Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 84 of 335
Found at i:27802244 original size:2 final size:2
Alignment explanation
Indices: 27802237--27802265 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27802227 ACCTATTCGA
27802237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27802266 AATCATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27803451 original size:43 final size:41
Alignment explanation
Indices: 27803304--27803463 Score: 144
Period size: 43 Copynumber: 3.8 Consensus size: 41
27803294 ATATCGTACA
* * * *
27803304 ATGCCAACGTCCCAGACGTGGTCTTACATGCT-ATCATATAGCG
1 ATGCCAATGTCCCA-ACATGGTCTTACACG-TAATCAAATA-CG
* *
27803347 ATGCCACTGTCCCAGACAGGGTCTTACACG-AATCAAATACG
1 ATGCCAATGTCCCA-ACATGGTCTTACACGTAATCAAATACG
** * *
27803388 ATATCGATGTCCCAAGCATGGTCTTACACGTAATCAAATATTG
1 ATGCCAATGTCCCAA-CATGGTCTTACACGTAATCAAATA-CG
*
27803431 ATGCCAATGTCCTATACATGGTCTTACACGTAA
1 ATGCCAATGTCCCA-ACATGGTCTTACACGTAA
27803464 CCATATATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
40 1 0.01
41 25 0.26
42 16 0.17
43 53 0.55
44 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (41 bp):
ATGCCAATGTCCCAACATGGTCTTACACGTAATCAAATACG
Found at i:27804605 original size:14 final size:15
Alignment explanation
Indices: 27804588--27804616 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27804578 TCACGAAAAT
27804588 TTCACACAT-ATAAA
1 TTCACACATAATAAA
27804602 TTCACACATAATAAA
1 TTCACACATAATAAA
27804617 CAAAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:27806935 original size:26 final size:26
Alignment explanation
Indices: 27806906--27806963 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
27806896 TGATACAAAT
27806906 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
27806932 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27806958 TGATAA
1 TGATAA
27806964 GAATTTCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:27808456 original size:25 final size:26
Alignment explanation
Indices: 27808428--27808479 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
27808418 TTTACAGTTT
27808428 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
27808453 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
27808479 T
1 T
27808480 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:27822062 original size:20 final size:20
Alignment explanation
Indices: 27822037--27822076 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
27822027 ACTTTTATAT
27822037 TTTTAC-TTTTAAGAATTTAA
1 TTTTACTTTTTAA-AATTTAA
27822057 TTTTACTTTTTAAAATTTAA
1 TTTTACTTTTTAAAATTTAA
27822077 GCTCATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTACTTTTTAAAATTTAA
Found at i:27823030 original size:29 final size:29
Alignment explanation
Indices: 27822988--27823045 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
27822978 CACTCGATCA
27822988 CTTTAGCTTGTATTTGAGTGATTAAATCT
1 CTTTAGCTTGTATTTGAGTGATTAAATCT
27823017 CTTTAGCTTGTATTTGAGTGATTAAATCT
1 CTTTAGCTTGTATTTGAGTGATTAAATCT
27823046 TTATTGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (29 bp):
CTTTAGCTTGTATTTGAGTGATTAAATCT
Found at i:27828167 original size:28 final size:28
Alignment explanation
Indices: 27828136--27828225 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
27828126 TAACCCAATA
27828136 AAATAGTTACATGTGAAAATAATAAAAT
1 AAATAGTTACATGTGAAAATAATAAAAT
* * *
27828164 AAATAAATCATACA--TGAAATTAAAAAAAT
1 AAAT-AGT--TACATGTGAAAATAATAAAAT
*
27828193 AAATAGTTACATGTGAATATAATAAAAT
1 AAATAGTTACATGTGAAAATAATAAAAT
27828221 AAATA
1 AAATA
27828226 AATCATACAT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
26 4 0.08
28 23 0.46
29 19 0.38
31 4 0.08
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (28 bp):
AAATAGTTACATGTGAAAATAATAAAAT
Found at i:27828198 original size:57 final size:57
Alignment explanation
Indices: 27828136--27828247 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
27828126 TAACCCAATA
27828136 AAATAGTTACATGTGAAAATAATAAAATAAATAAATCATACATGAAATTAAAAAAAT
1 AAATAGTTACATGTGAAAATAATAAAATAAATAAATCATACATGAAATTAAAAAAAT
*
27828193 AAATAGTTACATGTGAATATAATAAAATAAATAAATCATACATGAAATTAAAAAA
1 AAATAGTTACATGTGAAAATAATAAAATAAATAAATCATACATGAAATTAAAAAA
27828248 TAACTCTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (57 bp):
AAATAGTTACATGTGAAAATAATAAAATAAATAAATCATACATGAAATTAAAAAAAT
Found at i:27828247 original size:28 final size:29
Alignment explanation
Indices: 27828149--27828250 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
27828139 TAGTTACATG
*
27828149 TGAAAATAATAAAATAAATAAATCATACA
1 TGAAATTAATAAAATAAATAAATCATACA
* *
27828178 TGAAATTAAAAAAATAAAT-AGT--TACA
1 TGAAATTAATAAAATAAATAAATCATACA
*
27828204 TGTGAATATAATAAAATAAATAAATCATACA
1 TG-AAAT-TAATAAAATAAATAAATCATACA
27828235 TGAAATTAA-AAAATAA
1 TGAAATTAATAAAATAA
27828251 CTCTTAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
26 6 0.10
27 3 0.05
28 21 0.34
29 22 0.36
30 3 0.05
31 6 0.10
ACGTcount: A:0.63, C:0.05, G:0.06, T:0.26
Consensus pattern (29 bp):
TGAAATTAATAAAATAAATAAATCATACA
Found at i:27829573 original size:26 final size:26
Alignment explanation
Indices: 27829531--27829588 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
