAAGG
*
1264634 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1264665 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1264694 TTCAAAATTT
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:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1264785 original size:19 final size:19
Alignment explanation
Indices: 1264758--1264804 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1264748 AATGTTTTTA
* *
1264758 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
1264777 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
1264796 TGAACAGTA
1 TGAACAGTA
1264805 CCCCGAGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1264949 original size:21 final size:21
Alignment explanation
Indices: 1264911--1264952 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1264901 ATTTGAATAT
*
1264911 TATGAAGGGGTTTCGATTCCC
1 TATGAAGGGGTTACGATTCCC
1264932 TATGAAGGGG-TACAGATTCCC
1 TATGAAGGGGTTAC-GATTCCC
1264953 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTTACGATTCCC
Found at i:1267611 original size:19 final size:19
Alignment explanation
Indices: 1267584--1267630 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1267574 AATATTTTTA
* *
1267584 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
1267603 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
1267622 TGAACAGTA
1 TGAACAGTA
1267631 CCCCGAGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1267762 original size:21 final size:21
Alignment explanation
Indices: 1267736--1267777 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1267726 ATTTGAATAT
* *
1267736 TATGAAGGGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
1267757 TATGAAGAGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
1267778 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:1267839 original size:21 final size:21
Alignment explanation
Indices: 1267806--1267845 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1267796 TTTTTGCAGA
*
1267806 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1267828 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1267846 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1273056 original size:36 final size:36
Alignment explanation
Indices: 1273009--1273077 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1272999 TTCTTCGGTT
*
1273009 TTTTTGGCCCAATAGGGCTTTTAGATTGAAAATAAC
1 TTTTTGGCCCAATAGAGCTTTTAGATTGAAAATAAC
1273045 TTTTTGGCCCAATAGAGCTTTTAGATTGAAAAT
1 TTTTTGGCCCAATAGAGCTTTTAGATTGAAAAT
1273078 TTAGGGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (36 bp):
TTTTTGGCCCAATAGAGCTTTTAGATTGAAAATAAC
Found at i:1275269 original size:34 final size:34
Alignment explanation
Indices: 1275226--1275294 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1275216 TTTCGAAGGT
1275226 GTATCTCAGAGTGTGTTAAGTACACCTCCTCAAC
1 GTATCTCAGAGTGTGTTAAGTACACCTCCTCAAC
1275260 GTATCTCAGAGTGTGTTAAGTACACCTCCTCAAC
1 GTATCTCAGAGTGTGTTAAGTACACCTCCTCAAC
1275294 G
1 G
1275295 AGATGAAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (34 bp):
