Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 100 of 120
Found at i:29494639 original size:48 final size:48
Alignment explanation
Indices: 29494548--29494639 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
29494538 ATTGAACCCT
* * * * *
29494548 TCATTCATTCTTCAGAGGATAAGATTTCACATCCTTTATGGGATATTA
1 TCATTCATCCATCAGAGGATAAGATTTCACATCCCTCAAGGGATATTA
*
29494596 TCATTCATCCATCAGGGGATAAGATTTCACATCCCTCAAGGGAT
1 TCATTCATCCATCAGAGGATAAGATTTCACATCCCTCAAGGGAT
29494640 CATATTTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (48 bp):
TCATTCATCCATCAGAGGATAAGATTTCACATCCCTCAAGGGATATTA
Found at i:29495514 original size:31 final size:31
Alignment explanation
Indices: 29495476--29495538 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
29495466 GCCTAAGAAG
29495476 TAAGTAAATATATTTCAGAATTTATTAGAGC
1 TAAGTAAATATATTTCAGAATTTATTAGAGC
29495507 TAAGTAAATATATTTCAGAATTTATTAGAGC
1 TAAGTAAATATATTTCAGAATTTATTAGAGC
29495538 T
1 T
29495539 TGATAGACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (31 bp):
TAAGTAAATATATTTCAGAATTTATTAGAGC
Found at i:29499615 original size:22 final size:20
Alignment explanation
Indices: 29499590--29499629 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29499580 CCAACCCAAT
29499590 TTTTAATAAACACAAAAAATTA
1 TTTTAA-AAACA-AAAAAATTA
*
29499612 TTTTAAAAATAAAAAAAT
1 TTTTAAAAACAAAAAAAT
29499630 AAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTTAAAAACAAAAAAATTA
Found at i:29502666 original size:22 final size:22
Alignment explanation
Indices: 29502635--29502677 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29502625 TGAATATATA
*
29502635 TAATATAAT-AATAAAGTAAATT
1 TAATAAAATAAAT-AAGTAAATT
29502657 TAATAAAATAAATAAGTAAAT
1 TAATAAAATAAATAAGTAAAT
29502678 GAAATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
TAATAAAATAAATAAGTAAATT
Found at i:29502683 original size:22 final size:21
Alignment explanation
Indices: 29502648--29502689 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29502638 TATAATAATA
**
29502648 AAGTAAATTTAATAAAATAAAT
1 AAGTAAATGAAAT-AAATAAAT
29502670 AAGTAAATGAAATAAATAAA
1 AAGTAAATGAAATAAATAAA
29502690 GAATAGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
AAGTAAATGAAATAAATAAAT
Found at i:29503461 original size:9 final size:9
Alignment explanation
Indices: 29503445--29503491 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
29503435 TTTATGGAAT
29503445 TTATATTGA
1 TTATATTGA
*
29503454 TTAAATTGGTA
1 TTATATT-G-A
29503465 TATATATTGA
1 T-TATATTGA
29503475 TTATATTGA
1 TTATATTGA
29503484 TTAT-TTGA
1 TTATATTGA
29503492 ATTGAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 4 0.12
9 18 0.55
10 3 0.09
11 3 0.09
12 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (9 bp):
TTATATTGA
Found at i:29503737 original size:40 final size:40
Alignment explanation
Indices: 29503614--29503753 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
29503604 GACTTCGAGT
* * *
29503614 CGATGAGACACTAGGTGTC-AATTTATTATTTCGGATATATT
1 CGATGAGACACTGGGTGTCAAATTT-TTACTTCGGAT-TATC
* * * * *
29503655 CAATGAGGCACTGGGTG-CCAA--TTTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATC
* *
29503692 TGATGAGACACTGGGTGTCAAATTTTTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATC
* * *
29503732 CGATGAGGCATTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
29503754 CTGGTGTGTT
Statistics
Matches: 77, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 16 0.21
38 12 0.16
39 1 0.01
40 32 0.42
41 16 0.21
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATC
Found at i:29508907 original size:43 final size:43
Alignment explanation
Indices: 29508808--29508935 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 43
29508798 AGCTTGTACA
* *
29508808 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGTAAACACATATCG
*
29508851 ATGCC-ACTATCCCAAACAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACGTAAACACATA-TCG
*
29508894 ATGCCAACGTCCCAGACGTGGTCTTACACG-ACAACACATATC
1 ATGCCAACATCCCAGACGTGGTCTTACACGTA-AACACATATC
29508936 AGAAGTCCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
42 5 0.07
43 64 0.88
44 4 0.05
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGTAAACACATATCG
Found at i:29513127 original size:25 final size:27
Alignment explanation
Indices: 29513076--29513129 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 27
29513066 CGAGCACATA
*
29513076 AACGGGAAGCTCTCTCTCGAGCTATAT
1 AACGGGAAGCTCTATCTCGAGCTATAT
29513103 AACGGGAAGCT-TATC-CGAGCTATAT
1 AACGGGAAGCTCTATCTCGAGCTATAT
29513128 AA
1 AA
29513130 TGGAAAACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 12 0.46
26 3 0.12
27 11 0.42
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AACGGGAAGCTCTATCTCGAGCTATAT
Found at i:29513146 original size:25 final size:25
Alignment explanation
Indices: 29513093--29513147 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
29513083 AGCTCTCTCT
* * * *
29513093 CGAGCTATATAACGGGAAGCTTATC
1 CGAGCTATATAACGGAAAACTCATA
*
29513118 CGAGCTATATAATGGAAAACTCATA
1 CGAGCTATATAACGGAAAACTCATA
29513143 CGAGC
1 CGAGC
29513148 CATAATTAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (25 bp):
CGAGCTATATAACGGAAAACTCATA
Found at i:29513834 original size:5 final size:5
Alignment explanation
Indices: 29513817--29513848 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
29513807 AATTTAATAA
29513817 AATTC ATATTC AATTC AATTC AATTC AATTC A
1 AATTC A-ATTC AATTC AATTC AATTC AATTC A
29513849 CATCTTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTC
Found at i:29524398 original size:15 final size:16
Alignment explanation
Indices: 29524364--29524400 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
29524354 TGGGTGAAAG
*
29524364 AAAATATTTTATGTTA
1 AAAATATTTGATGTTA
*
29524380 AAAATATTTGATTTTA
1 AAAATATTTGATGTTA
29524396 AAAAT
1 AAAAT
29524401 GATTCAATAA
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:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
AAAATATTTGATGTTA
Found at i:29534362 original size:17 final size:17
Alignment explanation
Indices: 29534340--29534372 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29534330 ATATTTAATA
29534340 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
29534357 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
29534373 TAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:29535508 original size:45 final size:46
Alignment explanation
Indices: 29535444--29535539 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 46
29535434 TACTTAATCA
29535444 AGTATAAATAATAAATAATAAATACCATGTAATTTAGTTAA-ATTT
1 AGTATAAATAATAAATAATAAATACCATGTAATTTAGTTAATATTT
** * *
29535489 AGTATAAATAATTTATAATAAATACTATTTAATTTAGTTAATTATTT
1 AGTATAAATAATAAATAATAAATACCATGTAATTTAGTTAA-TATTT
29535536 AGTA
1 AGTA
29535540 AGTCAAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 37 0.82
47 8 0.18
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (46 bp):
AGTATAAATAATAAATAATAAATACCATGTAATTTAGTTAATATTT
Found at i:29540037 original size:15 final size:15
Alignment explanation
Indices: 29540012--29540046 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29540002 AACTCTATTT
*
29540012 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
29540026 TAATTAATATTAAGA
1 TAATTAATATTAAGA
29540041 TAATTA
1 TAATTA
29540047 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:29541696 original size:4 final size:4
Alignment explanation
Indices: 29541687--29541749 Score: 60
Period size: 4 Copynumber: 15.5 Consensus size: 4
29541677 CAACCCAATT
*
29541687 TTTA TTTA TTTA -TT- TTTA TTTTA TTTTA TTTA CTTTA TTTA TTAA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA -TTTA TTTA TTTA TTTA
29541736 TTT- TATTA TTTA TT
1 TTTA T-TTA TTTA TT
29541750 ACTTACTTGG
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
3 5 0.10
4 32 0.63
5 14 0.27
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:29541748 original size:33 final size:29
Alignment explanation
Indices: 29541687--29541753 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
29541677 CAACCCAATT
*
29541687 TTTA-TTTATTTATTTTTATTTTATTTTA
1 TTTACTTTATTTATTTTTATTTTATTATA
*
29541715 TTTACTTTATTTATTAATTTATTTTATTATT
1 TTTACTTTATTTATT--TTTATTTTATTATA
29541746 TATTACTT
1 T-TTACTT
29541754 ACTTGGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 4 0.12
29 10 0.30
31 13 0.39
32 6 0.18
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTACTTTATTTATTTTTATTTTATTATA
Found at i:29542988 original size:20 final size:20
Alignment explanation
Indices: 29542955--29543002 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
29542945 CTAAAGCATA
* *
29542955 AAAAATATAAAAAATAAATAAAT
1 AAAAAT-TAAAAGA-AAA-AAAG
29542978 AAAAATTAAAAGAAAAAAAG
1 AAAAATTAAAAGAAAAAAAG
29542998 AAAAA
1 AAAAA
29543003 AATATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
22 6 0.26
23 6 0.26
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (20 bp):
AAAAATTAAAAGAAAAAAAG
Found at i:29543582 original size:15 final size:15
Alignment explanation
