Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008844.1 Hibiscus syriacus cultivar Beakdansim tig00112051_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 694789
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 1 of 2
Found at i:3614 original size:32 final size:31
Alignment explanation
Indices: 3578--3654 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
3568 CGGGGCCGTG
*
3578 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
3610 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
3641 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3655 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3637 original size:63 final size:63
Alignment explanation
Indices: 3531--3654 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
3521 CCCTAAGGGA
* * ** *
3531 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
3594 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
3655 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:4534 original size:13 final size:13
Alignment explanation
Indices: 4516--4541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4506 AAGAAAGTCA
4516 ACGGTCAACGGTC
1 ACGGTCAACGGTC
4529 ACGGTCAACGGTC
1 ACGGTCAACGGTC
4542 GGGTCGGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:4553 original size:17 final size:17
Alignment explanation
Indices: 4531--4588 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
4521 CAACGGTCAC
4531 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4548 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
4565 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4582 GGTCAAC
1 GGTCAAC
4589 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:4558 original size:7 final size:7
Alignment explanation
Indices: 4512--4541 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4502 GTCAAAGAAA
4512 GTCAACG
1 GTCAACG
4519 GTCAACG
1 GTCAACG
4526 GTC-ACG
1 GTCAACG
4532 GTCAACG
1 GTCAACG
4539 GTC
1 GTC
4542 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:9604 original size:42 final size:43
Alignment explanation
Indices: 9514--9629 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
9504 AAAAAATGAC
* * * * *
9514 GCTAATTATCCTATCTTTAGTGGCTTTTTTTTTCCACAAACGCT
1 GCTAATTATCATGTCTTTAGTGGC-ATTTTTTGCCACAAACGCA
*
9558 GCTAATTAT-ATGTCTTTAGTGGCATTTTTTGCTACAAACGCA
1 GCTAATTATCATGTCTTTAGTGGCATTTTTTGCCACAAACGCA
* * * *
9600 GCTAATTCTCTTGTTTTTAGTGGCGTTTTT
1 GCTAATTATCATGTCTTTAGTGGCATTTTT
9630 AATACAAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 23 0.38
43 29 0.48
44 9 0.15
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.47
Consensus pattern (43 bp):
GCTAATTATCATGTCTTTAGTGGCATTTTTTGCCACAAACGCA
Found at i:9636 original size:42 final size:42
Alignment explanation
Indices: 9549--9637 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
9539 TTTTTTTTCC
* * **
9549 ACAAACGCTGCTAATTATATGTCTTTAGTGGCATTTTTTGCT
1 ACAAACGCAGCTAATTATATGTCTTTAGTGGCAGTTTTTAAT
* * *
9591 ACAAACGCAGCTAATTCTCTTGTTTTTAGTGGC-GTTTTTAAT
1 ACAAACGCAGCTAATTAT-ATGTCTTTAGTGGCAGTTTTTAAT
9633 ACAAA
1 ACAAA
9638 ACACCGCTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 27 0.69
43 12 0.31
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (42 bp):
ACAAACGCAGCTAATTATATGTCTTTAGTGGCAGTTTTTAAT
Found at i:11360 original size:83 final size:79
Alignment explanation
Indices: 11214--11449 Score: 283
Period size: 83 Copynumber: 2.9 Consensus size: 79
11204 AAACCCAAAC
* * * * *
11214 GCCACAAACATACCAAATTATTGTTGTGTTTGTAAAAATATGCCGCTAAAGTACTAGTATGTTGC
1 GCCAC-AACATACCAAATTATTGTGGCGTTTGTAAAAA-ACGCTGCTAAAGTACTAATATGTTGC
11279 GGCGTTTGTTGAAAAAA
64 GGCGTTTGTTG-AAAAA
* * *
11296 TGCCACAATCATACCAAACTATTGTGGCGTTTGTAAAAAACCGCTGCTAAAGTACTACTTTGTTG
1 -GCCACAA-CATACCAAATTATTGTGGCGTTTGTAAAAAA-CGCTGCTAAAGTACTAATATGTTG
* *
11361 CTGCATTTGTTGAAAAA
63 CGGCGTTTGTTGAAAAA
* * *
11378 GGCACAACATACCAAATTATTGCGGCGTTTGTAAAAAAAACACTGCTAAAGTACTAATATGTTGC
1 GCCACAACATACCAAATTATTGTGGCGTTTGT--AAAAAACGCTGCTAAAGTACTAATATGTTGC
11443 GGCGTTT
64 GGCGTTT
11450 TATACTACTC
Statistics
Matches: 132, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
80 23 0.17
81 33 0.25
82 14 0.11
83 62 0.47
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (79 bp):
GCCACAACATACCAAATTATTGTGGCGTTTGTAAAAAACGCTGCTAAAGTACTAATATGTTGCGG
CGTTTGTTGAAAAA
Found at i:11416 original size:39 final size:39
Alignment explanation
Indices: 11275--11416 Score: 88
Period size: 39 Copynumber: 3.5 Consensus size: 39
11265 TACTAGTATG
* * *
11275 TTGCGGCGTTTGTTGAAAAAATGCCACAATCATACCAAACTA
1 TTGCGGCGTTTG-T-AAAAAAAGGCACAA-CATACCAAATTA
* ** * * ** *
11317 TTGTGGCGTTTGTAAAAAACCGCTGCTAA-AGTACTACTTTG
1 TTGCGGCGTTTGTAAAAAAAGGC-AC-AACA-TACCAAATTA
* * **
11358 TTGCTGCATTTGTTGAAAAAGGCACAACATACCAAATTA
1 TTGCGGCGTTTGTAAAAAAAGGCACAACATACCAAATTA
11397 TTGCGGCGTTTGTAAAAAAA
1 TTGCGGCGTTTGTAAAAAAA
11417 ACACTGCTAA
Statistics
Matches: 70, Mismatches: 26, Indels: 11
0.65 0.24 0.10
Matches are distributed among these distances:
39 24 0.34
40 10 0.14
41 23 0.33
42 13 0.19
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (39 bp):
TTGCGGCGTTTGTAAAAAAAGGCACAACATACCAAATTA
Found at i:17180 original size:19 final size:20
Alignment explanation
Indices: 17156--17206 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
17146 CGGCCAAGAG
* *
17156 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
17175 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
17195 CATGTATTTTCA
1 CATGTATTTTCA
17207 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:21375 original size:19 final size:20
Alignment explanation
Indices: 21351--21401 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
21341 CGGCCAAGAG
* *
21351 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
21370 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
21390 CATGTATTTTCA
1 CATGTATTTTCA
21402 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:25805 original size:147 final size:148
Alignment explanation
Indices: 25536--25825 Score: 501
Period size: 147 Copynumber: 2.0 Consensus size: 148
25526 CCGAAGTGCC
* *
25536 CCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAATCATATACATATA
1 CCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCATATA-ATATA
* *
25601 CTATGGATCAAGTATGTTTCTTTCAAAACCTCAAACATGTTCCAAAGAATATACATATGTCCCAA
65 CTAAGGATCAAGTATGTGTCTTTCAAAACCTCAAACATGTTCCAAAGAATATACATATGTCCCAA
*
25666 AGAACTGCGTAGAATTGCA
130 AGAACCGCGTAGAATTGCA
*
25685 CCGTAGTGCCCTATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCATAT-ATATAC
1 CCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCATATAATATAC
*
25749 TAAGGATCAAGTATGTGTCTTTCAAAACCTCACACATGTTCCAAAGAATATACATATGTCCCAAA
66 TAAGGATCAAGTATGTGTCTTTCAAAACCTCAAACATGTTCCAAAGAATATACATATGTCCCAAA
25814 GAACCGCGTAGA
131 GAACCGCGTAGA
25826 CCCTCTACCC
Statistics
Matches: 134, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
147 79 0.59
149 55 0.41
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (148 bp):
CCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCATATAATATAC
TAAGGATCAAGTATGTGTCTTTCAAAACCTCAAACATGTTCCAAAGAATATACATATGTCCCAAA
GAACCGCGTAGAATTGCA
Found at i:32911 original size:23 final size:23
Alignment explanation
Indices: 32885--32929 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
32875 CACCACAGCT
*
32885 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
32908 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
32930 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:33178 original size:149 final size:149
Alignment explanation
Indices: 32908--33211 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
32898 CGAAGTGCCC
* *
32908 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
32973 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAAACCTCAAACATGTTCCAAAGAATATA
66 CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAAACCTCAAACATGTTCCAAAGAATATA
33038 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
*
33057 CGTAGAATTGCACCGTAGTGCCCTATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
33122 CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAAACCTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAAACCTCAAACATGTTCCAAAGAATATA
33187 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
33206 CGTAGA
1 CGTAGA
33212 CCCTCTACCC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAAACCTCAAACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:33724 original size:19 final size:20
Alignment explanation
Indices: 33687--33724 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33677 TTTTTTCTTA
*
33687 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
33707 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
33725 TCTTGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:42243 original size:2 final size:2
Alignment explanation
Indices: 42238--42275 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
42228 AACCTAAACG
*
42238 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42276 GCAGATTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44310 original size:33 final size:34
Alignment explanation
Indices: 44256--44321 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
44246 TACCTAACTC
*
44256 TCACCTAACTAATTTGATGTAAGCAATGACATCT
1 TCACCTAACTAAATTGATGTAAGCAATGACATCT
44290 TCACCTAAC-AAATTGATGTAAGCAATGACATC
1 TCACCTAACTAAATTGATGTAAGCAATGACATC
44322 AAATTAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 22 0.71
34 9 0.29
