Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002022.1 Hibiscus syriacus cultivar Beakdansim tig00004131_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: 86359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:3412 original size:20 final size:20
Alignment explanation
Indices: 3387--3431 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3377 TTATTATTTT
* **
3387 ATATTGTTTGCTTCTGTTTG
1 ATATTGCTTGCTTCTACTTG
3407 ATATTGCTTGCTTCTACTTG
1 ATATTGCTTGCTTCTACTTG
3427 ATATT
1 ATATT
3432 TGTAAGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.56
Consensus pattern (20 bp):
ATATTGCTTGCTTCTACTTG
Found at i:3543 original size:22 final size:23
Alignment explanation
Indices: 3515--3561 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3505 GTATGTTTTC
3515 TTAATGC-AGGATGATTGCTGAA
1 TTAATGCAAGGATGATTGCTGAA
* *
3537 TTAATGCAATGATGCTTGCTGAA
1 TTAATGCAAGGATGATTGCTGAA
3560 TT
1 TT
3562 GGTACATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (23 bp):
TTAATGCAAGGATGATTGCTGAA
Found at i:4186 original size:19 final size:20
Alignment explanation
Indices: 4162--4202 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
4152 TTTATAATAT
*
4162 AAGAATTATAATTAATA-AA
1 AAGAATTAGAATTAATATAA
*
4181 AAGAATTGGAATTAATATAA
1 AAGAATTAGAATTAATATAA
4201 AA
1 AA
4203 ACTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (20 bp):
AAGAATTAGAATTAATATAA
Found at i:4690 original size:26 final size:26
Alignment explanation
Indices: 4632--4681 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4622 GAATATCGAA
*
4632 TGCATTTTATGCATCGATACACTCAG
1 TGCATTTGATGCATCGATACACTCAG
* *
4658 TGCATTTGATGCATTGATGCACTC
1 TGCATTTGATGCATCGATACACTC
4682 TGGCTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (26 bp):
TGCATTTGATGCATCGATACACTCAG
Found at i:5518 original size:16 final size:16
Alignment explanation
Indices: 5499--5537 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
5489 TGAGTTAATT
*
5499 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
5515 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
5531 ACAGGTC
1 ACAGGTC
5538 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:6105 original size:16 final size:16
Alignment explanation
Indices: 6084--6116 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6074 ATTCATACAG
6084 AACATTTGAATCATTC
1 AACATTTGAATCATTC
6100 AACATTTGAATCATTC
1 AACATTTGAATCATTC
6116 A
1 A
6117 GCGCTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (16 bp):
AACATTTGAATCATTC
Found at i:10918 original size:7 final size:7
Alignment explanation
Indices: 10906--10932 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
10896 TGTCACACCC
10906 CAATTTT
1 CAATTTT
10913 CAATTTT
1 CAATTTT
10920 CAATTTT
1 CAATTTT
10927 CAATTT
1 CAATTT
10933 ATAGAATTAA
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:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (7 bp):
CAATTTT
Found at i:13601 original size:25 final size:25
Alignment explanation
Indices: 13567--13619 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
13557 AGGTTTGTTT
* * *
13567 CTTGAAGTTGAAGTATAGTATGATA
1 CTTGAAGTTGAAGCAAAATATGATA
13592 CTTGAAGTTGAAGCAAAATATGATA
1 CTTGAAGTTGAAGCAAAATATGATA
13617 CTT
1 CTT
13620 TGCGGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (25 bp):
CTTGAAGTTGAAGCAAAATATGATA
Found at i:14844 original size:18 final size:19
Alignment explanation
Indices: 14821--14856 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
14811 TACATATGAA
14821 AAATATAATT-TAAAAATT
1 AAATATAATTGTAAAAATT
14839 AAATATAATTGTAAAAAT
1 AAATATAATTGTAAAAAT
14857 AAAACATCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AAATATAATTGTAAAAATT
Found at i:15424 original size:16 final size:15
Alignment explanation
Indices: 15373--15432 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 15
15363 ATTTAAATAC
*
15373 TAAACATATAATTCACT
1 TAAA-ATAT-ATTTACT
15390 TAAAATTATATATTA-T
1 TAAAA-TATAT-TTACT
15406 TAAAATATATTTATCT
1 TAAAATATATTTA-CT
15422 TAAAA-ATATTT
1 TAAAATATATTT
15433 TTAAATCAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 3 0.08
15 11 0.29
16 15 0.39
17 9 0.24
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATATATTTACT
Found at i:18474 original size:14 final size:14
Alignment explanation
Indices: 18455--18495 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
18445 CCGAACCGAA
18455 CCGAACCGAAAAAC
1 CCGAACCGAAAAAC
18469 CCGAACCGTTAAAAAAC
1 CCGAACCG---AAAAAC
18486 CCGAACCGAA
1 CCGAACCGAA
18496 CCGAAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
17 14 0.58
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (14 bp):
CCGAACCGAAAAAC
Found at i:19053 original size:3 final size:3
Alignment explanation
Indices: 19045--19081 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
19035 GCTGATACCG
19045 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19082 AAGAATGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:20153 original size:57 final size:57
Alignment explanation
Indices: 19927--20153 Score: 289
Period size: 57 Copynumber: 4.0 Consensus size: 57
19917 TATGTTTCTT
* * * *
19927 AATTTATATATTT-TGT-AATTTTAATTTGAAAGTTTCAAATTCTGACGTAATTCCTTTA
1 AATTT-TATATTTAT-TAAATTTGAACTTGAAAGTTTCAAATTCTGAGGTAATT-TTTTA
* * *
19985 AA-TTTATATTTATTAAATCTGAATTTGAAAGTTTCAAATTCTGAGGTAATTTTTAA
1 AATTTTATATTTATTAAATTTGAACTTGAAAGTTTCAAATTCTGAGGTAATTTTTTA
* *
20041 AATTTTATGTTTATTAAATTTCAACTTGAAAGTTTCAAATTCTGAGGTAATTTTTTA
1 AATTTTATATTTATTAAATTTGAACTTGAAAGTTTCAAATTCTGAGGTAATTTTTTA
* * * *
20098 AATTTTATTTTTATTAAATTTGAACTTGATAGTTTCAAATTCTTAGGTTATTTTTT
1 AATTTTATATTTATTAAATTTGAACTTGAAAGTTTCAAATTCTGAGGTAATTTTTT
20154 TACCGGTGAA
Statistics
Matches: 151, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
56 13 0.09
57 136 0.90
58 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (57 bp):
AATTTTATATTTATTAAATTTGAACTTGAAAGTTTCAAATTCTGAGGTAATTTTTTA
Found at i:21496 original size:7 final size:7
Alignment explanation
Indices: 21457--21538 Score: 73
Period size: 7 Copynumber: 11.7 Consensus size: 7
21447 TGTCCTTATA
21457 ATAAACC
1 ATAAACC
*
21464 CTAAACTC
1 ATAAAC-C
21472 -TAAATCC
1 ATAAA-CC
21479 -TAAACTC
1 ATAAAC-C
21486 -TAAACC
1 ATAAACC
*
21492 ATAAATC
1 ATAAACC
*
21499 ATAAATC
1 ATAAACC
21506 ATAAATCC
1 ATAAA-CC
21514 -TAAACC
1 ATAAACC
21520 ATAAACC
1 ATAAACC
21527 ATAAACC
1 ATAAACC
21534 ATAAA
1 ATAAA
21539 ACCCTAAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
6 4 0.06
7 59 0.89
8 3 0.05
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (7 bp):
ATAAACC
Found at i:21529 original size:28 final size:28
Alignment explanation
Indices: 21458--21538 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
21448 GTCCTTATAA
* *
21458 TAAACCCTAAACTC-TAAATCCTAAACTC
1 TAAACCATAAAC-CATAAATCATAAACTC
*
21486 TAAACCATAAATCATAAATCATAAA-TCC
1 TAAACCATAAACCATAAATCATAAACT-C
*
21514 TAAACCATAAACCATAAACCATAAA
1 TAAACCATAAACCATAAATCATAAA
21539 ACCCTAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.04
28 44 0.96
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (28 bp):
TAAACCATAAACCATAAATCATAAACTC
Found at i:23398 original size:11 final size:11
Alignment explanation
Indices: 23382--23420 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
23372 GCACTCGAGT
23382 TTGAATTGAGC
1 TTGAATTGAGC
**
23393 TTGAATTGAAT
1 TTGAATTGAGC
23404 TTGAATTGAGC
1 TTGAATTGAGC
23415 TTGAAT
1 TTGAAT
23421 CAAGCTCGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (11 bp):
