Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 62
Found at i:2319530 original size:16 final size:16
Alignment explanation
Indices: 2319493--2319535 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2319483 ATACTTTAAC
*
2319493 TTTTATTTTATATTTA
1 TTTTTTTTTATATTTA
*
2319509 TTTTTTTTTGTATTTTTA
1 -TTTTTTTT-TATATTTA
2319527 TTTTTTTTT
1 TTTTTTTTT
2319536 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 15 0.65
18 7 0.30
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTATATTTA
Found at i:2319534 original size:22 final size:23
Alignment explanation
Indices: 2319496--2319539 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2319486 CTTTAACTTT
2319496 TATTTTATATTTATTTTTTTTTG
1 TATTTTATATTTATTTTTTTTTG
*
2319519 TATTTT-TATTTTTTTTTTTTT
1 TATTTTATATTTATTTTTTTTT
2319540 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (23 bp):
TATTTTATATTTATTTTTTTTTG
Found at i:2320998 original size:13 final size:13
Alignment explanation
Indices: 2320964--2320998 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2320954 TCTTAAATTC
*
2320964 ATATATTTTTTAA
1 ATATATTTTATAA
2320977 ATATA-TTTATAA
1 ATATATTTTATAA
2320989 ATATATTTTA
1 ATATATTTTA
2320999 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATATTTTATAA
Found at i:2321007 original size:13 final size:11
Alignment explanation
Indices: 2320966--2321001 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2320956 TTAAATTCAT
*
2320966 ATATTTTTTAA
1 ATATATTTTAA
2320977 ATATATTTATAA
1 ATATATTT-TAA
2320989 ATATATTTTAA
1 ATATATTTTAA
2321000 AT
1 AT
2321002 TCATATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATATTTTAA
Found at i:2321069 original size:62 final size:60
Alignment explanation
Indices: 2320996--2321111 Score: 187
Period size: 62 Copynumber: 1.9 Consensus size: 60
2320986 TAAATATATT
*
2320996 TTAAATTCATATATTAAATTTAATTCACATCTTAACATTGAGAAATAAATTTTATTTTTACC
1 TTAAATACATATATTAAATTTAATTCACATCTTAACATT-A-AAATAAATTTTATTTTTACC
* *
2321058 TTAAATACATATATTAAATTTAATTCACATCTTAATATTAAAATATATTTTATT
1 TTAAATACATATATTAAATTTAATTCACATCTTAACATTAAAATAAATTTTATT
2321112 CTTATATGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 13 0.25
61 1 0.02
62 37 0.73
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (60 bp):
TTAAATACATATATTAAATTTAATTCACATCTTAACATTAAAATAAATTTTATTTTTACC
Found at i:2321092 original size:31 final size:31
Alignment explanation
Indices: 2320996--2321092 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
2320986 TAAATATATT
2320996 TTAAATTCATATATTAAATTTAATTCACATC
1 TTAAATTCATATATTAAATTTAATTCACATC
* * * * *** *
2321027 TTAACATTGAGA-AATAAATTTTATTTTTACC
1 TTAA-ATTCATATATTAAATTTAATTCACATC
*
2321058 TTAAATACATATATTAAATTTAATTCACATC
1 TTAAATTCATATATTAAATTTAATTCACATC
2321089 TTAA
1 TTAA
2321093 TATTAAAATA
Statistics
Matches: 47, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
30 4 0.09
31 38 0.81
32 5 0.11
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (31 bp):
TTAAATTCATATATTAAATTTAATTCACATC
Found at i:2321514 original size:19 final size:19
Alignment explanation
Indices: 2321489--2321537 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
2321479 ATTTTTAAGT
2321489 GGGTTTTGAA-CTCCTATA
1 GGGTTTTGAACCTCCTATA
*
2321507 GTGGTTTTGAAACCTCCTCTA
1 G-GGTTTTG-AACCTCCTATA
2321528 GGGTTTTGAA
1 GGGTTTTGAA
2321538 ACCACTGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 9 0.33
20 9 0.33
21 8 0.30
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.39
Consensus pattern (19 bp):
GGGTTTTGAACCTCCTATA
Found at i:2321534 original size:20 final size:20
Alignment explanation
Indices: 2321489--2321540 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2321479 ATTTTTAAGT
2321489 GGGTTTTG-AA-CTCCTATA
1 GGGTTTTGAAACCTCCTATA
*
2321507 GTGGTTTTGAAACCTCCTCTA
1 G-GGTTTTGAAACCTCCTATA
2321528 GGGTTTTGAAACC
1 GGGTTTTGAAACC
2321541 ACTGTGTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 14 0.47
21 8 0.27
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (20 bp):
GGGTTTTGAAACCTCCTATA
Found at i:2323655 original size:57 final size:55
Alignment explanation
Indices: 2323569--2323682 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 55
2323559 GGCATTCAAG
2323569 TCCCTCACACTTACTCCTACCATTACAGATCATCCTTAGCTCTTACGATCCTTAA
1 TCCCTCACACTTACTCCTACCATTACAGATCATCCTTAGCTCTTACGATCCTTAA
2323624 TCCCTCACAGACTTACTCCTACCATTACAGATCATCCTTAGCTCTTACGATCCTTAA
1 TCCCTCAC--ACTTACTCCTACCATTACAGATCATCCTTAGCTCTTACGATCCTTAA
2323681 TC
1 TC
2323683 GGGTCAAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 8 0.14
57 49 0.86
ACGTcount: A:0.25, C:0.36, G:0.06, T:0.32
Consensus pattern (55 bp):
TCCCTCACACTTACTCCTACCATTACAGATCATCCTTAGCTCTTACGATCCTTAA
Found at i:2326349 original size:23 final size:23
Alignment explanation
Indices: 2326322--2326430 Score: 146
Period size: 23 Copynumber: 4.7 Consensus size: 23
2326312 TGCTACATAA
* *
2326322 TTGTCCCGACGGACCACATAGGT
1 TTGTCCCGAAGGACCACATAGTT
*
2326345 TTGTCCCAAAGGACCACATAGTT
1 TTGTCCCGAAGGACCACATAGTT
*
2326368 TTGTCCCAAAGGACCACATAGTT
1 TTGTCCCGAAGGACCACATAGTT
**
2326391 TTGTCTTGAAGGACCACATAGTT
1 TTGTCCCGAAGGACCACATAGTT
* *
2326414 TTATCCCGAATGACCAC
1 TTGTCCCGAAGGACCAC
2326431 TTAGAACCCT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGTT
Found at i:2331078 original size:32 final size:33
Alignment explanation
Indices: 2331034--2331103 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
2331024 ACCTTACAAC
* *
2331034 TCCCTAGATTTT-ATGGGCTAAACTAGAACCTT
1 TCCCTAGATTTTAACGGGATAAACTAGAACCTT
* *
2331066 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGATTTTA-ACGGGATAAACTAGAACCTT
2331100 TCCC
1 TCCC
2331104 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
34 21 0.66
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (33 bp):
TCCCTAGATTTTAACGGGATAAACTAGAACCTT
Found at i:2331343 original size:20 final size:22
Alignment explanation
Indices: 2331318--2331357 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2331308 TGTTGTATAT
2331318 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
2331338 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
2331358 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:2331701 original size:29 final size:29
Alignment explanation
Indices: 2331669--2331731 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
2331659 GAAACTTTTT
2331669 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
2331699 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
2331729 AAA
1 AAA
2331732 CATTTTACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:2331727 original size:30 final size:29
Alignment explanation
Indices: 2331680--2331737 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
2331670 AAACTTTGAA
*
2331680 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
2331709 TAAATTCAATTCAAGTCCAAAAACATTTT
1 TAAATTCAATT-AAGTCCAAAAACATTTT
2331738 ACCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:2334566 original size:34 final size:32
Alignment explanation
Indices: 2334499--2334568 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2334489 ACCTTACAAC
* *
2334499 TCCCTAGATTTTCCGAGCTAAACTATAACCTT
1 TCCCTAGATTTTCCGAGATAAACTAGAACCTT
* *
2334531 TCCCTAGCTTTTACACGAGATAAGCTAGAACCTT
1 TCCCTAGATTTT-C-CGAGATAAACTAGAACCTT
2334565 TCCC
1 TCCC
2334569 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.31
Consensus pattern (32 bp):
TCCCTAGATTTTCCGAGATAAACTAGAACCTT
Found at i:2335163 original size:29 final size:29
Alignment explanation
Indices: 2335131--2335193 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
2335121 GAAACCTTTT
2335131 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
* *
2335161 AAATATTTTGTAAATTTAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
2335191 AAA
1 AAA
2335194 CATTTTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.34
30 14 0.48
31 5 0.17
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:2335189 original size:30 final size:29
Alignment explanation
Indices: 2335142--2335199 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
2335132 AAACTTTGAA
*
2335142 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
*
2335171 TAAATTTAATTCAAGTCCAAAAACATTTT
1 TAAATTCAATT-AAGTCCAAAAACATTTT
2335200 TCCTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:2336750 original size:23 final size:23
Alignment explanation
Indices: 2336667--2336737 Score: 115
Period size: 23 Copynumber: 3.1 Consensus size: 23
2336657 TGCCACACAA
* *
2336667 TTGTCTCGAAGGACCACATAGGT
1 TTGTCCCGAAGGACCACATAGTT
*
2336690 TTGTCCCGATGGACCACATAGTT
1 TTGTCCCGAAGGACCACATAGTT
2336713 TTGTCCCGAAGGACCACATAGTT
1 TTGTCCCGAAGGACCACATAGTT
2336736 TT
1 TT
2336738 ATCTCGAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGTT
Found at i:2336756 original size:23 final size:23
Alignment explanation
Indices: 2336673--2336750 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