GTATCTCAGAGTGTGTTAAGTACACCTCCTCAAC
Found at i:1276905 original size:21 final size:21
Alignment explanation
Indices: 1276881--1276926 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1276871 AAAATTTAAG
1276881 ATTTT-TTTAAATATAA-AAAAT
1 ATTTTATTTAAA-A-AATAAAAT
1276902 ATTTTATTTAAAAAATAAAAT
1 ATTTTATTTAAAAAATAAAAT
1276923 ATTT
1 ATTT
1276927 ATAAAACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 15 0.65
22 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTTATTTAAAAAATAAAAT
Found at i:1277938 original size:30 final size:31
Alignment explanation
Indices: 1277899--1277960 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
1277889 TAAAATTATT
*
1277899 AAATTTAAAT-TCTAAATAA-TATTTTATAAA
1 AAATCTAAATATC-AAATAATTATTTTATAAA
*
1277929 AAATCTAAATAATCAAATAATTTTTTTATAAA
1 AAATCTAAAT-ATCAAATAATTATTTTATAAA
1277961 TGAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 9 0.33
31 6 0.22
32 12 0.44
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (31 bp):
AAATCTAAATATCAAATAATTATTTTATAAA
Found at i:1278442 original size:148 final size:151
Alignment explanation
Indices: 1278166--1278478 Score: 404
Period size: 148 Copynumber: 2.1 Consensus size: 151
1278156 CTTAACCGGT
** * * *
1278166 TAAAATAAAATAGG-AGTTACCTATTATGTTAAACTATCTACCGGTTTGTTTGAAGGTTACTAAT
1 TAAAATAAAATAGGCAGTTACCTATTACATTAAACTAGCTACCGATTTGTTTAAAGGTTACTAAT
* ** *
1278230 AATGTAAACGGTAAAATAAAATAGATGCTACATATTACGTTAAAATACCTACTTGTTTGTTTAAA
66 AATGTAAACGGTAAAATAAAATAGATGCTACATATTACATTAAAATACCTACCAGCTTGTTTAAA
* * *
1278295 -GTTTACTAATAATGTAAATAA
131 TG-TTAATAACAATGTAAACAA
*
1278316 TAAAAT-AAATAGGCAG-TACCTATTACATTAAACTAGCTACCGATTT-TTTAAATGTTACTAAT
1 TAAAATAAAATAGGCAGTTACCTATTACATTAAACTAGCTACCGATTTGTTTAAAGGTTACTAAT
* * *
1278378 AATGTAAACGGTAAAATAAAATAGGA-GCTACCTATTACATTAAACTAGCTACCAGCTTGTTTAA
66 AATGTAAACGGTAAAATAAAATA-GATGCTACATATTACATTAAAATACCTACCAGCTTGTTTAA
**
1278442 ATGTTAATAACAATGTAAACGG
130 ATGTTAATAACAATGTAAACAA
1278464 TAAAATAAAATAGGC
1 TAAAATAAAATAGGC
1278479 GCTGCCTATT
Statistics
Matches: 141, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
148 89 0.63
149 44 0.31
150 8 0.06
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (151 bp):
TAAAATAAAATAGGCAGTTACCTATTACATTAAACTAGCTACCGATTTGTTTAAAGGTTACTAAT
AATGTAAACGGTAAAATAAAATAGATGCTACATATTACATTAAAATACCTACCAGCTTGTTTAAA
TGTTAATAACAATGTAAACAA
Found at i:1278496 original size:75 final size:74
Alignment explanation
Indices: 1278166--1278497 Score: 386
Period size: 75 Copynumber: 4.5 Consensus size: 74
1278156 CTTAACCGGT
* * * * *
1278166 TAAAATAAAATAGGAGTTACCTATTATGTTAAACTATCTACCGGTTTGTTTGAAGGTTACTAATA
1 TAAAATAAAATAGGAGCTACCTATTACGTTAAACTAGCTACC-GTTTGTTTAAATGTTACTAATA
1278231 ATGTAAACGG
65 ATGTAAACGG
* * * *
1278241 TAAAATAAAATA-GATGCTACATATTACGTTAAAATACCTACTTGTTTGTTTAAA-GTTTACTAA
1 TAAAATAAAATAGGA-GCTACCTATTACGTTAAACTAGCTAC-CGTTTGTTTAAATG-TTACTAA
***
1278304 TAATGTAAATAA
63 TAATGTAAACGG
*
1278316 TAAAAT-AAATAGGCAG-TACCTATTACATTAAACTAGCTACCGATTT-TTTAAATGTTACTAAT
