Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 44 of 161
Found at i:13353281 original size:41 final size:41
Alignment explanation
Indices: 13353236--13353386 Score: 121
Period size: 41 Copynumber: 3.7 Consensus size: 41
13353226 GAGTGTAAAT
13353236 AGGGGCACGCATGTGCT-ATTCAAGGGTA-CTAAAGTACAAAA
1 AGGGGCACGCATGTG-TAATTCAAGGGTATC-AAAGTACAAAA
* * * *
13353277 AGGGGCACGTATGTGTAATTCAGGGGTATCGAAGTACAAAT
1 AGGGGCACGCATGTGTAATTCAAGGGTATCAAAGTACAAAA
** ** * * *
13353318 AGGGGCACATATGTGGCATT-TAGGGTTATCGAAGTACAAAT
1 AGGGGCACGCATGTGTAATTCAAGGG-TATCAAAGTACAAAA
** *
13353359 AGGGGCACGTGTGTGCAATTC-AGGGTAT
1 AGGGGCACGCATGTGTAATTCAAGGGTAT
13353387 AATTAATTAT
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
40 7 0.08
41 85 0.91
42 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (41 bp):
AGGGGCACGCATGTGTAATTCAAGGGTATCAAAGTACAAAA
Found at i:13367862 original size:16 final size:17
Alignment explanation
Indices: 13367843--13367875 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13367833 TAAATGTAAG
13367843 TAAAAC-TAAAGAAAAT
1 TAAAACATAAAGAAAAT
*
13367859 TAAAACATAACGAAAAT
1 TAAAACATAAAGAAAAT
13367876 GCTTGTATTC
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:0.67, C:0.09, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAACATAAAGAAAAT
Found at i:13373488 original size:6 final size:6
Alignment explanation
Indices: 13373468--13373533 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
13373458 TTTCTTTTCT
* * *
13373468 TTTTTG TTTTATA TTTTTA --TTTA TTTTTA TCTTTA TTTTTG TTTTTCA
1 TTTTTA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A
13373516 TTGCTTTA TTTTTA TTTT
1 TT--TTTA TTTTTA TTTT
13373534 CTTAGACTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.08
6 32 0.65
7 7 0.14
8 3 0.06
9 3 0.06
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:13374519 original size:8 final size:7
Alignment explanation
Indices: 13374484--13374518 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
13374474 TTCTCTTGTA
13374484 AAAAAAGG
1 AAAAAA-G
13374492 AAAAAAG
1 AAAAAAG
13374499 AAAAAAG
1 AAAAAAG
13374506 AAAAAAG
1 AAAAAAG
13374513 AAAAAA
1 AAAAAA
13374519 AATAATGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:13387829 original size:22 final size:22
Alignment explanation
Indices: 13387776--13387821 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13387766 ATTTAATGAT
13387776 TTGTGGTTAAATAGAAGATTAA
1 TTGTGGTTAAATAGAAGATTAA
13387798 TTGTGGTTAAATAGAAGATTAA
1 TTGTGGTTAAATAGAAGATTAA
13387820 TT
1 TT
13387822 AGGTTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (22 bp):
TTGTGGTTAAATAGAAGATTAA
Found at i:13389149 original size:20 final size:20
Alignment explanation
Indices: 13389124--13389190 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
13389114 GGCTTATGCC
*
13389124 AAGTAAGTGGAATGGAAAGT
1 AAGTAAATGGAATGGAAAGT
* *
13389144 AAGTAAATGAAATGAAAAGT
1 AAGTAAATGGAATGGAAAGT
*
13389164 AAGAAAATGGAAT-GATAAGT
1 AAGTAAATGGAATGGA-AAGT
13389184 AAG-AAAT
1 AAGTAAAT
13389191 AGAGTAGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 5 0.12
20 35 0.88
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.19
Consensus pattern (20 bp):
AAGTAAATGGAATGGAAAGT
Found at i:13411254 original size:14 final size:14
Alignment explanation
Indices: 13411226--13411254 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13411216 GTTGAGTGGC
13411226 TTTTGACTTGATTT
1 TTTTGACTTGATTT
13411240 TTTTG-CTTGATTT
1 TTTTGACTTGATTT
13411253 TT
1 TT
13411255 AAGCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (14 bp):
TTTTGACTTGATTT
Found at i:13423881 original size:65 final size:65
Alignment explanation
Indices: 13423788--13423914 Score: 245
Period size: 65 Copynumber: 2.0 Consensus size: 65
13423778 ATTTTAGATG
*
13423788 CCACACAACTCAGGACTGAGACTCGGTCAATCATAAATCTTTGAGAAAATCTCTAATTTCTTCAA
1 CCACACAACTCAGGACTGAGACCCGGTCAATCATAAATCTTTGAGAAAATCTCTAATTTCTTCAA
13423853 CCACACAACTCAGGACTGAGACCCGGTCAATCATAAATCTTTGAGAAAATCTCTAATTTCTT
1 CCACACAACTCAGGACTGAGACCCGGTCAATCATAAATCTTTGAGAAAATCTCTAATTTCTT
13423915 GGTTTAAATG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.28
Consensus pattern (65 bp):
CCACACAACTCAGGACTGAGACCCGGTCAATCATAAATCTTTGAGAAAATCTCTAATTTCTTCAA
Found at i:13429393 original size:20 final size:19
Alignment explanation
Indices: 13429346--13429397 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
13429336 TTTACTGAAA
*
13429346 ATGAATCAATATATATGTT
1 ATGAAACAATATATATGTT
* * *
13429365 ATTATACAATTTATCATGTT
1 ATGAAACAATATAT-ATGTT
13429385 ATGAAACAATATA
1 ATGAAACAATATA
13429398 AATCCAACGA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (19 bp):
ATGAAACAATATATATGTT
Found at i:13431670 original size:27 final size:27
Alignment explanation
Indices: 13431638--13431927 Score: 330
Period size: 27 Copynumber: 10.7 Consensus size: 27
13431628 TTCATTTCAA
**
13431638 TCATTTTACCCTATGGGGGTATTTTTG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
13431665 TTATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * ** *
13431692 TCATTTTAACATATTAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
13431719 CCATTTTACTCTATAGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
13431746 CCATTTTACCCTATGGAGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
13431773 TTATTTTACCCAATAGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
13431800 TCTTTTTACCCTAAGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
13431827 TCATTTTACCTTAAT-AGGGTATTTCGG
1 TCATTTTACCCT-ATGGGGGTATTTCGG
*
13431854 TCATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
13431881 TCATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
13431908 TCATTTTACCCTATGGGGGT
1 TCATTTTACCCTATGGGGGT
13431928 CTCGGTGCAG
Statistics
Matches: 221, Mismatches: 40, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 2 0.01
27 218 0.99
28 1 0.00
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:13431832 original size:108 final size:108
Alignment explanation
Indices: 13431639--13431927 Score: 388
Period size: 108 Copynumber: 2.7 Consensus size: 108
13431629 TCATTTCAAT
* * * *
13431639 CATTTTACCCTATGGGGGTATTTTTGTTATTTTACCCTATAGGGGTATTTCGGTCATTTTAACAT
1 CATTTTACCCTATGGAGGTATTTTGGTTATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCT
** *
13431704 ATTAGGGTATTTCGACCATTTTA-CTCT-ATAGGGGTATTTTGGC
66 ATGGGGGTATTTCGACCATTTTACCT-TAATA-GGGTATTTCGGC
* *
13431747 CATTTTACCCTATGGAGGTATTTTGGTTATTTTACCCAATAGGGGTATTTCGGTCTTTTTACCCT
1 CATTTTACCCTATGGAGGTATTTTGGTTATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCT
* * *
13431812 AAGGGGGTATTTCGATCATTTTACCTTAATAGGGTATTTCGGT
66 ATGGGGGTATTTCGACCATTTTACCTTAATAGGGTATTTCGGC
* *
13431855 CATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACC
1 CATTTTACCCTATGGA-GGTATTTTGGTTATTTTACCCTATAG-GGGTATTTCGGTCATTTTACC
13431918 CTATGGGGGT
64 CTATGGGGGT
13431928 CTCGGTGCAG
Statistics
Matches: 160, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
107 3 0.02
108 152 0.95
109 5 0.03
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (108 bp):
CATTTTACCCTATGGAGGTATTTTGGTTATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCT
ATGGGGGTATTTCGACCATTTTACCTTAATAGGGTATTTCGGC
Found at i:13436444 original size:20 final size:21
Alignment explanation
Indices: 13436419--13436457 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13436409 GAGCAAAACT
*
13436419 GCCCTT-GATGTCTCGACACG
1 GCCCTTCGATGTCGCGACACG
13436439 GCCCTTCGATGTCGCGACA
1 GCCCTTCGATGTCGCGACA
13436458 TCAGACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (21 bp):
GCCCTTCGATGTCGCGACACG
Found at i:13443003 original size:27 final size:27
Alignment explanation
Indices: 13442973--13443140 Score: 150
Period size: 27 Copynumber: 6.3 Consensus size: 27
13442963 ACCCTATAGT
* *
13442973 GGTAATTCGATAATTTTACCTATCGGG
1 GGTATTTCGATAATTTTACCTATCGAG
* **
13443000 GGTATTTC-AGTAATTTTATCTATTAAG
1 GGTATTTCGA-TAATTTTACCTATCGAG
*
13443027 GGTATTTCTG-TAATTTTACCCATCGAG
1 GGTATTTC-GATAATTTTACCTATCGAG
*
13443054 GGTATTTCGATAATTTTACCCATCGAG
1 GGTATTTCGATAATTTTACCTATCGAG
* *
13443081 GGTATTTTGGTAATTTTA-CTATCG-G
1 GGTATTTCGATAATTTTACCTATCGAG
* *
13443106 GAGTATTT-TAGTTATTTTATCC-ATCGAG
1 G-GTATTTCGA-TAATTTTA-CCTATCGAG
13443134 GGTATTT
1 GGTATTT
13443141 TGGTAGTTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
25 2 0.02
26 20 0.17
27 92 0.79
28 3 0.03
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACCTATCGAG
Found at i:13443057 original size:54 final size:53
Alignment explanation
Indices: 13442983--13443150 Score: 198
Period size: 54 Copynumber: 3.1 Consensus size: 53
13442973 GGTAATTCGA
* **
13442983 TAATTTTACCTATCGGGGGTATTTCAGTAATTTTATCTATTAAGGGTATTTCT-G
1 TAATTTTACCTATC-GGGGTATTTCAGTAATTTTATCCATCGAGGGTATTT-TGG
* *
13443037 TAATTTTACCCATCGAGGGTATTTC-GATAATTTTACCCATCGAGGGTATTTTGG
1 TAATTTTACCTATCG-GGGTATTTCAG-TAATTTTATCCATCGAGGGTATTTTGG
* *
13443091 TAATTTTA-CTATCGGGAGTATTTTAGTTATTTTATCCATCGAGGGTATTTTGG
1 TAATTTTACCTATCGGG-GTATTTCAGTAATTTTATCCATCGAGGGTATTTTGG
*
13443144 TAGTTTT
1 TAATTTT
13443151 CCTGCACGAG
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
52 2 0.02
53 45 0.45
54 52 0.53
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (53 bp):
TAATTTTACCTATCGGGGTATTTCAGTAATTTTATCCATCGAGGGTATTTTGG
Found at i:13443084 original size:81 final size:80
Alignment explanation
Indices: 13442973--13443140 Score: 214
Period size: 81 Copynumber: 2.1 Consensus size: 80
13442963 ACCCTATAGT
* * *
13442973 GGTAATTCGATAATTTTACCTATCGGGGGTATTTCAGTAATTTTATCTATTAAGG-GTATTTCT-
1 GGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTA-CTA-TAAGGAGTATTT-TA
13443036 GTAATTTTACCCATCGAG
63 GTAATTTTACCCATCGAG
** ** *
13443054 GGTATTTCGATAATTTTACCCATCGAGGGTATTTTGGTAATTTTACTATCGGGAGTATTTTAGTT
1 GGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACTATAAGGAGTATTTTAGTA
*
13443119 ATTTTATCCATCGAG
66 ATTTTACCCATCGAG
13443134 GGTATTT
1 GGTATTT
13443141 TGGTAGTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
