Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 113 of 170
Found at i:34765676 original size:42 final size:43
Alignment explanation
Indices: 34765615--34765719 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 43
34765605 GATTTGAGAT
* *
34765615 TTACGTGTAAGACCATGTCTGGAACATTGGCGTCG-TATATGA
1 TTACGTGTAAGACCATGTCTGGAACAGTGGCATCGTTATATGA
* * *
34765657 TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGAACAGTGGCATCGTTATATGA
* * *
34765700 TTACATGGAAGACCACGTCT
1 TTACGTGTAAGACCATGTCT
34765720 AGGACGTTGG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 31 0.58
43 22 0.42
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGAACAGTGGCATCGTTATATGA
Found at i:34765731 original size:43 final size:43
Alignment explanation
Indices: 34765574--34765732 Score: 141
Period size: 43 Copynumber: 3.7 Consensus size: 43
34765564 AATGTGATAT
* *
34765574 CGTGTAAGACCACATCTAGGACGTTGGCAT--TGATTTGAGATTTA
1 CGTGTAAGACCACGTCTAGGACGTTGGCATCGTTATTT--GA-TTA
* * * *
34765618 CGTGTAAGACCATGTCT-GGAACATTGGCGTCG-TATATGATTA
1 CGTGTAAGACCACGTCTAGG-ACGTTGGCATCGTTATTTGATTA
*
34765660 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGTTATTTGATTA
1 CGTGTAAGACCAC-GTCTAGGAC-GTTGGCATCGTTATTTGATTA
* *
34765703 CATGGAAGACCACGTCTAGGACGTTGGCAT
1 CGTGTAAGACCACGTCTAGGACGTTGGCAT
34765733 TGTACGAGCT
Statistics
Matches: 93, Mismatches: 13, Indels: 19
0.74 0.10 0.15
Matches are distributed among these distances:
42 28 0.30
43 38 0.41
44 24 0.26
45 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTAGGACGTTGGCATCGTTATTTGATTA
Found at i:34767539 original size:42 final size:42
Alignment explanation
Indices: 34767487--34767681 Score: 168
Period size: 42 Copynumber: 4.7 Consensus size: 42
34767477 TATGATTACG
* * * * *
34767487 TGTAAGACCATGTCTGGGACATTGGCTTTGTTATGTGATTCA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATCCA
* *
34767529 TGTAAGACCATGTCTGGGACATTGACATCGATATGAGATCCG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATCCA
* * * *
34767571 CGTAAGACCATGTCTGGGAAATTGGTATCGATATGAGAAT-CG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAG-ATCCA
* *
34767613 TGTAAGACCATAG-CT-AG-CTATTGGCATCGATAT-ATGATAGCA
1 TGTAAGACCAT-GTCTGGGAC-ATTGGCATCGATATGA-GAT-CCA
* *
34767655 TGTAAGACCATATCTGGGATA-TGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
34767682 TGTGCGAGTT
Statistics
Matches: 125, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
40 3 0.02
41 15 0.12
42 102 0.82
43 5 0.04
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATCCA
Found at i:34784135 original size:39 final size:40
Alignment explanation
Indices: 34784092--34784227 Score: 163
Period size: 40 Copynumber: 3.5 Consensus size: 40
34784082 CTATAGGTCA
* *
34784092 AGCATTAGCAGCGCTTTTTG-AAAATGCCGCTATAAATCG
1 AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCG
* *
34784131 AGCATTAGCGGCCCTTTTTGAAAAACGCCGCTATAGATC-
1 AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCG
* * *
34784170 ATGTATTAGCGGCG-TTTCTCGAAAAACGCCGCAAT-AATCG
1 A-GCATTAGCGGCGCTTT-TTGAAAAACGCCGCTATAAATCG
34784210 AGCATTAGCGGCGCTTTT
1 AGCATTAGCGGCGCTTTT
34784228 CAGAAAACAC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
39 37 0.45
40 45 0.55
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (40 bp):
AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCG
Found at i:34784234 original size:40 final size:38
Alignment explanation
Indices: 34784092--34784242 Score: 144
Period size: 39 Copynumber: 3.8 Consensus size: 38
34784082 CTATAGGTCA
* * *
34784092 AGCATTAGCAGCGCTTTTTGAAAATGCCGCTATAAATCG
1 AGCATTAGCGGCGCTTTTTGAAAACGCCGCAAT-AATCG
* *
34784131 AGCATTAGCGGCCCTTTTTGAAAAACGCCGCTATAGATC-
1 AGCATTAGCGGCGCTTTTTG-AAAACGCCGCAATA-ATCG
* *
34784170 ATGTATTAGCGGCG-TTTCTCGAAAAACGCCGCAATAATCG
1 A-GCATTAGCGGCGCTTT-TTG-AAAACGCCGCAATAATCG
* *
34784210 AGCATTAGCGGCGCTTTTCAGAAAACACCGCAA
1 AGCATTAGCGGCGCTTTT-TGAAAACGCCGCAA
34784243 AAAATTTAAG
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
39 49 0.52
40 46 0.48
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (38 bp):
AGCATTAGCGGCGCTTTTTGAAAACGCCGCAATAATCG
Found at i:34784515 original size:195 final size:195
Alignment explanation
Indices: 34784206--34784567 Score: 469
Period size: 195 Copynumber: 1.9 Consensus size: 195
34784196 CGCCGCAATA
* * *
34784206 ATCGAGCATTAGCGGCGCTTTTCAGAAAACACCGCAAAAAATTTAAGCAAAACACGTCGTTTGTT
1 ATCGAGCATTAGCGACACTTTTCAGAAAACACCGCAAAAAAATTAAGCAAAACACGTCGTTTGTT
* * *
34784271 GTTGAGCTTTAGTGGCATTAGCGGCACTTTTAAAAAAATGCCGCAATAGATCAAGCATTA-CGAC
66 GTTGAGCTTTAGTGGCATTAGCGGCACTTTTAAAAAAACGCCACAATAGATCAAGAATTAGCGAC
* * *
34784335 GCTT-TTAAAAAATGCCGCAATAGATTGAGAATTAGCTGTGCTTTGTCGAAAAACATGTCTATAG
131 ACTTGTTAAAAAACGCCGCAATAGATTCAGAATTAGCTGTGCTTTGTCGAAAAACATGTCTATAG
* *
34784399 ATCGAGCATTAGCGACACTTTTCAGAAAA-ATGCCGCAAAAAAATTGAGCAAAACAATGTCGTTT
1 ATCGAGCATTAGCGACACTTTTCAGAAAACA--CCGCAAAAAAATTAAGCAAAAC-ACGTCGTTT
* * * * * ** *
34784463 TTTTTTTAGCTTTAGTTGCATTAGCGGCGCTTTTGTAAAAACGCCACAATAGATCGAGAATTAGC
63 GTTGTTGAGCTTTAGTGGCATTAGCGGCACTTTTAAAAAAACGCCACAATAGATCAAGAATTAGC
* * * *
34784528 GGCACTTGTTGAAAAACGCCGCTATAGATTCAGCATTAGC
128 GACACTTGTTAAAAAACGCCGCAATAGATTCAGAATTAGC
34784568 GGCGCTTTTC
Statistics
Matches: 141, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
192 1 0.01
193 27 0.19
194 20 0.14
195 60 0.43
196 6 0.04
197 27 0.19
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (195 bp):
ATCGAGCATTAGCGACACTTTTCAGAAAACACCGCAAAAAAATTAAGCAAAACACGTCGTTTGTT
GTTGAGCTTTAGTGGCATTAGCGGCACTTTTAAAAAAACGCCACAATAGATCAAGAATTAGCGAC
ACTTGTTAAAAAACGCCGCAATAGATTCAGAATTAGCTGTGCTTTGTCGAAAAACATGTCTATAG
Found at i:34784543 original size:40 final size:40
Alignment explanation
Indices: 34784482--34784576 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
34784472 CTTTAGTTGC
*
34784482 ATTAGCGGCGCTTTTGTAAAAACGCCACAATAGA-TCGAGA
1 ATTAGCGGCACTTTTGTAAAAACGCCACAATAGATTC-AGA
* * *
34784522 ATTAGCGGCACTTGTTG-AAAAACGCCGCTATAGATTCAGC
1 ATTAGCGGCACTT-TTGTAAAAACGCCACAATAGATTCAGA
*
34784562 ATTAGCGGCGCTTTT
1 ATTAGCGGCACTTTT
34784577 CGCAAAATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
39 2 0.04
40 41 0.85
41 5 0.10
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (40 bp):
ATTAGCGGCACTTTTGTAAAAACGCCACAATAGATTCAGA
Found at i:34784678 original size:7 final size:7
Alignment explanation
Indices: 34784663--34784723 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
34784653 TTCATTTTAT
34784663 TTTAAGG
1 TTTAAGG
*
34784670 TTTAGGG
1 TTTAAGG
**
34784677 TTTAATA
1 TTTAAGG
34784684 TTTAAGG
1 TTTAAGG
*
34784691 TTTAATG
1 TTTAAGG
* *
34784698 TCTATGG
1 TTTAAGG
34784705 TTTAAGG
1 TTTAAGG
34784712 TTTTAAGG
1 -TTTAAGG
34784720 TTTA
1 TTTA
34784724 TGATATAATG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
7 34 0.83
8 7 0.17
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (7 bp):
TTTAAGG
Found at i:34784904 original size:21 final size:22
Alignment explanation
Indices: 34784878--34784932 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
34784868 AACAGCAGTG
34784878 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
34784899 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
*
34784920 GCAGTGAGATTAG
1 GCGGTGAGATTAG
34784933 AAACAGCGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:34785123 original size:18 final size:17
Alignment explanation
Indices: 34785096--34785212 Score: 68
Period size: 18 Copynumber: 7.0 Consensus size: 17
34785086 TTATTATTAA
34785096 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
34785113 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
* *
34785131 -TATAATAT-ATAATATT
1 ATATAATTTAATAA-AAT
* *
34785147 ATAAAATATAATTCAAAAT
1 ATATAATTTAA-T-AAAAT
* *
34785166 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
*
34785178 ATATAATTTAACAAAAAT
1 ATATAATTTAA-TAAAAT
34785196 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
34785213 TCTTAGTATT
Statistics
Matches: 74, Mismatches: 14, Indels: 24
0.66 0.12 0.21
Matches are distributed among these distances:
12 1 0.01
13 5 0.07
14 2 0.03
15 5 0.07
16 7 0.09
17 22 0.30
18 26 0.35
19 4 0.05
20 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:34785285 original size:119 final size:120
Alignment explanation
Indices: 34785112--34785353 Score: 441
Period size: 119 Copynumber: 2.0 Consensus size: 120
34785102 TTTAATAAAA
* *
34785112 TATATGAATTTACTAAAATTATAATATATAATATTATAAAATATAATTCAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAATTATTATTA
34785177 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
**
34785232 TATATGAATTTACTAAAATCATAAT-TATAATACTATAAAATATAATTTTAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAATTATTATTA
34785296 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
34785351 TAT
1 TAT
34785354 GATTGTATCA
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
119 94 0.80
120 24 0.20
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAATTATTATTA
AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
Found at i:34788475 original size:18 final size:18
Alignment explanation
Indices: 34788442--34788495 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
34788432 TTTGCAAACC
34788442 AAGGGGAACGGG-AAAGGG
1 AAGGGGAA-GGGAAAAGGG
34788460 AAGGGGAAGGGAAAAGGG
1 AAGGGGAAGGGAAAAGGG
* **
34788478 GAGAAGAAGGGAAAAGGG
1 AAGGGGAAGGGAAAAGGG
34788496 GAGAAGAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 3 0.09
18 29 0.91
ACGTcount: A:0.44, C:0.02, G:0.54, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGAAAAGGG
Found at i:34788496 original size:18 final size:18
Alignment explanation
Indices: 34788465--34788506 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
34788455 AAGGGAAGGG
34788465 GAAGGGAAAAGGGGAGAA
1 GAAGGGAAAAGGGGAGAA
34788483 GAAGGGAAAAGGGGAGAA
1 GAAGGGAAAAGGGGAGAA
34788501 GAAGGG
1 GAAGGG
34788507 TAACCAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (18 bp):
GAAGGGAAAAGGGGAGAA
Found at i:34789031 original size:28 final size:28
Alignment explanation
Indices: 34789000--34789053 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
34788990 GAAGTTTATG
