Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 190 of 193
Found at i:59425943 original size:62 final size:59
Alignment explanation
Indices: 59425840--59425954 Score: 167
Period size: 62 Copynumber: 1.9 Consensus size: 59
59425830 CACTTTAATG
* * * *
59425840 TTAAAGTAATATAATATTTGTCACGATAAATATTAGATTAAATTTAATATTAAATTTTA
1 TTAAAATAATAAAATATTTATCACGATAAATATTAAATTAAATTTAATATTAAATTTTA
59425899 TTAAAATAATAAAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAA
1 TTAAAATAATAAAATATTTATC-AC--GATAAATATTAAATTAAATTTAATATTAA
59425955 TATAATCACT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 19 0.39
60 2 0.04
62 28 0.57
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (59 bp):
TTAAAATAATAAAATATTTATCACGATAAATATTAAATTAAATTTAATATTAAATTTTA
Found at i:59427065 original size:363 final size:363
Alignment explanation
Indices: 59426400--59427124 Score: 1263
Period size: 363 Copynumber: 2.0 Consensus size: 363
59426390 AATAAGTATC
* *
59426400 ATGATTGAAAACACCTTATTGTATACTCTTTACGGAAGCAATTCATCCAACTGCTTTATCCAATG
1 ATGATTGAAAACACCTAATTGTATACTCTTTACGAAAGCAATTCATCCAACTGCTTTATCCAATG
* **
59426465 ACCTCGTCATGTGTGTTACCCTCATATGATATTCTTGATTCCTTTGAGTTAAATTGGTTCACTCA
66 ACCTCGTCATGTGTGTTACCCTCATATGATATCCTTGATTCCTTTGAGTTAAATACGTTCACTCA
* *
59426530 ATACAATCCTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATATGACCACTGTCA
131 ATACAATCCTATTTTATCTCATTCTCACCATTGTGTATTCTTAATGATTAATATGACCACTGTCA
*
59426595 ACAAATGACTGTGGTAAATTGCTAGTTCGAAAACAAGCAACCCGTATCCACGTTCCATATTTATC
196 ACAAATGACTATGGTAAATTGCTAGTTCGAAAACAAGCAACCCGTATCCACGTTCCATATTTATC
59426660 AATCCACACAATGCCAATAAGAGGATATCATTAACTCTTTAATTGAGCTATGAATTCCACTATTG
261 AATCCACACAATGCCAATAAGAGGATATCATTAACTCTTTAATTGAGCTATGAATTCCACTATTG
** *
59426725 CTAGTAAAGTTATGCCATACATAAGTCATGTACCCAAT
326 CTAGTAAAGCCATGCCATACACAAGTCATGTACCCAAT
59426763 ATGATTGAAAACACCTAATTGTATACTCTTTACGAAAGCAATTCATCCAACTGCTTTATCCAATG
1 ATGATTGAAAACACCTAATTGTATACTCTTTACGAAAGCAATTCATCCAACTGCTTTATCCAATG
*
59426828 TCCTCGTCATGTGTGTTACCCTCATATGATATCCTTGATTCCTTTGAGTTAAATACGTTCACTCA
66 ACCTCGTCATGTGTGTTACCCTCATATGATATCCTTGATTCCTTTGAGTTAAATACGTTCACTCA
*
59426893 ATACAATCCTATTTTATCTCATTCTCACCATTGTGTATTCTTAATGATTAATATGATCACTGTCA
131 ATACAATCCTATTTTATCTCATTCTCACCATTGTGTATTCTTAATGATTAATATGACCACTGTCA
* * * *
59426958 ACAAATGACTATGGTAAATTGCTCGTTCGAGAATAAGCAACCTGTGA-CCACGTTCCATATTTAT
196 ACAAATGACTATGGTAAATTGCTAGTTCGAAAACAAGCAACCCGT-ATCCACGTTCCATATTTAT
*
59427022 CAATCCACACAATGCCAATAAGAGGATATCATTAACTCTTTAATTGAGCTATGAATTCTACTATT
260 CAATCCACACAATGCCAATAAGAGGATATCATTAACTCTTTAATTGAGCTATGAATTCCACTATT
*
59427087 GCTAGTAAAGCCATGTCATACACAAGTCATGTACCCAA
325 GCTAGTAAAGCCATGCCATACACAAGTCATGTACCCAA
59427125 CATACCGGCT
Statistics
Matches: 342, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
363 341 1.00
364 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (363 bp):
ATGATTGAAAACACCTAATTGTATACTCTTTACGAAAGCAATTCATCCAACTGCTTTATCCAATG
ACCTCGTCATGTGTGTTACCCTCATATGATATCCTTGATTCCTTTGAGTTAAATACGTTCACTCA
ATACAATCCTATTTTATCTCATTCTCACCATTGTGTATTCTTAATGATTAATATGACCACTGTCA
ACAAATGACTATGGTAAATTGCTAGTTCGAAAACAAGCAACCCGTATCCACGTTCCATATTTATC
AATCCACACAATGCCAATAAGAGGATATCATTAACTCTTTAATTGAGCTATGAATTCCACTATTG
CTAGTAAAGCCATGCCATACACAAGTCATGTACCCAAT
Found at i:59428822 original size:11 final size:11
Alignment explanation
Indices: 59428806--59428862 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
59428796 ATTCAAAAAA
59428806 TAATAATATTT
1 TAATAATATTT
59428817 TAATAATA-TT
1 TAATAATATTT
* *
59428827 TAATATTAAATT
1 TAATAAT-ATTT
** *
59428839 TAATTTTATGT
1 TAATAATATTT
59428850 TAATAATATTT
1 TAATAATATTT
59428861 TA
1 TA
59428863 TTGATTTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 8 0.22
11 21 0.57
12 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TAATAATATTT
Found at i:59429029 original size:10 final size:9
Alignment explanation
Indices: 59429006--59429039 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
59428996 TCTCTCTTTT
59429006 TTTTTATAA
1 TTTTTATAA
59429015 TTTTTATAA
1 TTTTTATAA
59429024 TGTTTTATAA
1 T-TTTTATAA
*
59429034 ATTTTA
1 TTTTTA
59429040 ATGATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:59433099 original size:23 final size:23
Alignment explanation
Indices: 59433068--59433152 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
59433058 TCCTAAATCG
*
59433068 AGAACAAGAATAAGAAATGGGAA
1 AGAACAAGAAGAAGAAATGGGAA
* ***
59433091 AGAATAAGAAGAAGAAA-GGTCT
1 AGAACAAGAAGAAGAAATGGGAA
* * *
59433113 GGAACAAAAACAAGAAATGGGAA
1 AGAACAAGAAGAAGAAATGGGAA
*
59433136 AGAATAAGAAGAAGAAA
1 AGAACAAGAAGAAGAAA
59433153 GGTTTGCGCT
Statistics
Matches: 45, Mismatches: 16, Indels: 2
0.71 0.25 0.03
Matches are distributed among these distances:
22 15 0.33
23 30 0.67
ACGTcount: A:0.61, C:0.05, G:0.26, T:0.08
Consensus pattern (23 bp):
AGAACAAGAAGAAGAAATGGGAA
Found at i:59433118 original size:45 final size:45
Alignment explanation
Indices: 59433069--59433155 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
59433059 CCTAAATCGA
* *
59433069 GAACAAGAATAAGAAATGGGAAAGAATAAGAAGAAGAAAGGTCTG
1 GAACAAAAACAAGAAATGGGAAAGAATAAGAAGAAGAAAGGTCTG
59433114 GAACAAAAACAAGAAATGGGAAAGAATAAGAAGAAGAAAGGT
1 GAACAAAAACAAGAAATGGGAAAGAATAAGAAGAAGAAAGGT
59433156 TTGCGCTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.59, C:0.05, G:0.28, T:0.09
Consensus pattern (45 bp):
GAACAAAAACAAGAAATGGGAAAGAATAAGAAGAAGAAAGGTCTG
Found at i:59434873 original size:32 final size:31
Alignment explanation
Indices: 59434778--59434864 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 31
59434768 GGTTCTTAGG
**
59434778 TTTGGGGATTTT-A-GTTTAGGTTTTTAAAT
1 TTTGGGGATTTTCAGGTTTAGGTTTCAAAAT
* *
59434807 TTTGGGGATTTTCGGGTTTTAGATTTCAAAAT
1 TTTGGGGATTTTCAGG-TTTAGGTTTCAAAAT
59434839 TTTGGGGATTTTCAGGATTTAGGTTT
1 TTTGGGGATTTTCAGG-TTTAGGTTT
59434865 GGAGATTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 12 0.25
31 1 0.02
32 35 0.73
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.51
Consensus pattern (31 bp):
TTTGGGGATTTTCAGGTTTAGGTTTCAAAAT
Found at i:59435842 original size:31 final size:29
Alignment explanation
Indices: 59435807--59435868 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
59435797 ATTAAAATTA
*
59435807 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-AATTT-AAAAAAATAAT
*
59435838 TTTAATAATTTTAAATTTTAAAAAATAAT
1 TTTAATAATTTTAAATTTAAAAAAATAAT
59435867 TT
1 TT
59435869 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.41
30 4 0.14
31 13 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTAATAATTTTAAATTTAAAAAAATAAT
Found at i:59435869 original size:19 final size:20
Alignment explanation
Indices: 59435841--59435900 Score: 95
Period size: 19 Copynumber: 3.0 Consensus size: 20
59435831 AAATAATTTT
59435841 AATAATTTTAAATTTTAAAA
1 AATAATTTTAAATTTTAAAA
*
59435861 AATAA-TTTATATTTTAAAA
1 AATAATTTTAAATTTTAAAA
59435880 AATAATTTTAATATTTTAAAA
1 AATAATTTTAA-ATTTTAAAA
59435901 TCATTTGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 18 0.50
20 9 0.25
21 9 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATTTTAAATTTTAAAA
Found at i:59436891 original size:160 final size:161
Alignment explanation
Indices: 59436634--59436929 Score: 420
Period size: 159 Copynumber: 1.8 Consensus size: 161
59436624 CTATTGTTAA
* * * * *
59436634 AACATTCAATTTGATACTTTTACAATATTTTTAATAATAATTCTGAAAATTCATTGTTTAGTTTT
1 AACATTCAATTTGATACTGTCACAACATTTTTAACAATAATTCTGAAAATTCATTGTTCAGTTTT
* * * *
59436699 TGAAATTATAAAATATTTTTTTAAATTTATAATTATGT-AAAATTTAAAAAATTCTA-AAAATAT
66 TGAAATTATAAAATATTATTTTAAAATTATAATTATGTAAAAATTAAAAAAAATCTACAAAATAT
59436762 ATAATACATATTATTTATTATGTAATTTTAC
131 ATAATACATATTATTTATTATGTAATTTTAC
* * * *
59436793 AACATTCAATTTGGTACTGTCACAACCTTTTTAACAATAATT-TTAAAATTCATTGTTCATTTAT
1 AACATTCAATTTGATACTGTCACAACATTTTTAACAATAATTCTGAAAATTCATTGTTCA-GT-T
59436857 TTTGAAATTATAAAA-ATATATTTTAAAATTATAATTATGTAAAAATTAAAAAAAATCTACAAAA
64 TTTGAAATTATAAAATAT-TATTTTAAAATTATAATTATGTAAAAATTAAAAAAAATCTACAAAA
59436921 TATATAATA
128 TATATAATA
59436930 AACAAAACAC
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
158 15 0.13
159 39 0.33
160 36 0.30
161 16 0.13
162 13 0.11
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (161 bp):
AACATTCAATTTGATACTGTCACAACATTTTTAACAATAATTCTGAAAATTCATTGTTCAGTTTT
TGAAATTATAAAATATTATTTTAAAATTATAATTATGTAAAAATTAAAAAAAATCTACAAAATAT
ATAATACATATTATTTATTATGTAATTTTAC
Found at i:59438931 original size:6 final size:6
Alignment explanation
Indices: 59438920--59438956 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
59438910 GGTGAGGTGA
* *
59438920 GATTCG GATTCG GATTAG GATTAG GATTAG GATTAG G
1 GATTAG GATTAG GATTAG GATTAG GATTAG GATTAG G
59438957 GAGCCGCCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.32
Consensus pattern (6 bp):
GATTAG
Found at i:59443991 original size:3 final size:3
Alignment explanation
Indices: 59443983--59444020 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
59443973 GTTGCTTCAC
* *
59443983 ATT ATT ATT ATT ACT ATT ATT ACT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
59444021 AGTTAATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:59445506 original size:16 final size:16
Alignment explanation
Indices: 59445485--59445518 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59445475 AGTTCAACTC
*
59445485 TATTTTTAAGTATTTT
1 TATTTTTAAGAATTTT
*
59445501 TATTTTTATGAATTTT
1 TATTTTTAAGAATTTT
59445517 TA
1 TA
59445519 ATAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTTTTAAGAATTTT
Found at i:59459539 original size:23 final size:23
Alignment explanation
Indices: 59459513--59459557 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
59459503 ATAGTAGCGA
*
59459513 ATGTCAACTTTTATGGCACGGTT
1 ATGTCAACTTCTATGGCACGGTT
***
59459536 ATGTTTGCTTCTATGGCACGGT
1 ATGTCAACTTCTATGGCACGGT
59459558 AATTTGAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (23 bp):
ATGTCAACTTCTATGGCACGGTT
Found at i:59460373 original size:16 final size:17
Alignment explanation
Indices: 59460332--59460379 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
59460322 ATTTAAGAGC
59460332 TTTTTAGTTTCTTGATA
1 TTTTTAGTTTCTTGATA
* * *
59460349 TTCTT-GTTTCTT-TTT
1 TTTTTAGTTTCTTGATA
59460364 TTTTTAGTTTCTTGAT
1 TTTTTAGTTTCTTGAT
59460380 GTCTTCTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 5 0.21
16 14 0.58
17 5 0.21
ACGTcount: A:0.10, C:0.08, G:0.10, T:0.71
Consensus pattern (17 bp):
TTTTTAGTTTCTTGATA
Found at i:59460583 original size:22 final size:21
Alignment explanation
Indices: 59460540--59460583 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
59460530 AACTTTGAAT
* *
59460540 TTTCTCTTTGATTTTTTAATC
1 TTTCACTTTGATTTGTTAATC
*
59460561 TTTCACTTTGAATTTGTTCATC
1 TTTCACTTTG-ATTTGTTAATC
59460583 T
1 T
59460584 CTTTAAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.16, C:0.16, G:0.07, T:0.61
Consensus pattern (21 bp):
TTTCACTTTGATTTGTTAATC
Found at i:59461553 original size:13 final size:13
Alignment explanation
Indices: 59461535--59461559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59461525 ATTATGTATC
