Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 51
Found at i:5181447 original size:42 final size:42
Alignment explanation
Indices: 5181388--5181645 Score: 306
Period size: 42 Copynumber: 6.0 Consensus size: 42
5181378 GCTTTTTGAA
**
5181388 AACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTT
1 AACATCCTGCACTGGAGGTCTTACAGATGACCCGGAGGATTT
*
5181430 AACATCTTGCACTGGAGGTCTTACAGATGACCCGGAGGATTTT
1 AACATCCTGCACTGGAGGTCTTACAGATGACCCGGAGGA-TTT
**
5181473 AAACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTT
1 -AACATCCTGCACTGGAGGTCTTACAGATGACCCGGAGGATTT
* *
5181516 AACATCTTGCACTGGAGGTCTTACAGATGACCTGGAGGATTTT
1 AACATCCTGCACTGGAGGTCTTACAGATGACCCGGAGGA-TTT
* *
5181559 AAACATCCTGCACTGGAGGTCTTA-TGTATGACCCTGTA-G-TCTT
1 -AACATCCTGCACTGGAGGTCTTACAG-ATGACCC-GGAGGAT-TT
* * * * *
5181602 ATCATCTTGCACTGTAGGTCTTACAGATGACCCGAAAGATTT
1 AACATCCTGCACTGGAGGTCTTACAGATGACCCGGAGGATTT
5181644 AA
1 AA
5181646 GATCAAGAAA
Statistics
Matches: 186, Mismatches: 20, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
41 2 0.01
42 103 0.55
43 14 0.08
44 65 0.35
45 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (42 bp):
AACATCCTGCACTGGAGGTCTTACAGATGACCCGGAGGATTT
Found at i:5181643 original size:86 final size:86
Alignment explanation
Indices: 5181387--5181635 Score: 421
Period size: 86 Copynumber: 2.9 Consensus size: 86
5181377 GGCTTTTTGA
5181387 AAACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTTAACATCTTGCACTGGAGGTCTT
1 AAACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTTAACATCTTGCACTGGAGGTCTT
5181452 ACAGATGACCCGGAGGATTTT
66 ACAGATGACCCGGAGGATTTT
5181473 AAACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTTAACATCTTGCACTGGAGGTCTT
1 AAACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTTAACATCTTGCACTGGAGGTCTT
*
5181538 ACAGATGACCTGGAGGATTTT
66 ACAGATGACCCGGAGGATTTT
* * * *
5181559 AAACATCCTGCACTGGAGGTCTTATGTATGACCCTGTA-G-TCTTATCATCTTGCACTGTAGGTC
1 AAACATCCTGCACTGGAGGTCTTATGGATGACCC-GGAGGAT-TTAACATCTTGCACTGGAGGTC
5181622 TTACAGATGACCCG
64 TTACAGATGACCCG
5181636 AAAGATTTAA
Statistics
Matches: 155, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
85 1 0.01
86 152 0.98
87 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (86 bp):
AAACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTTAACATCTTGCACTGGAGGTCTT
ACAGATGACCCGGAGGATTTT
Found at i:5181749 original size:45 final size:45
Alignment explanation
Indices: 5181685--5181809 Score: 214
Period size: 45 Copynumber: 2.8 Consensus size: 45
5181675 TAAAATCTCA
* * *
5181685 TTTGAAAACATCCTGCACTGGAGGTCTTACATATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
5181730 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
*
5181775 TTTGAAAACATCTTGCACTGAAGGTCTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATG
5181810 TGGGAAATAG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
Found at i:5181752 original size:25 final size:25
Alignment explanation
Indices: 5181724--5181799 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
5181714 CATATGACCC
5181724 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
* * *
5181749 GAAGGTCTT----ACA-GATG-ACCC
1 GAAGGTTTTGAAAACATCATGCA-CT
*
5181769 GAAGGTTTTGAAAACATCTTGCACT
1 GAAGGTTTTGAAAACATCATGCACT
5181794 GAAGGT
1 GAAGGT
5181800 CTTACAGATG
Statistics
Matches: 37, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
19 1 0.03
20 12 0.32
21 3 0.08
24 3 0.08
25 17 0.46
26 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (25 bp):
GAAGGTTTTGAAAACATCATGCACT
Found at i:5182508 original size:22 final size:23
Alignment explanation
Indices: 5182483--5182535 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
5182473 AATAAAGCTT
5182483 ATCTTTGAAAAGAA-AATCTATC
1 ATCTTTGAAAAGAAGAATCTATC
5182505 ATCTTTG--AAGAATGAATCTATC
1 ATCTTTGAAAAGAA-GAATCTATC
*
5182527 ATTTTTGAA
1 ATCTTTGAA
5182536 TAATGTAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.19
22 21 0.81
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (23 bp):
ATCTTTGAAAAGAAGAATCTATC
Found at i:5182540 original size:22 final size:22
Alignment explanation
Indices: 5182497--5182540 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5182487 TTGAAAAGAA
5182497 AATCTATCATCTTTGAAGAATG
1 AATCTATCATCTTTGAAGAATG
* *
5182519 AATCTATCATTTTTGAATAATG
1 AATCTATCATCTTTGAAGAATG
5182541 TAGATGTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAATG
Found at i:5183920 original size:75 final size:75
Alignment explanation
Indices: 5183826--5183966 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 75
5183816 TCTAATATAG
* * *
5183826 ACGTTCAAAATGCGCCAATATT-CTAATTTCTGATTTAAATGAGCTTTCAGTATACCCCAACATT
1 ACGTTCAAAATGCGCCAATATTCCTAA-TTATGATTGAAATGAGCTTTCAGCATACCCCAACATT
5183890 TGTTGATACAA
65 TGTTGATACAA
* * * *
5183901 ACGTTCAAAATGCGTCAATATTCCTGATTATGATTGAAATGGGCTTTCAGCATGCCCCAACATTT
1 ACGTTCAAAATGCGCCAATATTCCTAATTATGATTGAAATGAGCTTTCAGCATACCCCAACATTT
5183966 G
66 G
5183967 CTTTTTTGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 55 0.95
76 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (75 bp):
ACGTTCAAAATGCGCCAATATTCCTAATTATGATTGAAATGAGCTTTCAGCATACCCCAACATTT
GTTGATACAA
Found at i:5185441 original size:18 final size:17
Alignment explanation
Indices: 5185387--5185435 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
5185377 TTGGAACCTT
* *
5185387 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
5185405 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
5185423 AGTGCATTCGATG
1 AGTGCA-TCGATG
5185436 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:5185540 original size:65 final size:65
Alignment explanation
Indices: 5185406--5185616 Score: 200
Period size: 65 Copynumber: 3.3 Consensus size: 65
5185396 GTGCACTAAG
*
5185406 AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCATAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCATAGTGCATCGATGCATGGCT
* * * * *
5185470 GGTGCATCGATGCATTAAATGTATTCGATGTTTTCATAAA-ATCC-TCAGTGCATCGGTGCATGG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAT-AGTGCATCGATGCATGG
5185533 -T
64 CT
* * ** ** *
5185534 AAGTGCATCGATGCATGAAATGCATTCAATG--TTCAATTTAATTCATGGTGCATCGATGCATGG
1 -AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT-AGCCATAGTGCATCGATGCATGG
*
5185597 ATT
64 -CT
*
5185600 GGTGCATCGATGCATCA
1 AGTGCATCGATGCATCA
5185617 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.38
65 66 0.55
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCATAGTGCATCGATGCATGGCT
Found at i:5187729 original size:13 final size:13
Alignment explanation
Indices: 5187701--5187739 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5187691 TGGGCAATGT
*
5187701 TTTGAAAA-ACTA
1 TTTGAAAATAATA
5187713 TTTGAAAATAATA
1 TTTGAAAATAATA
*
5187726 TTTGTAAATAATA
1 TTTGAAAATAATA
5187739 T
1 T
5187740 GTATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:5194097 original size:17 final size:18
Alignment explanation
Indices: 5194075--5194110 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5194065 GTGCACTAAG
5194075 AGTGCA-TCGATGTATCA
1 AGTGCATTCGATGTATCA
*
5194092 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTATCA
5194110 A
1 A
5194111 AATAGCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTGCATTCGATGTATCA
Found at i:5194274 original size:65 final size:63
Alignment explanation
Indices: 5194076--5194285 Score: 203
Period size: 65 Copynumber: 3.3 Consensus size: 63
5194066 TGCACTAAGA
* * * * *
5194076 GTGCATCGATGTATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGGGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
5194139 G
63 G
* **
5194140 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTTG
* **
5194205 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
5194268 TG
62 TG
*
5194270 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
5194286 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 47 0.39
65 64 0.52
66 4 0.03
67 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:5198007 original size:13 final size:13
Alignment explanation
Indices: 5197989--5198041 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
5197979 CAATGCAAAT
5197989 ATGAAAATATAAA
1 ATGAAAATATAAA
*
5198002 ATGAAAATGT-AA
1 ATGAAAATATAAA
5198014 ATGAAAATATAAA
1 ATGAAAATATAAA
* *
5198027 GATGCAAACATAAA
1 -ATGAAAATATAAA
5198041 A
1 A
5198042 AATGCAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 11 0.32
13 12 0.35
14 11 0.32
ACGTcount: A:0.64, C:0.04, G:0.11, T:0.21
Consensus pattern (13 bp):
ATGAAAATATAAA
Found at i:5198017 original size:12 final size:12
Alignment explanation
Indices: 5197989--5198026 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
5197979 CAATGCAAAT
5197989 ATGAAAATATAAA
1 ATGAAAATAT-AA
*
5198002 ATGAAAATGTAA
1 ATGAAAATATAA
5198014 ATGAAAATATAA
1 ATGAAAATATAA
5198026 A
1 A
5198027 GATGCAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (12 bp):
ATGAAAATATAA
Found at i:5200354 original size:31 final size:31
Alignment explanation
Indices: 5200319--5200381 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
5200309 AAAAATTTTC
5200319 ACACAAAAATTAATAT-CTAAAAAGT-AATTAA
1 ACACAAAAATTAATATAC-AAAAA-TAAATTAA
