Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 14 of 32
Found at i:2018082 original size:11 final size:11
Alignment explanation
Indices: 2018046--2018088 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
2018036 TCGTAATTTA
2018046 TATATTTATAAT
1 TATATTT-TAAT
* *
2018058 GATAATTTACAT
1 TATATTTTA-AT
2018070 TATATTTTAAT
1 TATATTTTAAT
2018081 TATATTTT
1 TATATTTT
2018089 TTTCATGTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (11 bp):
TATATTTTAAT
Found at i:2018365 original size:2 final size:2
Alignment explanation
Indices: 2018358--2018394 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2018348 ACTTCTACAA
2018358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2018395 GAGTGCCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2020643 original size:16 final size:16
Alignment explanation
Indices: 2020619--2020660 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2020609 TTTTTTTTTT
*
2020619 TTTTGAATTTAAATTA
1 TTTTGAATTTAAATAA
*
2020635 TTTTAAATTTAAATAA
1 TTTTGAATTTAAATAA
2020651 TTTTGAATTT
1 TTTTGAATTT
2020661 GAGATATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTTGAATTTAAATAA
Found at i:2020807 original size:21 final size:22
Alignment explanation
Indices: 2020783--2020825 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2020773 TTTTTTTAAA
2020783 AATTTATATCAT-TTTAAATTT
1 AATTTATATCATATTTAAATTT
* *
2020804 AATTTTTTTCATATTTAAATTT
1 AATTTATATCATATTTAAATTT
2020826 TTCAAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTTATATCATATTTAAATTT
Found at i:2021657 original size:22 final size:22
Alignment explanation
Indices: 2021632--2021679 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2021622 CATAATTCAA
2021632 ATTTATATCAAATTAAATTTTC
1 ATTTATATCAAATTAAATTTTC
* *
2021654 ATTTATATTAAATTAATTTTTC
1 ATTTATATCAAATTAAATTTTC
2021676 ATTT
1 ATTT
2021680 TTTTAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTATATCAAATTAAATTTTC
Found at i:2023021 original size:44 final size:41
Alignment explanation
Indices: 2022930--2023022 Score: 100
Period size: 44 Copynumber: 2.2 Consensus size: 41
2022920 CCTAATTTAC
* *
2022930 AAAATAAA-ATAATATTTTTTATTAAATTTTAATTATAATA
1 AAAATAAATATAATATTTTTTATTAAATTTTAATAAAAATA
* *
2022970 TATATAAATATTAATATAATTTTT-TTAATATTTTAATAAAAATA
1 AAAATAAATA-TAATAT--TTTTTATTAA-ATTTTAATAAAAATA
2023014 AAAATAAAT
1 AAAATAAAT
2023023 TAAGACTAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
40 6 0.14
41 1 0.02
42 6 0.14
43 4 0.10
44 25 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (41 bp):
AAAATAAATATAATATTTTTTATTAAATTTTAATAAAAATA
Found at i:2023269 original size:3 final size:3
Alignment explanation
Indices: 2023261--2023292 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2023251 GCATGTTCTC
2023261 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2023293 TCTTCAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2023881 original size:30 final size:29
Alignment explanation
Indices: 2023841--2023900 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
2023831 TTTATAAAAA
2023841 TTTTTTAAAATAGATA-TATATAATTTTAT
1 TTTTTTAAAAT-GATATTATATAATTTTAT
* *
2023870 TTTTATTAAAATTATATTATTTAATTTTAT
1 TTTT-TTAAAATGATATTATATAATTTTAT
2023900 T
1 T
2023901 GATAATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTTTAAAATGATATTATATAATTTTAT
Found at i:2024317 original size:20 final size:19
Alignment explanation
Indices: 2024292--2024361 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
2024282 ATTAAATTTT
2024292 TTTAAAATTTTATTTTATTA
1 TTTAAAA-TTTATTTTATTA
* * *
2024312 TTTAAAATATATTATAATA
1 TTTAAAATTTATTTTATTA
2024331 TTTAAAATTTATTTTTATTA
1 TTTAAAATTTA-TTTTATTA
*
2024351 -TTAATATTTAT
1 TTTAAAATTTAT
2024362 AAATTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.02
19 28 0.67
20 13 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAAAATTTATTTTATTA
Found at i:2024340 original size:26 final size:27
Alignment explanation
Indices: 2024311--2024367 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
2024301 TTATTTTATT
2024311 ATTTAAAATATATTA-TAATATTTA-AA
1 ATTT-AAATATATTATTAATATTTATAA
** *
2024337 ATTTATTTTTATTATTAATATTTATAA
1 ATTTAAATATATTATTAATATTTATAA
2024364 ATTT
1 ATTT
2024368 TTATACATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 7 0.27
26 13 0.50
27 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTAAATATATTATTAATATTTATAA
Found at i:2025817 original size:6 final size:6
Alignment explanation
Indices: 2025806--2025833 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2025796 TATTTTCCAC
2025806 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
2025834 CAGCTAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2029365 original size:2 final size:2
Alignment explanation
Indices: 2029358--2029403 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2029348 GACATTGGAT
* *
2029358 TA TA TA TA TA CA TA TA TA CA 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
2029400 TA TA
1 TA TA
2029404 ATTTAATGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2034631 original size:14 final size:14
Alignment explanation
Indices: 2034612--2034645 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2034602 ATTAATTCAT
2034612 ATAAAT-ATATTTTA
1 ATAAATAATA-TTTA
2034626 ATAAATAATATTTA
1 ATAAATAATATTTA
2034640 ATAAAT
1 ATAAAT
2034646 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAATAATATTTA
Found at i:2034677 original size:29 final size:30
Alignment explanation
Indices: 2034631--2034689 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2034621 TTTTAATAAA
2034631 TAATATTTAATA-AATTTTAATTTTAATTT
1 TAATATTTAATATAATTTTAATTTTAATTT
* ** *
2034660 TAATATTTATTATTTTTTTAATTTTGATTT
1 TAATATTTAATATAATTTTAATTTTAATTT
2034690 CTTTTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (30 bp):
TAATATTTAATATAATTTTAATTTTAATTT
Found at i:2037093 original size:21 final size:21
Alignment explanation
Indices: 2037064--2037106 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2037054 TGTTACTTAT
*
2037064 TATTGTATAATAGAAGCAAAG
1 TATTATATAATAGAAGCAAAG
*
2037085 TATTATATAATAGGAGCAAAG
1 TATTATATAATAGAAGCAAAG
2037106 T
1 T
2037107 TATGGGCAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.30
Consensus pattern (21 bp):
TATTATATAATAGAAGCAAAG
Found at i:2039222 original size:84 final size:84
Alignment explanation
Indices: 2039066--2039223 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
2039056 TTTGATATTT
* * * * * * * *
2039066 ATATTTAATATTTATTCGAACATATTTATTCGTATATATATTTATATTTTATATTTATACTCGAA
1 ATATTCAACATTTATTCGAACATATCTATTCATACATATATTCATATTTGATATTTATACTCCAA
*
2039131 TCTAAATAAATATTGATAC
66 ACTAAATAAATATTGATAC
*
2039150 ATATTCAACATTTATTCGAACATATCTATTCATGCATATATTCATATTTGATATTTATA-TCCAA
1 ATATTCAACATTTATTCGAACATATCTATTCATACATATATTCATATTTGATATTTATACTCCAA
2039214 ACTCAAATAA
66 ACT-AAATAA
2039224 GTGTTTTCTG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
83 6 0.10
84 57 0.90
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (84 bp):
ATATTCAACATTTATTCGAACATATCTATTCATACATATATTCATATTTGATATTTATACTCCAA
ACTAAATAAATATTGATAC
Found at i:2040492 original size:6 final size:6
Alignment explanation
Indices: 2040457--2040490 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2040447 AGGCAATATT
* *
2040457 TGCCAA TGCCAA TGCCAA TGCCGA TGCCGA TGCC
1 TGCCAA TGCCAA TGCCAA TGCCAA TGCCAA TGCC
2040491 GAGGCAGTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.18
Consensus pattern (6 bp):
TGCCAA
Found at i:2045955 original size:21 final size:20