59461535 ATTAAAAAAATGG
1 ATTAAAAAAATGG
59461548 ATTAAAAAAATG
1 ATTAAAAAAATG
59461560 ACATAAACAT
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:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
ATTAAAAAAATGG
Found at i:59466787 original size:56 final size:56
Alignment explanation
Indices: 59466701--59466814 Score: 149
Period size: 56 Copynumber: 2.0 Consensus size: 56
59466691 TATTTCCACT
** *
59466701 ATTTATTTTCCTGCCAGTTTAGGTATGAAATCTAC-ATATAGTATAATTGAACATGG
1 ATTTATTTTCCCACCAGTTTAGGTATGAAATCT-CGAAATAGTATAATTGAACATGG
* * * *
59466757 ATTTATTTTCCCACCATTTTATGTTTGAAATCTCGAAATAGTATCATTGAACATGG
1 ATTTATTTTCCCACCAGTTTAGGTATGAAATCTCGAAATAGTATAATTGAACATGG
59466813 AT
1 AT
59466815 CACAGTCTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
55 1 0.02
56 49 0.98
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (56 bp):
ATTTATTTTCCCACCAGTTTAGGTATGAAATCTCGAAATAGTATAATTGAACATGG
Found at i:59476308 original size:25 final size:27
Alignment explanation
Indices: 59476248--59476308 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 27
59476238 TTTTTGCATC
59476248 AATAATATAGAAAACTTTTATTTACCAA
1 AATAATATAGAAAAC-TTTATTTACCAA
59476276 AATAATATA-AAAA-TTTATTTA-CAA
1 AATAATATAGAAAACTTTATTTACCAA
59476300 AATTAATAT
1 AA-TAATAT
59476309 GTGATTGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.16
25 14 0.44
27 4 0.12
28 9 0.28
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (27 bp):
AATAATATAGAAAACTTTATTTACCAA
Found at i:59480230 original size:13 final size:12
Alignment explanation
Indices: 59480176--59480241 Score: 55
Period size: 13 Copynumber: 5.4 Consensus size: 12
59480166 ATATATTAGT
*
59480176 TAATAATAA-TA
1 TAATATTAATTA
*
59480187 TAATACTAATTA
1 TAATATTAATTA
*
59480199 -AATAATAATTTA
1 TAATATTAA-TTA
*
59480211 TATTATTATATTA
1 TAATATTA-ATTA
59480224 TAATATTAATTAA
1 TAATATTAATT-A
59480237 TAATA
1 TAATA
59480242 AATTAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
11 15 0.33
12 8 0.18
13 21 0.47
14 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATTAATTA
Found at i:59480918 original size:2 final size:2
Alignment explanation
Indices: 59480913--59480939 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59480903 AAAAAAAAAA
59480913 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59480940 AAAGCTTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59481457 original size:30 final size:30
Alignment explanation
Indices: 59481421--59481546 Score: 95
Period size: 29 Copynumber: 4.3 Consensus size: 30
59481411 AAAATTACCA
59481421 TTTTACCCTCGAACCTT-CCAAAATTTCATT
1 TTTTACCC-CGAACCTTCCCAAAATTTCATT
* * *
59481451 TTTTACCCCG-A-TTTCACCAAAATTAC-TA
1 TTTTACCCCGAACCTTC-CCAAAATTTCATT
**
59481479 TTTTACCCCCGAACCTT-CCAAAATCCCATT
1 TTTTA-CCCCGAACCTTCCCAAAATTTCATT
* **
59481509 TTTAACCCC-AAATTTCCCCAAAATTTCA-T
1 TTTTACCCCGAACCTT-CCCAAAATTTCATT
59481538 TTTTACCCC
1 TTTTACCCC
59481547 CGATAGTCAA
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
27 2 0.03
28 11 0.15
29 37 0.49
30 23 0.31
31 2 0.03
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTTACCCCGAACCTTCCCAAAATTTCATT
Found at i:59481473 original size:58 final size:58
Alignment explanation
Indices: 59481384--59481549 Score: 192
Period size: 58 Copynumber: 2.9 Consensus size: 58
59481374 AACTGTCTAG
* * * *
59481384 AAATTACA-TTTTGACCTCGATTTAACCAAAATTACCATTTTACCCTCGAACCTTCCA
1 AAATTACATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAACCTTCCA
* * *
59481441 AAATTTCATTTTTTACCCCGATTTCACCAAAATTACTATTTTACCCCCGAACCTTCCA
1 AAATTACATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAACCTTCCA
** * * *
59481499 AAATCCCATTTTTAACCCCAAATTTCCCCAAAATT-TCATTTTTACCCCCGA
1 AAATTACATTTTTAACCCC-GATTTCACCAAAATTACCA-TTTTACCCCCGA
59481550 TAGTCAAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
57 7 0.08
58 61 0.66
59 25 0.27
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (58 bp):
AAATTACATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAACCTTCCA
Found at i:59481490 original size:29 final size:27
Alignment explanation
Indices: 59481384--59481487 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 27
59481374 AACTGTCTAG
*
59481384 AAATTAC-ATTTTGACCTCGATTTAACCA
1 AAATTACTATTTT-ACCCCGATTT-ACCA
* *
59481412 AAATTACCATTTTACCCTCGAACCTT-CCA
1 AAATTACTATTTTACCC-CG-A-TTTACCA
* *
59481441 AAATTTCATTTTTTACCCCGATTTCACCA
1 AAATTAC-TATTTTACCCCGATTT-ACCA
59481470 AAATTACTATTTTACCCC
1 AAATTACTATTTTACCCC
59481488 CGAACCTTCC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.03
28 21 0.34
29 27 0.44
30 9 0.15
31 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (27 bp):
AAATTACTATTTTACCCCGATTTACCA
Found at i:59481499 original size:29 final size:29
Alignment explanation
Indices: 59481409--59481502 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
59481399 CTCGATTTAA
* *
59481409 CCAAAATTACCATTTTACCCTCGAACCTT
1 CCAAAATTACTATTTTACCCCCGAACCTT
* * *
59481438 CCAAAATTTCATTTTTTA-CCCCG-A-TTT
1 CCAAAATTAC-TATTTTACCCCCGAACCTT
59481465 CACCAAAATTACTATTTTACCCCCGAACCTT
1 --CCAAAATTACTATTTTACCCCCGAACCTT
59481496 CCAAAAT
1 CCAAAAT
59481503 CCCATTTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
27 2 0.04
28 7 0.14
29 34 0.67
30 6 0.12
31 2 0.04
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.33
Consensus pattern (29 bp):
CCAAAATTACTATTTTACCCCCGAACCTT
Found at i:59481511 original size:29 final size:30
Alignment explanation
Indices: 59481479--59481549 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
59481469 AAAATTACTA
*
59481479 TTTTACCCCCGAACCTT-CCAAAATCCCAT
1 TTTTACCCCCGAAACTTCCCAAAATCCCAT
* * **
59481508 TTTTAACCCC-AAATTTCCCCAAAATTTCAT
1 TTTTACCCCCGAAACTT-CCCAAAATCCCAT
59481538 TTTTACCCCCGA
1 TTTTACCCCCGA
59481550 TAGTCAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 4 0.12
29 9 0.27
30 19 0.58
31 1 0.03
ACGTcount: A:0.28, C:0.37, G:0.03, T:0.32
Consensus pattern (30 bp):
TTTTACCCCCGAAACTTCCCAAAATCCCAT
Found at i:59490147 original size:32 final size:30
Alignment explanation
Indices: 59490097--59490205 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 30
59490087 ATTTTAATAA
*
59490097 TATTTATATTAAAAATATTATTAATTATATAT
1 TATTT-TATTAAATATA-TATTAATTATATAT
*
59490129 TATTTTATTAAAT-TATATTTAATAATA-AT
1 TATTTTATTAAATATATA-TTAATTATATAT
* *
59490158 TATGTTA--AAATATA-ATTAAATTATTTAT
1 TATTTTATTAAATATATATT-AATTATATAT
59490186 TATTTTTATTAAAT-TATATT
1 TA-TTTTATTAAATATATATT
59490206 TAATAATAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
26 2 0.03
27 10 0.16
28 6 0.10
29 14 0.22
30 12 0.19
31 14 0.22
32 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
TATTTTATTAAATATATATTAATTATATAT
Found at i:59490171 original size:26 final size:27
Alignment explanation
Indices: 59490084--59490171 Score: 81
Period size: 30 Copynumber: 3.1 Consensus size: 27
59490074 TTTACTAATT
*
59490084 TATATTTTAATAATATTTATATTAAAA
1 TATATTTTAATAATAATTATATTAAAA
* *
59490111 -ATATTATTAATTATATATTATTTTATTAAA
1 TATATT-TTAATAATA-ATTATATTA--AAA
*
59490141 T-TATATTTAATAATAATTATGTTAAAA
1 TATAT-TTTAATAATAATTATATTAAAA
59490168 TATA
1 TATA
59490172 ATTAAATTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
26 5 0.10
27 12 0.24
28 9 0.18
29 8 0.16
30 14 0.29
31 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
TATATTTTAATAATAATTATATTAAAA
Found at i:59490180 original size:57 final size:58
Alignment explanation
Indices: 59490062--59490225 Score: 208
Period size: 58 Copynumber: 2.8 Consensus size: 58
59490052 TCTAATATTA
* * * * *
59490062 TATATTATGATTTTTACTAATTTATATTTTAATAATATTTATATTAAAAATATTATTAAT
1 TATA-TATTATTTTTATTAAATTATA-TTTAATAATAATTATATTAAAAATATAATTAAT
*
59490122 TATATATTA-TTTTATTAAATTATATTTAATAATAATTATGTT-AAAATATAATTAAAT
1 TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATT-AAT
*
59490179 TATTTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAA
1 TATATATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAA
59490226 TTTAATAACA
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
56 10 0.11
57 27 0.29
58 43 0.47
59 8 0.09
60 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (58 bp):
TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAT
Found at i:59490221 original size:32 final size:31
Alignment explanation
Indices: 59490131--59490221 Score: 77
Period size: 32 Copynumber: 3.0 Consensus size: 31
59490121 TTATATATTA
59490131 TTTTATTAAATTATATTTAATAATAA-TTA-
1 TTTTATTAAATTATATTTAATAATAATTTAT
* * * *
59490160 TGTTA--AAA-TATAATTAA-ATTATTTATTAT
1 TTTTATTAAATTATATTTAATAATA-AT-TTAT
59490189 TTTTATTAAATTATATTTAATAATAATCTTAT
1 TTTTATTAAATTATATTTAATAATAAT-TTAT
59490221 T
1 T
59490222 AAAATTTAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 3 0.07
28 3 0.07
29 8 0.18
31 3 0.07
32 14 0.31
33 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (31 bp):
TTTTATTAAATTATATTTAATAATAATTTAT
Found at i:59494172 original size:29 final size:28
Alignment explanation
Indices: 59494104--59494178 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 28
59494094 TATTTTAATC
**
59494104 TATAATATAATTTGAT-ATTTATATTTT
1 TATAATATAATTAAATAATTTATATTTT
*
59494131 TATAATATTATTAAATAATTTGATATTTT
1 TATAATATAATTAAATAATTT-ATATTTT
* *
59494160 TATAATGTAATTAATTAAT
1 TATAATATAATTAAATAAT
59494179 ATAAATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 13 0.32
28 4 0.10
29 23 0.57
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TATAATATAATTAAATAATTTATATTTT
Found at i:59507276 original size:16 final size:18
Alignment explanation
Indices: 59507237--59507270 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59507227 TAAGTTTATA
59507237 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
59507254 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
59507271 AATTTAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:59513017 original size:48 final size:47
Alignment explanation
Indices: 59512911--59513019 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 47
59512901 ATTGTTCCAA
*
59512911 AAATAATAATATTTTAATAATTTAATATTAAATTTAATTTAATACTT
1 AAATTATAATATTTTAATAATTTAATATTAAATTTAATTTAATACTT
** *
59512958 ATCTTAATAATATTTTATTAATTTAATATTAAGATGATT-ATCTTAATA-TT
1 AAATT-ATAATATTTTAATAATTTAATATTAA-AT--TTAAT-TTAATACTT
59513008 AAATT-TAATATT
1 AAATTATAATATT
59513020 AGAGTGATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
47 2 0.04
48 32 0.63
49 2 0.04
50 7 0.14
51 8 0.16
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (47 bp):
AAATTATAATATTTTAATAATTTAATATTAAATTTAATTTAATACTT
Found at i:59513455 original size:28 final size:23
Alignment explanation
Indices: 59513393--59513442 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
59513383 TTTCCAACAA
*
59513393 ATATCTGTTAATATAAATTCCAT
1 ATATCTGCTAATATAAATTCCAT
*
59513416 ATATCTGCTAATGTAAATTCCAT
1 ATATCTGCTAATATAAATTCCAT
59513439 ATAT
1 ATAT
59513443 ACCCATGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (23 bp):
ATATCTGCTAATATAAATTCCAT
Found at i:59527275 original size:2 final size:2
Alignment explanation
