Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008941.1 Hibiscus syriacus cultivar Beakdansim tig00112260_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: 348581
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4540 original size:59 final size:58
Alignment explanation
Indices: 4460--4575 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 58
4450 ACCCTCGAAC
* * * * * *
4460 TATGATTCTTATTCTAAATTGGTTTCTAAA-TTTTAAATATTTCTATTTTATCCTCAAAT
1 TATGATCCTCATTCTAAATTGG-TCCTAAACTTTTAAACATTTCAATTTCATCC-CAAAT
*
4519 TATGATCCTCATTTTAAATTGGTCCTAAACTTTTAAACATTTCAATTTCATCCCAAA
1 TATGATCCTCATTCTAAATTGGTCCTAAACTTTTAAACATTTCAATTTCATCCCAAA
4576 CTATCATTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 10 0.20
59 39 0.80
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (58 bp):
TATGATCCTCATTCTAAATTGGTCCTAAACTTTTAAACATTTCAATTTCATCCCAAAT
Found at i:5936 original size:25 final size:27
Alignment explanation
Indices: 5902--5952 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
5892 AATGATGAAT
5902 TTATAAAA-TTTC-AAGAATAAAAAAA
1 TTATAAAATTTTCAAAGAATAAAAAAA
*
5927 TTATACAATTTTCAGAAGAATAAAAA
1 TTATAAAATTTTCA-AAGAATAAAAA
5953 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
28 11 0.50
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (27 bp):
TTATAAAATTTTCAAAGAATAAAAAAA
Found at i:7935 original size:20 final size:21
Alignment explanation
Indices: 7912--7953 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7902 ATTTGAACAC
7912 TTAT-TTTTTAATTAATTTTT
1 TTATATTTTTAATTAATTTTT
* *
7932 TTATATTTTTATTTTATTTTT
1 TTATATTTTTAATTAATTTTT
7953 T
1 T
7954 AGTATAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (21 bp):
TTATATTTTTAATTAATTTTT
Found at i:10750 original size:14 final size:15
Alignment explanation
Indices: 10731--10765 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
10721 AATAAAAAAT
*
10731 AAAAAAAA-ATTAGA
1 AAAAAAAACATAAGA
10745 AAAAAAAACATAAGA
1 AAAAAAAACATAAGA
10760 AAAAAA
1 AAAAAA
10766 GAAAGCAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAAAAAACATAAGA
Found at i:10769 original size:23 final size:23
Alignment explanation
Indices: 10724--10769 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
10714 CAATAACAAT
10724 AAAAAATAAAAAAAAATTAGAAAA
1 AAAAAATAAAAAAAAA-TAGAAAA
*
10748 AAAAACATAAGAAAAAA-AGAAA
1 AAAAA-ATAAAAAAAAATAGAAA
10770 GCAACTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 5 0.25
25 10 0.50
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAAAATAAAAAAAAATAGAAAA
Found at i:13384 original size:59 final size:58
Alignment explanation
Indices: 13304--13419 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 58
13294 ACCCTCGAAC
* * * * *
13304 TATGATTCTTATTCTAAATTGGTTTCTAAA-TTTTAAATATTTCAATTTTATCCTCAAAT
1 TATGATCCTCATTCTAAATTGG-TCCTAAACTTTTAAACATTTCAATTTCATCC-CAAAT
*
13363 TATGATCCTCATTTTAAATTGGTCCTAAACTTTTAAACATTTCAATTTCATCCCAAA
1 TATGATCCTCATTCTAAATTGGTCCTAAACTTTTAAACATTTCAATTTCATCCCAAA
13420 CTATCATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 10 0.20
59 40 0.80
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46
Consensus pattern (58 bp):
TATGATCCTCATTCTAAATTGGTCCTAAACTTTTAAACATTTCAATTTCATCCCAAAT
Found at i:27059 original size:60 final size:60
Alignment explanation
Indices: 26939--27107 Score: 175
Period size: 60 Copynumber: 2.8 Consensus size: 60
26929 ATTTGGGGAC
* * ** * * * **
26939 GAAATTGGAAGATTCAAAAGTTTG-GGTACCGATTTAG-ATGAGTGTCATAGTTTGGGGAT
1 GAAATTGAAATATTCAAAAGTTTGAGG-ACTAACTTAGAATGAGAGTCATAATTTGAAGAT
*
26998 GAATTTGAAATGA-TCAAAAGTTT-AGAGACTAACTTAGAATGAGAGTCATAATTTGAAGAT
1 GAAATTGAAAT-ATTCAAAAGTTTGAG-GACTAACTTAGAATGAGAGTCATAATTTGAAGAT
* *
27058 GAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAGAATGAGGGTCATA
1 GAAATTGAAATATTCAAAAGTTTGAGGACTAACTTAGAATGAGAGTCATA
27108 GTTTAAGGAT
Statistics
Matches: 91, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
59 27 0.30
60 62 0.68
61 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (60 bp):
GAAATTGAAATATTCAAAAGTTTGAGGACTAACTTAGAATGAGAGTCATAATTTGAAGAT
Found at i:27306 original size:29 final size:29
Alignment explanation
Indices: 27261--27318 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
27251 GTGTTGGCCG
**
27261 TAGGTCGCCATGCCTTCTGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
*
27290 TAGGTCGCCATGTCTTCCCGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
27319 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.26, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:27426 original size:33 final size:33
Alignment explanation
Indices: 27374--27458 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
27364 GACCATCCGA
* * * * *
27374 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
27407 CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
27440 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
27459 GGTAGGCTCG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.36, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
Found at i:27516 original size:14 final size:14
Alignment explanation
Indices: 27494--27526 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
27484 CCTCGCATAG
*
27494 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
27508 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
27522 CTCGG
1 CTCGG
27527 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:31747 original size:39 final size:39
Alignment explanation
Indices: 31699--31792 Score: 179
Period size: 39 Copynumber: 2.4 Consensus size: 39
31689 TGAAGAGCTA
31699 ATGGGCGTTTGGGGGCTCGGATCACATAATGACCTAATT
1 ATGGGCGTTTGGGGGCTCGGATCACATAATGACCTAATT
31738 ATGGGCGTTTGGGGGCTCGGATCACATAATGACCTAATT
1 ATGGGCGTTTGGGGGCTCGGATCACATAATGACCTAATT
*
31777 AAGGGCGTTTGGGGGC
1 ATGGGCGTTTGGGGGC
31793 GTTTGGAGAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.21, C:0.17, G:0.35, T:0.27
Consensus pattern (39 bp):
ATGGGCGTTTGGGGGCTCGGATCACATAATGACCTAATT
Found at i:69310 original size:15 final size:16
Alignment explanation
Indices: 69279--69309 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
69269 TGTTATAATT
69279 TTAATTTTTTTAAAAA
1 TTAATTTTTTTAAAAA
69295 TTAATTTTTTTAAAA
1 TTAATTTTTTTAAAA
69310 TAAAACTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATTTTTTTAAAAA
Found at i:74520 original size:67 final size:66
Alignment explanation
Indices: 74373--74721 Score: 522
Period size: 67 Copynumber: 5.2 Consensus size: 66
74363 GTGACCTAAA
* * *
74373 CTAATTCAGGTTCAGCCTTTCGTTGTTGCTTTCTATCG--TAGAAGACCTTGCTCCGTGTGACAT
1 CTAATTCAGCTTCAG-CTTTCGTTGTTGCTTTCTATCGCATA-AAGGCCTTGCTCAGTGTGACAT
74436 GAG
64 GAG
* *
74439 CTAATTCAGGTTCAGTCTTTAGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG
1 CTAATTCAGCTTCAG-CTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG
74504 AG
65 AG
* *
74506 ATAATTCAGCTTCAGCTTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGTTCAGTGTGACATG
1 CTAATTCAGCTTCAGC-TTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG
74571 AG
65 AG
*
74573 ATAATTCAGCTTCAGCTTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG
1 CTAATTCAGCTTCAGC-TTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG
74638 AG
65 AG
* * * *
74640 CTAATTCAGCTCCAACCTTTTGTTGTTGCTTTCTATCGTATAAAGGCCTTGCTCAGTGTGACATG
1 CTAATTCAGCTTC-AGCTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG
74705 AG
65 AG
74707 CTAATTCAGCTTCAG
1 CTAATTCAGCTTCAG
74722 GTTTTAGTTC
Statistics
Matches: 263, Mismatches: 16, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
66 38 0.14
67 221 0.84
68 4 0.02
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (66 bp):
CTAATTCAGCTTCAGCTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATGA
G
Found at i:79881 original size:106 final size:106
Alignment explanation
Indices: 79696--79901 Score: 376
Period size: 106 Copynumber: 1.9 Consensus size: 106
79686 ATTCATCGCT
* *
79696 GCCGTCTCTGAAGGTAAGAGGTTTTCTCCCACCCTTGACATATATATTACTAGTTTTGTGTATTC
1 GCCGTCTCTGAAGGTAAGAGGTTTTCTCCCACCCTTGACATATATATTACTAGATTTCTGTATTC
*
79761 TCAGACAGAATTAGCAAATTCGTAGAATAAATCTTATCTGA
66 TCAGACAGAATTAGCAAATTCATAGAATAAATCTTATCTGA
*
79802 GCCGTCTCTGAAGGTACGAGGTTTTCTCCCACCCTTGACATATATATTACTAGATTTCTGTATTC
1 GCCGTCTCTGAAGGTAAGAGGTTTTCTCCCACCCTTGACATATATATTACTAGATTTCTGTATTC
79867 TCAGACAGAATTAGCAAATTCATAGAATAAATCTT
66 TCAGACAGAATTAGCAAATTCATAGAATAAATCTT
79902 CTTTGACTTG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (106 bp):
GCCGTCTCTGAAGGTAAGAGGTTTTCTCCCACCCTTGACATATATATTACTAGATTTCTGTATTC
TCAGACAGAATTAGCAAATTCATAGAATAAATCTTATCTGA
Found at i:94558 original size:22 final size:21
Alignment explanation
Indices: 94519--94575 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
94509 AAGAGGGAGG
94519 AAAAAAATATAATAATAAATA
1 AAAAAAATATAATAATAAATA
94540 AAAAAAATA-AATAAT--AT-
1 AAAAAAATATAATAATAAATA
*
94557 AAATAAATATAATAATAAA
1 AAAAAAATATAATAATAAA
94576 GAAGTAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 8 0.25
18 8 0.25
20 7 0.22
21 9 0.28
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAAAATATAATAATAAATA
Found at i:94571 original size:13 final size:12
Alignment explanation