Alignment explanation
Indices: 2045915--2045956 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2045905 TCAATATAAA
**
2045915 AATATTTTTTAAATTTTTAT
1 AATATTTTTTAAATAATTAT
2045935 AATATTATTTTAAATAATTAT
1 AATATT-TTTTAAATAATTAT
2045956 A
1 A
2045957 CAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATTTTTTAAATAATTAT
Found at i:2046478 original size:2 final size:2
Alignment explanation
Indices: 2046471--2046501 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2046461 CATACATTCT
2046471 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2046502 ATAGCAGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2051041 original size:23 final size:22
Alignment explanation
Indices: 2051015--2051083 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 22
2051005 AATGTTATAA
2051015 TTATATTTAAAATTATATATATT
1 TTATA-TTAAAATTATATATATT
2051038 TTATA-TAAAATT-TA-ATATAT
1 TTATATTAAAATTATATATAT-T
*
2051058 TAATAATATAAAATTAT-TAATATT
1 TTAT-AT-TAAAATTATAT-ATATT
2051082 TT
1 TT
2051084 TTTATTCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
19 4 0.11
20 6 0.16
21 8 0.22
23 12 0.32
24 3 0.08
25 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATATTAAAATTATATATATT
Found at i:2051048 original size:21 final size:21
Alignment explanation
Indices: 2051022--2051083 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
2051012 TAATTATATT
2051022 TAAAATTATATATATTTTATA
1 TAAAATTATATATATTTTATA
*
2051043 TAAAATT-TAATATATTAATAATA
1 TAAAATTAT-ATATATT--TTATA
2051066 TAAAATTAT-TAATATTTT
1 TAAAATTATAT-ATATTTT
2051084 TTTATTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
20 1 0.03
21 15 0.44
22 1 0.03
23 16 0.47
24 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAATTATATATATTTTATA
Found at i:2051601 original size:15 final size:16
Alignment explanation
Indices: 2051571--2051606 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2051561 ATCTAATAAA
2051571 ATAAA-ATAAAATTAT
1 ATAAATATAAAATTAT
2051586 ATAAATATAAAA-TAT
1 ATAAATATAAAATTAT
2051601 ATAAAT
1 ATAAAT
2051607 TAATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAATATAAAATTAT
Found at i:2053343 original size:2 final size:2
Alignment explanation
Indices: 2053336--2053363 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2053326 GCAATTTGCA
2053336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2053364 TTGTTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2057451 original size:21 final size:22
Alignment explanation
Indices: 2057427--2057482 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
2057417 TTAATATAAA
* *
2057427 ATTTAATTATTTTAAAA-TTTT
1 ATTTAATTATTTAAAAAGTTAT
*
2057448 ATTTTATATATTTAAAAAGTTAT
1 ATTTAAT-TATTTAAAAAGTTAT
2057471 ATTTAA-TATTTA
1 ATTTAATTATTTA
2057483 TGTTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 12 0.41
22 9 0.31
23 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTAATTATTTAAAAAGTTAT
Found at i:2057479 original size:23 final size:22
Alignment explanation
Indices: 2057427--2057479 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
2057417 TTAATATAAA
* *
2057427 ATTTAAT-TATTTTAAAATTTT
1 ATTTAATATATTTAAAAATTAT
*
2057448 ATTTTATATATTTAAAAAGTTAT
1 ATTTAATATATTTAAAAA-TTAT
2057471 ATTTAATAT
1 ATTTAATAT
2057480 TTATGTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 6 0.23
22 9 0.35
23 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTAATATATTTAAAAATTAT
Found at i:2059209 original size:6 final size:6
Alignment explanation
Indices: 2059198--2059231 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2059188 GTATAAATAC
* *
2059198 TTTATT TTTATT ATTATT TTTATT TTGATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
2059232 AGTAATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:2062829 original size:19 final size:19
Alignment explanation
Indices: 2062805--2062847 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2062795 GTAATATTAT
*
2062805 AATATATATTAATATATCA
1 AATATAAATTAATATATCA
* *
2062824 AATATAAATTTATATATTA
1 AATATAAATTAATATATCA
2062843 AATAT
1 AATAT
2062848 CATGATAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATAAATTAATATATCA
Found at i:2064004 original size:3 final size:3
Alignment explanation
Indices: 2063996--2064031 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2063986 GAGGAATCCG
* *
2063996 ATT ATT ATT ATT AGT ATT ATT ATA ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2064032 TCTGTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2064397 original size:14 final size:14
Alignment explanation
Indices: 2064378--2064412 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
2064368 CACTAACATC
2064378 GTAATTTATACACT
1 GTAATTTATACACT
2064392 GTAATTTATACACT
1 GTAATTTATACACT
2064406 GTCAATT
1 GT-AATT
2064413 AGTTAAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (14 bp):
GTAATTTATACACT
Found at i:2065358 original size:2 final size:2
Alignment explanation
Indices: 2065351--2065375 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2065341 AAACTTGCTT
2065351 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2065376 GAAGAGAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2066124 original size:19 final size:19
Alignment explanation
Indices: 2066100--2066139 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2066090 ATATAACTTA
*
2066100 ATTTAAATAAAAATATTTT
1 ATTTAAATAAAAATAATTT
2066119 ATTTAAATAAAAATAATTT
1 ATTTAAATAAAAATAATTT
2066138 AT
1 AT
2066140 ATTATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAATAATTT
Found at i:2066719 original size:21 final size:21
Alignment explanation
Indices: 2066695--2066741 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
2066685 ATTAAAAATT
2066695 ATTATATGTTTT-ATATTTTTA
1 ATTATATGTTTTAATA-TTTTA
*
2066716 ATTA-ATTTTTTAATATTTTA
1 ATTATATGTTTTAATATTTTA
2066736 A-TATAT
1 ATTATAT
2066742 CTTAAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 14 0.61
21 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTATATGTTTTAATATTTTA
Found at i:2068334 original size:3 final size:3
Alignment explanation
Indices: 2068322--2068358 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2068312 TAGGCTTTTA
2068322 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2068359 GCATTAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2068698 original size:2 final size:2
Alignment explanation
Indices: 2068659--2068689 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2068649 ACCGTCAGGC
2068659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2068690 CACATATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2069582 original size:12 final size:12
Alignment explanation
Indices: 2069551--2069630 Score: 61
Period size: 12 Copynumber: 6.7 Consensus size: 12
2069541 TGCTGGTGGA
* *
2069551 GGAGGTGGAGTT
1 GGAGTTGGAGGT
*
2069563 GGACTTGGAGGT
1 GGAGTTGGAGGT
* *
2069575 GGTGTTGGCGGT
1 GGAGTTGGAGGT
* *
2069587 GCAGTTGGAGTT
1 GGAGTTGGAGGT
*
2069599 GGAGGTGGAGGT
1 GGAGTTGGAGGT
* *
2069611 GGAGCTGGCGGT
1 GGAGTTGGAGGT
*
2069623 GGTGTTGG
1 GGAGTTGG
2069631 GACTGGTGTC
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.11, C:0.06, G:0.56, T:0.26
Consensus pattern (12 bp):
GGAGTTGGAGGT
Found at i:2069623 original size:18 final size:18
Alignment explanation
Indices: 2069551--2069624 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
2069541 TGCTGGTGGA
*
2069551 GGAGGTGGAGTTGGAC-TT
1 GGAGGTGGAGTTGG-CGGT
*
2069569 GGAGGTGGTGTTGGCGGT
1 GGAGGTGGAGTTGGCGGT
* * *
2069587 GCAGTTGGAGTTGGAGGT
1 GGAGGTGGAGTTGGCGGT