Indices: 59527268--59527294 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59527258 AATATAAATT
59527268 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
59527295 GATAAGATTG
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:59530334 original size:19 final size:19
Alignment explanation
Indices: 59530288--59530339 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
59530278 CCATTTAATG
* * *
59530288 ATTATATTTAAATATTTAA
1 ATTAAATTTATATATTCAA
*
59530307 AATATAATTTATATATTCAA
1 ATTA-AATTTATATATTCAA
59530327 ATTAAATTT-TATA
1 ATTAAATTTATATA
59530340 AATAATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 4 0.15
19 8 0.30
20 15 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAAATTTATATATTCAA
Found at i:59530355 original size:23 final size:23
Alignment explanation
Indices: 59530325--59530383 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
59530315 TTATATATTC
*
59530325 AAATTAAATTTTATAAATAATTA
1 AAATTAAATTTTAGAAATAATTA
* * *
59530348 ATATTAAATACTTAGAAATATTTA
1 AAATTAAAT-TTTAGAAATAATTA
59530372 AAATTAATATTT
1 AAATTAA-ATTT
59530384 CATATATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 8 0.29
24 18 0.64
25 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATTAAATTTTAGAAATAATTA
Found at i:59542905 original size:17 final size:17
Alignment explanation
Indices: 59542875--59542910 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
59542865 TTTAAAAGTT
59542875 TTTTTGAGTCAAAAATA
1 TTTTTGAGTCAAAAATA
59542892 TTTTTGAGAT-AAAAATA
1 TTTTTGAG-TCAAAAATA
59542909 TT
1 TT
59542911 ATTAAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTTTGAGTCAAAAATA
Found at i:59554480 original size:21 final size:21
Alignment explanation
Indices: 59554456--59554506 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
59554446 GTGTTAGCTT
59554456 TACCGATACAAGT-ATG-ATTTC
1 TACCGATACAAGTCATGCA--TC
59554477 TACCGATACAAGTCATGCATC
1 TACCGATACAAGTCATGCATC
59554498 TACCGATAC
1 TACCGATAC
59554507 CAAAAACTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (21 bp):
TACCGATACAAGTCATGCATC
Found at i:59556417 original size:29 final size:30
Alignment explanation
Indices: 59556360--59556418 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
59556350 GATAGGAGGG
* *
59556360 GAGTAAAAGTTTTGGGGGGAAAGTGAAAAT
1 GAGTAAAAATTTTGGGGGAAAAGTGAAAAT
*
59556390 GAGTAAAAATTTTGGGGGAAAAGTAAAAA
1 GAGTAAAAATTTTGGGGGAAAAGTGAAAA
59556419 GATTTGGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (30 bp):
GAGTAAAAATTTTGGGGGAAAAGTGAAAAT
Found at i:59557465 original size:15 final size:16
Alignment explanation
Indices: 59557435--59557473 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
59557425 TAGTAAAAAT
59557435 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
59557452 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
59557467 ATAATTT
1 ATAATTT
59557474 TTAAAAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:59557582 original size:83 final size:83
Alignment explanation
Indices: 59557430--59557587 Score: 201
Period size: 83 Copynumber: 1.9 Consensus size: 83
59557420 TATGATAGTA
* * * * ***
59557430 AAAATATAATTTTATTATTTTAATAATTTATATTTTTATAATTTTTAAAAAGTTAAATCAAATTT
1 AAAATATAATTTTATTA-TTTAATAATTTAAAATTTTATAATTATAAAAAAGTTAAATCAAAAAA
59557495 TTATCATTTTGAGAGAAAT
65 TTATCATTTTGAGAGAAAT
* * *
59557514 AAAATATAATTTTATTA-TTATTAATTTAAAATTTTATAAATTATAAAAAATTTAAATTAAAAAA
1 AAAATATAATTTTATTATTTAATAATTTAAAATTTTAT-AATTATAAAAAAGTTAAATCAAAAAA
59557578 TTATCATTTT
65 TTATCATTTT
59557588 AGGAGATCGT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
82 17 0.27
83 29 0.46
84 17 0.27
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.49
Consensus pattern (83 bp):
AAAATATAATTTTATTATTTAATAATTTAAAATTTTATAATTATAAAAAAGTTAAATCAAAAAAT
TATCATTTTGAGAGAAAT
Found at i:59557625 original size:13 final size:13
Alignment explanation
Indices: 59557607--59557631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59557597 TGGATCTCCA
59557607 AGATTTTTCATGT
1 AGATTTTTCATGT
59557620 AGATTTTTCATG
1 AGATTTTTCATG
59557632 CGCGTCTCGA
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:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (13 bp):
AGATTTTTCATGT
Found at i:59557867 original size:3 final size:3
Alignment explanation
Indices: 59557859--59557888 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
59557849 GTGAATTCTT
59557859 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59557889 CTTTTTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59563101 original size:19 final size:19
Alignment explanation
Indices: 59563079--59563123 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
59563069 TTATATTAGG
59563079 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
59563098 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
59563117 ATTTAAT
1 ATTTAAT
59563124 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:59563953 original size:16 final size:16
Alignment explanation
Indices: 59563932--59563962 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59563922 CTATTTTCTA
59563932 TTTCTTTTAGTTTTAT
1 TTTCTTTTAGTTTTAT
*
59563948 TTTCTTTTATTTTTA
1 TTTCTTTTAGTTTTA
59563963 ATTCTGTTTC
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:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTCTTTTAGTTTTAT
Found at i:59564804 original size:40 final size:40
Alignment explanation
Indices: 59564721--59564804 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
59564711 ATGTAAACAT
* *
59564721 TAAAAAATATTAAGATAATTAAATATAGAATTTTAATAAA
1 TAAAAAATATTAAAATAATTAAATATAGAATTTAAATAAA
* *
59564761 TAAAAAATATATAAAATCATTAAATATTA-AA-TTAAATATA
1 TAAAAAATAT-TAAAATAATTAAATA-TAGAATTTAAATAAA
59564801 TAAA
1 TAAA
59564805 TATATATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 21 0.55
41 15 0.39
42 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (40 bp):
TAAAAAATATTAAAATAATTAAATATAGAATTTAAATAAA
Found at i:59566923 original size:11 final size:11
Alignment explanation
Indices: 59566892--59566933 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
59566882 CCCAACTTGG
59566892 ATTTTAAATTA
1 ATTTTAAATTA
* *
59566903 AGTTTGAATTA
1 ATTTTAAATTA
*
59566914 ATTTTAAATTT
1 ATTTTAAATTA
59566925 A-TTTAAATT
1 ATTTTAAATT
59566934 TAAATTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:59566933 original size:17 final size:17
Alignment explanation
Indices: 59566894--59566955 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
59566884 CAACTTGGAT
*
59566894 TTTAAA-TTAAGTTTGA
1 TTTAAATTTAAATTTGA
* *
59566910 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
59566926 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
59566943 TTTAAATTTAAAT
1 TTTAAATTTAAAT
59566956 ACATTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:59566936 original size:22 final size:22
Alignment explanation
Indices: 59566892--59566933 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59566882 CCCAACTTGG
*
59566892 ATTTTAAATTAAGTTTGAATTA
1 ATTTTAAATTAAGTTTAAATTA
*
59566914 ATTTTAAATTTA-TTTAAATT
1 ATTTTAAATTAAGTTTAAATT
59566934 TAAATTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAATTAAGTTTAAATTA
Found at i:59566939 original size:27 final size:27
Alignment explanation
Indices: 59566898--59566989 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
59566888 TTGGATTTTA
* *
59566898 AATTAAGTTTGAATTAATTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* **
59566925 ATTTAAATTTAAATTTGTTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* * * *
59566952 AAATACATTTAAAATAATTTGAAACTTT
1 AATTAAATTTAAATTAATTTTAAA-TTT
59566980 AAATTAAATT
1 -AATTAAATT
59566990 AATAATGTCC
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
27 39 0.80
28 3 0.06
29 7 0.14
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (27 bp):
AATTAAATTTAAATTAATTTTAAATTT
Found at i:59566964 original size:16 final size:16
Alignment explanation
Indices: 59566911--59566964 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
59566901 TAAGTTTGAA
* *
59566911 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
59566927 TTAAATTTAAATTTGTT
1 TTAAATTTAAA-TTCAT
*
59566944 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
59566960 TTAAA
1 TTAAA
59566965 ATAATTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:59567755 original size:19 final size:18
Alignment explanation
Indices: 59567731--59567796 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 18
59567721 AACATTTTAA
59567731 TAATAATAATAAATGTTT
1 TAATAATAATAAATGTTT
59567749 CTAATAATAATAAATGATTT
1 -TAATAATAATAAATG-TTT
*
59567769 TAATAATAATGAAATTTTT
1 TAATAATAAT-AAATGTTT
59567788 TAATAATAA
1 TAATAATAA
59567797 GGTAATAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
19 37 0.84
20 7 0.16
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATGTTT
Found at i:59568151 original size:28 final size:28
Alignment explanation
Indices: 59568119--59568173 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
59568109 TGTTGTTTGA
* * *
59568119 AATAAAGAATAAAGAACAAGAGAAAAGG
1 AATAAAAAAAAAAGAACAAAAGAAAAGG
*
59568147 AATAAAAAAAAAAGAAGAAAAGAAAAG
1 AATAAAAAAAAAAGAACAAAAGAAAAG
59568174 AAACAGTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (28 bp):
AATAAAAAAAAAAGAACAAAAGAAAAGG
Found at i:59568984 original size:29 final size:29
Alignment explanation
Indices: 59568942--59569220 Score: 170
Period size: 29 Copynumber: 9.7 Consensus size: 29
59568932 AAACTTCAAA
59568942 AAAATTCCATTTTTAACCCCAAACTTTCC
1 AAAATTCCATTTTTAACCCCAAACTTTCC
* *
59568971 AAAATCCCATTTTTAACCTCGAAAC-TTCC
1 AAAATTCCATTTTTAACC-CCAAACTTTCC
* * *
59569000 AAAATTAC-TATTTGACCCCAAACTTTCC
1 AAAATTCCATTTTTAACCCCAAACTTTCC
*** *
59569028 AAAATTCCATTTTTAA-CCTTGATTTTCC
1 AAAATTCCATTTTTAACCCCAAACTTTCC
* *
59569056 AAAAATTACCA-TTTT-ACCCTTAAACTTTCA
1 -AAAATT-CCATTTTTAACCC-CAAACTTTCC
*
59569086 AAAATTCCATTTTTAACCCC-GA-TTTCAC
1 AAAATTCCATTTTTAACCCCAAACTTTC-C
* * * *
59569114 CAAATTAC-TATTTTACCCCCGAACTTTCC
1 AAAATTCCAT-TTTTAACCCCAAACTTTCC
* **
59569143 AAAATAT-CATTTTTTAACTCC--GGTTTCACC
1 AAAAT-TCCA-TTTTTAACCCCAAACTTT--CC
*
59569173 AAAATTACC-GTTTT-ACCCTCAAACTTTCC
1 AAAATT-CCATTTTTAACCC-CAAACTTTCC
*
59569202 AAAATCCCATTTTTAACCC
1 AAAATTCCATTTTTAACCC
59569221 TAATTTCATA
Statistics
Matches: 189, Mismatches: 36, Indels: 49
0.69 0.13 0.18
Matches are distributed among these distances:
27 10 0.05
28 54 0.29
29 78 0.41
30 42 0.22
31 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTAACCCCAAACTTTCC
Found at i:59569032 original size:28 final size:29
Alignment explanation
Indices: 59568912--59569147 Score: 114
Period size: 29 Copynumber: 8.2 Consensus size: 29
59568902 GAACTGTCTA
* *
59568912 AAAATTATAT-TTTAACCCCAAAAC-TTCAAA
1 AAAATTACATATTTAACCCC-AAACTTTC--C
* *
59568942 AAAATTCCATTTTTAACCCCAAACTTTCC
1 AAAATTACATATTTAACCCCAAACTTTCC
** * *
59568971 AAAATCCCATTTTTAACCTCGAAAC-TTCC
1 AAAATTACATATTTAACC-CCAAACTTTCC
*
59569000 AAAATTAC-TATTTGACCCCAAACTTTCC
1 AAAATTACATATTTAACCCCAAACTTTCC
* * *** *
59569028 AAAATTCCATTTTTAA-CCTTGATTTTCC
1 AAAATTACATATTTAACCCCAAACTTTCC
* *
59569056 AAAAATTACCAT-TTT-ACCCTTAAACTTTCA