79 4 0.05
80 32 0.42
81 40 0.53
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (80 bp):
GGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACTATAAGGAGTATTTTAGTA
ATTTTACCCATCGAG
Found at i:13444091 original size:25 final size:25
Alignment explanation
Indices: 13444063--13444111 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13444053 TTCAAATTCC
*
13444063 CAAATTCTCTCCTA-AAATCACTCCT
1 CAAATCCTCTCCTAGAAATC-CTCCT
13444088 CAAATCCTCTCCTAGAAATCCTCC
1 CAAATCCTCTCCTAGAAATCCTCC
13444112 ATGATCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.31, C:0.39, G:0.02, T:0.29
Consensus pattern (25 bp):
CAAATCCTCTCCTAGAAATCCTCCT
Found at i:13444108 original size:14 final size:13
Alignment explanation
Indices: 13444064--13444110 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
13444054 TCAAATTCCC
*
13444064 AAATTCTCTCCTA
1 AAATCCTCTCCTA
* *
13444077 AAAT-CACTCCTC
1 AAATCCTCTCCTA
13444089 AAATCCTCTCCTA
1 AAATCCTCTCCTA
13444102 GAAATCCTC
1 -AAATCCTC
13444111 CATGATCCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 10 0.36
13 10 0.36
14 8 0.29
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (13 bp):
AAATCCTCTCCTA
Found at i:13445140 original size:25 final size:25
Alignment explanation
Indices: 13445112--13445160 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13445102 TTCAAATTCC
*
13445112 CAAATTCTCTCCTA-AAATCACTCCT
1 CAAATCCTCTCCTAGAAATC-CTCCT
13445137 CAAATCCTCTCCTAGAAATCCTCC
1 CAAATCCTCTCCTAGAAATCCTCC
13445161 ATGATCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.31, C:0.39, G:0.02, T:0.29
Consensus pattern (25 bp):
CAAATCCTCTCCTAGAAATCCTCCT
Found at i:13445157 original size:14 final size:13
Alignment explanation
Indices: 13445113--13445159 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
13445103 TCAAATTCCC
*
13445113 AAATTCTCTCCTA
1 AAATCCTCTCCTA
* *
13445126 AAAT-CACTCCTC
1 AAATCCTCTCCTA
13445138 AAATCCTCTCCTA
1 AAATCCTCTCCTA
13445151 GAAATCCTC
1 -AAATCCTC
13445160 CATGATCCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 10 0.36
13 10 0.36
14 8 0.29
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (13 bp):
AAATCCTCTCCTA
Found at i:13445764 original size:25 final size:25
Alignment explanation
Indices: 13445727--13445780 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
13445717 TGAATCTCTG
*
13445727 ACCTCTTTACCACACCTGTGACGCC
1 ACCTCCTTACCACACCTGTGACGCC
* * *
13445752 ACCTCCTTGCCACACTTGTGTCGCC
1 ACCTCCTTACCACACCTGTGACGCC
13445777 ACCT
1 ACCT
13445781 TGCCACTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.17, C:0.44, G:0.13, T:0.26
Consensus pattern (25 bp):
ACCTCCTTACCACACCTGTGACGCC
Found at i:13448468 original size:18 final size:19
Alignment explanation
Indices: 13448445--13448486 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
13448435 ATAATAATTT
* *
13448445 ATATTATGTTATTTTTAA-
1 ATATTATGTAATTTGTAAC
13448463 ATATTATGTAATTTGTAAC
1 ATATTATGTAATTTGTAAC
13448482 ATATT
1 ATATT
13448487 GACAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (19 bp):
ATATTATGTAATTTGTAAC
Found at i:13450479 original size:12 final size:12
Alignment explanation
Indices: 13450462--13450492 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13450452 AAACAATATC
13450462 ATAATAATCCTA
1 ATAATAATCCTA
13450474 ATAATAATCCTA
1 ATAATAATCCTA
*
13450486 AAAATAA
1 ATAATAA
13450493 AATTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATAATCCTA
Found at i:13452558 original size:23 final size:22
Alignment explanation
Indices: 13452521--13452565 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
13452511 ATGTAAGAAA
13452521 ATAAAGAAAATAAAATATAAAAT
1 ATAAAGAAAATAAAATA-AAAAT
13452544 ATAAA-AAAATAAAAATAAAAAT
1 ATAAAGAAAAT-AAAATAAAAAT
13452566 CAAATTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (22 bp):
ATAAAGAAAATAAAATAAAAAT
Found at i:13452564 original size:14 final size:14
Alignment explanation
Indices: 13452527--13452564 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
13452517 GAAAATAAAG
*
13452527 AAAAT-AAAATATA
1 AAAATAAAAAAATA
13452540 AAATATAAAAAAATA
1 AAA-ATAAAAAAATA
13452555 AAAATAAAAA
1 AAAATAAAAA
13452565 TCAAATTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 10 0.45
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:13452565 original size:22 final size:23
Alignment explanation
Indices: 13452521--13452563 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
13452511 ATGTAAGAAA
13452521 ATAAAGAAAATAAAATATAAAAT
1 ATAAAGAAAATAAAATATAAAAT
13452544 ATAAA-AAAATAAAA-ATAAAA
1 ATAAAGAAAATAAAATATAAAA
13452564 ATCAAATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (23 bp):
ATAAAGAAAATAAAATATAAAAT
Found at i:13453964 original size:21 final size:21
Alignment explanation
Indices: 13453940--13453982 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
13453930 TTTATAGATG
13453940 CCTCTATTTTCTATTGAAAAT
1 CCTCTATTTTCTATTGAAAAT
*
13453961 CCTCTATTTTCTTTTGAAAAT
1 CCTCTATTTTCTATTGAAAAT
13453982 C
1 C
13453983 AATAGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (21 bp):
CCTCTATTTTCTATTGAAAAT
Found at i:13467503 original size:18 final size:16
Alignment explanation
Indices: 13467480--13467526 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
13467470 TATAATGATG
13467480 ATTATAATCTCATATGTT
1 ATTATAATCTCATA--TT
*
13467498 ATTATAATATC-TATT
1 ATTATAATCTCATATT
*
13467513 AATATAATCTCATA
1 ATTATAATCTCATA
13467527 AATATTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 2 0.08
18 10 0.40
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTATAATCTCATATT
Found at i:13467717 original size:24 final size:24
Alignment explanation
Indices: 13467682--13467760 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
13467672 CATTTATATA
13467682 TTATTACTTTATATATTACCTATTT
1 TTATTA-TTTATATATTACCTATTT
* **
13467707 TTATTTTTTATATATTATTTATTT
1 TTATTATTTATATATTACCTATTT
* **
13467731 TAAACTTATACATATATTACCTATTT
1 T-TA-TTATTTATATATTACCTATTT
13467757 TTAT
1 TTAT
13467761 ATATATAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
24 18 0.43
25 7 0.17
26 17 0.40
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTATTTATATATTACCTATTT
Found at i:13471226 original size:18 final size:16
Alignment explanation
Indices: 13471203--13471249 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
13471193 TATAATGATG
13471203 ATTATAATCTCATATGTT
1 ATTATAATCTCATA--TT
*
13471221 ATTATAATATC-TATT
1 ATTATAATCTCATATT
*
13471236 AATATAATCTCATA
1 ATTATAATCTCATA
13471250 AATATTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 2 0.08
18 10 0.40
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTATAATCTCATATT
Found at i:13471440 original size:24 final size:24
Alignment explanation
Indices: 13471405--13471483 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
13471395 CATTTATATA
13471405 TTATTACTTTATATATTACCTATTT
1 TTATTA-TTTATATATTACCTATTT
* **
13471430 TTATTTTTTATATATTATTTATTT
1 TTATTATTTATATATTACCTATTT
* **
13471454 TAAACTTATACATATATTACCTATTT
1 T-TA-TTATTTATATATTACCTATTT
13471480 TTAT
1 TTAT
13471484 ATATATAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
24 18 0.43
25 7 0.17
26 17 0.40
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTATTTATATATTACCTATTT
Found at i:13479658 original size:24 final size:24
Alignment explanation
Indices: 13479608--13479658 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
13479598 TGGCATTACG
* *
13479608 AATGTAAATGATGAATTGATGGAA
1 AATGTAAAGGATGAATTGACGGAA
*
13479632 AATGTAAAGGATGAATTGACGGCA
1 AATGTAAAGGATGAATTGACGGAA
13479656 AAT
1 AAT
13479659 TACCCAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.25
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGGAA
Found at i:13480717 original size:181 final size:181
Alignment explanation
Indices: 13480379--13480740 Score: 636
Period size: 181 Copynumber: 2.0 Consensus size: 181
13480369 CTGTAGATTT
*
13480379 ATTCACTTAGTGAGTTGCTAAATATAACTTCATGAATATTGTGGCAGCAACATTAGATTATTCTT
1 ATTCACTTAGTGAGTTGCTAAATATAACTTCATGAATATTGTGGCAACAACATTAGATTATTCTT
* *
13480444 GATAAGTATAAATTTCATATTTGAAAGGAAGTATTATGATTAAATTTTATACGAGCTTATTAAGC
66 GATAAGTATAAATTTCATATTTGAAAGGAAGTATTATGATTAAAGTTTATACGAGCTTACTAAGC
* *
13480509 ATTCATTACTTATGTATTTGTTTTTCTTCTACTTTTTAGATTATTGGAAGC
131 ATTCATTACTTATGTATTTGTTTTTCTTCTACTTTTCAGATTATCGGAAGC
*
13480560 ATTCACTTAGTGAGTTGTTAAATATAACTTCATGAATATTGTGGCAACAACATTAGATTATTCTT
1 ATTCACTTAGTGAGTTGCTAAATATAACTTCATGAATATTGTGGCAACAACATTAGATTATTCTT
*
13480625 GATAAGTATAAATTTCATATTTGAAAAGGAAGTATTATGATTAAAGTTTATATGAGCTTACTAAG
66 GATAAGTATAAATTTCATATTTG-AAAGGAAGTATTATGATTAAAGTTTATACGAGCTTACTAAG
*
13480690 CATTCATTGCTTATGTATTTG-TTTTCTTCTACTTTTCAGATTATCGGAAGC
130 CATTCATTACTTATGTATTTGTTTTTCTTCTACTTTTCAGATTATCGGAAGC
13480741 TCGATTGGGT
Statistics
Matches: 172, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
181 114 0.66
182 58 0.34
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (181 bp):
ATTCACTTAGTGAGTTGCTAAATATAACTTCATGAATATTGTGGCAACAACATTAGATTATTCTT
GATAAGTATAAATTTCATATTTGAAAGGAAGTATTATGATTAAAGTTTATACGAGCTTACTAAGC
ATTCATTACTTATGTATTTGTTTTTCTTCTACTTTTCAGATTATCGGAAGC
Found at i:13491676 original size:50 final size:50
Alignment explanation
Indices: 13491621--13492218 Score: 427
Period size: 50 Copynumber: 12.0 Consensus size: 50
13491611 TAATGAATTT
*
13491621 TTAAAAAGATTGAAGCTACAACGGCGAATCCTACTTCCCCGACATTGCAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * * * * *
13491671 TTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAGTACAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
** * * * * *
13491721 TGGAACATATTGAAGCTACAACGGTGAATCATGCTTCCCCGACATTGCAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* ** *
13491771 TTAAAAAGATTGAAG-TCACAACGGCGAATCTTACTTCCCAGACGGTGCAG
1 TTAAAAAGATTGAAGCT-ACAACGGCGAATCTTACTTCCCCGACATTGCAA
** * * * *
13491821 TGGAACAGATTGAAGCTACAACGGCAAATCCTACTTCCCCGACATTGTAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * * * ** *
