Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008213.1 Hibiscus syriacus cultivar Beakdansim tig00110839_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: 2348840
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:2107031 original size:24 final size:23
Alignment explanation
Indices: 2106960--2107033 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 23
2106950 CATAGTCTTG
* *
2106960 TGCATTGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
2106983 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
2107004 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
2107028 TGCATC
1 TGCATC
2107034 AATGTATTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
20 4 0.10
21 13 0.32
23 10 0.25
24 11 0.28
25 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:2111611 original size:18 final size:17
Alignment explanation
Indices: 2111557--2111605 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2111547 TTGGACTCCT
* *
2111557 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2111575 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2111593 AGTGCATTCGATG
1 AGTGCA-TCGATG
2111606 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2111681 original size:55 final size:56
Alignment explanation
Indices: 2111622--2111767 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 56
2111612 AAATAGCCTG
2111622 GTGCATCGATGCATGGATTGTGCATCG-ATGCATTCGATGTTTTAATTAAATCAGA
1 GTGCATCGATGCATGGATTGTGCATCGAATGCATTCGATGTTTTAATTAAATCAGA
*
2111677 GTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTTAATTAAATCAGA
1 GTGCATCGATGCAT-G-GA-T---T--GTGCATCGAATGCATTCGATGTTTTAATTAAATCAGA
**
2111741 GTGCATCGATGCATGGAGAGTGCATCG
1 GTGCATCGATGCATGGATTGTGCATCG
2111768 GAGCATGGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
55 14 0.18
56 8 0.10
57 2 0.03
58 1 0.01
61 1 0.01
62 2 0.03
63 8 0.10
64 42 0.54
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (56 bp):
GTGCATCGATGCATGGATTGTGCATCGAATGCATTCGATGTTTTAATTAAATCAGA
Found at i:2111688 original size:36 final size:36
Alignment explanation
Indices: 2111641--2111754 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
2111631 TGCATGGATT
2111641 GTGCATCGATGCATTCGATGTTTTAATTAAATCAGA
1 GTGCATCGATGCATTCGATGTTTTAATTAAATCAGA
* * **
2111677 GTGCATCGATGCA-TGGA-G-----AGTGCATC-G-
1 GTGCATCGATGCATTCGATGTTTTAATTAAATCAGA
*
2111704 GTGCATGGAATGCATTCGATGTTTTAATTAAATCAGA
1 GTGCATCG-ATGCATTCGATGTTTTAATTAAATCAGA
2111741 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2111755 GGAGAGTGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 20
0.66 0.11 0.23
Matches are distributed among these distances:
27 7 0.12
28 6 0.10
29 8 0.14
30 1 0.02
34 1 0.02
35 8 0.14
36 20 0.34
37 7 0.12
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (36 bp):
GTGCATCGATGCATTCGATGTTTTAATTAAATCAGA
Found at i:2111698 original size:19 final size:19
Alignment explanation
Indices: 2111674--2111724 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2111664 TAATTAAATC
2111674 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2111693 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2111712 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2111725 TTTTAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2111717 original size:64 final size:64
Alignment explanation
Indices: 2111641--2111796 Score: 278
Period size: 64 Copynumber: 2.5 Consensus size: 64
2111631 TGCATGGATT
*
2111641 GTGCATCG-ATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGAGTGCATCG
1 GTGCATGGAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGAGTGCATCG
2111704 GTGCATGGAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGAGTGCATCG
1 GTGCATGGAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGAGTGCATCG
* *
2111768 GAGCATGGAATGCATTCGATGTTTCAATT
1 GTGCATGGAATGCATTCGATGTTTTAATT
2111797 TATTCATTGA
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 7 0.08
64 82 0.92
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (64 bp):
GTGCATGGAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGAGTGCATCG
Found at i:2111762 original size:19 final size:19
Alignment explanation
Indices: 2111738--2111788 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2111728 TAATTAAATC
2111738 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
2111757 AGAGTGCATCGGA-GCATGG
1 AGAGTGCATC-GATGCATGG
2111776 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2111789 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.21
18 4 0.14
19 17 0.59
20 2 0.07
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2111848 original size:21 final size:21
Alignment explanation
Indices: 2111802--2111842 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2111792 CAATTTATTC
*
2111802 ATTGATTCATCGATGCATGCT
1 ATTGATGCATCGATGCATGCT
*
2111823 ATTGATGCATCGGTGCATGC
1 ATTGATGCATCGATGCATGC
2111843 CTTTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGCT
Found at i:2114788 original size:17 final size:17
Alignment explanation
Indices: 2114754--2114805 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2114744 ACTGGACAAA
* *
2114754 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
2114771 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
2114788 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
2114803 TTT
1 TTT
2114806 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:2116226 original size:18 final size:17
Alignment explanation
Indices: 2116201--2116251 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
2116191 ACCCGTTTAC
2116201 CCGTTTACCCGACCCGA
1 CCGTTTACCCGACCCGA
2116218 CCAGTTTACCCGACCCGA
1 CC-GTTTACCCGACCCGA
*
2116236 CCGTTGACCCGACCCG
1 CCGTTTACCCGACCCG
2116252 TTGACCGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (17 bp):
CCGTTTACCCGACCCGA
Found at i:2116254 original size:13 final size:12
Alignment explanation
Indices: 2116229--2116271 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
2116219 CAGTTTACCC
2116229 GACCCGACCGTT
1 GACCCGACCGTT
2116241 GACCCGACCCGTT
1 GACCCGA-CCGTT
*
2116254 GACCGTTGACCGTT
1 GACC--CGACCGTT
2116268 GACC
1 GACC
2116272 GTTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 9 0.33
15 2 0.07
ACGTcount: A:0.16, C:0.40, G:0.26, T:0.19
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:2116259 original size:7 final size:7
Alignment explanation