*
2069605 GGAGGTGGAGCTGGCGGT
1 GGAGGTGGAGTTGGCGGT
2069623 GG
1 GG
2069625 TGTTGGGACT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 1 0.02
18 44 0.98
ACGTcount: A:0.12, C:0.07, G:0.57, T:0.24
Consensus pattern (18 bp):
GGAGGTGGAGTTGGCGGT
Found at i:2070848 original size:15 final size:14
Alignment explanation
Indices: 2070825--2070895 Score: 69
Period size: 15 Copynumber: 5.1 Consensus size: 14
2070815 TTATAATACT
2070825 TAATAATATTAAATA
1 TAATAATA-TAAATA
*
2070840 TAATTATATAAATA
1 TAATAATATAAATA
*
2070854 T--T-ATATATATA
1 TAATAATATAAATA
2070865 TAATAATA-AAATA
1 TAATAATATAAATA
2070878 TAATATAATATAAATA
1 T-A-ATAATATAAATA
2070894 TA
1 TA
2070896 TATTTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
11 9 0.19
12 1 0.02
13 6 0.13
14 11 0.23
15 14 0.30
16 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATAATATAAATA
Found at i:2070855 original size:21 final size:21
Alignment explanation
Indices: 2070829--2070894 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 21
2070819 AATACTTAAT
2070829 AATATTAAATATAATTATATA
1 AATATTAAATATAATTATATA
2070850 AATATT--ATAT-A-TATAT-
1 AATATTAAATATAATTATATA
*
2070866 AATAATAAAATATAATATAATATA
1 AAT-ATTAAATATAAT-T-ATATA
2070890 AATAT
1 AATAT
2070895 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
16 3 0.08
17 7 0.19
18 1 0.03
19 8 0.22
20 1 0.03
21 6 0.17
22 1 0.03
23 6 0.17
24 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATTAAATATAATTATATA
Found at i:2072207 original size:18 final size:20
Alignment explanation
Indices: 2072175--2072213 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
2072165 ACGTCAATTT
2072175 TTATATTTAATATAAAAATA
1 TTATATTTAATATAAAAATA
2072195 TTAT-TTTAA-ATAAAAATA
1 TTATATTTAATATAAAAATA
2072213 T
1 T
2072214 AATTAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATATTTAATATAAAAATA
Found at i:2074020 original size:2 final size:2
Alignment explanation
Indices: 2074013--2074041 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2074003 AAATAAAGAA
2074013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2074042 GATACATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2074272 original size:26 final size:24
Alignment explanation
Indices: 2074204--2074272 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 24
2074194 TACGATATAA
* * *
2074204 ATATAATATAGTAAAATTTAAATT
1 ATATAATATATTAAATTTTAAAAT
2074228 ATATAAATTATATTAAAATTTATATAAAT
1 ATAT-AA-TATATT-AAATTT-TA-AAAT
2074257 ATATAATATATTAAAT
1 ATATAATATATTAAAT
2074273 AAAAAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 4 0.11
25 2 0.05
26 9 0.24
27 11 0.30
28 4 0.11
29 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
ATATAATATATTAAATTTTAAAAT
Found at i:2076305 original size:43 final size:43
Alignment explanation
Indices: 2076239--2076331 Score: 141
Period size: 43 Copynumber: 2.1 Consensus size: 43
2076229 TCTCATGCTT
* *
2076239 TAATGAGTCAAATCACTTTGTTTGTCACCCACCCCCATCGTGAA
1 TAAT-AGTCAAATCACTTTGTTTGTCACCAACCCCCATCATGAA
* *
2076283 TAATAGTCAAATCACTTTGTTTGTCTCCAACTCCCATCATGAA
1 TAATAGTCAAATCACTTTGTTTGTCACCAACCCCCATCATGAA
2076326 TAATAG
1 TAATAG
2076332 GTGTCGTTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 41 0.91
44 4 0.09
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (43 bp):
TAATAGTCAAATCACTTTGTTTGTCACCAACCCCCATCATGAA
Found at i:2076439 original size:2 final size:2
Alignment explanation
Indices: 2076432--2076464 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2076422 GCCTTCCACC
2076432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2076465 CTAACTATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2078513 original size:25 final size:25
Alignment explanation
Indices: 2078470--2078533 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
2078460 TTTAAAGTGT
*
2078470 TAAATATT-ATATA--TATATTTTT
1 TAAATATTAATATATTTATATTTTA
2078492 TAATATATTAATA-ATTTATATTTTA
1 TAA-ATATTAATATATTTATATTTTA
*
2078517 TAAATTTTAATATATTT
1 TAAATATTAATATATTT
2078534 TTTATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 3 0.09
23 6 0.17
24 11 0.31
25 15 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TAAATATTAATATATTTATATTTTA
Found at i:2079389 original size:22 final size:22
Alignment explanation
Indices: 2079346--2079395 Score: 57
Period size: 25 Copynumber: 2.2 Consensus size: 22
2079336 AATTAAATTA
2079346 AATAAA-AAAATTATTAATAAT
1 AATAAATAAAATTATTAATAAT
*
2079367 ATTAAATAAAATTTATTTAAATAAT
1 AATAAATAAAA-TTA-TT-AATAAT
2079392 AATA
1 AATA
2079396 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 5 0.22
22 4 0.17
23 3 0.13
24 2 0.09
25 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAATAAAATTATTAATAAT
Found at i:2081473 original size:2 final size:2
Alignment explanation
Indices: 2081466--2081506 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2081456 CTTAAAAGCA
2081466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2081507 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2084422 original size:21 final size:21
Alignment explanation
Indices: 2084397--2084480 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
2084387 GAATTTAAAG
*
2084397 TTAAATTCAATTGACTTATAT
1 TTAAATTCAATTGATTTATAT
* * * *
2084418 TTAAATTTAA--GAATTCAAAA
1 TTAAATTCAATTG-ATTTATAT
2084438 TTAAATTCAATTGATTTATAT
1 TTAAATTCAATTGATTTATAT
*
2084459 TTAAATTCAGTTGATTTATAT
1 TTAAATTCAATTGATTTATAT
2084480 T
1 T
2084481 ATTATCCAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.02
20 13 0.26
21 35 0.70
22 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (21 bp):
TTAAATTCAATTGATTTATAT
Found at i:2084442 original size:41 final size:41
Alignment explanation
Indices: 2084385--2084465 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
2084375 AAAAATTTAA
* *
2084385 AAGAATTTAAAGTTAAATTCAATTGACTTATATTTAAATTT
1 AAGAATTCAAAATTAAATTCAATTGACTTATATTTAAATTT
*
2084426 AAGAATTCAAAATTAAATTCAATTGATTTATATTTAAATT
1 AAGAATTCAAAATTAAATTCAATTGACTTATATTTAAATT
2084466 CAGTTGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (41 bp):
AAGAATTCAAAATTAAATTCAATTGACTTATATTTAAATTT
Found at i:2087276 original size:8 final size:9
Alignment explanation
Indices: 2087261--2087297 Score: 65
Period size: 9 Copynumber: 4.0 Consensus size: 9
2087251 AATTCAAACA
2087261 TTCTTTTTT
1 TTCTTTTTT
2087270 TTCTTTTTT
1 TTCTTTTTT
2087279 TTCTTTTTT
1 TTCTTTTTT
2087288 TTCTCTTTTT
1 TTCT-TTTTT
2087298 CGAGCACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 22 0.81
10 5 0.19
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:2089598 original size:12 final size:12
Alignment explanation
Indices: 2089581--2089607 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2089571 ATATATATAT
2089581 ATCCTAAAATGA
1 ATCCTAAAATGA
2089593 ATCCTAAAATGA
1 ATCCTAAAATGA
2089605 ATC
1 ATC
2089608 TAGGTTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (12 bp):
ATCCTAAAATGA
Found at i:2090661 original size:6 final size:6
Alignment explanation
Indices: 2090650--2090682 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2090640 CGGTAACCGA
*
2090650 TTGCTG TTGCTG TTGCTG TTGCTG TTGTTG TTG
1 TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTG
2090683 ATGATGATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.33, T:0.55
Consensus pattern (6 bp):
TTGCTG
Found at i:2092698 original size:18 final size:18
Alignment explanation
Indices: 2092677--2092733 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 18
2092667 TTATTTTATT
*
2092677 TTTTACATTTTAAATATA
1 TTTTAAATTTTAAATATA