13491871 TTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGGTGCAC
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
** * * * * *
13491921 TGGAATAGAATGAAGCCACAATGGCGAATCTT-CTCTCCCCGACATTCCAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACT-TCCCCGACATTGCAA
* * * * * * * * * *
13491971 TTTAAAAGATCGAAGCCACAATGGCAAATCTTACTT-CCCAAGA-GGTACC
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCA-A
* * * * * *
13492020 GTAGAATAGATTGAAGCTAGAACGGTGAATCTTA-TTTCCCGAAACTTGCAA
1 TTA-AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA-TTGCAA
* * * * * ** *
13492071 TCAAAAAGATTGAGGCCACAACGGTGAATCTTATTTCCCC-AGCGGTGCAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGA-CATTGCAA
** * * * * * **
13492121 TGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCTGACACTGCGG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * *
13492171 TT-AATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCAACATTGCA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCA
13492219 GTTGAACAGA
Statistics
Matches: 413, Mismatches: 123, Indels: 25
0.74 0.22 0.04
Matches are distributed among these distances:
48 1 0.00
49 51 0.12
50 349 0.85
51 10 0.02
52 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (50 bp):
TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
Found at i:13491802 original size:100 final size:99
Alignment explanation
Indices: 13491627--13492208 Score: 675
Period size: 100 Copynumber: 5.8 Consensus size: 99
13491617 ATTTTTAAAA
13491627 AGATTGAAGCTACAACGGCGAATCCTACTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAAT-CTACTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* *
13491692 CGGCGAATCTTACTTCCCAGGCAGTACAGTGGAAC
65 CGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAC
* * * *
13491727 ATATTGAAGCTACAACGGTGAATCATGCTTCCCCGACATTGCAATTAAAAAGATTGAAGTCACAA
1 AGATTGAAGCTACAACGGCGAATC-TACTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
*
13491792 CGGCGAATCTTACTTCCCAGACGGTGCAGTGGAAC
65 CGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAC
* *
13491827 AGATTGAAGCTACAACGGCAAATCCTACTTCCCCGACATTGTAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAAT-CTACTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * *
13491892 CGACGAATCTTACTTCCCAGGCGGTGCACTGGAAT
65 CGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAC
* * * * * * *
13491927 AGAATGAAGCCACAATGGCGAATCTTCTCTCCCCGACATTCCAATTTAAAAGATCGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTACT-TCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * * * * * * *
13491992 TGGCAAATCTTACTTCCCAAGAGGTACCGTAGAAT
65 CGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAC
* * * * * *
13492027 AGATTGAAGCTAGAACGGTGAATCTTA-TTTCCCGAAACTTGCAATCAAAAAGATTGAGGCCACA
1 AGATTGAAGCTACAACGGCGAATC-TACTTCCCCGACA-TTGCAATTAAAAAGATTGAAGCCACA
* *
13492091 ACGGTGAATCTTATTTCCCCA-GCGGTGCAGTGGAAC
64 ACGGCGAATCTTACTT-CCCAGGCGGTGCAGTGGAAC
* * * * ** * *
13492127 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCTGACACTGCGGTT-AATAGATTGAAGCTACAA
1 AGATTGAAGCTACAACGGCGAATC-TACTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
*
13492191 CAGCGAATCTTACTTCCC
65 CGGCGAATCTTACTTCCC
13492209 CAACATTGCA
Statistics
Matches: 401, Mismatches: 74, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
98 3 0.01
99 39 0.10
100 346 0.86
101 13 0.03
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (99 bp):
AGATTGAAGCTACAACGGCGAATCTACTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAAC
GGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAC
Found at i:13494025 original size:51 final size:50
Alignment explanation
Indices: 13493911--13494020 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 50
13493901 TATTATTACC
13493911 ACTATTATTAAT-TATTATTAGTTTTATTTTCTTTTTATTTATTTGTTATT
1 ACTA-TATTAATGTATTATTAGTTTTATTTTCTTTTTATTTATTTGTTATT
* *
13493961 ATTATATTAATGTATTAATTAGTTTTATATTTTTTTTTCAACTTTATTT-TTATT
1 ACTATATTAATGTATT-ATTAGTTTTAT-TTTCTTTTT--A-TTTATTTGTTATT
13494015 -CTATAT
1 ACTATAT
13494021 ATGTACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
49 7 0.14
50 7 0.14
51 11 0.22
52 8 0.16
53 5 0.10
54 6 0.12
55 7 0.14
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (50 bp):
ACTATATTAATGTATTATTAGTTTTATTTTCTTTTTATTTATTTGTTATT
Found at i:13504908 original size:13 final size:13
Alignment explanation
Indices: 13504890--13504914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13504880 CAATCAAATG
13504890 CACACAAAATAAA
1 CACACAAAATAAA
13504903 CACACAAAATAA
1 CACACAAAATAA
13504915 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:13510710 original size:41 final size:41
Alignment explanation
Indices: 13510665--13510770 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
13510655 ACTGGCAATT
* *
13510665 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTAAAGTCCGAAACATTTCACCGGCATCA
*
13510706 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCCGAAACATTTCACCGGCATCA
*
13510747 AGCCTGCTAGATGTAAAGTCCGAA
1 AGCCTGCTAGACGTAAAGTCCGAA
13510771 TTATCTCATT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCCGAAACATTTCACCGGCATCA
Found at i:13511205 original size:122 final size:122
Alignment explanation
Indices: 13511066--13511310 Score: 481
Period size: 122 Copynumber: 2.0 Consensus size: 122
13511056 ATACACTTTA
13511066 CATTCCAACATATTAAAATTATACACACATATATATACATGATCAAAACTAACATATGCAAATAT
1 CATTCCAACATATTAAAATTATACACACATATATATACATGATCAAAACTAACATATGCAAATAT
*
13511131 CATCTAATAACAAATTTCAAAACTAAATCTTATACATGCATACATTTACACTCAAAC
66 CATCTAATAACAAATTTCAAAACTAAATCTTATACATGCATACATATACACTCAAAC
13511188 CATTCCAACATATTAAAATTATACACACATATATATACATGATCAAAACTAACATATGCAAATAT
1 CATTCCAACATATTAAAATTATACACACATATATATACATGATCAAAACTAACATATGCAAATAT
13511253 CATCTAATAACAAATTTCAAAACTAAATCTTATACATGCATACATATACACTCAAAC
66 CATCTAATAACAAATTTCAAAACTAAATCTTATACATGCATACATATACACTCAAAC
13511310 C
1 C
13511311 GCATATACTT
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (122 bp):
CATTCCAACATATTAAAATTATACACACATATATATACATGATCAAAACTAACATATGCAAATAT
CATCTAATAACAAATTTCAAAACTAAATCTTATACATGCATACATATACACTCAAAC
Found at i:13512719 original size:13 final size:13
Alignment explanation
Indices: 13512701--13512725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13512691 CAATCAAATG
13512701 CACACAAAATAAA
1 CACACAAAATAAA
13512714 CACACAAAATAA
1 CACACAAAATAA
13512726 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:13515151 original size:50 final size:50
Alignment explanation
Indices: 13515096--13515692 Score: 420
Period size: 50 Copynumber: 12.0 Consensus size: 50
13515086 TAATGAATTT
* *
13515096 TTAAAAAGATTGAAGCTACAACGGCGAATCCTGCTTCCCCGACATTGCAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * * * *
13515146 TTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAGT-AAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
** * * * * *
13515195 GTGGAACAG-TTGAAGCTACAACGGAGAATCATGCTTCCCTGACATTGCAA
1 -TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * * ** *
13515245 TTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGACGGTGCAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
** * * *
13515295 TGGAACAGATTGAAGCTACAACGGCGAATCCTACTTCCCCGACATTGTAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* ** * * ** *
13515345 TTAAAAAGATTGAAGCCACAACGATGAATCTTACTTCCCAGGCGGTGCAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
** * * * *
13515395 TGGAATAGAATGAAGCTACAACGGCGAATCTT-CTCTCCTCGACATTGGAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACT-TCCCCGACATTGCAA
* * * * * * **
13515445 TTTAAAAGATCGAAACCACAACGGCTAATCTTACTTCCCAGGA-GGTGTC--
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC-CGACATTG-CAA
* * * * *
13515494 GTAGAATAGATTGAAGCTAGAACGGTGAATCTT-CTTTCCCTGACATTGCAA
1 TTA-AAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCCGACATTGCAA
* * * * * * * *
13515545 TCAAAAAGATTGAGGCCACAACGGTGAATCTTATTTCCCC-AGCAGTGTAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGA-CATTGCAA
** * ** * **
13515595 TGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCTGACATTGCGG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * * *
13515645 TT-AATAGATTGAAGCTACAACAGTGAATCTTACTTTCCCGACATTGCA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCA
13515693 GTTGAACAGG
Statistics
Matches: 407, Mismatches: 125, Indels: 31
0.72 0.22 0.06
Matches are distributed among these distances:
49 83 0.20
50 318 0.78
51 6 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (50 bp):
TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
Found at i:13515367 original size:100 final size:99
Alignment explanation
Indices: 13515102--13515701 Score: 701
Period size: 100 Copynumber: 6.0 Consensus size: 99
13515092 ATTTTTAAAA
13515102 AGATTGAAGCTACAACGGCGAATCCTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAAT-CTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * **
13515167 CGGCGAATCTTACTTCCCAGGCAGTAAAGTGGAAC
65 CGGTGAATCTTACTTCCCAGACAGTGCAGTGGAAC
* *
13515202 AG-TTGAAGCTACAACGGAGAATCATGCTTCCCTGACATTGCAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATC-TGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
*
13515266 CGGTGAATCTTACTTCCCAGACGGTGCAGTGGAAC
65 CGGTGAATCTTACTTCCCAGACAGTGCAGTGGAAC
* *
13515301 AGATTGAAGCTACAACGGCGAATCCTACTTCCCCGACATTGTAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAAT-CTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * * *
13515366 CGATGAATCTTACTTCCCAGGCGGTGCAGTGGAAT
65 CGGTGAATCTTACTTCCCAGACAGTGCAGTGGAAC
* * * * * * *
13515401 AGAATGAAGCTACAACGGCGAATCTTCTCTCCTCGACATTGGAATTTAAAAGATCGAAACCACAA
1 AGATTGAAGCTACAACGGCGAATCTGCT-TCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * *
13515466 CGGCT-AATCTTACTTCCCAGGA-GGTGTC-GTAGAAT
65 CGG-TGAATCTTACTTCCCA-GACAGTG-CAGTGGAAC
* * * * * *
13515501 AGATTGAAGCTAGAACGGTGAATCTTCTTTCCCTGACATTGCAATCAAAAAGATTGAGGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTGC-TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* *