1 TAAAATAAAATAGG-AGCTACCTATTACGTTAAACTAGCTACCG-TTTGTTTAAATGTTACTAAT
1278378 AATGTAAACGG
64 AATGTAAACGG
* * * *
1278389 TAAAATAAAATAGGAGCTACCTATTACATTAAACTAGCTACCAGCTTGTTTAAATGTTAATAACA
1 TAAAATAAAATAGGAGCTACCTATTACGTTAAACTAGCTACC-GTTTGTTTAAATGTTACTAATA
1278454 ATGTAAACGG
65 ATGTAAACGG
* * *
1278464 TAAAATAAAATAGGCGCTGCCTATTATGTTAAAC
1 TAAAATAAAATAGGAGCTACCTATTACGTTAAAC
1278498 AATTACTACC
Statistics
Matches: 221, Mismatches: 25, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
73 31 0.14
74 66 0.30
75 123 0.56
76 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (74 bp):
TAAAATAAAATAGGAGCTACCTATTACGTTAAACTAGCTACCGTTTGTTTAAATGTTACTAATAA
TGTAAACGG
Found at i:1278605 original size:98 final size:98
Alignment explanation
Indices: 1278503--1278689 Score: 302
Period size: 98 Copynumber: 1.9 Consensus size: 98
1278493 TAAACAATTA
*
1278503 CTACCTATTACGTTAAATAGACGCTACCTATTAAGTTAAACTAGCTACCGGTTTGTTTAAAGGTG
1 CTACCTATTACGTTAAATAGACGCTACCTATTAAGTTAAACTAGCTACCGGTTTGTTTAAAAGTG
*
1278568 AATAATAATGTTAACGGTAAAATAAAATAGGCG
66 AATAATAATGTAAACGGTAAAATAAAATAGGCG
* * * * * *
1278601 CTACCTATTATGTTAAATAGACGTTACCTATTACGTTAGATTAGCTACCGGTTTGTTTAAAAGTT
1 CTACCTATTACGTTAAATAGACGCTACCTATTAAGTTAAACTAGCTACCGGTTTGTTTAAAAGTG
1278666 AATAATAATGTAAACGGTAAAATA
66 AATAATAATGTAAACGGTAAAATA
1278690 TATACAACTT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 81 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (98 bp):
CTACCTATTACGTTAAATAGACGCTACCTATTAAGTTAAACTAGCTACCGGTTTGTTTAAAAGTG
AATAATAATGTAAACGGTAAAATAAAATAGGCG
Found at i:1278610 original size:121 final size:121
Alignment explanation
Indices: 1278396--1278617 Score: 349
Period size: 121 Copynumber: 1.8 Consensus size: 121
1278386 CGGTAAAATA
* *
1278396 AAATAGGAGCTACCTATTACATTAAACTAGCTACCAGCTTGTTTAAATGTTAATAACAATGTAAA
1 AAATAGGAGCTACCTATTACATTAAACTAGCTACCAGCTTGTTTAAAGGTGAATAACAATGTAAA
*
1278461 CGGTAAAATAAAATAGGCGCTGCCTATTATGTTAAACAATTACTACCTATTACGTT
66 CGGTAAAATAAAATAGGCGCTACCTATTATGTTAAACAATTACTACCTATTACGTT
* * * *
1278517 AAATA-GACGCTACCTATTA-AGTTAAACTAGCTACCGGTTTGTTTAAAGGTGAATAATAATGTT
1 AAATAGGA-GCTACCTATTACA-TTAAACTAGCTACCAGCTTGTTTAAAGGTGAATAACAATGTA
1278580 AACGGTAAAATAAAATAGGCGCTACCTATTATGTTAAA
64 AACGGTAAAATAAAATAGGCGCTACCTATTATGTTAAA
1278618 TAGACGTTAC
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
120 3 0.03
121 89 0.97
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (121 bp):
AAATAGGAGCTACCTATTACATTAAACTAGCTACCAGCTTGTTTAAAGGTGAATAACAATGTAAA
CGGTAAAATAAAATAGGCGCTACCTATTATGTTAAACAATTACTACCTATTACGTT
Found at i:1278618 original size:23 final size:23
Alignment explanation
Indices: 1278592--1278638 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1278582 CGGTAAAATA
* *
1278592 AAATAGGCGCTACCTATTATGTT
1 AAATAGACGCTACCTATTACGTT
*
1278615 AAATAGACGTTACCTATTACGTT
1 AAATAGACGCTACCTATTACGTT
1278638 A
1 A
1278639 GATTAGCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (23 bp):
AAATAGACGCTACCTATTACGTT