Indices: 94523--94575 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
94513 GGGAGGAAAA
94523 AAATATAATAAT
1 AAATATAATAAT
* *
94535 AAATAAAAAAAAT
1 AAAT-ATAATAAT
94548 AAATA-ATATAAAT
1 AAATATA-AT-AAT
94561 AAATATAATAAT
1 AAATATAATAAT
94573 AAA
1 AAA
94576 GAAGTAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 1 0.03
12 12 0.35
13 20 0.59
14 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:94629 original size:12 final size:12
Alignment explanation
Indices: 94612--94650 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
94602 AAATGTGTAC
94612 ATATATACATAT
1 ATATATACATAT
*
94624 ATATATATATAT
1 ATATATACATAT
94636 ATAATATAACATAT
1 AT-ATAT-ACATAT
94650 A
1 A
94651 AGTGAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 13 0.57
13 4 0.17
14 6 0.26
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATACATAT
Found at i:94651 original size:12 final size:13
Alignment explanation
Indices: 94612--94651 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
94602 AAATGTGTAC
94612 ATATATACATATA
1 ATATATACATATA
*
94625 TATATATATATATA
1 -ATATATACATATA
94639 ATATA-ACATATA
1 ATATATACATATA
94651 A
1 A
94652 GTGAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 7 0.29
13 5 0.21
14 12 0.50
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATACATATA
Found at i:96317 original size:105 final size:104
Alignment explanation
Indices: 96167--97361 Score: 2041
Period size: 105 Copynumber: 11.4 Consensus size: 104
96157 ATATTGTTCC
* * * * **
96167 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCCGAAATTGAGGAATGTTTGTTGACAGT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
96232 CAGCGGTCCCTTCGTCGTGAAGTTGAACCTATAC-TGTCTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAA-CT-TGCGTGTCTG
*
96272 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
96337 AAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC-GTGTCTG
96377 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
96442 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
96482 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
96547 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* *
96587 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
96652 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* * *
96692 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGATAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
96757 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
96797 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
96862 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* * *
96902 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAGATTTTTGTGGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
96967 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
97007 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
97072 AAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* *
97112 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
97177 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* * *
97217 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAGATTTTTGTGGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
97282 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
97322 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
97362 GGTATGCCTA
Statistics
Matches: 1051, Mismatches: 36, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
103 2 0.00
104 2 0.00
105 1047 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (104 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTGTCTG
Found at i:98154 original size:14 final size:13
Alignment explanation
Indices: 98134--98187 Score: 74
Period size: 14 Copynumber: 4.1 Consensus size: 13
98124 CGTTCTTCTC
98134 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
98147 TGTTTTG-TTTTTT
1 T-TTTTGTTTTTTT
*
98160 TCTTTGTTTTTTT
1 TTTTTGTTTTTTT
98173 TTCTTTGTTTTTTT
1 TT-TTTGTTTTTTT
98187 T
1 T
98188 CCAACTTAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
12 4 0.11
13 15 0.42
14 17 0.47
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:98166 original size:26 final size:26
Alignment explanation
Indices: 98136--98186 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
98126 TTCTTCTCTT
98136 TTTGTTTTTTTTGT-TTTGTTTTTTTC
1 TTTGTTTTTTTT-TCTTTGTTTTTTTC
98162 TTTGTTTTTTTTTCTTTGTTTTTTT
1 TTTGTTTTTTTTTCTTTGTTTTTTT
98187 TCCAACTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (26 bp):
TTTGTTTTTTTTTCTTTGTTTTTTTC
Found at i:98187 original size:13 final size:13
Alignment explanation
Indices: 98136--98188 Score: 72
Period size: 13 Copynumber: 4.0 Consensus size: 13
98126 TTCTTCTCTT
*
98136 TTTGTTTTTTTTG
1 TTTGTTTTTTTTC
98149 TTT-TGTTTTTTTC
1 TTTGT-TTTTTTTC
98162 TTTGTTTTTTTTTC
1 TTTG-TTTTTTTTC
98176 TTTGTTTTTTTTC
1 TTTGTTTTTTTTC
98189 CAACTTAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
12 1 0.03
13 22 0.61
14 12 0.33
15 1 0.03
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (13 bp):
TTTGTTTTTTTTC
Found at i:105347 original size:15 final size:13
Alignment explanation
Indices: 105307--105353 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
105297 AATACGAATG
105307 TAAAAACATGAAA
1 TAAAAACATGAAA
*
105320 -AAAAACATAAAA
1 TAAAAACATGAAA
105332 TAAACAGACATGAAA
1 TAAA-A-ACATGAAA
105347 TATAAAA
1 TA-AAAA
105354 TGCAAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 11 0.39
13 3 0.11
14 2 0.07
15 10 0.36
16 2 0.07
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (13 bp):
TAAAAACATGAAA
Found at i:107492 original size:10 final size:10
Alignment explanation
Indices: 107467--107500 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
107457 AAGGTTAGTA
*
107467 AAATAGAAAT
1 AAATAAAAAT
*
107477 AGATAAAAAT
1 AAATAAAAAT
107487 AAATAAAAAT
1 AAATAAAAAT
107497 AAAT
1 AAAT
107501 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:108351 original size:55 final size:53
Alignment explanation
Indices: 108267--108374 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 53
108257 CTTGAACTGC
* *
108267 CCTTTCGGTACTATGTAGTTCCAGTTGTCTTTAATAAGAAAGTTGTAACTTTAAA
1 CCTTTCGGTACTATGTAATTCCAGTTGTCTTTAA-AAG-AAGTTGTAAATTTAAA
108322 CCTTTCGGTACTATGTAATTCCAGTTGTCTTTAAAAGAAGTTGTAAATTTAAA
1 CCTTTCGGTACTATGTAATTCCAGTTGTCTTTAAAAGAAGTTGTAAATTTAAA
108375 TTAAAATGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 15 0.29
54 3 0.06
55 33 0.65
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (53 bp):
CCTTTCGGTACTATGTAATTCCAGTTGTCTTTAAAAGAAGTTGTAAATTTAAA
Found at i:108838 original size:18 final size:18
Alignment explanation
Indices: 108815--108863 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
108805 AGAGGGAGGA
108815 AAAAAAATATAATATAAT
1 AAAAAAATATAATATAAT
108833 AAAAAAA-ATAA-ATAAT
1 AAAAAAATATAATATAAT
*
108849 ATAAATAATATAATA
1 A-AAAAAATATAATA
108864 ATAAAGAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.22
17 9 0.33
18 11 0.41
19 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAAAATATAATATAAT
Found at i:108852 original size:9 final size:9
Alignment explanation
Indices: 108820--108866 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
108810 GAGGAAAAAA
108820 AATATAATAT
1 AATATAA-AT
108830 AATA-AAA-
1 AATATAAAT
*
108837 AAAATAAAT
1 AATATAAAT
108846 AATATAAAT
1 AATATAAAT
108855 AATAT-AAT
1 AATATAAAT
108863 AATA
1 AATA
108867 AAGAAGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 3 0.09
8 11 0.33
9 15 0.45
10 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AATATAAAT
Found at i:117045 original size:19 final size:19
Alignment explanation
Indices: 117012--117083 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
117002 GCTAATAAAC
117012 AAAAAATGAATAAAATATATA
1 AAAAAAT-AATAAAATA-ATA
117033 AAAAAATAA-AAAATAATA
1 AAAAAATAATAAAATAATA
** *
117051 ATGAAAGAA-AGAAATAATA
1 AAAAAATAATA-AAATAATA
117070 AAAAAATAATAAAA
1 AAAAAATAATAAAA
117084 GGTTAAGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 10 0.23
19 23 0.53
20 3 0.07
21 7 0.16
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (19 bp):
AAAAAATAATAAAATAATA
Found at i:117078 original size:11 final size:11
Alignment explanation
Indices: 117004--117083 Score: 56
Period size: 11 Copynumber: 6.7 Consensus size: 11
116994 AACAAAATGC
117004 TAATAAACAAAA
1 TAATAAA-AAAA
*
117016 -AATGAATAAAA
1 TAAT-AAAAAAA
117027 TATATAAAAAAA
1 TA-ATAAAAAAA
*
117039 TAA-AAAATAA
1 TAATAAAAAAA
117049 TAATGAAAGAAAGAAA
1 TAAT---A-AAA-AAA
117065 TAATAAAAAAA
1 TAATAAAAAAA
117076 TAATAAAA
1 TAATAAAA
117084 GGTTAAGTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
10 9 0.16
11 19 0.35
12 14 0.25
13 3 0.05
14 1 0.02
15 3 0.05
16 6 0.11
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (11 bp):
TAATAAAAAAA
Found at i:118362 original size:12 final size:12
Alignment explanation
Indices: 118345--118374 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
118335 TGACTGGATT
118345 TGGACCCGTTTA
1 TGGACCCGTTTA
*
118357 TGGACCCGTTTT
1 TGGACCCGTTTA
118369 TGGACC
1 TGGACC
118375 TGGAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.27, G:0.27, T:0.33
Consensus pattern (12 bp):
TGGACCCGTTTA
Found at i:118410 original size:5 final size:5