13515566 CGGTGAATCTTATTTCCCCAG-CAGTGTAGTGGAAC
65 CGGTGAATCTTACTT-CCCAGACAGTGCAGTGGAAC
* ** * *
13515601 AGATTGAAGCTACAACGGCGAATCTCGCTTCCCTGACATTGCGGTT-AATAGATTGAAGCTACAA
1 AGATTGAAGCTACAACGGCGAATCT-GCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * *
13515665 CAGTGAATCTTACTTTCCC-GACATTGCAGTTGAAC
65 CGGTGAATCTTAC-TTCCCAGACAGTGCAGTGGAAC
13515700 AG
1 AG
13515702 GTTGGAGGTG
Statistics
Matches: 431, Mismatches: 54, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
98 2 0.00
99 137 0.32
100 282 0.65
101 10 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (99 bp):
AGATTGAAGCTACAACGGCGAATCTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAAC
GGTGAATCTTACTTCCCAGACAGTGCAGTGGAAC
Found at i:13518989 original size:21 final size:22
Alignment explanation
Indices: 13518965--13519007 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13518955 ATTAATCATT
13518965 TTAAAAAAAT-ATTTTGATTTA
1 TTAAAAAAATGATTTTGATTTA
* *
13518986 TTAAAATAATGATTTTGGTTTA
1 TTAAAAAAATGATTTTGATTTA
13519008 CAAAATTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
TTAAAAAAATGATTTTGATTTA
Found at i:13519752 original size:26 final size:24
Alignment explanation
Indices: 13519684--13519755 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
13519674 AATTATATAT
* *
13519684 ATAAAAATAGGTAATATATGTATAAG
1 ATAAAAATAGGTAATATA--TAAAAA
* * **
13519710 TTTAAAATAAATAATATATAAAAA
1 ATAAAAATAGGTAATATATAAAAA
13519734 ATAAAAATAGGTAATATATAAA
1 ATAAAAATAGGTAATATATAAA
13519756 GTAATAATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 22 0.61
26 14 0.39
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (24 bp):
ATAAAAATAGGTAATATATAAAAA
Found at i:13519962 original size:18 final size:17
Alignment explanation
Indices: 13519918--13519964 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
13519908 TACAAATATT
*
13519918 TATGAGATTAT-ATTAA
1 TATGAGATTATAATAAA
*
13519934 TA-GATATTATAATAACA
1 TATGAGATTATAATAA-A
13519951 TATGAGATTATAAT
1 TATGAGATTATAAT
13519965 CATCATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 7 0.28
16 5 0.20
17 3 0.12
18 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (17 bp):
TATGAGATTATAATAAA
Found at i:13524801 original size:26 final size:24
Alignment explanation
Indices: 13524733--13524804 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
13524723 AATTATATAT
* *
13524733 ATAAAAATAGGTAATATATGTATAAG
1 ATAAAAATAGGTAATATA--TAAAAA
* * **
13524759 TTTAAAATAAATAATATATAAAAA
1 ATAAAAATAGGTAATATATAAAAA
13524783 ATAAAAATAGGTAATATATAAA
1 ATAAAAATAGGTAATATATAAA
13524805 GTAATAATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 22 0.61
26 14 0.39
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (24 bp):
ATAAAAATAGGTAATATATAAAAA
Found at i:13537295 original size:5 final size:5
Alignment explanation
Indices: 13537285--13537344 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
13537275 AGGCAACCCA
* *
13537285 ATTTT ATTTT ATTTT A-TAT ATTTT ATTTT TTTTT ATTTTCT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A-TTT-T ATTTT ATTTT
*
13537336 -CTTT ATTTT
1 ATTTT ATTTT
13537345 CTTACATGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 6 0.13
5 31 0.69
6 6 0.13
7 2 0.04
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:13537309 original size:19 final size:18
Alignment explanation
Indices: 13537285--13537335 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
13537275 AGGCAACCCA
13537285 ATTTTATTTTATTTTATAT
1 ATTTTATTTTATTTT-TAT
13537304 ATTTTATTTT-TTTTTAT
1 ATTTTATTTTATTTTTAT
13537321 -TTTCTATTTTATTTT
1 ATTT-TATTTTATTTT
13537336 CTTTATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.10
17 9 0.30
18 8 0.27
19 10 0.33
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTTATTTTATTTTTAT
Found at i:13537318 original size:24 final size:23
Alignment explanation
Indices: 13537285--13537344 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
13537275 AGGCAACCCA
*
13537285 ATTTTATTTTATTTTATATATTTT
1 ATTTTTTTTTATTTT-TATATTTT
*
13537309 ATTTTTTTTTA-TTTTCTATTTT
1 ATTTTTTTTTATTTTTATATTTT
*
13537331 A-TTTTCTTTATTTT
1 ATTTTTTTTTATTTT
13537345 CTTACATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 8 0.25
22 11 0.34
23 3 0.09
24 10 0.31
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (23 bp):
ATTTTTTTTTATTTTTATATTTT
Found at i:13538952 original size:41 final size:40
Alignment explanation
Indices: 13538862--13538954 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 40
13538852 TGAACTTTCG
* * * *
13538862 GGGCTTTAGTGGCGTTTTTGAAAAAGTGCCACTAATGATC
1 GGGCTTTAGCGGCATTTTTAAAAAAGTGCCACTAATGACC
* *
13538902 GGACTTTTAGCGGCATTTTTAAAAAAGTG-CAGCTAATGCCC
1 GGGC-TTTAGCGGCATTTTTAAAAAAGTGCCA-CTAATGACC
13538943 TGGGCTTTAGCG
1 -GGGCTTTAGCG
13538955 ACGTTTTCGT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
40 5 0.12
41 35 0.81
42 3 0.07
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (40 bp):
GGGCTTTAGCGGCATTTTTAAAAAAGTGCCACTAATGACC
Found at i:13539052 original size:40 final size:40
Alignment explanation
Indices: 13538967--13539091 Score: 153
Period size: 40 Copynumber: 3.1 Consensus size: 40
13538957 GTTTTCGTCA
* *
13538967 CTAATGCTCAGAGTTTTAGCAGCGTTTTTGAAAAAGCGTCG
1 CTAATGCTCAGA-TTTTAGCAGCATTTTTGAAAAAGCGCCG
* *
13539008 CTAATGCTCAGATCTTTAGCGGCATTTTT-AAAAATCGCCG
1 CTAATGCTCAGAT-TTTAGCAGCATTTTTGAAAAAGCGCCG
* * * *
13539048 CTAATACTCGGCTTTTAGCTGCATTTTTGAAAAAGCGCCG
1 CTAATGCTCAGATTTTAGCAGCATTTTTGAAAAAGCGCCG
13539088 CTAA
1 CTAA
13539092 AACATTTTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 14 0.19
40 34 0.47
41 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (40 bp):
CTAATGCTCAGATTTTAGCAGCATTTTTGAAAAAGCGCCG
Found at i:13539644 original size:60 final size:62
Alignment explanation
Indices: 13539580--13539694 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 62
13539570 AGGTTAGGCT
*
13539580 TTAGGGTTTATATTAATTAGTGTGATTT-AA-TT-TATATTAAATAAGATTTAGGGATTTGGG
1 TTAGGGTTTAGATTAATTAGTGT-ATTTAAATTTATATATTAAATAAGATTTAGGGATTTGGG
* *
13539640 TTAGGGTTTAGATTAATTAGTGTTTTTAAATTTATATATTAAATAAGGTTTAGGG
1 TTAGGGTTTAGATTAATTAGTGTATTTAAATTTATATATTAAATAAGATTTAGGG
13539695 GTTAATAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 3 0.06
60 24 0.49
61 2 0.04
62 20 0.41
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (62 bp):
TTAGGGTTTAGATTAATTAGTGTATTTAAATTTATATATTAAATAAGATTTAGGGATTTGGG
Found at i:13539739 original size:21 final size:21
Alignment explanation
Indices: 13539688--13539737 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
13539678 TTAAATAAGG
* *
13539688 TTTAGGGGTTAATAGTTAGGG
1 TTTAGGGGTTAAGAGTTAGGA
*
13539709 GTTAGGGGTTAAGAGTTAGTGA
1 TTTAGGGGTTAAGAGTTAG-GA
13539731 TTTAGGG
1 TTTAGGG
13539738 TTTAGAGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (21 bp):
TTTAGGGGTTAAGAGTTAGGA
Found at i:13539844 original size:7 final size:7
Alignment explanation
Indices: 13539832--13539874 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
13539822 ATTGTAAAAG
13539832 AGGGGTT
1 AGGGGTT
13539839 AGGGGTT
1 AGGGGTT
*
13539846 AGAGGTT
1 AGGGGTT
* *
13539853 AAGGATT
1 AGGGGTT
*
13539860 AAGGGTT
1 AGGGGTT
13539867 AGGGGTT
1 AGGGGTT
13539874 A
1 A
13539875 TGGATAGGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.47, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:13542174 original size:43 final size:43
Alignment explanation
Indices: 13542062--13542215 Score: 181
Period size: 43 Copynumber: 3.6 Consensus size: 43
13542052 ATATATTTTT
* * * *
13542062 TAAAGGTTATG-TTTTTAGCGGCGTTTTTG-CGAGAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGACTA-AAGCGCCGC
* * *
13542104 TAAAGGT-TTGTTCTTTCGCGGCGTTTGTGACTAAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGACTAAAGCGCCGC
*
13542146 TAAAGGTCATGATCTTTAGCGGCGTTTGTGA-TAAAAGGGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGACT-AAAGCGCCGC
*
13542189 TAAAGGTCAAGATCTTTAGCGGCGTTT
1 TAAAGGTCATGATCTTTAGCGGCGTTT
13542216 TTTCACATAA
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
41 2 0.02
42 39 0.40
43 57 0.58
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (43 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTGTGACTAAAGCGCCGC
Found at i:13543960 original size:19 final size:18
Alignment explanation
Indices: 13543918--13543960 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
13543908 AAGTAGTTTT
13543918 ATTCATTTGCTCGAAAAA
1 ATTCATTTGCTCGAAAAA
13543936 AGTTCATTTGCT-GCAACAAA
1 A-TTCATTTGCTCG-AA-AAA
13543956 ATTCA
1 ATTCA
13543961 GAAAATCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.09
19 16 0.73
20 4 0.18
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (18 bp):
ATTCATTTGCTCGAAAAA
Found at i:13544589 original size:18 final size:19
Alignment explanation
Indices: 13544553--13544594 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
13544543 TTATTTTTTC
* *
13544553 AATATGTTACAAATTACAT
1 AATATGTTAAAAATAACAT
13544572 AATAT-TTAAAAATAACAT
1 AATATGTTAAAAATAACAT
13544590 AATAT
1 AATAT
13544595 AAATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
AATATGTTAAAAATAACAT
Found at i:13549353 original size:46 final size:45
Alignment explanation
Indices: 13549240--13549402 Score: 159
Period size: 45 Copynumber: 3.6 Consensus size: 45
13549230 TCGAAGTGTA
* * **
13549240 CCATGGTGTCTTTCAACCATGGTCTTATTTATTCTTGTTTTGATG
1 CCATAGTGTCTTTCAACCATGGTCTTATTCATTCTTGTCGTGATG
* * *
13549285 CCATAGTGTCTTTAAACCATGGTCTTATTCATTTTTCGTCGTGTTG
1 CCATAGTGTCTTTCAACCATGGTCTTATTCATTCTT-GTCGTGATG
* * * *
13549331 TCATAGTGTCTTTCAACTATGGTCTTATTC-GT-TTGATTCGTGAAG
1 CCATAGTGTCTTTCAACCATGGTCTTATTCATTCTTG--TCGTGATG
* * *
13549376 CCATAGCGTCTTTCAGCTATGGTCTTA
1 CCATAGTGTCTTTCAACCATGGTCTTA
13549403 CTCAATAGAA
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 63 0.64
46 33 0.33
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (45 bp):
CCATAGTGTCTTTCAACCATGGTCTTATTCATTCTTGTCGTGATG
