Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 96 of 106
Found at i:36494973 original size:4 final size:4
Alignment explanation
Indices: 36494964--36494990 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
36494954 GATGGGAAAT
36494964 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
36494991 TATGTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:36509400 original size:30 final size:29
Alignment explanation
Indices: 36509337--36509402 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
36509327 TTTAAGAAAA
* * *
36509337 TTTTTATTTTTTTATTATATTTAATCAAG
1 TTTTTATTTTTTTATTAAATTAAATCAAC
36509366 TTTTTATTTTTTTATTTTAAATTAAAT-AAC
1 TTTTTATTTTTTTA--TTAAATTAAATCAAC
36509396 TTTTTAT
1 TTTTTAT
36509403 AATAAACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.44
30 9 0.28
31 9 0.28
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (29 bp):
TTTTTATTTTTTTATTAAATTAAATCAAC
Found at i:36511474 original size:20 final size:20
Alignment explanation
Indices: 36511446--36511489 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
36511436 GTTCTAAGCT
*
36511446 AAATGTATCGATACATTTAG
1 AAATATATCGATACATTTAG
* *
36511466 AAATATATCGATATATTTTG
1 AAATATATCGATACATTTAG
36511486 AAAT
1 AAAT
36511490 GTATTTGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (20 bp):
AAATATATCGATACATTTAG
Found at i:36511710 original size:21 final size:21
Alignment explanation
Indices: 36511639--36511711 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
36511629 AACCTAATTT
*
36511639 AAACAAGTTTTAAAAA-CTATTC
1 AAACAA-TTTCAAAAATC-ATTC
*
36511661 AAACAAGTTCAAAAATCATT-
1 AAACAATTTCAAAAATCATTC
36511681 AAAGCAATTTCAAAAATCATTC
1 AAA-CAATTTCAAAAATCATTC
*
36511703 AAATAATTT
1 AAACAATTT
36511712 TGAAACTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.07
21 31 0.70
22 10 0.23
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (21 bp):
AAACAATTTCAAAAATCATTC
Found at i:36511776 original size:21 final size:21
Alignment explanation
Indices: 36511767--36511843 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
36511757 AAAAAAGTTT
36511767 AAAAACTATTCAAACAAATTC
1 AAAAACTATTCAAACAAATTC
* *
36511788 AAAAACTCATTCAAGCAACTTC
1 AAAAACT-ATTCAAACAAATTC
* * *
36511810 AAATATTATTCAAACAAGTTC
1 AAAAACTATTCAAACAAATTC
36511831 AAAAA-TCATTCAA
1 AAAAACT-ATTCAA
36511844 GTAATTTTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 29 0.62
22 17 0.36
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAAACTATTCAAACAAATTC
Found at i:36512228 original size:81 final size:81
Alignment explanation
Indices: 36512123--36512327 Score: 306
Period size: 81 Copynumber: 2.5 Consensus size: 81
36512113 ACTTAAATTG
* *
36512123 GACCAACCAAAATTTAATTATTGGTCACATAATTTGTCTCTAAATAAATG-AAGATAATTTAGAG
1 GACCAATCAAAATTTAATTATTGGTCACATAATTTGTCTCTAAATAAA-GCAAGATAATTTAAAG
36512187 ATAATATTCATATTTTT
65 ATAATATTCATATTTTT
* * * *
36512204 GATCAATCAAAATTTAGTTATTGGTCATATAATTTGTCTATAAATAAAGCAAGATAATTTAAAGA
1 GACCAATCAAAATTTAATTATTGGTCACATAATTTGTCTCTAAATAAAGCAAGATAATTTAAAGA
36512269 TAATATTCATATTTTT
66 TAATATTCATATTTTT
* *
36512285 GACCAATCTAAATTTAATTATTGGTCATC-TAATTTATCTCTAA
1 GACCAATCAAAATTTAATTATTGGTCA-CATAATTTGTCTCTAA
36512328 TAATTATGCC
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.01
81 109 0.99
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (81 bp):
GACCAATCAAAATTTAATTATTGGTCACATAATTTGTCTCTAAATAAAGCAAGATAATTTAAAGA
TAATATTCATATTTTT
Found at i:36512524 original size:9 final size:9
Alignment explanation
Indices: 36512484--36512520 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
36512474 TTGTAGACAC
36512484 TAAA-AAAA
1 TAAATAAAA
36512492 TAAATAAAA
1 TAAATAAAA
36512501 TAAATAAAA
1 TAAATAAAA
*
36512510 TATATAAAA
1 TAAATAAAA
36512519 TA
1 TA
36512521 TATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 4 0.15
9 23 0.85
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAATAAAA
Found at i:36514293 original size:19 final size:19
Alignment explanation
Indices: 36514232--36514288 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
36514222 AAATCATCGA
* *
36514232 AAAATAATAAATAAACAAAT
1 AAAATAAAAAAT-AATAAAT
36514252 AATAGATAAAAAATAATAAAT
1 AA-A-ATAAAAAATAATAAAT
36514273 AAAATAAAACAATAAT
1 AAAATAAAA-AATAAT
36514289 GATAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 6 0.19
20 9 0.28
21 9 0.28
22 8 0.25
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATAAAAAATAATAAAT
Found at i:36514576 original size:31 final size:30
Alignment explanation
Indices: 36514541--36514622 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 30
36514531 AATTAGAAAT
*
36514541 ATAAAAAGAAAATATGATAATAAAGAAT-AAA
1 ATAAAAA-AAAATA-GATAATAAACAATAAAA
36514572 ATAAAATAAAAATA-ATAATTAAACAATAAAA
1 ATAAAA-AAAAATAGATAA-TAAACAATAAAA
*
36514603 ATAACAATAAAATAGATAAT
1 ATAA-AAAAAAATAGATAAT
36514623 TGCATTAGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 4 0.09
30 7 0.16
31 26 0.59
32 7 0.16
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (30 bp):
ATAAAAAAAAATAGATAATAAACAATAAAA
Found at i:36514580 original size:20 final size:19
Alignment explanation
Indices: 36514522--36514621 Score: 64
Period size: 20 Copynumber: 5.1 Consensus size: 19
36514512 TAAAGTATGA
36514522 AAAAATAATAATTAGAAAT-AT
1 AAAAATAA-AA-TA-AAATAAT
* **
36514543 AAAAAGAAAATATGATAAT
1 AAAAATAAAATAAAATAAT
36514562 AAAGAATAAAAT--AA-AAT
1 AAA-AATAAAATAAAATAAT
* *
36514579 AAAAATAATAATTAAACAAT
1 AAAAATAA-AATAAAATAAT
36514599 AAAAATAACAATAAAATAGAT
1 AAAAATAA-AATAAAATA-AT
36514620 AA
1 AA
36514622 TTGCATTAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
16 5 0.08
17 9 0.14
18 3 0.05
19 9 0.14
20 27 0.42
21 11 0.17
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (19 bp):
AAAAATAAAATAAAATAAT
Found at i:36514585 original size:11 final size:11
Alignment explanation
Indices: 36514569--36514616 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 11
36514559 AATAAAGAAT
36514569 AAAATAAAATA
1 AAAATAAAATA
36514580 AAAATAATAATTA
1 AAAATAA-AA-TA
36514593 AACAATAAAAATA
1 AA-AAT-AAAATA
*
36514606 ACAATAAAATA
1 AAAATAAAATA
36514617 GATAATTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
11 13 0.41
12 5 0.16
13 7 0.22
14 5 0.16
15 2 0.06
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:36514610 original size:12 final size:12
Alignment explanation
Indices: 36514559--36514614 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
36514549 AAAATATGAT
36514559 AATAAAGAATAA-
1 AATAAA-AATAAC
*
36514571 AAT-AAAATAAA
1 AATAAAAATAAC
*
36514582 AATAATAATTAAAC
1 AATAA-AAAT-AAC
36514596 AATAAAAATAAC
1 AATAAAAATAAC
36514608 AATAAAA
1 AATAAAA
36514615 TAGATAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 5 0.14
11 5 0.14
12 14 0.38
13 6 0.16
14 7 0.19
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (12 bp):
AATAAAAATAAC
Found at i:36516181 original size:29 final size:29
Alignment explanation
Indices: 36516115--36516184 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
36516105 TGAACTTCAC
* * *
36516115 TGTCGCTTGACCTTGATAACGAACTTCGT
1 TGTCGCTTGATCTTAATAACAAACTTCGT
* * *
36516144 TGCCACTTGATCTTAATCACAAACTTCGT
1 TGTCGCTTGATCTTAATAACAAACTTCGT
36516173 TGTCGCTTGATC
1 TGTCGCTTGATC
36516185 ACGAACTTCG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (29 bp):
TGTCGCTTGATCTTAATAACAAACTTCGT
Found at i:36516191 original size:23 final size:23
Alignment explanation
Indices: 36516159--36516215 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
36516149 CTTGATCTTA
*
36516159 ATCACAAACTTCGTTGTCGCTTG
1 ATCACGAACTTCGTTGTCGCTTG
* *
36516182 ATCACGAACTTCGTTTTTGCTTG
1 ATCACGAACTTCGTTGTCGCTTG
*
36516205 AACACGAACTT
1 ATCACGAACTT
36516216 TGCTGCTGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (23 bp):
ATCACGAACTTCGTTGTCGCTTG
Found at i:36516256 original size:29 final size:29
Alignment explanation
Indices: 36516201--36516258 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
36516191 TTCGTTTTTG
* **
36516201 CTTGAACACGAACTTTGCTGCTGCTTGAT
1 CTTGAACACAAACTTTGCTGCCACTTGAT
* *
36516230 CTTGATCACAAACTTTGTTGCCACTTGAT
1 CTTGAACACAAACTTTGCTGCCACTTGAT
36516259 TTTCACTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (29 bp):
CTTGAACACAAACTTTGCTGCCACTTGAT
Found at i:36516647 original size:57 final size:57
Alignment explanation
Indices: 36516533--36516647 Score: 126
