Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 63 of 127
Found at i:12327585 original size:11 final size:11
Alignment explanation
Indices: 12327554--12327589 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
12327544 GATAAATTTT
12327554 ATAATAAAAAA
1 ATAATAAAAAA
12327565 ATCAATAAAAAA
1 AT-AATAAAAAA
*
12327577 ATAACAAAAAA
1 ATAATAAAAAA
12327588 AT
1 AT
12327590 CTATATCCGA
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:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (11 bp):
ATAATAAAAAA
Found at i:12327770 original size:16 final size:15
Alignment explanation
Indices: 12327739--12327782 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
12327729 GTATATATAA
12327739 ATATATATTTATTATTT
1 ATATAT-TTTA-TATTT
*
12327756 ATTTAATTTTATATTT
1 ATAT-ATTTTATATTT
12327772 ATATATTTTAT
1 ATATATTTTAT
12327783 TTAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 7 0.29
18 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATATTTTATATTT
Found at i:12327795 original size:25 final size:23
Alignment explanation
Indices: 12327736--12327797 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 23
12327726 ATGGTATATA
12327736 TAAATATATATTTATTATTTATT
1 TAAATATATATTTATTATTTATT
* *
12327759 TAATTTTATATTTATATATTTTATT
1 TAAATATATATTTAT-TA-TTTATT
12327784 TAAA-ATATTATTTA
1 TAAATATA-TATTTA
12327798 ATACATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 13 0.41
24 4 0.12
25 15 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TAAATATATATTTATTATTTATT
Found at i:12327878 original size:17 final size:16
Alignment explanation
Indices: 12327846--12327879 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12327836 TTTTCTTATC
*
12327846 ATTTTTTAAAAAATTT
1 ATTTATTAAAAAATTT
12327862 ATTTATTAAATAAATTT
1 ATTTATTAAA-AAATTT
12327879 A
1 A
12327880 AAAAAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATTAAAAAATTT
Found at i:12328127 original size:30 final size:31
Alignment explanation
Indices: 12328092--12328167 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
12328082 ATTTAATTTA
*
12328092 TATTTATATGTATT-ATATTAAT-AAAAATAT
1 TATTTATATATATTAAT-TTAATAAAAAATAT
*
12328122 TATTTA-ATATCTTAATTTAATAAAAAATAT
1 TATTTATATATATTAATTTAATAAAAAATAT
12328152 T-TTTATATATAATTAA
1 TATTTATATAT-ATTAA
12328168 GTTATAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 14 0.36
30 21 0.54
31 4 0.10
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
TATTTATATATATTAATTTAATAAAAAATAT
Found at i:12337660 original size:24 final size:24
Alignment explanation
Indices: 12337633--12337704 Score: 90
Period size: 25 Copynumber: 3.0 Consensus size: 24
12337623 TTGTGGGTTG
* *
12337633 TGGTTTAATAAAACTGAGTTTTTA
1 TGGTTTGATAAAACTGAGTTTTCA
*
12337657 TGGTTTGATAAAAACTAAGTTTTCA
1 TGGTTTGAT-AAAACTGAGTTTTCA
* *
12337682 TGGTCTGATAAAACTGAGGTTTC
1 TGGTTTGATAAAACTGAGTTTTC
12337705 GTTTTAAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (24 bp):
TGGTTTGATAAAACTGAGTTTTCA
Found at i:12341846 original size:24 final size:24
Alignment explanation
Indices: 12341791--12341847 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
12341781 TATATTATTC
12341791 TAAAAAATTAAAATATTTAAAAAA
1 TAAAAAATTAAAATATTTAAAAAA
** * *
12341815 TATTAAATTAATAT-TTTAAATATA
1 TAAAAAATTAAAATATTTAAA-AAA
12341839 TAAAAAATT
1 TAAAAAATT
12341848 TTCTAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAAAATTAAAATATTTAAAAAA
Found at i:12342296 original size:15 final size:17
Alignment explanation
Indices: 12342278--12342312 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
12342268 CTTTGGGATG
12342278 TGAGAT-TTTGAGTT-A
1 TGAGATATTTGAGTTGA
12342293 TGAGATATTTGAGTTGA
1 TGAGATATTTGAGTTGA
12342310 TGA
1 TGA
12342313 CTTTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (17 bp):
TGAGATATTTGAGTTGA
Found at i:12351193 original size:71 final size:71
Alignment explanation
Indices: 12351129--12351289 Score: 177
Period size: 71 Copynumber: 2.3 Consensus size: 71
12351119 AAAACGTAGT
* * * *
12351129 TCTTGTTGAAACTAT-AGAATTTTGAAAATATAATT-TCAACATCTATTATATTTTTATGTAAAA
1 TCTTGTTGAAACTATGA-AATTCTAAAAATATAATTGT-AACATCCATTACATTTTTATGTAAAA
*
12351192 AATACAAC
64 AACACAAC
* * *
12351200 TCTTGTTGAAATTATGAAATTCTAAAAATATAATTGTAACATCCATTACATTTTTATCTTAAAAA
1 TCTTGTTGAAACTATGAAATTCTAAAAATATAATTGTAACATCCATTACATTTTTATGTAAAAAA
**
12351265 TGCAA-
66 CACAAC
12351270 TCATTGTTGAAACTAT-AAAT
1 TC-TTGTTGAAACTATGAAAT
12351290 AACAAAAATC
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
70 6 0.08
71 70 0.90
72 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (71 bp):
TCTTGTTGAAACTATGAAATTCTAAAAATATAATTGTAACATCCATTACATTTTTATGTAAAAAA
CACAAC
Found at i:12351730 original size:20 final size:20
Alignment explanation
Indices: 12351691--12351730 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12351681 TTTATTAATA
* *
12351691 TTATATATATAAATATAAAT
1 TTATATAAATAAATAAAAAT
*
12351711 TTATATAAATAATTAAAAAT
1 TTATATAAATAAATAAAAAT
12351731 ATTTACATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTATATAAATAAATAAAAAT
Found at i:12352826 original size:16 final size:16
Alignment explanation
Indices: 12352805--12352835 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12352795 AAAGTAATTT
12352805 TTTATTAGTTTTTAAA
1 TTTATTAGTTTTTAAA
*
12352821 TTTATTATTTTTTAA
1 TTTATTAGTTTTTAA
12352836 TTATAATTTT
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTATTAGTTTTTAAA
Found at i:12352839 original size:14 final size:15
Alignment explanation
Indices: 12352805--12352847 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
12352795 AAAGTAATTT
*
12352805 TTTATTAGTTTTTAAA
1 TTTATTA-TTTTTTAA
12352821 TTTATTATTTTTTAA
1 TTTATTATTTTTTAA
*
12352836 -TTATAATTTTTT
1 TTTATTATTTTTT
12352848 TCATTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.44
15 7 0.28
16 7 0.28
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTATTATTTTTTAA
Found at i:12356751 original size:7 final size:7
Alignment explanation
Indices: 12356729--12356784 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
12356719 ATTTCAAATC
*
12356729 AAATTCA
1 AAATTAA
*
12356736 AATTTAA
1 AAATTAA
12356743 AAATTAA
1 AAATTAA
*
12356750 AATTTAA
1 AAATTAA
12356757 AAATTAA
1 AAATTAA
*
12356764 AATTTAA
1 AAATTAA
12356771 AAATTAA
1 AAATTAA
*
12356778 AATTTAA
1 AAATTAA
12356785 TTAAATTTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (7 bp):
AAATTAA
Found at i:12356752 original size:14 final size:14
Alignment explanation
Indices: 12356729--12356784 Score: 103
Period size: 14 Copynumber: 4.0 Consensus size: 14
12356719 ATTTCAAATC
*
12356729 AAATTCAAATTTAA
1 AAATTAAAATTTAA
12356743 AAATTAAAATTTAA
1 AAATTAAAATTTAA
12356757 AAATTAAAATTTAA
1 AAATTAAAATTTAA
12356771 AAATTAAAATTTAA
1 AAATTAAAATTTAA
12356785 TTAAATTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTAAAATTTAA
Found at i:12357997 original size:22 final size:23
Alignment explanation
Indices: 12357954--12358002 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
12357944 TTTTCTCATC
12357954 TTTGGGGGCGTCCAAAGAAAAAT
1 TTTGGGGGCGTCCAAAGAAAAAT
* **
12357977 TTTGGGGGTGTCCAGTGAAAAAT
1 TTTGGGGGCGTCCAAAGAAAAAT
12358000 TTT
1 TTT
12358003 CCTTTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.31
Consensus pattern (23 bp):
TTTGGGGGCGTCCAAAGAAAAAT
Found at i:12362462 original size:213 final size:213
Alignment explanation
Indices: 12362095--12362521 Score: 836
Period size: 213 Copynumber: 2.0 Consensus size: 213
12362085 ATAGTGTAGT
12362095 ATACGGTAGGCAGCTTGTAGGTGCCCTTTTTTAGGATTATGTATAAATTGACTTATCACACTCGC
1 ATACGGTAGGCAGCTTGTAGGTGCCCTTTTTTAGGATTATGTATAAATTGACTTATCACACTCGC
12362160 ATCATAAGCTATATCAAGCGTAGTATGTGAGAGATAAATAAGTCTTCCAACTAATCTTTGGTACA
66 ATCATAAGCTATATCAAGCGTAGTATGTGAGAGATAAATAAGTCTTCCAACTAATCTTTGGTACA
12362225 TGTCTCTATCTACAGCAGCATTTTCGTTAGCTTCTCCGAGTTTATGATTAAGATCTATAGGGGTA
131 TGTCTCTATCTACAGCAGCATTTTCGTTAGCTTCTCCGAGTTTATGATTAAGATCTATAGGGGTA
12362290 TTTGCAAGTTTACATGTG
196 TTTGCAAGTTTACATGTG
*
12362308 ATACGGTAGGCAGCTTGTAGGTGCCCTTTTTTAGGATTATGTGTAAATTGACTTATCACACTCGC
1 ATACGGTAGGCAGCTTGTAGGTGCCCTTTTTTAGGATTATGTATAAATTGACTTATCACACTCGC
*
12362373 ATCATAAGCTATATCAAGCGTAGTATGTGAGAGATAAATGAGTCTTCCAACTAATCTTTGGTACA
66 ATCATAAGCTATATCAAGCGTAGTATGTGAGAGATAAATAAGTCTTCCAACTAATCTTTGGTACA
12362438 TGTCTCTATCTACAGCAGCATTTTCGTTAGCTTCTCCGAGTTTATGATTAAGATCTATAGGGGTA
131 TGTCTCTATCTACAGCAGCATTTTCGTTAGCTTCTCCGAGTTTATGATTAAGATCTATAGGGGTA
12362503 TTTGCAAGTTTACATGTG
196 TTTGCAAGTTTACATGTG
12362521 A
1 A
12362522 GCTTCCTAGT
Statistics
Matches: 212, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 212 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (213 bp):
ATACGGTAGGCAGCTTGTAGGTGCCCTTTTTTAGGATTATGTATAAATTGACTTATCACACTCGC
ATCATAAGCTATATCAAGCGTAGTATGTGAGAGATAAATAAGTCTTCCAACTAATCTTTGGTACA
TGTCTCTATCTACAGCAGCATTTTCGTTAGCTTCTCCGAGTTTATGATTAAGATCTATAGGGGTA
TTTGCAAGTTTACATGTG
Found at i:12364484 original size:19 final size:19
Alignment explanation
Indices: 12364460--12364497 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12364450 AGAGGGACCA
12364460 CATGTCACTATGAATCAAG
1 CATGTCACTATGAATCAAG
12364479 CATGTCACTATGAATCAAG
1 CATGTCACTATGAATCAAG
12364498 TAAAGAGTAG
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:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (19 bp):
CATGTCACTATGAATCAAG
Found at i:12364767 original size:16 final size:16
Alignment explanation
Indices: 12364746--12364778 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12364736 TTGTGTTGTT
12364746 TGATGTCTCAAGATAG
1 TGATGTCTCAAGATAG
12364762 TGATGTCTCAAGATAG
1 TGATGTCTCAAGATAG
12364778 T
1 T
12364779 ATAGTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (16 bp):
TGATGTCTCAAGATAG
Found at i:12369884 original size:22 final size:22