TTGAATTGAGC
Found at i:23515 original size:20 final size:20
Alignment explanation
Indices: 23492--23557 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
23482 GTTTGAGTCG
23492 AGTTTTAATATTATCTTTTT
1 AGTTTTAATATTATCTTTTT
** *
23512 AGTTCGAATATTATCTTTTG
1 AGTTTTAATATTATCTTTTT
23532 AGTTTTAATATTATCTTTTT
1 AGTTTTAATATTATCTTTTT
23552 AGTTTT
1 AGTTTT
23558 GAGTTCGAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (20 bp):
AGTTTTAATATTATCTTTTT
Found at i:23778 original size:24 final size:24
Alignment explanation
Indices: 23751--23796 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
23741 GGTTATTTTT
23751 TAAAAAATA-AAAAAAATTATTACG
1 TAAAAAATACAAAAAAA-TATTACG
23775 TAAAAAATACAAAAAAATATTA
1 TAAAAAATACAAAAAAATATTA
23797 TCATATCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
TAAAAAATACAAAAAAATATTACG
Found at i:24222 original size:206 final size:205
Alignment explanation
Indices: 23826--24215 Score: 615
Period size: 206 Copynumber: 1.9 Consensus size: 205
23816 CACTTTCATT
* * ** *
23826 TTGGTAGAGTGTAAGGCTCTTAACTTTGTGGTCGTGGGATCGAGTCTTACGGTGGGCAATTCATA
1 TTGGTAGAGCGTAAGGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCACGGTAGGCAATTCATA
* * * *
23891 ATTCGGAGGTCTCCCACGGAAGATACTCTTAATCTGGTTTTGGGGACAGCCTATTATCCTACCTT
66 ATTCGGAGATCTCCCACGAAAGATACTCTCAATCTGGTTTTGGGGACAGCCTACTATCCTACCTT
*
23956 TCCCTTATCCCATTACATATGGGAATAAGTGTAAGCTATTATTGATATGAGATTTTGAATTGCCC
131 TCCCTTATCCCATTACATATGGGAATAAGGGTAA-CTATTATTGATATGAGATTTTGAATTGCCC
24021 GTCTAGCTCAG
195 GTCTAGCTCAG
24032 TTGGTAGAGCGTAAGGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCACGGTAGGCAATTCATA
1 TTGGTAGAGCGTAAGGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCACGGTAGGCAATTCATA
* *
24097 ATTCGGAGATCTCCCACGAAAGATATTCTCAATCTGGTTTTAAGGGTA-A-CCTACTATCCTACC
66 ATTCGGAGATCTCCCACGAAAGATACTCTCAATCTGGTTTT--GGGGACAGCCTACTATCCTACC
*
24160 TTTCCCTTATCCCATTACATATGGGAATAAGGGTCA-TATTATTGATATGAGATTTT
129 TTTCCCTTATCCCATTACATATGGGAATAAGGGTAACTATTATTGATATGAGATTTT
24216 TTGAATTCTA
Statistics
Matches: 169, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
204 20 0.12
206 144 0.85
207 1 0.01
208 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (205 bp):
TTGGTAGAGCGTAAGGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCACGGTAGGCAATTCATA
ATTCGGAGATCTCCCACGAAAGATACTCTCAATCTGGTTTTGGGGACAGCCTACTATCCTACCTT
TCCCTTATCCCATTACATATGGGAATAAGGGTAACTATTATTGATATGAGATTTTGAATTGCCCG
TCTAGCTCAG
Found at i:24543 original size:13 final size:13
Alignment explanation
Indices: 24525--24556 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
24515 TTCTAGAAAA
24525 TATTTTCTATTTT
1 TATTTTCTATTTT
24538 TATTTTCTATTTT
1 TATTTTCTATTTT
*
24551 TGTTTT
1 TATTTT
24557 TAGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.78
Consensus pattern (13 bp):
TATTTTCTATTTT
Found at i:26332 original size:16 final size:18
Alignment explanation
Indices: 26311--26375 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 18
26301 CATTCTCCCA
26311 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
26327 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
*
26347 GTAATCTTACATTCTCACTG
1 GTAATCTT--ATTCCCACTG
*
26367 ATAATCTTA
1 GTAATCTTA
26376 CATTCTCATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 8 0.19
18 4 0.09
19 2 0.05
20 29 0.67
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:26349 original size:20 final size:20
Alignment explanation
Indices: 26328--26401 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
26318 TATTCCCTGG
*
26328 TAATCTTACATTCCCACTGG
1 TAATCTTACATTCCCACTGA
*
26348 TAATCTTACATTCTCACTGA
1 TAATCTTACATTCCCACTGA
* *
26368 TAATCTTACATTCTCATTGA
1 TAATCTTACATTCCCACTGA
26388 TAATCTTACATTCC
1 TAATCTTACATTCC
26402 GTGAACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATCTTACATTCCCACTGA
Found at i:27469 original size:4 final size:4
Alignment explanation
Indices: 27462--27616 Score: 51
Period size: 4 Copynumber: 38.5 Consensus size: 4
27452 ATAGTAAGTA
* * * * *
27462 AAAT AAAT AAAT AAA- ATAT AAAAT AAAT AAAG AAAA AGAAG AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
* * *
27511 ATAT AAAT AAA- ATAAT -AAT AAA- AAGT -AA- AAAT AATAT ATAT ATAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT A-AAT
* *
27557 AAAT AAA- AACAT AAA- AATAGT AAAT ATATAT AAAT TAAT AAA- ACAT
1 AAAT AAAT AA-AT AAAT AA-A-T AAAT A-A-AT AAAT AAAT AAAT AAAT
27603 ATAAT AAA- AAAT AA
1 A-AAT AAAT AAAT AA
27617 CATATATATA
Statistics
Matches: 113, Mismatches: 17, Indels: 42
0.66 0.10 0.24
Matches are distributed among these distances:
3 20 0.18
4 68 0.60
5 20 0.18
6 5 0.04
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:27473 original size:20 final size:20
Alignment explanation
Indices: 27460--27497 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27450 AAATAGTAAG
27460 TAAAATAAATAAATAAAATA
1 TAAAATAAATAAATAAAATA
*
27480 TAAAATAAATAAAGAAAA
1 TAAAATAAATAAATAAAA
27498 AGAAGAAAAA
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:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
TAAAATAAATAAATAAAATA
Found at i:27488 original size:25 final size:25
Alignment explanation
Indices: 27447--27611 Score: 66
Period size: 25 Copynumber: 6.7 Consensus size: 25
27437 GAAAACAAAG
*
27447 ATAAAATAGT-AAGTAAAATAAATAA
1 ATAAAATA-TAAAATAAAATAAATAA
*
27472 ATAAAATATAAAAT-AAATAAAGAA
1 ATAAAATATAAAATAAAATAAATAA
* * *
27496 A-AAGA-A-GAAA-AAAATATATAA
1 ATAAAATATAAAATAAAATAAATAA
*
27517 ATAAAATA-ATAATAAAA-AGTAA-AA
1 ATAAAATATAAAATAAAATA--AATAA
*
27541 ATAATATATATATAAT-AAATAAA-AA
1 ATAA-A-ATATAAAATAAAATAAATAA
* *
27566 CATAAAA-ATAGTAAATATATATAAATTA
1 -ATAAAATATA--AAATA-AAATAAATAA
* *
27594 ATAAAACATATAATAAAA
1 ATAAAATATAAAATAAAA
27612 AATAACATAT
Statistics
Matches: 107, Mismatches: 15, Indels: 36
0.68 0.09 0.23
Matches are distributed among these distances:
21 12 0.11
22 4 0.04
23 10 0.09
24 22 0.21
25 23 0.21
26 14 0.13
27 18 0.17
28 4 0.04
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (25 bp):
ATAAAATATAAAATAAAATAAATAA
Found at i:27510 original size:57 final size:58
Alignment explanation
Indices: 27403--27533 Score: 137
Period size: 57 Copynumber: 2.3 Consensus size: 58
27393 AATGAAGAAA
* ** * * *
27403 AAAACAAATTAAATAAAAGATATGATAAAATAAAGAAAACAAAGATAAAATA-GTAAGT
1 AAAATAAA-TAAATAAAAGATAAAATAAAATAAAGAAAACAAAGAAAAAATATATAAAT
*
27461 AAAATAAATAAATAAAATATAAAAT-AAATAAAGAAAA-AGAAGAAAAAAATATATAAAT
1 AAAATAAATAAATAAAAGATAAAATAAAATAAAGAAAACA-AAG-AAAAAATATATAAAT
27519 AAAAT-AAT-AATAAAA
1 AAAATAAATAAATAAAA
27534 AGTAAAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
55 1 0.02
56 22 0.35
57 24 0.38
58 16 0.25
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.19
Consensus pattern (58 bp):
AAAATAAATAAATAAAAGATAAAATAAAATAAAGAAAACAAAGAAAAAATATATAAAT
Found at i:27541 original size:33 final size:35
Alignment explanation
Indices: 27474--27563 Score: 84
Period size: 37 Copynumber: 2.6 Consensus size: 35
27464 ATAAATAAAT
27474 AAAATATA-AAAT-AAATAAAGAAAAAGAAG-AAA
1 AAAATATATAAATAAAATAAAGAAAAAGAAGAAAA
*
27506 AAAATATATAAATAAAATAATA-ATAAA-AAGTAAAA
1 AAAATATATAAATAAAATAA-AGAAAAAGAAG-AAAA
27541 ATAATATATATATAAT-AAATAAA
1 A-AA-ATATATA-AATAAAATAAA
27564 AACATAAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
32 8 0.16
33 7 0.14
34 10 0.20
35 5 0.10
36 3 0.06
37 13 0.27
38 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (35 bp):