34789000 GTTTAATATTTATGCTTTAGGGTTTAAA
1 GTTTAATATTTATGCTTTAGGGTTTAAA
* * *
34789028 GTTTAGTGTTTATGCTTTGGGGTTTA
1 GTTTAATATTTATGCTTTAGGGTTTA
34789054 CTTATGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (28 bp):
GTTTAATATTTATGCTTTAGGGTTTAAA
Found at i:34789039 original size:21 final size:20
Alignment explanation
Indices: 34788993--34789039 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
34788983 TTAAGATGAA
*
34788993 GTTTATGGTTTAATATTTAT
1 GTTTAGGGTTTAATATTTAT
34789013 GCTTTAGGGTTTAA-AGTTTAGT
1 G-TTTAGGGTTTAATA-TTTA-T
34789035 GTTTA
1 GTTTA
34789040 TGCTTTGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.23, C:0.02, G:0.21, T:0.53
Consensus pattern (20 bp):
GTTTAGGGTTTAATATTTAT
Found at i:34792544 original size:43 final size:41
Alignment explanation
Indices: 34792497--34792630 Score: 128
Period size: 43 Copynumber: 3.1 Consensus size: 41
34792487 GAACGGTACT
* *
34792497 TTTAGCGACGTTTGTCATAAAAGCGCCACTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTAATAAAAGCGCCA-TAAAG-TCATGTTC
* *
34792540 TTTAGCGGCGTTTGTGAAAAAAAGTCGCTA-AAAGTCAT-TCTC
1 TTTAGCGGCGTTTGT-AATAAAAG-CGCCATAAAGTCATGT-TC
* * *
34792582 TATAGCGGCGTTTGTGATAAAAGCGCCGTTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTAATAAAAGCGCC-ATAAA-GTCATGTTC
34792625 TTTAGC
1 TTTAGC
34792631 AATATTTGTG
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
40 3 0.04
41 7 0.09
42 23 0.31
43 30 0.41
44 7 0.09
45 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTGTAATAAAAGCGCCATAAAGTCATGTTC
Found at i:34795714 original size:36 final size:36
Alignment explanation
Indices: 34795642--34795716 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
34795632 CTAATGTAAT
* * **
34795642 TGTTAATTTAATTGAATGAAAGTTTATGGATGTATA
1 TGTTAATTCAATTGAATGAAAGTTTATAGAAATATA
* *
34795678 TGTTAATTCAATTGAATGGAATTTTATAGAAATATA
1 TGTTAATTCAATTGAATGAAAGTTTATAGAAATATA
34795714 TGT
1 TGT
34795717 ATTTAGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.44
Consensus pattern (36 bp):
TGTTAATTCAATTGAATGAAAGTTTATAGAAATATA
Found at i:34795991 original size:76 final size:70
Alignment explanation
Indices: 34795831--34795998 Score: 176
Period size: 70 Copynumber: 2.3 Consensus size: 70
34795821 TAGATATCCA
* * * *
34795831 ACTAGCGCTAGGCGCAATAATTTGTTGACTCGTTCAACTAGTGTCGGACACAACTATCGTCAGTT
1 ACTAGCGTTAGGCGCAATAACTTGTCGACTCGTTCAACTAGTGTCGGACACAAATATCGTCAGTT
**
34795896 ATTTG
66 AAATG
* * * *
34795901 ACTAACGTTTGGCGCAATAACTTGTCGACTCGTTCGACTAGTGCTGGGCACACAAATGATCTTGT
1 ACTAGCGTTAGGCGCAATAACTTGTCGACTCGTTCAACTAGTG-TCGG-ACACAAAT-ATC--GT
34795966 CGAGTTAAATG
61 C-AGTTAAATG
*
34795977 ACTAGCGTTGGGCGCAA-AACTT
1 ACTAGCGTTAGGCGCAATAACTT
34795999 TATTCACGGT
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
70 37 0.46
71 3 0.04
72 7 0.09
73 3 0.04
75 8 0.10
76 22 0.28
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (70 bp):
ACTAGCGTTAGGCGCAATAACTTGTCGACTCGTTCAACTAGTGTCGGACACAAATATCGTCAGTT
AAATG
Found at i:34798002 original size:18 final size:18
Alignment explanation
Indices: 34797976--34798019 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
34797966 AACAAAAATA
* *
34797976 TTGAGAGAGTTGAGA-AG
1 TTGAAAGAGCTGAGAGAG
34797993 TTTGAAAGAGCTGAGAGAG
1 -TTGAAAGAGCTGAGAGAG
34798012 TTGAAAGA
1 TTGAAAGA
34798020 AAGATACGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.39, C:0.02, G:0.36, T:0.23
Consensus pattern (18 bp):
TTGAAAGAGCTGAGAGAG
Found at i:34807156 original size:16 final size:17
Alignment explanation
Indices: 34807122--34807156 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34807112 AATAAATATA
*
34807122 TTATTTTTAATCTTTTC
1 TTATTTTTAATCTTATC
34807139 TTATTTTTAAT-TTATC
1 TTATTTTTAATCTTATC
34807155 TT
1 TT
34807157 TAATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTTAATCTTATC
Found at i:34811209 original size:23 final size:23
Alignment explanation
Indices: 34811174--34811230 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
34811164 TATATATATT
*
34811174 ATATAATATATGTACATATAAAAA
1 ATAT-ATATATGTACACATAAAAA
**
34811198 ATATATATATGTATGCATAAAAA
1 ATATATATATGTACACATAAAAA
*
34811221 ATATGTATAT
1 ATATATATAT
34811231 ATATAGGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.37
Consensus pattern (23 bp):
ATATATATATGTACACATAAAAA
Found at i:34813305 original size:252 final size:252
Alignment explanation
Indices: 34812860--34813381 Score: 805
Period size: 252 Copynumber: 2.1 Consensus size: 252
34812850 ACTGCAACTA
* **
34812860 CTCCACTGCAA-CTTCAGGGAAATAAGGTTTGTGGTTTTACTCTGCTCTATGGTTCAACCTACTC
1 CTCCACTG-AATCTTCAGGGAAATAAGGTTTGTGGTTTTAATCTGCTCTATACTTCAACCTACTC
*
34812924 CGCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAATCGCTATCTACTACCCGCTCCACTA
65 CGCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTACCCGCTCCACTA
* * * *
34812989 CAACTTTAGAGAGACACGACTTGTTGTTTTCAGTCTACTCCATTGTATCTTTAGGGAAATAAGAC
130 CAACTTTAGAGAGACACAACTTGTTGTTTTCAGTCTACTCCACTGCATCTTCAGGGAAATAAGAC
* *
34813054 TTATATCTTCAACCTGCTCCACTACAACTTTAGGGAAATAAGATTCGCAGTCGATCTG
195 TTATATCTTCAACCTGCTCCACTACAACTTCAGGGAAATAAGATTCGCAGCCGATCTG
* **
34813112 CTCCACTGAATCTTTAGGGAGGTAAGGTTTGTGGTTTTAATCTGC-CTCATACTTCAACCTACTC
1 CTCCACTGAATCTTCAGGGAAATAAGGTTTGTGGTTTTAATCTGCTCT-ATACTTCAACCTACTC
* ** *
34813176 CGCTGTAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGTCTGCTCCACTA
65 CGCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTACCCGCTCCACTA
*
34813241 CAACTTTAGGGAGACACAACTTGTTGTTTTCAGTCTACTCCACTGCATCTTCAGGGAAATAAGAC
130 CAACTTTAGAGAGACACAACTTGTTGTTTTCAGTCTACTCCACTGCATCTTCAGGGAAATAAGAC
* * * *
34813306 TTGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAAATAGGATTCGTAGCCGATCTG
195 TTATATCTTCAACCTGCTCCACTACAACTTCAGGGAAATAAGATTCGCAGCCGATCTG
*
34813364 CTCCACTGCATCTTCAGG
1 CTCCACTGAATCTTCAGG
34813382 AAGATACGAC
Statistics
Matches: 244, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
251 4 0.02
252 240 0.98
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (252 bp):
CTCCACTGAATCTTCAGGGAAATAAGGTTTGTGGTTTTAATCTGCTCTATACTTCAACCTACTCC
GCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTACCCGCTCCACTAC
AACTTTAGAGAGACACAACTTGTTGTTTTCAGTCTACTCCACTGCATCTTCAGGGAAATAAGACT
TATATCTTCAACCTGCTCCACTACAACTTCAGGGAAATAAGATTCGCAGCCGATCTG
Found at i:34813379 original size:42 final size:43
Alignment explanation
Indices: 34813278--34813381 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 43
34813268 TTTCAGTCTA
*
34813278 CTCCACTGCATCTTCAGGGAAATAAGACTTGTATCTTCAACCTG
1 CTCCACTGCATCTTCAGGGAAATAAGACTTGTAGC-TCAACCTG
* * * *
34813322 CTCCACTGCAACTTCAGGGAAATAGGA-TTCGTAGC-CGATCTG
1 CTCCACTGCATCTTCAGGGAAATAAGACTT-GTAGCTCAACCTG
34813364 CTCCACTGCATCTTCAGG
1 CTCCACTGCATCTTCAGG
34813382 AAGATACGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 22 0.42
43 2 0.04
44 29 0.55
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (43 bp):
CTCCACTGCATCTTCAGGGAAATAAGACTTGTAGCTCAACCTG
Found at i:34824021 original size:16 final size:16
Alignment explanation
Indices: 34823988--34824022 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34823978 TTTTATAATG
* *
34823988 AAATGCCATGTAGTCA
1 AAATGCCATGCAGCCA
34824004 AAATGCCATGCAGCCA
1 AAATGCCATGCAGCCA
34824020 AAA
1 AAA
34824023 CAAAACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:34825667 original size:20 final size:20
Alignment explanation
Indices: 34825642--34825680 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34825632 GACGATAAAT
34825642 AAAATAAAT-AAAATTATATA
1 AAAATAAATGAAAA-TATATA
*
34825662 AAAATATATGAAAATATAT
1 AAAATAAATGAAAATATAT
34825681 GTATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAATAAATGAAAATATATA
Found at i:34825759 original size:28 final size:29
Alignment explanation
Indices: 34825711--34825768 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
34825701 TATGAAAATA
34825711 AAAAATATATGTGTACATATACATAGTTAT
1 AAAAATATATGTGTA-ATATACATAGTTAT
*
34825741 AAAAATATATGTGT-ATATATATAGTTAT
1 AAAAATATATGTGTAATATACATAGTTAT
34825769 GAATTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 13 0.48
30 14 0.52
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (29 bp):
AAAAATATATGTGTAATATACATAGTTAT
Found at i:34828041 original size:19 final size:19
Alignment explanation
Indices: 34828003--34828041 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
34827993 TGTTTTTTTA
* * *
34828003 TTTTTAAAATTAACATATT
1 TTTTTAAAATAAAAAAATT
34828022 TTTTTAAAATAAAAAAATT
1 TTTTTAAAATAAAAAAATT
34828041 T
1 T
34828042 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTAAAATAAAAAAATT
Found at i:34848856 original size:16 final size:15
Alignment explanation
Indices: 34848809--34848879 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
34848799 AAATAAAAAC
*
34848809 ATAAAAAGTTTTAAA
1 ATAAAAAATTTTAAA
* *
34848824 ATTATAATATTTTAAA
1 A-TAAAAAATTTTAAA
34848840 ATAAAAAATTTTGAAAA
1 ATAAAAAATTTT--AAA
****
34848857 ATAATTTTTTTTAAA
1 ATAAAAAATTTTAAA
34848872 ATAAAAAA
1 ATAAAAAA
34848880 ATAAAAAATG
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
15 17 0.43
16 12 0.30
17 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAAAAATTTTAAA
Found at i:34848887 original size:30 final size:31
Alignment explanation
Indices: 34848833--34848894 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
34848823 AATTATAATA
* *
34848833 TTTTAAAATAAAAAATTTTGAAAAATAATTTT
1 TTTTAAAATAAAAAA-TATAAAAAATAATTTT
*
34848865 TTTTAAAATAAAAAA-ATAAAAAATGATTTT
1 TTTTAAAATAAAAAATATAAAAAATAATTTT
34848895 AAAAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 12 0.44
32 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (31 bp):
TTTTAAAATAAAAAATATAAAAAATAATTTT
Found at i:34860734 original size:18 final size:17
Alignment explanation
Indices: 34860697--34860735 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
34860687 ACTATACAAG
*
34860697 GCTCGCACCTTTGATGA
1 GCTCGCACCCTTGATGA
*
34860714 GCTCGCACCACTTGCTGA
1 GCTCGCACC-CTTGATGA
34860732 GCTC
1 GCTC
34860736 ATAGCTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.15, C:0.36, G:0.23, T:0.26
Consensus pattern (17 bp):
GCTCGCACCCTTGATGA
Found at i:34860766 original size:25 final size:25