Alignment explanation
Indices: 12369856--12369899 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12369846 ATTTTCTGTT
* *
12369856 CTTAATTGTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
12369878 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
12369900 TAAATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:12373960 original size:22 final size:22
Alignment explanation
Indices: 12373935--12373978 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12373925 ATTTTTTATC
*
12373935 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
12373957 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
12373979 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:12376066 original size:22 final size:21
Alignment explanation
Indices: 12376030--12376071 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
12376020 ACTGCATTTT
12376030 GAAAAAAAAAAAATGAAAAAG
1 GAAAAAAAAAAAATGAAAAAG
*
12376051 GAAAGAAAGAAAAATGAAAAA
1 GAAA-AAAAAAAAATGAAAAA
12376072 AGCCACCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (21 bp):
GAAAAAAAAAAAATGAAAAAG
Found at i:12385182 original size:20 final size:20
Alignment explanation
Indices: 12385146--12385184 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12385136 ATTAAAAATT
*
12385146 AATATTTTATATTTTTAAAA
1 AATATTTTATATATTTAAAA
12385166 AATATTTTAT-TAATTTAAA
1 AATATTTTATAT-ATTTAAA
12385185 TCCGATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTTTATATATTTAAAA
Found at i:12386810 original size:24 final size:24
Alignment explanation
Indices: 12386778--12386825 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
12386768 ACTCGACTCT
12386778 AACTCTAATTCCTAGCTAATTCAC
1 AACTCTAATTCCTAGCTAATTCAC
12386802 AACTCTAATTCCTAGCTAATTCAC
1 AACTCTAATTCCTAGCTAATTCAC
12386826 TATTGCCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (24 bp):
AACTCTAATTCCTAGCTAATTCAC
Found at i:12389303 original size:13 final size:13
Alignment explanation
Indices: 12389285--12389326 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
12389275 TTCGCAACTA
*
12389285 TTTATTTATTTAT
1 TTTATTTGTTTAT
*
12389298 TTTATTTGTTTGT
1 TTTATTTGTTTAT
12389311 TTGT-TTTGTTTAT
1 TT-TATTTGTTTAT
12389324 TTT
1 TTT
12389327 CATTCATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.79
Consensus pattern (13 bp):
TTTATTTGTTTAT
Found at i:12389317 original size:17 final size:17
Alignment explanation
Indices: 12389283--12389325 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
12389273 GTTTCGCAAC
12389283 TATTTATTTATTTATTT
1 TATTTATTTATTTATTT
* * *
12389300 TATTTGTTTGTTTGTTT
1 TATTTATTTATTTATTT
*
12389317 TGTTTATTT
1 TATTTATTT
12389326 TCATTCATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (17 bp):
TATTTATTTATTTATTT
Found at i:12389378 original size:17 final size:17
Alignment explanation
Indices: 12389326--12389385 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 17
12389316 TTGTTTATTT
*
12389326 TCATTCATTTCATGCATC
1 TCATTCATTTAAT-CATC
12389344 TCATTCATTCATAGATCATC
1 TCATTCATT--TA-ATCATC
*
12389364 ATCATTCATTT-ATCATG
1 -TCATTCATTTAATCATC
12389381 TCATT
1 TCATT
12389386 GCAAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 5 0.14
17 5 0.14
18 9 0.25
19 1 0.03
20 5 0.14
21 11 0.31
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (17 bp):
TCATTCATTTAATCATC
Found at i:12390408 original size:13 final size:14
Alignment explanation
Indices: 12390376--12390408 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
12390366 ATCCAATAGA
12390376 TTTTAGGAATTTTC
1 TTTTAGGAATTTTC
12390390 TTTTAGGAATTTT-
1 TTTTAGGAATTTTC
12390403 TTTTAG
1 TTTTAG
12390409 TGTTAATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.61
Consensus pattern (14 bp):
TTTTAGGAATTTTC
Found at i:12394955 original size:21 final size:20
Alignment explanation
Indices: 12394921--12394964 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12394911 GGTAAATCTA
12394921 TCAGTAACAATAAAAATTATG
1 TCAGTAACAAT-AAAATTATG
* * *
12394942 TCAGTAATAGTAAAATTTTG
1 TCAGTAACAATAAAATTATG
12394962 TCA
1 TCA
12394965 ATAAATTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (20 bp):
TCAGTAACAATAAAATTATG
Found at i:12395902 original size:12 final size:14
Alignment explanation
Indices: 12395880--12395917 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
12395870 CATCAATAAT
12395880 AAAAATACACAAA-
1 AAAAATACACAAAC
12395893 AAAAAT-CACAAAC
1 AAAAATACACAAAC
*
12395906 AAAAATATACAA
1 AAAAATACACAA
12395918 TAATTTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 6 0.27
13 12 0.55
14 4 0.18
ACGTcount: A:0.74, C:0.16, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAATACACAAAC
Found at i:12396103 original size:93 final size:93
Alignment explanation
Indices: 12395995--12396183 Score: 335
Period size: 93 Copynumber: 2.0 Consensus size: 93
12395985 TTATGGCTAT
12395995 ATATTATTAAAATATATGA-TTTATCAATAAGCACAATACACAACCATCATTACAATGCAAAAAA
1 ATATTATTAAAATATAT-ACTTTATCAATAAGCACAATACACAACCATCATTACAATGCAAAAAA
12396059 ATGCAATACTTGATCAATAATTACAATAC
65 ATGCAATACTTGATCAATAATTACAATAC
* * *
12396088 ATATTATTAACATATATACTTTATCAATAATCGCAATACACAACCATCATTACAATGCAAAAAAA
1 ATATTATTAAAATATATACTTTATCAATAAGCACAATACACAACCATCATTACAATGCAAAAAAA
12396153 TGCAATACTTGATCAATAATTACAATAC
66 TGCAATACTTGATCAATAATTACAATAC
12396181 ATA
1 ATA
12396184 ACTGTTATCA
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
92 1 0.01
93 91 0.99
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.30
Consensus pattern (93 bp):
ATATTATTAAAATATATACTTTATCAATAAGCACAATACACAACCATCATTACAATGCAAAAAAA
TGCAATACTTGATCAATAATTACAATAC
Found at i:12397799 original size:3 final size:3
Alignment explanation
Indices: 12397791--12397853 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
12397781 CATGTGTTTT
* ** * *
12397791 ATC ATC ATC ATC ATC ATC ATT ATC ATC ATC ATC GGC ATG ATC ATC ATT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
12397839 ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC
12397854 TTCTTGTTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:12402256 original size:28 final size:27
Alignment explanation
Indices: 12402212--12402265 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
12402202 AATCTAGAAA
*
12402212 ATATTAAATATAAAATATCCATACAAAT
1 ATATTAAATATAAAATATACAT-CAAAT
*
12402240 ATATATAAATAT-TAATATACATCAAA
1 ATAT-TAAATATAAAATATACATCAAA
12402266 CCCAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 12 0.52
29 7 0.30
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.33
Consensus pattern (27 bp):
ATATTAAATATAAAATATACATCAAAT
Found at i:12402580 original size:2 final size:2
Alignment explanation
Indices: 12402573--12402598 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12402563 ATCCATACAA
12402573 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
12402599 TTAAAGCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12402679 original size:2 final size:2
Alignment explanation
Indices: 12402674--12402700 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12402664 TATATATATA
12402674 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
12402701 ATAAAACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12404941 original size:3 final size:3
Alignment explanation
Indices: 12404933--12404962 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12404923 ATCGTTGTGT
12404933 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12404963 CAATTCCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12407802 original size:16 final size:16
Alignment explanation
Indices: 12407781--12407813 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12407771 AAACTCGAAA
*
12407781 TTAAAATAATTTGAAC
1 TTAAAATAATTTAAAC
12407797 TTAAAATAATTTAAAC
1 TTAAAATAATTTAAAC
12407813 T
1 T
12407814 CAATGATTTC
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:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAAAATAATTTAAAC
Found at i:12407876 original size:14 final size:14
Alignment explanation
Indices: 12407849--12407884 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12407839 AAATTGATTT
12407849 AATTTTAA-AAAAA
1 AATTTTAACAAAAA
12407862 AATTTTAACAAAAA
1 AATTTTAACAAAAA
*
12407876 AATTATAAC
1 AATTTTAAC
12407885 CTAAATAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
AATTTTAACAAAAA
Found at i:12409140 original size:3 final size:3
Alignment explanation
Indices: 12409134--12409160 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12409124 TGTTCTTCTT
12409134 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
12409161 CTTGGATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12409371 original size:13 final size:13
Alignment explanation
Indices: 12409353--12409379 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12409343 GCTGTGAGTT
12409353 AACTCAGAGATGC
1 AACTCAGAGATGC
12409366 AACTCAGAGATGC
1 AACTCAGAGATGC
12409379 A
1 A
12409380 GGTGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (13 bp):
AACTCAGAGATGC
Found at i:12412383 original size:2 final size:2
Alignment explanation
Indices: 12412376--12412420 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12412366 CTCTCGTTGC
12412376 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12412418 TA T
1 TA T
12412421 GATAGAGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12412998 original size:21 final size:18
Alignment explanation
Indices: 12412969--12413010 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
12412959 ATCATATCAT
12412969 ATAATTA-TTATTAAAAA
1 ATAATTATTTATTAAAAA
12412986 ATAATTATTTATTAAAAA
1 ATAATTATTTATTAAAAA
12413004 ATAATTA
1 ATAATTA
12413011 ATAAATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTATTTATTAAAAA
Found at i:12413458 original size:13 final size:14
Alignment explanation
Indices: 12413435--12413512 Score: 50