Indices: 29543557--29543591 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29543547 AACTCTATTT
*
29543557 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
29543571 TAATTAATATTAAGA
1 TAATTAATATTAAGA
29543586 TAATTA
1 TAATTA
29543592 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:29544793 original size:40 final size:39
Alignment explanation
Indices: 29544738--29544854 Score: 137
Period size: 40 Copynumber: 3.0 Consensus size: 39
29544728 GCGTTTGGAC
*
29544738 AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTA
1 AAAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTA
** * * *
29544778 AAAAAACGCCGCTAAAGGTAGAGCATTAGCGGCGCCTATC
1 AAAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTA
* *
29544818 CAAAAACGCCGCTAAAAATAAGCATTAGCGGCG-TTTT
1 AAAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTT
29544855 CTGAAAAGCA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 2 0.03
39 13 0.20
40 49 0.77
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTA
Found at i:29544969 original size:41 final size:41
Alignment explanation
Indices: 29544910--29545148 Score: 252
Period size: 41 Copynumber: 5.8 Consensus size: 41
29544900 GAGTTTTTAG
* *
29544910 GGCCTTTAGCGGCATTTTTGAATAAACGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAGAAACGCCGCTAATGCTCT
* *
29544951 GGCCTTTAGCCGCGTTTTTG-AGTAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAG-AAACGCCGCTAATGCTCT
29544992 GGCCTTTAGCGGCGTTTTTGAA-AAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAGAAA-CGCCGCTAATGCTCT
** * * * *
29545033 ATCTTTTAGCGGCGTTTTTGAAGAAGCGCCGCTGATGCTCA
1 GGCCTTTAGCGGCGTTTTTGAAGAAACGCCGCTAATGCTCT
** * * * *
29545074 GATCTTTAGCGGCGTTTTTAAAGAAGCGCCGGTATTGCTGC-
1 GGCCTTTAGCGGCGTTTTTGAAGAAACGCCGCTAATGCT-CT
* *
29545115 AGCCTTTAGCGGCGTTTTT-AAAAAAGCGCCGCTA
1 GGCCTTTAGCGGCGTTTTTGAAGAAA-CGCCGCTA
29545149 GTAATAATAA
Statistics
Matches: 166, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
40 7 0.04
41 155 0.93
42 4 0.02
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (41 bp):
GGCCTTTAGCGGCGTTTTTGAAGAAACGCCGCTAATGCTCT
Found at i:29545048 original size:82 final size:81
Alignment explanation
Indices: 29544910--29545148 Score: 286
Period size: 82 Copynumber: 2.9 Consensus size: 81
29544900 GAGTTTTTAG
* * *
29544910 GGCCTTTAGCGGCATTTTTGAATAAA-CGCCGCTAATGCTCTGGCCTTTAGCCGCGTTTTTGAGT
1 GGCCTTTAGCGGCGTTTTTGAA-AAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTGAG-
*
29544974 AAGCGCCGCTAATGCTCT
64 AAGCGCCGCTAATGCTCA
* *
29544992 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATCTTTTAGCGGCGTTTTTGAAGA
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTG-AGA
*
29545057 AGCGCCGCTGATGCTCA
65 AGCGCCGCTAATGCTCA
** * * *
29545074 GATCTTTAGCGGCGTTTTT-AAAGAAGCGCCGGTATTGCTGC-AGCCTTTAGCGGCGTTTTTAAA
1 GGCCTTTAGCGGCGTTTTTGAAA-AAGCGCCGCTAATGCT-CTAGCCTTTAGCGGCGTTTTT-GA
*
29545137 AAAGCGCCGCTA
63 GAAGCGCCGCTA
29545149 GTAATAATAA
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
81 6 0.04
82 127 0.93
83 3 0.02
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (81 bp):
GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTGAGAA
GCGCCGCTAATGCTCA
Found at i:29545133 original size:123 final size:123
Alignment explanation
Indices: 29544914--29545148 Score: 321
Period size: 123 Copynumber: 1.9 Consensus size: 123
29544904 TTTTAGGGCC
* * * *
29544914 TTTAGCGGCATTTTTGAATAAACGCCGCTAATGCTCTGGCCTTTAGCCGCGTTTTTGAGTAAGCG
1 TTTAGCGGCATTTTTGAAGAAACGCCGCTAATGCTCAGACCTTTAGCCGCGTTTTTAAGTAAGCG
* *
29544979 CCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATCT
66 CCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTATCT
* * * * *
29545037 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTGATGCTCAGATCTTTAGCGGCGTTTTTAAAG-AAGC
1 TTTAGCGGCATTTTTGAAGAAACGCCGCTAATGCTCAGACCTTTAGCCGCGTTTTT-AAGTAAGC
* *
29545101 GCCGGTATTGCTGC-AGCCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTA
65 GCCGCTAATGCT-CTAGCCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTA
29545149 GTAATAATAA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
123 94 0.97
124 3 0.03
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (123 bp):
TTTAGCGGCATTTTTGAAGAAACGCCGCTAATGCTCAGACCTTTAGCCGCGTTTTTAAGTAAGCG
CCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTATCT
Found at i:29556313 original size:66 final size:65
Alignment explanation
Indices: 29556206--29556376 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 65
29556196 GAGCAAATTA
* * * * *
29556206 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGTTGAGGTTCAAA-AAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAG-TATGAAGAACTCCA
29556270 G
65 G
*
29556271 CTACAACTAAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCA
29556336 G
65 G
* * * *
29556337 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
29556377 CGGCAGCGAA
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.02
66 86 0.93
67 4 0.04
ACGTcount: A:0.42, C:0.18, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCAG
Found at i:29556373 original size:21 final size:21
Alignment explanation
Indices: 29556347--29556459 Score: 84
Period size: 21 Copynumber: 5.4 Consensus size: 21
29556337 CAGCAGCTTA
*
29556347 AAGCAGATGCGGCAGC-AAGAG
1 AAGCAGAGGCGGCAGCGAA-AG
29556368 AAGCAGAGGCGGCAGCGAAAG
1 AAGCAGAGGCGGCAGCGAAAG
* * * **
29556389 AAGTACAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAAAG
*** **
29556410 AAGCAGAGGCTAAAGCGAGGG
1 AAGCAGAGGCGGCAGCGAAAG
* **
29556431 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAAAG
29556452 AAGCAGAG
1 AAGCAGAG
29556460 CAGCGTCAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
21 77 0.97
22 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAAAG
Found at i:29556427 original size:42 final size:42
Alignment explanation
Indices: 29556358--29556459 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
29556348 AGCAGATGCG
* * ** *
29556358 GCAGCAAGAGAAGCAGAGGCGGCAGCGAAAGAAGTACAGGCT
1 GCAGCGAGGGAAGCAGAGGCGAAAGCGAAAGAAGCACAGGCT
* ** *
29556400 GCAGCGAGGGAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCGAAAGCGAAAGAAGCACAGGCT
29556442 GCAGCGAGGGAAGCAGAG
1 GCAGCGAGGGAAGCAGAG
29556460 CAGCGTCAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (42 bp):
GCAGCGAGGGAAGCAGAGGCGAAAGCGAAAGAAGCACAGGCT
Found at i:29556852 original size:43 final size:43
Alignment explanation
Indices: 29556805--29557116 Score: 315
Period size: 43 Copynumber: 7.3 Consensus size: 43
29556795 AGGTGTTAGC
* * *
29556805 CTTTAGTGGCGTTTTTGGTCAAAGCGTCGCTAAAGATAAGGGT
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
29556848 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
29556891 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *
29556934 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
29556977 CTATT-GTGGCGTTTGAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *
29557020 CTTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * ** *
29557063 CTATT-GCGGCGCTTCT-CCCAAAAACGCCGCTAAAGATCAGGGT
1 CT-TTAGTGGCGTTTGTGGTC-AAAGCGCCGCTAAAGATCAGGGT
*
29557106 CTTTAGCGGCG
1 CTTTAGTGGCG
29557117 CTTCCACTAA
Statistics
Matches: 223, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
42 5 0.02
43 214 0.96
44 4 0.02
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (43 bp):
CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:29556915 original size:86 final size:86
Alignment explanation
Indices: 29556825--29557116 Score: 361
Period size: 86 Copynumber: 3.4 Consensus size: 86
29556815 GTTTTTGGTC
* * ** * * *
29556825 AAAGCGTCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGG
1 AAAGCGCCGCTAAAGATTAGGGTCTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
29556890 TCT-TTAGCGGCGTTTGTGGGG
66 TCTATT-GCGGCGTTTGTGGGG
* * *
29556911 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGGTCTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
* *
29556976 TCTATTGTGGCGTTTGAGGGG
66 TCTATTGCGGCGTTTGTGGGG
* * *
29556997 AAAGCGCCGCTAAAGATTAGGTTCTTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGGTCTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
* * ****
29557062 TCTATTGCGGCGCTTCTCCCA
66 TCTATTGCGGCGTTTGTGGGG
* *
29557083 AAAACGCCGCTAAAGATCAGGGTCTTTAGCGGCG
1 AAAGCGCCGCTAAAGATTAGGGTCTTTAGCGGCG
29557117 CTTCCACTAA
Statistics
Matches: 178, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
86 176 0.99
87 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.26
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATTAGGGTCTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
TCTATTGCGGCGTTTGTGGGG
Found at i:29557117 original size:43 final size:42
Alignment explanation
Indices: 29557044--29557139 Score: 131
Period size: 43 Copynumber: 2.3 Consensus size: 42
29557034 GTGGTCAAAG
* *
29557044 CGCCGCTATAGATCAGGGTCTATTGCGGCGCTTCTCCCAAAAA
1 CGCCGCTAAAGATCAGGGTCTATTGCGGCGCTTC-CACAAAAA
* *
29557087 CGCCGCTAAAGATCAGGGTCT-TTAGCGGCGCTTCCACTAAAG
1 CGCCGCTAAAGATCAGGGTCTATT-GCGGCGCTTCCACAAAAA
29557129 CGCCGCTAAAG
1 CGCCGCTAAAG
29557140 GTCTTAGTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