Alignment explanation
Indices: 34860738--34860798 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
34860728 CTGAGCTCAT
*
34860738 AGCTTGCACTTCTCGCTAAGCTCGC
1 AGCTTGCACATCTCGCTAAGCTCGC
* * *
34860763 AGCTTTG-ACATCTTGCTGAGCTTGC
1 AGC-TTGCACATCTCGCTAAGCTCGC
34860788 AGCTTGCACAT
1 AGCTTGCACAT
34860799 TGTAAAGCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 3 0.10
25 24 0.80
26 3 0.10
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.31
Consensus pattern (25 bp):
AGCTTGCACATCTCGCTAAGCTCGC
Found at i:34869414 original size:17 final size:17
Alignment explanation
Indices: 34869392--34869432 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
34869382 CTAAATCTGC
* *
34869392 TTTGGGCTTCTGTTTGG
1 TTTGGGCTTCAGTTGGG
34869409 TTTGGGCTTCAGTTGGG
1 TTTGGGCTTCAGTTGGG
34869426 TTTGGGC
1 TTTGGGC
34869433 CACATAGGTT
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:0.02, C:0.12, G:0.39, T:0.46
Consensus pattern (17 bp):
TTTGGGCTTCAGTTGGG
Found at i:34874861 original size:3 final size:3
Alignment explanation
Indices: 34874855--34874910 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
34874845 GTCGTCGTCG
* * *
34874855 TCA TCA TCA TCA TCA TCA TCA TCA TCT TGA TCA TCA TCA -GA GTCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA -TCA
34874900 TCA TCA TCA TC
1 TCA TCA TCA TC
34874911 TTTACCCTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:34886395 original size:22 final size:22
Alignment explanation
Indices: 34886369--34886415 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
34886359 TTTAGGTAAG
*
34886369 AAAA-TAGGTGTTTTAAAGGGTT
1 AAAATTAGGTGTATT-AAGGGTT
*
34886391 AAAATTGGGTGTATTAAGGGTT
1 AAAATTAGGTGTATTAAGGGTT
34886413 AAA
1 AAA
34886416 CCACCGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (22 bp):
AAAATTAGGTGTATTAAGGGTT
Found at i:34887740 original size:31 final size:31
Alignment explanation
Indices: 34887651--34887744 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
34887641 AGATAATTTT
* *
34887651 AAAGAGTTTTATTAGGATTCAATTACCCTTT
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
34887682 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
34887714 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
34887745 TAATTTGCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:34888067 original size:12 final size:11
Alignment explanation
Indices: 34888048--34888077 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
34888038 TCTATCCTTT
34888048 TTATTTATTTA
1 TTATTTATTTA
34888059 TTCATTTATTTA
1 TT-ATTTATTTA
34888071 TTATTTA
1 TTATTTA
34888078 CCTAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:34899793 original size:31 final size:31
Alignment explanation
Indices: 34899758--34899837 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
34899748 ACAGTGAAAA
34899758 TGGGCCCACAAGCCCATGACATTTCCCCGTG
1 TGGGCCCACAAGCCCATGACATTTCCCCGTG
* *
34899789 TGGGCCCACATGCCCATGACATTTGCCCGTG
1 TGGGCCCACAAGCCCATGACATTTCCCCGTG
*
34899820 TGGGCCCACACGCCCATG
1 TGGGCCCACAAGCCCATG
34899838 TGGCCCACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.17, C:0.39, G:0.25, T:0.19
Consensus pattern (31 bp):
TGGGCCCACAAGCCCATGACATTTCCCCGTG
Found at i:34903767 original size:11 final size:11
Alignment explanation
Indices: 34903751--34903780 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
34903741 AAATTTGGGG
34903751 TTTTGAAACTA
1 TTTTGAAACTA
*
34903762 TTTTGAAACTG
1 TTTTGAAACTA
34903773 TTTTGAAA
1 TTTTGAAA
34903781 ACTCTCGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (11 bp):
TTTTGAAACTA
Found at i:34903837 original size:20 final size:18
Alignment explanation
Indices: 34903812--34903882 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 18
34903802 AAAACCCAAT
34903812 AAGTATCGATATTTTTAGA
1 AAGTATCGATATTTTTA-A
*
34903831 CAAGTATCAATTATTTTATAA
1 -AAGTATCGA-TATTTT-TAA
34903852 AAGTATCGATATTTTTAA
1 AAGTATCGATATTTTTAA
34903870 AATGGTATCGATA
1 AA--GTATCGATA
34903883 CCAAATTCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
18 5 0.11
19 6 0.13
20 25 0.56
21 7 0.16
22 2 0.04
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (18 bp):
AAGTATCGATATTTTTAA
Found at i:34913519 original size:29 final size:30
Alignment explanation
Indices: 34913472--34913532 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
34913462 GTTTGACTAG
34913472 ATTATAATTAATCATTTTATTAAGATAAAT
1 ATTATAATTAATCATTTTATTAAGATAAAT
34913502 ATTA-AATTAATCATTTTATTAAGATAAAT
1 ATTATAATTAATCATTTTATTAAGATAAAT
34913531 AT
1 AT
34913533 CTACATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
ATTATAATTAATCATTTTATTAAGATAAAT
Found at i:34913551 original size:29 final size:29
Alignment explanation
Indices: 34913472--34913551 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
34913462 GTTTGACTAG
* **
34913472 ATTATAATTAATCATTTTATTAAGATAAAT
1 ATTA-AATAAATCATTAAATTAAGATAAAT
* **
34913502 ATTAAATTAATCATTTTATTAAGATAAAT
1 ATTAAATAAATCATTAAATTAAGATAAAT
*
34913531 ATCTACATAAAT-ATTAAATTA
1 AT-TAAATAAATCATTAAATTA
34913552 CAAATATCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 34 0.76
30 11 0.24
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTAAATAAATCATTAAATTAAGATAAAT
Found at i:34915452 original size:47 final size:47
Alignment explanation
Indices: 34915347--34915458 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 47
34915337 CACAATAATT
** * * *
34915347 TAGATAAACTATCAATAGTCAAAATTGTGGACAAGCCACCAAAATCG
1 TAGATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCA
* *
34915394 CAGATATACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCA
1 TAGATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCA
*
34915441 TAGATAAACTGCAAATAA
1 TAGATAAACTGCCAATAA
34915459 CTTTCACCTT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (47 bp):
TAGATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCA
Found at i:34917971 original size:188 final size:188
Alignment explanation
Indices: 34917654--34918013 Score: 675
Period size: 188 Copynumber: 1.9 Consensus size: 188
34917644 CCAAGACTAG
34917654 TCATCTTCCTAATCGAAATTGTAGAAGACATAATAATCCTTCTATATATTTGAATCAAATGTTCA
1 TCATCTTCCTAATCGAAATTGTAGAAGACATAATAATCCTTCTATATATTTGAATCAAATGTTCA
* * *
34917719 CTTTGATTCTTTTACAGGGTTACGAACTCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTCG
66 CTTTGATTCTTTTACAAGATAACGAACTCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTCG
34917784 CAATGAAAATATTCTTGCAGTGCCACTTATCATCAGCTTGAACTTAGACAAACAATGT
131 CAATGAAAATATTCTTGCAGTGCCACTTATCATCAGCTTGAACTTAGACAAACAATGT
* *
34917842 TCATCTTCCTAATTGAAATTGTAGACGACATAATAATCCTTCTATATATTTGAATCAAATGTTCA
1 TCATCTTCCTAATCGAAATTGTAGAAGACATAATAATCCTTCTATATATTTGAATCAAATGTTCA
34917907 CTTTGATTCTTTTACAAGATAACGAACTCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTCG
66 CTTTGATTCTTTTACAAGATAACGAACTCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTCG
34917972 CAATGAAAATATTCTTGCAGTGCCACTTATCATCAGCTTGAA
131 CAATGAAAATATTCTTGCAGTGCCACTTATCATCAGCTTGAA
34918014 AAGGTCTTTT
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 167 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (188 bp):
TCATCTTCCTAATCGAAATTGTAGAAGACATAATAATCCTTCTATATATTTGAATCAAATGTTCA
CTTTGATTCTTTTACAAGATAACGAACTCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTCG
CAATGAAAATATTCTTGCAGTGCCACTTATCATCAGCTTGAACTTAGACAAACAATGT
Found at i:34920084 original size:36 final size:37
Alignment explanation
Indices: 34919978--34920395 Score: 436
Period size: 36 Copynumber: 11.4 Consensus size: 37
34919968 AAAAATGGAA
*
34919978 TACTGATTCTACT-AAAGTACTC-AACGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
*
34920013 TACTGATTCTACTAAAAGTGCTTAAACGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* *
34920050 TACTGATTTTACAAAAAGTGCTC-AACGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* * * *
34920086 TATTGA-TCTTACTAAATGTGCTC-AGCGAGCAATATT
1 TACTGATTC-TACTAAAAGTGCTCAAACGAGCAATATC
* * * *
34920122 TACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* *
34920159 TACTGATTCTACTGAAAGTGCTCAAATGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* * *
34920196 TACTAATTCTACTAAAAGTGTTC-AACAAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* * * * * * * *
34920232 TACCGATCCCATTGAATGTGCTCAAATGAGCAATGTC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
*
34920269 TACTGATTCTACT-GAAGTGCTCAAACGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
*
34920305 TACTGATTCTACTAAATAGTTGCTCAAATGAGCAATATC
1 TACTGATTCTACTAAA-AG-TGCTCAAACGAGCAATATC
* * * * *
34920344 CACTGATTATACTGAATGCTTGCTCAAACGAGCATTATC
1 TACTGATTCTACTAAAAG--TGCTCAAACGAGCAATATC
* *
34920383 TAATGATTATACT
1 TACTGATTCTACT
34920396 GAATAAGTTT
Statistics
Matches: 318, Mismatches: 55, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
35 14 0.04
36 124 0.39
37 117 0.37
38 3 0.01
39 60 0.19
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (37 bp):
TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
Found at i:34920099 original size:73 final size:72
Alignment explanation
Indices: 34919978--34920351 Score: 410
Period size: 73 Copynumber: 5.1 Consensus size: 72
34919968 AAAAATGGAA
* * * *
34919978 TACTGATTCTACTAAAGTACTCAACGAGCAATATCTACTGATTCTACTAAAAGTGCTTAAACGAG
1 TACTGATTCTACAAAAGTGCTCAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATGAG
34920043 CAATATC
66 CAATATC
* * * **
34920050 TACTGATTTTACAAAAAGTGCTCAACGAGCAATATCTATTGA-TCTTACTAAATGTGCTC-AGCG
1 TACTGATTCTAC-AAAAGTGCTCAACGAGCAATATCTACTGATTC-TACTAAAAGTGCTCAAATG
*
34920113 AGCAATATT
64 AGCAATATC
* * * * *
34920122 TACTGATCCTACTGAATGTGCTCAAACGAGCAATGTCTACTGATTCTACTGAAAGTGCTCAAATG
1 TACTGATTCTAC-AAAAGTGCTC-AACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATG
34920187 AGCAATATC
64 AGCAATATC
* * * * * * * * *
34920196 TACTAATTCTACTAAAAGTGTTCAACAAGCAATATCTACCGATCCCATTGAATGTGCTCAAATGA
1 TACTGATTCTAC-AAAAGTGCTCAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATGA
*
34920261 GCAATGTC
65 GCAATATC
**
34920269 TACTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACTAAATAGTTGCTCAAAT
1 TACTGATTCTACAAAAGTGCTC-AACGAGCAATATCTACTGATTCTACTAAA-AG-TGCTCAAAT