Period size: 16 Copynumber: 5.1 Consensus size: 14
12413425 ATAAATAAAA
12413435 TATTAATAATAATT
1 TATTAATAATAATT
12413449 TATT-ATAATAATT
1 TATTAATAATAATT
*
12413462 AAATATTATTAATTAATAT
1 ---TATTAATAA-TAAT-T
*
12413481 TATATATTAATATATT
1 TAT-TAATAATA-ATT
* *
12413497 AATTAATATTAATT
1 TATTAATAATAATT
12413511 TA
1 TA
12413513 ATAAATTGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
13 9 0.18
14 8 0.16
15 6 0.12
16 12 0.24
17 11 0.22
18 4 0.08
19 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTAATAATAATT
Found at i:12413478 original size:21 final size:21
Alignment explanation
Indices: 12413463--12413600 Score: 52
Period size: 21 Copynumber: 6.8 Consensus size: 21
12413453 ATAATAATTA
12413463 AATATTATTAATTAAT-ATT-
1 AATATTATTAATTAATAATTA
*
12413482 -ATA-TATTAATATATTAATT-
1 AATATTATTAAT-TAATAATTA
* *
12413501 AATATTA--ATTTAATAAATTG
1 AATATTATTAATTAAT-AATTA
*
12413521 AATATTAATTTAATTGAATTA-TA
1 AATATT-A-TTAATT-AATAATTA
*
12413544 TAATAAT-TTAATT--TAATTA
1 -AATATTATTAATTAATAATTA
12413563 AATATTAGTTTAATT-AT-ATTA
1 AATATTA--TTAATTAATAATTA
12413584 AATATTAATTAA-TAATA
1 AATATT-ATTAATTAATA
12413601 TTTTATCTTA
Statistics
Matches: 90, Mismatches: 9, Indels: 38
0.66 0.07 0.28
Matches are distributed among these distances:
17 7 0.08
18 16 0.18
19 12 0.13
20 15 0.17
21 25 0.28
22 2 0.02
23 1 0.01
24 9 0.10
25 3 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATTATTAATTAATAATTA
Found at i:12413502 original size:62 final size:62
Alignment explanation
Indices: 12413436--12413617 Score: 180
Period size: 62 Copynumber: 3.0 Consensus size: 62
12413426 TAAATAAAAT
*
12413436 ATTAATAATAATTTATTATAATAATTAAATATT-ATTAATTAATATTATATATTAATAT-A-TTA
1 ATTAATATTAATTTA--AT-ATAATTAAATATTAATTAATTAATATTATATATTAATATAATTTA
* * * *
12413498 ATTAATATTAATTTAATA-AATTGAATATTAATTTAATTGA-ATTATATAATAATTTAATTTA
1 ATTAATATTAATTTAATATAATTAAATATTAA-TTAATTAATATTATATATTAATATAATTTA
* * * *
12413559 ATTAAATATTAGTTTAAT-TATATTAAATATTAATTAA-TAATATTTTATCTTAATTTAAT
1 ATT-AATATTAATTTAATATA-ATTAAATATTAATTAATTAATATTATATATTAATATAAT
12413618 AATATTCTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
58 10 0.10
59 15 0.15
60 10 0.10
61 8 0.08
62 47 0.47
63 11 0.11
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (62 bp):
ATTAATATTAATTTAATATAATTAAATATTAATTAATTAATATTATATATTAATATAATTTA
Found at i:12413537 original size:16 final size:15
Alignment explanation
Indices: 12413457--12413597 Score: 88
Period size: 16 Copynumber: 9.6 Consensus size: 15
12413447 TTTATTATAA
12413457 TAATTAAATATT-A-T
1 TAATT-AATATTAATT
12413471 TAATTAATATTATATAT
1 TAATTAATATTA-AT-T
12413488 TAA-T-ATATTAATT
1 TAATTAATATTAATT
*
12413501 AATATTAAT-TTAA-T
1 TA-ATTAATATTAATT
*
12413515 AAATTGAATATTAATT
1 TAATT-AATATTAATT
* *
12413531 TAATTGA-ATT-ATA
1 TAATTAATATTAATT
12413544 TAA-TAAT-TTAATT
1 TAATTAATATTAATT
*
12413557 TAATTAAATATTAGTT
1 TAATT-AATATTAATT
12413573 TAATT-ATATTAAATAT
1 TAATTAATATT-AAT-T
12413589 TAATTAATA
1 TAATTAATA
12413598 ATATTTTATC
Statistics
Matches: 101, Mismatches: 8, Indels: 33
0.71 0.06 0.23
Matches are distributed among these distances:
12 4 0.04
13 21 0.21
14 23 0.23
15 22 0.22
16 24 0.24
17 7 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TAATTAATATTAATT
Found at i:12413560 original size:13 final size:14
Alignment explanation
Indices: 12413441--12413560 Score: 70
Period size: 13 Copynumber: 8.3 Consensus size: 14
12413431 AAAATATTAA
*
12413441 TAATAATTTATTA-
1 TAATAATTTAATAT
*
12413454 TAATAATTAAATAT
1 TAATAATTTAATAT
*
12413468 TATTAA-TTAATAT
1 TAATAATTTAATAT
*
12413481 T-ATATATTAATATAT
1 TAATA-ATTTA-ATAT
12413496 TAATTAATATTAAT-T
1 TAA-TAAT-TTAATAT
*
12413511 TAATAAATTGAATAT
1 TAAT-AATTTAATAT
*
12413526 TAATTTAATTGAATTAT
1 TAA--TAATTTAA-TAT
12413543 ATAATAATTTAAT-T
1 -TAATAATTTAATAT
12413557 TAAT
1 TAAT
12413561 TAAATATTAG
Statistics
Matches: 85, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
12 2 0.02
13 23 0.27
14 13 0.15
15 17 0.20
16 19 0.22
17 8 0.09
18 3 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TAATAATTTAATAT
Found at i:12413577 original size:26 final size:24
Alignment explanation
Indices: 12413457--12413569 Score: 90
Period size: 21 Copynumber: 4.5 Consensus size: 24
12413447 TTTATTATAA
*
12413457 TAATTAAATATTATTAATTAATATT
1 TAATTAAATATTATTAATTTA-ATT
12413482 ATATATTAATATATTAATTAATATTAATT
1 -TA-ATTAA-ATATT-ATTAAT-TTAATT
*
12413511 TAA-TAAATTGAATATTAATTTAATT
1 TAATTAAA-T-ATTATTAATTTAATT
* *
12413536 GAATT--ATA-TAATAATTTAATT
1 TAATTAAATATTATTAATTTAATT
12413557 TAATTAAATATTA
1 TAATTAAATATTA
12413570 GTTTAATTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
21 16 0.22
22 1 0.01
23 4 0.06
24 3 0.04
25 9 0.12
26 13 0.18
27 8 0.11
28 7 0.10
29 9 0.12
30 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TAATTAAATATTATTAATTTAATT
Found at i:12413593 original size:42 final size:41
Alignment explanation
Indices: 12413439--12413805 Score: 252
Period size: 42 Copynumber: 8.9 Consensus size: 41
12413429 ATAAAATATT
*
12413439 AATAATAATTTATTATAATAATTAAATATT-A-TTAATTAATATTA
1 AATATTAATTTA--ATAAT-ATTAAATATTAATTTAA-TAA-ATTA
* * * *
12413483 TATATTAATAT-ATTA-ATT-AATATTAATTTAATAAATTG
1 AATATTAATTTAATAATATTAAATATTAATTTAATAAATTA
* * * *
12413521 AATATTAATTTAATTGA-ATTATATAATAATTTAATTTAATTA
1 AATATTAATTTAA-TAATATTAAATATTAATTTAA-TAAATTA
* * *
12413563 AATATTAGTTTAATTATATTAAATATTAA-TTAATAATATTT
1 AATATTAATTTAATAATATTAAATATTAATTTAATAA-ATTA
* * ** * * * *
12413604 TATCTTAATTTAATAATATTCTATATTCACTTAAAAATATTC
1 AATATTAATTTAATAATATTAAATATTAATTTAATAA-ATTA
* * * * *
12413646 AATTTTAATTTAATAATATTCAATATCAAATTAATATTATTA
1 AATATTAATTTAATAATATTAAATATTAATTTAATA-AATTA
*
12413688 AATATTAATTTAATAATATTAACTA-TAATTTAAT-AATATA
1 AATATTAATTTAATAATATTAAATATTAATTTAATAAAT-TA
* * * *
12413728 AAAATT-ATTGAACAATATTAAATATTAATTTAGT-AATATA
1 AATATTAATTTAATAATATTAAATATTAATTTAATAAAT-TA
*
12413768 AATATTCAATTTACTAATATTAAATATTAATTATAATA
1 AATATT-AATTTAATAATATTAAATATTAATT-TAATA
12413806 TTTTATGTTA
Statistics
Matches: 255, Mismatches: 52, Indels: 32
0.75 0.15 0.09
Matches are distributed among these distances:
38 18 0.07
39 25 0.10
40 37 0.15
41 52 0.20
42 112 0.44
43 3 0.01
44 8 0.03
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (41 bp):
AATATTAATTTAATAATATTAAATATTAATTTAATAAATTA
Found at i:12413618 original size:21 final size:21
Alignment explanation
Indices: 12413501--12413805 Score: 225
Period size: 21 Copynumber: 14.7 Consensus size: 21
12413491 TATATTAATT
*
12413501 AATATTAATTTAATAA-ATTG
1 AATATTAATTTAATAATATTC
*
12413521 AATATTAATTTAATTGA-ATT-
1 AATATTAATTTAA-TAATATTC
* * *
12413541 ATATAATAATTTAAT-TTAATTA
1 A-ATATTAATTTAATAAT-ATTC
* * *
12413563 AATATTAGTTTAATTATATTA
1 AATATTAATTTAATAATATTC
*
12413584 AATATTAA-TTAATAATATTT
1 AATATTAATTTAATAATATTC
* *
12413604 TATCTTAATTTAATAATATTC
1 AATATTAATTTAATAATATTC
* * * *
12413625 TATATTCACTTAAAAATATTC
1 AATATTAATTTAATAATATTC
*
12413646 AATTTTAATTTAATAATATTC
1 AATATTAATTTAATAATATTC
* * * *
12413667 AATATCAAATTAATATTATTA
1 AATATTAATTTAATAATATTC
12413688 AATATTAATTTAATAATATT-
1 AATATTAATTTAATAATATTC
*
12413708 AACTA-TAATTTAATAATA-TA
1 AA-TATTAATTTAATAATATTC
* * * *
12413728 AAAATT-ATTGAACAATATTA
1 AATATTAATTTAATAATATTC
* *
12413748 AATATTAATTTAGTAATA-TA
1 AATATTAATTTAATAATATTC
* *
12413768 AATATTCAATTTACTAATATTA
1 AATATT-AATTTAATAATATTC
12413790 AATATTAATTATAATA
1 AATATTAATT-TAATA
12413806 TTTTATGTTA
Statistics
Matches: 232, Mismatches: 38, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
19 11 0.05
20 64 0.28
21 143 0.62
22 14 0.06
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
AATATTAATTTAATAATATTC
Found at i:12413898 original size:36 final size:37
Alignment explanation
Indices: 12413784--12413899 Score: 100
Period size: 36 Copynumber: 3.2 Consensus size: 37
12413774 CAATTTACTA
*
12413784 ATATTAAATATTAA--TT-ATAATATTTT-ATGTTAAT
1 ATATTAAATATTAATTTTCATAATATTTTAATATT-AT
* *
12413818 AATAATTTAATATTATTTTTCATAATATTTTAATATTAT
1 -AT-ATTAAATATTAATTTTCATAATATTTTAATATTAT
* **
12413857 GTATTAAATATTAATTTTGTTAATA-TTTAATATTGA-
1 ATATTAAATATTAATTTTCATAATATTTTAATATT-AT
12413893 ATATTAA
1 ATATTAA
12413900 TTAAACATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
35 2 0.03
36 25 0.38
37 20 0.30
38 3 0.05
39 12 0.18
40 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (37 bp):
ATATTAAATATTAATTTTCATAATATTTTAATATTAT
Found at i:12413950 original size:8 final size:8
Alignment explanation
Indices: 12413908--12413977 Score: 60
Period size: 8 Copynumber: 9.2 Consensus size: 8
12413898 AATTAAACAT
*
12413908 TTTTATTA
1 TTTTAATA
12413916 TTTTAATA
1 TTTTAATA
12413924 ---TAA-A
1 TTTTAATA
12413928 TTTTAATA
1 TTTTAATA
**
12413936 TAATAATA
1 TTTTAATA
12413944 TTTTAATA
1 TTTTAATA
*
12413952 TTATAA-A
1 TTTTAATA
12413959 TTTATAATA
1 TTT-TAATA
12413968 TTTTAATA
1 TTTTAATA
12413976 TT
1 TT
12413978 AACTATGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
7 6 0.12
8 35 0.71
9 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTAATA
Found at i:12413969 original size:16 final size:15
Alignment explanation
Indices: 12413922--12413969 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
12413912 ATTATTTTAA
12413922 TATAAATTTTAATAT
1 TATAAATTTTAATAT
*
12413937 AATAATATTTTAATAT
1 TATAA-ATTTTAATAT
12413953 TATAAATTTATAATAT
1 TATAAATTT-TAATAT
12413969 T
1 T
12413970 TTAATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATAAATTTTAATAT
Found at i:12414133 original size:18 final size:18
Alignment explanation
Indices: 12414112--12414150 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12414102 CTAAATATTA
* *
12414112 ATTTAGTAATATTTTAAT
1 ATTTAATAATACTTTAAT
*
12414130 ATTTAATATTACTTTAAT
1 ATTTAATAATACTTTAAT
12414148 ATT
1 ATT