*
5200350 ACACAAACATTAATATACAAAAATAAATTAA
1 ACACAAAAATTAATATACAAAAATAAATTAA
5200381 A
1 A
5200382 AGAAATCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.93
32 1 0.03
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (31 bp):
ACACAAAAATTAATATACAAAAATAAATTAA
Found at i:5201260 original size:17 final size:17
Alignment explanation
Indices: 5201235--5201269 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5201225 ATAGCATGAC
5201235 TAAAATAAAATAATAAT
1 TAAAATAAAATAATAAT
* *
5201252 TAAAGTAAAATACTAAT
1 TAAAATAAAATAATAAT
5201269 T
1 T
5201270 TAAACATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
TAAAATAAAATAATAAT
Found at i:5204467 original size:2 final size:2
Alignment explanation
Indices: 5204462--5204486 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5204452 ACAAACACAC
5204462 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5204487 ATATTACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5215222 original size:29 final size:29
Alignment explanation
Indices: 5215180--5215261 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
5215170 AAACTAAATT
*
5215180 GATGTCACTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
5215209 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
5215238 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
5215262 GTTAGGTAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:5217591 original size:3 final size:3
Alignment explanation
Indices: 5217585--5217632 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
5217575 TTTACTCATT
*
5217585 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5217633 AAAAATAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5219037 original size:15 final size:15
Alignment explanation
Indices: 5219017--5219046 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5219007 TTATGTAGTC
*
5219017 ATAAATATATATATA
1 ATAAATAAATATATA
5219032 ATAAATAAATATATA
1 ATAAATAAATATATA
5219047 TTTTTTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAATAAATATATA
Found at i:5223094 original size:15 final size:15
Alignment explanation
Indices: 5223074--5223105 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5223064 ATCAATACCT
5223074 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
5223089 TTTTGCATACATTCA
1 TTTTGCATACATGCA
5223104 TT
1 TT
5223106 ATTCATTTCA
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:5230457 original size:22 final size:22
Alignment explanation
Indices: 5230430--5230500 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 22
5230420 ATTATGCTTG
5230430 AAGAGAAAAAGAAAAGAAAAAA
1 AAGAGAAAAAGAAAAGAAAAAA
*
5230452 AAGAGAAAAAGAAAAAAGAAAAA
1 AAGAGAAAAAGAAAAGA-AAAAA
*
5230475 AAGAGAAAAAAAAAAGAAGAAAA
1 AAGAGAAAAAGAAAAGAA-AAAA
5230498 AAG
1 AAG
5230501 GGGGGTCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 17 0.39
23 27 0.61
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AAGAGAAAAAGAAAAGAAAAAA
Found at i:5230463 original size:17 final size:16
Alignment explanation
Indices: 5230435--5230499 Score: 73
Period size: 15 Copynumber: 4.1 Consensus size: 16
5230425 GCTTGAAGAG
5230435 AAAAAG-AAAAGAAAA
1 AAAAAGAAAAAGAAAA
5230450 AAAAGAGAAAAAGAAAA
1 AAAA-AGAAAAAGAAAA
*
5230467 AAGAA-AAAAAGAGAAA
1 AAAAAGAAAAAGA-AAA
*
5230483 AAAAA-AAGAAGAAAA
1 AAAAAGAAAAAGAAAA
5230498 AA
1 AA
5230500 GGGGGGTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
15 16 0.36
16 16 0.36
17 12 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAA
Found at i:5232008 original size:115 final size:115
Alignment explanation
Indices: 5231652--5231966 Score: 560
Period size: 115 Copynumber: 2.7 Consensus size: 115
5231642 GAATGTGCTC
5231652 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
*
5231717 TCATTGGATTTGAAAGATGAATTTGCTTATAGTAGAAATAAGGAGACTCA
66 TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCA
*
5231767 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
5231832 TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCA
66 TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCA
* * *
5231882 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GGAACTATAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
* *
5231946 TCATTGGAATTAAAAGATGAA
66 TCATTGGATTTGAAAGATGAA
5231967 CTGCATGATC
Statistics
Matches: 192, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
114 32 0.17
115 160 0.83
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (115 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCA
Found at i:5232853 original size:113 final size:113
Alignment explanation
Indices: 5232681--5233556 Score: 1479
Period size: 113 Copynumber: 7.8 Consensus size: 113
5232671 GGATCAACAG
5232681 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
1 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
5232746 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
66 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
* *
5232794 TGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAAAA
1 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
5232859 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
66 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
5232907 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
1 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
5232972 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
66 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
5233020 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
1 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
5233085 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
66 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
5233133 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
1 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
5233198 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
66 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
* *
5233246 TGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAA
1 TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
* * *
5233311 GAATTTGTTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTT
66 GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
* * *
5233359 CT-CCAGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 -TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
* * * * * * * *
5233423 AGAACTTGTTCAA-TTTTTCGCTCGAATTCATCACTCGATAGATCAACTT
65 AGAATTTGTTCAACCTTTT-GCTCAAATCCATCACTTGATGGATTAGCTT
* * * *
5233472 T-TCAGAAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TGCCAGAA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
** *
5233536 AGAGCTTGTTCGACCTTTTGC
65 AGAATTTGTTCAACCTTTTGC
5233557 ATAACCCTAT
Statistics
Matches: 729, Mismatches: 30, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
112 10 0.01
113 714 0.98
114 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (113 bp):
TGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
GAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT
Found at i:5233905 original size:3 final size:3
Alignment explanation
Indices: 5233899--5233943 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5233889 TTTACTCATT
5233899 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5233944 AAAAATAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5235354 original size:19 final size:20
Alignment explanation
Indices: 5235330--5235370 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
5235320 TTATGTAGTC
5235330 ATAAATATATA-TATAATAA
1 ATAAATATATATTATAATAA
* *
5235349 ATAAATATTTATTTTAATAA
1 ATAAATATATATTATAATAA
5235369 AT
1 AT
5235371 TATTTTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATATATATTATAATAA
Found at i:5238353 original size:29 final size:29
Alignment explanation
Indices: 5238311--5238392 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
5238301 AAACTAAATT
5238311 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
5238340 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
5238369 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
5238393 GTTAGGTAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:5240091 original size:2 final size:2
Alignment explanation
Indices: 5240078--5240120 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
5240068 TAATTTAACC
*
5240078 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5240121 TTGTTCATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5240848 original size:17 final size:17
Alignment explanation
Indices: 5240826--5240866 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
5240816 ATAAACAACC
*
5240826 ACTCCACAATCAAATAA
1 ACTCCACAATCAAACAA
*
5240843 ACTCCACGATCAAACAA
1 ACTCCACAATCAAACAA
5240860 ACTCCAC
1 ACTCCAC
5240867 CTATACTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.37, G:0.02, T:0.15
Consensus pattern (17 bp):
ACTCCACAATCAAACAA
Found at i:5240896 original size:11 final size:11
Alignment explanation
Indices: 5240860--5240896 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5240850 GATCAAACAA
5240860 ACTCCACCTAT
1 ACTCCACCTAT
5240871 ACTCTCA-CT-T
1 ACTC-CACCTAT
5240881 ACTCCACCTAT
1 ACTCCACCTAT
