Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007853.1 Hibiscus syriacus cultivar Beakdansim tig00110213_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: 2309479
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:1160199 original size:14 final size:14
Alignment explanation
Indices: 1160180--1160216 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1160170 CATCAATTAC
1160180 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1160194 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1160208 ACAAATCAA
1 ACAAATCAA
1160217 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1162216 original size:14 final size:14
Alignment explanation
Indices: 1162197--1162253 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1162187 GCGAAATGAA
*
1162197 AATCGCAACGACAG
1 AATCGCAACGAAAG
1162211 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1162228 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1162244 AATCGCAACG
1 AATCGCAACG
1162254 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1162224 original size:33 final size:33
Alignment explanation
Indices: 1162178--1162270 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1162168 GCGAAACCAA
*
1162178 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1162211 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1162244 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1162271 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1162235 original size:19 final size:19
Alignment explanation
Indices: 1162141--1162275 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1162131 TAGTTTACTT
* *
1162141 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1162161 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1162180 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1162199 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1162213 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1162232 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1162246 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1162265 TCGCAATGCGA
1 TCGCAACGCGA
1162276 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1162293 original size:19 final size:19
Alignment explanation
Indices: 1162271--1162399 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1162261 AAAATCGCAA
1162271 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1162290 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1162304 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1162323 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1162337 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1162356 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1162375 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1162395 TGCGA
1 TGCGA
1162400 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1162313 original size:33 final size:33
Alignment explanation
Indices: 1162271--1162362 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1162261 AAAATCGCAA
1162271 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1162304 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1162337 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1162363 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1162563 original size:93 final size:93
Alignment explanation
Indices: 1162447--1162636 Score: 355
Period size: 93 Copynumber: 2.1 Consensus size: 93
1162437 ATGGATTGCA
1162447 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1162511 TAGCAGAATTGGCAGCAACCGAACAAAT
66 CAGCAGAATTGGCAGCAACCGAACAAAT
1162539 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1162604 CAGCAGAATTGGCAGCAACCGAATAAAT
66 CAGCAGAATTGGCAGCAACCGAACAAAT
1162632 TTACT
1 TTACT
1162637 AAGCAATCTA
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 4 0.04
93 91 0.96
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
CAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1164362 original size:14 final size:14
Alignment explanation
Indices: 1164343--1164399 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1164333 TTGAAATGAA
1164343 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1164357 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1164376 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1164390 AATCGCAACG
1 AATCGCAACG
1164400 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1164375 original size:33 final size:33
Alignment explanation
Indices: 1164335--1164416 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
1164325 TCTTTTGGTT
1164335 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1164368 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1164401 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1164417 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1164381 original size:19 final size:19
Alignment explanation
Indices: 1164357--1164421 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1164347 GCAACGAGAG
1164357 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1164376 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1164390 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1164409 AATCGCAATGCGA
1 AATCGCAACGCGA
1164422 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1164452 original size:14 final size:14
Alignment explanation
Indices: 1164433--1164489 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1164423 TTTGGTTTCG
1164433 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1164447 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1164466 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1164480 CATTGCGATT
1 CGTTGCGATT
1164490 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1164465 original size:33 final size:33
Alignment explanation
Indices: 1164417--1164538 Score: 136
Period size: 33 Copynumber: 3.5 Consensus size: 33
1164407 AAAATCGCAA
**
1164417 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1164450 TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1164483 TGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCGT
1164524 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1164539 TCTCGTTGCG
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 41 0.54
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 20 0.26
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1164498 original size:21 final size:21
Alignment explanation
Indices: 1164474--1164570 Score: 142
Period size: 21 Copynumber: 4.7 Consensus size: 21
1164464 CGCGTTGCGA
*
1164474 TTCTCTCATTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1164495 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1164515 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1164536 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1164557 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1164571 CTCTTCTGCA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.25
21 50 0.75
ACGTcount: A:0.12, C:0.25, G:0.15, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1164692 original size:33 final size:33
Alignment explanation
Indices: 1164650--1164720 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1164640 AATACTAACT
*
1164650 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1164683 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1164716 TGAAA
1 TGAAA
1164721 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1164954 original size:22 final size:22
Alignment explanation
Indices: 1164902--1164956 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1164892 TGGTTGTGAG
**
1164902 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1164924 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1164946 GGATTTCTTCG
1 GGATTTCTTCG
1164957 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1165128 original size:20 final size:20
Alignment explanation
Indices: 1165103--1165256 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1165093 CTTTAAATAT
1165103 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1165123 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1165145 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1165164 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1165184 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1165204 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1165224 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1165244 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1165257 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1165230 original size:40 final size:40
Alignment explanation
Indices: 1165102--1165256 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1165092 GCTTTAAATA
*
1165102 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
1165143 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
1165183 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
1165223 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
1165257 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:1165273 original size:21 final size:21
Alignment explanation
Indices: 1165243--1165325 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1165233 ATTTTCATAT
*