1 -AAAATTA-CATATTTAACCC-CAAACTTTCC
* * *
59569086 AAAATTCCATTTTTAACCCC-GA-TTTCAC
1 AAAATTACATATTTAACCCCAAACTTTC-C
* * *
59569114 CAAATTAC-TATTTTACCCCCGAACTTTCC
1 AAAATTACATA-TTTAACCCCAAACTTTCC
59569143 AAAAT
1 AAAAT
59569148 ATCATTTTTT
Statistics
Matches: 159, Mismatches: 32, Indels: 31
0.72 0.14 0.14
Matches are distributed among these distances:
27 10 0.06
28 45 0.28
29 58 0.36
30 34 0.21
31 12 0.08
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTACATATTTAACCCCAAACTTTCC
Found at i:59569103 original size:58 final size:58
Alignment explanation
Indices: 59568941--59569304 Score: 345
Period size: 59 Copynumber: 6.3 Consensus size: 58
59568931 AAAACTTCAA
* *
59568941 AAAAATT-CCATTTTTAACCC-CAAACTTTCCAAAATCCCATTTTTAACCTCGAAACTTCC
1 AAAAATTACCA-TTTT-ACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCG-AATTTCC
* * * *
59569000 -AAAATTACTATTTGACCC-CAAACTTTCCAAAATTCCATTTTTAACCTTGATTTTCC
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGAATTTCC
* * *
59569056 AAAAATTACCATTTTACCCTTAAACTTTCAAAAATTCCATTTTTAACCCCG-ATTT-C
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGAATTTCC
* * * * *
59569112 ACCAAATTACTATTTTACCCCCGAACTTTCCAAAATAT-CATTTTTTAA-CTCCG-GTTTCAC
1 A-AAAATTACCATTTTACCCTCAAACTTTCCAAAAT-TCCA-TTTTTAACCT-CGAATTTC-C
* * * * *
59569172 CAAAATTACCGTTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACC-CTAATTTCATA
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGAATTTC--C
* * *
59569231 AAAAATTACCATTTTA-CCTCTAAACTTTCCAAAATTTCATTTTTGACCTCGATTTTCC
1 AAAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCTCGAATTTCC
59569289 TAAAAATTACCATTTT
1 -AAAAATTACCATTTT
59569305 GCCCCTGGGC
Statistics
Matches: 249, Mismatches: 40, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
56 7 0.03
57 84 0.34
58 64 0.26
59 87 0.35
60 7 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGAATTTCC
Found at i:59577988 original size:3 final size:3
Alignment explanation
Indices: 59577980--59578011 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
59577970 ATTCAGGGAA
59577980 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
59578012 AAAGCCGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:59579168 original size:31 final size:29
Alignment explanation
Indices: 59579104--59579172 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
59579094 ACCACTTCGT
*
59579104 AAGTGACTAAAATGTAACATTTCAAGCAA
1 AAGTGACTAAAATGTAACATTGCAAGCAA
* *
59579133 AAGTGACTAAAATGTAACCTGATGCAATCAA
1 AAGTGACTAAAATGTAACAT--TGCAAGCAA
59579164 AAGTGACTA
1 AAGTGACTA
59579173 TTTTTGCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATTGCAAGCAA
Found at i:59589672 original size:2 final size:2
Alignment explanation
Indices: 59589665--59589692 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59589655 GTTTCTTGTT
59589665 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
59589693 CTTGTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59593137 original size:87 final size:88
Alignment explanation
Indices: 59592982--59593179 Score: 285
Period size: 87 Copynumber: 2.3 Consensus size: 88
59592972 TTTTTAGACA
* **
59592982 TTCG-GGGTTAAAATGGTAATTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTTAG
1 TTCGAGGGTAAAAAT-GTAATTTTGAAAGTTCGAGGGTCAAAAATGGAATTTTTGGAAGTTTTAG
*
59593046 GGTTAGAAA-TTTAATTTTTGAAAG
65 GGTTA-AAACTGTAATTTTTGAAAG
*
59593070 TTCGAGGGTAAAAATGTAATTTTGAAAGTTCGAGGGT-AAAAATGTAATTTTTGGAAGTTTTAGG
1 TTCGAGGGTAAAAATGTAATTTTGAAAGTTCGAGGGTCAAAAATGGAATTTTTGGAAGTTTTAGG
*
59593134 GTTAAAACTGTAATTTTTGGAAG
66 GTTAAAACTGTAATTTTTGAAAG
* *
59593157 TTCGAGAGTAAAAATGCAATTTT
1 TTCGAGGGTAAAAATGTAATTTT
59593180 TGGATAGTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
86 3 0.03
87 64 0.64
88 24 0.24
89 9 0.09
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (88 bp):
TTCGAGGGTAAAAATGTAATTTTGAAAGTTCGAGGGTCAAAAATGGAATTTTTGGAAGTTTTAGG
GTTAAAACTGTAATTTTTGAAAG
Found at i:59593182 original size:29 final size:29
Alignment explanation
Indices: 59592982--59593188 Score: 204
Period size: 30 Copynumber: 7.1 Consensus size: 29
59592972 TTTTTAGACA
* *
59592982 TTCG-GGGTTAAAATGGTAA-TTTTGAAAG
1 TTCGAGGGTAAAAAT-GTAATTTTTGGAAG
** *
59593010 TTTTAGGGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGGT-AAAAATGTAATTTTTGGAAG
** * * *
59593040 TTTTAGGGTTAGAAATTTAATTTTTGAAAG
1 TTCGAGGG-TAAAAATGTAATTTTTGGAAG
*
59593070 TTCGAGGGTAAAAATGTAA-TTTTGAAAG
1 TTCGAGGGTAAAAATGTAATTTTTGGAAG
59593098 TTCGAGGGTAAAAATGTAATTTTTGGAAG
1 TTCGAGGGTAAAAATGTAATTTTTGGAAG
** *
59593127 TTTTAGGGTTAAAACTGTAATTTTTGGAAG
1 TTCGAGGG-TAAAAATGTAATTTTTGGAAG
* *
59593157 TTCGAGAGTAAAAATGCAATTTTTGGATAG
1 TTCGAGGGTAAAAATGTAATTTTTGGA-AG
59593187 TT
1 TT
59593189 TAAGGACCTT
Statistics
Matches: 150, Mismatches: 22, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
28 30 0.20
29 47 0.31
30 72 0.48
31 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (29 bp):
TTCGAGGGTAAAAATGTAATTTTTGGAAG
Found at i:59594984 original size:19 final size:19
Alignment explanation
Indices: 59594957--59595005 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
59594947 GAACCCCAAT
* *
59594957 TTGGGCCTTTGATTTGTAA
1 TTGGACCTTTGACTTGTAA
*
59594976 TTGGACCTTGGACTTGTAA
1 TTGGACCTTTGACTTGTAA
*
59594995 ATGGA-CTTTGA
1 TTGGACCTTTGA
59595006 GTTTTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (19 bp):
TTGGACCTTTGACTTGTAA
Found at i:59595800 original size:201 final size:201
Alignment explanation
Indices: 59595444--59596371 Score: 1356
Period size: 201 Copynumber: 4.6 Consensus size: 201
59595434 CTCTGGTTTC
* * * * *
59595444 ATTGACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGATTCGAAGATTTGCTCGTATC
1 ATTG-CTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCTGGGG-TTCGAAGATTTACTCGCATT
59595509 GAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATT
64 GAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATT
*
59595574 CGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCAACTTCTC-GATATCTCATCAGGAAGCT
129 CGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAG-TATCTCATCAGGAAGCT
59595638 AACCATTTT
193 AACCATTTT
** * * * **
59595647 ATTGCTTTAACCTGCTTCTCAGTGTCTTATTAGGAAGCTGGGGTTTGAAGCTTCGCTCGCATTGA
1 ATTGCTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCTGGGGTTCGAAGATTTACTCGCATTGA
* * * *
59595712 GCGTTGAGTTGGTATACTTCTCTGTATCTCTTCAAGAAGATTATCGCCTCACTTGTTTCAATTCG
66 GCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCG
*
59595777 CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
131 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
59595842 CATTTT
196 CATTTT
* * *
59595848 ATTGCTTCGACCTGCTTCTCAATGTTTTATCAGGAAGCTGGAGCTGGATTCGAAGATTTACTCAC
1 ATTGCTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCT-G-G--GG-TTCGAAGATTTACTCGC
* * *
59595913 ATTGAGCGTTGAATTGGTATACTTCTCTATATCTCATCAGGAAGATGACCACCTCACTTGTTTCA
61 ATTGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCA
* *
59595978 ATTCGCTTCTTTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAG
126 ATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAG
59596043 CTAACCATTTT
191 CTAACCATTTT
* * * * * *
59596054 ATTGCTTCGACCTACTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTCACTCTCATTGG
1 ATTGCTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCTGGGGTTCGAAGATTTACTCGCATTGA
* * *
59596119 GCGTTGAGTTGGTATACTTCTTTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCG
66 GCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCG
* *
59596184 TTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
131 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
59596249 CATTTT
196 CATTTT
* * * * *
59596255 ATTGCTTTGGCCTGCTTCTCAGTATCTTATCAGGAAGCT-GGGTTTGAAGATTTACTCGCATCGA
1 ATTGCTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCTGGGGTTCGAAGATTTACTCGCATTGA
* * * *
59596319 GCGTCGAGTTGGCATACTTCTTTGTATCTCATCAGGAAGATGACTGCCTCACT
66 GCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACT
59596372 CGCATCGAGC
Statistics
Matches: 652, Mismatches: 67, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
200 71 0.11
201 357 0.55
202 38 0.06
203 5 0.01
204 1 0.00
205 3 0.00
206 177 0.27
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (201 bp):
ATTGCTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCTGGGGTTCGAAGATTTACTCGCATTGA
GCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCG
CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
CATTTT
Found at i:59596241 original size:407 final size:405
Alignment explanation
Indices: 59595444--59596371 Score: 1404
Period size: 407 Copynumber: 2.3 Consensus size: 405
59595434 CTCTGGTTTC
* * *
59595444 ATTGACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GG-GGATTCGAAGATTTGCTCGTA
1 ATTG-CTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGTGGATTCGAAGATTTACTCGCA
59595507 TCGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAA
65 TCGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAA
*
59595572 TTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCAACTTCTCGATATCTCATCAGGAAGC
130 TTCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCAACTTCTCGATATCTCATCAGGAAGC
* * * * * * * *
59595637 TAACCATTTTATTGCTTTAACCTGCTTCTCAGTGTCTTATTAGGAAGCTGGGGTTTGAAGCTTCG
195 TAACCATTTTATTGCTTCAACCTACTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTCA
* *
59595702 CTCGCATTGAGCGTTGAGTTGGTATACTTCTCTGTATCTCTTCAAGAAGATTATCGCCTCACTTG
260 CTCGCATTGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGATCGCCTCACTTG
* *
59595767 TTTCAATTCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCA
325 TTTCAATCCGCTTCTCTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCA
59595832 GGAAGCTAACCATTTT
390 GGAAGCTAACCATTTT
* * * *
59595848 ATTGCTTCGACCTGCTTCTCAATGTTTTATCAGGAAGCTGGAGCTGGATTCGAAGATTTACTCAC
1 ATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGG-G-TGGATTCGAAGATTTACTCGC
* * * *
59595913 ATTGAGCGTTGAATTGGTATACTTCTCTATATCTCATCAGGAAGATGACCACCTCACTTGTTTCA
64 ATCGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCA
* *
59595978 ATTCGCTTCTTTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTC-AGTATCTCATCAGGAA
129 ATTCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCAACTTCTCGA-TATCTCATCAGGAA
*
59596042 GCTAACCATTTTATTGCTTCGACCTACTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATT
193 GCTAACCATTTTATTGCTTCAACCTACTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATT
* * * *
59596107 CACTCTCATTGGGCGTTGAGTTGGTATACTTCTTTGTATCTCATCAGGAAGATGA-CTGCCTCAC
258 CACTCGCATTGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGATC-GCCTCAC
* *
59596171 TTGTTTCAATCCGTTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
322 TTGTTTCAATCCGCTTCTCTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
59596236 TCAGGAAGCTAACCATTTT
387 TCAGGAAGCTAACCATTTT
* *
59596255 ATTGCTTTGGCCTGCTTCTCAGTATCTTATCAGGAAGCTGGGT---TT-GAAGATTTACTCGCAT
1 ATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGTGGATTCGAAGATTTACTCGCAT
* * * *
59596316 CGAGCGTCGAGTTGGCATACTTCTTTGTATCTCATCAGGAAGATGACTGCCTCACT