5240892 ACTCC
1 ACTCC
5240897 CAATTATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 12 0.52
12 2 0.09
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (11 bp):
ACTCCACCTAT
Found at i:5244689 original size:21 final size:21
Alignment explanation
Indices: 5244660--5244699 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5244650 TTTTTATTAT
* *
5244660 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
5244681 TTTAGTAAAACATTTGGTA
1 TTTAGTAAAACAATTGGTA
5244700 CATTTAGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:5245573 original size:24 final size:23
Alignment explanation
Indices: 5245529--5245574 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
5245519 AAATGAGTTT
*
5245529 AATATTTTATTTTTTAAAATTAA
1 AATATTTTATTTTTCAAAATTAA
* *
5245552 AATATTTTCCTTTTTCACAATTA
1 AATATTTT-ATTTTTCAAAATTA
5245575 TGTCTATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTTATTTTTCAAAATTAA
Found at i:5249128 original size:30 final size:30
Alignment explanation
Indices: 5249094--5249154 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5249084 TTAATCCAAT
** *
5249094 ATATGAAATATGTGGATATTTTATACGTGA
1 ATATGAAATATGTAAATATGTTATACGTGA
* *
5249124 ATATGATATATGTAAATGTGTTATACGTGA
1 ATATGAAATATGTAAATATGTTATACGTGA
5249154 A
1 A
5249155 AATATCTATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (30 bp):
ATATGAAATATGTAAATATGTTATACGTGA
Found at i:5249602 original size:20 final size:20
Alignment explanation
Indices: 5249579--5249640 Score: 124
Period size: 20 Copynumber: 3.1 Consensus size: 20
5249569 GAAATTTGAA
5249579 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
5249599 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
5249619 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
5249639 TT
1 TT
5249641 TTCTGAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:5249896 original size:33 final size:30
Alignment explanation
Indices: 5249832--5249901 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 30
5249822 ATTTATTATT
* *
5249832 AAATATT-ATTTTTATAATTTTATTAATAA
1 AAATATTAATATTGATAATTTTATTAATAA
5249861 AAATATTAATATTGATATATTTTATTGAAATAA
1 AAATATTAATATTGATA-ATTTTATT--AATAA
5249894 AAATATTA
1 AAATATTA
5249902 TAAATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 7 0.20
30 7 0.20
31 8 0.23
33 13 0.37
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
AAATATTAATATTGATAATTTTATTAATAA
Found at i:5249911 original size:31 final size:29
Alignment explanation
Indices: 5249843--5249973 Score: 79
Period size: 31 Copynumber: 4.3 Consensus size: 29
5249833 AATATTATTT
*
5249843 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
5249873 TGATATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
* * * * * *
5249906 TTATATTAATTATTTATTAAAGTAATAGT-G
1 TTATATT--TTATTAATAAAAATATTAATAA
* * *
5249936 TTATATTATATT-TTAAAAATATTAATTA
1 TTATATTTTATTAATAAAAATATTAATAA
5249964 TTATATTTTA
1 TTATATTTTA
5249974 AATATCTTTA
Statistics
Matches: 77, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
27 9 0.12
28 13 0.17
30 8 0.10
31 22 0.29
32 6 0.08
33 19 0.25
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:5249919 original size:33 final size:33
Alignment explanation
Indices: 5249856--5249919 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
5249846 TAATTTTATT
* *
5249856 AATAAAAATATTAATATTGATATATTTTATTGA
1 AATAAAAATATTAAAATTGATATATATTATTGA
5249889 AATAAAAATATTATAAATT-ATAT-TAATTATT
1 AATAAAAATATTA-AAATTGATATAT-ATTATT
5249920 TATTAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 22 0.81
34 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (33 bp):
AATAAAAATATTAAAATTGATATATATTATTGA
Found at i:5249992 original size:23 final size:23
Alignment explanation
Indices: 5249943--5249993 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5249933 GTGTTATATT
**
5249943 ATATTTTAAAAATATTAATTATT
1 ATATTTTAAAAATATTAATTAAA
* * *
5249966 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
5249989 ATATT
1 ATATT
5249994 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:5250005 original size:19 final size:20
Alignment explanation
Indices: 5249981--5250051 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
5249971 TTAAATATCT
*
5249981 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTAAA
* *
5250000 TTATT-ATATTAATATTAAA
1 TTATTAATAATATTATTAAA
* *
5250019 TATATAAATAATATTATT-CA
1 T-TATTAATAATATTATTAAA
5250039 TTATTAATAATAT
1 TTATTAATAATAT
5250052 AATCATATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 1 0.02
19 26 0.63
20 5 0.12
21 9 0.22
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
TTATTAATAATATTATTAAA
Found at i:5250086 original size:27 final size:25
Alignment explanation
Indices: 5250006--5250086 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 25
5249996 TAGATTATTA
*
5250006 TATTAATATTAAATATATAAATAATAT
1 TATTCATA-TAAATA-ATAAATAATAT
* *
5250033 TATTCATTATTAATAATATAATCATAT
1 TATTCA-TATAAATAATA-AATAATAT
5250060 TATTTC-TATGAAATTAATAAATAATAT
1 TA-TTCATAT-AAA-TAATAAATAATAT
5250087 AAATTTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
26 6 0.14
27 28 0.64
28 10 0.23
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (25 bp):
TATTCATATAAATAATAAATAATAT
Found at i:5250151 original size:18 final size:19
Alignment explanation
Indices: 5250128--5250176 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
5250118 AAAATAAAAA
5250128 TATAATATAATAT-ATTAT
1 TATAATATAATATGATTAT
5250146 TATAATATAAT-TGATTAT
1 TATAATATAATATGATTAT
* *
5250164 TTTATTATAATAT
1 TATAATATAATAT
5250177 TAAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATAATATAATATGATTAT
Found at i:5250156 original size:23 final size:23
Alignment explanation
Indices: 5250126--5250176 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
5250116 TTAAAATAAA
5250126 AATATAATAT-AATATATTATTAT
1 AATATAAT-TGAATATATTATTAT
* *
5250149 AATATAATTGATTATTTTATTAT
1 AATATAATTGAATATATTATTAT
5250172 AATAT
1 AATAT
5250177 TAAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AATATAATTGAATATATTATTAT
Found at i:5250191 original size:22 final size:22
Alignment explanation
Indices: 5250161--5250209 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
5250151 TATAATTGAT
*
5250161 TATTTTATTATAATATTAAAAA
1 TATTATATTATAATATTAAAAA
* *
5250183 TATTATATTATATTATTAGAAA
1 TATTATATTATAATATTAAAAA
5250205 TATTA
1 TATTA
5250210 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:5253564 original size:17 final size:18
Alignment explanation
Indices: 5253523--5253564 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5253513 TTTTTTTTAT
*
5253523 TTTTATAATGTTTAAATA
1 TTTTATTATGTTTAAATA
**
5253541 TAATATTAT-TTTAAATA
1 TTTTATTATGTTTAAATA
5253558 TTTTATT
1 TTTTATT
5253565 GAACTTTTTA
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTATTATGTTTAAATA
Found at i:5255768 original size:21 final size:21
Alignment explanation
Indices: 5255742--5255783 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5255732 GAATATTTTC
5255742 TCTTTTATTACTAAAAATATT
1 TCTTTTATTACTAAAAATATT
5255763 TCTTTTATTACTAAAAATATT
1 TCTTTTATTACTAAAAATATT
5255784 CGATGAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (21 bp):
TCTTTTATTACTAAAAATATT
Found at i:5257329 original size:35 final size:35
Alignment explanation
Indices: 5257287--5257399 Score: 108
Period size: 35 Copynumber: 3.3 Consensus size: 35
5257277 AGTGTATTTC
5257287 TTAACTTTTTTATCTCTATATCTAATGAATCTATT
1 TTAACTTTTTTATCTCTATATCTAATGAATCTATT
* * * * *
5257322 TTAACTTTTTTA--ACAATAGTGTAGTGTAT-T-TT
1 TTAACTTTTTTATCTCTATA-TCTAATGAATCTATT
** *
5257354 GTTATTTTTTTTATCTCTATATCTAATGAATCTACT
1 -TTAACTTTTTTATCTCTATATCTAATGAATCTATT
5257390 TTAACTTTTT
1 TTAACTTTTT
5257400 AAAAATATTG
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
32 2 0.04
33 15 0.26
34 14 0.25
35 25 0.44
36 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.56
Consensus pattern (35 bp):
TTAACTTTTTTATCTCTATATCTAATGAATCTATT
Found at i:5258272 original size:38 final size:37
Alignment explanation
Indices: 5258191--5258287 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 37
5258181 CCGATAAAAG
* *
5258191 TAGTACAATAAAT-TGTAATGACTTGGTCAAATTCAAT
1 TAGTACAATAAATAT-TAATGATTTGGTCAAATTCAAA
* *
5258228 TGGTACAATGAATATTAATGATTTGGGTCAAATTCAAA
1 TAGTACAATAAATATTAATGATTT-GGTCAAATTCAAA
*
5258266 TAGTACAATAAATATGAATGAT
1 TAGTACAATAAATATTAATGAT
5258288 CTAAGTTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 19 0.37
38 32 0.63
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (37 bp):
TAGTACAATAAATATTAATGATTTGGTCAAATTCAAA
Found at i:5259744 original size:2 final size:2
Alignment explanation
Indices: 5259737--5259774 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5259727 ACAATATAAG
5259737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5259775 GTTATAATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5267522 original size:24 final size:24
Alignment explanation
Indices: 5267490--5267558 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
5267480 ACATTACCTA
* *
5267490 AATTTTGTTATGATTTCTTATCTG
1 AATTCTGTTATGATTTCTGATCTG
* * *
5267514 TATTCTGTTCTGATATCTGATCTG