AAAATATATAAATAAAATAAAGAAAAAGAAGAAAA
Found at i:27546 original size:27 final size:29
Alignment explanation
Indices: 27516--27589 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
27506 AAAATATATA
*
27516 AATAAA-ATAATAATAAAAA-GTAAAAAT
1 AATAAATATAATAATAAAAACATAAAAAT
27543 AATATATATATAATAAATAAAAACATAAAAAT
1 AATA-A-ATATAAT-AATAAAAACATAAAAAT
*
27575 AGTAAATATATATAA
1 AATAAATATA-ATAA
27590 ATTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 4 0.10
28 1 0.03
29 1 0.03
30 12 0.31
31 11 0.28
32 10 0.26
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (29 bp):
AATAAATATAATAATAAAAACATAAAAAT
Found at i:27558 original size:38 final size:38
Alignment explanation
Indices: 27479--27629 Score: 116
Period size: 38 Copynumber: 4.0 Consensus size: 38
27469 TAAATAAAAT
* * *
27479 ATAAAATAAATAAAGAAAAAG-AAGAAAAAAATATATA-A
1 ATAAAATAAAT-AATAAAAAGTAA-AAATATATATATATA
27517 ATAAAAT-AATAATAAAAAGTAAAAATAATATATATATA
1 ATAAAATAAATAATAAAAAGTAAAAAT-ATATATATATA
* * *
27555 AT-AAATAAAAACATAAAAA-TAGTAAATATATATAAATTA
1 ATAAAATAAATA-ATAAAAAGTA-AAAATATATATATA-TA
* * * *
27594 ATAAAACATATAATAAAAAAT-AACATATATATATAT
1 ATAAAATAAATAATAAAAAGTAAAAATATATATATAT
27630 GTAATCTAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
36 11 0.12
37 18 0.20
38 34 0.37
39 22 0.24
40 7 0.08
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (38 bp):
ATAAAATAAATAATAAAAAGTAAAAATATATATATATA
Found at i:27562 original size:34 final size:34
Alignment explanation
Indices: 27470--27599 Score: 108
Period size: 32 Copynumber: 3.9 Consensus size: 34
27460 TAAAATAAAT
* * *
27470 AAATAA-A-ATATAAAATAAATAAAGAAAAAGAAGA
1 AAATAATATATATATAATAAAT-AATAAAAAGTA-A
* * *
27504 AAAAAATATATAAATAAAATAATAATAAAAAGTAA
1 AAATAATATATATATAATA-AATAATAAAAAGTAA
*
27539 AAATAATATATATATAATAAATAA-AAACA-TAA
1 AAATAATATATATATAATAAATAATAAAAAGTAA
* *
27571 AAATAGTAAATATAT-ATAAATTAATAAAA
1 AAATAATATATATATAATAAA-TAATAAAA
27600 CATATAATAA
Statistics
Matches: 78, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
31 5 0.06
32 19 0.24
33 7 0.09
34 10 0.13
35 18 0.23
36 16 0.21
37 3 0.04
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.24
Consensus pattern (34 bp):
AAATAATATATATATAATAAATAATAAAAAGTAA
Found at i:27622 original size:36 final size:35
Alignment explanation
Indices: 27537--27626 Score: 101
Period size: 35 Copynumber: 2.5 Consensus size: 35
27527 AATAAAAAGT
27537 AAAAATAATATATATATAATAAATAAAAACATAAA
1 AAAAATAATATATATATAATAAATAAAAACATAAA
* * * *
27572 AATAGTAA-ATATATATAAATTAATAAAACATATAATA
1 AAAAATAATATATATAT-AATAAATAAAA-ACATAA-A
*
27609 AAAAATAACATATATATA
1 AAAAATAATATATATATA
27627 TATGTAATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
34 8 0.18
35 16 0.36
36 5 0.11
37 8 0.18
38 8 0.18
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (35 bp):
AAAAATAATATATATATAATAAATAAAAACATAAA
Found at i:28227 original size:37 final size:37
Alignment explanation
Indices: 28177--28288 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
28167 ATTCTTATGG
*
28177 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
28214 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
28251 ATCATATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
28288 A
1 A
28289 ACGCTATGTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:28972 original size:83 final size:84
Alignment explanation
Indices: 28783--29038 Score: 277
Period size: 83 Copynumber: 3.1 Consensus size: 84
28773 ACTCGACAAT
* * * * * * * *
28783 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTG-TCTCTG-AGTTG
1 TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCCT-TGAAGCTG
** * *
28846 AATGTAATCAAAATCAAAGGTC
63 AGCGTAATCAAACTCGAAGGTC
* * ** *
28868 TTTGATGACTGATAACCCTTCTTTCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGC
1 TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGC
* *
28932 GTAGTCGAACTCGAAGGTC
66 GTAATCAAACTCGAAGGTC
*
28951 TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGT
1 TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGC
29016 GTAATCAAACTCGAAGG-C
66 GTAATCAAACTCGAAGGTC
29034 TTTGT
1 TTTGT
29039 GTTTCAAGAG
Statistics
Matches: 145, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
82 2 0.01
83 80 0.55
84 27 0.19
85 36 0.25
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (84 bp):
TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGC
GTAATCAAACTCGAAGGTC
Found at i:29153 original size:36 final size:36
Alignment explanation
Indices: 29104--29340 Score: 165
Period size: 36 Copynumber: 6.7 Consensus size: 36
29094 TTTTTTTTTG
* *
29104 TGTTTCAAGAGAAACTGTCTCGAGAGGGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGGACAAAATT
*
29140 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGGACAAAA-TT
* *
29177 AG-TTCTAAAAGAAACTGTCTCAAG-GGAGACGAAATT
1 TGTTTC-AAAAGAAACTGTCTCAAGAGG-GACAAAATT
* *
29213 TGTTTCAAGGAA-AAGA-TAT-TCAA-A--G----ATTT
1 TGTTTCAA--AAGAA-ACTGTCTCAAGAGGGACAAAATT
** * * *
29242 TGTTTCAAGGGAAACTATCCCAAGAGAGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGGACAAAATT
** * *
29278 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGGACAA-AATT
**
29315 TGTTTCAAGGGAAACTGTCTCAAGAG
1 TGTTTCAAAAGAAACTGTCTCAAGAG
29341 AGAATTGTCT
Statistics
Matches: 166, Mismatches: 16, Indels: 37
0.76 0.07 0.17
Matches are distributed among these distances:
27 1 0.01
28 5 0.03
29 14 0.08
30 1 0.01
32 1 0.01
33 1 0.01
36 77 0.46
37 63 0.38
38 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGGGACAAAATT
Found at i:29317 original size:102 final size:102
Alignment explanation
Indices: 29138--29324 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
29128 AGGGACAAAA
* * *
29138 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTATCCCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
29203 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
** * **
29240 TTTGTTTCAAGGGAAACTATCCCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTCAAGA
1 TTTGTTTCAAAAGAAACTATCCCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCTCAAGA
29303 GAGAC-AAGATTTTGTTTCAAGG
65 GAGACGAA-A-TTTGTTTCAAGG
29325 GAAACTGTCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 3 0.04
101 27 0.36
102 44 0.59
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTATCCCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:30588 original size:32 final size:32
Alignment explanation
Indices: 30552--30640 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
30542 CCCAATATTC
*
30552 GATGTTGAATCTCAAAAAATACCCTAACATTT
1 GATGTTGAATCTCAAAAAATACCCTAACATCT
* * *
30584 GATGTTAAATCTCAAAAAATGCCCCAACATCT
1 GATGTTGAATCTCAAAAAATACCCTAACATCT
*
30616 GATGTTGAATCTTC-AAATATACCCT
1 GATGTTGAATC-TCAAAAAATACCCT
30641 CATTGTTCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 46 0.96
33 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATACCCTAACATCT
Found at i:31705 original size:14 final size:13
Alignment explanation
Indices: 31673--31723 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
31663 TTTTCTTCAA
31673 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
*
31685 GTTTCTCTTTGCTT
1 TTTTCTCTTTG-TT
31699 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
* *
31711 TTCTCTTTTTGTT
1 TTTTCTCTTTGTT
31724 CTGATTGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 14 0.44
13 7 0.22
14 11 0.34
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.75
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:34952 original size:33 final size:31