Alignment explanation
Indices: 118402--118427 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
118392 AAATTAAATT
118402 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
118428 TAATATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:118440 original size:19 final size:18
Alignment explanation
Indices: 118418--118457 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
118408 ATAAAATAAA
118418 ATAAAATAAATAATATGAT
1 ATAAAATAAATAATAT-AT
* *
118437 ATAAACTATATAATATAT
1 ATAAAATAAATAATATAT
118455 ATA
1 ATA
118458 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATAATATAT
Found at i:118619 original size:38 final size:38
Alignment explanation
Indices: 118439--118748 Score: 183
Period size: 38 Copynumber: 8.5 Consensus size: 38
118429 AATATGATAT
* *
118439 AAACTATATAATATATATATTTCA-AAAATATGTTTTAGA
1 AAACTATATATTATATA-ATTTCACAAAAAATGTTTTA-A
* * * * **
118478 AAACTATATA-T-TAT-ACTTAAAAAAAAAAGTTTCCA
1 AAACTATATATTATATAATTTCACAAAAAATGTTTTAA
* * * *
118513 AAACTATATATTACATAGTTT-TC--AAAACGTTTTAA
1 AAACTATATATTATATAATTTCACAAAAAATGTTTTAA
* *
118548 AAA-TAT-TA-TATA-AGTTTTCA-AAAAAATGTTTTTA
1 AAACTATATATTATATA-ATTTCACAAAAAATGTTTTAA
*
118582 AAACTATATATTATATAATTTCACAAAAAATGTTTTTA
1 AAACTATATATTATATAATTTCACAAAAAATGTTTTAA
* **
118620 AAACTATATACTATAT-ATGTTTTC--AAAATGTTTTAA
1 AAACTATATATTATATAAT-TTCACAAAAAATGTTTTAA
* * *
118656 AAACTATATAATATATAAACGTTT-TC--AAAATGTTTTCA
1 AAACTATATATTATAT-AA--TTTCACAAAAAATGTTTTAA
* * *
118694 AAACTATATATTATATATATTTTA-AAAATAT-TTTCAA
1 AAACTATATATTATATA-ATTTCACAAAAAATGTTTTAA
*
118731 AAACTATATAATATATAA
1 AAACTATATATTATATAA
118749 ATTTTTGAAA
Statistics
Matches: 217, Mismatches: 32, Indels: 47
0.73 0.11 0.16
Matches are distributed among these distances:
31 1 0.00
32 6 0.03
33 2 0.01
34 16 0.07
35 30 0.14
36 42 0.19
37 37 0.17
38 70 0.32
39 12 0.06
40 1 0.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (38 bp):
AAACTATATATTATATAATTTCACAAAAAATGTTTTAA
Found at i:118659 original size:74 final size:72
Alignment explanation
Indices: 118569--118748 Score: 227
Period size: 74 Copynumber: 2.4 Consensus size: 72
118559 AAGTTTTCAA
* * *
118569 AAAAATGTTTTTAAAACTATATATTATATAA-TTTCACAAAAAATGTTTTTAAAACTATATACTA
1 AAAAATGTTTTAAAAACTATATAATATATAACTTT-AC--AAAATGTTTTCAAAACTATATACTA
*
118633 TATATGTTTT
63 TATATATTTT
* * *
118643 CAAAATGTTTTAAAAACTATATAATATATAAACGTTTTCAAAATGTTTTCAAAACTATATATTAT
1 AAAAATGTTTTAAAAACTATATAATATAT-AAC-TTTACAAAATGTTTTCAAAACTATATACTAT
118708 ATATATTTT
64 ATATATTTT
*
118717 AAAAATATTTTCAAAAACTATATAATATATAA
1 AAAAATGTTTT-AAAAACTATATAATATATAA
118749 ATTTTTGAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
74 69 0.74
75 20 0.22
76 1 0.01
77 3 0.03
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (72 bp):
AAAAATGTTTTAAAAACTATATAATATATAACTTTACAAAATGTTTTCAAAACTATATACTATAT
ATATTTT
Found at i:118760 original size:74 final size:74
Alignment explanation
Indices: 118608--118786 Score: 234
Period size: 74 Copynumber: 2.4 Consensus size: 74
118598 AATTTCACAA
* * * * *
118608 AAAATGTTTTTAAAACTATATACTATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATA
1 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTAAAAACTATATAATATATA
118673 AACGTTTTC
66 AACGTTTTC
118682 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTCAAAAACTATATAATATAT
1 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTT-AAAAACTATATAATATAT
* *
118747 AAA-TTTTTG
65 AAACGTTTTC
* *
118756 AAAATCATTTTCTGAAAATTATATATTATAT
1 AAAAT-GTTTTC--AAAACTATATATTATAT
118787 TTTGTCAAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
74 50 0.54
75 26 0.28
77 16 0.17
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTAAAAACTATATAATATATA
AACGTTTTC
Found at i:118779 original size:75 final size:73
Alignment explanation
Indices: 118608--118814 Score: 213
Period size: 74 Copynumber: 2.8 Consensus size: 73
118598 AATTTCACAA
* * * * *
118608 AAAATGTTTTTAAAACTATATACTATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATA
1 AAAATATTTTCAAAACTATATA-TATATATATTTTAAAAATATTTTAAAAACTATATAATATATA
118673 AACGTTTTC
65 AACGTTTTC
*
118682 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTCAAAAACTATATAATATAT
1 AAAATATTTTCAAAACTATATA-TATATATATTTTAAAAATATTTT-AAAAACTATATAATATAT
* *
118747 AAA-TTTTTG
64 AAACGTTTTC
* * *
118756 AAAATCATTTTCTGAAAATTATATAT-TATAT-TTTGTCAAAAACATTTTTACAAACTATA
1 AAAAT-ATTTTC--AAAACTATATATATATATATTT-T-AAAAATA-TTTTAAAAACTATA
118815 ATAAAAAAAC
Statistics
Matches: 115, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
74 53 0.46
75 32 0.28
76 16 0.14
77 14 0.12
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (73 bp):
AAAATATTTTCAAAACTATATATATATATATTTTAAAAATATTTTAAAAACTATATAATATATAA
ACGTTTTC
Found at i:119805 original size:10 final size:10
Alignment explanation
Indices: 119790--119814 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
119780 TAATAAAAGG
119790 TATTTTTTAA
1 TATTTTTTAA
119800 TATTTTTTAA
1 TATTTTTTAA
119810 TATTT
1 TATTT
119815 CCGGTAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:119865 original size:20 final size:20
Alignment explanation
Indices: 119826--119865 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
119816 CGGTAAAGTG
* *
119826 TTACCTAAAATATTATTTTC
1 TTACCGAAAATATTAATTTC
*
119846 TTACCGAAAATGTTAATTTC
1 TTACCGAAAATATTAATTTC
119866 GCTATCTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (20 bp):
TTACCGAAAATATTAATTTC
Found at i:123733 original size:34 final size:34
Alignment explanation
Indices: 123690--123774 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
123680 TATGATTGAT
123690 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
123724 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
123758 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
123775 GCTGTGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:123828 original size:22 final size:22
Alignment explanation
Indices: 123796--123853 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
123786 GACTGGACGT
* *
123796 GAGAAATCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTACAAG
* *
123818 GAGAGAGCACGAGTTCTACAAG
1 GAGAAAGCACGGGTTCTACAAG
*
123840 GAGAAATCACGGGT
1 GAGAAAGCACGGGT
123854 CCTGGGTCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (22 bp):
GAGAAAGCACGGGTTCTACAAG
Found at i:123920 original size:23 final size:23
Alignment explanation
Indices: 123871--123920 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
123861 CCTGCAGGGC
****
123871 TGCACGTCTGCATGTGGGGGTCC
1 TGCACGTCTGCATGTGGGGAAAA
123894 TGCACGTCTGCATGTGGGGAAAA
1 TGCACGTCTGCATGTGGGGAAAA
123917 TGCA
1 TGCA
123921 ACTGTTGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.24
Consensus pattern (23 bp):
TGCACGTCTGCATGTGGGGAAAA
Found at i:124658 original size:172 final size:173
Alignment explanation
Indices: 124371--124729 Score: 560
Period size: 172 Copynumber: 2.1 Consensus size: 173
124361 TTGTAAAGTT
* * * *
124371 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
*
124436 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
124499 GGATTAAATTTCTAACTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
* * *
124543 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
* *
124608 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
124673 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
*
124716 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
124730 ATATTTGATG
Statistics
Matches: 170, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
172 110 0.65
173 59 0.35
174 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (173 bp):
TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:126994 original size:42 final size:42
Alignment explanation
Indices: 126945--127038 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
126935 ATATATTTAC
* *
126945 TATTATTATATCAGT-AAATATAAATAATTAAAGTCAAGTAAT
1 TATTATTAAATCAGTAAAAT-TAAATAATTAAAATCAAGTAAT
* * *
126987 TATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAAT
1 TATTATTAAATCAGTAAAATTAAATAATTAAAATCAAGTAAT
127029 TATTATTAAA
1 TATTATTAAA
127039 ATTAAATCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (42 bp):
TATTATTAAATCAGTAAAATTAAATAATTAAAATCAAGTAAT
Found at i:127002 original size:14 final size:14
Alignment explanation
Indices: 126985--127281 Score: 118
Period size: 14 Copynumber: 20.9 Consensus size: 14
126975 AAGTCAAGTA
126985 ATTATTATTAAATC
1 ATTATTATTAAATC
**
126999 ATTAAAATTAAATC
1 ATTATTATTAAATC
** * *
127013 ATTAAAATTAAGTA
1 ATTATTATTAAATC
127027 ATTATTATTAAA--
1 ATTATTATTAAATC
* *
127039 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
127056 ATTATTATTAAATC
1 ATTATTATTAAATC
*
127070 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
* *
127086 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
127103 ATTATTATTAAATC
1 ATTATTATTAAATC
*
127117 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
*
127131 ATTAAATCATTAAA--
1 ATT--ATTATTAAATC
* *
127145 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
127162 ATTATTATTAAATC
1 ATTATTATTAAATC
*
127176 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* *