Period size: 57 Copynumber: 2.0 Consensus size: 57
36516523 AAGTTAGGTA
* * * * **
36516533 TTATCTTTAAATTATCTTAATTTATTTAGAGATAAATTAAATAATCAAATTTGATTT
1 TTATCTTTAAATTAGCATAATTTATTTAAAGATAAATTAAATAATAAAATTAAATTT
* *
36516590 TTATCTTTAAATTAGCATAA-TTA-TTAAAGATAAATTAGATGACTAATAATTAAATTT
1 TTATCTTTAAATTAGCATAATTTATTTAAAGATAAATTAAAT-AATAA-AATTAAATTT
36516647 T
1 T
36516648 GATTGGTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
55 15 0.31
56 6 0.12
57 27 0.56
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (57 bp):
TTATCTTTAAATTAGCATAATTTATTTAAAGATAAATTAAATAATAAAATTAAATTT
Found at i:36516681 original size:79 final size:79
Alignment explanation
Indices: 36516590--36516753 Score: 197
Period size: 81 Copynumber: 2.1 Consensus size: 79
36516580 AATTTGATTT
* * *
36516590 TTATCTTTAAATTAGCAT-AATTA-TTAAAGATAAATTAGATGACTAATAATTAAATTTTGATTG
1 TTATCTCTAAATTAGCATGAATTATTTAAAGACAAATTAGATGACCAATAATTAAATTTTGATTG
36516653 GTCAAAAATATAAATA
66 GTC--AAATATAAATA
* * * * * *
36516669 TTATCTCTAAATTATCTTGATTTATTTAGAGACAAATTATATGACCAATAATTAAATTTTGATTT
1 TTATCTCTAAATTAGCATGAATTATTTAAAGACAAATTAGATGACCAATAATTAAATTTTGATTG
* *
36516734 GTCCAATTTAAATA
66 GTCAAATATAAATA
36516748 TTATCT
1 TTATCT
36516754 TCAATTATCT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
79 30 0.42
80 4 0.06
81 38 0.53
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (79 bp):
TTATCTCTAAATTAGCATGAATTATTTAAAGACAAATTAGATGACCAATAATTAAATTTTGATTG
GTCAAATATAAATA
Found at i:36518850 original size:20 final size:22
Alignment explanation
Indices: 36518822--36518876 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
36518812 GAAAAAAGTT
*
36518822 AAATTAAAATATATA-ATA-AA
1 AAATAAAAATATATATATATAA
36518842 AAATAAAAATA-ATATATATAA
1 AAATAAAAATATATATATATAA
* *
36518863 TATTAAAAATATAT
1 AAATAAAAATATAT
36518877 TTAAAGGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 11 0.38
22 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAAAAATATATATATATAA
Found at i:36554429 original size:21 final size:21
Alignment explanation
Indices: 36554403--36554445 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36554393 CGACTTGGAC
* *
36554403 CATTTTTAGAATCAGTTTCAT
1 CATTTTCAGAATCACTTTCAT
*
36554424 CATTTTCAGGATCACTTTCAT
1 CATTTTCAGAATCACTTTCAT
36554445 C
1 C
36554446 TTCACTACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (21 bp):
CATTTTCAGAATCACTTTCAT
Found at i:36555456 original size:3 final size:3
Alignment explanation
Indices: 36555448--36555473 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36555438 GGCCAATCCC
36555448 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
36555474 GGCTAATTTT
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:36563489 original size:55 final size:56
Alignment explanation
Indices: 36563424--36563537 Score: 194
Period size: 55 Copynumber: 2.1 Consensus size: 56
36563414 AGAAAAACTA
* *
36563424 ATTAAGTAATGAGGGAGATGAAGAAATTACAACGATAAGAGTTGGGCATTAG-AAT
1 ATTAAGTAATGAGGGAGACGAAGAAATTACAACGATAAGAGTTAGGCATTAGAAAT
*
36563479 ATTAAGTAATGAGGGAGACGAAGAAATTACAATGATAAGAGTTAGGCATTAGAAAT
1 ATTAAGTAATGAGGGAGACGAAGAAATTACAACGATAAGAGTTAGGCATTAGAAAT
36563535 ATT
1 ATT
36563538 GAAGCCACCT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 49 0.89
56 6 0.11
ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25
Consensus pattern (56 bp):
ATTAAGTAATGAGGGAGACGAAGAAATTACAACGATAAGAGTTAGGCATTAGAAAT
Found at i:36574021 original size:6 final size:6
Alignment explanation
Indices: 36574006--36574038 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
36573996 TTTTTTTTTT
36574006 TAATTA -AATTA TAATTA TAATTA TAATTA TAAT
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAAT
36574039 AATATTACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAATTA
Found at i:36577355 original size:16 final size:16
Alignment explanation
Indices: 36577336--36577378 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
36577326 TATGAAAATT
36577336 TATTAATTAATTGATA
1 TATTAATTAATTGATA
*
36577352 TATTATTTAATTGATA
1 TATTAATTAATTGATA
*
36577368 AATTAA-TAATT
1 TATTAATTAATT
36577379 TATTAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
TATTAATTAATTGATA
Found at i:36577636 original size:19 final size:20
Alignment explanation
Indices: 36577614--36577663 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
36577604 TTAAGTTATG
*
36577614 TATATATAAAATT-TTGATA
1 TATATATAAAATTATTAATA
* *
36577633 TATA-AGAAAATTATTAATT
1 TATATATAAAATTATTAATA
*
36577652 TATTTATAAAAT
1 TATATATAAAAT
36577664 GAGACTTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 7 0.29
19 11 0.46
20 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATATAAAATTATTAATA
Found at i:36581446 original size:5 final size:5
Alignment explanation
Indices: 36581436--36581465 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
36581426 ATCGTCATGG
36581436 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
36581466 AGTCTGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:36581584 original size:6 final size:6
Alignment explanation
Indices: 36581573--36581597 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36581563 CTAGTAAAAG
36581573 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
36581598 CTAGATGTAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:36589066 original size:2 final size:2
Alignment explanation
Indices: 36589061--36589101 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
36589051 AAAAAATGAT
36589061 TA TA TA TA TA 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 TA TA TA TA TA
36589102 GGACAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36589487 original size:31 final size:29
Alignment explanation
Indices: 36589448--36589577 Score: 134
Period size: 31 Copynumber: 4.6 Consensus size: 29
36589438 AAATATAAAT
36589448 TAAAAAAATAAATTTTTTACATTTCAAAAA
1 TAAAAAAAT-AATTTTTTACATTTCAAAAA
*
36589478 TAAAAAAAATCAATTTTTTACATTTTAAAAA
1 T-AAAAAAAT-AATTTTTTACATTTCAAAAA
*
36589509 T----ANAT-A-TTTTTACATTT-AAAAA
1 TAAAAAAATAATTTTTTACATTTCAAAAA
36589531 T-AAAAAATAA-TTTTTACATTTCAAAAA
1 TAAAAAAATAATTTTTTACATTTCAAAAA
36589558 TAAAAAAAATCAATTTTTTA
1 T-AAAAAAAT-AATTTTTTA
36589578 ACTTAAAAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
22 6 0.07
23 11 0.13
24 1 0.01
25 3 0.03
26 15 0.17
27 6 0.07
29 7 0.08
30 3 0.03
31 34 0.40
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAAAAAATAATTTTTTACATTTCAAAAA
Found at i:36589507 original size:22 final size:22
Alignment explanation
Indices: 36589482--36589561 Score: 81
Period size: 22 Copynumber: 3.4 Consensus size: 22
36589472 CAAAAATAAA
*
36589482 AAAAATCAAT-TTTTTACATTTT
1 AAAAATAAATATTTTTACA-TTT
*
36589504 AAAAATANATATTTTTACATTT
1 AAAAATAAATATTTTTACATTT
36589526 AAAAATAAAAAATAATTTTTACATTT
1 AAAAAT---AAAT-ATTTTTACATTT
36589552 CAAAAATAAA
1 -AAAAATAAA
36589562 AAAAATCAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 17 0.35
23 8 0.16
24 3 0.06
25 3 0.06
26 12 0.24
27 6 0.12
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATAAATATTTTTACATTT
Found at i:36589518 original size:23 final size:24
Alignment explanation
Indices: 36589478--36589561 Score: 84
Period size: 26 Copynumber: 3.4 Consensus size: 24
36589468 ATTTCAAAAA
36589478 TAAAAA-AAATCAATTTTTTACATTT
1 TAAAAATAAAT-AA-TTTTTACATTT
*
36589503 TAAAAATANAT-ATTTTTACA-TT
1 TAAAAATAAATAATTTTTACATTT
36589525 TAAAAATAAAAAATAATTTTTACATTT
1 TAAAAAT---AAATAATTTTTACATTT
*
36589552 CAAAAATAAA
1 TAAAAATAAA
36589562 AAAAATCAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
22 9 0.18
23 8 0.16
24 4 0.08
25 9 0.18
26 12 0.24
27 8 0.16
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAAATAAATAATTTTTACATTT
Found at i:36589587 original size:30 final size:29
Alignment explanation
Indices: 36589514--36589588 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 29
36589504 AAAAATANAT
*
36589514 ATTTTTACA-TTTAAAAAT--AAAAAATA
1 ATTTTTACACTTAAAAAATAAAAAAAATA
* *
36589540 ATTTTTACATTTCAAAAATAAAAAAAATCA
1 ATTTTTACACTTAAAAAATAAAAAAAAT-A
36589570 ATTTTTTA-ACTTAAAAAAT
1 A-TTTTTACACTTAAAAAAT
36589589 TGTACATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 9 0.22
27 8 0.20
29 7 0.17
30 11 0.27
31 6 0.15
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTTTTACACTTAAAAAATAAAAAAAATA
Found at i:36589658 original size:2 final size:2