34920334 GAGCAATATC
63 GAGCAATATC
*
34920344 CACTGATT
1 TACTGATT
34920352 ATACTGAATG
Statistics
Matches: 248, Mismatches: 46, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
72 49 0.20
73 143 0.58
74 31 0.12
75 25 0.10
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (72 bp):
TACTGATTCTACAAAAGTGCTCAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATGAG
CAATATC
Found at i:34920289 original size:146 final size:145
Alignment explanation
Indices: 34919978--34920343 Score: 491
Period size: 146 Copynumber: 2.5 Consensus size: 145
34919968 AAAAATGGAA
* * * *
34919978 TACTGATTCTACTAAAGTACTC-AACGAGCAATATCTACTGATTCTACTAAAAGTGCTTAAACGA
1 TACTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATGA
* * * ** **
34920042 GCAATATCTACTGATTTTACAAAAAGTGCTCAACGAGCAATATCTATTGATCTTACTAAATGTGC
66 GCAATATCTACTAATTCTACAAAAAGTGCTCAACAAGCAATATCTACCGATCCCACTAAATGTGC
* *
34920107 TCAGCGAGCAATATT
131 TCAACGAGCAATATC
* * *
34920122 TACTGATCCTACTGAATGTGCTCAAACGAGCAATGTCTACTGATTCTACTGAAAGTGCTCAAATG
1 TACTGATTCTACTGAA-GTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATG
* * * *
34920187 AGCAATATCTACTAATTCTACTAAAAGTGTTCAACAAGCAATATCTACCGATCCCATTGAATGTG
65 AGCAATATCTACTAATTCTACAAAAAGTGCTCAACAAGCAATATCTACCGATCCCACTAAATGTG
* *
34920252 CTCAAATGAGCAATGTC
130 CTC-AACGAGCAATATC
34920269 TACTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACTAAATAGTTGCTCAAAT
1 TACTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACTAAA-AG-TGCTCAAAT
34920334 GAGCAATATC
64 GAGCAATATC
34920344 CACTGATTAT
Statistics
Matches: 192, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
144 14 0.07
145 5 0.03
146 128 0.67
147 26 0.14
148 19 0.10
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (145 bp):
TACTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATGA
GCAATATCTACTAATTCTACAAAAAGTGCTCAACAAGCAATATCTACCGATCCCACTAAATGTGC
TCAACGAGCAATATC
Found at i:34931592 original size:56 final size:56
Alignment explanation
Indices: 34931486--34931686 Score: 224
Period size: 56 Copynumber: 3.6 Consensus size: 56
34931476 TATTTGTAAA
* * * * * * *
34931486 ATAGCCTTGACAAATTTCCACTTATAATATATTTCTGAA-AAACTTTCACATATAAG
1 ATAGTCTTGACAGACTTCCACATATAAGATAGTTCT-AATGAACTTTCACATATAAG
** * * *
34931542 ATAGTCTTGATGGACTTCCACATATAAGATAGTTTTAATGGACTTCCACATATAAG
1 ATAGTCTTGACAGACTTCCACATATAAGATAGTTCTAATGAACTTTCACATATAAG
* * * *
34931598 ATAGTTTTGACAAACTTTCACATATAAGATAGTTCTGATGAACTTTCACATATAAG
1 ATAGTCTTGACAGACTTCCACATATAAGATAGTTCTAATGAACTTTCACATATAAG
* *
34931654 ATAGTCTTGGCAGACTTCTACATATAAGATAGT
1 ATAGTCTTGACAGACTTCCACATATAAGATAGT
34931687 CCTTACGGAC
Statistics
Matches: 118, Mismatches: 26, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
55 2 0.02
56 116 0.98
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (56 bp):
ATAGTCTTGACAGACTTCCACATATAAGATAGTTCTAATGAACTTTCACATATAAG
Found at i:34931648 original size:84 final size:85
Alignment explanation
Indices: 34931501--34931686 Score: 243
Period size: 84 Copynumber: 2.2 Consensus size: 85
34931491 CTTGACAAAT
* * *
34931501 TTCCACTTATAATATA-TTTCTGAAAAACTTTCACATATAAGATAGTCTTGATGGACTTCCACAT
1 TTCCACATATAAGATAGTTTCTGAAAAACTTTCACATATAAGATAGTCTTGATGAACTTCCACAT
* **
34931565 ATAAGATAGTTTTAATGGAC
66 ATAAGATAGTCTTAACAGAC
* *
34931585 TTCCACATATAAGATAGTTT-TGACAAACTTTCACATATAAGATAGT-TCTGATGAACTTTCACA
1 TTCCACATATAAGATAGTTTCTGAAAAACTTTCACATATAAGATAGTCT-TGATGAACTTCCACA
**
34931648 TATAAGATAGTCTTGGCAGAC
65 TATAAGATAGTCTTAACAGAC
*
34931669 TTCTACATATAAGATAGT
1 TTCCACATATAAGATAGT
34931687 CCTTACGGAC
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
83 1 0.01
84 85 0.96
85 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (85 bp):
TTCCACATATAAGATAGTTTCTGAAAAACTTTCACATATAAGATAGTCTTGATGAACTTCCACAT
ATAAGATAGTCTTAACAGAC
Found at i:34931657 original size:28 final size:28
Alignment explanation
Indices: 34931508--34931658 Score: 169
Period size: 28 Copynumber: 5.4 Consensus size: 28
34931498 AATTTCCACT
* * **
34931508 TATAATATATTTCTGAAAAACTTTCACA
1 TATAAGATAGTTCTGATGAACTTTCACA
* *
34931536 TATAAGATAG-TCTTGATGGACTTCCACA
1 TATAAGATAGTTC-TGATGAACTTTCACA
* * * *
34931564 TATAAGATAGTTTTAATGGACTTCCACA
1 TATAAGATAGTTCTGATGAACTTTCACA
* **
34931592 TATAAGATAGTTTTGACAAACTTTCACA
1 TATAAGATAGTTCTGATGAACTTTCACA
34931620 TATAAGATAGTTCTGATGAACTTTCACA
1 TATAAGATAGTTCTGATGAACTTTCACA
34931648 TATAAGATAGT
1 TATAAGATAGT
34931659 CTTGGCAGAC
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
27 2 0.02
28 102 0.97
29 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36
Consensus pattern (28 bp):
TATAAGATAGTTCTGATGAACTTTCACA
Found at i:34931670 original size:28 final size:28
Alignment explanation
Indices: 34931527--34931687 Score: 166
Period size: 28 Copynumber: 5.8 Consensus size: 28
34931517 TTTCTGAAAA
**
34931527 ACTTTCACATATAAGATAGTCTTGATGG
1 ACTTTCACATATAAGATAGTCTTGACAG
* * * **
34931555 ACTTCCACATATAAGATAGTTTTAATGG
1 ACTTTCACATATAAGATAGTCTTGACAG
* * *
34931583 ACTTCCACATATAAGATAGTTTTGACAA
1 ACTTTCACATATAAGATAGTCTTGACAG
*
34931611 ACTTTCACATATAAGATAGT-TCTGA-TG
1 ACTTTCACATATAAGATAGTCT-TGACAG
*
34931638 AACTTTCACATATAAGATAGTCTTGGCAG
1 -ACTTTCACATATAAGATAGTCTTGACAG
34931667 AC-TTCTACATATAAGATAGTC
1 ACTTTC-ACATATAAGATAGTC
34931688 CTTACGGACT
Statistics
Matches: 116, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.03
28 110 0.95
29 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (28 bp):
ACTTTCACATATAAGATAGTCTTGACAG
Found at i:34931697 original size:28 final size:28
Alignment explanation
Indices: 34931533--34931707 Score: 160
Period size: 28 Copynumber: 6.2 Consensus size: 28
34931523 AAAAACTTTC
* *
34931533 ACATATAAGATAGTCTTGATGGACTTCC
1 ACATATAAGATAGTCTTGACGGACTTCT
* * * *
34931561 ACATATAAGATAGTTTTAATGGACTTCC
1 ACATATAAGATAGTCTTGACGGACTTCT
* **
34931589 ACATATAAGATAGTTTTGACAAACTT-T
1 ACATATAAGATAGTCTTGACGGACTTCT
* *
34931616 CACATATAAGATAGT-TCTGATGAACTT-T
1 -ACATATAAGATAGTCT-TGACGGACTTCT
* *
34931644 CACATATAAGATAGTCTTGGCAGACTTCT
1 -ACATATAAGATAGTCTTGACGGACTTCT
34931673 ACATATAAGATAGTCCTT-ACGGACTTCT
1 ACATATAAGATAGT-CTTGACGGACTTCT
*
34931701 GCATATA
1 ACATATA
34931708 TTTCATAACT
Statistics
Matches: 126, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
27 1 0.01
28 120 0.95
29 5 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (28 bp):
ACATATAAGATAGTCTTGACGGACTTCT
Found at i:34931706 original size:56 final size:55
Alignment explanation
Indices: 34931533--34931707 Score: 183
Period size: 56 Copynumber: 3.1 Consensus size: 55
34931523 AAAAACTTTC
** * * *
34931533 ACATATAAGATAGTCTTGATGGACTTCCACATATAAGATAGTTTTAATGGACTTCC
1 ACATATAAGATAGTCTTGACAGACTTCTACATATAAGATAGTCTT-ATGGACTTCT
* * * *
34931589 ACATATAAGATAGTTTTGACAAACTT-TCACATATAAGATAGTTCTGATGAACTT-T
1 ACATATAAGATAGTCTTGACAGACTTCT-ACATATAAGATAG-TCTTATGGACTTCT
* *
34931644 CACATATAAGATAGTCTTGGCAGACTTCTACATATAAGATAGTCCTTACGGACTTCT
1 -ACATATAAGATAGTCTTGACAGACTTCTACATATAAGATAGT-CTTATGGACTTCT
*
34931701 GCATATA
1 ACATATA
34931708 TTTCATAACT
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
55 1 0.01
56 92 0.95
57 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (55 bp):
ACATATAAGATAGTCTTGACAGACTTCTACATATAAGATAGTCTTATGGACTTCT
Found at i:34933061 original size:27 final size:27
Alignment explanation
Indices: 34933023--34933077 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
34933013 TGGTGCCACA
34933023 AATTAACTCGACATCAACTTAGTATTG
1 AATTAACTCGACATCAACTTAGTATTG
34933050 AATTAACTCGACATCAACTTAGTATTG
1 AATTAACTCGACATCAACTTAGTATTG
34933077 A
1 A
34933078 TAACAACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (27 bp):
AATTAACTCGACATCAACTTAGTATTG
Found at i:34934533 original size:108 final size:108
Alignment explanation
Indices: 34934344--34934560 Score: 407
Period size: 108 Copynumber: 2.0 Consensus size: 108
34934334 GAGTAAAGCG
*
34934344 TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGTTCCATTGCCAT
1 TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGCTCCATTGCCAT
*
34934409 CCCTACTTAGAAAAACTATGAAAATGTCATTCCGTATTTAAAA
66 CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
*
34934452 TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGCTCCATTGTCAT
1 TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGCTCCATTGCCAT
34934517 CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
66 CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
34934560 T
1 T
34934561 AAGTTATATT
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (108 bp):
TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGCTCCATTGCCAT
CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
Found at i:34937730 original size:22 final size:21
Alignment explanation
Indices: 34937686--34937740 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
34937676 TATTCACTAA
*
34937686 TTAATTTCTATAATGGATGTT
1 TTAATTTCTATAATGAATGTT
34937707 TTAATTTCTTGATAAT-AATGTT
1 TTAATTTC-T-ATAATGAATGTT
*
34937729 TT-ATTTCAATAA
1 TTAATTTCTATAA
34937741 CTTCACTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.13
21 13 0.43
22 8 0.27
23 5 0.17
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (21 bp):
TTAATTTCTATAATGAATGTT
Found at i:34938140 original size:18 final size:18
Alignment explanation
Indices: 34938100--34938142 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
34938090 AATATTACTT
* * *
34938100 CTAAAAGGTATTTTTGGG
1 CTAAAAAGTACTTTTGAG
*
34938118 ATAAAAAGTACTTTTGAG
1 CTAAAAAGTACTTTTGAG
34938136 CTAAAAA
1 CTAAAAA
34938143 TATTGCTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.33
Consensus pattern (18 bp):
CTAAAAAGTACTTTTGAG
Found at i:34938460 original size:40 final size:42
Alignment explanation
Indices: 34938407--34938489 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 42
34938397 GAGCAAAATC
*
34938407 ATATTTGAATAATGTAAAAT-AAAAAT-AAA-AAAAAACCAA
1 ATATTTGAATAATGGAAAATAAAAAATAAAATAAAAAACCAA
*
34938446 ATATATTGAATAATGGAAACTAAAAAATAAAATAAAAAACCAA
1 ATAT-TTGAATAATGGAAAATAAAAAATAAAATAAAAAACCAA
34938489 A
1 A
34938490 GGATAGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 4 0.11
40 14 0.37
41 6 0.16
42 3 0.08
43 11 0.29
