Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1354983 original size:34 final size:33
Alignment explanation
Indices: 1354928--1355029 Score: 116
Period size: 34 Copynumber: 3.0 Consensus size: 33
1354918 AGTTTATATT
*
1354928 AGCATTAGAGTGTA-ACCCCAAGACACTTAGTGTA
1 AGCACTAGAGTGTATA--CCAAGACACTTAGTGTA
* * *
1354962 GGCACTAGAGTGTATAGCCAAGACACATAGTGCA
1 AGCACTAGAGTGTATA-CCAAGACACTTAGTGTA
*
1354996 AGCGCTAGAGTGTATACTCAAGACACTTAGTGTA
1 AGCACTAGAGTGTATAC-CAAGACACTTAGTGTA
1355030 TATGGTGGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 1 0.02
34 55 0.96
35 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (33 bp):
AGCACTAGAGTGTATACCAAGACACTTAGTGTA
Found at i:1359006 original size:30 final size:30
Alignment explanation
Indices: 1358970--1359027 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1358960 CCGTAATTGG
1358970 AATTACGGAATTAGTTTTCCTTGAATTCCC
1 AATTACGGAATTAGTTTTCCTTGAATTCCC
1359000 AATTACGGAATTAGTTTTCCTTGAATTC
1 AATTACGGAATTAGTTTTCCTTGAATTC
1359028 ACGTGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (30 bp):
AATTACGGAATTAGTTTTCCTTGAATTCCC
Found at i:1359088 original size:42 final size:42
Alignment explanation
Indices: 1359029--1359144 Score: 205
Period size: 42 Copynumber: 2.8 Consensus size: 42
1359019 CTTGAATTCA
*
1359029 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
* *
1359071 CGTGTTTGTTTAACGTAATTCATTTTCCGGAAAACGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1359113 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1359145 TGTAATTCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
Found at i:1359241 original size:13 final size:14
Alignment explanation
Indices: 1359206--1359240 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1359196 ACTTACGGAT
1359206 TCATTTTTCGTAAG
1 TCATTTTTCGTAAG
1359220 TCATTTTTCGTAAG
1 TCATTTTTCGTAAG
1359234 TCATTTT
1 TCATTTT
1359241 CCGAACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.54
Consensus pattern (14 bp):
TCATTTTTCGTAAG
Found at i:1359452 original size:79 final size:79
Alignment explanation
Indices: 1359364--1359510 Score: 172
Period size: 79 Copynumber: 1.8 Consensus size: 79
1359354 AAAATATATT
* * *
1359364 TATTAATA-TTTATAATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TATTAATATTTTATAATAATAATAT-ATAATAAATTTTTAATA-TATATAAAATAATCAATAATA
1359428 TTATAATAATATAAGA
64 TTATAATAATATAAGA
** * ** *
1359444 TATT-ATATTTTTATTTTAATAATATATAATAAATTTTTTATATATATTTAATAATGAATAATAT
1 TATTAATA-TTTTATAATAATAATATATAATAAATTTTTAATATATATAAAATAATCAATAATAT
1359508 TAT
65 TAT
1359511 TTTATATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
79 24 0.43
80 18 0.32
81 14 0.25
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (79 bp):
TATTAATATTTTATAATAATAATATATAATAAATTTTTAATATATATAAAATAATCAATAATATT
ATAATAATATAAGA
Found at i:1359473 original size:54 final size:52
Alignment explanation
Indices: 1359378--1359478 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 52
1359368 AATATTTATA
*
1359378 ATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATATT
1 ATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATATT
*
1359430 ATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 ATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
1359479 TTTTATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
52 14 0.33
53 7 0.16
54 22 0.51
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
ATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATATT
Found at i:1359494 original size:32 final size:30
Alignment explanation
Indices: 1359375--1359530 Score: 112
Period size: 29 Copynumber: 5.2 Consensus size: 30
1359365 ATTAATATTT
* *
1359375 ATAATA-ATAATATAATATTATAT-TTTTA
1 ATAATATATAATATTATTTTATATATTTTA
* * * ** *
1359403 ATATTATATAA-AATAATCAATTATATTATA
1 ATAATATATAATATTATTTTA-TATATTTTA
1359433 ATAATATA-AGATATTATATTT-T-TATTTTA
1 ATAATATATA-ATATTAT-TTTATATATTTTA
1359462 ATAATATATAATAAATT-TTTTATATATATTTA
1 ATAATATATAAT--ATTATTTTATATAT-TTTA
*
1359494 ATAATGA-ATAATATTATTTTATATATTTCA
1 ATAAT-ATATAATATTATTTTATATATTTTA
1359524 ATAATAT
1 ATAATAT
1359531 TTTAGTAAAG
Statistics
Matches: 98, Mismatches: 15, Indels: 28
0.70 0.11 0.20
Matches are distributed among these distances:
28 8 0.08
29 28 0.29
30 27 0.28
31 19 0.19
32 15 0.15
33 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
ATAATATATAATATTATTTTATATATTTTA
Found at i:1359774 original size:20 final size:20
Alignment explanation
Indices: 1359696--1359765 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1359686 TTTCCAGATG
1359696 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1359716 TTTTCCAGAAATGTAATTAA
1 TTTTCCAGAAATGTAATTCA
*
1359736 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1359756 TTTTCCAGAA
1 TTTTCCAGAA
1359766 TTCAAATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1359784 original size:15 final size:15
Alignment explanation
Indices: 1359748--1359829 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
1359738 TTACAGAAAT
**
1359748 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1359763 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
1359777 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1359792 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1359807 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1359822 GTAATTCA
1 GTAATTCA
1359830 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1359800 original size:30 final size:30
Alignment explanation
Indices: 1359748--1359829 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
1359738 TTACAGAAAT
1359748 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
1359777 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1359807 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1359830 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1359815 original size:45 final size:44
Alignment explanation
Indices: 1359748--1359834 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
1359738 TTACAGAAAT
**
1359748 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1359792 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
1359835 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:1367952 original size:7 final size:7
Alignment explanation
Indices: 1367940--1367966 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1367930 GAGGGCATGG
1367940 AGAATGA
1 AGAATGA
1367947 AGAATGA
1 AGAATGA
1367954 AGAATGA
1 AGAATGA
1367961 AGAATG
1 AGAATG
1367967 GGCTCTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (7 bp):
AGAATGA
Found at i:1373243 original size:20 final size:19
Alignment explanation
Indices: 1373209--1373254 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1373199 TTCGGATCTA
* *
1373209 AAAAATCTTTGTAAAAAAT
1 AAAAATATTTGTAAAAAAG
*
1373228 AAAAATATTTGATAAAAGAG
1 AAAAATATTTG-TAAAAAAG
1373248 AAAAATA
1 AAAAATA
1373255 AATATACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (19 bp):
AAAAATATTTGTAAAAAAG
Found at i:1373570 original size:49 final size:49
Alignment explanation
Indices: 1373480--1373573 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 49
1373470 TGATTGATCT
* * * *
1373480 TTTATGTTATCATTTTATTCGATTTTAGTCTTTCAATCGTTAAATAACA
1 TTTACGTTATCATTTTATTCGATTTTAATCCTTCAACCGTTAAATAACA
* *
1373529 TTTACGTTATCATTTTATTCTATTTTAATCCTTCAGCCGTTAAAT
1 TTTACGTTATCATTTTATTCGATTTTAATCCTTCAACCGTTAAAT
1373574 CATAAGCTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (49 bp):
TTTACGTTATCATTTTATTCGATTTTAATCCTTCAACCGTTAAATAACA
Found at i:1375913 original size:15 final size:14
Alignment explanation
Indices: 1375893--1375987 Score: 57
Period size: 15 Copynumber: 6.4 Consensus size: 14
1375883 TATTATTTAA
1375893 ATTTAATTTGAATTT
1 ATTTAATTT-AATTT
*
1375908 ATTTAAATTAAGTTT
1 ATTTAATTTAA-TTT
**
1375923 ATAAAATTTGAATTT
1 ATTTAATTT-AATTT
*
1375938 ATTTAAATTAAGTTT
1 ATTTAATTTAA-TTT
** *
1375953 ATAAAATTTGAATTAA
1 ATTTAATTT-AATT-T
*
1375969 ATTTAATAT-ATTT
1 ATTTAATTTAATTT
1375982 ATTTAA
1 ATTTAA
1375988 GTTTTGTTTA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
13 6 0.10
14 7 0.12
15 37 0.62
16 10 0.17
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
ATTTAATTTAATTT
Found at i:1375932 original size:30 final size:30
Alignment explanation
Indices: 1375897--1375966 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
1375887 ATTTAAATTT
1375897 AATTTGAATTTATTTAAATTAAGTTTATAA
1 AATTTGAATTTATTTAAATTAAGTTTATAA
1375927 AATTTGAATTTATTTAAATTAAGTTTATAA
1 AATTTGAATTTATTTAAATTAAGTTTATAA
1375957 AATTTGAATT
1 AATTTGAATT
1375967 AAATTTAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (30 bp):
AATTTGAATTTATTTAAATTAAGTTTATAA
Found at i:1375981 original size:20 final size:20
Alignment explanation
Indices: 1375926--1375982 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1375916 TAAGTTTATA
*
1375926 AAATTTGAATTTATTTAAATT
1 AAATTT-AATATATTTAAATT
* * *
1375947 AAGTTT-ATAAAATTTGAATT
1 AAATTTAAT-ATATTTAAATT
1375967 AAATTTAATATATTTA
1 AAATTTAATATATTTA
1375983 TTTAAGTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
19 2 0.07
20 18 0.67
21 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AAATTTAATATATTTAAATT
Found at i:1378393 original size:54 final size:58
Alignment explanation
Indices: 1378321--1378451 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 58
1378311 TATCAATTTA
* * * * * *
1378321 TAACAAAATGATCCCTAATTTTTAAGT-A-TTTT-TTTTT-CACTACATTTTCAAAAG
1 TAACAAATTAATCACTAATGTTTAAGTAAGTTTTATTTTTCCACTAAAGTTTCAAAAG
1378375 TAACAAATTAATCACTAATGTTTAAGTAAGTTTTCATTTTTCCACTAAAGTTTCAAAAG
1 TAACAAATTAATCACTAATGTTTAAGTAAGTTTT-ATTTTTCCACTAAAGTTTCAAAAG