Alignment explanation
Indices: 34915--35032 Score: 82
Period size: 30 Copynumber: 3.7 Consensus size: 31
34905 GAAAAAGAAG
34915 AAAAAATATATAAATAAAATAATAATAAAAATT
1 AAAAAATA-ATAAAT-AAATAATAATAAAAATT
* * *
34948 -AAAAATAATATATATATAATAAATAAAAACAT
1 AAAAAATAATAAATAAATAAT-AATAAAAA-TT
* * *
34980 AAAAAATAGTAAATATAT-AT-ATATAAATT
1 AAAAAATAATAAATAAATAATAATAAAAATT
* *
35009 AATAAAA-CATATAATAAAAAATAA
1 AA-AAAATAATA-AATAAATAATAA
35033 CACATATATA
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
29 5 0.07
30 21 0.31
31 15 0.22
32 11 0.16
33 15 0.22
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.28
Consensus pattern (31 bp):
AAAAAATAATAAATAAATAATAATAAAAATT
Found at i:34954 original size:16 final size:16
Alignment explanation
Indices: 34875--34992 Score: 69
Period size: 18 Copynumber: 6.9 Consensus size: 16
34865 AAATAGTAAG
34875 TAAATAAATAATAAAATA
1 TAAA-AAATAATAAAA-A
*
34893 TAAATAAATAAAGAAAAA
1 TAAA-AAAT-AATAAAAA
*
34911 GAAGAAAA-AATATATAAA
1 TAA-AAAATAATA-A-AAA
34929 TAAAATAATAATAAAAA
1 TAAAA-AATAATAAAAA
* *
34946 TTAAAAATAATATATATA
1 TAAAAAATAATA-A-AAA
* *
34964 TAATAAATAA-AAACA
1 TAAAAAATAATAAAAA
*
34979 TAAAAAATAGTAAA
1 TAAAAAATAATAAA
34993 TATATATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
15 10 0.12
16 14 0.17
17 12 0.15
18 33 0.41
19 11 0.14
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAATAATAAAAA
Found at i:34963 original size:39 final size:40
Alignment explanation
Indices: 34920--35047 Score: 111
Period size: 42 Copynumber: 3.2 Consensus size: 40
34910 AGAAGAAAAA
* *
34920 ATATATAAATAAA-ATAATA-ATAAAAATTA-AAAATA-AT
1 ATATATAAATAAATA-AAAACATAAAAAATAGAAAATATAT
*
34957 ATATATATAATAAATAAAAACATAAAAAATAGTAAATATAT
1 ATATATA-AATAAATAAAAACATAAAAAATAGAAAATATAT
* * * * * *
34998 ATATATAAATTAATAAAACATATAATAAAAAATAACACATAT
1 ATATATAAATAAATAAAA-ACATAA-AAAATAGAAAATATAT
35040 ATATATAA
1 ATATATAA
35048 TCTAAAAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
37 7 0.09
38 9 0.12
39 10 0.14
40 15 0.20
41 14 0.19
42 19 0.26
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (40 bp):
ATATATAAATAAATAAAAACATAAAAAATAGAAAATATAT
Found at i:34985 original size:66 final size:66
Alignment explanation
Indices: 34862--34987 Score: 150
Period size: 65 Copynumber: 1.9 Consensus size: 66
34852 GAAAGCAAAG
* * *
34862 ATAAAATAGTAAGTAAATAAATAATAAAATATAAATAAATAAAGAAAAAGAAGAAAAAATATATA
1 ATAAAATAATAAGTAAATAAATAAAAAAATATAAATAAATAAAGAAAAACAAGAAAAAATATATA
34927 A
66 A
* * * *
34928 ATAAAATAATAA-TAAA-AATTAAAAATAATATATATATAATAAATAAAAAC-ATAAAAAATA
1 ATAAAATAATAAGTAAATAAATAAAAA-AATATAAATA-AATAAAGAAAAACAAGAAAAAATA
34988 GTAAATATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
64 7 0.14
65 22 0.43
66 22 0.43
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (66 bp):
ATAAAATAATAAGTAAATAAATAAAAAAATATAAATAAATAAAGAAAAACAAGAAAAAATATATA
A
Found at i:35650 original size:37 final size:37
Alignment explanation
Indices: 35600--35711 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
35590 ATGCTTCTGG
*
35600 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
35637 ATCCTATTTTTAGGAGTTTGAATCCTAGTACAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
35674 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
35711 A
1 A
35712 ACGCTATGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:43352 original size:45 final size:45
Alignment explanation
Indices: 43281--43368 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
43271 GTATTGAGCC
* *
43281 AGCAACAGATGTGTGCAGCAGCCCTGCTGAACCCAATACTGATGA
1 AGCAACAGATGCGTGCAACAGCCCTGCTGAACCCAATACTGATGA
* * **
43326 AGCAACAGATGCGTGTAACAGTCCTGCTGAACCTGATACTGAT
1 AGCAACAGATGCGTGCAACAGCCCTGCTGAACCCAATACTGAT
43369 AATCATCGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (45 bp):
AGCAACAGATGCGTGCAACAGCCCTGCTGAACCCAATACTGATGA
Found at i:45783 original size:43 final size:41
Alignment explanation
Indices: 45709--45937 Score: 137
Period size: 36 Copynumber: 6.0 Consensus size: 41
45699 TATATACATC
**
45709 TATATAT-TATATAA-TTTGCAAATGATTTTTGAAAAAATATA
1 TATATATATATATAATTTTG-AAAACA-TTTTGAAAAAATATA
*
45750 TATATATATAATATAATTTTGAAAACATGTTTGAAAACAT-T-
1 TATATATAT-ATATAATTTTGAAAACAT-TTTGAAAAAATATA
*
45791 TATATAT-TATATAGTTTT-AAAACATTTTG-AAAAATATA
1 TATATATATATATAATTTTGAAAACATTTTGAAAAAATATA
* *
45829 TAGT-T-T-T-T-TAA----AAAAACATTTTGAAAACATATA
1 TA-TATATATATATAATTTTGAAAACATTTTGAAAAAATATA
* *
45862 GATAT-TATAT--AATTTTGAAATCATTTT--AAAAAT-T-
1 TATATATATATATAATTTTGAAAACATTTTGAAAAAATATA
* * * *
45896 TATATA-ATATATAGTTTTAAAAACATTTTTAAAAACTATA
1 TATATATATATATAATTTTGAAAACATTTTGAAAAAATATA
45936 TA
1 TA
45938 ATTTTGAAAA
Statistics
Matches: 149, Mismatches: 16, Indels: 47
0.70 0.08 0.22
Matches are distributed among these distances:
32 12 0.08
33 11 0.07
34 11 0.07
35 4 0.03
36 25 0.17
37 7 0.05
38 24 0.16
39 11 0.07
40 3 0.02
41 14 0.09
42 3 0.02
43 20 0.13
44 4 0.03
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (41 bp):
TATATATATATATAATTTTGAAAACATTTTGAAAAAATATA
Found at i:45913 original size:105 final size:110
Alignment explanation
Indices: 45749--45942 Score: 299
Period size: 108 Copynumber: 1.8 Consensus size: 110
45739 GAAAAAATAT
* *
45749 ATATATATATAATATAATTTTGAAAACATGTTTGAAAACATTTATATATTATATAGTTTT-AAAA
1 ATATAGATATAATATAATTTTGAAAACATGTTTGAAAACATTTATATAATATATAGTTTTAAAAA
*
45813 CATTTTGAAAAA-TATATAGTTTTTTAAAAAAACATTTTGAAAAC
66 CATTTTGAAAAACTATATAATTTTTTAAAAAAACATTTTGAAAAC
* *
45857 ATATAGATATTATATAATTTTGAAATCAT-TTT-AAAA-ATTTATATAATATATAGTTTTAAAAA
1 ATATAGATATAATATAATTTTGAAAACATGTTTGAAAACATTTATATAATATATAGTTTTAAAAA
*
45919 CATTTTTAAAAACTATATAATTTT
66 CATTTTGAAAAACTATATAATTTT
45943 GAAAACATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
105 20 0.26
106 19 0.24
107 13 0.17
108 26 0.33
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (110 bp):
ATATAGATATAATATAATTTTGAAAACATGTTTGAAAACATTTATATAATATATAGTTTTAAAAA
CATTTTGAAAAACTATATAATTTTTTAAAAAAACATTTTGAAAAC
Found at i:45926 original size:29 final size:29
Alignment explanation
Indices: 45903--45959 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
45893 ATTTATATAA
*
45903 TATATAGTTTTAAAAACATTTTTAAAAAC
1 TATATAATTTTAAAAACATTTTTAAAAAC
*
45932 TATATAATTTTGAAAACATTTTTAAAAA
1 TATATAATTTTAAAAACATTTTTAAAAA
45960 AAATTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (29 bp):
TATATAATTTTAAAAACATTTTTAAAAAC
Found at i:45968 original size:30 final size:29
Alignment explanation
Indices: 45904--45969 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
45894 TTTATATAAT
* **
45904 ATATAGTTTTAAAAACATTTTTAAAAACT
1 ATATAATTTTAAAAACATTTTTAAAAAAA
*
45933 ATATAATTTTGAAAACATTTTTAAAAAAA
1 ATATAATTTTAAAAACATTTTTAAAAAAA
45962 ATTATAAT
1 A-TATAAT
45970 ATATATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (29 bp):
ATATAATTTTAAAAACATTTTTAAAAAAA
Found at i:46004 original size:68 final size:65
Alignment explanation
Indices: 45867--45997 Score: 167
Period size: 68 Copynumber: 2.0 Consensus size: 65
45857 ATATAGATAT
* * * *
45867 TATATAATTTTGAAATCATTTTAAAAATTTATATAATATATAGTTTTAAAAACATTTTTAAAAAC
1 TATATAATTTTGAAAACATTTTAAAAAATTATATAATATATAATTTTAAAAACATTTTGAAAAAC
45932 TATATAATTTTGAAAACATTTTTAAAAAAAATTATA-ATATATATAATTTTAAAATAC-TTTTGA
1 TATATAATTTTGAAAACA-TTTT--AAAAAATTATATA-ATATATAATTTTAAAA-ACATTTTGA
45995 AAA
61 AAA
45998 TATATATTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
65 17 0.30
66 4 0.07