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (42 bp):
ATATTTGAATAATGGAAAATAAAAAATAAAATAAAAAACCAA
Found at i:34945246 original size:16 final size:16
Alignment explanation
Indices: 34945225--34945256 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34945215 TTTATAACTG
*
34945225 CTATGTATTTATATAT
1 CTATGTATGTATATAT
34945241 CTATGTATGTATATAT
1 CTATGTATGTATATAT
34945257 TTGAAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.53
Consensus pattern (16 bp):
CTATGTATGTATATAT
Found at i:34963738 original size:21 final size:21
Alignment explanation
Indices: 34963709--34963749 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34963699 TTGGAGTAAC
* *
34963709 TCTATCATTAGCGCTAGTTGA
1 TCTAGCATTACCGCTAGTTGA
*
34963730 TCTAGCATTACCTCTAGTTG
1 TCTAGCATTACCGCTAGTTG
34963750 TTCAAATATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (21 bp):
TCTAGCATTACCGCTAGTTGA
Found at i:34964378 original size:10 final size:10
Alignment explanation
Indices: 34964364--34964400 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
34964354 AAAATAAAAT
*
34964364 AAAATAATTA
1 AAAATAATGA
*
34964374 CAAATAATGA
1 AAAATAATGA
34964384 AAAATAATGA
1 AAAATAATGA
34964394 AAAATAA
1 AAAATAA
34964401 AAATTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (10 bp):
AAAATAATGA
Found at i:34964380 original size:20 final size:19
Alignment explanation
Indices: 34964354--34964403 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
34964344 GTAACTAAAT
*
34964354 AAAATAAAATAAAATAATTA
1 AAAATAAAA-AAAATAATGA
* *
34964374 CAAATAATGAAAAATAATGA
1 AAAATAA-AAAAAATAATGA
34964394 AAAATAAAAA
1 AAAATAAAAA
34964404 TTAATATACT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.08
20 21 0.88
21 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAATAAAAAAAATAATGA
Found at i:34966034 original size:15 final size:15
Alignment explanation
Indices: 34966014--34966048 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34966004 GTTTTCCTTT
*
34966014 CAACGGTCACTATTC
1 CAACGGTAACTATTC
*
34966029 CAACGGTAACTTTTC
1 CAACGGTAACTATTC
34966044 CAACG
1 CAACG
34966049 ACTACTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (15 bp):
CAACGGTAACTATTC
Found at i:34966253 original size:7 final size:7
Alignment explanation
Indices: 34966180--34966253 Score: 64
Period size: 7 Copynumber: 10.6 Consensus size: 7
34966170 TCCAATCCCC
34966180 ATTTTCTA
1 ATTTTC-A
34966188 ATTTT-A
1 ATTTTCA
34966194 TATTTTCA
1 -ATTTTCA
*
34966202 ATCTTCA
1 ATTTTCA
*
34966209 ATCTTCAA
1 ATTTTC-A
34966217 ATTTT-A
1 ATTTTCA
34966223 ATTTT-A
1 ATTTTCA
34966229 ATTTTCA
1 ATTTTCA
* *
34966236 CTTTCCA
1 ATTTTCA
34966243 ATTTTCA
1 ATTTTCA
34966250 ATTT
1 ATTT
34966254 CAGAATTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
6 13 0.23
7 32 0.57
8 11 0.20
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTCA
Found at i:34968759 original size:20 final size:19
Alignment explanation
Indices: 34968713--34968759 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
34968703 TACAAAAAGT
*
34968713 TTCAAAATAATTTTTAAAA
1 TTCAAAATAATTTATAAAA
34968732 TTCAAAAT-ATTTATAGAAA
1 TTCAAAATAATTTATA-AAA
34968751 TTACAAAAT
1 TT-CAAAAT
34968760 TTATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 13 0.52
20 6 0.24
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (19 bp):
TTCAAAATAATTTATAAAA
Found at i:34968767 original size:24 final size:24
Alignment explanation
Indices: 34968738--34968785 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
34968728 AAAATTCAAA
34968738 ATATTTATAGAAATTACAAAATTT
1 ATATTTATAGAAATTACAAAATTT
* ** *
34968762 ATATTTTTTTAAATTATAAAATTT
1 ATATTTATAGAAATTACAAAATTT
34968786 CAAAAACGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATTTATAGAAATTACAAAATTT
Found at i:34971593 original size:14 final size:14
Alignment explanation
Indices: 34971572--34971605 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
34971562 TGGTATGGGT
34971572 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
34971585 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
34971599 TTATAGG
1 TTATAGG
34971606 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:34973919 original size:20 final size:18
Alignment explanation
Indices: 34973879--34973915 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
34973869 TTATGCCAGG
*
34973879 TGTGTATCCTATCCCTTA
1 TGTGTATCCTAACCCTTA
34973897 TGTGTATCCTAACCCTTA
1 TGTGTATCCTAACCCTTA
34973915 T
1 T
34973916 ATGTTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (18 bp):
TGTGTATCCTAACCCTTA
Found at i:34973924 original size:18 final size:18
Alignment explanation
Indices: 34973881--34973924 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
34973871 ATGCCAGGTG
* *
34973881 TGTATCCTATCCCTTATG
1 TGTATCCTAACCCTTATA
34973899 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
34973917 TGTTTCCT
1 TGTATCCT
34973925 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:34977672 original size:126 final size:125
Alignment explanation
Indices: 34977441--34977814 Score: 534
Period size: 126 Copynumber: 3.0 Consensus size: 125
34977431 GGTCAAACAA
*
34977441 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATTAATTTTGCTGACAGTACATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCA-TAATTTTGCTGACAGTGCATC
*
34977506 CTGCTTGAAGTGTTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
* * * * *
34977567 TAACTACTATAAAAAAAGAGCGTCCACATGGGAGCTTTTTTCATCAGTTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAT-AATTTTGCTGACAGTGCATC
* * * *
34977632 TTGCTTGAAGCATTTTTGACACTATTTGTTCAAAATCGTCTTCTCAAAATTATTTTTTTAG
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
* * * *
34977693 GAACTACGGTAGAAAAAGAGCATCCACGTGAGAGCTCTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCA-TAATTTTGCTGACAGTGCATC
* * * *
34977758 CTGCTTGAAGCGTTTTTCACATTATCTT-TTCAGAACCGTCTTCTCAAAATTAATTTT
65 CTGCTTGAAGCGTTTTTGACACTAT-TTGTTCAAAACCGTCTTCTCAAAATTATTTTT
34977815 CCTAAAACAA
Statistics
Matches: 218, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
125 1 0.00
126 214 0.98
127 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATAATTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
Found at i:34977945 original size:34 final size:31
Alignment explanation
Indices: 34977899--34978005 Score: 108
Period size: 34 Copynumber: 3.2 Consensus size: 31
34977889 TTTTTTTTAA
34977899 ACTAAACCCTAATTTAATTAATTTTCTTAAAAAC
1 ACTAAA-CCTAATTTAATT-ATTTT-TTAAAAAC
* *
34977933 TCTAAACTCTAATTTAATTTATTTATTTAAAACC
1 ACTAAAC-CTAATTTAA-TTATTT-TTTAAAAAC
*
34977967 CCTAAAACCTAATTTAAATT-TTTTTTAAAAAC
1 ACT-AAACCTAATTT-AATTATTTTTTAAAAAC
34977999 ACTAAAC
1 ACTAAAC
34978006 GCTGATTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
31 4 0.06
32 10 0.16
33 4 0.06
34 36 0.57
35 9 0.14
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (31 bp):
ACTAAACCTAATTTAATTATTTTTTAAAAAC
Found at i:34979141 original size:29 final size:29
Alignment explanation
Indices: 34979013--34979151 Score: 79
Period size: 28 Copynumber: 4.7 Consensus size: 29
34979003 CTTTTAATTT
* **
34979013 TTTTTCTGAAAATTTCAATTAAACT-TCATT
1 TTTTT-TGAAAATTTC-ATTAAACTCTTAAA
* * * *
34979043 TTTTTTGAAATTTTTATTAATCTCATAAA
1 TTTTTTGAAAATTTCATTAAACTCTTAAA
* * * *
34979072 ATTTTT-AAAATTT--TTAATTAGTTTTCAA
1 TTTTTTGAAAATTTCATTAA--ACTCTTAAA
34979100 TTTTTTGGAAAAATTTCATTAAACTCTTAAA
1 TTTTTT-G-AAAATTTCATTAAACTCTTAAA
*
34979131 TTTTTTGAAAACTTTAATTAA
1 TTTTTTGAAAA-TTTCATTAA
34979152 CCCCAAAACT
Statistics
Matches: 81, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
26 4 0.05
28 22 0.27
29 18 0.22
30 14 0.17
31 19 0.23
33 4 0.05
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTTTTGAAAATTTCATTAAACTCTTAAA
Found at i:34979718 original size:2 final size:2
Alignment explanation
Indices: 34979711--34979742 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
34979701 TCTTAGAATA
*
34979711 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34979743 TAAAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34993462 original size:20 final size:20
Alignment explanation
Indices: 34993437--34993476 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34993427 TGTAAAATGA
*
34993437 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
34993457 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
34993477 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:34993465 original size:34 final size:35
Alignment explanation
Indices: 34993422--34993488 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
34993412 CAGTAAAATA
* *
34993422 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTACTAGAAAATATTTTAC
34993456 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
34993489 TTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:34998719 original size:16 final size:16
Alignment explanation
Indices: 34998698--34998734 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
34998688 TTGGTTGAAT
*
34998698 GTAATGGAATAGAGGC
1 GTAATGAAATAGAGGC
*
34998714 GTAATGAAATAGAGGT
1 GTAATGAAATAGAGGC
34998730 GTAAT
1 GTAAT
34998735 AGCAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.32, T:0.24
Consensus pattern (16 bp):
GTAATGAAATAGAGGC
Found at i:34998726 original size:61 final size:61
Alignment explanation
Indices: 34998653--34998779 Score: 227
Period size: 61 Copynumber: 2.1 Consensus size: 61
34998643 GGTTATAAGT
*
34998653 GTAATGGAATAGAGGTGTAATAAAAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGC
1 GTAATGAAATAGAGGTGTAATAAAAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGC
**
34998714 GTAATGAAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGC
1 GTAATGAAATAGAGGTGTAATAAAAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGC
34998775 GTAAT
1 GTAAT
34998780 AATAATCTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (61 bp):
GTAATGAAATAGAGGTGTAATAAAAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGC
Found at i:34999056 original size:157 final size:157
Alignment explanation
Indices: 34998855--34999171 Score: 598
Period size: 157 Copynumber: 2.0 Consensus size: 157
34998845 TAGAATACCC
*
34998855 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