1165243 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1165264 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1165285 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1165306 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1165326 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1165316 original size:42 final size:43
Alignment explanation
Indices: 1165223--1165321 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1165213 ATTTATGTGT
* *
1165223 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1165264 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1165306 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1165322 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1177851 original size:17 final size:18
Alignment explanation
Indices: 1177817--1177852 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1177807 AGAGTTTGGA
1177817 TTGGGAATGTGGAATTTAC
1 TTGGGAATGT-GAATTTAC
1177836 TTGGGAATGT-AATTTAC
1 TTGGGAATGTGAATTTAC
1177853 ATTCCCCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.39
Consensus pattern (18 bp):
TTGGGAATGTGAATTTAC
Found at i:1188712 original size:32 final size:29
Alignment explanation
Indices: 1188651--1188713 Score: 72
Period size: 32 Copynumber: 2.1 Consensus size: 29
1188641 TATAATATTG
* *
1188651 ATTTTAAAAATATAAAATAAAACATATAT
1 ATTTTAAAAATATAAAATAAAAAACATAT
*
1188680 ATTTCTAATAAATATCAAGATAAAAAACATAT
1 ATTT-TAA-AAATAT-AAAATAAAAAACATAT
1188712 AT
1 AT
1188714 AAAACATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.14
30 3 0.11
31 6 0.21
32 15 0.54
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (29 bp):
ATTTTAAAAATATAAAATAAAAAACATAT
Found at i:1188867 original size:9 final size:10
Alignment explanation
Indices: 1188847--1188910 Score: 73
Period size: 9 Copynumber: 6.7 Consensus size: 10
1188837 TTGAATTTAA
1188847 AAAAAATCAT
1 AAAAAATCAT
1188857 AAAAAAT-AT
1 AAAAAATCAT
*
1188866 AAAAAATCAG
1 AAAAAATCAT
1188876 AAAAAATACA-
1 AAAAAAT-CAT
*
1188886 AAAAAAT-AC
1 AAAAAATCAT
1188895 AAAAAATCA-
1 AAAAAATCAT
1188904 AAAAAAT
1 AAAAAAT
1188911 TACAAAACAA
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
8 1 0.02
9 23 0.47
10 23 0.47
11 2 0.04
ACGTcount: A:0.77, C:0.08, G:0.02, T:0.14
Consensus pattern (10 bp):
AAAAAATCAT
Found at i:1188889 original size:29 final size:28
Alignment explanation
Indices: 1188846--1188917 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 28
1188836 CTTGAATTTA
*
1188846 AAAAAAAT-CATAAAAAATATAAAAAATC
1 AAAAAAATACA-AAAAAATACAAAAAATC
1188874 AGAAAAAATACAAAAAAATACAAAAAATC
1 A-AAAAAATACAAAAAAATACAAAAAATC
1188903 AAAAAAATTACAAAA
1 AAAAAAA-TACAAAA
1188918 CAATTAGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 7 0.17
29 31 0.77
30 2 0.05
ACGTcount: A:0.76, C:0.08, G:0.01, T:0.14
Consensus pattern (28 bp):
AAAAAAATACAAAAAAATACAAAAAATC
Found at i:1188909 original size:19 final size:19
Alignment explanation
Indices: 1188844--1188917 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 19
1188834 TACTTGAATT
*
1188844 TAAAAAAAATCATAAAAAA
1 TAAAAAAAATCACAAAAAA
* *
1188863 TATAAAAAATCAGAAAAAA
1 TAAAAAAAATCACAAAAAA
1188882 TACAAAAAAAT-ACAAAAAA
1 TA-AAAAAAATCACAAAAAA
* *
1188901 TCAAAAAAATTACAAAA
1 TAAAAAAAATCACAAAA
1188918 CAATTAGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 8 0.17
19 33 0.69
20 7 0.15
ACGTcount: A:0.76, C:0.08, G:0.01, T:0.15
Consensus pattern (19 bp):
TAAAAAAAATCACAAAAAA
Found at i:1188917 original size:10 final size:10
Alignment explanation
Indices: 1188847--1188923 Score: 61
Period size: 10 Copynumber: 7.9 Consensus size: 10
1188837 TTGAATTTAA
* *
1188847 AAAAAATCAT
1 AAAAAATTAC
*
1188857 AAAAAA-TAT
1 AAAAAATTAC
* *
1188866 AAAAAATCAG
1 AAAAAATTAC
1188876 AAAAAA-TAC
1 AAAAAATTAC
*
1188885 AAAAAAATAC
1 AAAAAATTAC
*
1188895 AAAAAATCA-
1 AAAAAATTAC
1188904 AAAAAATTAC
1 AAAAAATTAC
1188914 AAAACAATTA
1 AAAA-AATTA
1188924 GTATATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
9 23 0.42
10 27 0.49
11 5 0.09
ACGTcount: A:0.74, C:0.09, G:0.01, T:0.16
Consensus pattern (10 bp):
AAAAAATTAC
Found at i:1207604 original size:41 final size:43
Alignment explanation
Indices: 1207538--1207632 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 43
1207528 TTTTTTCATA
*
1207538 TAATTCGTTTTTTGAAAAATAATTTT-CAGTGTTTGTTTCACG
1 TAATTCGTTTTTTGAAAAATAATTTTCCAGTGTTTATTTCACG
* *
1207580 TAATTCGTTTTTTGAAAAAT-ATTTTCCCGTGTTTATTTCATG
1 TAATTCGTTTTTTGAAAAATAATTTTCCAGTGTTTATTTCACG
*
1207622 TAATTGGTTTT
1 TAATTCGTTTT
1207633 CCGGAACATA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 5 0.10
42 43 0.90
ACGTcount: A:0.24, C:0.09, G:0.14, T:0.53
Consensus pattern (43 bp):
TAATTCGTTTTTTGAAAAATAATTTTCCAGTGTTTATTTCACG
Found at i:1207986 original size:28 final size:26
Alignment explanation
Indices: 1207932--1207995 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 26
1207922 TTTATTTTAA
1207932 TAATATATAATAAAATTTTTATATATT
1 TAATA-ATAATAAAATTTTTATATATT
*
1207959 TAATAATGAATAATATTATTTATATATT
1 TAATAAT-AATAAAATT-TTTATATATT
1207987 TAAATAATA
1 T-AATAATA
1207996 TTTTAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 2 0.06
27 13 0.39
28 12 0.36
29 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TAATAATAATAAAATTTTTATATATT
Found at i:1208025 original size:23 final size:23
Alignment explanation
Indices: 1207999--1208043 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1207989 AATAATATTT
1207999 TAATAAAAATATTTAAAATATAC
1 TAATAAAAATATTTAAAATATAC
* * *
1208022 TAATTAATATTTTTAAAATATA
1 TAATAAAAATATTTAAAATATA
1208044 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAAATATTTAAAATATAC
Found at i:1208170 original size:19 final size:20
Alignment explanation
Indices: 1208138--1208176 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1208128 TAATAAAATT
1208138 ATAAAAAATATA-TTTAATA
1 ATAAAAAATATATTTTAATA
1208157 ATAAATAAAT-TATTTTAATA
1 ATAAA-AAATATATTTTAATA
1208177 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAAAATATATTTTAATA
Found at i:1209566 original size:21 final size:21
Alignment explanation
Indices: 1209542--1209585 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1209532 TTTAAGTATT
* *
1209542 ATATTGTAAATTGAAAATATA
1 ATATTGTAAAATAAAAATATA
*
1209563 ATATTTTAAAATAAAAATATA
1 ATATTGTAAAATAAAAATATA
1209584 AT
1 AT
1209586 TTTATCTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
ATATTGTAAAATAAAAATATA
Found at i:1210457 original size:20 final size:18
Alignment explanation
Indices: 1210413--1210503 Score: 128
Period size: 20 Copynumber: 4.8 Consensus size: 18
1210403 AACATTCCCA
1210413 GTAATCTTACATTCCTTG
1 GTAATCTTACATTCCTTG
*
1210431 ATAATCTTACATTCCTACTG
1 GTAATCTTACATTCCT--TG
1210451 GTAATCTTACATTCCTTG
1 GTAATCTTACATTCCTTG
*
1210469 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTC-C-TTG
1210489 GTAATCTTACATTCC
1 GTAATCTTACATTCC
1210504 GTGAACCAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
18 31 0.47
19 2 0.03
20 33 0.50
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (18 bp):
GTAATCTTACATTCCTTG
Found at i:1210457 original size:38 final size:38
Alignment explanation
Indices: 1210413--1210503 Score: 157
Period size: 38 Copynumber: 2.4 Consensus size: 38
1210403 AACATTCCCA
1210413 GTAATCTTACATTCCTTGATAATCTTACATTC-CTACTG
1 GTAATCTTACATTCCTTGATAATCTTACATTCTC-ACTG
*
1210451 GTAATCTTACATTCCTTGGTAATCTTACATTCTCACTG
1 GTAATCTTACATTCCTTGATAATCTTACATTCTCACTG
1210489 GTAATCTTACATTCC
1 GTAATCTTACATTCC
1210504 GTGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 50 0.98
39 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (38 bp):
GTAATCTTACATTCCTTGATAATCTTACATTCTCACTG
Found at i:1210655 original size:44 final size:44
Alignment explanation
Indices: 1210589--1210672 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
1210579 GAATCTGTCA
* * * *
1210589 GGAATTTAAATCCAATTTCATATTCTGTTTGGTTGGCAGAAAAT
1 GGAATTGAAATCCAATTCCATATTCTGTCTGGTTCGCAGAAAAT
1210633 GGAATTGAAATCCAATTCCATATTCTGTCTGGTTCGCAGA
1 GGAATTGAAATCCAATTCCATATTCTGTCTGGTTCGCAGA
1210673 CATATCAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (44 bp):
GGAATTGAAATCCAATTCCATATTCTGTCTGGTTCGCAGAAAAT
Found at i:1228132 original size:39 final size:39
Alignment explanation
Indices: 1228044--1228120 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
1228034 TCATTAAACT
*
1228044 TTTTAT-ATTTTAAATTTTGTAAAAAAAAATTATATAAA
1 TTTTATCAATTTAAATTTTGTAAAAAAAAATTATATAAA
* * * *
1228082 TTTTATGAATTTAATTTTTTTAAAATAAAA-TATATAAA
1 TTTTATCAATTTAAATTTTGTAAAAAAAAATTATATAAA
1228120 T
1 T
1228121 ATTTTCCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 15 0.44
39 19 0.56
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (39 bp):
TTTTATCAATTTAAATTTTGTAAAAAAAAATTATATAAA
Found at i:1237773 original size:14 final size:13
Alignment explanation
Indices: 1237754--1237792 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1237744 TATATGGATA
1237754 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
1237768 TTTTATTATTTAT
1 TTTTATTATTTAT
1237781 GTTATTATTATT
1 -TT-TTATTATT
1237793 ATATGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:1237791 original size:18 final size:17
Alignment explanation