Found at i:13549417 original size:45 final size:45
Alignment explanation
Indices: 13549368--13549541 Score: 251
Period size: 45 Copynumber: 3.9 Consensus size: 45
13549358 TTCGTTTGAT
* *
13549368 TCGTGAAGCCATAGCGTCTTTCAG-CTATGGTCTTACTCAATAGAA
1 TCGTGAAGCCATAACATCTTTCAGTC-ATGGTCTTACTCAATAGAA
* ** *
13549413 TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTTGATAAAA
1 TCGTGAAGCCATAACATCTTTCAGTCATGGTCTTACTCAATAGAA
* *
13549458 TTGTGAAGCCATAACATCTTTCAGTCATGATCTTACTCAATAGAA
1 TCGTGAAGCCATAACATCTTTCAGTCATGGTCTTACTCAATAGAA
*
13549503 TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCA
1 TCGTGAAGCCATAACATCTTTCAGTCATGGTCTTACTCA
13549542 TTTCTAGTAT
Statistics
Matches: 113, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
45 112 0.99
46 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (45 bp):
TCGTGAAGCCATAACATCTTTCAGTCATGGTCTTACTCAATAGAA
Found at i:13549464 original size:90 final size:90
Alignment explanation
Indices: 13549370--13549539 Score: 297
Period size: 90 Copynumber: 1.9 Consensus size: 90
13549360 CGTTTGATTC
* * *
13549370 GTGAAGCCATAGCGTCTTTCAG-CTATGGTCTTACTCAATAGAATCGTGATGCCATAACATCTTT
1 GTGAAGCCATAACATCTTTCAGTC-ATGATCTTACTCAATAGAATCGTGATGCCATAACATCTTT
13549434 CAGTCATGGTCTTACTTGATAAAATT
65 CAGTCATGGTCTTACTTGATAAAATT
13549460 GTGAAGCCATAACATCTTTCAGTCATGATCTTACTCAATAGAATCGTGATGCCATAACATCTTTC
1 GTGAAGCCATAACATCTTTCAGTCATGATCTTACTCAATAGAATCGTGATGCCATAACATCTTTC
13549525 AGTCATGGTCTTACT
66 AGTCATGGTCTTACT
13549540 CATTTCTAGT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
90 75 0.99
91 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (90 bp):
GTGAAGCCATAACATCTTTCAGTCATGATCTTACTCAATAGAATCGTGATGCCATAACATCTTTC
AGTCATGGTCTTACTTGATAAAATT
Found at i:13549558 original size:45 final size:43
Alignment explanation
Indices: 13549375--13549560 Score: 146
Period size: 45 Copynumber: 4.1 Consensus size: 43
13549365 GATTCGTGAA
* * *
13549375 GCCATAGCGTCTTTCAG-CTATGGTCTTACTCA-ATAGAATCGTGAT
1 GCCATAACATCTTTCAGTC-ATGGTCTTACTCATATAGTAT-G-G-T
* * * *
13549420 GCCATAACATCTTTCAGTCATGGTCTTACTTGATAAAAT-TGTGAA
1 GCCATAACATCTTTCAGTCATGGTCTTAC-TCATATAGTATG-G-T
* *
13549465 GCCATAACATCTTTCAGTCATGATCTTACTCA-ATAGAATCGTGAT
1 GCCATAACATCTTTCAGTCATGGTCTTACTCATATAGTAT-G-G-T
*
13549510 GCCATAACATCTTTCAGTCATGGTCTTACTCATTTCTAGTATGGT
1 GCCATAACATCTTTCAGTCATGGTCTTACTCA--TATAGTATGGT
13549555 GCCATA
1 GCCATA
13549561 GTGTCTTTCA
Statistics
Matches: 117, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 99 0.85
46 5 0.04
47 3 0.03
48 5 0.04
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (43 bp):
GCCATAACATCTTTCAGTCATGGTCTTACTCATATAGTATGGT
Found at i:13549582 original size:90 final size:90
Alignment explanation
Indices: 13549371--13549582 Score: 266
Period size: 90 Copynumber: 2.4 Consensus size: 90
13549361 GTTTGATTCG
*
13549371 TGAAGCCATAGCGTCTTTCAGCTATGGTCTTACTCAATAGAATCGTGATGCCATAACATCTTTCA
1 TGAAGCCATAGCGTCTTTCAACTATGGTCTTACTCAATAGAATCGTGATGCCATAACATCTTTCA
* * *
13549436 GTCATGGTCTTACTTGATAAAATTG
66 GTCATGGTCTTACTTCATAAAAGTA
* * * *
13549461 TGAAGCCATAACATCTTTC-AGTCATGATCTTACTCAATAGAATCGTGATGCCATAACATCTTTC
1 TGAAGCCATAGCGTCTTTCAACT-ATGGTCTTACTCAATAGAATCGTGATGCCATAACATCTTTC
***
13549525 AGTCATGGTCTTAC-TCATTTCTAGTA
65 AGTCATGGTCTTACTTCA-TAAAAGTA
** *
13549551 TGGTGCCATAGTGTCTTTCAACTATGGTCTTA
1 TGAAGCCATAGCGTCTTTCAACTATGGTCTTA
13549583 TTTATTCTCT
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
89 3 0.03
90 96 0.95
91 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (90 bp):
TGAAGCCATAGCGTCTTTCAACTATGGTCTTACTCAATAGAATCGTGATGCCATAACATCTTTCA
GTCATGGTCTTACTTCATAAAAGTA
Found at i:13549615 original size:46 final size:45
Alignment explanation
Indices: 13549529--13549635 Score: 151
Period size: 46 Copynumber: 2.4 Consensus size: 45
13549519 TCTTTCAGTC
* *
13549529 ATGGTCTTACTCATTTCTAGTATGGTGCCATAGTGTCTTTCAACT
1 ATGGTCTTACTCATTTCTAGTATAGTGCCATAGTGCCTTTCAACT
* * *
13549574 ATGGTCTTATTTATTCTCTGGTATAGTGCCATAGTGCCTTTCAACT
1 ATGGTCTTACTCATT-TCTAGTATAGTGCCATAGTGCCTTTCAACT
*
13549620 ATGGTCTTAATCATTT
1 ATGGTCTTACTCATTT
13549636 TCCTTCAAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 14 0.26
46 40 0.74
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.44
Consensus pattern (45 bp):
ATGGTCTTACTCATTTCTAGTATAGTGCCATAGTGCCTTTCAACT
Found at i:13555595 original size:21 final size:20
Alignment explanation
Indices: 13555553--13555595 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
13555543 ACTTATAATG
* * *
13555553 ATGATTTGAATGATGTTTTA
1 ATGATATGAATGATGATATA
13555573 ATGATATGAAATGATGATATA
1 ATGATATG-AATGATGATATA
13555594 AT
1 AT
13555596 TGTGGTACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (20 bp):
ATGATATGAATGATGATATA
Found at i:13558950 original size:57 final size:57
Alignment explanation
Indices: 13558889--13559052 Score: 163
Period size: 57 Copynumber: 2.9 Consensus size: 57
13558879 TTTTTATAAT
* * * *
13558889 ATTATATATTATGATTT-TTTAATT-CATATAATAATAATTATATTAGAATCTTATTAA
1 ATTATATATTAT--TTTATTAAATTGCATATAATAATAATTATATTAAAATATGATTAA
* *
13558946 ATTATATATTATTTTATTAAATTGTATTTAATAATAATTATATTAAAATATGATTAA
1 ATTATATATTATTTTATTAAATTGCATATAATAATAATTATATTAAAATATGATTAA
* ** * * *
13559003 ATTAT-TCATTATTTTTATTAAAATATATTTAACAATAATTTTATTAAAAT
1 ATTATAT-ATTA-TTTTATTAAATTGCATATAATAATAATTATATTAAAAT
13559053 TTAATAACAA
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
55 3 0.03
56 7 0.08
57 49 0.53
58 34 0.37
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (57 bp):
ATTATATATTATTTTATTAAATTGCATATAATAATAATTATATTAAAATATGATTAA
Found at i:13559002 original size:26 final size:25
Alignment explanation
Indices: 13558917--13559002 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 25
13558907 TTAATTCATA
* *
13558917 TAATAATAATTATATTAGAATCTTAT
1 TAATAATAATTATATTAAAAT-TGAT
* *
13558943 TAAATTATATATTATTTTATTAAATTGTATT
1 T-AATAATA-ATTATATTA--AAATTG-A-T
13558974 TAATAATAATTATATTAAAATATGAT
1 TAATAATAATTATATTAAAAT-TGAT
13559000 TAA
1 TAA
13559003 ATTATTCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
26 5 0.11
27 11 0.23
28 10 0.21
29 9 0.19
30 10 0.21
31 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (25 bp):
TAATAATAATTATATTAAAATTGAT
Found at i:13559044 original size:26 final size:26
Alignment explanation
Indices: 13558956--13559065 Score: 78
Period size: 26 Copynumber: 4.0 Consensus size: 26
13558946 ATTATATATT
* * *
13558956 ATTTTATTAAATTGTATTTAATAATA
1 ATTTTATTAAAATATATTTAACAATA
* * *
13558982 ATTATATTAAAATATGATTAAATTATTCATTA
1 ATTTTATTAAAATAT-A-T---TTA-ACAATA
*
13559014 TTTTTATTAAAATATATTTAACAATA
1 ATTTTATTAAAATATATTTAACAATA
* *
13559040 ATTTTATTAAAATTTA-ATAACAATA
1 ATTTTATTAAAATATATTTAACAATA
13559065 A
1 A
13559066 CAATAATTAT
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
25 9 0.14
26 30 0.46
27 4 0.06
28 1 0.02
30 1 0.02
31 4 0.06
32 16 0.25
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTTTATTAAAATATATTTAACAATA
Found at i:13559048 original size:58 final size:57
Alignment explanation
Indices: 13558921--13559052 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 57
13558911 TTCATATAAT
* * * * * *
13558921 AATAATTATATTAGAATCTTATTAAATTATATATTATTTTATTAAATTGTATTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTAAC
13558978 AATAATTATATTAAAATATGATTAAATTAT-TCATTATTTTTATTAAAATATATTTAAC
1 AATAATTATATTAAAATATGATTAAATTATAT-ATTA-TTTTATTAAAATATATTTAAC
*
13559036 AATAATTTTATTAAAAT
1 AATAATTATATTAAAAT
13559053 TTAATAACAA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
56 1 0.02
57 31 0.47
58 34 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (57 bp):
AATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTAAC
Found at i:13559261 original size:16 final size:16
Alignment explanation
Indices: 13559222--13559267 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
13559212 GAAATTACTA
* * *
13559222 ATTACAACTCTATTCT
1 ATTACAATTTTATTCC
13559238 ATTACAATTTTATTCC
1 ATTACAATTTTATTCC
13559254 ATTACAATTTTATT
1 ATTACAATTTTATT
13559268 ACCTAAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTACAATTTTATTCC
Found at i:13559289 original size:90 final size:89
Alignment explanation
Indices: 13559195--13559367 Score: 328
Period size: 90 Copynumber: 1.9 Consensus size: 89
13559185 CTATTTCATT
13559195 CCATTCAATCAAATAATGAAATTACTAATTACAACTCTATTCTATTACAATTTTATTCCATTACA
1 CCATTCAATCAAATAATGAAATTACTAATTACAACTCTATTCTATTA-AATTTTATTCCATTACA
*
13559260 ATTTTATTACCTAAGAGTTTTAGAA
65 ATTTTATTACCTAAAAGTTTTAGAA
13559285 CCATTCAATCAAATAATGAAATTACTAATTACAACTCTATTCTATTAAATTTTATTCCATTACAA
1 CCATTCAATCAAATAATGAAATTACTAATTACAACTCTATTCTATTAAATTTTATTCCATTACAA
13559350 TTTTATTACCTAAAAGTT
66 TTTTATTACCTAAAAGTT
13559368 GAACAGCAAT
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
89 35 0.43
90 47 0.57
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.40
Consensus pattern (89 bp):
CCATTCAATCAAATAATGAAATTACTAATTACAACTCTATTCTATTAAATTTTATTCCATTACAA
TTTTATTACCTAAAAGTTTTAGAA
Found at i:13559353 original size:16 final size:16
Alignment explanation
Indices: 13559312--13559356 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
13559302 GAAATTACTA
* * *
13559312 ATTACAACTCTATTCT
1 ATTACAATTTTATTCC
13559328 ATTA-AATTTTATTCC
1 ATTACAATTTTATTCC
13559343 ATTACAATTTTATT
1 ATTACAATTTTATT
13559357 ACCTAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTACAATTTTATTCC
Found at i:13564871 original size:40 final size:40
Alignment explanation
Indices: 13564816--13564899 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
13564806 CTTCAACAAT
13564816 TTACGCCCATGTAACGATATATATGTAAATATATTATATC
1 TTACGCCCATGTAACGATATATATGTAAATATATTATATC
13564856 TTACGCCCATGTAACGATATATATGTAAATATATTATATC
1 TTACGCCCATGTAACGATATATATGTAAATATATTATATC
13564896 TTAC
1 TTAC
13564900 CAGCCAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (40 bp):
TTACGCCCATGTAACGATATATATGTAAATATATTATATC
Found at i:13569036 original size:24 final size:24