34998920 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAA
34998985 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
34999012 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
34999077 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAA
*
34999142 TATATAATTTAATAAAATTTTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
34999169 TTA
1 TTA
34999172 ATATTCTTAT
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:34999166 original size:17 final size:18
Alignment explanation
Indices: 34999125--34999159 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34999115 TTATTATTAA
*
34999125 ATATATTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
34999143 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
34999160 TTTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:34999245 original size:15 final size:16
Alignment explanation
Indices: 34999224--34999279 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
34999214 GTAAAATATA
34999224 AATTAAAATA-ATTATT
1 AATTAAAATATATT-TT
34999240 -ATT-AAATATATTTT
1 AATTAAAATATATTTT
34999254 AATTAAAATATATAATTT
1 AATTAAAATATAT--TTT
34999272 AA-TAAAAT
1 AATTAAAAT
34999280 TCTTAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
14 7 0.20
15 9 0.26
16 8 0.23
17 6 0.17
18 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAAAATATATTTT
Found at i:34999245 original size:120 final size:120
Alignment explanation
Indices: 34999105--34999519 Score: 726
Period size: 120 Copynumber: 3.5 Consensus size: 120
34999095 TTAATCATAT
*
34999105 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTTTTAATAAT
1 TTAAA-ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
34999170 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
34999226 TTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT
1 TTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT
*
34999291 AATATTCTTATATGAATTTACTCAAATAATAATATATGATACTGT-AAATATAAA
66 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
*
34999345 TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
1 TTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT
* *
34999410 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAA
66 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
* * *
34999464 TTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -TTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
34999520 TAAAATAATT
Statistics
Matches: 282, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
119 119 0.42
120 158 0.56
121 5 0.02
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (120 bp):
TTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT
AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
Found at i:34999266 original size:18 final size:17
Alignment explanation
Indices: 34999245--34999279 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34999235 TTATTATTAA
*
34999245 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
34999263 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
34999280 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:34999303 original size:37 final size:38
Alignment explanation
Indices: 34999262--34999429 Score: 94
Period size: 37 Copynumber: 4.3 Consensus size: 38
34999252 TTAATTAAAA
*
34999262 TATATAATTTAATAAAATTCTTAATAAT-TAATATTCT
1 TATATAATTTAATAAAATTATTAATAATATAATATTCT
* * * * * *
34999299 TATATGAATTTACTCAAA-TAATAAT-ATATGATACTGT
1 TATAT-AATTTAATAAAATTATTAATAATATAATATTCT
* * * **
34999336 AAATATAAATTAA-AATAATTATTATTAAATATATTATAATTAAAA
1 -TATATAATTTAATAA-AATTATTAAT-AATATA--AT-ATT--CT
*
34999381 TATATAATTTAATAAAATTCTTAATAAT-TAATATTCT
1 TATATAATTTAATAAAATTATTAATAATATAATATTCT
34999418 TATATGAATTTA
1 TATAT-AATTTA
34999430 CTCAAATCAT
Statistics
Matches: 94, Mismatches: 23, Indels: 27
0.65 0.16 0.19
Matches are distributed among these distances:
36 3 0.03
37 28 0.30
38 25 0.27
39 3 0.03
40 6 0.06
42 4 0.04
43 5 0.05
44 18 0.19
45 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (38 bp):
TATATAATTTAATAAAATTATTAATAATATAATATTCT
Found at i:34999364 original size:15 final size:16
Alignment explanation
Indices: 34999343--34999385 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
34999333 TGTAAATATA
34999343 AATTAAAATA-ATTAT
1 AATTAAAATATATTAT
*
34999358 TATT-AAATATATTAT
1 AATTAAAATATATTAT
34999373 AATTAAAATATAT
1 AATTAAAATATAT
34999386 AATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 11 0.46
16 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:34999629 original size:101 final size:93
Alignment explanation
Indices: 34999462--34999742 Score: 286
Period size: 91 Copynumber: 3.0 Consensus size: 93
34999452 TATAAAAGAA
* * * *
34999462 AATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATT-TAAAA
1 AATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTCT----
* * * *
34999525 TAATTATAACTAATAAATTATATTTTATGAATTTGTAT
61 T-A--ATAA-T-ATAAATTTTATTATATGAATTTATAC
* *
34999563 AATTTAAAATAA-TAATTATTACATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT
1 AATTTAAAATAATTAA-TATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAAT
*
34999627 -A-ATAAATTTTCTTATATGAATTTATAC
65 AATATAAATTTTATTATATGAATTTATAC
* *
34999654 AATTTAAAATAATTAATATTAAATATAATTTAATAGTGATATATAATTTCATAAAATTCTTAATA
1 AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
* *
34999719 ATA-AAATGTTCTTATATGAATTTA
66 ATATAAATTTTATTATATGAATTTA
34999743 CTAAAATCAA
Statistics
Matches: 158, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
91 77 0.49
92 24 0.15
93 1 0.01
94 1 0.01
95 2 0.01
98 1 0.01
100 6 0.04
101 45 0.28
102 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (93 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
ATATAAATTTTATTATATGAATTTATAC
Found at i:35001794 original size:30 final size:29
Alignment explanation
Indices: 35001719--35001890 Score: 134
Period size: 30 Copynumber: 5.8 Consensus size: 29
35001709 TTTCTTTTCA
* *
35001719 TTTATTTTTGAAGCCCTTGTTTCACTTATTT
1 TTTATTTTT-AAGCCCTTATTTCAATT-TTT
*
35001750 TTTTTCTTTTAAGCCCTTATTTCAATTTTT
1 TTTAT-TTTTAAGCCCTTATTTCAATTTTT
*
35001780 TTTATTTTTGAAGCCCTTATTT-AACCTTTT
1 TTTATTTTT-AAGCCCTTATTTCAA-TTTTT
** * *
35001810 TTTGCTTTTAAGTCCTTATTTC-ACTTTT
1 TTTATTTTTAAGCCCTTATTTCAATTTTT
* * *
35001838 TTAATTTTTAAAGCCCTAATTT-AACTTATT
1 TTTATTTTT-AAGCCCTTATTTCAA-TTTTT
** *
35001868 TTTGCTTTTAAGTCCTTATTTCA
1 TTTATTTTTAAGCCCTTATTTCA
35001891 TTACTTTTTT
Statistics
Matches: 113, Mismatches: 20, Indels: 17
0.75 0.13 0.11
Matches are distributed among these distances:
28 11 0.10
29 39 0.35
30 40 0.35
31 19 0.17
32 4 0.04
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.58
Consensus pattern (29 bp):
TTTATTTTTAAGCCCTTATTTCAATTTTT
Found at i:35001809 original size:29 final size:28
Alignment explanation
Indices: 35001719--35001902 Score: 143
Period size: 29 Copynumber: 6.1 Consensus size: 28
35001709 TTTCTTTTCA
* *
35001719 TTTATTTTTGAAGCCCTTGTTTCACTTATTT
1 TTTATTTTT-AAGCCCTTATTTAAC-T-TTT
* *
35001750 TTTTTCTTTTAAGCCCTTATTTCAATTTTT
1 TTTAT-TTTTAAGCCCTTATTT-AACTTTT
35001780 TTTATTTTTGAAGCCCTTATTTAACCTTTT
1 TTTATTTTT-AAGCCCTTATTTAA-CTTTT
** * *
35001810 TTTGCTTTTAAGTCCTTATTTCACTTTT
1 TTTATTTTTAAGCCCTTATTTAACTTTT
* *
35001838 TTAATTTTTAAAGCCCTAATTTAACTTATT
1 TTTATTTTT-AAGCCCTTATTTAACTT-TT
** *
35001868 TTTGCTTTTAAGTCCTTATTTCATTACTTTT
1 TTTATTTTTAAGCCCTTATTT-A--ACTTTT
35001899 TTTA
1 TTTA
35001903 ACTTTTAATG
Statistics
Matches: 122, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
28 11 0.09
29 42 0.34
30 39 0.32
31 21 0.17
32 9 0.07
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.59
Consensus pattern (28 bp):
TTTATTTTTAAGCCCTTATTTAACTTTT
Found at i:35001845 original size:58 final size:58
Alignment explanation
Indices: 35001722--35001890 Score: 214
Period size: 58 Copynumber: 2.9 Consensus size: 58
35001712 CTTTTCATTT
* * * * * * *
35001722 ATTTTTGAAGCCCTTGTTTCACTTATTTTTTTTCTTTTAAGCCCTTATTTCAATTTTTTTT
1 ATTTTTGAAGCCCTTATTTAAC--CTTTTTTTGCTTTTAAGTCCTTATTTC-ACTTTTTTA
35001783 ATTTTTGAAGCCCTTATTTAACCTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTA
1 ATTTTTGAAGCCCTTATTTAACCTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTA
* *
35001841 ATTTTTAAAGCCCTAATTTAA-CTTATTTTTGCTTTTAAGTCCTTATTTCA
1 ATTTTTGAAGCCCTTATTTAACCTT-TTTTTGCTTTTAAGTCCTTATTTCA
35001891 TTACTTTTTT
Statistics
Matches: 98, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
57 3 0.03
58 51 0.52
59 24 0.24
61 20 0.20
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (58 bp):
ATTTTTGAAGCCCTTATTTAACCTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTA
Found at i:35001928 original size:58 final size:56
Alignment explanation
Indices: 35001747--35001927 Score: 163
Period size: 58 Copynumber: 3.1 Consensus size: 56
35001737 GTTTCACTTA
* * * * * *
35001747 TTTTTTTT-CTTTTAAGCCCTTATTTCAATTTTTTTTATTTTTGAAGCCCTTATTTAAC
1 TTTTTTTTGCTTTTAAGTCCTTATTTC-ACTTTTTTAACTTTTAAAG-CC-AATTTAAC
* *
35001805 CTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTAATTTTTAAAGCCCTAATTTAAC
1 TTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTAACTTTTAAAG-CC-AATTTAAC
* *
35001863 TTATTTTTGCTTTTAAGTCCTTATTTCATTACTTTTTTTAACTTTTAATG-C-A-TTAAC
1 TTTTTTTTGCTTTTAAGTCCTTATTTC---AC-TTTTTTAACTTTTAAAGCCAATTTAAC
35001920 TTTTTTTT
1 TTTTTTTT
35001928 TAGTTTTAAG
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
57 12 0.11
58 60 0.56
59 17 0.16
60 1 0.01
61 2 0.02
62 15 0.14
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.60
Consensus pattern (56 bp):
TTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTAACTTTTAAAGCCAATTTAAC
Found at i:35001979 original size:32 final size:32
Alignment explanation
Indices: 35001943--35002003 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
35001933 TTAAGTATTT
*
35001943 ATTTTTAAAGCCCATGTTCAACTTTTTTTAAA
1 ATTTTTAAAGCCCATATTCAACTTTTTTTAAA
* * *
35001975 ATTTTTGAAGCCCTTATTTAACTTTTTTT
1 ATTTTTAAAGCCCATATTCAACTTTTTTT
35002004 GCTTTTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (32 bp):
ATTTTTAAAGCCCATATTCAACTTTTTTTAAA
Found at i:35002031 original size:28 final size:29