Alignment explanation
Indices: 36589651--36589676 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36589641 TTTATTTTCT
36589651 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
36589677 CCTGTGCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:36590422 original size:21 final size:21
Alignment explanation
Indices: 36590398--36590437 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36590388 TCCTTTCAAA
36590398 TTCTAGTTT-TGTTTTTCTTCT
1 TTCT-GTTTATGTTTTTCTTCT
*
36590419 TTCTTTTTATGTTTTTCTT
1 TTCTGTTTATGTTTTTCTT
36590438 GCACTATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.75
Consensus pattern (21 bp):
TTCTGTTTATGTTTTTCTTCT
Found at i:36601994 original size:12 final size:12
Alignment explanation
Indices: 36601977--36602001 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36601967 CTTCATACAG
36601977 AACCAGAGAAGA
1 AACCAGAGAAGA
36601989 AACCAGAGAAGA
1 AACCAGAGAAGA
36602001 A
1 A
36602002 TGCAAACCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.24, T:0.00
Consensus pattern (12 bp):
AACCAGAGAAGA
Found at i:36604214 original size:53 final size:53
Alignment explanation
Indices: 36604134--36604241 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
36604124 AGTGGGGTTT
36604134 TTATGGTTGGAGATAGGTATTATCTCCCTTTGTGTAGCTCAAGCACAATGAAC
1 TTATGGTTGGAGATAGGTATTATCTCCCTTTGTGTAGCTCAAGCACAATGAAC
36604187 TTATGGTTGGAGATAGGTATTATCTCCCTTTGTGTAGCTCAAGCACAATGAAC
1 TTATGGTTGGAGATAGGTATTATCTCCCTTTGTGTAGCTCAAGCACAATGAAC
36604240 TT
1 TT
36604242 TCACCTGTGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (53 bp):
TTATGGTTGGAGATAGGTATTATCTCCCTTTGTGTAGCTCAAGCACAATGAAC
Found at i:36605670 original size:6 final size:6
Alignment explanation
Indices: 36605659--36605683 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36605649 GCAAATAAGT
36605659 AATATA AATATA AATATA AATATA A
1 AATATA AATATA AATATA AATATA A
36605684 TGATTGATGA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:36637685 original size:43 final size:44
Alignment explanation
Indices: 36637617--36637717 Score: 109
Period size: 43 Copynumber: 2.3 Consensus size: 44
36637607 ATTAAGAATA
* * *
36637617 ATCAAGGATATC-ATCTATTATACTTA-AAATCGTAATACCACAT
1 ATCAAGGATATCAAGCTATTAGACTTAGAAAT-GTAACACCACAT
* *
36637660 ATCAAGGATATCAAGC-ATTAGACTTAGAAGTGTAACACTACAT
1 ATCAAGGATATCAAGCTATTAGACTTAGAAATGTAACACCACAT
* *
36637703 AACAAGGATGTCAAG
1 ATCAAGGATATCAAG
36637718 TATAATGATT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 44 0.90
44 5 0.10
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.27
Consensus pattern (44 bp):
ATCAAGGATATCAAGCTATTAGACTTAGAAATGTAACACCACAT
Found at i:36643343 original size:13 final size:13
Alignment explanation
Indices: 36643325--36643349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36643315 GGTAAATTTC
36643325 TTTTTATAAGTTT
1 TTTTTATAAGTTT
36643338 TTTTTATAAGTT
1 TTTTTATAAGTT
36643350 ATAATTTTGG
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTTTATAAGTTT
Found at i:36644534 original size:34 final size:35
Alignment explanation
Indices: 36644491--36644557 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
36644481 GGGAAGGTCC
36644491 GATCGGCGCATAGGGAGAGAGAG-GAGGAAATACT
1 GATCGGCGCATAGGGAGAGAGAGAGAGGAAATACT
*
36644525 GATCTGCGCATAGGGAGAGAGAGATGAGGAAAT
1 GATCGGCGCATAGGGAGAGAGAGA-GAGGAAAT
36644558 TTCGATCGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 22 0.73
36 8 0.27
ACGTcount: A:0.36, C:0.10, G:0.40, T:0.13
Consensus pattern (35 bp):
GATCGGCGCATAGGGAGAGAGAGAGAGGAAATACT
Found at i:36645979 original size:3 final size:3
Alignment explanation
Indices: 36645971--36646048 Score: 57
Period size: 3 Copynumber: 28.7 Consensus size: 3
36645961 AGTATGAAAA
*
36645971 AAT AAT AAT AAGA AAT AA- AAT AA- AA- AAT -AT AAT AAT AA- AA-
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
36646011 AAT AA- AAT AA- AAT AAA AAT AAT AAT TA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36646049 ATGACAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
2 17 0.28
3 42 0.69
4 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:36645997 original size:27 final size:27
Alignment explanation
Indices: 36645967--36646068 Score: 105
Period size: 27 Copynumber: 3.5 Consensus size: 27
36645957 GTAAAGTATG
*
36645967 AAAAAATAATAATAAGAAATAAAATAA
1 AAAAAATAATAATAAAAAATAAAATAA
*
36645994 AAAATATAATAATAAAAAATAAAATAAA
1 AAAAAATAATAATAAAAAATAAAAT-AA
*
36646022 ATAAAAATAATAATTAAATAATAATAAATGACA
1 A-AAAAATAATAA-TAAAAAAT-A-AAAT-A-A
36646055 AAAAAATAGATAAT
1 AAAAAATA-ATAAT
36646069 TGCATTAACA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
27 23 0.37
28 3 0.05
29 10 0.16
30 7 0.11
31 1 0.02
32 13 0.21
33 6 0.10
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.23
Consensus pattern (27 bp):
AAAAAATAATAATAAAAAATAAAATAA
Found at i:36645998 original size:12 final size:12
Alignment explanation
Indices: 36645967--36646031 Score: 69
Period size: 13 Copynumber: 5.2 Consensus size: 12
36645957 GTAAAGTATG
36645967 AAAAAATAATAAT
1 AAAAAATAA-AAT
*
36645980 AAGAAATAAAAT
1 AAAAAATAAAAT
36645992 AAAAAATATAATAAT
1 -AAAAA-ATAA-AAT
36646007 AAAAAATAAAAT
1 AAAAAATAAAAT
*
36646019 AAAATA-AAAAT
1 AAAAAATAAAAT
36646030 AA
1 AA
36646032 TAATTAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
11 7 0.15
12 11 0.24
13 16 0.35
14 9 0.20
15 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:36646015 original size:37 final size:37
Alignment explanation
Indices: 36645967--36646050 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 37
36645957 GTAAAGTATG
36645967 AAAAAATAATAATAAGAA-ATAAAATAAAAAATATAATAAT
1 AAAAAATAA-AATAA-AATA-AAAATAAAAAATA-AATAAT
* *
36646007 AAAAAATAAAATAAAATAAAAATAATAATTAAATAAT
1 AAAAAATAAAATAAAATAAAAATAAAAAATAAATAAT
*
36646044 AATAAAT
1 AAAAAAT
36646051 GACAAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 12 0.30
38 13 0.32
39 6 0.15
40 9 0.22
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (37 bp):
AAAAAATAAAATAAAATAAAAATAAAAAATAAATAAT
Found at i:36646040 original size:17 final size:17
Alignment explanation
Indices: 36645988--36646048 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
36645978 ATAAGAAATA
36645988 AAATAAAAA-ATATAA-T
1 AAATAAAAATA-ATAATT
*
36646004 -AATAAAAAATAA-AATA
1 AAAT-AAAAATAATAATT
36646020 AAATAAAAATAATAATT
1 AAATAAAAATAATAATT
*
36646037 AAATAATAATAA
1 AAATAAAAATAA
36646049 ATGACAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 5 0.14
16 14 0.38
17 18 0.49
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAAAATAATAATT
Found at i:36646310 original size:24 final size:23
Alignment explanation
Indices: 36646266--36646312 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 23
36646256 TCATAAACGA
36646266 AAAATAAAAAAAATGATAAAAATT
1 AAAATAAAAAAAATGA-AAAAATT
36646290 AAAATAAAGAAGAAATGAAAAAA
1 AAAATAAA-AA-AAATGAAAAAA
36646313 GAGGGGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 7 0.33
26 6 0.29
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.15
Consensus pattern (23 bp):
AAAATAAAAAAAATGAAAAAATT
Found at i:36646654 original size:25 final size:25
Alignment explanation
Indices: 36646580--36646654 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
36646570 GAGGAAGGGG
* *
36646580 GAGATCTTGGGTGAGAGAGCAAAAG
1 GAGATCTTGGGTGAGAAAGCAAAAA
36646605 GAGATCTTGGGTGAGAAAGCAAAAA
1 GAGATCTTGGGTGAGAAAGCAAAAA
*
36646630 GAGATTTTGGGTGAGAAAGCAAAAA
1 GAGATCTTGGGTGAGAAAGCAAAAA
36646655 AAGAAACGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.41, C:0.07, G:0.35, T:0.17
Consensus pattern (25 bp):
GAGATCTTGGGTGAGAAAGCAAAAA
Found at i:36646665 original size:24 final size:25
Alignment explanation
Indices: 36646613--36646666 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
36646603 AGGAGATCTT
* ***
36646613 GGGTGAGAAAGCAAAAAGAGATTTT
1 GGGTGAGAAAGCAAAAAAAGATAAC
36646638 GGGTGAGAAAGCAAAAAAAGA-AAC
1 GGGTGAGAAAGCAAAAAAAGATAAC
36646662 GGGTG
1 GGGTG
36646667 GAGAGGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.46, C:0.06, G:0.35, T:0.13
Consensus pattern (25 bp):
GGGTGAGAAAGCAAAAAAAGATAAC
Found at i:36647705 original size:27 final size:28
Alignment explanation
Indices: 36647675--36647727 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
36647665 AAAATTACTC
* *
36647675 GATAAAAATAATAAAT-AAATAATAAAT