12414151 ATTTTAGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTAATAATACTTTAAT
Found at i:12414138 original size:29 final size:29
Alignment explanation
Indices: 12414125--12414401 Score: 110
Period size: 29 Copynumber: 10.0 Consensus size: 29
12414115 TAGTAATATT
* *
12414125 TTAATATTTAATATTACTTTAATATTATT
1 TTAATATTTAATATTAATTTAATAATATT
* * * *
12414154 TTAGTATTTAACA-TATTTTAAGAATATT
1 TTAATATTTAATATTAATTTAATAATATT
* * * *
12414182 TGAATA-TTAGATATTATTTTATTAGTATT
1 TTAATATTTA-ATATTAATTTAATAATATT
* **
12414211 TTATTATTTTAATATTAATTTAATGGTATT
1 TTAATA-TTTAATATTAATTTAATAATATT
* *
12414241 TTAATA-TT-AT-TTAA--AAACATATCATT
1 TTAATATTTAATATTAATTTAATA-AT-ATT
*
12414267 TT-ATTTATTAATATT-ATTT-A-AATA-T
1 TTAATAT-TTAATATTAATTTAATAATATT
* *
12414292 TCAATA-TTAGT-TTAA--T-AT--T-TT
1 TTAATATTTAATATTAATTTAATAATATT
* * *
12414313 TTGAAAATTTAATATTAAGTTAAT-ATTTT
1 TT-AATATTTAATATTAATTTAATAATATT
* *
12414342 TTGAAAATTTAATATTAAGTTAATAATATT
1 TT-AATATTTAATATTAATTTAATAATATT
* * *
12414372 TAAATATTAAATATTATTTTAATAATATT
1 TTAATATTTAATATTAATTTAATAATATT
12414401 T
1 T
12414402 ATTATATTAT
Statistics
Matches: 188, Mismatches: 35, Indels: 50
0.69 0.13 0.18
Matches are distributed among these distances:
21 3 0.02
22 5 0.03
23 6 0.03
24 11 0.06
25 5 0.03
26 13 0.07
27 11 0.06
28 25 0.13
29 80 0.43
30 26 0.14
31 3 0.02
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (29 bp):
TTAATATTTAATATTAATTTAATAATATT
Found at i:12414171 original size:155 final size:160
Alignment explanation
Indices: 12414003--12414314 Score: 338
Period size: 155 Copynumber: 2.0 Consensus size: 160
12413993 AAATTTAAAA
* *
12414003 ATTTAATATTATTTAAATG-ATATTTCCAT-TCTAAATATTATATTAATAGTAATTTAATATTTT
1 ATTTAACATTATTTAAA-GAATATTTCAATAT-TAAATATTATATTAATAGTAATTTAATATTTT
*
12414066 AATATT-ATTTGAATAATATTTTAAGAATATTT-TAAACTAAAT-A-TTAATTTAGTAATA-T-T
64 AATATTAATTT-AATAATATTTTAAGAATATTTAAAAAC-AAATCATTTAATTTAGTAATATTAT
*
12414125 TT-AATATTTAATATTACTTTAATATTATTTTAGT
127 TTAAATATTCAATATTACTTTAATATT-TTTTAGT
* * * * * * *
12414159 ATTTAACA-TATTTTAAGAATATTTGAATATTAGATATTATTTTATTAGTATTTTATTATTTTAA
1 ATTTAACATTATTTAAAGAATATTTCAATATTAAATATTATATTAATAGTAATTTAATATTTTAA
** * * * * *
12414223 TATTAATTTAATGGTATTTTAATATTATTTAAAAACATATCATTTTATTTATTAATATTATTTAA
66 TATTAATTTAATAATATTTTAAGAATATTTAAAAACAAATCATTTAATTTAGTAATATTATTTAA
*
12414288 ATATTCAATATTAGTTTAATATTTTTT
131 ATATTCAATATTACTTTAATATTTTTT
12414315 GAAAATTTAA
Statistics
Matches: 128, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
154 1 0.01
155 68 0.53
156 17 0.13
157 12 0.09
158 1 0.01
159 7 0.05
160 22 0.17
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (160 bp):
ATTTAACATTATTTAAAGAATATTTCAATATTAAATATTATATTAATAGTAATTTAATATTTTAA
TATTAATTTAATAATATTTTAAGAATATTTAAAAACAAATCATTTAATTTAGTAATATTATTTAA
ATATTCAATATTACTTTAATATTTTTTAGT
Found at i:12414182 original size:28 final size:26
Alignment explanation
Indices: 12414080--12414182 Score: 73
Period size: 28 Copynumber: 3.7 Consensus size: 26
12414070 TTATTTGAAT
**
12414080 AATATTTTAAGAATATTTTA-AACTA
1 AATATTTTAAGAATATTTTATATTTA
*
12414105 AATATTAATTTAGTAATATTTTAATATTTA
1 AATATT--TTAAG-AATATTTT-ATATTTA
* * *
12414135 ATATTACTTTAATATTATTTTAGTATTTA
1 A-A-TATTTTAAGAATATTTTA-TATTTA
12414164 ACATATTTTAAGAATATTT
1 A-ATATTTTAAGAATATTT
12414183 GAATATTAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
25 6 0.10
27 4 0.07
28 22 0.37
29 16 0.27
30 7 0.12
31 1 0.02
32 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (26 bp):
AATATTTTAAGAATATTTTATATTTA
Found at i:12414297 original size:18 final size:17
Alignment explanation
Indices: 12414272--12414310 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
12414262 TCATTTTATT
12414272 TATTAATATTA-TTTAAA
1 TATTAATATTAGTTT-AA
12414289 TATTCAATATTAGTTTAA
1 TATT-AATATTAGTTTAA
12414307 TATT
1 TATT
12414311 TTTTGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 13 0.65
19 3 0.15
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TATTAATATTAGTTTAA
Found at i:12414308 original size:11 final size:10
Alignment explanation
Indices: 12414036--12414423 Score: 85
Period size: 11 Copynumber: 39.0 Consensus size: 10
12414026 TTCCATTCTA
12414036 AATATTATATT
1 AATATTAT-TT
*
12414047 AATAGTAATTT
1 AATA-TTATTT
12414058 AATA-T-TTT
1 AATATTATTT
12414066 AATATTATTT
1 AATATTATTT
*
12414076 GAATAATATTTT
1 -AATATTA-TTT
* *
12414088 AAGAATATTTT
1 AATATTA-TTT
*
12414099 AA-ACTA---
1 AATATTATTT
12414105 AATATTAATTT
1 AATATT-ATTT
* *
12414116 AGTAATATTT
1 AATATTATTT
*
12414126 --TAATATTT
1 AATATTATTT
12414134 AATATTACTTT
1 AATATTA-TTT
12414145 AATATTATTT
1 AATATTATTT
*
12414155 --TAGTATTT
1 AATATTATTT
*
12414163 AACA-TATTTT
1 AATATTA-TTT
* *
12414173 AAGAATATTT
1 AATATTATTT
12414183 GAATATTA---
1 -AATATTATTT
*
12414191 GATATTATTTT
1 AATATTA-TTT
* *
12414202 ATTAGTATTT
1 AATATTATTT
12414212 --TATTATTTT
1 AATATTA-TTT
12414221 AATATTAATTT
1 AATATT-ATTT
**
12414232 AATGGTATTTT
1 AATATTA-TTT
12414243 AATATTATTT
1 AATATTATTT
*
12414253 AAAAACATATCATTT
1 ----A-ATATTATTT
*
12414268 TAT-TTA-TT
1 AATATTATTT
12414276 AATATTATTT
1 AATATTATTT
*
12414286 AA-A-TATTC
1 AATATTATTT
12414294 AATATTAGTTT
1 AATATTA-TTT
*
12414305 AATATTTTTT
1 AATATTATTT
12414315 GAA-A--ATTT
1 -AATATTATTT
*
12414323 AATATTAAGTT
1 AATATT-ATTT
*
12414334 AATATTTTTT
1 AATATTATTT
12414344 GAA-A--ATTT
1 -AATATTATTT
*
12414352 AATATTAAGTT
1 AATATT-ATTT
*
12414363 AATAATATTT
1 AATATTATTT
*
12414373 AA-A-TATTA
1 AATATTATTT
12414381 AATATTATTTT
1 AATATTA-TTT
*
12414392 AATAATATTT
1 AATATTATTT
*
12414402 ATTATATTATAT
1 A--ATATTATTT
*
12414414 AATAATATTT
1 AATATTATTT
12414424 TATTTAAAAA
Statistics
Matches: 280, Mismatches: 45, Indels: 105
0.65 0.10 0.24
Matches are distributed among these distances:
6 2 0.01
7 12 0.04
8 51 0.18
9 15 0.05
10 67 0.24
11 109 0.39
12 15 0.05
14 1 0.00
15 8 0.03
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (10 bp):
AATATTATTT
Found at i:12414402 original size:29 final size:28
Alignment explanation
Indices: 12414274--12414402 Score: 134
Period size: 29 Copynumber: 4.5 Consensus size: 28
12414264 ATTTTATTTA
*
12414274 TTAATATTATTTAAATATTCAATATT-AG
1 TTAATATTATTTAAA-ATTTAATATTAAG
*
12414302 TTTAATATTTTTTGAAAATTTAATATTAAG
1 -TTAATATTATTT-AAAATTTAATATTAAG
*
12414332 TTAATATTTTTTGAAAATTTAATATTAAG
1 TTAATATTATTT-AAAATTTAATATTAAG
* * **
12414361 TTAATAATATTTAAATATTAAATATTATT
1 TTAATATTATTTAAA-ATTTAATATTAAG
*
12414390 TTAATAATATTTA
1 TTAATATTATTTA
12414403 TTATATTATA
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
28 3 0.03
29 82 0.91
30 5 0.06
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (28 bp):
TTAATATTATTTAAAATTTAATATTAAG
Found at i:12414448 original size:11 final size:10
Alignment explanation
Indices: 12414361--12414452 Score: 54
Period size: 10 Copynumber: 9.5 Consensus size: 10
12414351 TAATATTAAG
12414361 TTAATAATAT
1 TTAATAATAT
12414371 TT-A-AATAT
1 TTAATAATAT
* *
12414379 TAAATATTATT
1 TTAATAATA-T
12414390 TTAATAATAT
1 TTAATAATAT
*
12414400 TTATTATATTAT
1 TTA--ATAATAT
*
12414412 ATAATAATA-
1 TTAATAATAT
12414421 TT--T--TAT
1 TTAATAATAT
*
12414427 TTAAAAATAT
1 TTAATAATAT
12414437 TGTAATAATAT
1 T-TAATAATAT
12414448 TTAAT
1 TTAAT
12414453 TAGTGTATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 22
0.66 0.11 0.24
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 1 0.02
8 6 0.10
9 3 0.05
10 22 0.36
11 17 0.28
12 8 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (10 bp):
TTAATAATAT
Found at i:12414500 original size:22 final size:21
Alignment explanation
Indices: 12414472--12414516 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
12414462 TAATGTTTAA
12414472 TATAATTTAATTAATTAGTAAT
1 TATAATTTAATTAA-TAGTAAT
*
12414494 TATAATTTAATTAATATTAAT
1 TATAATTTAATTAATAGTAAT
12414515 TA
1 TA
12414517 ATTATCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATAATTTAATTAATAGTAAT
Found at i:12415219 original size:72 final size:69
Alignment explanation
Indices: 12415059--12415265 Score: 238
Period size: 67 Copynumber: 3.0 Consensus size: 69
12415049 TGAAAATAGT
* * * *
12415059 TTTTATCTTAAAAACATCATTTTTATTGAATTCT-GAAAT-TTTTTTTATGTTTTCAACAAAAAC
1 TTTTATATTAGAAACATCATCTTTATTGAATTCTAAAAATATTTTTTTATGTTTTCAACAAAAAC
*
12415122 TGCA
66 TACA
* *
12415126 TTTTATCTTAGAAACATCATCTTTATTGAATTCTAAAAACTATTTTTTTATATTTTCAACAAAAA
1 TTTTATATTAGAAACATCATCTTTATTGAATTCTAAAAA-TATTTTTTTATGTTTTCAACAAAAA
12415191 CTACA
65 CTACA
** * * * *
12415196 TTTTTTATATTAGAAATGTCATCTTTGTTGAATTATAGAAAATAGTTTTTTCATGTTTTTAACAA
1 --TTTTATATTAGAAACATCATCTTTATTGAATTCTA-AAAATA-TTTTTTTATGTTTTCAACAA
12415261 AAACT
62 AAACT
12415266 TTATTTTTAT
Statistics
Matches: 120, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
67 32 0.27
68 3 0.03
69 1 0.01
70 26 0.22
72 32 0.27
73 26 0.22
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (69 bp):
TTTTATATTAGAAACATCATCTTTATTGAATTCTAAAAATATTTTTTTATGTTTTCAACAAAAAC
TACA
Found at i:12415273 original size:72 final size:71
Alignment explanation
Indices: 12415058--12415284 Score: 230
Period size: 72 Copynumber: 3.2 Consensus size: 71
12415048 ATGAAAATAG
* * * * *
12415058 TTTTTATCTTAAAAACATCATTTTTATTGAATTCT-GAAA-T-TTTTTTTATGTTTTCAACAAAA
1 TTTTTATATTAGAAACATCATCTTTATTGAATTATAAAAACTATTTTTTTATGTTTTCAACAAAA
*
12415120 ACTGCA
66 ACTACA
* * *
12415126 -TTTTATCTTAGAAACATCATCTTTATTGAATTCTAAAAACTATTTTTTTATATTTTCAACAAAA
1 TTTTTATATTAGAAACATCATCTTTATTGAATTATAAAAACTATTTTTTTATGTTTTCAACAAAA
12415190 ACTACA
66 ACTACA
** * * *
12415196 TTTTTTATATTAGAAATGTCATCTTTGTTGAATTATAGAAAA-TAGTTTTTTCATGTTTTTAACA
1 -TTTTTATATTAGAAACATCATCTTTATTGAATTATA-AAAACTA-TTTTTTTATGTTTTCAACA
**
12415260 AAAACTTTA
63 AAAACTACA
* *
12415269 TTTTTATCTTAAAAAC
1 TTTTTATATTAGAAAC
12415285 GTCTTTTAAA