2092695 TTTTAAATTTTATATATTATA
1 TTTTAAATTTTA-A-A-TATA
*
2092716 TTTAAAATTATTAAATAT
1 TTTTAAATT-TTAAATAT
2092734 TAATGAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 11 0.33
19 4 0.12
20 2 0.06
21 13 0.39
22 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAATTTTAAATATA
Found at i:2092717 original size:21 final size:22
Alignment explanation
Indices: 2092691--2092735 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2092681 ACATTTTAAA
* *
2092691 TATATTTTAAATT-TTATATAT
1 TATATTTAAAATTATTAAATAT
2092712 TATATTTAAAATTATTAAATAT
1 TATATTTAAAATTATTAAATAT
2092734 TA
1 TA
2092736 ATGAAACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATTTAAAATTATTAAATAT
Found at i:2095085 original size:61 final size:61
Alignment explanation
Indices: 2095007--2095124 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 61
2094997 TTTTTTTAAA
*
2095007 AAGAGAATTACATTTTTAAGGAATAAAATTTTATAAATTTATGAGTATTTAAAAAAGAATC
1 AAGAAAATTACATTTTTAAGGAATAAAATTTTATAAATTTATGAGTATTTAAAAAAGAATC
* * *
2095068 AAGAAAATTATATTTTTAAGTAATAAAATTTTATATATTTATGAGTATTTAAAAAAG
1 AAGAAAATTACATTTTTAAGGAATAAAATTTTATAAATTTATGAGTATTTAAAAAAG
2095125 GTAATACTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (61 bp):
AAGAAAATTACATTTTTAAGGAATAAAATTTTATAAATTTATGAGTATTTAAAAAAGAATC
Found at i:2096159 original size:17 final size:18
Alignment explanation
Indices: 2096124--2096170 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
2096114 ATATAATTTT
2096124 AAAAA-AAGATAAT--AA
1 AAAAATAAGATAATGGAA
2096139 AAAAATAA-ATAATGGAA
1 AAAAATAAGATAATGGAA
*
2096156 AAAAGTAAGATAATG
1 AAAAATAAGATAATG
2096171 TTAGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 9 0.33
18 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (18 bp):
AAAAATAAGATAATGGAA
Found at i:2098055 original size:17 final size:16
Alignment explanation
Indices: 2098029--2098061 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2098019 TTATTTAATG
2098029 AATTGATATAAATTTA
1 AATTGATATAAATTTA
2098045 AATTAGATATAAATTTA
1 AATT-GATATAAATTTA
2098062 TAACATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AATTGATATAAATTTA
Found at i:2098886 original size:8 final size:8
Alignment explanation
Indices: 2098875--2098919 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
2098865 TATTAAAATT
2098875 TATATAAA
1 TATATAAA
*
2098883 TATATAAT
1 TATATAAA
2098891 TA-ATAAA
1 TATATAAA
*
2098898 -ACATAAA
1 TATATAAA
2098905 TATATAAA
1 TATATAAA
2098913 T-TATAAA
1 TATATAAA
2098920 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
6 1 0.03
7 15 0.47
8 16 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (8 bp):
TATATAAA
Found at i:2098926 original size:22 final size:22
Alignment explanation
Indices: 2098878--2098920 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2098868 TAAAATTTAT
2098878 ATAAATATATAATTAATAAAAC
1 ATAAATATATAATTAATAAAAC
2098900 ATAAATATATAAATT-ATAAAA
1 ATAAATATAT-AATTAATAAAA
2098921 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATATATAATTAATAAAAC
Found at i:2099029 original size:2 final size:2
Alignment explanation
Indices: 2099022--2099046 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2099012 TGTAAAGGAC
2099022 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2099047 TCTTATGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2113198 original size:2 final size:2
Alignment explanation
Indices: 2113191--2113222 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2113181 TATCTGAGAA
2113191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2113223 GTAACATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2114093 original size:171 final size:171
Alignment explanation
Indices: 2113808--2114150 Score: 686
Period size: 171 Copynumber: 2.0 Consensus size: 171
2113798 AGAACGAGGC
2113808 TAGGGAATGGAATATATTATTAAAATTAAATATTCACCATAGATGCGGGAAGCTGATGGCGACGA
1 TAGGGAATGGAATATATTATTAAAATTAAATATTCACCATAGATGCGGGAAGCTGATGGCGACGA
2113873 AGTTCATCACGAAATTGAGTTCCAGCCTCCTTATACATTTCCTGGAAAAGAAATTATTTGATCAG
66 AGTTCATCACGAAATTGAGTTCCAGCCTCCTTATACATTTCCTGGAAAAGAAATTATTTGATCAG
2113938 AAATATGCCACCAGATATGACAAACCTTAATGTATGAACCA
131 AAATATGCCACCAGATATGACAAACCTTAATGTATGAACCA
2113979 TAGGGAATGGAATATATTATTAAAATTAAATATTCACCATAGATGCGGGAAGCTGATGGCGACGA
1 TAGGGAATGGAATATATTATTAAAATTAAATATTCACCATAGATGCGGGAAGCTGATGGCGACGA
2114044 AGTTCATCACGAAATTGAGTTCCAGCCTCCTTATACATTTCCTGGAAAAGAAATTATTTGATCAG
66 AGTTCATCACGAAATTGAGTTCCAGCCTCCTTATACATTTCCTGGAAAAGAAATTATTTGATCAG
2114109 AAATATGCCACCAGATATGACAAACCTTAATGTATGAACCA
131 AAATATGCCACCAGATATGACAAACCTTAATGTATGAACCA
2114150 T
1 T
2114151 GAAATCTCTA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 172 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (171 bp):
TAGGGAATGGAATATATTATTAAAATTAAATATTCACCATAGATGCGGGAAGCTGATGGCGACGA
AGTTCATCACGAAATTGAGTTCCAGCCTCCTTATACATTTCCTGGAAAAGAAATTATTTGATCAG
AAATATGCCACCAGATATGACAAACCTTAATGTATGAACCA
Found at i:2118844 original size:15 final size:15
Alignment explanation
Indices: 2118824--2118854 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2118814 TATTAAAATT
*
2118824 TTTAAATTTTATAAA
1 TTTAAATTTTAAAAA
2118839 TTTAAATTTTAAAAA
1 TTTAAATTTTAAAAA
2118854 T
1 T
2118855 ATTTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAAATTTTAAAAA
Found at i:2120309 original size:22 final size:23
Alignment explanation
Indices: 2120259--2120311 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 23
2120249 TTTAAATTTA
*
2120259 ATTAAAA-AAAATATTTTTAACT
1 ATTAAAATAAAATATTTTAAACT
2120281 ATT---ATAAAATATTTTAAAC-
1 ATTAAAATAAAATATTTTAAACT
2120300 ATTAAAATAAAA
1 ATTAAAATAAAA
2120312 CTTTCCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
19 4 0.15
20 13 0.50
22 9 0.35
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTAAAATAAAATATTTTAAACT
Found at i:2120594 original size:25 final size:25
Alignment explanation
Indices: 2120559--2120613 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
2120549 TATTATTTTT
2120559 TAAAAAAAATTAT-AAT-TTAAAAA
1 TAAAAAAAATTATAAATATTAAAAA
*
2120582 TAAAAAAGTAATTATAAATATTAAAAT
1 TAAAAAA--AATTATAAATATTAAAAA
2120609 TAAAA
1 TAAAA
2120614 TTTATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 7 0.26
25 6 0.22
26 3 0.11
27 11 0.41
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TAAAAAAAATTATAAATATTAAAAA
Found at i:2122103 original size:22 final size:21
Alignment explanation
Indices: 2122013--2122106 Score: 73
Period size: 22 Copynumber: 4.1 Consensus size: 21
2122003 CAGATTAAAT
* *
2122013 ATTTATAATATTTAAACTTAA
1 ATTTATATTATTTAAATTTAA
2122034 ATTTATAAAATTATTTCAACATTTAA
1 ATTTAT---ATTATTT-AA-ATTTAA
**
2122060 ATTTATTTATTATTTGTA-TTAA
1 ATTTA--TATTATTTAAATTTAA
2122082 ATTTATATTATTTAAAATTTAA
1 ATTTATATTATTT-AAATTTAA
2122104 ATT
1 ATT
2122107 AAATAATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
20 8 0.14
21 7 0.12
22 16 0.28
23 1 0.02
24 6 0.10
25 9 0.16
26 10 0.17
28 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (21 bp):
ATTTATATTATTTAAATTTAA
Found at i:2123184 original size:18 final size:17
Alignment explanation
Indices: 2123161--2123199 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2123151 AGCTTTTATT
2123161 TTATTTATTAAAAATAAA
1 TTATTTATTAAAAA-AAA
* *
2123179 TTATTTTTTTAAAAAAA
1 TTATTTATTAAAAAAAA
2123196 TTAT
1 TTAT
2123200 CCGACCCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTTATTAAAAAAAA
Found at i:2123455 original size:3 final size:3
Alignment explanation
Indices: 2123442--2123504 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
