Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 31
Found at i:2730 original size:21 final size:21
Alignment explanation
Indices: 2704--2743 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2694 CCCCCTTTGA
*
2704 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2725 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2744 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:9129 original size:19 final size:18
Alignment explanation
Indices: 9101--9141 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
9091 TGATTGAGAT
9101 TTATCCTAACAATAATTC
1 TTATCCTAACAATAATTC
*
9119 ATTATCTTAACAATAATTC
1 -TTATCCTAACAATAATTC
9138 TTAT
1 TTAT
9142 TTCTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATCCTAACAATAATTC
Found at i:13419 original size:22 final size:22
Alignment explanation
Indices: 13392--13443 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
13382 TTCAACTAAA
13392 ATATAATTACACATTGTGTACC
1 ATATAATTACACATTGTGTACC
*
13414 ATATAATTACACATTGTTTACC
1 ATATAATTACACATTGTGTACC
13436 ATATAATT
1 ATATAATT
13444 TTATCGCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (22 bp):
ATATAATTACACATTGTGTACC
Found at i:15125 original size:20 final size:20
Alignment explanation
Indices: 15100--15138 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15090 TGACATACGA
15100 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
15120 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
15139 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:15132 original size:9 final size:9
Alignment explanation
Indices: 15100--15138 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
15090 TGACATACGA
15100 ATACGAGCC
1 ATACGAGCC
*
15109 ATACAAGCC
1 ATACGAGCC
15118 ATATACGAGCC
1 --ATACGAGCC
15129 ATACGAGCC
1 ATACGAGCC
15138 A
1 A
15139 ATGGAGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (9 bp):
ATACGAGCC
Found at i:15189 original size:29 final size:29
Alignment explanation
Indices: 15145--15248 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
15135 GCCAATGGAG
* **
15145 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
15174 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
* **
15203 AGGTTGCCATGTAGTCCCGGCGACCAAGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
15232 AGGTCGCCATGTAGTCC
1 AGGTCGCCATGTAGTCC
15249 TAGCTCACGA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.16, C:0.29, G:0.32, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:15600 original size:25 final size:26
Alignment explanation
Indices: 15550--15600 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
15540 CTTGGTCGCC
**
15550 GAGATTGCAGCCGAAGAAAGGGAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
*
15576 GAGATTGCAGCCG-AGAAATAAAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
15601 AGGGAGAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.45, C:0.12, G:0.33, T:0.10
Consensus pattern (26 bp):
GAGATTGCAGCCGAAGAAAGAAAGAA
Found at i:15886 original size:45 final size:47
Alignment explanation
Indices: 15824--15914 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
15814 TTATATAGTT
*
15824 AAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATATA
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATA
*
15868 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
15915 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 6 0.15
45 15 0.37
46 5 0.12
47 7 0.17
48 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (47 bp):
AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATA
Found at i:16103 original size:16 final size:16
Alignment explanation
Indices: 16071--16117 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
16061 TTTAAAAAGT
*
16071 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
16087 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
16103 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
16118 AAGTTTAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:16112 original size:15 final size:14
Alignment explanation
Indices: 16092--16122 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
16082 GTTTATTAGT
16092 TTATTATATTATAAG
1 TTATTATATTA-AAG
16107 TTATTATATTAAAG
1 TTATTATATTAAAG
16121 TT
1 TT
16123 TAGTTGTAAA
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:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:18269 original size:17 final size:17
Alignment explanation
Indices: 18247--18279 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18237 CAATGATTTT
*
18247 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
18264 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
18280 AATATTTAAA
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:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:18504 original size:14 final size:14
Alignment explanation
Indices: 18485--18524 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
18475 TAGTAATAAT
18485 TATTAAATCATTAG
1 TATTAAATCATTAG
*
18499 TATTAAATCATTAT
1 TATTAAATCATTAG
*
18513 TA-TAAATAATTA
1 TATTAAATCATTA
18525 CTAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:18647 original size:26 final size:25
Alignment explanation
Indices: 18613--19076 Score: 374
Period size: 26 Copynumber: 18.6 Consensus size: 25
18603 TATTTAAATC
*
18613 ATTATTAAATCATTTTTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
18639 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
18665 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
18691 ATTATCAAATCATTACTA-AATCATC
1 ATTAT-AAATCATTATTATAATGATT
* * * * *
18716 A-AATCATTAAATATT-TAA--ATT
1 ATTATAAATCATTATTATAATGATT
*
18737 ATTATTAAATCATTTTTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
18763 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
18789 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
18815 ATTATCAAATCATTACTA-AATCATCAA
1 ATTAT-AAATCATTATTATAATGAT--T
* *
18842 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
*
18864 A-T-TAAATCATTTTTATAATGATT
1 ATTATAAATCATTATTATAATGATT
18887 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
18913 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
18939 ATTATCAAATCATTACTA-AATCATCAA
1 ATTAT-AAATCATTATTATAATGAT--T
* *
18966 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
*
18988 A-T-TAAATCATTTTTATAATGATT
1 ATTATAAATCATTATTATAATGATT
19011 ATTACT-AATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
19036 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
19062 ATTATCAAATCATTA
1 ATTAT-AAATCATTA
19077 CTAAATCATC
Statistics
Matches: 368, Mismatches: 39, Indels: 62
0.78 0.08 0.13
Matches are distributed among these distances:
19 10 0.03
20 2 0.01
21 5 0.01
22 9 0.02
23 29 0.08
24 24 0.07
25 43 0.12
26 230 0.62
27 14 0.04
28 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (25 bp):
ATTATAAATCATTATTATAATGATT
Found at i:18730 original size:124 final size:124
Alignment explanation
Indices: 18541--19126 Score: 1122
Period size: 124 Copynumber: 4.7 Consensus size: 124
18531 AATAACTAAA
* *
18541 TATTATAAAATCATTATTATAATGATTATTATC-AATCATTACTAAATCATCAAATCATTAAATA
1 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
18605 TTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGAT
66 TTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGAT
18664 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
1 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
*
18729 TTTAAATTATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGAT
66 TTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGAT
18788 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
1 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
18853 TTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGAT
66 TTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGAT
18912 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
1 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
18977 TTTAAATCATTATTAAATCATTTTTATAATGATTATTACT-AATCATTATTATAATGAT
66 TTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGAT
19035 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
1 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
*
19100 TTTAAATCATTATTAAATAATTTTTAT
66 TTTAAATCATTATTAAATCATTTTTAT
19127 GATTAATAAA
Statistics
Matches: 457, Mismatches: 5, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
123 140 0.31
124 317 0.69
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (124 bp):
TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
TTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGAT
Found at i:21962 original size:27 final size:28
Alignment explanation
Indices: 21897--21962 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 28
21887 TATAATATAC
21897 TATTAACTTGATCAAATAAAATTATTAAA
1 TATTAACTTGATCAAATAAAATTATT-AA
21926 TATTAA--TGATCAAATAAAATTTATT-A
1 TATTAACTTGATCAAATAAAA-TTATTAA
21952 T-TTAACTTGAT
1 TATTAACTTGAT
21963 TGATTGCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
25 4 0.12
26 2 0.06
27 17 0.50
28 5 0.15
29 6 0.18
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (28 bp):
TATTAACTTGATCAAATAAAATTATTAA
Found at i:22044 original size:27 final size:27
Alignment explanation
Indices: 21983--22047 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
21973 CTAATAAACC
*
21983 TAATAATGATTTGATAATTACTATTAA
1 TAATAATGATTTGATAATTAATATTAA
* *
22010 T-CTAATGATTTGATATTTAATGATTAA