Indices: 2116249--2116279 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2116239 TTGACCCGAC
2116249 CCGTTGA
1 CCGTTGA
2116256 CCGTTGA
1 CCGTTGA
2116263 CCGTTGA
1 CCGTTGA
2116270 CCGTTGA
1 CCGTTGA
2116277 CCG
1 CCG
2116280 GTGCTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:2116340 original size:29 final size:29
Alignment explanation
Indices: 2116279--2116345 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
2116269 ACCGTTGACC
*** *
2116279 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATA
2116308 GGTGCTATTCTGGGAATTAATTCGAAATA
1 GGTGCTATTCTGGGAATTAATTCGAAATA
2116337 GGTGCTATT
1 GGTGCTATT
2116346 TTAGTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATA
Found at i:2116354 original size:29 final size:28
Alignment explanation
Indices: 2116279--2116362 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 28
2116269 ACCGTTGACC
* *** *
2116279 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTAGGAATT-ATTCGAAATA
*
2116308 GGTGCTATTCTGGGAATTAATTCGAAATA
1 GGTGCTATTCTAGGAATT-ATTCGAAATA
* * *
2116337 GGTGCTATTTTAGTAATTTTTCGAAA
1 GGTGCTATTCTAGGAATTATTCGAAA
2116363 AAAATAATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 7 0.15
29 40 0.85
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.42
Consensus pattern (28 bp):
GGTGCTATTCTAGGAATTATTCGAAATA
Found at i:2123484 original size:20 final size:19
Alignment explanation
Indices: 2123445--2123495 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
2123435 ACTGGAAACT
2123445 GGTTTTGACCGGTTTAACC
1 GGTTTTGACCGGTTTAACC
* *
2123464 GGTTTTGAACCGTTTTGACC
1 GGTTTTG-ACCGGTTTAACC
2123484 GG-TTTGACCGGT
1 GGTTTTGACCGGT
2123496 CACGACCCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 12 0.43
ACGTcount: A:0.14, C:0.20, G:0.29, T:0.37
Consensus pattern (19 bp):
GGTTTTGACCGGTTTAACC
Found at i:2123505 original size:29 final size:29
Alignment explanation
Indices: 2123446--2123507 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2123436 CTGGAAACTG
***
2123446 GTTTTGACCGGTTTAACCGGTTTTGAACC
1 GTTTTGACCGGTTTAACCGGTCACGAACC
* *
2123475 GTTTTGACCGGTTTGACCGGTCACGACCC
1 GTTTTGACCGGTTTAACCGGTCACGAACC
2123504 GTTT
1 GTTT
2123508 ACCCGTTTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (29 bp):
GTTTTGACCGGTTTAACCGGTCACGAACC
Found at i:2123535 original size:18 final size:17
Alignment explanation
Indices: 2123512--2123560 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
2123502 CCGTTTACCC
2123512 GTTTACCCGACCCGACCA
1 GTTTACCCGACCCGA-CA
*
2123530 GTTTACCCGACCCGACT
1 GTTTACCCGACCCGACA
*
2123547 GTTGACCCGACCCG
1 GTTTACCCGACCCG
2123561 TTGACCGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.18, C:0.43, G:0.20, T:0.18
Consensus pattern (17 bp):
GTTTACCCGACCCGACA
Found at i:2123556 original size:17 final size:18
Alignment explanation
Indices: 2123516--2123560 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
2123506 TTACCCGTTT
*
2123516 ACCCGACCCGACCAGTTT
1 ACCCGACCCGACCAGTTG
*
2123534 ACCCGACCCGA-CTGTTG
1 ACCCGACCCGACCAGTTG
2123551 ACCCGACCCG
1 ACCCGACCCG
2123561 TTGACCGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCAGTTG
Found at i:2123635 original size:29 final size:29
Alignment explanation
Indices: 2123574--2123640 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
2123564 ACCGTTGACC
*** *
2123574 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATA
2123603 GGTGCTATTCTGGGAATTAATTCGAAATA
1 GGTGCTATTCTGGGAATTAATTCGAAATA
2123632 GGTGCTATT
1 GGTGCTATT
2123641 TTAGTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATA
Found at i:2123698 original size:29 final size:29
Alignment explanation
Indices: 2123575--2123698 Score: 92
Period size: 29 Copynumber: 4.3 Consensus size: 29
2123565 CCGTTGACCG
* **** *
2123575 GTGCTATTCTGGGAATTAATTCGGTTTTG
1 GTGCTATTTTGGGAATTAATTCGAAAATA
*
2123604 GTGCTATTCTGGGAATTAATTCG-AAATA
1 GTGCTATTTTGGGAATTAATTCGAAAATA
* * *
2123632 GGTGCTATTTTAGTAATT-TTTCGCAAAA-A
1 -GTGCTATTTTGGGAATTAATTCG-AAAATA
* **
2123661 ATAATATTTTGGGAATTAATTCGAAAATA
1 GTGCTATTTTGGGAATTAATTCGAAAATA
2123690 GTGCTATTT
1 GTGCTATTT
2123699 GTGTAAAATG
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
28 21 0.29
29 49 0.67
30 3 0.04
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (29 bp):
GTGCTATTTTGGGAATTAATTCGAAAATA
Found at i:2132198 original size:16 final size:16
Alignment explanation
Indices: 2132177--2132207 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2132167 GTGCATTGTA
2132177 TTAAAAAATAAAAATT
1 TTAAAAAATAAAAATT
*
2132193 TTAAAAACTAAAAAT
1 TTAAAAAATAAAAAT
2132208 AGATTTATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAAAATAAAAATT
Found at i:2136539 original size:9 final size:9
Alignment explanation
Indices: 2136525--2136551 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2136515 ATAACTGGAA
2136525 AACCGGTTT
1 AACCGGTTT
2136534 AACCGGTTT
1 AACCGGTTT
2136543 AACCGGTTT
1 AACCGGTTT
2136552 TGAATCGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (9 bp):
AACCGGTTT
Found at i:2136601 original size:22 final size:22
Alignment explanation
Indices: 2136561--2136603 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2136551 TTGAATCGGT
*
2136561 CCGACCCGACCCGATTGTTGAG
1 CCGACCCGACCCGACTGTTGAG
**
2136583 CCGACCCGACTTGACTGTTGA
1 CCGACCCGACCCGACTGTTGA
2136604 CCGTTGATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.21
Consensus pattern (22 bp):
CCGACCCGACCCGACTGTTGAG
Found at i:2151218 original size:27 final size:27
Alignment explanation
Indices: 2151169--2151221 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2151159 TATAGGATCT
*
2151169 CTAAATTATAATTATTTTCGTTAAGAG
1 CTAAATTAAAATTATTTTCGTTAAGAG
*
2151196 CTAATATTAAAATTA-TTTGGTTAAGA
1 CTAA-ATTAAAATTATTTTCGTTAAGA
2151222 AATTACGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (27 bp):
CTAAATTAAAATTATTTTCGTTAAGAG
Found at i:2152631 original size:24 final size:24
Alignment explanation
Indices: 2152604--2152690 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
2152594 TTCAATTTGA
* *
2152604 ATTCTAATATGATATTTGACATGG
1 ATTCTGATCTGATATTTGACATGG
* *
2152628 ATTCTGATCTGATATCTGAAATGG
1 ATTCTGATCTGATATTTGACATGG
* *
2152652 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATATTTGACATGG
*
2152676 ATTTTGATCTGATAT
1 ATTCTGATCTGATAT
2152691 CTGAAACAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (24 bp):
ATTCTGATCTGATATTTGACATGG