2123432 TATTATCGTC
2123442 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
2123489 ACA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
2123505 AGCAGAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2131349 original size:23 final size:23
Alignment explanation
Indices: 2131321--2131373 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2131311 CTTAATAAAT
2131321 TATTTAAAAATATTTTAT-ATTAA
1 TATTTAAAAAT-TTTTATAATTAA
* *
2131344 TATTTATATATTTTTATAATTAA
1 TATTTAAAAATTTTTATAATTAA
2131367 -ATTTAAA
1 TATTTAAA
2131374 TAAAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTAAAAATTTTTATAATTAA
Found at i:2137291 original size:3 final size:3
Alignment explanation
Indices: 2137285--2137312 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2137275 AAAAAAAAAA
2137285 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2137313 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2137317 original size:3 final size:3
Alignment explanation
Indices: 2137311--2137338 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2137301 ATAATAATAA
2137311 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2137339 CTAAATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2138241 original size:2 final size:2
Alignment explanation
Indices: 2138234--2138258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2138224 TCTTATATTT
2138234 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2138259 GATTTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2139513 original size:22 final size:21
Alignment explanation
Indices: 2139467--2139515 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2139457 TGTGTACTTT
* * *
2139467 TAAATTTAAAAAATAATATAT
1 TAAATATAAAAAATAAAATAA
2139488 TAAATATAAAAAATTAAAATAA
1 TAAATATAAAAAA-TAAAATAA
2139510 TAAATA
1 TAAATA
2139516 AATAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATATAAAAAATAAAATAA
Found at i:2139699 original size:5 final size:5
Alignment explanation
Indices: 2139677--2139734 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
2139667 ATATTAAATT
* *
2139677 ATTT- ATTTA A-TAA ATTTA ATTTA ATTTA ATTTA ATTAAA ATATT- ATTTAA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATT-TA AT-TTA ATTT-A
2139727 ATTTA ATT
1 ATTTA ATT
2139735 ATAAAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
4 9 0.20
5 27 0.61
6 7 0.16
7 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTTA
Found at i:2139745 original size:26 final size:25
Alignment explanation
Indices: 2139664--2139743 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 25
2139654 TATGAAAAAA
*
2139664 AAAATATTAAATT-ATTT-ATTTAAT
1 AAAATATT-ATTTAATTTAATTTAAT
2139688 -AAAT-TTAATTTAATTTAATTTAATT
1 AAAATATT-ATTTAATTTAATTTAA-T
2139713 AAAATATTATTTAAATTTAA-TT-AT
1 AAAATATTATTT-AATTTAATTTAAT
2139737 AAAATAT
1 AAAATAT
2139744 ATAAAAATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
22 6 0.12
23 8 0.16
24 14 0.29
25 2 0.04
26 10 0.20
27 9 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAAATATTATTTAATTTAATTTAAT
Found at i:2139769 original size:20 final size:21
Alignment explanation
Indices: 2139739--2139781 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2139729 TTAATTATAA
*
2139739 AATATATAAAAATAAATTTTT
1 AATATATAAAAAGAAATTTTT
*
2139760 AATA-ATAAAACGAAATTTTT
1 AATATATAAAAAGAAATTTTT
2139780 AA
1 AA
2139782 AAAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AATATATAAAAAGAAATTTTT
Found at i:2141581 original size:17 final size:18
Alignment explanation
Indices: 2141559--2141601 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2141549 ACAATTTTTT
*
2141559 TATATTAATTTT-TTAAA
1 TATATTAATTTTATAAAA
2141576 TATATT-ATTTTATAAAA
1 TATATTAATTTTATAAAA
*
2141593 TTTATTAAT
1 TATATTAAT
2141602 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 15 0.68
18 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTAATTTTATAAAA
Found at i:2142414 original size:25 final size:21
Alignment explanation
Indices: 2142395--2142436 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
2142385 TTTAAATATC
2142395 ATTTATATATTATCAATTAAAAA
1 ATTTATA-ATTAT-AATTAAAAA
2142418 ATTTATAATTATAATTAAA
1 ATTTATAATTATAATTAAA
2142437 CAATAACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTATAATTATAATTAAAAA
Found at i:2143470 original size:2 final size:2
Alignment explanation
Indices: 2143463--2143499 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2143453 AGAAACACAA
2143463 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2143500 AGACATGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2147906 original size:17 final size:18
Alignment explanation
Indices: 2147868--2147912 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
2147858 TATAAATTTT
*
2147868 TAAAAATATTTTAAATACA
1 TAAAAAT-TTTTAAATAAA
2147887 TAAAAATTTTTAAA-AAA
1 TAAAAATTTTTAAATAAA
*
2147904 TAAATATTT
1 TAAAAATTT
2147913 CTACGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.42
18 7 0.29
19 7 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAAATTTTTAAATAAA
Found at i:2154214 original size:2 final size:2
Alignment explanation
Indices: 2154207--2154255 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2154197 TGGTGAAGGG
2154207 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2154249 GA GA GA G
1 GA GA GA G
2154256 GGAAGCATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2155140 original size:2 final size:2
Alignment explanation
Indices: 2155086--2155122 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2155076 TTCGGGTAGA
*
2155086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2155123 ACCCTTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2156523 original size:3 final size:3
Alignment explanation
Indices: 2156515--2156540 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2156505 TTTTATACCC
2156515 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2156541 CCATTTACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2161738 original size:25 final size:25
Alignment explanation
Indices: 2161710--2161760 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2161700 GGGAGGCATT
2161710 ATCCAAGGCCGGTCATGGTTTTGAG
1 ATCCAAGGCCGGTCATGGTTTTGAG
**
2161735 ATCCAAGGGTGGTCATGGTTTTGAG
1 ATCCAAGGCCGGTCATGGTTTTGAG
2161760 A
1 A
2161761 GAGAATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (25 bp):
ATCCAAGGCCGGTCATGGTTTTGAG
Found at i:2162880 original size:13 final size:13
Alignment explanation
Indices: 2162862--2162889 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2162852 TTTGAAAATG
2162862 TATTGAATATAAA
1 TATTGAATATAAA
2162875 TATTGAATATAAA
1 TATTGAATATAAA
2162888 TA
1 TA
2162890 CTTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (13 bp):
TATTGAATATAAA
Found at i:2163166 original size:2 final size:2
Alignment explanation
Indices: 2163153--2163187 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2163143 AAAGATTAAC
*
2163153 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2163188 GCCAAGTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2163759 original size:4 final size:4
Alignment explanation
Indices: 2163745--2163774 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2163735 GCTTATTGGC
*
2163745 TTAT ATAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
2163775 TGCATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:2164151 original size:13 final size:13
Alignment explanation
Indices: 2164133--2164157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2164123 ATCTGTCTAA
2164133 ATTTAAAATTTAT