42 18 0.38
43 30 0.62
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21
Consensus pattern (42 bp):
CGCCGCTAAAGATCAGGGTCTATTGCGGCGCTTCCACAAAAA
Found at i:29557150 original size:42 final size:43
Alignment explanation
Indices: 29557044--29557158 Score: 108
Period size: 42 Copynumber: 2.7 Consensus size: 43
29557034 GTGGTCAAAG
* * * *
29557044 CGCCGCTATAGATCAGGGTCTAT-TGCGGCGCTTCTCCCAAAAA
1 CGCCGCTAAAGATCAGAGTCT-TCAGCGGCGCTTCTCACAAAAA
* * * *
29557087 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTC-CACTAAAG
1 CGCCGCTAAAGATCAGAGTCTTCAGCGGCGCTTCTCACAAAAA
* **
29557129 CGCCGCTAAAGGTCTTAGTCTTCAGCGGCG
1 CGCCGCTAAAGATCAGAGTCTTCAGCGGCG
29557159 TTTGTGCTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 31 0.51
43 30 0.49
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.23
Consensus pattern (43 bp):
CGCCGCTAAAGATCAGAGTCTTCAGCGGCGCTTCTCACAAAAA
Found at i:29561476 original size:14 final size:14
Alignment explanation
Indices: 29561444--29561476 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29561434 ATATATGATA
*
29561444 ATAAATTTAAAAAT
1 ATAATTTTAAAAAT
29561458 ATAATTTTAAAAAT
1 ATAATTTTAAAAAT
29561472 ATAAT
1 ATAAT
29561477 AATAATTTTA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATTTTAAAAAT
Found at i:29565098 original size:20 final size:20
Alignment explanation
Indices: 29565069--29565108 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29565059 TGAACAGAAT
* *
29565069 AGAACGGAACGGAGCAAAAC
1 AGAACAGAACAGAGCAAAAC
29565089 AGAACAGAACAGAGCAAAAC
1 AGAACAGAACAGAGCAAAAC
29565109 GAAGCATGTA
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:0.55, C:0.20, G:0.25, T:0.00
Consensus pattern (20 bp):
AGAACAGAACAGAGCAAAAC
Found at i:29565491 original size:104 final size:103
Alignment explanation
Indices: 29565303--29565536 Score: 263
Period size: 104 Copynumber: 2.3 Consensus size: 103
29565293 TTATCAACAT
* * * * * * *
29565303 GGCCTGGTCACACGCCCATGTTCTTACTTGTGTGTCTCACACGGCCTGGGCACACCCCCATGTCC
1 GGCCTGGACACACGCCCATGTCCTT-GTTGTGTGGCACACACAGCCTAGGCACACCCCCATGTCC
** * * *
29565368 CTAGCTGTATGGTTTTAAAGTGTAAACAGTGAGTTATAC
65 CTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTACAC
*
29565407 GGCCCT-GACACACGCCCATGTCCTTGTTCGTGTGGCACACACAGCCTAGGCACACGCCCATGTC
1 GG-CCTGGACACACGCCCATGTCCTTGTT-GTGTGGCACACACAGCCTAGGCACACCCCCATGTC
* * *
29565471 CCTGGCCATGTGGTTCTAAAGCGTAAATAGTGAGTTACAC
64 CCTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTACAC
* **
29565511 GGCCTGGACACATGTTCATGTCCTTG
1 GGCCTGGACACACGCCCATGTCCTTG
29565537 CCCATGTGGC
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
103 5 0.05
104 100 0.93
105 3 0.03
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (103 bp):
GGCCTGGACACACGCCCATGTCCTTGTTGTGTGGCACACACAGCCTAGGCACACCCCCATGTCCC
TAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTACAC
Found at i:29565545 original size:104 final size:104
Alignment explanation
Indices: 29565340--29565575 Score: 249
Period size: 104 Copynumber: 2.3 Consensus size: 104
29565330 TTGTGTGTCT
* * * ** * * *
29565340 CACACGGCCTGGGCACACCCCCATGTCCCTAGCTGTATGGTTTTAAAGTGTAAACAGTGAGTTAT
1 CACACAGCCTAGGCACACACCCATGTCCCTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTAC
** *
29565405 ACGGCCCTGACACACGCCCATGTCCTTGTTCGTGTGGCA
66 ACGGCCCTGACACACGCCCATGTCCTTGCCCATGTGGCA
* * * *
29565444 CACACAGCCTAGGCACACGCCCATGTCCCTGGCCATGTGGTTCTAAAGCGTAAATAGTGAGTTAC
1 CACACAGCCTAGGCACACACCCATGTCCCTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTAC
* ** *
29565509 ACGG-CCTGGACACATGTTCATGTCCTTGCCCATGTGGCT
66 ACGGCCCT-GACACACGCCCATGTCCTTGCCCATGTGGCA
* * * *
29565548 TATACAGTCTAGGCACACACCTATGTCC
1 CACACAGCCTAGGCACACACCCATGTCC
29565576 TTGCCCGTGT
Statistics
Matches: 108, Mismatches: 23, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
103 3 0.03
104 105 0.97
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (104 bp):
CACACAGCCTAGGCACACACCCATGTCCCTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTAC
ACGGCCCTGACACACGCCCATGTCCTTGCCCATGTGGCA
Found at i:29565605 original size:42 final size:42
Alignment explanation
Indices: 29565527--29565620 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
29565517 GACACATGTT
* * *
29565527 CATGTCCTTGCCCATGTGGCTTATACAGTCTAGGCACAC-AC
1 CATGTCCTTGCCCATGTGGCTCACACAGCCTAGGCACACGAC
* * *
29565568 CTATGTCCTTGCCCGTGTGGCTCACAC-GACCTGGGCACACGTC
1 C-ATGTCCTTGCCCATGTGGCTCACACAG-CCTAGGCACACGAC
29565611 CATGTCCTTG
1 CATGTCCTTG
29565621 GTCGTATGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 2 0.05
42 40 0.91
43 2 0.05
ACGTcount: A:0.17, C:0.34, G:0.22, T:0.27
Consensus pattern (42 bp):
CATGTCCTTGCCCATGTGGCTCACACAGCCTAGGCACACGAC
Found at i:29565605 original size:146 final size:145
Alignment explanation
Indices: 29565415--29565767 Score: 440
Period size: 146 Copynumber: 2.4 Consensus size: 145
29565405 ACGGCCCTGA
** * *
29565415 CACACGCCCATGTCCTTGTTCGTGTGGCACACAC-AGCCTAGGCACACGCCCATGTCCCTGGCCA
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACGA-CCTGGGCACACGCCCATGTCCCTGGCCA
* * * * * *
29565479 TGTGGTTCTAAAGCGTAAATAGTGAGTTACACGGCCTGGACACATGTTCATGTCCTTGCCCATGT
65 TATGATTCTAAAGCATAAACAGTGAGTTACACGGCCTGGACACATGCTCATGTCCTTACCCATGT
* * *
29565544 GGCTTATACAGTCTAGG
130 GGCTCACAC-GGCTAGG
* * * * * *
29565561 CACACACCTATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGTCCATGTCCTTGGTCGT
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGCCCATGTCCCTGGCCAT
**
29565626 ATGATTCTAAAGCATAAACAGTGAGTTACACGGCCTGGACACATGCTCATGTCCTTACCTGTGTG
66 ATGATTCTAAAGCATAAACAGTGAGTTACACGGCCTGGACACATGCTCATGTCCTTACCCATGTG
*
29565691 GCTCACACGGCTGGG
131 GCTCACACGGCTAGG
* * * *
29565706 AACACGCCCATGTCCTTGCCC-TATGGCTCACACGGCCTGGGCACACGCTCATGTCCCTGGCC
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGCCCATGTCCCTGGCC
29565768 GTGTAGCGTC
Statistics
Matches: 175, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
144 35 0.20
145 23 0.13
146 116 0.66
147 1 0.01
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (145 bp):
CACACGCCCATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGCCCATGTCCCTGGCCAT
ATGATTCTAAAGCATAAACAGTGAGTTACACGGCCTGGACACATGCTCATGTCCTTACCCATGTG
GCTCACACGGCTAGG
Found at i:29565720 original size:41 final size:41
Alignment explanation
Indices: 29565653--29565761 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 41
29565643 ACAGTGAGTT
* * * *
29565653 ACACGGCCT-GGACACATGCTCATGTCCTTACCTGTGTGGCTC
1 ACACGGCCTGGGA-ACACGCCCATGTCCTTACC-CTATGGCTC
*
29565695 ACACGG-CTGGGAACACGCCCATGTCCTTGCCCTATGGCTC
1 ACACGGCCTGGGAACACGCCCATGTCCTTACCCTATGGCTC
* *
29565735 ACACGGCCTGGGCACACGCTCATGTCC
1 ACACGGCCTGGGAACACGCCCATGTCC
29565762 CTGGCCGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 13 0.22
41 36 0.62
42 9 0.16
ACGTcount: A:0.17, C:0.37, G:0.25, T:0.21
Consensus pattern (41 bp):
ACACGGCCTGGGAACACGCCCATGTCCTTACCCTATGGCTC
Found at i:29568968 original size:6 final size:6
Alignment explanation
Indices: 29568957--29568982 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29568947 TTTTGGGTTT
29568957 TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TT
29568983 TAAGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:29569555 original size:124 final size:125
Alignment explanation
Indices: 29569165--29569572 Score: 638
Period size: 125 Copynumber: 3.3 Consensus size: 125
29569155 ATTTATTATG
* *
29569165 GAAATCGCCCCCACGTGGACGCGCTGTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
* * *
29569230 ATTTCTGAGCAAATAGTATAAAAAATGCTTCTAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTCT
* * * * *
29569290 GAAATCACTCCTACGTGGACTCGCTTTTGCTACAGTAGGTCTTGAAAAAATAATTTTGACTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
*
29569355 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGTTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTCT
* * * *
29569415 GAAATCGCTCCTACGTGGACGCGTTTTTGCTACAGTAGATCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
* * *
29569480 GTTTTTGAGCAAATAGTAT-AAAAATGCTTCAAGTAGGATGCTTTATTAGAATAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTCT
*
29569539 GAAATCGCTCCCACGTGGACGCGTTTTTGCTACA
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACA
29569573 ATAGCATGAG
Statistics
Matches: 260, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
124 70 0.27
125 190 0.73
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTCT
Found at i:29572985 original size:49 final size:49
Alignment explanation
Indices: 29572769--29572987 Score: 375
Period size: 49 Copynumber: 4.5 Consensus size: 49
29572759 TAAGAATATT
* *
29572769 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
* * *
29572818 AACTATTTTTTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
29572867 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
29572916 AACTATTTTGTATTTTATTACATCAAATAATATCAAATTATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
29572965 AACTATTTTGTATTATATTACAT
1 AACTATTTTGTATTTTATTACAT
29572988 TAATATAAAC
Statistics
Matches: 164, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 164 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
