Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 98 of 126
Found at i:29911409 original size:18 final size:19
Alignment explanation
Indices: 29911377--29911415 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
29911367 AATATAAAAT
* *
29911377 AATTTAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
29911396 AATTAAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
29911414 AA
1 AA
29911416 ATTCTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:29911475 original size:43 final size:43
Alignment explanation
Indices: 29911382--29911475 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
29911372 AAAATAATTT
* *
29911382 AAAATA-ATTTTTAAAATTAAAAATATTTATAAAAATTCTAAA
1 AAAATATATTTTAAAAATTAAAAATATTTATAAAAATTATAAA
***
29911424 ATTTTATATTTTAAAAATTATAAAA-ATTTCA-AAAAATTATAAA
1 AAAATATATTTTAAAAATTA-AAAATATTT-ATAAAAATTATAAA
29911467 AAAATATAT
1 AAAATATAT
29911476 AAATGAAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
42 3 0.07
43 33 0.80
44 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (43 bp):
AAAATATATTTTAAAAATTAAAAATATTTATAAAAATTATAAA
Found at i:29912238 original size:18 final size:18
Alignment explanation
Indices: 29912215--29912252 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
29912205 TTTTATGTGT
29912215 TATAAAAATTAA-ATAATA
1 TATAAAAA-TAATATAATA
29912233 TATAAAAATAATATAATA
1 TATAAAAATAATATAATA
29912251 TA
1 TA
29912253 AAATATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TATAAAAATAATATAATA
Found at i:29912243 original size:13 final size:15
Alignment explanation
Indices: 29912225--29912257 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
29912215 TATAAAAATT
29912225 AAATAATAT-ATA-A
1 AAATAATATAATATA
29912238 AAATAATATAATATA
1 AAATAATATAATATA
29912253 AAATA
1 AAATA
29912258 TTACAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 3 0.17
15 6 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAATATAATATA
Found at i:29912245 original size:16 final size:18
Alignment explanation
Indices: 29912215--29912260 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 18
29912205 TTTTATGTGT
29912215 TATAAAAATTAAATA-ATA
1 TATAAAAATTAAATATA-A
29912233 TATAAAAA-T-AATATAA
1 TATAAAAATTAAATATAA
29912249 TATAAAATATTA
1 TATAAAA-ATTA
29912261 CAAACTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 12 0.50
17 3 0.12
18 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAAAAATTAAATATAA
Found at i:29918497 original size:27 final size:27
Alignment explanation
Indices: 29918450--29918540 Score: 166
Period size: 27 Copynumber: 3.4 Consensus size: 27
29918440 AAATATTCTC
*
29918450 TAAATTAAT-AAATATTAATTTATCGA
1 TAAATTAATAAAATATTCATTTATCGA
29918476 TAAATTAATAAAATATTCATTTATCGA
1 TAAATTAATAAAATATTCATTTATCGA
29918503 TAAATTAATAAAATATTCATTTATCGA
1 TAAATTAATAAAATATTCATTTATCGA
29918530 TAAATTAATAA
1 TAAATTAATAA
29918541 CCTCGAAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
26 9 0.14
27 54 0.86
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAATTAATAAAATATTCATTTATCGA
Found at i:29925636 original size:17 final size:17
Alignment explanation
Indices: 29925616--29925648 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29925606 AAACTTTTCC
29925616 TTTAT-TTTCTATTTTAG
1 TTTATCTTT-TATTTTAG
29925633 TTTATCTTTTATTTTA
1 TTTATCTTTTATTTTA
29925649 TGCTTTGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTATCTTTTATTTTAG
Found at i:29930714 original size:16 final size:16
Alignment explanation
Indices: 29930693--29930736 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
29930683 TTGGTTCAAG
29930693 TTTTATATAATATTTA
1 TTTTATATAATATTTA
29930709 TTTTATATAATATTTA
1 TTTTATATAATATTTA
29930725 TTTTATATAATA
1 TTTTATATAATA
29930737 AAGATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATATAATATTTA
Found at i:29937158 original size:127 final size:127
Alignment explanation
Indices: 29936932--29937184 Score: 434
Period size: 127 Copynumber: 2.0 Consensus size: 127
29936922 AACAATGTTC
*
29936932 CAACTCAAGGGGTATGGGCCAAAAGCTCACCTCATCCTAATGGTTAGGATGTCTTGTAACCAGGG
1 CAACTCAAGGGGTATGGGCCAAAAGCTCACCTCATCCTAACGGTTAGGATGTCTTGTAACCAGGG
29936997 GCAGATTTAAGTGGATTGGTATGGGCCCCGACCCCCTCTAAAATGAAATTTTGATCTTTTTT
66 GCAGATTTAAGTGGATTGGTATGGGCCCCGACCCCCTCTAAAATGAAATTTTGATCTTTTTT
* * * *
29937059 CAACTCAAGGGGTATGGGCGAAACGCTCACCTCATCTTAACGGTTAGGATGTCTTGTAACTAGGG
1 CAACTCAAGGGGTATGGGCCAAAAGCTCACCTCATCCTAACGGTTAGGATGTCTTGTAACCAGGG
* * *
29937124 GTAGATTTAAGTGGATTGGTATGGGCCTCGACCCCCTCTAAAATGGAATTTTGATCTTTTT
66 GCAGATTTAAGTGGATTGGTATGGGCCCCGACCCCCTCTAAAATGAAATTTTGATCTTTTT
29937185 CTGCTTTAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 118 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (127 bp):
CAACTCAAGGGGTATGGGCCAAAAGCTCACCTCATCCTAACGGTTAGGATGTCTTGTAACCAGGG
GCAGATTTAAGTGGATTGGTATGGGCCCCGACCCCCTCTAAAATGAAATTTTGATCTTTTTT
Found at i:29939787 original size:127 final size:126
Alignment explanation
Indices: 29939562--29939815 Score: 445
Period size: 127 Copynumber: 2.0 Consensus size: 126
29939552 AGGAACAATG
*
29939562 TTCCAACTCAAGGGGTATGGGCCAAAAGCTCACCTCATCCTAAGGTTAGGATGTCTTGTAACTAG
1 TTCCAACTCAAGGGGTATGGGCCAAAAGCTCACCTCATCCTAAGGTTAGGATGTCTTGTAACCAG
* *
29939627 GGGCAGCTTTAAGTGGATTGGTTTGGGCCCCGACCCCCTCTAAAATGAAATTTTGATCTTT
66 GGGCAGATTTAAGTGGATTGGTATGGGCCCCGACCCCCTCTAAAATGAAATTTTGATCTTT
*
29939688 TTCCAACTCAAGGGGTATGGGCCAAACGCTCACCTCATCCTAAGGGTTAGGATGTCTTGTAACCA
1 TTCCAACTCAAGGGGTATGGGCCAAAAGCTCACCTCATCCTAA-GGTTAGGATGTCTTGTAACCA
* *
29939753 GGGGTAGATTTAAGTGGATTGGTATGGGCCCCGACCCCCTCTAAAATGGAATTTTGATCTTT
65 GGGGCAGATTTAAGTGGATTGGTATGGGCCCCGACCCCCTCTAAAATGAAATTTTGATCTTT
29939815 T
1 T
29939816 CCGCTTTAAA
Statistics
Matches: 121, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
126 42 0.35
127 79 0.65
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (126 bp):
TTCCAACTCAAGGGGTATGGGCCAAAAGCTCACCTCATCCTAAGGTTAGGATGTCTTGTAACCAG
GGGCAGATTTAAGTGGATTGGTATGGGCCCCGACCCCCTCTAAAATGAAATTTTGATCTTT
Found at i:29944734 original size:6 final size:6
Alignment explanation
Indices: 29944715--29944794 Score: 51
Period size: 6 Copynumber: 13.8 Consensus size: 6
29944705 TATCTTAAGA
* ** *
29944715 TTAAAT TT-ATT TTAAAT TTAAAT TT-GTT TTAAGT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * *
29944760 TTAAGT TTAAAA TT-ATT TTAAACT TAAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAA
29944795 AAAGTATCCC
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
5 14 0.26
6 35 0.65
7 5 0.09
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:29944735 original size:34 final size:34
Alignment explanation
Indices: 29944697--29944794 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 34
29944687 TAAACCTTTT
* **
29944697 TTTAAATTTATCTTAAGATTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTAAATTAAA
* * *
29944731 TTTAAATTTGTTTTAAGTTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAGATTAAATTTAAATTAAA
*
29944765 TTTAAAATTATTTTAA-ACTTAAAATTTAAA
1 TTTAAATTTATTTTAAGA-TT-AAATTTAAA
29944795 AAAGTATCCC
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
34 44 0.83
35 9 0.17
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGATTAAATTTAAATTAAA
Found at i:29944786 original size:17 final size:17
Alignment explanation
Indices: 29944697--29944792 Score: 95
Period size: 17 Copynumber: 5.6 Consensus size: 17
29944687 TAAACCTTTT
*
29944697 TTTAAATTTATCTTAAGA
1 TTTAAATTTATTTTAA-A
29944715 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
29944731 TTTAAATTTGTTTTAAG
1 TTTAAATTTATTTTAAA
** *
29944748 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
*
29944765 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
*
29944782 CTTAAAATTTA
1 -TTTAAATTTA
29944793 AAAAAGTATC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
16 1 0.02
17 55 0.86
18 8 0.12
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:29945486 original size:15 final size:15
Alignment explanation
Indices: 29945466--29945505 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
29945456 TAAAAAAAAT
*
29945466 TAATAATAATGGTAA
1 TAATAATAATGCTAA
29945481 TAATAA-ATATGCTAA
1 TAATAATA-ATGCTAA
29945496 TAATAATAAT
1 TAATAATAAT
29945506 AATAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (15 bp):
TAATAATAATGCTAA
Found at i:29950060 original size:2 final size:2
Alignment explanation
Indices: 29950045--29950081 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
29950035 TTTCTAGTTT
29950045 TA TA TA GTA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29950082 TTGCATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29952406 original size:29 final size:30
Alignment explanation
Indices: 29952346--29952406 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
29952336 AGATGGGAGG
***
29952346 GGAGTAAAAGTTTTAGGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTAGGGGGAAAGTAAAAA
29952376 GGAGTAAAAGTTTTA-GGGGAAAGTAAAAA
1 GGAGTAAAAGTTTTAGGGGGAAAGTAAAAA
29952405 GG
1 GG
29952407 TTTGGAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (30 bp):
GGAGTAAAAGTTTTAGGGGGAAAGTAAAAA
Found at i:29952558 original size:18 final size:18
Alignment explanation
Indices: 29952524--29952569 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
29952514 TTGAGAAAAA
*
29952524 AATTCGAGTTGACTCGAAT
1 AATTCGA-TTAACTCGAAT
29952543 AATTCGATTAACTCGAAT
1 AATTCGATTAACTCGAAT
*
29952561 AACTCGATT
1 AATTCGATT
29952570 CATTTAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (18 bp):
AATTCGATTAACTCGAAT
Found at i:29958132 original size:31 final size:29
Alignment explanation
Indices: 29958076--29958134 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 29
29958066 TATTTTTTAT
29958076 AATTTTAAAGGACTAAATCAAAATTTTAAC
1 AATTTTAAAGGACTAAATC-AAATTTTAAC
29958106 AATTTTAAGAGGATCTAAATGC-AATTTTA
1 AATTTTAA-AGGA-CTAAAT-CAAATTTTA
29958135 CCTTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.31
31 11 0.42
32 6 0.23
33 1 0.04
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (29 bp):
AATTTTAAAGGACTAAATCAAATTTTAAC
Found at i:29958841 original size:20 final size:20
Alignment explanation
Indices: 29958812--29958980 Score: 108
Period size: 20 Copynumber: 8.8 Consensus size: 20
29958802 CCATATTTTT
*
29958812 TAATTATTTACAATTTTAAA
1 TAATTTTTTACAATTTTAAA
* * *
29958832 TAATGTTTTATAATTTTTAA
1 TAATTTTTTACAATTTTAAA
*
29958852 TAATTTTTTACAATTTTTAA
1 TAATTTTTTACAATTTTAAA
* *
29958872 CAATTTTTTTACAATTTT-TA
1 TAA-TTTTTTACAATTTTAAA
* *
29958892 TAA--TTTTAGTAACTTTAAA
1 TAATTTTTTA-CAATTTTAAA
*
29958911 T-ATTTTTTACAATTTT-TA
1 TAATTTTTTACAATTTTAAA
* *
29958929 T-ATGTTTTAAATATTTTAAA
1 TAATTTTTTACA-ATTTTAAA
*
29958949 T-ATTTTTATGC-ATTTT-AA
1 TAATTTTT-TACAATTTTAAA
29958967 T-A-TTTTTACAATTT
1 TAATTTTTTACAATTT
29958981 ACAATTTTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
16 2 0.02
17 13 0.11
18 20 0.17
19 17 0.14
20 51 0.43
21 15 0.13
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (20 bp):
TAATTTTTTACAATTTTAAA
Found at i:29958844 original size:10 final size:9
Alignment explanation
Indices: 29958806--29958980 Score: 72
Period size: 9 Copynumber: 18.4 Consensus size: 9
29958796 TCCAATCCAT
29958806 ATTTTT-TA
1 ATTTTTATA
*
29958814 ATTATTTACA
1 ATT-TTTATA
*
29958824 ATTTTAAATA
1 ATTTT-TATA
29958834 ATGTTTTATA
1 AT-TTTTATA
29958844 ATTTTTAATA
1 ATTTTT-ATA
*
29958854 ATTTTTTACA
1 A-TTTTTATA
*
29958864 ATTTTTAACA
1 ATTTTT-ATA
*
29958874 ATTTTTTTACA
1 A--TTTTTATA
29958885 ATTTTTATA
1 ATTTTTATA
29958894 A-TTTTAGTA
1 ATTTTTA-TA
**
29958903 ACTTTAAATA
1 A-TTTTTATA
* *