Alignment explanation
Indices: 13568985--13569039 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
13568975 CGTCTTCATG
* *
13568985 ATCATCATCTTCATCATCAGAAAT
1 ATCATCATCTTCATCACCAGAAAC
*
13569009 ATCATCATCTTCAATCACCA-AAGC
1 ATCATCATCTTC-ATCACCAGAAAC
13569033 ATCATCA
1 ATCATCA
13569040 ATCTCCACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (24 bp):
ATCATCATCTTCATCACCAGAAAC
Found at i:13572358 original size:24 final size:24
Alignment explanation
Indices: 13572307--13572365 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
13572297 CGTCTTCATG
* *
13572307 ATCATCATCTTCATCATCAGAAAT
1 ATCATCATCTTCATCACCAGAAAC
*
13572331 ATCATCATCTTCAATCACCA-AAGC
1 ATCATCATCTTC-ATCACCAGAAAC
13572355 ATCATCGATCT
1 ATCATC-ATCT
13572366 CCACAGGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 20 0.67
25 10 0.33
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.31
Consensus pattern (24 bp):
ATCATCATCTTCATCACCAGAAAC
Found at i:13576928 original size:6 final size:6
Alignment explanation
Indices: 13576917--13576962 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
13576907 TTGTCTCTAT
* * *
13576917 TATCCC TATCCC TATCTC TATCCC TATCTC TATCTC TATCTC TATC
1 TATCTC TATCTC TATCTC TATCTC TATCTC TATCTC TATCTC TATC
13576963 GCAAGCACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.43
Consensus pattern (6 bp):
TATCTC
Found at i:13576937 original size:12 final size:12
Alignment explanation
Indices: 13576917--13576962 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
13576907 TTGTCTCTAT
*
13576917 TATCCCTATCCC
1 TATCTCTATCCC
13576929 TATCTCTATCCC
1 TATCTCTATCCC
*
13576941 TATCTCTATCTC
1 TATCTCTATCCC
13576953 TATCTCTATC
1 TATCTCTATC
13576963 GCAAGCACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.43
Consensus pattern (12 bp):
TATCTCTATCCC
Found at i:13576940 original size:18 final size:18
Alignment explanation
Indices: 13576917--13576962 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
13576907 TTGTCTCTAT
13576917 TATCCCTATCCCTATCTC
1 TATCCCTATCCCTATCTC
*
13576935 TATCCCTATCTCTATCTC
1 TATCCCTATCCCTATCTC
*
13576953 TATCTCTATC
1 TATCCCTATC
13576963 GCAAGCACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.43
Consensus pattern (18 bp):
TATCCCTATCCCTATCTC
Found at i:13578128 original size:31 final size:31
Alignment explanation
Indices: 13578066--13578128 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
13578056 AAAATGCAAT
* *
13578066 TTAAATAAAAAATTTTAAATAGTTTAATGAC
1 TTAAATAAAAAATTTTAAATAATTCAATGAC
* * *
13578097 TTAAATGAAAATTTTTAAATAATTCAGTGAC
1 TTAAATAAAAAATTTTAAATAATTCAATGAC
13578128 T
1 T
13578129 ATTTTGTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (31 bp):
TTAAATAAAAAATTTTAAATAATTCAATGAC
Found at i:13583404 original size:37 final size:37
Alignment explanation
Indices: 13583282--13583462 Score: 271
Period size: 36 Copynumber: 5.0 Consensus size: 37
13583272 GGTAAGCCNA
* *
13583282 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT-
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* * *
13583318 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT-
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
13583354 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
13583391 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
13583428 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
13583463 ATCATACGTA
Statistics
Matches: 137, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
35 12 0.09
36 72 0.53
37 53 0.39
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:13585430 original size:39 final size:39
Alignment explanation
Indices: 13585342--13585416 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
13585332 CAAATATCTT
*
13585342 AAAAAACGTCGTAAAAGAACATCTTTAGTGGCGTTTTTA
1 AAAAAACGCCGTAAAAGAACATCTTTAGTGGCGTTTTTA
13585381 AAAAAACGCCGTAAAAGAACATCTTTAGTGGCGTTT
1 AAAAAACGCCGTAAAAGAACATCTTTAGTGGCGTTT
13585417 ATTTTTAAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (39 bp):
AAAAAACGCCGTAAAAGAACATCTTTAGTGGCGTTTTTA
Found at i:13588534 original size:23 final size:23
Alignment explanation
Indices: 13588495--13588540 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13588485 GCTCGATTCT
*
13588495 TCGTATTTATAGATTTGGTTTTG
1 TCGTATTTATAGATTTGATTTTG
*
13588518 TCGTATTTTTA-ATTTTGATTTTG
1 TCGTATTTATAGA-TTTGATTTTG
13588541 CTTTCTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.61
Consensus pattern (23 bp):
TCGTATTTATAGATTTGATTTTG
Found at i:13588726 original size:44 final size:46
Alignment explanation
Indices: 13588650--13588737 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 46
13588640 GCTTCTATTA
13588650 TTGTTCATTACAGATTTTGGTCGAATGGTTTAGGGTGTTAGGAAAT
1 TTGTTCATTACAGATTTTGGTCGAATGGTTTAGGGTGTTAGGAAAT
* *
13588696 TTGTTCATTACTG-TTTT-GTTGAATGGTTTAGGGTGTTAGGAA
1 TTGTTCATTACAGATTTTGGTCGAATGGTTTAGGGTGTTAGGAA
13588738 CCGTTTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 24 0.60
45 4 0.10
46 12 0.30
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (46 bp):
TTGTTCATTACAGATTTTGGTCGAATGGTTTAGGGTGTTAGGAAAT
Found at i:13589995 original size:17 final size:17
Alignment explanation
Indices: 13589973--13590005 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13589963 TTAATATCTA
13589973 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
13589990 TATAAGTTTTCTAAAT
1 TATAAGTTTTCTAAAT
13590006 AAGTTTTGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:13590281 original size:32 final size:32
Alignment explanation
Indices: 13590245--13590343 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 32
13590235 TTAAATAACT
** *
13590245 TACATAATTTATTATGTAACAACATAATAAAC
1 TACATAATACATTATATAACAACATAATAAAC
*
13590277 TACATAATACATTATATAATAACATAAT-AAC
1 TACATAATACATTATATAACAACATAATAAAC
* *
13590308 T-TA-AATA-ACTTATATAATAACATAAT-AAC
1 TACATAATACA-TTATATAACAACATAATAAAC
13590337 TAACATA
1 T-ACATA
13590344 CAATATATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
28 1 0.02
29 25 0.44
30 1 0.02
31 5 0.09
32 25 0.44
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (32 bp):
TACATAATACATTATATAACAACATAATAAAC
Found at i:13590315 original size:20 final size:21
Alignment explanation
Indices: 13590274--13590343 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
13590264 CAACATAATA
*
13590274 AACT-ACATAAT-ACATTATAT
1 AACTAACATAATAAC-TTAAAT
13590294 AA-TAACATAATAACTTAAAT
1 AACTAACATAATAACTTAAAT
* * *
13590314 AACTTATATAATAACAT-AAT
1 AACTAACATAATAACTTAAAT
13590334 AACTAACATA
1 AACTAACATA
13590344 CAATATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 27 0.66
21 13 0.32
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (21 bp):
AACTAACATAATAACTTAAAT
Found at i:13590350 original size:29 final size:28
Alignment explanation
Indices: 13590255--13590353 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 28
13590245 TACATAATTT
* *
13590255 ATTATGTAACAACATAATAAACTACATAATAC
1 ATTATATAATAACATAAT-AACT--A-AATAC
13590287 ATTATATAATAACATAATAACTTAAATA-
1 ATTATATAATAACATAATAAC-TAAATAC
13590315 ACTTATATAATAACATAATAACTAACATAC
1 A-TTATATAATAACATAATAACTAA-ATAC
*
13590345 AATATATAA
1 ATTATATAA
13590354 ACATATATAG
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
28 4 0.07
29 34 0.57
30 2 0.03
31 3 0.05
32 17 0.28
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (28 bp):
ATTATATAATAACATAATAACTAAATAC
Found at i:13590393 original size:9 final size:9
Alignment explanation
Indices: 13590365--13590638 Score: 250
Period size: 9 Copynumber: 30.2 Consensus size: 9
13590355 CATATATAGA
*
13590365 AACTAACAT
1 AACTTACAT
* *
13590374 AAATTAAAT
1 AACTTACAT
*
13590383 AAGTTACAT
1 AACTTACAT
13590392 AACTTACAT
1 AACTTACAT
* *
13590401 AAATTAAAT
1 AACTTACAT
13590410 AACTTACAT
1 AACTTACAT
13590419 AACTTACAT
1 AACTTACAT
*
13590428 AAAC-AACAT
1 -AACTTACAT
*
13590437 AAATTACAT
1 AACTTACAT
*
13590446 AACTTAAAT
1 AACTTACAT
* *
13590455 AGGA-ATGCAT
1 A--ACTTACAT
13590465 AACTTACAT
1 AACTTACAT
*
13590474 AACCTACAT
1 AACTTACAT
* *
13590483 AAATTAAAT
1 AACTTACAT
13590492 AACTTACAT
1 AACTTACAT
*
13590501 GACTTACAT
1 AACTTACAT
*
13590510 AAATTA-AGT
1 AACTTACA-T
*
13590519 AACCTACAT
1 AACTTACAT
13590528 AACTTACAT
1 AACTTACAT
*
13590537 AAACTTGCAT
1 -AACTTACAT
* *
13590547 AAATTAAAT
1 AACTTACAT
13590556 AACTTACAT
1 AACTTACAT
*
13590565 AACCTACAT
1 AACTTACAT
* *
13590574 AAATTAAAT
1 AACTTACAT
13590583 AACTTACAT
1 AACTTACAT
13590592 AACTTACAT
1 AACTTACAT
*
13590601 AAATTA-AGT
1 AACTTACA-T
13590610 AACTTACAT
1 AACTTACAT
13590619 AACTTACAT
1 AACTTACAT
13590628 AACTTACAT
1 AACTTACAT
13590637 AA
1 AA
13590639 TACATAAAAA
Statistics
Matches: 209, Mismatches: 46, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
8 5 0.02
9 186 0.89
10 17 0.08
11 1 0.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:13590483 original size:91 final size:90
Alignment explanation
Indices: 13590387--13590638 Score: 312
Period size: 91 Copynumber: 2.8 Consensus size: 90
13590377 TTAAATAAGT
* * * * * * *
13590387 TACATAACTTACATAAATTAAATAACTTACATAACTTACA-TAAACAACATAAATTACATAACTT
1 TACATAAATTAAATAACTTACATAACTTACATAAATTA-AGTAAACTACATAACTTACATAACTT
**
13590451 AAATAGGAA-TGCATAACTTACATAACC
65 AAATA--AATTAAATAACTTACATAACC
* *
13590478 TACATAAATTAAATAACTTACATGACTTACATAAATTAAGTAACCTACATAACTTACATAAACTT
1 TACATAAATTAAATAACTTACATAACTTACATAAATTAAGTAAACTACATAACTTACAT-AACTT
**
13590543 GCATAAATTAAATAACTTACATAACC
65 AAATAAATTAAATAACTTACATAACC
13590569 TACATAAATTAAATAACTTACATAACTTACATAAATTAAGT-AACTTACATAACTTACATAACTT
1 TACATAAATTAAATAACTTACATAACTTACATAAATTAAGTAAAC-TACATAACTTACATAACTT
*
13590633 ACATAA
65 AAATAA
13590639 TACATAAAAA
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
90 15 0.11
91 118 0.84
92 8 0.06
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.31
Consensus pattern (90 bp):
TACATAAATTAAATAACTTACATAACTTACATAAATTAAGTAAACTACATAACTTACATAACTTA
AATAAATTAAATAACTTACATAACC