Found at i:29573434 original size:18 final size:18
Alignment explanation
Indices: 29573408--29573450 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
29573398 GACTAGAAAA
* * *
29573408 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
29573426 AGGATACATAAAATGGCT
1 AGGATACATAAAAGGGCT
29573444 AGGATAC
1 AGGATAC
29573451 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:29575260 original size:22 final size:22
Alignment explanation
Indices: 29575218--29575266 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
29575208 TCTTTTAAAT
* *
29575218 AGAAATTTGAGAGGAATTTGAG
1 AGAAATTAGAGAGGAAATTGAG
29575240 AGAATATTAGAGA-GAAATTGAG
1 AGAA-ATTAGAGAGGAAATTGAG
29575262 AGAAA
1 AGAAA
29575267 ATATTTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (22 bp):
AGAAATTAGAGAGGAAATTGAG
Found at i:29575262 original size:10 final size:10
Alignment explanation
Indices: 29575218--29575266 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
29575208 TCTTTTAAAT
29575218 AGAAATTTGAG
1 AGAAA-TTGAG
*
29575229 AGGAATTTGAG
1 A-GAAATTGAG
29575240 AGAATATTAGAG
1 AGAA-ATT-GAG
29575252 AGAAATTGAG
1 AGAAATTGAG
29575262 AGAAA
1 AGAAA
29575267 ATATTTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 11 0.33
11 12 0.36
12 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (10 bp):
AGAAATTGAG
Found at i:29577799 original size:18 final size:19
Alignment explanation
Indices: 29577762--29577822 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
29577752 AAGAATTCTA
* *
29577762 AAAAATATAAAAAA-ACAT
1 AAAAATTTAAAAAATAGAT
* *
29577780 AAATATTTTAAAAATA-AT
1 AAAAATTTAAAAAATAGAT
29577798 AATAAATTTAAAAAATAGAT
1 AA-AAATTTAAAAAATAGAT
29577818 AAAAA
1 AAAAA
29577823 AAAGTATTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.43
19 16 0.46
20 4 0.11
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATTTAAAAAATAGAT
Found at i:29578145 original size:27 final size:27
Alignment explanation
Indices: 29578073--29578157 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
29578063 GTATGGGGTA
* * *
29578073 GGTGGCGCCTATCTGACAAGCGCGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
29578100 GGTGGAGCTTATCTGACAGGCGCGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
* *
29578127 GGTGGAGCTTATCTGACAGGTGTGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
29578154 GGTG
1 GGTG
29578158 CTTAATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.18, C:0.21, G:0.38, T:0.24
Consensus pattern (27 bp):
GGTGGAGCTTATCTGACAGGCGCGACT
Found at i:29581697 original size:33 final size:33
Alignment explanation
Indices: 29581599--29581723 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 33
29581589 AACTTGAGCC
* * *
29581599 GAGAGGAGTGGAGTACGGCAGTAGATACGGG-CT
1 GAGAGGAGTGGAGTACGAC-GTGGATACGGGCCA
* *
29581632 GAGAGGAGTGAAGTACGATGGTGGATACGGGCCA
1 GAGAGGAGTGGAGTACGA-CGTGGATACGGGCCA
*
29581666 G-GAGGAGTGGAGTACGACGTTGGATACGGGCCT
1 GAGAGGAGTGGAGTACGACG-TGGATACGGGCCA
* * *
29581699 GA-ATGAGCGGAGTACTGAGGTGGAT
1 GAGAGGAGTGGAGTAC-GACGTGGAT
29581724 GTGAGCTGGG
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
32 1 0.01
33 70 0.92
34 5 0.07
ACGTcount: A:0.26, C:0.12, G:0.45, T:0.17
Consensus pattern (33 bp):
GAGAGGAGTGGAGTACGACGTGGATACGGGCCA
Found at i:29582876 original size:15 final size:14
Alignment explanation
Indices: 29582851--29582892 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
29582841 ACATTTTTAT
29582851 AAATC-AATAAAAA
1 AAATCAAATAAAAA
*
29582864 ATTATCAAATAAATAA
1 A-AATCAAATAAA-AA
29582880 AAATCAAATAAAA
1 AAATCAAATAAAA
29582893 TTACATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 4 0.17
15 16 0.67
16 3 0.12
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATCAAATAAAAA
Found at i:29582883 original size:18 final size:18
Alignment explanation
Indices: 29582847--29582882 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29582837 ATCAACATTT
*
29582847 TTATAAATCAATAAAAAA
1 TTATAAATAAATAAAAAA
29582865 TTATCAAATAAATAAAAA
1 TTAT-AAATAAATAAAAA
29582883 TCAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
TTATAAATAAATAAAAAA
Found at i:29583168 original size:103 final size:105
Alignment explanation
Indices: 29582889--29583179 Score: 425
Period size: 104 Copynumber: 2.8 Consensus size: 105
29582879 AAAATCAAAT
* *
29582889 AAAATTACATTA-AAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAATC
1 AAAATTACATTACTAAAAAATCACAAAACACTATACTAAACACTAACAATTTATATAACCTAATC
* **
29582953 ATAAATTACTAACAAAATAACTATAAAATTATTATTTTTT
66 ATAAATTATTAACAAAATAACTATAAAATTATTATTTTAA
*
29582993 AAAA-TACATTACTAAAAAATCACAAAACAC-ATAACTAAACCCTAACAATTTATATAACCTAAT
1 AAAATTACATTACTAAAAAATCACAAAACACTAT-ACTAAACACTAACAATTTATATAACCTAAT
29583056 CATAAATTATTAACAAAATAACTATAAAATTA-T-TTTTAA
65 CATAAATTATTAACAAAATAACTATAAAATTATTATTTTAA
* * *
29583095 AAAATTACATTACTAAAAAATCACAAAACCCTATACTAAACACTAACAA-TT-TGTAACATAATC
1 AAAATTACATTACTAAAAAATCACAAAACACTATACTAAACACTAACAATTTATATAACCTAAT-
29583158 CCATAAATTATTAACAAAATAA
65 -CATAAATTATTAACAAAATAA
29583180 ATAACTATAA
Statistics
Matches: 171, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
101 9 0.05
102 10 0.06
103 69 0.40
104 83 0.49
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (105 bp):
AAAATTACATTACTAAAAAATCACAAAACACTATACTAAACACTAACAATTTATATAACCTAATC
ATAAATTATTAACAAAATAACTATAAAATTATTATTTTAA
Found at i:29583789 original size:27 final size:27
Alignment explanation
Indices: 29583754--29583835 Score: 121
Period size: 27 Copynumber: 3.0 Consensus size: 27
29583744 AGGGGGTAGG
*
29583754 CAGTGGCGCCTACCT-ATCAGGCGCGAC
1 CAGTTGCGCCTACCTGA-CAGGCGCGAC
*
29583781 TAGTTGCGCCTACCTGACAGGCGCGAC
1 CAGTTGCGCCTACCTGACAGGCGCGAC
*
29583808 CAGTTGCGCCTATCTGACAGGCGCGAC
1 CAGTTGCGCCTACCTGACAGGCGCGAC
29583835 C
1 C
29583836 TGTCTCAGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.17
Consensus pattern (27 bp):
CAGTTGCGCCTACCTGACAGGCGCGAC
Found at i:29600389 original size:28 final size:28
Alignment explanation
Indices: 29600358--29600413 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
29600348 AAAAGTTATA
*
29600358 AAAAGATTATAAAAATCGTAAAAAAAAT
1 AAAAGATTATAAAAATCATAAAAAAAAT
** *
29600386 AAAATTTTATAAAAATCATACAAAAAAT
1 AAAAGATTATAAAAATCATAAAAAAAAT
29600414 TATAAAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAAGATTATAAAAATCATAAAAAAAAT
Found at i:29607999 original size:20 final size:19
Alignment explanation
Indices: 29607961--29607999 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29607951 TTAATTTCTT
*
29607961 TTAAAATTTAAAAACATTA
1 TTAAAATTAAAAAACATTA
*
29607980 TTAAAATTAATAAAATATTA
1 TTAAAATTAA-AAAACATTA
29608000 AATAAAGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAATTAAAAAACATTA
Found at i:29608931 original size:15 final size:15
Alignment explanation
Indices: 29608907--29608940 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29608897 ATTTATTTTT
29608907 AATTATTTAAAT-AA
1 AATTATTTAAATGAA
29608921 AATTAATTTAAATGAA
1 AATT-ATTTAAATGAA
29608937 AATT
1 AATT
29608941 GAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATGAA
Found at i:29611635 original size:54 final size:54
Alignment explanation
Indices: 29611553--29611673 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 54
29611543 TTTATATTGC
*
29611553 ATGCATGACATTTAATTTGAATATAGGATATTGAAATATAAATATTAATTAATT
1 ATGCATGAAATTTAATTTGAATATAGGATATTGAAATATAAATATTAATTAATT
* *
29611607 ATGCATGAGATTTAATTTGAATATAGGATATTGAAATATGAATATTAATTAATT
1 ATGCATGAAATTTAATTTGAATATAGGATATTGAAATATAAATATTAATTAATT
29611661 ATGCATGAAATTT
1 ATGCATGAAATTT
29611674 TGGTCTTTAC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.40
Consensus pattern (54 bp):
ATGCATGAAATTTAATTTGAATATAGGATATTGAAATATAAATATTAATTAATT
Found at i:29621249 original size:15 final size:13
Alignment explanation
Indices: 29621219--29621253 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
29621209 TATGTTTAAA
29621219 TTTTAATTTTATT
1 TTTTAATTTTATT
29621232 TTTTATATTTTAATT
1 TTTTA-ATTTT-ATT
29621247 TTTTAAT
1 TTTTAAT
29621254 ATAATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 7 0.35
15 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTAATTTTATT
Found at i:29621290 original size:25 final size:23
Alignment explanation
Indices: 29621237--29621290 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 23
29621227 TTATTTTTTA
29621237 TATTTTAATTTTTTAATATAATT
1 TATTTTAATTTTTTAATATAATT
*
29621260 TGATTTCTATATTTTTATAATATTA-T
1 T-ATTT-TA-ATTTTT-TAATATAATT
29621286 TATTT
1 TATTT
29621291 AGTCCAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.04
24 4 0.15
25 6 0.23
26 8 0.31
27 7 0.27
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TATTTTAATTTTTTAATATAATT
Found at i:29621989 original size:58 final size:58
Alignment explanation
Indices: 29621885--29622011 Score: 184
Period size: 58 Copynumber: 2.2 Consensus size: 58
29621875 CAGTAGAGGG
* * * * *
29621885 CACCCAACTATGGTTTTTTTTTTTTTGGTTACCCAATTATGAAAAGTTACAAAATGGT
1 CACCCAACTATGGTTTTTTTTCTTTTGATCACCCAACTATGAAAAGTTACAAAATGAT