2336663 ACAATTGTCT
* *
2336673 CGAAGGACCACATAGGTTTGTCC
1 CGAAGGACCACATAGTTTTATCC
* *
2336696 CGATGGACCACATAGTTTTGTCC
1 CGAAGGACCACATAGTTTTATCC
*
2336719 CGAAGGACCACATAGTTTTATCT
1 CGAAGGACCACATAGTTTTATCC
*
2336742 CGAATGACC
1 CGAAGGACC
2336751 TAATAGAACC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (23 bp):
CGAAGGACCACATAGTTTTATCC
Found at i:2343157 original size:19 final size:20
Alignment explanation
Indices: 2343133--2343179 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2343123 AAACGATTTT
**
2343133 ATTTTGAAAA-CAAAATTGA
1 ATTTTGAAAATCAAAATAAA
2343152 ATTTTGAAAATCAAAATAAA
1 ATTTTGAAAATCAAAATAAA
2343172 ATTTTGAA
1 ATTTTGAA
2343180 GAATGATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (20 bp):
ATTTTGAAAATCAAAATAAA
Found at i:2344455 original size:20 final size:19
Alignment explanation
Indices: 2344432--2344475 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2344422 GTTTTGAAAC
2344432 CCCCTGAATGGTTTCTAAA
1 CCCCTGAATGGTTTCTAAA
***
2344451 TCCCCTTTTTGGTTTCTAAA
1 -CCCCTGAATGGTTTCTAAA
2344471 CCCCT
1 CCCCT
2344476 TGTTTCAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39
Consensus pattern (19 bp):
CCCCTGAATGGTTTCTAAA
Found at i:2345163 original size:28 final size:29
Alignment explanation
Indices: 2345108--2345163 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2345098 CGAGCCTAAC
** *
2345108 AATATATTAAAATATATTTTTATTTTTAT
1 AATATATTAAAATATATTTAAATATTTAT
2345137 AATAT-TTAAAATATATTTAAATATTTA
1 AATATATTAAAATATATTTAAATATTTA
2345164 AAAAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
AATATATTAAAATATATTTAAATATTTAT
Found at i:2345179 original size:19 final size:19
Alignment explanation
Indices: 2345137--2345179 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2345127 TTATTTTTAT
* *
2345137 AATATTTAAAATATATTTA
1 AATATTTAAAAAATATATA
2345156 AATATTTAAAAAATA-ATA
1 AATATTTAAAAAATATATA
2345174 ATATAT
1 A-ATAT
2345180 GAATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATTTAAAAAATATATA
Found at i:2345216 original size:21 final size:21
Alignment explanation
Indices: 2345159--2345208 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 21
2345149 ATATTTAAAT
2345159 ATTTAAAAAATAATAATATATGA
1 ATTTAAAAAATAA-AA-ATATGA
2345182 ATTTAAAAAATAAAAATATGA
1 ATTTAAAAAATAAAAATATGA
2345203 ATTTAA
1 ATTTAA
2345209 GATATAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 12 0.44
22 2 0.07
23 13 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
ATTTAAAAAATAAAAATATGA
Found at i:2345283 original size:21 final size:21
Alignment explanation
Indices: 2345210--2345285 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
2345200 TGAATTTAAG
* *
2345210 ATATAAATTTAGAAAATAAAA
1 ATATGAATTTAAAAAATAAAA
* * * * *
2345231 ATGTAAATTTAATAAATTTAAT
1 ATATGAATTTAA-AAAATAAAA
2345253 ATATGAATTTAAAAAATAAAA
1 ATATGAATTTAAAAAATAAAA
*
2345274 ATACGAATTTAA
1 ATATGAATTTAA
2345286 GACTAAAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
21 27 0.63
22 16 0.37
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.34
Consensus pattern (21 bp):
ATATGAATTTAAAAAATAAAA
Found at i:2345283 original size:43 final size:43
Alignment explanation
Indices: 2345202--2345285 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
2345192 TAAAAATATG
* **
2345202 AATTTAAGATATAAATTTAGAAAATAAAAATGTAAATTTAATA
1 AATTTAAGATATAAATTTAAAAAATAAAAATACAAATTTAATA
* * *
2345245 AATTTAATATATGAATTTAAAAAATAAAAATACGAATTTAA
1 AATTTAAGATATAAATTTAAAAAATAAAAATACAAATTTAA
2345286 GACTAAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (43 bp):
AATTTAAGATATAAATTTAAAAAATAAAAATACAAATTTAATA
Found at i:2345284 original size:34 final size:34
Alignment explanation
Indices: 2345172--2345285 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 34
2345162 TAAAAAATAA
2345172 TAATATATGAATTTAAAAAATAAAAATATGAATT
1 TAATATATGAATTTAAAAAATAAAAATATGAATT
* * * *
2345206 TAAGATATAAATTTAGAAAATAAAAATGTAAATTTAATAAATT
1 TAATATATGAATTT--AAAA-AATAA---AAA--T-ATGAATT
*
2345249 TAATATATGAATTTAAAAAATAAAAATACGAATT
1 TAATATATGAATTTAAAAAATAAAAATATGAATT
2345283 TAA
1 TAA
2345286 GACTAAAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
34 20 0.32
35 1 0.02
36 4 0.06
37 7 0.11
40 7 0.11
41 4 0.06
42 1 0.02
43 18 0.29
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (34 bp):
TAATATATGAATTTAAAAAATAAAAATATGAATT
Found at i:2349433 original size:43 final size:43
Alignment explanation
Indices: 2349372--2349458 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
2349362 TATAAAATAC
2349372 ATAAACTACTAATAAAACCATAGTAGTATACCACCCTCATATT
1 ATAAACTACTAATAAAACCATAGTAGTATACCACCCTCATATT
2349415 ATAAACTACTAATAAAACCATAGTAGTATACCACCCTCATATT
1 ATAAACTACTAATAAAACCATAGTAGTATACCACCCTCATATT
2349458 A
1 A
2349459 GTACTATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (43 bp):
ATAAACTACTAATAAAACCATAGTAGTATACCACCCTCATATT
Found at i:2352154 original size:20 final size:20
Alignment explanation
Indices: 2352129--2352181 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2352119 GATTTTCCAG
* *
2352129 AATCGCATCGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
2352149 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
2352169 AATCGCAACGCGA
1 AATCGCAACGCGA
2352182 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:2352233 original size:81 final size:80
Alignment explanation
Indices: 2352148--2352360 Score: 241
Period size: 81 Copynumber: 2.6 Consensus size: 80
2352138 GCGAATATGA
* * * * *
2352148 AAATCGCAACGCGAACATATAAATCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATCCGTAAA
1 AAATCGCAACGAGAACACATAAATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACGT-AA
2352211 ATCGCAACGCGTATCCGT
63 ATCGCAACGCGTATCCGT
* * * *
2352229 AAATCACAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCGTAACGAGAATACGTAAATC
1 AAATCGCAACGAGAACACATAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATC
*
2352294 GCAATGCGTATCCGT
66 GCAACGCGTATCCGT
* * * * *
2352309 AAATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTAAATCGCAACG
1 AAATCGCAACGAGAACACAT-AAATCGCAACGCGTATCTGTAAATCGCAACG
2352361 CGATTTTTAA
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
80 37 0.32
81 75 0.66
82 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (80 bp):
AAATCGCAACGAGAACACATAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATC
GCAACGCGTATCCGT
Found at i:2352238 original size:20 final size:20
Alignment explanation
Indices: 2352190--2352362 Score: 186
Period size: 20 Copynumber: 8.6 Consensus size: 20
2352180 GATTCTGACT
*
2352190 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
2352211 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
2352231 ATCACAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
2352251 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
2352271 ATCGTAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
2352291 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
2352311 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
2352332 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
2352352 ATCGCAACGCG
1 ATCGCAACGCG
2352363 ATTTTTAAAG
Statistics
Matches: 122, Mismatches: 27, Indels: 7
0.78 0.17 0.04
Matches are distributed among these distances:
20 89 0.73
21 33 0.27
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:2352254 original size:121 final size:121
Alignment explanation
Indices: 2352129--2352360 Score: 279
Period size: 121 Copynumber: 1.9 Consensus size: 121
2352119 GATTTTCCAG
* * * * *
2352129 AATCGCATCGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGT-A-AAT
** *
2352192 CGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTA
64 CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTA
* * * * * * *
2352250 AATCGCAACGCGTATCTGTAAATCGTAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATCG
* *
2352315 CAACGACAATACGTAAAATCGCAATGCGTATCCGTAAATCGCAACG
66 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACG
2352361 CGATTTTTAA
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
121 87 0.95
122 4 0.04
123 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (121 bp):
AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATCG
CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTA
Found at i:2352262 original size:40 final size:41
Alignment explanation
Indices: 2352190--2352360 Score: 256
Period size: 40 Copynumber: 4.2 Consensus size: 41
2352180 GATTCTGACT
* *
2352190 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
2352231 ATCACAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
2352271 ATCGTAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
2352311 ATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
2352352 ATCGCAACG
1 ATCGCAACG
2352361 CGATTTTTAA
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 73 0.61
41 46 0.39
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:2352985 original size:21 final size:20