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (34 bp):
TCACCTAACTAAATTGATGTAAGCAATGACATCT
Found at i:51365 original size:23 final size:23
Alignment explanation
Indices: 51335--51393 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
51325 GAATCGATCA
51335 CCCTTTGAAGGGGAACCGATTCC
1 CCCTTTGAAGGGGAACCGATTCC
51358 CCCTTTGAAGGGGAACCGATTCC
1 CCCTTTGAAGGGGAACCGATTCC
51381 CCCTTTGAAGGGG
1 CCCTTTGAAGGGG
51394 TTCTGGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (23 bp):
CCCTTTGAAGGGGAACCGATTCC
Found at i:58463 original size:33 final size:34
Alignment explanation
Indices: 58405--58470 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
58395 TACCTAACTC
*
58405 TCACCTAACAAATTTGATGTAAGCAATGACATCT
1 TCACCTAACAAATTTAATGTAAGCAATGACATCT
*
58439 TCACCTAACAAA-TTAATGTAAGCAATGCCATC
1 TCACCTAACAAATTTAATGTAAGCAATGACATC
58471 ATATTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 18 0.60
34 12 0.40
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (34 bp):
TCACCTAACAAATTTAATGTAAGCAATGACATCT
Found at i:59536 original size:8 final size:8
Alignment explanation
Indices: 59523--59564 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
59513 TCACAATCAT
59523 TTATTTAA
1 TTATTTAA
59531 TTATTTAA
1 TTATTTAA
59539 TTATTT-A
1 TTATTTAA
* *
59546 TTTTTCTAT
1 TTATT-TAA
59555 TTATTTAA
1 TTATTTAA
59563 TT
1 TT
59565 TGAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 19 0.68
9 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATTTAA
Found at i:64546 original size:2 final size:2
Alignment explanation
Indices: 64539--64572 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
64529 AGTTATTTTC
*
64539 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64573 ATTATTACGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65909 original size:23 final size:23
Alignment explanation
Indices: 65879--65959 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 23
65869 CTCTATTCCT
65879 TCTTTATTTCATTTCATTTCTTA
1 TCTTTATTTCATTTCATTTCTTA
* *
65902 TCTTTA-TT-ATTTCATTTATTCT
1 TCTTTATTTCATTTCATTTCTT-A
*
65924 TCCTTTATTAATCATCTTCCTTTTCTTA
1 T-CTTTATT--TCAT-TT-CATTTCTTA
65952 TCTTTATT
1 TCTTTATT
65960 GCAGCCAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 11 0.24
22 3 0.07
23 11 0.24
24 1 0.02
26 1 0.02
27 9 0.20
28 3 0.07
29 6 0.13
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (23 bp):
TCTTTATTTCATTTCATTTCTTA
Found at i:65915 original size:26 final size:26
Alignment explanation
Indices: 65882--65959 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
65872 TATTCCTTCT
65882 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
65908 TTATTTCATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
* *
65931 TTA-ATCATCTTCCTTTTCTTATCTTTA
1 TTATTTCAT-TT-CATTTCTTATCTTTA
65958 TT
1 TT
65960 GCAGCCAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 4 0.09
23 10 0.23
24 5 0.12
25 1 0.02
26 16 0.37
27 7 0.16
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTATCTTTA
Found at i:66217 original size:26 final size:28
Alignment explanation
Indices: 66188--66251 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
66178 CATAAAGAAA
*
66188 AGAAAAGGCA-AAAAGAAAAA-AAATTC
1 AGAAAAGGAAGAAAAGAAAAAGAAATTC
66214 AGAAAA-GAAGAAAAGAAAAAGAAATTC
1 AGAAAAGGAAGAAAAGAAAAAGAAATTC
66241 A-AAAAGAGAAG
1 AGAAAAG-GAAG
66252 GCAAGCCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 2 0.06
26 20 0.61
27 7 0.21
28 4 0.12
ACGTcount: A:0.70, C:0.05, G:0.19, T:0.06
Consensus pattern (28 bp):
AGAAAAGGAAGAAAAGAAAAAGAAATTC
Found at i:69172 original size:2 final size:2
Alignment explanation
Indices: 69165--69198 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
69155 ATTTTCATAC
*
69165 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69199 GTTATTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70331 original size:23 final size:25
Alignment explanation
Indices: 70291--70341 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 25
70281 TATCCCTTCT
70291 TTATTTCATTTTATTTCTTATCTTTA
1 TTATTTCATTTTATTTCTTAT-TTTA
70317 TTATTT-A-TTTA-TTCTTATTTTA
1 TTATTTCATTTTATTTCTTATTTTA
70339 TTA
1 TTA
70342 ATCATCTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.28
23 7 0.28
24 4 0.16
25 1 0.04
26 6 0.24
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (25 bp):
TTATTTCATTTTATTTCTTATTTTA
Found at i:73235 original size:25 final size:24
Alignment explanation
Indices: 73181--73262 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
73171 ATCTTTGGGT
* *
73181 ACTCCTGTATCAATGCAAATATGC
1 ACTCCTGTATCAGTGCAAGTATGC
*
73205 ACTCCTGTATACAGTACAAGTATGC
1 ACTCCTGTAT-CAGTGCAAGTATGC
* *
73230 ATTCCTGTGTCAGTGCAAGTATGC
1 ACTCCTGTATCAGTGCAAGTATGC
* *
73254 TCTCATGTA
1 ACTCCTGTA
73263 AATAGTGCAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 28 0.60
25 19 0.40
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (24 bp):
ACTCCTGTATCAGTGCAAGTATGC
Found at i:75528 original size:12 final size:12
Alignment explanation
Indices: 75511--75546 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
75501 CCTACTACCA
75511 TCTCTTCTTCCT
1 TCTCTTCTTCCT
75523 TCTCTTCTTCCT
1 TCTCTTCTTCCT
75535 TCTCTTCTTCCT
1 TCTCTTCTTCCT
75547 CCACTGCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTCTTCTTCCT
Found at i:78102 original size:183 final size:183
Alignment explanation
Indices: 77865--78262 Score: 625
Period size: 183 Copynumber: 2.2 Consensus size: 183
77855 TACAATTAAT
* * * *
77865 ATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGCCATATTTTAACCTGTTA
1 ATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTACCATATTTTAACCTGTTA
* * * * *
77930 TATTGTTATGTATCGAAACATTTTTATAAAGTATCGATACTTTGTAGGCGCTATTACTGCTTTTC
66 TATTGTTATGTATCGAAACATGTTTATAAAATATCGATACTTTATAGGCGCTATTACTGATGTTC
* *
77995 TTTTAAATTACGAAAGTGTCGATACTTATTTAAATGGAATCGATATTTTCAAC
131 TTTTAAATTACAAAAGTGTCGATACTTATTTAAATGGAATCGATACTTTCAAC
* * *
78048 ATATCCGGTAGCGCTTTACCGGTTTTGTCATTATGAAACCGATTTTATCATATTTTTACCTGTTA
1 ATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTACCATATTTTAACCTGTTA
*
78113 TATTGTTATGTATCGATACATGTTTATAAAATATCGATACTTTATAGGCGCTATTACTGATGTTC
66 TATTGTTATGTATCGAAACATGTTTATAAAATATCGATACTTTATAGGCGCTATTACTGATGTTC
* * *
78178 TTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATTGATACTTTCAAC
131 TTTTAAATTACAAAAGTGTCGATACTTATTTAAATGGAATCGATACTTTCAAC
*
78231 ATATCCGGTAGCGCTTTACCGGTGTTGTCATA
1 ATATCCGGTAGCGCTTTACCGGTTTTGTCATA
78263 TTTTTACCAA
Statistics
Matches: 195, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
183 195 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.41
Consensus pattern (183 bp):
ATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTACCATATTTTAACCTGTTA
TATTGTTATGTATCGAAACATGTTTATAAAATATCGATACTTTATAGGCGCTATTACTGATGTTC
TTTTAAATTACAAAAGTGTCGATACTTATTTAAATGGAATCGATACTTTCAAC
Found at i:78470 original size:11 final size:11
Alignment explanation
Indices: 78454--78478 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
78444 TTCCGATAAC
78454 GTCGTATATTA
1 GTCGTATATTA
78465 GTCGTATATTA
1 GTCGTATATTA
78476 GTC
1 GTC
78479 CGCCCTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (11 bp):
GTCGTATATTA
Found at i:85186 original size:11 final size:10
Alignment explanation
Indices: 85162--85204 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
85152 TTTTTGAAAA
85162 TTTTGGCTTT
1 TTTTGGCTTT
85172 TTTTGGCTCTT
1 TTTTGGCT-TT
85183 TTTT-G-TTT
1 TTTTGGCTTT
*
85191 TTTTGCCTTT
1 TTTTGGCTTT
85201 TTTT
1 TTTT
85205 TTTTTTGCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 6 0.21
9 1 0.03
10 16 0.55
11 6 0.21
ACGTcount: A:0.00, C:0.12, G:0.14, T:0.74
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:85191 original size:17 final size:16
Alignment explanation
Indices: 85170--85241 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
85160 AATTTTGGCT
85170 TTTTTTGGCTCTTTTTTG
1 TTTTTT-GC-CTTTTTTG
*
85188 TTTTTTTGCCTTTTTTT
1 -TTTTTTGCCTTTTTTG
85205 TTTTTTGCCTTTTTTTG
1 TTTTTTGCC-TTTTTTG
85222 TTTTTTG--TTTTTTG
1 TTTTTTGCCTTTTTTG
85236 TTTTTT
1 TTTTTT
85242 TGAAAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
14 13 0.26
16 9 0.18
17 20 0.40
18 2 0.04
19 6 0.12
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (16 bp):
TTTTTTGCCTTTTTTG
Found at i:85201 original size:16 final size:16
Alignment explanation
Indices: 85182--85243 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
85172 TTTTGGCTCT
85182 TTTTTGTTTTTTTGCC
1 TTTTTGTTTTTTTGCC
*
85198 TTTTTTTTTTTTTGCC
1 TTTTTGTTTTTTTGCC
* *
85214 TTTTTTTGTTTTTTG-T
1 TTTTTGT-TTTTTTGCC
85230 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
85244 AAAAAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
15 7 0.17
16 28 0.67
17 7 0.17
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.82
Consensus pattern (16 bp):
TTTTTGTTTTTTTGCC
Found at i:85217 original size:10 final size:9
Alignment explanation
Indices: 85162--85243 Score: 63
Period size: 7 Copynumber: 9.7 Consensus size: 9
85152 TTTTTGAAAA
*
85162 TTTTGGCTT
1 TTTTTGCTT
85171 TTTTTGGCTCT
1 TTTTT-GCT-T
85182 TTTTTG-TT
1 TTTTTGCTT
*
85190 TTTTTGCCT
1 TTTTTGCTT
85199 TTTTT--TT
1 TTTTTGCTT
85206 TTTTTGCCTT
1 TTTTTG-CTT
85216 TTTTTG--T
1 TTTTTGCTT
85223 TTTTTG--T
1 TTTTTGCTT
85230 TTTTTG-TT
1 TTTTTGCTT
85238 TTTTTG
1 TTTTTG
85244 AAAAAAAATA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
7 20 0.32
8 14 0.22
9 11 0.17
10 12 0.19
11 6 0.10
ACGTcount: A:0.00, C:0.09, G:0.13, T:0.78