Found at i:1279372 original size:104 final size:98
Alignment explanation
Indices: 1279298--1279478 Score: 249
Period size: 98 Copynumber: 1.9 Consensus size: 98
1279288 AAGACTCCAT
*
1279298 CTTAAATTTTGGTAACATTTTAAGCGCTACCT-ATATGTTGATAATATTAATAACAAAATAAGTA
1 CTTAAACTTTGGTAACATTTTAAGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTA
* *
1279362 ATTAACATATTTTGTTATCATAATACCCATCAG
66 ATTAACATATTTTATTATCATAATACACATCAG
* * * * * *
1279395 CTTACACTTTGGTAATATTTTAGGCTCTACCTAATATGTTGATAATATTAATAACAAATTACGTA
1 CTTAAACTTTGGTAACATTTTAAGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTA
*
1279460 ATTAATC-TATTTTGTTATC
66 ATTAA-CATATTTTATTATC
1279479 GTCATATTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
97 27 0.36
98 47 0.63
99 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (98 bp):
CTTAAACTTTGGTAACATTTTAAGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTA
ATTAACATATTTTATTATCATAATACACATCAG
Found at i:1280757 original size:18 final size:19
Alignment explanation
Indices: 1280709--1280758 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1280699 AATTAAATTA
*
1280709 TTATTATAAATAAATCAGTT
1 TTATTATAAATAAA-CACTT
* *
1280729 TTAGTACAAATAAA-ACTT
1 TTATTATAAATAAACACTT
1280747 TTATTATAAATA
1 TTATTATAAATA
1280759 GGAATAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 13 0.52
20 12 0.48
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (19 bp):
TTATTATAAATAAACACTT
Found at i:1281780 original size:24 final size:26
Alignment explanation
Indices: 1281748--1281797 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1281738 GCCACACATA
* *
1281748 TTAACATATAAT-GTACAAACATGAC
1 TTAACATATAATAATAAAAACATGAC
1281773 TTAA-ATATAATAATAAAAACATGAC
1 TTAACATATAATAATAAAAACATGAC
1281798 ATGCAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (26 bp):
TTAACATATAATAATAAAAACATGAC
Found at i:1282257 original size:26 final size:26
Alignment explanation
Indices: 1282222--1282288 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
1282212 GGAGGTCAAT
1282222 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1282248 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1282274 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
1282289 CGTACGAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:1284064 original size:55 final size:55
Alignment explanation
Indices: 1283959--1284548 Score: 877
Period size: 55 Copynumber: 10.7 Consensus size: 55
1283949 TGGTTTTATC
* * **
1283959 CCCTATTGCTTCAGGGAGTA-AA-ACTCGAA-AATCTTCGTCAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * * * * * *
1284011 CCCCATTT-TTCCAGAGAGTACAAGACTCAAACGAT-TCTCGATAATCATGTCTGCT
1 CCCTATTTCTT-CAGAGAGTATAAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
* * * *
1284066 CCCTATTTTTTCAGAGAGTATGAGACTCGAACAAT-TCTCAATAATCGTGCCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
* *