29621943 CACCCAACTATGGTTTTTTTATCTTTTGATCACCCAACTATG-AAAGTTACAAAATGAT
1 CACCCAACTATGGTTTTTTT-TCTTTTGATCACCCAACTATGAAAAGTTACAAAATGAT
*
29622001 CATCCAACTAT
1 CACCCAACTAT
29622012 TCAAATTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
58 45 0.73
59 17 0.27
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (58 bp):
CACCCAACTATGGTTTTTTTTCTTTTGATCACCCAACTATGAAAAGTTACAAAATGAT
Found at i:29622311 original size:18 final size:18
Alignment explanation
Indices: 29622288--29622327 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
29622278 GTGCAATGAT
29622288 AAGGTACATTACATTTCC
1 AAGGTACATTACATTTCC
29622306 AAGGTACATTACATTTCC
1 AAGGTACATTACATTTCC
29622324 AAGG
1 AAGG
29622328 AGAGATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (18 bp):
AAGGTACATTACATTTCC
Found at i:29624775 original size:6 final size:6
Alignment explanation
Indices: 29624764--29624809 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
29624754 CAGCCTAAAA
* * *
29624764 AACAGC AACAGC AACATC AACATC AACATC AACATC AACACC AACA
1 AACATC AACATC AACATC AACATC AACATC AACATC AACATC AACA
29624810 ACAAGCCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.52, C:0.35, G:0.04, T:0.09
Consensus pattern (6 bp):
AACATC
Found at i:29634604 original size:72 final size:72
Alignment explanation
Indices: 29634514--29634685 Score: 231
Period size: 72 Copynumber: 2.4 Consensus size: 72
29634504 AAAATCACAT
* *
29634514 ATAAACAACTATTGATAAAACTAATTTA-ATAAAAAATAAGTAGAATATAAATTCAATATCTAAA
1 ATAAACAACTATTGATAAAACTAATTTACA-AAAAAATAAGTAGAACATAAATTCAATATCCAAA
*
29634578 GACCAAAC
65 AACCAAAC
* * * *
29634586 ATAAACAACTTTTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTA-ATTTACAAAAAAATAAGTAGAACATAAATTCAATATCCAAA
29634650 AACCAAAC
65 AACCAAAC
* *
29634658 ATAAATAACTATTGATAAAACTAGTTTA
1 ATAAACAACTATTGATAAAACTAATTTA
29634686 GCATTGTTGT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
72 84 0.98
73 2 0.02
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAATTTACAAAAAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:29643372 original size:3 final size:3
Alignment explanation
Indices: 29643364--29643394 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
29643354 GTAATGTGCT
*
29643364 TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29643395 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:29652483 original size:16 final size:16
Alignment explanation
Indices: 29652458--29652492 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29652448 ATTATTTTTT
29652458 CAAAAACAAAGGAAAA
1 CAAAAACAAAGGAAAA
* *
29652474 CAAAATCAAATGAAAA
1 CAAAAACAAAGGAAAA
29652490 CAA
1 CAA
29652493 TAAAAGAACA
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:0.71, C:0.14, G:0.09, T:0.06
Consensus pattern (16 bp):
CAAAAACAAAGGAAAA
Found at i:29653258 original size:13 final size:13
Alignment explanation
Indices: 29653240--29653275 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
29653230 TTCTTTATTG
29653240 CTTTTGAGAAGTA
1 CTTTTGAGAAGTA
*
29653253 CTTTTGAGAAGTG
1 CTTTTGAGAAGTA
29653266 CTTTTGAGAA
1 CTTTTGAGAA
29653276 ATTTGAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (13 bp):
CTTTTGAGAAGTA
Found at i:29653546 original size:19 final size:20
Alignment explanation
Indices: 29653502--29653551 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
29653492 ATTAATTATT
*
29653502 TATAAAATTTAATTAGAATA
1 TATAAAATATAATTAGAATA
*
29653522 TATAAAATATATTTA-AATA
1 TATAAAATATAATTAGAATA
*
29653541 T-TTAAATATAA
1 TATAAAATATAA
29653552 AAATTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 8 0.31
19 5 0.19
20 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TATAAAATATAATTAGAATA
Found at i:29656754 original size:46 final size:46
Alignment explanation
Indices: 29656676--29656998 Score: 502
Period size: 46 Copynumber: 7.0 Consensus size: 46
29656666 ACAATGCTAT
* * *
29656676 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCCACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* *
29656722 AACTCAGTATGGTTTTCTTTATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
*
29656768 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* * * *
29656814 AACTCAGTATGATTTTCTTTACCGAAACACCATATCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* *
29656860 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
*
29656906 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* * *
29656952 AACTCAATATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
29656998 A
1 A
29656999 CTTTGCCATG
Statistics
Matches: 257, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 257 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
Found at i:29663688 original size:78 final size:78
Alignment explanation
Indices: 29663554--29663931 Score: 502
Period size: 78 Copynumber: 4.9 Consensus size: 78
29663544 AACTAATAGT
* * *
29663554 GGATAATATATGTATATACATGTATAAGTTCTTGAATTTAGTTAAAATTATGTATGTTATATTTA
1 GGAT-ATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTA
*
29663619 TATATATGAAGTTC
65 TATATATAAAGTTC
29663633 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
29663698 ATATATAAAGTTC
66 ATATATAAAGTTC
29663711 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
29663776 ATATATAAAGTTC
66 ATATATAAAGTTC
* * * *
29663789 GGATATATGTGTATATACATGAATAAGTTC-TGAATTTAGTT-AATGT-TGAATGTTATA--TAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
* * *
29663849 GTTTACAAGAGGTTC
66 ATATATAA-A-GTTC
** * * * *
29663864 GGATAGGTATGTATAT--ATGAGTATAAATTCTTGGATTTA-TTAAAAGTATGGATGTTACATAT
1 GGATATATATGTATATACATGA--ATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTT
29663926 ATATAT
64 ATATAT
29663932 GTATAATATA
Statistics
Matches: 269, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
73 12 0.04
74 1 0.00
75 36 0.13
76 15 0.06
77 20 0.07
78 176 0.65
79 9 0.03
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (78 bp):
GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
ATATATAAAGTTC
Found at i:29664631 original size:41 final size:41
Alignment explanation
Indices: 29664528--29664784 Score: 338
Period size: 41 Copynumber: 6.2 Consensus size: 41
29664518 CATTTCGGAC
* ** **
29664528 TATAAGTCTAGCAGGCTAAAAGCCGGTG-TACTGAATAAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGAT-CTGAACCAGGT
* * *
29664569 TTTAAAACCTAGCAGGCTAAGTGTCGGTGATCTGAACCAGGT
1 TAT-AAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
* *
29664611 TATAAGCCTAGCAGGCTAAGTGCCAGTGATCTAAACCAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
*
29664652 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGC
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
* *
29664693 TATAAGCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
* *
29664734 TATAAGCCTAGCATGCTAAGTGCCGGTGATCTGAATCAGGCT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGG-T
29664776 T-TAAGCCTA
1 TATAAGCCTA
29664785 ACAGATATGA
Statistics
Matches: 192, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
41 158 0.82
42 33 0.17
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (41 bp):
TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
Found at i:29675557 original size:4 final size:4
Alignment explanation
Indices: 29675548--29675575 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
29675538 ATCTTTTATT
29675548 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
29675576 ATCCTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:29679039 original size:67 final size:67
Alignment explanation
Indices: 29678931--29679065 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
29678921 TTTTCAATTC
*
29678931 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGTAGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
29678996 CA
66 CA
*
29678998 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
29679063 CA
66 CA
29679065 A
1 A
29679066 CGACAATTAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:29680051 original size:16 final size:16
Alignment explanation
Indices: 29680030--29680063 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
29680020 GTTTGTTCCT
29680030 TTTTAAAATATACTTA
1 TTTTAAAATATACTTA
29680046 TTTTAAAATATACTTA
1 TTTTAAAATATACTTA
29680062 TT
1 TT
29680064 AAGGATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAATATACTTA
Found at i:29682889 original size:21 final size:21
Alignment explanation
Indices: 29682865--29682906 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29682855 TTGTTATTAA
29682865 TGTGTTACCCTCATACAATAT
1 TGTGTTACCCTCATACAATAT
29682886 TGTGTTACCCTCATACAATAT
1 TGTGTTACCCTCATACAATAT
29682907 CCTTAATCAT
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:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (21 bp):
TGTGTTACCCTCATACAATAT
Found at i:29685577 original size:19 final size:18
Alignment explanation
Indices: 29685541--29685578 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
29685531 TTGTTCGAAC
29685541 ATTTTAATATTTTGTAAA
1 ATTTTAATATTTTGTAAA
29685559 ATTTTAAATAATTTT-TAAA
1 ATTTT-AAT-ATTTTGTAAA
29685578 A
1 A