67 1 0.02
68 33 0.58
69 2 0.04
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (65 bp):
TATATAATTTTGAAAACATTTTAAAAAATTATATAATATATAATTTTAAAAACATTTTGAAAAAC
Found at i:46033 original size:2 final size:2
Alignment explanation
Indices: 46024--46052 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
46014 TTTTTGGAAA
46024 AT AT -T 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
46053 TATTGTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:46147 original size:15 final size:15
Alignment explanation
Indices: 46127--46162 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
46117 TGTAGGGTCT
*
46127 GGTCCAGTCCAGCAG
1 GGTCCAGTCCAACAG
46142 GGTCCAGTCCAACAG
1 GGTCCAGTCCAACAG
*
46157 AGTCCA
1 GGTCCA
46163 AATGAAGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.14
Consensus pattern (15 bp):
GGTCCAGTCCAACAG
Found at i:47372 original size:5 final size:5
Alignment explanation
Indices: 47362--47394 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
47352 TTATTATTTA
47362 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTA
47395 TTTGGTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:47418 original size:3 final size:3
Alignment explanation
Indices: 47406--47447 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
47396 TTGGTATACA
*
47406 TAT T-T TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
47448 TTCTTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:48529 original size:38 final size:35
Alignment explanation
Indices: 48487--48568 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 35
48477 TATTTTCAAA
* *
48487 ATTATATAGTTTTCAAAAATGTTTTTTTAAAACTATAT
1 ATTATATAGTTTT-AAAAATG--ATTTCAAAACTATAT
*
48525 ATTATATAAGTTTTTAAAATGATTTCAAAACTATAT
1 ATTATAT-AGTTTTAAAAATGATTTCAAAACTATAT
*
48561 AATATATA
1 ATTATATA
48569 TATATATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
35 1 0.03
36 19 0.49
38 13 0.33
39 6 0.15
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (35 bp):
ATTATATAGTTTTAAAAATGATTTCAAAACTATAT
Found at i:48657 original size:37 final size:37
Alignment explanation
Indices: 48565--48799 Score: 211
Period size: 37 Copynumber: 6.3 Consensus size: 37
48555 CTATATAATA
* *
48565 TATATATATATATTTTTTTTCAAAATATTTTTTTAAAA-
1 TATATA-ATATATTTATTTTCAAAATA-TTTTTAAAAAC
* *
48603 TA-CT-ATATA--T-TTTTCAAAATATTTTTAAAAAT
1 TATATAATATATTTATTTTCAAAATATTTTTAAAAAC
48635 TATATAATATATTTATTTTCAAAA-ATATTTTAAAAAC
1 TATATAATATATTTATTTTCAAAATAT-TTTTAAAAAC
*
48672 TATATATTATATTTATTTTCAAAATA-TTTTAAAAAC
1 TATATAATATATTTATTTTCAAAATATTTTTAAAAAC
* * *
48708 TATATAATATATAAATATTTTCAAACAT-GTTTTCAAAAC
1 TATATAATATAT--TTATTTTCAAA-ATATTTTTAAAAAC
* *
48747 TATATATTATATATATATATTTTCAAAA-ACTATTTACAAAC
1 TATATA--ATATAT-T-TATTTTCAAAATA-TTTTTAAAAAC
48788 TATATAATATAT
1 TATATAATATAT
48800 ATATAGATGT
Statistics
Matches: 167, Mismatches: 13, Indels: 33
0.78 0.06 0.15
Matches are distributed among these distances:
31 9 0.05
32 13 0.08
33 2 0.01
34 5 0.03
35 5 0.03
36 24 0.14
37 42 0.25
38 13 0.08
39 23 0.14
40 2 0.01
41 29 0.17
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (37 bp):
TATATAATATATTTATTTTCAAAATATTTTTAAAAAC
Found at i:48660 original size:116 final size:114
Alignment explanation
Indices: 48449--48688 Score: 265
Period size: 115 Copynumber: 2.1 Consensus size: 114
48439 ATTTTAAAAT
* *
48449 TATATATATTATAGTTTTTTTTTAAAAATATTTTCAAAATTATATAGTTTTCAAAAATGTTTTTT
1 TATATATATTATAGTTTTTTTTCAAAAATATTTTCAAAATTATATAGTTTTCAAAAATGATTTTT
* * * *
48514 TAAAACTATATATTATATAAGTTTTTAAAATGA-TTTCAAAACTATATAA
66 AAAAACTATATAATATATAAGTTTTAAAAAT-ATTTTAAAAACTATATAA
* * *
48563 TATATATATATATA-TTTTTTTTCAAAATATTTTTTTAAAATACTATATATTTTTC-AAAAT-AT
1 TATATATAT-TATAGTTTTTTTTCAAAA-ATATTTTCAAAAT--TATATAGTTTTCAAAAATGAT
* * *
48625 TTTTAAAAATTATATAATATATTTA-TTTTCAAAAATATTTTAAAAACTATATAT
62 TTTTAAAAACTATATAATATA-TAAGTTTT-AAAAATATTTTAAAAACTATATAA
*
48679 TATATTTATT
1 TATATATATT
48689 TTCAAAATAT
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
114 21 0.20
115 40 0.38
116 34 0.32
117 11 0.10
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (114 bp):
TATATATATTATAGTTTTTTTTCAAAAATATTTTCAAAATTATATAGTTTTCAAAAATGATTTTT
AAAAACTATATAATATATAAGTTTTAAAAATATTTTAAAAACTATATAA
Found at i:48746 original size:75 final size:79
Alignment explanation
Indices: 48606--48800 Score: 253
Period size: 75 Copynumber: 2.5 Consensus size: 79
48596 TTTAAAATAC
* * *
48606 TATATAT-TTTTCAAAATATTTTTAAAAATTATATAATATAT-TTATTTTCAAAAATATTTTAAA
1 TATATATATTTTCAAAATACTTTTAAAAACTATATAATATATAATATTTTCAAAAATATTTTAAA
48669 AACTATATA-T-TA
66 AACTATATATTATA
* * *
48681 TAT-T-TATTTTCAAAATA-TTTTAAAAACTATATAATATATAAATATTTTCAAACATGTTTTCA
1 TATATATATTTTCAAAATACTTTTAAAAACTATATAATATAT-AATATTTTCAAAAATATTTTAA
48743 AAACTATATATTATA
65 AAACTATATATTATA
*
48758 TATATATATTTTCAAAA-ACTATTTACAAACTATATAATATATA
1 TATATATATTTTCAAAATACT-TTTAAAAACTATATAATATATA
48801 TATAGATGTA
Statistics
Matches: 105, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
73 22 0.21
74 12 0.11
75 30 0.29
76 1 0.01
77 5 0.05
78 2 0.02
79 13 0.12
80 20 0.19
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.46
Consensus pattern (79 bp):
TATATATATTTTCAAAATACTTTTAAAAACTATATAATATATAATATTTTCAAAAATATTTTAAA
AACTATATATTATA
Found at i:48803 original size:39 final size:38
Alignment explanation
Indices: 48601--48804 Score: 222
Period size: 39 Copynumber: 5.3 Consensus size: 38
48591 ATTTTTTTAA
* *
48601 AATACTATATAT-TTTTCAAAATATTTTTAAAAATTATAT
1 AATA-TATATATATTTTCAAAA-ATATTTAAAAACTATAT
48640 AATATAT-T-TATTTTCAAAAATATTTTAAAAACTATAT
1 AATATATATATATTTTCAAAAATA-TTTAAAAACTATAT
*
48677 -AT-TATATTTATTTTC-AAAATATTTTAAAAACTATAT
1 AATATATATATATTTTCAAAAATA-TTTAAAAACTATAT
* * * *
48713 AATATATAAATATTTTCAAACATGTTTTCAAAACTATAT
1 AATATATATATATTTTCAAAAAT-ATTTAAAAACTATAT
*
48752 ATTATATATATATATTTTCAAAAACTATTTACAAACTATAT
1 A--ATATATATATATTTTCAAAAA-TATTTAAAAACTATAT
48793 AATATATATATA
1 AATATATATATA
48805 GATGTAATAA
Statistics
Matches: 142, Mismatches: 12, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
35 3 0.02
36 27 0.19
37 32 0.23
38 14 0.10
39 33 0.23
41 32 0.23
42 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (38 bp):
AATATATATATATTTTCAAAAATATTTAAAAACTATAT
Found at i:52645 original size:20 final size:20
Alignment explanation
Indices: 52620--52673 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
52610 GACCAACAAA
52620 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
52640 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
*
52660 TTCGCAACGTGAAT
1 TTCGCAACGCGAAT
52674 ATGTAAATCG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:52720 original size:20 final size:20
Alignment explanation
Indices: 52697--52781 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
52687 TGCGATTTTC
52697 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*** *
52717 CAAATTCGCGTTGCGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
*
52739 -AAA-TCGCAACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
*
52757 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
52777 CAAAT
1 CAAAT
52782 GTTTTTACGC
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
18 2 0.04
19 4 0.08
20 36 0.75
21 4 0.08
22 2 0.04
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:52731 original size:41 final size:41
Alignment explanation
Indices: 52652--52766 Score: 103
Period size: 41 Copynumber: 2.8 Consensus size: 41
52642 CGCAACCCAG