Found at i:2152656 original size:48 final size:48
Alignment explanation
Indices: 2152604--2152696 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
2152594 TTCAATTTGA
*
2152604 ATTCTAATATGATATTTGACATGGATTCTGATCTGATATCTGAAATGG
1 ATTCTAATATGATACTTGACATGGATTCTGATCTGATATCTGAAATGG
* * * *
2152652 ATTCTGATCTGATACTTGACTTGGATTTTGATCTGATATCTGAAA
1 ATTCTAATATGATACTTGACATGGATTCTGATCTGATATCTGAAA
2152697 CAACACCAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (48 bp):
ATTCTAATATGATACTTGACATGGATTCTGATCTGATATCTGAAATGG
Found at i:2162238 original size:28 final size:28
Alignment explanation
Indices: 2162198--2162253 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2162188 GAAGGACAAG
2162198 ATATGTAAAACACGTTGGAGTGCAACGA
1 ATATGTAAAACACGTTGGAGTGCAACGA
2162226 ATATGTAAAACACGTTGGAGTGCAACGA
1 ATATGTAAAACACGTTGGAGTGCAACGA
2162254 TGGAATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (28 bp):
ATATGTAAAACACGTTGGAGTGCAACGA
Found at i:2194718 original size:12 final size:11
Alignment explanation
Indices: 2194703--2194736 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
2194693 TTCAATTCTG
2194703 TTATATTTTTTT
1 TTAT-TTTTTTT
2194715 TTATTTTTTCTT
1 TTATTTTTT-TT
2194727 TTATTTTTTT
1 TTATTTTTTT
2194737 CCCGATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:2195930 original size:18 final size:18
Alignment explanation
Indices: 2195907--2195948 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2195897 TTGACCGGTT
*
2195907 TTGACCCGACCCAACCCG
1 TTGACCAGACCCAACCCG
*
2195925 TTGACCAGACCCGACCCG
1 TTGACCAGACCCAACCCG
2195943 TTGACC
1 TTGACC
2195949 GTTGACCAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.45, G:0.19, T:0.14
Consensus pattern (18 bp):
TTGACCAGACCCAACCCG
Found at i:2195991 original size:29 final size:29
Alignment explanation
Indices: 2195957--2196012 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2195947 CCGTTGACCA
* *
2195957 GGTGACATTTTAGT-AATTATTTTGAAACT
1 GGTGACATATT-GTGAATTAATTTGAAACT
2195986 GGTGACATATTGTGAATTAATTTGAAA
1 GGTGACATATTGTGAATTAATTTGAAA
2196013 AGGGTGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (29 bp):
GGTGACATATTGTGAATTAATTTGAAACT
Found at i:2196093 original size:28 final size:26
Alignment explanation
Indices: 2196027--2196112 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
2196017 TGTTATTTTT
* *
2196027 TAATTTTTTAAAAAATGCTATTTTCG
1 TAATTTTTGAAAAAATGCTATTTTAG
2196053 TAATTTTTGGAAAAAATGAC-ATTTTAG
1 TAATTTTT-GAAAAAATG-CTATTTTAG
** * *
2196080 TAAATATTTTGAAAATGTGCTATATTGG
1 T-AAT-TTTTGAAAAAATGCTATTTTAG
2196108 TAATT
1 TAATT
2196113 AATTTTAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
26 9 0.18
27 19 0.39
28 17 0.35
29 4 0.08
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (26 bp):
TAATTTTTGAAAAAATGCTATTTTAG
Found at i:2196161 original size:109 final size:110
Alignment explanation
Indices: 2195959--2196164 Score: 267
Period size: 109 Copynumber: 1.9 Consensus size: 110
2195949 GTTGACCAGG
* *
2195959 TGACATTTTAGTAATTATTTTGAAACTGGTGACATATTGTGAATTAATTTGAAAAGGGTGTTATT
1 TGACATTTTAGTAAATATTTTGAAAATGGTGACATATTGTGAATTAATTTGAAAAGGGTGTTATT
* ** * *
2196024 TTTTAATTTTTTAAAAAATGCTATTTTCGTAATTTTTGGAAAAAA
66 TTATAATTTTAAAAAAAATACTAATTTCGTAATTTTTGGAAAAAA
* *
2196069 TGACATTTTAGTAAATATTTTGAAAAT-GTG-CTATATTG-GTAATTAATTTTAAAATGGTGTTA
1 TGACATTTTAGTAAATATTTTGAAAATGGTGAC-ATATTGTG-AATTAATTTGAAAAGGGTGTTA
*
2196131 TTTTCATAA-TTTAAAAAAAATATTAATTTCGTAA
64 TTTT-ATAATTTTAAAAAAAATACTAATTTCGTAA
2196165 AATGGTTTAC
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
108 2 0.02
109 53 0.64
110 28 0.34
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (110 bp):
TGACATTTTAGTAAATATTTTGAAAATGGTGACATATTGTGAATTAATTTGAAAAGGGTGTTATT
TTATAATTTTAAAAAAAATACTAATTTCGTAATTTTTGGAAAAAA
Found at i:2197503 original size:17 final size:19
Alignment explanation
Indices: 2197478--2197516 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2197468 ATATTTGTAT
2197478 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
2197496 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
2197515 TA
1 TA
2197517 AGTTTGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:2200990 original size:19 final size:19
Alignment explanation
Indices: 2200966--2201003 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2200956 CACTACTTTT
2200966 ATCCAATCACCAAAATGTG
1 ATCCAATCACCAAAATGTG
2200985 ATCCAATCACCAAAATGTG
1 ATCCAATCACCAAAATGTG
2201004 TAGGTTCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (19 bp):
ATCCAATCACCAAAATGTG
Found at i:2201102 original size:43 final size:40
Alignment explanation
Indices: 2201039--2201242 Score: 207
Period size: 41 Copynumber: 4.8 Consensus size: 40
2201029 CTATACACCA
* *
2201039 GTAAGGCTTAACGTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACAAAGCAAAGGGA-CCT-GG-AAACT
*
2201083 GTAAGGTTTATCCTTGCACACAA-CAAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACA-AAGC-AAAGGGACCT-GGAAACT
2201126 GTAAGGCTTACCCTTGCACACAA-CAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACA-AAGCAAAGGGACCTGG-AAACT
* *
2201168 GTAAGGCTTACCTTCGCACATAGCAAAGGAACCTGGAAACT
1 GTAAGGCTTACCTT-GCACAAAGCAAAGGGACCTGGAAACT
*
2201209 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCT
1 GTAAGGCTTACCTT-GCACAAAGCAAAGGGACCT
2201243 AATAATACTT
Statistics
Matches: 143, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
41 44 0.31
42 42 0.29
43 35 0.24
44 19 0.13
45 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.19
Consensus pattern (40 bp):
GTAAGGCTTACCTTGCACAAAGCAAAGGGACCTGGAAACT
Found at i:2201167 original size:42 final size:41
Alignment explanation
Indices: 2201078--2201242 Score: 226
Period size: 41 Copynumber: 4.0 Consensus size: 41
2201068 GAGCCTAGGA
*
2201078 AAACTGTAAGGTTTATCCTT-GCACACAACAAAAGGGACCTGGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAAC-AAAGGGACCT-GG
2201121 AAACTGTAAGGCTTACCCTT-GCACACAACAAAGGGACCTGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCTGG
* * *
2201162 TAAACTGTAAGGCTTACCTTCGCACATAGCAAAGGAACCTGG
1 -AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGG
*
2201204 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCT
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCT
2201243 AATAATACTT
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
41 43 0.38
42 43 0.38
43 27 0.24
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (41 bp):
AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGG
Found at i:2201217 original size:83 final size:85
Alignment explanation
Indices: 2201078--2201242 Score: 239
Period size: 83 Copynumber: 2.0 Consensus size: 85
2201068 GAGCCTAGGA
* *
2201078 AAACTGTAAGGTTTATCCTTGCACACAACAAAAGGGACCTGGGAAACTGTAAGGCTTACCCTT-G
1 AAACTGTAAGGCTTATCCTTGCACACAACAAAAGGAACCTGGGAAACTGTAAGGCTTA-CCTTCG
2201142 CACACAACAAAGGGACCTGGT
65 CACACAACAAAGGGACCTGGT
* *
2201163 AAACTGTAAGGCTTA-CCTTCGCACATAGC-AAAGGAACCT-GGAAACTGTAAGGCTTACCTTCG
1 AAACTGTAAGGCTTATCCTT-GCACACAACAAAAGGAACCTGGGAAACTGTAAGGCTTACCTTCG
*
2201225 CACACAGCAAAGGGACCT
65 CACACAACAAAGGGACCT
2201243 AATAATACTT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
82 4 0.05
83 35 0.48
84 13 0.18
85 21 0.29
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (85 bp):
AAACTGTAAGGCTTATCCTTGCACACAACAAAAGGAACCTGGGAAACTGTAAGGCTTACCTTCGC
ACACAACAAAGGGACCTGGT
Found at i:2201220 original size:41 final size:43
Alignment explanation
Indices: 2201039--2201243 Score: 208
Period size: 42 Copynumber: 4.8 Consensus size: 43
2201029 CTATACACCA
* * * *
2201039 GTAAGGCTTAACGTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCTAGGAAAACT
* * * *
2201083 GTAAGGTTTATCCTTGCACACAACAAAAGGGACCT-GGGAAACT
1 GTAAGGCTTACCCTTGCACACAGC-AAAGGGACCTAGGAAAACT
* *
2201126 GTAAGGCTTACCCTTGCACACAACAAAGGGACCT-GGTAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGAAAACT
* *
2201168 GTAAGGCTTA-CCTTCGCACATAGCAAAGGAACCT-GG-AAACT
1 GTAAGGCTTACCCTT-GCACACAGCAAAGGGACCTAGGAAAACT
2201209 GTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTA
1 GTAAGGCTTACCCTT-GCACACAGCAAAGGGACCTA
2201244 ATAATACTTC
Statistics
Matches: 142, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
41 41 0.29
42 45 0.32
43 37 0.26
44 16 0.11
45 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (43 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGAAAACT
Found at i:2202267 original size:28 final size:29
Alignment explanation
Indices: 2202197--2202300 Score: 131
Period size: 29 Copynumber: 3.6 Consensus size: 29
2202187 TTTTTTTTAA
*
2202197 AATTAATTACCAAAATAGCACCT-TTTTCG
1 AATTAATTCCCAAAATAGCACCTATTTT-G
** *
2202226 AATTAATTTACAAAATAG-AACTATTTTG
1 AATTAATTCCCAAAATAGCACCTATTTTG
* *
2202254 AATTAATTCCCAAAATAGCACCCATTTCG
1 AATTAATTCCCAAAATAGCACCTATTTTG
2202283 AATTAATTCCCAAAATAG
1 AATTAATTCCCAAAATAG
2202301 TACACAGTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
28 20 0.31
29 45 0.69
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (29 bp):
AATTAATTCCCAAAATAGCACCTATTTTG
Found at i:2208559 original size:42 final size:41
Alignment explanation
Indices: 2208468--2208634 Score: 239
Period size: 41 Copynumber: 4.0 Consensus size: 41
2208458 GATGAGCCTA
*
2208468 GGAAACTGTAAGGTTTATCCTT-GCACACAACAAAAGGGACCT
1 GGAAACTGTAAGGCTTA-CCTTCGCACACAAC-AAAGGGACCT
2208510 GGGAAACTGTAAGGCTTACCCTT-GCACACAACAAAGGGACCT
1 -GGAAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCT
* *
2208552 GGTAAACTGTAAGGCTTACCTTCGCACACAGCAAAGGAACCT
1 GG-AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCT
*
2208594 GGAAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCT
1 GGAAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCT
2208635 AATAATACTT
Statistics
Matches: 117, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
41 44 0.38
42 44 0.38
43 29 0.25
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (41 bp):
GGAAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCT
Found at i:2208611 original size:83 final size:85
Alignment explanation
Indices: 2208470--2208634 Score: 248
Period size: 83 Copynumber: 2.0 Consensus size: 85
2208460 TGAGCCTAGG
* *
2208470 AAACTGTAAGGTTTATCCTTGCACACAACAAAAGGGACCTGGGAAACTGTAAGGCTTACCCTT-G
1 AAACTGTAAGGCTTATCCTTGCACACAACAAAAGGAACCTGGGAAACTGTAAGGCTTA-CCTTCG
2208534 CACACAACAAAGGGACCTGGT
65 CACACAACAAAGGGACCTGGT
*
2208555 AAACTGTAAGGCTTA-CCTTCGCACACAGC-AAAGGAACCT-GGAAACTGTAAGGCTTACCTTCG
1 AAACTGTAAGGCTTATCCTT-GCACACAACAAAAGGAACCTGGGAAACTGTAAGGCTTACCTTCG
*
2208617 CACACAGCAAAGGGACCT
65 CACACAACAAAGGGACCT
2208635 AATAATACTT
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
82 4 0.05
83 35 0.47
84 13 0.18
85 22 0.30
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (85 bp):
AAACTGTAAGGCTTATCCTTGCACACAACAAAAGGAACCTGGGAAACTGTAAGGCTTACCTTCGC
ACACAACAAAGGGACCTGGT
Found at i:2209620 original size:29 final size:28
Alignment explanation
Indices: 2209585--2209683 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
2209575 TTTTTAAAAA
2209585 TAATTACCAAAATAGCACATTTTTGAAT
1 TAATTACCAAAATAGCACATTTTTGAAT
*
2209613 TAATTTA-CAAAATAGCAC-TATTTTAAAT
1 TAA-TTACCAAAATAGCACAT-TTTTGAAT
*
2209641 TAATTCCCAAAATAGCACCCA-TTTTGAAT
1 TAATTACCAAAATAGCA--CATTTTTGAAT
*
2209670 TAATTCCCAAAATA
1 TAATTACCAAAATA
2209684 ACACTAGGTC
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
27 3 0.05
28 34 0.55
29 24 0.39
30 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (28 bp):
TAATTACCAAAATAGCACATTTTTGAAT
Found at i:2209671 original size:57 final size:57
Alignment explanation
Indices: 2209564--2209689 Score: 157
Period size: 57 Copynumber: 2.2 Consensus size: 57
2209554 CATTTTATAG
* *
2209564 AAATAGCACCTTTTTTAAAAATAATTACCAAAATAGCACATTTTTGAATTAATTTACA
1 AAATAGCA-CTATTTTAAAAATAATTACCAAAATAGCACATTTTTGAATTAATTCACA
* * *
2209622 AAATAGCACTATTTT-AAATTAATTCCCAAAATAGCACCCA-TTTTGAATTAATTCCCA
1 AAATAGCACTATTTTAAAAATAATTACCAAAATAGCA--CATTTTTGAATTAATTCACA
*
2209679 AAATAACACTA
1 AAATAGCACTA
2209690 GGTCAACGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
56 19 0.32
57 31 0.52
58 10 0.17
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.33
Consensus pattern (57 bp):
AAATAGCACTATTTTAAAAATAATTACCAAAATAGCACATTTTTGAATTAATTCACA
Found at i:2209712 original size:17 final size:18
Alignment explanation
Indices: 2209690--2209723 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2209680 AATAACACTA
2209690 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
2209707 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
2209724 AAAACCGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:2209718 original size:13 final size:13
Alignment explanation
Indices: 2209700--2209725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2209690 GGTCAACGGT
2209700 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