1 GATAAAAAAAAGAAATAAAATAATAAAT
*
36647702 GATAAAAAAAAGAGATAAAATAATAA
1 GATAAAAAAAAGAAATAAAATAATAA
36647728 CAATTTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (28 bp):
GATAAAAAAAAGAAATAAAATAATAAAT
Found at i:36647955 original size:14 final size:14
Alignment explanation
Indices: 36647936--36647999 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
36647926 TTGCTTATGG
36647936 AAAATATAATAAAA
1 AAAATATAATAAAA
36647950 AAAATAT-A-AAAA
1 AAAATATAATAAAA
* * *
36647962 TATATAAAATAAAA
1 AAAATATAATAAAA
** *
36647976 GTAGTATAATAAAA
1 AAAATATAATAAAA
*
36647990 AATATATAAT
1 AAAATATAAT
36648000 TTTTGTTCAC
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
12 8 0.22
13 2 0.06
14 26 0.72
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AAAATATAATAAAA
Found at i:36648113 original size:13 final size:12
Alignment explanation
Indices: 36648088--36648159 Score: 65
Period size: 13 Copynumber: 5.6 Consensus size: 12
36648078 AATGTAAAGT
*
36648088 ATAAAAAAAATA
1 ATAATAAAAATA
36648100 ATAATAAGAAATA
1 ATAATAA-AAATA
*
36648113 AGAATAGAAAATA
1 ATAATA-AAAATA
36648126 TGATAAT-AAAATA
1 --ATAATAAAAATA
36648139 TATAATAAAAATA
1 -ATAATAAAAATA
36648152 ATTAATAA
1 A-TAATAA
36648160 TAACAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 12 0.24
13 33 0.66
14 1 0.02
15 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (12 bp):
ATAATAAAAATA
Found at i:36648145 original size:12 final size:13
Alignment explanation
Indices: 36648120--36648148 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
36648110 ATAAGAATAG
36648120 AAAATATGATAAT
1 AAAATATGATAAT
36648133 AAAATAT-ATAAT
1 AAAATATGATAAT
36648145 AAAA
1 AAAA
36648149 ATAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAATATGATAAT
Found at i:36658475 original size:14 final size:13
Alignment explanation
Indices: 36658456--36658486 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
36658446 AAAAAAACAC
*
36658456 AAAAAAACAGAAA
1 AAAAAAAAAGAAA
36658469 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
36658482 AAAAA
1 AAAAA
36658487 GGAAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:36658475 original size:23 final size:22
Alignment explanation
Indices: 36658446--36658493 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
36658436 TCCAAAGCTT
*
36658446 AAAAAAACACAAAAAAACAGAAA
1 AAAAAAAAACAAAAAAA-AGAAA
* *
36658469 AAAAAAAAAGAAAAAAAAGGAA
1 AAAAAAAAACAAAAAAAAGAAA
36658491 AAA
1 AAA
36658494 TACAACTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACAAAAAAAAGAAA
Found at i:36676066 original size:51 final size:51
Alignment explanation
Indices: 36676007--36676109 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
36675997 CTTGTCCTCT
36676007 GCATTAATTTGAGCCTAACAATGAACTAACAATGCTAATTAAAATAAATAA
1 GCATTAATTTGAGCCTAACAATGAACTAACAATGCTAATTAAAATAAATAA
*
36676058 GCATTAATTTGAGCCTAACAATGAACTGACAATGCTAATTAAAATAAATAA
1 GCATTAATTTGAGCCTAACAATGAACTAACAATGCTAATTAAAATAAATAA
36676109 G
1 G
36676110 GCTATTTGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.27
Consensus pattern (51 bp):
GCATTAATTTGAGCCTAACAATGAACTAACAATGCTAATTAAAATAAATAA
Found at i:36679158 original size:23 final size:23
Alignment explanation
Indices: 36679132--36679247 Score: 73
Period size: 23 Copynumber: 5.0 Consensus size: 23
36679122 ACTTTATTCC
36679132 TATTTTATTTTTATTTTTGTTTT
1 TATTTTATTTTTATTTTTGTTTT
* * *
36679155 TATTTT-TTTATA-TTTT-ATAT
1 TATTTTATTTTTATTTTTGTTTT
*
36679175 TATTATATTCTTTATTTTT-TCATTT
1 TATTTTATT-TTTATTTTTGT--TTT
36679200 T-TTATCTATTTATTATTTTTGTTATT
1 TATT-T-TATTT-TTATTTTTGTT-TT
* *
36679226 TATATT-TTTTTATTATTGTTTT
1 TATTTTATTTTTATTTTTGTTTT
36679248 ATCTTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 23
0.69 0.10 0.22
Matches are distributed among these distances:
20 7 0.10
21 6 0.08
22 10 0.14
23 20 0.28
24 5 0.07
25 6 0.08
26 16 0.22
27 2 0.03
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (23 bp):
TATTTTATTTTTATTTTTGTTTT
Found at i:36679161 original size:7 final size:7
Alignment explanation
Indices: 36679134--36679261 Score: 59
Period size: 7 Copynumber: 17.3 Consensus size: 7
36679124 TTTATTCCTA
36679134 TTTTA-T
1 TTTTATT
36679140 TTTTATT
1 TTTTATT
36679147 TTTGT-TT
1 TTT-TATT
36679154 TTATT-TT
1 TT-TTATT
36679161 TTTATATT
1 TTT-TATT
*
36679169 TTATATT
1 TTTTATT
*
36679176 ATTATATT
1 -TTTTATT
*
36679184 CTTTATT
1 TTTTATT
36679191 TTTTCATT
1 TTTT-ATT
36679199 TTTTATCT
1 TTTTAT-T
*
36679207 ATTTATT
1 TTTTATT
36679214 ATTTT-TGT
1 -TTTTAT-T
*
36679222 TATTTATA
1 T-TTTATT
36679230 TTTT-TT
1 TTTTATT
*
36679236 TATTATT
1 TTTTATT
36679243 GTTTTATCTT
1 -TTTTA--TT
36679253 TTTTATT
1 TTTTATT
36679260 TT
1 TT
36679262 AAATTTCTCT
Statistics
Matches: 96, Mismatches: 10, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
6 10 0.10
7 40 0.42
8 38 0.40
9 6 0.06
10 2 0.02
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (7 bp):
TTTTATT
Found at i:36679164 original size:8 final size:8
Alignment explanation
Indices: 36679134--36679261 Score: 73
Period size: 9 Copynumber: 15.1 Consensus size: 8
36679124 TTTATTCCTA
36679134 TTTTATTT
1 TTTTATTT
*
36679142 TTATTTTTGT
1 TT-TTATT-T
36679152 TTTTATTT
1 TTTTATTT
*
36679160 TTTTA-TA
1 TTTTATTT
*
36679167 TTTTATAT
1 TTTTATTT
*
36679175 TATTATATT
1 TTTTAT-TT
*
36679184 CTTTATTT
1 TTTTATTT
*
36679192 TTTCA-TT
1 TTTTATTT
36679199 TTTTATCTAT
1 TTTTAT-T-T
36679209 TTATTATTT
1 TT-TTATTT
36679218 TTGTTATTT
1 TT-TTATTT
36679227 ATATTT-TTT
1 -T-TTTATTT
* *
36679236 TATTATTG
1 TTTTATTT
36679244 TTTTATCTT
1 TTTTAT-TT
36679253 TTTTATTT
1 TTTTATTT
36679261 T
1 T
36679262 AAATTTCTCT
Statistics
Matches: 91, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
7 14 0.15
8 29 0.32
9 33 0.36
10 10 0.11
11 5 0.05
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTATTT
Found at i:36679170 original size:15 final size:15
Alignment explanation
Indices: 36679152--36679262 Score: 59
Period size: 15 Copynumber: 7.3 Consensus size: 15
36679142 TTATTTTTGT
36679152 TTTTATTTTTTTATA
1 TTTTATTTTTTTATA
* *
36679167 TTTTATATTATTATA
1 TTTTATTTTTTTATA
* *
36679182 TTCTTTATTTTTTCATT
1 -T-TTTATTTTTTTATA
* *
36679199 TTTTATCTATTTATTA
1 TTTTATTTTTTTA-TA
*
36679215 TTTT-TGTTATTTATA
1 TTTTAT-TTTTTTATA
* *
36679230 -TTT-TTTTATTATTG
1 TTTTATTTTTTTA-TA
*
36679244 TTTTATCTTTTT-TA
1 TTTTATTTTTTTATA
36679258 TTTTA
1 TTTTA
36679263 AATTTCTCTT
Statistics
Matches: 72, Mismatches: 17, Indels: 15
0.69 0.16 0.14
Matches are distributed among these distances:
13 5 0.07
14 11 0.15
15 28 0.39
16 18 0.25
17 10 0.14
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTATTTTTTTATA
Found at i:36679219 original size:18 final size:16
Alignment explanation
Indices: 36679151--36679242 Score: 75
Period size: 17 Copynumber: 5.7 Consensus size: 16
36679141 TTTATTTTTG
*
36679151 TTTTTATTTTTTTATAT
1 TTTTTA-TTATTTATAT
*
36679168 TTTATATTA-TTATAT
1 TTTTTATTATTTATAT
*
36679183 TCTTTATT-TTT-TCAT
1 TTTTTATTATTTAT-AT
36679198 TTTTTATCTATTTAT-T
1 TTTTTAT-TATTTATAT
*
36679214 ATTTTTGTTATTTATATT
1 -TTTTTATTATTTATA-T
36679232 TTTTTATTATT
1 TTTTTATTATT
36679243 GTTTTATCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
14 1 0.02
15 22 0.37
16 11 0.18
17 24 0.40
18 2 0.03
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTTTATTATTTATAT
Found at i:36679241 original size:13 final size:12
Alignment explanation
Indices: 36679132--36679247 Score: 57
Period size: 12 Copynumber: 9.7 Consensus size: 12
36679122 ACTTTATTCC
*
36679132 TATTTTATTT-T
1 TATTTTTTTTAT
36679143 TATTTTTGTTT-T
1 TATTTTT-TTTAT
36679155 TA-TTTTTTTA-
1 TATTTTTTTTAT
*
36679165 TATTTTATATTAT
1 TATTTT-TTTTAT
* *
36679178 TATATTCTTTAT
1 TATTTTTTTTAT
36679190 T-TTTTCATTTT-T
1 TATTTT--TTTTAT
* *
36679202 TA-TCTATTTAT
1 TATTTTTTTTAT
*
36679213 TATTTTTGTTATT
1 TATTTTTTTTA-T
36679226 TATATTTTTTTAT
1 TAT-TTTTTTTAT
36679239 TATTGTTTT
1 TATT-TTTT
36679248 ATCTTTTTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
10 8 0.10
11 19 0.24
12 25 0.32
13 20 0.25
14 7 0.09
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (12 bp):
TATTTTTTTTAT
Found at i:36679614 original size:9 final size:9
Alignment explanation
Indices: 36679585--36679629 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
36679575 TGGGTATTAA
36679585 TATTTTTAT
1 TATTTTTAT
* *
36679594 AAATTCTTAT