1 ATTTAAAATTTAT
2164146 ATTTAAAATTTA
1 ATTTAAAATTTA
2164158 ATCAATAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAAAATTTAT
Found at i:2164735 original size:7 final size:7
Alignment explanation
Indices: 2164725--2164756 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2164715 ATGGGCCAAT
2164725 CCTAGTC
1 CCTAGTC
2164732 CCTAGTC
1 CCTAGTC
2164739 CCTAGT-
1 CCTAGTC
2164745 CCTAGTC
1 CCTAGTC
2164752 CCTAG
1 CCTAG
2164757 AAGGGGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.16, C:0.41, G:0.16, T:0.28
Consensus pattern (7 bp):
CCTAGTC
Found at i:2164750 original size:13 final size:14
Alignment explanation
Indices: 2164725--2164756 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2164715 ATGGGCCAAT
2164725 CCTAGTCCCTAGTC
1 CCTAGTCCCTAGTC
2164739 CCTAGT-CCTAGTC
1 CCTAGTCCCTAGTC
2164752 CCTAG
1 CCTAG
2164757 AAGGGGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.16, C:0.41, G:0.16, T:0.28
Consensus pattern (14 bp):
CCTAGTCCCTAGTC
Found at i:2165887 original size:2 final size:2
Alignment explanation
Indices: 2165882--2165925 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
2165872 TTTTACTCCT
*
2165882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
2165925 T
1 T
2165926 GCAGGCATGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2167250 original size:2 final size:2
Alignment explanation
Indices: 2167243--2167270 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2167233 GGGGAGACAC
2167243 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2167271 GCCTTACAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2170752 original size:35 final size:35
Alignment explanation
Indices: 2170707--2170778 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
2170697 AGAAGAAAGA
2170707 AAAAAGAACAAGAAAGAAGTAAACACAGATTCACC
1 AAAAAGAACAAGAAAGAAGTAAACACAGATTCACC
2170742 AAAAAGAACAAGAAAGAAGTAAACACAGATTCACC
1 AAAAAGAACAAGAAAGAAGTAAACACAGATTCACC
2170777 AA
1 AA
2170779 TATGCATGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.61, C:0.17, G:0.14, T:0.08
Consensus pattern (35 bp):
AAAAAGAACAAGAAAGAAGTAAACACAGATTCACC
Found at i:2172259 original size:2 final size:2
Alignment explanation
Indices: 2172246--2172276 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2172236 AATAGGACAA
*
2172246 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2172277 TATATATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:2176360 original size:233 final size:233
Alignment explanation
Indices: 2175953--2176431 Score: 931
Period size: 233 Copynumber: 2.1 Consensus size: 233
2175943 TGGCAATTGA
2175953 TGCACCTTCTCTTTTTAGATTTCTCTTTTCCCATCATTCTTCCATCAAATTTCCTCTCCTGCTTT
1 TGCACCTTCTCTTTTTAGATTTCTCTTTTCCCATCATTCTTCCATCAAATTTCCTCTCCTGCTTT
2176018 CAAGCTCAGCATTTTATACCATAATCCTCATCAATCAGGTTTTCTCCCTTTAAATTTTTCCATGA
66 CAAGCTCAGCATTTTATACCATAATCCTCATCAATCAGGTTTTCTCCCTTTAAATTTTTCCATGA
2176083 GAATAAAGCATCAAGATGCCCTTACCATTATATCTTCTATATAGCATGAAAATAACAATGCATAC
131 GAATAAAGCATCAAGATGCCCTTACCATTATATCTTCTATATAGCATGAAAATAACAATGCATAC
2176148 TTAATGCAACATCTTACGTTAAGTACAGAAAAGAGTTT
196 TTAATGCAACATCTTACGTTAAGTACAGAAAAGAGTTT
*
2176186 TGCACCTTCTCTTTTTAGATTTCTCTTTTCCCATCATTCTTCCATCAAATTTCCTCTCCTGTTTT
1 TGCACCTTCTCTTTTTAGATTTCTCTTTTCCCATCATTCTTCCATCAAATTTCCTCTCCTGCTTT
2176251 CAAGCTCAGCATTTTATACCATAATCCTCATCAATCAGGTTTTCTCCCTTTAAATTTTTCCATGA
66 CAAGCTCAGCATTTTATACCATAATCCTCATCAATCAGGTTTTCTCCCTTTAAATTTTTCCATGA
*
2176316 GAATAAAGCATCAAGATGCCCTTACCATTTTATCTTCTATATAGCATGAAAATAACAATGCATAC
131 GAATAAAGCATCAAGATGCCCTTACCATTATATCTTCTATATAGCATGAAAATAACAATGCATAC
2176381 TTAATGCAACATCTTACGTTAAGTACAGAAAAGAGTTT
196 TTAATGCAACATCTTACGTTAAGTACAGAAAAGAGTTT
*
2176419 TGCACCTTGTCTT
1 TGCACCTTCTCTT
2176432 ATCCAAAGTT
Statistics
Matches: 243, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
233 243 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (233 bp):
TGCACCTTCTCTTTTTAGATTTCTCTTTTCCCATCATTCTTCCATCAAATTTCCTCTCCTGCTTT
CAAGCTCAGCATTTTATACCATAATCCTCATCAATCAGGTTTTCTCCCTTTAAATTTTTCCATGA
GAATAAAGCATCAAGATGCCCTTACCATTATATCTTCTATATAGCATGAAAATAACAATGCATAC
TTAATGCAACATCTTACGTTAAGTACAGAAAAGAGTTT
Found at i:2185450 original size:17 final size:17
Alignment explanation
Indices: 2185423--2185473 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2185413 CATCATACTA
2185423 TTTAGTTAAATATATATT
1 TTTAGTTAAATAT-TATT
2185441 TTTA-TTAAATATTA-T
1 TTTAGTTAAATATTATT
*
2185456 TATAGTT-AATATTTATT
1 TTTAGTTAAATA-TTATT
2185473 T
1 T
2185474 AATATGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 8 0.28
16 7 0.24
17 10 0.34
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTAGTTAAATATTATT
Found at i:2185632 original size:5 final size:6
Alignment explanation
Indices: 2185616--2185640 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2185606 AAAAGCTATA
2185616 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
2185641 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:2185942 original size:34 final size:33
Alignment explanation
Indices: 2185884--2185948 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
2185874 TATATTTATA
* *
2185884 TTTATATTTTATAATTAAATTTAAATTAAATGC
1 TTTATATTTTATAATAAAATTTAAACTAAATGC
2185917 TTTATATTATTA-AATAATAATTTAAACTAAAT
1 TTTATATT-TTATAATAA-AATTTAAACTAAAT
2185949 AATTTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (33 bp):
TTTATATTTTATAATAAAATTTAAACTAAATGC
Found at i:2185951 original size:14 final size:14
Alignment explanation
Indices: 2185932--2185961 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2185922 ATTATTAAAT
2185932 AATAATTTAAACTA
1 AATAATTTAAACTA
*
2185946 AATAATTTAAATTA
1 AATAATTTAAACTA
2185960 AA
1 AA
2185962 AAGAAAATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAATTTAAACTA
Found at i:2186328 original size:37 final size:36
Alignment explanation
Indices: 2186225--2186335 Score: 113
Period size: 37 Copynumber: 3.1 Consensus size: 36
2186215 TGTTTTATAT
* *
2186225 ATATTTTTAATATTAATAATATAAATA-TAAT-TTAA
1 ATATATTT-ATATTAATAATATAAATATTAATATAAA
* * *
2186260 AT-TATTTAT-TTAAAAATTTAAATATAAATATAAA
1 ATATATTTATATTAATAATATAAATATTAATATAAA
* *
2186294 ATATATATTATATTAATTATATAAATATTAATATAAT
1 ATATAT-TTATATTAATAATATAAATATTAATATAAA
2186331 ATATA
1 ATATA
2186336 GTTTTAAATC
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
32 13 0.21
33 5 0.08
34 9 0.15
35 5 0.08
36 4 0.07
37 25 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
ATATATTTATATTAATAATATAAATATTAATATAAA
Found at i:2186507 original size:11 final size:11
Alignment explanation
Indices: 2186488--2186605 Score: 58
Period size: 11 Copynumber: 11.5 Consensus size: 11
2186478 AAAATTTTAT
2186488 ATATAATATAA
1 ATATAATATAA
*
2186499 ATATGATATAA
1 ATATAATATAA
2186510 A-A-AAT-TAA
1 ATATAATATAA
* *
2186518 TTAAAATAT-A
1 ATATAATATAA
*
2186528 ATATTATATAA
1 ATATAATATAA
2186539 ATATAA-A-AA
1 ATATAATATAA
2186548 ATAT-AT-TAA
1 ATATAATATAA
* *
2186557 AAATTATATAA
1 ATATAATATAA
* *
2186568 AAATAAATTATTA
1 ATAT-AA-TATAA
*
2186581 ATAT-TTA-AA
1 ATATAATATAA
*
2186590 ATGTAATATAA
1 ATATAATATAA
2186601 ATATA
1 ATATA
2186606 TAATATATTA
Statistics
Matches: 79, Mismatches: 16, Indels: 24
0.66 0.13 0.20
Matches are distributed among these distances:
8 4 0.05
9 18 0.23
10 18 0.23
11 31 0.39
12 1 0.01
13 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATATAATATAA
Found at i:2186562 original size:29 final size:29
Alignment explanation
Indices: 2186530--2186620 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