127190 ---ATTA--AAGTA
1 ATTATTATTAAATC
127199 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
127213 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
127227 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
127241 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
* *
127255 ATTA-AATTTAAATA
1 ATTATTA-TTAAATC
127269 ATTATTATTAAAT
1 ATTATTATTAAAT
127282 ATGTACTCGA
Statistics
Matches: 225, Mismatches: 32, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
9 3 0.01
11 1 0.00
12 8 0.04
13 4 0.02
14 142 0.63
15 26 0.12
16 30 0.13
17 11 0.05
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (14 bp):
ATTATTATTAAATC
Found at i:127004 original size:8 final size:8
Alignment explanation
Indices: 126991--127246 Score: 150
Period size: 8 Copynumber: 34.8 Consensus size: 8
126981 AGTAATTATT
126991 ATTAAATC
1 ATTAAATC
126999 ATTAAA--
1 ATTAAATC
127005 ATTAAATC
1 ATTAAATC
127013 ATTAAA--
1 ATTAAATC
* *
127019 ATTAAGTA
1 ATTAAATC
*
127027 ATT--ATT
1 ATTAAATC
127033 ATTAAA--
1 ATTAAATC
127039 ATTAAATC
1 ATTAAATC
*
127047 ATTAAAGTA
1 ATTAAA-TC
*
127056 ATT--ATT
1 ATTAAATC
127062 ATTAAATC
1 ATTAAATC
127070 ATTAAATC
1 ATTAAATC
127078 ATTAAATC
1 ATTAAATC
127086 ATTAAATC
1 ATTAAATC
*
127094 ATTAAAGTA
1 ATTAAA-TC
*
127103 ATT--ATT
1 ATTAAATC
127109 ATTAAATC
1 ATTAAATC
127117 ATTAAA--
1 ATTAAATC
*
127123 GTTAAATC
1 ATTAAATC
127131 ATTAAATC
1 ATTAAATC
127139 ATTAAA--
1 ATTAAATC
127145 ATTAAATC
1 ATTAAATC
*
127153 ATTAAAGTA
1 ATTAAA-TC
*
127162 ATT--ATT
1 ATTAAATC
127168 ATTAAATC
1 ATTAAATC
127176 ATTAAA--
1 ATTAAATC
*
127182 GTTAAATC
1 ATTAAATC
*
127190 ATTAAAGTA
1 ATTAAA-TC
*
127199 ATT--ATT
1 ATTAAATC
127205 ATTAAATC
1 ATTAAATC
127213 ATTAAA--
1 ATTAAATC
* *
127219 GTTAAATA
1 ATTAAATC
*
127227 ATT--ATT
1 ATTAAATC
127233 ATTAAATC
1 ATTAAATC
127241 ATTAAA
1 ATTAAA
127247 GTTAAATAAT
Statistics
Matches: 195, Mismatches: 23, Indels: 60
0.70 0.08 0.22
Matches are distributed among these distances:
6 63 0.32
7 4 0.02
8 112 0.57
9 16 0.08
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:127016 original size:28 final size:28
Alignment explanation
Indices: 126965--127282 Score: 145
Period size: 28 Copynumber: 11.2 Consensus size: 28
126955 TCAGTAAATA
* * * * *
126965 TAAATAATTAAAGTCAAGTAATTATTAT
1 TAAATAATTAAAATTAAATCATTATAAT
* *
126993 TAAATCATTAAAATTAAATCATTAAAAT
1 TAAATAATTAAAATTAAATCATTATAAT
* ** *
127021 TAAGTAATTATTATTAAA--ATTAAATCAT
1 TAAATAATTAAAATTAAATCATT--ATAAT
** *
127049 TAAAGTAATTATTATTAAATCATTAAATCAT
1 TAAA-TAATTAAAATTAAATCATT--ATAAT
* * *
127080 TAAATCATTAAATCATTAAAGTAATTATTAT
1 TAAATAATTAAA--ATTAAA-TCATTATAAT
* *
127111 TAAATCATTAAAGTTAAATCATTA-AAT
1 TAAATAATTAAAATTAAATCATTATAAT
* * *
127138 CATTAA-AATTAAATCATTAAAGTAATTATTAT
1 --TAAATAATTAAA--ATTAAA-TCATTATAAT
* * *
127170 TAAATCATTAAAGTTAAATCATTA-AAG
1 TAAATAATTAAAATTAAATCATTATAAT
*
127197 T-AATTATT---ATTAAATCATTA-AAGT
1 TAAATAATTAAAATTAAATCATTATAA-T
**
127221 TAAATAATTATTATTAAATCATTA-AAGT
1 TAAATAATTAAAATTAAATCATTATAA-T
* * *
127249 TAAATAATTAAATTTAAATAATTATTAT
1 TAAATAATTAAAATTAAATCATTATAAT
127277 TAAATA
1 TAAATA
127283 TGTACTCGAG
Statistics
Matches: 227, Mismatches: 42, Indels: 42
0.73 0.14 0.14
Matches are distributed among these distances:
23 13 0.06
24 1 0.00
25 6 0.03
26 9 0.04
27 4 0.02
28 100 0.44
29 28 0.12
30 13 0.06
31 41 0.18
32 8 0.04
33 4 0.02
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (28 bp):
TAAATAATTAAAATTAAATCATTATAAT
Found at i:127172 original size:37 final size:37
Alignment explanation
Indices: 127109--127230 Score: 185
Period size: 37 Copynumber: 3.3 Consensus size: 37
127099 AGTAATTATT
*
127109 ATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAA
1 ATTAAATCATTAAAG-TAATTATTATTAAATCATTAAA
127145 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
1 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
*
127182 GTTAAATCATTAAAGTAATTATTATTAAATCATTAAA
1 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
* *
127219 GTTAAATAATTA
1 ATTAAATCATTA
127231 TTATTAAATC
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
35 3 0.04
36 15 0.19
37 63 0.78
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (37 bp):
ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
Found at i:130652 original size:18 final size:18
Alignment explanation
Indices: 130629--130675 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
130619 AAATTATTAG
130629 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
130647 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
130665 TCTCACGCTTC
1 TCTCACGCTTC
130676 GGCCACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:131127 original size:43 final size:43
Alignment explanation
Indices: 131078--131181 Score: 190
Period size: 43 Copynumber: 2.4 Consensus size: 43
131068 GACGACAGGT
131078 GAAGACGCCGAGAGATCCACATTGGCATTCCTTGTAGCATGCA
1 GAAGACGCCGAGAGATCCACATTGGCATTCCTTGTAGCATGCA
*
131121 GAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCA
1 GAAGACGCCGAGAGATCCACATTGGCATTCCTTGTAGCATGCA
*
131164 GAAGACGCCGAGATATCC
1 GAAGACGCCGAGAGATCC
131182 CACAGTCCAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (43 bp):
GAAGACGCCGAGAGATCCACATTGGCATTCCTTGTAGCATGCA
Found at i:132236 original size:23 final size:24
Alignment explanation
Indices: 132181--132237 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
132171 ATATTATAAT
* *
132181 AGATAAATA-TATATAATTTTAGA
1 AGATAAAAACTATAAAATTTTAGA
*
132204 ATATACAAAACTATAAAATTTTA-A
1 AGATA-AAAACTATAAAATTTTAGA
132228 AGATAAAAAC
1 AGATAAAAAC
132238 ATATTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 9 0.32
24 8 0.29
25 11 0.39
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (24 bp):
AGATAAAAACTATAAAATTTTAGA
Found at i:135947 original size:3 final size:3
Alignment explanation
Indices: 135939--136000 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
135929 GTTCCCTTTC
135939 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
135987 TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TC
136001 CCCATTGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:138030 original size:25 final size:25
Alignment explanation
Indices: 138002--138051 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
137992 ATTTTATGCG
*
138002 TTTT-CTTTTTTAGTTTAGTATATAT
1 TTTTACTTTTTTAGATTA-TATATAT
*
138027 TTTTATTTTTTTAGATTATATATAT
1 TTTTACTTTTTTAGATTATATATAT
138052 ATATATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (25 bp):
TTTTACTTTTTTAGATTATATATAT
Found at i:138050 original size:27 final size:29
Alignment explanation
Indices: 138007--138069 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
137997 ATGCGTTTTC
138007 TTTTTTAGTTTAGTATATAT-T-T-TTAT
1 TTTTTTAGTTTAGTATATATATATATTAT
138033 TTTTTTAGATTATA-TATATATATATATTAT
1 TTTTTTAG-TT-TAGTATATATATATATTAT
138063 TTTTTTA
1 TTTTTTA
138070 TTATCAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.25
27 9 0.28
28 3 0.09
29 1 0.03
30 11 0.34
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTTTTAGTTTAGTATATATATATATTAT
Found at i:138125 original size:22 final size:22
Alignment explanation
Indices: 138100--138157 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
138090 TATATATATA
*
138100 TATATATACTATT-TTTTTATTT
1 TATATATA-TATTATTTTTACTT
138122 TATATATATATTATTTTTACTT
1 TATATATATATTATTTTTACTT
138144 TAT-TAT-TATTATTT
1 TATATATATATTATTT
138158 ATTATTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 8 0.24
21 7 0.21
22 19 0.56
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (22 bp):
TATATATATATTATTTTTACTT
Found at i:138178 original size:16 final size:15
Alignment explanation
Indices: 138119--138230 Score: 77
Period size: 16 Copynumber: 7.1 Consensus size: 15
138109 TATTTTTTTA
*
138119 TTTTATATATATATTAT
1 TTTTATTTAT-TATT-T
138136 TTTTACTTTATTATTAT
1 TTTTA-TTTATTATT-T
138153 TATTTA-TTATTATTT
1 T-TTTATTTATTATTT
138168 GTTTTATTTATATATTT
1 -TTTTATTTAT-TATTT
*
138185 TTTTCTTTATT-TTT
1 TTTTATTTATTATTT
*
138199 TATTTTTTTA-TATTT
1 T-TTTATTTATTATTT
* *
138214 ATTTTACTTACTATTT
1 -TTTTATTTATTATTT
138230 T
1 T
138231 ATCTTTGCTT
Statistics
Matches: 81, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
14 5 0.06
15 23 0.28
16 28 0.35
17 17 0.21
18 8 0.10
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (15 bp):
TTTTATTTATTATTT
Found at i:138194 original size:29 final size:30
Alignment explanation
Indices: 138162--138218 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
138152 TTATTTATTA
138162 TTATTTGTTT-TATTTATATATTT-TTTTCT
1 TTATTT-TTTATATTTATATATTTATTTTCT
* *
138191 TTATTTTTTATTTTTTTATATTTATTTT
1 TTATTTTTTATATTTATATATTTATTTT
138219 ACTTACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 17 0.71
30 4 0.17
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (30 bp):
TTATTTTTTATATTTATATATTTATTTTCT
Found at i:138219 original size:46 final size:50
Alignment explanation
Indices: 138115--138219 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
138105 ATACTATTTT
138115 TTTATTTTATATATATATTATTTTTACTTTATTATTATTATTTATTATTA
1 TTTATTTTATATATATATTATTTTTACTTTATTATTATTATTTATTATTA
* * *