1 -TATTTTTAT
36679604 TATTTTTAT
1 TATTTTTAT
36679613 TATTTTTAT
1 TATTTTTAT
36679622 TATTTTTA
1 TATTTTTA
36679630 CGATAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 24 0.77
10 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TATTTTTAT
Found at i:36679670 original size:17 final size:18
Alignment explanation
Indices: 36679648--36679681 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36679638 TAAATATAAG
36679648 ATTTATT-TTTTATTTTA
1 ATTTATTATTTTATTTTA
36679665 ATTTATTATTTTATTTT
1 ATTTATTATTTTATTTT
36679682 TTGACTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTATTATTTTATTTTA
Found at i:36680596 original size:2 final size:2
Alignment explanation
Indices: 36680589--36680622 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
36680579 GCTCGGTCCC
*
36680589 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
36680623 TGTTACCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:36681184 original size:16 final size:17
Alignment explanation
Indices: 36681165--36681207 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
36681155 GTTTTTCTCA
36681165 TTATTTTATTTTA-TAT
1 TTATTTTATTTTATTAT
36681181 TTA-TTTATTTTATTAT
1 TTATTTTATTTTATTAT
*
36681197 TT-TTTGATTTT
1 TTATTTTATTTT
36681208 TTTGGGTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TTATTTTATTTTATTAT
Found at i:36681189 original size:15 final size:15
Alignment explanation
Indices: 36681168--36681207 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
36681158 TTTCTCATTA
36681168 TTTTATTTTA-TATT
1 TTTTATTTTATTATT
36681182 TATTTATTTTATTATT
1 T-TTTATTTTATTATT
36681198 TTTTGATTTT
1 TTTT-ATTTT
36681208 TTTGGGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.04
15 12 0.52
16 10 0.43
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTATTTTATTATT
Found at i:36681655 original size:46 final size:46
Alignment explanation
Indices: 36681587--36681674 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
36681577 CCTTTGATTG
* * * *
36681587 AATCATACTTAAACTCTACCAACGTCTATCTGACTGAGTATAATCA
1 AATCAGACTCAAACTCTACCAACGTCTACCTGACTGAATATAATCA
* *
36681633 AATCAGACTCAAACTCTCCCAACGTTTACCTGACTGAATATA
1 AATCAGACTCAAACTCTACCAACGTCTACCTGACTGAATATA
36681675 CATGCTGATC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.28
Consensus pattern (46 bp):
AATCAGACTCAAACTCTACCAACGTCTACCTGACTGAATATAATCA
Found at i:36681686 original size:135 final size:135
Alignment explanation
Indices: 36681444--36681701 Score: 408
Period size: 135 Copynumber: 1.9 Consensus size: 135
36681434 TTTCTCAGCT
* * *
36681444 TTTGATTGAATTAGACCTAAACTCTACCAATGTCTATTTGACTGAGTATAATCAAATCAAACTCA
1 TTTGATTGAATCAGACCTAAACTCTACCAACGTCTATCTGACTGAGTATAATCAAATCAAACTCA
* * * *
36681509 AACTCTCCTAACATCTACCTGACTGAGTATACTTGTTGATCAGTTTTTTCTCAACTCCGCTTACT
66 AACTCTCCCAACATCTACCTGACTGAATATACATGCTGATCAGTTTTTTCTCAACTCCGCTTACT
36681574 CAACC
131 CAACC
* * *
36681579 TTTGATTGAATCATACTTAAACTCTACCAACGTCTATCTGACTGAGTATAATCAAATCAGACTCA
1 TTTGATTGAATCAGACCTAAACTCTACCAACGTCTATCTGACTGAGTATAATCAAATCAAACTCA
* *
36681644 AACTCTCCCAACGTTTACCTGACTGAATATACATGCTGATCAGTTTTTTCTCAACTCC
66 AACTCTCCCAACATCTACCTGACTGAATATACATGCTGATCAGTTTTTTCTCAACTCC
36681702 CTTGATTTGG
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 111 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (135 bp):
TTTGATTGAATCAGACCTAAACTCTACCAACGTCTATCTGACTGAGTATAATCAAATCAAACTCA
AACTCTCCCAACATCTACCTGACTGAATATACATGCTGATCAGTTTTTTCTCAACTCCGCTTACT
CAACC
Found at i:36681740 original size:30 final size:30
Alignment explanation
Indices: 36681704--36681761 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
36681694 TCAACTCCCT
36681704 TGATTTGGTGCAACATTCACCTTATTCTTC
1 TGATTTGGTGCAACATTCACCTTATTCTTC
** *
36681734 TGATTTGGTGCAATGTTCACTTTATTCT
1 TGATTTGGTGCAACATTCACCTTATTCT
36681762 ACCTATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (30 bp):
TGATTTGGTGCAACATTCACCTTATTCTTC
Found at i:36682207 original size:291 final size:290
Alignment explanation
Indices: 36681623--36682447 Score: 1202
Period size: 290 Copynumber: 2.8 Consensus size: 290
36681613 TATCTGACTG
* * * * * *
36681623 AGTATAATCAAATCAGACTCAAACTCTCCCAACGTTTACCTGACTGAATATACATGCTGA-TCAG
1 AGTATAATCAAATCAAACTCAAACTTTCCCAACGTCTACTTGACTGAGTATAAATGCTGACT-AG
* * * * *
36681687 TTTTTTCTCAACTCCCTTGATTTGGTGCAACATTCACCTTATTCTTCTGATTTGGTGCAATGTTC
65 TTTTTTCTCAACTCCCCTGATTTGGTGCAACTTTCACCTCATTCTCCTGATTTGGTGCAACGTTC
* * * * ** * *
36681752 ACTTTAT--TCTACCTATAAATACAGCCTCTCTACCTCTA-TCACAACACACA-A-ACCAAGCAA
130 AATTCATCCTTTGCCTATAAATACAATCTCCCTACCTC-AGTCACAACACACACACACTAAGCAA
* ** * * * **
36681812 AGCTTCTCTA-TA-TTTAAGTTTTGTCAACCTTTGAT-TAAATCAAACTTA-AACTCTACCAACG
194 CGCTTCTCTACTACTTT---CCTT-TCAAGCTTT--TCT---GCATA-TTATTTCTCTACCAACG
36681873 TACTTAAACTCTTCAGACTTAAACTTTACCAACATCTTCCTA
249 TACTTAAACTCTTCAGACTTAAACTTTACCAACATCTTCCTA
36681915 AGTATAATCAAATCAAACTCAAACTTTCCCAACGTCTACTTGACTGAGTATAAATGCTGACTAGT
1 AGTATAATCAAATCAAACTCAAACTTTCCCAACGTCTACTTGACTGAGTATAAATGCTGACTAG-
36681980 TTTTTTCTCAACTCCCCTGATTTGGTGCAACTTTCACCTCATTCTCCTGATTTGGTGCAACGTTC
65 TTTTTTCTCAACTCCCCTGATTTGGTGCAACTTTCACCTCATTCTCCTGATTTGGTGCAACGTTC
36682045 AATTCATCCTTTGCCTATAAATACAATCTCCCTACCTCAGTCACAACACACACACACTAAGCAAC
130 AATTCATCCTTTGCCTATAAATACAATCTCCCTACCTCAGTCACAACACACACACACTAAGCAAC
36682110 GCTTCTCTACTACTTTCCTTTCAAGCTTTTCTGCATATTATTTCTCTACCAACGTACTTAAACTC
195 GCTTCTCTACTACTTTCCTTTCAAGCTTTTCTGCATATTATTTCTCTACCAACGTACTTAAACTC
36682175 TTCAGACTTAAACTTTACCAACATCTTCCTA
260 TTCAGACTTAAACTTTACCAACATCTTCCTA
36682206 AGTATAATCAAATCAAACTCAAACTTTCCCAACGTCTACTTGACTGAGTATAAATGCTGACTAGT
1 AGTATAATCAAATCAAACTCAAACTTTCCCAACGTCTACTTGACTGAGTATAAATGCTGACTAGT
* *
36682271 TTTTTCTCAACTCTCCTGATTTGGTGCAACTTTCACCTCATTCTCCTGTTTTGGTGCAACGTTCA
66 TTTTTCTCAACTCCCCTGATTTGGTGCAACTTTCACCTCATTCTCCTGATTTGGTGCAACGTTCA
36682336 ATTCATCCTTTGCCTATAAATACAATCTCCCTACCTCAGTCACAACACACACACACTAAGCAACG
131 ATTCATCCTTTGCCTATAAATACAATCTCCCTACCTCAGTCACAACACACACACACTAAGCAACG
36682401 CTTCTCTACTACTTTCCTTTCAAGCTTTTCTGCATATTATTTCTCTA
196 CTTCTCTACTACTTTCCTTTCAAGCTTTTCTGCATATTATTTCTCTA
36682448 TTTTCATTCC
Statistics
Matches: 493, Mismatches: 29, Indels: 24
0.90 0.05 0.04
Matches are distributed among these distances:
290 179 0.36
291 120 0.24
292 56 0.11
293 67 0.14
294 2 0.00
295 44 0.09
296 3 0.01
297 17 0.03
298 2 0.00
299 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.35
Consensus pattern (290 bp):
AGTATAATCAAATCAAACTCAAACTTTCCCAACGTCTACTTGACTGAGTATAAATGCTGACTAGT
TTTTTCTCAACTCCCCTGATTTGGTGCAACTTTCACCTCATTCTCCTGATTTGGTGCAACGTTCA
ATTCATCCTTTGCCTATAAATACAATCTCCCTACCTCAGTCACAACACACACACACTAAGCAACG
CTTCTCTACTACTTTCCTTTCAAGCTTTTCTGCATATTATTTCTCTACCAACGTACTTAAACTCT
TCAGACTTAAACTTTACCAACATCTTCCTA
Found at i:36685825 original size:14 final size:14
Alignment explanation
Indices: 36685806--36685832 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36685796 CAAAAATTAT
36685806 AACTTATAAAAAAG
1 AACTTATAAAAAAG
36685820 AACTTATAAAAAA
1 AACTTATAAAAAA
36685833 AATTTTACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AACTTATAAAAAAG
Found at i:36688992 original size:36 final size:37
Alignment explanation
Indices: 36688925--36688998 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
36688915 ATTTATTAGT
* *
36688925 TATAAAAATTTAATTTAAATTTAAACTAAAATAAAAA
1 TATAAAAATTTAATTTAAATGTAAACAAAAATAAAAA
*
36688962 TATAAGAATTTAA-TTAAATGTAATA-AAAAATAAAAA
1 TATAAAAATTTAATTTAAATGTAA-ACAAAAATAAAAA
36688998 T
1 T
36688999 TTATTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 20 0.61
37 13 0.39
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (37 bp):
TATAAAAATTTAATTTAAATGTAAACAAAAATAAAAA
Found at i:36688999 original size:28 final size:29
Alignment explanation
Indices: 36688954--36689008 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
36688944 TTTAAACTAA
*
36688954 AATAAAAATATAAGAATTTAATTAAATGT
1 AATAAAAATATAAAAATTTAATTAAATGT
*
36688983 AATAAAAA-ATAAAAATTTATTTAAAT
1 AATAAAAATATAAAAATTTAATTAAAT
36689009 TTTTATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (29 bp):
AATAAAAATATAAAAATTTAATTAAATGT
Found at i:36689016 original size:29 final size:28
Alignment explanation
Indices: 36688954--36689035 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
36688944 TTTAAACTAA
* *
36688954 AATAAAAATATAAGAATTTAATTAAATGT