* * * *
52652 TTTCCAATTTCGCAACGTGAATATGT-AAA-TCGTATTGCGAT
1 TTTCCAAATTCGCAACGCGAA-A-GTCAAATTCGCATTGCGAA
*
52693 TTTCCAAATTCGCAACGCGAAAGTCAAATTCGCGTTGCGAA
1 TTTCCAAATTCGCAACGCGAAAGTCAAATTCGCATTGCGAA
** *
52734 TTTGTAAA-TCGCAACAC-AGAAGTCAAATTCGCA
1 TTTCCAAATTCGCAACGCGA-AAGTCAAATTCGCA
52767 ACGTGAAAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
39 3 0.05
40 25 0.40
41 34 0.55
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (41 bp):
TTTCCAAATTCGCAACGCGAAAGTCAAATTCGCATTGCGAA
Found at i:52939 original size:22 final size:22
Alignment explanation
Indices: 52914--52960 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
52904 GGCGACATCT
*
52914 GTCCCCATCTCCGTCAAAATCC
1 GTCCCCATCTCCGACAAAATCC
* *
52936 GTCCCCATTTCCGACGAAATCC
1 GTCCCCATCTCCGACAAAATCC
52958 GTC
1 GTC
52961 TATCTCCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.43, G:0.13, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCC
Found at i:53289 original size:40 final size:40
Alignment explanation
Indices: 53234--53317 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
53224 AATGCAAAAA
*
53234 TCGCAATGCGAAAATTAAATCACGTTGCGATTTTCATTTT
1 TCGCAATGCAAAAATTAAATCACGTTGCGATTTTCATTTT
53274 TCGCAATGCAAAAATTAAATCACGTTGCGATTTTCATTTT
1 TCGCAATGCAAAAATTAAATCACGTTGCGATTTTCATTTT
53314 TCGC
1 TCGC
53318 GTTGCGATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (40 bp):
TCGCAATGCAAAAATTAAATCACGTTGCGATTTTCATTTT
Found at i:53336 original size:20 final size:21
Alignment explanation
Indices: 53296--53344 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
53286 AATTAAATCA
53296 CGTTGCGATTTTCATTTTTCG
1 CGTTGCGATTTTCATTTTTCG
53317 CGTTGCGATTTTCA-TTTTCG
1 CGTTGCGATTTTCATTTTTCG
*
53337 CATTGCGA
1 CGTTGCGA
53345 ATTTAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (21 bp):
CGTTGCGATTTTCATTTTTCG
Found at i:53348 original size:21 final size:21
Alignment explanation
Indices: 53298--53344 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
53288 TTAAATCACG
*
53298 TTGCGATTTTCATTTTTCGCG
1 TTGCGATTTTCATTTTTCGCA
53319 TTGCGATTTTCA-TTTTCGCA
1 TTGCGATTTTCATTTTTCGCA
53339 TTGCGA
1 TTGCGA
53345 ATTTAAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (21 bp):
TTGCGATTTTCATTTTTCGCA
Found at i:53355 original size:20 final size:20
Alignment explanation
Indices: 53312--53355 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
53302 GATTTTCATT
* * * *
53312 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTGCGAATTTAAG
53332 TTTCGCATTGCGAATTTAAG
1 TTTCGCATTGCGAATTTAAG
53352 TTTC
1 TTTC
53356 AGAAACTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTAAG
Found at i:55608 original size:21 final size:21
Alignment explanation
Indices: 55559--55614 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
55549 GAATCCCCTC
55559 CCACCGTTCAAGAGGTCCCCG
1 CCACCGTTCAAGAGGTCCCCG
* *
55580 TCATCGTTCAAGAGGT-CCCG
1 CCACCGTTCAAGAGGTCCCCG
*
55600 CCCGCCGTTCAAGAG
1 -CCACCGTTCAAGAG
55615 CCCGATTCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.20, C:0.38, G:0.25, T:0.18
Consensus pattern (21 bp):
CCACCGTTCAAGAGGTCCCCG
Found at i:57234 original size:20 final size:20
Alignment explanation
Indices: 57211--57253 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
57201 AATTTTCGGT
*
57211 TTGCGAATTTGACTTTCGTG
1 TTGCGAATTTGACTTTCGCG
57231 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
57251 TTG
1 TTG
57254 ATCGCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:57481 original size:39 final size:39
Alignment explanation
Indices: 57427--57513 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
57417 TCAAGTTGTA
* *
57427 GATTTTAATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
57466 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
57505 GATTTTGAT
1 GATTTTGAT
57514 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:57787 original size:25 final size:25
Alignment explanation
Indices: 57757--57814 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
57747 ATTTATACAT
*
57757 ACAATGTTCAAATAATGTACCCATA
1 ACAATGTTCAAATAATGTACCCACA
57782 ACAATGTTCAAATAATGTACCCACA
1 ACAATGTTCAAATAATGTACCCACA
57807 ACAATGTT
1 ACAATGTT
57815 TAATTGATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (25 bp):
ACAATGTTCAAATAATGTACCCACA
Found at i:57968 original size:20 final size:20
Alignment explanation
Indices: 57904--57960 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
57894 AAATAAGCGT
*
57904 TGCGATAGTCAAATTCGCAA
1 TGCGAAAGTCAAATTCGCAA
57924 TGCGAAAGTCAAATTCGCAA
1 TGCGAAAGTCAAATTCGCAA
*
57944 CGCGAAAGTCAAATTCG
1 TGCGAAAGTCAAATTCG
57961 GTTTGCGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TGCGAAAGTCAAATTCGCAA
Found at i:58307 original size:18 final size:18
Alignment explanation
Indices: 58284--58319 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58274 AAGCCGGTTG
*
58284 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
58302 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
58320 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:60378 original size:3 final size:3
Alignment explanation
Indices: 60370--60409 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
60360 TCTTCGGGGA
60370 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
60410 AGGGTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:60784 original size:12 final size:12
Alignment explanation
Indices: 60763--60796 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
60753 AGTTGTGGGT
*
60763 TTTGAGATTGTG
1 TTTGATATTGTG
60775 TTTGATATTGTG
1 TTTGATATTGTG
*
60787 TTTGGTATTG
1 TTTGATATTG
60797 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:61477 original size:20 final size:21
Alignment explanation
Indices: 61440--61479 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
61430 AAATTAAGTT
61440 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
61461 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
61480 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:61714 original size:19 final size:19
Alignment explanation
Indices: 61690--61728 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
61680 TCGAATGCAT
61690 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
61709 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
61728 T
1 T
61729 GAATATTTTC
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:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:61853 original size:64 final size:65
Alignment explanation
Indices: 61676--61838 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
61666 GAATTAATTG
* * * *
61676 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
61741 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
61804 A
65 A
61805 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
61839 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:62736 original size:19 final size:19
Alignment explanation
Indices: 62714--62802 Score: 133
Period size: 19 Copynumber: 4.6 Consensus size: 19
62704 CTAAATTTGT
62714 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
62733 GTTGCGATTTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
62752 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
62771 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
62792 GTTGCGAATTT
1 GTTGCGAATTT
62803 TTGACTTTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 51 0.81
20 1 0.02
21 11 0.17
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.39