Indices: 1237752--1237794 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1237742 ATTATATGGA
1237752 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
1237768 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
1237786 TATTATTAT
1 TATTATTAT
1237795 ATGTGTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1237807 original size:2 final size:2
Alignment explanation
Indices: 1237800--1237824 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1237790 ATTATATGTG
1237800 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1237825 TTCTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1240813 original size:8 final size:8
Alignment explanation
Indices: 1240800--1240838 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1240790 GAACATTTCA
*
1240800 TGCATTCT
1 TGCATTTT
1240808 TGCA-TTT
1 TGCATTTT
1240815 TGCATTTT
1 TGCATTTT
*
1240823 TGCCTTTT
1 TGCATTTT
1240831 TGCATTTT
1 TGCATTTT
1240839 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:1242665 original size:22 final size:22
Alignment explanation
Indices: 1242637--1242687 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1242627 CCCCATCAAT
1242637 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
1242659 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
1242681 CCTTTGA
1 CCTTTGA
1242688 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:1243595 original size:36 final size:36
Alignment explanation
Indices: 1243548--1243652 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
1243538 GTGCTCACCA
1243548 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* *
1243584 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
1243621 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1243653 TAAACATTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
36 31 0.50
37 31 0.50
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:1243642 original size:37 final size:37
Alignment explanation
Indices: 1243548--1243657 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
1243538 GTGCTCACCA
1243548 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
1243584 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
1243621 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
1243658 ATTGAAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 30 0.46
37 32 0.49
38 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:1243742 original size:102 final size:102
Alignment explanation
Indices: 1243566--1243957 Score: 651
Period size: 102 Copynumber: 3.9 Consensus size: 102
1243556 CTTGAGACAG
** * * * *
1243566 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1243631 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
1243668 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
1243733 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1243770 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
1243835 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
1243872 TTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
1243936 TGAGACAGCTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
1243958 CAAAACCTTT
Statistics
Matches: 274, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
101 35 0.13
102 239 0.87
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:1243743 original size:37 final size:37
Alignment explanation
Indices: 1243684--1243754 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
1243674 TTGAAATGAG
* *
1243684 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
* *
1243721 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
1243755 TAAACATTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:1243837 original size:37 final size:37
Alignment explanation
Indices: 1243770--1243856 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
1243760 ATTGGAAACA
** * *
1243770 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1243806 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1243843 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
1243857 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:1243916 original size:204 final size:203
Alignment explanation
Indices: 1243566--1244024 Score: 675
Period size: 204 Copynumber: 2.2 Consensus size: 203
1243556 CTTGAGACAG
* *
1243566 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * * *
1243631 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTTGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
* * *
1243696 TGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
131 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACATAAACA
1243761 TTGGAAACA
195 TTGGAAACA
** * *
1243770 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1243835 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
* *
1243900 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACACAAAACC
131 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACA-TAAACA
* ***
1243965 TTTGAGATTG
195 TTGGA-AACA
* * * * *
1243975 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1244025 CAAAATCTTT
Statistics
Matches: 227, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
203 35 0.15
204 148 0.65
205 44 0.19
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (203 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACATAAACAT
TGGAAACA
Found at i:1243926 original size:36 final size:36
Alignment explanation
Indices: 1243871--1243940 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
1243861 CATTGAAAAC
** *
1243871 ATTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGATA
* *
1243907 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGA
1243941 CAGCTTCTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGATA
Found at i:1243953 original size:36 final size:36
Alignment explanation
Indices: 1243886--1243957 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1243876 CCTAGAAATG
* * *
1243886 AATTTCGTCTCTCTTGAGATAATTTCCCTTGAAACA
1 AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
* * *
1243922 AATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACA
1 AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
1243958 CAAAACCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (36 bp):
AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
Found at i:1244048 original size:67 final size:67
Alignment explanation
Indices: 1243899--1244057 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
1243889 TTCGTCTCTC
** *
1243899 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
1243964 CT
66 CT
* * *
1243966 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
1244031 CT
66 CT
*
1244033 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
1244058 ATTTCGTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
CT
Found at i:1245256 original size:105 final size:104
Alignment explanation
Indices: 1244891--1245963 Score: 1542
Period size: 105 Copynumber: 10.3 Consensus size: 104
1244881 GCCATCCGCG
* * * * * *
1244891 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
1244956 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAA-TTCAGAGCCA
* *
1245000 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
1245065 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAA-CTTCCCAA-TTCAGAGCCA
*
1245107 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1245172 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
1245212 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1245277 ACCGTTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
1245317 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1245382 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* *
1245417 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1245482 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
1245522 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1245587 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* *
1245622 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1245687 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
* *
1245727 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
1245792 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* *
1245827 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA-GAACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG-ACGAAGG
* * * **
1245891 GACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
65 GACCGCTGCTTGTCAAC-AACAACTTCCCAATT-CAGAGCCA
* *
1245933 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1245964 TGGAACAATG
Statistics
Matches: 891, Mismatches: 53, Indels: 43
0.90 0.05 0.04
Matches are distributed among these distances:
99 1 0.00
100 258 0.29
101 12 0.01
102 9 0.01
103 10 0.01
104 12 0.01
105 377 0.42
106 93 0.10
107 97 0.11
109 22 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
Found at i:1245499 original size:205 final size:205
Alignment explanation
Indices: 1244891--1245963 Score: 1612
Period size: 205 Copynumber: 5.2 Consensus size: 205
1244881 GCCATCCGCG
* * * * * *
1244891 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
1244956 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAAC-AA-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTCACAACGAAGG
** * * *
1245021 ATATTGGACTCCAGACAACACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACA
122 ATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* *
1245086 ATTTTCCCAATTTCAGAGCCA
186 ACTTT-CCAATCTCAGAGCCA
*
1245107 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1245172 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
1245237 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGTTGCTTGTCAACAACAACTTT
126 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
1245302 CCAATCTCAGAGCCA
191 CCAATCTCAGAGCCA
1245317 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1245382 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
1245447 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
1245512 CTCAGAGCCA
196 CTCAGAGCCA
1245522 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1245587 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
1245652 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
1245717 CCCAGAGCCA
196 CTCAGAGCCA
* *
1245727 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
1245792 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** * *
1245857 TCGAGACAACACAAGTTCAACTTCA-GAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCC
131 TCCAGACAATGCAAGTTCAACTTCACG-ACGAAGGGACCGCTGCTTGTCAAC-AACAACTTT-CC
**
1245920 GGT-TCCAGAGCCA
193 AATCT-CAGAGCCA
* *
1245933 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1245964 TGGAACAATG
Statistics
Matches: 810, Mismatches: 42, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
204 1 0.00
205 485 0.60
206 46 0.06
207 1 0.00
208 2 0.00
209 2 0.00
210 95 0.12
211 9 0.01
212 96 0.12
213 49 0.06
214 3 0.00
216 21 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (205 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
CTCAGAGCCA
Found at i:1245505 original size:310 final size:311
Alignment explanation
Indices: 1244891--1245963 Score: 1569
Period size: 310 Copynumber: 3.4 Consensus size: 311
1244881 GCCATCCGCG
* * * * *
1244891 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACACAAGTTCAACTTCACGACGAA
* * *
1244956 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAACAAACAATTTC-CAA-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* * * *
1245021 ATATTGGACTCCAGACAACACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACA
126 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* *
1245086 ATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
190 ACTTT--CAA-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAA
*
1245151 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
252 GTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-CCAATCTCAGAGCCA
**
1245212 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGG
*
1245277 ACCGTTGCTTGTCAAC-AACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 ACCGCTGCTTGTCAACAAACAA-TTTCCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATA
1245341 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
1245404 TC-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAAC
194 TCAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAAC
1245468 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
259 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAAC-TTCCAATCTCAGAGCCA
*
1245522 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGG
*
1245587 ACCGCTGCTTGTCAAC-AA-AATTT-C-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 ACCGCTGCTTGTCAACAAACAATTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* * *
1245648 GGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-T
* * *
1245713 CAATCCCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAATGCAAGTTCAAC
195 CAAT-TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAAC
* **
1245778 TTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTTC-AT-TCAGATTCA
259 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCA
*
1245827 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA-GAACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG-ACGAAGG
* * ** * *
1245891 GACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGAT
65 GACCGCTGCTTGTCAACAAACAATTT-CCAATT-CAGAGCCAATTTCAACTTCACAACGAAGGAT
1245956 ATTGGACT
128 ATTGGACT
1245964 TGGAACAATG
Statistics
Matches: 700, Mismatches: 37, Indels: 40
0.90 0.05 0.05
Matches are distributed among these distances:
304 1 0.00
305 171 0.24
306 8 0.01
307 11 0.02
308 4 0.01
309 7 0.01
310 282 0.40
311 39 0.06
312 1 0.00
314 3 0.00
315 2 0.00
316 3 0.00
317 94 0.13
318 49 0.07
319 3 0.00
321 22 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (311 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAACAATTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
AATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTT
CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCA
Found at i:1246981 original size:14 final size:13
Alignment explanation
Indices: 1246962--1247000 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1246952 TATATGGATA
1246962 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
1246976 TTTTATTATTTAT
1 TTTTATTATTTAT
1246989 GTTATTATTATT
1 -TT-TTATTATT
1247001 ATGTGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:1246999 original size:18 final size:17
Alignment explanation
Indices: 1246960--1247002 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1246950 ATTATATGGA
1246960 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
1246976 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
1246994 TATTATTAT
1 TATTATTAT
1247003 GTGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1247013 original size:2 final size:2
Alignment explanation
Indices: 1247006--1247078 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
1246996 TTATTATGTG
*
1247006 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1247048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1247079 TTCTTTAATA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1247320 original size:24 final size:24
Alignment explanation
Indices: 1247276--1247321 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1247266 ATATATATTA
* *
1247276 TTATTATTATTTTCGTTTTTTTAT
1 TTATTATTATTATCATTTTTTTAT
1247300 TTATTATTATTAT-ATTATTTTT
1 TTATTATTATTATCATT-TTTTT
1247322 TTAGAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (24 bp):
TTATTATTATTATCATTTTTTTAT
Found at i:1247481 original size:2 final size:2
Alignment explanation
Indices: 1247476--1247506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1247466 TACTTTGACG
1247476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1247507 TTCCTTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1247598 original size:31 final size:31
Alignment explanation
Indices: 1247550--1247609 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1247540 ACTTTACTAT
* *
1247550 TTTTTTCCTTTATCTTATTT-ATTTATTTTA
1 TTTTTCCCTTTACCTTATTTGATTTATTTTA
*
1247580 TTTTTCCCTTTTACCTTATTTGTTTTATTT
1 TTTTTCCC-TTTACCTTATTTGATTTATTT
1247610 ACCTTGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 11 0.44
32 7 0.28
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (31 bp):
TTTTTCCCTTTACCTTATTTGATTTATTTTA
Found at i:1251650 original size:16 final size:19
Alignment explanation
Indices: 1251621--1251660 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
1251611 CCGAAACCGA
1251621 TTTTTTAGATCGGTTC-GG
1 TTTTTTAGATCGGTTCGGG
1251639 TTTTTTA-A-CGGTTCGGG
1 TTTTTTAGATCGGTTCGGG
1251656 TTTTT
1 TTTTT
1251661 CGGTTTACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.10, C:0.10, G:0.25, T:0.55
Consensus pattern (19 bp):
TTTTTTAGATCGGTTCGGG
Found at i:1256021 original size:21 final size:22
Alignment explanation
Indices: 1255984--1256024 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1255974 ATAACATTTC
1255984 TATTTTCTTATTATTTAAAAAT
1 TATTTTCTTATTATTTAAAAAT
*
1256006 TATTTT-TTATTTTTTAAAA
1 TATTTTCTTATTATTTAAAA
1256025 TATACTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTCTTATTATTTAAAAAT
Found at i:1256045 original size:2 final size:2
Alignment explanation
Indices: 1256038--1256080 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1256028 ACTTAAACAG
1256038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1256080 A
1 A
1256081 ATCCTCCCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1257939 original size:19 final size:20
Alignment explanation
Indices: 1257901--1257940 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1257891 CACGAATTGG
*
1257901 ATTAAGTTAGTGTGTATTTCT
1 ATTAAGATAGTGTG-ATTTCT
1257922 ATTAAGATAGTGTG-TTTCT
1 ATTAAGATAGTGTGATTTCT
1257941 GTAATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (20 bp):
ATTAAGATAGTGTGATTTCT
Found at i:1268039 original size:2 final size:2
Alignment explanation
Indices: 1267982--1268023 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1267972 TTTATATACA
1267982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1268024 TATGATTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1275831 original size:34 final size:30
Alignment explanation
Indices: 1275793--1275861 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
1275783 TTGATATAAC