66 CGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACT
59596372 CGCATCGAGC
Statistics
Matches: 471, Mismatches: 47, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
401 63 0.13
402 2 0.00
403 31 0.07
404 5 0.01
405 2 0.00
406 3 0.01
407 365 0.77
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (405 bp):
ATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGTGGATTCGAAGATTTACTCGCAT
CGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAAT
TCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCAACTTCTCGATATCTCATCAGGAAGCT
AACCATTTTATTGCTTCAACCTACTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTCAC
TCGCATTGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGATCGCCTCACTTGT
TTCAATCCGCTTCTCTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG
GAAGCTAACCATTTT
Found at i:59596393 original size:61 final size:61
Alignment explanation
Indices: 59596308--59596429 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
59596298 TTGAAGATTT
59596308 ACTCGCATCGAGCGTCGAGTTGGCATACTTCTTTGTATCTCATCAGGAAGATGACTGCCTC
1 ACTCGCATCGAGCGTCGAGTTGGCATACTTCTTTGTATCTCATCAGGAAGATGACTGCCTC
59596369 ACTCGCATCGAGCGTCGAGTTGGCATACTTCTTTGTATCTCATCAGGAAGATGACTGCCTC
1 ACTCGCATCGAGCGTCGAGTTGGCATACTTCTTTGTATCTCATCAGGAAGATGACTGCCTC
59596430 GCTATTTGTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (61 bp):
ACTCGCATCGAGCGTCGAGTTGGCATACTTCTTTGTATCTCATCAGGAAGATGACTGCCTC
Found at i:59596819 original size:49 final size:49
Alignment explanation
Indices: 59596761--59596998 Score: 305
Period size: 49 Copynumber: 4.9 Consensus size: 49
59596751 GTACCGGGTT
* * ** **
59596761 CGCCATTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTGGATC
1 CGCCGTTGCGGCTTAAATATTTCCCTTCATGTCTTCGTGGTACTGGATC
* * * * *
59596810 TGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTGTGGTATTGGATC
1 CGCCGTTGCGGCTTAAATATTTCCCTTCATGTCTTCGTGGTACTGGATC
* *
59596859 CGCCGTCGCGGCTTAAATATTTCCCTTTATGTCTTCGTGGTACTGGATC
1 CGCCGTTGCGGCTTAAATATTTCCCTTCATGTCTTCGTGGTACTGGATC
*
59596908 CGCCGTTGTGGCTTAAATATTTCCCTTCATGTCTTCGTGGTACTGGATC
1 CGCCGTTGCGGCTTAAATATTTCCCTTCATGTCTTCGTGGTACTGGATC
** * * *
59596957 CGCCGTTATGGCTTAGATCTTTCCCTTCATGTCTTCGAGGTA
1 CGCCGTTGCGGCTTAAATATTTCCCTTCATGTCTTCGTGGTA
59596999 TAAGGTTCAC
Statistics
Matches: 166, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 166 1.00
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (49 bp):
CGCCGTTGCGGCTTAAATATTTCCCTTCATGTCTTCGTGGTACTGGATC
Found at i:59597032 original size:98 final size:98
Alignment explanation
Indices: 59596780--59597032 Score: 233
Period size: 98 Copynumber: 2.6 Consensus size: 98
59596770 GACTTAAACC
** * ** * * * *
59596780 TTTCCCTTCAAATCTTCGTGGTACTGGATCTGCCGTTGCGGCTTAGATC-TTTCCCTTCATGTCT
1 TTTCCCTTCATGTCTTCGAGGTACTGGATCCACCGTTGTGACTTA-AACATTACCCTTCATGTCT
* * *
59596844 TTGTGGTATTGGATCCGCCGTCGCGGCTTAAATA
65 TCGTGGTACTGGATCCGCCGTCACGGCTTAAATA
* * * * * *
59596878 TTTCCCTTTATGTCTTCGTGGTACTGGATCCGCCGTTGTGGCTTAAATATTTCCCTTCATGTCTT
1 TTTCCCTTCATGTCTTCGAGGTACTGGATCCACCGTTGTGACTTAAACATTACCCTTCATGTCTT
* * * *
59596943 CGTGGTACTGGATCCGCCGTTATGGCTTAGATC
66 CGTGGTACTGGATCCGCCGTCACGGCTTAAATA
* * *
59596976 TTTCCCTTCATGTCTTCGAGGTA-TAAGG-TTCACCTTTGTGACTTAAACCTTACCCTT
1 TTTCCCTTCATGTCTTCGAGGTACT--GGATCCACCGTTGTGACTTAAACATTACCCTT
59597033 TGTATCTTTA
Statistics
Matches: 129, Mismatches: 23, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
97 2 0.02
98 125 0.97
99 2 0.02
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (98 bp):
TTTCCCTTCATGTCTTCGAGGTACTGGATCCACCGTTGTGACTTAAACATTACCCTTCATGTCTT
CGTGGTACTGGATCCGCCGTCACGGCTTAAATA
Found at i:59597062 original size:147 final size:148
Alignment explanation
Indices: 59596780--59597120 Score: 337
Period size: 147 Copynumber: 2.3 Consensus size: 148
59596770 GACTTAAACC
** * *
59596780 TTTCCCTTCAAATCTTCGTGGTACTGGATCTGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTT
1 TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTACGGCTTAGATCTTTCCCTTCATGTCTT
* * * * * * * * ** *
59596845 TGTGGTATTGGATCCGCCGTCGCGGCTTAAATATTTCCCTTTATGTCTTCGTGGTACTGGATCCG
66 CGAGGTATAGGATCCACCGTCGCGACTTAAACATTACCCTTTATATCTTCACGGTACTGGATCCA
* *
59596910 CCGTTGTGG-CTTAAATA
131 CCGTTGCGGTCTCAAATA
*
59596927 TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTATGGCTTAGATCTTTCCCTTCATGTCTT
1 TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTACGGCTTAGATCTTTCCCTTCATGTCTT
* * * * * * * *
59596992 CGAGGTATAAGG-TTCACCTTTGTGACTTAAACCTTACCCTTTGTATCTTTACGGTACTGGATCT
66 CGAGGTAT-AGGATCCACCGTCGCGACTTAAACATTACCCTTTATATCTTCACGGTACTGGATCC
* * *
59597056 ATCGTTGCGGTCTCAGATC
130 ACCGTTGCGGTCTCAAATA
* * **
59597075 TTTCTCTTC-TGTATCTTTGTGGTACTGGATCCGCCGTCGCGGCTTA
1 TTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCCGTTACGGCTTA
59597121 AATTCTTCCC
Statistics
Matches: 156, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
147 112 0.72
148 15 0.10
149 29 0.19
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (148 bp):
TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTACGGCTTAGATCTTTCCCTTCATGTCTT
CGAGGTATAGGATCCACCGTCGCGACTTAAACATTACCCTTTATATCTTCACGGTACTGGATCCA
CCGTTGCGGTCTCAAATA
Found at i:59597778 original size:106 final size:107
Alignment explanation
Indices: 59597656--59597864 Score: 314
Period size: 106 Copynumber: 2.0 Consensus size: 107
59597646 AGGCGAATGA
*
59597656 AATTTTATTGAAGGCAAAGCTCACATAAATGAAAAGATTAAAAATGAC-CTATATTAGTCAAAGG
1 AATTTTATTGAAGGCAAAGCTCACATAAATGAAAAGATTAAAAATGACTC-ATATTAGTCAAAGA
* *
59597720 A-TGCCAAATATAAAGTGAGCAAAGAATAGAGTTAGGTGGATG
65 ATTGCCAAACACAAAGTGAGCAAAGAATAGAGTTAGGTGGATG
* ** * *
59597762 AATTTTATTGGAGGCAAAGCTTGCATGAATGAAAAGATTAAAAATGACTCATATTGGTCAAAGAA
1 AATTTTATTGAAGGCAAAGCTCACATAAATGAAAAGATTAAAAATGACTCATATTAGTCAAAGAA
*
59597827 TTGCCAAACACAAAGTGAGCAAAGAATAGGGTTAGGTG
66 TTGCCAAACACAAAGTGAGCAAAGAATAGAGTTAGGTG
59597865 CCCCAGATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
106 57 0.62
107 35 0.38
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (107 bp):
AATTTTATTGAAGGCAAAGCTCACATAAATGAAAAGATTAAAAATGACTCATATTAGTCAAAGAA
TTGCCAAACACAAAGTGAGCAAAGAATAGAGTTAGGTGGATG
Found at i:59598131 original size:6 final size:6
Alignment explanation
Indices: 59598129--59598182 Score: 90
Period size: 6 Copynumber: 8.8 Consensus size: 6
59598119 CTTTTTTTCT
*
59598129 TTTTTC TTTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTT-TTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
59598178 TTTTT
1 TTTTT
59598183 TCTTTTCTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
6 41 0.89
7 5 0.11
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:59598188 original size:6 final size:6
Alignment explanation
Indices: 59598136--59598182 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
59598126 TCTTTTTTCT
59598136 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
59598183 TCTTTTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:59598193 original size:18 final size:18
Alignment explanation
Indices: 59598129--59598193 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
59598119 CTTTTTTTCT
59598129 TTTTTCTTTTTTGTTTTTG
1 TTTTTC-TTTTTGTTTTTG
*
59598148 TTTTTGTTTTTGTTTTTG
1 TTTTTCTTTTTGTTTTTG
*
59598166 TTTTTGTTTTTGTTTTT-
1 TTTTTCTTTTTGTTTTTG
59598183 TCTTTTCTTTT
1 T-TTTTCTTTT
59598194 ATTCATTGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
17 1 0.02
18 37 0.86
19 5 0.12
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.85
Consensus pattern (18 bp):
TTTTTCTTTTTGTTTTTG
Found at i:59603948 original size:30 final size:29
Alignment explanation
Indices: 59603879--59604092 Score: 116
Period size: 29 Copynumber: 7.7 Consensus size: 29
59603869 GGGCATCCGA
59603879 GGGT-AAAATGGTAA-TTTTGAAAGTTTTG
1 GGGTAAAAATGG-AATTTTTGAAAGTTTTG
* *
59603907 GGGTCAAAATGGAATTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGAAAGTTTTG
*
59603936 AGGTTAAAAATGGAATTTTT---A------
1 -GGGTAAAAATGGAATTTTTGAAAGTTTTG
** *
59603957 GGTCAAAAATGGAATTTTT-AAAGTTTAG
1 GGGTAAAAATGGAATTTTTGAAAGTTTTG
* * **
59603985 AGGTAAAAATGTAATTTTCAAAAGTTTAT-
1 GGGTAAAAATGGAATTTTTGAAAGTTT-TG
** *
59604014 GGGTAAAAATATAATTTTTGGAAGTTTTAG
1 GGGTAAAAATGGAATTTTTGAAAGTTTT-G
* *
59604044 GGTTAAAAATGTAATTTTT-AGAAG-TTTG
1 GGGTAAAAATGGAATTTTTGA-AAGTTTTG
* *
59604072 AGGGTATAAATGTAATTTTTG
1 -GGGTAAAAATGGAATTTTTG
59604093 GATAGTTTAG
Statistics
Matches: 148, Mismatches: 20, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
20 18 0.12
22 1 0.01
27 1 0.01
28 22 0.15
29 69 0.47
30 37 0.25
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.39
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGAAAGTTTTG
Found at i:59603959 original size:20 final size:20
Alignment explanation
Indices: 59603925--59603976 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
59603915 ATGGAATTTT
* *
59603925 TGGAAGTTTTGAGGTTAAAAA
1 TGGAA-TTTTTAGGTCAAAAA
59603946 TGGAATTTTTAGGTCAAAAA
1 TGGAATTTTTAGGTCAAAAA
59603966 TGGAATTTTTA
1 TGGAATTTTTA
59603977 AAGTTTAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (20 bp):
TGGAATTTTTAGGTCAAAAA
Found at i:59603982 original size:49 final size:48
Alignment explanation
Indices: 59603908--59604002 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
59603898 AAAGTTTTGG
* *
59603908 GGTCAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGAATTTTTA
1 GGTCAAAATGGAATTTTTGAAAGTTTAGAGG-TAAAAATGGAATTTTTA
*
59603957 GGTCAAAAATGGAATTTTT-AAAGTTTAGAGGTAAAAATGTAATTTT
1 GGTC-AAAATGGAATTTTTGAAAGTTTAGAGGTAAAAATGGAATTTT
59604003 CAAAAGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 14 0.33
49 14 0.33
50 14 0.33
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (48 bp):
GGTCAAAATGGAATTTTTGAAAGTTTAGAGGTAAAAATGGAATTTTTA
Found at i:59604054 original size:59 final size:58
Alignment explanation
Indices: 59603978--59604104 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 58
59603968 GAATTTTTAA
59603978 AGTTTAGAGGTAAAAATGTAATTTTCAAAAGTTT-ATGGGTAAAAATATAATTTTTGGA-
1 AGTTTAG-GGTAAAAATGTAATTTTCAAAAGTTTGA-GGGTAAAAATATAATTTTTGGAT
* * * *
59604036 AGTTTTAGGGTTAAAAATGTAATTTTTAGAAGTTTGAGGGTATAAATGTAATTTTTGGAT
1 AG-TTTAGGG-TAAAAATGTAATTTTCAAAAGTTTGAGGGTAAAAATATAATTTTTGGAT
59604096 AGTTTAGGG
1 AGTTTAGGG
59604105 ACCTTTGATG
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
58 4 0.07
59 54 0.89
60 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.40
Consensus pattern (58 bp):
AGTTTAGGGTAAAAATGTAATTTTCAAAAGTTTGAGGGTAAAAATATAATTTTTGGAT
Found at i:59604104 original size:29 final size:28
Alignment explanation
Indices: 59603953--59604104 Score: 155
Period size: 29 Copynumber: 5.2 Consensus size: 28
59603943 AAATGGAATT
* *
59603953 TTTA-GGTCAAAAATGGAATTTTT-AAAG
1 TTTAGGGT-AAAAATGTAATTTTTGGAAG
***
59603980 TTTAGAGGTAAAAATGTAATTTTCAAAAG
1 TTTAG-GGTAAAAATGTAATTTTTGGAAG
*
59604009 TTTATGGGTAAAAATATAATTTTTGGAAG
1 TTTA-GGGTAAAAATGTAATTTTTGGAAG
*
59604038 TTTTAGGGTTAAAAATGTAATTTTTAGAAG
1 -TTTAGGG-TAAAAATGTAATTTTTGGAAG
*
59604068 TTTGAGGGTATAAATGTAATTTTTGGATAG
1 TTT-AGGGTAAAAATGTAATTTTTGGA-AG
59604098 TTTAGGG
1 TTTAGGG
59604105 ACCTTTGATG