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:62737 original size:38 final size:38
Alignment explanation
Indices: 62695--62802 Score: 101
Period size: 38 Copynumber: 2.8 Consensus size: 38
62685 AAACATTTGT
**
62695 GTTGCGAAACT-AAATTTGTGTTGCGAATTTGAAATTCA
1 GTTGCGAAACTGAAA-TTCAGTTGCGAATTTGAAATTCA
*** *
62733 GTTGCGATTTTGAAATTCAGTTGTGAATTTGAAATTCA
1 GTTGCGAAACTGAAATTCAGTTGCGAATTTGAAATTCA
** *
62771 GTTGCGAATTTGAAATTCCGCGTTGCGAATTT
1 GTTGCGAAACTGAAATT-C-AGTTGCGAATTT
62803 TTGACTTTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
38 44 0.76
39 4 0.07
40 10 0.17
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (38 bp):
GTTGCGAAACTGAAATTCAGTTGCGAATTTGAAATTCA
Found at i:62827 original size:20 final size:20
Alignment explanation
Indices: 62802--62860 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
62792 GTTGCGAATT
62802 TTTGACTTTTGTGTTACGAA
1 TTTGACTTTTGTGTTACGAA
* * *
62822 TTTGACTATTGCGTTGCGAA
1 TTTGACTTTTGTGTTACGAA
*
62842 TTTGACTTCTGTGTTACGA
1 TTTGACTTTTGTGTTACGA
62861 TTTACAAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.46
Consensus pattern (20 bp):
TTTGACTTTTGTGTTACGAA
Found at i:62876 original size:40 final size:43
Alignment explanation
Indices: 62775--62877 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 43
62765 AATTCAGTTG
*
62775 CGAATTTG--AAATTCCGCGTTGCGAATTTTTGACTTTTGTGTTA
1 CGAATTTGACAAATT-CGCGTTGCGAA-TTTTGACTTCTGTGTTA
*
62818 CGAATTTGAC-TATT-GCGTTGCGAA-TTTGACTTCTGTGTTA
1 CGAATTTGACAAATTCGCGTTGCGAATTTTGACTTCTGTGTTA
62858 CG-ATTT-ACAAATTCGCGTTG
1 CGAATTTGACAAATTCGCGTTG
62878 TGATTTACAG
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
38 2 0.04
39 7 0.13
40 23 0.43
42 10 0.19
43 8 0.15
44 3 0.06
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (43 bp):
CGAATTTGACAAATTCGCGTTGCGAATTTTGACTTCTGTGTTA
Found at i:62884 original size:20 final size:20
Alignment explanation
Indices: 62859--62897 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
62849 TCTGTGTTAC
62859 GATTTACAAATTCGCGTTGT
1 GATTTACAAATTCGCGTTGT
*
62879 GATTTACAGATTCGCGTTG
1 GATTTACAAATTCGCGTTG
62898 CGAAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (20 bp):
GATTTACAAATTCGCGTTGT
Found at i:62923 original size:21 final size:21
Alignment explanation
Indices: 62897--62963 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
62887 GATTCGCGTT
62897 GCGAAATTGGAAAA-CTGCAAC
1 GCGAAATTGGAAAATC-GCAAC
62918 GCGAAATTGGAAAATCGCAAC
1 GCGAAATTGGAAAATCGCAAC
* *
62939 GCGAATTTGGAAAATCGCAAT
1 GCGAAATTGGAAAATCGCAAC
62960 GCGA
1 GCGA
62964 TTTACATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
GCGAAATTGGAAAATCGCAAC
Found at i:66374 original size:77 final size:77
Alignment explanation
Indices: 66287--66449 Score: 204
Period size: 77 Copynumber: 2.1 Consensus size: 77
66277 TATATATAAG
* * * * *
66287 AAATACGGTTGCGCCCAATAATATCATGGTTCAGTAAGAAA-CATATTGCAATAT-GTAATGTTA
1 AAATA-GGTTGCGCCCAAAAATATCACGATTCAGTAAGAAATCAGATTGCAATATCG-AATCTTA
66350 ATATTTTTATTAATA
64 ATATTTTTA-TAATA
* * * *
66365 AAATAGGTTGTGCCCAAAAATATCACGATTCATTAAGAAATCAGGTTGTAATATCGAATCTTAAT
1 AAATAGGTTGCGCCCAAAAATATCACGATTCAGTAAGAAATCAGATTGCAATATCGAATCTTAAT
66430 ATTTTTATAATA
66 ATTTTTATAATA
66442 AAATAGGT
1 AAATAGGT
66450 GTGCCTAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
77 43 0.58
78 30 0.41
79 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (77 bp):
AAATAGGTTGCGCCCAAAAATATCACGATTCAGTAAGAAATCAGATTGCAATATCGAATCTTAAT
ATTTTTATAATA
Found at i:66629 original size:77 final size:76
Alignment explanation
Indices: 66529--66765 Score: 232
Period size: 81 Copynumber: 3.0 Consensus size: 76
66519 TACGATTGCA
* * *
66529 CCCAAGAATGTCATAGTTCACTAAGAAATAGGTTGTGATC-TGAAATGTTAATATTTTTATTAAT
1 CCCAAGAATGTCATGGTTCACTAAGAAATAGGTTGCGATCATGTAATGTTAATATTTTTATTAAT
66593 ACAATGAGTTGTG
66 A-AAT-AGTTGTG
* * * * *
66606 TCCAAGAATGTTATGGTACACTAAGAAAGTTGGTTGCAATCTTTAATGTAATGTTAAT-TTTTT-
1 CCCAAGAATGTCATGGTTCACTAAGAAA-TAGGTTGCGATC----ATGTAATGTTAATATTTTTA
*
66669 TTAATAAAATAGATTGCG
61 TTAAT-AAATAG-TTGTG
* * *
66687 CCCAAGAATGTCATGGTTCACAAAGAAATAAGTTGCGA-CATGTTATGTTAATATTTTTA-TAAT
1 CCCAAGAATGTCATGGTTCACTAAGAAATAGGTTGCGATCATGTAATGTTAATATTTTTATTAA-
66750 TAAATAAGTTGTG
65 TAAAT-AGTTGTG
66763 CCC
1 CCC
66766 TAAAATATAA
Statistics
Matches: 130, Mismatches: 18, Indels: 25
0.75 0.10 0.14
Matches are distributed among these distances:
75 12 0.09
76 19 0.15
77 27 0.21
78 9 0.07
79 1 0.01
80 9 0.07
81 36 0.28
82 6 0.05
83 11 0.08
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (76 bp):
CCCAAGAATGTCATGGTTCACTAAGAAATAGGTTGCGATCATGTAATGTTAATATTTTTATTAAT
AAATAGTTGTG
Found at i:67436 original size:77 final size:77
Alignment explanation
Indices: 67290--67438 Score: 212
Period size: 77 Copynumber: 1.9 Consensus size: 77
67280 AATTTCAATT
* *
67290 TTTTATAATAAAAATATTAACATTCTAGATCGCAACTTACTTTCTTATTGAACCATAACATTCTT
1 TTTTATAATAAAAATATTAACATTCTAGATCACAACTTACTTTCTTAGTGAACCATAACATTCTT
67355 GGGTGCATCCCA
66 GGGTGCATCCCA
* * * *
67367 TTTTATTAATAAAAATATTAACATT-TCATATCACAACTTA-TTTCTTAGTGGATCATTACATTC
1 TTTTA-TAATAAAAATATTAACATTCT-AGATCACAACTTACTTTCTTAGTGAACCATAACATTC
67430 TTGGGTGCA
64 TTGGGTGCA
67439 ACCGTATTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
77 34 0.53
78 30 0.47
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (77 bp):
TTTTATAATAAAAATATTAACATTCTAGATCACAACTTACTTTCTTAGTGAACCATAACATTCTT
GGGTGCATCCCA
Found at i:67788 original size:18 final size:18
Alignment explanation
Indices: 67752--67785 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
67742 TATTAAACTT
*
67752 TCTAATTACATGAAATTA
1 TCTAATTACATCAAATTA
67770 TCTAATT-CATCAAATT
1 TCTAATTACATCAAATT
67786 TATAGGGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (18 bp):
TCTAATTACATCAAATTA
Found at i:67849 original size:18 final size:19
Alignment explanation
Indices: 67814--67850 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
67804 CACGGAATGT
67814 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
67834 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
67851 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:74022 original size:36 final size:36
Alignment explanation
Indices: 73975--74047 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
73965 CTGCCTCAAA
*
73975 ACTAAGAGATTGATGCTCTTTACCTCAGAATCCAAC
1 ACTAAGAGATTGATGCTCTGTACCTCAGAATCCAAC
74011 ACTAAGAGATTGATGCTCTGTACCTCAGAATCCAAC
1 ACTAAGAGATTGATGCTCTGTACCTCAGAATCCAAC
74047 A
1 A
74048 TTCTTTCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (36 bp):
ACTAAGAGATTGATGCTCTGTACCTCAGAATCCAAC
Found at i:76668 original size:111 final size:111
Alignment explanation
Indices: 76538--76760 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
76528 TTTTATAATT
76538 ATAATTATTATATTTTATAATAAGTGATGTAAATTTTAAAAAGAATTTACGTCTGTGACAATTAC
1 ATAATTATTATATTTTATAATAAGTGATGTAAATTTTAAAAAGAATTTACGTCTGTGACAATTAC
76603 GATAATATCTGTAACATTTGTAATCGGGATGAGAGCATCGTGACTA
66 GATAATATCTGTAACATTTGTAATCGGGATGAGAGCATCGTGACTA
76649 ATAATTATTATATTTTATAATAAGTGATGTAAATTTTAAAAAGAATTTACGTCTGTGACAATTAC
1 ATAATTATTATATTTTATAATAAGTGATGTAAATTTTAAAAAGAATTTACGTCTGTGACAATTAC
76714 GATAATATCTGTAACATTTGTAATCGGGATGAGAGCATCGTGACTA
66 GATAATATCTGTAACATTTGTAATCGGGATGAGAGCATCGTGACTA
76760 A
1 A
76761 AAATGAGACG
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (111 bp):
ATAATTATTATATTTTATAATAAGTGATGTAAATTTTAAAAAGAATTTACGTCTGTGACAATTAC