1275793 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
*
1275827 AATTT-ATAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1275856 AATTTA
1 AATTTA
1275862 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 12 0.36
31 5 0.15
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1275872 original size:29 final size:30
Alignment explanation
Indices: 1275803--1275862 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1275793 AATTTAAGGC
1275803 AAAATGGTTTTTGGACTTGAATTGAATTTAT
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAT
1275834 AAAATGTTTTTGGACTT-AATTGAATTTAT
1 AAAATGTTTTTGGACTTGAATTGAATTTAT
1275863 TCAAAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 12 0.41
30 12 0.41
31 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAT
Found at i:1276067 original size:20 final size:20
Alignment explanation
Indices: 1276042--1276112 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1276032 GCAATTAGAA
1276042 CATCGATGCATCCTTCTGTG
1 CATCGATGCATCCTTCTGTG
* **
1276062 CATCGATACATCAAGGT-TGTG
1 CATCGATGCATC--CTTCTGTG
*
1276083 CATCGATGCATCCTGCTGTG
1 CATCGATGCATCCTTCTGTG
*
1276103 CATCCATGCA
1 CATCGATGCA
1276113 CGAAGGCTGC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
20 24 0.60
21 15 0.38
22 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (20 bp):
CATCGATGCATCCTTCTGTG
Found at i:1281926 original size:165 final size:166
Alignment explanation
Indices: 1281654--1281984 Score: 655
Period size: 165 Copynumber: 2.0 Consensus size: 166
1281644 AATTTCTTGC
1281654 AGGTAAGAAGCAGCTTTGGGTTACAGACGTGATCTGCATGTTGTGAAATGATCTGATCGTAAAGA
1 AGGTAAGAAGCAGCTTTGGGTTACAGACGTGATCTGCATGTTGTGAAATGATCTGATCGTAAAGA
1281719 GTGTTGTGTTGGTAAAGTTAAGAGGATAAGTTTAGTATATGTTCAGAATTTTCTTAATC-ATTGA
66 GTGTTGTGTTGGTAAAGTTAAGAGGATAAGTTTAGTATATGTTCAGAATTTTCTTAATCAATTGA
1281783 TCATGTACACACATTTTGTAGACGATATGTTTCAAA
131 TCATGTACACACATTTTGTAGACGATATGTTTCAAA
1281819 AGGTAAGAAGCAGCTTTGGGTTACAGACGTGATCTGCATGTTGTGAAATGATCTGATCGTAAAGA
1 AGGTAAGAAGCAGCTTTGGGTTACAGACGTGATCTGCATGTTGTGAAATGATCTGATCGTAAAGA
1281884 GTGTTGTGTTGGTAAAGTTAAGAGGATAAGTTTAGTATATGTTCAGAATTTTCTTAATCAATTGA
66 GTGTTGTGTTGGTAAAGTTAAGAGGATAAGTTTAGTATATGTTCAGAATTTTCTTAATCAATTGA
1281949 TCATGTACACACATTTTGTAGACGATATGTTTCAAA
131 TCATGTACACACATTTTGTAGACGATATGTTTCAAA
1281985 CCAAAGATCT
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 124 0.75
166 41 0.25
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (166 bp):
AGGTAAGAAGCAGCTTTGGGTTACAGACGTGATCTGCATGTTGTGAAATGATCTGATCGTAAAGA
GTGTTGTGTTGGTAAAGTTAAGAGGATAAGTTTAGTATATGTTCAGAATTTTCTTAATCAATTGA
TCATGTACACACATTTTGTAGACGATATGTTTCAAA
Found at i:1282602 original size:58 final size:60
Alignment explanation
Indices: 1282529--1282641 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 60
1282519 TCTCTTAGGC
1282529 ATATTGTTATGAAATTTTATTATTAGCTCTTTAT-CTTTTAAGTATTT-TCTCTTTAAAT
1 ATATTGTTATGAAATTTTATTATTAGCTCTTTATACTTTTAAGTATTTATCTCTTTAAAT
* * * * *
1282587 ATATTGTTTTTAAATTTTATTATTGGTTCTTTATATTTTTAAGTATTTATCTCTT
1 ATATTGTTATGAAATTTTATTATTAGCTCTTTATACTTTTAAGTATTTATCTCTT
1282642 AAGCAAAGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 30 0.62
59 12 0.25
60 6 0.12
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (60 bp):
ATATTGTTATGAAATTTTATTATTAGCTCTTTATACTTTTAAGTATTTATCTCTTTAAAT
Found at i:1287484 original size:24 final size:23
Alignment explanation
Indices: 1287460--1287504 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1287450 GAAAAACACT
*
1287460 TTTCAAAGAAACATTTACCAAAC
1 TTTCAAAAAAACATTTACCAAAC
* *
1287483 TTTGAAAAAAACATTTTCCAAA
1 TTTCAAAAAAACATTTACCAAA
1287505 GTTGGTTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (23 bp):
TTTCAAAAAAACATTTACCAAAC
Found at i:1298751 original size:23 final size:23
Alignment explanation
Indices: 1298719--1298768 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1298709 AGTAAAAATC
* *
1298719 GAAACAACAGATCATTTTCTTGA
1 GAAACAACAGATAATTTTCTCGA
*
1298742 GAAACCACAGATAATTTTCTCGA
1 GAAACAACAGATAATTTTCTCGA
1298765 GAAA
1 GAAA
1298769 AGGCTCAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (23 bp):
GAAACAACAGATAATTTTCTCGA
Found at i:1305884 original size:30 final size:32
Alignment explanation
Indices: 1305848--1305910 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
1305838 CAACCTCATT
* *
1305848 GTTTTCTTATTACAATA-CAA-GTCTTCTTTG
1 GTTTTCTTATGACAATATCAATGGCTTCTTTG
1305878 GTTTTCTTATGACAATATCAATGGCTTCTTTG
1 GTTTTCTTATGACAATATCAATGGCTTCTTTG
1305910 G
1 G
1305911 CTTTGTCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.55
31 3 0.10
32 10 0.34
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (32 bp):
GTTTTCTTATGACAATATCAATGGCTTCTTTG
Found at i:1307658 original size:20 final size:19
Alignment explanation
Indices: 1307622--1307691 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
1307612 AAAGAATTAA
*
1307622 AAAAATATAATTT-TTTTT
1 AAAATTATAATTTATTTTT
*
1307640 AAGATTTATAATTTA-TTTT
1 AA-AATTATAATTTATTTTT
**
1307659 AAAATTATAAAATATTTTT
1 AAAATTATAATTTATTTTT
1307678 AAAAATTATAATTT
1 -AAAATTATAATTT
1307692 CAAGAAAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 11 0.27
19 19 0.46
20 11 0.27
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (19 bp):
AAAATTATAATTTATTTTT
Found at i:1308738 original size:52 final size:52
Alignment explanation
Indices: 1308621--1308738 Score: 182
Period size: 53 Copynumber: 2.2 Consensus size: 52
1308611 TATTATTTTT
* *
1308621 ATTAAAAACTCAACTTTTTTTTAGAGGAAATGAATGAATTTGGTTTACCTGG
1 ATTAAAAACTCAACCTTTTTTTAGAGGAAATGAATGAATTTGGTTTACCTAG
* * *
1308673 ATTAAAAAACTCAACCTTTTTTTAGTGGTAATGAATGAATTTGGTTTACTTAG
1 ATT-AAAAACTCAACCTTTTTTTAGAGGAAATGAATGAATTTGGTTTACCTAG
1308726 ATTAAAAACTCAA
1 ATTAAAAACTCAA
1308739 ATGAGTTCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 13 0.22
53 47 0.78
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.38
Consensus pattern (52 bp):
ATTAAAAACTCAACCTTTTTTTAGAGGAAATGAATGAATTTGGTTTACCTAG
Found at i:1317798 original size:31 final size:31
Alignment explanation
Indices: 1317760--1317838 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1317750 TATTTATAAA
*
1317760 TAATATTTTATCTAAAATTCAAATGTCAAAT
1 TAATATTTTATCTAAAATTCAAAGGTCAAAT
*
1317791 TAATATTTTATTTAAAATTCAAAGGTCAAAT
1 TAATATTTTATCTAAAATTCAAAGGTCAAAT
1317822 TAATATTTTATCTAAAA
1 TAATATTTTATCTAAAA
1317839 CTCATTAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (31 bp):
TAATATTTTATCTAAAATTCAAAGGTCAAAT
Found at i:1317853 original size:31 final size:29
Alignment explanation
Indices: 1317756--1317853 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 29
1317746 TTATTATTTA
1317756 TAAA-TAATATTTTATCTAAAATTCAAAT
1 TAAATTAATATTTTATCTAAAATTCAAAT
*
1317784 GTCAAATTAATATTTTATTTAAAATTCAAAGGT
1 -T-AAATTAATATTTTATCTAAAATTCAAA--T
* *
1317817 CAAATTAATATTTTATCTAAAACTCATTAAT
1 TAAATTAATATTTTATCTAAAATTCA--AAT
1317848 TAAATT
1 TAAATT
1317854 TAAAATTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
29 1 0.02
30 3 0.05
31 51 0.88
33 3 0.05
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAATTAATATTTTATCTAAAATTCAAAT
Found at i:1348786 original size:22 final size:22
Alignment explanation
Indices: 1348744--1348786 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1348734 TGCAACTAAA
*
1348744 AATTAAAAAAATATACGAAATC
1 AATTAAAAAAATATACAAAATC
*
1348766 AATTAAAATAATAATA-AAAAT
1 AATTAAAAAAAT-ATACAAAAT
1348787 GCCAAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (22 bp):
AATTAAAAAAATATACAAAATC
Found at i:1348912 original size:29 final size:29
Alignment explanation
Indices: 1348846--1348912 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1348836 ATTTAATATC
* **
1348846 TAAAGTTTAATGATTAAATTAGAAATTCA
1 TAAAGTTTAATGATTAAATAAGAAATGAA
* *
1348875 TATATTTTAATGATTAAAATAAGAAA-GAA
1 TAAAGTTTAATGATT-AAATAAGAAATGAA
1348904 TAAAGTTTA
1 TAAAGTTTA
1348913 GTGAGAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.37
Consensus pattern (29 bp):
TAAAGTTTAATGATTAAATAAGAAATGAA
Found at i:1351268 original size:18 final size:19
Alignment explanation
Indices: 1351245--1351284 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1351235 AAATGGGTAC
* *
1351245 TTAAATT-ATTTTTTATTT
1 TTAAATTAATATTTAATTT
1351263 TTAAATTAATATTTAATTT
1 TTAAATTAATATTTAATTT
1351282 TTA
1 TTA
1351285 TTGTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTAAATTAATATTTAATTT
Found at i:1351685 original size:3 final size:3
Alignment explanation
Indices: 1351677--1351702 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1351667 ATTCGGGCTT
1351677 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1351703 GAGGTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1357994 original size:26 final size:26
Alignment explanation
Indices: 1357950--1358049 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 26
1357940 AAATTTTAAC
*
1357950 ATAAAATATATATATTTTTAAATGAAA
1 ATAAAATA-AAATATTTTTAAATGAAA
* *
1357977 ATAAAATAAAATATTTTTAAATTAAG
1 ATAAAATAAAATATTTTTAAATGAAA
* * * **
1358003 TTAATAATAAAATATATTTAATAAGTTA
1 ATAA-AATAAAATATTTTTAA-ATGAAA
*
1358031 ATATAA-AAAATATTTTTAA
1 ATAAAATAAAATATTTTTAA
1358050 GTTAATATAT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