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
27 4 0.04
28 13 0.12
29 57 0.53
30 33 0.31
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.40
Consensus pattern (28 bp):
TTTAGGGTAAAAATGTAATTTTTGGAAG
Found at i:59606566 original size:17 final size:18
Alignment explanation
Indices: 59606528--59606569 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
59606518 AGTGCTTTTT
*
59606528 AAAAGCACTTTTGACATA
1 AAAAACACTTTTGACATA
*
59606546 AAAAACACTTTTGA-ATC
1 AAAAACACTTTTGACATA
59606563 AAAAACA
1 AAAAACA
59606570 ATGCTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (18 bp):
AAAAACACTTTTGACATA
Found at i:59606974 original size:13 final size:13
Alignment explanation
Indices: 59606956--59607017 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
59606946 TAAACCAAGC
59606956 TTTTCAAAAGTAT
1 TTTTCAAAAGTAT
*
59606969 TTTTCAAAA-TCAA
1 TTTTCAAAAGT-AT
* *
59606982 TTTTCCAAAGCAT
1 TTTTCAAAAGTAT
* *
59606995 TTTTTAAAAATAT
1 TTTTCAAAAGTAT
*
59607008 TTCTCAAAAG
1 TTTTCAAAAG
59607018 CATTGCTAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
12 1 0.03
13 35 0.97
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (13 bp):
TTTTCAAAAGTAT
Found at i:59618113 original size:5 final size:5
Alignment explanation
Indices: 59618103--59618143 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
59618093 TGCAAGGAAA
59618103 ACGTC ACGTC ACGTC ACGTC ACGTC ACGTC ACGTC ACGTC A
1 ACGTC ACGTC ACGTC ACGTC ACGTC ACGTC ACGTC ACGTC A
59618144 TAGTGGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.22, C:0.39, G:0.20, T:0.20
Consensus pattern (5 bp):
ACGTC
Found at i:59621033 original size:84 final size:83
Alignment explanation
Indices: 59620892--59621049 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 83
59620882 TTAAATTCGG
* * *
59620892 TGAATTCATCGAGTTCTTTTCAATAGGACCATCCAAACTCTGAGATATGAACTCATTAAAAGTAA
1 TGAATTCATCAAGTTCGTCTCAATAGGACCATCCAAACTCTGAGATATGAACTCATTAAAAGTAA
59620957 GAAACTCAACCTCACATGT
66 -AAACTCAACCTCACATGT
* * **
59620976 TGAATTCATCAAGTTCGTCTCAATAGGATCA-CTCAAAC-CTTGGGATATGAGGTCATTAAAAGT
1 TGAATTCATCAAGTTCGTCTCAATAGGACCATC-CAAACTC-TGAGATATGAACTCATTAAAAGT
59621039 AAAAACTCAAC
64 AAAAACTCAAC
59621050 TTTATGCATG
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
83 11 0.17
84 54 0.83
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (83 bp):
TGAATTCATCAAGTTCGTCTCAATAGGACCATCCAAACTCTGAGATATGAACTCATTAAAAGTAA
AAACTCAACCTCACATGT
Found at i:59622964 original size:34 final size:34
Alignment explanation
Indices: 59622921--59622993 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
59622911 AAACTAAACT
59622921 CAAATATTTTTAATTTTTTACCTTTTATCTTACC
1 CAAATATTTTTAATTTTTTACCTTTTATCTTACC
*
59622955 CAAATATTTTTAATTTTTTATCTTTTATCTTACC
1 CAAATATTTTTAATTTTTTACCTTTTATCTTACC
59622989 CAAAT
1 CAAAT
59622994 GTTGTTTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (34 bp):
CAAATATTTTTAATTTTTTACCTTTTATCTTACC
Found at i:59625346 original size:18 final size:18
Alignment explanation
Indices: 59625299--59625346 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
59625289 TTTTTCTTTT
59625299 AAAAA-ATTTTTT-TCTC
1 AAAAATATTTTTTATCTC
* *
59625315 AAAAATATATTTTATCTT
1 AAAAATATTTTTTATCTC
*
59625333 AAAAGTATTTTTTA
1 AAAAATATTTTTTA
59625347 AAAATAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 15 0.58
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (18 bp):
AAAAATATTTTTTATCTC
Found at i:59625432 original size:6 final size:6
Alignment explanation
Indices: 59625421--59625455 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
59625411 AGGAAACCAT
59625421 GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GAGGC
1 GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GAGGC
59625456 CTAGCCTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.51, T:0.00
Consensus pattern (6 bp):
GAGGCA
Found at i:59627305 original size:1 final size:1
Alignment explanation
Indices: 59627299--59627329 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
59627289 ATTGGGTTTT
59627299 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
59627330 TATTTGGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:59641421 original size:15 final size:15
Alignment explanation
Indices: 59641401--59641436 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
59641391 ATTTTATAAA
*
59641401 AAAATTATAATTTCC
1 AAAATTAAAATTTCC
*
59641416 AAAATTAAAATTTTC
1 AAAATTAAAATTTCC
59641431 AAAATT
1 AAAATT
59641437 TTCAAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTAAAATTTCC
Found at i:59645672 original size:37 final size:38
Alignment explanation
Indices: 59645626--59645725 Score: 125
Period size: 37 Copynumber: 2.7 Consensus size: 38
59645616 TATTGAAAAA
* *
59645626 ATAAATAAAAATTA-ATGGCCAAAAAAGACTCAAATAT
1 ATAATTAAAAATTATATGGACAAAAAAGACTCAAATAT
* *
59645663 ATAATT-AAAATTATTTTGACAAAAAAGACTCAAATAT
1 ATAATTAAAAATTATATGGACAAAAAAGACTCAAATAT
* *
59645700 ATAATT-AAAATTATTTTGACAAAAAA
1 ATAATTAAAAATTATATGGACAAAAAA
59645726 TAAATAAACG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 7 0.12
37 51 0.88
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (38 bp):
ATAATTAAAAATTATATGGACAAAAAAGACTCAAATAT
Found at i:59645767 original size:16 final size:16
Alignment explanation
Indices: 59645744--59645799 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
59645734 CGTTTGGTCC
*
59645744 GCTGTAATGGAATATA
1 GCTGTAATGGAATAAA
*
59645760 GGTGTAATGGAATAAA
1 GCTGTAATGGAATAAA
* *
59645776 ACTGTAATGGAATAGA
1 GCTGTAATGGAATAAA
59645792 GCTGTAAT
1 GCTGTAAT
59645800 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAAA
Found at i:59645834 original size:46 final size:44
Alignment explanation
Indices: 59645781--59645874 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
59645771 ATAAAACTGT
* *
59645781 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
59645827 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
59645871 AATG
1 AATG
59645875 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:59646036 original size:26 final size:26
Alignment explanation
Indices: 59646007--59646093 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
59645997 ATTAATTTAT
59646007 TTAATTATATTTTAATATAATTATTA
1 TTAATTATATTTTAATATAATTATTA
* * * *
59646033 TTAAATACAATTTAATAAAATAATATGTAA
1 TTAATTATATTTTAATATAAT--TAT-T-A
*
59646063 TTTAATAATATTTTAATATAATTATTA
1 -TTAATTATATTTTAATATAATTATTA
59646090 TTAA
1 TTAA
59646094 AATATGAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
26 21 0.45
27 1 0.02
28 4 0.09
29 4 0.09
30 1 0.02
31 16 0.34
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
TTAATTATATTTTAATATAATTATTA
Found at i:59646037 original size:58 final size:58
Alignment explanation
Indices: 59645968--59646112 Score: 197
Period size: 57 Copynumber: 2.5 Consensus size: 58
59645958 AAATTTAATG
* * *
59645968 ATTATTATTAAATATAATTTAATAAAAATATTAAT-TTATTTAATTATATTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAAT-ATGTAATTTAATAATATTTTAATATA
*
59646026 ATTATTATTAAATACAATTTAAT-AAAATAATATGTAATTTAATAATATTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATGTAATTTAATAATATTTTAATATA
*
59646083 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
59646113 TATAATATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
56 2 0.03
57 37 0.48
58 31 0.40
59 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATGTAATTTAATAATATTTTAATATA
Found at i:59652559 original size:24 final size:22
Alignment explanation
Indices: 59652507--59652560 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
59652497 GAATGATGCT
59652507 AACAGAGAGTTTAAATGGCCAA
1 AACAGAGAGTTTAAATGGCCAA
59652529 AACAGAGAGTTTAAATGGCCAA
1 AACAGAGAGTTTAAATGGCCAA
59652551 AACAGAGAGT
1 AACAGAGAGT
59652561 ATCAAAACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.17
Consensus pattern (22 bp):
AACAGAGAGTTTAAATGGCCAA
Found at i:59653641 original size:7 final size:7
Alignment explanation
Indices: 59653629--59653658 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
59653619 ATGGAGAGGG
59653629 TCCCTAC
1 TCCCTAC
59653636 TCCCTAC
1 TCCCTAC
59653643 TCCCTAC
1 TCCCTAC
59653650 TCCCTAC
1 TCCCTAC
59653657 TC
1 TC
59653659 GCAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.57, G:0.00, T:0.30
Consensus pattern (7 bp):
TCCCTAC
Found at i:59657199 original size:41 final size:41
Alignment explanation
Indices: 59657149--59657229 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
59657139 TTTCCTTAGC
59657149 TATAAATTAATCATGAAAACAACTCAATAATTAATCCTTAT
1 TATAAATTAATCATGAAAACAACTCAATAATTAATCCTTAT
* * *
59657190 TATAAATTAATTATGAAAATAATTCAATAATTAATCCTTA
1 TATAAATTAATCATGAAAACAACTCAATAATTAATCCTTA
59657230 CCAGTTGAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.37
Consensus pattern (41 bp):
TATAAATTAATCATGAAAACAACTCAATAATTAATCCTTAT
Found at i:59673208 original size:21 final size:21
Alignment explanation
Indices: 59673184--59673226 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
59673174 ATGTGTTTGG
59673184 GTTTAAATGAATTTAAATTTT
1 GTTTAAATGAATTTAAATTTT
*
59673205 GTTTAAATGAGTTTAAATTTT
1 GTTTAAATGAATTTAAATTTT
59673226 G
1 G
59673227 ATTCATGATG
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:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (21 bp):
GTTTAAATGAATTTAAATTTT
Found at i:59673495 original size:11 final size:10
Alignment explanation
Indices: 59673465--59673498 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
59673455 ATAACTTGAA
59673465 AAATGTTTTT
1 AAATGTTTTT
59673475 AAATGTTTTT
1 AAATGTTTTT
*
59673485 AAATTTATTTT
1 AAATGT-TTTT
59673496 AAA
1 AAA
59673499 GCTTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (10 bp):
AAATGTTTTT
Found at i:59674532 original size:20 final size:19
Alignment explanation
Indices: 59674497--59674534 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
59674487 GCTTACAACC
*
59674497 AATAAAAATATTTTAATTT
1 AATAAAAATATATTAATTT
59674516 AATAAAAATAATATTAATT
1 AATAAAAAT-ATATTAATT
59674535 ATGTTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAAAATATATTAATTT
Found at i:59677744 original size:10 final size:11
Alignment explanation
Indices: 59677709--59677741 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
59677699 CTCAATTAAC
59677709 ATTTAAATATA
1 ATTTAAATATA
59677720 ATTATAAAT-TA
1 ATT-TAAATATA
59677731 ATTTAAATATA
1 ATTTAAATATA
59677742 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.25
11 10 0.50
12 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTTAAATATA
Found at i:59679603 original size:29 final size:29
Alignment explanation
Indices: 59679545--59679604 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
59679535 TTATTATTTT
*
59679545 TTTATTTTTAAAAATTTAATTTAATTTAA
1 TTTATTTTTAAAAATTTAATTTAATCTAA
*
59679574 TTTA-TTTT-AAATTTTAAATTTAAATCTAA
1 TTTATTTTTAAAAATTT-AATTT-AATCTAA
59679603 TT
1 TT
59679605 GTTAACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.22
28 9 0.33
29 12 0.44
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTATTTTTAAAAATTTAATTTAATCTAA
Found at i:59689618 original size:21 final size:21