Consensus pattern (9 bp):
TTTTTGCTT
Found at i:85219 original size:34 final size:33
Alignment explanation
Indices: 85169--85243 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 33
85159 AAATTTTGGC
*
85169 TTTTTTTGGCTCTTTTTTGTTTTTTTGCCTTTTTT-
1 TTTTTTTGCCTCTTTTTTG-TTTTTTG--TTTTTTG
85204 TTTTTTTGCCT-TTTTTTGTTTTTTGTTTTTTG
1 TTTTTTTGCCTCTTTTTTGTTTTTTGTTTTTTG
85236 TTTTTTTG
1 TTTTTTTG
85244 AAAAAAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 6 0.16
32 8 0.21
33 7 0.18
34 7 0.18
35 10 0.26
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (33 bp):
TTTTTTTGCCTCTTTTTTGTTTTTTGTTTTTTG
Found at i:94595 original size:44 final size:42
Alignment explanation
Indices: 94507--94690 Score: 160
Period size: 42 Copynumber: 4.3 Consensus size: 42
94497 ATTAGCGGAA
* * *
94507 TTTGTGGAAAAAATGCCACTAAAGACCAGAGAATCAGC-GACG
1 TTTGTGGAAAAAACGCCACTAAAGACAAGAGAATTAGCAG-CG
* *
94549 TTTATGGTAAAAAAGCGCCACTAAAGATAAGAGAATTAGCAGCG
1 TTTGTGG-AAAAAA-CGCCACTAAAGACAAGAGAATTAGCAGCG
* * * *
94593 TTTGT-GACCAAAACACCACTAAAGACAAGAGAGTTAG-AGGCA
1 TTTGTGGA-AAAAACGCCACTAAAGACAAGAGAATTAGCA-GCG
** *
94635 TTTGTGGGCTAAAACG-CACTAAAGATAAGAGAATTAGCAGCG
1 TTTGT-GGAAAAAACGCCACTAAAGACAAGAGAATTAGCAGCG
*
94677 TTTGTTGACAAAAA
1 TTTGTGGA-AAAAA
94691 ATGCTACTAT
Statistics
Matches: 113, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
41 2 0.02
42 65 0.58
43 17 0.15
44 28 0.25
45 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (42 bp):
TTTGTGGAAAAAACGCCACTAAAGACAAGAGAATTAGCAGCG
Found at i:96144 original size:18 final size:18
Alignment explanation
Indices: 96086--96145 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
96076 AATATGAACT
96086 ATATAATATGTGGATATA--
1 ATATAATATGT--ATATACC
*
96104 ATATAATATGATTTACGTACC
1 ATATAATATG-TATA--TACC
96125 ATATAATATGTATATACC
1 ATATAATATGTATATACC
96143 ATA
1 ATA
96146 ATTTGAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 2 0.06
18 17 0.49
19 3 0.09
20 3 0.09
21 10 0.29
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (18 bp):
ATATAATATGTATATACC
Found at i:98331 original size:14 final size:15
Alignment explanation
Indices: 98288--98339 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
98278 CATATTACAT
98288 TCATTGTCTTTATCT-
1 TCATTGTCTTTAT-TA
98303 T-ATT-T-TTTCATTA
1 TCATTGTCTTT-ATTA
98316 TC-TTGTCTTTATTA
1 TCATTGTCTTTATTA
98330 TCATTGTCTT
1 TCATTGTCTT
98340 AACCTTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
12 4 0.13
13 6 0.19
14 10 0.32
15 11 0.35
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.63
Consensus pattern (15 bp):
TCATTGTCTTTATTA
Found at i:104050 original size:17 final size:17
Alignment explanation
Indices: 104030--104082 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
104020 TTAATAAAGT
104030 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* * *
104047 TAGTCCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
104064 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
104081 TA
1 TA
104083 AATCTTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:106106 original size:2 final size:2
Alignment explanation
Indices: 106099--106202 Score: 208
Period size: 2 Copynumber: 52.0 Consensus size: 2
106089 CATGAGTAGA
106099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106183 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
106203 GAATTAAAAT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112169 original size:111 final size:111
Alignment explanation
Indices: 111975--112188 Score: 311
Period size: 111 Copynumber: 1.9 Consensus size: 111
111965 GTTGGAGGAA
* * *
111975 GAATACTTGCAGGTTCCTCGGCTTTGTGTTGAGAGCCTTATTGTTCGTGACGGGGAAGAATACTT
1 GAATACTTGCAGGTTCCTCGACTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGAAGAATACTT
* *
112040 GTAGGTTCCTCGGCTTTGTGCTTAGAGCCTTACTGTTCATGATGGT
66 GCAGGTTCCTCGGCTTTGTGCTCAGAGCCTTACTGTTCATGATGGT
** * ** *
112086 GAATACTTGTTGGTTCCTCGACTTTGTGCTGAGAGCCTTACTGTTTGTGACGGGGTTGATTACTT
1 GAATACTTGCAGGTTCCTCGACTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGAAGAATACTT
* *
112151 GCAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTC
66 GCAGGTTCCTCGGCTTTGTGCTCAGAGCCTTACTGTTC
112189 GTGACGGGGT
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
111 90 1.00
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.37
Consensus pattern (111 bp):
GAATACTTGCAGGTTCCTCGACTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGAAGAATACTT
GCAGGTTCCTCGGCTTTGTGCTCAGAGCCTTACTGTTCATGATGGT
Found at i:112198 original size:57 final size:57
Alignment explanation
Indices: 111975--112200 Score: 287
Period size: 57 Copynumber: 4.0 Consensus size: 57
111965 GTTGGAGGAA
* * **
111975 GAATACTTGCAGGTTCCTCGGCTTTGTGTTGAGAGCCTTATTGTTCGTGACGGGGAA
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * * *
112032 GAATACTTGTAGGTTCCTCGGCTTTGTGCTTAGAGCCTTACTGTTCATGA--TGG-T
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
** * *
112086 GAATACTTGTTGGTTCCTCGACTTTGTGCTGAGAGCCTTACTGTTTGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * * *
112143 GATTACTTGCAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
112200 G
1 G
112201 TAAGCCTACA
Statistics
Matches: 145, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
54 45 0.31
55 2 0.01
56 2 0.01
57 96 0.66
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.37
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
Found at i:114009 original size:85 final size:85
Alignment explanation
Indices: 113903--114063 Score: 232
Period size: 85 Copynumber: 1.9 Consensus size: 85
113893 AATATAATTC
* * * * *
113903 TTAATATAATATCTTAAATCCTAATTAAAACACTTACAACCATTTAAACTAAAATATCTAAAACA
1 TTAAAATAATACCCTAAATCCTAATTAAAACACTAACAACCATTTAAACTAAAATACCTAAAACA
*
113968 TAGATAAAATAAAACACTAT
66 AAGATAAAATAAAACACTAT
* * * *
113988 TTAAAATAATACCCTAAATCCTAATTGAAATACTAACATCTATTTAAACTAAAATACCTAAAACA
1 TTAAAATAATACCCTAAATCCTAATTAAAACACTAACAACCATTTAAACTAAAATACCTAAAACA
114053 AAGATAAAATA
66 AAGATAAAATA
114064 TAATGTTTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 66 1.00
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (85 bp):
TTAAAATAATACCCTAAATCCTAATTAAAACACTAACAACCATTTAAACTAAAATACCTAAAACA
AAGATAAAATAAAACACTAT
Found at i:117945 original size:22 final size:22
Alignment explanation
Indices: 117920--117979 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
117910 AAAGTTTGCT
*
117920 AAAAATAGAATGGAAATAAAAC
1 AAAAATAGAATGAAAATAAAAC
*
117942 AAAAATAAAATGAAAATAAAAC
1 AAAAATAGAATGAAAATAAAAC
*
117964 CAAAATAGAAT-AAAAT
1 AAAAATAGAATGAAAAT
117980 GGGTTGCCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.15
22 29 0.85
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAAATAGAATGAAAATAAAAC
Found at i:124454 original size:24 final size:24
Alignment explanation
Indices: 124422--124467 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
124412 CCAGTTACGG
124422 AGTTACTATAGTAAGAAGTGACAA
1 AGTTACTATAGTAAGAAGTGACAA
124446 AGTTACTATAGTAAGAAGTGAC
1 AGTTACTATAGTAAGAAGTGAC
124468 TCCTACGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (24 bp):
AGTTACTATAGTAAGAAGTGACAA
Found at i:128302 original size:30 final size:30
Alignment explanation
Indices: 128246--128315 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
128236 GAGAATGACC
* * *
128246 ACTTTGGTC-CCTGAACTTTCCCAATTTTAT
1 ACTTTGGTCACCTAAACTTT-CAAAATTTAT
128276 ACTTTGGTCACC-AAACTTTCAAAATTTAT
1 ACTTTGGTCACCTAAACTTTCAAAATTTAT
**
128305 GGTTTGGTCAC
1 ACTTTGGTCAC
128316 TAACAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 17 0.50
30 15 0.44
31 2 0.06
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (30 bp):
ACTTTGGTCACCTAAACTTTCAAAATTTAT
Found at i:134304 original size:158 final size:158
Alignment explanation
Indices: 134012--134327 Score: 587
Period size: 158 Copynumber: 2.0 Consensus size: 158
134002 CTACATCCAG
134012 GAAAGCATTAGTCGTTGTGTCATCTTAATGACAAACCACGATTTAAACCACTCTAAAGATAAGTA
1 GAAAGCATTAGTCGTTGTGTCATCTTAATGACAAACCACGATTTAAACCACTCTAAAGATAAGTA
*
134077 TGCTTTTATCTATGTTGATTATATTCTTATCAACTTCTTTTATTTTAACCAGGTTCAAATAGTAG
66 TGCTTTTATCTATGTTGATTATATTCTTATCAACTTCTTTTATTTTAACCAGGTTCAAATAGTAA
134142 AAGTTTGGCAACACAAGATACTTTCACA
131 AAGTTTGGCAACACAAGATACTTTCACA
* *
134170 GAAAGCATTAGTCGTTGTGTCATCTTAATGACAAACCACTATTTAAACTACTCTAAAGATAAGTA
1 GAAAGCATTAGTCGTTGTGTCATCTTAATGACAAACCACGATTTAAACCACTCTAAAGATAAGTA
*
134235 TGTTTTTATCTATGTTGATTATATTCTTATCAACTTCTTTTATTTTAACCAGGTTCAAATAGTAA
66 TGCTTTTATCTATGTTGATTATATTCTTATCAACTTCTTTTATTTTAACCAGGTTCAAATAGTAA
*
134300 AAGTTTGTCAACACAAGATACTTTCACA
131 AAGTTTGGCAACACAAGATACTTTCACA
134328 AAGGTTATCA
Statistics
Matches: 153, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 153 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (158 bp):
GAAAGCATTAGTCGTTGTGTCATCTTAATGACAAACCACGATTTAAACCACTCTAAAGATAAGTA
TGCTTTTATCTATGTTGATTATATTCTTATCAACTTCTTTTATTTTAACCAGGTTCAAATAGTAA
AAGTTTGGCAACACAAGATACTTTCACA
Found at i:136775 original size:7 final size:6
Alignment explanation
Indices: 136759--136830 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
136749 TTCACTTTGG
* * * * *
136759 TTTTTC TTTTTC TTTTT- TTCTATC TTATTC TTATTC TTTTCC TTTTCC
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * *
136807 TTTTTC TTATTC TATTTA TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC
136831 CTCTTTTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
5 2 0.04
6 48 0.92
7 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:136813 original size:24 final size:26