1 AATTCTGTTATGATTTCTGATCTG
*
5267538 AATTCTGTTTTGATTTCTGAT
1 AATTCTGTTATGATTTCTGAT
5267559 ATCTCCATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.55
Consensus pattern (24 bp):
AATTCTGTTATGATTTCTGATCTG
Found at i:5267735 original size:2 final size:2
Alignment explanation
Indices: 5267717--5267772 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
5267707 GATAGAGGTG
* *
5267717 TA TA TA GA TA TA GA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5267758 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
5267773 GTTTTTTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5268200 original size:30 final size:30
Alignment explanation
Indices: 5268164--5268230 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 30
5268154 TGTAATTGTA
5268164 TTTTATTTTATATATGAGTCTGAAAACTTG
1 TTTTATTTTATATATGAGTCTGAAAACTTG
5268194 TTTTA-TTTATATATGAGTCTGAAAACTTG
1 TTTTATTTTATATATGAGTCTGAAAACTTG
5268223 TTTTATTT
1 TTTTATTT
5268231 CTAAACATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 29 0.81
30 7 0.19
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (30 bp):
TTTTATTTTATATATGAGTCTGAAAACTTG
Found at i:5272278 original size:24 final size:24
Alignment explanation
Indices: 5272243--5272314 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
5272233 AATATATTAC
* *
5272243 CTGAATTTTGTTCTGATTTCTGGT
1 CTGAATTATGTTCTGATTTCTGAT
* * * *
5272267 CTGGATTCTGTTCTGATATCTTAT
1 CTGAATTATGTTCTGATTTCTGAT
*
5272291 CTGAATTATGTTTTGATTTCTGAT
1 CTGAATTATGTTCTGATTTCTGAT
5272315 ATCTCTGTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.53
Consensus pattern (24 bp):
CTGAATTATGTTCTGATTTCTGAT
Found at i:5273404 original size:50 final size:50
Alignment explanation
Indices: 5273329--5273428 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
5273319 ATCTGAGAAA
5273329 TTCTGACTCGACTCCGGAAATGAAATTGGGATATGCTACTGCTCTATGAG
1 TTCTGACTCGACTCCGGAAATGAAATTGGGATATGCTACTGCTCTATGAG
5273379 TTCTGACTCGACTCCGGAAATGAAATTGGGATATGCTACTGCTCTATGAG
1 TTCTGACTCGACTCCGGAAATGAAATTGGGATATGCTACTGCTCTATGAG
5273429 CCTATTCTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (50 bp):
TTCTGACTCGACTCCGGAAATGAAATTGGGATATGCTACTGCTCTATGAG
Found at i:5274854 original size:30 final size:31
Alignment explanation
Indices: 5274754--5274891 Score: 219
Period size: 31 Copynumber: 4.5 Consensus size: 31
5274744 CATAGATTCT
* *
5274754 GAAGAACCTAGGTAATCAGTCC--ATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
5274783 GAAGGACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
5274814 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
5274845 GAA-AACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
5274875 GAACAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
5274892 CCTCGACCCT
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
29 19 0.19
30 30 0.29
31 53 0.52
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:5274870 original size:61 final size:60
Alignment explanation
Indices: 5274754--5274891 Score: 215
Period size: 61 Copynumber: 2.3 Consensus size: 60
5274744 CATAGATTCT
* * *
5274754 GAAGAACCTAGGTAATCAGTCCATGTCCCGAAGGACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
5274814 GAAGAACATAGGTAAACAGTCCATATGTCCCGAA-AACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCC--ATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
*
5274875 GAACAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
5274892 CCTCGACCCT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
60 20 0.28
61 42 0.58
62 10 0.14
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (60 bp):
GAAGAACATAGGTAAACAGTCCATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:5275531 original size:21 final size:21
Alignment explanation
Indices: 5275507--5275551 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5275497 TGTTGTTCGT
* *
5275507 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5275528 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5275549 TTG
1 TTG
5275552 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5279263 original size:24 final size:24
Alignment explanation
Indices: 5279229--5279301 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
5279219 ATACATTACC
* *
5279229 TGAATTTTGTTCTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* * *
5279253 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTATGATTTCTGATA
* *
5279277 TGAATTCTGTTTTGATTTTTGATA
1 TGAATTCTGTTATGATTTCTGATA
5279301 T
1 T
5279302 CTCCGTTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.08, G:0.18, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:5279264 original size:48 final size:47
Alignment explanation
Indices: 5279185--5279301 Score: 121
Period size: 48 Copynumber: 2.4 Consensus size: 47
5279175 TCACATAAAT
* * *
5279185 ATTTTATTTGATTTCTGACT-TGAATTTTGTTATGATA-CATTACCTGA
1 ATTTTGTTTGATTTCTGA-TATGAATTCTGTTATGATATC-TGACCTGA
* *
5279232 ATTTTGTTCTGATTTCTGATATGGATTCTGTTATGATATCTGATCTGA
1 ATTTTGTT-TGATTTCTGATATGAATTCTGTTATGATATCTGACCTGA
* *
5279280 ATTCTGTTTTGATTTTTGATAT
1 ATTTTG-TTTGATTTCTGATAT
5279302 CTCCGTTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
47 8 0.14
48 48 0.81
49 3 0.05
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.53
Consensus pattern (47 bp):
ATTTTGTTTGATTTCTGATATGAATTCTGTTATGATATCTGACCTGA
Found at i:5281965 original size:18 final size:18
Alignment explanation
Indices: 5281937--5281986 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
5281927 CTCATTTTTG
5281937 TAACTAACTTGAAACAACC
1 TAAC-AACTTGAAACAACC
5281956 TAACAACTTGAAACAACC
1 TAACAACTTGAAACAACC
*
5281974 TAATAACTTGAAA
1 TAACAACTTGAAA
5281987 ACTGATTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (18 bp):
TAACAACTTGAAACAACC
Found at i:5294997 original size:107 final size:107
Alignment explanation
Indices: 5294811--5295025 Score: 430
Period size: 107 Copynumber: 2.0 Consensus size: 107
5294801 TATTTTTCAC
5294811 CATAACCCGAATCCGACCTGAACACCACCTTTTAAAAAAACCCGGCTCGAATCCAATTTTTTTTT
1 CATAACCCGAATCCGACCTGAACACCACCTTTTAAAAAAACCCGGCTCGAATCCAATTTTTTTTT
5294876 AAAAACCCAAGCCGATTGTGTCTGGCCGGAACCCGTAGGATT
66 AAAAACCCAAGCCGATTGTGTCTGGCCGGAACCCGTAGGATT
5294918 CATAACCCGAATCCGACCTGAACACCACCTTTTAAAAAAACCCGGCTCGAATCCAATTTTTTTTT
1 CATAACCCGAATCCGACCTGAACACCACCTTTTAAAAAAACCCGGCTCGAATCCAATTTTTTTTT
5294983 AAAAACCCAAGCCGATTGTGTCTGGCCGGAACCCGTAGGATT
66 AAAAACCCAAGCCGATTGTGTCTGGCCGGAACCCGTAGGATT
5295025 C
1 C
5295026 GGGTCCCATG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (107 bp):
CATAACCCGAATCCGACCTGAACACCACCTTTTAAAAAAACCCGGCTCGAATCCAATTTTTTTTT
AAAAACCCAAGCCGATTGTGTCTGGCCGGAACCCGTAGGATT
Found at i:5295167 original size:42 final size:42
Alignment explanation
Indices: 5295108--5295243 Score: 229
Period size: 42 Copynumber: 3.2 Consensus size: 42
5295098 TTCCCTAAAA
5295108 TCTCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
1 TCTCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
5295150 TCTCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
1 TCTCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
* * *
5295192 TCTCGTGTTTGTTTCACATAATTCATTTTCCGGAAAATGTTT
1 TCTCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
5295234 TC-CAGTGTTT
1 TCTC-GTGTTT
5295244 AGTTGGAGGA
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
41 1 0.01
42 89 0.99
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (42 bp):
TCTCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
Found at i:5295503 original size:22 final size:23
Alignment explanation
Indices: 5295465--5295519 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
5295455 TAAAATATTT
5295465 AAAATAT-ATAGTAATATTTCTA
1 AAAATATAATAGTAATATTTCTA
* *
5295487 AAAATATAATA-TTATATTTTTA
1 AAAATATAATAGTAATATTTCTA
* *
5295509 ATATTATAATA
1 AAAATATAATA
5295520 AAATAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AAAATATAATAGTAATATTTCTA
Found at i:5295587 original size:50 final size:48
Alignment explanation
Indices: 5295533--5295674 Score: 132
Period size: 50 Copynumber: 2.9 Consensus size: 48
5295523 TAATCAATTA
5295533 TATTATAATAATATAAGATATTATTTTTATTTTAATAATATATAATAAAT
1 TATTATAATAAT-TAA-ATATTATTTTTATTTTAATAATATATAATAAAT
* * * *
5295583 TATTAATAA-AATT-TATATTATTTATGAATTTCATATAATATATATTAAAT
1 TATT-ATAATAATTAAATATTATTT-T-TATTTTA-ATAATATATAATAAAT
* *
5295633 TA-T-TAATAATGAAATATTATTTATA-TTTAATAATATAATAAT
1 TATTATAATAATTAAATATTATTTTTATTTTAATAATAT-ATAAT
5295675 CTAATAATAT
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
45 7 0.09
46 7 0.09
47 13 0.17
48 4 0.05
49 16 0.21
50 24 0.32
51 4 0.05
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (48 bp):
TATTATAATAATTAAATATTATTTTTATTTTAATAATATATAATAAAT
Found at i:5295686 original size:32 final size:31
Alignment explanation
Indices: 5295623--5295686 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
5295613 TCATATAATA
* * *
5295623 TATATTAAATTATTAATAATGAAATATTATT
1 TATATTAAATAATTAATAATCAAATAATATT
* *
5295654 TATATTTAATAATATAATAATCTAATAATATT
1 TATATTAAATAAT-TAATAATCAAATAATATT
5295686 T
1 T
5295687 TACAATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
TATATTAAATAATTAATAATCAAATAATATT