*
1378434 TAGCAAATTAATCACTAA
1 TAACAAATTAATCACTAA
1378452 CATTATCTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
54 23 0.35
55 1 0.02
56 4 0.06
58 5 0.08
59 32 0.49
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.40
Consensus pattern (58 bp):
TAACAAATTAATCACTAATGTTTAAGTAAGTTTTATTTTTCCACTAAAGTTTCAAAAG
Found at i:1378519 original size:90 final size:90
Alignment explanation
Indices: 1378386--1378570 Score: 241
Period size: 90 Copynumber: 2.1 Consensus size: 90
1378376 AACAAATTAA
* * * *
1378386 TCACTAATGTTTAAGTAAGTTTTCATTTTTCCACTAAAGTTTCAAAAGTAGCAAATTAATCACTA
1 TCACTAATGTTTAAGTAAGTTTTCATTTTCCCACTAAAATTTCAAAAGCAACAAATTAATCACTA
* *
1378451 ACATTATCTATTTGTAACAAAATGG
66 ACATTATCGATTTATAACAAAATGG
*
1378476 TCACTAATG-TTAGAGTACA-TATTT-ATTTTCCCACTAAAATTTCAAAAGCAACAAATTGATCA
1 TCACTAATGTTTA-AGTA-AGT-TTTCATTTTCCCACTAAAATTTCAAAAGCAACAAATTAATCA
* *
1378538 TTAACGTTATCGATTTATAACAAAATGG
63 CTAACATTATCGATTTATAACAAAATGG
1378566 TCACT
1 TCACT
1378571 CCACCGTCAT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
89 3 0.04
90 76 0.92
91 4 0.05
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (90 bp):
TCACTAATGTTTAAGTAAGTTTTCATTTTCCCACTAAAATTTCAAAAGCAACAAATTAATCACTA
ACATTATCGATTTATAACAAAATGG
Found at i:1379217 original size:15 final size:15
Alignment explanation
Indices: 1379180--1379209 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1379170 TTTATTATTT
*
1379180 CTTTTAACATTTTAA
1 CTTTTAATATTTTAA
1379195 CTTTTAATATTTTAA
1 CTTTTAATATTTTAA
1379210 TTTCTAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
CTTTTAATATTTTAA
Found at i:1379301 original size:26 final size:26
Alignment explanation
Indices: 1379265--1379343 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
1379255 TTAATTTTTG
*
1379265 ATTGAAACATACTATATTAGATAACA
1 ATTGAAACATACTATATTAGATAAAA
* *
1379291 ATTGAAACATACTGTATTTGATAAAA
1 ATTGAAACATACTATATTAGATAAAA
* *
1379317 ATTGGAACATTCTATATTAGATAAAA
1 ATTGAAACATACTATATTAGATAAAA
1379343 A
1 A
1379344 CCGTTAATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (26 bp):
ATTGAAACATACTATATTAGATAAAA
Found at i:1386325 original size:30 final size:28
Alignment explanation
Indices: 1386259--1386331 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 28
1386249 TATGGTCAAT
*
1386259 AATCAAT-ATGACCACCGAACTTTTTTTG
1 AATCAATCA-GACCACCAAACTTTTTTTG
1386287 AATCAATCAGACCACCAAACTTTTTAATTG
1 AATCAATCAGACCACCAAACTTTTT--TTG
*
1386317 ATTCAATCAGACCAC
1 AATCAATCAGACCAC
1386332 TCTCCGTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 22 0.55
29 1 0.03
30 17 0.43
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (28 bp):
AATCAATCAGACCACCAAACTTTTTTTG
Found at i:1388479 original size:13 final size:13
Alignment explanation
Indices: 1388452--1388584 Score: 72
Period size: 13 Copynumber: 10.0 Consensus size: 13
1388442 CATTAACACG
*
1388452 ATAACAGTATGCA
1 ATAACAATATGCA
*
1388465 ATAACAATATTCA
1 ATAACAATATGCA
**
1388478 ATTATTTTAATATGCA
1 A-TA--ACAATATGCA
* *
1388494 ATAACAGTAGGC-
1 ATAACAATATGCA
*
1388506 ATGAACAATATGTA
1 AT-AACAATATGCA
*
1388520 ATAACAGTATGC-
1 ATAACAATATGCA
*
1388532 ATGAACAATATGTA
1 AT-AACAATATGCA
* * *
1388546 ATAATATTATGTA
1 ATAACAATATGCA
* *
1388559 GTAACAATATGTA
1 ATAACAATATGCA
*
1388572 ATAACACTATGCA
1 ATAACAATATGCA
1388585 TGAAGAATAT
Statistics
Matches: 89, Mismatches: 24, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
12 4 0.04
13 69 0.78
14 6 0.07
15 2 0.02
16 8 0.09
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (13 bp):
ATAACAATATGCA
Found at i:1388522 original size:26 final size:26
Alignment explanation
Indices: 1388486--1388597 Score: 145
Period size: 26 Copynumber: 4.3 Consensus size: 26
1388476 CAATTATTTT
* *
1388486 AATATGCAATAACAGTAGGCATGAAC
1 AATATGTAATAACAGTATGCATGAAC
1388512 AATATGTAATAACAGTATGCATGAAC
1 AATATGTAATAACAGTATGCATGAAC
* * *
1388538 AATATGTAATAATATTATGTA-GTAAC
1 AATATGTAATAACAGTATGCATG-AAC
* *
1388564 AATATGTAATAACACTATGCATGAAG
1 AATATGTAATAACAGTATGCATGAAC
1388590 AATATGTA
1 AATATGTA
1388598 TTAGCAAGTT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
25 1 0.01
26 73 0.97
27 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (26 bp):
AATATGTAATAACAGTATGCATGAAC
Found at i:1390116 original size:18 final size:18
Alignment explanation
Indices: 1390095--1390134 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1390085 CTTGTGTTGT
1390095 CATTTGTTCTAAACTTCA
1 CATTTGTTCTAAACTTCA
1390113 CATTTGTTCTAAACTTCA
1 CATTTGTTCTAAACTTCA
1390131 CATT
1 CATT
1390135 ATACCTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.45
Consensus pattern (18 bp):
CATTTGTTCTAAACTTCA
Found at i:1390557 original size:45 final size:45
Alignment explanation
Indices: 1390487--1390596 Score: 175
Period size: 45 Copynumber: 2.4 Consensus size: 45
1390477 CACCTCATCA
*
1390487 GGTTCTGGTTCATTAATTCCAGGTTCATTAATTTCTGGCTCAACT
1 GGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTGGCTCAACT
* ** *
1390532 GGTTCTGGTTCATCAATTTTGGGTTCATTAATTTCTGGCTCAATT
1 GGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTGGCTCAACT
1390577 GGTTCTGGTTCATTAATTTC
1 GGTTCTGGTTCATTAATTTC
1390597 TGGCTCAGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.45
Consensus pattern (45 bp):
GGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTGGCTCAACT
Found at i:1390612 original size:75 final size:75
Alignment explanation
Indices: 1390508--1390671 Score: 274
Period size: 75 Copynumber: 2.2 Consensus size: 75
1390498 ATTAATTCCA
* *
1390508 GGTTCATTAATTTCTGGCTCAACTGGTTCTGGTTCATCAATTTTGGGTTCATTAATTTCTGGCTC
1 GGTTCATTAATTTCTGGCTCAACTGGTTCTGGTTCATCAATTTCGGGTTCACTAATTTCTGGCTC
*
1390573 AATTGGTTCT
66 AACTGGTTCT
* *
1390583 GGTTCATTAATTTCTGGCTCAGCTGGTTCTGGTTCATTAATTTCGGGTTCACTAATTTCTGGCTC
1 GGTTCATTAATTTCTGGCTCAACTGGTTCTGGTTCATCAATTTCGGGTTCACTAATTTCTGGCTC
1390648 AACTGGTTCT
66 AACTGGTTCT
*
1390658 GGTTCATCAATTTC
1 GGTTCATTAATTTC
1390672 AGGTTCATTA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (75 bp):
GGTTCATTAATTTCTGGCTCAACTGGTTCTGGTTCATCAATTTCGGGTTCACTAATTTCTGGCTC
AACTGGTTCT
Found at i:1390613 original size:45 final size:44
Alignment explanation
Indices: 1390487--1390659 Score: 125
Period size: 45 Copynumber: 3.8 Consensus size: 44
1390477 CACCTCATCA
* * * * ** *
1390487 GGTTCTGGTTCATTAATTCCAGGTTCATTAATTTCTGGCTCAACT
1 GGTTCTGGTTCATTAATTTCTGGCTCACT-GGTTCTGGCTCAATT
* * * **
1390532 GGTTCTGGTTCATCAATTT-TGGGTTCATTAATTTCTGGCTCAATT
1 GGTTCTGGTTCATTAATTTCT-GGCTCACT-GGTTCTGGCTCAATT
*
1390577 GGTTCTGGTTCATTAATTTCTGGCTCAGCTGGTTCTGGTTC-ATT
1 GGTTCTGGTTCATTAATTTCTGGCTCA-CTGGTTCTGGCTCAATT
** * *
1390621 AATTTCGGGTTCACTAATTTCTGGCTCAACTGGTTCTGG
1 -GGTTCTGGTTCATTAATTTCTGGCTC-ACTGGTTCTGG
1390660 TTCATCAATT
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
44 3 0.03
45 103 0.94
46 3 0.03
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.43
Consensus pattern (44 bp):
GGTTCTGGTTCATTAATTTCTGGCTCACTGGTTCTGGCTCAATT
Found at i:1390643 original size:30 final size:30
Alignment explanation
Indices: 1390489--1390644 Score: 106
Period size: 30 Copynumber: 5.2 Consensus size: 30
1390479 CCTCATCAGG
* * *
1390489 TTCTGGTTCATTAATTCCAGGTTCATTAAT
1 TTCTGGTTCATTAATTTCTGGTTCACTAAT
* *
1390519 TTCTGGCTCA--ACTGGTTCTGGTTCA-TCAAT
1 TTCTGGTTCATTAAT--TTCTGGTTCACT-AAT
* * ***
1390549 TT-TGGGTTCATTAATTTCTGGCTCAATTGG
1 TTCT-GGTTCATTAATTTCTGGTTCACTAAT
* **
1390579 TTCTGGTTCATTAATTTCTGGCTCAGCT-GG
1 TTCTGGTTCATTAATTTCTGGTTCA-CTAAT
*
1390609 TTCTGGTTCATTAATTTCGGGTTCACTAAT
1 TTCTGGTTCATTAATTTCTGGTTCACTAAT
1390639 TTCTGG
1 TTCTGG
1390645 CTCAACTGGT
Statistics
Matches: 101, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
28 2 0.02
29 4 0.04
30 90 0.89
31 3 0.03
32 2 0.02
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (30 bp):
TTCTGGTTCATTAATTTCTGGTTCACTAAT
Found at i:1390660 original size:45 final size:45
Alignment explanation
Indices: 1390583--1390678 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
1390573 AATTGGTTCT
* * * *
1390583 GGTTCATTAATTTCTGGCTCAGCTGGTTCTGGTTCATTAATTTCG
1 GGTTCACTAATTTCTGGCTCAACTGGTTCTGGTTCATCAATTTCA
1390628 GGTTCACTAATTTCTGGCTCAACTGGTTCTGGTTCATCAATTTCA
1 GGTTCACTAATTTCTGGCTCAACTGGTTCTGGTTCATCAATTTCA
1390673 GGTTCA
1 GGTTCA
1390679 TTATGTTCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (45 bp):
GGTTCACTAATTTCTGGCTCAACTGGTTCTGGTTCATCAATTTCA
Found at i:1391390 original size:17 final size:17
Alignment explanation
Indices: 1391370--1391413 Score: 65
Period size: 15 Copynumber: 2.7 Consensus size: 17
1391360 TTCACTAAAC
1391370 ACATATATTCATGCAGA
1 ACATATATTCATGCAGA
*
1391387 ACATATA--CATGCAGT
1 ACATATATTCATGCAGA
1391402 ACATATATTCAT
1 ACATATATTCAT
1391414 TGACTTCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 14 0.58
17 10 0.42
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (17 bp):
ACATATATTCATGCAGA
Found at i:1391466 original size:18 final size:17
Alignment explanation
Indices: 1391445--1391478 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1391435 TATTCATGCA
1391445 AACAAATAATTCTATCAC
1 AACAAAT-ATTCTATCAC
*
1391463 AACATATATTCTATCA
1 AACAAATATTCTATCA
1391479 ATAAACATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (17 bp):
AACAAATATTCTATCAC
Found at i:1391487 original size:19 final size:19
Alignment explanation
Indices: 1391463--1391560 Score: 68
Period size: 19 Copynumber: 5.4 Consensus size: 19
1391453 ATTCTATCAC
1391463 AACATATATTCTATCAATA
1 AACATATATTCTATCAATA
* *
1391482 AACATA-AAT-TATCCAAATG
1 AACATATATTCTAT-C-AATA
1391501 AACATATATTCTAT--A-A
1 AACATATATTCTATCAATA