1284121 CCCTATTTTCTTCAGAGAGAATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTA-TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1284177 CCCTATTTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTA-TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1284233 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1284288 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1284343 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1284398 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1284453 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1284508 CCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTCAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
1284549 TTATCGTTGG
Statistics
Matches: 500, Mismatches: 30, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.00
52 14 0.03
53 2 0.00
54 7 0.01
55 368 0.74
56 106 0.21
57 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:1285572 original size:9 final size:9
Alignment explanation
Indices: 1285549--1285598 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
1285539 GAACCCTTCC
*
1285549 TTTTTTCCA
1 TTTTTTTCA
1285558 -TTTTTTCA
1 TTTTTTTCA
1285566 TTTTTTT-A
1 TTTTTTTCA
*
1285574 TTATTTTTTTA
1 -T-TTTTTTCA
1285585 TTTTTTTCA
1 TTTTTTTCA
1285594 TTTTT
1 TTTTT
1285599 CATTTTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 8 0.23
9 19 0.54
10 7 0.20
11 1 0.03
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1297374 original size:24 final size:26
Alignment explanation
Indices: 1297342--1297391 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1297332 GCCACACATA
* *
1297342 TTAACATATAAT-GTACAAACATGAC
1 TTAACATATAATAATAAAAACATGAC
1297367 TTAA-ATATAATAATAAAAACATGAC
1 TTAACATATAATAATAAAAACATGAC
1297392 ATGCAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (26 bp):
TTAACATATAATAATAAAAACATGAC
Found at i:1297848 original size:26 final size:26
Alignment explanation
Indices: 1297813--1297879 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
1297803 GGAGGTCAAT
1297813 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1297839 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1297865 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
1297880 CGTACGAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:1300031 original size:24 final size:24
Alignment explanation
Indices: 1299998--1300044 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1299988 TTTATTAGTT
*
1299998 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
* *
1300022 TAATTAAATATGTAATATTATTA
1 TAATTAAATATATAAAATTATTA
1300045 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:1300777 original size:73 final size:73
Alignment explanation
Indices: 1300650--1300786 Score: 240
Period size: 73 Copynumber: 1.9 Consensus size: 73
1300640 CTAAGGTGAT
1300650 TATAATAATTAATTTTAGTGTAACAAAAATAATATATATGATCTCTATAAATAACTATTATTTTA
1 TATAATAATTAATTTTAGTGTAACAAAAATAATATATATGATCTCTATAAATAACTATT-TTTTA
1300715 GTGTAACAA
65 GTGTAACAA
* *
1300724 TATAATAATTAATTTTAGTGTAAC-AATATAATATATATTATCTCTATAAATAACTATTTTTTA
1 TATAATAATTAATTTTAGTGTAACAAAAATAATATATATGATCTCTATAAATAACTATTTTTTA