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
67 32 0.24
68 3 0.02
69 1 0.01
70 26 0.19
72 45 0.34
73 27 0.20
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.48
Consensus pattern (71 bp):
TTTTTATATTAGAAACATCATCTTTATTGAATTATAAAAACTATTTTTTTATGTTTTCAACAAAA
ACTACA
Found at i:12421978 original size:12 final size:12
Alignment explanation
Indices: 12421961--12421986 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12421951 ACTCAAAATT
12421961 AACCTAAAACCC
1 AACCTAAAACCC
12421973 AACCTAAAACCC
1 AACCTAAAACCC
12421985 AA
1 AA
12421987 TTACATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.38, G:0.00, T:0.08
Consensus pattern (12 bp):
AACCTAAAACCC
Found at i:12425241 original size:3 final size:3
Alignment explanation
Indices: 12425233--12425283 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
12425223 TCTTTATCAA
12425233 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12425281 ATT
1 ATT
12425284 TGAAGTTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12430417 original size:19 final size:21
Alignment explanation
Indices: 12430388--12430428 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12430378 TTATACCTTA
12430388 TATTCGATAAA-AAACTTAAT
1 TATTCGATAAATAAACTTAAT
*
12430408 TATT-GATAAATAAATTTAAT
1 TATTCGATAAATAAACTTAAT
12430428 T
1 T
12430429 TATGTATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
TATTCGATAAATAAACTTAAT
Found at i:12439250 original size:16 final size:16
Alignment explanation
Indices: 12439223--12439263 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
12439213 CGATAAACAA
*
12439223 ATGATAATGATGATTT
1 ATGATGATGATGATTT
*
12439239 ATTATGATGATGATTT
1 ATGATGATGATGATTT
12439255 ATGATGATG
1 ATGATGATG
12439264 TTAAAGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
ATGATGATGATGATTT
Found at i:12439346 original size:47 final size:47
Alignment explanation
Indices: 12439232--12439333 Score: 134
Period size: 48 Copynumber: 2.2 Consensus size: 47
12439222 AATGATAATG
*
12439232 ATGATTTAT-TATGATGATGATTTATGATGATGTTAAAGATTGATCC
1 ATGATTTGTATATGATGATGATTTATGATGATGTTAAAGATTGATCC
* * * * *
12439278 ATGATTTGTATATAAAGATGATTTATGATGATTTTTATAGTTTGATCC
1 ATGATTTGTATATGATGATGATTTATGATGA-TGTTAAAGATTGATCC
12439326 ATGATTTG
1 ATGATTTG
12439334 GTTTGATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 8 0.17
47 19 0.40
48 21 0.44
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (47 bp):
ATGATTTGTATATGATGATGATTTATGATGATGTTAAAGATTGATCC
Found at i:12443779 original size:8 final size:8
Alignment explanation
Indices: 12443766--12443794 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12443756 TACTTTCCTA
12443766 TTGCAGGG
1 TTGCAGGG
12443774 TTGCAGGG
1 TTGCAGGG
12443782 TTGCAGGG
1 TTGCAGGG
12443790 TTGCA
1 TTGCA
12443795 TGGCTATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.45, T:0.28
Consensus pattern (8 bp):
TTGCAGGG
Found at i:12451709 original size:16 final size:17
Alignment explanation
Indices: 12451690--12451729 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
12451680 AAATTATATA
12451690 AATTTTAA-AAATAAAT
1 AATTTTAATAAATAAAT
12451706 AATTTTAATAAATAAAT
1 AATTTTAATAAATAAAT
*
12451723 TATTTTA
1 AATTTTA
12451730 TCATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTAATAAATAAAT
Found at i:12458609 original size:17 final size:17
Alignment explanation
Indices: 12458587--12458625 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
12458577 GTATTTTAAT
12458587 ATTTATATATAATAAAA
1 ATTTATATATAATAAAA
12458604 ATTTATATATAATAAAA
1 ATTTATATATAATAAAA
*
12458621 TTTTA
1 ATTTA
12458626 AAATAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTATATATAATAAAA
Found at i:12458631 original size:16 final size:17
Alignment explanation
Indices: 12458587--12458631 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
12458577 GTATTTTAAT
*
12458587 ATTTATATATAATAAAA
1 ATTTATAAATAATAAAA
*
12458604 ATTTATATATAATAAAA
1 ATTTATAAATAATAAAA
*
12458621 TTTTA-AAATAA
1 ATTTATAAATAA
12458632 AAGAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTATAAATAATAAAA
Found at i:12459510 original size:22 final size:22
Alignment explanation
Indices: 12459480--12459551 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
12459470 TAAATCATCA
* *
12459480 ATAACTTAATAGTTAATTAATT
1 ATAATTTAATAGTTAATTAATG
12459502 ATAATTTAATAGTTAATT-ATGG
1 ATAATTTAATAGTTAATTAAT-G
* *
12459524 ATAATTTAATA-TAAATCAATG
1 ATAATTTAATAGTTAATTAATG
12459545 ATAATTT
1 ATAATTT
12459552 GGATAGTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 14 0.32
22 30 0.68
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (22 bp):
ATAATTTAATAGTTAATTAATG
Found at i:12460672 original size:193 final size:194
Alignment explanation
Indices: 12460326--12460750 Score: 699
Period size: 193 Copynumber: 2.2 Consensus size: 194
12460316 TACCACATTT
*
12460326 CAAGTCATTAAGAGCTAAGAAAACTTATTACTTCTATTTACCATCTTATCCAAGCATTAAAGAGC
1 CAAG-CATTAAGAGCCAAGAAAACTTATTACTTCTATTTACCATCTTATCCAAGCATTAAAGAGC
* * * *
12460391 ATTTTTGTTGTGTGAAAAGTGTAAAAATTCATCTTATTTTTGTTTTTCTCCTGATAATCTTTTTA
65 ATTTTTGCTGTGTGAAAAGTGCAAAAATTCATCTTATATTTGTTTCTCTCCTGATAATCTTTTTA
** *
12460456 ATCTTGATTTGTACTTCAAATTAGTAAACACTTAACCTTAAAGAGGTTTTATTTACCATCTTCTC
130 ATCTTGATTTGTACTTCAAATTAGTAAACACCCAACCTTAAAGAAGTTTTATTTACCATCTTCTC
12460521 CAAGCATTAAGAGCCAAGAAAACTTATTACTTCTATTTACCATCTTATCCAAGCATTAAAGAGCA
1 CAAGCATTAAGAGCCAAGAAAACTTATTACTTCTATTTACCATCTTATCCAAGCATTAAAGAGCA
** * * *
12460586 -TTTTGCTGTGTGAAAAGTGCAAATTTTCATCTTGTATTTGTTTCTCTCTTGATAATTTTTTTAA
66 TTTTTGCTGTGTGAAAAGTGCAAAAATTCATCTTATATTTGTTTCTCTCCTGATAATCTTTTTAA
*
12460650 TCTTGATTTGTACTTTAAATTAGTAAACACCCAACCTTAAAGAAGTTTTATTTACCATCTTCTC
131 TCTTGATTTGTACTTCAAATTAGTAAACACCCAACCTTAAAGAAGTTTTATTTACCATCTTCTC
*
12460714 CAAGCATTAAGAGCCAAGAAAACTTATTTCTTCTATT
1 CAAGCATTAAGAGCCAAGAAAACTTATTACTTCTATT
12460751 GTATTTGTTT
Statistics
Matches: 215, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
193 151 0.70
194 60 0.28
195 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (194 bp):
CAAGCATTAAGAGCCAAGAAAACTTATTACTTCTATTTACCATCTTATCCAAGCATTAAAGAGCA
TTTTTGCTGTGTGAAAAGTGCAAAAATTCATCTTATATTTGTTTCTCTCCTGATAATCTTTTTAA
TCTTGATTTGTACTTCAAATTAGTAAACACCCAACCTTAAAGAAGTTTTATTTACCATCTTCTC
Found at i:12469203 original size:22 final size:22
Alignment explanation
Indices: 12469178--12469220 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12469168 ATTTATAATT
*
12469178 TAATAATAAATTACTAATAACA
1 TAATAATAAATAACTAATAACA
* *
12469200 TAATAGTAAATAATTAATAAC
1 TAATAATAAATAACTAATAAC
12469221 TTAGTTGTAA
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:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATAATAAATAACTAATAACA
Found at i:12469230 original size:22 final size:22
Alignment explanation
Indices: 12469192--12469311 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 22
12469182 AATAAATTAC
* *
12469192 TAATAACATAATAGTAAATAAT
1 TAATAACTTAGTAGTAAATAAT
* ***
12469214 TAATAACTTAGTTGTAAATTGG
1 TAATAACTTAGTAGTAAATAAT
* * * *
12469236 TGATAATTTAATAGTAAATCAT
1 TAATAACTTAGTAGTAAATAAT
* * *
12469258 TAATAGCTTAGTAGTAAATTAC
1 TAATAACTTAGTAGTAAATAAT
12469280 TAATAA-TATAGTAGTAAATCAA-
1 TAATAACT-TAGTAGTAAAT-AAT
12469302 TAATAACTTA
1 TAATAACTTA
12469312 AACATTGTTT
Statistics
Matches: 74, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
21 1 0.01
22 71 0.96
23 2 0.03
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (22 bp):
TAATAACTTAGTAGTAAATAAT
Found at i:12469247 original size:66 final size:66
Alignment explanation
Indices: 12469172--12469298 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
12469162 CTAACAATTT
* * *
12469172 ATAATTTAATAATAAATTACTAATAACATAATAGTAAATAATTAATAACT-TAGTTGTAAATTGG
1 ATAATTTAATAATAAATCACTAATAACATAATAGTAAATAACTAATAA-TATAGTAGTAAATTGG
12469236 TG
65 TG
* * * * * *
12469238 ATAATTTAATAGTAAATCATTAATAGCTTAGTAGTAAATTACTAATAATATAGTAGTAAAT
1 ATAATTTAATAATAAATCACTAATAACATAATAGTAAATAACTAATAATATAGTAGTAAAT
12469299 CAATAATAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 50 0.98
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (66 bp):
ATAATTTAATAATAAATCACTAATAACATAATAGTAAATAACTAATAATATAGTAGTAAATTGGT
G
Found at i:12469249 original size:44 final size:44
Alignment explanation
Indices: 12469184--12469311 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 44
12469174 AATTTAATAA
* *
12469184 TAAATTACTAATAACATAATAGTAAATAATTAATAACTTAGTTG
1 TAAATTACTAATAATATAATAGTAAATAATTAATAACTTAGTAG
** * * * *
12469228 TAAATTGGTGATAATTTAATAGTAAATCATTAATAGCTTAGTAG
1 TAAATTACTAATAATATAATAGTAAATAATTAATAACTTAGTAG
*
12469272 TAAATTACTAATAATATAGTAGTAAATCAA-TAATAACTTA
1 TAAATTACTAATAATATAATAGTAAAT-AATTAATAACTTA
12469312 AACATTGTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
44 67 0.99
45 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (44 bp):
TAAATTACTAATAATATAATAGTAAATAATTAATAACTTAGTAG
Found at i:12469842 original size:6 final size:6
Alignment explanation
Indices: 12469833--12469864 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12469823 GTAAAAGTAG
*
12469833 TAATTC TAATAC TAATAC TAATAC TAATAC TA
1 TAATAC TAATAC TAATAC TAATAC TAATAC TA
12469865 GTGGAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (6 bp):
TAATAC
Found at i:12473884 original size:14 final size:15
Alignment explanation
Indices: 12473856--12473884 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12473846 CAGTCGTGCT
12473856 ACCACTAGTTGGGCA
1 ACCACTAGTTGGGCA
12473871 ACCACTAG-TGGGCA
1 ACCACTAGTTGGGCA
12473885 TTAGAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (15 bp):
ACCACTAGTTGGGCA
Found at i:12474806 original size:4 final size:4
Alignment explanation
Indices: 12474792--12474825 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
12474782 AAGAAAATGG
* *