* *
1391517 AACAAATTATTCTAT---TGG
1 AACATA-TATTCTATCAAT-A
1391535 AACATATATTCTATCAATA
1 AACATATATTCTATCAATA
1391554 AACATAT
1 AACATAT
1391561 CATTAATAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
16 5 0.08
17 20 0.33
18 8 0.13
19 22 0.36
20 3 0.05
21 3 0.05
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (19 bp):
AACATATATTCTATCAATA
Found at i:1391505 original size:38 final size:39
Alignment explanation
Indices: 1391463--1391559 Score: 125
Period size: 34 Copynumber: 2.6 Consensus size: 39
1391453 ATTCTATCAC
1391463 AACATATATTCTATCAATAAACATAAATTATCCAAAT-G
1 AACATATATTCTATCAATAAACATAAATTATCCAAATGG
* * *
1391501 AACATATATTCTAT--A-AAAC--AAATTATTCTATTGG
1 AACATATATTCTATCAATAAACATAAATTATCCAAATGG
1391535 AACATATATTCTATCAATAAACATA
1 AACATATATTCTATCAATAAACATA
1391560 TCATTAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
33 10 0.20
34 15 0.30
35 4 0.08
36 2 0.04
37 4 0.08
38 14 0.28
39 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.34
Consensus pattern (39 bp):
AACATATATTCTATCAATAAACATAAATTATCCAAATGG
Found at i:1391544 original size:17 final size:17
Alignment explanation
Indices: 1391500--1391548 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1391490 TTATCCAAAT
1391500 GAACATATATTCTA-TA
1 GAACATATATTCTATTA
* * *
1391516 AAACAAATTATTCTATTG
1 GAACATA-TATTCTATTA
1391534 GAACATATATTCTAT
1 GAACATATATTCTAT
1391549 CAATAAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (17 bp):
GAACATATATTCTATTA
Found at i:1392174 original size:20 final size:20
Alignment explanation
Indices: 1392151--1392188 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1392141 GATCTTTATT
1392151 TCTCAGAATCTCTCTAAAGC
1 TCTCAGAATCTCTCTAAAGC
*
1392171 TCTCTGAATCTCTCTAAA
1 TCTCAGAATCTCTCTAAA
1392189 CCAGTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (20 bp):
TCTCAGAATCTCTCTAAAGC
Found at i:1394306 original size:21 final size:20
Alignment explanation
Indices: 1394276--1394315 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1394266 ACTTCTGCCG
*
1394276 CTCATTTCTTCTTTATTTTT
1 CTCATTTCTTCATTATTTTT
1394296 CTCATGTTCTTCATTATTTT
1 CTCAT-TTCTTCATTATTTT
1394316 ATTCGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.12, C:0.20, G:0.03, T:0.65
Consensus pattern (20 bp):
CTCATTTCTTCATTATTTTT
Found at i:1394985 original size:39 final size:39
Alignment explanation
Indices: 1394929--1395005 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
1394919 CGGGGAATTG
* *
1394929 AAAAGGCTCTTGCACACTCGGATTCCTCCTTTCTTATGA
1 AAAAGGCTCTTGAACACTCGGATTCCCCCTTTCTTATGA
1394968 AAAAGGCTCTTGAACACTCGGATTCCCCCTTTCTTATG
1 AAAAGGCTCTTGAACACTCGGATTCCCCCTTTCTTATG
1395006 GACCTAGGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (39 bp):
AAAAGGCTCTTGAACACTCGGATTCCCCCTTTCTTATGA
Found at i:1395065 original size:3 final size:3
Alignment explanation
Indices: 1395059--1395105 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
1395049 TACCAAAAAA
1395059 ATT ATT ATT ATT -TT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1395104 AT
1 AT
1395106 GTTTTTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:1395648 original size:136 final size:132
Alignment explanation
Indices: 1395234--1395659 Score: 504
Period size: 130 Copynumber: 3.2 Consensus size: 132
1395224 CCTGGTTCCA
* * *
1395234 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCATCCACATCACGTAGGAAGCGTGTTAT
1 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCACATCACGTAGGAACCGTGTTAT
* * * *
1395299 CATTT-TTAAAGATGGCC-TGACGTCCTCATCGCGTAGGAACCGTGTCATCCCCGACCAGACCTC
66 CATTTCCTAAAGATGGCCAAGACATCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGACCTC
1395362 CT
131 CT
* * * *
1395364 CATCACGTAGGAGCCGTGTCA-CCTTCAGATAACAAGCCGTCCTCATCACGTAGGAGCCGTGTTA
1 CATCACGTAGGAGCCGTGTCACCCCT-AGATAACCAGCCGTCCACATCACGTAGGAACCGTGTTA
* * * *
1395428 TCA-TCCCTAAAGATGG-CATA-TCATCCTCATCATGTAAGAACCGTGTCATCCCCCGACCAGAC
65 TCATTTCCTAAAGATGGCCA-AGACATCCTCATCACGTAGGAACCGTGTCAT-CCCCGACCAGAC
1395490 CTCCT
128 CTCCT
** * * ** *
1395495 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTTGTCCCCATCGCACAGGAATCGTGTTAT
1 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCACATCACGTAGGAACCGTGTTAT
* **
1395560 CACCATTTCCTAAAGATGGCCAAGCCATCCTCATCACGTAGGAACATTGTCATCCACCGACCAGA
66 ---CATTTCCTAAAGATGGCCAAGACATCCTCATCACGTAGGAACCGTGTCATCC-CCGACCAGA
*
1395625 TCTCCT
127 CCTCCT
*
1395631 CATCACGTAGGAGCCGTGTCACCCTTAGA
1 CATCACGTAGGAGCCGTGTCACCCCTAGA
1395660 CGACCAAACC
Statistics
Matches: 250, Mismatches: 33, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
129 5 0.02
130 89 0.36
131 68 0.27
132 3 0.01
134 2 0.01
135 15 0.06
136 68 0.27
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.23
Consensus pattern (132 bp):
CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCACATCACGTAGGAACCGTGTTAT
CATTTCCTAAAGATGGCCAAGACATCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGACCTC
CT
Found at i:1397526 original size:30 final size:30
Alignment explanation
Indices: 1397443--1397633 Score: 176
Period size: 30 Copynumber: 6.5 Consensus size: 30
1397433 TTTGTAATTA
* * *
1397443 CTATTTTAGTCCTTTTAGATTCT-CTTTT-
1 CTATTTTAGTCCTTTAAGTTTCTATTTTTG
* * * *
1397471 -TAATATAGTCCTTTAAATGTCTATTTTTG
1 CTATTTTAGTCCTTTAAGTTTCTATTTTTG
*
1397500 CTATTTTAGTTCC-TTAAGTTTTTATTTTTG
1 CTATTTTAG-TCCTTTAAGTTTCTATTTTTG
1397530 CTATTTTAG-CTCTTTAAGTTTCTATTTTTG
1 CTATTTTAGTC-CTTTAAGTTTCTATTTTTG
* *
1397560 CTATTTTAGTCCTTTAAATTTCTATTTTAG
1 CTATTTTAGTCCTTTAAGTTTCTATTTTTG
* * * * *
1397590 CTATTTTGGTCCTTTAATTTTTTGTTTTTC
1 CTATTTTAGTCCTTTAAGTTTCTATTTTTG
* *
1397620 CCATTCTAGTCCTT
1 CTATTTTAGTCCTT
1397634 GCAGTTATAA
Statistics
Matches: 132, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
27 16 0.12
28 5 0.04
29 1 0.01
30 106 0.80
31 4 0.03
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (30 bp):
CTATTTTAGTCCTTTAAGTTTCTATTTTTG
Found at i:1403023 original size:38 final size:36
Alignment explanation
Indices: 1402968--1403075 Score: 137
Period size: 36 Copynumber: 3.0 Consensus size: 36
1402958 TAGAGACAGT
* *
1402968 TTTCT-TAAAAACAAATTTTATTTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* *
1403003 CTTTCTCTAAAAAAAAAATTTTGTCTCGCTTAAGACAA
1 -TTTCTCT-AAAAACAAATTTTGTCTCGCTTGAGACAA
* *
1403041 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
1403076 TTTTTTTCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 29 0.47
37 8 0.13
38 25 0.40
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:1403513 original size:40 final size:40
Alignment explanation
Indices: 1403383--1403528 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
1403373 TGGTCTATCG
* * * *
1403383 TCCTCATCGCGTAGCAACCGTGTCATCCCTTGGCCAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACC
* * ** **
1403423 TCCTCACCACGTAAGATTCGTGTCA-CTTTCAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTC-G---ACCAGACC
1403465 GTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACC
1 -TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACC
* *
1403506 TCCTCATCACATAGGAACTGTGT
1 TCCTCATCACGTAGGAACCGTGT
1403529 TAACCATAGA
Statistics
Matches: 81, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
39 2 0.02
40 46 0.57
41 2 0.02
42 2 0.02
43 26 0.32
44 3 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACC
Found at i:1403540 original size:83 final size:83
Alignment explanation
Indices: 1403381--1403571 Score: 215
Period size: 83 Copynumber: 2.3 Consensus size: 83
1403371 GATGGTCTAT
* * * * * *
1403381 CGTCCTCATCGCGTAGCAACCGTGTCATCCCTTGGCCAGACCTCCTCACCACGTAAGATTCGTGT
1 CGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCACCACATAAGACTCGTGT
* ** *
1403446 CACTTTCAGATAACCAGC
66 AACCATCAGATAACCAAC
* *
1403464 CGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCATCACATAGGAACT-GTG
1 CGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCACCACATAAG-ACTCGTG
1403528 TTAACCAT-AGATAACCAAC
65 -TAACCATCAGATAACCAAC
* * *
1403547 CATCCACATCACGTAAGAACCGTGT
1 CGTCCTCATCACGTAGGAACCGTGT
1403572 TATCATTTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
83 85 0.93
84 6 0.07
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.23
Consensus pattern (83 bp):
CGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCACCACATAAGACTCGTGT
AACCATCAGATAACCAAC
Found at i:1403719 original size:131 final size:131
Alignment explanation
Indices: 1403476--1403721 Score: 307
Period size: 131 Copynumber: 1.9 Consensus size: 131
1403466 TCCTCATCAC
* * *
1403476 GTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCATCACATAGGAACTGTGTTAACCATAGATA
1 GTAGGAACCGTATCATCCCTCGACCAAACCTCCTCATCACATAGGAACCGTGTTAACCATAGATA
***
1403541 ACCAACCATCCACATCACGTAAGAACCGTGTTATCATTTTTAAAGATGGCCTACCATCTTCATCG
66 ACCAACCATCCACATCACGTAAGAACCGTGTTATCATCCCTAAAGATGGCCTACCATCTTCATCG
1403606 T
131 T
* * * *
1403607 GTAGGAACCGTATCATCCCTCGACCAAACCTCCTCATCACGTAGGAGCCGTG-TCACCTTCAGAT
1 GTAGGAACCGTATCATCCCTCGACCAAACCTCCTCATCACATAGGAACCGTGTTAACCAT-AGAT
* * * * * * *
1403671 AACTAGCCGTCCTCATCATGTATA-AATCGTGTTATCATCCCTAGAGATGGC
65 AACCAACCATCCACATCACGTA-AGAACCGTGTTATCATCCCTAAAGATGGC
1403722 ATGCCGTACT
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
130 5 0.05
131 90 0.94
132 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (131 bp):
GTAGGAACCGTATCATCCCTCGACCAAACCTCCTCATCACATAGGAACCGTGTTAACCATAGATA
ACCAACCATCCACATCACGTAAGAACCGTGTTATCATCCCTAAAGATGGCCTACCATCTTCATCG
T
Found at i:1403745 original size:131 final size:130
Alignment explanation
Indices: 1403462--1403746 Score: 295
Period size: 131 Copynumber: 2.2 Consensus size: 130