29958913 TTTTTTACA
1 ATTTTTATA
29958922 ATTTTTAT-
1 ATTTTTATA
29958930 ATGTTTTA-A
1 AT-TTTTATA
*
29958939 ATATTTTAAA
1 AT-TTTTATA
*
29958949 TATTTTTATGC
1 -ATTTTTAT-A
*
29958960 ATTTTAAT-
1 ATTTTTATA
*
29958968 ATTTTTACA
1 ATTTTTATA
29958977 ATTT
1 ATTT
29958981 ACAATTTTTT
Statistics
Matches: 129, Mismatches: 20, Indels: 35
0.70 0.11 0.19
Matches are distributed among these distances:
8 16 0.12
9 52 0.40
10 39 0.30
11 17 0.13
12 5 0.04
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (9 bp):
ATTTTTATA
Found at i:29959090 original size:21 final size:21
Alignment explanation
Indices: 29959043--29959105 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
29959033 TAATATCTTC
* *
29959043 ACAATTTGTAATAATTTTAAA
1 ACAATTTGTAATAATTTTTAT
* *
29959064 AAAATTTGAAATAATTTTTAT
1 ACAATTTGTAATAATTTTTAT
*
29959085 ACAATTTTTAAT-ATTTTTAT
1 ACAATTTGTAATAATTTTTAT
29959105 A
1 A
29959106 TTTTAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
20 9 0.26
21 26 0.74
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (21 bp):
ACAATTTGTAATAATTTTTAT
Found at i:29959102 original size:10 final size:9
Alignment explanation
Indices: 29959088--29959174 Score: 78
Period size: 9 Copynumber: 9.7 Consensus size: 9
29959078 TTTTTATACA
29959088 ATTTTTAAT
1 ATTTTTAAT
29959097 ATTTTT-AT
1 ATTTTTAAT
29959105 A-TTTTAAT
1 ATTTTTAAT
29959113 -TTTTTACA-
1 ATTTTTA-AT
29959121 ATTTTTATAT
1 ATTTTTA-AT
29959131 ATTTTTAAAT
1 ATTTTT-AAT
29959141 ACTTTTT-AT
1 A-TTTTTAAT
29959150 GATTTTTAAT
1 -ATTTTTAAT
29959160 ATTTTTTAAT
1 A-TTTTTAAT
29959170 -TTTTT
1 ATTTTT
29959175 GGTCCGGTTA
Statistics
Matches: 67, Mismatches: 1, Indels: 21
0.75 0.01 0.24
Matches are distributed among these distances:
7 4 0.06
8 15 0.22
9 22 0.33
10 20 0.30
11 6 0.09
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:29962639 original size:22 final size:22
Alignment explanation
Indices: 29962587--29962640 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
29962577 TCCTCCCATC
29962587 TCAATATCTCCAAACATAAAAG
1 TCAATATCTCCAAACATAAAAG
* **
29962609 AC-ATAATCTCCAAACATAAATT
1 TCAAT-ATCTCCAAACATAAAAG
29962631 TCAATATCTC
1 TCAATATCTC
29962641 AATATATAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (22 bp):
TCAATATCTCCAAACATAAAAG
Found at i:29963646 original size:19 final size:20
Alignment explanation
Indices: 29963622--29963663 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
29963612 TTTTTGTTCC
*
29963622 TTATTTTTTATAATTTC-TT
1 TTATTTTTGATAATTTCATT
*
29963641 TTATTTTTGATATTTTCATT
1 TTATTTTTGATAATTTCATT
29963661 TTA
1 TTA
29963664 AAATTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (20 bp):
TTATTTTTGATAATTTCATT
Found at i:29963842 original size:7 final size:7
Alignment explanation
Indices: 29963830--29963857 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29963820 TAGGTTCAAA
29963830 TTAATTT
1 TTAATTT
29963837 TTAATTT
1 TTAATTT
29963844 TTAATTT
1 TTAATTT
29963851 TTAATTT
1 TTAATTT
29963858 AGTTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTAATTT
Found at i:29964018 original size:22 final size:23
Alignment explanation
Indices: 29963961--29964018 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
29963951 AAGTCTAAAT
*
29963961 TTTAAA-TTATATTAGATTTTGA
1 TTTAAATTTAGATTAGATTTTGA
29963983 TTTGAAATTT-GATTA-ATTTATG-
1 TTT-AAATTTAGATTAGATTT-TGA
29964005 TTTAAATTTAGATT
1 TTTAAATTTAGATT
29964019 TGATAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 6 0.19
22 14 0.45
23 9 0.29
24 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAGATTAGATTTTGA
Found at i:29964154 original size:23 final size:23
Alignment explanation
Indices: 29964096--29964154 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
29964086 TAAATTTTAA
* *
29964096 ATTTAGATTTCAAGTTTTATTAG
1 ATTTAGATTTTAAGTATTATTAG
* * **
29964119 AATAAGAGCTTAAGTATTATTAG
1 ATTTAGATTTTAAGTATTATTAG
29964142 ATTTAGATTTTAA
1 ATTTAGATTTTAA
29964155 ATTTCTTTAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (23 bp):
ATTTAGATTTTAAGTATTATTAG
Found at i:29964781 original size:4 final size:4
Alignment explanation
Indices: 29964774--29964840 Score: 57
Period size: 4 Copynumber: 16.8 Consensus size: 4
29964764 CGGGCAGAAG
* * *
29964774 AAGA AAGA AAGA AAGAA AAGA AAGA AA-A AAGG AAGA AGGA GAGGA AAGA
1 AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAGA -AAGA AAGA
* *
29964823 AAG- AAGA ATGA GAGA AAG
1 AAGA AAGA AAGA AAGA AAG
29964841 GTAGTGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
3 6 0.12
4 37 0.73
5 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:29964795 original size:9 final size:9
Alignment explanation
Indices: 29964769--29964801 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
29964759 ACGAACGGGC
29964769 AGAAGAAGAA
1 AGAA-AAGAA
29964779 AG-AAAGAA
1 AGAAAAGAA
29964787 AGAAAAGAA
1 AGAAAAGAA
29964796 AGAAAA
1 AGAAAA
29964802 AAGGAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.32
9 13 0.59
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AGAAAAGAA
Found at i:29964798 original size:24 final size:25
Alignment explanation
Indices: 29964771--29964840 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 25
29964761 GAACGGGCAG
29964771 AAGAAGAAAGAAAGAAAGA-AAAGA
1 AAGAAGAAAGAAAGAAAGAGAAAGA
* *
29964795 AAGAAAAAAGGAAGAAGGAGAGGAAAGA
1 AAGAAGAAAGAAAGAA--AGA-GAAAGA
* *
29964823 AAGAAGAATGAGAGAAAG
1 AAGAAGAAAGAAAGAAAG
29964841 GTAGTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
24 14 0.39
26 5 0.14
28 17 0.47
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.01
Consensus pattern (25 bp):
AAGAAGAAAGAAAGAAAGAGAAAGA
Found at i:29967842 original size:28 final size:28
Alignment explanation
Indices: 29967811--29967900 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
29967801 TCTAACTTAT
29967811 GGTTTAAGGTTTTAAATTTAGGGTTTAG
1 GGTTTAAGGTTTTAAATTTAGGGTTTAG
* *
29967839 GGTTT-AGTATTTTAAATTTAGGGTTTAA
1 GGTTTAAG-GTTTTAAATTTAGGGTTTAG
* * * *
29967867 GGTGTACGG-TATAAGCTTTAGGGTTTAG
1 GGTTTAAGGTTTTAA-ATTTAGGGTTTAG
29967895 GGTTTA
1 GGTTTA
29967901 TAAGTATAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 6 0.12
28 43 0.86
29 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.44
Consensus pattern (28 bp):
GGTTTAAGGTTTTAAATTTAGGGTTTAG
Found at i:29967844 original size:14 final size:14
Alignment explanation
Indices: 29967827--29967900 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
29967817 AGGTTTTAAA
*
29967827 TTTAGGGTTTAGGG
1 TTTAGGGTTTAAGG
** *
29967841 TTTAGTATTTTAA-A
1 TTTAG-GGTTTAAGG
29967855 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
* * * *
29967869 TGTACGGTATAAGC
1 TTTAGGGTTTAAGG
*
29967883 TTTAGGGTTTAGGG
1 TTTAGGGTTTAAGG
29967897 TTTA
1 TTTA
29967901 TAAGTATAAA
Statistics
Matches: 42, Mismatches: 16, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
13 5 0.12
14 33 0.79
15 4 0.10
ACGTcount: A:0.23, C:0.03, G:0.30, T:0.45
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:29970087 original size:16 final size:15
Alignment explanation
Indices: 29970066--29970115 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
29970056 GGATGGGGAT
29970066 ATTATTTTGGTAATTA
1 ATTATTTT-GTAATTA
*
29970082 ATTATTTTTTATATT-
1 ATTATTTTGTA-ATTA
29970097 A-TATTTTAGTAATTA
1 ATTATTTT-GTAATTA
29970112 ATTA
1 ATTA
29970116 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (15 bp):
ATTATTTTGTAATTA
Found at i:29970615 original size:16 final size:15
Alignment explanation
Indices: 29970578--29970615 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
29970568 CTTAATTTAC
29970578 TCAATTAAATAAAAA
1 TCAATTAAATAAAAA
29970593 -C-ATTAAATAACAAA
1 TCAATTAAATAA-AAA
29970607 TCAATTAAA
1 TCAATTAAA
29970616 AATTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 9 0.45
14 4 0.20
15 1 0.05
16 6 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (15 bp):
TCAATTAAATAAAAA
Found at i:29970867 original size:12 final size:11
Alignment explanation
Indices: 29970845--29970885 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 11
29970835 ATTTCTCTCC
29970845 TTCTTCTTTCT
1 TTCTTCTTTCT
29970856 TTCTTCCTTTCT
1 TTCTT-CTTTCT
29970868 TTCTT-TTT-T
1 TTCTTCTTTCT
29970877 TTCTTCTTT
1 TTCTTCTTT
29970886 TTCTTTGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.21
10 6 0.21
11 5 0.18
12 11 0.39
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTCTTCTTTCT
Found at i:29971426 original size:12 final size:12
Alignment explanation
Indices: 29971411--29971447 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
29971401 CTTAGTTTGG
29971411 TTAGATTTAGAT
1 TTAGATTTAGAT
29971423 TTAGATTTA-AT
1 TTAGATTTAGAT
*
29971434 TTAGGTTTAGAT
1 TTAGATTTAGAT
29971446 TT
1 TT
29971448 TAAGTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (12 bp):
TTAGATTTAGAT
Found at i:29971437 original size:17 final size:17
Alignment explanation
Indices: 29971415--29971447 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29971405 GTTTGGTTAG
29971415 ATTTAGATTTAGATTTA
1 ATTTAGATTTAGATTTA
*
29971432 ATTTAGGTTTAGATTT
1 ATTTAGATTTAGATTT
29971448 TAAGTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (17 bp):
ATTTAGATTTAGATTTA
Found at i:29971823 original size:72 final size:72
Alignment explanation
Indices: 29971737--29971881 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
29971727 AACTCGTTTG
29971737 AAATTATTTCCCTAACCAATAAATAACCTTGTAACTCAACACCCAATATTTAACTTACCGACGAC
1 AAATTATTTCCCTAACCAATAAATAACCTTGTAACTCAACACCCAATATTTAACTTACCGACGAC
29971802 ATTAAGA
66 ATTAAGA
29971809 AAATTATTTCCCTAACCAATAAATAACCTTGTAACTCAACACCCAATATTTAACTTACCGACGAC
1 AAATTATTTCCCTAACCAATAAATAACCTTGTAACTCAACACCCAATATTTAACTTACCGACGAC
29971874 ATTAAGA
66 ATTAAGA
29971881 A
1 A
29971882 CAAGAGAGAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (72 bp):
AAATTATTTCCCTAACCAATAAATAACCTTGTAACTCAACACCCAATATTTAACTTACCGACGAC
ATTAAGA
Found at i:29983687 original size:41 final size:41
Alignment explanation
Indices: 29983588--29983815 Score: 242
Period size: 41 Copynumber: 5.5 Consensus size: 41
29983578 GGTGTATAAA
* * * * * *
29983588 AAGGAAGACTCATGTCTCGGGTTGAGCATAAGA-AATTGTAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTA-TGAAT
* * *
29983629 AAATGGAAGACTTATGTCTCGAGATAAGAATGAGATTACGAAT
1 -AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
*
29983672 AAGGAAGACTCATGTCTTGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * *
29983713 AAGGAAGACTCATGTCTTGAAATGAGAATGAGATTTTGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * **
29983754 AAGGAAGACTCATGTCTCAAGATGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* *
29983795 AAAGGAAGACTTATGACTCGA
1 -AAGGAAGACTCATGTCTCGA
29983816 AAGAGCATAA
Statistics
Matches: 158, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
41 108 0.68
42 21 0.13
43 28 0.18
44 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
Found at i:29989452 original size:3 final size:3
Alignment explanation
Indices: 29989432--29989466 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
29989422 GTCCCCTATG
* *
29989432 TAT TAA TAT TAC TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29989467 AATTTCAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:29990148 original size:13 final size:13
Alignment explanation
Indices: 29990130--29990159 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29990120 GGATTAAATC
*
29990130 AAAATTCATGTAT
1 AAAATTCATATAT
29990143 AAAATTCATATAT
1 AAAATTCATATAT
29990156 AAAA
1 AAAA
29990160 CTGCATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATTCATATAT
Found at i:29997030 original size:43 final size:43
Alignment explanation
Indices: 29996982--29997070 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
29996972 ATAGTTTTAA
* * * *
29996982 ATTAAATTATAATTT-TTTTAAATGTTTAATTATTACAATTTCT
1 ATTAAATTAT-ATTTAATTTAAATATATAATTATCACAATTTCT
* *
29997025 ATTAAATTATATTTAATTTAATTATATAATTATCATAATTTCT
1 ATTAAATTATATTTAATTTAAATATATAATTATCACAATTTCT
29997068 ATT
1 ATT
29997071 TTACTTAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 4 0.10
43 35 0.90
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (43 bp):
ATTAAATTATATTTAATTTAAATATATAATTATCACAATTTCT
Found at i:29998667 original size:16 final size:15
Alignment explanation
Indices: 29998646--29998710 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 15
29998636 TTTTAAAAAT
*
29998646 TTGATTAATAGTTAA
1 TTGATTAATAATTAA
29998661 TTCGATTCAA-AATTAA
1 TT-GATT-AATAATTAA
29998677 TTGATTAATCAAATTAA
1 TTGATTAAT--AATTAA
*
29998694 TTGAATTAATAAATAA
1 TTG-ATTAATAATTAA
29998710 T
1 T
29998711 ATTATAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 2 0.05
15 6 0.14
16 17 0.40
17 11 0.26
18 6 0.14
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (15 bp):
TTGATTAATAATTAA
Found at i:29998692 original size:17 final size:17
Alignment explanation
Indices: 29998670--29998707 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
29998660 ATTCGATTCA
29998670 AAATTAATTG-ATTAAT
1 AAATTAATTGAATTAAT
29998686 CAAATTAATTGAATTAAT
1 -AAATTAATTGAATTAAT
29998704 AAAT
1 AAAT
29998708 AATATTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (17 bp):
AAATTAATTGAATTAAT
Found at i:30005045 original size:22 final size:22
Alignment explanation
Indices: 30005019--30005060 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30005009 TTAATATACT
30005019 ATTTGGTA-TATGAGTTTTTTCA
1 ATTTGGTACT-TGAGTTTTTTCA
*
30005041 ATTTGTTACTTGAGTTTTTT
1 ATTTGGTACTTGAGTTTTTT
30005061 TTCCATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.19, C:0.05, G:0.17, T:0.60
Consensus pattern (22 bp):
ATTTGGTACTTGAGTTTTTTCA
Found at i:30006593 original size:18 final size:19
Alignment explanation
Indices: 30006557--30006595 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30006547 AAACATTATC
* *
30006557 TAAATAAAAAGTATGAAAA
1 TAAAAAAAAAGTATAAAAA
30006576 TAAAAAAAAAGTA-AAAAA
1 TAAAAAAAAAGTATAAAAA
30006594 TA
1 TA
30006596 TTAGAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (19 bp):
TAAAAAAAAAGTATAAAAA
Found at i:30013215 original size:59 final size:59
Alignment explanation
Indices: 30013138--30013305 Score: 264
Period size: 59 Copynumber: 2.8 Consensus size: 59
30013128 TGGGTTCTCA
* * * * * *
30013138 ATTAAATGTTACAGTATAAATATCATGTGTACAAAAATATTCAAAAGAATTTTTATTTT
1 ATTAAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTATATTTT
*
30013197 ATTAAATGATATAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTATATTTT
1 ATTAAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTATATTTT
*
30013256 ATTAAAAGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAAC
1 ATTAAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAAC
30013306 ATCAATGCAT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 100 1.00
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.34
Consensus pattern (59 bp):
ATTAAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTATATTTT
Found at i:30017196 original size:16 final size:16
Alignment explanation
Indices: 30017175--30017220 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
30017165 GTATATTTTA
30017175 ATTTAATATTAAAGTG
1 ATTTAATATTAAAGTG
30017191 ATTTAATATT--A---
1 ATTTAATATTAAAGTG
30017202 ATTTAATATTAAAGTG
1 ATTTAATATTAAAGTG
30017218 ATT
1 ATT
30017221 AAGTTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
11 10 0.40
13 1 0.04
14 1 0.04
16 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
ATTTAATATTAAAGTG
Found at i:30017205 original size:11 final size:11
Alignment explanation
Indices: 30017144--30017213 Score: 54
Period size: 11 Copynumber: 6.2 Consensus size: 11
30017134 TATTAAATTA
30017144 AATTTAATACTT
1 AATTTAATA-TT
*
30017156 ATTTTAATAGTAT
1 AATTTAATA-T-T
*
30017169 ATTTTAAT-TT
1 AATTTAATATT
*
30017179 AATATTAA-AGT
1 AAT-TTAATATT
*
30017190 GATTTAATATT
1 AATTTAATATT
30017201 AATTTAATATT
1 AATTTAATATT
30017212 AA
1 AA
30017214 AGTGATTAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 7 0.15
11 22 0.47
12 9 0.19
13 9 0.19
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (11 bp):
AATTTAATATT
Found at i:30017948 original size:38 final size:38
Alignment explanation
Indices: 30017904--30018010 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 38
30017894 CCACCCTATT
* *
30017904 GAATACATGTTGGA-CATGTTTACTATTAGTGATGGATG
1 GAATACATGTT-GACCATGTTTACTACTAGTGATGAATG
* * * *
30017942 GAATACATGATGACCATGTTTGCTGCTAGTGATGAATT
1 GAATACATGTTGACCATGTTTACTACTAGTGATGAATG
* * * *
30017980 GAATATATGTTAAGCATGTTTACTGCTAGTG
1 GAATACATGTTGACCATGTTTACTACTAGTG
30018011 TTGTTTTGTT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 2 0.04
38 55 0.96
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.36
Consensus pattern (38 bp):
GAATACATGTTGACCATGTTTACTACTAGTGATGAATG
Found at i:30018209 original size:119 final size:119
Alignment explanation
Indices: 30017998--30018233 Score: 436
Period size: 119 Copynumber: 2.0 Consensus size: 119
30017988 GTTAAGCATG
30017998 TTTACTGCTAGTGTTGTTTTGTTCCATTACAAAGCATGTCATGCATTGCATGGGGTGGGATGCTA
1 TTTACTGCTAGTGTTGTTTTGTTCCATTACAAAGCATGTCATGCATTGCATGGGGTGGGATGCTA
* * * *
30018063 TGTATGGAGGAAGAGTGGCAGTCTATTAATCTGTAAATAGTGTGGTTCGTTCTT
66 TGTATGGAGGAAGAGTGGCAATCTATTAATCTATAAACAGTGCGGTTCGTTCTT
30018117 TTTACTGCTAGTGTTGTTTTGTTCCATTACAAAGCATGTCATGCATTGCATGGGGTGGGATGCTA
1 TTTACTGCTAGTGTTGTTTTGTTCCATTACAAAGCATGTCATGCATTGCATGGGGTGGGATGCTA
30018182 TGTATGGAGGAAGAGTGGCAATCTATTAATCTATAAACAGTGCGGTTCGTTC
66 TGTATGGAGGAAGAGTGGCAATCTATTAATCTATAAACAGTGCGGTTCGTTC
30018234 ATGAACCAAG
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 113 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (119 bp):
TTTACTGCTAGTGTTGTTTTGTTCCATTACAAAGCATGTCATGCATTGCATGGGGTGGGATGCTA
TGTATGGAGGAAGAGTGGCAATCTATTAATCTATAAACAGTGCGGTTCGTTCTT
Found at i:30018287 original size:42 final size:43
Alignment explanation
Indices: 30018236--30018336 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 43
30018226 GTTCGTTCAT
*
30018236 GAACCAAGTGGCAATTATTATATGCAAATATGTTGTGC-ATCCAC
1 GAACCAAGTGGCAATT-TTATATGCAAATATGTGGTGCAAT-CAC
* * *
30018280 -AA-CAAGTGGC-AGTTTATCTGCAAATATGTGGTTCAATCAC
1 GAACCAAGTGGCAATTTTATATGCAAATATGTGGTGCAATCAC
30018320 GAACCAAGTGGCAATTT
1 GAACCAAGTGGCAATTT
30018337 ATCTATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
40 21 0.44
41 6 0.12
42 16 0.33
43 5 0.10
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (43 bp):
GAACCAAGTGGCAATTTTATATGCAAATATGTGGTGCAATCAC
Found at i:30018338 original size:42 final size:42
Alignment explanation
Indices: 30018236--30018340 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
30018226 GTTCGTTCAT
* *
30018236 GAACCAAGTGGCAATTATTATATGCAAATATGTTGTGCATCCAC
1 GAACCAAGTGGCAA-T-TTATCTGCAAATATGTGGTGCATCCAC
* *
30018280 -AA-CAAGTGGCAGTTTATCTGCAAATATGTGGTTCAAT-CAC
1 GAACCAAGTGGCAATTTATCTGCAAATATGTGGTGC-ATCCAC
30018320 GAACCAAGTGGCAATTTATCT
1 GAACCAAGTGGCAATTTATCT
30018341 ATAAATGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
40 21 0.40
41 5 0.09
42 25 0.47
43 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (42 bp):
GAACCAAGTGGCAATTTATCTGCAAATATGTGGTGCATCCAC
Found at i:30019517 original size:24 final size:24
Alignment explanation
Indices: 30019474--30019520 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
30019464 GTATATATAC
30019474 TTTTTAATATTGAACAATTAATTGT
1 TTTTTAATATT-AACAATTAATTGT
30019499 TTTTTAATATT-ACATATTAATT
1 TTTTTAATATTAACA-ATTAATT
30019521 TTTAATAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 7 0.33
25 11 0.52
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTTTAATATTAACAATTAATTGT
Found at i:30020301 original size:19 final size:19
Alignment explanation
Indices: 30020277--30020331 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
30020267 TAAAAAATTT
*
30020277 AATTTTTATATTTTTTAAC
1 AATTTTTATATTTTTTAAA
* *
30020296 AATTTTTA-AATTTTAAAA
1 AATTTTTATATTTTTTAAA
30020314 ATATTTTTTATATTTTTT
1 A-A-TTTTTATATTTTTT
30020332 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 8 0.29
19 9 0.32
20 6 0.21
21 5 0.18
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTTTTATATTTTTTAAA
Found at i:30020341 original size:39 final size:39
Alignment explanation
Indices: 30020255--30020353 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
30020245 GAATTTAATT
* * *
30020255 AATTTTTAAAATTAAAAAATTTAATTTTTATATTTTTTAAC
1 AATTTTTAAATTTTAAAAA--TATTTTTTATATTTTTTAAC
30020296 AATTTTTAAATTTTAAAAATATTTTTTATATTTTTTGAA-
1 AATTTTTAAATTTTAAAAATATTTTTTATATTTTTT-AAC
**
30020335 TTTTTTTAAATTTTAAAAA
1 AATTTTTAAATTTTAAAAA
30020354 ATTAATTAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
39 33 0.63
40 2 0.04
41 17 0.33
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (39 bp):
AATTTTTAAATTTTAAAAATATTTTTTATATTTTTTAAC
Found at i:30020348 original size:9 final size:9
Alignment explanation
Indices: 30020279--30020348 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
30020269 AAAAATTTAA
*
30020279 TTTTTATAT
1 TTTTTAAAT
*
30020288 TTTTTAACAA
1 TTTTTAA-AT
30020298 TTTTTAAAT
1 TTTTTAAAT
**
30020307 TTTAAAAATAT
1 TTT-TTAA-AT
*
30020318 TTTTTATAT
1 TTTTTAAAT
*
30020327 TTTTTGAATT
1 TTTTT-AAAT
30020337 TTTTTAAAT
1 TTTTTAAAT
30020346 TTT
1 TTT
30020349 AAAAAATTAA
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
9 23 0.50
10 18 0.39
11 5 0.11
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:30033238 original size:7 final size:8
Alignment explanation
Indices: 30033219--30033244 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
30033209 AAATAGTGGA
30033219 AAAAATTG
1 AAAAATTG
30033227 AAAAATTG
1 AAAAATTG
30033235 AAAAATTG
1 AAAAATTG
30033243 AA
1 AA
30033245 CACACAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (8 bp):
AAAAATTG
Found at i:30044950 original size:29 final size:28
Alignment explanation
Indices: 30044914--30045013 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 28
30044904 GCAAAATTGT
30044914 AATTTTGGAGAAATCGGGGTTAAAAATGG
1 AATTTTGGA-AAATCGGGGTTAAAAATGG
* * *
30044943 AACTTTGGAAAGTTCGAGGGGTAAAAATGG
1 AATTTTGGAAA-ATCG-GGGTTAAAAATGG
* *
30044973 TAAATTTTGGTAAAACCGGGGTTAAAAATGA
1 --AATTTTGG-AAAATCGGGGTTAAAAATGG
30045004 AATTTTGGAA
1 AATTTTGGAA
30045014 GGTTTTGGGG
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
28 4 0.07
29 19 0.33
30 12 0.21
31 11 0.19
32 9 0.16
33 3 0.05
ACGTcount: A:0.39, C:0.05, G:0.28, T:0.28
Consensus pattern (28 bp):
AATTTTGGAAAATCGGGGTTAAAAATGG
Found at i:30045026 original size:30 final size:30
Alignment explanation
Indices: 30044990--30045158 Score: 171
Period size: 30 Copynumber: 5.6 Consensus size: 30
30044980 TGGTAAAACC
* * *
30044990 GGGGTTAAAAATGAAATTTT-GGAAGGTTTT
1 GGGGTT-AAAATGTAATTTTAGAAAAGTTTT
* **
30045020 GGGGTTAAAATATAATTTTAGAAAAAATTT
1 GGGGTTAAAATGTAATTTTAGAAAAGTTTT
* *
30045050 AGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTTAAAATGTAATTTTAGAAAAGTTTT
* *
30045080 AGGGTCAAAATGTAATTTTAGAAAAGTTTT
1 GGGGTTAAAATGTAATTTTAGAAAAGTTTT
* * *
30045110 GAGGTTAAAATGTAATTTTCA-AAGACTTTT
1 GGGGTTAAAATGTAATTTT-AGAAAAGTTTT
* *
30045140 AGGGTTAAAATATAATTTT
1 GGGGTTAAAATGTAATTTT
30045159 GGATAGTTTA