GATAATATCTGTAACATTTGTAATCGGGATGAGAGCATCGTGACTA
Found at i:76980 original size:20 final size:20
Alignment explanation
Indices: 76963--77000 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
76953 ATCCAAGATA
76963 AATCAAATGAAGAAAAGAAG
1 AATCAAATGAAGAAAAGAAG
**
76983 AATCGGATGAAGAAAAGA
1 AATCAAATGAAGAAAAGA
77001 GATCTGGAAA
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:0.61, C:0.05, G:0.24, T:0.11
Consensus pattern (20 bp):
AATCAAATGAAGAAAAGAAG
Found at i:77532 original size:28 final size:27
Alignment explanation
Indices: 77483--77536 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
77473 AATATGATAG
* * *
77483 TTTTAAAAAGTTTCTTTTTAAAAAAAT
1 TTTTAAAAAATTTATTTATAAAAAAAT
77510 TTTTAAAAAATTATATTTATAAAAAAA
1 TTTTAAAAAATT-TATTTATAAAAAAA
77537 CCTTTATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TTTTAAAAAATTTATTTATAAAAAAAT
Found at i:77542 original size:28 final size:27
Alignment explanation
Indices: 77484--77542 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
77474 ATATGATAGT
* * * **
77484 TTTAAAAAGTTTCTTTTTAAAAAAATT
1 TTTAAAAAATTTATTTATAAAAAAACC
77511 TTTAAAAAATTATATTTATAAAAAAACC
1 TTTAAAAAATT-TATTTATAAAAAAACC
77539 TTTA
1 TTTA
77543 TTTCTTTTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (27 bp):
TTTAAAAAATTTATTTATAAAAAAACC
Found at i:78075 original size:22 final size:22
Alignment explanation
Indices: 78030--78074 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
78020 AAGCTTGAAA
* *
78030 TTAATCTAAAAATTATCTGATT
1 TTAATCCAAAAATTATATGATT
78052 TTAATCCAAAAATTATAT-ATT
1 TTAATCCAAAAATTATATGATT
78073 TT
1 TT
78075 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAATCCAAAAATTATATGATT
Found at i:78710 original size:64 final size:63
Alignment explanation
Indices: 78588--78710 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 63
78578 TAGTTATGTT
* * *
78588 ATATCATTTAACCAGAAATATTATCAAGTATAATAATATATTAGGTATCACTTATATAAAAAA
1 ATATCATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCACTTATATAAAAAA
* * *
78651 ATATGCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTTTATAA
1 ATAT-CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCACTTATATAA
78711 TGTAATAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 4 0.08
64 49 0.92
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (63 bp):
ATATCATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCACTTATATAAAAAA
Found at i:79075 original size:198 final size:198
Alignment explanation
Indices: 78726--79446 Score: 874
Period size: 198 Copynumber: 3.6 Consensus size: 198
78716 TAAGTAGCGC
* *
78726 TTATATTGACCTATTTTCTAAGT-AAACCGGTATATTTATACCGGTAACATTGC-AAATTTACCT
1 TTATGTTGACATATTTTCTAA-TAAAACCGGTATATTTATACCGGT-ACATT-CTAAATTTACCT
* * *
78789 ATTACATTATAATTATCGGTTTCGATATTTTTTGGATCGATACATTT--TAAATGTATCGACACT
63 ATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACT
* * * *
78852 TTATGCGTGCACATCGTTGGGCATTCATTCTGGA-AAAAAATATCGACACAAACTTAAAAAGTGT
128 TTATGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAA-TTAACAAGTGT
**
78916 TAATACA
192 CGATACA
* * *
78923 TTAT-TTAGACATATTTTCTTATAAAACCGATATATTTATACATGGTACATTCTAAATTTACCTA
1 TTATGTT-GACATATTTTCTAATAAAACCGGTATATTTATAC-CGGTACATTCTAAATTTACCTA
* * *
78987 TCACATTGTAATCT-TC-GTTTCGATGTTTTTGGGATCGATAGTTTTAATAAATGTATCGACACT
64 TTACATTATAAT-TATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACT
* * * * *
79050 CTATGCGTGCACCCCGTTTGGCATTCATTATGGACAAAATGTATCGACAAAAATTTAACAAGTGT
128 TTATGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAA-TTAACAAGTGT
*
79115 CGATACT
192 CGATACA
* * * * * *
79122 TTATGCTGGCATATTTTCTCATAAAACTGGTATATTTATATCGGTTACATTGTAAATTTACCTAT
1 TTATGTTGACATATTTTCTAATAAAACCGGTATATTTATACCGG-TACATTCTAAATTTACCTAT
79187 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
65 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
* * *
79252 ATGCGTGCACCTCGTTTGGGTATTCATTCTGGACAATAAGTATCGACACAAATTCCACAAGTGTC
130 ATGCGTGCACCTCGTTT-GGCATTCATTCTGGACAAAAAGTATCGACACAAATT-AACAAGTGTC
79317 GATACA
193 GATACA
* * * *
79323 TTATGTTGA-ACTATTTTCTAAT-TAACCGG-ATATTTATACCGTTACATTGTTAATTTACCTAT
1 TTATGTTGACA-TATTTTCTAATAAAACCGGTATATTTATACCGGTACATTCTAAATTTACCTAT
* * *
79385 TACATTATAATTATTGGTTTCGATGTTTTTTTGG-TCGATACTTTTAGA-AAATGTATCAACAC
65 TACATTATAATTATCGGTTTCGATG-TTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
79447 ATATTTAGGT
Statistics
Matches: 453, Mismatches: 54, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
196 29 0.06
197 61 0.13
198 120 0.26
199 111 0.25
200 72 0.16
201 60 0.13
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (198 bp):
TTATGTTGACATATTTTCTAATAAAACCGGTATATTTATACCGGTACATTCTAAATTTACCTATT
ACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTA
TGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAATTAACAAGTGTCGAT
ACA
Found at i:82321 original size:19 final size:21
Alignment explanation
Indices: 82269--82312 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
82259 CCCCTTTTGC
82269 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
82290 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
82311 CT
1 CT
82313 TGATTGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.14, T:0.39
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCGACT
Found at i:85005 original size:178 final size:179
Alignment explanation
Indices: 84637--85297 Score: 949
Period size: 179 Copynumber: 3.7 Consensus size: 179
84627 TACGCGTACT
* * *
84637 TATTAAAGTATCGACACTTTCAATATCCGGTAGCTCTA-ACCGGTTTT-TCCTTCGAGATCGGTT
1 TATTAAAGTATCGACACTTTCAATATCCGGTAGCTCTATACCGGTTTTGTCTTTCGAGACCGATT
*
84700 TTGTCATATTTTTATATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTTA
66 TTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTTA
* * *
84765 TAGGCG-TAAAAACTGTTTATCTTTTAAATTTACAAAGTGTCGATACTTA
131 TAGGCGCT-AAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* *
84814 TATTAAAGTATCGACACTTTCATATATCCGATAGCTCTATACCGGTTTTGTCATTTCGAGACCGG
1 TATTAAAGTATCGACACTTTCA-ATATCCGGTAGCTCTATACCGGTTTTGTC-TTTCGAGACCGA
* *
84879 TTTTGTCATATTTTTACCTG-TATATCG-TGTGGATCGATACATTGTTATAAAGTATCAACACTT
64 TTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTT
*
84942 TATAGGCGCTAAAACTGCTTCTC-TTTAAATTCACAAAATGTCGATACTTA
129 TATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
84992 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCTCTATACCGATTTTGTCCTTTTGAGACTG
1 TATTAAAGTATCGACACTTTC-A-ATATCCGGTAGCTCTATACCGGTTTTGT-CTTTCGAGACCG
* * *
85057 ATTTTGTCATATTTTTACCTGTTATATCGTTGTAGATCGATACATTGTTATAAAATATCGACACT
63 ATTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
85122 TTATA-GCACAAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
128 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * *
85173 TATTAAAGTATCGACACTTTTAATATCCGGTAACACTTTACCGCTTTTGTCTTTTGAGACCGATT
1 TATTAAAGTATCGACACTTTCAATATCCGGTAGCTCTATACCGGTTTTGTCTTTCGAGACCGATT
* * * *
85238 TTGTCATATTTTTACATGTTATATTGATATGGATCGATACATTTTTATAAAGTATCGACA
66 TTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACA
85298 TAAACCGACA
Statistics
Matches: 440, Mismatches: 34, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
177 22 0.05
178 128 0.29
179 144 0.33
180 35 0.08
181 111 0.25
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (179 bp):
TATTAAAGTATCGACACTTTCAATATCCGGTAGCTCTATACCGGTTTTGTCTTTCGAGACCGATT
TTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTTA
TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Done.