2209713 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
2209726 AACCGGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:2212683 original size:29 final size:29
Alignment explanation
Indices: 2212649--2212734 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
2212639 GAATTTATTG
* *
2212649 ATTTTGGTGTTATTCTAGGAATTAATTCA
1 ATTTTGGTGCTATTATAGGAATTAATTCA
*
2212678 ATTTTGGTGCTATTATGGGAATTAATTCA
1 ATTTTGGTGCTATTATAGGAATTAATTCA
** * *
2212707 AAATGGGTGCTATT-TTGGTAATTAATTC
1 ATTTTGGTGCTATTATAGG-AATTAATTC
2212735 GAAAAGGAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 3 0.06
29 46 0.94
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (29 bp):
ATTTTGGTGCTATTATAGGAATTAATTCA
Found at i:2212749 original size:30 final size:29
Alignment explanation
Indices: 2212666--2212751 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
2212656 TGTTATTCTA
** * *
2212666 GGAATTAATTCAATTTTGGTGCTATTATG
1 GGAATTAATTCAAAATGGGTGCTATTTTG
2212695 GGAATTAATTCAAAATGGGTGCTATTTTG
1 GGAATTAATTCAAAATGGGTGCTATTTTG
*
2212724 GTAATTAATTCGAAAA-GGAGTGCTATTT
1 GGAATTAATTC-AAAATGG-GTGCTATTT
2212752 CTGTAAAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 37 0.74
30 13 0.26
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (29 bp):
GGAATTAATTCAAAATGGGTGCTATTTTG
Found at i:2223954 original size:29 final size:29
Alignment explanation
Indices: 2223934--2224015 Score: 114
Period size: 29 Copynumber: 2.8 Consensus size: 29
2223924 GCACCCTTTT
2223934 CGAATTATTTACCAGAATAGCA-CCAAAA
1 CGAATTATTTACCAGAATAGCACCCAAAA
*
2223962 CTGATTTATTTACCAGAATAGCA-CCAAAA
1 C-GAATTATTTACCAGAATAGCACCCAAAA
*
2223991 CCGAATTATTTACCAAAATAGCACC
1 -CGAATTATTTACCAGAATAGCACC
2224016 GGTCAACGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
28 1 0.02
29 45 0.94
30 2 0.04
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.24
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCCAAAA
Found at i:2224038 original size:17 final size:17
Alignment explanation
Indices: 2224016--2224082 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
2224006 AAATAGCACC
2224016 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2224033 GGTCAA----CGGGTCG
1 GGTCAACGGTCGGGTCG
2224046 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
**
2224063 GGTCAACTATCGGGTCG
1 GGTCAACGGTCGGGTCG
2224080 GGT
1 GGT
2224083 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
13 13 0.30
17 31 0.70
ACGTcount: A:0.13, C:0.22, G:0.45, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2224058 original size:12 final size:13
Alignment explanation
Indices: 2224026--2224061 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2224016 GGTCAACGGT
2224026 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
2224039 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
2224052 C-GGTCGGGTC
1 CGGGTCGGGTC
2224062 GGGTCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.11, C:0.25, G:0.47, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:2231224 original size:29 final size:29
Alignment explanation
Indices: 2231183--2231264 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
2231173 CACCCTTTTT
2231183 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
2231212 TGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
2231241 CGAATTATTTACCAAAATAGCACC
1 CGAATTATTTACCAGAATAGCACC
2231265 GGTCAACAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:2231295 original size:17 final size:17
Alignment explanation
Indices: 2231273--2231325 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
2231263 CCGGTCAACA
2231273 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
2231290 GTCAA----CGGGTCGG
1 GTCAACGGTCGGGTCGG
2231303 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
2231320 GTCAAC
1 GTCAAC
2231326 TATCGAAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 13 0.41
17 19 0.59
ACGTcount: A:0.15, C:0.25, G:0.43, T:0.17
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:2231314 original size:12 final size:13
Alignment explanation
Indices: 2231282--2231317 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2231272 AGTCAACGGT
2231282 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
2231295 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
2231308 C-GGTCGGGTC
1 CGGGTCGGGTC
2231318 GGGTCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.11, C:0.25, G:0.47, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:2233648 original size:17 final size:18
Alignment explanation
Indices: 2233613--2233649 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2233603 GGATTAATAA
2233613 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
2233631 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
2233648 AT
1 AT
2233650 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Found at i:2235329 original size:48 final size:48
Alignment explanation
Indices: 2235273--2235377 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
2235263 TAATATTTTA
* *
2235273 TCTGATTTCCGA-CTTGAATTTTGTTCTTATA-CATGACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTCTGATATC-TGACCTGAATTCTGT
* * **
2235321 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
*
2235369 TTTGATTTC
1 TCTGATTTC
2235378 TGATATCTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.50
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:2235330 original size:12 final size:12
Alignment explanation
Indices: 2235310--2235379 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
2235300 TATACATGAC
*
2235310 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2235322 CTGATTTCTGAT
1 CTGATTTCTGTT
2235334 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
*
2235346 CTGATATCTGTT
1 CTGATTTCTGTT
*
2235358 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2235370 TTGATTTCTG
1 CTGATTTCTG
2235380 ATATCTCCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:2235341 original size:24 final size:24
Alignment explanation
Indices: 2235310--2235381 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
2235300 TATACATGAC
2235310 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* * *
2235334 CTGGATTCTGTTCTGATATCTGTT
1 CTGAATTCTGTTCTGATTTCTGAT
*
2235358 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
2235382 ATCTCCGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:2238452 original size:19 final size:19