27829521 TTTTTTTTTG
27829531 TATAA-TTATATACATAAGACT-AAAAT
1 TATAATTTATATACATAA-A-TAAAAAT
*
27829557 TATAATTTA-ATATATAAATAAAAAT
1 TATAATTTATATACATAAATAAAAAT
27829582 T-TAATTT
1 TATAATTT
27829589 TTAATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 7 0.24
25 7 0.24
26 12 0.41
27 3 0.10
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (26 bp):
TATAATTTATATACATAAATAAAAAT
Found at i:27829750 original size:26 final size:29
Alignment explanation
Indices: 27829720--27829772 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
27829710 TTAATTTTTT
27829720 AATTATAAT-T-TA-TTAAATTTATAATA
1 AATTATAATATATATTTAAATTTATAATA
*
27829746 AATTATAATATATATTTAATTTTATAA
1 AATTATAATATATATTTAAATTTATAA
27829773 ATATCTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 1 0.04
28 2 0.09
29 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AATTATAATATATATTTAAATTTATAATA
Found at i:27829804 original size:34 final size:35
Alignment explanation
Indices: 27829758--27829826 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
27829748 TTATAATATA
* *
27829758 TATTTAATTTTATAA-ATATCTTTGTTTTAAATTTT
1 TATTTAATTTTATAATATATATTTGGTTT-AATTTT
27829793 TATTT-ATTTTATAATATATATTTGGTTTAATTTT
1 TATTTAATTTTATAATATATATTTGGTTTAATTTT
27829827 GCCAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 15 0.48
35 16 0.52
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (35 bp):
TATTTAATTTTATAATATATATTTGGTTTAATTTT
Found at i:27829821 original size:18 final size:18
Alignment explanation
Indices: 27829748--27829815 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
27829738 TTATAATAAA
27829748 TTATAATATATATTTAATT
1 TTATAATATATATTT-ATT
* *
27829767 TTATAA-ATATCTTTGTT
1 TTATAATATATATTTATT
* *
27829784 TTA-AATTTTTATTTATT
1 TTATAATATATATTTATT
27829801 TTATAATATATATTT
1 TTATAATATATATTT
27829816 GGTTTAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
16 2 0.05
17 15 0.38
18 16 0.41
19 6 0.15
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (18 bp):
TTATAATATATATTTATT
Found at i:27836204 original size:20 final size:21
Alignment explanation
Indices: 27836165--27836204 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27836155 TAAAATATTC
*
27836165 GAAAATTTTCATATATGATAG
1 GAAAATTTTCATAAATGATAG
*
27836186 GAAAATTTTGA-AAATGATA
1 GAAAATTTTCATAAATGATA
27836205 TTCTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (21 bp):
GAAAATTTTCATAAATGATAG
Found at i:27842271 original size:14 final size:15
Alignment explanation
Indices: 27842252--27842287 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
27842242 ATGTTATTAC
27842252 TAATTAAATTAA-AA
1 TAATTAAATTAACAA
27842266 TAATTAAA-TAACAA
1 TAATTAAATTAACAA
27842280 T-ATTAAAT
1 TAATTAAAT
27842288 GATTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATTAAATTAACAA
Found at i:27842896 original size:23 final size:23
Alignment explanation
Indices: 27842866--27842911 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
27842856 CAGGGCCATG
27842866 AAATCTCAAATAATTAAAAACTT
1 AAATCTCAAATAATTAAAAACTT
27842889 AAATCTCAAATAATTAAAAACTT
1 AAATCTCAAATAATTAAAAACTT
27842912 TTATTTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATCTCAAATAATTAAAAACTT
Found at i:27844757 original size:46 final size:46
Alignment explanation
Indices: 27844690--27844859 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 46
27844680 TGTAACCTGC
*
27844690 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGAGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCAT
* *
27844736 CCATAAGTGAAATCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACA-
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-G-C--GTTCGCAT
* * * * * *
27844785 GC-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCAT
27844829 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
27844860 TTCGGATGCT
Statistics
Matches: 101, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 2 0.02
45 2 0.02
46 57 0.56
47 26 0.26
48 3 0.03
49 2 0.02
50 2 0.02
51 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCAT
Found at i:27844811 original size:93 final size:93
Alignment explanation
Indices: 27844698--27844868 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
27844688 GCCCATAAGT
* *
27844698 GAACTCAGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAGTGAAATCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAAATCGGACTCAACTCAA
27844763 CGAGCTCGGATGCCTAGTTACAGCTCAC
66 CGAGCTCGGATGCCTAGTTACAGCTCAC
* * *
27844791 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAAATCGGACTCAACTCAA
*
27844856 CGAGTTCGGATGC
66 CGAGCTCGGATGC
27844869 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAAATCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACAGCTCAC
Found at i:27853471 original size:134 final size:136
Alignment explanation
Indices: 27853280--27853630 Score: 498
Period size: 135 Copynumber: 2.6 Consensus size: 136
27853270 CAACTTCACA
* * *
27853280 TGTTTAAAAGCCCAAGAGTTTAG-AATCAAAATCTAGGGTGAAGATTTTG-AAGACTAAAAGTTT
1 TGTTTAGAAGTCCAAGAGTTTAGAAATCAAAGTCTAGGGTGAAGATTTTGAAAGACTAAAAGTTT
* * * *
27853343 TCTCTAAAATCCCAAGAAATCTCT-TAG-ATTTCTAAAAACTCAAAGAAATATTGAAGAACATAA