29685579 AAACTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTTAATATTTTGTAAA
Found at i:29690414 original size:31 final size:31
Alignment explanation
Indices: 29690376--29690450 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
29690366 ATGTTAATGG
*
29690376 GTGACTGATTTGTCACTTTTCGATAACGTTA
1 GTGACTGATTTGTCACTTTTCGATAACATTA
29690407 GTGACTGATTTGTCACTTTTCGATAACATTA
1 GTGACTGATTTGTCACTTTTCGATAACATTA
29690438 GTGACTGATTTGT
1 GTGACTGATTTGT
29690451 TATTTTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.43
Consensus pattern (31 bp):
GTGACTGATTTGTCACTTTTCGATAACATTA
Found at i:29690528 original size:20 final size:20
Alignment explanation
Indices: 29690505--29690543 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29690495 CAACGTGGCA
29690505 AGTTAACTGG-CTACGTCACT
1 AGTTAACTGGTC-ACGTCACT
29690525 AGTTAACTGGTCACGTCAC
1 AGTTAACTGGTCACGTCAC
29690544 CTGTCCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
AGTTAACTGGTCACGTCACT
Found at i:29697817 original size:12 final size:12
Alignment explanation
Indices: 29697800--29697824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29697790 GGTGTTCATT
29697800 CGGTTAACCGAC
1 CGGTTAACCGAC
29697812 CGGTTAACCGAC
1 CGGTTAACCGAC
29697824 C
1 C
29697825 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:29697999 original size:9 final size:9
Alignment explanation
Indices: 29697985--29698024 Score: 80
Period size: 9 Copynumber: 4.4 Consensus size: 9
29697975 TTTGGTTAAA
29697985 AATTACCCG
1 AATTACCCG
29697994 AATTACCCG
1 AATTACCCG
29698003 AATTACCCG
1 AATTACCCG
29698012 AATTACCCG
1 AATTACCCG
29698021 AATT
1 AATT
29698025 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:29700754 original size:19 final size:19
Alignment explanation
Indices: 29700730--29700793 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
29700720 ATTAAGCTTA
29700730 AAAATTATTAAAATATTAT
1 AAAATTATTAAAATATTAT
*
29700749 AAAATT-TGTGTAAA-ATTAT
1 AAAATTAT-T-AAAATATTAT
*
29700768 AGAAATTTATTAAAATTTTATT
1 A-AAA-TTATTAAAATATTA-T
29700790 AAAA
1 AAAA
29700794 ATGATAGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
18 1 0.03
19 13 0.37
20 9 0.26
21 9 0.26
22 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
AAAATTATTAAAATATTAT
Found at i:29701202 original size:19 final size:20
Alignment explanation
Indices: 29701156--29701203 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
29701146 ATAATATGCT
29701156 AATAATTTTCGACAACTTTC
1 AATAATTTTCGACAACTTTC
* *
29701176 AGTGATTTTC-ACAA-TTTGC
1 AATAATTTTCGACAACTTT-C
29701195 AATAATTTT
1 AATAATTTT
29701204 TTTAGAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.13
19 12 0.52
20 8 0.35
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (20 bp):
AATAATTTTCGACAACTTTC
Found at i:29701647 original size:3 final size:3
Alignment explanation
Indices: 29701639--29701664 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29701629 CTTTACTCTT
29701639 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
29701665 TTCTTTCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29704546 original size:3 final size:3
Alignment explanation
Indices: 29704538--29704586 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
29704528 AGTTTACCCT
29704538 TTA 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 TTA
29704586 T
1 T
29704587 GTGGCATTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29704843 original size:17 final size:20
Alignment explanation
Indices: 29704803--29704843 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
29704793 TAATCAATAA
29704803 AAATTATATAAAATATCATT
1 AAATTATATAAAATATCATT
29704823 AAATT-TAT-AAATATC-TT
1 AAATTATATAAAATATCATT
29704840 AAAT
1 AAAT
29704844 ATACTTACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 7 0.33
19 3 0.14
20 5 0.24
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTATATAAAATATCATT
Found at i:29710444 original size:40 final size:40
Alignment explanation
Indices: 29710389--29710469 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
29710379 TTACACACTT
29710389 AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
1 AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
29710429 AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
1 AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
29710469 A
1 A
29710470 TACACACCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (40 bp):
AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
Found at i:29710592 original size:23 final size:23
Alignment explanation
Indices: 29710566--29710634 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
29710556 ATAAGTGCCA
29710566 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
29710589 CACTGATATGTAGACGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
29710612 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
29710635 ACATGCTAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:29717923 original size:51 final size:51
Alignment explanation
Indices: 29717797--29717984 Score: 245
Period size: 51 Copynumber: 3.7 Consensus size: 51
29717787 ACCATTCGAT
* * ** * **
29717797 ACACATAGTAGCCTTCACATAGTACTACACACGTGTTCA--AACTTTCCGGT
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAA-TATCCGAA
* *
29717847 TCATGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGAA
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGAA
* * *
29717898 ACACGTAGTAGCCTGCACATTGTACTACACAAGTGACCATTAATATCCGAT
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGAA
29717949 ACACGTAGTAGCCTGCACATAGTACTACACACGTGA
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGA
29717985 TCGAAGCTAT
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
50 33 0.28
51 85 0.71
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (51 bp):
ACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGAA
Found at i:29724643 original size:23 final size:23
Alignment explanation
Indices: 29724617--29724685 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
29724607 ATAAGTGCCA
29724617 CACTAATATGTAGCCGAAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
* * *
29724640 CACTGATATGTAGCCGTAGCCAC
1 CACTAATATGTAGCCGAAGCTAC
*
29724663 CACTAAAATGTAGCCGAAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
29724686 TCATGCTAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (23 bp):
CACTAATATGTAGCCGAAGCTAC
Found at i:29726539 original size:10 final size:10
Alignment explanation
Indices: 29726526--29726582 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
29726516 TTAAAATTAA
*
29726526 TTTTTATAGTT
1 TTTTTATA-AT
*
29726537 TTTTTATAAG
1 TTTTTATAAT
*
29726547 TTTTTA-CAT
1 TTTTTATAAT
29726556 TATTTTATAAT
1 T-TTTTATAAT
*
29726567 TTTTTACAAT
1 TTTTTATAAT
29726577 TTTTTA
1 TTTTTA
29726583 AATCTATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.05
10 25 0.66
11 11 0.29
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:29726581 original size:20 final size:19
Alignment explanation
Indices: 29726536--29726582 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
29726526 TTTTTATAGT
29726536 TTTTTTATAAGTTTTTACA
1 TTTTTTATAAGTTTTTACA
*
29726555 TTATTTTATAATTTTTTACAA
1 TT-TTTTATAAGTTTTTAC-A
29726576 TTTTTTA
1 TTTTTTA
29726583 AATCTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTTATAAGTTTTTACA
Found at i:29726899 original size:33 final size:33
Alignment explanation
Indices: 29726851--29726915 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
29726841 GACGCTCACG
* *
29726851 GTATCGGCTCGCAGGAATCGAAGGGAGCTTGCC
1 GTATCAGCTCACAGGAATCGAAGGGAGCTTGCC
*
29726884 GTATCAGCTCACAGGAATCGAAGGGAGTTTGC
1 GTATCAGCTCACAGGAATCGAAGGGAGCTTGC
29726916 AGTCCTAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.34, T:0.20
Consensus pattern (33 bp):
GTATCAGCTCACAGGAATCGAAGGGAGCTTGCC
Found at i:29728581 original size:163 final size:163
Alignment explanation
Indices: 29728311--29728639 Score: 550
Period size: 163 Copynumber: 2.0 Consensus size: 163
29728301 TTCAATGAAA
*
29728311 TAATGCTAGTCAAAATCAGCATCCCATTCATGACTCCAAATTTTGTTATTCATTTTCAACCTAAT
1 TAATGCTAGTCAAAATAAGCATCCCATTCATGACTCCAAATTTTGTTATTCATTTTCAACCTAAT
* * *
29728376 GTGTTGACAGATGTACTTAGGACTCAATTAAATTAATTTGATGCATTGAAGGTTTTTATCAGCAT
66 GTGTTCACAGATATACCTAGGACTCAATTAAATTAATTTGATGCATTGAAGGTTTTTATCAGCAT
29728441 TCATTAATTATTATTTTAAGAAATCGTTTTTAT
131 TCATTAATTATTATTTTAAGAAATCGTTTTTAT
* *
29728474 TAATGCTAGTCAAAATAAGCATCCCATTGATGACTCCAATTTTTGTTATTCATTTTCAACCTAAT
1 TAATGCTAGTCAAAATAAGCATCCCATTCATGACTCCAAATTTTGTTATTCATTTTCAACCTAAT
* * * *
29728539 GTGTTCACAGATATCCCTAGGATTCAATTCAATTAATTTGATGCATTGACGGTTTTTATCAGCAT
66 GTGTTCACAGATATACCTAGGACTCAATTAAATTAATTTGATGCATTGAAGGTTTTTATCAGCAT
* *
29728604 TCATTAATTATTATTTTAAGAACTTGTTTTTAT
131 TCATTAATTATTATTTTAAGAAATCGTTTTTAT
29728637 TAA
1 TAA
29728640 ATTCAAATTT
Statistics
Matches: 154, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 154 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (163 bp):
TAATGCTAGTCAAAATAAGCATCCCATTCATGACTCCAAATTTTGTTATTCATTTTCAACCTAAT
GTGTTCACAGATATACCTAGGACTCAATTAAATTAATTTGATGCATTGAAGGTTTTTATCAGCAT