1403452 CAGATAACCA
* * *
1403462 GCCGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCATCACATAGGAACTGT
1 GCCGT-CTCATCACGTAGGAACCGTATCATCCCTCGACCAAACCTCCTCATCACATAGGAACCGT
*** *
1403527 GTTAACCATAGATAACCAACCATCCACATCACGTAAGAACCGTGTTATCATTTTTAAAGATGGCC
65 GTTAACCATAGATAACCAACCATCCACATCACGTAAGAACCGTGTTATCATCCCTAAAGATGGCA
1403592 T
130 T
* * ** * *
1403593 ACCATCTTCATCGTGTAGGAACCGTATCATCCCTCGACCAAACCTCCTCATCACGTAGGAGCCGT
1 GCCGTC-TCATCACGTAGGAACCGTATCATCCCTCGACCAAACCTCCTCATCACATAGGAACCGT
* * * * * * * * *
1403658 G-TCACCTTCAGATAACTAGCCGTCCTCATCATGTATA-AATCGTGTTATCATCCCTAGAGATGG
65 GTTAACCAT-AGATAACCAACCATCCACATCACGTA-AGAACCGTGTTATCATCCCTAAAGATGG
1403721 CAT
128 CAT
* *
1403724 GCCGTACTCCTCACGTCGGAACC
1 GCCGT-CTCATCACGTAGGAACC
1403747 ATGTTATCTA
Statistics
Matches: 122, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
130 6 0.05
131 114 0.93
132 2 0.02
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (130 bp):
GCCGTCTCATCACGTAGGAACCGTATCATCCCTCGACCAAACCTCCTCATCACATAGGAACCGTG
TTAACCATAGATAACCAACCATCCACATCACGTAAGAACCGTGTTATCATCCCTAAAGATGGCAT
Found at i:1404193 original size:4 final size:4
Alignment explanation
Indices: 1404184--1404209 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1404174 ATATTATTAT
1404184 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
1404210 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1404220 original size:12 final size:13
Alignment explanation
Indices: 1404177--1404218 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
1404167 CAAAAAAATA
1404177 TTATTATT-TTAT
1 TTATTATTATTAT
1404189 TTATTTATTTATTTAT
1 TTA-TTA-TTA-TTAT
1404205 TTATTATTATTAT
1 TTATTATTATTAT
1404218 T
1 T
1404219 ATGTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.12
13 8 0.31
14 5 0.19
15 3 0.12
16 7 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:1404543 original size:18 final size:18
Alignment explanation
Indices: 1404520--1404560 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1404510 TTAACATCAA
*
1404520 CCACCAACATCAG-TTCAG
1 CCACCAACACCAGCTT-AG
1404538 CCACCAACACCAGCTTAG
1 CCACCAACACCAGCTTAG
1404556 CCACC
1 CCACC
1404561 GCCACTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.32, C:0.46, G:0.10, T:0.12
Consensus pattern (18 bp):
CCACCAACACCAGCTTAG
Found at i:1405782 original size:30 final size:29
Alignment explanation
Indices: 1405728--1405887 Score: 133
Period size: 30 Copynumber: 5.3 Consensus size: 29
1405718 TGTTTTAATA
* * *
1405728 TTTAGTCCTTTAAATGTCTGTTTTTGCTAT
1 TTTAGTCC-TTAAGTTTCTATTTTTGCTAT
*
1405758 TTTAGTTCCTTAAGTTTTTATTTTTGCTAT
1 TTTAG-TCCTTAAGTTTCTATTTTTGCTAT
* * * *
1405788 TTTAACTCTTTGAGTTTCTATTTTTTCTAT
1 TTT-AGTCCTTAAGTTTCTATTTTTGCTAT
* *
1405818 TTTAGTCCTTTAAATTTCTATTTTAGCTAT
1 TTTAGTCC-TTAAGTTTCTATTTTTGCTAT
* * *
1405848 TTT-GATCCTTTAGTTTTCTATTTTTCCCAT
1 TTTAG-TCCTTAAG-TTTCTATTTTTGCTAT
*
1405878 TCTAGTCCTT
1 TTTAGTCCTT
1405888 GTAATTATAA
Statistics
Matches: 103, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
29 7 0.07
30 91 0.88
31 5 0.05
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (29 bp):
TTTAGTCCTTAAGTTTCTATTTTTGCTAT
Found at i:1405818 original size:60 final size:60
Alignment explanation
Indices: 1405696--1405887 Score: 162
Period size: 60 Copynumber: 3.2 Consensus size: 60
1405686 TTTTTTATTA
* * * * ** * *
1405696 CTATTTTAGTCCTTTTAGATTT-TGTTTTA-ATA-TTTAGTCCTTTAAATGTCTGTTTTTG
1 CTATTTTAGTCC-TTTAAATTTCTATTTTAGCTATTTTAATCCTTTAGTTTTCTATTTTTG
* * * *
1405754 CTATTTTAGTTCC-TTAAGTTTTTATTTTTGCTATTTTAA-CTCTTTGAG-TTTCTATTTTTT
1 CTATTTTAG-TCCTTTAAATTTCTATTTTAGCTATTTTAATC-CTTT-AGTTTTCTATTTTTG
* *
1405814 CTATTTTAGTCCTTTAAATTTCTATTTTAGCTATTTTGATCCTTTAGTTTTCTATTTTTC
1 CTATTTTAGTCCTTTAAATTTCTATTTTAGCTATTTTAATCCTTTAGTTTTCTATTTTTG
* *
1405874 CCATTCTAGTCCTT
1 CTATTTTAGTCCTT
1405888 GTAATTATAA
Statistics
Matches: 108, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
57 6 0.06
58 14 0.13
59 11 0.10
60 75 0.69
61 2 0.02
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.59
Consensus pattern (60 bp):
CTATTTTAGTCCTTTAAATTTCTATTTTAGCTATTTTAATCCTTTAGTTTTCTATTTTTG
Found at i:1417193 original size:21 final size:21
Alignment explanation
Indices: 1417167--1417207 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1417157 AGGTATATTT
1417167 TTAACAATTAGTATCCTTTTG
1 TTAACAATTAGTATCCTTTTG
* *
1417188 TTAACAATTGGTATCTTTTT
1 TTAACAATTAGTATCCTTTT
1417208 CATTAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
TTAACAATTAGTATCCTTTTG
Found at i:1417532 original size:64 final size:64
Alignment explanation
Indices: 1417419--1417584 Score: 246
Period size: 64 Copynumber: 2.6 Consensus size: 64
1417409 CAAAAATGTT
* * *
1417419 AAGA-GGTGCCGATA-CCCCCAGGGGTATCCATACCCCCTTGAAGGCAAAAATTCCAGAATGCA
1 AAGAGGGTACCGATACCCCCCAGGGGTATCCATACCCCCTAGAAGGAAAAAATTCCAGAATGCA
* ** *
1417481 AAGAGGGTACCGATACCCCCCAGGGGTATCCCTACCCCCTAGTTGGAAAAAATTCTAGAATGCA
1 AAGAGGGTACCGATACCCCCCAGGGGTATCCATACCCCCTAGAAGGAAAAAATTCCAGAATGCA
*
1417545 AAGAGGGTACCAATACCCCCCAGGGGTATCCATACCCCCT
1 AAGAGGGTACCGATACCCCCCAGGGGTATCCATACCCCCT
1417585 GGCTGCAACG
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
62 4 0.04
63 9 0.10
64 80 0.86
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.17
Consensus pattern (64 bp):
AAGAGGGTACCGATACCCCCCAGGGGTATCCATACCCCCTAGAAGGAAAAAATTCCAGAATGCA
Found at i:1422161 original size:25 final size:25
Alignment explanation
Indices: 1422133--1422182 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1422123 GCCTTTGCTC
1422133 CCCCTAACCCTGGATCTTTAATAAG
1 CCCCTAACCCTGGATCTTTAATAAG
1422158 CCCCTAACCCTGGATCTTTAATAAG
1 CCCCTAACCCTGGATCTTTAATAAG
1422183 TTCCTTGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (25 bp):
CCCCTAACCCTGGATCTTTAATAAG
Found at i:1428977 original size:13 final size:13
Alignment explanation
Indices: 1428959--1428983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1428949 TACTTAGCAT
1428959 ATAAAATAAAGAA
1 ATAAAATAAAGAA
1428972 ATAAAATAAAGA
1 ATAAAATAAAGA
1428984 CGATGAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
ATAAAATAAAGAA
Found at i:1432431 original size:21 final size:21
Alignment explanation
Indices: 1432407--1432497 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
1432397 TCGAGGGATT
1432407 GATCCTTTTCTCCAAGAGATC
1 GATCCTTTTCTCCAAGAGATC
1432428 GATCCTTTTCTCCAAGAGATC
1 GATCCTTTTCTCCAAGAGATC
* ***
1432449 GATCATTTT-GAAAATG-GATC
1 GATCCTTTTCTCCAA-GAGATC
*
1432469 GATCC-TTTCTCCTGAGAGATC
1 GATCCTTTTCTCC-AAGAGATC
1432490 GATCCTTT
1 GATCCTTT
1432498 ATTGGACAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.05
20 11 0.20
21 40 0.71
22 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (21 bp):
GATCCTTTTCTCCAAGAGATC
Found at i:1434269 original size:22 final size:24
Alignment explanation
Indices: 1434220--1434267 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1434210 TATTTAACTT
**
1434220 AATATTTATATATTTAAAATTTAA
1 AATATTTATATATTTAAAAAATAA
*
1434244 AATATTTTTAT-TTTAAAAAATAA
1 AATATTTATATATTTAAAAAATAA
1434267 A
1 A
1434268 TAAGCCCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATATTTATATATTTAAAAAATAA
Found at i:1434405 original size:21 final size:21
Alignment explanation
Indices: 1434363--1434406 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1434353 CGTCACCGAC
* * *
1434363 CACTATGGATTGCCATGTCAA
1 CACTATAGATTGCCACGCCAA
1434384 CACTATAGATTGCCACGCCAA
1 CACTATAGATTGCCACGCCAA
1434405 CA
1 CA
1434407 TTATGAAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (21 bp):
CACTATAGATTGCCACGCCAA
Found at i:1436048 original size:17 final size:17
Alignment explanation
Indices: 1436026--1436065 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1436016 TCCCTTGAAA
*
1436026 ATTTTA-ATTTTTTATAT
1 ATTTTAGATATTTT-TAT
1436043 ATTTTAGATATTTTTAT
1 ATTTTAGATATTTTTAT
1436060 ATTTTA
1 ATTTTA
1436066 TCCTGATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTAGATATTTTTAT
Found at i:1436053 original size:9 final size:9
Alignment explanation
Indices: 1436026--1436066 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
1436016 TCCCTTGAAA
1436026 ATTTTA-AT
1 ATTTTATAT
*
1436034 TTTTTATAT
1 ATTTTATAT
*
1436043 ATTTTAGAT
1 ATTTTATAT
1436052 ATTTT-TAT
1 ATTTTATAT
1436060 ATTTTAT
1 ATTTTAT
1436067 CCTGATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTATAT
Found at i:1438196 original size:21 final size:20
Alignment explanation
Indices: 1438170--1438214 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
1438160 CATTGACAAG
1438170 TTATCAGCACTATCCTCTTCA
1 TTATCA-CACTATCCTCTTCA
1438191 TTAT--CACTATCCTCTTCA
1 TTATCACACTATCCTCTTCA
1438209 TTATCA
1 TTATCA
1438215 AACCAGCCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 18 0.82
21 4 0.18
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (20 bp):
TTATCACACTATCCTCTTCA
Found at i:1438200 original size:18 final size:18
Alignment explanation
Indices: 1438177--1438214 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1438167 AAGTTATCAG
1438177 CACTATCCTCTTCATTAT
1 CACTATCCTCTTCATTAT
1438195 CACTATCCTCTTCATTAT
1 CACTATCCTCTTCATTAT
1438213 CA
1 CA
1438215 AACCAGCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (18 bp):
CACTATCCTCTTCATTAT
Found at i:1442118 original size:21 final size:21
Alignment explanation
Indices: 1442094--1442192 Score: 112
Period size: 23 Copynumber: 4.5 Consensus size: 21
1442084 CCTCGCTATA
1442094 TATCGATACA-CTATGAATGTG
1 TATCGATACATCT-TGAATGTG
1442115 TATCGATACATTCCTTGAATGTG
1 TATCGATACA-T-CTTGAATGTG
1442138 TATCGATACATTCCTTGAATGTG
1 TATCGATACA-T-CTTGAATGTG
*