Found at i:5295804 original size:27 final size:28
Alignment explanation
Indices: 5295770--5295828 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
5295760 TATAATTTAT
*
5295770 AATATTTTTATT-TCAATAAAA-TATACA
1 AATATTTTT-TTATCAATAAAATTATAAA
*
5295797 AATATTTTTTTATTAATAAAATTATAAA
1 AATATTTTTTTATCAATAAAATTATAAA
5295825 AATA
1 AATA
5295829 ATATATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 17 0.61
28 9 0.32
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
AATATTTTTTTATCAATAAAATTATAAA
Found at i:5295836 original size:21 final size:21
Alignment explanation
Indices: 5295812--5295872 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
5295802 TTTTTTATTA
5295812 ATAAAATTATAAAAATAATAT
1 ATAAAATTATAAAAATAATAT
*
5295833 ATAATAA-TATAAAAATTAT-T
1 ATAA-AATTATAAAAATAATAT
* * *
5295853 TTAATATTTTAAAAATAATA
1 ATAAAATTATAAAAATAATA
5295873 ATATTAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.44
21 15 0.47
22 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAATTATAAAAATAATAT
Found at i:5295857 original size:20 final size:21
Alignment explanation
Indices: 5295819--5295872 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
5295809 TTAATAAAAT
5295819 TATAAAAATAATATATAATAA
1 TATAAAAATAATATATAATAA
* * *
5295840 TATAAAAATTAT-TTTAATAT
1 TATAAAAATAATATATAATAA
*
5295860 TTTAAAAATAATA
1 TATAAAAATAATA
5295873 ATATTAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAAAAATAATATATAATAA
Found at i:5299808 original size:3 final size:3
Alignment explanation
Indices: 5299802--5299878 Score: 58
Period size: 3 Copynumber: 26.3 Consensus size: 3
5299792 TATTCCTTAA
* *
5299802 TAT TAT TAT TAT TAT T-T TA- TAT T-T TAT TTT TAT T-T ATAT ACAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT
5299845 GTAT TAT TAT TAT TAT T-T TAT TATT TAT T-T TAT T
1 -TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
5299879 TATATGTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
2 11 0.18
3 41 0.67
4 9 0.15
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:5299840 original size:49 final size:49
Alignment explanation
Indices: 5299765--5299893 Score: 131
Period size: 49 Copynumber: 2.6 Consensus size: 49
5299755 TTAATGTTAC
* * *
5299765 ATTATAATATTTATATATTT-TTTATATTAT-TCCTTAATATTATTATTATT
1 ATTATTATATTT-TATTTTTATTTATATTATGT-ATTAATATTATTATT-TT
* *
5299815 ATT-TTATATTTTATTTTTATTTATATACATGTATTATTATTATTATTTT
1 ATTATTATATTTTATTTTTATTTATAT-TATGTATTAATATTATTATTTT
*
5299864 ATTATT-TATTTTATTTATATGTTATATTAT
1 ATTATTATATTTTATTTTTAT-TTATATTAT
5299894 ATATATATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
48 6 0.09
49 34 0.51
50 26 0.39
51 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (49 bp):
ATTATTATATTTTATTTTTATTTATATTATGTATTAATATTATTATTTT
Found at i:5299898 original size:16 final size:15
Alignment explanation
Indices: 5299808--5299911 Score: 54
Period size: 14 Copynumber: 7.7 Consensus size: 15
5299798 TTAATATTAT
5299808 TATTAT-TAT-TTTA
1 TATTATATATATTTA
*
5299821 TATT-T-TATTTTTA
1 TATTATATATATTTA
* *
5299834 T-TTATATACATGTA
1 TATTATATATATTTA
5299848 TTATTAT-TATTATTT-
1 -TATTATATA-TATTTA
5299863 TATTAT-T-TATTT-
1 TATTATATATATTTA
*
5299875 TATT-TATAT-GTTA
1 TATTATATATATTTA
*
5299888 TATTATATATATATA
1 TATTATATATATTTA
5299903 TA-TATATAT
1 TATTATATAT
5299912 TTGCTTAATA
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
11 1 0.01
12 18 0.25
13 15 0.21
14 24 0.33
15 7 0.10
16 7 0.10
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (15 bp):
TATTATATATATTTA
Found at i:5300018 original size:9 final size:9
Alignment explanation
Indices: 5300006--5300103 Score: 69
Period size: 9 Copynumber: 10.8 Consensus size: 9
5299996 CTCGTTTTTG
5300006 TTTATTTAT
1 TTTATTTAT
5300015 TTTATTTTTAT
1 TTTA--TTTAT
*
5300026 TTTCTTTA-
1 TTTATTTAT
5300034 TTTATTTAT
1 TTTATTTAT
*
5300043 TTTCTTTAT
1 TTTATTTAT
5300052 TTT-TCTTAT
1 TTTAT-TTAT
5300061 TTTATTTA-
1 TTTATTTAT
* *
5300069 CTTATCTTTT
1 TTTAT-TTAT
*
5300079 TTTCTTTA-
1 TTTATTTAT
5300087 TTTATCTTAT
1 TTTAT-TTAT
*
5300097 TCTATTT
1 TTTATTT
5300104 TGTCTTTATT
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
8 16 0.23
9 38 0.54
10 8 0.11
11 8 0.11
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:5300060 original size:22 final size:23
Alignment explanation
Indices: 5300035--5300094 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
5300025 TTTTCTTTAT
5300035 TTATTTATTTTCTTTAT-TTTTC
1 TTATTTATTTTCTTTATCTTTTC
* *
5300057 TTATTTTATTTAC-TTATCTTTTT
1 TTA-TTTATTTTCTTTATCTTTTC
*
5300080 TTCTTTATTTATCTT
1 TTATTTATTT-TCTT
5300095 ATTCTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 14 0.47
23 15 0.50
24 1 0.03
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTTATTTTCTTTATCTTTTC
Found at i:5300062 original size:18 final size:18
Alignment explanation
Indices: 5300022--5300097 Score: 109
Period size: 18 Copynumber: 4.3 Consensus size: 18
5300012 TATTTTATTT
5300022 TTATTTTCTTTATTTAT-
1 TTATTTTCTTTATTTATC
*
5300039 TTATTTTCTTTATTTTTC
1 TTATTTTCTTTATTTATC
* *
5300057 TTATTTTATTTACTTATC
1 TTATTTTCTTTATTTATC
*
5300075 TTTTTTTCTTTATTTATC
1 TTATTTTCTTTATTTATC
5300093 TTATT
1 TTATT
5300098 CTATTTTGTC
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
17 16 0.32
18 34 0.68
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTTTCTTTATTTATC
Found at i:5300072 original size:13 final size:13
Alignment explanation
Indices: 5300001--5300073 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 13
5299991 TTTTCCTCGT
* *
5300001 TTTTGTTTATTTA
1 TTTTATTTACTTA
5300014 TTTTATTT--TTA
1 TTTTATTTACTTA
* *
5300025 TTTTCTTTATTTA
1 TTTTATTTACTTA
*
5300038 -TTTATTTTCTT-
1 TTTTATTTACTTA
*
5300049 TATT-TTT-CTTA
1 TTTTATTTACTTA
5300060 TTTTATTTACTTA
1 TTTTATTTACTTA
5300073 T
1 T
5300074 CTTTTTTTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
10 3 0.06
11 16 0.34
12 13 0.28
13 15 0.32
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (13 bp):
TTTTATTTACTTA
Found at i:5300118 original size:31 final size:30
Alignment explanation
Indices: 5300007--5300119 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 30
5299997 TCGTTTTTGT
* *
5300007 TTATTTATTTTATTTTTA-TTTTCTTTAT-
1 TTATTTATTTTATCTTTATTTTTATTTATC
* *
5300035 TTATTTA-TTT-TCTTTATTTTT-CTTATT
1 TTATTTATTTTATCTTTATTTTTATTTATC
* *
5300062 TTATTTA-CTTATCTTTTTTTCTTTATTTATC
1 TTATTTATTTTATC-TTTATT-TTTATTTATC
*
5300093 TTATTCTATTTTGTCTTTATTTTTATT
1 TTATT-TATTTTATCTTTATTTTTATT
5300120 CCTTTCATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
26 9 0.13
27 16 0.24
28 9 0.13
29 5 0.07
30 3 0.04
31 15 0.22
32 7 0.10
33 4 0.06
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (30 bp):
TTATTTATTTTATCTTTATTTTTATTTATC
Found at i:5300193 original size:14 final size:14
Alignment explanation
Indices: 5300174--5300222 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
5300164 TTGTCTTTAT
5300174 TTTATTTGT-TATTA
1 TTTATTT-TCTATTA
*
5300188 TTTATTTTCTATTC
1 TTTATTTTCTATTA
*
5300202 TTTA-TTTC-ATTT
1 TTTATTTTCTATTA
5300214 TTTATTTTC
1 TTTATTTTC
5300223 AATTTATCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 7 0.23
13 9 0.29
14 15 0.48
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTATTTTCTATTA
Found at i:5306572 original size:176 final size:176
Alignment explanation
Indices: 5306278--5306626 Score: 698
Period size: 176 Copynumber: 2.0 Consensus size: 176
5306268 ATAAGAGTTA
5306278 TTGGTGACTAATTATAAATAGAGAATATTTATTAGTTTTTAGAATTATGAGATATAATTATAAAG
1 TTGGTGACTAATTATAAATAGAGAATATTTATTAGTTTTTAGAATTATGAGATATAATTATAAAG
5306343 ATGTAATATTCTTGTAGCCTCTGTAACTTTTGGGGTCGAGATGAGTTTTGTAGGGATATTGGGAG
66 ATGTAATATTCTTGTAGCCTCTGTAACTTTTGGGGTCGAGATGAGTTTTGTAGGGATATTGGGAG
5306408 AGTGTTTTGGGATACATTAGGTTTTGATATATATATATATATATAT
131 AGTGTTTTGGGATACATTAGGTTTTGATATATATATATATATATAT
5306454 TTGGTGACTAATTATAAATAGAGAATATTTATTAGTTTTTAGAATTATGAGATATAATTATAAAG
1 TTGGTGACTAATTATAAATAGAGAATATTTATTAGTTTTTAGAATTATGAGATATAATTATAAAG
5306519 ATGTAATATTCTTGTAGCCTCTGTAACTTTTGGGGTCGAGATGAGTTTTGTAGGGATATTGGGAG
66 ATGTAATATTCTTGTAGCCTCTGTAACTTTTGGGGTCGAGATGAGTTTTGTAGGGATATTGGGAG
5306584 AGTGTTTTGGGATACATTAGGTTTTGATATATATATATATATA
131 AGTGTTTTGGGATACATTAGGTTTTGATATATATATATATATA
5306627 ATATATATAT
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 173 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.42
Consensus pattern (176 bp):
TTGGTGACTAATTATAAATAGAGAATATTTATTAGTTTTTAGAATTATGAGATATAATTATAAAG
ATGTAATATTCTTGTAGCCTCTGTAACTTTTGGGGTCGAGATGAGTTTTGTAGGGATATTGGGAG
AGTGTTTTGGGATACATTAGGTTTTGATATATATATATATATATAT
Found at i:5306617 original size:2 final size:2
Alignment explanation
Indices: 5306610--5306640 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5306600 TTAGGTTTTG
5306610 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5306641 CAGGTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5306630 original size:15 final size:15
Alignment explanation
Indices: 5306612--5306640 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5306602 AGGTTTTGAT
5306612 ATATATATATATATA
1 ATATATATATATATA
5306627 ATATATATATATAT
1 ATATATATATATAT
5306641 CAGGTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:5311996 original size:32 final size:32