TCATTAATTATTATTTTAAGAAATCGTTTTTAT
Found at i:29729417 original size:16 final size:15
Alignment explanation
Indices: 29729387--29729420 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
29729377 ATAGTTTTAA
29729387 TTAATTTAATTTATT
1 TTAATTTAATTTATT
*
29729402 TTAATATTATTTTATT
1 TTAAT-TTAATTTATT
29729418 TTA
1 TTA
29729421 TAAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTAATTTAATTTATT
Found at i:29729618 original size:14 final size:15
Alignment explanation
Indices: 29729586--29729619 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29729576 ATTTTATAAC
* *
29729586 TTTTCAATACTTAAT
1 TTTTCAACACCTAAT
29729601 TTTTCAACACCTAAT
1 TTTTCAACACCTAAT
29729616 TTTT
1 TTTT
29729620 TAATTTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTCAACACCTAAT
Found at i:29729684 original size:5 final size:5
Alignment explanation
Indices: 29729674--29729698 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29729664 AAGAAAAAGT
29729674 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
29729699 TAATTATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:29729803 original size:2 final size:2
Alignment explanation
Indices: 29729793--29729845 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
29729783 ATCTATTTTT
29729793 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29729834 TA TA TA TA TA TA
1 TA TA TA TA TA TA
29729846 AGTGTAAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29733006 original size:22 final size:21
Alignment explanation
Indices: 29732960--29733007 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
29732950 GCCCGTTTTT
* * *
29732960 AATTAAAATTATTTTTTATAA
1 AATTAAAACTAATTGTTATAA
29732981 AATTAAAACTAATTGTTATTAA
1 AATTAAAACTAATTGTTA-TAA
29733003 AATTA
1 AATTA
29733008 GTTGTTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AATTAAAACTAATTGTTATAA
Found at i:29733051 original size:9 final size:9
Alignment explanation
Indices: 29733037--29733069 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
29733027 ATTATCAAAT
29733037 TATTAATTG
1 TATTAATTG
29733046 TATTAATTG
1 TATTAATTG
29733055 --TTAATTG
1 TATTAATTG
29733062 TATTAATT
1 TATTAATT
29733070 ATTATAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (9 bp):
TATTAATTG
Found at i:29733058 original size:16 final size:16
Alignment explanation
Indices: 29733034--29733073 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
29733024 AAAATTATCA
29733034 AATTATTAATTGTATT
1 AATTATTAATTGTATT
*
29733050 AATTGTTAATTGTATT
1 AATTATTAATTGTATT
29733066 AATTATTA
1 AATTATTA
29733074 TAACAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
AATTATTAATTGTATT
Found at i:29735008 original size:22 final size:22
Alignment explanation
Indices: 29734978--29735028 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
29734968 GGTATTTTGT
*
29734978 AATTTAAT-AAAA-TATAATAAA
1 AATTAAATAAAAATTATAA-AAA
29734999 ATATTAAATAAAAATTATAAAAA
1 A-ATTAAATAAAAATTATAAAAA
29735022 AATTAAA
1 AATTAAA
29735029 CATTAGTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 12 0.46
23 8 0.31
24 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTAAATAAAAATTATAAAAA
Found at i:29735022 original size:11 final size:12
Alignment explanation
Indices: 29734978--29735026 Score: 54
Period size: 11 Copynumber: 4.4 Consensus size: 12
29734968 GGTATTTTGT
29734978 AATT-TAAT-AA
1 AATTATAATAAA
29734988 AA-TATAATAAA
1 AATTATAATAAA
29734999 ATATTA-AATAAA
1 A-ATTATAATAAA
29735011 AATTATAA-AAA
1 AATTATAATAAA
29735022 AATTA
1 AATTA
29735027 AACATTAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.03
10 6 0.18
11 15 0.44
12 10 0.29
13 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATTATAATAAA
Found at i:29737054 original size:20 final size:20
Alignment explanation
Indices: 29737031--29737071 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29737021 AATTTATTTT
29737031 AAAATAATA-AAATTTATAAA
1 AAAATAATACAAATTT-TAAA
*
29737051 AAAATTATACAAATTTTAAA
1 AAAATAATACAAATTTTAAA
29737071 A
1 A
29737072 CTATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATAATACAAATTTTAAA
Found at i:29738602 original size:27 final size:27
Alignment explanation
Indices: 29738564--29738615 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
29738554 ATACAGGGGT
*
29738564 GTGGTGCCTATCTGATAGGCGGCACTG
1 GTGGTGCCTATCTGATAGGCAGCACTG
*
29738591 GTGGTGCTTATCTGATAGGCAGCAC
1 GTGGTGCCTATCTGATAGGCAGCAC
29738616 ACCTAGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (27 bp):
GTGGTGCCTATCTGATAGGCAGCACTG
Found at i:29740509 original size:2 final size:2
Alignment explanation
Indices: 29740502--29740529 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29740492 AGCTCTGCTT
29740502 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29740530 AGTTCGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:29742345 original size:2 final size:2
Alignment explanation
Indices: 29742338--29742363 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29742328 TTAAGGAGGA
29742338 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
29742364 GAAGGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29743109 original size:28 final size:29
Alignment explanation
Indices: 29743044--29743110 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
29743034 ATTGAACTTG
*
29743044 AATTTTAAAATTCAAAAATAGAGAGAATA
1 AATTTTAAAAATCAAAAATAGAGAGAATA
29743073 AATTCTTAAAAAT-AAAAATATG-G-GAATTA
1 AATT-TTAAAAATCAAAAATA-GAGAGAA-TA
29743102 AATTTTAAA
1 AATTTTAAA
29743111 TTTATAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 8 0.24
29 18 0.53
30 8 0.24
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (29 bp):
AATTTTAAAAATCAAAAATAGAGAGAATA
Found at i:29743382 original size:17 final size:17
Alignment explanation
Indices: 29743349--29743382 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29743339 ATTATTTTGA
*
29743349 TTAAATTTTGGTAAAGG
1 TTAAATTTTAGTAAAGG
*
29743366 TTAAATTTTAGTTAAGG
1 TTAAATTTTAGTAAAGG
29743383 AGCTATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TTAAATTTTAGTAAAGG
Found at i:29746854 original size:44 final size:44
Alignment explanation
Indices: 29746787--29746880 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
29746777 GTCTCGACTT
*
29746787 TCATTTTCATATGCTTATCAAATATAAGTATTATATTAACCAAC
1 TCATTTTCATATGCTTATCAAATATAAGTATTATATTAACCAAA
* * *
29746831 TCATTTTCATATGCTTATTAAATATAAGTATTGTATTAATCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTATATTAACCAAA
29746875 TCATTT
1 TCATTT
29746881 ATTGAATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (44 bp):
TCATTTTCATATGCTTATCAAATATAAGTATTATATTAACCAAA
Found at i:29748616 original size:21 final size:21
Alignment explanation
Indices: 29748592--29748636 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
29748582 GCCATGCAAC
*
29748592 TTGTCGAAATCATTTTTAAAT
1 TTGTCGAAACCATTTTTAAAT
29748613 TTGTCGAAACCATTTTTAAAT
1 TTGTCGAAACCATTTTTAAAT
29748634 TTG
1 TTG
29748637 AAAAATGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (21 bp):
TTGTCGAAACCATTTTTAAAT
Found at i:29751143 original size:24 final size:24
Alignment explanation
Indices: 29751106--29751153 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29751096 GACTGTGGGC
29751106 ATTTTAAAATTTGGCTTTATTTTT
1 ATTTTAAAATTTGGCTTTATTTTT
*
29751130 ATTTATAAAA-TTGGGTTTATTTTT
1 ATTT-TAAAATTTGGCTTTATTTTT
29751154 GGTTTGCGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.60
Consensus pattern (24 bp):
ATTTTAAAATTTGGCTTTATTTTT
Found at i:29751982 original size:193 final size:194
Alignment explanation
Indices: 29751665--29752029 Score: 529
Period size: 193 Copynumber: 1.9 Consensus size: 194
29751655 AGTCCCGAGT
* * *
29751665 GAGAGAAGACATTTAGAAGAAATGAATTAAGAGACCTACATGCTTGAATAAAAGCATTAAAGAAA
1 GAGAGAAGACAGTTAGAAGAAATGAATTAAGAGACCTACATACTTGAACAAAAGCATTAAAGAAA
* * *
29751730 ATGTAGCAACCATAAACAGAAAGTATGAGATTAATGGGTGGAGCATTTCTCTAGATTTTAATACC
66 ATGTAGCAACCATAAACAAAAAGTAGGAGATTAATGGGTGGAGCATTTATCTAGATTTTAATACC
*
29751795 TCGTATGGAACCATTATGA-CCTACCACCAATTGTAGTGGTAGAAACTGATTTGAAGTATTGTGA
131 TCGTATGAAACCATTATGATCC-ACCACCAATTGTAGTGGTAGAAACTGATTTGAAGTATTGTGA
* * * *
29751859 GAGAGAAGACAGTTAGAAGAAATGATTTGAGAGACCT-CATACTTTAACAAAAGTATTAAAGAAA
1 GAGAGAAGACAGTTAGAAGAAATGAATTAAGAGACCTACATACTTGAACAAAAGCATTAAAGAAA
* * * * *
29751923 ATGTATCAACTATAAATAAAAAGTAGGTGATTAATGGGTGGAGCATTTAT-TGAGATTTTAATGC
66 ATGTAGCAACCATAAACAAAAAGTAGGAGATTAATGGGTGGAGCATTTATCT-AGATTTTAATAC
* *
29751987 CTTGTATGAAACCATTATGATCCACCGCCAATTGTAGTGGTAG
130 CTCGTATGAAACCATTATGATCCACCACCAATTGTAGTGGTAG
29752030 TTTAGGTACG
Statistics
Matches: 151, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
192 1 0.01
193 114 0.75
194 36 0.24
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (194 bp):
GAGAGAAGACAGTTAGAAGAAATGAATTAAGAGACCTACATACTTGAACAAAAGCATTAAAGAAA
ATGTAGCAACCATAAACAAAAAGTAGGAGATTAATGGGTGGAGCATTTATCTAGATTTTAATACC
TCGTATGAAACCATTATGATCCACCACCAATTGTAGTGGTAGAAACTGATTTGAAGTATTGTGA
Found at i:29758715 original size:19 final size:19
Alignment explanation