Found at i:13595410 original size:21 final size:21
Alignment explanation
Indices: 13595385--13595453 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
13595375 CAGCAACTTA
* *
13595385 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
**
13595406 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
*
13595427 AAGCAGAGGCCGCAGCAAGAG
1 AAGCAGAGGCCGCAGCGAGAG
13595448 AAGCAG
1 AAGCAG
13595454 CGAGAGAAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:13595453 original size:12 final size:12
Alignment explanation
Indices: 13595438--13595477 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
13595428 AGCAGAGGCC
13595438 GCAGCAAGAGAA
1 GCAGCAAGAGAA
*
13595450 GCAGCGAGAGAA
1 GCAGCAAGAGAA
*
13595462 GCAGCAATAGAA
1 GCAGCAAGAGAA
13595474 GCAG
1 GCAG
13595478 AGGTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.45, C:0.17, G:0.35, T:0.03
Consensus pattern (12 bp):
GCAGCAAGAGAA
Found at i:13595766 original size:15 final size:15
Alignment explanation
Indices: 13595746--13595779 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13595736 ATTTATTGTT
*
13595746 TTTGGTTAGTTTAGA
1 TTTGGTTACTTTAGA
*
13595761 TTTGGTTACTTTTGA
1 TTTGGTTACTTTAGA
13595776 TTTG
1 TTTG
13595780 CTGTTGCAGG
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:0.15, C:0.03, G:0.24, T:0.59
Consensus pattern (15 bp):
TTTGGTTACTTTAGA
Found at i:13595898 original size:42 final size:42
Alignment explanation
Indices: 13595835--13595993 Score: 239
Period size: 42 Copynumber: 3.8 Consensus size: 42
13595825 AATCCCAAAA
*
13595835 TTAGTGGCG-TTTTTTCTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
* *
13595876 TTAGCGGCGTTTTTTTCTAAGCGCCGCTGAAGAGCATGATCT
1 TTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
*
13595918 TTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
* *
13595960 TTAGCGGCGTTTTTTTATGTAAGCGCCGCAAAAG
1 TTAGCGGCG-TTTTTT-TCTAAGCGCCGCTAAAG
13595994 TTAGTGGCGT
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
41 8 0.08
42 77 0.73
43 6 0.06
44 15 0.14
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (42 bp):
TTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
Found at i:13596088 original size:21 final size:22
Alignment explanation
Indices: 13596064--13596107 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
13596054 TTAGTGGCGT
*
13596064 TAAAAAG-CGCCGCTAAAGACC
1 TAAAAAGACGCCGCTAAAAACC
13596085 TAAAAAGACGCCGCTAAAAACC
1 TAAAAAGACGCCGCTAAAAACC
13596107 T
1 T
13596108 GTTCTACTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.45, C:0.27, G:0.16, T:0.11
Consensus pattern (22 bp):
TAAAAAGACGCCGCTAAAAACC
Found at i:13604688 original size:48 final size:48
Alignment explanation
Indices: 13604617--13604716 Score: 166
Period size: 48 Copynumber: 2.1 Consensus size: 48
13604607 CAGTCGAAAA
*
13604617 CATTTAAACCTCATATGATTCAACATGTTAAT-GTAATCATAAACCAAT
1 CATTTAAACCTCATATGATTCAACATGTTAATACT-ATCATAAACCAAT
*
13604665 CATTTAAACCTCATATTATTCAACATGTTAATACTATCATAAACCAAT
1 CATTTAAACCTCATATGATTCAACATGTTAATACTATCATAAACCAAT
13604713 CATT
1 CATT
13604717 CACATGCATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 48 0.98
49 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (48 bp):
CATTTAAACCTCATATGATTCAACATGTTAATACTATCATAAACCAAT
Found at i:13605813 original size:20 final size:20
Alignment explanation
Indices: 13605790--13605970 Score: 64
Period size: 20 Copynumber: 9.1 Consensus size: 20
13605780 AAGTATAATT
13605790 AGGGGCACGTATGTGCAATC
1 AGGGGCACGTATGTGCAATC
* * * * *
13605810 AGGGGTATC-AAAGTACAACC
1 AGGGGCA-CGTATGTGCAATC
* * *
13605830 ATGGGCACATATGTGCAATT
1 AGGGGCACGTATGTGCAATC
* *
13605850 AGGGGTGC-CG-AAGTACAATC
1 A-GGG-GCACGTATGTGCAATC
*
13605870 AGGGGCACATATGTGCAATC
1 AGGGGCACGTATGTGCAATC
* ** * * *
13605890 AGGGGTACCAAAGTACAAAC
1 AGGGGCACGTATGTGCAATC
** * *
13605910 ATAGACACGTATGGGCAATC
1 AGGGGCACGTATGTGCAATC
* * * *
13605930 AGGGGTACCG-AAGTACAAAC
1 AGGGGCA-CGTATGTGCAATC
*
13605950 AGGGACACGTATGTGCAATC
1 AGGGGCACGTATGTGCAATC
13605970 A
1 A
13605971 TATAATAATT
Statistics
Matches: 104, Mismatches: 49, Indels: 16
0.62 0.29 0.09
Matches are distributed among these distances:
18 2 0.02
19 7 0.07
20 87 0.84
21 6 0.06
22 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (20 bp):
AGGGGCACGTATGTGCAATC
Found at i:13605885 original size:80 final size:80
Alignment explanation
Indices: 13605768--13605970 Score: 280
Period size: 80 Copynumber: 2.5 Consensus size: 80
13605758 GAAAGTGCAT
* * * * * *
13605768 TCAGGGGTATCGAAGTATAATTAGGGGCACGTATGTGCAATCAGGGGTATCAAAGTACAACCATG
1 TCAGGGGTACCGAAGTACAATCAGGGGCACGTATGTGCAATCAGGGGTACCAAAGTACAAACATA
* *
13605833 GGCACATATGTGCAA
66 GACACATATGGGCAA
* * *
13605848 TTAGGGGTGCCGAAGTACAATCAGGGGCACATATGTGCAATCAGGGGTACCAAAGTACAAACATA
1 TCAGGGGTACCGAAGTACAATCAGGGGCACGTATGTGCAATCAGGGGTACCAAAGTACAAACATA
*
13605913 GACACGTATGGGCAA
66 GACACATATGGGCAA
* *
13605928 TCAGGGGTACCGAAGTACAAACAGGGACACGTATGTGCAATCA
1 TCAGGGGTACCGAAGTACAATCAGGGGCACGTATGTGCAATCA
13605971 TATAATAATT
Statistics
Matches: 106, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 106 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (80 bp):
TCAGGGGTACCGAAGTACAATCAGGGGCACGTATGTGCAATCAGGGGTACCAAAGTACAAACATA
GACACATATGGGCAA
Found at i:13605905 original size:40 final size:40
Alignment explanation
Indices: 13605741--13605970 Score: 244
Period size: 40 Copynumber: 5.8 Consensus size: 40
13605731 GAGTTGCTAG
* * * * * *
13605741 AGTATAAATAGGGGCACGAAAGTGCATTCAGGGGTATCGA
1 AGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCGA
* ** * *
13605781 AGTATAATTAGGGGCACGTATGTGCAATCAGGGGTATCAA
1 AGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCGA
* * * * *
13605821 AGTACAACCATGGGCACATATGTGCAATTAGGGGTGCCGA
1 AGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCGA
* * *
13605861 AGTACAATCAGGGGCACATATGTGCAATCAGGGGTACCAA
1 AGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCGA
** * *
13605901 AGTACAAACATAGACACGTATGGGCAATCAGGGGTACCGA
1 AGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCGA
*
13605941 AGTACAAACAGGGACACGTATGTGCAATCA
1 AGTACAAACAGGGGCACGTATGTGCAATCA
13605971 TATAATAATT
Statistics
Matches: 161, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 161 1.00
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (40 bp):
AGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCGA
Found at i:13612460 original size:22 final size:22
Alignment explanation
Indices: 13612449--13612493 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
13612439 AACTATTTCC
13612449 TCTTCCCATATTAGATAGTTAA
1 TCTTCCCATATTAGATAGTTAA
*
13612471 TCTTCCCATATTAGACAGTTAA
1 TCTTCCCATATTAGATAGTTAA
13612493 T
1 T
13612494 TTAATAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (22 bp):
TCTTCCCATATTAGATAGTTAA
Found at i:13615381 original size:31 final size:31
Alignment explanation
Indices: 13615346--13615409 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
13615336 ATTATGGTAA
* * *
13615346 AAATGTGAAAATCAATTTGTATGTTCAAATT
1 AAATGTGAAAATCAAATTGTAAGCTCAAATT
13615377 AAATGTGAAAATCAAATTGTAAGCTCAAATT
1 AAATGTGAAAATCAAATTGTAAGCTCAAATT
13615408 AA
1 AA
13615410 GGGATACGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (31 bp):
AAATGTGAAAATCAAATTGTAAGCTCAAATT
Found at i:13615608 original size:46 final size:46
Alignment explanation
Indices: 13615490--13615767 Score: 445
Period size: 46 Copynumber: 6.0 Consensus size: 46
13615480 CATGGCAAAG
* *
13615490 TGTGAAACGTAGGTATGGTATTTCAATAAAGAAAACCATACTAAG-
1 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGT
13615535 TGTTGAAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGT
1 TG-TG-AAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGT
13615583 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAG-
1 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGT
*
13615628 TGTTGAAAAAGTAGGTATGGTATCTCAATAAA-AAAACCATACTGAGT
1 TG-TG-AAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGT
* *
13615675 TGTGAAAAGTAGGTATGATATTTCAATAAAGAAAACCATACTGGGT
1 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGT
*
13615721 TGTGAAAAGTAGGTATCGTATTTCAATAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGT
13615767 T
1 T
13615768 AGAGTATAGT
Statistics
Matches: 217, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
45 28 0.13
46 119 0.55
47 68 0.31
48 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGT
Found at i:13615649 original size:93 final size:93
Alignment explanation
Indices: 13615490--13615767 Score: 472
Period size: 93 Copynumber: 3.0 Consensus size: 93
13615480 CATGGCAAAG
* *
13615490 TGTGAAACGTAGGTATGGTATTTCAATAAAGAAAACCATACTAAGTGTTGAAAAAGTAGGTATGG
1 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTGTTGAAAAAGTAGGTATGG
13615555 TATTTCAATAAAGAAAACCATACTGAGT
66 TATTTCAATAAAGAAAACCATACTGAGT
13615583 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTGTTGAAAAAGTAGGTATGG
1 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTGTTGAAAAAGTAGGTATGG
*
13615648 TATCTCAATAAA-AAAACCATACTGAGT
66 TATTTCAATAAAGAAAACCATACTGAGT
* * *
13615675 TGTGAAAAGTAGGTATGATATTTCAATAAAGAAAACCATACTG-G-GTTGTGAAAAGTAGGTATC
1 TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTGTTG-AAAAAGTAGGTATG
13615738 GTATTTCAATAAAGAAAACCATACTGAGT
65 GTATTTCAATAAAGAAAACCATACTGAGT
13615767 T
1 T
13615768 AGAGTATAGT
Statistics
Matches: 176, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
90 4 0.02
91 25 0.14
92 73 0.41
93 74 0.42
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.28
Consensus pattern (93 bp):
TGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTGTTGAAAAAGTAGGTATGG
TATTTCAATAAAGAAAACCATACTGAGT
Found at i:13617084 original size:7 final size:7
Alignment explanation
Indices: 13617063--13617097 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
13617053 AAGCAAAGAA
13617063 AAATAAT
1 AAATAAT
13617070 AGAATAAT
1 A-AATAAT
13617078 AAATAAT
1 AAATAAT
13617085 AAATAAT
1 AAATAAT
13617092 AAATAA
1 AAATAA