1442161 TATCGATACATTCCTTGAATATG
1 TATCGATACA-T-CTTGAATGTG
1442184 TATCG-TACA
1 TATCGATACA
1442193 CTCAAGAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
21 10 0.14
22 4 0.05
23 58 0.78
24 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (21 bp):
TATCGATACATCTTGAATGTG
Found at i:1442137 original size:23 final size:23
Alignment explanation
Indices: 1442107--1442192 Score: 156
Period size: 23 Copynumber: 3.8 Consensus size: 23
1442097 CGATACACTA
1442107 TGAATGTGTATCGATACATTCCT
1 TGAATGTGTATCGATACATTCCT
1442130 TGAATGTGTATCGATACATTCCT
1 TGAATGTGTATCGATACATTCCT
1442153 TGAATGTGTATCGATACATTCCT
1 TGAATGTGTATCGATACATTCCT
*
1442176 TGAATATGTATCG-TACA
1 TGAATGTGTATCGATACA
1442193 CTCAAGAGTG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 4 0.06
23 58 0.94
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (23 bp):
TGAATGTGTATCGATACATTCCT
Found at i:1445508 original size:14 final size:15
Alignment explanation
Indices: 1445489--1445540 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1445479 TTGAAAAGGT
1445489 ATAATAA-AAATAAA
1 ATAATAATAAATAAA
1445503 ATAATAATAAATAAA
1 ATAATAATAAATAAA
**
1445518 AGGGA-AATATAATAAA
1 A-TAATAATA-AATAAA
1445534 ATAATAA
1 ATAATAA
1445541 ATAATAGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.23
15 13 0.43
16 10 0.33
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
ATAATAATAAATAAA
Found at i:1445605 original size:18 final size:18
Alignment explanation
Indices: 1445584--1445632 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
1445574 AAGTTATTTC
1445584 TTAAATAAATAATAATAA
1 TTAAATAAATAATAATAA
*
1445602 TTAAATAAA-AGAAAATAA
1 TTAAATAAATA-ATAATAA
1445620 TTAAATAAATAAT
1 TTAAATAAATAAT
1445633 CTAAAGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
TTAAATAAATAATAATAA
Found at i:1452884 original size:43 final size:43
Alignment explanation
Indices: 1452813--1452929 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
1452803 TAGGAATACA
* * * *
1452813 ATGCAACTTTA-ATTTTTCTAA-GTGGAAGACGTATGTATTACC
1 ATGCAACTTTAGGTTTTTC-AAGGTTGAAGACGCATGAATTACC
1452855 ATGCAACTTTAGGTTTTTCAAGGTTGAAGACGCATGAATTACC
1 ATGCAACTTTAGGTTTTTCAAGGTTGAAGACGCATGAATTACC
* * * *
1452898 ATGCGACTTT-GGCTTTCCAAGGTTGAAAACGC
1 ATGCAACTTTAGGTTTTTCAAGGTTGAAGACGC
1452930 CTAGAAATCT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
42 32 0.49
43 33 0.51
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (43 bp):
ATGCAACTTTAGGTTTTTCAAGGTTGAAGACGCATGAATTACC
Found at i:1453638 original size:33 final size:33
Alignment explanation
Indices: 1453596--1453664 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1453586 TATAAAAAGA
1453596 TGATATACCATAAATTACTCTTGAGAATGTGAG
1 TGATATACCATAAATTACTCTTGAGAATGTGAG
1453629 TGATATACCATAAATTACTCTTGAGAATGTGAG
1 TGATATACCATAAATTACTCTTGAGAATGTGAG
1453662 TGA
1 TGA
1453665 ATTACAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (33 bp):
TGATATACCATAAATTACTCTTGAGAATGTGAG
Found at i:1453845 original size:43 final size:44
Alignment explanation
Indices: 1453792--1453927 Score: 150
Period size: 43 Copynumber: 3.1 Consensus size: 44
1453782 TGAGAACAAA
* * * *
1453792 AAACACCGCAATAGGTCAAGATCTATTGCGACGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGATAC
** * * * *
1453835 AAGTGCCGCAAAAGGTTAATATCTATAGTGGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGATAC
* *
1453879 AAACGCCGCAAAATGTC-ATATCTATAGCGATGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGATAC
1453922 AAACGC
1 AAACGC
1453928 TGCTAATTAC
Statistics
Matches: 74, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
43 59 0.80
44 15 0.20
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (44 bp):
AAACGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGATAC
Found at i:1455722 original size:11 final size:11
Alignment explanation
Indices: 1455706--1455735 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1455696 TTAGTTTAAA
1455706 TATTTTTTTAT
1 TATTTTTTTAT
*
1455717 TATTTTTATAT
1 TATTTTTTTAT
1455728 TATTTTTT
1 TATTTTTT
1455736 AACTAACACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TATTTTTTTAT
Found at i:1455775 original size:27 final size:27
Alignment explanation
Indices: 1455745--1455818 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
1455735 TAACTAACAC
1455745 TTTTACTTT-TTTATTTT-ATTCATTTTA
1 TTTT-CTTTCTTTATTTTAATT-ATTTTA
*
1455772 TTTTCTTTCTTTATTTTAATTTTTTTA
1 TTTTCTTTCTTTATTTTAATTATTTTA
*
1455799 TTTT-TATT-TTAATTTTAATT
1 TTTTCT-TTCTTTATTTTAATT
1455819 TTAAGTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 16 0.38
27 23 0.55
28 3 0.07
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTCTTTCTTTATTTTAATTATTTTA
Found at i:1455800 original size:14 final size:13
Alignment explanation
Indices: 1455745--1455846 Score: 66
Period size: 12 Copynumber: 7.9 Consensus size: 13
1455735 TAACTAACAC
*
1455745 TTTTACTTTTTTA
1 TTTTATTTTTTTA
*
1455758 TTTTATTCATTTTA
1 TTTTATT-TTTTTA
* *
1455772 TTTTCTTTCTTTA
1 TTTTATTTTTTTA
1455785 TTTTAATTTTTTTA
1 TTTT-ATTTTTTTA
* *
1455799 TTTT-TATTTTAA
1 TTTTATTTTTTTA
* *
1455811 TTTTA-ATTTTAA
1 TTTTATTTTTTTA
* *
1455823 GTTT-TTTGTTTA
1 TTTTATTTTTTTA
*
1455835 TTTTCTTTTTTT
1 TTTTATTTTTTT
1455847 TACTAACTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
12 27 0.39
13 20 0.29
14 22 0.32
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:1455816 original size:26 final size:27
Alignment explanation
Indices: 1455767--1455820 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
1455757 ATTTTATTCA
*
1455767 TTTTATTTTCTTTCTTTATTTTAATTT
1 TTTTATTTTCTTTCTTAATTTTAATTT
1455794 TTTTATTTT-TATT-TTAATTTTAATTT
1 TTTTATTTTCT-TTCTTAATTTTAATTT
1455820 T
1 T
1455821 AAGTTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTATTTTCTTTCTTAATTTTAATTT
Found at i:1455848 original size:14 final size:14
Alignment explanation
Indices: 1455751--1455848 Score: 63
Period size: 14 Copynumber: 6.5 Consensus size: 14
1455741 ACACTTTTAC
1455751 TTTTTTATTTTATT
1 TTTTTTATTTTATT
** *
1455765 CATTTTATTTT-CT
1 TTTTTTATTTTATT
* *
1455778 TTCTTTATTTTAAT
1 TTTTTTATTTTATT
1455792 TTTTTTATTTTTATT
1 TTTTTTA-TTTTATT
1455807 TTAATTTTAATTTTAAGTTT
1 TT--TTTT-ATTTT-A--TT
*
1455827 TTTGTTTATTTTCTT
1 TTT-TTTATTTTATT
1455842 TTTTTTA
1 TTTTTTA
1455849 CTAACTTTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
13 9 0.14
14 20 0.31
15 13 0.20
17 8 0.12
18 8 0.12
19 3 0.05
20 4 0.06
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTTATTTTATT
Found at i:1455998 original size:7 final size:7
Alignment explanation
Indices: 1455986--1456023 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
1455976 CGAATCGATG
1455986 TTTTAAA
1 TTTTAAA
1455993 TTTTAAA
1 TTTTAAA
1456000 TTTT-AA
1 TTTTAAA
*
1456006 TTTTTAA
1 TTTTAAA
*
1456013 TTTTTAA
1 TTTTAAA
1456020 TTTT
1 TTTT
1456024 CGCCGTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTAAA
Found at i:1456014 original size:20 final size:20
Alignment explanation
Indices: 1455986--1456023 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1455976 CGAATCGATG
1455986 TTTTAAATTTTAAATTTTAA
1 TTTTAAATTTTAAATTTTAA
* *
1456006 TTTTTAATTTTTAATTTT
1 TTTTAAATTTTAAATTTT
1456024 CGCCGTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAAATTTTAAATTTTAA
Found at i:1461190 original size:37 final size:36
Alignment explanation
Indices: 1461149--1461326 Score: 202
Period size: 36 Copynumber: 4.9 Consensus size: 36
1461139 ACAAGGGGTC
* *
1461149 GTCTCGCTTAAGACTAATTTACTC-AAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CTCTAAAACAAAGTTTT
1461186 GTCTCTCTTGAGACAATTTCTCTTAAAACAAAGTTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAAGTTTT
1461223 GTCTCTCTTGAGACAATTTCTCTTAAAACAAA-TTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAAGTTTT
** *
1461259 GTCTCTCTTGAGACAGCTTC-CATTGAAACAAA-TTTT
1 GTCTCTCTTGAGACAATTTCTC--TAAAACAAAGTTTT
* *
1461295 GTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAA
1461327 ATCTTTGAAT
Statistics
Matches: 130, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
35 4 0.03
36 68 0.52
37 58 0.45
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (36 bp):
GTCTCTCTTGAGACAATTTCTCTAAAACAAAGTTTT
Found at i:1461266 original size:36 final size:37
Alignment explanation
Indices: 1461173--1461326 Score: 233
Period size: 36 Copynumber: 4.2 Consensus size: 37
1461163 TAATTTACTC
1461173 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTT
1 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTT
1461210 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTT
1 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTT
**
1461247 AAAACAAA-TTTTGTCTCTCTTGAGACAGCTTC-CATT
1 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTC-TT
* * *
1461283 GAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTT
1461319 AAAACAAA
1 AAAACAAA
1461327 ATCTTTGAAT
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
35 1 0.01
36 63 0.57
37 46 0.42
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (37 bp):
AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTT
Found at i:1461435 original size:129 final size:130
Alignment explanation
Indices: 1461292--1461537 Score: 413
Period size: 130 Copynumber: 1.9 Consensus size: 130
1461282 TGAAACAAAT
*
1461292 TTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATATG-TTTTACTTTAAACAAA
1 TTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATATGTTTTTACTTGAAACAAA
* * *
1461356 TTTCGTTTCCCTTGAGACAATTTCTTTAGGAACTAAGTTTTGTCTCTCTTGAAACAAATTTTGTC
66 TTTCGTCTCCCTTGAGACAATTTCTTTAGAAACAAAGTTTTGTCTCTCTTGAAACAAATTTTGTC
* *