1 TAATAATGATTTGATAATTAAT-ATTAA
22037 TAAT-ATGATTT
1 TAATAATGATTT
22048 AGTCATAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 17 0.53
27 14 0.44
28 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (27 bp):
TAATAATGATTTGATAATTAATATTAA
Found at i:22820 original size:41 final size:46
Alignment explanation
Indices: 22765--22875 Score: 124
Period size: 48 Copynumber: 2.4 Consensus size: 46
22755 GTTTAAAGAC
* *
22765 ACTAACAAATTAATTAATATTTTTT-TATAT-T-TA-ATAACTTAA
1 ACTAATAAACTAATTAATATTTTTTATATATATATATATAACTTAA
*
22807 ACTAA-GAACTAATTAACTAATTTTTTATATATATAATATATAACTTAA
1 ACTAATAAACTAATTAA-T-ATTTTTTATATATAT-ATATATAACTTAA
22855 ACTAATAAACTAATATAATAT
1 ACTAATAAACTAAT-TAATAT
22876 AACTTAAACT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
41 9 0.16
42 6 0.11
43 7 0.12
44 5 0.09
45 1 0.02
47 2 0.04
48 16 0.28
49 8 0.14
50 3 0.05
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (46 bp):
ACTAATAAACTAATTAATATTTTTTATATATATATATATAACTTAA
Found at i:22881 original size:28 final size:28
Alignment explanation
Indices: 22844--22897 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
22834 TATATATAAT
*
22844 ATATAACTTAAACTAATAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
22872 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
22898 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:22904 original size:28 final size:28
Alignment explanation
Indices: 22839--22904 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
22829 TTTTATATAT
*
22839 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
22867 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
22895 ATAATTTATA
1 ATAATATATA
22905 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:22907 original size:21 final size:21
Alignment explanation
Indices: 22874--22922 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
22864 CTAATATAAT
22874 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
22895 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
22916 ATTAACT
1 A-TAACT
22923 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:23468 original size:20 final size:20
Alignment explanation
Indices: 23443--23480 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23433 ACGTGCATGG
*
23443 CCCATGCACAGTTCCCACGT
1 CCCATGCACAGCTCCCACGT
23463 CCCATGCACAGCTCCCAC
1 CCCATGCACAGCTCCCAC
23481 AACTCCCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.50, G:0.13, T:0.16
Consensus pattern (20 bp):
CCCATGCACAGCTCCCACGT
Found at i:23588 original size:29 final size:29
Alignment explanation
Indices: 23555--23658 Score: 190
Period size: 29 Copynumber: 3.6 Consensus size: 29
23545 AACACCACAT
*
23555 AGGTCGCTCGGATGCCATGGCAACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
*
23584 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
23613 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
23642 AGGTCGCTCGGATGCCA
1 AGGTCGCTCGGATGCCA
23659 CTGTCGAATT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (29 bp):
AGGTCGCTCGGATGCCATGGCGACCTCCA
Found at i:27726 original size:49 final size:45
Alignment explanation
Indices: 27624--27744 Score: 134
Period size: 49 Copynumber: 2.6 Consensus size: 45
27614 GTAACCATGC
*
27624 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
* * * * **
27669 AAAAAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAA
*
27718 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
27745 AAGGTAAGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
45 23 0.37
46 1 0.02
48 1 0.02
49 37 0.60
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
Found at i:29289 original size:29 final size:29
Alignment explanation
Indices: 29244--29307 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
29234 TAAATTTGGT
*
29244 AAAGTTTGGTGAACAAAGTATAACTTTAA
1 AAAGTTTGGTGAACAAAATATAACTTTAA
* * * *
29273 AAAGTTTAGG-GACCAAAATTTAATTTTAG
1 AAAGTTT-GGTGAACAAAATATAACTTTAA
29302 AAAGTT
1 AAAGTT
29308 ACACATGGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (29 bp):
AAAGTTTGGTGAACAAAATATAACTTTAA
Found at i:37607 original size:13 final size:13
Alignment explanation
Indices: 37574--37607 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
37564 AAATGTCGTC
*
37574 TGTTCACGGGTAT
1 TGTTCACTGGTAT
*
37587 TGTTCACTGTTAT
1 TGTTCACTGGTAT
37600 TGTTCACT
1 TGTTCACT
37608 ATTCACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.47
Consensus pattern (13 bp):
TGTTCACTGGTAT
Found at i:51729 original size:44 final size:44
Alignment explanation
Indices: 51680--51764 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
51670 TATTACATGC
* * *
51680 ACCTTTCTGCCAATAATGCACCATTTTGCATTTTCATTTATGGA
1 ACCTTTATGCCAATAATACACCATTATGCATTTTCATTTATGGA
* *
51724 ACCTTTATGTCAATAATACACCGTTATGCATTTTCATTTAT
1 ACCTTTATGCCAATAATACACCATTATGCATTTTCATTTAT
51765 TCATTCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.42
Consensus pattern (44 bp):
ACCTTTATGCCAATAATACACCATTATGCATTTTCATTTATGGA
Found at i:54274 original size:13 final size:13
Alignment explanation
Indices: 54256--54294 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
54246 GTCATAAATC
*
54256 TATGACGTGCATT
1 TATGACGCGCATT
*
54269 TATGACACGCATT
1 TATGACGCGCATT
*
54282 TATGACGCACATT
1 TATGACGCGCATT
54295 GCGCGTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:54358 original size:98 final size:98
Alignment explanation
Indices: 54198--54436 Score: 264
Period size: 98 Copynumber: 2.4 Consensus size: 98
54188 ACACAAATGA
* ** * *
54198 GCGTCATTGAAGCCACCGTCATAAATCTCAGATGACACACAATTATGTGTCATAAATCTATGACG
1 GCGTCATTGAAGCCCCCGTCATAAAT-AAAGATGACACACATTTATGTGTCATAAATCTATGACA
* * *
54263 TGCATTTATGACACGCATTTATGACGCACATTGC
65 CGCATTTATGACACACATTTACGACGCACATTGC
* * * *
54297 GCGTCATTGAAGCCCCCGTCATAAATGAAGATGACACACATTTGTTTGTCATAAATTTATGACAC
1 GCGTCATTGAAGCCCCCGTCATAAATAAAGATGACACACATTTATGTGTCATAAATCTATGACAC
** ** *
54362 GCATTTATGACTTACATTTACGACTTACATTGT
66 GCATTTATGACACACATTTACGACGCACATTGC
* * * *
54395 GTGTCATTGAAGCACACGTCGTTAAA-AAAGATGACACACATT
1 GCGTCATTGAAGCCCCCGTC-ATAAATAAAGATGACACACATT
54437 CGTGTGTCGT
Statistics
Matches: 118, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
98 89 0.75
99 29 0.25
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (98 bp):
GCGTCATTGAAGCCCCCGTCATAAATAAAGATGACACACATTTATGTGTCATAAATCTATGACAC
GCATTTATGACACACATTTACGACGCACATTGC
Found at i:54379 original size:13 final size:13
Alignment explanation
Indices: 54363--54392 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54353 TTATGACACG
*
54363 CATTTATGACTTA
1 CATTTACGACTTA
54376 CATTTACGACTTA
1 CATTTACGACTTA
54389 CATT
1 CATT
54393 GTGTGTCATT
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:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
CATTTACGACTTA
Found at i:54471 original size:2 final size:2
Alignment explanation
Indices: 54464--54490 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54454 TGTCGTAAAT
54464 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 T
54491 TGTAGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61360 original size:30 final size:29
Alignment explanation
Indices: 61299--61388 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 29
61289 AACTATATAT
* *
61299 AACTTTTCAAAATTACATTTTGGAC-CTTA
1 AACTTTTCAAAATTATATTTTAGACAC-TA
*
61328 AACTTTTCAAAGTTTATATTTTAGACACTA
1 AACTTTTCAAA-ATTATATTTTAGACACTA
* *
61358 AACTTTTAGAAAATTATATTTTAGTCACTA
1 AACTTTT-CAAAATTATATTTTAGACACTA
61388 A
1 A
61389 CCAAAGTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
29 11 0.21
30 37 0.71
31 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (29 bp):
AACTTTTCAAAATTATATTTTAGACACTA
Found at i:66799 original size:23 final size:23
Alignment explanation
Indices: 66768--66828 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
66758 CATAATTTTC
66768 CCGAAGGACCACATAGGTTTTG-T
1 CCGAAGGACCACATA-GTTTTGTT
*
66791 CTGAAGGACCACATAGTTTTGTT
1 CCGAAGGACCACATAGTTTTGTT
*
66814 CCGAAAGACCACATA
1 CCGAAGGACCACATA
66829 AAACCCTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 6 0.18
23 28 0.82
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (23 bp):
CCGAAGGACCACATAGTTTTGTT
Found at i:73653 original size:24 final size:24
Alignment explanation
Indices: 73604--73687 Score: 100
Period size: 23 Copynumber: 3.6 Consensus size: 24
73594 TAATTATCCT
* * *
73604 GAAGTACCACATAGG-GTTGTCTC
1 GAAGGACCACATAGGTTTTGTCCC
*
73627 GAAGGACCATATAGGTTTTGTCCC
1 GAAGGACCACATAGGTTTTGTCCC
*
73651 GAAGGATCACATA-GTTTTGTCCC
1 GAAGGACCACATAGGTTTTGTCCC
*
73674 AAAGGACCACATAG
1 GAAGGACCACATAG
73688 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
23 34 0.67
24 17 0.33
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (24 bp):
GAAGGACCACATAGGTTTTGTCCC
Found at i:77338 original size:25 final size:25
Alignment explanation
Indices: 77310--77365 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
77300 AAATTACTAA
*
77310 ATACCCTACAAGAGACACTTACTTG
1 ATACCCTACAAGAGACACTTACCTG
*
77335 ATACCTTACAAGAGACACTTACCTG
1 ATACCCTACAAGAGACACTTACCTG
77360 ATACCC
1 ATACCC
77366 AAATTACTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (25 bp):
ATACCCTACAAGAGACACTTACCTG
Found at i:80396 original size:993 final size:995
Alignment explanation
Indices: 78468--80448 Score: 3585
Period size: 993 Copynumber: 2.0 Consensus size: 995
78458 ATCTTTTCAA
*
78468 AGAGTTGACGATAACCAAAAATCTATCGGTCATAGATTTGATATTCATTCAGACTCATCTTGAAG