66 TCTCTAAAATCCCAAGAAATCTATGAAGAATTT-GAAAAACTCAAAGAAATATTGAAGAACACAA
27853406 TACCACT
130 TACCACT
* * *
27853413 TGTTTAGAAGTCCAAAAGTTTAGAAATCAAAGTCTAAGGTGAAGATTTTGAAAG-CTAAAAATTT
1 TGTTTAGAAGTCCAAGAGTTTAGAAATCAAAGTCTAGGGTGAAGATTTTGAAAGACTAAAAGTTT
* * *
27853477 TCTCTAAAATCCCAAGAAATCTATGAAGAATTTGAAAAACTTAAAGAAATTTTGAAGAACACCAT
66 TCTCTAAAATCCCAAGAAATCTATGAAGAATTTGAAAAACTCAAAGAAATATTGAAGAACACAAT
*
27853542 ACCATT
131 ACCACT
* * *
27853548 TGTTTAGAAGTCCAAGAGTTTAGAAATCAAAGTCTAGGGTGAATATTTT-AAAGATTAGAAGTTT
1 TGTTTAGAAGTCCAAGAGTTTAGAAATCAAAGTCTAGGGTGAAGATTTTGAAAGACTAAAAGTTT
27853612 TCTCTAAAATCCCAAGAAA
66 TCTCTAAAATCCCAAGAAA
27853631 GCTACTCTTC
Statistics
Matches: 193, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
133 20 0.10
134 60 0.31
135 109 0.56
136 4 0.02
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (136 bp):
TGTTTAGAAGTCCAAGAGTTTAGAAATCAAAGTCTAGGGTGAAGATTTTGAAAGACTAAAAGTTT
TCTCTAAAATCCCAAGAAATCTATGAAGAATTTGAAAAACTCAAAGAAATATTGAAGAACACAAT
ACCACT
Found at i:27854879 original size:11 final size:11
Alignment explanation
Indices: 27854865--27854905 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
27854855 TGTTTTCTCT
27854865 CTATTTTGCTA
1 CTATTTTGCTA
*
27854876 CTATTTTACTA
1 CTATTTTGCTA
* *
27854887 TTATGTTGCTA
1 CTATTTTGCTA
27854898 CTATTTTG
1 CTATTTTG
27854906 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:27855159 original size:12 final size:12
Alignment explanation
Indices: 27855144--27855177 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27855134 TATATATATT
*
27855144 AAAATTATATAA
1 AAAATAATATAA
27855156 AAAATAATATAA
1 AAAATAATATAA
*
27855168 AAATTAATAT
1 AAAATAATAT
27855178 GGGCGGACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:27856591 original size:13 final size:13
Alignment explanation
Indices: 27856573--27856597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27856563 AGTAACAAAC
27856573 CAGAACAATACTA
1 CAGAACAATACTA
27856586 CAGAACAATACT
1 CAGAACAATACT
27856598 TCTCTTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (13 bp):
CAGAACAATACTA
Found at i:27861754 original size:2 final size:2
Alignment explanation
Indices: 27861747--27861785 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27861737 AATAAACATA
27861747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27861786 AACTCACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27862236 original size:59 final size:58
Alignment explanation
Indices: 27862109--27862249 Score: 140
Period size: 59 Copynumber: 2.4 Consensus size: 58
27862099 AAGCATTAAT
* * ****
27862109 GCTGAAA-ATATATAACATATATTATCCTTTGATTTAATGTAATTTATCTCATTTTCC
1 GCTGAAATATATATAACATATATTATCCTTTAATTGAATGTAATTTATCTCATTGGAA
* * * * *
27862166 CCTCAAAATATATATACCCTATATTATCCTTTAATTGAATGTAATTTATGTCATTGGAA
1 GCT-GAAATATATATAACATATATTATCCTTTAATTGAATGTAATTTATCTCATTGGAA
*
27862225 GCTGAATATATATATATATATATAT
1 GCTGAA-ATATATATA-ACATATAT
27862250 ATATATATAT
Statistics
Matches: 64, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
57 2 0.03
58 5 0.08
59 52 0.81
60 5 0.08
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (58 bp):
GCTGAAATATATATAACATATATTATCCTTTAATTGAATGTAATTTATCTCATTGGAA
Found at i:27862237 original size:2 final size:2
Alignment explanation
Indices: 27862230--27862286 Score: 75
Period size: 2 Copynumber: 30.0 Consensus size: 2
27862220 TGGAAGCTGA
*
27862230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
27862271 AT AG AT -T AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT
27862287 TAAATTTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:27868331 original size:2 final size:2
Alignment explanation
Indices: 27868324--27868362 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27868314 AACTCAACCA
27868324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27868363 AATTACACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27876221 original size:23 final size:24
Alignment explanation
Indices: 27876195--27876241 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
27876185 AATTGGACTT
* *
27876195 AATTTTAAGATTT-AATTCTTATA
1 AATTTTAAAATTTCAATTATTATA
27876218 AATTTTAAAATTTCAATTATTATA
1 AATTTTAAAATTTCAATTATTATA
27876242 GTGAGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
AATTTTAAAATTTCAATTATTATA
Found at i:27881814 original size:6 final size:6
Alignment explanation
Indices: 27881803--27881843 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
27881793 AAGTAGTAGT
* * *
27881803 CTCAGG CTCAGG CTAAGG CTAAGG CTAAGG CTCAGG CTCAG
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAG
27881844 ACTCTATAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (6 bp):
CTCAGG
Found at i:27881827 original size:12 final size:12
Alignment explanation
Indices: 27881806--27881840 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
27881796 TAGTAGTCTC
27881806 AGGCTCAGGCTA
1 AGGCTCAGGCTA
*
27881818 AGGCTAAGGCTA
1 AGGCTCAGGCTA
27881830 AGGCTCAGGCT
1 AGGCTCAGGCT
27881841 CAGACTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.34, T:0.17
Consensus pattern (12 bp):
AGGCTCAGGCTA