2186520 AAAATATAAT
*
2186530 ATTATATAAATATAAAAAATATATTAAAA
1 ATTATATAAATATAAATAATATATTAAAA
* * *
2186559 ATTATATAAAAATAAATTATTAATATTTAAA
1 ATTATATAAATATAAA-TAAT-ATATTAAAA
2186590 ATGTAATATAAATAT--ATAATATATTAAAA
1 AT-T-ATATAAATATAAATAATATATTAAAA
2186619 AT
1 AT
2186621 AATTATTGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 25 0.49
30 5 0.10
31 11 0.22
32 1 0.02
33 9 0.18
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (29 bp):
ATTATATAAATATAAATAATATATTAAAA
Found at i:2186574 original size:35 final size:35
Alignment explanation
Indices: 2186488--2186625 Score: 92
Period size: 35 Copynumber: 3.9 Consensus size: 35
2186478 AAAATTTTAT
*
2186488 ATATAATAT-AAATATGATATAAAAAATTAATTAAA
1 ATATAATATAAAATA-AATATAAAAAATTAATTAAA
* *
2186523 ATATAATATTATATAAATATAAAAAA-TATATTAAA
1 ATATAATATAAAATAAATATAAAAAATTA-ATTAAA
* ** *
2186558 A-ATTATATAAAAATAAAT-T-ATTAA-TATTTAAA
1 ATATAATAT-AAAATAAATATAAAAAATTAATTAAA
*
2186590 ATGTAATATAAATATATAATATATTAAAAA-TAATTA
1 ATATAATATAAA-ATA-AATATA--AAAAATTAATTA
2186626 TTGACACTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
32 9 0.11
33 13 0.16
34 12 0.15
35 34 0.43
36 4 0.05
38 8 0.10
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (35 bp):
ATATAATATAAAATAAATATAAAAAATTAATTAAA
Found at i:2186585 original size:31 final size:35
Alignment explanation
Indices: 2186550--2186616 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 35
2186540 TATAAAAAAT
2186550 ATATTAAAAAT-T-ATATAAAAATA-AAT-TATTA
1 ATATTAAAAATGTAATATAAAAATATAATATATTA
* *
2186581 ATATTTAAAATGTAATATAAATATATAATATATTA
1 ATATTAAAAATGTAATATAAAAATATAATATATTA
2186616 A
1 A
2186617 AAATAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 10 0.33
32 1 0.03
33 10 0.33
34 3 0.10
35 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (35 bp):
ATATTAAAAATGTAATATAAAAATATAATATATTA
Found at i:2186621 original size:11 final size:11
Alignment explanation
Indices: 2186504--2186625 Score: 50
Period size: 11 Copynumber: 11.5 Consensus size: 11
2186494 TATAAATATG
*
2186504 ATATAAAAAAT
1 ATATTAAAAAT
2186515 -TAATTAAAATAT
1 AT-ATTAAAA-AT
2186527 AATATTATATAAAT
1 -ATATTA-A-AAAT
2186541 ATA--AAAAAT
1 ATATTAAAAAT
2186550 ATATTAAAAAT
1 ATATTAAAAAT
2186561 -TATATAAAAAT
1 ATAT-TAAAAAT
* **
2186572 AAATTATTAAT
1 ATATTAAAAAT
2186583 AT-TT-AAAAT
1 ATATTAAAAAT
* * *
2186592 GTAATATAAAT
1 ATATTAAAAAT
2186603 ATA-T---AAT
1 ATATTAAAAAT
2186610 ATATTAAAAAT
1 ATATTAAAAAT
2186621 A-ATTA
1 ATATTA
2186626 TTGACACTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 33
0.66 0.09 0.26
Matches are distributed among these distances:
7 6 0.07
8 1 0.01
9 11 0.13
10 13 0.15
11 36 0.43
12 4 0.05
13 7 0.08
14 4 0.05
15 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
ATATTAAAAAT
Found at i:2188337 original size:16 final size:17
Alignment explanation
Indices: 2188271--2188338 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
2188261 TTATTATAAA
* *
2188271 TTAATTTAATATATTAT
1 TTAATTTAATAAAATAT
* *
2188288 ATTAAGTTAATATAATAAT
1 -TTAATTTAATAAAAT-AT
* *
2188307 TTAATTTTATTAAATAT
1 TTAATTTAATAAAATAT
2188324 TT-ATTTAATAAAATA
1 TTAATTTAATAAAATA
2188339 ATCGATTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 11 0.27
17 4 0.10
18 24 0.59
19 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (17 bp):
TTAATTTAATAAAATAT
Found at i:2188447 original size:20 final size:21
Alignment explanation
Indices: 2188418--2188468 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2188408 AATATTAATC
*
2188418 AAAATATAAAATTATCTTA-T-
1 AAAATTTAAAATT-TCTTATTA
*
2188438 AAAATTTAAAATTTTTTATTA
1 AAAATTTAAAATTTCTTATTA
2188459 AAAATTTAAA
1 AAAATTTAAA
2188469 TCTTATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTTAAAATTTCTTATTA
Found at i:2189309 original size:24 final size:23
Alignment explanation
Indices: 2189228--2189315 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 23
2189218 TAGATAATAT
2189228 TATTAAATAAA-ATAA-TTAAAA
1 TATTAAATAAATATAATTTAAAA
2189249 TA-TAACGTTATAAATATTAATTTAAAA
1 TATTAA----ATAAATA-TAATTTAAAA
* * *
2189276 TTTTATATAAATATAATATTAATA
1 TATTAAATAAATATAAT-TTAAAA
2189300 TATTAAATAAAATATA
1 TATTAAAT-AAATATA
2189316 TAAATCTACT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
20 3 0.06
21 2 0.04
23 4 0.08
24 23 0.44
25 8 0.15
26 3 0.06
27 7 0.13
28 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
TATTAAATAAATATAATTTAAAA
Found at i:2194752 original size:2 final size:2
Alignment explanation
Indices: 2194745--2194776 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2194735 AACCTGTAAA
2194745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2194777 CAATTCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2195451 original size:2 final size:2
Alignment explanation
Indices: 2195444--2195476 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2195434 GCTTGTCTGG
2195444 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2195477 TTGTTAGTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2204482 original size:216 final size:215
Alignment explanation
Indices: 2204085--2204930 Score: 1042
Period size: 215 Copynumber: 4.0 Consensus size: 215
2204075 TCTCAACCCC
* * ** *
2204085 CCAGTAATTATCGTCGCAGGTTTGAATTGAAACTGAATTTAGATTTTTGAATTTTATCCTTTTTT
1 CCAGTAATTGTTGTCGCAGGTCGGAATTGAAACTGAATTTAGATTTTTGAATTTTAT-C-TTTTC
* *
2204150 ATTTTCTTTTCGCGTTTGTG-TTGTTT--ATCACTAAGAAAGTTTAGAATTATAGATTTTGGTTT
64 ATTTTCTTTTCGCGTTTGTGTTTATTTGGATCACTAAGAAAGTTTAGAATTCTAGATTTTGGTTT
* **
2204212 GAGCTAAATCCTATTCCGTAGCTTGAATTGATCTAATTGTGAATCACTTATTTTGTAGATTTCTT
129 TAGCTAAATCCTATTCCGTAGCTTGAATTGATCTAATTACGAATCACTTATTTTGTAGATTTCTT
2204277 GTTTATACATTACTTCATGTTT
194 GTTTATACATTACTTCATGTTT
* * * **
2204299 TCAGTAGTTGTTGTCGGAGGTCGGAATTGAAACTGAATTTAGATTTCGGGAATTTTATCTTTTCA
1 CCAGTAATTGTTGTCGCAGGTCGGAATTGAAACTGAATTTAGATTT-TTGAATTTTATCTTTTCA
* **
2204364 TTTTCTTTTCGCATTTGTGTTTATTTGGATCACTAAGAAAGTCCAGAATTCTAGATTTTGGTTTT
65 TTTTCTTTTCGCGTTTGTGTTTATTTGGATCACTAAGAAAGTTTAGAATTCTAGATTTTGGTTTT
* * * * *
2204429 AGTTAAATCCTATTCCGTAGCTTGAATTTATCTAATTGCGCATCACCTATTTTGTCA-ATTTCTT
130 AGCTAAATCCTATTCCGTAGCTTGAATTGATCTAATTACGAATCACTTATTTTGT-AGATTTCTT
* * * * *
2204493 GTTTGTACATTGCATAATGCTTC
194 GTTTATACATTACTTCATG-TTT
** * * * *
2204516 CCAGTAATTGTCATCGCAGATAGGAATTGAAACTGAATTTAGATTTTTGAATATTTTTCTTATCA
1 CCAGTAATTGTTGTCGCAGGTCGGAATTGAAACTGAATTTAGATTTTTGAAT-TTTATCTTTTCA
*
2204581 TTTT-TTTT-GCGCTTT-TATTTATTTGGATCACTAAGAAAGTTTAGAATTCTAGATTTTGGTTT
65 TTTTCTTTTCGCG-TTTGTGTTTATTTGGATCACTAAGAAAGTTTAGAATTCTAGATTTTGGTTT
*
2204643 TAGCTAAATCCTATTCTGTAGCTTGAATTGATCTAATTACGAATCACTTATTTTGTAGATTTCTT
129 TAGCTAAATCCTATTCCGTAGCTTGAATTGATCTAATTACGAATCACTTATTTTGTAGATTTCTT
*
2204708 GTTTATACATTACTTCATGCTT
194 GTTTATACATTACTTCATGTTT
* * *
2204730 CCAGTAATTGTTGTTGCAGGTCGGAATTGAAACTGAATTTAGATTTTTTGAATTTT-GC-CTTC-
1 CCAGTAATTGTTGTCGCAGGTCGGAATTGAAACTGAATTTAGA-TTTTTGAATTTTATCTTTTCA
* * * * *
2204792 TTTTTTTTTCGGGTTTGTGTTGT-TTTGGATCAGTAATAAAGGTTAGCAA-TCTAGATTTTGGTT
65 TTTTCTTTTCGCGTTTGTGTT-TATTTGGATCACTAAGAAAGTTTAG-AATTCTAGATTTTGGTT
* * * *
2204855 TT-GCTAAATCCTATTCCGTAGATTGAATTGATCTAATTATGCATCA---ATTATGTAGATTTCT
128 TTAGCTAAATCCTATTCCGTAGCTTGAATTGATCTAATTACGAATCACTTATTTTGTAGATTTCT
2204916 TGTTTAT-CATTACTT
193 TGTTTATACATTACTT
2204931 TGTGCTTACT
Statistics
Matches: 546, Mismatches: 71, Indels: 36
0.84 0.11 0.06
Matches are distributed among these distances:
208 8 0.01
209 21 0.04
211 4 0.01
212 49 0.09
213 65 0.12
214 91 0.17
215 136 0.25
216 116 0.21
217 56 0.10