Statistics
Matches: 116, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
29 11 0.09
30 104 0.90
31 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTAGAAAAGTTTT
Found at i:30045059 original size:60 final size:58
Alignment explanation
Indices: 30044991--30045158 Score: 201
Period size: 60 Copynumber: 2.8 Consensus size: 58
30044981 GGTAAAACCG
* *
30044991 GGGTTAAAAATGAAATTTTGGAAGGTTTTGGGGTTAAAATATAATTTTAGAAAAAATTTA
1 GGGTT-AAAATGTAATTTTGGAAGGTTTTAGGGTTAAAATATAATTTTAG-AAAAATTTA
* * * * *
30045051 GGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTT
1 GGGTTAAAATGTAATTTTGG-AAGGTTTTAGGGTTAAAATATAATTTTAGAAAAATTTA
** *
30045110 GAGGTTAAAATGTAATTTTCAAAGACTTTTAGGGTTAAAATATAATTTT
1 G-GGTTAAAATGTAATTTTGGAAG-GTTTTAGGGTTAAAATATAATTTT
30045159 GGATAGTTTA
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 24 0.26
60 68 0.74
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (58 bp):
GGGTTAAAATGTAATTTTGGAAGGTTTTAGGGTTAAAATATAATTTTAGAAAAATTTA
Found at i:30045109 original size:90 final size:89
Alignment explanation
Indices: 30044997--30045161 Score: 224
Period size: 90 Copynumber: 1.8 Consensus size: 89
30044987 ACCGGGGTTA
* * *
30044997 AAAATGAAATTTTGGAAGGTTTTGGGGTTAAAATATAATTTT-AGAAAAAATTTAGGGTTAAAAT
1 AAAATGAAATTTTGAAAAGTTTTGAGGTTAAAATATAATTTTCA-AAAAAATTTAGGGTTAAAAT
*
30045061 GTAATTTTGGAAAAGTTTTAGGGTC
65 ATAATTTTGGAAAAGTTTTAGGGTC
* * * **
30045086 AAAATGTAATTTTAGAAAAGTTTTGAGGTTAAAATGTAATTTTCAAAGACTTTTAGGGTTAAAAT
1 AAAATGAAATTTT-GAAAAGTTTTGAGGTTAAAATATAATTTTCAAAAAAATTTAGGGTTAAAAT
30045151 ATAATTTTGGA
65 ATAATTTTGGA
30045162 TAGTTTAGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
89 12 0.18
90 52 0.80
91 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (89 bp):
AAAATGAAATTTTGAAAAGTTTTGAGGTTAAAATATAATTTTCAAAAAAATTTAGGGTTAAAATA
TAATTTTGGAAAAGTTTTAGGGTC
Found at i:30046250 original size:15 final size:15
Alignment explanation
Indices: 30046233--30046284 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
30046223 CCTTCTTTTT
*
30046233 TTATTATAAATATTT
1 TTATTATAAATATTA
*
30046248 TTATT-TAAACCATTA
1 TTATTATAAA-TATTA
* *
30046263 TTATTATTATTATTA
1 TTATTATAAATATTA
30046278 TTATTAT
1 TTATTAT
30046285 TATTAATGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 4 0.13
15 24 0.80
16 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATAAATATTA
Found at i:30046267 original size:3 final size:3
Alignment explanation
Indices: 30046259--30046289 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30046249 TATTTAAACC
30046259 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
30046290 ATGGCTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:30047007 original size:6 final size:6
Alignment explanation
Indices: 30046996--30047041 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
30046986 TTATAATAAT
** *
30046996 TTTAAA TTTAAA -TTAAA TCCAAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
30047042 ATAAATTCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:30047011 original size:11 final size:11
Alignment explanation
Indices: 30046997--30047048 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
30046987 TATAATAATT
30046997 TTAAATTTAAA
1 TTAAATTTAAA
**
30047008 TTAAATCCAAA
1 TTAAATTTAAA
30047019 TTTAAA-TTAAA
1 -TTAAATTTAAA
30047030 TTCAAATTTAAA
1 TT-AAATTTAAA
*
30047042 ATAAATT
1 TTAAATT
30047049 CAAAATGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
10 2 0.06
11 20 0.61
12 11 0.33
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:30047019 original size:17 final size:17
Alignment explanation
Indices: 30046999--30047052 Score: 90
Period size: 17 Copynumber: 3.2 Consensus size: 17
30046989 TAATAATTTT
*
30046999 AAATTTAAATTAAATCC
1 AAATTTAAATTAAATTC
30047016 AAATTTAAATTAAATTC
1 AAATTTAAATTAAATTC
*
30047033 AAATTTAAAATAAATTC
1 AAATTTAAATTAAATTC
30047050 AAA
1 AAA
30047053 ATGGTTTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTAAATTAAATTC
Found at i:30047471 original size:92 final size:92
Alignment explanation
Indices: 30047353--30047951 Score: 993
Period size: 92 Copynumber: 6.5 Consensus size: 92
30047343 AATGATTTGA
* ** * * *
30047353 TATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAATGATGTTTATGCTTCATCTTACTCTCAC
1 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
*
30047418 TTCAACTGT-AGAGGGACGAAGGCTTGT
66 TTCAA-TTTCAGAGGGACGAAGGCTTGT
* * *
30047445 TATCTAACTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGATCCTTCTTCTTACTCTTAC
1 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
*
30047510 TTCGATTTCAGAGGGACGAAGGCTTGT
66 TTCAATTTCAGAGGGACGAAGGCTTGT
*
30047537 TATCCAGCTTTACTTCAATTTCAAAAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
1 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
*
30047602 TTCGATTTCAGAGGGACGAAGAAGGCTTGT
66 TTCAATTTCAGAGGGAC---GAAGGCTTGT
30047632 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
1 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
*
30047697 TTCGATTTCAGAGGGACGAAGGCTTGT
66 TTCAATTTCAGAGGGACGAAGGCTTGT
30047724 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
1 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
30047789 TTCAATTTCAGAGGGACGAAGGCTTGT
66 TTCAATTTCAGAGGGACGAAGGCTTGT
* *
30047816 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTAC
1 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
* *
30047881 TTTAATTTCAGAGGAACGAAGGCTTGT
66 TTCAATTTCAGAGGGACGAAGGCTTGT
30047908 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTT
1 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTT
30047952 AGATTGATGT
Statistics
Matches: 484, Mismatches: 19, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
91 2 0.00
92 391 0.81
95 91 0.19
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (92 bp):
TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
TTCAATTTCAGAGGGACGAAGGCTTGT
Found at i:30047853 original size:279 final size:276
Alignment explanation
Indices: 30047315--30047951 Score: 994
Period size: 279 Copynumber: 2.3 Consensus size: 276
30047305 CGAGGTTTCG
* ** * *
30047315 TCTTGCTCTTACTTCAATTTCA-A--AAAGGAATGATTTGATATCCAGCTCTACTTCAATTTCAA
1 TCTTACTCTTACTTCAATTTCAGAGGAAA-GAA-GGCTTGTTATCCAGCTTTACTTCAATTTCAA
* *
30047377 GAGGATAGGAAAATGATGTTTATGCTTCATCTTACTCTCACTTCAACTGTAGAGGGACGAAGGCT
64 GAGGATAGGAAAATGATGTTGATCCTTCATCTTACTCTCACTTCAACTGTAGAGGGACGAAGGCT
*
30047442 TGTTATCTAACTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGATCCTTCTTCTTACTCT
129 TGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGATCCTTCTTCTTACTCT
*
30047507 TACTTCGATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAAAGGATAGGAA
194 TACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAAAGGATAGGAA
*
30047572 AATGATGTTGGTCCTTCT
259 AATGATGTTGGTCCTTCA
*
30047590 TCTTACTCTTACTTCGATTTCAGAGGGACGAAGAAGGCTTGTTATCCAGCTTTACTTCAATTTCA
1 TCTTACTCTTACTTCAATTTCAGA-GGA--AAGAAGGCTTGTTATCCAGCTTTACTTCAATTTCA
* * * * *
30047655 AGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTACTTCGA-TTTCAGAGGGACGAAGG
63 AGAGGATAGGAAAATGATGTTGATCCTTCATCTTACTCTCACTTCAACTGT-AGAGGGACGAAGG
* *
30047719 CTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACT
127 CTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGATCCTTCTTCTTACT
*
30047784 CTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGG
192 CTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAAAGGATAGG
*
30047849 AAAATGATGTTGGTGCTTCA
257 AAAATGATGTTGGTCCTTCA
* *
30047869 TCTTACTCTTACTTTAATTTCAGAGGAACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGAAAGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
30047934 GGATAGGAAAATGATGTT
66 GGATAGGAAAATGATGTT
30047952 AGATTGATGT
Statistics
Matches: 332, Mismatches: 23, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
275 20 0.06
276 56 0.17
278 5 0.02
279 246 0.74
280 3 0.01
281 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (276 bp):
TCTTACTCTTACTTCAATTTCAGAGGAAAGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
GGATAGGAAAATGATGTTGATCCTTCATCTTACTCTCACTTCAACTGTAGAGGGACGAAGGCTTG
TTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGATCCTTCTTCTTACTCTTA
CTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAAAGGATAGGAAAA
TGATGTTGGTCCTTCA
Found at i:30060109 original size:30 final size:30
Alignment explanation
Indices: 30060057--30060211 Score: 199
Period size: 30 Copynumber: 5.2 Consensus size: 30
30060047 TCAAAAACAA
* *
30060057 AATTTTGG-AAGGTTTTGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTTGAGGTTAAAATGT
30060086 AATTTTGGAAAAGTTTTGAGGTTAAAATGT
1 AATTTTGGAAAAGTTTTGAGGTTAAAATGT
* *
30060116 AATTTTGGAAAGGTTTT-AGGGTCAAAATGT
1 AATTTTGGAAAAGTTTTGA-GGTTAAAATGT
* *
30060146 AATTTTAGAATAGTTTTGAGGTTAAAATGT
1 AATTTTGGAAAAGTTTTGAGGTTAAAATGT
* *
30060176 AATTTT-CAAAGAGTTTTGAGGTTAAAATAT
1 AATTTTGGAAA-AGTTTTGAGGTTAAAATGT
30060206 AATTTT
1 AATTTT
30060212 TGGATAGTTT
Statistics
Matches: 111, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
29 11 0.10
30 99 0.89
31 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTTGAGGTTAAAATGT
Found at i:30060113 original size:90 final size:88
Alignment explanation
Indices: 30059989--30060211 Score: 222
Period size: 90 Copynumber: 2.5 Consensus size: 88
30059979 ATTAGGGCTA
* * *
30059989 AAAATGGAACTTTGG-AAAG-TTTGAGGGGTAAAAATGGTAAATTTTGGTAAA-ATTAGGGTCAA
1 AAAATGTAATTTTGGAAAAGTTTTGA--GGTTAAAAT-GT-AATTTTGG-AAAGATTAGGGTC-A
* * *
30060051 AAACAAAATTTTGGAA-GGTTTTGGGGTT
60 AAACAAAATTTTAGAATAGTTTTGAGGTT
* *
30060079 AAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGTAATTTTGGAAAGGTTTTAGGGTCAAAAT
1 AAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGTAATTTTGGAAA-G-ATTAGGGTCAAAAC
**
30060144 GTAATTTTAGAATAGTTTTGAGGTT
64 AAAATTTTAGAATAGTTTTGAGGTT
* *
30060169 AAAATGTAATTTT-CAAAGAGTTTTGAGGTTAAAATATAATTTT
1 AAAATGTAATTTTGGAAA-AGTTTTGAGGTTAAAATGTAATTTT
30060212 TGGATAGTTT
Statistics
Matches: 114, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
87 3 0.03
88 8 0.07
89 18 0.16
90 76 0.67
91 4 0.04
92 5 0.04
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (88 bp):
AAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGTAATTTTGGAAAGATTAGGGTCAAAACAA
AATTTTAGAATAGTTTTGAGGTT
Found at i:30060129 original size:60 final size:60
Alignment explanation
Indices: 30060057--30060211 Score: 224
Period size: 60 Copynumber: 2.6 Consensus size: 60
30060047 TCAAAAACAA
*
30060057 AATTTTGG-AAGGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGT
1 AATTTTGGAAAGGTTTTGGGGTTAAAATGTAATTTTAGAAAAGTTTTGAGGTTAAAATGT
* * *
30060116 AATTTTGGAAAGGTTTTAGGGTCAAAATGTAATTTTAGAATAGTTTTGAGGTTAAAATGT
1 AATTTTGGAAAGGTTTTGGGGTTAAAATGTAATTTTAGAAAAGTTTTGAGGTTAAAATGT
* * *
30060176 AATTTT-CAAAGAGTTTTGAGGTTAAAATATAATTTT
1 AATTTTGGAAAG-GTTTTGGGGTTAAAATGTAATTTT
30060212 TGGATAGTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
59 12 0.14
60 73 0.86
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (60 bp):
AATTTTGGAAAGGTTTTGGGGTTAAAATGTAATTTTAGAAAAGTTTTGAGGTTAAAATGT
Found at i:30061856 original size:16 final size:17
Alignment explanation
Indices: 30061835--30061866 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
30061825 CAGGGCATGG
30061835 TGGAGCTGGTG-GCAGA
1 TGGAGCTGGTGAGCAGA
30061851 TGGAGCTGGTGAGCAG
1 TGGAGCTGGTGAGCAG
30061867 CAAATCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.19, C:0.12, G:0.50, T:0.19
Consensus pattern (17 bp):
TGGAGCTGGTGAGCAGA
Found at i:30062072 original size:6 final size:6
Alignment explanation
Indices: 30062061--30062123 Score: 51