Alignment explanation
Indices: 136781--136837 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
136771 TTTTTTTCTA
*
136781 TCTTATTCTTATTCT-TTTCCTTTTCC
1 TCTT-TTCTTATTCTATTTACTTTTCC
*
136807 T-TTTTCTTATTCTATTTATTTTTCC
1 TCTTTTCTTATTCTATTTACTTTTCC
136832 TCTTTT
1 TCTTTT
136838 TTTGTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 10 0.37
25 12 0.44
26 5 0.19
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (26 bp):
TCTTTTCTTATTCTATTTACTTTTCC
Found at i:138426 original size:27 final size:27
Alignment explanation
Indices: 138388--138443 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
138378 CAATATGAAT
138388 TAAAATAACTAATCAAACCTCCAACAA
1 TAAAATAACTAATCAAACCTCCAACAA
138415 TAAAATAACTAATCAAACCTCCAACAA
1 TAAAATAACTAATCAAACCTCCAACAA
138442 TA
1 TA
138444 CAATCACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (27 bp):
TAAAATAACTAATCAAACCTCCAACAA
Found at i:141186 original size:35 final size:35
Alignment explanation
Indices: 141001--141188 Score: 141
Period size: 35 Copynumber: 5.3 Consensus size: 35
140991 TATTGTGGAC
* ** *
141001 TTTGGAAGCACCTTTTCAGAGTGAAAAGTTATGACC
1 TTTGGAAGCACCTATT-AGAGTGAAAAGGCATGACT
* * * *
141037 CTTGGAAGCATC-ACTT-GAAGTGAAAAGACACGACT
1 TTTGGAAGCACCTA-TTAG-AGTGAAAAGGCATGACT
* * * *
141072 TTTGGAGGCACC-ACTTGGAGTGAAAAGACACGACT
1 TTTGGAAGCACCTA-TTAGAGTGAAAAGGCATGACT
* *
141107 TTTGGAAGTACCTCTTAGAGTGAAAAGGCATGACT
1 TTTGGAAGCACCTATTAGAGTGAAAAGGCATGACT
** *
141142 TTTAAAAGCACCTATTATG-GTGAAAAGGTATGACT
1 TTTGGAAGCACCTATTA-GAGTGAAAAGGCATGACT
*
141177 TTCGGAAGCACC
1 TTTGGAAGCACC
141189 CTTTGGTGAA
Statistics
Matches: 123, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
34 1 0.01
35 108 0.88
36 14 0.11
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (35 bp):
TTTGGAAGCACCTATTAGAGTGAAAAGGCATGACT
Found at i:148568 original size:32 final size:32
Alignment explanation
Indices: 148506--148568 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
148496 AGAAATTAAT
* **
148506 ATTTGTTATAAATTATTATTTTGATTAAATAA
1 ATTTGTCATAAATTATTATTTTGACAAAATAA
* *
148538 ATTTGTCATAATTTTTTATTTTGACAAAATA
1 ATTTGTCATAAATTATTATTTTGACAAAATA
148569 TTGTGAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (32 bp):
ATTTGTCATAAATTATTATTTTGACAAAATAA
Found at i:148707 original size:197 final size:197
Alignment explanation
Indices: 148231--149010 Score: 854
Period size: 198 Copynumber: 3.9 Consensus size: 197
148221 CTTTTTACTA
* * *
148231 TGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAAGTTTTTATAA
1 TGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCATAA-TTTTTATAT
* * * * *
148296 TGAGAAATTAATATTTTTTATAAATTTTTATTTTGATTAAATAAATTTGTCACT-ATTTTTTATT
65 TAAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCA-TAATTTTTTATT
* * * * * * *
148360 TCGACAAAATATTGGGAGGAAATAAATTTGAGA-GAATTGTTTACTTTGACTAAATTTAAC-GTG
129 TTGACAAAATATTGTGACGAAATAAATTTGACATAAATT-TTTATTTTGACTAAATTT-ACTATG
148423 TTATTG
192 TTATTG
* * * * * * *
148429 TGACTAAATCATTTTGTTGCAATTTGTTATTGTGAAAGAGTATTACTTGTTATAGATTTATATGA
1 TGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCATA-ATTTTTAT-A
* * *
148494 -TAAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCATAATTTTTTATT
64 TTAAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCATAATTTTTTATT
* * * * *
148558 TTGACAAAATATTGTGA-AAAATAAAGTTGTCATAAATTTTGATTTTGACTAAATTTTCTATGTT
129 TTGACAAAATATTGTGACGAAATAAATTTGACATAAATTTTTATTTTGACTAAATTTACTATGTT
148622 ATTG
194 ATTG
* * * *
148626 TAAATAAATAAATTTGTTGCAATTTGTTAGTGTGAAAGAATATTATTTGTCATAATTTTTTATAT
1 TGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCATAA-TTTTTATAT
* * * * * *
148691 TAAGGATTTAATATTTGTTATAAATTGTTATTATGACTAACTAAATTTGTCAAAAGTTGTTATTT
65 TAAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCATAATTTTTTATTT
* * * * *
148756 TGAAAAAACAATTGTGACGAAATAAATTTAACATAAATTTTTATTTTGATTAAATTTAATATGTT
130 TGACAAAA-TATTGTGACGAAATAAATTTGACATAAATTTTTATTTTGACTAAATTTACTATGTT
148821 ATTG
194 ATTG
* * * * *
148825 TGACTAAATAAAATT-TTATAA-TTGATTATTGTGAAAAAATATTATTTTTCATAACTTTTAATA
1 TGACTAAATAAATTTGTTACAATTTG-TTATTGTGAAAGAATATTATTTGTCATAA-TTTTTATA
* * * * ** *
148888 TTAAGAAATTAATATTTATTATAATTTGTTAGTATAACTATTTAAATTTGTCATAACTTTTTATT
64 TTAAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCATAATTTTTTATT
* * * * **
148953 TTGATAAAATATTTTGACTAAATAAATTTGACATAATTTTTTATTTCAACTAAATTTA
129 TTGACAAAATATTGTGACGAAATAAATTTGACATAAATTTTTATTTTGACTAAATTTA
149011 ATTTGTTAAT
Statistics
Matches: 493, Mismatches: 79, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
196 3 0.01
197 195 0.40
198 238 0.48
199 57 0.12
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (197 bp):
TGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCATAATTTTTATATT
AAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCATAATTTTTTATTTT
GACAAAATATTGTGACGAAATAAATTTGACATAAATTTTTATTTTGACTAAATTTACTATGTTAT
TG
Found at i:148965 original size:395 final size:395
Alignment explanation
Indices: 148235--149009 Score: 916
Period size: 395 Copynumber: 2.0 Consensus size: 395
148225 TTACTATGAC
* * *
148235 TAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAAGTTTTTATAATGAG
1 TAAATAAATTTGTTACAATTTGTTAGTGTGAAAGAATATTATTTGTCACAAGTTTTTATAATAAG
* * * * ** * * *
148300 AAATTAATATTTTTTATAAATTTTTATTTTGATTAAATAAATTTGTCACTATTTTTTATTTCGAC
66 AAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTCGAA
* * * * * *
148365 AAAATATTGGGAGGAAATAAATTTGAGAGAATTGTTTACTTTGACTAAATTTAACGTGTTATTGT
131 AAAAAATTGGGACGAAATAAATTTAACAAAATTGTTTACTTTGACTAAATTTAACATGTTATTGT
* ** * * *
148430 GACTAAATCATTTTGTTGCAATTTGTTATTGTGAAAGAGTATTACTTGTTATAGATTTATATGAT
196 GACTAAATAAAATTGTTACAATTTGTTATTGTGAAAAAATATTACTTGTTATAGATTTATAT-AT
* * * * * *
148495 AAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCATAATTTTTTATTTT
260 AAGAAATTAATATTTATTATAAATTATTAGTATAACTAAATAAATTTGTCATAACTTTTTATTTT
* **
148560 GACAAAATATTGTGA-AAAATAAAGTTGTCATAAATTTTGATTTTGACTAAATTTTCTATGTTAT
325 GACAAAATATTGTGACAAAATAAAGTTGACATAAATTTTGATTTCAACTAAATTTTCTATGTTAT
148624 TGTAAA
390 TGTAAA
* * * *
148630 TAAATAAATTTGTTGCAATTTGTTAGTGTGAAAGAATATTATTTGTCATAATTTTTTATATTAAG
1 TAAATAAATTTGTTACAATTTGTTAGTGTGAAAGAATATTATTTGTCACAAGTTTTTATAATAAG
* * * *
148695 GATTTAATATTTGTTATAAATTGTTATTATGACTAACTAAATTTGTCAAAAGTTGTTATTTTGAA
66 AAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTCGAA
* * * *
148760 AAAACAATTGTGACGAAATAAATTTAACATAAATT-TTTATTTTGATTAAATTTAATATGTTATT
131 AAAA-AATTGGGACGAAATAAATTTAACA-AAATTGTTTACTTTGACTAAATTTAACATGTTATT
* *
148824 GTGACTAAATAAAATT-TTATAA-TTGATTATTGTGAAAAAATATTA-TTTTTCATA-ACTTT-T
194 GTGACTAAATAAAATTGTTACAATTTG-TTATTGTGAAAAAATATTACTTGTT-ATAGA-TTTAT
* * **
148884 AATATTAAGAAATTAATATTTATTATAATTTGTTAGTATAACTATTTAAATTTGTCATAACTTTT
256 -ATA-TAAGAAATTAATATTTATTATAAATTATTAGTATAACTAAATAAATTTGTCATAACTTTT
* * * * * *
148949 TATTTTGATAAAATATTTTGACTAAATAAATTTGACATAATTTTTTATTTCAACTAAATTT
319 TATTTTGACAAAATATTGTGACAAAATAAAGTTGACATAAATTTTGATTTCAACTAAATTT
149010 AATTTGTTAA
Statistics
Matches: 315, Mismatches: 57, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
394 10 0.03
395 212 0.67
396 89 0.28
397 4 0.01
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (395 bp):
TAAATAAATTTGTTACAATTTGTTAGTGTGAAAGAATATTATTTGTCACAAGTTTTTATAATAAG
AAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTCGAA
AAAAAATTGGGACGAAATAAATTTAACAAAATTGTTTACTTTGACTAAATTTAACATGTTATTGT
GACTAAATAAAATTGTTACAATTTGTTATTGTGAAAAAATATTACTTGTTATAGATTTATATATA
AGAAATTAATATTTATTATAAATTATTAGTATAACTAAATAAATTTGTCATAACTTTTTATTTTG
ACAAAATATTGTGACAAAATAAAGTTGACATAAATTTTGATTTCAACTAAATTTTCTATGTTATT
GTAAA
Found at i:158545 original size:22 final size:20
Alignment explanation
Indices: 158499--158545 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
158489 AACTTGAAAA
158499 TAAAAGAAAAATGAAAACTT
1 TAAAAGAAAAATGAAAACTT
* *
158519 GAAAAGTAAAAATAGAAAGCTT
1 TAAAAG-AAAAAT-GAAAACTT
158541 TAAAA
1 TAAAA
158546 AATTAGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 6 0.27
22 11 0.50
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.19
Consensus pattern (20 bp):
TAAAAGAAAAATGAAAACTT
Found at i:159840 original size:25 final size:25
Alignment explanation
Indices: 159803--159856 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
159793 AAAAATTAAT
*
159803 AAAATATAGTATT-TTAAGAA-TTTA
1 AAAATATAATATTATTAA-AATTTTA
159827 AAAATATTAATATTATTAAAATTTTA
1 AAAATA-TAATATTATTAAAATTTTA
159853 AAAA
1 AAAA
159857 GTAATGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 8 0.31
26 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
AAAATATAATATTATTAAAATTTTA
Found at i:160318 original size:24 final size:24
Alignment explanation
Indices: 160291--160342 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
160281 TGGGACTAAT
160291 CTTTGATCGGACATAGTGTCAATA
1 CTTTGATCGGACATAGTGTCAATA
*
160315 CTTTTATCGGACATAGTGTCAATA
1 CTTTGATCGGACATAGTGTCAATA
160339 CTTT
1 CTTT
160343 CATTGCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
CTTTGATCGGACATAGTGTCAATA
Found at i:171680 original size:23 final size:22
Alignment explanation
Indices: 171653--171696 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
171643 TCTCAATTTC
* *
171653 ATCATTTTTTATACAGAGTTTTT
1 ATCATTCTTTAT-CAAAGTTTTT
171676 ATCATTCTTTATCAAAGTTTT
1 ATCATTCTTTATCAAAGTTTT
171697 ATGCCAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (22 bp):
ATCATTCTTTATCAAAGTTTTT
Found at i:181420 original size:22 final size:22