1461421 TTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATCTTTGAATATGTTTTTCCTTGAAACAAA
1 TTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATATGTTTTTACTTGAAACAAA
* *
1461486 TTTCGTCTCCCTTGAGACAGTTTCTTTTGAAACAAAGTTTTGTCTCTCTTGA
66 TTTCGTCTCCCTTGAGACAATTTCTTTAGAAACAAAGTTTTGTCTCTCTTGA
1461538 GACAGTTTTC
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 47 0.44
130 61 0.56
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (130 bp):
TTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATATGTTTTTACTTGAAACAAA
TTTCGTCTCCCTTGAGACAATTTCTTTAGAAACAAAGTTTTGTCTCTCTTGAAACAAATTTTGTC
Found at i:1461537 original size:37 final size:37
Alignment explanation
Indices: 1461468--1461580 Score: 144
Period size: 37 Copynumber: 3.1 Consensus size: 37
1461458 CTTTGAATAT
* * *
1461468 GTTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCTCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
1461505 GTTTCT-TTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
1461542 GTTT-TCCTTGAAACAAA--TTGTCTCTCTTGAGATA
1 GTTTCTCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1461576 GTTTC
1 GTTTC
1461581 CCATGGAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
34 20 0.30
36 11 0.16
37 36 0.54
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (37 bp):
GTTTCTCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:1461712 original size:37 final size:37
Alignment explanation
Indices: 1461607--1461716 Score: 168
Period size: 36 Copynumber: 3.0 Consensus size: 37
1461597 TTTTGGAACT
*
1461607 AAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
* * *
1461644 AA-TTTTTTCTCTCTTGAGACGGTTTCCCTTGAAACA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
*
1461680 AAGTTTTGTCTCTCTTGAGACAGCTTCTCTTGAAACA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1461717 CCAATCTTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (37 bp):
AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
Found at i:1461815 original size:15 final size:15
Alignment explanation
Indices: 1461795--1461844 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1461785 AAAAAAACCT
*
1461795 TTGAAATTGTTTCTC
1 TTGAAAATGTTTCTC
** *
1461810 TTGAAAAAATATCT-
1 TTGAAAATGTTTCTC
1461824 TTGAAAATGTTTCTC
1 TTGAAAATGTTTCTC
1461839 TTGAAA
1 TTGAAA
1461845 CACAAAACCT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (15 bp):
TTGAAAATGTTTCTC
Found at i:1461826 original size:29 final size:28
Alignment explanation
Indices: 1461785--1461844 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
1461775 CTTGAAACAC
*
1461785 AAAAAAACCTTTGAAATTGTTTCTCTTG
1 AAAAAAACCTTTGAAAATGTTTCTCTTG
*
1461813 AAAAAATATCTTTGAAAATGTTTCTCTTG
1 AAAAAA-ACCTTTGAAAATGTTTCTCTTG
1461842 AAA
1 AAA
1461845 CACAAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (28 bp):
AAAAAAACCTTTGAAAATGTTTCTCTTG
Found at i:1463210 original size:22 final size:23
Alignment explanation
Indices: 1463180--1463229 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
1463170 TAACTAACCC
1463180 TTTTACTTTT-TTTATTTTATTCA
1 TTTTACTTTTCTTTA-TTTATTCA
*
1463203 TTTT-CTTTTCTTTATTTATTTA
1 TTTTACTTTTCTTTATTTATTCA
1463225 TTTTA
1 TTTTA
1463230 ATTAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTACTTTTCTTTATTTATTCA
Found at i:1466540 original size:42 final size:41
Alignment explanation
Indices: 1466395--1466550 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 41
1466385 AACCCTATTA
* *
1466395 CGGCATTTGTATAAAAAATGCCGCTAAAGTACTAATCTATCG
1 CGGCATTTGTAT-AAAAACGCCGCTAAAGTACTACTCTATCG
* * *
1466437 CGGCATTTGT-TGGAAAAACGCCACTATAAATGA-TAC-CTATTG
1 CGGCATTTGTAT--AAAAACGCCGCTA-AAGT-ACTACTCTATCG
* * *
1466479 CGGCGTTTATATAAAAACGCCGGTAAAGTACTACTCTATCG
1 CGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATCG
* * *
1466520 CGGCTTTTGTTTAAGAAACGCCGTTAAAGTA
1 CGGCATTTGTATAA-AAACGCCGCTAAAGTA
1466551 TTATTTTGTG
Statistics
Matches: 91, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
39 1 0.01
40 6 0.07
41 28 0.31
42 49 0.54
43 6 0.07
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
CGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATCG
Found at i:1469872 original size:81 final size:80
Alignment explanation
Indices: 1469786--1470035 Score: 252
Period size: 81 Copynumber: 3.1 Consensus size: 80
1469776 TTTTTATTCA
* * * * * *
1469786 AAACGCCGCGAGAGAGTAGTACTTTAACAGCGTTTGTATAAAAACGCCGCAATATGTTTCATCCA
1 AAACGCCGTGACAGAGTATTACTTTAACGGCGTTTGTATAAAAATGCCGCAATA-GGTTCATCCA
1469851 TAGTGGCGTTTTCAAC
65 TAGTGGCGTTTTCAAC
* * * * * *
1469867 AAACGCCGTAACATAATATTACTTT-A-GGCGATGTTTTATACAAATGCCACAATAGGTTCATCC
1 AAACGCCGTGACAGAGTATTACTTTAACGGCG-T-TTGTATAAAAATGCCGCAATAGGTTCATCC
1469930 ATAGTGGCGTTTCTCAAC
64 ATAGTGGCGTTT-TCAAC
* * * * *
1469948 AAACGCCGTGACAGAGTTTTACTTTAGCGGTGTTTGTATAAAAATGCCGTAATAGGGTTCATCTA
1 AAACGCCGTGACAGAGTATTACTTTAACGGCGTTTGTATAAAAATGCCGCAATA-GGTTCATCCA
* * *
1470013 TAGTGTCATTTTATAAC
65 TAGTGGCGTTTT-CAAC
1470030 AAACGC
1 AAACGC
1470036 TACAAAAACG
Statistics
Matches: 136, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
79 3 0.02
80 22 0.16
81 80 0.59
82 28 0.21
83 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (80 bp):
AAACGCCGTGACAGAGTATTACTTTAACGGCGTTTGTATAAAAATGCCGCAATAGGTTCATCCAT
AGTGGCGTTTTCAAC
Found at i:1472320 original size:43 final size:43
Alignment explanation
Indices: 1472237--1472533 Score: 352
Period size: 43 Copynumber: 6.9 Consensus size: 43
1472227 ATGGTAATTA
* * *
1472237 GCGGCGTTTGTATCCAAAAATGCCACTATTGATAT-GACCTTTT
1 GCGGCGTTTGT-TCCAAAAATGCCGCTATAGATCTCGACCTTTT
* *
1472280 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTTT
1 GCGGCGTTTGTTCCAAAAATGCCGCTATAGATCTCGACC-TTTT
* * * *
1472324 GTGACATTTGTATCGAAAACA--CCGCTATAGATCT-GACCTTTT
1 GCGGCGTTTGT-TCCAAAA-ATGCCGCTATAGATCTCGACCTTTT
* *
1472366 GCAGCGTTTGTTCCAAAAATGGCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCCAAAAATGCCGCTATAGATCTCGACCTTTT
** * * *
1472409 GCATCGTTTGTTCCAAAAACGCCACTATAGATC-AGACCTTTT
1 GCGGCGTTTGTTCCAAAAATGCCGCTATAGATCTCGACCTTTT
1472451 GCGGCGTTTGTTCCAAAAATGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCCAAAAATGCCGCTATAGATCTCGACCTTTT
* * *
1472494 GCGGCATTTGTTCCAAAAATGCCGCTATATATCTTGACCT
1 GCGGCGTTTGTTCCAAAAATGCCGCTATAGATCTCGACCT
1472534 ATTGAGACGT
Statistics
Matches: 217, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
40 1 0.00
41 6 0.03
42 79 0.36
43 99 0.46
44 25 0.12
45 6 0.03
46 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAATGCCGCTATAGATCTCGACCTTTT
Found at i:1472458 original size:85 final size:85
Alignment explanation
Indices: 1472243--1472522 Score: 352
Period size: 85 Copynumber: 3.3 Consensus size: 85
1472233 ATTAGCGGCG
* * *
1472243 TTTGTATCCAAAAATGCCACTATTGAT-ATGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTA
1 TTTGTATCCAAAAACGCCACTATAGATCA-GACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTA
* *
1472307 TAGATCTCAACCTTTTTGTGACA
65 TAGATCTCGACC-TTTTG-CACA
* * * * * *
1472330 TTTGTAT-CGAAAACACCGCTATAGATCTGACCTTTTGCAGCGTTTGTTCCAAAAATGGCGCTAT
1 TTTGTATCCAAAAACGCCACTATAGATCAGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTAT
*
1472394 AGATCTCGACCTTTTGCATCG
66 AGATCTCGACCTTTTGCA-CA
1472415 TTTGT-TCCAAAAACGCCACTATAGATCAGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTAT
1 TTTGTATCCAAAAACGCCACTATAGATCAGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTAT
*
1472479 AGATCTCGACCTTTTGCGGCA
66 AGATCTCGACCTTTTGC-ACA
* *
1472500 TTTGT-TCCAAAAATGCCGCTATA
1 TTTGTATCCAAAAACGCCACTATA
1472523 TATCTTGACC
Statistics
Matches: 167, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
84 2 0.01
85 101 0.60
86 57 0.34
87 7 0.04
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (85 bp):
TTTGTATCCAAAAACGCCACTATAGATCAGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTAT
AGATCTCGACCTTTTGCACA
Found at i:1479162 original size:23 final size:20
Alignment explanation
Indices: 1479111--1479170 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
1479101 TTTTGGTGCA
*
1479111 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
1479130 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
1479151 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
1479171 CCACAGGGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:1484021 original size:97 final size:97
Alignment explanation
Indices: 1483848--1484026 Score: 304
Period size: 97 Copynumber: 1.8 Consensus size: 97
1483838 GAAGGGAAAG
* *
1483848 TGTAGAAACGAGCTCCATAACTGGTACATTAGGATATATTTTTCCTAAGAAATAGGAACAGTCGT
1 TGTAGAAACGAGCTCCATAACTGATACATTAGGATATATTTTTCCTAAGAAATAGGAACAGTCAT
* *
1483913 TAGCTGTTTCCTATTTAGTTACTTTTCTACTT
66 TAACTGCTTCCTATTTAGTTACTTTTCTACTT
* *
1483945 TGTAGAATCGAGCTCCATAACTGATACATTAGGATTTATTTTTCCTAAGAAATAGGAACAGTCAT
1 TGTAGAAACGAGCTCCATAACTGATACATTAGGATATATTTTTCCTAAGAAATAGGAACAGTCAT
1484010 TAACTGCTTCCTATTTA
66 TAACTGCTTCCTATTTA
1484027 CTAGCATATG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 76 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (97 bp):
TGTAGAAACGAGCTCCATAACTGATACATTAGGATATATTTTTCCTAAGAAATAGGAACAGTCAT
TAACTGCTTCCTATTTAGTTACTTTTCTACTT
Found at i:1486476 original size:18 final size:19
Alignment explanation
Indices: 1486438--1486478 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1486428 TCATGGAAAT
*
1486438 GGAGGAAAATAGATTGTGGA
1 GGAGAAAAATAGA-TGTGGA
1486458 GGAGAAAAATAGA-GTGGA
1 GGAGAAAAATAGATGTGGA
1486476 GGA
1 GGA
1486479 CAGGAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (19 bp):
GGAGAAAAATAGATGTGGA
Found at i:1500649 original size:22 final size:22
Alignment explanation