1 AGAGTTGACGATAACAAAAAATCTATCGGTCATAGATTTGATATTCATTCAGACTCATCTTGAAG
*
78533 TTTTTGTAATTGTGATTGAGAATATTAGTTTTAGTTTCTCTCACTTCATTGGTTCCTTCATGAGT
66 TTTTTGTAATTGTGATTGAGAATACTAGTTTTAGTTTCTCTCACTTCATTGGTTCCTTCATGAGT
* *
78598 GACTTCAAGATTATCACAAATTTCCTTGGCATTGGAATAAGAATAGACTTTTCCATATTCATTTG
131 GACTTCAAGATTATCACAAATTTCCTAGGCATTGGAATAAGAATAGACTTTTCCATATTCATTCG
78663 CGCCAAATGTGCATGGCCTTGCAATTTAGTTAGAACTTCTTTCTTCTTCACTCTAATTGTCTATC
196 CGCCAAATGTGCATGGCCTTGCAATTTAGTTAGAACTTCTTTCTTCTTCACTCTAATTGTCTATC
78728 TAATTGGTTGAAGTATTAAAACCTTTCATGATAGAGTTCCATGCTCCTAAATCATCTGCTTGAAT
261 TAATTGGTTGAAGTATTAAAACCTTTCATGATAGAGTTCCATGCTCCTAAATCATCTGCTTGAAT
*
78793 GAAAAACTTCATTGTATTCTTCCAATAGGCATAATTTTCCCTATTAAATATGGTGGCTTGTTAAC
326 GAAAAACTTCATTGTATTCTTCCAATAGGCATAATTTTCCATATTAAATATGGTGGCTTGTTAAC
* *
78858 CGATTGTAAACCTTAATGTAGTAGGACCCGAAGGTTGAAGTCATCTTTCTTGGTTGAATGTAGAA
391 CGATTGTAAACCTTAATGTAGTAGGACCCGAAGATTGAAGTCAACTTTCTTGGTTGAATGTAGAA
* * *
78923 TTTGGTAGATACCTCTTAAGAAATTCTCAAGGTTATTATATCATCGATAGAAACCCACTCTAATA
456 TTTGATAGATACCTCTTAAGAAATTCTCAAGGTTATTAAACCATCGATAGAAACCCACTCTAATA
*
78988 CCAATTATTAGCTCTATAGATCAATCAAAATACGTCAAGAAGGGGTGGATTGGTCTTTTAAAAAA
521 CCAATTATTAGCTCTATAGATAAATCAAAATACGTCAAGAAGGGGTGGATTGGTCTTTTAAAAAA
*
79053 TTTGATAGAATTCACTGAAAAATAGAAAGATTTACATAATGATTTACAGTGGTTTGACTTTTAAA
586 TTTGATAGAATTCACTAAAAAATAGAAAGATTTACATAATGATTTACAGTGGTTTGACTTTTAAA
79118 CCGAATCTATGAACACTACCTTAGCATCCACACTAAGAATTTTTCAAATCCACATTTAAGGACAA
651 CCGAATCTATGAACACTACCTTAGCATCCACACTAAGAATTTTTCAAATCCACATTTAAGGACAA
79183 GGTGTAATCTTACAAACACTTCAAGGTTTATATCAAAACCTTGAATACACATTCTCCCAAATATT
716 GGTGTAATCTTACAAACACTTCAAGGTTTATATCAAAACCTTGAATACACATTCTCCCAAATATT
*
79248 AATTACAAATTAAATAAACAAAGAGAAAATCTCATAAGGCTAAATGTGTTTGCAAATATTAAGCA
781 AATTACAAATTAAATAAACAAAGAGAAAATCTCATAAGGCTAAATGTGTTTGCAAAAATTAAGCA
*
79313 CTCACCCAATTCACATTTAAGCAATGTAACATACTAATGCTGTCAGACCTGAATACCAAAGGATT
846 CTCACCCAATTCACATTTAAGCAATGTAACATACTAATGATGTCAGACCTGAATACCAAAGGATT
*
79378 AAAGTGACACACTGGACAACAGAAGTGACATCCCTAAAAATTTTCTTTTTAAACAACTGTAAAGC
911 AAAGTGACACACGGGACAACAGAAGTGACATCCCTAAAAATTTTCTTTTTAAACAACTGTAAAGC
79443 GTCATTTAAAACCTTTTGAG
976 GTCATTTAAAACCTTTTGAG
79463 AGAGTTGACGATAACAAAAAATCTA-CTGGTCATAGATTTGATATTCATTCAGACTCATCTTGAA
1 AGAGTTGACGATAACAAAAAATCTATC-GGTCATAGATTTGATATTCATTCAGACTCATCTTGAA
*
79527 GTTTTTGTAATTGTGATTGATAATACTAGTTTTAGTTTCTCTCACTTCATTGGTTCCTTCATGAG
65 GTTTTTGTAATTGTGATTGAGAATACTAGTTTTAGTTTCTCTCACTTCATTGGTTCCTTCATGAG
*
79592 TGACTTCAAGTTTATCACAAATTTCCTAGGCATTGGAATAAGAATAGACTTTTCCATATTCATCT
130 TGACTTCAAGATTATCACAAATTTCCTAGGCATTGGAATAAGAATAGACTTTTCCATATTCAT-T
79657 CG-GCCAAATGTGCATGGCCTTGCAATTTAGTTAGAACTTCTTTCTTCTTCACTCTAATT-TCTA
194 CGCGCCAAATGTGCATGGCCTTGCAATTTAGTTAGAACTTCTTTCTTCTTCACTCTAATTGTCTA
*
79720 TCTAATTGGTTGAAGTATTAAAACCTTTCATGATAGAGTTCCATGCTCCTAAATCATCTTCTTGA
259 TCTAATTGGTTGAAGTATTAAAACCTTTCATGATAGAGTTCCATGCTCCTAAATCATCTGCTTGA
79785 ATGAAAAACTTCATTGTATTCTTCCAATAGGCATAATTTTCCATATTAAATATGGT-GCTTGTTA
324 ATGAAAAACTTCATTGTATTCTTCCAATAGGCATAATTTTCCATATTAAATATGGTGGCTTGTTA
79849 ACCGATTGTAAACCTTAATGTAGTAGGACCCGAAGATTGAAGTCAACTTTCTTGGTTGAATGTAG
389 ACCGATTGTAAACCTTAATGTAGTAGGACCCGAAGATTGAAGTCAACTTTCTTGGTTGAATGTAG
* * *
79914 AATTTGATAGATACCTCTTAGGAAATTCTCAAGGTTATTAAACCATCGATAGAAACCCATTCTGA
454 AATTTGATAGATACCTCTTAAGAAATTCTCAAGGTTATTAAACCATCGATAGAAACCCACTCTAA
* * *
79979 TACTAATTGTTAGCTCTATAGATAAATCAAAATATGTCAA-AAGGGGGTGGATTGGTCTTTTAAA
519 TACCAATTATTAGCTCTATAGATAAATCAAAATACGTCAAGAA-GGGGTGGATTGGTCTTTTAAA
* * *
80043 AATTTTGATAGAATTCATTAAAAAATAGAAAGATTTACATAATGATTTAGAGTGGTTTGACTTTT
583 AAATTTGATAGAATTCACTAAAAAATAGAAAGATTTACATAATGATTTACAGTGGTTTGACTTTT
*
80108 AAACCGAATCTATGAACACTACCTTAGCATCTACACTAAGAATTTTTCAAATCCACATTTAAGGA
648 AAACCGAATCTATGAACACTACCTTAGCATCCACACTAAGAATTTTTCAAATCCACATTTAAGGA
80173 CAAGGTGTAATCTTACAAACACTTCAAGGTTTATATCAAAACCTTGAATACACATTCTCCCAAAT
713 CAAGGTGTAATCTTACAAACACTTCAAGGTTTATATCAAAACCTTGAATACACATTCTCCCAAAT
*
80238 ATTAATTACAAATTAAATAAACGAAGAGAAAATCTCATAAGGCTAAATGTGTTTGCAAAAATTAA
778 ATTAATTACAAATTAAATAAACAAAGAGAAAATCTCATAAGGCTAAATGTGTTTGCAAAAATTAA
* * * *
80303 GCACTCACCCAATTCACATTTAAGCAATGTAATATACTAATGATGTCCGACCTGAATACCGAAGT
843 GCACTCACCCAATTCACATTTAAGCAATGTAACATACTAATGATGTCAGACCTGAATACCAAAGG
*
80368 ATTAAAGTGTCACACGGGACAACAGAAGTGACATCCCTAAAAATTTTCTTTTTAAACAACTGTAA
908 ATTAAAGTGACACACGGGACAACAGAAGTGACATCCCTAAAAATTTTCTTTTTAAACAACTGTAA
*
80433 AGCGTCATTTTAAACC
973 AGCGTCATTTAAAACC
80449 ATCCATAAAG
Statistics
Matches: 948, Mismatches: 35, Indels: 8
0.96 0.04 0.01
Matches are distributed among these distances:
992 2 0.00
993 578 0.61
994 124 0.13
995 242 0.26
996 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (995 bp):
AGAGTTGACGATAACAAAAAATCTATCGGTCATAGATTTGATATTCATTCAGACTCATCTTGAAG
TTTTTGTAATTGTGATTGAGAATACTAGTTTTAGTTTCTCTCACTTCATTGGTTCCTTCATGAGT
GACTTCAAGATTATCACAAATTTCCTAGGCATTGGAATAAGAATAGACTTTTCCATATTCATTCG
CGCCAAATGTGCATGGCCTTGCAATTTAGTTAGAACTTCTTTCTTCTTCACTCTAATTGTCTATC
TAATTGGTTGAAGTATTAAAACCTTTCATGATAGAGTTCCATGCTCCTAAATCATCTGCTTGAAT
GAAAAACTTCATTGTATTCTTCCAATAGGCATAATTTTCCATATTAAATATGGTGGCTTGTTAAC
CGATTGTAAACCTTAATGTAGTAGGACCCGAAGATTGAAGTCAACTTTCTTGGTTGAATGTAGAA
TTTGATAGATACCTCTTAAGAAATTCTCAAGGTTATTAAACCATCGATAGAAACCCACTCTAATA
CCAATTATTAGCTCTATAGATAAATCAAAATACGTCAAGAAGGGGTGGATTGGTCTTTTAAAAAA
TTTGATAGAATTCACTAAAAAATAGAAAGATTTACATAATGATTTACAGTGGTTTGACTTTTAAA
CCGAATCTATGAACACTACCTTAGCATCCACACTAAGAATTTTTCAAATCCACATTTAAGGACAA
GGTGTAATCTTACAAACACTTCAAGGTTTATATCAAAACCTTGAATACACATTCTCCCAAATATT
AATTACAAATTAAATAAACAAAGAGAAAATCTCATAAGGCTAAATGTGTTTGCAAAAATTAAGCA
CTCACCCAATTCACATTTAAGCAATGTAACATACTAATGATGTCAGACCTGAATACCAAAGGATT
AAAGTGACACACGGGACAACAGAAGTGACATCCCTAAAAATTTTCTTTTTAAACAACTGTAAAGC
GTCATTTAAAACCTTTTGAG
Found at i:82974 original size:40 final size:40
Alignment explanation
Indices: 82929--83039 Score: 168
Period size: 40 Copynumber: 2.8 Consensus size: 40
82919 AAGGACAATA
* * *
82929 AGTGTACATGGTGGGCATGACCTTATGTGTAATACACTTT
1 AGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTC
* * *
82969 GGTGTATATGGTGGACACGACCTTATGTGCAATACACTTC
1 AGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTC
83009 AGTGTATATGGTGGGCACGACCTTATGTGTA
1 AGTGTATATGGTGGGCACGACCTTATGTGTA
83040 GCATTAAGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (40 bp):
AGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTC
Found at i:83743 original size:22 final size:22
Alignment explanation
Indices: 83678--83743 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
83668 GTAGCGCATC
*
83678 GGTACTGTTTATCACTGTTCAC
1 GGTACTGTTTATCACTGTTCAT
83700 GGTACTGTTTATCACTGTTCAT
1 GGTACTGTTTATCACTGTTCAT
* * *
83722 GGTACTATTCATCACTATTCAT
1 GGTACTGTTTATCACTGTTCAT
83744 AAAAAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (22 bp):
GGTACTGTTTATCACTGTTCAT
Found at i:89709 original size:17 final size:17
Alignment explanation
Indices: 89686--89730 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 17
89676 TATAATTTTA
89686 AAAAATAATTAGATTAT
1 AAAAATAATTAGATTAT
*
89703 CAAAATAA--A-ATTAT
1 AAAAATAATTAGATTAT
89717 AAAAATAATTAGAT
1 AAAAATAATTAGAT
89731 ACTAAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 12 0.52
15 1 0.04
16 1 0.04
17 9 0.39
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAAATAATTAGATTAT
Found at i:90645 original size:8 final size:8
Alignment explanation
Indices: 90595--90675 Score: 58
Period size: 8 Copynumber: 10.0 Consensus size: 8
90585 TTTATAACTG
*
90595 TAAAAAAA
1 TAAAATAA
90603 TAAAATAA
1 TAAAATAA
*
90611 TTAAAAAAA
1 -TAAAATAA
90620 TAATAA-AA
1 TAA-AATAA
*
90628 -AAATTAAA
1 TAAAAT-AA
90636 TAAAATAA
1 TAAAATAA
*
90644 TAAAAAAA
1 TAAAATAA
*
90652 TTAAATAA
1 TAAAATAA
*
90660 TACAATAA
1 TAAAATAA
*
90668 TTAAATAA
1 TAAAATAA
90676 AATACTAACA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 41 0.72
9 13 0.23
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (8 bp):
TAAAATAA
Found at i:90661 original size:16 final size:16
Alignment explanation
Indices: 90595--90675 Score: 76
Period size: 16 Copynumber: 5.0 Consensus size: 16
90585 TTTATAACTG
*
90595 TAAAAAAATAAAATAA
1 TAAAAAAATTAAATAA
90611 TTAAAAAAA-T-AATAA
1 -TAAAAAAATTAAATAA
* *
90626 AAAAATTAAATAAAATAA
1 TAAAA--AAATTAAATAA
90644 TAAAAAAATTAAATAA
1 TAAAAAAATTAAATAA
* *
90660 TACAATAATTAAATAA
1 TAAAAAAATTAAATAA
90676 AATACTAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
14 4 0.08
15 5 0.09
16 27 0.51
17 8 0.15
18 9 0.17
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAAAAATTAAATAA
Found at i:90667 original size:21 final size:21
Alignment explanation
Indices: 90595--90659 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
90585 TTTATAACTG
* *
90595 TAAAAAAATAAAATAATTAAA
1 TAAAATAATAAAAAAATTAAA
90616 -AAAATAATAAAAAAATTAAA
1 TAAAATAATAAAAAAATTAAA
90636 TAAAATAATAAAAAAATTAAA
1 TAAAATAATAAAAAAATTAAA
90657 TAA
1 TAA
90660 TACAATAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 18 0.44
21 23 0.56
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAATAATAAAAAAATTAAA
Found at i:90689 original size:37 final size:37
Alignment explanation
Indices: 90617--90689 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
90607 ATAATTAAAA
90617 AAATAATAAAAAAATTAAATAAAATAATAAAAAAATT
1 AAATAATAAAAAAATTAAATAAAATAATAAAAAAATT
* * * *
90654 AAATAATACAATAATTAAATAAAATACTAACAAAAT
1 AAATAATAAAAAAATTAAATAAAATAATAAAAAAAT