12474792 AGAA GGAA AGAA AGAA AGAA AGAG AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
12474826 CTATATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:12476544 original size:11 final size:11
Alignment explanation
Indices: 12476528--12476577 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
12476518 CTTTAAAAAC
12476528 AAAATAATATA
1 AAAATAATATA
12476539 AAAATAAATATA
1 AAAAT-AATATA
*
12476551 ATAATAATACT-
1 AAAATAATA-TA
*
12476562 AAACTAATA-A
1 AAAATAATATA
12476572 AAAATA
1 AAAATA
12476578 TAGGAAAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
10 5 0.16
11 16 0.50
12 11 0.34
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATAATATA
Found at i:12477092 original size:201 final size:202
Alignment explanation
Indices: 12476588--12477116 Score: 771
Period size: 204 Copynumber: 2.6 Consensus size: 202
12476578 TAGGAAAAGG
* *
12476588 AAATTTTTATCTGACGATGAGATTCAAAGGTATTCCGAGTAGTGATGCCTACGAAA-CTTCTAGG
1 AAATTTTTATCTAACGATGAGATTCAAAGGTATTCCGAGTAGTGATGCATACGAAATC-TCTAGG
* *
12476652 TGAAAAGATTTTTTTAAAAATACTACCAGTGTATTAGAGTATTTATAAAAAATTTTCAATACAGT
65 TGAGAAGATTTTTTT-AAAATACTACCAGTGTATTGGAGTATTTATAAAAAATTTTCAATACAGT
*
12476717 AAAGATTTTTTTTTAAATAATAAATAAAAATTAGTTAATAAATTAAAAATATATGTAATAAAAAT
129 AAAGATTTTTTTTAAAATAATAAATAAAAATTAGTTAATAAATTAAAAATATATGTAATAAAAAT
12476782 AGGAAGAAA
194 AGGAAGAAA
* *
12476791 AGAAATTTTATCCAACGATGAGATTCAAAGGTATTCCGAGTAGTGATGCATACGAAATCTCTAGG
1 A-AATTTTTATCTAACGATGAGATTCAAAGGTATTCCGAGTAGTGATGCATACGAAATCTCTAGG
*
12476856 TGAGAAGATTTTTCTAAAATACTACCAGTGTATTGGAGTATTTATAAAAAATTTTCAATACAGTA
65 TGAGAAGATTTTTTTAAAATACTACCAGTGTATTGGAGTATTTATAAAAAATTTTCAATACAGTA
* *
12476921 AAGA-TTTTTTTAAAATAATAAATAAAAATTGGTTAATCAATT-AAAATATATGTAATAAAAATA
130 AAGATTTTTTTTAAAATAATAAATAAAAATTAGTTAATAAATTAAAAATATATGTAATAAAAATA
12476984 -GAA-AAA
195 GGAAGAAA
* * * * ** *
12476990 AAATTTTTATCTAATGATGGGATTCTAAAAGTATTCCGAGTAGAGATGTTTTAAGAAATCTCTAG
1 AAATTTTTATCTAACGATGAGATTC-AAAGGTATTCCGAGTAGTGATG-CATACGAAATCTCTAG
* * * * *
12477055 GTGAGAAGATTTTTTGTAAAATATTACCAGCGTATTGGAATATTTATAGAAAATCTTCAATA
64 GTGAGAAGATTTTTT-TAAAATACTACCAGTGTATTGGAGTATTTATAAAAAATTTTCAATA
12477117 TAAATAAATT
Statistics
Matches: 296, Mismatches: 25, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
198 20 0.07
199 24 0.08
200 30 0.10
201 62 0.21
202 35 0.12
203 54 0.18
204 70 0.24
205 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (202 bp):
AAATTTTTATCTAACGATGAGATTCAAAGGTATTCCGAGTAGTGATGCATACGAAATCTCTAGGT
GAGAAGATTTTTTTAAAATACTACCAGTGTATTGGAGTATTTATAAAAAATTTTCAATACAGTAA
AGATTTTTTTTAAAATAATAAATAAAAATTAGTTAATAAATTAAAAATATATGTAATAAAAATAG
GAAGAAA
Found at i:12477168 original size:12 final size:12
Alignment explanation
Indices: 12477153--12477183 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
12477143 TTTAATTAAA
12477153 AATAAAACAATT
1 AATAAAACAATT
12477165 AATAAAACAATT
1 AATAAAACAATT
12477177 AATAAAA
1 AATAAAA
12477184 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAAACAATT
Found at i:12477934 original size:22 final size:21
Alignment explanation
Indices: 12477898--12477939 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
12477888 CATTTTTAGT
*
12477898 AAAAAAAAAATCAAAAAAATA
1 AAAAAAAAAAGCAAAAAAATA
12477919 AAAAATAAAAAGCAAAAAAAT
1 AAAAA-AAAAAGCAAAAAAAT
12477940 TCACACACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (21 bp):
AAAAAAAAAAGCAAAAAAATA
Found at i:12484693 original size:14 final size:15
Alignment explanation
Indices: 12484665--12484717 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
12484655 TATTTTCATC
12484665 TTCATTTTACTTTCCA
1 TTCATTTT-CTTTCCA
12484681 TTC-TTTTCTTTCCA
1 TTCATTTTCTTTCCA
*
12484695 -TCATTTTCTTGCCA
1 TTCATTTTCTTTCCA
12484709 TTCCATTTT
1 TT-CATTTT
12484718 TGTGTGCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.06
14 17 0.52
15 5 0.15
16 9 0.27
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.58
Consensus pattern (15 bp):
TTCATTTTCTTTCCA
Found at i:12487644 original size:17 final size:17
Alignment explanation
Indices: 12487622--12487658 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12487612 TTATCAAATA
*
12487622 CAATATTTACCAATTAT
1 CAATATTAACCAATTAT
*
12487639 CAATATTAATCAATTAT
1 CAATATTAACCAATTAT
12487656 CAA
1 CAA
12487659 ATTCAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (17 bp):
CAATATTAACCAATTAT
Found at i:12487644 original size:40 final size:40
Alignment explanation
Indices: 12487578--12487660 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
12487568 CCAACTTTTC
* ** *
12487578 AATATAATATTTACCTGTTACAAATATTGATCAATTATCA
1 AATACAATATTTACCAATTACAAATATTAATCAATTATCA
12487618 AATACAATATTTACCAATTATC-AATATTAATCAATTATCA
1 AATACAATATTTACCAATTA-CAAATATTAATCAATTATCA
12487658 AAT
1 AAT
12487661 TCAAACCCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 37 0.97
41 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (40 bp):
AATACAATATTTACCAATTACAAATATTAATCAATTATCA
Found at i:12488159 original size:62 final size:61
Alignment explanation
Indices: 12488059--12488196 Score: 181
Period size: 62 Copynumber: 2.2 Consensus size: 61
12488049 TTAAAAGCAC
* * *
12488059 ATTTTTGTAATTATAGTAAGAGTGTATTATAGTAATTTTGATCAATTATAATATTAA-AGGA
1 ATTTTTGTAATTATAGTAAGAGAGCATTATAGTAATTTTGATCAATTATAATA-AAATAGGA
* * *
12488120 ATTTTTGTAATTAT-GATAGGAGGAGCATTATAGTAATTTTGATCAATTATAATAAAATATGT
1 ATTTTTGTAATTATAG-TAAGA-GAGCATTATAGTAATTTTGATCAATTATAATAAAATAGGA
12488182 ATTTTTGTAATTATA
1 ATTTTTGTAATTATA
12488197 ACAAGGGTGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 1 0.01
61 20 0.30
62 46 0.69
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.45
Consensus pattern (61 bp):
ATTTTTGTAATTATAGTAAGAGAGCATTATAGTAATTTTGATCAATTATAATAAAATAGGA
Found at i:12488219 original size:62 final size:61
Alignment explanation
Indices: 12488050--12488222 Score: 172
Period size: 62 Copynumber: 2.8 Consensus size: 61
12488040 ATGAAGCAAT
* * * *
12488050 TAAAAGCACATTTTTGTAATTATAGTAAGAGT-GTATTATAGTAATTTTGATCAATTATAATA
1 TAAAAGGA-ATTTTTGTAATTATA-AAAGGGTGGCATTATAGTAATTTTGATCAATTATAATA
* * *
12488112 TTAAAGGAATTTTTGTAATTATGATAGGAG-GAGCATTATAGTAATTTTGATCAATTATAATA
1 TAAAAGGAATTTTTGTAATTATAAAAGG-GTG-GCATTATAGTAATTTTGATCAATTATAATA
* * * *
12488174 -AAATATGTATTTTTGTAATTATAACAAGGGTGGCAATATAATAATTTTG
1 TAAA-AGGAATTTTTGTAATTATAA-AAGGGTGGCATTATAGTAATTTTG
12488223 GCTATTTATG
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
60 2 0.02
61 17 0.19
62 68 0.75
63 4 0.04
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (61 bp):
TAAAAGGAATTTTTGTAATTATAAAAGGGTGGCATTATAGTAATTTTGATCAATTATAATA
Found at i:12488528 original size:61 final size:60
Alignment explanation
Indices: 12488448--12488589 Score: 164
Period size: 61 Copynumber: 2.3 Consensus size: 60
12488438 AATTGAAAAT
* * * **
12488448 GGTATTTTTGTAATAATGATCAAAG-GGTATTATAGTAATTTTGATCCA-TTATAGTATTA-AG
1 GGTATTTTCGTAATTATGATAAAAGAAATATTATAGTAATTTTGAT-CATTTAT-GTA--AGAG
*
12488509 GGTATTTTCATAATTATGATAAAAGAAATATTATAGTAATTTTGATCATTTATGTAAGAG
1 GGTATTTTCGTAATTATGATAAAAGAAATATTATAGTAATTTTGATCATTTATGTAAGAG
12488569 GGATATTTTCGTAATTATGAT
1 GG-TATTTTCGTAATTATGAT
12488590 TGTAGTGGTA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
59 1 0.01
60 4 0.06
61 43 0.61
62 22 0.31
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (60 bp):
GGTATTTTCGTAATTATGATAAAAGAAATATTATAGTAATTTTGATCATTTATGTAAGAG
Found at i:12489384 original size:31 final size:31
Alignment explanation
Indices: 12489348--12489414 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
12489338 AGATATAAGT
* *
12489348 ATATTATAATTATTTGTTATTTAAAAGAGGG
1 ATATTATAATGATTTGATATTTAAAAGAGGG
* *
12489379 GTATTATAATGATTTGATATTTATAAGAGGG
1 ATATTATAATGATTTGATATTTAAAAGAGGG
12489410 ATATT
1 ATATT
12489415 TTTGTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (31 bp):
ATATTATAATGATTTGATATTTAAAAGAGGG
Found at i:12489477 original size:24 final size:25
Alignment explanation
Indices: 12489450--12489508 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
12489440 CATTAAAAAA
*
12489450 TTTATCATTTA-A-AAGAGAGATATT
1 TTTATCATTTACATAAGA-AGACATT
12489474 TTTATCATTTACATAAGAAGACATT
1 TTTATCATTTACATAAGAAGACATT
*
12489499 ATTATCATTT
1 TTTATCATTT
12489509 TAAACACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 11 0.35
25 16 0.52
26 4 0.13
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTATCATTTACATAAGAAGACATT
Found at i:12489782 original size:24 final size:24
Alignment explanation
Indices: 12489737--12489782 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12489727 GTTAAAATTA
* *
12489737 AATATATAATAATTAATTATTTAT
1 AATACATAATAATAAATTATTTAT
12489761 AATACATAAT-ATAAATTCATTT
1 AATACATAATAATAAATT-ATTT
12489783 GCAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
AATACATAATAATAAATTATTTAT
Found at i:12490214 original size:17 final size:16
Alignment explanation
Indices: 12490194--12490297 Score: 55
Period size: 15 Copynumber: 6.8 Consensus size: 16
12490184 ATAATTTTAT
12490194 TAATTTAATATAATAAA
1 TAATTT-ATATAATAAA
*
12490211 TAATTT-TAT--TATA
1 TAATTTATATAATAAA
*
12490224 TAATATAT-TAATAAA
1 TAATTTATATAATAAA
*
12490239 TAATTTAAATAA-AATA
1 TAATTTATATAATAA-A
* *
12490255 TGTTATTT-TTTAATAAA
1 --TAATTTATATAATAAA
12490272 T--TTTATATAATAAA
1 TAATTTATATAATAAA
12490286 TAAATTT-TATAA
1 T-AATTTATATAA
12490298 ATGTTAAATC
Statistics
Matches: 66, Mismatches: 9, Indels: 25
0.66 0.09 0.25
Matches are distributed among these distances:
13 12 0.18
14 10 0.15
15 15 0.23
16 9 0.14
17 13 0.20
18 7 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (16 bp):
TAATTTATATAATAAA
Found at i:12490244 original size:28 final size:26
Alignment explanation
Indices: 12490182--12490244 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 26