Alignment explanation
Indices: 2352924--2352999 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
2352914 TTCTAAACTT
*
2352924 AAAATTGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
2352944 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
2352964 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
2352985 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
2353000 TAATCGCAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 29 0.60
21 19 0.40
ACGTcount: A:0.51, C:0.17, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:2353063 original size:14 final size:14
Alignment explanation
Indices: 2353044--2353100 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2353034 TTTCATTTCG
2353044 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
2353058 CGTTGCGATTTTAATTTCG
1 CGTTGCGA---T--TCTCT
2353077 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2353091 CGTTGCGATT
1 CGTTGCGATT
2353101 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
16 1 0.03
17 1 0.03
19 11 0.32
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2353069 original size:33 final size:33
Alignment explanation
Indices: 2353027--2353159 Score: 176
Period size: 33 Copynumber: 3.8 Consensus size: 33
2353017 CAAAATCACA
2353027 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2353060 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2353093 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGAT--TC---T-CTCG
*
2353132 TTGCGATTTTCATTCTCTCGTTGCGATT
1 TTGCGATTTTCATT-TCGCGTTGCGATT
2353160 TTCATTTCAA
Statistics
Matches: 89, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
33 57 0.64
35 2 0.02
38 2 0.02
39 17 0.19
40 11 0.12
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2353133 original size:20 final size:19
Alignment explanation
Indices: 2353091--2353158 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
2353081 GCGATTCTCT
**
2353091 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
2353110 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
** *
2353130 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATAGTCATT-TCG
2353150 CGTTGCGAT
1 CGTTGCGAT
2353159 TTTCATTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.36
20 26 0.62
21 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:2353159 original size:20 final size:19
Alignment explanation
Indices: 2353027--2353167 Score: 140
Period size: 19 Copynumber: 7.8 Consensus size: 19
2353017 CAAAATCACA
2353027 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
2353046 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
*
2353060 TTGCGATTTTAATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
2353079 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
2353093 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
2353112 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
*
2353132 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
2353152 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2353168 AACCAAAAGA
Statistics
Matches: 99, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
14 20 0.20
16 5 0.05
17 5 0.05
19 35 0.35
20 33 0.33
21 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:2355200 original size:21 final size:21
Alignment explanation
Indices: 2355176--2355242 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2355166 TCATTCCTCG
2355176 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2355197 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2355218 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2355239 AGAG
1 AGAG
2355243 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2355200 original size:42 final size:42
Alignment explanation
Indices: 2355124--2355242 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
2355114 GACTCGCCTG
* * * * * * *
2355124 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
2355166 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
2355208 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2355243 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:2356606 original size:14 final size:14
Alignment explanation
Indices: 2356587--2356622 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2356577 ATTGTTTAAT
2356587 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2356601 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2356615 TGATTTGT
1 TGATTTGT
2356623 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2356775 original size:33 final size:32
Alignment explanation
Indices: 2356733--2356821 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 32
2356723 ATGACTATCA
* *
2356733 CAATGCGAAATGAAAATCGCAACAAGAGAATCG
1 CAATGCGAAAT-AAAATCGCAACAACAAAATCG
* *
2356766 CAATGCGAAATTAAAATCGCAACGACAAAATTG
1 CAATGCGAAA-TAAAATCGCAACAACAAAATCG
*
2356799 CAACGCGAAACTAAAATCGCAAC
1 CAATGCGAAA-TAAAATCGCAAC
2356822 GCAAAACTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 48 0.98
34 1 0.02
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.13
Consensus pattern (32 bp):
CAATGCGAAATAAAATCGCAACAACAAAATCG
Found at i:2356820 original size:19 final size:19
Alignment explanation
Indices: 2356761--2356837 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
2356751 GCAACAAGAG
* *
2356761 AATCGCAATGCGAAATTAA
1 AATCGCAACGCGAAACTAA
2356780 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
2356794 AATTGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
2356813 AATCGCAACGCAAAACTAA
1 AATCGCAACGCGAAACTAA
*
2356832 ATTCGC
1 AATCGC
2356838 GTTGCGATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 32 0.67
ACGTcount: A:0.47, C:0.23, G:0.14, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:2356855 original size:19 final size:19
Alignment explanation
Indices: 2356833--2356930 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
2356823 CAAAACTAAA
*
2356833 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
2356852 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
2356868 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2356885 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
2356901 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2356918 TTCGCATTGCGAT
1 TTCGCATTGCGAT
2356931 AGTTGCATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 12 0.19
16 13 0.21
17 13 0.21
19 24 0.39
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:2356879 original size:33 final size:33
Alignment explanation
Indices: 2356837--2356930 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
2356827 ACTAAATTCG
2356837 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
2356870 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
2356903 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2356931 AGTTGCATTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:2359191 original size:14 final size:14
Alignment explanation
Indices: 2359172--2359198 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2359162 TCCCGTGGTA
2359172 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
2359186 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
2359199 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:2359432 original size:24 final size:24
Alignment explanation
Indices: 2359398--2359451 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2359388 CTGAAAAATC
2359398 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2359422 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2359446 ATCAAA
1 ATCAAA
2359452 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2359465 original size:24 final size:24
Alignment explanation
Indices: 2359398--2359465 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2359388 CTGAAAAATC
* * *
2359398 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2359422 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2359446 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2359466 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2360512 original size:20 final size:20
Alignment explanation
Indices: 2360308--2360599 Score: 268
Period size: 20 Copynumber: 14.5 Consensus size: 20
2360298 GTCAGAATCT
* *
2360308 CGTTGCGATTTACATATTTG
1 CGTTGCGATTTACGTATTCG
*
2360328 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
* *
2360348 CATTGCGATTTACGTATTTG
1 CGTTGCGATTTACGTATTCG
* *
2360368 CATTGAGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
* *
2360388 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
* *
2360408 TGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTAC-GTATTCG
*
2360428 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
* *
2360448 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCG
2360468 CGTTGCGATTTTACGTATT-G
1 CGTTGCGA-TTTACGTATTCG
* *
2360488 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGTATTCG
* * *
2360509 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATTCG
* *