1300787 TTAATATAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
72 5 0.08
73 32 0.52
74 24 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (73 bp):
TATAATAATTAATTTTAGTGTAACAAAAATAATATATATGATCTCTATAAATAACTATTTTTTAG
TGTAACAA
Found at i:1301197 original size:32 final size:32
Alignment explanation
Indices: 1301161--1301223 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1301151 ATGGGTTTTA
* *
1301161 TGAATGACGCGTCCTATGGAACACGCCTCCCT
1 TGAATGACGCGTCATACGGAACACGCCTCCCT
** *
1301193 TGAATGGTGCGTCATACGGAACGCGCCTCCC
1 TGAATGACGCGTCATACGGAACACGCCTCCC
1301224 ATGCCAGGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (32 bp):
TGAATGACGCGTCATACGGAACACGCCTCCCT
Found at i:1304563 original size:83 final size:81
Alignment explanation
Indices: 1304466--1305185 Score: 591
Period size: 83 Copynumber: 8.7 Consensus size: 81
1304456 GGAACATGCA
1304466 CCTTTCATTTCGGATGGGATAGAACACTATGACATGATAACGATTCTCTGAATAATAATGGAAAA
1 CCTTTCATTTCGGATGGGATAGAACACTATGACATGATAA-GATTCTCTGAATAATAATGGAAAA
*
1304531 CACTTTTCCTAGAACACG
65 -ACTTTCCCTAGAACACG
* * **
1304549 CCTTTCATTTCGGATGGGATATAACACTATGAAATGGCAGAGATTCTCTGAATAATAAT-GAAAA
1 CCTTTCATTTCGGATGGGATAGAACACTATGACATGATA-AGATTCTCTGAATAATAATGGAAAA
* ** *
1304613 ATGTTTCCCCTAGAATGCA
65 A-CTTT-CCCTAGAACACG
* ** * * * *
1304632 CCTTTAATTTTAGATGGAATATAACACTATGACATGACATATATTCTCTGAATAATAATGGAAAA
1 CCTTTCATTTCGGATGGGATAGAACACTATGACATGATA-AGATTCTCTGAATAATAATGGAAAA
** * *
1304697 TGTTTTCCCCTGGAACACT
65 -ACTTT-CCCTAGAACACG
* *
1304716 TCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAT-AGATTCTCTGAATAATAATGAGAA
1 CCTTTCATTTCGGATGGGATAGAACACTATGACAT-G-ATAAGATTCTCTGAATAATAATG-GAA
** * *
1304780 ACGCTTCCCCTAGAACGCG
63 AAACTTTCCCTAGAACACG
** * * * * *
1304799 CCTTTCATTTAAGATGGGATGGAAAACTATGACGTGGTCGAGATTCTCTGAATAATAATGGAAAA
1 CCTTTCATTTCGGATGGGATAGAACACTATGACATGAT-AAGATTCTCTGAATAATAATGGAAAA
** * *
1304864 TGTTTTCCTTAGAACGCG
65 -ACTTTCCCTAGAACACG
* *
1304882 CCTTTCATTTCAGATGGGAT-GAAACACTATGACATG-TCAGAGATTCTCTGAATAATAATAGAA
1 CCTTTCATTTCGGATGGGATAG-AACACTATGACATGAT-A-AGATTCTCTGAATAATAATGGAA
* *
1304945 AACACTTCCCCTAGAACACA
63 AA-ACTTTCCCTAGAACACG
* * * **
1304965 CCTTTCATTTCGGATGGGAT-GAAACATTATGACATGGAAAAGATTCTTTGAATAATAATATAAA
1 CCTTTCATTTCGGATGGGATAG-AACACTATGACAT-GATAAGATTCTCTGAATAATAATGGAAA
* **
1305029 ATACTTCCCCTAGAATGCG
64 A-ACTTTCCCTAGAACACG
* * * *
1305048 CCTCTCATTTCGAATGGGATAGAATACTATGATATGGCA-AAGATT-TCTGAATAATAATGGAAA
1 CCTTTCATTTCGGATGGGATAGAACACTATGACAT-G-ATAAGATTCTCTGAATAATAATGGAAA
* *
1305111 ATGC-TTCCACT-GAA-ATGTG
64 A-ACTTTCC-CTAGAACA--CG
*
1305130 CCTTTCATTTCGGATGGGAT-GAAACACTATGACATGGA-AGAGATTTTCTGAATAAT
1 CCTTTCATTTCGGATGGGATAG-AACACTATGACAT-GATA-AGATTCTCTGAATAAT
1305186 GGAAAACACT
Statistics
Matches: 529, Mismatches: 85, Indels: 46
0.80 0.13 0.07
Matches are distributed among these distances:
81 11 0.02
82 73 0.14
83 367 0.69
84 72 0.14
85 5 0.01
86 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (81 bp):