Period size: 6 Copynumber: 11.0 Consensus size: 6
30062051 TTATAATAAT
** **
30062061 TTTAAA TTTAAA -TTAAA TCCAAA TTTAAA -TTAAA TCCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
30062107 -ATAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA
30062124 ACAAATTCAA
Statistics
Matches: 42, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
5 14 0.33
6 28 0.67
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:30062084 original size:17 final size:17
Alignment explanation
Indices: 30062064--30062112 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
30062054 TAATAATTTT
30062064 AAATTTAAATTAAATCC
1 AAATTTAAATTAAATCC
30062081 AAATTTAAATTAAATCC
1 AAATTTAAATTAAATCC
*
30062098 AAATTTAAAATAAAT
1 AAATTTAAATTAAAT
30062113 TTAATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTAAATTAAATCC
Found at i:30062121 original size:17 final size:17
Alignment explanation
Indices: 30062048--30062134 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
30062038 TTGGACATTG
* * *
30062048 AATTTATAATAATTTTA
1 AATTTAAAATAAATTCA
* *
30062065 AATTTAAATTAAATCCA
1 AATTTAAAATAAATTCA
* *
30062082 AATTTAAATTAAATCCA
1 AATTTAAAATAAATTCA
*
30062099 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* *
30062116 ATTTTAAAACAAATTCA
1 AATTTAAAATAAATTCA
30062133 AA
1 AA
30062135 ATGGTTTGAT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 58 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:30064158 original size:14 final size:15
Alignment explanation
Indices: 30064139--30064167 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30064129 ATATCAAATC
30064139 AATAAA-TTTAACAA
1 AATAAATTTTAACAA
30064153 AATAAATTTTAACAA
1 AATAAATTTTAACAA
30064168 TTAGACTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAATTTTAACAA
Found at i:30065057 original size:368 final size:366
Alignment explanation
Indices: 30064382--30065121 Score: 1300
Period size: 368 Copynumber: 2.0 Consensus size: 366
30064372 TATTTTTATT
* *
30064382 AGATATAATATTTTGGTGTAAAATGGTTAAAGGAAGAATAGTTTAGTTAATACTTGTGATAAAAA
1 AGATATAACATTTTGGTGTAAAATGGTTAAAGGAAGAATAGTTTAGTTAATACTTGTGAAAAAAA
*
30064447 AAGGGGTAGAACCATGAGGTGTGGTGTGTTGTGATGGTTGCTCATCTTATCCCTTAATCATGAGG
66 AAGGGGTAGAACCATGAGGTGTGATGTGTTGTGATGGTTGCTCATCTTATCCCTTAATCATGAGG
* * * *
30064512 TCGAGTATTCGGTCATTGCTTATGAGAATGGAGCACATTTCATGGTCAACCATTTACCTTTTCGA
131 TCGAGGATTCGGTCATTGCTTATGAGAATGGAACACATTTCATGGCCAACCATTTACCTCTTCGA
* *
30064577 AGAGCACATGCGATGAGATGATTAGTCATTACTATCGAAGGTGGAGATGTCCAAGTTTCAATAAA
196 AGAGCACATGCGATGAGATGATTAGTCATTACTACCGAAGGTGGAGATATCCAAGTTTCAATAAA
* * *
30064642 AATAGAAAAGGACAGGGTTAGATACCAAGTTGGGAAAAGGGTATAGTCTAATTTAAGGTTAAGCC
261 AATAAAAAAGGACAGGATTAGATACCAAGTTGAGAAAAGGGTATAGTCTAATTTAAGGTTAAGCC
30064707 TTTAAAAAATAAAGTTAATAATTTGACTAATGGTTGGATTG
326 TTTAAAAAATAAAGTTAATAATTTGACTAATGGTTGGATTG
30064748 AGATATAACATTTTGGTGTAAAATGGTTAAAGGAAGAATAGTTTAGTTAATACTTGTGACAAAAA
1 AGATATAACATTTTGGTGTAAAATGGTTAAAGGAAGAATAGTTTAGTTAATACTTGTG--AAAAA
*
30064813 AAAAGGGGTAGAACCATGAGGTGTGATGTGTTGTGGTGGTTGCTCATCTTATCCCTTAATCATGA
64 AAAAGGGGTAGAACCATGAGGTGTGATGTGTTGTGATGGTTGCTCATCTTATCCCTTAATCATGA
*
30064878 GGTCGAGGGTTCGGTCATTGCTTATGAGAATGGAACACATTTCATGGCCAACCATTTACCTCTTC
129 GGTCGAGGATTCGGTCATTGCTTATGAGAATGGAACACATTTCATGGCCAACCATTTACCTCTTC
* *
30064943 GAAGAGCACATGCGATGAGATGATTATTCATTGCTACCGAAGGTGGAGATATCCAAGTTTCAATA
194 GAAGAGCACATGCGATGAGATGATTAGTCATTACTACCGAAGGTGGAGATATCCAAGTTTCAATA
* *
30065008 AAAATAAAAAAGGAGAGGATTAGGTACCAAGTTGAGAAAAGGGTATAGTCTAATTTAAGGTTAAG
259 AAAATAAAAAAGGACAGGATTAGATACCAAGTTGAGAAAAGGGTATAGTCTAATTTAAGGTTAAG
30065073 CCTTTAAAAAATAAAGTTAATAATTTGACTAATGGTTGGATTG
324 CCTTTAAAAAATAAAGTTAATAATTTGACTAATGGTTGGATTG
30065116 AGATAT
1 AGATAT
30065122 TACCTTAAGA
Statistics
Matches: 354, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
366 57 0.16
368 297 0.84
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (366 bp):
AGATATAACATTTTGGTGTAAAATGGTTAAAGGAAGAATAGTTTAGTTAATACTTGTGAAAAAAA
AAGGGGTAGAACCATGAGGTGTGATGTGTTGTGATGGTTGCTCATCTTATCCCTTAATCATGAGG
TCGAGGATTCGGTCATTGCTTATGAGAATGGAACACATTTCATGGCCAACCATTTACCTCTTCGA
AGAGCACATGCGATGAGATGATTAGTCATTACTACCGAAGGTGGAGATATCCAAGTTTCAATAAA
AATAAAAAAGGACAGGATTAGATACCAAGTTGAGAAAAGGGTATAGTCTAATTTAAGGTTAAGCC
TTTAAAAAATAAAGTTAATAATTTGACTAATGGTTGGATTG
Found at i:30070331 original size:12 final size:12
Alignment explanation
Indices: 30070314--30070339 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30070304 AGTGGAATGG
30070314 CAATCTGACATC
1 CAATCTGACATC
30070326 CAATCTGACATC
1 CAATCTGACATC
30070338 CA
1 CA
30070340 GGCTTGCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.23
Consensus pattern (12 bp):
CAATCTGACATC
Found at i:30071394 original size:103 final size:103
Alignment explanation
Indices: 30071320--30071545 Score: 335
Period size: 103 Copynumber: 2.2 Consensus size: 103
30071310 ACAAAAGGAT
* * * *
30071320 ATTGCCTCGATTTTAAAATAGGATATTCTATTATTTAGGTCCAAAGAAAAATCATACCCAGTACG
1 ATTGCCTCGATTTTAAAATAGGATATTCAATTACTTAGATCCAAAGAAAAATCATACCCAGTACA
30071385 TTTGAGCACAATTTTTCGAGTTTCCTAAATAAAGAAAC
66 TTTGAGCACAATTTTTCGAGTTTCCTAAATAAAGAAAC
* * * * *
30071423 ATTGCCTCGTTTTTCAAATAGGATATTCAATTACTTCGATTCAAAGAAAAATTATACCCAGTACA
1 ATTGCCTCGATTTTAAAATAGGATATTCAATTACTTAGATCCAAAGAAAAATCATACCCAGTACA
* * *
30071488 TTTGAGCACAATTTATCGAATTCCCTAAATAAAGAAAC
66 TTTGAGCACAATTTTTCGAGTTTCCTAAATAAAGAAAC
30071526 ATTGCCTCGATTTTGAAAAT
1 ATTGCCTCGATTTT-AAAAT
30071546 TTTAGTTCTA
Statistics
Matches: 108, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
103 104 0.96
104 4 0.04
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (103 bp):
ATTGCCTCGATTTTAAAATAGGATATTCAATTACTTAGATCCAAAGAAAAATCATACCCAGTACA
TTTGAGCACAATTTTTCGAGTTTCCTAAATAAAGAAAC
Found at i:30073059 original size:60 final size:60
Alignment explanation
Indices: 30072962--30073131 Score: 227
Period size: 60 Copynumber: 2.8 Consensus size: 60
30072952 TTGGGAGTCA
* *
30072962 AAAATGTAATTTTAGAAAAATTTAAAGGTTAAAAATGTAATTTTAGAGAAGTTTAAGGGTT
1 AAAATGTAATTTTAGAAAAATTT-AAGGTTAAAAATGTAATTTTAGAAAAGTATAAGGGTT
**
30073023 AAAATGTAATTTTA-AAAAAGTTTAAGGTTAAAAATGTAATTTTAGAAAAGTATGGGGGTT
1 AAAATGTAATTTTAGAAAAA-TTTAAGGTTAAAAATGTAATTTTAGAAAAGTATAAGGGTT
* * ** *
30073083 GAAATGTAATTTTAGAAAAATGTGGGGTT-AAAATGTCATTTTAGAAAAG
1 AAAATGTAATTTTAGAAAAATTTAAGGTTAAAAATGTAATTTTAGAAAAG
30073132 CTTATGGTCA
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
59 19 0.19
60 57 0.58
61 22 0.22
ACGTcount: A:0.45, C:0.01, G:0.20, T:0.35
Consensus pattern (60 bp):
AAAATGTAATTTTAGAAAAATTTAAGGTTAAAAATGTAATTTTAGAAAAGTATAAGGGTT
Found at i:30073144 original size:29 final size:29
Alignment explanation
Indices: 30072896--30073167 Score: 206
Period size: 30 Copynumber: 9.1 Consensus size: 29
30072886 TAGATGTTCG
* **
30072896 AGGG-TAAAATAGTAATTTTGGATGAGTTT
1 AGGGTTAAAAT-GTAATTTTAGAAAAGTTT
* * * *
30072925 GGGGTAAAAATTTAATTTTAGGAAAGTTT
1 AGGGTTAAAATGTAATTTTAGAAAAGTTT
* * *
30072954 GGGAGTCAAAAATGTAATTTTAGAAAAATTT
1 AGG-GT-TAAAATGTAATTTTAGAAAAGTTT
* *
30072985 AAAGGTTAAAAATGTAATTTTAGAGAAGTTT
1 -AGGGTT-AAAATGTAATTTTAGAAAAGTTT
*
30073016 AAGGGTTAAAATGTAATTTTAAAAAAGTTT
1 -AGGGTTAAAATGTAATTTTAGAAAAGTTT
* *
30073046 AAGGTTAAAAATGTAATTTTAGAAAAGTATG
1 AGGGTT-AAAATGTAATTTTAGAAAAGT-TT
* * * *
30073077 GGGGTTGAAATGTAATTTTAGAAAAATGT
1 AGGGTTAAAATGTAATTTTAGAAAAGTTT
* * *
30073106 GGGGTTAAAATGTCATTTTAGAAAAGCTT
1 AGGGTTAAAATGTAATTTTAGAAAAGTTT
* * * * *
30073135 ATGGTCAAAATATGATTTTTAG-AAAGTTC
1 AGGGTTAAAATGT-AATTTTAGAAAAGTTT
30073164 AGGG
1 AGGG
30073168 ACCTTTTGGG
Statistics
Matches: 194, Mismatches: 41, Indels: 16
0.77 0.16 0.06
Matches are distributed among these distances:
29 65 0.34
30 73 0.38
31 55 0.28
32 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (29 bp):
AGGGTTAAAATGTAATTTTAGAAAAGTTT
Found at i:30074048 original size:14 final size:14
Alignment explanation
Indices: 30074026--30074067 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
30074016 TCGAATCCCC
*
30074026 TTTTCTTATATTTA
1 TTTTATTATATTTA
*
30074040 TTTTATTATAATTA
1 TTTTATTATATTTA
30074054 -TTTATT-TATTTA
1 TTTTATTATATTTA
30074066 TT
1 TT
30074068 ATGCTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 12 0.50
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTATATTTA
Found at i:30075353 original size:39 final size:39
Alignment explanation
Indices: 30075305--30075670 Score: 192
Period size: 39 Copynumber: 9.4 Consensus size: 39
30075295 TTTACCCCAA
*
30075305 GCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCTAG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAG
* * ** *
30075344 GCTCAGGGTAAAAGATT---AAATGGCTGCAATCTGCCC-AA
1 GCTCGGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCTAG
* * * **** *
30075382 GCTCGGGGTAAAAGATCGGAC-GGTTACAATCTGCCCAAG
1 GCTCGGGGTAAGAGATTGG-CTGATGGTGATCTGCCCTAG
*
30075421 GCTCGGGGTAAGAGATTGGCTGATGGTGATTTG-CCTCAG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCT-AG
* * * * ** *
30075460 GCTCGGGGTAAAAGATCGGAC-GGTTGCAATATG-CCTCAG
1 GCTCGGGGTAAGAGATTGG-CTGATGGTGATCTGCCCT-AG
** * * * *
30075499 GCTCTAGGTAAGAGATTGGCTAATAGTGATCTGCCCCAA
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAG
* * * *
30075538 GCTCGAGGTAAGAGATTGGCTGATGGTGATCTACCCCAA
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAG
* * * * * * *
30075577 GCTCGGGGTAAAAGATCGAACAG-TTGTAATCTGCCTTAG
1 GCTCGGGGTAAGAGATTG-GCTGATGGTGATCTGCCCTAG
* * * *
30075616 GGTCGGGGTAAGAGATTGGCTGATGATGATTTGCCCTAA
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAG
* *
30075655 GCTCGGGATAAAAGAT
1 GCTCGGGGTAAGAGAT
30075671 CGAAATCTTT
Statistics
Matches: 241, Mismatches: 71, Indels: 30
0.70 0.21 0.09
Matches are distributed among these distances:
36 4 0.02
37 2 0.01
38 30 0.12
39 199 0.83
40 5 0.02
41 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (39 bp):
GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAG
Found at i:30075412 original size:38 final size:38
Alignment explanation
Indices: 30075368--30075980 Score: 186
Period size: 39 Copynumber: 15.8 Consensus size: 38
30075358 ATTAAATGGC
30075368 TGCAATCTGCCCAAGCTCGGGGTAAAAGATCGGACGGT
1 TGCAATCTGCCCAAGCTCGGGGTAAAAGATCGGACGGT
* * * *
30075406 TACAATCTGCCCAAGGCTCGGGGTAAGAGATTGG-CTGAT
1 TGCAATCTGCCCAA-GCTCGGGGTAAAAGATCGGAC-GGT
* ** * *
30075445 GGTGATTTGCCTCAGGCTCGGGGTAAAAGATCGGACGGT
1 TGCAATCTGCC-CAAGCTCGGGGTAAAAGATCGGACGGT
* * ** * * **
30075484 TGCAATATGCCTCAGGCTCTAGGTAAGAGATTGG-CTAAT
1 TGCAATCTGCC-CAAGCTCGGGGTAAAAGATCGGAC-GGT
* ** * * * *
30075523 AGTGATCTGCCCCAAGCTCGAGGTAAGAGATTGG-CTGAT
1 TGCAATCTG-CCCAAGCTCGGGGTAAAAGATCGGAC-GGT
* ** * * *
30075562 GGTGATCTACCCCAAGCTCGGGGTAAAAGATCGAACAGT
1 TGCAATCT-GCCCAAGCTCGGGGTAAAAGATCGGACGGT
* * * * * * * *
30075601 TGTAATCTGCCTTAGGGTCGGGGTAAGAGATTGG-CTGA
1 TGCAATCTGCC-CAAGCTCGGGGTAAAAGATCGGACGGT
* * * ***
30075639 TG-ATGATTTGCCCTAAGCTCGGGATAAAAGATCGAAATCT
1 TGCA--ATCTGCCC-AAGCTCGGGGTAAAAGATCGGACGGT
* * *
30075679 T-TAATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGAT
1 TGCAATCTG-CCCAAGCTCGGGGTAAAAGATCGGACGGT
* * * ** * * *
30075717 TGAAATCTACCCTAGGCTCAAGGTAAAAGATCGAATGGC
1 TGCAATCTGCCC-AAGCTCGGGGTAAAAGATCGGACGGT
* ** ** **
30075756 TGTAATCTGCCCCAAGCTTAGGGTAAAAGATCAAACGAC
1 TGCAATCTG-CCCAAGCTCGGGGTAAAAGATCGGACGGT
* * * * *
30075795 TGCAATCTGCCCAGGCTCGAGGTAAGAGATTC--ACTGA
1 TGCAATCTGCCCAAGCTCGGGGTAAAAGA-TCGGACGGT
* * * * *
30075832 TG-ATGATCTACTCCAAACTCGGGGTAAAAGATCGAAAGGC
1 TGCA--ATCTGC-CCAAGCTCGGGGTAAAAGATCGGACGGT
* * * * *
30075872 TGCAATCTGCCTCAGGCTCGGAGTAAGAGATTGG-CTGAT