90690 ATGATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (37 bp):
AAATAATAAAAAAATTAAATAAAATAATAAAAAAATT
Found at i:92986 original size:14 final size:15
Alignment explanation
Indices: 92967--92996 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
92957 TCTCCATGTT
92967 ATATATA-AAAAAAA
1 ATATATAGAAAAAAA
92981 ATATATAGAAAAAAA
1 ATATATAGAAAAAAA
92996 A
1 A
92997 GCACATCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
ATATATAGAAAAAAA
Found at i:92987 original size:16 final size:16
Alignment explanation
Indices: 92966--92996 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
92956 TTCTCCATGT
*
92966 TATATATAAAAAAAAA
1 TATATAGAAAAAAAAA
92982 TATATAGAAAAAAAA
1 TATATAGAAAAAAAA
92997 GCACATCCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
TATATAGAAAAAAAAA
Found at i:93623 original size:9 final size:9
Alignment explanation
Indices: 93609--93638 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
93599 TGGAATTATT
93609 ATATATTAA
1 ATATATTAA
*
93618 ATATATTAT
1 ATATATTAA
93627 ATATATTAA
1 ATATATTAA
93636 ATA
1 ATA
93639 CATATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATATTAA
Found at i:93631 original size:18 final size:19
Alignment explanation
Indices: 93603--93638 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
93593 ATTAATTGGA
93603 ATTATTATATATTAAATAT
1 ATTATTATATATTAAATAT
93622 ATTA-TATATATTAAATA
1 ATTATTATATATTAAATA
93639 CATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATTATATATTAAATAT
Found at i:93907 original size:30 final size:29
Alignment explanation
Indices: 93856--93915 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
93846 TAATATTTTC
*
93856 AAGAAAAAAAGTTCGGTTTAATTAACAATTA
1 AAGAAAAAAAGTTCGGATTAATT--CAATTA
93887 AAGAAAAAAAGTTC-GATTAATTCAATTA
1 AAGAAAAAAAGTTCGGATTAATTCAATTA
93915 A
1 A
93916 TTAAATTCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.25
30 7 0.25
31 14 0.50
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (29 bp):
AAGAAAAAAAGTTCGGATTAATTCAATTA
Found at i:111854 original size:59 final size:59
Alignment explanation
Indices: 111779--111906 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 59
111769 GTAGTGCTAA
* * * * *
111779 CCCGAGTATGACACATAAGGTCATGTCCACCATCTATACTAAGTATCCTTAAGTACAGT
1 CCCGAATATGAAACATAAGGTCATGCCCACCATATACACTAAGTATCCTTAAGTACAGT
* * * ** *
111838 CCCGAATATGAAACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATT
1 CCCGAATATGAAACATAAGGTCATGCCCACCATATACACTAAGTATCCTTAAGTACAGT
111897 CCCGAATATG
1 CCCGAATATG
111907 CAGCCTGCTG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (59 bp):
CCCGAATATGAAACATAAGGTCATGCCCACCATATACACTAAGTATCCTTAAGTACAGT
Found at i:120454 original size:58 final size:59
Alignment explanation
Indices: 120372--120537 Score: 201
Period size: 58 Copynumber: 2.8 Consensus size: 59
120362 TGGCACTTTG
* * *
120372 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGAT-
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCA-TGATA
* * *** * * **
120431 TGTGCT-AAATGGTAAGGGGATCATATTGAAAATATGGATTTTCAGATAGGGCATTTTA
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCATGATA
120489 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATA
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATA
120538 AAACCCTAAG
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
57 2 0.02
58 43 0.49
59 42 0.48
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.32
Consensus pattern (59 bp):
TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCATGATA
Found at i:120628 original size:59 final size:59
Alignment explanation
Indices: 120565--120677 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
120555 CAAAGATAAG
* * *
120565 AAAATCATACT-AATGGTATGGA-TTTTCACATAGGGCATTTCATGTGCTAAAATGGTAAC
1 AAAATCATACTAAAT-GTATGAATTTTTCA-ATAGGGAACTTCATGTGCTAAAATGGTAAC
* *
120624 AAAATCATACTAAATGTATGAATTTTTGAATAGGGAACTTCGTGTGCTAAAATG
1 AAAATCATACTAAATGTATGAATTTTTCAATAGGGAACTTCATGTGCTAAAATG
120678 AAAGGGGAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 39 0.83
60 8 0.17
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (59 bp):
AAAATCATACTAAATGTATGAATTTTTCAATAGGGAACTTCATGTGCTAAAATGGTAAC
Found at i:123882 original size:18 final size:18
Alignment explanation
Indices: 123859--123899 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
123849 GTTGATAAAC
* *
123859 ATAAGCATGCTATGAAGT
1 ATAAGCATGCTAAGAAGA
*
123877 ATAAGCATGTTAAGAAGA
1 ATAAGCATGCTAAGAAGA
123895 ATAAG
1 ATAAG
123900 AAAATGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (18 bp):
ATAAGCATGCTAAGAAGA
Found at i:127685 original size:15 final size:15
Alignment explanation
Indices: 127665--127696 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
127655 TAAAAGACTC
127665 TTGGAGAGGAAAGTT
1 TTGGAGAGGAAAGTT
127680 TTGGAGAGGAAAGTT
1 TTGGAGAGGAAAGTT
127695 TT
1 TT
127697 AAAGAGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (15 bp):
TTGGAGAGGAAAGTT
Found at i:127702 original size:15 final size:15
Alignment explanation
Indices: 127669--127702 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
127659 AGACTCTTGG
**
127669 AGAGGAAAGTTTTGG
1 AGAGGAAAGTTTTAA
127684 AGAGGAAAGTTTTAA
1 AGAGGAAAGTTTTAA
127699 AGAG
1 AGAG
127703 TACAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (15 bp):
AGAGGAAAGTTTTAA
Found at i:131072 original size:37 final size:37
Alignment explanation
Indices: 131021--131093 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
131011 GAGTATTTAC
* * *
131021 AGAAGGCATGTATTCTATATGGATCTTGTGTATTTGT
1 AGAAGACATATATTCTATATGGACCTTGTGTATTTGT
131058 AGAAGACATATATTCTATATGGACCTTGTGTATTTG
1 AGAAGACATATATTCTATATGGACCTTGTGTATTTG
131094 AGTCATGTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (37 bp):
AGAAGACATATATTCTATATGGACCTTGTGTATTTGT
Found at i:137003 original size:23 final size:23
Alignment explanation
Indices: 136977--137020 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
136967 ACAACAAATT
*
136977 CTAA-AATAAGAATGAATAAGGGC
1 CTAATAATAA-AATGAACAAGGGC
*
137000 CTAATATTAAAATGAACAAGG
1 CTAATAATAAAATGAACAAGG
137021 ATGAGATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.20
Consensus pattern (23 bp):
CTAATAATAAAATGAACAAGGGC
Found at i:140133 original size:21 final size:22
Alignment explanation
Indices: 140107--140149 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
140097 TAGTCTCAAT
140107 AAACC-AAACAAGTTAGAAATA
1 AAACCAAAACAAGTTAGAAATA
140128 AAACCAAAAAACAAGTTAGAAA
1 AAACC--AAAACAAGTTAGAAA
140150 GGGGGGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
24 14 0.74
ACGTcount: A:0.65, C:0.14, G:0.09, T:0.12
Consensus pattern (22 bp):
AAACCAAAACAAGTTAGAAATA
Found at i:144098 original size:27 final size:27
Alignment explanation
Indices: 144068--144122 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
144058 GCACATTATA
* *
144068 CATTTCACTTATGGCATCCTTTCTTGC
1 CATTCCACTTATGGCATCCTTTCATGC
** *
144095 CATTCCTTTTATGGCATCTTTTCATGC
1 CATTCCACTTATGGCATCCTTTCATGC
144122 C
1 C
144123 TTTAATGCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.29, G:0.11, T:0.45
Consensus pattern (27 bp):
CATTCCACTTATGGCATCCTTTCATGC
Found at i:144353 original size:54 final size:53
Alignment explanation
Indices: 144245--144772 Score: 538
Period size: 54 Copynumber: 9.8 Consensus size: 53
144235 CACACGGTCA
* ** ** * * *
144245 TTCATAAACATATTATGAATTTCGTTAGTTGCACACATAATG-CTTAAACTGTTG
1 TTCATCAACATAGGATGAATTT-GTGGGTTGCACACATAGTGTC-GAAACGGTTG
* * * ** *
144299 TTCGTTAACATATGATGAATTATGTGGGTTGCACACATAGTCCCGAAACAGTTG
1 TTCATCAACATAGGATGAATT-TGTGGGTTGCACACATAGTGTCGAAACGGTTG
* * * * * *
144353 TTCATCAACATAGGATGAATTCTATGAGTTGTACAAATAGTGTCGAAACTGTTT
1 TTCATCAACATAGGATGAATT-TGTGGGTTGCACACATAGTGTCGAAACGGTTG
* * *
144407 TTTATCAACATAAGATGAATTTCGTGGGTTGCACACATAGTG-CTAAAACGGTTG
1 TTCATCAACATAGGATGAATTT-GTGGGTTGCACACATAGTGTC-GAAACGGTTG
** * * *
144461 TTCATCAACATAGGATGAATTACATGGGTTGCACAAATAGTGTCAAAATGGTTG
1 TTCATCAACATAGGATGAATT-TGTGGGTTGCACACATAGTGTCGAAACGGTTG
* * *
144515 TTCATCAACATAGGATGAATTTCGTGGGTTGCACATATAGTGTCGAAATGGTTA
1 TTCATCAACATAGGATGAATTT-GTGGGTTGCACACATAGTGTCGAAACGGTTG
* ** * * *
144569 TTCATCAACATATGATGAATTTCGTGGGTTGTTCACATAGTTTCAAAATGGTTG
1 TTCATCAACATAGGATGAATTT-GTGGGTTGCACACATAGTGTCGAAACGGTTG
* *
144623 TTCATCAGCATAGGATGAATTCTGTGGGTTGCACACATAGTGTCGAAATGGTTG
1 TTCATCAACATAGGATGAATT-TGTGGGTTGCACACATAGTGTCGAAACGGTTG
*
144677 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAGTGTCGAAACGGTTG
1 TTCATCAACATAGGATGAA-TTTGTGGGTTGCACACATAGTGTCGAAACGGTTG
* * * *
144731 TTCATCAACATATGATGAGTTCTATAGGTTGCACACATAGTG
1 TTCATCAACATAGGATGAATT-TGTGGGTTGCACACATAGTG
144773 CCCATACAAA
Statistics
Matches: 404, Mismatches: 60, Indels: 20
0.83 0.12 0.04
Matches are distributed among these distances:
53 4 0.01
54 394 0.98
55 6 0.01
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (53 bp):
TTCATCAACATAGGATGAATTTGTGGGTTGCACACATAGTGTCGAAACGGTTG
Found at i:144687 original size:27 final size:27
Alignment explanation
Indices: 144657--144742 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
144647 TGGGTTGCAC
144657 ACATAGTGTCGAAATGGTTGTTCATCA
1 ACATAGTGTCGAAATGGTTGTTCATCA
* * *
144684 ACATA-TGAT-GAATTTTGTGGGTTGCA-C-
1 ACATAGTG-TCGAA-ATGGT-TGTT-CATCA
*
144711 ACATAGTGTCGAAACGGTTGTTCATCA
1 ACATAGTGTCGAAATGGTTGTTCATCA
144738 ACATA
1 ACATA
144743 TGATGAGTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 2 0.05
26 9 0.20
27 22 0.50
28 9 0.20
29 2 0.05