2360530 CGTTGCGATAGT-CAG-AATCG
1 CGTTGCGAT-TTAC-GTATTCG
** *
2360550 CGTTGCGATTTATATGTTCG
1 CGTTGCGATTTACGTATTCG
* *
2360570 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCG
2360590 CGTTGCGATT
1 CGTTGCGATT
2360600 CTGGAAAATC
Statistics
Matches: 227, Mismatches: 35, Indels: 20
0.80 0.12 0.07
Matches are distributed among these distances:
19 2 0.01
20 186 0.82
21 39 0.17
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:2362313 original size:34 final size:34
Alignment explanation
Indices: 2362255--2362336 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
2362245 CTGATTATAT
*
2362255 ATATATAATATTTTTTTATTTTTTATATTAATTAG
1 ATATATAATA-TTTTTTATATTTTATATTAATTAG
*
2362290 ATATATAATATTTTTTATATTTTATATTAATTAT
1 ATATATAATATTTTTTATATTTTATATTAATTAG
2362324 ATATATAATATTT
1 ATATATAATATTT
2362337 CGGGTCGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 35 0.78
35 10 0.22
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
ATATATAATATTTTTTATATTTTATATTAATTAG
Found at i:2367530 original size:3 final size:3
Alignment explanation
Indices: 2367522--2367561 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2367512 GGATAAAAAC
2367522 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2367562 TTGCATCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2371492 original size:3 final size:3
Alignment explanation
Indices: 2371486--2371560 Score: 71
Period size: 3 Copynumber: 24.7 Consensus size: 3
2371476 TTCATTTAAA
* * *
2371486 TAT TATT TAT TAT TAT TAT TAT AAT TAT TA- TAT TAG TAA TAT TATT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * *
2371532 TAT TAT TAA TAT TAT TAT AAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2371561 CAAGCCAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2376512 original size:26 final size:26
Alignment explanation
Indices: 2376483--2376536 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2376473 AAAGAAAGAG
2376483 AAAACTTTTATTAAAACAAAGTAACA
1 AAAACTTTTATTAAAACAAAGTAACA
2376509 AAAACTTTTATTAAAACAAAGTAACA
1 AAAACTTTTATTAAAACAAAGTAACA
2376535 AA
1 AA
2376537 GCAAAACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (26 bp):
AAAACTTTTATTAAAACAAAGTAACA
Found at i:2378087 original size:62 final size:64
Alignment explanation
Indices: 2378017--2378141 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
2378007 CATGCAATTT
2378017 AACTATCAAGAATGTTTAAATTC-AAATA-TTACAGCTTAAACAATTACAACATGTTAAAGATC
1 AACTATCAAGAATGTTTAAATTCAAAATATTTACAGCTTAAACAATTACAACATGTTAAAGATC
2378079 AACTATCAAGAATGTTTAAATTCAAAATATTTACAGCTTAAACAATTACAACATGTTAAAGAT
1 AACTATCAAGAATGTTTAAATTCAAAATATTTACAGCTTAAACAATTACAACATGTTAAAGAT
2378142 AATCGATGGA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 23 0.38
63 5 0.08
64 33 0.54
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (64 bp):
AACTATCAAGAATGTTTAAATTCAAAATATTTACAGCTTAAACAATTACAACATGTTAAAGATC
Found at i:2378162 original size:62 final size:62
Alignment explanation
Indices: 2378034--2378165 Score: 162
Period size: 64 Copynumber: 2.1 Consensus size: 62
2378024 AAGAATGTTT
* * ***
2378034 AAATTC-AAATATTACAGCTTAAACAATTACAACATGTTAAAGATCAACTATCAAGAATGTTT
1 AAATTCAAAATATTACAGCTTAAACAATTACAACATGTTAAAGATCAACGAT-AAGAAAGGAA
*
2378096 AAATTCAAAATATTTACAGCTTAAACAATTACAACATGTTAAAGAT-AATCGAT-GGAAAGGAA
1 AAATTCAAAATA-TTACAGCTTAAACAATTACAACATGTTAAAGATCAA-CGATAAGAAAGGAA
2378158 AAATTCAA
1 AAATTCAA
2378166 CCAAACATTC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
62 18 0.30
63 7 0.11
64 36 0.59
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (62 bp):
AAATTCAAAATATTACAGCTTAAACAATTACAACATGTTAAAGATCAACGATAAGAAAGGAA
Found at i:2386913 original size:91 final size:91
Alignment explanation
Indices: 2386755--2386924 Score: 254
Period size: 91 Copynumber: 1.9 Consensus size: 91
2386745 TTGTTTATGA
* *
2386755 TCTTTTATGCAGGCCTTAAGCAAATATGTTAAATATTAATTACATATCAACTGTTTTACATCTTT
1 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTACATATCAACTGTTTTACATCATT
2386820 TGTTGTTGTATTTTATGATCTTTCAT
66 TGTTGTTGTATTTTATGATCTTTCAT
* * *
2386846 TCTTTTATGTAGGCCTTAAACAAATATGTTAAGTA-TATATT-CATTGTCAACTGTTTTACATCA
1 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTA-ATTACA-TATCAACTGTTTTACATCA
*
2386909 TTTGTTGTTGTTTTTT
64 TTTGTTGTTGTATTTT
2386925 TCTTGAAGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
90 4 0.06
91 67 0.94
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.49
Consensus pattern (91 bp):
TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTACATATCAACTGTTTTACATCATT
TGTTGTTGTATTTTATGATCTTTCAT
Found at i:2389985 original size:2 final size:2
Alignment explanation
Indices: 2389978--2390011 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2389968 TGTCAAACTA
*
2389978 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2390012 ATTTACGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2391264 original size:5 final size:5
Alignment explanation
Indices: 2391254--2391289 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
2391244 ACAGGTTTCT
2391254 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
2391290 TTGGAATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.22, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:2397733 original size:105 final size:105
Alignment explanation
Indices: 2397529--2397987 Score: 338
Period size: 105 Copynumber: 4.4 Consensus size: 105
2397519 TTGGTCATTT
* * * * * *
2397529 TTTTCGTGACCATCAATATTGTCACACTAAGTATTTTTTAATGACCAAATATTTGATACTATTAT
1 TTTT-GTGACCATCAATGTTGTCACATTAAGTATTTTTTAGTGACCAAATATTCGACACTACTAT
*
2397594 CAATACAAATTGTGATAAATTTATTTAACACTAAAAATCTA
65 CAATACAAATTGTGATAAATTTACTTAACACTAAAAATCTA
* *
2397635 TTTTGTGACCATCAATGTTGTCACATTAAGTATTATTCTAGTGACCAAATATTCGACACTACTCT
1 TTTTGTGACCATCAATGTTGTCACATTAAGTATT-TTTTAGTGACCAAATATTCGACACTACTAT
* * * *
2397700 CAATA-AAATTTGTGATGAATTTGCTTGAC-CTAAAAATTTA
65 CAATACAAA-TTGTGATAAATTTACTTAACACTAAAAATCTA
* * * * * ** *
2397740 TTTTGTGACCATCAATGTTGCCACATTAAATATTGTTTTAGTGATCACATGTTCGGTACT-GTAA
1 TTTTGTGACCATCAATGTTGTCACATTAAGTATT-TTTTAGTGACCAAATATTCGACACTACT-A
* * * ** *
2397804 CCAATAGAAATTGTGATAACTTTGTTTGACACTTAAAAA--TA
64 TCAATACAAATTGTGATAAATTTACTTAACAC-TAAAAATCTA
* * * * * ** * * *
2397845 TTTTGTGACCATAAATATTATCACAATAATTATTTTTGTAGCAACCAAATGTTTGACACTATTAT
1 TTTTGTGACCATCAATGTTGTCACATTAAGTATTTTT-TAGTGACCAAATATTCGACACTACTAT
* * * ** * * *
2397910 GAATAGAAATTATGACGAATTT-GTTCGACACTGAAAATAC-A
65 CAATACAAATTGTGATAAATTTACTT-AACACTAAAAAT-CTA
* * * * *
2397951 TTATGTGACCATCAATGGTGCCACACTAGGTATTTTT
1 TTTTGTGACCATCAATGTTGTCACATTAAGTATTTTT
2397988 AATAATCAAT
Statistics
Matches: 282, Mismatches: 59, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
104 11 0.04
105 182 0.65
106 83 0.29
107 6 0.02
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (105 bp):
TTTTGTGACCATCAATGTTGTCACATTAAGTATTTTTTAGTGACCAAATATTCGACACTACTATC
AATACAAATTGTGATAAATTTACTTAACACTAAAAATCTA
Found at i:2397932 original size:210 final size:211
Alignment explanation
Indices: 2397594--2397975 Score: 475
Period size: 210 Copynumber: 1.8 Consensus size: 211
2397584 ATACTATTAT
* * *
2397594 CAATACAAATTGTGATAAATTTATTTAACACTAAAAATCTATTTTGTGACCATCAATGTTGTCAC
1 CAATACAAATTGTGATAAATTTATTTAACACTAAAAA-CTATTTTGTGACCATAAATATTATCAC
* ** * * *
2397659 ATTAAGTATTATTCTAGTGACCAAATATTCGACACTACTCTCAATAAAATTTGTGATGAATTTGC
65 AATAAGTATTATTCTAGCAACCAAATATTCGACACTACTATCAATAAAATTTATGACGAATTTG-
** * *
2397724 TT-GAC-CTAAAAATTTATTTTGTGACCATCAATGTTGCCACATTAAATATTGTTTTAGTGATCA
129 TTCGACACTAAAAATACATTATGTGACCATCAATGGTGCCACATTAAATATTGTTTTAGTGATCA
2397787 CATGTTCGGTACTGTAAC
194 CATGTTCGGTACTGTAAC
* * * *
2397805 CAATAGAAATTGTGATAACTTTGTTTGACACTTAAAAA-TATTTTGTGACCATAAATATTATCAC
1 CAATACAAATTGTGATAAATTTATTTAACAC-TAAAAACTATTTTGTGACCATAAATATTATCAC
* * * * * * *
2397869 AATAATTATTTTTGTAGCAACCAAATGTTTGACACTATTATGAATAGAAA-TTATGACGAATTTG
65 AATAAGTATTATTCTAGCAACCAAATATTCGACACTACTATCAATA-AAATTTATGACGAATTTG
*
2397933 TTCGACACTGAAAATACATTATGTGACCATCAATGGTGCCACA
129 TTCGACACTAAAAATACATTATGTGACCATCAATGGTGCCACA
2397976 CTAGGTATTT
Statistics
Matches: 142, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
209 2 0.01
210 73 0.51
211 61 0.43
212 6 0.04
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (211 bp):
CAATACAAATTGTGATAAATTTATTTAACACTAAAAACTATTTTGTGACCATAAATATTATCACA
ATAAGTATTATTCTAGCAACCAAATATTCGACACTACTATCAATAAAATTTATGACGAATTTGTT
CGACACTAAAAATACATTATGTGACCATCAATGGTGCCACATTAAATATTGTTTTAGTGATCACA
TGTTCGGTACTGTAAC
Found at i:2406122 original size:16 final size:17
Alignment explanation
Indices: 2406098--2406133 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2406088 GCCTTATTCA
*
2406098 CATGGTATCTACCC-AT
1 CATGATATCTACCCAAT
2406114 CATGATATCTACCCAAT
1 CATGATATCTACCCAAT
2406131 CAT
1 CAT
2406134 ACTTTAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (17 bp):
CATGATATCTACCCAAT
Found at i:2409375 original size:3 final size:3