Alignment explanation
Indices: 5311950--5312024 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
5311940 ACAACTGACT
*
5311950 GCAATTTTGAAACTCAACTTACAGCTGCATCA
1 GCAACTTTGAAACTCAACTTACAGCTGCATCA
*
5311982 GCAACTTTGAAACTCATCTTACAGCTGCATCA
1 GCAACTTTGAAACTCAACTTACAGCTGCATCA
5312014 GCAACTTTGAA
1 GCAACTTTGAA
5312025 CACAAATCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (32 bp):
GCAACTTTGAAACTCAACTTACAGCTGCATCA
Found at i:5316338 original size:45 final size:45
Alignment explanation
Indices: 5316272--5316368 Score: 185
Period size: 45 Copynumber: 2.2 Consensus size: 45
5316262 CGAATATCGG
*
5316272 ATCTGATTTGATCTAATGATTTTGATACCTAAAATAGTTATTCGT
1 ATCTGATTTGATCTAAAGATTTTGATACCTAAAATAGTTATTCGT
5316317 ATCTGATTTGATCTAAAGATTTTGATACCTAAAATAGTTATTCGT
1 ATCTGATTTGATCTAAAGATTTTGATACCTAAAATAGTTATTCGT
5316362 ATCTGAT
1 ATCTGAT
5316369 CTGAAAATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (45 bp):
ATCTGATTTGATCTAAAGATTTTGATACCTAAAATAGTTATTCGT
Found at i:5316380 original size:40 final size:42
Alignment explanation
Indices: 5316289--5316380 Score: 134
Period size: 45 Copynumber: 2.2 Consensus size: 42
5316279 TTGATCTAAT
*
5316289 GATTTTGATACCTAAAATAGTTATTCGTATCTGATTTGATCTAAA
1 GATTTTGATACCTAAAATAGTTATTCGTATCTGATCTG---TAAA
5316334 GATTTTGATACCTAAAATAGTTATTCGTATCTGATCTG-AAA
1 GATTTTGATACCTAAAATAGTTATTCGTATCTGATCTGTAAA
5316375 -ATTTTG
1 GATTTTG
5316381 GATATATGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
40 6 0.13
41 3 0.07
45 37 0.80
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (42 bp):
GATTTTGATACCTAAAATAGTTATTCGTATCTGATCTGTAAA
Found at i:5324851 original size:14 final size:14
Alignment explanation
Indices: 5324832--5324915 Score: 69
Period size: 14 Copynumber: 5.4 Consensus size: 14
5324822 ACAAAGGGCT
5324832 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
5324846 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
*
5324860 CGTTCGTGAACGTTCGATTATA
1 ---T-GT--TCGTTC-ATT-TA
*
5324882 TGTTCGTTTATTTA
1 TGTTCGTTCATTTA
*
5324896 TATTCGTTCATTTA
1 TGTTCGTTCATTTA
5324910 TGTTCG
1 TGTTCG
5324916 AACATAGGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
14 33 0.59
15 3 0.05
16 4 0.07
17 1 0.02
18 4 0.07
19 1 0.02
20 5 0.09
21 3 0.05
22 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (14 bp):
TGTTCGTTCATTTA
Found at i:5324902 original size:36 final size:34
Alignment explanation
Indices: 5324836--5324902 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 34
5324826 AGGGCTTGTT
*
5324836 CGTTCATTTATGTTCGTTCATTTACGTTCGTGAA
1 CGTTCATTTATGTTCGTTCATTTACATTCGTGAA
* *
5324870 CGTTCGATTATATGTTCGTTTATTTATATTCGT
1 CGTTC-ATT-TATGTTCGTTCATTTACATTCGT
5324903 TCATTTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 5 0.18
35 3 0.11
36 20 0.71
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (34 bp):
CGTTCATTTATGTTCGTTCATTTACATTCGTGAA
Found at i:5329758 original size:15 final size:14
Alignment explanation
Indices: 5329734--5329766 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
5329724 AGTTTAAGAT
5329734 TATAATTAATTAAA
1 TATAATTAATTAAA
5329748 TATAGATTAATTAAA
1 TATA-ATTAATTAAA
5329763 TATA
1 TATA
5329767 TAAATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TATAATTAATTAAA
Found at i:5335274 original size:14 final size:14
Alignment explanation
Indices: 5335255--5335287 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5335245 TGGGGAGTAA
*
5335255 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
5335269 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
5335283 TCCCT
1 TCCCT
5335288 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:5340878 original size:7 final size:7
Alignment explanation
Indices: 5340866--5340899 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
5340856 TATTTTTTAA
5340866 AAATTTT
1 AAATTTT
5340873 AAATTTT
1 AAATTTT
5340880 AAATTTT
1 AAATTTT
5340887 ATATATTTT
1 A-A-ATTTT
5340896 AAAT
1 AAAT
5340900 ATTTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 17 0.68
8 2 0.08
9 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AAATTTT
Found at i:5340881 original size:16 final size:18
Alignment explanation
Indices: 5340860--5340935 Score: 72
Period size: 18 Copynumber: 4.3 Consensus size: 18
5340850 GATAGTTATT
5340860 TTTTAAAAATTTTA-A-A
1 TTTTAAAAATTTTATATA
5340876 TTTT--AAATTTTATATA
1 TTTTAAAAATTTTATATA
*
5340892 TTTTAAATATTTT-TATA
1 TTTTAAAAATTTTATATA
*
5340909 TTTTTATCAAAAATTTATATA
1 -TTTTA--AAAATTTTATATA
5340930 TTTTAA
1 TTTTAA
5340936 TATAAAATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.16
15 1 0.02
16 9 0.18
17 4 0.08
18 12 0.24
20 11 0.22
21 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAAAAATTTTATATA
Found at i:5340942 original size:21 final size:21
Alignment explanation
Indices: 5340879--5340943 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
5340869 TTTTAAATTT
*
5340879 TAAATTTTATATATTTTAA-A
1 TAAAATTTATATATTTTAATA
* *
5340899 T---ATTTTTATATTTTTATCA
1 TAAAATTTATATATTTTAAT-A
5340918 -AAAATTTATATATTTTAATA
1 TAAAATTTATATATTTTAATA
5340938 TAAAAT
1 TAAAAT
5340944 CATGTGTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 11
0.68 0.10 0.22
Matches are distributed among these distances:
17 12 0.35
19 1 0.03
20 2 0.06
21 19 0.56
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAATTTATATATTTTAATA
Found at i:5342851 original size:23 final size:23
Alignment explanation
Indices: 5342825--5342868 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5342815 CCTAAAAGCA
5342825 TTCACAAACATATTCATTTAACG
1 TTCACAAACATATTCATTTAACG
*
5342848 TTCACGAACATATTCATTTAA
1 TTCACAAACATATTCATTTAA
5342869 TGTTTGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (23 bp):
TTCACAAACATATTCATTTAACG
Found at i:5348345 original size:23 final size:23
Alignment explanation
Indices: 5348318--5348428 Score: 72
Period size: 23 Copynumber: 5.0 Consensus size: 23
5348308 GAATATATCA
5348318 ATATTTTAAATAATTAAAATAAT
1 ATATTTTAAATAATTAAAATAAT
** *
5348341 ATATTTT--ATAATGT--TTTATT
1 ATATTTTAAATAAT-TAAAATAAT
* *
5348361 ATATTTCAAATTATTAAAATAAT
1 ATATTTTAAATAATTAAAATAAT
* *
5348384 ATACTTTATAAT-ATT-AAATAAA
1 ATATTTTA-AATAATTAAAATAAT
* *
5348406 ATATTTTAACATTATAAAAATAA
1 ATATTTTAA-ATAATTAAAATAA
5348429 AAATATTTAA
Statistics
Matches: 66, Mismatches: 13, Indels: 17
0.69 0.14 0.18
Matches are distributed among these distances:
20 9 0.14
21 7 0.11
22 20 0.30
23 21 0.32
24 9 0.14
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATTTTAAATAATTAAAATAAT
Found at i:5352353 original size:2 final size:2
Alignment explanation
Indices: 5352348--5352388 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5352338 ATACACACAA
5352348 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5352389 AAGAAAAGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5361443 original size:11 final size:12
Alignment explanation
Indices: 5361427--5361477 Score: 70
Period size: 11 Copynumber: 4.3 Consensus size: 12
5361417 TATCAAGATT
5361427 AAATAATATTA-
1 AAATAATATTAG
5361438 AAATAATATTAG
1 AAATAATATTAG
*
5361450 AAAGTAATTTTA-
1 AAA-TAATATTAG
5361462 AAATAATATTAG
1 AAATAATATTAG
5361474 AAAT
1 AAAT
5361478 TAATTAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 18 0.51
12 10 0.29
13 7 0.20
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (12 bp):
AAATAATATTAG
Found at i:5361482 original size:24 final size:24
Alignment explanation
Indices: 5361430--5361482 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
5361420 CAAGATTAAA
*
5361430 TAATATTAAAATAATATTAGAAAG
1 TAATTTTAAAATAATATTAGAAAG
*
5361454 TAATTTTAAAATAATATTAGAAAT
1 TAATTTTAAAATAATATTAGAAAG
5361478 TAATT
1 TAATT
5361483 AATATTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
TAATTTTAAAATAATATTAGAAAG
Found at i:5362901 original size:9 final size:9
Alignment explanation
Indices: 5362887--5362912 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5362877 GAAATCGGTT
5362887 AATTAACCG
1 AATTAACCG
5362896 AATTAACCG
1 AATTAACCG
5362905 AATTAACC
1 AATTAACC
5362913 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:5363049 original size:17 final size:17
Alignment explanation
Indices: 5363027--5363065 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5363017 TGAATCAAAT
5363027 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
5363044 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
5363061 -AATTA
1 TAATTA
5363066 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:5364107 original size:16 final size:16
Alignment explanation
Indices: 5364082--5364118 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5364072 ATTTGGGGAT
5364082 AAAA-TTGAAATATCC
1 AAAATTTGAAATATCC
*
5364097 AAAATTTGAAATATTC
1 AAAATTTGAAATATCC
5364113 AAAATT
1 AAAATT
5364119 CTATGGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (16 bp):
AAAATTTGAAATATCC
Found at i:5364206 original size:60 final size:60
Alignment explanation
Indices: 5364110--5364223 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
5364100 ATTTGAAATA
* * *
5364110 TTCAAAATTCTATGGATTAATTTAGAAATAGGGTCATAGTTTAGGGATGAAACTAGAATG