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (27 bp):
ACATAGTGTCGAAATGGTTGTTCATCA
Found at i:144789 original size:54 final size:54
Alignment explanation
Indices: 144623--144805 Score: 123
Period size: 54 Copynumber: 3.4 Consensus size: 54
144613 AAAATGGTTG
* * * * * * ******
144623 TTCATCAGCATAGGATGAATTCTGTGGGTTGCACACATAGTGTCGAAATGGTTG
1 TTCATCAACATATGATGAATTCTATAGGTTGCACACATAGTGCCCAAACAAAAA
* * * * * *****
144677 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAGTGTCGAAACGGTTG
1 TTCATCAACATATGATGAATTCTATAGGTTGCACACATAGTGCCCAAACAAAAA
* *
144731 TTCATCAACATATGATGAGTTCTATAGGTTGCACACATAGTGCCCATACAAAAA
1 TTCATCAACATATGATGAATTCTATAGGTTGCACACATAGTGCCCAAACAAAAA
* * *
144785 TTCATAAACTTATTATGAATT
1 TTCATCAACATATGATGAATT
144806 TTTTAGTTTT
Statistics
Matches: 109, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 109 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTCTATAGGTTGCACACATAGTGCCCAAACAAAAA
Found at i:144805 original size:162 final size:162
Alignment explanation
Indices: 144238--144774 Score: 646
Period size: 162 Copynumber: 3.3 Consensus size: 162
144228 TAGTGCCCAC
* * * ** * ** * *
144238 ACGGTCATTCATAAACATATTATGAATTTCGTTAGTTGCACACATAATGCTTAAACTGTTGTTCG
1 ACGGTTATTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCA
* * * ** **
144303 TTAACATATGATGAATTATGTGGGTTGCACACATAGTCCCGAAACAGTTGTTCATCAACATAGGA
66 TCAACATAGGATGAATTCTGTGGGTTGCACACATAGTGTCGAAATGGTTGTTCATCAACATAGGA
* * * *
144368 TGAATTCTATGAGTTGTACAAATAGTGTCGAA
131 TGAATTTTGTGGGTTGCACAAATAGTGTCGAA
* * * * *
144400 ACTGTTTTTTATCAACATAAGATGAATTTCGTGGGTTGCACACATAGTGCTAAAACGGTTGTTCA
1 ACGGTTATTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCA
* * *
144465 TCAACATAGGATGAATTAC-ATGGGTTGCACAAATAGTGTCAAAATGGTTGTTCATCAACATAGG
66 TCAACATAGGATGAATT-CTGTGGGTTGCACACATAGTGTCGAAATGGTTGTTCATCAACATAGG
* *
144529 ATGAATTTCGTGGGTTGCACATATAGTGTCGAA
130 ATGAATTTTGTGGGTTGCACAAATAGTGTCGAA
* ** ** *
144562 ATGGTTATTCATCAACATATGATGAATTTCGTGGGTTGTTCACATAGTTTCAAAATGGTTGTTCA
1 ACGGTTATTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCA
* *
144627 TCAGCATAGGATGAATTCTGTGGGTTGCACACATAGTGTCGAAATGGTTGTTCATCAACATATGA
66 TCAACATAGGATGAATTCTGTGGGTTGCACACATAGTGTCGAAATGGTTGTTCATCAACATAGGA
*
144692 TGAATTTTGTGGGTTGCACACATAGTGTCGAA
131 TGAATTTTGTGGGTTGCACAAATAGTGTCGAA
* * * *
144724 ACGGTTGTTCATCAACATATGATG-AGTTCTATAGGTTGCACACATAGTGCC
1 ACGGTTATTCATCAACATATGATGAATTTC-GTGGGTTGCACACATAGTGCC
144775 CATACAAAAA
Statistics
Matches: 316, Mismatches: 56, Indels: 6
0.84 0.15 0.02
Matches are distributed among these distances:
161 5 0.02
162 311 0.98
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (162 bp):
ACGGTTATTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCA
TCAACATAGGATGAATTCTGTGGGTTGCACACATAGTGTCGAAATGGTTGTTCATCAACATAGGA
TGAATTTTGTGGGTTGCACAAATAGTGTCGAA
Found at i:145212 original size:22 final size:22
Alignment explanation
Indices: 145170--145214 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
145160 ACCCCTACCA
* *
145170 TGGTATCGATACTTCTATATTG
1 TGGTACCGATACTCCTATATTG
145192 TGGTACCGATACTCCCT-TATTG
1 TGGTACCGATACT-CCTATATTG
145214 T
1 T
145215 ATCAATACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (22 bp):
TGGTACCGATACTCCTATATTG
Found at i:149426 original size:12 final size:12
Alignment explanation
Indices: 149409--149487 Score: 51
Period size: 12 Copynumber: 6.8 Consensus size: 12
149399 TATTATAAGA
149409 AGAAAAAAAAAT
1 AGAAAAAAAAAT
149421 AGAAAAAGAAAAT
1 AGAAAAA-AAAAT
* *
149434 -GAAAACGAAGA-
1 AGAAAA-AAAAAT
149445 AG-AAAAAAAAT
1 AGAAAAAAAAAT
*
149456 -GAAAAAGAGAA-
1 AGAAAAA-AAAAT
* *
149467 AGAAAAGAAAAG
1 AGAAAAAAAAAT
149479 AGAAAAAAA
1 AGAAAAAAA
149488 TGAGAGATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
10 4 0.08
11 10 0.20
12 32 0.63
13 5 0.10
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (12 bp):
AGAAAAAAAAAT
Found at i:149431 original size:18 final size:17
Alignment explanation
Indices: 149408--149487 Score: 72
Period size: 18 Copynumber: 4.6 Consensus size: 17
149398 ATATTATAAG
149408 AAGAAAAAAAAATAGAAA
1 AAGAAAAAAAAA-AGAAA
* * *
149426 AAGAAAATGAAAACGAAG
1 AAGAAAA-AAAAAAGAAA
*
149444 AAG-AAAAAAAATGAAA
1 AAGAAAAAAAAAAGAAA
* *
149460 AAGAGAAAGAAAAGAAA
1 AAGAAAAAAAAAAGAAA
149477 AGAGAAAAAAA
1 A-AGAAAAAAA
149488 TGAGAGATGA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
16 10 0.21
17 14 0.29
18 20 0.42
19 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.04
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:149454 original size:22 final size:23
Alignment explanation
Indices: 149424--149477 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
149414 AAAAAATAGA
*
149424 AAAAGAAAATGAAAACGA-AGAAG
1 AAAAGAAAATGAAAAAGAGA-AAG
149447 AAAA-AAAATGAAAAAGAGAAAG
1 AAAAGAAAATGAAAAAGAGAAAG
149469 AAAAGAAAA
1 AAAAGAAAA
149478 GAGAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.04
Consensus pattern (23 bp):
AAAAGAAAATGAAAAAGAGAAAG
Found at i:149490 original size:33 final size:34
Alignment explanation
Indices: 149405--149490 Score: 115
Period size: 33 Copynumber: 2.5 Consensus size: 34
149395 TATATATTAT
149405 AAGAAGAAAAAAAAATAGAAAAAGAAAATGAAAACG
1 AAGAAG-AAAAAAAAT-GAAAAAGAAAATGAAAACG
149441 AAGAAGAAAAAAAATGAAAAAGAGAAA-GAAAA-G
1 AAGAAGAAAAAAAATGAAAAAGA-AAATGAAAACG
149474 AA-AAGAGAAAAAAATGA
1 AAGAAGA-AAAAAAATGA
149491 GAGATGAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
32 4 0.08
33 13 0.27
34 13 0.27
35 12 0.25
36 6 0.12
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.05
Consensus pattern (34 bp):
AAGAAGAAAAAAAATGAAAAAGAAAATGAAAACG
Found at i:153692 original size:47 final size:45
Alignment explanation
Indices: 153598--153723 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 45
153588 GTAACCATGG
* * *
153598 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
153642 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
153689 AAATAAGCTTACGAGCTTATAGG-ATAAATGGTAAG
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
153724 AGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 36 0.50
48 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:155175 original size:2 final size:2
Alignment explanation
Indices: 155168--155192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
155158 CCAGAAAAGC
155168 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 T
155193 TTCTAACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:160978 original size:21 final size:21
Alignment explanation
Indices: 160952--160992 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
160942 CCAGTATGCT
*
160952 CAGAGGGAACTGATTCCCCCC
1 CAGAGGGAACCGATTCCCCCC
*
160973 CAGAGGGTACCGATTCCCCC
1 CAGAGGGAACCGATTCCCCC
160993 TTGTGTAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.39, G:0.24, T:0.15
Consensus pattern (21 bp):
CAGAGGGAACCGATTCCCCCC
Found at i:162779 original size:20 final size:20
Alignment explanation
Indices: 162754--162809 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
162744 GCAACCCCTT
162754 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
162774 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
* *
162793 TGAAAGTACATGCTTTT
1 TGAAAATACATGATTTT
162810 GGCCAAATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:163752 original size:21 final size:21
Alignment explanation
Indices: 163703--163752 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
163693 TGTTTCCATG
163703 ATATGTAAATGATATAAAAAC
1 ATATGTAAATGATATAAAAAC
*
163724 ATA-ATAAATGA-ATATAAAAC
1 ATATGTAAATGATATA-AAAAC
163744 ATATGTAAA
1 ATATGTAAA
163753 ACATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.12
20 15 0.60
21 7 0.28
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (21 bp):
ATATGTAAATGATATAAAAAC
Found at i:165200 original size:81 final size:81
Alignment explanation
Indices: 165072--165342 Score: 411
Period size: 81 Copynumber: 3.3 Consensus size: 81
165062 TATGCCAACT
* *
165072 ATGCACAGCTAGG-CATTTAGTCTTTTATCTCAAAGGTAGTTAACCTTTCATCTAATTGGCATAA
1 ATGCACAGCTAGGCCA-TTAATCTTTTA-CTCAAAGGTATTTAACCTTTCATCTAATTGGCATAA
**
165136 TTGACATGTTTCTGTCAA
64 TTGACACATTTCTGTCAA
*
165154 ATGCACAAG-TAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAAT
1 ATGCAC-AGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAAT
* *
165218 TGACACCTTTCTATCAA
65 TGACACATTTCTGTCAA
*
165235 ATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATTATT
1 ATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATT
165300 GACACATTTCTGTCAA
66 GACACATTTCTGTCAA
* *
165316 ATGCACGGCTAGGCCATTAATATTTTA
1 ATGCACAGCTAGGCCATTAATCTTTTA
165343 TTTAAAATAG
Statistics
Matches: 174, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
80 2 0.01
81 148 0.85
82 20 0.11
83 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (81 bp):
ATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATT
GACACATTTCTGTCAA
Found at i:168926 original size:21 final size:20
Alignment explanation
Indices: 168900--168943 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
168890 TGGCCTATCT
168900 CATGTTTGATATGCACTTATG
1 CATGTTTGATATGCACTT-TG
*
168921 CATGTTTGATATGTACTTTG
1 CATGTTTGATATGCACTTTG
168941 CAT
1 CAT
168944 TCCATCATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (20 bp):
CATGTTTGATATGCACTTTG
Found at i:169652 original size:28 final size:28
Alignment explanation
Indices: 169620--169676 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