1 AATAAAAA-ATAAAAATTTATTTAAATGT
*
36688983 AATAAAAAATAAAAATTTATTTAAATTTT
1 AATAAAAAATAAAAATTTATTTAAA-TGT
* * *
36689012 TATAAATAATTAAAATTT-TTTAAA
1 AATAAAAAATAAAAATTTATTTAAA
36689036 ATATTATATC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 21 0.46
29 25 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
AATAAAAAATAAAAATTTATTTAAATGT
Found at i:36692490 original size:14 final size:14
Alignment explanation
Indices: 36692446--36692498 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
36692436 ATTTTAATGA
*
36692446 ATTTTTTAAAATAT
1 ATTTTTAAAAATAT
* * * *
36692460 -TATATAAAATTAA
1 ATTTTTAAAAATAT
36692473 ATTTTTAAAAATAT
1 ATTTTTAAAAATAT
36692487 ATTTTTAAAAAT
1 ATTTTTAAAAAT
36692499 TTTGAAGCCC
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTTTAAAAATAT
Found at i:36693591 original size:15 final size:15
Alignment explanation
Indices: 36693571--36693604 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
36693561 ATGTTAATAT
*
36693571 TTATATTAAATTTTA
1 TTATATTAAATGTTA
*
36693586 TTATATTAGATGTTA
1 TTATATTAAATGTTA
36693601 TTAT
1 TTAT
36693605 TATTTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
TTATATTAAATGTTA
Found at i:36693627 original size:26 final size:26
Alignment explanation
Indices: 36693580--36693634 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
36693570 TTTATATTAA
*
36693580 ATTTTATTATATTAGATGTTATTATT
1 ATTTTATTATATTAGATGTTATAATT
* *
36693606 ATTTTATTATAATTA-TTTTTATAATT
1 ATTTTATTAT-ATTAGATGTTATAATT
36693632 ATT
1 ATT
36693635 GATTTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (26 bp):
ATTTTATTATATTAGATGTTATAATT
Found at i:36693822 original size:21 final size:24
Alignment explanation
Indices: 36693776--36693833 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
36693766 CGTATTGTGT
*
36693776 TATAAA-ATTATTAAATATATTTA
1 TATAAATATTATTAAATATATTAA
36693799 TATAAATATT-TTAAAT-T-TTAA
1 TATAAATATTATTAAATATATTAA
36693820 TATAAATAATTATT
1 TATAAAT-ATTATT
36693834 TGTAACGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 10 0.32
22 4 0.13
23 14 0.45
24 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATAAATATTATTAAATATATTAA
Found at i:36699290 original size:24 final size:25
Alignment explanation
Indices: 36699257--36699305 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
36699247 GGTTTTTATT
36699257 TGAAAAAT-AAAAAATTTAATTAAA
1 TGAAAAATAAAAAAATTTAATTAAA
* *
36699281 TGAAATATAAAAAAATTTATTTAAA
1 TGAAAAATAAAAAAATTTAATTAAA
36699306 ATTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
TGAAAAATAAAAAAATTTAATTAAA
Found at i:36699974 original size:3 final size:3
Alignment explanation
Indices: 36699966--36699995 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
36699956 TTAGTTGTAA
36699966 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36699996 AATTTCTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36704680 original size:6 final size:6
Alignment explanation
Indices: 36704664--36704695 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
36704654 GGGAGAGAGA
36704664 GAAGGG G-AGGG GAAGGG GAAGGG GAAGGG GAA
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAA
36704696 ATGTTGAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:36706089 original size:6 final size:6
Alignment explanation
Indices: 36706080--36706108 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
36706070 GGATAGGGAA
36706080 CGAGAT CGAGAT CGAGAT CGAGAT CGAGA
1 CGAGAT CGAGAT CGAGAT CGAGAT CGAGA
36706109 CCGAAGCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.14
Consensus pattern (6 bp):
CGAGAT
Found at i:36711618 original size:41 final size:40
Alignment explanation
Indices: 36711551--36711629 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
36711541 TATATTGTGT
* *
36711551 TATTAGATTGAACATTGAGATATAATATATTATGATAGGC
1 TATTAGATTGAACATTAAAATATAATATATTATGATAGGC
* *
36711591 TATTGGATTGAACTATTAAAATATAATATGTTATGATAG
1 TATTAGATTGAAC-ATTAAAATATAATATATTATGATAG
36711630 ACTTAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 12 0.35
41 22 0.65
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (40 bp):
TATTAGATTGAACATTAAAATATAATATATTATGATAGGC
Found at i:36712059 original size:22 final size:23
Alignment explanation
Indices: 36712033--36712093 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
36712023 TAAAATCATC
*
36712033 GAAAATAAAATTCATA-TAA-TA
1 GAAAATAAAAATCATAGTAAGTA
* *
36712054 GAAAAAAGAAAAACATAGTAAGTA
1 GAAAATA-AAAATCATAGTAAGTA
*
36712078 GAAAATAAAACTCATA
1 GAAAATAAAAATCATA
36712094 AAAGACATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 6 0.19
22 7 0.23
23 10 0.32
24 8 0.26
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.20
Consensus pattern (23 bp):
GAAAATAAAAATCATAGTAAGTA
Found at i:36725118 original size:6 final size:6
Alignment explanation
Indices: 36725107--36725148 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
36725097 CTGCTTCAGG
*
36725107 TTTTTC TTTTTC TTTTTC TTTTT- TTCTTT- TTTGTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC T
36725149 CTTAATCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:36725143 original size:17 final size:16
Alignment explanation
Indices: 36725107--36725151 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
36725097 CTGCTTCAGG
36725107 TTTTTCTTTTTCT-TT
1 TTTTTCTTTTTCTCTT
*
36725122 TTCTT-TTTTTCT-TT
1 TTTTTCTTTTTCTCTT
*
36725136 TTTGTCTTTTTCTCTT
1 TTTTTCTTTTTCTCTT
36725152 AATCAGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 11 0.44
16 2 0.08
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTTCTCTT
Found at i:36726042 original size:32 final size:31
Alignment explanation
Indices: 36726006--36726066 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
36725996 AATATACGAA
* *
36726006 ATTATATTAAAGAAATGAAAATAAACTATAAG
1 ATTATAATAAA-AAATGAAAATAAAATATAAG
* *
36726038 ATTATAATAAAAATTTAAAATAAAATATA
1 ATTATAATAAAAAATGAAAATAAAATATA
36726067 TGACATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (31 bp):
ATTATAATAAAAAATGAAAATAAAATATAAG
Found at i:36750450 original size:12 final size:12
Alignment explanation
Indices: 36750435--36750475 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
36750425 ATATTTGATG
*
36750435 TTATTATTATTA
1 TTATTATTATAA
36750447 TTATTTATTATAA
1 TTA-TTATTATAA
*
36750460 TTATTTTTATAA
1 TTATTATTATAA
36750472 TTAT
1 TTAT
36750476 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTATTATAA
Found at i:36750454 original size:13 final size:13
Alignment explanation
Indices: 36750438--36750475 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
36750428 TTTGATGTTA
*
36750438 TTATTATTATTAT
1 TTATTATAATTAT
36750451 TTATTATAATTAT
1 TTATTATAATTAT
36750464 TT-TTATAATTAT
1 TTATTATAATTAT
36750476 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATAATTAT
Found at i:36755897 original size:93 final size:92
Alignment explanation
Indices: 36755739--36755920 Score: 283
Period size: 93 Copynumber: 2.0 Consensus size: 92
36755729 AAATAAGGGA
* * * *
36755739 ACCCAATTGCCCAATTAACAAGACACTATGAACGGTGTGCTACGAGGAATTAATATATGGATCAT
1 ACCCAATTGCCCAATTAACAAAACACTATGAACGGTCTGCTACAAGGAATTAATATATAGATCAT
36755804 GTTTCTTGATTCTGCAAACTCCTGGGT
66 GTTTCTTGATTCTGCAAACTCCTGGGT
* * * *
36755831 ACCCAATTGTCCTATTAACAAAAACACTATGGACGGTCTGCTACAAGGAATTCATATATAGATCA
1 ACCCAATTGCCCAATTAAC-AAAACACTATGAACGGTCTGCTACAAGGAATTAATATATAGATCA
36755896 TGTTTCTTGATTCTGCAAACTCCTG
65 TGTTTCTTGATTCTGCAAACTCCTG
36755921 AGTAGCAGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 17 0.21
93 64 0.79
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (92 bp):
ACCCAATTGCCCAATTAACAAAACACTATGAACGGTCTGCTACAAGGAATTAATATATAGATCAT
GTTTCTTGATTCTGCAAACTCCTGGGT
Found at i:36782585 original size:2 final size:2
Alignment explanation
Indices: 36782578--36782608 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
36782568 GAACAAAGTA
*
36782578 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
36782609 AGTTAAATTG
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:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36792692 original size:18 final size:18
Alignment explanation
Indices: 36792671--36792710 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
36792661 AATTTTTTTT
*
36792671 TTATAAATTTTT-TTTAAA
1 TTAT-AATTTTTATTAAAA
36792689 TTATAATTTTTATTAAAA
1 TTATAATTTTTATTAAAA