138165 TTTGTTTTATTTATATATT-TTTTT-CTTTATT-TT-TTATTT-TTTTATA
1 TTTATTTTATATATATATTATTTTTACTTTATTATTATTATTTATTAT-TA
138211 TTTATTTTA
1 TTTATTTTA
138220 CTTACTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
45 3 0.06
46 16 0.32
47 2 0.04
48 7 0.14
49 5 0.10
50 17 0.34
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (50 bp):
TTTATTTTATATATATATTATTTTTACTTTATTATTATTATTTATTATTA
Found at i:144396 original size:30 final size:31
Alignment explanation
Indices: 144362--144436 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 31
144352 AACAAATGAA
* *
144362 AGTTTAGGTACTAAAATGAAAT-AAACTTAT
1 AGTTTAAGTACTAAAATAAAATAAAACTTAT
144392 AGTTTAAGTACT-AAATAAAATAAAACTTAT
1 AGTTTAAGTACTAAAATAAAATAAAACTTAT
*
144422 AGTTTAAGCACTAAA
1 AGTTTAAGTACTAAA
144437 CGTGTAGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.20
30 30 0.75
31 2 0.05
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (31 bp):
AGTTTAAGTACTAAAATAAAATAAAACTTAT
Found at i:146970 original size:23 final size:23
Alignment explanation
Indices: 146938--147006 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
146928 ATTCGATTTA
*
146938 TTAGCGTTTATGAATATGTTCAT
1 TTAGCATTTATGAATATGTTCAT
*
146961 TTAGCATTTACGAATATGTTCAT
1 TTAGCATTTATGAATATGTTCAT
* * *
146984 TTAACATTTGTGAACATGTTCAT
1 TTAGCATTTATGAATATGTTCAT
147007 CGATATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (23 bp):
TTAGCATTTATGAATATGTTCAT
Found at i:147235 original size:21 final size:21
Alignment explanation
Indices: 147209--147248 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
147199 AAGAATCAGG
*
147209 TAAACAAGCTTATAAACAAGT
1 TAAACAAACTTATAAACAAGT
*
147230 TAAACAAACTTATGAACAA
1 TAAACAAACTTATAAACAA
147249 TAATGATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (21 bp):
TAAACAAACTTATAAACAAGT
Found at i:150064 original size:56 final size:55
Alignment explanation
Indices: 149997--150107 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
149987 ATGTATGCAT
149997 GTTTATGCTTTGCTAATTTGC-TTTACAGATTAGAGAGAGATCGTGTGAAAGAAAAG
1 GTTTATGCTTTGCTAATTTGCTTTTACAGATT--AGAGAGATCGTGTGAAAGAAAAG
150053 GTTTATGCTTTGCTAATTTGCTTTTACAGATTAGAGAGATCGTGTGAAAGAAAAG
1 GTTTATGCTTTGCTAATTTGCTTTTACAGATTAGAGAGATCGTGTGAAAGAAAAG
150108 CAAAAGTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
55 23 0.43
56 21 0.39
57 10 0.19
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (55 bp):
GTTTATGCTTTGCTAATTTGCTTTTACAGATTAGAGAGATCGTGTGAAAGAAAAG
Found at i:150399 original size:12 final size:12
Alignment explanation
Indices: 150384--150427 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
150374 CAGGTATACA
*
150384 TATATATATATT
1 TATATATATAAT
150396 TATATATATAAT
1 TATATATATAAT
* *
150408 TATGTATACAAT
1 TATATATATAAT
150420 TATATATA
1 TATATATA
150428 GCTTATAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (12 bp):
TATATATATAAT
Found at i:153151 original size:68 final size:67
Alignment explanation
Indices: 153042--153183 Score: 241
Period size: 68 Copynumber: 2.1 Consensus size: 67
153032 AACATCTTAG
153042 TATAAAATGCTTAGGATGCAAAATTAGATATTAAAAAGATATAAAAAATATTTAAATTATATAAA
1 TATAAAATGCTTAGGATGCAAAATTAGATATTAAAAAGATAT-AAAAATATTTAAATTATATAAA
153107 AAT
65 AAT
* * *
153110 TATAAAATGTTTGGGATGCAAAATTAGATATTAAAAAGATATAAAAATATTTAAATTATATAGAA
1 TATAAAATGCTTAGGATGCAAAATTAGATATTAAAAAGATATAAAAATATTTAAATTATATAAAA
153175 AT
66 AT
153177 T-TAAAAT
1 TATAAAAT
153184 TTACAAAAGA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 6 0.08
67 25 0.35
68 40 0.56
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (67 bp):
TATAAAATGCTTAGGATGCAAAATTAGATATTAAAAAGATATAAAAATATTTAAATTATATAAAA
AT
Found at i:158958 original size:6 final size:6
Alignment explanation
Indices: 158947--159043 Score: 194
Period size: 6 Copynumber: 16.2 Consensus size: 6
158937 GACACGTATT
158947 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
158995 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
159043 A
1 A
159044 GCCGAGCCGA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:159051 original size:5 final size:5
Alignment explanation
Indices: 159041--159084 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
159031 ACCACGACCA
159041 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
159085 ACGGACGGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.20, C:0.39, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:160951 original size:27 final size:26
Alignment explanation
Indices: 160910--160960 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
160900 AGTATATATC
* * *
160910 ATTTTTTTAATTTAAGTATTTAAAGT
1 ATTTTTTTAAATTAAATATCTAAAGT
160936 ATTTTTTTCAAATTAAATATCTAAA
1 ATTTTTTT-AAATTAAATATCTAAA
160961 TTCATCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTTTTTAAATTAAATATCTAAAGT
Found at i:161152 original size:29 final size:29
Alignment explanation
Indices: 161111--161203 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
161101 ATTAAATATT
*
161111 TTTAAGTACCTATTTTGACAAAAAAATAC
1 TTTAAGTATCTATTTTGACAAAAAAATAC
* **
161140 TTTAAATATCTATTTTGACCAAAAAGGTAAC
1 TTTAAGTATCTATTTTGA-CAAAAAAAT-AC
* * * *
161171 TTTAGGTATTTATTTTGACTAAAATATAC
1 TTTAAGTATCTATTTTGACAAAAAAATAC
161200 TTTA
1 TTTA
161204 GGTACTTAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 22 0.42
30 13 0.25
31 17 0.33
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.41
Consensus pattern (29 bp):
TTTAAGTATCTATTTTGACAAAAAAATAC
Found at i:165552 original size:4 final size:4
Alignment explanation
Indices: 165533--165588 Score: 55
Period size: 4 Copynumber: 14.2 Consensus size: 4
165523 TCTACAAAAA
*
165533 TATT ATATT ATATT TATT TATT TATT TATT TA-T TA-T TA-T TATT AATT
1 TATT -TATT -TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
*
165580 TTTT TATT T
1 TATT TATT T
165589 TTATTTTTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
3 9 0.20
4 28 0.61
5 9 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:165574 original size:21 final size:21
Alignment explanation
Indices: 165550--165593 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
165540 TTATATTTAT
*
165550 TTATTTATTTATTTATTATTA
1 TTATTAATTTATTTATTATTA
* *
165571 TTATTAATTTTTTTATTTTTA
1 TTATTAATTTATTTATTATTA
165592 TT
1 TT
165594 TTTGCAAGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTAATTTATTTATTATTA
Found at i:165574 original size:25 final size:26
Alignment explanation
Indices: 165533--165593 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
165523 TCTACAAAAA
*
165533 TATTATATTA-TATTTATTTATTTATT
1 TATT-TATTATTATTTATTAATTTATT
*
165559 TATTTATTATTA-TTATTAATTTTTT
1 TATTTATTATTATTTATTAATTTATT
165584 TATTT-TTATT
1 TATTTATTATT
165594 TTTGCAAGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 5 0.16
25 21 0.66
26 6 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
TATTTATTATTATTTATTAATTTATT
Found at i:165701 original size:33 final size:33
Alignment explanation
Indices: 165664--165727 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
165654 TTTGACTCCT
* *
165664 ATTGAAACACTAAAACCAACGTATTTGAGTCAA
1 ATTGAAACACTAAAACCAAAGCATTTGAGTCAA
* *
165697 ATTGAAATACTAAAACTAAAGCATTTGAGTC
1 ATTGAAACACTAAAACCAAAGCATTTGAGTC
165728 CAAGTAGGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (33 bp):
ATTGAAACACTAAAACCAAAGCATTTGAGTCAA
Found at i:165892 original size:21 final size:21
Alignment explanation
Indices: 165868--165923 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
165858 CCGAGGTAAT
165868 TATTTTATA-TA-TATATATATA
1 TATTTTATATTATTATAT-TA-A
*
165889 TATTTAATATTATTATATTAA
1 TATTTTATATTATTATATTAA
*
165910 TATTTTTTATTATT
1 TATTTTATATTATT
165924 CTTTTCTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 21 0.70
22 4 0.13
23 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATATTATTATATTAA
Found at i:168847 original size:13 final size:13
Alignment explanation
Indices: 168802--168865 Score: 71
Period size: 12 Copynumber: 5.0 Consensus size: 13
168792 TTCAATCAAG
* *
168802 AACAAAAAGAGAA
1 AACAAAGAGAAAA
168815 AA-AAAGAGAAAA
1 AACAAAGAGAAAA
168827 AAGCAAAGAGAAAA
1 AA-CAAAGAGAAAA
168841 TAA-AAAGAGAAAA
1 -AACAAAGAGAAAA
168854 AACAAAG-GAAAA
1 AACAAAGAGAAAA
168866 TTGAAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
12 17 0.38
13 16 0.36
14 10 0.22
15 2 0.04
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.02
Consensus pattern (13 bp):
AACAAAGAGAAAA
Found at i:168851 original size:27 final size:25
Alignment explanation
Indices: 168815--168866 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
168805 AAAAAGAGAA
168815 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAA-CAAAG-GAAAAT
168842 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAACAAAGGAAAAT
168867 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAACAAAGGAAAAT
Found at i:169058 original size:69 final size:69
Alignment explanation
Indices: 168940--169077 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
168930 GATTCAAACT
* * * *
168940 ATGAGATTGATCAAGCATAATTATTTTCGAATCATTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
169005 TCAA
66 TCAA
*
169009 ATGAGATTGATCAAGCACAATCA-TTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGAGC
1 ATGAGATTGATCAAGCACAATCATTTTC-GAATCACTGAACCACTCCACTCGAAGATCATAGAGC
169073 ATCAA
65 ATCAA
169078 GAGAGAGACA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 4 0.06
69 59 0.94
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:170038 original size:32 final size:32
Alignment explanation
Indices: 169997--170091 Score: 145
Period size: 32 Copynumber: 2.9 Consensus size: 32
169987 TGAGGGCATC
169997 TTTGAAGATTCAACATCAAATGTTGGGGCATTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCATTT
* *
170030 TTTGAGATTTAACATAAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
* *
170062 TTTGAGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATGTTGGGGCAT
170092 CTTTGGGAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
32 52 0.93
33 4 0.07
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.37
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTT
Found at i:170104 original size:32 final size:32
Alignment explanation
Indices: 169990--170105 Score: 135
Period size: 32 Copynumber: 3.6 Consensus size: 32
169980 GGAACAATGA
* *
169990 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATTTTTGGAGATTCAACATCAAATGTTG
* * *
170022 GGGCATTTTTTGAGATTTAACATAAAATGTTG
1 GGGCATTTTTGGAGATTCAACATCAAATGTTG
* * *
170054 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCATTTTTGGAGATTCAACATCAAATGTTG
*
170086 GGGCATCTTTGG-GAATTCAA
1 GGGCATTTTTGGAG-ATTCAA
170106 TATCCTGATG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
31 1 0.01
32 71 0.99
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (32 bp):
GGGCATTTTTGGAGATTCAACATCAAATGTTG
Found at i:170834 original size:43 final size:43
Alignment explanation
Indices: 170773--170871 Score: 189
Period size: 43 Copynumber: 2.3 Consensus size: 43
170763 CAGAGCCAAT
170773 TTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAG
1 TTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAG
*
170816 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
1 TTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAG
170859 TTCAACTTCACAG
1 TTCAACTTCACAG
170872 TGAAAGGACA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (43 bp):
TTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAG
Found at i:171451 original size:36 final size:36
Alignment explanation
Indices: 171331--171540 Score: 207
Period size: 37 Copynumber: 5.9 Consensus size: 36
171321 CTCACCATTC
* * * *
171331 TCTCTCCTGAGATAGCTTCCCTTGAAACAAAATCTTA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT-TTG
171368 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT-TTG
*
171405 TCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTCG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTT-G
* * * * *
171441 TCTCACTTGAGACAGTTT-CTTTTAGAAC-TAAGTT-
1 TCTCTCTTGAGACAGTTTCCCTTGA-AACAAAATTTG
** *
171475 T-T-TCTTGAGACAGTTTCTTTTGAAACAAATTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTG
* *
171509 TCCCTCTTGAGACAGTTTCTCTTGAAACAAAA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
171541 AAAACCCTTG
Statistics
Matches: 146, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
32 16 0.11
33 8 0.05
34 2 0.01
35 6 0.04
36 54 0.37
37 60 0.41
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (36 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTG
Found at i:171497 original size:15 final size:15
Alignment explanation
Indices: 171447--171497 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
171437 TTCGTCTCAC
171447 TTGAGACAGTTTCTT
1 TTGAGACAGTTTCTT
171462 TT-AGAACTAAGTTT-TT
1 TTGAG-AC--AGTTTCTT
171478 CTTGAGACAGTTTCTT
1 -TTGAGACAGTTTCTT
171494 TTGA
1 TTGA
171498 AACAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
14 2 0.07
15 13 0.43
16 4 0.13
17 9 0.30
18 2 0.07
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (15 bp):
TTGAGACAGTTTCTT
Found at i:171597 original size:28 final size:29
Alignment explanation
Indices: 171538--171594 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
171528 TCTTGAAACA
*
171538 AAAAAAACCCTTGAAATTGTTTCTCTTGG
1 AAAAAAACCCTTGAAAATGTTTCTCTTGG
*
171567 AAAAAAACCTTTGAAAATGTTTCTCTTG
1 AAAAAAACCCTTGAAAATGTTTCTCTTG
171595 AAACATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (29 bp):
AAAAAAACCCTTGAAAATGTTTCTCTTGG
Found at i:171743 original size:83 final size:83
Alignment explanation
Indices: 171604--171861 Score: 335
Period size: 83 Copynumber: 3.1 Consensus size: 83
171594 GAAACATCAA
* * * * *
171604 ACCTTCGAGTTCGACTATGCTCAGCTTCAAGACACATCATTTACAGCATAACTCAAGGCTATAAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
171669 GGTTATCTGCCAACAAAG
66 GGTTATCTGCCAACAAAG
171687 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
*
171752 GGTTATCT-CTCAACAAGG
66 GGTTATCTGC-CAACAAAG
* * * * * * **
171770 ACCTCCGAGTTCGACTCCACTCAGCTCAAAGGCACCATCATTTACATCATAGCTCAAGGAAAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTACAGCATAACTCAAGGCTAGAA
*
171835 GGGTTATATG-C--CAAAG
65 GGGTTATCTGCCAACAAAG
171851 ACCTTCGAGTT
1 ACCTTCGAGTT
171862 TGATCCATTC
Statistics
Matches: 155, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
81 14 0.09
82 1 0.01
83 106 0.68
84 34 0.22
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (83 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTGCCAACAAAG
Found at i:172233 original size:8 final size:8
Alignment explanation
Indices: 172205--172278 Score: 69
Period size: 8 Copynumber: 8.9 Consensus size: 8
172195 ACAAAAACAT
172205 TTTATTATA
1 TTTATT-TA
172214 TTATATTATA
1 TT-TATT-TA
172224 TTTATTTA
1 TTTATTTA
172232 TTTATTTA
1 TTTATTTA
172240 TTTA-TTA
1 TTTATTTA
*
172247 TTTTTATTA
1 TTTAT-TTA
* *
172256 TTAATTTT
1 TTTATTTA
*
172264 TTTATTTT
1 TTTATTTA
172272 TTTATTT
1 TTTATTT
172279 TTACAGGCCC
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.11
8 30 0.53
9 12 0.21
10 9 0.16
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTATTTA
Found at i:172239 original size:12 final size:12
Alignment explanation
Indices: 172205--172278 Score: 69
Period size: 12 Copynumber: 5.9 Consensus size: 12
172195 ACAAAAACAT
172205 TTTATTATATTATA
1 TTTATT-TATT-TA
172219 TTATATTTATTTA
1 TT-TATTTATTTA
172232 TTTATTTATTTA
1 TTTATTTATTTA
*
172244 -TTATTTTTATTA
1 TTTATTTAT-TTA
* *
172256 TTAATTTTTTTA
1 TTTATTTATTTA
*
172268 TTTTTTTATTT
1 TTTATTTATTT
172279 TTACAGGCCC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
11 7 0.13
12 24 0.46
13 11 0.21
14 6 0.12
15 4 0.08
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:172248 original size:28 final size:27
Alignment explanation
Indices: 172214--172270 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
172204 TTTTATTATA
*
172214 TTATA-TTATATTTATTTATTTATTTAT
1 TTATATTTATA-TTATTAATTTATTTAT
* *
172241 TTATTATTTTTATTATTAATTTTTTTAT
1 TTA-TATTTATATTATTAATTTATTTAT
172269 TT
1 TT
172271 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 3 0.12
28 18 0.72
29 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (27 bp):
TTATATTTATATTATTAATTTATTTAT
Found at i:172378 original size:33 final size:33
Alignment explanation
Indices: 172331--172396 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
172321 GAAAATAAAT
*
172331 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACATATTTGAGTCCTATTGAAACACTAAAAC
172364 CAACATATTTGAGTCCTATTGAAACACTAAAAC
1 CAACATATTTGAGTCCTATTGAAACACTAAAAC
172397 TGAAGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (33 bp):
CAACATATTTGAGTCCTATTGAAACACTAAAAC
Found at i:172594 original size:8 final size:8
Alignment explanation
Indices: 172550--172596 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
172540 AACCAAGGTA
172550 ATTATTAT
1 ATTATTAT
172558 A-TATATAT
1 ATTAT-TAT
172566 ATATATATAT
1 AT-TAT-TAT
172576 ATTATTAAT
1 ATTATT-AT
172585 ATTATTAT
1 ATTATTAT
172593 ATTA
1 ATTA
172597 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.09
8 12 0.34
9 11 0.31
10 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATTATTAT
Found at i:172982 original size:3 final size:3
Alignment explanation
Indices: 172974--172999 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
172964 CCGACAAGCA
172974 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
173000 GAACAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:176337 original size:31 final size:31
Alignment explanation
Indices: 176299--176366 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
176289 AAAGTAAATC
176299 AAAACATATCTAAATAGTTAAAACACTAACT
1 AAAACATATCTAAATAGTTAAAACACTAACT
*
176330 AAAACATATCTAAATAGTTAAAATACTAACT
1 AAAACATATCTAAATAGTTAAAACACTAACT
176361 AAAACA
1 AAAACA
176367 CAATTTAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (31 bp):
AAAACATATCTAAATAGTTAAAACACTAACT
Found at i:179475 original size:6 final size:6
Alignment explanation
Indices: 179464--179502 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
179454 AGACACGTAT
179464 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GAC
179503 AAGGAAGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.49, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:190000 original size:3 final size:3
Alignment explanation
Indices: 189992--190027 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