Found at i:27885175 original size:15 final size:15
Alignment explanation
Indices: 27885139--27885173 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27885129 ACTGTCATGT
*
27885139 ATATATATTTTTTAA
1 ATATTTATTTTTTAA
27885154 ATATTTATTTTTT-A
1 ATATTTATTTTTTAA
27885168 ATATTT
1 ATATTT
27885174 TACTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATTTATTTTTTAA
Found at i:27894045 original size:49 final size:49
Alignment explanation
Indices: 27893992--27894090 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
27893982 CATTAGTTAG
*
27893992 TCCAAATAATTAGTTGTATTAATAAATTTAATAGTTAATGTGAATTTTT
1 TCCAAATAATTAGCTGTATTAATAAATTTAATAGTTAATGTGAATTTTT
* *
27894041 TCCAAATAATTAGCTGTATTAATAAATTTGATAGTTGATGTGAATTTTT
1 TCCAAATAATTAGCTGTATTAATAAATTTAATAGTTAATGTGAATTTTT
27894090 T
1 T
27894091 AAAAAGACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46
Consensus pattern (49 bp):
TCCAAATAATTAGCTGTATTAATAAATTTAATAGTTAATGTGAATTTTT
Found at i:27897526 original size:22 final size:22
Alignment explanation
Indices: 27897500--27897548 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
27897490 ATATCCAAAC
27897500 AATAACAATAAAATAGTAGCAA
1 AATAACAATAAAATAGTAGCAA
* * * *
27897522 TATAATAGTAAAATGGTAGCAA
1 AATAACAATAAAATAGTAGCAA
27897544 AATAA
1 AATAA
27897549 TGGCCGGGCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.22
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGCAA
Found at i:27897549 original size:22 final size:22
Alignment explanation
Indices: 27897508--27897549 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27897498 ACAATAACAA
*
27897508 TAAAATAGTAGCAATATAATAG
1 TAAAATAGTAGCAAAATAATAG
*
27897530 TAAAATGGTAGCAAAATAAT
1 TAAAATAGTAGCAAAATAAT
27897550 GGCCGGGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.26
Consensus pattern (22 bp):
TAAAATAGTAGCAAAATAATAG
Found at i:27907698 original size:42 final size:42
Alignment explanation
Indices: 27907550--27907699 Score: 156
Period size: 42 Copynumber: 3.5 Consensus size: 42
27907540 CGTACAGTGA
* * *
27907550 CATATCCCGGATATGGTCTTACATGTAATCTCATATCGATGTC
1 CATATCCCAGATATGGTCTTACACGTAATATCATATCGATG-C
* * * * * * *
27907593 AATAGCCCAGCTATGGTCTTACACGAAATTTCGTATCGATTC
1 CATATCCCAGATATGGTCTTACACGTAATATCATATCGATGC
* * * *
27907635 CATGTCACAGACATGGTCTTACACGTAATATCATACCGATGC
1 CATATCCCAGATATGGTCTTACACGTAATATCATATCGATGC
*
27907677 CATATCCCAGATATGGACTTACA
1 CATATCCCAGATATGGTCTTACA
27907700 TGTATTCTCA
Statistics
Matches: 83, Mismatches: 24, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
42 51 0.61
43 32 0.39
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
CATATCCCAGATATGGTCTTACACGTAATATCATATCGATGC
Found at i:27909365 original size:2 final size:2
Alignment explanation
Indices: 27909350--27909386 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
27909340 TTATTAATTA
27909350 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27909387 AGAGAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27912697 original size:26 final size:26
Alignment explanation
Indices: 27912661--27912744 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
27912651 TGATACAAAT
27912661 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
27912687 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
27912713 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
27912739 TGATAA
1 TGATAA
27912745 GAAATTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:27914264 original size:26 final size:26
Alignment explanation
Indices: 27914234--27914286 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
27914224 TTTATAGTTT
27914234 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
27914260 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
27914286 T
1 T
27914287 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:27915094 original size:21 final size:21
Alignment explanation
Indices: 27915068--27915153 Score: 109
Period size: 21 Copynumber: 4.1 Consensus size: 21
27915058 GGCTTTATCG
* *
27915068 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
27915089 ATCAGGCACCTCATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
27915110 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
* * * *
27915131 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
27915152 AT
1 AT
27915154 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (21 bp):
ATCAGGCACCTCATGTGTCGT
Found at i:27919584 original size:6 final size:5
Alignment explanation
Indices: 27919570--27919621 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
27919560 TTAGTTTAGG
* * *
27919570 TTTTC TTTTC ATTTTC TTTTC TCTTA TTTTC TTTTTT TTTTC TTTTTC
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC -TTTTC
27919618 TTTT
1 TTTT
27919622 TATTTTCGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 24 0.63
6 14 0.37
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:27919586 original size:11 final size:11
Alignment explanation
Indices: 27919570--27919628 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
27919560 TTAGTTTAGG
27919570 TTTTCTTTTCA
1 TTTTCTTTTCA
27919581 TTTTCTTTTC-
1 TTTTCTTTTCA
* * *
27919591 TCTTATTTTCT
1 TTTTCTTTTCA
* *