Indices: 1500624--1500665 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1500614 GCATTATGAC
1500624 TTTT-TTTCATGCACTTTATGGA
1 TTTTATTTCA-GCACTTTATGGA
*
1500646 TTTTATTTTAGCACTTTATG
1 TTTTATTTCAGCACTTTATG
1500666 TTGCCTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTATTTCAGCACTTTATGGA
Found at i:1507948 original size:19 final size:19
Alignment explanation
Indices: 1507924--1507962 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1507914 ACGATGAATG
*
1507924 TATATATGTGAGCATTGTA
1 TATATATGTAAGCATTGTA
1507943 TATATATGTAAGCATTGTA
1 TATATATGTAAGCATTGTA
1507962 T
1 T
1507963 TGCCTGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (19 bp):
TATATATGTAAGCATTGTA
Found at i:1514307 original size:17 final size:17
Alignment explanation
Indices: 1514268--1514372 Score: 83
Period size: 17 Copynumber: 6.1 Consensus size: 17
1514258 TTAATATGTG
* *
1514268 TCTGATAACTGTAAAACA
1 TCTGATATCTGT-AAATA
1514286 TCTGATATCTGTAAATA
1 TCTGATATCTGTAAATA
*
1514303 TCTGATAACTGT-AATCA
1 TCTGATATCTGTAAAT-A
*
1514320 TCTGATATATGTAAATA
1 TCTGATATCTGTAAATA
*
1514337 -CATGATAAT-TGAAAATCA
1 TC-TGAT-ATCTGTAAAT-A
1514355 TCTGAT-TACTGTAAATA
1 TCTGATAT-CTGTAAATA
1514372 T
1 T
1514373 TTAGAATTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
16 5 0.07
17 39 0.54
18 27 0.38
19 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (17 bp):
TCTGATATCTGTAAATA
Found at i:1514310 original size:35 final size:35
Alignment explanation
Indices: 1514268--1514372 Score: 128
Period size: 34 Copynumber: 3.0 Consensus size: 35
1514258 TTAATATGTG
1514268 TCTGATAACTGTAAAACATCTGATATCTGTAAATA
1 TCTGATAACTGTAAAACATCTGATATCTGTAAATA
* *
1514303 TCTGATAACTGT-AATCATCTGATATATGTAAATA
1 TCTGATAACTGTAAAACATCTGATATCTGTAAATA
*
1514337 -CATGATAATTG-AAAATCATCTGAT-TACTGTAAATA
1 TC-TGATAACTGTAAAA-CATCTGATAT-CTGTAAATA
1514372 T
1 T
1514373 TTAGAATTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
33 1 0.02
34 31 0.52
35 28 0.47
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (35 bp):
TCTGATAACTGTAAAACATCTGATATCTGTAAATA
Found at i:1515356 original size:21 final size:21
Alignment explanation
Indices: 1515332--1515377 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1515322 CGAGGGTTTC
*
1515332 TATGTAGTCCTTCAGGAT-ATA
1 TATGTAATCCTT-AGGATCATA
*
1515353 TATGTAATCCTTTGGATCATA
1 TATGTAATCCTTAGGATCATA
1515374 TATG
1 TATG
1515378 CGGTTCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (21 bp):
TATGTAATCCTTAGGATCATA
Found at i:1520959 original size:31 final size:30
Alignment explanation
Indices: 1520904--1520972 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
1520894 GTAAATTTTG
* *
1520904 AAAGTCTAGGGACAAAAGTGTAAATTTGCA
1 AAAGTTTAGGGACAAAAATGTAAATTTGCA
* *
1520934 AAAGTTTAGGTACTAAAAATGTAAATTTTCA
1 AAAGTTTAGGGAC-AAAAATGTAAATTTGCA
*
1520965 AAAATTTA
1 AAAGTTTA
1520973 TATTTTTGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.30
Consensus pattern (30 bp):
AAAGTTTAGGGACAAAAATGTAAATTTGCA
Found at i:1521195 original size:20 final size:19
Alignment explanation
Indices: 1521170--1521212 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
1521160 TGATATTTTT
*
1521170 AATTAGTGTAATTTGGTGTG
1 AATTAGTGAAATTTGGTG-G
1521190 AATTAGTGAAATTTGGTGG
1 AATTAGTGAAATTTGGTGG
1521209 AATT
1 AATT
1521213 TCCATGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (19 bp):
AATTAGTGAAATTTGGTGG
Found at i:1534890 original size:21 final size:21
Alignment explanation
Indices: 1534866--1534906 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1534856 GATCGACGTG
1534866 AATCGACGTAAAATCAATGAA
1 AATCGACGTAAAATCAATGAA
** *
1534887 AATCGATTTAAAATCGATGA
1 AATCGACGTAAAATCAATGA
1534907 TACTTCCAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (21 bp):
AATCGACGTAAAATCAATGAA
Found at i:1542463 original size:40 final size:39
Alignment explanation
Indices: 1542401--1542554 Score: 146
Period size: 40 Copynumber: 3.9 Consensus size: 39
1542391 GGAGTGATTT
* ** *
1542401 TGAATACTGATACTAACACTTTATGTGCATTACTGTTCAT
1 TGAATAATGATACTGGCACTTTATGTGCATTA-TGTTCAC
* * * *
1542441 TTAATATTGATATTGGCACTTTATGTGCATTATCATTCAC
1 TGAATAATGATACTGGCACTTTATGTGCATTAT-GTTCAC
* *
1542481 TGATTAATGATACTGGCACTTTATGTGCATTATTGTTTAC
1 TGAATAATGATACTGGCACTTTATGTGCATTA-TGTTCAC
* * * * *
1542521 TGAATACTAATAGTGACACTTTATGTGCAATATG
1 TGAATAATGATACTGGCACTTTATGTGCATTATG
1542555 GCAGTTATAT
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
39 3 0.03
40 89 0.96
41 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (39 bp):
TGAATAATGATACTGGCACTTTATGTGCATTATGTTCAC
Found at i:1542690 original size:17 final size:18
Alignment explanation
Indices: 1542668--1542704 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
1542658 ATTGTAAAAA
1542668 GATATAGTACAAT-AAAG
1 GATATAGTACAATGAAAG
1542685 GATATAGTACAATGAAAG
1 GATATAGTACAATGAAAG
1542703 GA
1 GA
1542705 ACAATACAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (18 bp):
GATATAGTACAATGAAAG
Found at i:1543020 original size:20 final size:22
Alignment explanation
Indices: 1542995--1543034 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1542985 GGATTTAATT
*
1542995 TGAAT-ATG-TATATATGTGTG
1 TGAATAATGTTATACATGTGTG
1543015 TGAATAATGTTATACATGTG
1 TGAATAATGTTATACATGTG
1543035 AAAGAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 3 0.18
22 9 0.53
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.42
Consensus pattern (22 bp):
TGAATAATGTTATACATGTGTG
Found at i:1548040 original size:18 final size:18
Alignment explanation
Indices: 1548017--1548053 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1548007 ACGATGTCGT
1548017 TTCCATCTCCAGGTATAA
1 TTCCATCTCCAGGTATAA
1548035 TTCCATCTCCAGGTATAA
1 TTCCATCTCCAGGTATAA
1548053 T
1 T
1548054 GCTCATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (18 bp):
TTCCATCTCCAGGTATAA
Found at i:1550690 original size:19 final size:19
Alignment explanation
Indices: 1550643--1550690 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1550633 ATTATAATGT
* *
1550643 TATTTAATA-TATCAAATA
1 TATTTAAAATTATAAAATA
*
1550661 TAATCTAAAATTATAAAATA
1 T-ATTTAAAATTATAAAATA
1550681 TATTTAAAAT
1 TATTTAAAAT
1550691 ATTATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 9 0.38
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTTAAAATTATAAAATA
Found at i:1551600 original size:23 final size:23
Alignment explanation
Indices: 1551553--1551602 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1551543 AATAACATAT
**
1551553 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
1551576 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
1551599 TAGG
1 TAGG
1551603 CATTTAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:1551662 original size:87 final size:87
Alignment explanation
Indices: 1551516--1551678 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
1551506 TATGTTATAT
* *
1551516 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGCACTTATATAATGTAATAGGT
1551581 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
1551603 CATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGCACTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGCACTTATATAATGTAATAGGT
1551668 AGCGCTTATAT
66 AGCGCTTATAT
1551679 TGACCTATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGCACTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:1552023 original size:198 final size:200
Alignment explanation
Indices: 1551702--1552393 Score: 895
Period size: 198 Copynumber: 3.5 Consensus size: 200
1551692 AAGTAAACCA
* * *
1551702 GTATATTTATACCAGTAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * * * *
1551767 TTGAATCGATACAATTT--GAAATGTATCGACACTTTATGTGTGCACCTTGTTGGGCATTCATTC
66 TGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGCATTCATTC
* *
1551830 TGGA-AAAAAGTATCGACACAAACTTAAAAAGTGTCGATATATTAT-TTAGACCTATTTTCTCAT
130 TGGACAAAAAGTATCAACACAAA-TTAACAAGTGTCGATATATTATGTTAGACCTATTTTCTCAT
1551893 AAAATCG
194 AAAATCG
* * * * * * *
1551900 GCATATTTCTATCGGGTACATTGTAAAATTGCCTATCACATTATAATTATCGGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* *
1551965 TGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC-CGTTTGGCATTCATTAT
66 TGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGCATTCATTCT
* * *
1552029 GGACAAAATGTATCAACA-AAATTTAACAAGTGTCGATACT-TTATGCT-GATCTATTTTCTCAT
131 GGACAAAAAGTATCAACACAAA-TTAACAAGTGTCGATA-TATTATGTTAGACCTATTTTCTCAT
1552091 AAAATCG
194 AAAATCG
*
1552098 GTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGAT-TTTA
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT-
1552162 TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGAGCATTCATT
65 TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTG-GCATTCATT
* * * * * *
1552227 CTGGACAATAAGTATCAACACAAATTCCACAAGTGTTGATACATTATGTTA-ACCTCTTTTCTAA
129 CTGGACAAAAAGTATCAACACAAATT-AACAAGTGTCGATATATTATGTTAGACCTATTTTCTCA
* *
1552291 T-TAACCG
193 TAAAATCG
* * * *
1552298 GTATATTTATACCGGTTAGATTGTTAATTTACCTATTACATTATAATTATTGGTTTTGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTT
*
1552363 TTGGG-TCGATACTTTTAAAAAATGTATCGAC
65 TTGGGATCGATACTTTTAATAAATGTATCGAC
1552394 GCATATTTAG
Statistics
Matches: 429, Mismatches: 51, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
197 6 0.01
198 224 0.52
199 47 0.11
200 112 0.26
201 37 0.09
202 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (200 bp):
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGCATTCATTCT
GGACAAAAAGTATCAACACAAATTAACAAGTGTCGATATATTATGTTAGACCTATTTTCTCATAA
AATCG
Found at i:1554919 original size:19 final size:19
Alignment explanation
Indices: 1554874--1554922 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1554864 TTAAATTCAC