12490172 GATTATTGTG
*
12490182 AAATAATTTTATTAATTTAATATAAT
1 AAATAATTTTATTAATATAATATAAT
12490208 AAATAATTTTATT-ATATAATATATTAAT
1 AAATAATTTTATTAATAT-A-ATA-TAAT
12490236 AAATAATTT
1 AAATAATTT
12490245 AAATAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 3 0.09
26 14 0.42
27 3 0.09
28 13 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATAATTTTATTAATATAATATAAT
Found at i:12490250 original size:24 final size:27
Alignment explanation
Indices: 12490182--12490255 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 27
12490172 GATTATTGTG
**
12490182 AAATAATTTTAT-TAATTTAATA-TAAT
1 AAATAATTTTATAT-ATAAAATATTAAT
*
12490208 AAATAATTTTATTATATAATATATTAAT
1 AAATAATTTTA-TATATAAAATATTAAT
12490236 AAATAA-TTTA-A-ATAAAATAT
1 AAATAATTTTATATATAAAATAT
12490256 GTTATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 8 0.20
25 1 0.02
26 11 0.27
27 10 0.24
28 11 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATAATTTTATATATAAAATATTAAT
Found at i:12490251 original size:13 final size:13
Alignment explanation
Indices: 12490182--12490251 Score: 52
Period size: 13 Copynumber: 5.2 Consensus size: 13
12490172 GATTATTGTG
*
12490182 AAATAATTTTATT
1 AAATAATTTTAAT
* *
12490195 AATTTAA-TATAAT
1 AA-ATAATTTTAAT
*
12490208 AAATAATTTTATT
1 AAATAATTTTAAT
*
12490221 ATATAATATATTAAT
1 AAATAAT-T-TTAAT
*
12490236 AAATAATTTAAAT
1 AAATAATTTTAAT
12490249 AAA
1 AAA
12490252 ATATGTTATT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
12 3 0.07
13 25 0.58
14 5 0.12
15 10 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATAATTTTAAT
Found at i:12491409 original size:3 final size:3
Alignment explanation
Indices: 12491401--12491468 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
12491391 ATAGTATTAC
12491401 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12491449 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
12491469 CATCATCATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12492420 original size:20 final size:20
Alignment explanation
Indices: 12492397--12492497 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
12492387 AAAAAATTCT
12492397 AAAAAAAATCTTTTCAAATA
1 AAAAAAAATCTTTTCAAATA
12492417 AAAAAAAATCTTTGT-AAAT-
1 AAAAAAAATCTTT-TCAAATA
*
12492436 -----AAA-GTTTTCAAAATA
1 AAAAAAAATCTTTTC-AAATA
12492451 ATAAAAAAATCTTTTC-AAT-
1 A-AAAAAAATCTTTTCAAATA
*
12492470 AAAAAAAGTCTTTT-AAATA
1 AAAAAAAATCTTTTCAAATA
*
12492489 AACAAAAAT
1 AAAAAAAAT
12492498 AATTTTTATC
Statistics
Matches: 63, Mismatches: 5, Indels: 27
0.66 0.05 0.28
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 7 0.11
18 15 0.24
19 8 0.13
20 20 0.32
21 4 0.06
22 5 0.08
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAAAAAATCTTTTCAAATA
Found at i:12492450 original size:34 final size:33
Alignment explanation
Indices: 12492407--12492472 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
12492397 AAAAAAAATC
12492407 TTTTCAAATAA-AAAAAAATCTTTGTAAATAAAG
1 TTTTCAAATAATAAAAAAATCTTT-TAAATAAAG
*
12492440 TTTTCAAAATAATAAAAAAATCTTTTCAATAAA
1 TTTTC-AAATAATAAAAAAATCTTTTAAATAAA
12492473 AAAAGTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 13 0.43
35 12 0.40
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.35
Consensus pattern (33 bp):
TTTTCAAATAATAAAAAAATCTTTTAAATAAAG
Found at i:12492470 original size:17 final size:18
Alignment explanation
Indices: 12492450--12492495 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
12492440 TTTTCAAAAT
*
12492450 AATAAAAAAA-TCTTTTC
1 AATAAAAAAAGTCTTTTA
12492467 AATAAAAAAAGTCTTTTA
1 AATAAAAAAAGTCTTTTA
12492485 AATAAACAAAA
1 AATAAA-AAAA
12492496 ATAATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (18 bp):
AATAAAAAAAGTCTTTTA
Found at i:12495376 original size:17 final size:17
Alignment explanation
Indices: 12495354--12495389 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12495344 CTTATCATCT
12495354 TAGATCTTTTGAGAATG
1 TAGATCTTTTGAGAATG
12495371 TAGATCTTTTGAGAATG
1 TAGATCTTTTGAGAATG
12495388 TA
1 TA
12495390 CTTAGGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (17 bp):
TAGATCTTTTGAGAATG
Found at i:12496363 original size:9 final size:9
Alignment explanation
Indices: 12496312--12496368 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
12496302 GAAAAATGTG
*
12496312 TAAAAAAAG
1 TAAAAAAAA
12496321 TAAAAAAAA
1 TAAAAAAAA
12496330 TAAAAAAATAA
1 T-AAAAAA-AA
*
12496341 GAAGCAAAATAA
1 TAA--AAAA-AA
12496353 TAAAAAAAA
1 TAAAAAAAA
12496362 TAAAAAA
1 TAAAAAA
12496369 GATGAGATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 18 0.44
10 12 0.29
11 2 0.05
12 9 0.22
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:12497264 original size:64 final size:64
Alignment explanation
Indices: 12497130--12497252 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
12497120 TCCATATCAT
* * * * *
12497130 TTTTTATGACTTGTGATTTCATTTCGATCATTTATTTTTGACCTCGACTCGATCTTGGTTGCCTA
1 TTTTT-TGACTCGTAATTTCATCTCGATCATTTATTTTTGACCTCAACTCGATCCTGGTTGCCTA
* *
12497195 TTTTTTGACTCGTAATTTCATCTCGATCATTTATTTTTTATCTCAACTC-AGTCCTGGT
1 TTTTTTGACTCGTAATTTCATCTCGATCATTTATTTTTGACCTCAACTCGA-TCCTGGT
12497253 CACTTTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.02
64 44 0.88
65 5 0.10
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.50
Consensus pattern (64 bp):
TTTTTTGACTCGTAATTTCATCTCGATCATTTATTTTTGACCTCAACTCGATCCTGGTTGCCTA
Found at i:12497805 original size:120 final size:120
Alignment explanation
Indices: 12497679--12498409 Score: 599
Period size: 120 Copynumber: 6.1 Consensus size: 120
12497669 CTTATGACTA
* * * * * * * *
12497679 GTGGTTTCATCTCGATCATTTGATTTTGGTTCAGTCTAGATTATTTCTTATGACTCAAGGTTTTA
1 GTGGTTTCATCTCGATCACTTAATTTTGGCTCAGTCCAAATCATTTCTTATGACTCATGGTTTCA
* * * * * *
12497744 TCTCGATAATTTATTTTTTACCTTGACTCGGTCCTAGTCACTTCATTTTTGATTT
66 TCCCGATCATTTATTTTTGACCTTGACTCGGTCTTAGTCACTTCATTTTTAACTT
* * * * ** * * *
12497799 GTGGTTTTATC-CTGATAACTTAATCTTAGCTCAGTCCAAATCGCTTCTTATGACTTAGGGTTTT
1 GTGGTTTCATCTC-GATCACTTAATTTTGGCTCAGTCCAAATCATTTCTTATGACTCATGGTTTC
*** * * ** * *
12497863 ATCTTAATCATTTATTTTTAACCTCGACTCGGTC-CCGATCGCTTCATTTTTTACTT
65 ATCCCGATCATTTATTTTTGACCTTGACTCGGTCTTAG-TCACTTCATTTTTAACTT
* * * * * * * ** *
12497919 TTGATTTTATCTCAATCACTTAATTTTGGTTCAGTTCAGATCATTTAGTATGACTCGTGGTTTCA
1 GTGGTTTCATCTCGATCACTTAATTTTGGCTCAGTCCAAATCATTTCTTATGACTCATGGTTTCA
* * * * * * *
12497984 TCCTGATCATTTATTTTCGATCTTGACTCGATCATGGTCGCTTCATTTTTAACTT
66 TCCCGATCATTTATTTTTGACCTTGACTCGGTCTTAGTCACTTCATTTTTAACTT
* ** * ** * * * ** *
12498039 GTGATTTTGTCTC-AGTCATTTGCTTTTAGCTTAGTCCAGATCGCTTCTTATGACTCATGATTTC
1 GTGGTTTCATCTCGA-TCACTTAATTTTGGCTCAGTCCAAATCATTTCTTATGACTCATGGTTTC
* ** * *
12498103 ATCCCGATCATTTATTTTT-AACTTCGACTCAATCTTGGTCACTTTATTTTT-ACTT
65 ATCCCGATCATTTATTTTTGACCTT-GACTCGGTCTTAGTCACTTCATTTTTAACTT
* * **
12498158 GTGGTTTCATTTCGATCATTTAATTTTGGCTCAGTCCAAATTGTTTCTTATGACTCATGGTTTCA
1 GTGGTTTCATCTCGATCACTTAATTTTGGCTCAGTCCAAATCATTTCTTATGACTCATGGTTTCA
* * * * *
12498223 TCCCGGTTATTTATTTTTGACCTTGACTCTGTCTTAATCGCTTCATTTTTAACTT
66 TCCCGATCATTTATTTTTGACCTTGACTCGGTCTTAGTCACTTCATTTTTAACTT
* * * * * * *
12498278 GTGATTTCATCTCGGTTACTTGATCTTGGCTCAGTCCAAATCATTTCTTATAACTCATAGTTTCA
1 GTGGTTTCATCTCGATCACTTAATTTTGGCTCAGTCCAAATCATTTCTTATGACTCATGGTTTCA
* ** * * *
12498343 TCCCAATCATTTATTTTTGACCTCAACTCAGTCTTAGTCACTTCATTCTTGACTT
66 TCCCGATCATTTATTTTTGACCTTGACTCGGTCTTAGTCACTTCATTTTTAACTT
12498398 GTGGTTTCATCT
1 GTGGTTTCATCT
12498410 TTACCGCATT
Statistics
Matches: 486, Mismatches: 116, Indels: 18
0.78 0.19 0.03
Matches are distributed among these distances:
119 98 0.20
120 386 0.79
121 2 0.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (120 bp):
GTGGTTTCATCTCGATCACTTAATTTTGGCTCAGTCCAAATCATTTCTTATGACTCATGGTTTCA
TCCCGATCATTTATTTTTGACCTTGACTCGGTCTTAGTCACTTCATTTTTAACTT
Found at i:12497809 original size:176 final size:175
Alignment explanation
Indices: 12497507--12497880 Score: 394
Period size: 176 Copynumber: 2.1 Consensus size: 175
12497497 TTATTTGTGA
* * * * * *
12497507 TTTCATCCCAATCATTTAATTTTAGCTCAAT-TCAGATCACTTT-TTATAACTCATGGTTTCATC
1 TTTCATCTCAATCATTT-ATTTTGGTTCAGTCT-AGATTA-TTTCTTATAACTCAAGGTTTCATC
* * * ** * *
12497570 TCGATCACTTATTTTTTATCTCGACTCGATCCTGGTTGCTTCATTTTTTACTTATGATTTTATCT
63 TCGATAACTTATTTTTTACCTCGACTCGATCCTAGTCACTTCATTTTTGACTTATGATTTTATCC
* * * * *
12497635 TGGTCACTTGATCTTAGCTAAGTCTATATAACTTCTTATGAC-TAGTGG
128 TGATAACTTAATCTTAGCTAAGTCCAAATAACTTCTTATGACTTAG-GG
* * *
12497683 TTTCATCTCGATCATTTGATTTTGGTTCAGTCTAGATTATTTCTTATGACTCAAGGTTTTATCTC
1 TTTCATCTCAATCATTT-ATTTTGGTTCAGTCTAGATTATTTCTTATAACTCAAGGTTTCATCTC
* * * * * *
12497748 GATAATTTATTTTTTACCTTGACTCGGTCCTAGTCACTTCATTTTTGATTTGTGGTTTTATCCTG
65 GATAACTTATTTTTTACCTCGACTCGATCCTAGTCACTTCATTTTTGACTTATGATTTTATCCTG
* **
12497813 ATAACTTAATCTTAGCTCAGTCCAAATCGCTTCTTATGACTTAGGG
130 ATAACTTAATCTTAGCTAAGTCCAAATAACTTCTTATGACTTAGGG
* *
12497859 TTTTATCTTAATCATTTATTTT
1 TTTCATCTCAATCATTTATTTT
12497881 TAACCTCGAC
Statistics
Matches: 161, Mismatches: 34, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
175 8 0.05
176 149 0.93
177 4 0.02
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.47
Consensus pattern (175 bp):
TTTCATCTCAATCATTTATTTTGGTTCAGTCTAGATTATTTCTTATAACTCAAGGTTTCATCTCG
ATAACTTATTTTTTACCTCGACTCGATCCTAGTCACTTCATTTTTGACTTATGATTTTATCCTGA
TAACTTAATCTTAGCTAAGTCCAAATAACTTCTTATGACTTAGGG
Found at i:12498114 original size:416 final size:408
Alignment explanation
Indices: 12497354--12498120 Score: 923
Period size: 416 Copynumber: 1.9 Consensus size: 408
12497344 TTTATATTCA
* * * * * * * *
12497354 ACCTCGACTTGGTCCTAATCACTTCATTTTTGACTTGTTGTTTCGTCGTGGTCACTTGATCTTGG
1 ACCTCGACTCGGTCCTAATCACTTCATTTTTGACTTGTGGTTTCATCCTGATAACTTAATCTTAG
* * * * * *
12497419 CTCAGTCCAAATCATTTCTTATGACTCATGATTTTATTTTGATCATTTATTTTTTATCTCGACTC