Alignment explanation
Indices: 2238428--2238467 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2238418 ATGACATTAG
*
2238428 TAGCTTTGACTTGCTTTAA
1 TAGCTTTGAATTGCTTTAA
2238447 TAGCTTTGAATTGCTTTAA
1 TAGCTTTGAATTGCTTTAA
2238466 TA
1 TA
2238468 AACACATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (19 bp):
TAGCTTTGAATTGCTTTAA
Found at i:2241083 original size:13 final size:13
Alignment explanation
Indices: 2241065--2241089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2241055 TCATAACCCG
2241065 ACCCGACCCGTTT
1 ACCCGACCCGTTT
2241078 ACCCGACCCGTT
1 ACCCGACCCGTT
2241090 GACCACTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:2243620 original size:24 final size:24
Alignment explanation
Indices: 2243552--2243660 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
2243542 AAATATTTTA
*
2243552 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTCCTGATC-TGAATTCTGT
* * * *
2243576 TCTGATACATTACCTGAATTCTGT
1 TCTGATTCCTGATCTGAATTCTGT
*
2243600 TCTGATTCCTGATCTGGATTCTGT
1 TCTGATTCCTGATCTGAATTCTGT
* * *
2243624 TATGATAT-CTTATCTGAATTATGT
1 TCTGAT-TCCTGATCTGAATTCTGT
* *
2243648 TTTGATTTCTGAT
1 TCTGATTCCTGAT
2243661 ATCTCCGTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 64 0.96
25 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGATTCCTGATCTGAATTCTGT
Found at i:2243623 original size:48 final size:49
Alignment explanation
Indices: 2243552--2243660 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
2243542 AAATATTTTA
* *
2243552 TCTGATTTCTGA-CTTGAATTCTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATATC-TTACCTGAATTATGT
* * *
2243600 TCTGATTCCTGATC-TGGATTCTGTTATGATATCTTATCTGAATTATGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATATCTTACCTGAATTATGT
*
2243648 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2243661 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 50 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTATGATATCTTACCTGAATTATGT
Found at i:2248264 original size:48 final size:48
Alignment explanation
Indices: 2248192--2248283 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
2248182 TCTGACTTGA
*
2248192 ATTCTGTTATGATACATTACCTGAATTATGTTCTGATTCCTGATCTGG
1 ATTCTGTTATGATACATGACCTGAATTATGTTCTGATTCCTGATCTGG
* * * *
2248240 ATTCTGTTATGATATC-TGATCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTATGATA-CATGACCTGAATTATGTTCTGATTCCTGAT
2248284 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
48 37 0.97
49 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (48 bp):
ATTCTGTTATGATACATGACCTGAATTATGTTCTGATTCCTGATCTGG
Found at i:2248281 original size:24 final size:24
Alignment explanation
Indices: 2248179--2248283 Score: 97
Period size: 24 Copynumber: 4.4 Consensus size: 24
2248169 ATTTTATCTA
2248179 ATTTCTGA-CTTGAATTCTGTTATG
1 ATTTCTGATC-TGAATTCTGTTATG
* * * * *
2248203 A-TACATTACCTGAATTATGTTCTG
1 ATTTC-TGATCTGAATTCTGTTATG
* *
2248227 ATTCCTGATCTGGATTCTGTTATG
1 ATTTCTGATCTGAATTCTGTTATG
* *
2248251 ATATCTGATCTGAATTCTGTTTTG
1 ATTTCTGATCTGAATTCTGTTATG
2248275 ATTTCTGAT
1 ATTTCTGAT
2248284 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
23 2 0.03
24 58 0.92
25 3 0.05
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (24 bp):
ATTTCTGATCTGAATTCTGTTATG
Found at i:2252079 original size:2 final size:2
Alignment explanation
Indices: 2252072--2252119 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2252062 CTTAATCATA
2252072 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
2252114 AT AT AT
1 AT AT AT
2252120 TTCGGGTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2253577 original size:38 final size:38
Alignment explanation
Indices: 2253502--2253577 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
2253492 ATAAACATTT
* * *
2253502 CAGAAAACCATATAAAACACATACATATCAAAGTATCA
1 CAGAAAACCATATAAAACACATACAGAACAAAATATCA
* ** *
2253540 CAGAAAACCTTATAAAACATTTACGGAACAAAATATCA
1 CAGAAAACCATATAAAACACATACAGAACAAAATATCA
2253578 GTAATACAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.54, C:0.20, G:0.07, T:0.20
Consensus pattern (38 bp):
CAGAAAACCATATAAAACACATACAGAACAAAATATCA
Found at i:2262071 original size:29 final size:29
Alignment explanation
Indices: 2262059--2262190 Score: 104
Period size: 29 Copynumber: 4.6 Consensus size: 29
2262049 TTAGAAAAAT
2262059 TTACAAAAATATCACCATTTTCAAAATAA
1 TTACAAAAATATCACCATTTTCAAAATAA
* *** * * *
2262088 TTACTAAAATATCATTTTTTTAAAAACAT
1 TTACAAAAATATCACCATTTTCAAAATAA
** * * * *
2262117 TTATGAAATTATCA-CTTTTTGAAAAAGAA
1 TTACAAAAATATCACCATTTT-CAAAATAA
* *
2262146 TTACGAAAATAACACCATTTTCAAAATAA
1 TTACAAAAATATCACCATTTTCAAAATAA
*
2262175 TTACCAAAATATCACC
1 TTACAAAAATATCACC
2262191 CGGTCAACGG
Statistics
Matches: 80, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
28 5 0.06
29 70 0.88
30 5 0.06
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (29 bp):
TTACAAAAATATCACCATTTTCAAAATAA
Found at i:2262222 original size:18 final size:18
Alignment explanation
Indices: 2262199--2262256 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
2262189 CCCGGTCAAC
* *
2262199 GGTCAACGGGTCTGATCG
1 GGTCAACGGGTCGGGTCG
* *
2262217 GGTCAACAGGTCGGGTTG
1 GGTCAACGGGTCGGGTCG
2262235 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
2262253 GGTC
1 GGTC
2262257 GGGTTGGAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.45, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:2264172 original size:13 final size:13
Alignment explanation
Indices: 2264154--2264197 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2264144 TTGACTTTTT
2264154 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
*
2264167 GGTCAAAGTCAAT
1 GGTCAAAGTCAAC
* *
2264180 AGTCAACGGTCAAC
1 GGTCAA-AGTCAAC
2264194 GGTC
1 GGTC
2264198 GGTTAACGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:2264185 original size:20 final size:19
Alignment explanation
Indices: 2264155--2264192 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
2264145 TGACTTTTTG
2264155 GTCAAAGTCAACGGTCAAA
1 GTCAAAGTCAACGGTCAAA
2264174 GTCAATAGTCAACGGTCAA
1 GTCAA-AGTCAACGGTCAA
2264193 CGGTCGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (19 bp):
GTCAAAGTCAACGGTCAAA
Found at i:2264252 original size:15 final size:15
Alignment explanation
Indices: 2264232--2264263 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2264222 GGGTCAACAT
*