1 TGCAATCTGCC-CAAGCTCGGGGTAAAAGATCGGAC-GGT
* ** **
30075911 GGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGACGAC
1 TGCAATCTG-CCCAAGCTCGGGGTAAAAGATCGGACGGT
* *
30075950 TGCAATCTACCCTAAGCTC-GGGTAAGAGATC
1 TGCAATCTGCCC-AAGCTCGGGGTAAAAGATC
30075981 AGAATCTTCA
Statistics
Matches: 423, Mismatches: 122, Indels: 60
0.70 0.20 0.10
Matches are distributed among these distances:
36 1 0.00
37 5 0.01
38 87 0.21
39 310 0.73
40 19 0.04
41 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (38 bp):
TGCAATCTGCCCAAGCTCGGGGTAAAAGATCGGACGGT
Found at i:30075484 original size:78 final size:78
Alignment explanation
Indices: 30075372--30075553 Score: 242
Period size: 78 Copynumber: 2.3 Consensus size: 78
30075362 AATGGCTGCA
* *
30075372 ATCTG-CCCAAGCTCGGGGTAAAAGATCGGACGGTTACAATCTGCC-CAAGGCTCGGGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGACGGTTACAATATGCCTC-AGGCTCGAGGTAAGAG
* *
30075435 ATTGGCTGATGGTG
65 ATTGGCTAATAGTG
* * * * *
30075449 ATTTGCCTCAGGCTCGGGGTAAAAGATCGGACGGTTGCAATATGCCTCAGGCTCTAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGACGGTTACAATATGCCTCAGGCTCGAGGTAAGAGA
30075514 TTGGCTAATAGTG
66 TTGGCTAATAGTG
* *
30075527 ATCTGCCCCAAGCTCGAGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGGGTAAAAGAT
30075554 TGGCTGATGG
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
77 4 0.04
78 84 0.94
79 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (78 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGGACGGTTACAATATGCCTCAGGCTCGAGGTAAGAGA
TTGGCTAATAGTG
Found at i:30075560 original size:117 final size:116
Alignment explanation
Indices: 30075299--30075670 Score: 392
Period size: 117 Copynumber: 3.2 Consensus size: 116
30075289 CTGTAATTTA
* * **
30075299 CCCCAAGCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCTAGGCTCAGGGTAAAAGATTAAA
1 CCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AGGCTCGGGGTAAAAGATCGAA
* * * * * * * **
30075364 TGGCTGCAATCTGCC-CAAGCTCGGGGTAAAAGATCGGACGGTTA-CAATCTG
65 CGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGG-CTGATAGTGATCTG
* *
30075415 -CCCAAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCTCAGGCTCGGGGTAAAAGATCGG
1 CCCCAA-GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCC-CAGGCTCGGGGTAAAAGATCGA
* ** *
30075479 ACGGTTGCAATATGCCTCAGGCTCTAGGTAAGAGATTGGCTAATAGTGATCTG
64 ACGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTG
* * *
30075532 CCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAGATCGAA
1 CCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCT-GCCCAGGCTCGGGGTAAAAGATCGAA
* * * * *
30075597 CAGTTGTAATCTGCCTTAGGGTCGGGGTAAGAGATTGGCTGAT-GATGATTTG
65 CGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATAG-TGATCTG
* * *
30075649 CCCTAAGCTCGGGATAAAAGAT
1 CCCCAAGCTCGGGGTAAGAGAT
30075671 CGAAATCTTT
Statistics
Matches: 212, Mismatches: 37, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
115 5 0.02
116 67 0.32
117 133 0.63
118 7 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (116 bp):
CCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCAGGCTCGGGGTAAAAGATCGAAC
GGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTG
Found at i:30075879 original size:155 final size:155
Alignment explanation
Indices: 30075689--30075979 Score: 338
Period size: 155 Copynumber: 1.9 Consensus size: 155
30075679 TTAATCTGCC
* * * *
30075689 CCAAGCTCGGGGTAAAAGATCGGATGATTGAAATCTACCCT-AGGCTCA-AGGTAAAAGATCGAA
1 CCAAACTCGGGGTAAAAGATCGAAAGACTGAAATCT-CCCTCAGGCTCAGA-GTAAAAGATCGAA
* * * *
30075752 TGGCT-GTAATCTGCCCCAAGCTTAGGGTAAAAGATCAAACGACTGCAATCTGCCC-AGGCTCGA
64 T-GATGGTAATCTGCCCCAAGCTCAGGGTAAAAGATCAAACGACTGCAATCTACCCTAAGCTCG-
30075815 GGTAAGAGATTCACTGATGATGATCTACT
127 GGTAAGAGATTCACTGATGATGATCTACT
* * * * * * **
30075844 CCAAACTCGGGGTAAAAGATCGAAAGGCTGCAATCTGCCTCAGGCTCGGAGTAAGAGATTGGCTG
1 CCAAACTCGGGGTAAAAGATCGAAAGACTGAAATCTCCCTCAGGCTCAGAGTAAAAGATCGAATG
* * **
30075909 ATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGACGACTGCAATCTACCCTAAGCTCGGGTA
66 ATGGTAATCTGCCCCAAGCTCAGGGTAAAAGATCAAACGACTGCAATCTACCCTAAGCTCGGGTA
30075974 AGAGAT
131 AGAGAT
30075980 CAGAATCTTC
Statistics
Matches: 112, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
154 5 0.04
155 100 0.89
156 7 0.06
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.21
Consensus pattern (155 bp):
CCAAACTCGGGGTAAAAGATCGAAAGACTGAAATCTCCCTCAGGCTCAGAGTAAAAGATCGAATG
ATGGTAATCTGCCCCAAGCTCAGGGTAAAAGATCAAACGACTGCAATCTACCCTAAGCTCGGGTA
AGAGATTCACTGATGATGATCTACT
Found at i:30075911 original size:78 final size:77
Alignment explanation
Indices: 30075776--30075979 Score: 252
Period size: 78 Copynumber: 2.6 Consensus size: 77
30075766 CCCAAGCTTA
30075776 GGGTAAAAGATC-AAACGACTGCAATCTGCCCAGGCTC-GAGGTAAGAGATTCACTGATGATGAT
1 GGGTAAAAGATCGAAA-GACTGCAATCTGCCCAGGCTCGGA-GTAAGAGATTCACTGATGATGAT
*
30075839 CTACTCCAAACTCG
64 CTACCCCAAACTCG
* ** *
30075853 GGGTAAAAGATCGAAAGGCTGCAATCTGCCTCAGGCTCGGAGTAAGAGATTGGCTGATGGTGATC
1 GGGTAAAAGATCGAAAGACTGCAATCTGCC-CAGGCTCGGAGTAAGAGATTCACTGATGATGATC
* *
30075918 TGCCCCAAGCTCG
65 TACCCCAAACTCG
* * * *
30075931 GGGTAAAAGATCGGACGACTGCAATCTACCCTAAGCTCGG-GTAAGAGAT
1 GGGTAAAAGATCGAAAGACTGCAATCTGCCC-AGGCTCGGAGTAAGAGAT
30075980 CAGAATCTTC
Statistics
Matches: 111, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
77 35 0.32
78 74 0.67
79 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (77 bp):
GGGTAAAAGATCGAAAGACTGCAATCTGCCCAGGCTCGGAGTAAGAGATTCACTGATGATGATCT
ACCCCAAACTCG
Found at i:30078341 original size:21 final size:21
Alignment explanation
Indices: 30078317--30078359 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
30078307 TTTCATATCT
30078317 TCTGGTCTATTTCTTTGATCA
1 TCTGGTCTATTTCTTTGATCA
30078338 TCTGGTCTATTTCTTTGATCA
1 TCTGGTCTATTTCTTTGATCA
30078359 T
1 T
30078360 TGAGGCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.53
Consensus pattern (21 bp):
TCTGGTCTATTTCTTTGATCA
Found at i:30083306 original size:52 final size:50
Alignment explanation
Indices: 30083220--30083318 Score: 119
Period size: 52 Copynumber: 1.9 Consensus size: 50
30083210 TTTTTACATA
* * * *
30083220 TATATATATAAAATAAAATCAAGATCTATGTATATATGTATGTGTATATACG
1 TATATAAAAAAAATAAAATCAAGATCTATCTATAT-T-TATATGTATATACG
*
30083272 TATATAAAAAAAATAAAATCAAGA-CGTGTCTATATTTATATGTATAT
1 TATATAAAAAAAATAAAATCAAGATC-TATCTATATTTATATGTATAT
30083319 TCATGCGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 10 0.24
51 2 0.05
52 29 0.71
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.37
Consensus pattern (50 bp):
TATATAAAAAAAATAAAATCAAGATCTATCTATATTTATATGTATATACG
Found at i:30084082 original size:13 final size:13
Alignment explanation
Indices: 30084058--30084100 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
30084048 TTTATAATTG
30084058 TAATA-ATATAAT
1 TAATATATATAAT
*
30084070 TAATATGTATAAT
1 TAATATATATAAT
* *
30084083 AAATATATAAAAT
1 TAATATATATAAT
30084096 TAATA
1 TAATA
30084101 ATTATTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
TAATATATATAAT
Found at i:30084101 original size:17 final size:16
Alignment explanation
Indices: 30084079--30084124 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
30084069 TTAATATGTA
30084079 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
*
30084096 TAATAATTATTAAAAT
1 TAATAAATATTAAAAT
30084112 CT-ATAAA-ATTAAA
1 -TAATAAATATTAAA
30084125 CCTTAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:30084111 original size:16 final size:17
Alignment explanation
Indices: 30084079--30084111 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30084069 TTAATATGTA
30084079 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
30084096 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
30084112 CTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:30085258 original size:27 final size:27
Alignment explanation
Indices: 30085221--30085285 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
30085211 ATCCAAAGAT
30085221 TGCCAAAAAGGCATCCTTTACAAGGAA
1 TGCCAAAAAGGCATCCTTTACAAGGAA
* * *
30085248 TGCCACAAAGGCGTCCTTTATAAGGAA
1 TGCCAAAAAGGCATCCTTTACAAGGAA
* *
30085275 TACCATAAAGG
1 TGCCAAAAAGG
30085286 TTTCCCTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (27 bp):
TGCCAAAAAGGCATCCTTTACAAGGAA
Found at i:30085295 original size:27 final size:27
Alignment explanation
Indices: 30085227--30085295 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 27
30085217 AGATTGCCAA
* * * *
30085227 AAAGGCATCCTTTACAAGGAATGCCAC
1 AAAGGCGTCCCTTATAAGGAATACCAC
* *
30085254 AAAGGCGTCCTTTATAAGGAATACCAT
1 AAAGGCGTCCCTTATAAGGAATACCAC
**
30085281 AAAGGTTTCCCTTAT
1 AAAGGCGTCCCTTAT
30085296 GGAGATTGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (27 bp):
AAAGGCGTCCCTTATAAGGAATACCAC
Found at i:30088882 original size:16 final size:16
Alignment explanation
Indices: 30088852--30088893 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
30088842 CTAGCAACAC
30088852 ATAAAAT-AT-TATTA
1 ATAAAATAATATATTA
30088866 A-AAAATTAATATATTA
1 ATAAAA-TAATATATTA
30088882 ATAAAATAATAT
1 ATAAAATAATAT
30088894 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 2 0.08
15 2 0.08
16 12 0.50
17 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAATAATATATTA
Found at i:30104919 original size:15 final size:14
Alignment explanation
Indices: 30104894--30104924 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
30104884 AAATGATTGT
30104894 AAAATTATTTTTTA
1 AAAATTATTTTTTA
30104908 AAAATATATTTTTTA
1 AAAAT-TATTTTTTA
30104923 AA
1 AA
30104925 TATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAAATTATTTTTTA
Found at i:30104940 original size:21 final size:22
Alignment explanation
Indices: 30104906--30104958 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
30104896 AATTATTTTT
*
30104906 TAAAAATATATTTTTT-AAAT-A
1 TAAAATTAT-TTTTTTGAAATAA
30104927 TAAAATTATTTTTTTGAAATAA
1 TAAAATTATTTTTTTGAAATAA
30104949 TAAAATTATT
1 TAAAATTATT
30104959 AAATAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 6 0.21
21 12 0.41
22 11 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTTTTTGAAATAA
Found at i:30107662 original size:33 final size:30
Alignment explanation
Indices: 30107592--30107666 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 30
30107582 TTTAAAATTC
30107592 AAAATAAAAAATATTTTAAAATGTTTCTTA
1 AAAATAAAAAATATTTTAAAATGTTTCTTA
*
30107622 AAAATAAAAATATATATTTAAATAT-TTTTTTA
1 AAAATAAAAA-ATAT-TTTAAA-ATGTTTCTTA
*
30107654 TAAGATAAAAAAT
1 -AAAATAAAAAAT
30107667 GATAAAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 10 0.26
31 4 0.10
32 14 0.36
33 11 0.28
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATAAAAAATATTTTAAAATGTTTCTTA
Found at i:30107778 original size:21 final size:19
Alignment explanation
Indices: 30107746--30107797 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
30107736 AAAAATTTAT
*
30107746 AAATTTTAATAAAAGTAAA
1 AAATTTTAATAAAAATAAA
30107765 AATATTTTATATAAAAATAAA
1 AA-ATTTTA-ATAAAAATAAA
30107786 AAATTTATAATA
1 AAATTT-TAATA
30107798 TTTACATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 13 0.45
21 14 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATTTTAATAAAAATAAA
Found at i:30118529 original size:193 final size:194
Alignment explanation
Indices: 30118185--30118629 Score: 540
Period size: 193 Copynumber: 2.3 Consensus size: 194
30118175 GAAACCGACG
* * *
30118185 CGATGGTTGAGGTACCGTATATGTTGCGAGTCCTCGACAGCTCGTGTGACCAGCATCGTGAGTCG
1 CGATGGCTGAGGTACCGTATATGTTGCGAGTCCTCGACAGCTTGTGTGAGCAGCATCGTGAGTCG
* * *