189982 TGGATGGTCT
*
189992 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
190028 ATCATCATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:196988 original size:2 final size:2
Alignment explanation
Indices: 196981--197018 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
196971 TATAATTTAA
196981 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
197019 TCAAGTGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:205631 original size:3 final size:3
Alignment explanation
Indices: 205623--205652 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
205613 ATCGTCATCC
*
205623 CTT CTT CTT CTT CTT CTT CTT CTT CCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
205653 TTTTAAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:207332 original size:21 final size:21
Alignment explanation
Indices: 207306--207355 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
207296 AGTTGAGTTA
207306 AACTCAACACTAATCGAATTC
1 AACTCAACACTAATCGAATTC
* *
207327 AACTCAACTCTAGTCGAATTC
1 AACTCAACACTAATCGAATTC
207348 AACTCAAC
1 AACTCAAC
207356 CATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.30, G:0.06, T:0.24
Consensus pattern (21 bp):
AACTCAACACTAATCGAATTC
Found at i:212531 original size:4 final size:4
Alignment explanation
Indices: 212524--212551 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
212514 TATTGAAGCT
212524 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
212552 CAAGCACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:228086 original size:2 final size:2
Alignment explanation
Indices: 228079--228106 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
228069 ATATTATAAT
228079 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
228107 AAAGTGGTTA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:230770 original size:21 final size:20
Alignment explanation
Indices: 230733--230876 Score: 116
Period size: 19 Copynumber: 7.2 Consensus size: 20
230723 AAATTTACGT
*
230733 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
230752 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
** *
230773 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
230792 TAGTCCAAGTTCACGTTGCGT
1 TAGTCCAAGTTC-CGTTGCGA
** *
230813 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
230832 TAGTCCAAGTTCACGTTGCGT
1 TAGTCCAAGTTC-CGTTGCGA
** *
230853 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
230872 TAGTC
1 TAGTC
230877 GAAGACACGT
Statistics
Matches: 95, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
19 50 0.53
21 45 0.47
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (20 bp):
TAGTCCAAGTTCCGTTGCGA
Found at i:230791 original size:40 final size:40
Alignment explanation
Indices: 230736--230876 Score: 255
Period size: 40 Copynumber: 3.5 Consensus size: 40
230726 TTTACGTTAG
* * *
230736 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
230776 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
230816 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
230856 TCCAAATTCGTTGCGATAGTC
1 TCCAAATTCGTTGCGATAGTC
230877 GAAGACACGT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (40 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
Found at i:231255 original size:22 final size:22
Alignment explanation
Indices: 231227--231283 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 22
231217 ACTATCGCAA
*
231227 CAACACATTTTTCAAACTCTCG
1 CAACACATTTTTCAAACTATCG
231249 CAACACA-TTTT--AACTATCG
1 CAACACATTTTTCAAACTATCG
231268 CAACACATTTTTCAAA
1 CAACACATTTTTCAAA
231284 ATCGCGTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 14 0.45
20 4 0.13
21 4 0.13
22 9 0.29
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.32
Consensus pattern (22 bp):
CAACACATTTTTCAAACTATCG
Found at i:231333 original size:21 final size:21
Alignment explanation
Indices: 231285--231338 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
231275 TTTTTCAAAA
*
231285 TCGCGTTGCGAATCTTATAAT
1 TCGCGTTGCGAATCTGATAAT
231306 T-GCGTTGCGAATCTGGAT-AT
1 TCGCGTTGCGAATCT-GATAAT
231326 TCGCGTTGCGAAT
1 TCGCGTTGCGAAT
231339 TTGAAAACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGAATCTGATAAT
Found at i:233358 original size:7 final size:7
Alignment explanation
Indices: 233346--233375 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
233336 AATTTATTAA
233346 AAATATT
1 AAATATT
233353 AAATATT
1 AAATATT
233360 AAATATT
1 AAATATT
*
233367 ATATATT
1 AAATATT
233374 AA
1 AA
233376 GTTAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATATT
Found at i:259061 original size:6 final size:6
Alignment explanation
Indices: 259050--259083 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
259040 TGCATAAATT
259050 CATGAA CATGAA CAAT-AA CATGAA CATGAA CATG
1 CATGAA CATGAA C-ATGAA CATGAA CATGAA CATG
259084 TGTTTGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.08
6 22 0.85
7 2 0.08
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.18
Consensus pattern (6 bp):
CATGAA
Found at i:259294 original size:13 final size:14
Alignment explanation
Indices: 259265--259295 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
259255 AACTATGCAA
259265 GTGATATGAACTAT
1 GTGATATGAACTAT
259279 GTGATATGAA-TAT
1 GTGATATGAACTAT
259292 GTGA
1 GTGA
259296 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:263237 original size:377 final size:377
Alignment explanation
Indices: 262010--263518 Score: 2804
Period size: 377 Copynumber: 4.0 Consensus size: 377
262000 TACTTCCATG
*
262010 ACACTCCTAAAATCGAAATATTATCTTATTTCAGCTAAATATAACTTTATATTCAACCACCATAA
1 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
*
262075 ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTTAGT
66 ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
* *
262140 GTAGAACATTTTATTATTTCATACTTTAGTCCAAATTCTCATTAAAATGTACC-AAAAATAAAAA
131 GTAGAACGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAAT-AAAA
* *
262204 AATAAAACCTTGCTCACCTTGGCTATGGAGTCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCT
195 AAGAAAACCTTGCTCACCTTGGCTATGGAATCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCT
*
262269 TGAAATTTCTTACAAAACATCTCCTTAAAAGTTCAATTTAAAATGAATTAAAATTTATTTTAGCC
260 TGAAATTTCTTACAAAACATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTTATTTTAGCC
262334 CAAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
325 CAAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
262387 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
1 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
262452 ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
66 ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
262517 GTAGAACGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAAATAAAA
131 GTAGAACGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACC-AAAAAATAAAA
262582 AAGAAAACCTTGCTCACCTTGGCTATGGAATCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCT
195 AAGAAAACCTTGCTCACCTTGGCTATGGAATCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCT
*
262647 TGAAATTTCTTACAAAACATCTCCTTAAAAGTCTAATTTAAAATGAATTAAAATTTATTTTAGCC
260 TGAAATTTCTTACAAAACATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTTATTTTAGCC
262712 CAAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
325 CAAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
262765 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
1 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
262830 ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
66 ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
*
262895 GTAGAACGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAAGAAAAA
131 GTAGAACGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
262960 AGAAAACCTTGCTCACCTTGGCTATGGAATCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCTT
196 AGAAAACCTTGCTCACCTTGGCTATGGAATCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCTT
*
263025 GAAATTTCTTACAAAATATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTTATTTTAGCCC
261 GAAATTTCTTACAAAACATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTTATTTTAGCCC
263090 AAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
326 AAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
*
263142 ACACTCCTAAAATCGAAATATTATCTTAGTTCAACTAAATATAACTTTATATTCAACCACCATAA
1 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
* *
263207 ATACCAATTTCACCATTTAAGCAAGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
66 ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
*
263272 GTAGATCGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
131 GTAGAACGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
* * *
263337 AGAAAACCTTGCTCACCTTGGCTATGGAGTCACGGCATGTTGTTGGAGAAGAGAAGAGTTCTCTT
196 AGAAAACCTTGCTCACCTTGGCTATGGAATCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCTT
* * *
263402 GAAATTTCTTACAAAATATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTCATTTTAACCC
261 GAAATTTCTTACAAAACATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTTATTTTAGCCC
*
263467 AAAAGTCAAAATTACTCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
326 AAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