169610 AGAATTTGTG
*
169620 AGTAGGTTGGGAATTTAAAGAAAGAGGC
1 AGTAGATTGGGAATTTAAAGAAAGAGGC
*
169648 AGTAGATTGGGAATTTAAAGAAAGTGGC
1 AGTAGATTGGGAATTTAAAGAAAGAGGC
169676 A
1 A
169677 AAATAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.33, T:0.23
Consensus pattern (28 bp):
AGTAGATTGGGAATTTAAAGAAAGAGGC
Found at i:181157 original size:25 final size:23
Alignment explanation
Indices: 181129--181208 Score: 56
Period size: 25 Copynumber: 3.3 Consensus size: 23
181119 TTGAAGAAAT
181129 TTGATGAAGAAATTTTAAAAAATAA
1 TTGATGAAG--ATTTTAAAAAATAA
* * *
181154 TTGAT-AATATTTTTTTACAAAATAT
1 TTGATGAAGA---TTTTAAAAAATAA
*
181179 TTGATGAAG-TTTTGAAAAATAA
1 TTGATGAAGATTTTAAAAAATAA
*
181201 TTTATGAA
1 TTGATGAA
181209 AGAATATTGA
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
22 18 0.42
24 2 0.05
25 21 0.49
26 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.41
Consensus pattern (23 bp):
TTGATGAAGATTTTAAAAAATAA
Found at i:203840 original size:8 final size:8
Alignment explanation
Indices: 203829--203863 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
203819 GAGAAAAATC
203829 AGAAAAGA
1 AGAAAAGA
203837 AGAAAAGA
1 AGAAAAGA
203845 AGAAAAGAAA
1 AGAAAAG--A
203855 AGAAAAGA
1 AGAAAAGA
203863 A
1 A
203864 AAAGTGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:203842 original size:16 final size:16
Alignment explanation
Indices: 203829--203863 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
203819 GAGAAAAATC
203829 AGAAAAGAAGAAAAGA
1 AGAAAAGAAGAAAAGA
203845 AGAAAAGAAAAGAAAAGA
1 AGAAAAG--AAGAAAAGA
203863 A
1 A
203864 AAAGTGAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAGAAAAGA
Found at i:203852 original size:13 final size:13
Alignment explanation
Indices: 203829--203863 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
203819 GAGAAAAATC
203829 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
203842 AGAAGAA-AAGAAA
1 AGAA-AAGAAGAAA
203855 AGAAAAGAA
1 AGAAAAGAA
203864 AAAGTGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:208393 original size:42 final size:41
Alignment explanation
Indices: 208346--208442 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
208336 ACAATTTAAG
* * *
208346 TCCTTCGGGCCATCAGTAAGTCTTTCGAG-AATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAA-AATGAT-AAA
* * *
208388 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAAATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAAATGATAAA
*
208429 TCTTTCGGGCCATC
1 TCCTTCGGGCCATC
208443 CATAAGACCT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 14 0.30
42 30 0.65
43 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAAATGATAAA
Found at i:208590 original size:22 final size:22
Alignment explanation
Indices: 208558--208624 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
208548 TTGCACTTAG
208558 TAAGTCTTTCGAGCATGATGAT
1 TAAGTCTTTCGAGCATGATGAT
* *
208580 TAAGTCCTTCGAGCCATCA-G--
1 TAAGTCTTTCGAG-CATGATGAT
*
208600 TAAGTCTTTCGAGTATGATGAT
1 TAAGTCTTTCGAGCATGATGAT
208622 TAA
1 TAA
208625 ATTCTTCGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 3 0.08
20 13 0.36
22 16 0.44
23 4 0.11
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (22 bp):
TAAGTCTTTCGAGCATGATGAT
Found at i:208691 original size:13 final size:13
Alignment explanation
Indices: 208673--208697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
208663 TGAAGAAAAT
208673 CCATCAGTAAGTG
1 CCATCAGTAAGTG
208686 CCATCAGTAAGT
1 CCATCAGTAAGT
208698 CTTTCGAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:208751 original size:93 final size:93
Alignment explanation
Indices: 208592--208777 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 93
208582 AGTCCTTCGA
** * * ** *
208592 GCCATCAGTAAGTCTTTCGAGTATGATGATTAAATTCTTCGGGTAATTTTTAAGCCTTCACGGAA
1 GCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACCGAA
208657 GAGTAGTGAAGAAAATCCATCAGTAAGT
66 GAGTAGTGAAGAAAATCCATCAGTAAGT
*
208685 GCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCGCCGAA
1 GCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACCGAA
*
208750 GAGTAGTGAAGCAAATCCATCAGTAAGT
66 GAGTAGTGAAGAAAATCCATCAGTAAGT
208778 CTTTCGAGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (93 bp):
GCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACCGAA
GAGTAGTGAAGAAAATCCATCAGTAAGT
Found at i:208826 original size:42 final size:41
Alignment explanation
Indices: 208767--208895 Score: 159
Period size: 42 Copynumber: 3.1 Consensus size: 41
208757 GAAGCAAATC
*
208767 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGTT
1 CATCAGTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGT
*
208809 CATCAGTAAGTCTTTCGAGCATGACGATTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGA-TAAATCCTTCGGGT
** * * * * *
208851 CATTTGTGAGTCTATCAAGCAAGATGATAAATCATTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGT
208892 CATC
1 CATC
208896 CATAAGACCT
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
41 16 0.21
42 58 0.77
43 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (41 bp):
CATCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGT
Found at i:209392 original size:53 final size:53
Alignment explanation
Indices: 209272--209585 Score: 380
Period size: 53 Copynumber: 5.9 Consensus size: 53
209262 GAATCACACT
*
209272 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAG-GAACCCGTAGAC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * *
209324 AGAAGATTGTTCGAGTTTTACTCCCTGAAGCGAGAGGGAGCGAACCCGTAGGT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * *
209377 AGAAGATTGTTCGAGTTCTACTCCTTGGAGCAAGAGGGAGTGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * *
209430 AGAAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCATAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * * ** ****
209483 AGAACATTATTCAAGTTCTACTCCCTGAAGCAATAGGGAGCAAACCTATTTTT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* *
209536 AGAAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCGGACCCGT
1 AGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
209586 CATTTAAATA
Statistics
Matches: 223, Mismatches: 36, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
52 38 0.17
53 160 0.72
54 15 0.07
55 10 0.04
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
Found at i:215885 original size:29 final size:29
Alignment explanation
Indices: 215828--215890 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
215818 TGCATGATAT
*
215828 AAATTAAAATGAATAAACATAAACAAATA
1 AAATAAAAATGAATAAACATAAACAAATA
*
215857 AAATAAAAATGGATAAACGA-AAA-ATAATA
1 AAATAAAAATGAATAAAC-ATAAACA-AATA
215886 AAATA
1 AAATA
215891 TGTGTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.70, C:0.05, G:0.06, T:0.19
Consensus pattern (29 bp):
AAATAAAAATGAATAAACATAAACAAATA
Found at i:216323 original size:39 final size:39
Alignment explanation
Indices: 216252--216347 Score: 160
Period size: 38 Copynumber: 2.5 Consensus size: 39
216242 ATAAAACTAA
216252 GGATTGAAATTGCAAAT-AACCACATCGACTGCAAATAG
1 GGATTGAAATTGCAAATAAACCACATCGACTGCAAATAG
216290 GGATTGAAATTGCAAATAAACCACATCGACTGCAAATAG
1 GGATTGAAATTGCAAATAAACCACATCGACTGCAAATAG
* *
216329 GGATT-AAAATGAAAATAAA
1 GGATTGAAATTGCAAATAAA
216348 GCAAAATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
38 29 0.53
39 26 0.47
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (39 bp):
GGATTGAAATTGCAAATAAACCACATCGACTGCAAATAG
Found at i:221038 original size:11 final size:11
Alignment explanation
Indices: 221024--221072 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
221014 AGTGTTAGAG
221024 TGTTATTAGTT
1 TGTTATTAGTT
*
221035 TGTTA-TGGTT
1 TGTTATTAGTT
*
221045 TGTTATTAGCT
1 TGTTATTAGTT
*
221056 TGTTATTAATT
1 TGTTATTAGTT
221067 TGTTAT
1 TGTTAT
221073 GGTTGTTGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.61
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:222647 original size:11 final size:11
Alignment explanation
Indices: 222633--222681 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
222623 AATGTTAGAG
222633 TGTTATTAGCT
1 TGTTATTAGCT
* *
222644 TGTTATGA-TT
1 TGTTATTAGCT
222654 TGTTATTAGCT
1 TGTTATTAGCT
*
222665 TGTTATTAGTT
1 TGTTATTAGCT
222676 TGTTAT
1 TGTTAT
222682 GGTTGTTGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 8 0.25
11 24 0.75
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.59
Consensus pattern (11 bp):
TGTTATTAGCT
Found at i:222658 original size:21 final size:22
Alignment explanation
Indices: 222633--222681 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
222623 AATGTTAGAG
222633 TGTTATTAGCTTGTTATGA-TT
1 TGTTATTAGCTTGTTATGAGTT
*
222654 TGTTATTAGCTTGTTATTAGTT
1 TGTTATTAGCTTGTTATGAGTT
222676 TGTTAT
1 TGTTAT
222682 GGTTGTTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.59
Consensus pattern (22 bp):
TGTTATTAGCTTGTTATGAGTT
Found at i:224249 original size:11 final size:11
Alignment explanation
Indices: 224235--224283 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
224225 AATGTTAGAG
224235 TGTTATTAGTT
1 TGTTATTAGTT
*
224246 TGTTA-TGGTT
1 TGTTATTAGTT
*
224256 TGTTATTAGCT
1 TGTTATTAGTT
*
224267 TGTTCTTAGTT
1 TGTTATTAGTT
224278 TGTTAT
1 TGTTAT
224284 GGTTGTTGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.14, C:0.04, G:0.20, T:0.61
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:229223 original size:46 final size:46
Alignment explanation
Indices: 228735--229210 Score: 657
Period size: 46 Copynumber: 10.3 Consensus size: 46