Alignment explanation
Indices: 2409367--2409412 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
2409357 TATAATTGTT
* *
2409367 ATA ATA ATA ATA ATA ATA AT- ATA ATA GTA ATA ATT ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2409413 TTTATAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:2409387 original size:29 final size:29
Alignment explanation
Indices: 2409348--2409412 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
2409338 TAAATGATAT
* * *
2409348 TAATACTAATATAATTGTTATAATAATAA
1 TAATAATAATATAATAGTAATAATAATAA
*
2409377 TAATAATAATATAATAGTAATAATTATAA
1 TAATAATAATATAATAGTAATAATAATAA
2409406 T-ATAATA
1 TAATAATA
2409413 TTTATAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (29 bp):
TAATAATAATATAATAGTAATAATAATAA
Found at i:2409419 original size:20 final size:20
Alignment explanation
Indices: 2409366--2409412 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2409356 ATATAATTGT
2409366 TATAATAATAATAATAATAA
1 TATAATAATAATAATAATAA
* *
2409386 TATAATAGTAATAATTATAA
1 TATAATAATAATAATAATAA
2409406 TATAATA
1 TATAATA
2409413 TTTATAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TATAATAATAATAATAATAA
Found at i:2411954 original size:24 final size:24
Alignment explanation
Indices: 2411879--2411956 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
2411869 AAACGAAGAT
*
2411879 ATCAGAACATAA-TCCAGATCAGAA
1 ATCAGAACATAATTCAAG-TCAGAA
* * *
2411903 ATCAAAACATAATTCAAGTAATG-T
1 ATCAGAACATAATTCAAGTCA-GAA
*
2411927 ATCAGAACAGAATTCAAGTCAGAA
1 ATCAGAACATAATTCAAGTCAGAA
2411951 ATCAGA
1 ATCAGA
2411957 TAAAATATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.02
24 37 0.86
25 5 0.12
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAACATAATTCAAGTCAGAA
Found at i:2414725 original size:20 final size:20
Alignment explanation
Indices: 2414700--2414747 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2414690 ACTGAAATTA
2414700 ACGACGAACGACAACGATTT
1 ACGACGAACGACAACGATTT
* *
2414720 ACGACGAACGATAATGATTT
1 ACGACGAACGACAACGATTT
*
2414740 ATGACGAA
1 ACGACGAA
2414748 TGGATTAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
ACGACGAACGACAACGATTT
Found at i:2416273 original size:24 final size:24
Alignment explanation
Indices: 2416246--2416354 Score: 96
Period size: 24 Copynumber: 4.5 Consensus size: 24
2416236 AAACGGAGAT
*
2416246 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
2416270 ATCAGATATCAGAATAGGATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
2416294 ATCAGAAATCAGAACAAAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
2416318 GTAATG-TATCATAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
2416341 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
2416355 TAAAATATTT
Statistics
Matches: 63, Mismatches: 19, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:2416328 original size:48 final size:47
Alignment explanation
Indices: 2416246--2416354 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 47
2416236 AAACGGAGAT
* * * * *
2416246 ATCAGAAATCAAAACAGAATTCAGATCAGATATCAGAATAGGATCCA
1 ATCAGAAATCAGAACAAAATTCAGATAAGATATCAGAACAGAATCCA
* * *
2416293 GATCAGAAATCAGAACAAAATTCAGGTAATG-TATCATAACAGAATTCA
1 -ATCAGAAATCAGAACAAAATTCAGATAA-GATATCAGAACAGAATCCA
2416341 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
2416355 TAAAATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 1 0.02
48 49 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAAAATTCAGATAAGATATCAGAACAGAATCCA
Found at i:2418604 original size:17 final size:18
Alignment explanation
Indices: 2418582--2418623 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2418572 TTTTGATCAA
2418582 AGTCAACGGTCAACGAT-
1 AGTCAACGGTCAACGATC
* *
2418599 AGTCAATGGTCAACGGTC
1 AGTCAACGGTCAACGATC
2418617 AGTCAAC
1 AGTCAAC
2418624 AGTTTTACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (18 bp):
AGTCAACGGTCAACGATC
Found at i:2425432 original size:17 final size:18
Alignment explanation
Indices: 2425406--2425441 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2425396 ACATTTCTCT
2425406 AAAATAATATAATTAATA
1 AAAATAATATAATTAATA
*
2425424 AAAAT-ATATAATTTATA
1 AAAATAATATAATTAATA
2425441 A
1 A
2425442 TTTATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATAATATAATTAATA
Found at i:2425655 original size:37 final size:36
Alignment explanation
Indices: 2425585--2425659 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 36
2425575 ATAAAAAAGC
*
2425585 AATTATAAATATAAAAAATTAAATTTAAAATTATTTA
1 AATTAAAAATATAAAAAATTAAA-TTAAAATTATTTA
2425622 AATTAAAAATA-AAAAATATTAAA-TAAATGATTATTTA
1 AATTAAAAATATAAAAA-ATTAAATTAAA--ATTATTTA
2425659 A
1 A
2425660 CTTATATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
35 4 0.12
36 5 0.15
37 25 0.74
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (36 bp):
AATTAAAAATATAAAAAATTAAATTAAAATTATTTA
Found at i:2425678 original size:12 final size:12
Alignment explanation
Indices: 2425663--2425713 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
2425653 TATTTAACTT
*
2425663 ATATAATAATTT
1 ATATAATAATTA
* *
2425675 ATATACTAACTA
1 ATATAATAATTA
2425687 ATATAATAA-TA
1 ATATAATAATTA
2425698 ATAATAATAATTA
1 AT-ATAATAATTA
2425711 ATA
1 ATA
2425714 CATAATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 25 0.76
13 4 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATAATAATTA
Found at i:2425697 original size:3 final size:3
Alignment explanation
Indices: 2425685--2425736 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
2425675 ATATACTAAC
2425685 TAA T-A TAA TAA TAA TAA TAA TAA TTAA TACA TAA TAA -AA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA-A TAA TAA TAA TAA TAA
2425729 -AA TAA TAA
1 TAA TAA TAA
2425737 AAAATAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.19
3 29 0.67
4 6 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2425712 original size:24 final size:24
Alignment explanation
Indices: 2425657--2425725 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
2425647 AATGATTATT
* * *
2425657 TAACTTATATAATAAT-TTATATAC
1 TAACTAATATAATAATAATA-ATAA
2425681 TAACTAATATAATAATAATAATAA
1 TAACTAATATAATAATAATAATAA
* *
2425705 TAATTAATA-CATAATAA-AATA
1 TAACTAATATAATAATAATAATA
2425726 TAAAATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 4 0.10
23 7 0.18
24 26 0.67
25 2 0.05
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
TAACTAATATAATAATAATAATAA
Found at i:2425735 original size:15 final size:16
Alignment explanation
Indices: 2425686--2425762 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 16
2425676 TATACTAACT
2425686 AATATAATAATAATAA
1 AATATAATAATAATAA
2425702 TAATAATTAATACATAATAA
1 -AAT-A-TAATA-ATAATAA
2425722 AATATAA-AATAATAA
1 AATATAATAATAATAA
* *
2425737 AAAATAACTAA-AATGA
1 AATATAA-TAATAATAA
*
2425753 AATAAAATAA
1 AATATAATAA
2425763 ACAGTGACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
15 16 0.31
16 10 0.20
17 8 0.16
18 2 0.04
19 8 0.16
20 7 0.14
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (16 bp):
AATATAATAATAATAA
Found at i:2425761 original size:26 final size:25
Alignment explanation
Indices: 2425715--2425790 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
2425705 TAATTAATAC
2425715 ATAA-TAAAATATAA-AATAATAAAAA
1 ATAACTAAAATA-AATAA-AATAAAAA
*
2425740 ATAACTAAAATGAAATAAAATAAACA
1 ATAACTAAAAT-AAATAAAATAAAAA
* * *
2425766 GTGACTAAAATAAATAAAATTAAAA
1 ATAACTAAAATAAATAAAATAAAAA
2425791 CTATAGTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 16 0.37
26 24 0.56
27 3 0.07
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (25 bp):
ATAACTAAAATAAATAAAATAAAAA
Found at i:2427038 original size:3 final size:3
Alignment explanation
Indices: 2427032--2427097 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
2427022 ATTATTTAAA
* * *
2427032 AAT AAT AAT AAT -AT AA- CAT AAT AAT AAT AAT AAT ATT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2427078 AAA AAT AAT AAT ACT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
2427098 AATGATATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
2 3 0.06
3 48 0.94
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2427600 original size:123 final size:119
Alignment explanation
Indices: 2427248--2427582 Score: 349
Period size: 123 Copynumber: 2.8 Consensus size: 119
2427238 CTTTAGGACT
* * * *
2427248 AGTTCTTTTTATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTTCTGTGATGTAATCTA
1 AGTTCTTCTCATTATGAACTCTTCCACTGGGGATGACAATTCATCTCCTTCTGTGATGTAATCTA
* * * *
2427313 GAAAAAATTTGAACAAA-TTCTTCTCATTATGAACTTCTTCTTCTTTTTCTGATG
66 G-AAAAAGTTGAACAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* * ** * *
2427367 AGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATG-CTGA-TCAATCTTCTTCTGTGATAG
1 AGTTCTTCTCATTATGAACT-CTTC---CACTGGGGATGAC-AATTC-ATCTCCTTCTGTGAT-G
** * * *
2427430 -CGTCGAGAAAAAGGTTG-ACCAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATG
59 TAATCTAGAAAAA-GTTGAACAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* *
2427490 AGTTCTTCTCATTATGAACTCTACCACCGGGGATGACAATTCATCTCCTTCTGTGATGTAATCTA
1 AGTTCTTCTCATTATGAACTCTTCCACTGGGGATGACAATTCATCTCCTTCTGTGATGTAATCTA
2427555 GCAAAAAGTTGAACAAAGTT-TTCTCATT
66 G-AAAAAGTTGAACAAAGTTCTTCTCATT
2427583 TTCAGATGAG
Statistics
Matches: 171, Mismatches: 31, Indels: 28
0.74 0.13 0.12
Matches are distributed among these distances:
118 1 0.01
119 55 0.32
120 18 0.11
122 14 0.08
123 82 0.48
124 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (119 bp):
AGTTCTTCTCATTATGAACTCTTCCACTGGGGATGACAATTCATCTCCTTCTGTGATGTAATCTA
GAAAAAGTTGAACAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
Found at i:2428626 original size:44 final size:44
Alignment explanation
Indices: 2428554--2428747 Score: 282
Period size: 44 Copynumber: 4.4 Consensus size: 44
2428544 AATCCAATAA
* * *
2428554 AGCTTTCATCTTTGAAAAGAGAATCTATCATCTTTGAAGAGA-GA
1 AGCTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGA-ATGT
* * * *
2428598 ATCTATCTTTTTTGAAGAGAGAAGCTATCATCTTTGAAGAATGT
1 AGCTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGT
*
2428642 AGCTATCATCTTTGAAGAGAAAATCTATCATCTTTGAAGAATGT
1 AGCTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGT
*
2428686 AGCTATCATCTTTGAATAGAGAATCTATCATCTTTGAAGAATGT
1 AGCTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGT
*
2428730 AGCTATCATCTTTTAAGA
1 AGCTATCATCTTTGAAGA
2428748 ATGTAGATAT
Statistics
Matches: 133, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
43 1 0.01
44 132 0.99
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (44 bp):
AGCTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGT
Found at i:2428735 original size:22 final size:22
Alignment explanation
Indices: 2428553--2428747 Score: 216
Period size: 22 Copynumber: 8.9 Consensus size: 22
2428543 AAATCCAATA
* *
2428553 AAGCTTTCATCTTTGAAAAGAG
1 AAGCTATCATCTTTGAAGAGAG
*
2428575 AATCTATCATCTTTGAAGAGAG
1 AAGCTATCATCTTTGAAGAGAG
* * *
2428597 AATCTATCTTTTTTGAAGAGAG
1 AAGCTATCATCTTTGAAGAGAG
2428619 AAGCTATCATCTTTGAAGA-ATG
1 AAGCTATCATCTTTGAAGAGA-G
* *
2428641 TAGCTATCATCTTTGAAGAGAA
1 AAGCTATCATCTTTGAAGAGAG
*
2428663 AATCTATCATCTTTGAAGA-ATG
1 AAGCTATCATCTTTGAAGAGA-G
* *
2428685 TAGCTATCATCTTTGAATAGAG
1 AAGCTATCATCTTTGAAGAGAG
*
2428707 AATCTATCATCTTTGAAGA-ATG
1 AAGCTATCATCTTTGAAGAGA-G
* *
2428729 TAGCTATCATCTTTTAAGA
1 AAGCTATCATCTTTGAAGA
2428748 ATGTAGATAT
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
21 3 0.02
22 141 0.97
23 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (22 bp):
AAGCTATCATCTTTGAAGAGAG
Found at i:2428736 original size:66 final size:66
Alignment explanation
Indices: 2428554--2428753 Score: 244
Period size: 66 Copynumber: 3.0 Consensus size: 66
2428544 AATCCAATAA
* * *
2428554 AGCTTTCATCTTTGAAAAGAGAATCTATCATCTTTGAAGAGAGAATCTATCTTTTTTGAAGAGA-
1 AGCTATCATCTTTGAAAAGAGAATCTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGA-AT
*
2428618 GA
65 GT
* * * *
2428620 AGCTATCATCTTTGAAGAA-TGTAGCTATCATCTTTGAAGAGAAAATCTATCATCTTTGAAGAAT
1 AGCTATCATCTTTGAA-AAGAGAATCTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAAT
2428684 GT
65 GT
* * * *
2428686 AGCTATCATCTTTGAATAGAGAATCTATCATCTTTGAAGA-ATGTAGCTATCATCTTTTAAGAAT
1 AGCTATCATCTTTGAAAAGAGAATCTATCATCTTTGAAGAGA-GAATCTATCATCTTTGAAGAAT
2428750 GT
65 GT
2428752 AG
1 AG
2428754 ATATAGATAT
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
65 3 0.03
66 109 0.96
67 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (66 bp):
AGCTATCATCTTTGAAAAGAGAATCTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATG
T
Found at i:2430228 original size:75 final size:75
Alignment explanation
Indices: 2430103--2430263 Score: 216
Period size: 75 Copynumber: 2.1 Consensus size: 75
2430093 TCTTCAACAA
* *
2430103 GCCCCAACATTGGCTAGTACAAACGTTCAAAATACATCAATATTCTTGATTCTGATTGAAAGGGG
1 GCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAATATTCTTGATTATGATTGAAAGGGG
2430168 CTTTCAGCAT
66 CTTTCAGCAT
* *** * *
2430178 GCCCCAACATTGGTTAATACAAACGTTCAAAATGTGTCAATATTAC-TGATTATGATTGACATGG
1 GCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAATATT-CTTGATTATGATTGAAAGGG
2430242 GCTTTCAGCAT
65 GCTTTCAGCAT
* *
2430253 GCTCCATCATT
1 GCCCCAACATT
2430264 TGCTTCTTGT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
75 74 0.99
76 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (75 bp):
GCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAATATTCTTGATTATGATTGAAAGGGG
CTTTCAGCAT
Found at i:2436590 original size:20 final size:20
Alignment explanation
Indices: 2436562--2436600 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2436552 GCAAAGATGC
* *
2436562 AAATGCAAAAATGAAAATGT
1 AAATACAAAAATAAAAATGT
*
2436582 AAATACAAACATAAAAATG
1 AAATACAAAAATAAAAATG
2436601 AAAAGATGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (20 bp):
AAATACAAAAATAAAAATGT
Found at i:2436869 original size:43 final size:43
Alignment explanation
Indices: 2436807--2436889 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
2436797 TGCATCAAAC
* *
2436807 AAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTCAAT
1 AAAACTTTTACATATAGGGGACAACTTTC-CTCCTAACTTCAAT
*
2436851 AAAAC-TTTACATATAGGGGATAACTTTCCTCCTAACTTC
1 AAAACTTTTACATATAGGGGACAACTTTCCTCCTAACTTC
2436890 TCTAAAGCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 10 0.28
43 21 0.58
44 5 0.14
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.33
Consensus pattern (43 bp):
AAAACTTTTACATATAGGGGACAACTTTCCTCCTAACTTCAAT
Found at i:2438182 original size:2 final size:2
Alignment explanation
Indices: 2438175--2438203 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2438165 ATAAAGAAGA
2438175 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2438204 ATAGTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2439136 original size:25 final size:27
Alignment explanation
Indices: 2439108--2439164 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
2439098 TAATAATAAT
*
2439108 AATAATAATTAAACA-T-A-TAAAATTA
1 AATAATAACTAAACAGTGACTAAAA-TA
2439133 AATAATAACTAAACAGTGACTAAAATA
1 AATAATAACTAAACAGTGACTAAAATA
2439160 AATAA
1 AATAA
2439165 ATTAAAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 14 0.50
26 1 0.04
27 8 0.29
28 5 0.18
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (27 bp):
AATAATAACTAAACAGTGACTAAAATA
Found at i:2439156 original size:28 final size:24
Alignment explanation
Indices: 2439100--2439164 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 24
2439090 AAAAATAATA
*
2439100 ATAATAAT-AATAATAATTAAACAT
1 ATAA-AATAAATAATAACTAAACAT
2439124 ATAAAATTAAATAATAACTAAACAGT
1 ATAAAA-TAAATAATAACTAAACA-T
2439150 GACTAAAATAAATAA
1 -A-TAAAATAAATAA
2439165 ATTAAAACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 2 0.06
24 5 0.14
25 14 0.40
26 1 0.03
27 8 0.23
28 5 0.14
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.28
Consensus pattern (24 bp):
ATAAAATAAATAATAACTAAACAT
Found at i:2440424 original size:3 final size:3
Alignment explanation
Indices: 2440418--2440498 Score: 71
Period size: 3 Copynumber: 28.0 Consensus size: 3
2440408 AATTATTATT
* * * *
2440418 TAA TAA TAA TAA TAA T-A TAA -CA TAA TAA -CA TAA TAA AAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2440463 TAA TAA TAA -AA TTAA TAA AAA TAA TAA TAC TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
2440499 AATGATATAA
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
2 6 0.10
3 53 0.87
4 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2440451 original size:27 final size:28
Alignment explanation
Indices: 2440419--2440512 Score: 90
Period size: 27 Copynumber: 3.4 Consensus size: 28
2440409 ATTATTATTT
* *
2440419 AATAATAATAATAATATAA-CATAATAA
1 AATAATAAAAATAATATAATAATAATAA
*
2440446 CATAATAAAAAT-AT-TAATAATAATAA
1 AATAATAAAAATAATATAATAATAATAA
*
2440472 AATTAATAAAAAT-A-ATAATACTAATAA
1 AA-TAATAAAAATAATATAATAATAATAA
2440499 AATGATATAAAAAT
1 AAT-A-ATAAAAAT
2440513 TTAGTGTCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
25 3 0.05
26 11 0.19
27 35 0.61
28 8 0.14
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (28 bp):
AATAATAAAAATAATATAATAATAATAA
Found at i:2442723 original size:24 final size:24
Alignment explanation
Indices: 2442696--2442747 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2442686 TAAAAGTAAT
2442696 ATATTTAATAAGTTAATATAAAAA
1 ATATTTAATAAGTTAATATAAAAA
** * *
2442720 ATATTTGTTAGGTTAATATATAAA
1 ATATTTAATAAGTTAATATAAAAA
2442744 ATAT
1 ATAT
2442748 GAATATATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (24 bp):
ATATTTAATAAGTTAATATAAAAA
Found at i:2443613 original size:74 final size:73
Alignment explanation
Indices: 2443492--2443638 Score: 285
Period size: 74 Copynumber: 2.0 Consensus size: 73
2443482 AATAAATATA
2443492 ATCTTCGAATCAGATCGTGCCACATGTCGCCATTCGATTGGAGGGTTTACTTTATTTAATTTAAT
1 ATCTTCGAATCAGATCGTGCCACATGTCGCCATTCGATTGGAGGGTTTAC-TTATTTAATTTAAT