26 30 0.52
27 25 0.43
28 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
ATAAAATAAAATATTTTTAAATGAAA
Found at i:1358033 original size:25 final size:25
Alignment explanation
Indices: 1357981--1358071 Score: 96
Period size: 27 Copynumber: 3.5 Consensus size: 25
1357971 ATGAAAATAA
*
1357981 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AA-TAAGTTAAT
1358008 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
* *
1358033 -ATAAAAAATATTT-TTAAGTTAATAT
1 AATAAAATATATTTAATAAGTT-A-AT
1358058 ATATAAAATATATT
1 A-ATAAAATATATT
1358072 CACGCATTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.11
24 13 0.23
25 11 0.20
26 2 0.04
27 24 0.43
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:1358054 original size:23 final size:24
Alignment explanation
Indices: 1357997--1358068 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 24
1357987 ATATTTTTAA
*
1357997 ATTAAGTTAATAATAAAATATATTT
1 ATTAAGTTAAT-ATAAAAAATATTT
*
1358022 AATAAGTTAATATAAAAAATATTT
1 ATTAAGTTAATATAAAAAATATTT
1358046 -TTAAGTTAATATATATAAAATAT
1 ATTAAGTTAATATA-A-AAAATAT
1358069 ATTCACGCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
23 12 0.29
24 13 0.31
25 17 0.40
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
ATTAAGTTAATATAAAAAATATTT
Found at i:1360343 original size:26 final size:26
Alignment explanation
Indices: 1360283--1360334 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1360273 ATAAATAATT
*
1360283 AATATAATTTATAATATTTTTATTTA
1 AATATAATATATAATATTTTTATTTA
*
1360309 AATAAAATATATCAATATTTTTATTT
1 AATATAATATAT-AATATTTTTATTT
1360335 TTATTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATAATATATAATATTTTTATTTA
Found at i:1360541 original size:14 final size:14
Alignment explanation
Indices: 1360519--1360553 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1360509 TAAACATCGT
*
1360519 AAAACGTTTTCCAG
1 AAAATGTTTTCCAG
*
1360533 AAAATGTTTTTCAG
1 AAAATGTTTTCCAG
1360547 AAAATGT
1 AAAATGT
1360554 AATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (14 bp):
AAAATGTTTTCCAG
Found at i:1361354 original size:23 final size:23
Alignment explanation
Indices: 1361324--1361374 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1361314 AAATAATTTA
1361324 TCTTTGTGACACATTTTTC-TCT
1 TCTTTGTGACACATTTTTCATCT
**
1361346 GTCTTTGTGACATGTTTTTCATCT
1 -TCTTTGTGACACATTTTTCATCT
1361370 TCTTT
1 TCTTT
1361375 CTAGGACGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.57
Consensus pattern (23 bp):
TCTTTGTGACACATTTTTCATCT
Found at i:1363755 original size:661 final size:655
Alignment explanation
Indices: 1362495--1363800 Score: 1594
Period size: 661 Copynumber: 2.0 Consensus size: 655
1362485 AAAGTTTACT
* * *
1362495 GTAAGGCCAATCCTAGTTATAATCTTACCATCAGACATGGTAAGGTTATTCTTGCTCCATCTAAT
1 GTAAGGCCAATCCTAATTATAATCTTACCATAAGACAAGGTAAGGTTATTCTTGCTCCATCTAAT
* * * **
1362560 CCTAATGATGAATTTCAGGTACCATATCAACATATCCCACTTAATCTCTTTTTTCTGAAGTTTTT
66 CCTAATGATGAATTCCAGG----ATATC-ACATAT-CCACTTAATCTCGTTTTTCTAAACCTTTT
* * * * * *
1362625 GAGTGCTAAAACTTAAGGTTTAGGAAAAACATGAATCTTATTTTGGTTTTGGTGTAAATCTTTGT
125 GAGTGCTAAAACTTAAGATTAAGGAAAAACACGAATCTTAGTTTGATTTTGATGTAAATCTTTGT
* * * * *
1362690 TGTTGTTTTAGCTTTGGTATAAAGATGAGACGTTCAGCTCAACTGTGAAAGATGAATCCGGTTTT
190 TGTTGTTTTAGCTCTGGTATAAAGATGAGAAGTACAGCTCAACTGTGAAAGATGAATACGGTTTC
* * * * *
1362755 CCCGGTTTTTCTCTGGTTAATAAAGCTACTGGTGAAGCTATTAAACATGCCATTGGAGCAACTCA
255 CCCAGTTTTTCTCTGATTAATAAAGCTACTGATGAAGCCATCAAACATGCCATTGGAGCAACTCA
** *
1362820 TCCCGTAAGAAATGCTTTGTTTATTCATACAATTGTTAAAAAAATCGTTTTGAATTTAGCCTTAA
320 TCCCGTAAGAAATGCTTCATTTATTCATACAATTGTTAAAAAAATCGTTTGGAATTTAGCCTTAA
* *** * *
1362885 AGTTTTGCTTTAAAATTATGGGATTTTGATCCGCAGGTCCAACTCGTACCCTACAAACCAGGCGT
385 AGTTTTGCTTAAAAATTAAAAGATTTTGATCCGCAGGTCCAACTCGCACCCTACAAACCAGACGT
* * * * *
1362950 TCTGGATGAGTCTTTATTATGGAGCGCGTCAAATGAAGTCAGTGATGGCTACAAAGCTATGCGTA
450 TCTGGACGAGTCTGTATTATGGAGCGCGTCAAATGAAGTCAGGGATGGCTACAAAGCCATACGTA
* * * * *
1363015 TGGTTAATAACATTAGCCTGAATCTCGATGCTTACATTGGCAATGGTAGCATAACTGATGGTACC
515 TGGTTAATAACATCAGCCTGAATCTCGATGCTTACATCGGCAATGGTAACATAACTAATGGCACC
* *
1363080 ACTGTTGGTGTATGGGAATGGAATGGCGGAGACAACCAAATATGGAAGATTGAACCAAATACTGT
580 ACTATTGGTGTATGGGAATGGAATGCCGGAGACAACCAAATATGGAAGATTGAACCAAATACTGT
1363145 GAAAATTCACA
645 GAAAATTCACA
* * *
1363156 GTAAGGCCGATCCTAATTATAATCTTACCATAAGACAAGGTAAGGTTGTTCTTGCTCCATCTGAT
1 GTAAGGCCAATCCTAATTATAATCTTACCATAAGACAAGGTAAGGTTATTCTTGCTCCATCTAAT
*
1363221 CCCT-CTGATGAATTCCAGG-TA-C-CAT-T-CACTTAATCTCGTTTTTCTAAACCTTTTGAGTG
66 -CCTAATGATGAATTCCAGGATATCACATATCCACTTAATCTCGTTTTTCTAAACCTTTTGAGTG
* **
1363280 CTATAACTTAAGATTAAAGG-AAAACACGGGTCTTAGTTTGATTTTGATGTAAATCTTTGTTGTT
130 CTAAAACTTAAGATT-AAGGAAAAACACGAATCTTAGTTTGATTTTGATGTAAATCTTTGTTGTT
* * * *
1363344 GTTTTAGGTCTGGTATAAAGATGAGAAGTACGGCTCAAGTGTGAAAGATG-ATGAGGGTTTCCCC
194 GTTTTAGCTCTGGTATAAAGATGAGAAGTACAGCTCAACTGTGAAAGATGAAT-ACGGTTTCCCC
* * *
1363408 AGTTTTTCTCTGATTAATAAAG-TCACTGATGAAGCCATCAAACATGCCCTTGGAGCATCT-TTG
258 AGTTTTTCTCTGATTAATAAAGCT-ACTGATGAAGCCATCAAACATGCCATTGGAGCAACTCAT-
* * * * * * *
1363471 CCTGTATGAAATTCTTCATTTGTTCATTC-CTCTGCTTTTGAAAAAATACGTTTGGAACTTATTA
321 CCCGTAAGAAATGCTTCATTTATTCATACAAT-TG---TTAAAAAAAT-CGTTTGGAA--T-TTA
* *
1363535 GCCTTAAATCTTAATTTGCTTAAAAATTAAAAGATTTTGATCCGCAGGTCCAACTGGCACCCTAC
378 GCCTTAAA--GT--TTTGCTTAAAAATTAAAAGATTTTGATCCGCAGGTCCAACTCGCACCCTAC
* * * *
1363600 CAATCAGACGTTTTGGACGAGTCTGTATTATGGAGCGCGTCCAATGAAGTCAGGGATGGCTACAA
439 AAACCAGACGTTCTGGACGAGTCTGTATTATGGAGCGCGTCAAATGAAGTCAGGGATGGCTACAA
* *
1363665 AGCCATACGTATGGTTAATAACACTCA-CCTGAATCTCGATGCTTTCATCGGCAGTGGTAACATT
504 AGCCATACGTATGGTTAATAACA-TCAGCCTGAATCTCGATGCTTACATCGGCAATGGTAACA-T
* * *
1363729 TA-TAATGGCATCACTATTGGTGTATGGGAATGGAATGCCGGAGACAACCAAATATGGATGATTG
567 AACTAATGGCACCACTATTGGTGTATGGGAATGGAATGCCGGAGACAACCAAATATGGAAGATTG
*
1363793 TACCAAAT
632 AACCAAAT
1363801 TGTAAGTTTC
Statistics
Matches: 548, Mismatches: 78, Indels: 38
0.83 0.12 0.06
Matches are distributed among these distances:
649 5 0.01
650 207 0.38
651 3 0.01
652 1 0.00
653 12 0.02
654 8 0.01
655 1 0.00
656 3 0.01
657 11 0.02
659 1 0.00
661 289 0.53
662 7 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (655 bp):
GTAAGGCCAATCCTAATTATAATCTTACCATAAGACAAGGTAAGGTTATTCTTGCTCCATCTAAT
CCTAATGATGAATTCCAGGATATCACATATCCACTTAATCTCGTTTTTCTAAACCTTTTGAGTGC
TAAAACTTAAGATTAAGGAAAAACACGAATCTTAGTTTGATTTTGATGTAAATCTTTGTTGTTGT
TTTAGCTCTGGTATAAAGATGAGAAGTACAGCTCAACTGTGAAAGATGAATACGGTTTCCCCAGT
TTTTCTCTGATTAATAAAGCTACTGATGAAGCCATCAAACATGCCATTGGAGCAACTCATCCCGT
AAGAAATGCTTCATTTATTCATACAATTGTTAAAAAAATCGTTTGGAATTTAGCCTTAAAGTTTT
GCTTAAAAATTAAAAGATTTTGATCCGCAGGTCCAACTCGCACCCTACAAACCAGACGTTCTGGA
CGAGTCTGTATTATGGAGCGCGTCAAATGAAGTCAGGGATGGCTACAAAGCCATACGTATGGTTA
ATAACATCAGCCTGAATCTCGATGCTTACATCGGCAATGGTAACATAACTAATGGCACCACTATT
GGTGTATGGGAATGGAATGCCGGAGACAACCAAATATGGAAGATTGAACCAAATACTGTGAAAAT
TCACA
Found at i:1370519 original size:33 final size:35
Alignment explanation
Indices: 1370477--1370543 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 35
1370467 CCGAAAGACT
*
1370477 ATTTTATAACTTTTAATCA-TGGG-GACTCCACAC
1 ATTTTATAACTTTTAATAATTGGGAGACTCCACAC
1370510 ATTTTATAACTTTTAATAATTGGGAGACTCCACA
1 ATTTTATAACTTTTAATAATTGGGAGACTCCACA
1370544 AAATAGTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 18 0.58
34 4 0.13
35 9 0.29
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (35 bp):
ATTTTATAACTTTTAATAATTGGGAGACTCCACAC
Found at i:1375144 original size:21 final size:20
Alignment explanation
Indices: 1375058--1375215 Score: 88
Period size: 21 Copynumber: 7.8 Consensus size: 20
1375048 AAATGACCAA
**
1375058 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1375077 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1375097 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1375117 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1375138 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1375159 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
*
1375179 CCAAAATCGCAACGCGAATATT
1 -CAAAATCGCAACGCG-ATTTT
1375201 -AAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1375216 ACACATAAAT
Statistics
Matches: 105, Mismatches: 27, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 17 0.16
20 40 0.38
21 44 0.42
22 4 0.04
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1375206 original size:20 final size:20
Alignment explanation
Indices: 1375118--1375234 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
1375108 ATCAGTTTCC
* *
1375118 AAAATCGCAACGCGATTCTT
1 AAAATCGCAACGCGAATATT
* *
1375138 GAAAATCGCAATGCG-ATAGT
1 -AAAATCGCAACGCGAATATT
** *
1375158 ACAAATTCGCATTGCG-ATTTT
1 A-AAA-TCGCAACGCGAATATT
1375179 CCAAAATCGCAACGCGAATATT
1 --AAAATCGCAACGCGAATATT
* *
1375201 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATT
1375220 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
1375235 TATCCGTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
20 35 0.45
21 33 0.42
22 7 0.09
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATT
Found at i:1375244 original size:20 final size:20
Alignment explanation
Indices: 1375202--1375451 Score: 254