30118250 AGAAATGAGAAATGAATCCAAGAATGGATTACAAGCCCTACGATGGCTAGGATTTATGCATAAGT
66 AAAAAAGAGAAATGAATCCAAGAATGGATTACAAGCCCTACGATGGCTAGGATTTATGCATAAGC
* * * ** * * *
30118315 GCATATTCTCGACAGCTCGTGTGAGCAGCATTGTTAGGGAACA-TTTATATGCACAGATACCGTA
131 GAATATTCTCAACAGCTCGTGTGAGCAACATCATTAGGGAACAGTTTACA-G-ACAGACACCATA
*
30118379 T
194 C
*
30118380 CGATGGCTGAGGT-CCGTATATGTTGCGAGTCCTCAACAGCTTGTGTGAGCAGCATCGTGAGTC-
1 CGATGGCTGAGGTACCGTATATGTTGCGAGTCCTCGACAGCTTGTGTGAGCAGCATCGTGAGTCG
* * * * * *
30118443 AAAAAAGAGATATGAAATCTAA-AATGGATTATAGGCCCTACGATGGCTGGGATTTATGCTTGAA
66 AAAAAAGAGAAATG-AATCCAAGAATGGATTACAAGCCCTACGATGGCTAGGATTTATGCAT-AA
* * *
30118507 -CGAATATTCTCAATAGCTCGTGTGAGCAACATCATTAGGGGACAGTTTACAGACAGACACTATA
129 GCGAATATTCTCAACAGCTCGTGTGAGCAACATCATTAGGGAACAGTTTACAGACAGACACCATA
30118571 C
194 C
* * * * * *
30118572 CGATGACTGGGGTATCGCATATGTTGTGAGTCTTCGACAGCTTGTGTGAGCAGCATCG
1 CGATGGCTGAGGTACCGTATATGTTGCGAGTCCTCGACAGCTTGTGTGAGCAGCATCG
30118630 GGTACTAGTA
Statistics
Matches: 214, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
192 20 0.09
193 122 0.57
194 60 0.28
195 12 0.06
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (194 bp):
CGATGGCTGAGGTACCGTATATGTTGCGAGTCCTCGACAGCTTGTGTGAGCAGCATCGTGAGTCG
AAAAAAGAGAAATGAATCCAAGAATGGATTACAAGCCCTACGATGGCTAGGATTTATGCATAAGC
GAATATTCTCAACAGCTCGTGTGAGCAACATCATTAGGGAACAGTTTACAGACAGACACCATAC
Found at i:30119934 original size:5 final size:6
Alignment explanation
Indices: 30119920--30119957 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
30119910 AGTACTAAAT
30119920 AAAACA AAAACA AAAACA AAAAC- AAAAC- AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
30119958 ATAAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:30121351 original size:30 final size:28
Alignment explanation
Indices: 30121280--30121351 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
30121270 TACGTAAAAT
* *
30121280 GTCCTCGAACTTTCCAAAAATAAATTTT
1 GTCCTCAAACTTTCCAAAAATAAATTTG
* **
30121308 GACCTCTAAACTTTCCAAAAATTTGGATTTG
1 GTCCTC-AAACTTTCCAAAAA--TAAATTTG
30121339 GTCCTCAAACTTT
1 GTCCTCAAACTTT
30121352 ATAAATATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.14
29 13 0.37
30 7 0.20
31 10 0.29
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (28 bp):
GTCCTCAAACTTTCCAAAAATAAATTTG
Found at i:30121411 original size:29 final size:29
Alignment explanation
Indices: 30121365--30121490 Score: 153
Period size: 29 Copynumber: 4.3 Consensus size: 29
30121355 AATATTACAT
* *
30121365 TTTAACCCCTAAAATTTCCAAAATTCAAA
1 TTTAACCCTTAAACTTTCCAAAATTCAAA
*
30121394 TTTAACCCTTAAACTTTCCAAAAAATCAAA
1 TTTAACCCTTAAACTTTCC-AAAATTCAAA
*
30121424 TTTAACCCTTAAACTTTCCAAATTTCAAA
1 TTTAACCCTTAAACTTTCCAAAATTCAAA
* * ** *
30121453 TTTAATCGTCGAACTTTCCAAAATTCAGA
1 TTTAACCCTTAAACTTTCCAAAATTCAAA
*
30121482 TTTGACCCT
1 TTTAACCCT
30121491 CGAAAGCTCC
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 54 0.66
30 28 0.34
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTAACCCTTAAACTTTCCAAAATTCAAA
Found at i:30121425 original size:30 final size:30
Alignment explanation
Indices: 30121365--30121445 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
30121355 AATATTACAT
* * *
30121365 TTTAACCCCTAAAATTTCC-AAAATTCAAA
1 TTTAACCCTTAAACTTTCCAAAAAATCAAA
30121394 TTTAACCCTTAAACTTTCCAAAAAATCAAA
1 TTTAACCCTTAAACTTTCCAAAAAATCAAA
30121424 TTTAACCCTTAAACTTTCCAAA
1 TTTAACCCTTAAACTTTCCAAA
30121446 TTTCAAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 17 0.35
30 31 0.65
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (30 bp):
TTTAACCCTTAAACTTTCCAAAAAATCAAA
Found at i:30121516 original size:30 final size:30
Alignment explanation
Indices: 30121472--30121552 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
30121462 CGAACTTTCC
*
30121472 AAAATTCAGA-TTTGACCCTCGAAAG-CTCCA
1 AAAATTCA-ATTTTGAACCTCGAAAGTC-CCA
*
30121502 AAAATTCAATTTTGAAACCT-GAACGTCCCA
1 AAAATTCAATTTTG-AACCTCGAAAGTCCCA
*
30121532 AAAATTCGAATTTTGATCCTC
1 AAAATTC-AATTTTGAACCTC
30121553 TTTTATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
29 1 0.02
30 30 0.70
31 12 0.28
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.28
Consensus pattern (30 bp):
AAAATTCAATTTTGAACCTCGAAAGTCCCA
Found at i:30127220 original size:111 final size:111
Alignment explanation
Indices: 30127070--30127275 Score: 301
Period size: 111 Copynumber: 1.9 Consensus size: 111
30127060 AATGTTTGTC
* *
30127070 ATTTTTAATCTTTTCATTCATGCGAGCTTTGCCTTAATAAAATTCAATTTTATCCACCTTA-AAA
1 ATTTTTAATATTTTCATTCATGCGAGCTTTGCCTCAATAAAATTCAATTTTATCCACCTTACAAA
* *
30127134 CCTTTTTCAAGCACGTTTT-CATTGAGATAACAGTTAGTGGACTAATG
66 CC-TGTTCAAGCA-GTTTTGCATTGAAATAACAGTTAGTGGACTAATG
*
30127181 ATTTTTAATATTTTCATTCATGCGAGC-TTGCCTCCAATAAAATTCAATTTTATCTACCTTACAA
1 ATTTTTAATATTTTCATTCATGCGAGCTTTGCCT-CAATAAAATTCAATTTTATCCACCTTACAA
* *
30127245 TCCTGTTCAAGCATTTTTGCATTGAAATAAC
65 ACCTGTTCAAGCAGTTTTGCATTGAAATAAC
30127276 GATATAACGA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
110 10 0.12
111 71 0.84
112 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (111 bp):
ATTTTTAATATTTTCATTCATGCGAGCTTTGCCTCAATAAAATTCAATTTTATCCACCTTACAAA
CCTGTTCAAGCAGTTTTGCATTGAAATAACAGTTAGTGGACTAATG
Found at i:30128021 original size:99 final size:99
Alignment explanation
Indices: 30127709--30128321 Score: 648
Period size: 99 Copynumber: 6.2 Consensus size: 99
30127699 AGGAAACATA
**
30127709 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGACATGATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAA
* * * * *
30127774 AGATCGAGATCGTAACGGTGGATCTAGTACCATGG
66 GGATTGAGGTCGCAACGGTGAATCTAGTACCAT-G
* * *
30127809 AA-ATA--AAGGGAAAGGTTGAGGCCGTAACGGCAAACTCGGTACCTTAGAAGATGTTATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAA
* * *** *
30127871 CGATTGA-GCCGCAACGAAAAAT-TCGGTACCATG
66 GGATTGAGGTCGCAACGGTGAATCT-AGTACCATG
* * * ** *
30127904 AAGATATGTAGGGAAAGGTTAAGACCAAAACGGTGAACCCGGTACC-TAGAAAGATGTGATGGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAG-AAGATGTGATGGGA
* * * * *
30127968 ATGATTAAGTTCGCAACGGTGAATCAAATACCATG
65 AGGATTGAGGTCGCAACGGTGAATCTAGTACCATG
* *
30128003 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCGGGTACCTTAGAAGATGTGATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAA
* * * *
30128068 GGATTGAGGTCGGAACGGTAAATC-CGATACCATA
66 GGATTGAGGTCGCAACGGTGAATCTAG-TACCATG
* * ** *
30128102 AAGATATGAAGGGAAAGGTTGAGGCCGCAACTGCGAACCCAATACCTTAGAAGATGTGATGGTAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAA
* * * *
30128167 GGACTGAGGCCGTAACGGCGAATCTAGTACCATG
66 GGATTGAGGTCGCAACGGTGAATCTAGTACCATG
* * * * *
30128201 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGTGAATCCAGTACCTTAAAAGATGTGATAGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAA
* *** *
30128266 GGATTGAGGCCGCAACGACAAATCTTGTACCATG
66 GGATTGAGGTCGCAACGGTGAATCTAGTACCATG
*
30128300 GAGATAT-AGAGGGAAAGGTTGA
1 AAGATATGA-AGGGAAAGGTTGA
30128322 AGTCGAAACG
Statistics
Matches: 426, Mismatches: 76, Indels: 23
0.81 0.14 0.04
Matches are distributed among these distances:
95 4 0.01
96 18 0.04
97 60 0.14
98 50 0.12
99 288 0.68
100 6 0.01
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (99 bp):
AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAA
GGATTGAGGTCGCAACGGTGAATCTAGTACCATG
Found at i:30128075 original size:50 final size:49
Alignment explanation
Indices: 30127705--30128282 Score: 320
Period size: 50 Copynumber: 11.8 Consensus size: 49
30127695 ATCGAGGAAA
* *
30127705 CATA-AAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTAC
1 CATAGAAGATATGATGGGAAAGGTTGAGGCCGTAACGGTGAA-CCGGTAC
* * * * ** * **
30127754 CTTAGAAGACATGATGGGAAAGATCGAGATCGTAACGGTGGATCTAGTAC
1 CATAGAAGATATGATGGGAAAGGTTGAGGCCGTAACGGT-GAACCGGTAC
* * **
30127804 CATGGAA-ATA--AAGGGAAAGGTTGAGGCCGTAACGGCAAACTCGGTAC
1 CATAGAAGATATGATGGGAAAGGTTGAGGCCGTAACGGTGAAC-CGGTAC
* * * * * * *** *
30127851 CTTAGAAGATGTTATGGGAACGATTGA-GCCGCAACGAAAAATTCGGTAC
1 CATAGAAGATATGATGGGAAAGGTTGAGGCCGTAACGGTGAA-CCGGTAC
* * **
30127900 CAT-GAAGATATG-TAGGGAAAGGTTAAGACCAAAACGGTGAACCCGGTAC
1 CATAGAAGATATGAT-GGGAAAGGTTGAGGCCGTAACGGTGAA-CCGGTAC
* * * * ** * ***
30127949 C-TAGAAAGATGTGATGGGAATGATTAAGTTCGCAACGGTGAATCAAATAC
1 CATAG-AAGATATGATGGGAAAGGTTGAGGCCGTAACGGTGAA-CCGGTAC
*
30127999 CAT-GAAGATATGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCGGGTAC
1 CATAGAAGATATGATGGGAAAGGTTGAGGCCGTAACGGTGAACC-GGTAC
* * * * * *
30128048 CTTAGAAGATGTGATGGG-AAGGATTGAGGTCGGAACGGTAAATCCGATAC
1 CATAGAAGATATGATGGGAAAGG-TTGAGGCCGTAACGGTGAA-CCGGTAC
* * * * **
30128098 CATA-AAGATATGAAGGGAAAGGTTGAGGCCGCAACTGCGAACCCAATAC
1 CATAGAAGATATGATGGGAAAGGTTGAGGCCGTAACGGTGAA-CCGGTAC
* * * * * **
30128147 CTTAGAAGATGTGAT-GGTAAGGACTGAGGCCGTAACGGCGAATCTAGTAC
1 CATAGAAGATATGATGGGAAAGG-TTGAGGCCGTAACGGTGAA-CCGGTAC
* *
30128197 CAT-GAAGATATGAAGGGAAAGGTTGAGGCCGTAACGGTGAATCCAGTAC
1 CATAGAAGATATGATGGGAAAGGTTGAGGCCGTAACGGTGAA-CCGGTAC
* * * * *
30128246 CTTAAAAGATGTGATAGG-AAGGATTGAGGCCGCAACG
1 CATAGAAGATATGATGGGAAAGG-TTGAGGCCGTAACG
30128283 ACAAATCTTG
Statistics
Matches: 396, Mismatches: 110, Indels: 45
0.72 0.20 0.08
Matches are distributed among these distances:
46 2 0.01
47 30 0.08
48 20 0.05
49 157 0.40
50 181 0.46
51 6 0.02
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (49 bp):
CATAGAAGATATGATGGGAAAGGTTGAGGCCGTAACGGTGAACCGGTAC
Found at i:30128218 original size:198 final size:196
Alignment explanation
Indices: 30127705--30128338 Score: 724
Period size: 198 Copynumber: 3.2 Consensus size: 196
30127695 ATCGAGGAAA
* **
30127705 CATAAAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGACATGATG
1 CATAAAGATATGAAGGGAAAGGTTGAGGCCGAAACGGCGAACCCGGTACCTTAGAAGATGTGATG
*
30127770 GGAAAGATCGAGATCGTAACGGTGGATCTAGTACCATGGAA-ATA--AAGGGAAAGGTTGAGGCC
66 GGAAAGAT-GAGATCGTAACGGTGAATCTAGTACCAT-GAAGATATGAAGGGAAAGGTTGAGGCC
** * * *
30127832 GTAACGGCAAACTCGGTACCTTAGAAGATGTTATGGGAACGATTGA-GCCGCAACGAAAAATTCG
129 GTAACGGTGAAC-CGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGCAACGAAAAATCCG
*
30127896 GTAC
193 ATAC
* * * * * *
30127900 CATGAAGATATGTAGGGAAAGGTTAAGACCAAAACGGTGAACCCGGTACC-TAGAAAGATGTGAT
1 CATAAAGATATGAAGGGAAAGGTTGAGGCCGAAACGGCGAACCCGGTACCTTAG-AAGATGTGAT
* * * * * *
30127964 GGGAATGATTAAGTTCGCAACGGTGAATCAAATACCATGAAGATATGAAGGGAAAGGTTGAGGCC
65 GGGAAAGA-TGAGATCGTAACGGTGAATCTAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCC
* * **
30128029 GTAACGGTGAACCGGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGTCGGAACGGTAAATCCG
129 GTAACGGTGAACC-GGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGCAACGAAAAATCCG
30128094 ATAC
193 ATAC
* * **
30128098 CATAAAGATATGAAGGGAAAGGTTGAGGCCGCAACTGCGAACCCAATACCTTAGAAGATGTGATG
1 CATAAAGATATGAAGGGAAAGGTTGAGGCCGAAACGGCGAACCCGGTACCTTAGAAGATGTGATG
* * ** *
30128163 GTAAGGACTGAGGCCGTAACGGCGAATCTAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCG
66 GGAAAGA-TGAGATCGTAACGGTGAATCTAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCG
* * * * *
30128228 TAACGGTGAATCCAGTACCTTAAAAGATGTGATAGGAAGGATTGAGGCCGCAACGACAAATCTTG
130 TAACGGTGAA-CCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGCAACGAAAAATC-CG
30128293 -TAC
193 ATAC
** * * *
30128296 CATGGAGATAT-AGAGGGAAAGGTTGAAGTCGAAACGACGAACC
1 CATAAAGATATGA-AGGGAAAGGTTGAGGCCGAAACGGCGAACC
30128339 TTATACCTTA
Statistics
Matches: 367, Mismatches: 61, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
194 6 0.02
195 83 0.23
196 2 0.01
197 59 0.16
198 211 0.57
199 6 0.02
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.19
Consensus pattern (196 bp):