Alignment explanation
Indices: 59689559--59689619 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 21
59689549 TTTATATTAT
* *
59689559 TGTTTTGGTGTTGCTTTTTAC
1 TGTTTTGGTATTGTTTTTTAC
* * *
59689580 TGTTTTGATTACTATTTTTTAC
1 TGTTTTG-GTATTGTTTTTTAC
59689602 TGTTTTGGTATTGTTTTT
1 TGTTTTGGTATTGTTTTT
59689620 GTTGTTATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.10, C:0.07, G:0.18, T:0.66
Consensus pattern (21 bp):
TGTTTTGGTATTGTTTTTTAC
Found at i:59692546 original size:43 final size:43
Alignment explanation
Indices: 59692421--59694350 Score: 915
Period size: 43 Copynumber: 45.1 Consensus size: 43
59692411 TATTAGCACC
* * * *
59692421 CACATAGTGCATCATTTG-ATAAACCGAAGCATATATACTGGCA
1 CACACAGTGCATCA-TCGAATAAACTGAAGCATCTATACTGGCA
* * * * * * * *
59692464 CCCATATAGTGCACCAT-TAGATAAACTGAATCTTTTATATTGGCA
1 --CACACAGTGCATCATCGA-ATAAACTGAAGCATCTATACTGGCA
* * * * * * *
59692509 CAAATAGTGCATCATCGGATACACCGAAACATCTATATTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* *
59692552 CACACAATGCATCATCGGATAAACTGAAGCATCTATACT-G-A
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
**
59692593 CACACAGTGCATCATCGAATAAACTGAAGCATC-ATACTGAAA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * * *
59692635 GACACAATGCATCATCGAATAAACTGAAGCATTTACACTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * *
59692678 CACATAGTGCATCATCGAACAAAGC-GAAACATCTATA-T----
1 CACACAGTGCATCATCGAATAAA-CTGAAGCATCTATACTGGCA
** * *
59692716 ---TTAGTGCATCGT--AAGGTAAA-TCGAAGCATCTTTACTGGCA
1 CACACAGTGCATCATCGAA--TAAACT-GAAGCATCTATACTGGCA
* * ** *
59692756 CACACAGTGCTTCGTCGGGTAAA-TCGAAGCATCTTTACTGGCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * * ** * * *
59692799 CACATAGTGTATCCTCGAATAAACCAAAGTATTTTTACTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * * *
59692842 CACACAGTGCATCATCAAATAAA-TCGAAGCATCTAAACGGGTA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * * * *
59692885 CACATAATGCATCGTCAAATAAA-TCGAAGCATCTATAC-CG-A
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* ** *
59692926 CACACAGTGCATCATCGAATAAACCGAAATATCTATACTAGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * * * * * *
59692969 CACACAATGCGTCCTCGGATAAGCCGAAGCATCTATATTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * * * * * * * * * **
59693012 AACACAATACTTCGTC-AGGTATACTGAAGTACCTATATTAACA
1 CACACAGTGCATCATCGA-ATAAACTGAAGCATCTATACTGGCA
* *
59693055 CACACAGTGCATCATCGAGTAAACT-AAGACATTTATACTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAG-CATCTATACTGGCA
** * *
59693098 CACACAGTGCATCATCGGGTAAACGGAGGCATCTATTA-TGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTA-TACTGGCA
* * * * * * *
59693141 CACATAGTGCATCATCTAATAAACCGAAGAATTTATATTAGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * **
59693184 CACATAATGCATCATCGGGTAAA-TCGAAGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * ** * * *
59693227 CACACAATGCATTATCGGGTAAACCGAGGCATCTATACTGACA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * * * ** * *
59693270 CACATAATGTATGATCGGGTAAACCGAGGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * * ** *
59693313 CACATAGTGCATAATTGGGTAAA-TCGAGGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * * * *
59693356 CACACAATGCACCATTCG-ATAAA-TCGAAACATTTATACAGGCA
1 CACACAGTGCATCA-TCGAATAAACT-GAAGCATCTATACTGGCA
* * * *
59693399 CACACAGTGTA-CAATCGAATAAA-TCGAGGAATCTATACTGACA
1 CACACAGTGCATC-ATCGAATAAACT-GAAGCATCTATACTGGCA
* * * * ** * * * * **
59693442 CATATAGTGCAACATAGGGTAAGCCGAGGCATCATCTATTCTAACA
1 CACACAGTGCATCATCGAATAAACTGA---AGCATCTATACTGGCA
* * ** * ** * *
59693488 CACATAATATATGATCGGGTAAACTGAGGCATCTATACTAGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * * * ** *
59693531 CACATAATGCATAATTGGGTAAA-TCGAGGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * *
59693574 CACACAGTGCACCATCTG-GTAAA-TCGAAGCATCTATACAGG--
1 CACACAGTGCATCATC-GAATAAACT-GAAGCATCTATACTGGCA
** * * *
59693615 CACACAGTATATAATCGGATAAA-TCGAGGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * * * * ** * * *
59693658 CATATAATGCAACATAGGGTAAGCCGAGGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
* * * ** *
59693701 CACAGAGTGTATCGTCGGGTAAAC-CAAGACATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAG-CATCTATACTGGCA
* ** *
59693744 CACACAATGCATCATCGGGTAAA-TCGAAGCATCTATATTGGCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * ** * *
59693787 CACATAGTGCATCATTGGGTAAA-TCGAAGAATCTATACTGCCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * *
59693830 CACACAGTGCATCATC-AGATAAACCT-AGGCATTTATACTTGCA
1 CACACAGTGCATCATCGA-ATAAA-CTGAAGCATCTATACTGGCA
* * ** * *
59693873 CACACAGTGCATTATTGGGTAAA-TCGAGGCATCTATAATGGCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
** * * * *
59693916 CTTATAATGCATCATCGAGTAAAC-CAAGGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACTGAA-GCATCTATACTGGCA
*
59693959 CACACAGTGCATCATC-AAGTAAACTGATGCATCTATACTGGCA
1 CACACAGTGCATCATCGAA-TAAACTGAAGCATCTATACTGGCA
* ** *
59694002 CACACAGTGCATAATCGGGTAAACTGAGGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
** *
59694045 CTTACAGTGCATCATC-AAGTAAA-TCGAGGCATCTATACTGGCA
1 CACACAGTGCATCATCGAA-TAAACT-GAAGCATCTATACTGGCA
* * * * *
59694088 TACACAGTGCATCATC-AGGTGAACCGAGGCATCTATACTGG--
1 CACACAGTGCATCATCGA-ATAAACTGAAGCATCTATACTGGCA
* ** * * *
59694129 CACACAGTGTATCATCGGGTAAA-TCAAGGCGTCTACACTGGACA
1 CACACAGTGCATCATCGAATAAACTGAA-GCATCTATACTGG-CA
* * ** * * ** *
59694173 CATACGGTGCATCATCGGGTAAACCGAGGTGTCTATATTGGCA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
*
59694216 CACACAGTGCATCATCAAATAAA-TCGAAGCATCTATACTGGCA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * * *
59694259 TACACAGTGCATCCTCGAATAAA-TCGAAGCATCTATATTGACA
1 CACACAGTGCATCATCGAATAAACT-GAAGCATCTATACTGGCA
* * * * * * **
59694302 AACACAGTGCATCATCGGATATACCGAAGTACCTATACTAACA
1 CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
59694345 CACACA
1 CACACA
59694351 ATGATACCTT
Statistics
Matches: 1468, Mismatches: 342, Indels: 152
0.75 0.17 0.08
Matches are distributed among these distances:
33 2 0.00
35 23 0.02
36 1 0.00
40 7 0.00
41 125 0.09
42 50 0.03
43 1152 0.78
44 45 0.03
45 34 0.02
46 29 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (43 bp):
CACACAGTGCATCATCGAATAAACTGAAGCATCTATACTGGCA
Found at i:59692626 original size:20 final size:20
Alignment explanation
Indices: 59692601--59692666 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
59692591 GACACACAGT
59692601 GCATCATCGAATAAACTGAA
1 GCATCATCGAATAAACTGAA
* **
59692621 GCATCATACTGAA-AGACACAA
1 GCATCAT-C-GAATAAACTGAA
59692642 TGCATCATCGAATAAACTGAA
1 -GCATCATCGAATAAACTGAA
59692663 GCAT
1 GCAT
59692667 TTACACTGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
20 14 0.39
21 12 0.33
22 10 0.28
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (20 bp):
GCATCATCGAATAAACTGAA
Found at i:59692888 original size:129 final size:127
Alignment explanation
Indices: 59692551--59692974 Score: 293
Period size: 121 Copynumber: 3.4 Consensus size: 127
59692541 CTATATTGGC
* * * ** *
59692551 ACACACAATGCATCATCGGATAAACTGAAGCATCTATACT-G-ACACACAGTGCATCATCGAATA
1 ACACACAGTGCATCATCGAATAAACCGAAATATCTATACTAGCACACACAGTGCATCATCAAATA
* * ** * * * * * *
59692614 AA-CTGAAGCATC-ATACTGAAAGACACAATGCATCATCGAATAAA-CTGAAGCATTTACACTGG
66 AATC-GAAGCATCTAAACGGGCACACACAATGCATCGTCAAATAAATC-GAAGCATCTATAC-CG
* * * * ** * *
59692676 CACACATAGTGCATCATCGAACAAAGCGAAACATCTATA-T-------TTAGTGCATCGT-AAGG
1 -ACACACAGTGCATCATCGAATAAACCGAAATATCTATACTAGCACACACAGTGCATCATCAA-A
** * * * *** * *
59692732 TAAATCGAAGCATCTTTACTGGCACACACAGTGCTTCGTCGGGTAAATCGAAGCATCTTTACTGG
64 TAAATCGAAGCATCTAAACGGGCACACACAATGCATCGTCAAATAAATCGAAGCATCTATAC-CG
* * * * * *
59692797 CACACATAGTGTATCCTCGAATAAACC-AAAGTATTTTTACTGGCACACACAGTGCATCATCAAA
1 -ACACACAGTGCATCATCGAATAAACCGAAA-TATCTATACTAGCACACACAGTGCATCATCAAA
* *
59692861 TAAATCGAAGCATCTAAACGGGTACACATAATGCATCGTCAAATAAATCGAAGCATCTATACCG
64 TAAATCGAAGCATCTAAACGGGCACACACAATGCATCGTCAAATAAATCGAAGCATCTATACCG
59692925 ACACACAGTGCATCATCGAATAAACCGAAATATCTATACTAGCACACACA
1 ACACACAGTGCATCATCGAATAAACCGAAATATCTATACTAGCACACACA
59692975 ATGCGTCCTC
Statistics
Matches: 230, Mismatches: 53, Indels: 29
0.74 0.17 0.09
Matches are distributed among these distances:
119 1 0.00
120 24 0.10
121 65 0.28
122 2 0.01
125 1 0.00
126 31 0.13
127 40 0.17
128 4 0.02
129 60 0.26
130 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (127 bp):
ACACACAGTGCATCATCGAATAAACCGAAATATCTATACTAGCACACACAGTGCATCATCAAATA
AATCGAAGCATCTAAACGGGCACACACAATGCATCGTCAAATAAATCGAAGCATCTATACCG
Found at i:59692972 original size:84 final size:84
Alignment explanation
Indices: 59692841--59693005 Score: 195
Period size: 84 Copynumber: 2.0 Consensus size: 84
59692831 TTTTACTGGC
* * * * * *
59692841 ACACACAGTGCATCATCAAATAAATCGAAGCATCTAAACGGGTACACATAATGCATCGTCAAATA
1 ACACACAGTGCATCATCAAATAAACCGAAACATCTAAACGAGCACACACAATGCATCCTCAAATA
*
59692906 AATCGAAGCATCTATACCG
66 AACCGAAGCATCTATACCG
* * * * * **
59692925 ACACACAGTGCATCATCGAATAAACCGAAATATCTATACTAGCACACACAATGCGTCCTCGGATA
1 ACACACAGTGCATCATCAAATAAACCGAAACATCTAAACGAGCACACACAATGCATCCTCAAATA
*
59692990 AGCCGAAGCATCTATA
66 AACCGAAGCATCTATA
59693006 TTGGCAAACA
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (84 bp):
ACACACAGTGCATCATCAAATAAACCGAAACATCTAAACGAGCACACACAATGCATCCTCAAATA
AACCGAAGCATCTATACCG
Found at i:59694330 original size:86 final size:86
Alignment explanation
Indices: 59692731--59694319 Score: 1175
Period size: 86 Copynumber: 18.5 Consensus size: 86
59692721 GCATCGTAAG
* * * * *
59692731 GTAAATCGAAGCATCTTTACTGGCACACACAGTGCTTCGTCGGGTAAATCGAAGCATCTTTACTG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
* * *
59692796 GCACACATAGTGTATCCTCGA
66 GCACACACAGTGCATCATCGA
* * * * * *** * *
59692817 ATAAACCAAAGTATTTTTACTGGCACACACAGTGCATCATCAAATAAATCGAAGCATCTAAACGG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
* * * * *
59692882 GTACACATAATGCATCGTCAA
66 GCACACACAGTGCATCATCGA
* * * ** * ** *
59692903 ATAAATCGAAGCATCTATAC-CG-ACACACAGTGCATCATCGAATAAACCGAAATATCTATACTA
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
* * *
59692966 GCACACACAATGCGTCCTCG-
66 GCACACACAGTGCATCATCGA
* * * * * * * * * * * *
59692986 GATAAGCCGAAGCATCTATATTGGCAAACACAATACTTCGTCAGGTATA-CTGAAGTACCTATAT
1 G-TAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAAGCATCTATAC
**
59693050 TAACACACACAGTGCATCATCGA
64 TGGCACACACAGTGCATCATCGA
* * *
59693073 GTAAA-CTAAGACATTTATACTGGCACACACAGTGCATCATCGGGTAAA-CGGAGGCATCTATTA
1 GTAAACCGAAG-CATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAAGCATCTA-TA
* *
59693136 -TGGCACACATAGTGCATCATCTA
63 CTGGCACACACAGTGCATCATCGA
* * * * * * *
59693159 ATAAACCGAAGAATTTATATTAGCACACATAATGCATCATCGGGTAAATCGAAGCATCTATACTG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
* * *
59693224 GCACACACAATGCATTATCGG
66 GCACACACAGTGCATCATCGA
* * * * * * * *
59693245 GTAAACCGAGGCATCTATACTGACACACATAATGTATGATCGGGTAAACCGAGGCATCTATACTG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
* * * *
59693310 GCACACATAGTGCATAATTGG
66 GCACACACAGTGCATCATCGA