13617098 AAACGGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:13620707 original size:13 final size:13
Alignment explanation
Indices: 13620689--13620722 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
13620679 ATGGGGGATT
*
13620689 AAATTAAAATAGA
1 AAATTAAAATAAA
13620702 AAATTAAAATAAA
1 AAATTAAAATAAA
13620715 AAATTAAA
1 AAATTAAA
13620723 CCAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAATTAAAATAAA
Found at i:13622626 original size:44 final size:44
Alignment explanation
Indices: 13622524--13622631 Score: 144
Period size: 44 Copynumber: 2.5 Consensus size: 44
13622514 CAACATGTAA
* *
13622524 TATGTATCGGTGTTGGCTATGTGCCATTTACATTCAGCAGGTAC
1 TATGTACCGGTGTTGGCTATGTGCCATTTACATTAAGCAGGTAC
*** * * *
13622568 TATGTACTAATGTTGGCTATGTGCCATTTATATTAAGTAGGTAT
1 TATGTACCGGTGTTGGCTATGTGCCATTTACATTAAGCAGGTAC
13622612 TATGTACCGGTGTTGGCTAT
1 TATGTACCGGTGTTGGCTAT
13622632 TACACCGTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (44 bp):
TATGTACCGGTGTTGGCTATGTGCCATTTACATTAAGCAGGTAC
Found at i:13624980 original size:51 final size:51
Alignment explanation
Indices: 13624904--13625006 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
13624894 TCTAAAGAGG
13624904 AATCCTATACGATATTTAAAATTAGTTTAAAACTCTAAATTCAAATGGTAT
1 AATCCTATACGATATTTAAAATTAGTTTAAAACTCTAAATTCAAATGGTAT
13624955 AATCCTATACGATATTTAAAATTAGTTTAAAACTCTAAATTCAAATGGTAT
1 AATCCTATACGATATTTAAAATTAGTTTAAAACTCTAAATTCAAATGGTAT
13625006 A
1 A
13625007 TAAGATCTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (51 bp):
AATCCTATACGATATTTAAAATTAGTTTAAAACTCTAAATTCAAATGGTAT
Found at i:13626303 original size:5 final size:5
Alignment explanation
Indices: 13626293--13626322 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13626283 CATTCTCCCT
*
13626293 TTTTC TTTTC TTTTC TTTTC TTTTC GTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
13626323 ATGTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:13627035 original size:42 final size:42
Alignment explanation
Indices: 13626988--13627166 Score: 227
Period size: 42 Copynumber: 4.3 Consensus size: 42
13626978 CTTTATATTC
* *
13626988 AATGTAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTT
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
13627030 AATGTAATGAAAAGTAAATAGG-CCTCCACACCTGAGG-CTCTA
1 AATGCAATGAAAAGTAAAT-GGACCTCCACACCTG-GGCCTCTA
* * * * *
13627072 AATACGATGAAAAGTAAATGGACCTACACATCTGGGCCTCAA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* *
13627114 AATGCAATGAAAAGTAAATAGACCTCCACACTTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
13627156 AATACAATGAA
1 AATGCAATGAA
13627167 TGCTTTCCTT
Statistics
Matches: 118, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
41 4 0.03
42 110 0.93
43 4 0.03
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
Found at i:13627140 original size:84 final size:84
Alignment explanation
Indices: 13626993--13627166 Score: 260
Period size: 84 Copynumber: 2.1 Consensus size: 84
13626983 TATTCAATGT
* ** * *
13626993 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTTAATGTAATGAAAAGTAAATAGGCCTCCA
1 AATGAAAAGTAAATGGACCTACACACCTGGGCCTCAAAATGCAATGAAAAGTAAATAGACCTCCA
13627058 CACCTGAGG-CTCTAAATAC
66 CACCTG-GGCCTCTAAATAC
* *
13627077 GATGAAAAGTAAATGGACCTACACATCTGGGCCTCAAAATGCAATGAAAAGTAAATAGACCTCCA
1 AATGAAAAGTAAATGGACCTACACACCTGGGCCTCAAAATGCAATGAAAAGTAAATAGACCTCCA
*
13627142 CACTTGGGCCTCTAAATAC
66 CACCTGGGCCTCTAAATAC
13627161 AATGAA
1 AATGAA
13627167 TGCTTTCCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
83 2 0.03
84 78 0.98
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (84 bp):
AATGAAAAGTAAATGGACCTACACACCTGGGCCTCAAAATGCAATGAAAAGTAAATAGACCTCCA
CACCTGGGCCTCTAAATAC
Found at i:13627684 original size:23 final size:23
Alignment explanation
Indices: 13627643--13627699 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
13627633 GTATGATTTT
*
13627643 ATTGATGCATAATTATAAGAGAAA
1 ATTGATGC-TGATTATAAGAGAAA
13627667 ATTGATGCTGATTATAAGAGAAA
1 ATTGATGCTGATTATAAGAGAAA
13627690 ATTGATGCTG
1 ATTGATGCTG
13627700 CTTTATCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 24 0.75
24 8 0.25
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (23 bp):
ATTGATGCTGATTATAAGAGAAA
Found at i:13630905 original size:17 final size:17
Alignment explanation
Indices: 13630883--13630915 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13630873 ACTAAGATTA
*
13630883 CAATGCAATGACAATAG
1 CAATGCAACGACAATAG
13630900 CAATGCAACGACAATA
1 CAATGCAACGACAATA
13630916 TTAACTAACA
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:0.48, C:0.21, G:0.15, T:0.15
Consensus pattern (17 bp):
CAATGCAACGACAATAG
Found at i:13636525 original size:17 final size:15
Alignment explanation
Indices: 13636494--13636527 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
13636484 ATAGTTAATT
13636494 AATTAAAAATGACAA
1 AATTAAAAATGACAA
13636509 AATTGAAAAATGTACAA
1 AATT-AAAAATG-ACAA
13636526 AA
1 AA
13636528 CTTGCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 7 0.41
17 6 0.35
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (15 bp):
AATTAAAAATGACAA
Found at i:13640427 original size:33 final size:33
Alignment explanation
Indices: 13640300--13640428 Score: 109
Period size: 33 Copynumber: 3.9 Consensus size: 33
13640290 AGTATAAATA
* *
13640300 CATGTGTAAGACCATAGCTGGGCTATTGC-ATT
1 CATGTGTAAGACCATAGCTGGGCTATGGCAATG
** * *
13640332 C-TGATAGTAAGACCATAATTGGGTTATGGCACTG
1 CATG-T-GTAAGACCATAGCTGGGCTATGGCAATG
** * * *
13640366 CAAATGTAAGACCATGGCAGGGCCATGGCAATG
1 CATGTGTAAGACCATAGCTGGGCTATGGCAATG
* *
13640399 CATGTGTAAGACCATAGTTGGACTATGGCA
1 CATGTGTAAGACCATAGCTGGGCTATGGCA
13640429 CAAAAAGAAC
Statistics
Matches: 71, Mismatches: 22, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
31 2 0.03
32 2 0.03
33 64 0.90
34 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (33 bp):
CATGTGTAAGACCATAGCTGGGCTATGGCAATG
Found at i:13643782 original size:24 final size:24
Alignment explanation
Indices: 13643750--13643801 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
13643740 TATTCTACCC
*
13643750 TAATTAGAGTTCGACTGGGACAAA
1 TAATTAGAGTTCGAATGGGACAAA
*
13643774 TAATTAGAGTTTGAATGGGACAAA
1 TAATTAGAGTTCGAATGGGACAAA
13643798 TAAT
1 TAAT
13643802 CAAAGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (24 bp):
TAATTAGAGTTCGAATGGGACAAA
Found at i:13644296 original size:15 final size:14
Alignment explanation
Indices: 13644268--13644294 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13644258 TAGTTTATGT
13644268 TTTTTTAATATTTA
1 TTTTTTAATATTTA
13644282 TTTTTTAATATTT
1 TTTTTTAATATTT
13644295 TACTATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:13644903 original size:14 final size:15
Alignment explanation
Indices: 13644871--13644913 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13644861 TGAATTTTTT
13644871 AATTTAACTCGAATA
1 AATTTAACTCGAATA
* *
13644886 AATTT-ACTCGATTC
1 AATTTAACTCGAATA
*
13644900 AATTCAACTCGAAT
1 AATTTAACTCGAAT
13644914 TTTCATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.35
Consensus pattern (15 bp):
AATTTAACTCGAATA
Found at i:13652824 original size:43 final size:43
Alignment explanation
Indices: 13652771--13652862 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
13652761 GTAATGAGTT
* ** * *
13652771 GTGGAGTTCATGGTAATCAGTTGTTGTACTTAATAGGGTATCA
1 GTGGAATTCATGGTAATCAACTGTTGCACGTAATAGGGTATCA
*
13652814 GTGGAATTCATGGTACTCAACTGTTGCACGTAATAGGGTATCA
1 GTGGAATTCATGGTAATCAACTGTTGCACGTAATAGGGTATCA
13652857 GTGGAA
1 GTGGAA
13652863 ACCATATTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (43 bp):
GTGGAATTCATGGTAATCAACTGTTGCACGTAATAGGGTATCA
Found at i:13658870 original size:6 final size:6
Alignment explanation
Indices: 13658861--13658886 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
13658851 TAATAAACCT
13658861 CCATTC CCATTC CCATTC CCATTC CC
1 CCATTC CCATTC CCATTC CCATTC CC
13658887 TACAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (6 bp):
CCATTC
Found at i:13663351 original size:2 final size:2
Alignment explanation
Indices: 13663344--13663376 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13663334 AGAATGCTAT
13663344 TA TA TA 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 T
13663377 TATGATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13674070 original size:91 final size:91
Alignment explanation
Indices: 13673914--13674089 Score: 228
Period size: 91 Copynumber: 1.9 Consensus size: 91
13673904 CCATCGTATC
** * * *
13673914 TATATTGTCCACCGCTAAATTGACATGCAACGTCCATCGTGGCTCTTGGATGCAAGACACTTCTC
1 TATATTGTCCACCGCTAAATCAACATGCAACGTCCATCGTGACTCTTGAATGCAAGACACCTCTC
13673979 CA-TCATTCGGAATTTCGAATGGAATG
66 CATTC-TTCGGAATTTCGAATGGAATG
* * * * **
13674005 TATATTGTCCACTGCTACATCAATATGCAATGTCCATCGTGACTCTTGAATGTGAGACACCTCTC
1 TATATTGTCCACCGCTAAATCAACATGCAACGTCCATCGTGACTCTTGAATGCAAGACACCTCTC
*
13674070 CATTCTTCGGAATTTTGAAT
66 CATTCTTCGGAATTTCGAAT
13674090 AAAATTTATA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
91 70 0.97
92 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (91 bp):
TATATTGTCCACCGCTAAATCAACATGCAACGTCCATCGTGACTCTTGAATGCAAGACACCTCTC
CATTCTTCGGAATTTCGAATGGAATG
Found at i:13680935 original size:16 final size:16
Alignment explanation
Indices: 13680914--13680955 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
13680904 TTATTAAATT
*
13680914 ATATATTTTAATTATA
1 ATATATTTTAATAATA
13680930 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
13680945 AT-TATGTTTAA
1 ATATAT-TTTAA
13680956 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:13680940 original size:15 final size:15
Alignment explanation
Indices: 13680905--13680946 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13680895 TTAAGAATTT
*
13680905 TATTAAATTAT-ATA
1 TATTTAATTATAATA
13680919 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
13680933 TATTTAATAATAAT
1 TATTTAATTATAAT
13680947 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Done.