Alignment explanation
Indices: 35001977--35002031 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
35001967 TTTTTAAAAT
**
35001977 TTTTGAAGCCCTTATTTAACTTTTTTTGC
1 TTTTGAAGCCCTTATTTAACTAATTTTGC
* *
35002006 TTTT-AAGTCCTTATTTCACTAATTTT
1 TTTTGAAGCCCTTATTTAACTAATTTT
35002032 TTGGGTAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.20, C:0.16, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTTGAAGCCCTTATTTAACTAATTTTGC
Found at i:35004059 original size:124 final size:123
Alignment explanation
Indices: 35003840--35004065 Score: 292
Period size: 124 Copynumber: 1.8 Consensus size: 123
35003830 TCTAAAGTCC
* * * *
35003840 TTATTTAAATTTTTTTTTTGGAACTTTTATGTCATTATTTCATTAATTTTACAGTTATAAAACAA
1 TTATTTAAATCTTTTTTTTGGAACTTTTAAGCCATTATTTCACTAATTTTACAGTTATAAAACAA
* * *
35003905 AATATGCCAAAATATTAAAATATTTCTTGAACTATTTCCTTCTTTTAAAAACAAATTT
66 AATATGCCAAAAAAGTAAAATAATTCTTGAACTATTTCCTTCTTTTAAAAACAAATTT
* * * * *
35003963 TTATTTAAATGCTTTTTTTTGGAACTTTTAAGCCCTTATTTCACTAATTTTATAGTTGTCAAATA
1 TTATTTAAAT-CTTTTTTTTGGAACTTTTAAGCCATTATTTCACTAATTTTACAGTTATAAAACA
** *
35004028 AAATA-GGGAAAACAAGTAAAATAATTCTTGAATTATTT
65 AAATATGCCAAAA-AAGTAAAATAATTCTTGAACTATTT
35004066 TAATCTTTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
123 15 0.17
124 71 0.83
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (123 bp):
TTATTTAAATCTTTTTTTTGGAACTTTTAAGCCATTATTTCACTAATTTTACAGTTATAAAACAA
AATATGCCAAAAAAGTAAAATAATTCTTGAACTATTTCCTTCTTTTAAAAACAAATTT
Found at i:35005631 original size:31 final size:31
Alignment explanation
Indices: 35005595--35005654 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
35005585 TGGATCACTA
35005595 AACTATTCGAAA-ATTTTCATTTAAGTCATCG
1 AACTATT-GAAATATTTTCATTTAAGTCATCG
* * *
35005626 AACTATTTAAATTTTTTTATTTAAGTCAT
1 AACTATTGAAATATTTTCATTTAAGTCAT
35005655 TGAATTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (31 bp):
AACTATTGAAATATTTTCATTTAAGTCATCG
Found at i:35007480 original size:71 final size:71
Alignment explanation
Indices: 35007375--35007510 Score: 193
Period size: 71 Copynumber: 1.9 Consensus size: 71
35007365 TGAAATATTT
* * *
35007375 TTTTTCACCTACATTGTGGAGATGATAAATTTTAATATTATAAAATCAACTAATTATTTCAAATA
1 TTTTTCACCTACACTGTGGAGATGATAAACTTTAATATTATAAAATCAAATAATTATTTCAAATA
35007440 TCATTA
66 TCATTA
* * * *
35007446 TTTTTCACCTGCACTGTGGATAT-AGTAAACTTTAATATTATAAAATTAAATAATTATTTCGAAT
1 TTTTTCACCTACACTGTGGAGATGA-TAAACTTTAATATTATAAAATCAAATAATTATTTCAAAT
35007510 A
65 A
35007511 CACATACAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 1 0.02
71 56 0.98
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (71 bp):
TTTTTCACCTACACTGTGGAGATGATAAACTTTAATATTATAAAATCAAATAATTATTTCAAATA
TCATTA
Found at i:35007858 original size:30 final size:30
Alignment explanation
Indices: 35007822--35007878 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
35007812 CAAACCTTTT
* * *
35007822 TACTTTCCTCCTAATACTTTTACTCCCTCC
1 TACTTTCCCCCCAAAACTTTTACTCCCTCC
35007852 TACTTTCCCCCCAAAACTTTTACTCCC
1 TACTTTCCCCCCAAAACTTTTACTCCC
35007879 CTCCCATCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.39
Consensus pattern (30 bp):
TACTTTCCCCCCAAAACTTTTACTCCCTCC
Found at i:35008609 original size:14 final size:14
Alignment explanation
Indices: 35008585--35008618 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35008575 ACCAAAATTA
35008585 GAAAG-AAAAGAAC
1 GAAAGAAAAAGAAC
*
35008598 GAAAGAAAAAGAAG
1 GAAAGAAAAAGAAC
35008612 GAAAGAA
1 GAAAGAA
35008619 GCAGACGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAGAAC
Found at i:35015566 original size:5 final size:5
Alignment explanation
Indices: 35015556--35015583 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
35015546 CATGAGTTAG
35015556 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
35015584 CTTGAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:35015984 original size:5 final size:5
Alignment explanation
Indices: 35015974--35016007 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
35015964 TTAAGCACAT
35015974 AAACC AAACC AAACC AAACC AAACC AAACC AAAC
1 AAACC AAACC AAACC AAACC AAACC AAACC AAAC
35016008 TTATTCTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:35020073 original size:29 final size:29
Alignment explanation
Indices: 35020040--35020104 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
35020030 AAAATAATTT
*
35020040 AATCTTTATCCAGCCAATTTCAAATCTTC
1 AATCTTTATCCAGCCAACTTCAAATCTTC
*
35020069 AATCTTTATCCAGTCAACTTCAAATCTTC
1 AATCTTTATCCAGCCAACTTCAAATCTTC
35020098 AATCTTT
1 AATCTTT
35020105 CAATCTACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (29 bp):
AATCTTTATCCAGCCAACTTCAAATCTTC
Found at i:35022294 original size:17 final size:16
Alignment explanation
Indices: 35022272--35022305 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35022262 TTTTATAAAT
35022272 AAAAGAGTTATTAATTA
1 AAAAGA-TTATTAATTA
*
35022289 AAAAGATTATTTATTA
1 AAAAGATTATTAATTA
35022305 A
1 A
35022306 TTATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
AAAAGATTATTAATTA
Found at i:35022302 original size:20 final size:20
Alignment explanation
Indices: 35022279--35022317 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35022269 AATAAAAGAG
35022279 TTATTAATTA-AAAAGATTAT
1 TTATTAATTATAAAA-ATTAT
35022299 TTATTAATTATAAAAATTA
1 TTATTAATTATAAAAATTA
35022318 ATTAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTATTAATTATAAAAATTAT
Found at i:35022990 original size:18 final size:18
Alignment explanation
Indices: 35022950--35022992 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35022940 GTTCAAGGTG
35022950 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
35022968 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
35022986 TAATTAA
1 TAATTAA
35022993 AAACCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:35025919 original size:6 final size:6
Alignment explanation
Indices: 35025908--35025964 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
35025898 CGGAGGAAGG
* * *
35025908 AGATGA AGATGA AGATGA AGATGA GGATCG- AGGTGA AGATGA AGACGA
1 AGATGA AGATGA AGATGA AGATGA AGAT-GA AGATGA AGATGA AGATGA
*
35025956 AGATAA AGA
1 AGATGA AGA
35025965 AGAGGAAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 1 0.02
6 40 0.95
7 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.35, T:0.14
Consensus pattern (6 bp):
AGATGA
Found at i:35025934 original size:30 final size:30
Alignment explanation
Indices: 35025900--35025959 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
35025890 CTCAACCACG
* *
35025900 GAGGAAGGAGATGAAGATGAAGATGAAGAT
1 GAGGAACGAGATGAAGATGAAGACGAAGAT
* *
35025930 GAGGATCGAGGTGAAGATGAAGACGAAGAT
1 GAGGAACGAGATGAAGATGAAGACGAAGAT
35025960 AAAGAAGAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.03, G:0.40, T:0.13
Consensus pattern (30 bp):
GAGGAACGAGATGAAGATGAAGACGAAGAT
Found at i:35028317 original size:7 final size:7
Alignment explanation
Indices: 35028285--35028316 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
35028275 TATTATTTTC
35028285 AACCTTA
1 AACCTTA
35028292 AACCTTA
1 AACCTTA
35028299 AACCTTA
1 AACCTTA
*
35028306 AACCCTA
1 AACCTTA
35028313 AACC
1 AACC
35028317 CAAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (7 bp):
AACCTTA
Found at i:35028490 original size:29 final size:29
Alignment explanation
Indices: 35028458--35028523 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
35028448 CCAAAATCAA
*
35028458 CCTATTCCAATAAATATGCCAAAAACTAG
1 CCTATTCCAATAAATATACCAAAAACTAG
* *
35028487 CCTATTCCGATAAATATACCAAAAACTGG
1 CCTATTCCAATAAATATACCAAAAACTAG
35028516 CCTATTCC
1 CCTATTCC
35028524 CTCAATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.26
Consensus pattern (29 bp):
CCTATTCCAATAAATATACCAAAAACTAG
Found at i:35036006 original size:175 final size:174
Alignment explanation
Indices: 35035714--35036110 Score: 544
Period size: 175 Copynumber: 2.3 Consensus size: 174
35035704 AAATTTGGTC
* *
35035714 AAAATTAAATATAGTGATAAAATTTCAAATTTGAGTGTAATATAATGACTAAAACTAAAATTGGA
1 AAAATTAAATATAGAGATAAAATTTCAAATTTGAGTGTAATATAATAACTAAAACTAAAATTGGA
** *
35035779 CCATTGTTTTATAATAAAGAACGTAAAGGGATCAAAATTGAAATTATACCATCATCTTAT-GAGA
66 CCATTGTTTTATAATAAAGAAAATAAAGGGATCAAAATTAAAATTATACCATCATCTTATAGAGA
* * *
35035843 GAGAGAATAGAAAAATGTGTATTGTTTGAGGTACCAAATTATGTTA
131 GAGAGAATAGAAAAATGTG--TCGCTCGAGGTACCAAATTATGTTA
* * *
35035889 AAAATTAAATATAGAGATAAAATTTCAAATTTGAATGTAGTATAATAACTAAAACTAAAATTTGA
1 AAAATTAAATATAGAGATAAAATTTCAAATTTGAGTGTAATATAATAACTAAAACTAAAATTGGA
* *
35035954 CTATTGTTTTATAATAAAGAAAATAAAGGGATCAAAATTAAAATTGTACCATCATCTTATAAGGG
66 CCATTGTTTTATAATAAAGAAAATAAAGGGATCAAAATTAAAATTATACCATCATCTTAT-A--G
* * * *
35036019 AGAGAGAGAATAGCAGAATGTGTCGCTCGATGTTCCAAATTATGTTA
128 AGAGAGAGAATAGAAAAATGTGTCGCTCGAGGTACCAAATTATGTTA
* * * * *
35036066 AAAATTATATATAAATATGAAATCTCAAATTTGAGTGTAATATAA
1 AAAATTAAATATAGAGATAAAATTTCAAATTTGAGTGTAATATAA
35036111 AGACCGAAAC
Statistics
Matches: 194, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
175 115 0.59
177 58 0.30
179 21 0.11
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.32
Consensus pattern (174 bp):
AAAATTAAATATAGAGATAAAATTTCAAATTTGAGTGTAATATAATAACTAAAACTAAAATTGGA
CCATTGTTTTATAATAAAGAAAATAAAGGGATCAAAATTAAAATTATACCATCATCTTATAGAGA
GAGAGAATAGAAAAATGTGTCGCTCGAGGTACCAAATTATGTTA
Found at i:35045026 original size:39 final size:40
Alignment explanation
Indices: 35044981--35045205 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
35044971 GCTCCTCGTT
* * * *
35044981 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
35045021 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
35045060 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
35045100 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
35045140 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
35045181 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
35045206 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:35045214 original size:41 final size:41
Alignment explanation
Indices: 35045137--35045214 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
35045127 CTTGTATCTC
* * *