2264232 GTCAGGTCAAAGCGG
1 GTCAGGTCAAACCGG
2264247 GTCAGGTCAAACCGG
1 GTCAGGTCAAACCGG
2264262 GT
1 GT
2264264 TAACGTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.38, T:0.16
Consensus pattern (15 bp):
GTCAGGTCAAACCGG
Found at i:2272846 original size:14 final size:15
Alignment explanation
Indices: 2272821--2272853 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2272811 ATCTTCTTAT
*
2272821 TTTTACTTTAATTAC
1 TTTTACTTTAATCAC
2272836 TTTTA-TTTAATCAC
1 TTTTACTTTAATCAC
2272850 TTTT
1 TTTT
2272854 TTATCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTACTTTAATCAC
Found at i:2286018 original size:13 final size:13
Alignment explanation
Indices: 2285999--2286056 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
2285989 GTCACAACCC
2285999 GACCCGACCCGTT
1 GACCCGACCCGTT
*
2286012 TACCCGACCCGTT
1 GACCCGACCCGTT
2286025 GACCCGACCCGTT
1 GACCCGACCCGTT
*
2286038 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
2286053 GACC
1 GACC
2286057 GTTGACCGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 28 0.70
15 12 0.30
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2286028 original size:8 final size:8
Alignment explanation
Indices: 2286017--2286063 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
2286007 CCGTTTACCC
2286017 GACCCGTT
1 GACCCGTT
2286025 GACCC---
1 GACCCGTT
2286030 GACCCGTT
1 GACCCGTT
2286038 GA-CCGTT
1 GACCCGTT
2286045 GACCCGTT
1 GACCCGTT
2286053 GA-CCGTT
1 GACCCGTT
2286060 GACC
1 GACC
2286064 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:2286045 original size:7 final size:7
Alignment explanation
Indices: 2286033--2286064 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2286023 TTGACCCGAC
2286033 CCGTTGA
1 CCGTTGA
2286040 CCGTTGA
1 CCGTTGA
2286047 CCCGTTGA
1 -CCGTTGA
2286055 CCGTTGA
1 CCGTTGA
2286062 CCG
1 CCG
2286065 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:2286050 original size:15 final size:15
Alignment explanation
Indices: 2286017--2286063 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
2286007 CCGTTTACCC
*
2286017 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
2286030 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2286045 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2286060 GACC
1 GACC
2286064 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:2287400 original size:18 final size:18
Alignment explanation
Indices: 2287374--2287409 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2287364 TCGAAAGGAC
*
2287374 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2287392 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
2287410 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2288585 original size:24 final size:24
Alignment explanation
Indices: 2288552--2288655 Score: 95
Period size: 24 Copynumber: 4.3 Consensus size: 24
2288542 ATATTTTATC
* *
2288552 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
2288576 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * *
2288600 TGAT-TCCT-AACTTGGATTCTGTTA
1 TGATAT-CTGATC-TGAATTCTGTTT
*
2288624 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
2288648 TGATATCT
1 TGATATCT
2288656 CCGTTTACCG
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
23 3 0.05
24 56 0.90
25 3 0.05
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.48
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:2288818 original size:2 final size:2
Alignment explanation
Indices: 2288811--2288843 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2288801 GGGATGGGGG
2288811 TA 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 TA T
2288844 GTTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2295062 original size:76 final size:77
Alignment explanation
Indices: 2294980--2295134 Score: 287
Period size: 77 Copynumber: 2.0 Consensus size: 77
2294970 AATTTATTCG
2294980 AAACT-AAGAAAAAAAATTGTGTAATGAGTACAA-ATAAAATGTCTATGGGAATCTAATATCTCA
1 AAACTAAAGAAAAAAAATTGTGTAATGAGTACAATA-AAAATGTCTATGGGAATCTAATATCTCA
2295043 TTCGGAAATGCTA
65 TTCGGAAATGCTA
2295056 AAACTAAAGAAAAAAAATTGTGTAATGAGTACAATAAAAATGTCTATGGGAATCTAATATCTCAT
1 AAACTAAAGAAAAAAAATTGTGTAATGAGTACAATAAAAATGTCTATGGGAATCTAATATCTCAT
2295121 TCGGAAATGCTA
66 TCGGAAATGCTA
2295133 AA
1 AA
2295135 TTTACAATGC
Statistics
Matches: 77, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
76 5 0.06
77 71 0.92
78 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.27
Consensus pattern (77 bp):
AAACTAAAGAAAAAAAATTGTGTAATGAGTACAATAAAAATGTCTATGGGAATCTAATATCTCAT
TCGGAAATGCTA
Found at i:2306371 original size:18 final size:18
Alignment explanation
Indices: 2306348--2306413 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
2306338 GTCACAACCT
2306348 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
2306366 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
*
2306384 -A----ACCCATTGACCC
1 GACCCGACCCGTTGACCC
2306397 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
2306414 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
17 1 0.03
18 27 0.69
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:2306388 original size:13 final size:13
Alignment explanation
Indices: 2306347--2306371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2306337 GGTCACAACC
2306347 TGACCCGACCCGT
1 TGACCCGACCCGT
2306360 TGACCCGACCCG
1 TGACCCGACCCG
2306372 ACCCGTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:2306397 original size:31 final size:31
Alignment explanation
Indices: 2306349--2306409 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2306339 TCACAACCTG
* *
2306349 ACCCGACCCGTTGACCCGACCCGACCCGTTT
1 ACCCAACCCATTGACCCGACCCGACCCGTTT
2306380 ACCCAACCCATTGACCCGACCCGACCCGTT
1 ACCCAACCCATTGACCCGACCCGACCCGTT
2306410 GACCGTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.49, G:0.16, T:0.15
Consensus pattern (31 bp):
ACCCAACCCATTGACCCGACCCGACCCGTTT
Found at i:2307653 original size:18 final size:18
Alignment explanation
Indices: 2307627--2307662 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2307617 TCGAAAGGAC
*
2307627 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2307645 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
2307663 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2308833 original size:23 final size:23
Alignment explanation
Indices: 2308807--2308889 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