Period size: 20 Copynumber: 12.5 Consensus size: 20
1375192 GCGAATATTA
* *
1375202 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1375222 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1375242 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1375262 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1375282 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1375302 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1375322 AAATCACAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1375342 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1375362 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1375382 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
1375402 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1375422 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1375442 AAATCACAAC
1 AAATCGCAAC
1375452 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 27, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 195 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1375246 original size:40 final size:40
Alignment explanation
Indices: 1375182--1375451 Score: 292
Period size: 40 Copynumber: 6.8 Consensus size: 40
1375172 CGATTTTCCA
* * * *
1375182 AAATCGCAACGCGAATAT-TAAAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATCTGT-AAATCGCAACGAGAATC-CGT
* * * * *
1375222 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATCCGT
* * ** * * *
1375262 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATCCGT
* * * * * *
1375302 ATATCGCAACGCGTATCCGTAAATCACAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATCCGT
*
1375342 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATCCGT
1375382 AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATCCGT
*
1375422 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCTGTAAATCGCAAC
1375452 ACTGAAATTT
Statistics
Matches: 203, Mismatches: 25, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
40 201 0.99
41 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATCCGT
Found at i:1376161 original size:24 final size:24
Alignment explanation
Indices: 1376134--1376180 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1376124 AAATTTGGTC
1376134 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
1376158 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
1376181 GATGTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:1376372 original size:12 final size:12
Alignment explanation
Indices: 1376355--1376379 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1376345 ATATAATCCT
1376355 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1376367 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1376379 G
1 G
1376380 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1378764 original size:33 final size:33
Alignment explanation
Indices: 1378660--1378767 Score: 164
Period size: 33 Copynumber: 3.2 Consensus size: 33
1378650 CGGAAATTAC
*
1378660 AATCGCAACGAGAGAATCGCAATACGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1378693 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
1378727 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1378760 AATCGCAA
1 AATCGCAA
1378768 TGCGAAATGA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
32 1 0.01
33 36 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1378765 original size:19 final size:19
Alignment explanation
Indices: 1378674--1378857 Score: 209
Period size: 19 Copynumber: 10.4 Consensus size: 19
1378664 GCAACGAGAG
*
1378674 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1378693 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1378707 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1378727 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1378741 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1378760 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1378779 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1378793 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
1378812 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1378831 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1378850 AATCGCAA
1 AATCGCAA
1378858 CGAGAGAATC
Statistics
Matches: 141, Mismatches: 8, Indels: 32
0.78 0.04 0.18
Matches are distributed among these distances:
14 32 0.23
15 2 0.01
16 4 0.03
17 4 0.03
18 3 0.02
19 83 0.59
20 13 0.09
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1378787 original size:52 final size:52
Alignment explanation
Indices: 1378702--1378838 Score: 256
Period size: 52 Copynumber: 2.6 Consensus size: 52
1378692 AAATCCCAAC
1378702 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1378755 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1378807 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1378839 TGCGAAATGA
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 67 0.81
53 16 0.19
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1378868 original size:52 final size:52
Alignment explanation
Indices: 1378704--1378879 Score: 223
Period size: 52 Copynumber: 3.4 Consensus size: 52
1378694 ATCCCAACAT
* *
1378704 GAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 GAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
* * *
1378757 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAAT
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
* * *
1378809 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAAC
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-AAATGCGAAAC
1378859 GAGAGAATCGCAATGCGAAAT
1 GA-A-AATCGCAATGCGAAAT
1378880 TATAAACGCA
Statistics
Matches: 113, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
50 6 0.05
51 7 0.06
52 86 0.76
53 14 0.12
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.14
Consensus pattern (52 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
Found at i:1378895 original size:71 final size:71
Alignment explanation
Indices: 1378741--1378879 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
1378731 GCAACGAGAG
*
1378741 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1378806 AATGAA
66 AATGAA
1378812 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1378877 AAT
66 AAT
1378880 TATAAACGCA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:1378998 original size:52 final size:53
Alignment explanation
Indices: 1378886--1379001 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
1378876 AAATTATAAA
1378886 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
*
1378939 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1378991 CGCATTGCGAT
1 CGCATTGCGAT
1379002 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:1379009 original size:19 final size:19
Alignment explanation
Indices: 1378904--1379001 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1378894 GATTATCTCG
1378904 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1378924 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1378943 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1378957 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1378976 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1378995 TTGCGAT
1 TTGCGAT
1379002 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1379127 original size:14 final size:14
Alignment explanation
Indices: 1379108--1379144 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1379098 CATCAATTAC
1379108 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1379122 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1379136 ACAAATCAA
1 ACAAATCAA
1379145 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1381109 original size:19 final size:19
Alignment explanation
Indices: 1381069--1381203 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1381059 TAGTTTACTT
* *
1381069 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1381089 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1381108 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1381127 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1381141 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1381160 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1381174 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1381193 TCGCAATGCGA
1 TCGCAACGCGA
1381204 TTTTGGTTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 8 0.08
17 8 0.08
18 1 0.01
19 49 0.51
20 12 0.12
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1381145 original size:33 final size:33
Alignment explanation
Indices: 1381103--1381198 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
1381093 AACGCGAAAC
1381103 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
*
1381136 CAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
1381169 -AAGAATCGCAACGCGAAATGAAAATCGCAA
1 CAA-AATCGCAACGCGAAATGAAAATCGCAA
1381199 TGCGATTTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 2 0.03
33 58 0.97
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (33 bp):
CAAAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1381177 original size:14 final size:14
Alignment explanation
Indices: 1381125--1381181 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