66 CTCAGTCCAAATCACTTCTTATGACTCAGGATTTTATCTTAATCATTTATTTTTAACCTCGACTC
*
12497484 GGTCCTGATTGTTTTATTTGTGATTTCATCCCAATCATTTAATTTTAGCTCAATTCAGATCACTT
131 GGTCCTGATTGTTTTATTTGTGATTTCATCCCAATCACTTAATTTTAGCTCAATTCAGATCACTT
* ** * *
12497549 TTTATAACTCATGGTTTCATCTCGATCACTTATTTTTTATCTCGACTCGATCCTGGTTGCTTCAT
196 TGTATAACTCATGGTTTCATCTCGATCACTTATTTTCGATCTCGACTCGATCATGGTCGCTTCAT
* ** * *
12497614 TTTTTACTTATGATTTTATCTTGGTCACTTGATCTTAGCTAAGTCTATATAACTTCTTATGACTA
261 TTTTAACTTATGATTTTATCTCAGTCACTTGATCTTAGCTAAGTCCAGATAACTTCTTATGACTA
* *
12497679 GTGGTTTCATCTCGATCATTTGATTTTGGTTCAGTCTAGATTATTTCTTATGACTCAAGGTTTTA
326 GTGATTTCATCCCGATCATTT-ATTTTGGTTCAGTCTAGATTATTTCTTATGACTCAAGGTTTTA
12497744 TCTCGATAATTTATTTTTT
390 TCTCGATAATTTATTTTTT
* * * *
12497763 ACCTTGACTCGGTCCTAGTCACTTCATTTTTGATTTGTGGTTTTATCCTGATAACTTAATCTTAG
1 ACCTCGACTCGGTCCTAATCACTTCATTTTTGACTTGTGGTTTCATCCTGATAACTTAATCTTAG
* * *
12497828 CTCAGTCCAAATCGCTTCTTATGACTTAGGGTTTTATCTTAATCATTTATTTTTAACCTCGACTC
66 CTCAGTCCAAATCACTTCTTATGACTCAGGATTTTATCTTAATCATTTATTTTTAACCTCGACTC
* * * * *
12497893 GGTCCCGATCGCTTCATT-TTTTACTTT-TGATTTTATCTCAATCACTTAATTTTGGTTCAGTTC
131 GGT-CC--T-G----ATTGTTTTA-TTTGTGATTTCATCCCAATCACTTAATTTTAGCTCAATTC
* * * *
12497956 AGATCA-TTTAGTATGACTCGTGGTTTCATC-CTGATCATTTATTTTCGATCTTGACTCGATCAT
187 AGATCACTTT-GTATAACTCATGGTTTCATCTC-GATCACTTATTTTCGATCTCGACTCGATCAT
* * * * * * **
12498019 GGTCGCTTCATTTTTAACTTGTGATTTTGTCTCAGTCATTTGCTTTTAGCTTAGTCCAGATCGCT
250 GGTCGCTTCATTTTTAACTTATGATTTTATCTCAGTCACTTGATCTTAGCTAAGTCCAGATAACT
12498084 TCTTATGACTCA-TGATTTCATCCCGATCATTTATTTT
315 TCTTATGACT-AGTGATTTCATCCCGATCATTTATTTT
12498121 TAACTTCGAC
Statistics
Matches: 295, Mismatches: 51, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
409 112 0.38
410 2 0.01
412 1 0.00
413 1 0.00
415 9 0.03
416 163 0.55
417 7 0.02
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (408 bp):
ACCTCGACTCGGTCCTAATCACTTCATTTTTGACTTGTGGTTTCATCCTGATAACTTAATCTTAG
CTCAGTCCAAATCACTTCTTATGACTCAGGATTTTATCTTAATCATTTATTTTTAACCTCGACTC
GGTCCTGATTGTTTTATTTGTGATTTCATCCCAATCACTTAATTTTAGCTCAATTCAGATCACTT
TGTATAACTCATGGTTTCATCTCGATCACTTATTTTCGATCTCGACTCGATCATGGTCGCTTCAT
TTTTAACTTATGATTTTATCTCAGTCACTTGATCTTAGCTAAGTCCAGATAACTTCTTATGACTA
GTGATTTCATCCCGATCATTTATTTTGGTTCAGTCTAGATTATTTCTTATGACTCAAGGTTTTAT
CTCGATAATTTATTTTTT
Found at i:12498389 original size:359 final size:360
Alignment explanation
Indices: 12497723--12498400 Score: 752
Period size: 359 Copynumber: 1.9 Consensus size: 360
12497713 TCTAGATTAT
* * * * **
12497723 TTCTTATGACTCAAGGTTTTATCTCGATAATTTATTTTTTACCTTGACTCGGTCCTAGTCACTTC
1 TTCTTATGACTCAAGATTTCATCCCGATAATTTATTTTTTAACTTGACTCAATCCTAGTCACTTC
* *
12497788 ATTTTTGATTTGTGGTTTTATCCTGATAACTTAATCTTAGCTCAGTCCAAATCGCTTCTTATGAC
66 ATTTTTGACTTGTGGTTTCATCCTGATAACTTAATCTTAGCTCAGTCCAAATCGCTTCTTATGAC
* * ** * *
12497853 TTAGGGTTTTATCTTAATCATTTATTTTTAACCTCGACTCGGTCCCGATCGCTTCATTTTTTACT
131 TCAGGGTTTCATCCCAATCATTTATTTTTAACCTCGACTCGGTCCCAATCGCTTCATTTTTAACT
* * * * * * * * *
12497918 TTTGATTTTATCTCAATCACTTAATTTTGGTTCAGTTCAGATCATTTAGTATGACTCGTGGTTTC
196 TGTGATTTCATCTCAATCACTTAATCTTGGCTCAGTCCAAATCATTTAGTATAACTCATAGTTTC
** * ** * * *
12497983 ATCCTGATCATTTATTTTCGATCTTGACTCGATCATGGTCGCTTCATTTTTAACTTGTGATTTTG
261 ATCCCAATCATTTATTTTCGACCTCAACTCGATCATAGTCACTTCATTCTTAACTTGTGATTTTG
12498048 TCTCAGTCATTTGCTTTTAGCTTAGTCCAGATCGC
326 TCTCAGTCATTTGCTTTTAGCTTAGTCCAGATCGC
* * * *
12498083 TTCTTATGACTCATGATTTCATCCCGATCATTTA-TTTTTAACTTCGACTCAATCTTGGTCACTT
1 TTCTTATGACTCAAGATTTCATCCCGATAATTTATTTTTTAACTT-GACTCAATCCTAGTCACTT
* * * * * * * *
12498147 TATTTTT-ACTTGTGGTTTCAT-TTCGATCATTTAATTTTGGCTCAGTCCAAATTGTTTCTTATG
65 CATTTTTGACTTGTGGTTTCATCCT-GATAACTTAATCTTAGCTCAGTCCAAATCGCTTCTTATG
* ** * * * * **
12498210 ACTCATGGTTTCATCCCGGTTATTTATTTTTGACCTTGACTCTGTCTTAATCGCTTCATTTTTAA
129 ACTCAGGGTTTCATCCCAATCATTTATTTTTAACCTCGACTCGGTCCCAATCGCTTCATTTTTAA
** * * **
12498275 CTTGTGATTTCATCTCGGTTACTTGATCTTGGCTCAGTCCAAATCATTTCTTATAACTCATAGTT
194 CTTGTGATTTCATCTCAATCACTTAATCTTGGCTCAGTCCAAATCATTTAGTATAACTCATAGTT
* * *
12498340 TCATCCCAATCATTTATTTTTGACCTCAACTC-AGTCTTAGTCACTTCATTCTTGACTTGTG
259 TCATCCCAATCATTTATTTTCGACCTCAACTCGA-TCATAGTCACTTCATTCTTAACTTGTG
12498401 GTTTCATCTT
Statistics
Matches: 254, Mismatches: 61, Indels: 7
0.79 0.19 0.02
Matches are distributed among these distances:
358 2 0.01
359 202 0.80
360 50 0.20
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (360 bp):
TTCTTATGACTCAAGATTTCATCCCGATAATTTATTTTTTAACTTGACTCAATCCTAGTCACTTC
ATTTTTGACTTGTGGTTTCATCCTGATAACTTAATCTTAGCTCAGTCCAAATCGCTTCTTATGAC
TCAGGGTTTCATCCCAATCATTTATTTTTAACCTCGACTCGGTCCCAATCGCTTCATTTTTAACT
TGTGATTTCATCTCAATCACTTAATCTTGGCTCAGTCCAAATCATTTAGTATAACTCATAGTTTC
ATCCCAATCATTTATTTTCGACCTCAACTCGATCATAGTCACTTCATTCTTAACTTGTGATTTTG
TCTCAGTCATTTGCTTTTAGCTTAGTCCAGATCGC
Found at i:12498693 original size:13 final size:12
Alignment explanation
Indices: 12498662--12498711 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
12498652 ATCATTTCTA
12498662 TTTTTCATTTTT
1 TTTTTCATTTTT
*
12498674 CATTTTCATTTTT
1 -TTTTTCATTTTT
*
12498687 TTCTTTCTTTTTT
1 TT-TTTCATTTTT
*
12498700 TTTTTGATTTTT
1 TTTTTCATTTTT
12498712 GGCATGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 9 0.29
13 22 0.71
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTCATTTTT
Found at i:12499669 original size:17 final size:17
Alignment explanation
Indices: 12499645--12499703 Score: 77
Period size: 16 Copynumber: 3.5 Consensus size: 17
12499635 GTTTTTAAAA
12499645 TAAT-AAAAAATCTTTT
1 TAATAAAAAAATCTTTT
12499661 TAATAAAAAAATC-TTT
1 TAATAAAAAAATCTTTT
* *
12499677 TAATAAAAAAGTATTTT
1 TAATAAAAAAATCTTTT
12499694 TAAATAAAAA
1 T-AATAAAAA
12499704 TAATAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 18 0.47
17 12 0.32
18 8 0.21
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (17 bp):
TAATAAAAAAATCTTTT
Found at i:12502660 original size:18 final size:18
Alignment explanation
Indices: 12502637--12502676 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
12502627 AATTATATTT
12502637 TAATTAATTATAATAAA-A
1 TAATTAATTAT-ATAAATA
12502655 TAATTAATTATATAAATA
1 TAATTAATTATATAAATA
12502673 TAAT
1 TAAT
12502677 ATTTAATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATTAATTATATAAATA
Found at i:12502677 original size:21 final size:19
Alignment explanation
Indices: 12502637--12502684 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
12502627 AATTATATTT
12502637 TAATTAA-TTATAATAAAA
1 TAATTAATTTATAATAAAA
*
12502655 TAATTAATTATATAAATATAA
1 TAATTAATT-TAT-AATAAAA
*
12502676 TATTTAATT
1 TAATTAATT
12502685 GCGATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 1 0.04
20 3 0.12
21 14 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATTAATTTATAATAAAA
Found at i:12504666 original size:3 final size:3
Alignment explanation
Indices: 12504652--12504706 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
12504642 TATAGGAATA
*
12504652 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12504700 TAT TAT T
1 TAT TAT T
12504707 GTGTAATAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12506205 original size:3 final size:3
Alignment explanation
Indices: 12506197--12506226 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12506187 TTATTGTTGA
*
12506197 ATG ATG ATG ATG ATG ATG ATG AGG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
12506227 GCTATCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:12507678 original size:7 final size:7
Alignment explanation
Indices: 12507668--12507692 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12507658 TTTATACATT
12507668 ATTATAG
1 ATTATAG
12507675 ATTATAG
1 ATTATAG
12507682 ATTATAG
1 ATTATAG
12507689 ATTA
1 ATTA
12507693 CAATTGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
ATTATAG
Found at i:12508011 original size:46 final size:45
Alignment explanation
Indices: 12507944--12508031 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 45
12507934 TCATCTTCAC
*
12507944 TTGATTTATAAGAATTGTAAGGATACTCGAGGTGACTTTTTTTTTA
1 TTGATTTATAAGAATTGTAAGGATACTAGAGGTGA-TTTTTTTTTA
*
12507990 TTGATTTATAA-AACCTT-TAAGGATACTAGATGTGATTTTTTT
1 TTGATTTATAAGAA--TTGTAAGGATACTAGAGGTGATTTTTTT
12508032 ATATAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
45 9 0.24
46 27 0.71
47 2 0.05
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (45 bp):
TTGATTTATAAGAATTGTAAGGATACTAGAGGTGATTTTTTTTTA
Found at i:12521239 original size:28 final size:28
Alignment explanation
Indices: 12521208--12521268 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
12521198 TTTTTCCTAA
* *
12521208 ATTTTAAATTCTTTTAGTTTTTAATCTT
1 ATTTTAAACTCTTTTAGCTTTTAATCTT
*
12521236 ATTTTGAACTCTTTTAGCTTTTAATCTT
1 ATTTTAAACTCTTTTAGCTTTTAATCTT
12521264 ATTTT
1 ATTTT
12521269 TTGACAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (28 bp):
ATTTTAAACTCTTTTAGCTTTTAATCTT
Found at i:12523797 original size:27 final size:26
Alignment explanation
Indices: 12523763--12523813 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12523753 TAAAAAAGAC
* * *
12523763 AAAAAAAATGAATATAATAAAAAATT
1 AAAAAAAAAGAAAAAAATAAAAAATT
12523789 AAAAGAAAAAGAAAAAAATAAAAAA
1 AAAA-AAAAAGAAAAAAATAAAAAA
12523814 AGTTGAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAATAAAAAATT
Found at i:12524945 original size:26 final size:25
Alignment explanation
Indices: 12524889--12524948 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
12524879 TTTAAATGAG
*
12524889 GTAAAAAACAAAAAAATAAAGAAAT
1 GTAAAAAAAAAAAAAATAAAGAAAT
*
12524914 GAAAAAAAAAAACAAAATAAA-AATAT
1 GTAAAAAAAAAA-AAAATAAAGAA-AT
*
12524940 TTAAAAAAA
1 GTAAAAAAA
12524949 GAGTTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.13
Consensus pattern (25 bp):
GTAAAAAAAAAAAAAATAAAGAAAT
Done.