Alignment explanation
Indices: 181371--181412 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
181361 ACCAAGTAAA
*
181371 TATATATATGTATGTGTGTGTG
1 TATATATATATATGTGTGTGTG
181393 TATATATATATATGTGTGTG
1 TATATATATATATGTGTGTG
181413 ATGGTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (22 bp):
TATATATATATATGTGTGTGTG
Found at i:193530 original size:13 final size:13
Alignment explanation
Indices: 193514--193544 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
193504 GTAAATGTAT
193514 GTCATCAATGCGC
1 GTCATCAATGCGC
193527 GTCATCAATGCGC
1 GTCATCAATGCGC
193540 GTCAT
1 GTCAT
193545 AGATTTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (13 bp):
GTCATCAATGCGC
Found at i:201563 original size:2 final size:2
Alignment explanation
Indices: 201556--201588 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
201546 ATTACATTTA
201556 AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
201589 TTATTGCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:210524 original size:28 final size:28
Alignment explanation
Indices: 210471--210525 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
210461 GCGTACTCTA
**
210471 GCTAGCTCTTGAAGTGCCTCGTGCACTT
1 GCTAGCTCTTGAAGTGCCTCCCGCACTT
210499 GCTAGCTCTTGAAGTGCCTCCCGCACT
1 GCTAGCTCTTGAAGTGCCTCCCGCACT
210526 GACCATGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.15, C:0.33, G:0.24, T:0.29
Consensus pattern (28 bp):
GCTAGCTCTTGAAGTGCCTCCCGCACTT
Found at i:221560 original size:22 final size:22
Alignment explanation
Indices: 221535--221595 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
221525 GTGGTTTTGG
221535 TAAAAAGATATTTAAA-TAATAA
1 TAAAAAGATATTTAAAGTAA-AA
221557 T-AAAAGCA-ATTTAAAGTAAAA
1 TAAAAAG-ATATTTAAAGTAAAA
*
221578 CATAAAAGAT-TTTAAAGT
1 TA-AAAAGATATTTAAAGT
221596 TGAAAATGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
21 14 0.42
22 14 0.42
23 5 0.15
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (22 bp):
TAAAAAGATATTTAAAGTAAAA
Found at i:221561 original size:21 final size:23
Alignment explanation
Indices: 221537--221595 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
221527 GGTTTTGGTA
*
221537 AAAAGATATTTAAA-TAATA-AT
1 AAAAGATATTTAAAGTAAAACAT
221558 AAAAGCA-ATTTAAAGTAAAACAT
1 AAAAG-ATATTTAAAGTAAAACAT
221581 AAAAGAT-TTTAAAGT
1 AAAAGATATTTAAAGT
221596 TGAAAATGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 12 0.36
22 14 0.42
23 7 0.21
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.29
Consensus pattern (23 bp):
AAAAGATATTTAAAGTAAAACAT
Found at i:222458 original size:26 final size:26
Alignment explanation
Indices: 222427--222479 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
222417 CCAGAGGGCA
* *
222427 CGCTGACTAGATCTTCTAGAAACTAC
1 CGCTGACTAGACCTTCTAAAAACTAC
*
222453 CGCTGACTGGACCTTCTAAAAACTAC
1 CGCTGACTAGACCTTCTAAAAACTAC
222479 C
1 C
222480 ACATCGGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (26 bp):
CGCTGACTAGACCTTCTAAAAACTAC
Found at i:231658 original size:22 final size:21
Alignment explanation
Indices: 231611--231668 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
231601 GGGTTTTGGT
* *
231611 AAAAAGATATTTAAATAATAAT
1 AAAAA-ATATTTAAATAAAAAG
231633 AAAAAATATTTAAAGTAAAAAG
1 AAAAAATATTTAAA-TAAAAAG
*
231655 AAAATAT-TTTAAAT
1 AAAAAATATTTAAAT
231669 TTTAAAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 16 0.50
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
AAAAAATATTTAAATAAAAAG
Found at i:231660 original size:20 final size:21
Alignment explanation
Indices: 231610--231668 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
231600 GGGGTTTTGG
231610 TAAAAAGATATTTAAATAATAA
1 TAAAAA-ATATTTAAATAATAA
231632 TAAAAAATATTTAAAGTAA-AA
1 TAAAAAATATTTAAA-TAATAA
*
231653 -AGAAAATATTTTAAAT
1 TAAAAAATA-TTTAAAT
231669 TTTAAAATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 8 0.24
21 17 0.50
22 9 0.26
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
TAAAAAATATTTAAATAATAA
Found at i:233876 original size:21 final size:23
Alignment explanation
Indices: 233851--233892 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
233841 AAATTTAATA
233851 TGAAAAAT-ATTTT-GAATATAT
1 TGAAAAATGATTTTGGAATATAT
*
233872 TGAAATATGATTTTGGAATAT
1 TGAAAAATGATTTTGGAATAT
233893 TAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (23 bp):
TGAAAAATGATTTTGGAATATAT
Found at i:233893 original size:21 final size:20
Alignment explanation
Indices: 233847--233900 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
233837 TTTTAAATTT
*
233847 AATA-TGAAAAATATTTTGA
1 AATATTGAAATATATTTTGA
*
233866 ATATATTGAAATATGATTTTGG
1 A-ATATTGAAATAT-ATTTTGA
*
233888 AATATTAAAATAT
1 AATATTGAAATAT
233901 TTCAATTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 3 0.10
21 18 0.62
22 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (20 bp):
AATATTGAAATATATTTTGA
Found at i:235799 original size:16 final size:16
Alignment explanation
Indices: 235762--235802 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
235752 AAAAATGAAG
*
235762 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
235778 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
235793 AATAAATAAA
1 AATAAATAAA
235803 TAAATAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:235807 original size:12 final size:13
Alignment explanation
Indices: 235738--235817 Score: 51
Period size: 13 Copynumber: 6.4 Consensus size: 13
235728 CAGAGGAAAA
*
235738 AAATGAATAAATG
1 AAATAAATAAATG
*
235751 AAA-AAATGAA-G
1 AAATAAATAAATG
* * *
235762 AATAAAAATAAGTA
1 AA-ATAAATAAATG
* *
235776 AAAAAAATAAAAG
1 AAATAAATAAATG
*
235789 GAA-AAATAAAT-
1 AAATAAATAAATG
235800 AAATAAATAAATG
1 AAATAAATAAATG
235813 AAATA
1 AAATA
235818 TTAATATATA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
11 5 0.10
12 21 0.41
13 23 0.45
14 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (13 bp):
AAATAAATAAATG
Found at i:235902 original size:18 final size:18
Alignment explanation
Indices: 235823--235906 Score: 57
Period size: 21 Copynumber: 4.4 Consensus size: 18
235813 AAATATTAAT
235823 ATATATAAATATAAATGAGTA
1 ATATA-AAATAT-AAT-AGTA
* * *
235844 AAATAGAA-A-AATAATA
1 ATATAAAATATAATAGTA
235860 ATCATAACAATAATAATAGTA
1 AT-ATAA-AAT-ATAATAGTA
235881 ATATGAAAATATAATA-TA
1 ATAT-AAAATATAATAGTA
235899 ATATAAAA
1 ATATAAAA
235907 AAAACCAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
16 4 0.08
17 10 0.20
18 8 0.16
19 7 0.14
20 8 0.16
21 14 0.27
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (18 bp):
ATATAAAATATAATAGTA
Found at i:235907 original size:18 final size:19
Alignment explanation
Indices: 235857--235907 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
235847 TAGAAAAATA
*
235857 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
235877 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
235896 ATAATATAAAAA
1 ATAATATAAAAA
235908 AAACCAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:236116 original size:2 final size:2
Alignment explanation
Indices: 236111--236154 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
236101 AAAAAAAAAG
236111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
236153 TA
1 TA
236155 GTATTAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:236209 original size:23 final size:24
Alignment explanation
Indices: 236178--236226 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
236168 ACTAAATGAA
236178 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
236201 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
236225 TA
1 TA
236227 AAAAAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:236784 original size:37 final size:37
Alignment explanation
Indices: 236691--236792 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
236681 GTGCTTGTGG
* * * * *
236691 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
236728 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
236765 ATCCTATTTTTAGGAGTTTGATTCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
236793 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:239107 original size:106 final size:106
Alignment explanation
Indices: 237525--239099 Score: 2232
Period size: 106 Copynumber: 14.9 Consensus size: 106
237515 GCATTGTTCT
* * ** * *
237525 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGAGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
* * * *
237589 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
237631 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTTTG-AA-TGA-AA--T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * * *
237690 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
237732 G-GTCCAAGATCCTTCGATGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
237796 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * ** *
237837 GAGTCCAATATTCTACGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAAATGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
237902 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
237943 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
238008 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
238049 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
238114 CCAGAGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
238155 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
238220 CTAGCGGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
238261 GAGTCCAATATCCTTCGTTGTTAAGTTAAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