1381115 GCGAAATGAA
1381125 AATCGCAACGACAA-
1 AATCGCAACGA-AAG
1381139 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1381156 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1381172 AATCGCAACG
1 AATCGCAACG
1381182 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 18 0.49
15 2 0.05
16 4 0.11
17 5 0.14
19 8 0.22
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1381221 original size:19 final size:19
Alignment explanation
Indices: 1381199--1381327 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1381189 AAAATCGCAA
*
1381199 TGCGATTTTGGTTTTGCGT
1 TGCGATTTTGGTTTCGCGT
*
1381218 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1381232 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1381251 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1381265 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1381284 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1381303 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1381323 TGCGA
1 TGCGA
1381328 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1381241 original size:33 final size:33
Alignment explanation
Indices: 1381199--1381290 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1381189 AAAATCGCAA
*
1381199 TGCGATTTTGGTTTTGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1381232 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1381265 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1381291 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1381491 original size:93 final size:93
Alignment explanation
Indices: 1381375--1381843 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
1381365 ATGGATTGCA
1381375 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1381439 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1381467 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1381532 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
1381560 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACTGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1381625 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1381653 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1381718 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1381746 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1381811 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1381839 TTACT
1 TTACT
1381844 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 369 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1383569 original size:14 final size:14
Alignment explanation
Indices: 1383550--1383639 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1383540 TTGAAATGAA
1383550 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1383564 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
1383583 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1383597 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1383616 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1383630 AATCGCAACG
1 AATCGCAACG
1383640 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1383587 original size:33 final size:33
Alignment explanation
Indices: 1383542--1383656 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1383532 TCTTTTGGTT
1383542 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1383575 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1383608 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1383641 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1383657 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1383588 original size:19 final size:19
Alignment explanation
Indices: 1383564--1383661 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1383554 GCAACGAGAG
*
1383564 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
1383583 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1383597 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1383616 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1383630 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1383649 AATCGCAATGCGA
1 AATCGCAACGCGA
1383662 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1383692 original size:14 final size:14
Alignment explanation
Indices: 1383673--1383729 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1383663 TTTGGTTTCG
1383673 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1383687 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1383706 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1383720 CGTTGCGATT
1 CGTTGCGATT
1383730 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:1383705 original size:33 final size:33
Alignment explanation
Indices: 1383657--1383737 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1383647 AAAATCGCAA
**
1383657 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1383690 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1383723 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1383738 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1383740 original size:21 final size:21
Alignment explanation
Indices: 1383714--1383789 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1383704 CGCGTTGCGA
1383714 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1383735 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1383755 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1383776 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1383790 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1383770 original size:41 final size:41
Alignment explanation
Indices: 1383713--1383790 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1383703 TCGCGTTGCG
*
1383713 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1383754 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1383791 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1383911 original size:33 final size:33
Alignment explanation
Indices: 1383869--1383939 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1383859 AATACTAACT
*
1383869 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1383902 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1383935 TGAAA
1 TGAAA
1383940 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1384173 original size:22 final size:22
Alignment explanation
Indices: 1384121--1384175 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1384111 TGGTTGTGAG
** *
1384121 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATCGGGAC
**
1384143 GGAAATCTTCGGAGATCGGGAC
1 GGATTTCTTCGGAGATCGGGAC
1384165 GGATTTCTTCG
1 GGATTTCTTCG
1384176 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATCGGGAC
Found at i:1384347 original size:20 final size:20
Alignment explanation
Indices: 1384322--1384515 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1384312 CTTTAAATAT
1384322 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1384342 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1384364 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1384383 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1384403 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1384423 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1384443 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1384463 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1384483 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1384503 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1384516 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1384509 original size:60 final size:60
Alignment explanation
Indices: 1384322--1384515 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1384312 CTTTAAATAT
**
1384322 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1384383 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1384443 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1384503 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1384516 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1384532 original size:21 final size:21
Alignment explanation
Indices: 1384502--1384584 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1384492 ATTTTCATAT
*
1384502 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1384523 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1384544 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1384565 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1384585 CTAATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1384575 original size:42 final size:43
Alignment explanation
Indices: 1384482--1384580 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1384472 ATTTATGTGT
* *
1384482 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1384523 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1384565 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1384581 GAAACTAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1387959 original size:3 final size:3
Alignment explanation
Indices: 1387944--1387978 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1387934 TTAGTTCGAT
*
1387944 ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1387979 GCAACGTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.