263519 TTTTTATCTC
Statistics
Matches: 1108, Mismatches: 22, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
377 736 0.66
378 366 0.33
379 6 0.01
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (377 bp):
ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
GTAGAACGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
AGAAAACCTTGCTCACCTTGGCTATGGAATCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCTT
GAAATTTCTTACAAAACATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTTATTTTAGCCC
AAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
Found at i:270624 original size:24 final size:22
Alignment explanation
Indices: 270558--270622 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
270548 AATTAATTTT
* *
270558 TATTATAAATCTTATATA--AA
1 TATTATTAATATTATATATTAA
*
270578 -ATTATTTATA-TATATATTAA
1 TATTATTAATATTATATATTAA
270598 TATTATTAATATTATATATTAA
1 TATTATTAATATTATATATTAA
270620 TAT
1 TAT
270623 ATAAATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 6 0.16
19 7 0.19
20 2 0.05
21 9 0.24
22 13 0.35
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTATTAATATTATATATTAA
Found at i:270631 original size:24 final size:22
Alignment explanation
Indices: 270588--270634 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
270578 ATTATTTATA
*
270588 TATATATTAATATTATTAATAT
1 TATATATTAATATTAATAATAT
270610 TATATATTAATATATAAATAATAT
1 TATATATTAATAT-T-AATAATAT
270634 T
1 T
270635 TTTGGATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 1 0.05
24 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATATTAATATTAATAATAT
Found at i:272494 original size:21 final size:21
Alignment explanation
Indices: 272465--272515 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
272455 ATCAAAAGCC
*
272465 TTAAACTTTTGATTAAATG-AT
1 TTAAACTTTTGA-TAAAAGAAT
*
272486 TTAATCTTTTGATAAAAGAAT
1 TTAAACTTTTGATAAAAGAAT
*
272507 TTAACCTTT
1 TTAAACTTT
272516 CCATAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (21 bp):
TTAAACTTTTGATAAAAGAAT
Found at i:272937 original size:14 final size:14
Alignment explanation
Indices: 272918--272954 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
272908 AGAAAGAAGG
272918 GAGAGCTTTCAGGA
1 GAGAGCTTTCAGGA
272932 GAGAGCTTTCAGGA
1 GAGAGCTTTCAGGA
*
272946 GAGTGCTTT
1 GAGAGCTTT
272955 TTTGAGAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.27
Consensus pattern (14 bp):
GAGAGCTTTCAGGA
Found at i:273321 original size:44 final size:44
Alignment explanation
Indices: 273271--273354 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
273261 TATAACAAAA
*
273271 ACAAAGAGAATATATATTTTAACAAATGCAAGCTTGTGAAGCTT
1 ACAAAGAGAATATATATTTTAACAAATACAAGCTTGTGAAGCTT
*
273315 ACAAAGAGAATATATATTTTAACAAATACAAGTTTGTGAA
1 ACAAAGAGAATATATATTTTAACAAATACAAGCTTGTGAA
273355 ATTTACTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (44 bp):
ACAAAGAGAATATATATTTTAACAAATACAAGCTTGTGAAGCTT
Found at i:276583 original size:15 final size:15
Alignment explanation
Indices: 276563--276604 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
276553 TTGTAGGAGT
*
276563 TTTTGGTTTGTTTTA
1 TTTTGGCTTGTTTTA
276578 TTTTGGCTTGTTTTA
1 TTTTGGCTTGTTTTA
276593 TTTTGGCGTTGT
1 TTTTGGC-TTGT
276605 CATGTGCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.05, C:0.05, G:0.24, T:0.67
Consensus pattern (15 bp):
TTTTGGCTTGTTTTA
Found at i:291948 original size:16 final size:16
Alignment explanation
Indices: 291927--291958 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
291917 GCACGAGAAA
291927 TATACACTTTCTGTTG
1 TATACACTTTCTGTTG
291943 TATACACTTTCTGTTG
1 TATACACTTTCTGTTG
291959 AATTCGACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (16 bp):
TATACACTTTCTGTTG
Found at i:295035 original size:2 final size:2
Alignment explanation
Indices: 295028--295085 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
295018 TACCTTACCA
* *
295028 AT AT AT AT AT AT TT GAG A- 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
295070 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
295086 TCTCAAATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:297153 original size:18 final size:18
Alignment explanation
Indices: 297130--297173 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
297120 TTCTGGTAAT
* * *
297130 TTTAAAAAATTTATTTTC
1 TTTAAAAAATATATTATA
297148 TTT-AAAAATATATTATA
1 TTTAAAAAATATATTATA
297165 TTTAAAAAA
1 TTTAAAAAA
297174 AACTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAAAAAATATATTATA
Found at i:299910 original size:26 final size:24
Alignment explanation
Indices: 299872--299924 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
299862 TAATAATTCC
299872 AAAAATAGATAATTCAGTT-TTTTT
1 AAAAATAGATAA-TCAGTTATTTTT
*
299896 AAAATATATGATAATCATTTATTTTT
1 AAAA-ATA-GATAATCAGTTATTTTT
299922 AAA
1 AAA
299925 TTTTGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 4 0.16
25 8 0.32
26 13 0.52
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (24 bp):
AAAAATAGATAATCAGTTATTTTT
Found at i:308392 original size:23 final size:21
Alignment explanation
Indices: 308339--308401 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
308329 TTTTGGTGCA
*
308339 GAGGGAATCGATTCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
* *
308360 GAGGGAACCGATTCCTCCTTT
1 GAGGGAACCGATTCCCCCCTT
308381 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
308402 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.54
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:315558 original size:28 final size:29
Alignment explanation
Indices: 315504--315567 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
315494 TAAGCATTAA
315504 AGTTTAAAATTTTAGATATTAGAGTCTAG
1 AGTTTAAAATTTTAGATATTAGAGTCTAG
*
315533 AGTTTAAAA-TTTAGA-ATCTAGTGTCTAG
1 AGTTTAAAATTTTAGATAT-TAGAGTCTAG
315561 -GTTTAAA
1 AGTTTAAA
315568 TTGCAAGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 9 0.27
28 15 0.45
29 9 0.27
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.41
Consensus pattern (29 bp):
AGTTTAAAATTTTAGATATTAGAGTCTAG
Found at i:318596 original size:20 final size:19
Alignment explanation
Indices: 318567--318606 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
318557 CAAATGGGTT
318567 CTTTTTGTTTTTG-GTTTTG
1 CTTTTTG-TTTTGAGTTTTG
318586 CTTTGTTGTTTTGAGTTTTG
1 CTTT-TTGTTTTGAGTTTTG
318606 C
1 C
318607 AAGTTCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.03, C:0.07, G:0.23, T:0.68
Consensus pattern (19 bp):
CTTTTTGTTTTGAGTTTTG
Found at i:325766 original size:159 final size:157
Alignment explanation
Indices: 325439--325748 Score: 444
Period size: 159 Copynumber: 2.0 Consensus size: 157
325429 CCGCAACCTG
* * * *
325439 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTTATCAACTTTCTTCTCCTCAATTCGATTAACAA
1 TTTAGCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
* **
325504 CCTTGTCATCTTGAGCTTCACTGATTTTCTTCTTCTTCTTGGTTTTCTTTTTGACAACTTTCGAT
66 CCTTGTCATCTCGAGCTTCACTGA--TTCTTCTTCTTCTTGGTTTTCTCCTTGACAACTTTCGAT
* *
325569 GTTTGGGAAGCATTTGGTGGTTCAACATA
129 ATTTGGGAAGCACTTGGTGGTTCAACATA
* * *
325598 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTTGATCCACAA
1 TTTAGCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
* *
325663 CCTTGTTATCTCGAGCTTCACTGA-TCTTCTTGTTCTTGGTTTTCTCCTTGACAACTTTCGGA-A
66 CCTTGTCATCTCGAGCTTCACTGATTCTTCTTCTTCTTGGTTTTCTCCTTGACAACTTTC-GATA
*
325726 TTTGTGAAGCACTTGGTGGTTCA
130 TTTGGGAAGCACTTGGTGGTTCA
325749 GCGTATTCTT
Statistics
Matches: 137, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
156 53 0.39
157 2 0.01
159 82 0.60
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.45
Consensus pattern (157 bp):
TTTAGCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
CCTTGTCATCTCGAGCTTCACTGATTCTTCTTCTTCTTGGTTTTCTCCTTGACAACTTTCGATAT
TTGGGAAGCACTTGGTGGTTCAACATA
Found at i:332420 original size:82 final size:81
Alignment explanation
Indices: 332329--332491 Score: 227
Period size: 82 Copynumber: 2.0 Consensus size: 81
332319 CATATATTAA
* *
332329 AATTATTATATGATGCAAATTCAGAGCATGAAGATGCAATATACATTAATGCAGATATAAATACC
1 AATTATTATATGATACAAATTCAGAGCATGAAAATGCAATATACATTAATGCAGATA-AAATACC
**
332394 ATGCATGTGACATACAT
65 ATGCATGCAACATACAT
* * * * * *
332411 AATTATTATATGATACAAATTCAGAGGATGAAAATGCACTATACATTTATTCAGATACACTACCA
1 AATTATTATATGATACAAATTCAGAGCATGAAAATGCAATATACATTAATGCAGATAAAATACCA
332476 TGCATGCAACATACAT
66 TGCATGCAACATACAT
332492 TTATGCAGAT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 20 0.28
82 51 0.72
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (81 bp):
AATTATTATATGATACAAATTCAGAGCATGAAAATGCAATATACATTAATGCAGATAAAATACCA
TGCATGCAACATACAT
Found at i:332490 original size:35 final size:36
Alignment explanation
Indices: 332451--332522 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
332441 AAAATGCACT
* *
332451 ATACATTTATTCAGATAC-ACTACCATGCATGCAAC
1 ATACATTTATGCAGATACAAATACCATGCATGCAAC
*
332486 ATACATTTATGCAGATACAAATACCATGCATGTAAC
1 ATACATTTATGCAGATACAAATACCATGCATGCAAC
332522 A
1 A
332523 CATTCATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (36 bp):
ATACATTTATGCAGATACAAATACCATGCATGCAAC
Done.