1 TTCAAAATTCTAAGGACTAATTTAGAAATAGAGTCATAGTTTAGGGATGAAACTAGAATG
* * *
5364170 TTCAAAATTTTAAGGACTAATTT-GGAATGAGAGTCATAGTTTATGGATGAAACT
1 TTCAAAATTCTAAGGACTAATTTAGAAAT-AGAGTCATAGTTTAGGGATGAAACT
5364224 CAAATAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (60 bp):
TTCAAAATTCTAAGGACTAATTTAGAAATAGAGTCATAGTTTAGGGATGAAACTAGAATG
Found at i:5364489 original size:21 final size:19
Alignment explanation
Indices: 5364463--5364504 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
5364453 TGATATAAAA
5364463 TTTTTAATATTTTCAATTATT
1 TTTTTAATATTTT-AA-TATT
5364484 TTTTTAATATTTTAATATT
1 TTTTTAATATTTTAATATT
5364503 TT
1 TT
5364505 ATAATTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTAATATTTTAATATT
Found at i:5364655 original size:14 final size:14
Alignment explanation
Indices: 5364636--5364665 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5364626 TCATTAGAAT
5364636 TAGTAAAATTTCAA
1 TAGTAAAATTTCAA
*
5364650 TAGTAAACTTTCAA
1 TAGTAAAATTTCAA
5364664 TA
1 TA
5364666 AAATTTTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
TAGTAAAATTTCAA
Found at i:5365070 original size:9 final size:8
Alignment explanation
Indices: 5365051--5365080 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5365041 AAATCTTATA
5365051 TATAATTT
1 TATAATTT
5365059 TATAATTTT
1 TATAA-TTT
5365068 TATAATTT
1 TATAATTT
5365076 TATAA
1 TATAA
5365081 ACCTAATAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATAATTT
Found at i:5365667 original size:13 final size:13
Alignment explanation
Indices: 5365649--5365676 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5365639 CTTGATATTT
5365649 ATATATTTTTAAA
1 ATATATTTTTAAA
5365662 ATATATTTTTAAA
1 ATATATTTTTAAA
5365675 AT
1 AT
5365677 TCTAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATTTTTAAA
Found at i:5367162 original size:23 final size:23
Alignment explanation
Indices: 5367132--5367204 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
5367122 ATAATTTACA
*
5367132 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
5367155 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
5367178 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
5367201 ATAT
1 ATAT
5367205 TTTTACCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:5367656 original size:23 final size:23
Alignment explanation
Indices: 5367621--5367693 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
5367611 ATACTTTACA
*
5367621 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
5367644 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
5367667 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
5367690 ATAT
1 ATAT
5367694 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:5367983 original size:490 final size:490
Alignment explanation
Indices: 5366733--5368054 Score: 2416
Period size: 489 Copynumber: 2.7 Consensus size: 490
5366723 TAATATGTTG
*
5366733 AAAGTGTCCATACTTTTT-TATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
1 AAAGTGTCCATACTTTTTATA-AAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
* * *
5366797 CAA-ATTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCACA
65 CAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACA
** *
5366861 AGTAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
130 AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTA
* *
5366926 ACCAAAGATAATAATAAATATGTAATATATATGTTTTTTGTTTTTAATTTAATAATAATATATAT
195 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATAC
5366991 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
260 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
* *
5367056 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATA
325 AAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATAGACACTCTTATAAAAAGGATA
5367121 GATAATTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
390 GATAATTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
*
5367186 GCTACCTATTACATCATATTTTTACCTATTATATTG
455 GCTACCTATTACATCATATTTTTACCTATTATATTA
*
5367222 AAAGTGTTCATACTTTTTAT-AAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTC
1 AAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTC
*
5367286 AATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
66 AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
5367351 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
131 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
* *
5367416 CCAAAGATAATAATAAATATGTAATATATATGTTTATTTTTTTTAATTTAATAATAATATATACA
196 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
*
5367481 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAACTCACTCAA
261 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
*
5367546 AAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACTCTTATAAAAAGGATAG
326 AAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATAGACACTCTTATAAAAAGGATAG
* *
5367611 ATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCG
391 ATAATTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCG
5367676 CTACCTATTACATCATATTTTTACCTATTATATTA
456 CTACCTATTACATCATATTTTTACCTATTATATTA
5367711 AAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTC
1 AAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTC
5367776 AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
66 AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
*
5367841 AAAATTATTTGATTATTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
131 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
*
5367906 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTACTTTAATAATAATATATACC
196 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
5367971 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
261 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
5368036 AAGATAACCTTAAATTAAT
326 AAGATAACCTTAAATTAAT
5368055 GTCCATACTC
Statistics
Matches: 803, Mismatches: 27, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
488 45 0.06
489 440 0.55
490 318 0.40
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (490 bp):
AAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTC
AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
AAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATAGACACTCTTATAAAAAGGATAG
ATAATTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCG
CTACCTATTACATCATATTTTTACCTATTATATTA
Found at i:5368087 original size:33 final size:33
Alignment explanation
Indices: 5368046--5368157 Score: 109
Period size: 33 Copynumber: 3.3 Consensus size: 33
5368036 AAGATAACCT
5368046 TAAATTAATGTCCATACTCACGCCTATAATTAC
1 TAAATTAATGTCCATACTCACGCCTATAATTAC
* * * * * * *
5368079 TAAATTAATATCTTAAAACTCAC-TCAAAAGATAACC
1 TAAATTAATGTC--CATACTCACGCCTATA-ATTA-C
5368115 TTAAATTAATGTCCATACTCACGCCTATAATTAC
1 -TAAATTAATGTCCATACTCACGCCTATAATTAC
5368149 TAAATTAAT
1 TAAATTAAT
5368158 ATCTTAAAAC
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
33 20 0.34
34 4 0.07
35 20 0.34
36 4 0.07
37 11 0.19
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (33 bp):
TAAATTAATGTCCATACTCACGCCTATAATTAC
Found at i:5368100 original size:35 final size:35
Alignment explanation
Indices: 5367995--5368171 Score: 132
Period size: 35 Copynumber: 5.1 Consensus size: 35
5367985 AAATCATTAG
5367995 ACGCCTATAATTACTAAATTAATATCTTAAAACTC
1 ACGCCTATAATTACTAAATTAATATCTTAAAACTC
* * * * * * *
5368030 AC-TCAAAAGATAACCTTAAATTAATGTC--CATACTC
1 ACGCCTATA-ATTA-C-TAAATTAATATCTTAAAACTC
5368065 ACGCCTATAATTACTAAATTAATATCTTAAAACTC
1 ACGCCTATAATTACTAAATTAATATCTTAAAACTC
* * * * * * *
5368100 AC-TCAAAAGATAACCTTAAATTAATGTC--CATACTC
1 ACGCCTATA-ATTA-C-TAAATTAATATCTTAAAACTC
5368135 ACGCCTATAATTACTAAATTAATATCTTAAAACTC
1 ACGCCTATAATTACTAAATTAATATCTTAAAACTC
5368170 AC
1 AC
5368172 TCAACATATT
Statistics
Matches: 102, Mismatches: 28, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
33 22 0.22
34 8 0.08
35 42 0.41
36 8 0.08
37 22 0.22
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (35 bp):
ACGCCTATAATTACTAAATTAATATCTTAAAACTC
Found at i:5368108 original size:70 final size:70
Alignment explanation
Indices: 5367995--5368175 Score: 362
Period size: 70 Copynumber: 2.6 Consensus size: 70
5367985 AAATCATTAG
5367995 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTCCA
1 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTCCA
5368060 TACTC
66 TACTC
5368065 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTCCA
1 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTCCA
5368130 TACTC
66 TACTC
5368135 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
1 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
5368176 CATATTAGGT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 111 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (70 bp):
ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTCCA
TACTC
Found at i:5368320 original size:87 final size:87
Alignment explanation
Indices: 5368174--5368393 Score: 413
Period size: 87 Copynumber: 2.5 Consensus size: 87
5368164 AAACTCACTC
*
5368174 AACATATTAGGTAACACTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
1 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
5368239 GGGAAATATTATCAAGTACAAT