CCTTTCATTTCGGATGGGATAGAACACTATGACATGATAAGATTCTCTGAATAATAATGGAAAAA
CTTTCCCTAGAACACG
Found at i:1304910 original size:250 final size:247
Alignment explanation
Indices: 1304464--1305185 Score: 848
Period size: 250 Copynumber: 2.9 Consensus size: 247
1304454 ATGGAACATG
*
1304464 CACCTTTCATTTCGGATGGGATAGAACACTATGACAT-GATAACGATTCTCTGAATAATAATG-G
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGAT-A-GATTCTCTGAATAATAATGAG
** * * * *
1304527 AAAACACTTTTCCTAGAACACGCCTTTCATTTCGGATGGGATATAACACTATGAAATGGCAGAGA
64 -AAACACTTCCCCTAGAACGCGCCTTTCATTT-AGATGGGATAGAAAACTATGAAATGGCAGAGA
* * * * * *
1304592 TTCTCTGAATAATAATGAAAAATGTTTCCCCTAGAATGCACCTTTAATTTTAGATGGAAT-ATAA
127 TTCTCTGAATAATAATGGAAAATGTTTCCCTTAGAATGCGCCTTTCATTTCAGATGGGATGA-AA
* * * *** *
1304656 CACTATGACATGACATATATTCTCTGAATAATAATGGAAAATGTTTTCCCCTGGAACA
191 CACTATGACATGACAGAGATTCTCTGAATAATAATAGAAAA-CACTTCCCCTAGAACA
**
1304714 CTTCTTTCATTTCGGATGGGATGGAACACTATGACATGGCATAGATTCTCTGAATAATAATGAGA
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGG-ATAGATTCTCTGAATAATAATGAGA
* * **
1304779 AACGCTTCCCCTAGAACGCGCCTTTCATTTAAGATGGGATGGAAAACTATGACGTGGTC-GAGAT
65 AACACTTCCCCTAGAACGCGCCTTTCATTT-AGATGGGATAGAAAACTATGAAATGG-CAGAGAT
* *
1304843 TCTCTGAATAATAATGGAAAATGTTTTCCTTAGAACGCGCCTTTCATTTCAGATGGGATGAAACA
128 TCTCTGAATAATAATGGAAAATGTTTCCCTTAGAATGCGCCTTTCATTTCAGATGGGATGAAACA
*
1304908 CTATGACATGTCAGAGATTCTCTGAATAATAATAGAAAACACTTCCCCTAGAACA
193 CTATGACATGACAGAGATTCTCTGAATAATAATAGAAAACACTTCCCCTAGAACA
* * * * *
1304963 CACCTTTCATTTCGGATGGGATGAAACATTATGACATGGAAAAGATTCTTTGAATAATAAT-ATA
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGG-ATAGATTCTCTGAATAATAATGA-G
* * * * * * *
1305027 AAATACTTCCCCTAGAATGCGCCTCTCATTTCGAATGGGATAGAATACTATGATATGGCAAAGAT
64 AAACACTTCCCCTAGAACGCGCCTTTCATTTAG-ATGGGATAGAAAACTATGAAATGGCAGAGAT
* * * *
1305092 T-TCTGAATAATAATGGAAAATGCTTCCACTGA-AATGTGCCTTTCATTTCGGATGGGATGAAAC
128 TCTCTGAATAATAATGGAAAATGTTTCC-CTTAGAATGCGCCTTTCATTTCAGATGGGATGAAAC
*
1305155 ACTATGACATGGA-AGAGATTTTCTGAATAAT
192 ACTATGACAT-GACAGAGATTCTCTGAATAAT
1305186 GGAAAACACT
Statistics
Matches: 406, Mismatches: 56, Indels: 22
0.84 0.12 0.05
Matches are distributed among these distances:
248 82 0.20
249 122 0.30
250 195 0.48
251 5 0.01
252 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (247 bp):
CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGATAGATTCTCTGAATAATAATGAGAA
ACACTTCCCCTAGAACGCGCCTTTCATTTAGATGGGATAGAAAACTATGAAATGGCAGAGATTCT
CTGAATAATAATGGAAAATGTTTCCCTTAGAATGCGCCTTTCATTTCAGATGGGATGAAACACTA
TGACATGACAGAGATTCTCTGAATAATAATAGAAAACACTTCCCCTAGAACA
Found at i:1304955 original size:166 final size:164
Alignment explanation
Indices: 1304463--1305185 Score: 751
Period size: 166 Copynumber: 4.4 Consensus size: 164
1304453 AATGGAACAT
* *
1304463 GCACCTTTCATTTCGGATGGGATAGAACACTATGACAT-GATAACGATTCTCTGAATAATAATGG
1 GCACCTTTCATTTCGGATGGGAT-GAAAACTATGACATGGA-AAAGATTCTCTGAATAATAATGG
** * *
1304527 AAAACACTTTT-CCTAGAACACGCCTTTCATTTCGGATGGGATATAACACTATGAAATGGCAGAG