* * * * * * * *
59693331 GTAAATCGAGGCATCTATACTGGCACACACAATGCACCATTC-GATAAATCGAAACATTTATACA
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCA-TCGGGTAAATCGAAGCATCTATACT
*
59693395 GGCACACACAGTGTA-CAATCGA
65 GGCACACACAGTGCATC-ATCGA
* * * * * * * * * ** * *
59693417 ATAAATCGAGGAATCTATACTGACACATATAGTGCAACATAGGGTAAGCCGAGGCATCATCTATT
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGA---AGCATCTATA
** * * ** * *
59693482 CTAACACACATAATATATGATCGG
63 CTGGCACACACAGTGCATCATCGA
* * * * * * * *
59693506 GTAAACTGAGGCATCTATACTAGCACACATAATGCATAATTGGGTAAATCGAGGCATCTATACTG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
*
59693571 GCACACACAGTGCACCATCTG-
66 GCACACACAGTGCATCATC-GA
* * ** * * *
59693592 GTAAATCGAAGCATCTATACAGG--CACACAGTATATAATCGGATAAATCGAGGCATCTATACTG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
* * * * * *
59693655 GCACATATAATGCAACATAGG
66 GCACACACAGTGCATCATCGA
* * * * * *
59693676 GTAAGCCGAGGCATCTATACTGGCACACAGAGTGTATCGTCGGGTAAA-CCAAGACATCTATACT
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAG-CATCTATACT
* *
59693740 GGCACACACAATGCATCATCGG
65 GGCACACACAGTGCATCATCGA
* * * * *
59693762 GTAAATCGAAGCATCTATATTGGCACACATAGTGCATCATTGGGTAAATCGAAGAATCTATACTG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
*
59693827 CCACACACAGTGCATCATC-A
66 GCACACACAGTGCATCATCGA
* * * * * * * *
59693847 GATAAACCTAGGCATTTATACTTGCACACACAGTGCATTATTGGGTAAATCGAGGCATCTATAAT
1 G-TAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACT
** * *
59693912 GGCACTTATAATGCATCATCGA
65 GGCACACACAGTGCATCATCGA
** *
59693934 GTAAACC-AAGGCATCTATACTGGCACACACAGTGCATCATCAAGTAAA-CTGATGCATCTATAC
1 GTAAACCGAA-GCATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAAGCATCTATAC
* *
59693997 TGGCACACACAGTGCATAATCGG
64 TGGCACACACAGTGCATCATCGA
* * ** ** *
59694020 GTAAACTGAGGCATCTATACTGGCACTTACAGTGCATCATCAAGTAAATCGAGGCATCTATACTG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
*
59694085 GCATACACAGTGCATCATC-A
66 GCACACACAGTGCATCATCGA
* * * * *
59694105 GGTGAACCGAGGCATCTATACTGG--CACACAGTGTATCATCGGGTAAATC-AAGGCGTCTACAC
1 -GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAA-GCATCTATAC
* * *
59694167 TGGACACATACGGTGCATCATCGG
64 TGG-CACACACAGTGCATCATCGA
* ** * ***
59694191 GTAAACCGAGGTGTCTATATTGGCACACACAGTGCATCATCAAATAAATCGAAGCATCTATACTG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
* *
59694256 GCATACACAGTGCATCCTCGA
66 GCACACACAGTGCATCATCGA
* * * * *
59694277 ATAAATCGAAGCATCTATATTGACAAACACAGTGCATCATCGG
1 GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGG
59694320 ATATACCGAA
Statistics
Matches: 1179, Mismatches: 288, Indels: 72
0.77 0.19 0.05
Matches are distributed among these distances:
83 2 0.00
84 163 0.14
85 50 0.04
86 850 0.72
87 51 0.04
88 2 0.00
89 61 0.05
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (86 bp):
GTAAACCGAAGCATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTATACTG
GCACACACAGTGCATCATCGA
Found at i:59694379 original size:8 final size:8
Alignment explanation
Indices: 59694366--59694426 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
59694356 ACCTTTTGTA
59694366 TTATACTT
1 TTATACTT
59694374 TTATACTT
1 TTATACTT
59694382 TTATA-TT
1 TTATACTT
*
59694389 ATATTACTT
1 TTA-TACTT
*
59694398 TAATA-TT
1 TTATACTT
* *
59694405 TAATAATT
1 TTATACTT
59694413 TTATACCTT
1 TTATA-CTT
59694422 TTATA
1 TTATA
59694427 TTTATTTGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
7 11 0.25
8 23 0.52
9 10 0.23
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATACTT
Found at i:59694427 original size:24 final size:22
Alignment explanation
Indices: 59694366--59694430 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
59694356 ACCTTTTGTA
*
59694366 TTATACTTTTATACTTTTATATT
1 TTATACTTTTATA-TTTAATATT
* *
59694389 ATATTACTTTAATATTTAATAATT
1 TTA-TACTTTTATATTTAAT-ATT
59694413 TTATACCTTTTATATTTA
1 TTATA-CTTTTATATTTA
59694431 TTTGATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 9 0.26
24 25 0.74
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATACTTTTATATTTAATATT
Found at i:59698115 original size:120 final size:120
Alignment explanation
Indices: 59697902--59698117 Score: 405
Period size: 120 Copynumber: 1.8 Consensus size: 120
59697892 CCGGCCACAC
59697902 TAGCCCGTCTAGCTCAGTCGGTAGAGCGCAAAGCTCTTAACCTTGTGGTCGTGGGTTCGAACCCC
1 TAGCCCGTCTAGCTCAGTCGGTAGAGCGCAAAGCTCTTAACCTTGTGGTCGTGGGTTCGAACCCC
59697967 ACGGTGGGCGGTTTATGTTATTTTATTTTAATGTAAATTCAGTAAGATAATATCG
66 ACGGTGGGCGGTTTATGTTATTTTATTTTAATGTAAATTCAGTAAGATAATATCG
* *
59698022 TAGCCCGTCTAGCTCAGTCGGTAGAGCGCAAGGCTCTTAACCTTGTGGTCGTGGGTTCGAGCCCC
1 TAGCCCGTCTAGCTCAGTCGGTAGAGCGCAAAGCTCTTAACCTTGTGGTCGTGGGTTCGAACCCC
*
59698087 ACGGTGGGCGGTTTCTGTTATTTTATTTTAA
66 ACGGTGGGCGGTTTATGTTATTTTATTTTAA
59698118 GTTTGGGCTT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 93 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (120 bp):
TAGCCCGTCTAGCTCAGTCGGTAGAGCGCAAAGCTCTTAACCTTGTGGTCGTGGGTTCGAACCCC
ACGGTGGGCGGTTTATGTTATTTTATTTTAATGTAAATTCAGTAAGATAATATCG
Found at i:59698544 original size:12 final size:12
Alignment explanation
Indices: 59698527--59698551 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59698517 CTCCTTTTAA
59698527 CCTTTTCCTCTT
1 CCTTTTCCTCTT
59698539 CCTTTTCCTCTT
1 CCTTTTCCTCTT
59698551 C
1 C
59698552 GTCTTCCGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (12 bp):
CCTTTTCCTCTT
Found at i:59704749 original size:18 final size:19
Alignment explanation
Indices: 59704717--59704755 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
59704707 GTCTCTACTC
* *
59704717 TTTAAAAATACATAAT-TT
1 TTTAAAAAAAAATAATCTT
59704735 TTTAAAAAAAAATAATCTT
1 TTTAAAAAAAAATAATCTT
59704754 TT
1 TT
59704756 CATATTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAAAAAAAAATAATCTT
Found at i:59705279 original size:17 final size:17
Alignment explanation
Indices: 59705248--59705344 Score: 85
Period size: 18 Copynumber: 5.5 Consensus size: 17
59705238 CTTTTTTCAT
59705248 ATTTTAAACAAATAAAAA
1 ATTTTAAA-AAATAAAAA
59705266 ATTTTAAAAAATAAAAA
1 ATTTTAAAAAATAAAAA
*
59705283 ATATATTTAAAAATAAAAA
1 AT-T-TTAAAAAATAAAAA
59705302 A---TAAAAAATTATAAAA
1 ATTTTAAAAAA-TA-AAAA
*
59705318 TATTTT-TAAAATATAAAA
1 -ATTTTAAAAAATA-AAAA
59705336 ATTTTAAAA
1 ATTTTAAAA
59705345 TTCAATATTA
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
16 4 0.06
17 17 0.26
18 18 0.27
19 18 0.27
20 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTTTAAAAAATAAAAA
Found at i:59705294 original size:19 final size:18
Alignment explanation
Indices: 59705250--59705344 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
59705240 TTTTTCATAT
59705250 TTTAAACAAATAAAAAAT-
1 TTTAAA-AAATAAAAAATA
59705268 TTTAAAAAATAAAAAATA
1 TTTAAAAAATAAAAAATA
*
59705286 TATTTAAAAATAAAAAATA
1 T-TTAAAAAATAAAAAATA
* *
59705305 ---AAAAATTATAAAATA
1 TTTAAAAAATAAAAAATA
**
59705320 TTTTTAAAATATAAAAAT-
1 TTTAAAAAATA-AAAAATA
59705338 TTTAAAA
1 TTTAAAA
59705345 TTCAATATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
15 12 0.20
17 11 0.18
18 17 0.28
19 21 0.34
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAAAAAATAAAAAATA
Found at i:59705318 original size:34 final size:34
Alignment explanation
Indices: 59705270--59705336 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
59705260 TAAAAAATTT
59705270 TAAAAAATAAAAAATATATTTAAAA-ATAAAAAA
1 TAAAAAATAAAAAATATATTTAAAATATAAAAAA
* *
59705303 TAAAAAATTATAAAATATTTTTAAAATATAAAAA
1 TAAAAAA-TAAAAAATATATTTAAAATATAAAAA
59705337 TTTTAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.23
34 16 0.53
35 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (34 bp):
TAAAAAATAAAAAATATATTTAAAATATAAAAAA
Found at i:59706777 original size:42 final size:42
Alignment explanation
Indices: 59706694--59706817 Score: 128
Period size: 42 Copynumber: 3.0 Consensus size: 42
59706684 GATTTGATTT
* **
59706694 TCAAGGCCATGAAA-TGATG-TTTTTGATTTTTCAAAACTGTC
1 TCAAGGCCAT-AAATTGATGCTTGTTGATTTTTCAAAGTTGTC
**
59706735 TTGAGAG-CATAAATTGATGCTTGTTGATTTTTCAAAGTTGTC
1 TCAAG-GCCATAAATTGATGCTTGTTGATTTTTCAAAGTTGTC
* * * *
59706777 TCAAGGCCATGAATTGATGCTTGCTAATTTTTAAAAGTTGT
1 TCAAGGCCATAAATTGATGCTTGTTGATTTTTCAAAGTTGT
59706818 ATCATTGTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
40 3 0.04
41 12 0.18
42 53 0.78
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (42 bp):
TCAAGGCCATAAATTGATGCTTGTTGATTTTTCAAAGTTGTC
Found at i:59709502 original size:16 final size:16
Alignment explanation
Indices: 59709481--59709512 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59709471 GGTAATTTTT
*
59709481 ATGTTAAAGGATTAAA
1 ATGTTAAAGGAATAAA
59709497 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
59709513 TTTATAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:59710020 original size:47 final size:47
Alignment explanation
Indices: 59709963--59710060 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 47
59709953 TCCAATTCTA
*
59709963 GGCTCATAAGAGATAATCAT-TCTAGGCTTGTAAGAGCT-ACC-ATTATG
1 GGCTCATAAGAGATAA-CATCT-TAGGCTCGTAAGAGCTAACCTATT-TG
* * *
59710010 GGCTCGTAAGAGCTAACATCTTGGGCTCGTAAGAGCTAACCTATTTG
1 GGCTCATAAGAGATAACATCTTAGGCTCGTAAGAGCTAACCTATTTG
59710057 GGCT
1 GGCT
59710061 TGTATGAGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
46 17 0.39
47 24 0.55
48 3 0.07
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (47 bp):
GGCTCATAAGAGATAACATCTTAGGCTCGTAAGAGCTAACCTATTTG
Found at i:59710069 original size:24 final size:23
Alignment explanation
Indices: 59709963--59710072 Score: 107
Period size: 23 Copynumber: 4.7 Consensus size: 23
59709953 TCCAATTCTA
* * * *
59709963 GGCTCATAAGAGATAATCATTCTA
1 GGCTCGTAAGAGCTAACCATT-TG
*
59709987 GGCTTGTAAGAGCT-ACCATTATG
1 GGCTCGTAAGAGCTAACCATT-TG
59710010 GGCTCGTAAGAGCTAA-CATCTTG
1 GGCTCGTAAGAGCTAACCAT-TTG
59710033 GGCTCGTAAGAGCTAACCTATTTG
1 GGCTCGTAAGAGCTAACC-ATTTG
* *
59710057 GGCTTGTATGAGCTAA
1 GGCTCGTAAGAGCTAA
59710073 TTTTGTCTGG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
23 40 0.55
24 31 0.42
25 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCTCGTAAGAGCTAACCATTTG
Found at i:59717647 original size:6 final size:6
Alignment explanation
Indices: 59717636--59717690 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
59717626 GTGAGAACCT
* * ** *
59717636 CACAAC CACAAC CACAGC CACAGC CACAGT CACAAC CACAAC CACAAT
1 CACAAC CACAAC CACAAC CACAAC CACAAC CACAAC CACAAC CACAAC
59717684 CACAAC C
1 CACAAC C
59717691 TCATGAACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.44, C:0.47, G:0.05, T:0.04
Consensus pattern (6 bp):
CACAAC
Found at i:59720998 original size:31 final size:31
Alignment explanation
Indices: 59720935--59720999 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
59720925 AAACGTATAT
* *
59720935 ATATCTAAATGAATATTAAAACCGAACTCAA
1 ATATCTAAATGAATATTAAAACCAAACGCAA
**
59720966 ATAT-TAAATTGAATATTAAAATTAAACGCAA
1 ATATCTAAA-TGAATATTAAAACCAAACGCAA
59720997 ATA
1 ATA
59721000 CCAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (31 bp):
ATATCTAAATGAATATTAAAACCAAACGCAA
Done.