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (215 bp):
CCAGTAATTGTTGTCGCAGGTCGGAATTGAAACTGAATTTAGATTTTTGAATTTTATCTTTTCAT
TTTCTTTTCGCGTTTGTGTTTATTTGGATCACTAAGAAAGTTTAGAATTCTAGATTTTGGTTTTA
GCTAAATCCTATTCCGTAGCTTGAATTGATCTAATTACGAATCACTTATTTTGTAGATTTCTTGT
TTATACATTACTTCATGTTT
Found at i:2204991 original size:431 final size:429
Alignment explanation
Indices: 2204114--2204928 Score: 1064
Period size: 431 Copynumber: 1.9 Consensus size: 429
2204104 GTTTGAATTG
* * * * * *
2204114 AAACTGAATTTAGATTTTTGAAT-TTTATCCTTTTTTATTTTCTTTT-CGCGTTTGTGTTGTTT-
1 AAACTGAATTTAGATTTTTGAATATTT-TTC-TTATCATTTT-TTTTGCGCTTTTAT-TTATTTG
2204176 -ATCACTAAGAAAGTTTAGAATTATAGATTTTGGTTTGAGCTAAATCCTATTCCGTAGCTTGAAT
62 GATCACTAAGAAAGTTTAGAATTATAGATTTTGGTTTGAGCTAAATCCTATTCCGTAGCTTGAAT
** * *
2204240 TGATCTAATTGTGAATCACTTATTTTGTAGATTTCTTGTTTATACATTACTTCATGTTTTCAGTA
127 TGATCTAATTACGAATCACTTATTTTGTAGATTTCTTGTTTATACATTACTTCATGCTTCCAGTA
* * * *
2204305 GTTGTTGTCGGAGGTCGGAATTGAAACTGAATTTAGATTTCGGGAATTTTATCTTTTCATTTTCT
192 ATTGTTGTCGCAGGTCGGAATTGAAACTGAATTTAGATTTCGGGAATTTTAGCTCTTCATTTTCT
*
2204370 TTTCGCATTTGTGTTTATTTGGATCACTAAGAAAGTCCAGAATTCTAGATTTTGGTTTTAGTTAA
257 TTTCGCATTTGTGTTTATTTGGATCACTAAGAAAGTCCAGAATTCTAGATTTTGGTTTTAGCTAA
* * * * *
2204435 ATCCTATTCCGTAGCTTGAATTTATCTAATTGCGCATCACCTATTTTGTCAATTTCTTGTTTGTA
322 ATCCTATTCCGTAGATTGAATTGATCTAATTACGCATCA-C-ATTATGTCAATTTCTTGTTTATA
* * ** * * **
2204500 CATTGCATAATGCTTCCCAGTAATTGTCATCGCAGATAGGAATTG
385 CATTACATAATGCTTACCAGTAAAGGTAATAGCAGATAGGAATAC
2204545 AAACTGAATTTAGATTTTTGAATATTTTTCTTATCATTTTTTTTGCGCTTTTATTTATTTGGATC
1 AAACTGAATTTAGATTTTTGAATATTTTTCTTATCATTTTTTTTGCGCTTTTATTTATTTGGATC
* * *
2204610 ACTAAGAAAGTTTAGAATTCTAGATTTTGGTTTTAGCTAAATCCTATTCTGTAGCTTGAATTGAT
66 ACTAAGAAAGTTTAGAATTATAGATTTTGGTTTGAGCTAAATCCTATTCCGTAGCTTGAATTGAT
2204675 CTAATTACGAATCACTTATTTTGTAGATTTCTTGTTTATACATTACTTCATGCTTCCAGTAATTG
131 CTAATTACGAATCACTTATTTTGTAGATTTCTTGTTTATACATTACTTCATGCTTCCAGTAATTG
* *** *
2204740 TTGTTGCAGGTCGGAATTGAAACTGAATTTAGATTTTTTGAATTTT-GC-CTTC-TTTTTTTTTC
196 TTGTCGCAGGTCGGAATTGAAACTGAATTTAGATTTCGGGAATTTTAGCTCTTCATTTTCTTTTC
** * * *
2204802 GGGTTTGTGTTGT-TTTGGATCAGTAATAAAGGT-TAGCAA-TCTAGATTTTGGTTTT-GCTAAA
261 GCATTTGTGTT-TATTTGGATCACTAAGAAA-GTCCAG-AATTCTAGATTTTGGTTTTAGCTAAA
*
2204863 TCCTATTCCGTAGATTGAATTGATCTAATTATGCATCA-ATTATGT-AGATTTCTTGTTTAT-CA
323 TCCTATTCCGTAGATTGAATTGATCTAATTACGCATCACATTATGTCA-ATTTCTTGTTTATACA
2204925 TTAC
387 TTAC
2204929 TTTGTGCTTA
Statistics
Matches: 341, Mismatches: 35, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
423 6 0.02
424 18 0.05
427 39 0.11
428 51 0.15
429 17 0.05
430 16 0.05
431 191 0.56
432 3 0.01
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (429 bp):
AAACTGAATTTAGATTTTTGAATATTTTTCTTATCATTTTTTTTGCGCTTTTATTTATTTGGATC
ACTAAGAAAGTTTAGAATTATAGATTTTGGTTTGAGCTAAATCCTATTCCGTAGCTTGAATTGAT
CTAATTACGAATCACTTATTTTGTAGATTTCTTGTTTATACATTACTTCATGCTTCCAGTAATTG
TTGTCGCAGGTCGGAATTGAAACTGAATTTAGATTTCGGGAATTTTAGCTCTTCATTTTCTTTTC
GCATTTGTGTTTATTTGGATCACTAAGAAAGTCCAGAATTCTAGATTTTGGTTTTAGCTAAATCC
TATTCCGTAGATTGAATTGATCTAATTACGCATCACATTATGTCAATTTCTTGTTTATACATTAC
ATAATGCTTACCAGTAAAGGTAATAGCAGATAGGAATAC
Found at i:2206188 original size:51 final size:51
Alignment explanation
Indices: 2206112--2206211 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
2206102 AACTTTATTG
* *
2206112 GTAGCTAATTTTTGTGGTATCTTATGGAAATCCTTACTGGAAATTGATAAA
1 GTAGCTAATTTTTGCGGTATCTTATGGAAATCCTCACTGGAAATTGATAAA
*
2206163 GTAGCTAATTTTTGCGGTATCTTATGGTAATCCTCACTGGAAATTGATA
1 GTAGCTAATTTTTGCGGTATCTTATGGAAATCCTCACTGGAAATTGATA
2206212 GTCCTAGAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (51 bp):
GTAGCTAATTTTTGCGGTATCTTATGGAAATCCTCACTGGAAATTGATAAA
Found at i:2214345 original size:2 final size:2
Alignment explanation
Indices: 2214338--2214365 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2214328 ATTGATGAGA
2214338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2214366 TGGGTTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2214597 original size:18 final size:18
Alignment explanation
Indices: 2214576--2214611 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2214566 TTTATTATTA
*
2214576 TTATTATTATTATTTCTT
1 TTATTATTATTACTTCTT
*
2214594 TTATTTTTATTACTTCTT
1 TTATTATTATTACTTCTT
2214612 ATAGTTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTATTATTACTTCTT
Found at i:2217303 original size:22 final size:24
Alignment explanation
Indices: 2217272--2217315 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
2217262 GAAAAAATAA
2217272 TTCAATTTAAAATAATA-TAAAAT
1 TTCAATTTAAAATAATAGTAAAAT
*
2217295 TTCAA-TTAAAATGATAGTAAA
1 TTCAATTTAAAATAATAGTAAA
2217316 TATATACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (24 bp):
TTCAATTTAAAATAATAGTAAAAT
Found at i:2217699 original size:16 final size:16
Alignment explanation
Indices: 2217674--2217710 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 16
2217664 TTTATGCATC
2217674 TATTATTTA-T-TTA-
1 TATTATTTATTATTAT
2217687 TATTATTTATTATTAT
1 TATTATTTATTATTAT
2217703 TATTATTT
1 TATTATTT
2217711 TCAAAAGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.43
14 1 0.05
15 3 0.14
16 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTTATTATTAT
Found at i:2218776 original size:2 final size:2
Alignment explanation
Indices: 2218769--2218796 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2218759 CGGGATCAAC
2218769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2218797 TAAATACGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2220244 original size:19 final size:17
Alignment explanation
Indices: 2220220--2220263 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
2220210 TTAATATAAA
2220220 TATTAAAATGAGTAATATT
1 TATTAAAAT-AGTAAT-TT
*
2220239 TATTAAAAATATTAATTT
1 TATT-AAAATAGTAATTT
2220257 TATTAAA
1 TATTAAA
2220264 CAGTGACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 6 0.26
19 9 0.39
20 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
TATTAAAATAGTAATTT
Found at i:2220683 original size:24 final size:23
Alignment explanation
Indices: 2220656--2220700 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2220646 TAATTTTAGT
2220656 TAAAAATATTTTAAAATTTTAAAA
1 TAAAAATA-TTTAAAATTTTAAAA
*
2220680 TAAAAATATTTAATATTTTAA
1 TAAAAATATTTAAAATTTTAA
2220701 TTTTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAAATATTTAAAATTTTAAAA
Found at i:2226221 original size:131 final size:131
Alignment explanation
Indices: 2226031--2226290 Score: 380
Period size: 131 Copynumber: 2.0 Consensus size: 131
2226021 CTTGAGGATG
* * *
2226031 CATACATGAATATAGTCACTGTGACTGGAAACAGTAAGCCGATGAGCAAATTTTAAATGAAATGA
1 CATACATGAAAATAGTCACAGTGACTGGAAACAGTAAGCCAATGAGCAAATTTTAAATGAAATGA
* *
2226096 TCAAACGGTTCA-TGTTTTATATTATAGATGAATCATCCAATACCATTTTAAAATATTACACATT
66 TCAAACAGTTCATTG-TTTATATTATAGATGAATCATCCAACACCATTTTAAAATATTACACATT
2226160 TT
130 TT
* * *
2226162 CATACATGAAAATAGTCACAGTGACTGGAAACAGTAGGCTAATGCA-CAAATTTTAAATGAAATT
1 CATACATGAAAATAGTCACAGTGACTGGAAACAGTAAGCCAATG-AGCAAATTTTAAATGAAATG
* * * *
2226226 ATCAAACAGTTCCTTGTTTATATTATAGATGAGTCATCCAACGCCATTTTAAAATATTAGACATT
65 ATCAAACAGTTCATTGTTTATATTATAGATGAATCATCCAACACCATTTTAAAATATTACACATT
2226291 CACTTGATTG
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
131 112 0.97
132 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (131 bp):
CATACATGAAAATAGTCACAGTGACTGGAAACAGTAAGCCAATGAGCAAATTTTAAATGAAATGA
TCAAACAGTTCATTGTTTATATTATAGATGAATCATCCAACACCATTTTAAAATATTACACATTT
T
Done.