64 AAAA-TGTTTTCCCTAGAACACGCCTTTCATTTCGGATGGGATAGAACACTATGACATGGCAGAG
* *
1304591 ATTCTCTGAATAATAATGAAAA-ATGTTTCCCCTAGAAT
128 ATTCTCTGAATAATAATGAAAACA--CTTCCCCTAGAAC
* ** * * *
1304629 GCACCTTTAATTTTAGATGGAAT-ATAACACTATGACAT-GACATATATTCTCTGAATAATAATG
1 GCACCTTTCATTTCGGATGGGATGA-AA-ACTATGACATGGA-AAAGATTCTCTGAATAATAATG
* ** * *
1304692 GAAAATGTTTTCCCCTGGAACACTTCTTTCATTTCGGATGGGATGGAACACTATGACATGGCATA
63 GAAAATGTTTT-CCCTAGAACACGCCTTTCATTTCGGATGGGATAGAACACTATGACATGGCAGA
*
1304757 GATTCTCTGAATAATAATGAGAAACGCTTCCCCTAGAAC
127 GATTCTCTGAATAATAATGA-AAACACTTCCCCTAGAAC
* ** * ***
1304796 GCGCCTTTCATTTAAGATGGGATGGAAAACTATGACGTGGTCGAGATTCTCTGAATAATAATGGA
1 GCACCTTTCATTTCGGATGGGAT-GAAAACTATGACATGGAAAAGATTCTCTGAATAATAATGGA
* * * *
1304861 AAATGTTTTCCTTAGAACGCGCCTTTCATTTCAGATGGGAT-GAAACACTATGACATGTCAGAGA
65 AAATGTTTTCCCTAGAACACGCCTTTCATTTCGGATGGGATAG-AACACTATGACATGGCAGAGA
1304925 TTCTCTGAATAATAATAGAAAACACTTCCCCTAGAAC
129 TTCTCTGAATAATAAT-GAAAACACTTCCCCTAGAAC
* * * **
1304962 ACACCTTTCATTTCGGATGGGATGAAACATTATGACATGGAAAAGATTCTTTGAATAATAATATA
1 GCACCTTTCATTTCGGATGGGATGAAA-ACTATGACATGGAAAAGATTCTCTGAATAATAATGGA
** * ** * * * * *
1305027 AAATACTTCCCCTAGAATGCGCCTCTCATTTCGAATGGGATAGAATACTATGATATGGCAAAGAT
65 AAATGTTTTCCCTAGAACACGCCTTTCATTTCGGATGGGATAGAACACTATGACATGGCAGAGAT
** * *
1305092 T-TCTGAATAATAATGGAAAATGCTTCCACT-GAAAT
130 TCTCTGAATAATAAT-GAAAACACTTCCCCTAG-AAC
** * *
1305127 GTGCCTTTCATTTCGGATGGGATGAAACACTATGACATGGAAGAGATTTTCTGAATAAT
1 GCACCTTTCATTTCGGATGGGATGAAA-ACTATGACATGGAAAAGATTCTCTGAATAAT
1305186 GGAAAACACT
Statistics
Matches: 468, Mismatches: 75, Indels: 29
0.82 0.13 0.05
Matches are distributed among these distances:
164 2 0.00
165 89 0.19
166 233 0.50
167 137 0.29
168 6 0.01
169 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (164 bp):
GCACCTTTCATTTCGGATGGGATGAAAACTATGACATGGAAAAGATTCTCTGAATAATAATGGAA
AATGTTTTCCCTAGAACACGCCTTTCATTTCGGATGGGATAGAACACTATGACATGGCAGAGATT
CTCTGAATAATAATGAAAACACTTCCCCTAGAAC
Found at i:1305205 original size:38 final size:37
Alignment explanation
Indices: 1305151--1305224 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 37
1305141 GGATGGGATG
* *
1305151 AAACACTATGACATGGAAGAGATTTTCTGAATAATGGA
1 AAACACTATGACATGGAAAAGATTCTCTGAA-AATGGA
*
1305189 AAACACTATGATATGGAAAAGATTCTCTGAAAATGG
1 AAACACTATGACATGGAAAAGATTCTCTGAAAATGG
1305225 GGAAAGTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 5 0.15
38 28 0.85
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (37 bp):
AAACACTATGACATGGAAAAGATTCTCTGAAAATGGA
Found at i:1306112 original size:26 final size:26
Alignment explanation
Indices: 1306062--1306112 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1306052 TGAACTATAA
* *
1306062 AAACAACAAACCATAAACATTACATT
1 AAACAACAAAACATAAACATGACATT
* *
1306088 AAACAATAAAACATAAATATGACAT
1 AAACAACAAAACATAAACATGACAT
1306113 GAAGCATACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.61, C:0.18, G:0.02, T:0.20
Consensus pattern (26 bp):
AAACAACAAAACATAAACATGACATT
Done.