27919602 TTTTTTTTTCT
1 TTTTCTTTTCA
*
27919613 TTTTCTTTTTA
1 TTTTCTTTTCA
27919624 TTTTC
1 TTTTC
27919629 GTTGTAGTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 8 0.20
11 32 0.80
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTCA
Found at i:27919599 original size:26 final size:25
Alignment explanation
Indices: 27919570--27919619 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
27919560 TTAGTTTAGG
27919570 TTTTCTTTTCATTTTCTTTTCTCTTA
1 TTTTCTTTTCATTTTCTTTT-TCTTA
**
27919596 TTTTCTTTTTTTTTTCTTTTTCTT
1 TTTTCTTTTCATTTTCTTTTTCTT
27919620 TTTATTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTCTTTTCATTTTCTTTTTCTTA
Found at i:27919616 original size:17 final size:17
Alignment explanation
Indices: 27919596--27919628 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27919586 TTTTCTCTTA
*
27919596 TTTTCTTTTTTTTTTCT
1 TTTTCTTTTTATTTTCT
27919613 TTTTCTTTTTATTTTC
1 TTTTCTTTTTATTTTC
27919629 GTTGTAGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTCTTTTTATTTTCT
Found at i:27919646 original size:6 final size:6
Alignment explanation
Indices: 27919570--27919627 Score: 57
Period size: 6 Copynumber: 9.5 Consensus size: 6
27919560 TTAGTTTAGG
*
27919570 TTTTC- TTTTCA TTTTCT TTTCTCTT ATTTTCT TTTT-T TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTT-TC-T -TTTTCT TTTTCT TTTTCT TTTTCT
*
27919619 TTTTAT TTT
1 TTTTCT TTT
27919628 CGTTGTAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
5 10 0.22
6 27 0.59
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:27921612 original size:20 final size:19
Alignment explanation
Indices: 27921586--27921630 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
27921576 TGAAAGTTCC
*
27921586 AAAAATAATAAAAGAAATAA
1 AAAAATAACAAAA-AAATAA
*
27921606 TAAAATAACAAAAAAATAA
1 AAAAATAACAAAAAAATAA
27921625 AAAAAT
1 AAAAAT
27921631 GAAATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAAATAACAAAAAAATAA
Found at i:27925760 original size:19 final size:19
Alignment explanation
Indices: 27925736--27925772 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27925726 AAATTAATGT
*
27925736 ATTTTCAGATTTTCTATTA
1 ATTTTCAAATTTTCTATTA
*
27925755 ATTTTCAAATTTTTTATT
1 ATTTTCAAATTTTCTATT
27925773 TAAAAAGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTTCAAATTTTCTATTA
Found at i:27929805 original size:19 final size:20
Alignment explanation
Indices: 27929763--27929811 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
27929753 TAATTATTTG
* * *
27929763 TAAAATTTAATTTGAATATA
1 TAAAATATATTTTAAATATA
27929783 TAAAATATATTTTAAATAT-
1 TAAAATATATTTTAAATATA
27929802 TAAAATATAT
1 TAAAATATAT
27929812 AATGTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAAATATATTTTAAATATA
Found at i:27930328 original size:2 final size:2
Alignment explanation
Indices: 27930321--27930358 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
27930311 GTACTTCTAG
*
27930321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27930359 TGATATTTTA
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:27930383 original size:8 final size:7
Alignment explanation
Indices: 27930322--27930383 Score: 54
Period size: 8 Copynumber: 8.3 Consensus size: 7
27930312 TACTTCTAGA
27930322 TATATAT
1 TATATAT
27930329 ATATATAT
1 -TATATAT
27930337 ATATATAT
1 -TATATAT
27930345 ATATATAT
1 -TATATAT
27930353 GTATAT-T
1 -TATATAT
* *
27930360 GATATTT
1 TATATAT
27930367 TATATAT
1 TATATAT
27930374 TATAATAT
1 TAT-ATAT
27930382 TA
1 TA
27930384 ACAAATTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
6 4 0.08
7 10 0.21
8 34 0.71
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:27930746 original size:29 final size:28
Alignment explanation
Indices: 27930653--27930747 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
27930643 GATTATTTTT
*
27930653 TTTAAATTTTAAAAATATATTTTTTTATAA
1 TTTAATTTTTAAAAATA-ATTTTTTT-TAA
* ** * *
27930683 TTTTATATTTTTTAAAATAATTTTAATGATT
1 -TTTA-ATTTTTAAAAATAATTTTTTTTA-A
27930714 TTTAATTTTTAAAAATAAGTTTTTTTTAA
1 TTTAATTTTTAAAAATAA-TTTTTTTTAA
27930743 TTTAA
1 TTTAA
27930748 GAAATAATTA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
29 18 0.36
30 11 0.22
31 10 0.20
32 11 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTAATTTTTAAAAATAATTTTTTTTAA
Found at i:27933415 original size:13 final size:13
Alignment explanation
Indices: 27933397--27933422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27933387 TTAAAAAATA
27933397 TTAAATTTTAACT
1 TTAAATTTTAACT
27933410 TTAAATTTTAACT
1 TTAAATTTTAACT
27933423 AATGTAAAGT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAATTTTAACT
Found at i:27933688 original size:29 final size:29
Alignment explanation
Indices: 27933656--27933713 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
27933646 GATTTGTTAA
*
27933656 AACGTAGAATTTTAT-TTGTAAAATTTATT
1 AACGAAGAATTTTATATT-TAAAATTTATT
*
27933685 AACGAATAATTTTATATTTAAAATTTATT
1 AACGAAGAATTTTATATTTAAAATTTATT
27933714 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (29 bp):
AACGAAGAATTTTATATTTAAAATTTATT
Found at i:27934802 original size:3 final size:3
Alignment explanation
Indices: 27934794--27934831 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