228725 AAAGTTAAAC
* ** ** *
228735 GCATAACGGTGCATTATTAGCATGAAAGGATATCATAAATGAAATT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
* *
228781 GAATAATGGTACATTATCGGCATGAAAGGATGCCATAAATGAAAAT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
* *
228827 GCATAATGGGGCATTA-CTGGCATGAAAGGATTCCATAAATGAAAAT
1 GCATAATGGTGCATTATC-GGCATGAAAGGATGCCATAAATGAAAAT
* * **
228873 ACATAATGGTGCATTATTGGCATGAAAGGATATCATAAATGAAAAT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
* *
228919 GCATAATGGTGCATTATCGGAAAGAAAGGATGCCATAAATGAAAAT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
*
228965 GCATAATGGTGCATTATCGGCATGAAAGGATGCCAAAAATGAAAAT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
* * * * *
229011 GCATAACGATGTATTATCGGTATGAAATGATGCCATAAATGAAAAT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
229057 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
* * * *
229103 GCATAACGATGCATTATCAGCATGAAAGGATTCCATAAATGAAAAT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
* * *
229149 ACATAATGGTGCATTATCAGCATGAAAGGATGTCATAAATGAAAAT
1 GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
* *
229195 GCATAACGGTGTATTA
1 GCATAATGGTGCATTA
229211 AAGGCATAAA
Statistics
Matches: 379, Mismatches: 49, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.00
46 378 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (46 bp):
GCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAT
Found at i:234421 original size:45 final size:45
Alignment explanation
Indices: 234255--234462 Score: 186
Period size: 45 Copynumber: 4.6 Consensus size: 45
234245 AATGAAAGTT
* * * * *
234255 AAATGCATAACGGTGAATTATTGGCATGAAAAGTTGCCATAAATGAA
1 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAA--AA
* * *
234302 AAATGCATAATGGTTCATTATCGACATGAAATGATGCCA-AAAATGA
1 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAAA--A
* *
234348 AAGTGCATAACGGTGCATTATC-AGCATGAAAGGATGCGATAAAAA
1 AAATGCATAACGGTGCATTATCGA-CATGAAAGGATGCCATAAAAA
* * * * * *
234393 AAATGCTTAACGGTGCATAATCGACATGAAAGAATGCTACAAATA
1 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAAAA
* * *
234438 AAATACATAACGGTGTATTAACGAC
1 AAATGCATAACGGTGCATTATCGAC
234463 GTTAAAGGGT
Statistics
Matches: 132, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
44 1 0.01
45 58 0.44
46 37 0.28
47 36 0.27
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (45 bp):
AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAAAA
Found at i:237458 original size:36 final size:35
Alignment explanation
Indices: 237401--237505 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 35
237391 GATACAATCT
237401 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCA-CATTATCACGCCTATATCATCACCATA
* *
237437 GTCTATCTCTATTATCACGCCTATATCATCACCATA
1 GTCCATCAC-ATTATCACGCCTATATCATCACCATA
* * *
237473 TTCCATCACAATATCACGCCTATATTATCACCA
1 GTCCATCACATTATCACGCCTATATCATCACCA
237506 ACTTATAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
35 23 0.38
36 38 0.62
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.31
Consensus pattern (35 bp):
GTCCATCACATTATCACGCCTATATCATCACCATA
Found at i:237972 original size:11 final size:11
Alignment explanation
Indices: 237956--237997 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
237946 GGAGTGCAAA
237956 AAAAAGAAAAG
1 AAAAAGAAAAG
237967 AAAAAG--AAG
1 AAAAAGAAAAG
**
237976 AAAATCAAAAG
1 AAAAAGAAAAG
237987 AAAAAGAAAAG
1 AAAAAGAAAAG
237998 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 7 0.28
11 18 0.72
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:243192 original size:35 final size:36
Alignment explanation
Indices: 243122--243202 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 36
243112 ATAAGATACA
*
243122 ATCATCACCATAGTCCATCACTATTATCACGCCTAT
1 ATCATCACCATAGTCCATCACCATTATCACGCCTAT
*
243158 ATCATCACCATATTCCATCACCA-TATCACGCCTAT
1 ATCATCACCATAGTCCATCACCATTATCACGCCTAT
*
243193 ATTATCACCA
1 ATCATCACCA
243203 ACTTATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 21 0.50
36 21 0.50
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.30
Consensus pattern (36 bp):
ATCATCACCATAGTCCATCACCATTATCACGCCTAT
Found at i:253680 original size:12 final size:12
Alignment explanation
Indices: 253663--253697 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
253653 TGATTGCGGA
253663 TGATATGAGTTG
1 TGATATGAGTTG
253675 TGATATGAGTTG
1 TGATATGAGTTG
253687 TGATATGAGTT
1 TGATATGAGTT
253698 ACGCCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (12 bp):
TGATATGAGTTG
Found at i:255488 original size:19 final size:21
Alignment explanation
Indices: 255466--255513 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
255456 TAGTTTTGTG
255466 TGTTATTTGA-GATTT-TAGA
1 TGTTATTTGAGGATTTATAGA
**
255485 TGTTATAAGAGGATTTATAGA
1 TGTTATTTGAGGATTTATAGA
*
255506 TGTAATTT
1 TGTTATTT
255514 AGTTGGATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 8 0.36
20 5 0.23
21 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (21 bp):
TGTTATTTGAGGATTTATAGA
Found at i:255740 original size:19 final size:19
Alignment explanation
Indices: 255716--255767 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
255706 ATTCAAGAAA
*
255716 TATCGATACTAGTGTGG-GG
1 TATCGATACTA-TGAGGAGG
*
255735 TATCGATATTATGAGGAAGG
1 TATCGATACTATGAGG-AGG
255755 TATCGATACTATG
1 TATCGATACTATG
255768 GATTCCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 10 0.36
20 14 0.50
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (19 bp):
TATCGATACTATGAGGAGG
Found at i:256250 original size:54 final size:54
Alignment explanation
Indices: 256163--256882 Score: 886
Period size: 54 Copynumber: 13.3 Consensus size: 54
256153 GCATTTTTTA
* * * * *
256163 CGTATCGGTACTAAGTATGCAACCCACAAAATTCATAATAAGTTTATAAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* *
256217 CGTATCGGCACTAAGTGTGCAACCAACAGAATTCATAATAAGTTTATGAAAGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * * * * *
256271 CGTATCGGTACGAAGAGTGCAACCTACGGAATTCATAATAAGTTTATGAATGAT
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * * * * *
256325 CATATCGACACTAAGTCTACAACCCACGGAATTCATAATAAGTTTATGAATAAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * *
256379 CGTATCGGCACTAAGTGTGCAACCTACAAAATTCATAATAAGTTTATGAATGAT
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * *
256433 CGTATTGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAATGAT
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * * * *
256487 TGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGAT
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * *
256541 CGTATCGACAC-AAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * * *
256594 TGTATTGGCACTAAGTGTGCAACCCA-TGAAATTCATAATAAGTTTTTGAATGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAATGAC
* *
256648 CATATCGGCACTAAGTGTTCAACCCACAGAATTCATAATAAGTTTATGAATGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * ** * *
256702 CGTATCGACACTAAGTGTGCAACCTATGGAATTCATAATAAGTTTATGAACGGC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
** *
256756 CGTATCGGCACTAAGTGTGCAACCCATGGAATTCATAACAAGTTTATGAATGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
* * * * * * **
256810 CGTATCAGAACTAAATGTACAACCCACAGAATTTCAAAATGAGCATATGAATGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAA-TTCATAATAAGTTTATGAATGAC
* *
256865 CGTATTGGCACTACGTGT
1 CGTATCGGCACTAAGTGT
256883 ACATCTCACA
Statistics
Matches: 579, Mismatches: 83, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
53 48 0.08
54 499 0.86
55 32 0.06
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (54 bp):
CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
Found at i:263465 original size:54 final size:54
Alignment explanation
Indices: 263383--263793 Score: 571
Period size: 54 Copynumber: 7.6 Consensus size: 54
263373 TCATTTTTTA
263383 CGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
1 CGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
*
263437 CGTATCGACACTAAGTGTACAACCCACGAAATTCATAATAAGTTTATGAACGAC
1 CGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
* *
263491 CGTATC-AGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAATGAT
1 CGTATCGA-CACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
** * **
263545 CGTATTAACACTAAGTGTGTAACCCAC-ATAATTCATAATAAGTTTATGAACGGT
1 CGTATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGAC
* * * *
263599 CGTATCGACAGTAAGTGTGAAACCCA-AAGAATTCATAATAAGTTTATGAATGAC
1 CGTATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGAC
* *
263653 CGTATCGGCACTAAGTGTGCAACCCAC-AGAATTCATAATAATTTTATGAACGAC
1 CGTATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGAC
* * * *
263707 TGTATCAACACTAAGTGTGCAACCCATGAAATTCATAACAAGTTTATGAACGAC
1 CGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
*
263761 CGTATCGGA-ACTAAGTGTGCAACCCACAAAATT
1 CGTATC-GACACTAAGTGTGCAACCCACGAAATT
263794 TCAAAATGAG
Statistics
Matches: 319, Mismatches: 31, Indels: 14
0.88 0.09 0.04
Matches are distributed among these distances:
53 2 0.01
54 314 0.98
55 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (54 bp):
CGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
Found at i:264797 original size:18 final size:18
Alignment explanation
Indices: 264774--264819 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
264764 CAATCGACCT
264774 TACTTTCAAAAATCAAAA
1 TACTTTCAAAAATCAAAA
264792 TACTTTCAAAAATCAAAA
1 TACTTTCAAAAATCAAAA
*