238326 CCAGCGGTCCCTTCGTTGTTAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
238367 GAGTCCAATATTCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
238432 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
238473 GAGTCCAATATCATTC-CTTGTAAAGTTAAAATTGGCCCTAAAATTGAGAAGTTTTTTATTGACA
1 GAGTCCAATATCCTTCGC-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
** *
238537 AGAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
238579 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
238644 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
238685 GAGTCCAATATCCTTCGCTATGAATTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
238750 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
238791 GAGTCCAATATCCTTCGTTGTTAAGTTAAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
238856 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
238897 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
238962 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
239003 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
239068 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
239100 TATTGTCTTG
Statistics
Matches: 1314, Mismatches: 144, Indels: 22
0.89 0.10 0.01
Matches are distributed among these distances:
100 78 0.06
101 5 0.00
102 2 0.00
103 4 0.00
104 2 0.00
105 6 0.00
106 1215 0.92
107 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:239943 original size:22 final size:22
Alignment explanation
Indices: 239917--239993 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
239907 TTATGTTTGG
239917 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
239939 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
239961 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
239983 TCAACGGTTTG
1 TCAAAGGTTTG
239994 ATGCGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:240685 original size:172 final size:173
Alignment explanation
Indices: 240388--240734 Score: 565
Period size: 172 Copynumber: 2.0 Consensus size: 173
240378 TAAATAAGCC
* *
240388 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTA
*
240453 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATATTCGAGTAAAGTGATTCAGTGATTCGGGAATG
240518 ATTATGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTATGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
* *
240563 CAAACAAGTGTTTCAGGGTGTTGAACCAATGATCAATTCATTATGATGTCTTC-A-A-TCCTACT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTACT
**
240625 CAAAATGTTTCTCTCTCTTGATGCTCTATGATATTCGAGTGTAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATATTCGAGTAAAGTGATTCAGTGATTCGGGAATG
*
240690 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTATGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
240735 TAGGGAATCT
Statistics
Matches: 162, Mismatches: 8, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
170 13 0.08
172 98 0.60
174 1 0.01
175 50 0.31
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTACT
CAAAATGTCTCTCTCTTGATGCTCTATGATATTCGAGTAAAGTGATTCAGTGATTCGGGAATGAT
TATGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:245409 original size:15 final size:16
Alignment explanation
Indices: 245375--245449 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
245365 TGTTAGAGGG
*
245375 AAAAAATGAAGAAATG
1 AAAAAATGAAGAAATA
245391 AAAAAATGAAG-AATA
1 AAAAAATGAAGAAATA
* *
245406 AAAATAAGTAAAAAAATA
1 AAAA-AA-TGAAGAAATA
* * *
245424 AATAAATAAATAAATA
1 AAAAAATGAAGAAATA
*
245440 AATAAATGAA
1 AAAAAATGAA
245450 ATATTAATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.14
16 31 0.62
17 5 0.10
18 7 0.14
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.17
Consensus pattern (16 bp):
AAAAAATGAAGAAATA
Found at i:245410 original size:13 final size:14
Alignment explanation
Indices: 245376--245433 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 14
245366 GTTAGAGGGA
245376 AAAAATGAAGAAAT
1 AAAAATGAAGAAAT
245390 GAAAAAATGAAG-AAT
1 --AAAAATGAAGAAAT
*
245405 AAAAAT-AAGTAA-
1 AAAAATGAAGAAAT
* *
245417 AAAAATAAATAAAT
1 AAAAATGAAGAAAT
245431 AAA
1 AAA
245434 TAAATAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 9 0.24
13 12 0.32
14 3 0.08
15 3 0.08
16 10 0.27
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (14 bp):
AAAAATGAAGAAAT
Found at i:245420 original size:12 final size:12
Alignment explanation
Indices: 245386--245452 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
245376 AAAAATGAAG
*
245386 AAATGAAAAAAT
1 AAATAAAAAAAT
* *
245398 GAAGAATAAAAAT
1 AAATAA-AAAAAT
*
245411 AAGTAAAAAAAT
1 AAATAAAAAAAT
*
245423 AAATAAATAAAT
1 AAATAAAAAAAT
*
245435 AAATAAATAAAT
1 AAATAAAAAAAT
245447 GAAATA
1 -AAATA
245453 TTAATATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
12 31 0.69
13 14 0.31
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.19
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:245428 original size:4 final size:4
Alignment explanation
Indices: 245407--245452 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
245397 TGAAGAATAA
* *
245407 AAAT AAGT AAAA AAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
245453 TTAATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:245769 original size:21 final size:20
Alignment explanation
Indices: 245742--245791 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
245732 GTAAAATATT
*
245742 TTAAAAAAAGTATATATA-TA
1 TTAAAAAAA-TAAATATAGTA
245762 TATAAAAATAATAAATATAGTA
1 T-TAAAAA-AATAAATATAGTA
245784 TTAAAAAA
1 TTAAAAAA
245792 TAACCAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
TTAAAAAAATAAATATAGTA
Found at i:245779 original size:19 final size:20
Alignment explanation
Indices: 245755--245848 Score: 66
Period size: 22 Copynumber: 4.4 Consensus size: 20
245745 AAAAAAGTAT
245755 ATATATATATAAAAATAATAA
1 ATATATATA-AAAAATAATAA
*
245776 ATATAGTATTAAAAAATAACCAA
1 ATATA-TA-TAAAAAATAA-TAA
*
245799 ATGA-ATATAAATAAATAAAAA
1 AT-ATATATAAA-AAATAATAA
* *
245820 ATATATGTATAGATAATAAT-A
1 ATATA--TATAAAAAATAATAA
245841 ATATATAT
1 ATATATAT
245849 TGTAAAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 20 0.33
22 23 0.38
23 12 0.20
24 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (20 bp):
ATATATATAAAAAATAATAA
Found at i:245835 original size:23 final size:23
Alignment explanation
Indices: 245755--245848 Score: 58
Period size: 23 Copynumber: 4.3 Consensus size: 23
245745 AAAAAAGTAT
*
245755 ATATATATATAAA-AATAAT-AA
1 ATATATGTATAAATAATAATAAA
* **
245776 ATATA-GTATTAAAAAATAACCAA
1 ATATATGTA-TAAATAATAATAAA
245799 ATGA-A--TATAAATAAATAA-AAA
1 AT-ATATGTATAAAT-AATAATAAA
* *
245820 ATATATGTATAGATAATAATAAT
1 ATATATGTATAAATAATAATAAA
245843 ATATAT
1 ATATAT
245849 TGTAAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
20 3 0.05
21 18 0.31
22 17 0.29
23 19 0.33
24 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
ATATATGTATAAATAATAATAAA
Found at i:246362 original size:37 final size:37
Alignment explanation
Indices: 246321--246425 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
246311 GTGCTTGTGG
* * *
246321 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
246358 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
246395 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
246426 GATGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:250405 original size:26 final size:26
Alignment explanation
Indices: 250376--250432 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
250366 CCATAGTGCT
* *
250376 TACACATAAGGTCGTGCCCACCATAA
1 TACACAAAAGGTCATGCCCACCATAA
250402 TACACAAAAGGTCATGCCCACCATAA
1 TACACAAAAGGTCATGCCCACCATAA
250428 TACAC
1 TACAC
250433 TTAGTGCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.32, G:0.12, T:0.18
Consensus pattern (26 bp):
TACACAAAAGGTCATGCCCACCATAA
Found at i:252110 original size:31 final size:31
Alignment explanation
Indices: 252060--252119 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
252050 AATTACTATT
*
252060 AAACCAACACACCTCAACCTTATCATCTTCC
1 AAACCAACAAACCTCAACCTTATCATCTTCC
* *
252091 AAACCAAGAAACCTTAACCTTATCATCTT
1 AAACCAACAAACCTCAACCTTATCATCTT
252120 GCTTAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.35, G:0.02, T:0.25
Consensus pattern (31 bp):
AAACCAACAAACCTCAACCTTATCATCTTCC
Found at i:254062 original size:11 final size:11
Alignment explanation
Indices: 254046--254073 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
254036 TCCTACTTGA
254046 CATTTTCTTAC
1 CATTTTCTTAC
254057 CATTTTCTTAC
1 CATTTTCTTAC
254068 CATTTT
1 CATTTT
254074 TACTTGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (11 bp):
CATTTTCTTAC
Found at i:262424 original size:19 final size:17
Alignment explanation
Indices: 262382--262422 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
262372 ATATATATTG
*
262382 TATATGTTTTCAAAACT
1 TATATATTTTCAAAACT
* *
262399 TATATATTTTTAAAACC
1 TATATATTTTCAAAACT
262416 TATATAT
1 TATATAT
262423 ATATATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATATTTTCAAAACT
Found at i:262449 original size:30 final size:30
Alignment explanation
Indices: 262401--262458 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
262391 TCAAAACTTA
* * *
262401 TATATTTTTAAAACCTATATATATATATAT
1 TATACTTTCAAAAACTATATATATATATAT
262431 TATACTTTCAAAAACTATATATATATAT
1 TATACTTTCAAAAACTATATATATATAT
262459 TGGAAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (30 bp):
TATACTTTCAAAAACTATATATATATATAT
Found at i:262465 original size:21 final size:21
Alignment explanation
Indices: 262422--262524 Score: 91