27934784 CCAGAAGCTG
27934794 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
27934832 ACGTTATCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:27944542 original size:113 final size:114
Alignment explanation
Indices: 27944406--27944631 Score: 310
Period size: 114 Copynumber: 2.0 Consensus size: 114
27944396 ATGAATTTGA
* * * * ** *
27944406 CATCATCATATAATGCAAATTAGTTTAAAAT-TTCAAATGTTTTTACTTTGATATTAAAATCAAA
1 CATCAGCATAAAATGCAAATTAGTTTAAAATATTAAAATATTTTTACTTCAACATTAAAATCAAA
*
27944470 GGCTTTCATGAGTAAAAACTACAAGTCGTGAGCTTATTTAACTACAAAG
66 GGCTTTCAGGAGTAAAAACTACAAGTCGTGAGCTTATTTAACTACAAAG
* *
27944519 CATCAGCATAAAATGTAAATTAGTTTAAATTATTAAAATATTTTTACTTCAACATTAAAATCAAA
1 CATCAGCATAAAATGCAAATTAGTTTAAAATATTAAAATATTTTTACTTCAACATTAAAATCAAA
* * * * *
27944584 GGCTTTCAGGAGTAAAAATTATATGTTGTGGGCTTATTTAACTACAAA
66 GGCTTTCAGGAGTAAAAACTACAAGTCGTGAGCTTATTTAACTACAAA
27944632 AATAGCATAA
Statistics
Matches: 97, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
113 27 0.28
114 70 0.72
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (114 bp):
CATCAGCATAAAATGCAAATTAGTTTAAAATATTAAAATATTTTTACTTCAACATTAAAATCAAA
GGCTTTCAGGAGTAAAAACTACAAGTCGTGAGCTTATTTAACTACAAAG
Found at i:27945040 original size:5 final size:5
Alignment explanation
Indices: 27945030--27945054 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27945020 TATAACATAC
27945030 ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT
27945055 CTATATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:27946368 original size:25 final size:25
Alignment explanation
Indices: 27946339--27946395 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
27946329 TAATTAAAAT
*
27946339 TAAAATTAAATAGTAAAATTTAATCA
1 TAAAATTAAATAGCAAAATTTAAT-A
* *
27946365 -AAAATTAAGTGGCAAAATTTAATA
1 TAAAATTAAATAGCAAAATTTAATA
27946389 TAAAATT
1 TAAAATT
27946396 GAAGTGGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (25 bp):
TAAAATTAAATAGCAAAATTTAATA
Found at i:27946400 original size:26 final size:25
Alignment explanation
Indices: 27946353--27946402 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
27946343 ATTAAATAGT
27946353 AAAATTTAATCAAAAATTAAGTGGC
1 AAAATTTAATCAAAAATTAAGTGGC
27946378 AAAATTTAAT-ATAAAATTGAAGTGG
1 AAAATTTAATCA-AAAATT-AAGTGG
27946403 AGTGATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.04
25 16 0.70
26 6 0.26
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (25 bp):
AAAATTTAATCAAAAATTAAGTGGC
Found at i:27948411 original size:29 final size:27
Alignment explanation
Indices: 27948365--27948428 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
27948355 TAATTTTTTA
*
27948365 ATATTAAAATTGTTAAT-ATATTTTCATTT
1 ATATT-AAATTGTTAATAATA-TTAC-TTT
*
27948394 ATATTAAATTTTTGAATAATATTACTTT
1 ATATTAAATTGTT-AATAATATTACTTT
27948422 ATATTAA
1 ATATTAA
27948429 TCACATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 17 0.55
29 11 0.35
30 3 0.10
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (27 bp):
ATATTAAATTGTTAATAATATTACTTT
Found at i:27968019 original size:21 final size:20
Alignment explanation
Indices: 27967979--27968027 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
27967969 ATAAATAAAA
*
27967979 TCATTCATGTCAATTCCCTG
1 TCATTCATGACAATTCCCTG
*
27967999 TCATTCACTGACAATTTCCTG
1 TCATTCA-TGACAATTCCCTG
27968020 TCATTCAT
1 TCATTCAT
27968028 AACTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.41
Consensus pattern (20 bp):
TCATTCATGACAATTCCCTG
Found at i:27968229 original size:21 final size:21
Alignment explanation
Indices: 27968200--27968330 Score: 167
Period size: 21 Copynumber: 6.3 Consensus size: 21
27968190 TGAATACACC
*
27968200 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
27968221 AACAAAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
27968242 AACAGAAGCTC-GAA-AGTTG
1 AACAGAAGCTCATAAGAGCTG
* *
27968261 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTG
* *
27968282 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
*
27968303 AATAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
27968324 AACAGAA
1 AACAGAA
27968331 AGTAGCATAA
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 15 0.16
20 4 0.04
21 73 0.79
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:27972113 original size:22 final size:22
Alignment explanation
Indices: 27972053--27972116 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
27972043 ACTAATGAAT
* *
27972053 AGAGAGCACTAAAGTGATATAC
1 AGAGAGCACTAAAGTGCTAAAC
* *
27972075 AGAGAGCACGAATGTGCTAAAC
1 AGAGAGCACTAAAGTGCTAAAC
27972097 AGAGAGCACTAAAGTGCTAA
1 AGAGAGCACTAAAGTGCTAA
27972117 TAATCGAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.16
Consensus pattern (22 bp):
AGAGAGCACTAAAGTGCTAAAC
Found at i:27972130 original size:25 final size:25
Alignment explanation
Indices: 27972099--27972188 Score: 112
Period size: 25 Copynumber: 3.5 Consensus size: 25
27972089 TGCTAAACAG
27972099 AGAGCACTAAAGTGCTAATAATCGA
1 AGAGCACTAAAGTGCTAATAATCGA
*
27972124 AGAGCACTAACA-TGCTAATAATCGG
1 AGAGCACTAA-AGTGCTAATAATCGA
*
27972149 AGAGCACTAACGTGCTAATAATC-A
1 AGAGCACTAAAGTGCTAATAATCGA