264810 TGCTTTCAAA
1 TACTTTCAAA
264820 TCATAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (18 bp):
TACTTTCAAAAATCAAAA
Found at i:269777 original size:21 final size:21
Alignment explanation
Indices: 269753--269798 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
269743 AAAAGCAAGA
269753 AGTGAAGCAGAAAGTTTAGCT
1 AGTGAAGCAGAAAGTTTAGCT
269774 AGTGAAGCAGAAAGTTTAGCT
1 AGTGAAGCAGAAAGTTTAGCT
269795 AGTG
1 AGTG
269799 CCTTTCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.09, G:0.30, T:0.24
Consensus pattern (21 bp):
AGTGAAGCAGAAAGTTTAGCT
Found at i:277459 original size:20 final size:21
Alignment explanation
Indices: 277407--277467 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
277397 TTCCCCTGTG
277407 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
277430 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
277450 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
277468 TACACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:283884 original size:39 final size:40
Alignment explanation
Indices: 283826--283904 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 40
283816 TGCAGGTTCA
*
283826 TAATACACTTCGGTGTATAT-GTGGGCACGACCTTATGTG
1 TAATACACTTCGGTATATATGGTGGGCACGACCTTATGTG
*
283865 TAATACACTTCGGTATATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTATATATGGTGGGCACGACCTTATGTG
283905 CTGCACTACG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 19 0.51
40 18 0.49
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTATATATGGTGGGCACGACCTTATGTG
Found at i:284075 original size:45 final size:45
Alignment explanation
Indices: 284011--284119 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 45
284001 GTAAGCATGC
*
284011 AAATAAGCTTACGAGCTTAT-GGA-ATATTGGAAAGTATATGGGTAA
1 AAATAAGCTTACGAGCTTATGGGACAAATT-GAAAGTATATGGGT-A
* * * *
284056 AAATAAGCTTACGAGCTTATGGGACAAATTGTAATTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGACAAATTGAAAGTATATGGGTA
284101 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
284120 CGAAAATAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 40 0.70
46 13 0.23
47 4 0.07
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGACAAATTGAAAGTATATGGGTA
Found at i:284591 original size:22 final size:22
Alignment explanation
Indices: 284566--284629 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
284556 GTTGTGCATC
**
284566 GGTACTCTGTTCACTGTTCACT
1 GGTACTCTCATCACTGTTCACT
* *
284588 GGTAGTGTCATCACTGTTCACT
1 GGTACTCTCATCACTGTTCACT
* *
284610 -GTACTGTTCATCACTATTCA
1 GGTACT-CTCATCACTGTTCA
284630 TAAAAAAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (22 bp):
GGTACTCTCATCACTGTTCACT
Found at i:287030 original size:2 final size:2
Alignment explanation
Indices: 287025--287054 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
287015 GAGATGATTA
287025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
287055 CACTGGTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:288736 original size:30 final size:31
Alignment explanation
Indices: 288697--288769 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
288687 AATGGATTTA
* *
288697 TTTA-GTGACCAAATTATAAA-TTTGGTAAAG
1 TTTAGGTGACCAAAGTATAAACTTT-GAAAAG
288727 TTT-GGTGACCAAAGTATAAACTTTGAAAAG
1 TTTAGGTGACCAAAGTATAAACTTTGAAAAG
288757 TTTAGG-GACCAAA
1 TTTAGGTGACCAAA
288770 ATGTAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 33 0.87
31 5 0.13
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (31 bp):
TTTAGGTGACCAAAGTATAAACTTTGAAAAG
Found at i:289277 original size:22 final size:22
Alignment explanation
Indices: 289252--289296 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
289242 GGGGTTATGT
289252 CGTGAAATAGGAAAATGATCTA
1 CGTGAAATAGGAAAATGATCTA
289274 CGTGAAATAGGAAAATGATCTA
1 CGTGAAATAGGAAAATGATCTA
289296 C
1 C
289297 CCCAAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (22 bp):
CGTGAAATAGGAAAATGATCTA
Found at i:289303 original size:22 final size:22
Alignment explanation
Indices: 289256--289303 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
289246 TTATGTCGTG
***
289256 AAATAGGAAAATGATCTACGTG
1 AAATAGGAAAATGATCTACCCC
289278 AAATAGGAAAATGATCTACCCC
1 AAATAGGAAAATGATCTACCCC
289300 AAAT
1 AAAT
289304 CTAACAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.21
Consensus pattern (22 bp):
AAATAGGAAAATGATCTACCCC
Found at i:290630 original size:40 final size:40
Alignment explanation
Indices: 290575--290656 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
290565 TGCAGGTTCA
*
290575 TAATATACATCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACATCGGTGTATATGGTGGGCACGACCTTATGTG
*
290615 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACATCGGTGTATATGGTGGGCACGACCTTATGTG
290655 TA
1 TA
290657 GCACTACGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACATCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:290825 original size:45 final size:45
Alignment explanation
Indices: 290761--290869 Score: 134
Period size: 45 Copynumber: 2.4 Consensus size: 45
290751 GTAAGCATAC
* *
290761 AAATAAGCTTACGAGCTTAT-GGA-ATATTGGA-AAGTATATGGGTAA
1 AAATAAGCTTACGAGCTTATGGGACA-AAT-GATAACTATATGGGT-A
* *
290806 AAATAAGCTTACGAGCTTATGGGACAAATGATAACTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGACAAATGATAACTATATGGGTA
290851 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
290870 CAAAAATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
45 42 0.74
46 14 0.25
47 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGACAAATGATAACTATATGGGTA
Found at i:300962 original size:19 final size:19
Alignment explanation
Indices: 300938--300979 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
300928 TACATGAGTC
300938 AAACATGCACCGAAGTACT
1 AAACATGCACCGAAGTACT
*
300957 AAACATGCACCGAAGTGCT
1 AAACATGCACCGAAGTACT
300976 AAAC
1 AAAC
300980 CAATTTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (19 bp):
AAACATGCACCGAAGTACT
Found at i:303252 original size:2 final size:2
Alignment explanation
Indices: 303245--303300 Score: 94
Period size: 2 Copynumber: 27.0 Consensus size: 2
303235 AGGTAAAATG
303245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
303287 AT GACT AT AT AT AT
1 AT -A-T AT AT AT AT
303301 GTGACTATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 49 0.94
3 2 0.04
4 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:308998 original size:23 final size:23
Alignment explanation
Indices: 308967--309023 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
308957 TTTATATGGA
*
308967 ACTTCGGTGCAATTCTACGCGGC
1 ACTTTGGTGCAATTCTACGCGGC
* **
308990 ACTTTGGTGTAATTCTACTTGGC
1 ACTTTGGTGCAATTCTACGCGGC
309013 ACTTTGGTGCA
1 ACTTTGGTGCA
309024 TTTATACGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (23 bp):
ACTTTGGTGCAATTCTACGCGGC
Found at i:312403 original size:64 final size:63
Alignment explanation
Indices: 312323--312475 Score: 150
Period size: 64 Copynumber: 2.4 Consensus size: 63
312313 GTGTGTATCA
* * *
312323 ATGCATAGGAAATGCATCGATGCACCCCTTAAAAATTGAAATATC-AA-ATGCAATTAGTGCATC
1 ATGCATAGGGAGTGCATCGATGCACCCCTT-AAAATTGAAACATCGAAGATGC--TTAGTGCATC
312386 G
63 G
* * * * * * *
312387 ATGCATAGGGAGTGCATCAATACACCCCCTTAAGATTTAAACATCGAAGGTGCTTTGTGTATCG
1 ATGCATAGGGAGTGCATCGATGCA-CCCCTTAAAATTGAAACATCGAAGATGCTTAGTGCATCG
312451 ATGCAT-GGGTAGTGCATCGATGCAC
1 ATGCATAGGG-AGTGCATCGATGCAC
312476 ATGTTAAGGG
Statistics
Matches: 73, Mismatches: 12, Indels: 9
0.78 0.13 0.10
Matches are distributed among these distances:
63 4 0.05
64 58 0.79
65 8 0.11
66 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (63 bp):
ATGCATAGGGAGTGCATCGATGCACCCCTTAAAATTGAAACATCGAAGATGCTTAGTGCATCG
Found at i:313588 original size:2 final size:2
Alignment explanation
Indices: 313581--313624 Score: 54
Period size: 2 Copynumber: 21.0 Consensus size: 2
313571 TGGTAGAATG
313581 AT AT AT AT AT AT AT AT AT A- ACT AT AT AT AT AT GACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT -A-T AT AT AT
313623 AT
1 AT
313625 GTGACTATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 1 0.03
2 33 0.87
3 3 0.08
4 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:313598 original size:12 final size:13
Alignment explanation
Indices: 313581--313624 Score: 65
Period size: 12 Copynumber: 3.5 Consensus size: 13
313571 TGGTAGAATG
313581 ATATATATA-TAT
1 ATATATATACTAT
313593 ATATATA-ACTAT
1 ATATATATACTAT
313605 ATATATATGACTAT
1 ATATATAT-ACTAT
313619 ATATAT
1 ATATAT
313625 GTGACTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.03
12 17 0.59
14 11 0.38
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (13 bp):
ATATATATACTAT
Found at i:313629 original size:14 final size:14
Alignment explanation
Indices: 313588--313632 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
313578 ATGATATATA
*
313588 TATATATATATAAC
1 TATATATATATGAC
313602 TATATATATATGAC
1 TATATATATATGAC
*
313616 TATATATATGTGAC
1 TATATATATATGAC
313630 TAT
1 TAT
313633 GAGTTGGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
TATATATATATGAC
Found at i:314172 original size:23 final size:23
Alignment explanation
Indices: 314139--314198 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
314129 CATTTTATAT
314139 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* **
314162 GGTACTTCGGTGCAATTCTACTT
1 GGCACTTCGGTGCAATTCTACGC
314185 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
314199 TTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Done.