Indices: 29758666--29758720 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
29758656 AATACAAAAT
*
29758666 AATTCAAAATAATTT-TCAA
1 AATTCAAAAT-ATTTATAAA
29758685 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
29758704 AATTCAAAATATATATA
1 AATTCAAAATATTTATA
29758721 TATATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.12
19 29 0.88
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:29762036 original size:2 final size:2
Alignment explanation
Indices: 29762031--29762071 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29762021 TGTATATATA
29762031 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
29762072 ATAGGGTTTT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:29770574 original size:23 final size:24
Alignment explanation
Indices: 29770533--29770580 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29770523 CAGTACAAAT
*
29770533 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
29770557 AACAAAAACTACAG-AAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
29770580 A
1 A
29770581 GCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.17, G:0.04, T:0.08
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:29771242 original size:14 final size:11
Alignment explanation
Indices: 29771206--29771238 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
29771196 CTCAACACCA
29771206 AAATTGAGAGG
1 AAATTGAGAGG
29771217 AAATTGAGAGG
1 AAATTGAGAGG
29771228 AAATTTGAGAG
1 AAA-TTGAGAG
29771239 AGGATTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.21
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:29773306 original size:42 final size:42
Alignment explanation
Indices: 29773168--29773306 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 42
29773158 CATGTCAGCA
* ** * *
29773168 AAAGCTCA-TCCAGCTGGATGTCCTTTCTTGCCAATTGTGCAG
1 AAAGCTCACT-CAGCTGGACGAGCTTTCCTGCCAACTGTGCAG
* ** **
29773210 AAAGCTCAC-CTAGCTGGACTAGCTTTCCTGAGAACTGTGTGG
1 AAAGCTCACTC-AGCTGGACGAGCTTTCCTGCCAACTGTGCAG
**
29773252 AAAGCTTGCTCAGCTGGACGAGCTTTCCTGCCAACTGTGCAG
1 AAAGCTCACTCAGCTGGACGAGCTTTCCTGCCAACTGTGCAG
* *
29773294 AAATCGCACTCAG
1 AAAGCTCACTCAG
29773307 TTGGGTGCGC
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
41 1 0.01
42 71 0.97
43 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (42 bp):
AAAGCTCACTCAGCTGGACGAGCTTTCCTGCCAACTGTGCAG
Found at i:29780746 original size:53 final size:53
Alignment explanation
Indices: 29780666--29780775 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
29780656 ACTGGACTTC
29780666 ACAAAGAGTGATAATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
1 ACAAAGAGTGATAATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
*
29780719 ACAAAGAGTGATGATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
1 ACAAAGAGTGATAATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
29780772 ACAA
1 ACAA
29780776 GGACGTATCT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (53 bp):
ACAAAGAGTGATAATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
Found at i:29782163 original size:32 final size:32
Alignment explanation
Indices: 29782118--29782181 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
29782108 TTTTTCGTCC
* *
29782118 TTTTTTTTGTTTTTA-ATAAATGGCCCAATAT
1 TTTTTTTTCTTTTTACATAAATGACCCAATAT
*
29782149 TTTTTTTTACTTTTTACGTAAATGACCCAATAT
1 TTTTTTTT-CTTTTTACATAAATGACCCAATAT
29782182 GTTTATACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 8 0.29
32 6 0.21
33 14 0.50
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (32 bp):
TTTTTTTTCTTTTTACATAAATGACCCAATAT
Found at i:29782936 original size:41 final size:41
Alignment explanation
Indices: 29782889--29782979 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
29782879 GTGGGTTTAA
29782889 GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
1 GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
29782930 GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
1 GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
29782971 GGAGCTTTG
1 GGAGCTTTG
29782980 GAAAATTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.21, C:0.10, G:0.40, T:0.30
Consensus pattern (41 bp):
GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
Found at i:29784188 original size:31 final size:31
Alignment explanation
Indices: 29784147--29784294 Score: 124
Period size: 31 Copynumber: 4.8 Consensus size: 31
29784137 TGCTCAAATC
* * *
29784147 AATTCAGCAATATATATTCATATACGAACAA
1 AATTCGGCAATGTATAATCATATACGAACAA
*
29784178 AATTCGGCAATGTAT-ATCTATATAC-AA-ATC
1 AATTCGGCAATGTATAATC-ATATACGAACA-A
* * *
29784208 AATTCGGCAATGTACAACCATATAAGAATC-A
1 AATTCGGCAATGTATAATCATATACGAA-CAA
* * **
29784239 AGTTCGGCAATGTATAATCATATACAAATTA
1 AATTCGGCAATGTATAATCATATACGAACAA
* *
29784270 AATTCAGCAATGTATAACCATATAC
1 AATTCGGCAATGTATAATCATATAC
29784295 AAATCAATTT
Statistics
Matches: 93, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
29 1 0.01
30 23 0.25
31 69 0.74
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (31 bp):
AATTCGGCAATGTATAATCATATACGAACAA
Found at i:29784295 original size:31 final size:31
Alignment explanation
Indices: 29784184--29784704 Score: 404
Period size: 31 Copynumber: 16.9 Consensus size: 31
29784174 ACAAAATTCG
* * * *
29784184 GCAATGTATATCTATATACAAATCAA-TTCG
1 GCAATGTATAACCATATACAAATTAATTTCA
* * * *
29784214 GCAATGTACAACCATATA-AGAATCAAGTTCG
1 GCAATGTATAACCATATACA-AATTAATTTCA
* *
29784245 GCAATGTATAATCATATACAAATTAAATTCA
1 GCAATGTATAACCATATACAAATTAATTTCA
* *
29784276 GCAATGTATAACCATATACAAATCAATTT-G
1 GCAATGTATAACCATATACAAATTAATTTCA
*
29784306 GCAACT-TATATCCATATAC-AATTCAATTTCA
1 GCAA-TGTATAACCATATACAAATT-AATTTCA
* *
29784337 ACAATGTATAACCATGTACAAATTAATTTCA
1 GCAATGTATAACCATATACAAATTAATTTCA
* ** * *
29784368 GCAATATATAATAATATACAAATCAA-TTCG
1 GCAATGTATAACCATATACAAATTAATTTCA
**
29784398 GCAACT-TATATTCATATAC-AATTCAATTTCA
1 GCAA-TGTATAACCATATACAAATT-AATTTCA
* * *
29784429 ACAATGTATAACCATGTACAAATTAATTTTA
1 GCAATGTATAACCATATACAAATTAATTTCA
** * *
29784460 GCAATACACAACAATGTATACAAATTAATTTCA
1 GCAATGTATAACCA--TATACAAATTAATTTCA
* ** * * *
29784493 GCAATATATAATAATATACGAATCAA-TTCG
1 GCAATGTATAACCATATACAAATTAATTTCA
**
29784523 GCAACT-TATATTCATATAC-AATTCAATTTCA
1 GCAA-TGTATAACCATATACAAATT-AATTTCA
* *
29784554 ACAATGTATAACCATGTACAAATTAATTTCA
1 GCAATGTATAACCATATACAAATTAATTTCA
* * * *
29784585 GCAATGTACAACCATATACGAATCAA-TTCG
1 GCAATGTATAACCATATACAAATTAATTTCA
**
29784615 GCAACT-TATATTCATATAC-AATTCAATTTCA
1 GCAA-TGTATAACCATATACAAATT-AATTTCA
*
29784646 ACAATGTATAACCATATACAAATTAATTTCA
1 GCAATGTATAACCATATACAAATTAATTTCA
* * *
29784677 GCAATGTACAATCATATACAAATCAATT
1 GCAATGTATAACCATATACAAATTAATT
29784705 CGGGAACTTA
Statistics
Matches: 393, Mismatches: 73, Indels: 49
0.76 0.14 0.10
Matches are distributed among these distances:
29 13 0.03
30 105 0.27
31 232 0.59
32 17 0.04
33 26 0.07
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (31 bp):
GCAATGTATAACCATATACAAATTAATTTCA
Found at i:29784490 original size:64 final size:60
Alignment explanation
Indices: 29784410--29784612 Score: 178
Period size: 61 Copynumber: 3.3 Consensus size: 60
29784400 AACTTATATT
*
29784410 CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTTAGCAATACACAA
1 CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATACA-AA
* * ** * * * * * *
29784471 CAATGTATACAAATT-AATTTCAGCAATATATAATAATATACGAATCAA-TTCGGCAACTTATAT
1 C-A--TATAC-AATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAA--TACAA
*
29784534 T
60 A
*
29784535 CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATGTACAAC
1 CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAA--TACAAA
29784597 CATATACGAA-TCAATT
1 CATATAC-AATTCAATT
29784613 CGGCAACTTA
Statistics
Matches: 108, Mismatches: 25, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
60 4 0.04
61 32 0.30
62 24 0.22
63 9 0.08
64 32 0.30
65 7 0.06
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (60 bp):
CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATACAAA
Found at i:29784507 original size:125 final size:125
Alignment explanation
Indices: 29784353--29784589 Score: 456
Period size: 125 Copynumber: 1.9 Consensus size: 125
29784343 TATAACCATG
29784353 TACAAATTAATTTCAGCAATATATAATAATATACAAATCAATTCGGCAACTTATATTCATATACA
1 TACAAATTAATTTCAGCAATATATAATAATATACAAATCAATTCGGCAACTTATATTCATATACA
*
29784418 ATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTTAGCAATACACAACAATGTA
66 ATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATACACAACAATGTA
*
29784478 TACAAATTAATTTCAGCAATATATAATAATATACGAATCAATTCGGCAACTTATATTCATATACA
1 TACAAATTAATTTCAGCAATATATAATAATATACAAATCAATTCGGCAACTTATATTCATATACA
29784543 ATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAAT
66 ATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAAT
29784590 GTACAACCAT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 110 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (125 bp):
TACAAATTAATTTCAGCAATATATAATAATATACAAATCAATTCGGCAACTTATATTCATATACA
ATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATACACAACAATGTA
Done.