27972173 GAGACCGCACTAAAGT
1 -AGA--GCACTAAAGT
27972189 TCCTTAATGG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
25 46 0.82
26 1 0.02
27 9 0.16
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (25 bp):
AGAGCACTAAAGTGCTAATAATCGA
Found at i:27973045 original size:13 final size:12
Alignment explanation
Indices: 27973018--27973058 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
27973008 TTGTTTAGTT
27973018 TTTC-CTTTTTC
1 TTTCTCTTTTTC
27973029 TTTCTCTTTTTC
1 TTTCTCTTTTTC
*
27973041 GTTTCTC-CTTTC
1 -TTTCTCTTTTTC
27973053 TTTCTC
1 TTTCTC
27973059 CCCTGTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 10 0.37
12 11 0.41
13 6 0.22
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTCTCTTTTTC
Found at i:27973140 original size:21 final size:18
Alignment explanation
Indices: 27973114--27973154 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
27973104 TTGTTTGTTT
27973114 TTATAATATAATATAATATCA
1 TTATAATAT--TATAATA-CA
27973135 TTATAATATTATAATACA
1 TTATAATATTATAATACA
27973153 TT
1 TT
27973155 TTAACTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
21 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATAATATTATAATACA
Found at i:27974262 original size:25 final size:25
Alignment explanation
Indices: 27974215--27974262 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
27974205 TTAGCCCTCT
*
27974215 CGAGCTTCCCGTTATATGGTTTTTA
1 CGAGCTTCCCGTTATATGCTTTTTA
*
27974240 CGAGCTTCCTGTTA-ATAGCTTTT
1 CGAGCTTCCCGTTATAT-GCTTTT
27974263 CGGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATGCTTTTTA
Found at i:27974600 original size:52 final size:50
Alignment explanation
Indices: 27974469--27974605 Score: 136
Period size: 50 Copynumber: 2.7 Consensus size: 50
27974459 ATTGGCTTGC
* * *
27974469 ATGAGCTTCCTA-AATATGGCTCTTATGAGCTTCCCGCTATACAGCCCGA
1 ATGAGCTTCCCATTATATGGCTCATATGAGCTTCCCGCTATACAGCCCGA
* * **
27974518 ATGAGCTTCCCATTATATGGCTCACATGAGCTTCCCGTTATATGGCCCGA
1 ATGAGCTTCCCATTATATGGCTCATATGAGCTTCCCGCTATACAGCCCGA
*
27974568 GA-GAGGGCTTCCCATT-TATGTGCTCGTATGAGCATTCC
1 -ATGA--GCTTCCCATTATATG-GCTCATATGAGC-TTCC
27974606 TGAATATGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
49 11 0.15
50 33 0.45
51 5 0.07
52 20 0.27
53 4 0.05
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (50 bp):
ATGAGCTTCCCATTATATGGCTCATATGAGCTTCCCGCTATACAGCCCGA
Found at i:27975520 original size:4 final size:4
Alignment explanation
Indices: 27975511--27975543 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
27975501 GTTAGCAAAT
27975511 ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC A
1 ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC A
27975544 ATACCTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTC
Found at i:27977438 original size:11 final size:12
Alignment explanation
Indices: 27977422--27977459 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
27977412 ATAAAGAAAT
27977422 AAATGAAAAA-A
1 AAATGAAAAACA
*
27977433 AAATGAAAAAGA
1 AAATGAAAAACA
*
27977445 AAAAGAAAAACA
1 AAATGAAAAACA
27977457 AAA
1 AAA
27977460 CGAACAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.05
Consensus pattern (12 bp):
AAATGAAAAACA
Found at i:27978142 original size:3 final size:3
Alignment explanation
Indices: 27978134--27978163 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
27978124 GAATGGTAAG
27978134 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27978164 GGTATTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27983418 original size:13 final size:14
Alignment explanation
Indices: 27983402--27983437 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
27983392 CAATCTCATA
27983402 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
27983415 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
27983428 TCTC-ATTTCA
1 TCTCAATTTCA
27983438 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:27983427 original size:18 final size:19
Alignment explanation
Indices: 27983389--27983429 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
27983379 TGGTTCATGT
27983389 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
27983408 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
27983426 TTTC
1 TTTC
27983430 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:27983619 original size:39 final size:38
Alignment explanation
Indices: 27983552--27983686 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
27983542 ACCAATATGG
* * *
27983552 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
27983591 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
27983629 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
27983670 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
27983687 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:27983952 original size:18 final size:19
Alignment explanation
Indices: 27983926--27983964 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
27983916 TTTCAATTCA
27983926 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
27983945 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
27983963 AT
1 AT
27983965 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:27985291 original size:5 final size:5