36792707 TTAT
1 TTAT
36792711 TATAGAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATAATTTTTATTAAAA
Found at i:36798014 original size:24 final size:24
Alignment explanation
Indices: 36797979--36798058 Score: 142
Period size: 24 Copynumber: 3.3 Consensus size: 24
36797969 CAAAAGCAGA
36797979 ACCTTAATAACTGATTATCAAGGG
1 ACCTTAATAACTGATTATCAAGGG
* *
36798003 ACTTTAATAACTGATTATCAAAGG
1 ACCTTAATAACTGATTATCAAGGG
36798027 ACCTTAATAACTGATTATCAAGGG
1 ACCTTAATAACTGATTATCAAGGG
36798051 ACCTTAAT
1 ACCTTAAT
36798059 CAATTAAGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (24 bp):
ACCTTAATAACTGATTATCAAGGG
Found at i:36800586 original size:15 final size:15
Alignment explanation
Indices: 36800566--36800626 Score: 86
Period size: 15 Copynumber: 4.1 Consensus size: 15
36800556 ACTTTACAAT
*
36800566 GTAATGTGATTACAG
1 GTAATGTGATTGCAG
*
36800581 GTAATGTAATTGCAG
1 GTAATGTGATTGCAG
* *
36800596 GTAATGTGATTGTAA
1 GTAATGTGATTGCAG
36800611 GTAATGTGATTGCAG
1 GTAATGTGATTGCAG
36800626 G
1 G
36800627 GAAGATAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (15 bp):
GTAATGTGATTGCAG
Found at i:36800813 original size:17 final size:17
Alignment explanation
Indices: 36800791--36800823 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
36800781 ATTTTTTTAT
36800791 TGTTAATTTTTAAATAA
1 TGTTAATTTTTAAATAA
36800808 TGTTAATTTTTAAATA
1 TGTTAATTTTTAAATA
36800824 TATTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TGTTAATTTTTAAATAA
Found at i:36800850 original size:33 final size:32
Alignment explanation
Indices: 36800800--36800884 Score: 77
Period size: 32 Copynumber: 2.6 Consensus size: 32
36800790 TTGTTAATTT
*
36800800 TTAAATA-ATGTTAATTTTTAAATATATTTTTAA
1 TTAAATATAT-TTTATTTTTAAATATATTTTT-A
* * *
36800833 TTAAATATATTTTATTTTT-CATTTCTTTTTA
1 TTAAATATATTTTATTTTTAAATATATTTTTA
36800864 -TAAGTATATATTTTATTTTTA
1 TTAA--ATATATTTTATTTTTA
36800885 TTTTTAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 3 0.07
31 1 0.02
32 23 0.52
33 15 0.34
34 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (32 bp):
TTAAATATATTTTATTTTTAAATATATTTTTA
Found at i:36802296 original size:15 final size:15
Alignment explanation
Indices: 36802276--36802307 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
36802266 GCTTAAAATG
*
36802276 ATTTCTCAACTTGAA
1 ATTTCTCAACTTAAA
36802291 ATTTCTCAACTTAAA
1 ATTTCTCAACTTAAA
36802306 AT
1 AT
36802308 GATGCTGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (15 bp):
ATTTCTCAACTTAAA
Found at i:36808961 original size:19 final size:19
Alignment explanation
Indices: 36808934--36808978 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
36808924 ATATAGGTAT
36808934 ATATAAATATGAAAAATAT-A
1 ATAT-AATAT-AAAAATATAA
*
36808954 ATATAATATAAAATTATAA
1 ATATAATATAAAAATATAA
36808973 ATATAA
1 ATATAA
36808979 AAAAATAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 12 0.52
20 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATATAATATAAAAATATAA
Found at i:36811619 original size:16 final size:14
Alignment explanation
Indices: 36811589--36811628 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
36811579 TTTTTTCCCA
36811589 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
36811603 TTTTTTTCTCTCTTTC
1 TTTTTTTCT-TC-TTC
*
36811619 TTTCTTTCTT
1 TTTTTTTCTT
36811629 GGCTCGCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 3 0.13
16 11 0.48
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTTCTTCTTC
Found at i:36812151 original size:20 final size:18
Alignment explanation
Indices: 36812126--36812165 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
36812116 AGTCCTTTCC
36812126 TTGTTTTCTCTCTTTTTTAT
1 TTGTTTT-TCT-TTTTTTAT
*
36812146 TTGTTTTTGTTTTTTTAT
1 TTGTTTTTCTTTTTTTAT
36812164 TT
1 TT
36812166 TTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.05, C:0.07, G:0.07, T:0.80
Consensus pattern (18 bp):
TTGTTTTTCTTTTTTTAT
Found at i:36812206 original size:25 final size:23
Alignment explanation
Indices: 36812138--36812207 Score: 61
Period size: 27 Copynumber: 2.8 Consensus size: 23
36812128 GTTTTCTCTC
36812138 TTTTTTATTTGTTTT-TGTTTTTT
1 TTTTTTATTTGTTTTAT-TTTTTT
*
36812161 TATTTTTAATTTATTTCTTATTTTTTAT
1 T-TTTTT-ATTT-GTT-TTATTTTTT-T
36812189 TTTTTTAGTTTGTTTTATT
1 TTTTTTA-TTTGTTTTATT
36812208 ATATTTCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
23 1 0.03
24 5 0.13
25 9 0.24
26 5 0.13
27 15 0.39
28 3 0.08
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (23 bp):
TTTTTTATTTGTTTTATTTTTTT
Found at i:36813815 original size:15 final size:14
Alignment explanation
Indices: 36813772--36813826 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
36813762 CATTTGGTAT
36813772 ATTGCTGAGGATGTG
1 ATTGCTG-GGATGTG
**
36813787 ATTATTGGGAATGTG
1 ATTGCTGGG-ATGTG
36813802 ATTGCTGCGGATGTG
1 ATTGCTG-GGATGTG
*
36813817 ACTGCTGGGA
1 ATTGCTGGGA
36813827 ATATAACTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 5 0.15
15 26 0.79
16 2 0.06
ACGTcount: A:0.20, C:0.09, G:0.38, T:0.33
Consensus pattern (14 bp):
ATTGCTGGGATGTG
Found at i:36813826 original size:30 final size:30
Alignment explanation
Indices: 36813772--36813828 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
36813762 CATTTGGTAT
* *
36813772 ATTGCTGAGGATGTGATTATTGGGAATGTG
1 ATTGCTGAGGATGTGACTACTGGGAATGTG
* *
36813802 ATTGCTGCGGATGTGACTGCTGGGAAT
1 ATTGCTGAGGATGTGACTACTGGGAAT
36813829 ATAACTTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.37, T:0.33
Consensus pattern (30 bp):
ATTGCTGAGGATGTGACTACTGGGAATGTG
Found at i:36814117 original size:18 final size:18
Alignment explanation
Indices: 36814094--36814129 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
36814084 ATATTTTATT
36814094 AAAATAT-TGAAATATTTA
1 AAAATATAT-AAATATTTA
36814112 AAAATATATAAATATTTA
1 AAAATATATAAATATTTA
36814130 TTTTTGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAATATATAAATATTTA
Found at i:36817066 original size:63 final size:62
Alignment explanation
Indices: 36816873--36817096 Score: 286
Period size: 62 Copynumber: 3.6 Consensus size: 62
36816863 AAGACAATTT
* * * * * * **
36816873 GGTAGTTATCGATAGATGCCAACATCAATTGATAGTTCTTCACTCGAGAGCAAAACAGGCTT
1 GGTAGCTATCGATAGATGACAACATCTATCGATAGTTCTTCACCCGAGAGCAAGACAGGCCC
* *
36816935 GGTAGCTATTGATAGATGACAACATCTATCGATACTTCTTCACCCGAGAGCAAGACAGGCCC
1 GGTAGCTATCGATAGATGACAACATCTATCGATAGTTCTTCACCCGAGAGCAAGACAGGCCC
** * *
36816997 GGTAGCTATCGATAGATCCCAACATCTATCGAATAGTTCTTCACCCAAGAGCAAGACAAGCCC
1 GGTAGCTATCGATAGATGACAACATCTATCG-ATAGTTCTTCACCCGAGAGCAAGACAGGCCC
* * *
36817060 GATAGCTATTGATAGATGACAACATCTATTGATAGTT
1 GGTAGCTATCGATAGATGACAACATCTATCGATAGTT
36817097 TCAAAGAGCT
Statistics
Matches: 140, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
62 86 0.61
63 54 0.39
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (62 bp):
GGTAGCTATCGATAGATGACAACATCTATCGATAGTTCTTCACCCGAGAGCAAGACAGGCCC
Found at i:36820868 original size:11 final size:11
Alignment explanation
Indices: 36820839--36820882 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
36820829 CTACACACCC
36820839 TAAACACTATA
1 TAAACACTATA
36820850 TGAAACACTATA
1 T-AAACACTATA
*
36820862 TAAACACAATA
1 TAAACACTATA
36820873 TAAACACTAT
1 TAAACACTAT
36820883 GAAACACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (11 bp):
TAAACACTATA
Found at i:36820990 original size:23 final size:23
Alignment explanation
Indices: 36820923--36820979 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
36820913 TTGTATCATA
36820923 TACCCTGAAACAGA-ATATAAACAC
1 TACCCT-AAACA-ACATATAAACAC
*
36820947 TACCCTAAACAACCTATAAACAC
1 TACCCTAAACAACATATAAACAC
*
36820970 TACTCTAAAC
1 TACCCTAAAC
36820980 GCTATATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 23 0.77
24 6 0.20
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (23 bp):
TACCCTAAACAACATATAAACAC
Found at i:36834092 original size:17 final size:18
Alignment explanation
Indices: 36834049--36834096 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
36834039 AAATATTAAA
36834049 AATTAATAAT-TTATTTAT
1 AATTAA-AATATTATTTAT
*
36834067 AATTTAAATATTA-TTAT
1 AATTAAAATATTATTTAT
*
36834084 GATTAAAATATTA
1 AATTAAAATATTA
36834097 AATATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATTAAAATATTATTTAT
Found at i:36834321 original size:21 final size:21
Alignment explanation