Period size: 21 Copynumber: 4.7 Consensus size: 21
262412 AACCTATATA
262422 TATATATATTATACTTTCAAAAAC
1 TATATATA-TATA--TTCAAAAAC
**
262446 TATATATATATATTGGAAAAC
1 TATATATATATATTCAAAAAC
* *
262467 TATATAATATGTTTTC-AAAAC
1 TATAT-ATATATATTCAAAAAC
*
262488 TATATTATATATTTTCAAAAAC
1 TATA-TATATATATTCAAAAAC
*
262510 CATATATCATATATT
1 TATATAT-ATATATT
262525 TTCATATATA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
21 33 0.49
22 22 0.33
23 4 0.06
24 8 0.12
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.43
Consensus pattern (21 bp):
TATATATATATATTCAAAAAC
Found at i:262485 original size:43 final size:45
Alignment explanation
Indices: 262423--262545 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 45
262413 ACCTATATAT
* * **
262423 ATATATATTATACTTTCAAAAACTATATATATATATTGGAAAA-C
1 ATATATAATATATTTTCAAAAACTATATATATATATTCAAAAACC
* *
262467 -TATATAATATGTTTTC-AAAACTATATTATATATTTTCAAAAACC
1 ATATATAATATATTTTCAAAAACTATA-TATATATATTCAAAAACC
* * *
262511 ATATATCATATATTTTCATATA-TATATATATATAT
1 ATATATAATATATTTTCAAAAACTATATATATATAT
262546 ATATATATAT
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
42 9 0.14
43 26 0.41
44 9 0.14
45 18 0.28
46 2 0.03
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (45 bp):
ATATATAATATATTTTCAAAAACTATATATATATATTCAAAAACC
Found at i:262533 original size:2 final size:2
Alignment explanation
Indices: 262528--262581 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
262518 ATATATTTTC
262528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
262570 AT AT AT AT AT AT
1 AT AT AT AT AT AT
262582 TAAAAGCCCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268049 original size:45 final size:45
Alignment explanation
Indices: 267967--268052 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
267957 GAAACTAAAA
*
267967 ATATAATGAAAATAAATAAATAGTATAAATAAAATAATAAACAAT
1 ATATAATAAAAATAAATAAATAGTATAAATAAAATAATAAACAAT
* *
268012 ATATATATAAAAATATAA-AAAT-GTATGAATAATATAATAAA
1 ATATA-ATAAAAATA-AATAAATAGTATAAATAAAATAATAAA
268053 ATACTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 22 0.61
46 12 0.33
47 2 0.06
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (45 bp):
ATATAATAAAAATAAATAAATAGTATAAATAAAATAATAAACAAT
Found at i:268051 original size:22 final size:22
Alignment explanation
Indices: 267962--268096 Score: 61
Period size: 23 Copynumber: 6.1 Consensus size: 22
267952 GAAAAGAAAC
267962 TAAAAATATAATGAA-AATA-AA
1 TAAAAATAT-ATGAATAATATAA
* *
267983 T--AAATAGTATAAATAAAATAA
1 TAAAAATA-TATGAATAATATAA
*
268004 TAAACAATATAT-ATATAA-AAATA
1 TAAA-AATATATGA-ATAATATA-A
*
268027 TAAAAATGTATGAATAATATAA
1 TAAAAATATATGAATAATATAA
* *
268049 TAAAATACTAAAT-AGTAATAATAA
1 TAAAA-A-TATATGAATAAT-ATAA
* *
268073 TAATAAATAAATGAAAAATA-AA
1 TAA-AAATATATGAATAATATAA
268095 TA
1 TA
268097 TACATATAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 29
0.70 0.08 0.23
Matches are distributed among these distances:
19 9 0.10
20 4 0.04
21 4 0.04
22 23 0.26
23 28 0.31
24 19 0.21
25 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (22 bp):
TAAAAATATATGAATAATATAA
Found at i:268268 original size:21 final size:21
Alignment explanation
Indices: 268227--268275 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
268217 AGATAAAAAA
* *
268227 ATAATAATATAATATATATAT
1 ATAATAATAGAAAATATATAT
268248 ATAATAATAGGAAAATAATATAAT
1 ATAATAATA-GAAAAT-ATAT-AT
268272 ATAA
1 ATAA
268276 CGCAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 4 0.17
24 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATAATAGAAAATATATAT
Found at i:268309 original size:19 final size:19
Alignment explanation
Indices: 268285--268327 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
268275 ACGCAAAGAA
268285 AAATAAAAAAAATTATAA-T
1 AAATAAAAAAAA-TATAATT
*
268304 AAATAAATAAAATATAATT
1 AAATAAAAAAAATATAATT
268323 AAATA
1 AAATA
268328 TATACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAAAAAAAATATAATT
Found at i:268785 original size:37 final size:37
Alignment explanation
Indices: 268744--268828 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
268734 GGATCATATC
* * *
268744 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAAATCTATCCTATT
* **
268781 TTTAGGAGTTTGAATCCTAGCAAAAATCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAAATCTATCCTATT
268818 TTTAGGAGTTT
1 TTTAGGAGTTT
268829 GAATCCTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAAATCTATCCTATT
Found at i:269774 original size:106 final size:106
Alignment explanation
Indices: 269590--270865 Score: 1881
Period size: 106 Copynumber: 12.0 Consensus size: 106
269580 GCATTGTTCC
* * * * * * *
269590 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGAGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
269655 CCAGCCGTCCCTTCAAT-GTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTC-GTCGTGAAGTTGAACTTGCGTTGTCTG
* *
269696 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
269761 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
269802 GAGTCCAATATCCTTTGCTGTGAAATTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
269867 CCAGCGGTCCCTTCGTCGTGAAGTTTAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * *
269908 GAGTCCAATATCCTTCGTTGTGAAGTTGAAAATACCTCTGAAATTGAGAAGTTGTTTGTTGCCAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
269973 CCAGCGGTCCCTTCG-CTGTGAAGTTGAACTTACGTTGTCCG
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTG
* ** * *
270014 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
270079 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTCTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
270120 GAGTCCAATATCTTTCGATGTGAAGTTGAAATTGGCTCCGAAATTAGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
270185 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
270226 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
270291 CCAGCGGTTCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
270332 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
270397 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
270438 GACTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
270503 CCAGCGGTCCCTTCATCATGAAGTTGAACTTTCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * ** * * *
270544 GTGTCCAATATCCTTCGATGTAAAGTTGAAATAAGCTCTGAAATTGGGAAATTGTTTATTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
270609 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
270650 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
270715 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
270756 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
270821 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
270862 GAGT
1 GAGT
270866 GGCACGATAT
Statistics
Matches: 1061, Mismatches: 106, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
105 2 0.00
106 1058 1.00
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:271863 original size:22 final size:22
Alignment explanation
Indices: 271809--271863 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
271799 TTGTGTTTGG
* *
271809 TCAAAGGTTTAGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATAC
271831 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATAC
271853 TCAAAGGTTTG
1 TCAAAGGTTTG
271864 ATGGGGTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATAC
Found at i:272476 original size:18 final size:17
Alignment explanation
Indices: 272452--272523 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 17
272442 TTGCATGTGC
272452 TTTTTTGTCCCTTT-TTT
1 TTTTTTGT-CCTTTCTTT
*
272469 TATTTTTGTTCTTTCTTT
1 T-TTTTTGTCCTTTCTTT
*
272487 TTTTTTGT--TTTCTTC
1 TTTTTTGTCCTTTCTTT
*
272502 TTTTTTGCTTCTTTTCTTT
1 TTTTTTG--TCCTTTCTTT
272521 TTT
1 TTT
272524 GTTTTTGCCC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
15 13 0.28
17 13 0.28
18 11 0.24
19 9 0.20
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTTGTCCTTTCTTT
Found at i:272491 original size:22 final size:22
Alignment explanation
Indices: 272462--272504 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
272452 TTTTTTGTCC
* *
272462 CTTTTTTTAT-TTTTGTTCTTT
1 CTTTTTTTTTGTTTTCTTCTTT
272483 CTTTTTTTTTGTTTTCTTCTTT
1 CTTTTTTTTTGTTTTCTTCTTT
272505 TTTGCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (22 bp):
CTTTTTTTTTGTTTTCTTCTTT
Found at i:272505 original size:16 final size:15
Alignment explanation
Indices: 272480--272528 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
272470 ATTTTTGTTC
*
272480 TTTCTTTTTTTTTGT
1 TTTCTTCTTTTTTGT
272495 TTTCTTCTTTTTTGCT
1 TTTCTTCTTTTTTG-T
272511 TCTT-TTCTTTTTTGT
1 T-TTCTTCTTTTTTGT
272526 TTT
1 TTT
272529 TGCCCTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 2 0.06
15 15 0.48
16 12 0.39
17 2 0.06
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTCTTCTTTTTTGT
Found at i:272507 original size:19 final size:19
Alignment explanation
Indices: 272465--272530 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 19
272455 TTTGTCCCTT
*
272465 TTTTTATTTTTGTTCT-TTC
1 TTTTT-TTTTTGTTTTCTTC
272484 -TTTTTTTTTGTTTTCTTC
1 TTTTTTTTTTGTTTTCTTC
** *
272502 TTTTTTGCTTCTTTTCTT-
1 TTTTTTTTTTGTTTTCTTC
*
272520 TTTTGTTTTTG
1 TTTTTTTTTTG
272531 CCCTTTTTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
17 9 0.24
18 14 0.38
19 14 0.38
ACGTcount: A:0.02, C:0.11, G:0.08, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTTGTTTTCTTC
Found at i:276845 original size:15 final size:16
Alignment explanation