CATAAAGATATGAAGGGAAAGGTTGAGGCCGAAACGGCGAACCCGGTACCTTAGAAGATGTGATG
GGAAAGATGAGATCGTAACGGTGAATCTAGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGT
AACGGTGAACCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGCAACGAAAAATCCGATA
C
Found at i:30128296 original size:50 final size:51
Alignment explanation
Indices: 30127817--30128282 Score: 231
Period size: 49 Copynumber: 9.4 Consensus size: 51
30127807 GGAAATAAAG
* * * *
30127817 GGAAAGG-TTGAGGCCGTAACGGC-AAACTCGGTACCTTAGAAGATGTTAT-
1 GGAAAGGATTGAGGCCGCAACGGCGAATC-CAGTACCTTAGAAGATGTGATA
* * *** * * * *
30127866 GGGAACGATTGA-GCCGCAACGAAAAATTCGGTACCAT-GAAGATATG-TA
1 GGAAAGGATTGAGGCCGCAACGGCGAATCCAGTACCTTAGAAGATGTGATA
* * ** * * *
30127914 GGGAAAGG-TTAAGACCAAAACGGTGAACCCGGTACC-TAGAAAGATGTGAT-
1 -GGAAAGGATTGAGGCCGCAACGGCGAATCCAGTACCTTAG-AAGATGTGATA
* * * ** * * * * *
30127964 GGGAATGATTAAGTTCGCAACGGTGAATCAAATACCAT-GAAGATATGA-A
1 GGAAAGGATTGAGGCCGCAACGGCGAATCCAGTACCTTAGAAGATGTGATA
* * *
30128013 GGGAAAGG-TTGAGGCCGTAACGGTGAA-CCGGGTACCTTAGAAGATGTGAT-
1 -GGAAAGGATTGAGGCCGCAACGGCGAATCC-AGTACCTTAGAAGATGTGATA
* * * ** * *
30128063 GGGAAGGATTGAGGTCGGAACGGTAAATCC-GATACCATA-AAGATATGA-A
1 GGAAAGGATTGAGGCCGCAACGGCGAATCCAG-TACCTTAGAAGATGTGATA
* * *
30128112 GGGAAAGG-TTGAGGCCGCAACTGCGAACCCAATACCTTAGAAGATGTGAT-
1 -GGAAAGGATTGAGGCCGCAACGGCGAATCCAGTACCTTAGAAGATGTGATA
* * * * * *
30128162 GGTAAGGACTGAGGCCGTAACGGCGAATCTAGTACCAT-GAAGATATGA-A
1 GGAAAGGATTGAGGCCGCAACGGCGAATCCAGTACCTTAGAAGATGTGATA
* * *
30128211 GGGAAAGG-TTGAGGCCGTAACGGTGAATCCAGTACCTTAAAAGATGTGATA
1 -GGAAAGGATTGAGGCCGCAACGGCGAATCCAGTACCTTAGAAGATGTGATA
30128262 GG-AAGGATTGAGGCCGCAACG
1 GGAAAGGATTGAGGCCGCAACG
30128283 ACAAATCTTG
Statistics
Matches: 311, Mismatches: 77, Indels: 57
0.70 0.17 0.13
Matches are distributed among these distances:
47 1 0.00
48 12 0.04
49 157 0.50
50 136 0.44
51 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (51 bp):
GGAAAGGATTGAGGCCGCAACGGCGAATCCAGTACCTTAGAAGATGTGATA
Found at i:30128385 original size:49 final size:49
Alignment explanation
Indices: 30128094--30128394 Score: 147
Period size: 49 Copynumber: 6.1 Consensus size: 49
30128084 GGTAAATCCG
* * **
30128094 ATACCATAAAGATAT-GAAGGGAAAGGTTGAGGCCGCAACTG-CGAACCCA
1 ATACCATAGAGATATAG-AGGGAAAGGTTGAGGCCGCAAC-GACGAATCTT
* * * * * * *
30128143 ATACCTTAGAAGATGT-GATGGTAAGGACTGAGGCCGTAACGGCGAATC-T
1 ATACCATAG-AGATATAGAGGGAAAGG-TTGAGGCCGCAACGACGAATCTT
* ** *
30128192 AGTACCAT-GAAGATAT-GAAGGGAAAGGTTGAGGCCGTAACGGTGAATC-C
1 A-TACCATAG-AGATATAG-AGGGAAAGGTTGAGGCCGCAACGACGAATCTT
* * * * *
30128241 AGTACCTTAAAAGATGT-GATAGG-AAGGATTGAGGCCGCAACGACAAATCTT
1 A-TACCAT-AGAGATATAGA-GGGAAAGG-TTGAGGCCGCAACGACGAATCTT
* * * * * *
30128292 GTACCATGGAGATATAGAGGGAAAGGTTGAAGTCGAAACGACGAACCTT
1 ATACCATAGAGATATAGAGGGAAAGGTTGAGGCCGCAACGACGAATCTT
* * *
30128341 ATACCTTAGAGATATTA-AGGGAAAGAG-TGAGGCCGCAACAACGAATCTC
1 ATACCATAGAGATA-TAGAGGGAAAG-GTTGAGGCCGCAACGACGAATCTT
30128390 ATACC
1 ATACC
30128395 CTGAAGATGA
Statistics
Matches: 193, Mismatches: 45, Indels: 28
0.73 0.17 0.11
Matches are distributed among these distances:
49 120 0.62
50 73 0.38
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (49 bp):
ATACCATAGAGATATAGAGGGAAAGGTTGAGGCCGCAACGACGAATCTT
Found at i:30128450 original size:21 final size:20
Alignment explanation
Indices: 30128426--30128479 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
30128416 TTAAAGCCGC
30128426 AAAGGCGAATCTCAAAGCTGT
1 AAAGGCGAATCT-AAAGCTGT
* *
30128447 AAAGGGCTAGAT-TGAAGCTGT
1 AAA-GGCGA-ATCTAAAGCTGT
30128468 AAAGGCGAATCT
1 AAAGGCGAATCT
30128480 TACGTCCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.07
20 5 0.19
21 13 0.48
22 5 0.19
23 2 0.07
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (20 bp):
AAAGGCGAATCTAAAGCTGT
Found at i:30128703 original size:42 final size:42
Alignment explanation
Indices: 30128640--30129033 Score: 409
Period size: 42 Copynumber: 9.6 Consensus size: 42
30128630 TTACCCCCGA
* * *
30128640 TGAAGACATCATTCAATCTCTTACCTCGATCATAGGGCAGAT
1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
*
30128682 TGAAGACATCATCCAAACTCTTACCCCGATCATGGGGCAGAT
1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
* *
30128724 TGAAGACA-CA-CCAATATCTTACCCTGATCATGGGGCAGAT
1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
* * * *
30128764 TGAAGACA-GAT-AAATCTCTAACCCCAATCATGGGGCAGAT
1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
** *
30128804 CAAAGATATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
** *
30128846 TGAAG-CAT--T-CAATCGT-TTACCCTAATCA-GAGGGCAAAT
1 TGAAGACATCATCCAATC-TCTTACCCCGATCATG-GGGCAGAT
* * * * * *
30128884 TGAAGACATCGTCCGATCTTTTACCCCAATCATGAGGTAGAT
1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
*
30128926 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGTAGAT
1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
* * * * * *
30128968 TGAAGACATTATCCAATCTCTTACCTCGATAATAGGGTAAAT
1 TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
*
30129010 TGAAG-C--CATCCGATCTCTTACCCC
1 TGAAGACATCATCCAATCTCTTACCCC
30129034 AATTAGGAGA
Statistics
Matches: 297, Mismatches: 44, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.00
38 27 0.09
39 20 0.07
40 65 0.22
41 9 0.03
42 174 0.59
43 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGAT
Found at i:30128820 original size:82 final size:83
Alignment explanation
Indices: 30128642--30128992 Score: 308
Period size: 80 Copynumber: 4.3 Consensus size: 83
30128632 ACCCCCGATG
* * *
30128642 AAGACATCATTCAATCTCTTA-CCTCGATCATAGGGCAGATTGAAGACATCATCCAAACTCTTAC
1 AAGACATCATCCAATCTCTTACCCT-GATCATGGGGCAGATTGAAGACATCAT-CAAACTCTAAC
* **
30128706 CCCGATCATGGGGCAGATTG
64 CCCAATCATGGGGCAGATCA
* *
30128726 AAGACA-CA-CCAATATCTTACCCTGATCATGGGGCAGATTGAAGACA-GAT-AAATCTCTAACC
1 AAGACATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATCATCAAA-CTCTAACC
30128787 CCAATCATGGGGCAGATCA
65 CCAATCATGGGGCAGATCA
* * * *
30128806 AAGATATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CAT--TCAATCGT-TTACC
1 AAGACATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATCATCAAAC-TCTAACC
* * **
30128867 CTAATCA-GAGGGCAAATTG
65 CCAATCATG-GGGCAGATCA
* * * ** * * * *
30128886 AAGACATCGTCCGATCTTTTACCCCAATCATGAGGTAGATTGAAGACATCATCCAATCTCTTACC
1 AAGACATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATCAT-CAAACTCTAACC
* * **
30128951 CCGATCATGGGGTAGATTG
65 CCAATCATGGGGCAGATCA
*
30128970 AAGACATTATCCAATCTCTTACC
1 AAGACATCATCCAATCTCTTACC
30128993 TCGATAATAG
Statistics
Matches: 221, Mismatches: 32, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
79 4 0.02
80 85 0.38
81 12 0.05
82 64 0.29
83 7 0.03
84 48 0.22
85 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (83 bp):
AAGACATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATCATCAAACTCTAACCC
CAATCATGGGGCAGATCA
Found at i:30128910 original size:122 final size:122
Alignment explanation
Indices: 30128640--30128977 Score: 407
Period size: 122 Copynumber: 2.8 Consensus size: 122
30128630 TTACCCCCGA
* * * * *
30128640 TGAAGACATCATTCAATCTCTTACCTCGATCATAGGGCAGATTGAAGACATCATCCAAACTCTTA
1 TGAAGACATC-GTCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCCAATCTCTTA
** * *
30128705 CCCCGATCATGGGGCAGATTGAAGACACACCAATATCTTACCCTGATCATGGGGCAGAT
65 CCCCGATCATGGGGCAGATTGAAGACA-TTCAATATCTTACCCTAATCATGGGGCAAAT
* * ** *
30128764 TGAAGACA--GATAAATCTCTAACCCCAATCATGGGGCAGATCAAAGATATCATCCAATCTCTTA
1 TGAAGACATCG-TCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCCAATCTCTTA
*
30128827 CCCCGATCATGGGGCAGATTGAAG-CATTCAATCGT-TTACCCTAATCA-GAGGGCAAAT
65 CCCCGATCATGGGGCAGATTGAAGACATTCAAT-ATCTTACCCTAATCATG-GGGCAAAT
* * * *
30128884 TGAAGACATCGTCCGATCTTTTACCCCAATCATGAGGTAGATTGAAGACATCATCCAATCTCTTA
1 TGAAGACATCGT-CAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCCAATCTCTTA
*
30128949 CCCCGATCATGGGGTAGATTGAAGACATT
65 CCCCGATCATGGGGCAGATTGAAGACATT
30128978 ATCCAATCTC
Statistics
Matches: 182, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
119 1 0.01
120 30 0.16
121 4 0.02
122 135 0.74
123 4 0.02
124 8 0.04
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (122 bp):
TGAAGACATCGTCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCCAATCTCTTAC
CCCGATCATGGGGCAGATTGAAGACATTCAATATCTTACCCTAATCATGGGGCAAAT
Found at i:30128946 original size:164 final size:162
Alignment explanation
Indices: 30128642--30129036 Score: 413
Period size: 164 Copynumber: 2.4 Consensus size: 162
30128632 ACCCCCGATG
*
30128642 AAGACATCATTCAATCTCTTACCTCGATCATAGGGCAGATTGAAGACATCATCCAAACTCTTACC
1 AAGACATCATCCAATCTCTTACCTCGATCATAGGGCAGATTGAAG-CAT-ATCCAAACTCTTACC
* * ** *
30128707 CCGATCATGGGGCAGATTGAAGACACACCAATATCTTACCCTGATCATGGGGCAGATTGAAGACA
64 CCAATCATGGGGCAAATTGAAGACACACCAATATCTTACCCCAATCATGAGGCAGATTGAAGACA
*
30128772 GATAAATCTCTAACCCCAATCATGGGGCAGATCA
129 CATAAATCTCTAACCCCAATCATGGGGCAGATCA
* * * *
30128806 AAGATATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCAT-T-CAATCGT-TTACCC
1 AAGACATCATCCAATCTCTTACCTCGATCATAGGGCAGATTGAAGCATATCCAAAC-TCTTACCC
* * * * * *
30128868 TAATCA-GAGGGCAAATTGAAGACATCGTCCGATCTTTTACCCCAATCATGAGGTAGATTGAAGA
65 CAATCATG-GGGCAAATTGAAGACA-C-ACCAATATCTTACCCCAATCATGAGGCAGATTGAAGA
* * * * **
30128932 CATCATCCAATCTCTTACCCCGATCATGGGGTAGATTG
127 CA-CAT-AAATCTCTAACCCCAATCATGGGGCAGATCA
* * * * * * *
30128970 AAGACATTATCCAATCTCTTACCTCGATAATAGGGTAAATTGAAGC-CATCCGATCTCTTACCCC
1 AAGACATCATCCAATCTCTTACCTCGATCATAGGGCAGATTGAAGCATATCCAAACTCTTACCCC
30129034 AAT
66 AAT
30129037 TAGGAGACAG
Statistics
Matches: 189, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
159 1 0.01
160 29 0.15
161 3 0.02
162 31 0.16
163 5 0.03
164 107 0.57
165 13 0.07
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (162 bp):
AAGACATCATCCAATCTCTTACCTCGATCATAGGGCAGATTGAAGCATATCCAAACTCTTACCCC
AATCATGGGGCAAATTGAAGACACACCAATATCTTACCCCAATCATGAGGCAGATTGAAGACACA
TAAATCTCTAACCCCAATCATGGGGCAGATCA
Found at i:30130728 original size:30 final size:29
Alignment explanation
Indices: 30130692--30130857 Score: 106
Period size: 30 Copynumber: 5.6 Consensus size: 29
30130682 TTAGAAGATT
30130692 CCTAAACTTTCCAAAAATCATATTTTGATC
1 CCTAAACTTTCCAAAAATCATA-TTTGATC
*
30130722 CCTAAACTTTCTAAAAATTCATATTTGAT-
1 CCTAAACTTTCCAAAAA-TCATATTTGATC
* * * *
30130751 CCTAAAACTTTCTAAATATTACAT-TTTAACC
1 CCT-AAACTTTCCAAA-AAT-CATATTTGATC
* * * * *
30130782 CCTAATCTTTCTAAAATTTAGATTTGAATC
1 CCTAAACTTTCCAAAAATCATATTTG-ATC
* * *
30130812 TC-AAACTTTCCAAAAAATTCAAATTT-AAC
1 CCTAAACTTTCC-AAAAA-TCATATTTGATC
30130841 CCTTAAACTTTCCAAAA
1 CC-TAAACTTTCCAAAA
30130858 TTTAGATTTG
Statistics
Matches: 108, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.01
29 19 0.18
30 61 0.56
31 27 0.25
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.37
Consensus pattern (29 bp):
CCTAAACTTTCCAAAAATCATATTTGATC
Found at i:30130747 original size:31 final size:31
Alignment explanation
Indices: 30130692--30130797 Score: 121
Period size: 30 Copynumber: 3.5 Consensus size: 31
30130682 TTAGAAGATT
*
30130692 CCTAAACTTTCCAAAAA-TCATATTTTGATC
1 CCTAAACTTTCTAAAAATTCATATTTTGATC
30130722 CCTAAACTTTCTAAAAATTCATA-TTTGAT-
1 CCTAAACTTTCTAAAAATTCATATTTTGATC
* * * *
30130751 CCTAAAACTTTCTAAATATT-ACATTTTAACC
1 CCT-AAACTTTCTAAAAATTCATATTTTGATC
*
30130782 CCTAATCTTTCTAAAA
1 CCTAAACTTTCTAAAA
30130798 TTTAGATTTG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
29 5 0.08
30 52 0.80
31 8 0.12
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.39
Consensus pattern (31 bp):
CCTAAACTTTCTAAAAATTCATATTTTGATC
Done.