Indices: 36834295--36834343 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
36834285 TCATTAAGGC
36834295 ATCAGATCGGTACTTTCCATG
1 ATCAGATCGGTACTTTCCATG
* *
36834316 ATCAGATCGGTATTTTTCATG
1 ATCAGATCGGTACTTTCCATG
36834337 ATCAGAT
1 ATCAGAT
36834344 TTGGTCGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (21 bp):
ATCAGATCGGTACTTTCCATG
Found at i:36835180 original size:118 final size:115
Alignment explanation
Indices: 36835012--36835230 Score: 314
Period size: 118 Copynumber: 1.9 Consensus size: 115
36835002 AATTATATAT
* * * * *
36835012 TTTCTTTTTTAATCTTTTAATTTTATTTTTATTAACATTTTACAATATTAATAATCTATTATTAA
1 TTTCTTTTTTAATCTTTTAATTTTATTTTCATCAAAAATTTACAACATTAATAATCTATTATTAA
*
36835077 ATTATTAATATGATTTTTTATTTCAATTTCTTTTTATTGTCTTTATTTGTAC
66 ATTATTAATAT-A-TTTTTATTTCAATTTATTTTTATTGTCTTTATTTGTAC
* *
36835129 TTTCTTTTTTTAATCTTTTAATTTCTATTTTCGTCAAAAATTTA-AACATTAATAATTTATTATT
1 TTTC-TTTTTTAATCTTTTAATTT-TATTTTCATCAAAAATTTACAACATTAATAATCTATTATT
*
36835193 AAATTATTAATATATTTTTATTTTAATTTATTTTTATT
64 AAATTATTAATATATTTTTATTTCAATTTATTTTTATT
36835231 TTTTAATTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
116 22 0.24
117 5 0.05
118 50 0.55
119 14 0.15
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (115 bp):
TTTCTTTTTTAATCTTTTAATTTTATTTTCATCAAAAATTTACAACATTAATAATCTATTATTAA
ATTATTAATATATTTTTATTTCAATTTATTTTTATTGTCTTTATTTGTAC
Found at i:36835203 original size:19 final size:17
Alignment explanation
Indices: 36835176--36835226 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
36835166 AAATTTAAAC
*
36835176 ATTAATAATTTATTATTAA
1 ATTATTAATTTATT-TT-A
* *
36835195 ATTATTAATATATTTTT
1 ATTATTAATTTATTTTA
36835212 ATT-TTAATTTATTTT
1 ATTATTAATTTATTTT
36835227 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 2 0.07
19 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTATTAATTTATTTTA
Found at i:36835239 original size:18 final size:16
Alignment explanation
Indices: 36835199--36835232 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
36835189 TATTAAATTA
*
36835199 TTAATATATTTTTATT
1 TTAATTTATTTTTATT
36835215 TTAATTTATTTTTATT
1 TTAATTTATTTTTATT
36835231 TT
1 TT
36835233 TTAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTAATTTATTTTTATT
Found at i:36837635 original size:35 final size:35
Alignment explanation
Indices: 36837592--36837703 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
36837582 AGTGTGGATA
*
36837592 ATGATATTGAAGTGTGCAAGTAGGGAGTGCACATG
1 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACATG
*
36837627 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACACG
1 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACATG
* * *
36837662 ATGATATAGAAATGTGCGAGTAGGGAATGCACATG
1 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACATG
*
36837697 ATAATAT
1 ATGATAT
36837704 ATAGTGTGCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.34, C:0.09, G:0.32, T:0.25
Consensus pattern (35 bp):
ATGATATTGAAGTGTGCGAGTAGGGAGTGCACATG
Found at i:36837751 original size:38 final size:38
Alignment explanation
Indices: 36837708--36837807 Score: 146
Period size: 38 Copynumber: 2.6 Consensus size: 38
36837698 TAATATATAG
* *
36837708 TGTGCGCGATGTGGGGGTGCACACGATGACTCCAGCTA
1 TGTGCGCTATGTGGGGGTGCACACGATGACTCCAACTA
*
36837746 TGTGCGCTATGTGGGAGTGCACACGATGACTCCAACTA
1 TGTGCGCTATGTGGGGGTGCACACGATGACTCCAACTA
* *
36837784 TGTGCACTATGTGAGGGTTGCACA
1 TGTGCGCTATGTG-GGGGTGCACA
36837808 TGAGCTGGTG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
38 47 0.85
39 8 0.15
ACGTcount: A:0.21, C:0.22, G:0.33, T:0.24
Consensus pattern (38 bp):
TGTGCGCTATGTGGGGGTGCACACGATGACTCCAACTA
Found at i:36839272 original size:15 final size:15
Alignment explanation
Indices: 36839240--36839300 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
36839230 TATATATGAA
**
36839240 TAAAATATTAATTTT
1 TAAAATATTAATAAT
36839255 TAAAATATTAATAAT
1 TAAAATATTAATAAT
*
36839270 TAAATTA-T-A-AAT
1 TAAAATATTAATAAT
* *
36839282 AAAAATATTAATATT
1 TAAAATATTAATAAT
36839297 TAAA
1 TAAA
36839301 TGATCTATTC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
12 8 0.22
13 2 0.06
14 2 0.06
15 24 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATATTAATAAT
Found at i:36839287 original size:42 final size:41
Alignment explanation
Indices: 36839183--36839300 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 41
36839173 ACTAATTTTA
* * * *
36839183 AATTAAAAATTAATTAAAATTATTAATATTTTAATCATAATAAT
1 AATTAAATA-TAAATAAAAATATTAAT-TTTTAA-AATAATAAT
* * * *
36839227 ATTTATATATGAAT-AAAATATTAATTTTTAAAATATTAAT
1 AATTAAATATAAATAAAAATATTAATTTTTAAAATAATAAT
*
36839267 AATTAAATTATAAATAAAAATATTAATATTTAAA
1 AATTAAA-TATAAATAAAAATATTAATTTTTAAA
36839301 TGATCTATTC
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
40 12 0.20
41 12 0.20
42 27 0.45
43 3 0.05
44 6 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (41 bp):
AATTAAATATAAATAAAAATATTAATTTTTAAAATAATAAT
Found at i:36839410 original size:17 final size:17
Alignment explanation
Indices: 36839383--36839430 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
36839373 TNNNNNTAAT
36839383 AATATTTAAATAATATAA
1 AATA-TTAAATAATATAA
** *
36839401 AATATTAAATTTTTTAA
1 AATATTAAATAATATAA
36839418 AATATT-AATAATA
1 AATATTAAATAATA
36839431 AATTATAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTAAATAATATAA
Found at i:36839412 original size:159 final size:159
Alignment explanation
Indices: 36839220--36839534 Score: 484
Period size: 159 Copynumber: 2.0 Consensus size: 159
36839210 ATTTTAATCA
*
36839220 TAATAATATTTATATATGAATAAAATATTAA-TTTTTAAAATATTAATAATTAAATTATAAATAA
1 TAATAATATTTAAATAT-AATAAAATATTAATTTTTTAAAATATTAATAA-TAAATTATAAATAA
36839284 AAATATTAATATTTAAATGATCTATTCTTAATA-TTTAAAT-AA-TTAAATAAATATTATAAT-A
64 AAATATTAATATTTAAATGATCTATTCTTAATATTTTAAATAAATTTAAATAAATATTATAATAA
36839345 AAAATA-TTCTC-TTTTATCACTTTTTGTTT
129 AAAATATTTCTCTTTTTATCACTTTTTGTTT
36839374 NNNNNTAATAATATTTAAATA-ATATAAAATATTAAATTTTTTAAAATATTAATAATAAATTATA
1 -----TAATAATATTTAAATATA-ATAAAATATT-AATTTTTTAAAATATTAATAATAAATTATA
36839438 AATAAAAATATTAATATTTAAATGATCTATTCTTAATATTTTAAATAAATTTAAATAAATATTAT
59 AATAAAAATATTAATATTTAAATGATCTATTCTTAATATTTTAAATAAATTTAAATAAATATTAT
36839503 AATAAAAAATATTTCTCTTTTTATCACTTTTT
124 AATAAAAAATATTTCTCTTTTTATCACTTTTT
36839535 TTTGTTTTTT
Statistics
Matches: 146, Mismatches: 1, Indels: 12
0.92 0.01 0.08
Matches are distributed among these distances:
157 1 0.01
158 10 0.07
159 64 0.44
160 25 0.17
161 2 0.01
162 18 0.12
163 7 0.05
164 5 0.03
165 14 0.10
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (159 bp):
TAATAATATTTAAATATAATAAAATATTAATTTTTTAAAATATTAATAATAAATTATAAATAAAA
ATATTAATATTTAAATGATCTATTCTTAATATTTTAAATAAATTTAAATAAATATTATAATAAAA
AATATTTCTCTTTTTATCACTTTTTGTTT
Found at i:36840933 original size:15 final size:16
Alignment explanation
Indices: 36840897--36840935 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
36840887 ATTCATTTTT
36840897 ATCA-AAATAACTAAA
1 ATCATAAATAACTAAA
36840912 A--ATAAATAA-TAAA
1 ATCATAAATAACTAAA
36840925 ATCATAAATAA
1 ATCATAAATAA
36840936 ACCAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 6 0.29
14 6 0.29
15 9 0.43
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (16 bp):
ATCATAAATAACTAAA
Found at i:36842220 original size:33 final size:32
Alignment explanation
Indices: 36842179--36842252 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
36842169 AGTGATGGTG
36842179 AAAAATATTTTTCACGAGA-TCATCCAAATAATA
1 AAAAATATTTTTCA-GA-ATTCATCCAAATAATA
* * *
36842212 AAAAATATTTTTTATAATTCATTCAAATAATA
1 AAAAATATTTTTCAGAATTCATCCAAATAATA
36842244 AAAAATATT
1 AAAAATATT
36842253 AAATTCTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 1 0.03
32 23 0.62
33 13 0.35
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.36
Consensus pattern (32 bp):
AAAAATATTTTTCAGAATTCATCCAAATAATA
Found at i:36842469 original size:18 final size:19
Alignment explanation
Indices: 36842428--36842470 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
36842418 TATAGATCTT
* *
36842428 TATTTATTTTTTTTTAGAA
1 TATTTATTTATTTGTAGAA
36842447 T-TTTATTTATTTGT-GAA
1 TATTTATTTATTTGTAGAA
36842464 TATTTAT
1 TATTTAT
36842471 AATTTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 16 0.76
19 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (19 bp):
TATTTATTTATTTGTAGAA
Done.