1554874 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
** **
1554893 ATGTAAAATTATAAATTTT
1 ATACAAAATTATAAATCGT
1554912 ATACAAAATTA
1 ATACAAAATTA
1554923 ACCCTACATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1556985 original size:200 final size:199
Alignment explanation
Indices: 1556526--1557293 Score: 1078
Period size: 200 Copynumber: 3.9 Consensus size: 199
1556516 CGCGTTATTT
* * * *
1556526 AAAAAGTATCGACACAACTT-TAAAAGTGTCGATACATTATGTTGACATATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * *
1556590 GGTGTATTTATACCGATTACATTGTAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
1556655 TTGGGATCGATACAATTT-CAAATGTATCGACACGTTGTGCCTGTACA-CCGTTTGGCATTCATT
131 TTGGGATCGATACATTTTAAAAATGTATCGACACTTTATG-C-GTACACCCGTTTGGCATTCATT
*
1556718 CTGGAC
194 TTGGAC
* * ** * * *
1556724 AAAATGTATCGACACAAA-TCTAAAATGTGTCGATACATTATGTTCAGCTATTTTCTCATAAAAT
1 AAAAAGTATCGACACAAATTCCAAAA-GTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
* * *
1556788 CGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCAATGTT
65 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* *
1556853 TTTGGGATCGATACCTTTTAAAAATGTAT-GAACACTTTATGCGTACAACCCTTTTGGCATTCAT
130 TTTGGGATCGATACATTTTAAAAATGTATCG-ACACTTTATGCGTAC-ACCCGTTTGGCATTCAT
1556917 TTTGGAC
193 TTTGGAC
* *
1556924 AAAAAGTATCGACACAAATTCCACAAGTGTCTATACATTATGTAGACCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * *
1556989 GGTATAGTTGTATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * *
1557054 CTGGGATCGATACATTTTAAAAATGTATCGACACTTTATGCGTGCACCACGTTTGGTATTCATTT
131 TTGGGATCGATACATTTTAAAAATGTATCGACACTTTATGCGTACACC-CGTTTGGCATTCATTT
1557119 TGGAC
195 TGGAC
* * * * *
1557124 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTATATCTATTTTCTCAAAAAACC
1 AAAAAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
*
1557189 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
1557254 TTGGGATCGATACTTTTTAAAAATGTATCAACACTTTATG
131 TTGGGATCGATACATTTTAAAAATGTATCGACACTTTATG
1557294 TTATGTGTCG
Statistics
Matches: 507, Mismatches: 54, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
197 1 0.00
198 25 0.05
199 115 0.23
200 360 0.71
201 6 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (199 bp):
AAAAAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
TTGGGATCGATACATTTTAAAAATGTATCGACACTTTATGCGTACACCCGTTTGGCATTCATTTT
GGAC
Found at i:1562106 original size:200 final size:199
Alignment explanation
Indices: 1561464--1562424 Score: 1203
Period size: 200 Copynumber: 4.8 Consensus size: 199
1561454 TTTTAAAATG
* * * * * * *
1561464 GTATCGACACAAATTT-AACAATTGTCGATACTTTATGTTGACCTATTTTCTCATAAAACCGGTA
1 GTATCGACACAAATTTCAA-AAGTGTTGATACATTATGTAGA-CTATTCTCACATAAAAACGGTA
** * * * *
1561528 TATTTATACCGGTTACATTGGAAATTTACCTATTACATTATAATCATAGGTTTTGATGTTTCTGG
64 TATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * *
1561593 GATCAATAGTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGTTTTGCATTCATTCT
129 GATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTG---GGCATTCATTCT
*
1561658 GGACAAAAT
191 GGACAAAAA
* * * *
1561667 GTATCGATACATAA-TTAAAAAGTATTGATACATTATGTAGACCTATTCTCACAT-AAAACTAGT
1 GTATCGACACA-AATTTCAAAAGTGTTGATACATTATGTAGA-CTATTCTCACATAAAAAC-GGT
* *
1561730 ATATTTATACCGGTTACATTACAAAATTACCTACTACATTATAATTATGGG-TTCGATGTCTCTG
63 ATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTG
* * * ** *
1561794 GGATTGACACTTTTTAAAAATGTATCGATTCTTTATGCGTTCACCATTTTGGGCATTCATTCTGG
128 GGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGG
1561859 ACAAAAA
193 ACAAAAA
* * *
1561866 GTATCGACACCAATTTCAAATGTGTTGATACATTATGTAGACTTATTCTCATATAAAAACGGTAT
1 GTATCGACACAAATTTCAAAAGTGTTGATACATTATGTAGAC-TATTCTCACATAAAAACGGTAT
* * ** *
1561931 ATTTATACCAGTTACATTACAAAATTACCTATTACATTATAGTTATGGGTTTCGATGCCTCTAGG
65 ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * * * * *
1561996 ATTGACACTTTTAAAAAATGTATCGACACTTTATGGGTGCACCCTTTTGGGCATTCCTTCTGGAC
130 ATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
*
1562061 AAACA
195 AAAAA
* * * * * *
1562066 TTATCGACACAAATTCCAGAAGTGTTAATACATTATGTAGACATATTCTCTCATAAAACCGGTAT
1 GTATCGACACAAATTTCAAAAGTGTTGATACATTATGTAGAC-TATTCTCACATAAAAACGGTAT
* ** *
1562131 AATTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
65 ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * *
1562196 ATCGATACATTTTATAAATGTATCGACACTTTTTGCGTTCACCATTTTGGGCATTCATTCTGGAT
130 ATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
1562261 AAAAA
195 AAAAA
* * *
1562266 GTATCGACACCAATTTCAAAAGTGTCT-ATACATTATGTACAACTATTCTCACATAAAATCGGTA
1 GTATCGACACAAATTTCAAAAGTGT-TGATACATTATGTA-GACTATTCTCACATAAAAACGGTA
* *
1562330 TATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
64 TATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
1562395 GATCGATACTTTTTATAAATGTATCGACAC
129 GATCGATACTTTTTATAAATGTATCGACAC
1562425 ATCTGCTTAC
Statistics
Matches: 656, Mismatches: 93, Indels: 21
0.85 0.12 0.03
Matches are distributed among these distances:
198 3 0.00
199 112 0.17
200 389 0.59
201 3 0.00
202 58 0.09
203 87 0.13
204 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (199 bp):
GTATCGACACAAATTTCAAAAGTGTTGATACATTATGTAGACTATTCTCACATAAAAACGGTATA
TTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGA
TCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACA
AAAA
Found at i:1562814 original size:19 final size:19
Alignment explanation
Indices: 1562790--1562838 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1562780 TTACATTCAC
1562790 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
1562809 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
1562828 ATACAAAATTA
1 ATACAAAATTA
1562839 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:1565767 original size:7 final size:7
Alignment explanation
Indices: 1565755--1565800 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
1565745 AGAATAGCAC
1565755 CGGTCAA
1 CGGTCAA
*
1565762 CGGTCAT
1 CGGTCAA
1565769 CGGTCAA
1 CGGTCAA
1565776 CGGTCAA
1 CGGTCAA
1565783 CGGGTC-A
1 C-GGTCAA
1565790 -GGTCAA
1 CGGTCAA
1565796 CGGTC
1 CGGTC
1565801 GGGTAAACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.12
6 1 0.03
7 25 0.74
8 4 0.12
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (7 bp):
CGGTCAA
Found at i:1565820 original size:18 final size:18
Alignment explanation
Indices: 1565797--1565850 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
1565787 TCAGGTCAAC
*
1565797 GGTCGGGTAAACGGGTTG
1 GGTCGGGTAAACGGGTCG
1565815 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
1565833 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
1565851 TGACCGTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.17, C:0.15, G:0.50, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:1565875 original size:10 final size:10
Alignment explanation
Indices: 1565860--1565896 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1565850 GTGACCGTTC
1565860 AAACCGGTCA
1 AAACCGGTCA
*
1565870 AAACCGGT-T
1 AAACCGGTCA
1565879 AAACCGGTCA
1 AAACCGGTCA
1565889 AAACCGGT
1 AAACCGGT
1565897 TTCCAGCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (10 bp):
AAACCGGTCA
Found at i:1565875 original size:19 final size:18
Alignment explanation
Indices: 1565853--1565894 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
1565843 ACGGGTCGTG
1565853 ACCGTTCAAACCGGTCAAA
1 ACCGTT-AAACCGGTCAAA
1565872 ACCGGTTAAACCGGTCAAA
1 ACC-GTTAAACCGGTCAAA
1565891 ACCG
1 ACCG
1565895 GTTTCCAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCGTTAAACCGGTCAAA
Found at i:1565895 original size:19 final size:19
Alignment explanation
Indices: 1565860--1565897 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1565850 GTGACCGTTC
1565860 AAACCGGTCAAAACCGGTT
1 AAACCGGTCAAAACCGGTT
1565879 AAACCGGTCAAAACCGGTT
1 AAACCGGTCAAAACCGGTT
1565898 TCCAGCGTTC
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:0.26, G:0.21, T:0.16
Consensus pattern (19 bp):
AAACCGGTCAAAACCGGTT
Found at i:1573068 original size:7 final size:7
Alignment explanation
Indices: 1573056--1573086 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1573046 AGAATAGCAC
1573056 CGGTCAA
1 CGGTCAA
*
1573063 CGGTCAT
1 CGGTCAA
1573070 CGGTCAA
1 CGGTCAA
1573077 CGGTCAA
1 CGGTCAA
1573084 CGG
1 CGG
1573087 GTCGGGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (7 bp):
CGGTCAA
Found at i:1573121 original size:18 final size:18
Alignment explanation
Indices: 1573098--1573133 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1573088 TCGGGTAAAT
1573098 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
1573116 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
1573134 TGACCGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:1573133 original size:13 final size:13
Alignment explanation
Indices: 1573082--1573118 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1573072 GTCAACGGTC
1573082 AACGGGTCGGGTA
1 AACGGGTCGGGTA
*
1573095 AA-TGGTCGGGTA
1 AACGGGTCGGGTA
1573107 AACGGGTCGGGT
1 AACGGGTCGGGT
1573119 CGGGTAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.22, C:0.14, G:0.46, T:0.19
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:1573158 original size:10 final size:10
Alignment explanation
Indices: 1573143--1573179 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1573133 GTGACCGTTC
1573143 AAACCGGTCA
1 AAACCGGTCA
*
1573153 AAACCGGT-T
1 AAACCGGTCA
1573162 AAACCGGTCA
1 AAACCGGTCA
1573172 AAACCGGT
1 AAACCGGT
1573180 TTCCAGCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (10 bp):
AAACCGGTCA
Done.