2443557 AATTTTATT
65 AATTTTATT
2443566 ATCTTCGAATCAGATCGTGCCACATGTCGCCATTCGATTGGAGGGTTTACTTATTTAATTTAATA
1 ATCTTCGAATCAGATCGTGCCACATGTCGCCATTCGATTGGAGGGTTTACTTATTTAATTTAATA
2443631 ATTTTATT
66 ATTTTATT
2443639 TCGCACCAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 23 0.32
74 50 0.68
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.41
Consensus pattern (73 bp):
ATCTTCGAATCAGATCGTGCCACATGTCGCCATTCGATTGGAGGGTTTACTTATTTAATTTAATA
ATTTTATT
Found at i:2444106 original size:36 final size:31
Alignment explanation
Indices: 2444028--2444101 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2444018 TTATTTTAAC
* * *
2444028 ATATTTTAATCTTATCTTATCTTAAAAATAT
1 ATATTTTATTTTTATCTTAACTTAAAAATAT
2444059 ATATTTTATTTTTATCTTAACTTATAAAA-AT
1 ATATTTTATTTTTATCTTAACTTA-AAAATAT
*
2444090 ATAGTTTATTTT
1 ATATTTTATTTT
2444102 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.55
Consensus pattern (31 bp):
ATATTTTATTTTTATCTTAACTTAAAAATAT
Found at i:2444128 original size:29 final size:28
Alignment explanation
Indices: 2444086--2444175 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
2444076 TAACTTATAA
* **
2444086 AAATATAGTTTATTTTATTTTAAATTATT
1 AAATATA-TTTATTCTAACTTAAATTATT
*
2444115 ACATATATTATATTCTAACTTAAATTATT
1 AAATATATT-TATTCTAACTTAAATTATT
* *
2444144 AAATATATTCTAGTCTTACCTTAAATTATT
1 AAATATATT-TATTC-TAACTTAAATTATT
2444174 AA
1 AA
2444176 TTAATCGTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.04
29 34 0.67
30 15 0.29
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (28 bp):
AAATATATTTATTCTAACTTAAATTATT
Found at i:2444377 original size:28 final size:29
Alignment explanation
Indices: 2444325--2444431 Score: 96
Period size: 28 Copynumber: 3.8 Consensus size: 29
2444315 AATATTTCAA
* * *
2444325 TTAAAGTAAGAATAAATTATGTTTTAAAG
1 TTAAAATAAGAATAAAATATATTTTAAAG
* * *
2444354 TTAATAA-AA-ATTAAAATATATTTTTAAT
1 TTAA-AATAAGAATAAAATATATTTTAAAG
2444382 TTAAAATAAGAATAAAATATATTTT-AA-
1 TTAAAATAAGAATAAAATATATTTTAAAG
**
2444409 TATATGATAAGAATAAAATATAT
1 T-TAAAATAAGAATAAAATATAT
2444432 ATTTTTAATG
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
27 3 0.05
28 41 0.63
29 20 0.31
30 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
TTAAAATAAGAATAAAATATATTTTAAAG
Found at i:2444393 original size:57 final size:59
Alignment explanation
Indices: 2444307--2444440 Score: 150
Period size: 57 Copynumber: 2.3 Consensus size: 59
2444297 TTATTACCAG
* * * * *
2444307 AAAATATAAATATTTCAA-TTAAAGTAAGAATAAATTATGTTTTAA-AGT-TAATAAAAAT
1 AAAATATATAT-TTTTAATTTAAAATAAGAATAAAATATATTTTAATA-TATAATAAAAAT
* * *
2444365 TAAA-ATATATTTTTAATTTAAAATAAGAATAAAATATATTTTAATATATGATAAGAAT
1 AAAATATATATTTTTAATTTAAAATAAGAATAAAATATATTTTAATATATAATAAAAAT
2444423 AAAATATATATTTTTAAT
1 AAAATATATATTTTTAAT
2444441 GTTTAGATGT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
56 5 0.08
57 30 0.48
58 15 0.24
59 13 0.21
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAATATATATTTTTAATTTAAAATAAGAATAAAATATATTTTAATATATAATAAAAAT
Found at i:2446532 original size:21 final size:21
Alignment explanation
Indices: 2446506--2446552 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2446496 ATCCGACAGA
2446506 TGAAGCAATAATTTATGAATT
1 TGAAGCAATAATTTATGAATT
*
2446527 TGAAGCAATAGTTTATGAATT
1 TGAAGCAATAATTTATGAATT
2446548 TGAAG
1 TGAAG
2446553 TAATGGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.36
Consensus pattern (21 bp):
TGAAGCAATAATTTATGAATT
Found at i:2457779 original size:16 final size:16
Alignment explanation
Indices: 2457758--2457790 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2457748 TTATCGGAGG
2457758 TTTATCAAGGACTTTT
1 TTTATCAAGGACTTTT
*
2457774 TTTATCAATGACTTTT
1 TTTATCAAGGACTTTT
2457790 T
1 T
2457791 GAAGATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (16 bp):
TTTATCAAGGACTTTT
Found at i:2459623 original size:14 final size:14
Alignment explanation
Indices: 2459604--2459630 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2459594 ACCCATTTCG
2459604 TTTTCTTTTAATTC
1 TTTTCTTTTAATTC
2459618 TTTTCTTTTAATT
1 TTTTCTTTTAATT
2459631 TATTTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTAATTC
Found at i:2459650 original size:13 final size:13
Alignment explanation
Indices: 2459629--2459662 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2459619 TTTCTTTTAA
*
2459629 TTTATTTTTAAAT
1 TTTAGTTTTAAAT
2459642 TTTAGTTTTAAAT
1 TTTAGTTTTAAAT
*
2459655 TTTCGTTT
1 TTTAGTTT
2459663 ATTATTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (13 bp):
TTTAGTTTTAAAT
Found at i:2462505 original size:10 final size:10
Alignment explanation
Indices: 2462490--2462518 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2462480 TCAAGCAGAT
2462490 GAAAAAAAGA
1 GAAAAAAAGA
2462500 GAAAAAAAGA
1 GAAAAAAAGA
2462510 -AAAAAAAGA
1 GAAAAAAAGA
2462519 ATGTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
GAAAAAAAGA
Found at i:2463494 original size:19 final size:20
Alignment explanation
Indices: 2463451--2463498 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2463441 ATTAGGATTT
*
2463451 ATATTATTTTTATGTTTAGG
1 ATATTATTTTTATGTTTAGA
2463471 A-ATTATCTTTTAT-TTT-GA
1 ATATTAT-TTTTATGTTTAGA
2463489 ATATTATTTT
1 ATATTATTTT
2463499 CTAGATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.20
19 13 0.52
20 7 0.28
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (20 bp):
ATATTATTTTTATGTTTAGA
Found at i:2466981 original size:58 final size:57
Alignment explanation
Indices: 2466779--2466989 Score: 169
Period size: 58 Copynumber: 3.6 Consensus size: 57
2466769 ATAATACTTT
* * * *
2466779 ATTCTCAAG-AAATAAATTCAATGATTTAATTTC-TTTTACAAAACAGAATCATATAAG
1 ATTCT-AAGAAAATAAATTCAACGATTT-ATTTCTTTTTACCAAACAAAATCATATCAG
* * * * ** *
2466836 ATTCTATGAAAATAAATTTAACAATTTATTTCCTTCTTA-CAAGATGAAATCGT-TCAAG
1 ATTCTAAGAAAATAAATTCAACGATTTATTT-CTTTTTACCAA-ACAAAATCATATC-AG
* ** *
2466894 ATTTCCAAGAAAATAAATTTTACGTTTTATTTCTTTTTACCAAACAAAATCATATCAG
1 A-TTCTAAGAAAATAAATTCAACGATTTATTTCTTTTTACCAAACAAAATCATATCAG
* * *
2466952 ATTAATAAGAAAATAAATTCAATGATTTATTCCTTTTT
1 ATT-CTAAGAAAATAAATTCAACGATTTATTTCTTTTT
2466990 CAAAGTTAGA
Statistics
Matches: 118, Mismatches: 27, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
56 6 0.05
57 26 0.22
58 56 0.47
59 30 0.25
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.39
Consensus pattern (57 bp):
ATTCTAAGAAAATAAATTCAACGATTTATTTCTTTTTACCAAACAAAATCATATCAG
Found at i:2468697 original size:26 final size:26
Alignment explanation
Indices: 2468639--2468689 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
2468629 AGATCAAGCC
2468639 AAATATTAGCCACTAGTCCACATAAG
1 AAATATTAGCCACTAGTCCACATAAG
*
2468665 AAATATTAGCCACTAGTTCACATAA
1 AAATATTAGCCACTAGTCCACATAA
2468690 TCAATATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (26 bp):
AAATATTAGCCACTAGTCCACATAAG
Found at i:2468837 original size:19 final size:19
Alignment explanation
Indices: 2468813--2468853 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2468803 CATAATCAAT
*
2468813 AAAAAA-AACACAAGTATTC
1 AAAAAACAAC-CAAATATTC
2468832 AAAAAACAACCAAATATTC
1 AAAAAACAACCAAATATTC
2468851 AAA
1 AAA
2468854 TAACCAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.66, C:0.17, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAAAACAACCAAATATTC
Found at i:2476427 original size:60 final size:60
Alignment explanation
Indices: 2476363--2476484 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
2476353 AAACCTCACA
2476363 AGGTAAGATGTTTGCACAATTCTAAAACAAAGAAAGAACGCTAAAAAATGAATATAATTG
1 AGGTAAGATGTTTGCACAATTCTAAAACAAAGAAAGAACGCTAAAAAATGAATATAATTG
*
2476423 AGGTAAGATGTTTGCACAATTCTAGAACAAAGAAAGAACGCTAAAAAATGAATATAATTG
1 AGGTAAGATGTTTGCACAATTCTAAAACAAAGAAAGAACGCTAAAAAATGAATATAATTG
2476483 AG
1 AG
2476485 CACAAATTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (60 bp):
AGGTAAGATGTTTGCACAATTCTAAAACAAAGAAAGAACGCTAAAAAATGAATATAATTG
Found at i:2483260 original size:31 final size:31
Alignment explanation
Indices: 2483224--2483282 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2483214 AACTTAAAAG
*
2483224 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
2483255 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2483283 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2483331 original size:22 final size:22
Alignment explanation
Indices: 2483306--2483759 Score: 621
Period size: 22 Copynumber: 20.6 Consensus size: 22
2483296 ATAATAAATT
2483306 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
2483328 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
2483350 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
2483372 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
2483394 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* ***
2483416 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
2483438 TTTTAAAATAAATCAATACATA
1 TTTTAAAATAAATCAATTCATA