66 GGGAAATATTATCAAGTACAAT
5368261 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
1 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
5368326 GGGAAATATTATCAAGTACAAT
66 GGGAAATATTATCAAGTACAAT
* *
5368348 AACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAT
1 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATAT
5368394 TGACCTATTT
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 130 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
GGGAAATATTATCAAGTACAAT
Found at i:5371968 original size:183 final size:182
Alignment explanation
Indices: 5371722--5372108 Score: 596
Period size: 183 Copynumber: 2.1 Consensus size: 182
5371712 TTAAAATTAG
* * *
5371722 CGACACAATATTAAAAAGTGTCGATATATGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCTCATAAAACAGGTATATTT
** * *
5371787 ATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGA-TGTATAAATGTCG
66 ATACCAATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATTGTATAAA--TCG
* *
5371851 ATACTTTTTGACAAGGTATCAACACATTTTTCTTCCATTCTGGACATAAAGTAC
129 ACACTTTTTGAAAAGGTATCAACACATTTTTCTTCCATTCTGGACATAAAGTAC
* *
5371905 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTTGCTCATAAAACATGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCTCATAAAACAGGTATATTT
* * *
5371970 ATACCAATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATTTTTTTCAATCGA
66 ATACCAATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA-TTGTATAAATCGA
* *
5372035 CACTTTTTGAAAATGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
130 CACTTTTTGAAAAGGTATCAACACATTTTTCTTCCATTCTGGACATAAAGTAC
5372088 CGACACAATATTAAAAAGTGT
1 CGACACAATATTAAAAAGTGT
5372109 GAAAACTTTG
Statistics
Matches: 186, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
183 181 0.97
185 5 0.03
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (182 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCTCATAAAACAGGTATATTT
ATACCAATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATTGTATAAATCGAC
ACTTTTTGAAAAGGTATCAACACATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:5373313 original size:3 final size:3
Alignment explanation
Indices: 5373305--5373349 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
5373295 ACTTGTTTGG
* * * *
5373305 ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
5373350 GTAATCTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.24, C:0.33, G:0.04, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:5373356 original size:12 final size:12
Alignment explanation
Indices: 5373309--5373357 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
5373299 GTTTGGATCA
* *
5373309 TCATCATCATCA
1 TCATCGTCATCT
5373321 TCATCGTCATCT
1 TCATCGTCATCT
5373333 TCATCGTCATCT
1 TCATCGTCATCT
*
5373345 TCATCGTAATCT
1 TCATCGTCATCT
5373357 T
1 T
5373358 TATCTTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.41
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:5374906 original size:200 final size:200
Alignment explanation
Indices: 5374582--5375727 Score: 1832
Period size: 200 Copynumber: 5.8 Consensus size: 200
5374572 AACATTAATC
* * * *
5374582 AGTGTCGATACA-TATTATATACCA-ATTCTCCCATAAAACCGGTATACTTATACCAGTTAGATT
1 AGTGTCGATACATTATT-TAGA-CATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATT
* * *
5374645 GAAAAATTACCTAATACATTATACTTTTGGGTTTCGATATTTATCGGATCGACACTTTTTATATA
64 GAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATA
* * *
5374710 TGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACAAAAAATATCGACACAAA
129 TGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAA
5374775 CTACAAA
194 CTACAAA
* * * *
5374782 AGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATATTTGTATCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
5374847 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATTGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
*
5374912 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGATACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
5374977 ACAAA
196 ACAAA
*
5374982 AGTGTCGATACATTATTTAGACTTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
5375047 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
5375112 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
5375177 ACAAA
196 ACAAA
*
5375182 AGTGTCGACACATTATTTAGAGC-TATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
1 AGTGTCGATACATTATTTAGA-CATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
5375246 AAAAATTACC---TACATTATACTTATGGGTTTCGATG-TTATCGGATCGACAC--TTT-TATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATAT
*
5375304 GTATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
5375369 TACAAA
195 TACAAA
* *
5375375 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCAGTTAGATTGA
1 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
5375440 AAAATTACCTATTAC-----A--TATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
* **
5375498 GATTGACACTTTATTGTTGCATACTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
5375563 ACAAA
196 ACAAA
* *
5375568 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAAACGGTTATACTTGTACCGATTAGATTG
1 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGG-TATACTTGTACCGGTTAGATTG
* *
5375633 AAAAATTACCTATTACATTATACTTTTGGGTTTCGATG-TT-TGGGATCGACAC-TTTT-TATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATAT
*
5375694 GGATCGACAC-TTATGGTTGCACCCTGTTTGCCAT
130 GGATCGACACTTTATTGTTGCACCCTGTTTGCCAT
5375728 ATTGTAAATT
Statistics
Matches: 884, Mismatches: 43, Indels: 42
0.91 0.04 0.04
Matches are distributed among these distances:
189 14 0.02
190 15 0.02
191 1 0.00
192 4 0.00
193 257 0.29
194 39 0.04
196 39 0.04
197 39 0.04
198 4 0.00
199 14 0.02
200 440 0.50
201 18 0.02
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:5375971 original size:17 final size:17
Alignment explanation
Indices: 5375949--5376005 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
5375939 TCTCATTCAT
5375949 AATTAT-ATCACATACAA
1 AATTATAATC-CATACAA
**
5375966 AATTATAATGTATACAA
1 AATTATAATCCATACAA
5375983 AATTATAATCCTATACAA
1 AATTATAATCC-ATACAA
5376001 AATTA
1 AATTA
5376006 ACCCTACATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 21 0.62
18 13 0.38
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (17 bp):
AATTATAATCCATACAA
Found at i:5375999 original size:18 final size:17
Alignment explanation
Indices: 5375960--5376005 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
5375950 ATTATATCAC
*
5375960 ATACAAAATTATAATGT
1 ATACAAAATTATAATCT
5375977 ATACAAAATTATAATCCT
1 ATACAAAATTATAAT-CT
5375995 ATACAAAATTA
1 ATACAAAATTA
5376006 ACCCTACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (17 bp):
ATACAAAATTATAATCT
Found at i:5377882 original size:21 final size:21
Alignment explanation
Indices: 5377856--5377908 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
5377846 TCTCAAGGTA
*
5377856 TCTTCGACTCTCTCAAGTTTC
1 TCTTCGACTCTATCAAGTTTC
5377877 TCTTCGACTCTATCAAGTTTC
1 TCTTCGACTCTATCAAGTTTC
5377898 TCTTCGACTCT
1 TCTTCGACTCT
5377909 TGATTGTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.32, G:0.09, T:0.43
Consensus pattern (21 bp):
TCTTCGACTCTATCAAGTTTC
Found at i:5380149 original size:19 final size:19
Alignment explanation
Indices: 5380104--5380161 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
5380094 TCCGGTATCG
5380104 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
5380123 TTGATACC-GTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
* *
5380143 TTTTACCTGTTATATCATT
1 TTTTACCGGTTTTATCATT
5380162 GTGGATCGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:5380330 original size:20 final size:19
Alignment explanation
Indices: 5380284--5380330 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
5380274 TCCGGTAACG
5380284 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
5380303 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
5380324 TTTTACC
1 TTTTACC
5380331 TGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:5380402 original size:181 final size:182
Alignment explanation
Indices: 5380071--5380542 Score: 743
Period size: 181 Copynumber: 2.6 Consensus size: 182
5380061 CGTACTTACG
*
5380071 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACC-GTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
5380135 TATCATATTTTTACCTGTTATATCATTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
5380200 AGGTGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGTGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
5380251 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
5380316 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
5380381 AGGAT-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGG-TGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * **
5380433 AAAGTATCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
5380498 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTT
5380543 AATTTGGATC
Statistics
Matches: 268, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
180 59 0.22
181 108 0.40
182 101 0.38
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGTGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Done.