Indices: 276825--276861 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
276815 TGAAAAAAAA
*
276825 ATAAAATTGAAT-AAG
1 ATAAAATTAAATGAAG
276840 ATAAAA-TAAATGAAG
1 ATAAAATTAAATGAAG
276855 ATAAAAT
1 ATAAAAT
276862 ATATATACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (16 bp):
ATAAAATTAAATGAAG
Found at i:276957 original size:21 final size:20
Alignment explanation
Indices: 276933--276985 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
276923 GCAGAGAAAC
276933 TAAA-AATATAATGAAAATAAA
1 TAAACAATATAAT-AAAAT-AA
*
276954 TAAATAATATAAATAAAATAA
1 TAAACAATAT-AATAAAATAA
276975 TAAACAATATA
1 TAAACAATATA
276986 TATATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.52
22 10 0.34
23 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAACAATATAATAAAATAA
Found at i:277222 original size:30 final size:30
Alignment explanation
Indices: 277188--277246 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
277178 ATAAGTAAAC
277188 ATAT-ATAAAAAAAATAATAATATAATATAT
1 ATATAATAAAAAAAA-AATAATATAATATAT
* **
277218 ATATAATAATACGAAAATAATATAATATA
1 ATATAATAAAAAAAAAATAATATAATATA
277247 ACGCAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (30 bp):
ATATAATAAAAAAAAAATAATATAATATAT
Found at i:277291 original size:23 final size:23
Alignment explanation
Indices: 277257--277303 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
277247 ACGCAAAGAA
277257 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
277280 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
277303 A
1 A
277304 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:279328 original size:67 final size:67
Alignment explanation
Indices: 279233--279371 Score: 271
Period size: 67 Copynumber: 2.1 Consensus size: 67
279223 ACAACTAACC
279233 CAACACGATCTAAGACCTTAAATAGTCCTATAAACCTCAAGATAAGCTTACCGTTACACCAAAAC
1 CAACACGATCTAAGACCTTAAATAGTCCTATAAACCTCAAGATAAGCTTACCGTTACACCAAAAC
279298 AT
66 AT
279300 CAACACGATCTAAGACCTTAAATAGTCCTATAAACCTCAAGATAAGCTTACCGTTACACCAAAAC
1 CAACACGATCTAAGACCTTAAATAGTCCTATAAACCTCAAGATAAGCTTACCGTTACACCAAAAC
279365 AT
66 AT
279367 -AACAC
1 CAACAC
279372 CTTCTTCCAA
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 5 0.07
67 67 0.93
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.22
Consensus pattern (67 bp):
CAACACGATCTAAGACCTTAAATAGTCCTATAAACCTCAAGATAAGCTTACCGTTACACCAAAAC
AT
Found at i:283321 original size:16 final size:17
Alignment explanation
Indices: 283294--283329 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
283284 TTAAATAAGG
*
283294 AAATATAATTTAGATTA
1 AAATATAATTTAGATGA
283311 AAATA-AATTTAGATGA
1 AAATATAATTTAGATGA
283327 AAA
1 AAA
283330 ATTGTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (17 bp):
AAATATAATTTAGATGA
Found at i:283330 original size:17 final size:17
Alignment explanation
Indices: 283294--283331 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
283284 TTAAATAAGG
*
283294 AAATATAATTTAGATTA
1 AAATATAATTTAGATAA
283311 AAATA-AATTTAGATGAA
1 AAATATAATTTAGAT-AA
283328 AAAT
1 AAAT
283332 TGTATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (17 bp):
AAATATAATTTAGATAA
Found at i:291009 original size:20 final size:21
Alignment explanation
Indices: 290979--291019 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
290969 TGGTTATCAT
290979 ATAATATGGGATTCATA-AATA
1 ATAATATGGGA-TCATATAATA
291000 ATAA-ATGGGATCATATAATA
1 ATAATATGGGATCATATAATA
291020 GTATCCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.32
Consensus pattern (21 bp):
ATAATATGGGATCATATAATA
Found at i:293599 original size:12 final size:12
Alignment explanation
Indices: 293579--293633 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
293569 TAGATAAGTG
293579 AGGTAGCTAGCT
1 AGGTAGCTAGCT
*
293591 AGGTGGCTA---
1 AGGTAGCTAGCT
293600 AGGTAGCTAGCT
1 AGGTAGCTAGCT
*
293612 AGGTGGCTA---
1 AGGTAGCTAGCT
293621 AGGTAGCTAGCT
1 AGGTAGCTAGCT
293633 A
1 A
293634 CGTGCCTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
9 16 0.48
12 17 0.52
ACGTcount: A:0.25, C:0.15, G:0.36, T:0.24
Consensus pattern (12 bp):
AGGTAGCTAGCT
Found at i:293603 original size:21 final size:21
Alignment explanation
Indices: 293579--293633 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
293569 TAGATAAGTG
293579 AGGTAGCTAGCTAGGTGGCTA
1 AGGTAGCTAGCTAGGTGGCTA
293600 AGGTAGCTAGCTAGGTGGCTA
1 AGGTAGCTAGCTAGGTGGCTA
293621 AGGTAGCTAGCTA
1 AGGTAGCTAGCTA
293634 CGTGCCTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.15, G:0.36, T:0.24
Consensus pattern (21 bp):
AGGTAGCTAGCTAGGTGGCTA
Found at i:312454 original size:16 final size:16
Alignment explanation
Indices: 312430--312470 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
312420 TAAATTTTTA
312430 TAGTACTTTTGAGTAT
1 TAGTACTTTTGAGTAT
*
312446 TATTACTTTTGAGTAT
1 TAGTACTTTTGAGTAT
312462 TAGTACTTT
1 TAGTACTTT
312471 AGATAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (16 bp):
TAGTACTTTTGAGTAT
Found at i:312764 original size:54 final size:54
Alignment explanation
Indices: 312705--313508 Score: 971
Period size: 54 Copynumber: 14.9 Consensus size: 54
312695 CTTTTTTTAT
* * *
312705 GTATCGACACTATGTGTACAACCCACGAAATTAATAATAAGTTTATGAACGATC
1 GTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* * * *
312759 GTATCGATACTATGAGT-CAACGCACGAAATTCATAACAAGTTTATGAACGACC
1 GTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* *
312812 GTATCTG-CACTATGTGTGCAATCAAC-ATAATTCATAATAAGTTTATGAACGACC
1 GTATC-GACACTATGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACC
* *
312866 GTATCGACACTATGTGTGTAACCCAC-ATAATTCATAATAAGTTGATGAACGACC
1 GTATCGACACTATGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACC
* * * * * *
312920 GTATCGGCAGTATGTTTGCTACCAAC-AGAATTCATAATAAGTTTATAAACGACC
1 GTATCGACACTATGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACC
* * *
312974 GTATC-AGCACAATGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACC
1 GTATCGA-CACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* * *
313028 ATATTGGCACTATGTGTGCAACCCAC-ATAATTCATAATAAGTTTATGAACGACC
1 GTATCGACACTATGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACC
* *
313082 ATATCGACACTATGTGTGCAACCCATGAAATTCATAATAAGTTTATGAACGACC
1 GTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* * * **
313136 GTATC-ATCACTATGTGTTCAACCCACGGAATTCATAATAAGTTTATAAACGATA
1 GTATCGA-CACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
** *
313190 GTATCGACACTATGTGTGCAACCCATAAAATTTATAATAAGTTTATGAACGACC
1 GTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
*
313244 CTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
1 GTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* ** * * *
313298 GTATCGGCACTATGTGTGTTACCCAC-ATAATTCATAATAAGCTTATAAATGACC
1 GTATCGACACTATGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACC
* * * * *
313352 ATATCGACACTGTGTTTGCAACCCATGAAATTCATAATAAGTTTATGAACGACT
1 GTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* * * *
313406 GTATCGGCACTATGTGTGCTACCCAC-ATAATTCATAATAAGCTTATAAACGACC
1 GTATCGACACTATGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACC
* * * * *
313460 ATATCAACACTATATATGCAACCCACAAAATTCATAATAAGTTTATGAA
1 GTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAA
313509 TAACAGTATG
Statistics
Matches: 638, Mismatches: 97, Indels: 30
0.83 0.13 0.04
Matches are distributed among these distances:
53 50 0.08
54 584 0.92
55 4 0.01
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (54 bp):
GTATCGACACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
Found at i:329483 original size:54 final size:54
Alignment explanation
Indices: 329403--329628 Score: 240
Period size: 54 Copynumber: 4.2 Consensus size: 54
329393 ATGTATCAGT
* * *
329403 ACTATGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATG-TCGATATCGGT
1 ACTATGTGTGCAACCCACGTAATTCATAATAAGTTTATGAATGATCG-TATCGGC
* ** * * *
329457 ACTATGTGTACAACCCACGTAATTCATAATAAGTTTATGAACAACCATATCAGC
1 ACTATGTGTGCAACCCACGTAATTCATAATAAGTTTATGAATGATCGTATCGGC
* * * * * *
329511 ACTATGTGTGCAACTCATGAAATTCATAATAAGTTTATAAATGACCGTATCGAC
1 ACTATGTGTGCAACCCACGTAATTCATAATAAGTTTATGAATGATCGTATCGGC
* * * *
329565 ACTATGTGTGCATCCCAC-TGAATTCATAATGAGCTTATGAATGATCGTATCGAC
1 ACTATGTGTGCAACCCACGT-AATTCATAATAAGTTTATGAATGATCGTATCGGC
*
329619 ACTACGTGTG
1 ACTATGTGTG
329629 TGCCCCACAG
Statistics
Matches: 142, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
54 141 0.99
55 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (54 bp):
ACTATGTGTGCAACCCACGTAATTCATAATAAGTTTATGAATGATCGTATCGGC
Found at i:329628 original size:108 final size:108
Alignment explanation
Indices: 329396--329605 Score: 289
Period size: 108 Copynumber: 1.9 Consensus size: 108
329386 ATTTTTTATG
* * * * **
329396 TATCAGTACTATGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGTCGATATCGGTACTA
1 TATCAGCACTATGTGTGCAACCCATGAAATTCATAATAAGTTTATAAATGCCGATATCGACACTA
*
329461 TGTGTACAACCCACGTAATTCATAATAAGTTTATGAACAACCA
66 TGTGTACAACCCACGTAATTCATAATAAGCTTATGAACAACCA
*
329504 TATCAGCACTATGTGTGCAACTCATGAAATTCATAATAAGTTTATAAATGACCG-TATCGACACT
1 TATCAGCACTATGTGTGCAACCCATGAAATTCATAATAAGTTTATAAATG-CCGATATCGACACT
* * *
329568 ATGTGTGCATCCCAC-TGAATTCATAATGAGCTTATGAA
65 ATGTGTACAACCCACGT-AATTCATAATAAGCTTATGAA
329606 TGATCGTATC
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
107 1 0.01
108 86 0.97
109 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (108 bp):
TATCAGCACTATGTGTGCAACCCATGAAATTCATAATAAGTTTATAAATGCCGATATCGACACTA
TGTGTACAACCCACGTAATTCATAATAAGCTTATGAACAACCA
Done.