35045137 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
35045178 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
35045215 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:35052963 original size:40 final size:39
Alignment explanation
Indices: 35052874--35053094 Score: 185
Period size: 40 Copynumber: 5.6 Consensus size: 39
35052864 CTCGTTCAAG
* * * *
35052874 TGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAA
1 TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAA
*
35052913 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AA
* * *
35052953 TGCCTTCGGGACTTTACCCGGATTTAGTATCTAGCACAAA
1 TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AA
* * * * *
35052993 GGCCTTCGGGGCTTAACCCGGAACTT-GTATCTTGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC-AA
** * * * *
35053033 TGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAA
1 TGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACAA
* *
35053073 AGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
35053095 CAGCATTCAA
Statistics
Matches: 149, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
39 36 0.24
40 102 0.68
41 11 0.07
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (39 bp):
TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAA
Found at i:35062627 original size:16 final size:17
Alignment explanation
Indices: 35062600--35062635 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
35062590 TTAGAATTGG
*
35062600 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
35062617 ATTGA-AAAATTAATTA
1 ATTGAGAAAATTAATTA
35062633 ATT
1 ATT
35062636 TAATAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:35071861 original size:19 final size:19
Alignment explanation
Indices: 35071839--35071880 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35071829 CAAAATTCGG
35071839 AATAAATAAATAATAAA-AT
1 AATAAA-AAATAATAAATAT
*
35071858 AATAAAAACTAATAAATAT
1 AATAAAAAATAATAAATAT
35071877 AATA
1 AATA
35071881 CTGTGCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAATAATAAATAT
Found at i:35073969 original size:52 final size:52
Alignment explanation
Indices: 35073911--35074014 Score: 126
Period size: 52 Copynumber: 2.0 Consensus size: 52
35073901 CCTAAGATTT
*
35073911 AATTTAAAAATATAATA-TT-AACATC-TAATTCAAT-ATAAAAAATTATAACCTA
1 AATTTAAAAA-ATAATATTTGAA-ATCTTAAAT-AATAATAAAAAA-TATAACCTA
*
35073963 AATTTAAAAACTAATATTTGAAATCTTAAATAATAATAAAAAATATAACCTA
1 AATTTAAAAAATAATATTTGAAATCTTAAATAATAATAAAAAATATAACCTA
35074015 GTGTATAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
51 5 0.11
52 27 0.59
53 14 0.30
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.34
Consensus pattern (52 bp):
AATTTAAAAAATAATATTTGAAATCTTAAATAATAATAAAAAATATAACCTA
Found at i:35074058 original size:19 final size:18
Alignment explanation
Indices: 35074036--35074088 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
35074026 AACCTAAAAG
35074036 AAATCTAAAATT-ATTCTTA
1 AAATCTAAAATTAATTC--A
35074055 AAATCT-AAATTAATTCA
1 AAATCTAAAATTAATTCA
35074072 AAATCCTAAAATCTAAT
1 AAAT-CTAAAAT-TAAT
35074089 ATCTAACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.17
18 7 0.23
19 14 0.47
20 4 0.13
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATCTAAAATTAATTCA
Found at i:35082076 original size:12 final size:12
Alignment explanation
Indices: 35082059--35082089 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
35082049 TATAACCTGA
35082059 ATATATATGTAT
1 ATATATATGTAT
*
35082071 ATATATATTTAT
1 ATATATATGTAT
35082083 ATATATA
1 ATATATA
35082090 GATAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:35083989 original size:88 final size:88
Alignment explanation
Indices: 35083870--35084359 Score: 684
Period size: 88 Copynumber: 5.6 Consensus size: 88
35083860 GGACCATTGG
* * * * *
35083870 CTTCGATATGCTTCACTGTCGATGTAGGAAGGCAAGACCTGCTGTCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACAGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
35083935 ACTGAGGGAGGCAAGGCTTGTGT
66 ACTGAGGGAGGCAAGGCTTGTGT
* * * *
35083958 CTTTGATTTACTTCGTC-GTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
1 CTTCGATCTGCTTC-ACAGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
* *
35084022 AACCGAGGGAGGCAAGGCTTGTGC
65 AACTGAGGGAGGCAAGGCTTGTGT
* ** *
35084046 CTTCGATCTGCTTCACTGTCGATGCAGGAATACAAGATCTGCTATCTTTAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACAGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
35084111 ACCGAGGGAGGCAAGGCTTGTGT
66 ACTGAGGGAGGCAAGGCTTGTGT
* * * *
35084134 CTTCAATCTGCTTCGCCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAA-CTAGCTTCACTAC
1 CTTCGATCTGCTTCACAGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCT-GCTCCACTAC
35084198 AACTGAGGGAGGCAAGGCTTGTGT
65 AACTGAGGGAGGCAAGGCTTGTGT
* *
35084222 CTTCGATCTGCTTCACAGTC-AGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
1 CTTCGATCTGCTTCACAGTCGA-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
35084286 AA-TCGAGGGAGGCAAGGCTTGTGT
65 AACT-GAGGGAGGCAAGGCTTGTGT
* *
35084310 CTTCGATCTGCTTCACTGTC-AGTACAGGAAGGCAAGATCTGCTATCTTCA
1 CTTCGATCTGCTTCACAGTCGA-TGCAGGAAGGCAAGATCTGCTATCTTCA
35084360 CTGATCTATT
Statistics
Matches: 363, Mismatches: 33, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
87 5 0.01
88 355 0.98
89 3 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.27
Consensus pattern (88 bp):
CTTCGATCTGCTTCACAGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
ACTGAGGGAGGCAAGGCTTGTGT
Found at i:35084343 original size:44 final size:44
Alignment explanation
Indices: 35084207--35084345 Score: 140
Period size: 44 Copynumber: 3.2 Consensus size: 44
35084197 CAACTGAGGG
* *
35084207 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACAGTCAGTACAAGA
1 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
* * * * * * * *
35084251 AGGCAA-GATCTGCTATCTTCAACCTGCTCCACT-ACAAT-CGAGGG
1 AGGCAAGGCT-TG-TGTCTTCGATCTGCTTCACTGTCAGTAC-AGGA
35084295 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
1 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
35084339 AGGCAAG
1 AGGCAAG
35084346 ATCTGCTATC
Statistics
Matches: 71, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
43 19 0.27
44 34 0.48
45 18 0.25
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (44 bp):
AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
Found at i:35095587 original size:34 final size:34
Alignment explanation
Indices: 35095549--35095619 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
35095539 TGGGTCTCCA
35095549 TAATTCGCCACTCCTTCGACACAGTAATAAAAAC
1 TAATTCGCCACTCCTTCGACACAGTAATAAAAAC
*
35095583 TAATTCGCCACTCCTTTGACACAGTAATAAAAAC
1 TAATTCGCCACTCCTTCGACACAGTAATAAAAAC
35095617 TAA
1 TAA
35095620 GGGAATAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
TAATTCGCCACTCCTTCGACACAGTAATAAAAAC
Found at i:35107452 original size:18 final size:18
Alignment explanation
Indices: 35107429--35107488 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
35107419 TTAAAACAAG
35107429 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
35107447 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
35107464 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
35107482 TTACATT
1 TTACATT
35107489 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:35111348 original size:41 final size:41
Alignment explanation
Indices: 35111211--35111570 Score: 466
Period size: 41 Copynumber: 8.9 Consensus size: 41
35111201 CAAAATATTT
* * * *
35111211 TTAGCGGCACTTTTCTAAAAACGCCGCTAAAGTCCCCAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAA
* * * *
35111252 TTAGCGGCTC-TTTCTC-AAAACGCCGCTAAATACCTCAGCA
1 TTAGCGGCGCTTTTC-CAAAAACGCCGCTAAAGACCCCAGAA
*
35111292 TTA-CGGCGCTTTTCCAAAAACGCCACTAAAGACCCCAGAA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAA
*
35111332 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAA
*
35111373 TTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGA-CCCA-ACA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGA-A
* *
35111413 TTAGCGGTGTTTTTCCAAAAACGCCGCTAAAGACCCCA-ATA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGA-A
* *
35111454 TTAGTGGCGCTTTT-CAAAAACACCGCTAAAGACCCCAGAA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAA
* *
35111494 TTAGCGGCGCTTTTCCAAAAACGCCGTTAAAGACCCCAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAA
**
35111535 TTAGCGGCGCTTTTTTAAAAACGCCGCTAAAG-CCCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCC
35111571 TAAAGGTAAG
Statistics
Matches: 282, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
39 6 0.02
40 130 0.46
41 146 0.52
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAA
Found at i:35111416 original size:81 final size:82
Alignment explanation
Indices: 35111211--35111570 Score: 491
Period size: 81 Copynumber: 4.5 Consensus size: 82
35111201 CAAAATATTT
* * * * *
35111211 TTAGCGGCACTTTTCTAAAAACGCCGCTAAAGTCCCCAGCATTAGCGGCTC-TTTCTC-AAAACG
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAATTAGCGGCGCTTTTC-CAAAAACG
* *
35111274 CCGCTAAATACCTCAGCA
65 CCGCTAAAGACCCCAGCA
*
35111292 TTA-CGGCGCTTTTCCAAAAACGCCACTAAAGACCCCAGAATTAGCGGCGCTTTTCCAAAAACGC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAATTAGCGGCGCTTTTCCAAAAACGC
35111356 CGCTAAAGACCCCAGCA
66 CGCTAAAGACCCCAGCA
* * *
35111373 TTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGA-CCCA-ACATTAGCGGTGTTTTTCCAAAAACG
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGA-ATTAGCGGCGCTTTTCCAAAAACG
**
35111436 CCGCTAAAGACCCCAATA
65 CCGCTAAAGACCCCAGCA
* *
35111454 TTAGTGGCGCTTTT-CAAAAACACCGCTAAAGACCCCAGAATTAGCGGCGCTTTTCCAAAAACGC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAATTAGCGGCGCTTTTCCAAAAACGC
*
35111518 CGTTAAAGACCCCAGCA
66 CGCTAAAGACCCCAGCA
**
35111535 TTAGCGGCGCTTTTTTAAAAACGCCGCTAAAG-CCCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCC
35111571 TAAAGGTAAG
Statistics
Matches: 247, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
80 60 0.24
81 144 0.58
82 43 0.17
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (82 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGAATTAGCGGCGCTTTTCCAAAAACGC
CGCTAAAGACCCCAGCA
Done.