* *
2483460 TTTTAAACTAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
2483482 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
2483504 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
2483526 TTTTAAAA-AATATCAATTCATA
1 TTTTAAAATAA-ATCAATTCATA
***
2483548 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
2483570 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
2483592 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
2483614 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATTCATA
*
2483636 TTTTAAAATAAATCAATACATA
1 TTTTAAAATAAATCAATTCATA
**
2483658 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
2483680 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
2483702 TTTTAAAAATAAATCAATCCATA
1 TTTT-AAAATAAATCAATTCATA
2483725 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
2483747 TTTTAAAATAAAT
1 TTTTAAAATAAAT
2483760 TTTAAAATAG
Statistics
Matches: 385, Mismatches: 37, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
21 9 0.02
22 350 0.91
23 25 0.06
24 1 0.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:2483763 original size:12 final size:12
Alignment explanation
Indices: 2483746--2483776 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2483736 ATCAATCTAT
2483746 ATTTTAAAATAA
1 ATTTTAAAATAA
*
2483758 ATTTTAAAATAG
1 ATTTTAAAATAA
2483770 ATTTTAA
1 ATTTTAA
2483777 TTTTCCCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:2484276 original size:2 final size:2
Alignment explanation
Indices: 2484269--2484313 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2484259 TATAAACCAA
2484269 AT AT AT AT AT AT AT AT AT AT AT A- 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
2484310 AT AT
1 AT AT
2484314 TCACACATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2484518 original size:25 final size:26
Alignment explanation
Indices: 2484483--2484617 Score: 150
Period size: 26 Copynumber: 5.3 Consensus size: 26
2484473 ATAGTGCTCA
**
2484483 TATCACTTGCACTCGTAAGTGCCACG
1 TATCACTTGCACTCAAAAGTGCCACG
*
2484509 TATCAC-TGCACTCAAAAGTGTCACG
1 TATCACTTGCACTCAAAAGTGCCACG
*
2484534 TATCACTTGCACT-AGTAAGTGCCACG
1 TATCACTTGCACTCA-AAAGTGCCACG
* * *
2484560 TATCGC-TACACTCAAAAGTGTCACG
1 TATCACTTGCACTCAAAAGTGCCACG
* * *
2484585 TATCACTTACACTTAAAAGTGCCACA
1 TATCACTTGCACTCAAAAGTGCCACG
2484611 TATCACT
1 TATCACT
2484618 GAATGTATAA
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
25 42 0.46
26 50 0.54
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (26 bp):
TATCACTTGCACTCAAAAGTGCCACG
Found at i:2484542 original size:51 final size:51
Alignment explanation
Indices: 2484483--2484618 Score: 202
Period size: 51 Copynumber: 2.7 Consensus size: 51
2484473 ATAGTGCTCA
*
2484483 TATCACTTGCACTCGTAAGTGCCACGTATCACTGCACTCAAAAGTGTCACG
1 TATCACTTGCACTAGTAAGTGCCACGTATCACTGCACTCAAAAGTGTCACG
* *
2484534 TATCACTTGCACTAGTAAGTGCCACGTATCGCTACACTCAAAAGTGTCACG
1 TATCACTTGCACTAGTAAGTGCCACGTATCACTGCACTCAAAAGTGTCACG
* * *
2484585 TATCACTTACACTTA-AAAGTGCCACATATCACTG
1 TATCACTTGCAC-TAGTAAGTGCCACGTATCACTG
2484619 AATGTATAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
51 74 0.97
52 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (51 bp):
TATCACTTGCACTAGTAAGTGCCACGTATCACTGCACTCAAAAGTGTCACG
Found at i:2487321 original size:29 final size:30
Alignment explanation
Indices: 2487272--2487328 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
2487262 ATCCTTAAAC
*
2487272 TTTTCCAAAATTTATTCTTTGGCCACTAAG
1 TTTTCCAAAATTTAATCTTTGGCCACTAAG
*
2487302 TTTT-CAAAATTTACAT-TTTGGTCACTA
1 TTTTCCAAAATTTA-ATCTTTGGCCACTA
2487329 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.46
Consensus pattern (30 bp):
TTTTCCAAAATTTAATCTTTGGCCACTAAG
Found at i:2489499 original size:21 final size:21
Alignment explanation
Indices: 2489475--2489516 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2489465 AACTAGGGGA
* *
2489475 AGGAAACACTTACCTTGGGTT
1 AGGAAAAACATACCTTGGGTT
2489496 AGGAAAAACATACCTTGGGTT
1 AGGAAAAACATACCTTGGGTT
2489517 GAGTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (21 bp):
AGGAAAAACATACCTTGGGTT
Found at i:2499509 original size:176 final size:174
Alignment explanation
Indices: 2499199--2499549 Score: 595
Period size: 173 Copynumber: 2.0 Consensus size: 174
2499189 TTAGCTCGCT
2499199 GCTCCTCTCGGATGCCTAGCTCGCCCTCCTGGAGCTTATCAATGGAGCAACACCACTCAAGGAAG
1 GCTCCTCTCGGATGCCTAGCTCGCCCTCCTGGAGCTTATCAATGGAGCAACACCACTCAAGGAAG
2499264 AAGAGGGAAACGGTGAAAAGAAAATAAATAAAGGTGAAATTCCTCTCTCTCTATACCGTATTCCC
66 AAGAGGGAAACGGTGAAAAGAAAATAAATAAAGGTGAAATTCCTCTCTCTC-ATACCGTATTCCC
2499329 TTCT-CCCATGAGGT-T-A-ATATAATAAAAATATCTAGGGGTAA
130 TTCTCCCCATGAGGTGTAATATATAATAAAAATATCTAGGGGTAA
2499370 GCTCCTCTCGGATGCCTAGCTCGCCACTCCTTGGAGCTTATCAATGGAGCAACACCACTCAAGGA
1 GCTCCTCTCGGATGCCTAGCTCGCC-CTCC-TGGAGCTTATCAATGGAGCAACACCACTCAAGGA
2499435 AGAAGAAGGGAAACGGTGAAAAAGAAAATAAAATAAAGGTGAAATTCCTCTCTGCTC-TACCGTA
64 AGAAG-AGGGAAACGGTG-AAAAGAAAAT-AAATAAAGGTGAAATTCCTCTCT-CTCATACCGTA
2499499 TTTCCCTTCTCCCCATGAGGTGTAATATATAATAAAAATATCTAGGGGTAA
125 -TTCCCTTCTCCCCATGAGGTGTAATATATAATAAAAATATCTAGGGGTAA
2499550 TGATGAGGTT
Statistics
Matches: 169, Mismatches: 0, Indels: 13
0.93 0.00 0.07
Matches are distributed among these distances:
171 25 0.15
172 4 0.02
173 39 0.23
174 12 0.07
175 17 0.10
176 32 0.19
177 13 0.08
178 1 0.01
179 1 0.01
180 25 0.15
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (174 bp):
GCTCCTCTCGGATGCCTAGCTCGCCCTCCTGGAGCTTATCAATGGAGCAACACCACTCAAGGAAG
AAGAGGGAAACGGTGAAAAGAAAATAAATAAAGGTGAAATTCCTCTCTCTCATACCGTATTCCCT
TCTCCCCATGAGGTGTAATATATAATAAAAATATCTAGGGGTAA
Found at i:2502320 original size:27 final size:27
Alignment explanation
Indices: 2502289--2502356 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
2502279 GAAGATGAAG
*
2502289 AAATGAGAGAGAAAAAGAAAAAGTTAC
1 AAATGAGAGAGAAAAAGAAAAAGTTAA
*
2502316 AAATGAAAGAGAAAAAGAAAAAGTTAA
1 AAATGAGAGAGAAAAAGAAAAAGTTAA
2502343 AAATGAGAGAGAAA
1 AAATGAGAGAGAAA
2502357 TGTGTGATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.10
Consensus pattern (27 bp):
AAATGAGAGAGAAAAAGAAAAAGTTAA
Found at i:2519756 original size:27 final size:28
Alignment explanation
Indices: 2519726--2519860 Score: 139
Period size: 29 Copynumber: 4.8 Consensus size: 28
2519716 TATCTTTATT
*
2519726 CTGATTCTGCATTAGATTATCA-AT-GTC
1 CTGATTCTGCATGAGATTAT-ATATCGTC
*
2519753 CTGATTCTGCATGAGATTATATCTCGTC
1 CTGATTCTGCATGAGATTATATATCGTC
* *
2519781 CTGATTCTGCATGGGATTATATTCTCGTC
1 CTGATTCTGCATGAGATTATA-TATCGTC
* **
2519810 CTGATTCTGCATGGGATTATATCCCCGTC
1 CTGATTCTGCATGAGATTATAT-ATCGTC
* * *
2519839 CTCATTCTGTATGGGATTATAT
1 CTGATTCTGCATGAGATTATAT
2519861 CTCTGTCTTG
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.01
27 20 0.20
28 24 0.24
29 53 0.54
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (28 bp):
CTGATTCTGCATGAGATTATATATCGTC
Found at i:2519861 original size:29 final size:29
Alignment explanation
Indices: 2519750--2519861 Score: 172
Period size: 29 Copynumber: 3.9 Consensus size: 29
2519740 GATTATCAAT
*
2519750 GTCCTGATTCTGCATGAGATTATAT-CTC
1 GTCCTGATTCTGCATGGGATTATATCCTC
*
2519778 GTCCTGATTCTGCATGGGATTATATTCTC
1 GTCCTGATTCTGCATGGGATTATATCCTC
*
2519807 GTCCTGATTCTGCATGGGATTATATCCCC
1 GTCCTGATTCTGCATGGGATTATATCCTC
* *
2519836 GTCCTCATTCTGTATGGGATTATATC
1 GTCCTGATTCTGCATGGGATTATATC
2519862 TCTGTCTTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
28 24 0.31
29 54 0.69
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (29 bp):
GTCCTGATTCTGCATGGGATTATATCCTC
Found at i:2519877 original size:29 final size:29
Alignment explanation
Indices: 2519749--2519876 Score: 170
Period size: 29 Copynumber: 4.4 Consensus size: 29
2519739 AGATTATCAA
*
2519749 TGTCCTGATTCTGCATGAGATTATATCTC
1 TGTCCTGATTCTGCATGGGATTATATCTC
2519778 -GTCCTGATTCTGCATGGGATTATAT-TC
1 TGTCCTGATTCTGCATGGGATTATATCTC
*
2519805 TCGTCCTGATTCTGCATGGGATTATATCCC
1 T-GTCCTGATTCTGCATGGGATTATATCTC
* * *
2519835 CGTCCTCATTCTGTATGGGATTATATCTC
1 TGTCCTGATTCTGCATGGGATTATATCTC
* *
2519864 TGTCTTGTTTCTG
1 TGTCCTGATTCTG
2519877 TTTAGATCAT
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
27 2 0.02
28 24 0.28
29 59 0.69
30 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (29 bp):
TGTCCTGATTCTGCATGGGATTATATCTC
Found at i:2522407 original size:2 final size:2
Alignment explanation
Indices: 2522400--2522445 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2522390 CGTTCTATTC
2522400 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
2522442 AT AT
1 AT AT
2522446 CCAACAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2526359 original size:4 final size:4
Alignment explanation
Indices: 2526350--2526391 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
2526340 TTCAACTATG
2526350 TATT TATT TA-T TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
2526392 ACATGCATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Done.