2308797 TCCGACTTGA
* *
2308807 ATTCTGTTATGATCCTGACCTGG
1 ATTCTGATATGATCATGACCTGG
* *
2308830 ATTCTGATCTGAT-ATTGACATGG
1 ATTCTGATATGATCA-TGACCTGG
*
2308853 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGAT-CATGACCTGG
*
2308877 ATTTTGATATGAT
1 ATTCTGATATGAT
2308890 ACTTGACTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
23 31 0.62
24 18 0.36
25 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (23 bp):
ATTCTGATATGATCATGACCTGG
Found at i:2308877 original size:24 final size:24
Alignment explanation
Indices: 2308822--2308896 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
2308812 GTTATGATCC
2308822 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
2308845 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
* *
2308869 TGACCTGGATTTTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
2308893 TGAC
1 TGAC
2308897 TTGAATTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:2311111 original size:18 final size:18
Alignment explanation
Indices: 2311088--2311152 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
2311078 TCACAACCTA
2311088 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
2311106 ACCCGACCCGTTTACCC-
1 ACCCGACCCGTTGACCCG
*
2311123 A----ACCCATTGACCCG
1 ACCCGACCCGTTGACCCG
2311137 ACCCGACCCGTTGACC
1 ACCCGACCCGTTGACC
2311153 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
17 1 0.03
18 26 0.68
ACGTcount: A:0.20, C:0.49, G:0.17, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:2311136 original size:31 final size:31
Alignment explanation
Indices: 2311088--2311148 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2311078 TCACAACCTA
* *
2311088 ACCCGACCCGTTGACCCGACCCGACCCGTTT
1 ACCCAACCCATTGACCCGACCCGACCCGTTT
2311119 ACCCAACCCATTGACCCGACCCGACCCGTT
1 ACCCAACCCATTGACCCGACCCGACCCGTT
2311149 GACCGTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.49, G:0.16, T:0.15
Consensus pattern (31 bp):
ACCCAACCCATTGACCCGACCCGACCCGTTT
Found at i:2311156 original size:7 final size:7
Alignment explanation
Indices: 2311144--2311174 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2311134 CCGACCCGAC
2311144 CCGTTGA
1 CCGTTGA
2311151 CCGTTGA
1 CCGTTGA
2311158 CCGTTGA
1 CCGTTGA
*
2311165 CTGTTGA
1 CCGTTGA
2311172 CCG
1 CCG
2311175 ACGTTGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:2312392 original size:18 final size:18
Alignment explanation
Indices: 2312366--2312401 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2312356 TCGAAAGGAC
*
2312366 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2312384 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
2312402 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2313616 original size:24 final size:24
Alignment explanation
Indices: 2313539--2313638 Score: 105
Period size: 23 Copynumber: 4.2 Consensus size: 24
2313529 TCTGATTTCC
* * *
2313539 GACTTGAATTCTGTTATGAT-CCT
1 GACTTGGATTCTGATATGATACTT
* *
2313562 GACCTGGATTCTGATCTGATA-TT
1 GACTTGGATTCTGATATGATACTT
* * *
2313585 GACATGGATTCTGATCTGATACAT
1 GACTTGGATTCTGATATGATACTT
*
2313609 GACTTGGATTTTGATATGATACTT
1 GACTTGGATTCTGATATGATACTT
2313633 GACTTG
1 GACTTG
2313639 AATTATGCTT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
23 37 0.58
24 27 0.42
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (24 bp):
GACTTGGATTCTGATATGATACTT
Found at i:2319554 original size:14 final size:13
Alignment explanation
Indices: 2319534--2319571 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2319524 GCTTAATCGG
2319534 AAAAAAATATAAA
1 AAAAAAATATAAA
2319547 AGAAAAAATA-AAA
1 A-AAAAAATATAAA
*
2319560 ATAAAAATATAA
1 AAAAAAATATAA
2319572 CGGAATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 7 0.32
13 7 0.32
14 8 0.36
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (13 bp):
AAAAAAATATAAA
Found at i:2325772 original size:13 final size:12
Alignment explanation
Indices: 2325740--2325773 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2325730 AATTCCGTTA
*
2325740 TATTTTTATTTT
1 TATTTTTTTTTT
*
2325752 TATTTTTTCTTT
1 TATTTTTTTTTT
2325764 TATTTTTTTT
1 TATTTTTTTT
2325774 CCCGATTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (12 bp):
TATTTTTTTTTT
Found at i:2326644 original size:18 final size:16
Alignment explanation
Indices: 2326609--2326664 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
2326599 TCTCCATCAC
*
2326609 AAAAAAAA-TGTT-GA
1 AAAAAAAACAGTTCGA
2326623 AAAAAAATAGCAGTTCGA
1 AAAAAAA-A-CAGTTCGA
*
2326641 AAAAAAAACTGTTCGA
1 AAAAAAAACAGTTCGA
2326657 AAAAAAAA
1 AAAAAAAA
2326665 GACATGAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 7 0.19
15 1 0.03
16 15 0.42
17 4 0.11
18 9 0.25
ACGTcount: A:0.64, C:0.07, G:0.12, T:0.16
Consensus pattern (16 bp):
AAAAAAAACAGTTCGA
Found at i:2328310 original size:14 final size:15
Alignment explanation
Indices: 2328285--2328317 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2328275 ATCTTCTTAT
*
2328285 TTTTACTTTAATTAC
1 TTTTACTTTAATCAC
2328300 TTTTA-TTTAATCAC
1 TTTTACTTTAATCAC
2328314 TTTT
1 TTTT
2328318 TTATCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTACTTTAATCAC
Found at i:2347190 original size:2 final size:2
Alignment explanation
Indices: 2347183--2347214 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2347173 CTTTTTAAAC
2347183 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2347215 CCCCCATCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2347405 original size:24 final size:24
Alignment explanation
Indices: 2347378--2347477 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
2347368 GATATCAAAA
*
2347378 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
2347402 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
2347426 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
2347450 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
2347474 ATCA
1 ATCA
2347478 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:2347477 original size:48 final size:48
Alignment explanation
Indices: 2347371--2347479 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
2347361 AAACGGAGAT
* * * * *
2347371 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
2347419 TTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
2347467 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2347480 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Done.