Alignment explanation
Indices: 27985281--27985333 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
27985271 TTACTTATTT
* *
27985281 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
27985329 ATATA
1 ATATA
27985334 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:27985297 original size:12 final size:12
Alignment explanation
Indices: 27985280--27985335 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
27985270 TTTACTTATT
27985280 TATATAATATAA
1 TATATAATATAA
27985292 TATATAATATAATA
1 TATATAATAT-A-A
27985306 TACTATAATATAA
1 TA-TATAATATAA
*
27985319 TA-ATAATTTAA
1 TATATAATATAA
27985330 TATATA
1 TATATA
27985336 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:27989869 original size:13 final size:14
Alignment explanation
Indices: 27989853--27989888 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
27989843 CAATCTCATA
27989853 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
27989866 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
27989879 TCTC-ATTTCA
1 TCTCAATTTCA
27989889 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:27989878 original size:18 final size:19
Alignment explanation
Indices: 27989840--27989880 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
27989830 TGGTTCATGT
27989840 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
27989859 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
27989877 TTTC
1 TTTC
27989881 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:27990070 original size:39 final size:38
Alignment explanation
Indices: 27990003--27990137 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
27989993 ACCAATATGG
* * *
27990003 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
27990042 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
27990080 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
27990121 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
27990138 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:27990403 original size:18 final size:19
Alignment explanation
Indices: 27990377--27990415 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
27990367 TTTCAATTCA
27990377 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
27990396 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
27990414 AT
1 AT
27990416 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:27991741 original size:5 final size:5
Alignment explanation
Indices: 27991731--27991783 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
27991721 TTACTTATTT
* *
27991731 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
27991779 ATATA
1 ATATA
27991784 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:27991747 original size:12 final size:12
Alignment explanation
Indices: 27991730--27991785 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
27991720 TTTACTTATT
27991730 TATATAATATAA
1 TATATAATATAA
27991742 TATATAATATAATA
1 TATATAATAT-A-A
27991756 TACTATAATATAA
1 TA-TATAATATAA
*
27991769 TA-ATAATTTAA
1 TATATAATATAA
27991780 TATATA
1 TATATA
27991786 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:27993146 original size:2 final size:2
Alignment explanation
Indices: 27993139--27993169 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27993129 AAGGTATTAA
27993139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27993170 AAAGGAAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27994173 original size:19 final size:20
Alignment explanation
Indices: 27994149--27994191 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
27994139 GGTGATTGTG
*
27994149 TATACATGTGTACA-AATAA
1 TATACATATGTACATAATAA
*
27994168 TATACATATGTATATAATAA
1 TATACATATGTACATAATAA
27994188 TATA
1 TATA
27994192 TGAATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
TATACATATGTACATAATAA
Found at i:27994221 original size:5 final size:5
Alignment explanation
Indices: 27994211--27994264 Score: 108
Period size: 5 Copynumber: 10.8 Consensus size: 5
27994201 AATATTTAAG
27994211 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
27994261 TATA
1 TATA
27994265 ATAACTAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 49 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:27994358 original size:11 final size:11
Alignment explanation
Indices: 27994342--27994366 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27994332 ACAGAGGGAA
27994342 AAAGAAAGGAG
1 AAAGAAAGGAG
27994353 AAAGAAAGGAG
1 AAAGAAAGGAG
27994364 AAA
1 AAA
27994367 AATTAGGGGT
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAAGAAAGGAG
Found at i:27995245 original size:41 final size:40
Alignment explanation
Indices: 27995194--27995307 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 40
27995184 CCTCGAGTTA
**
27995194 ATGAGACACTGGGTGTCAATTATTTACTTCGGATTAATTCG
1 ATGAGACACTGGGTGTCAATTA-TTACTTCGGATTAAGCCG
* * *
27995235 ATGA-AGCACTGGGTGCCAACTA--ACTTCGG-TTTAGCCG
1 ATGAGA-CACTGGGTGTCAATTATTACTTCGGATTAAGCCG
*
27995272 ATGAGACACTGGGTGTCAACTTATTACTTCGAATTA
1 ATGAGACACTGGGTGTCAA-TTATTACTTCGGATTA
27995308 TCTGATGAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
37 21 0.36
38 10 0.17
40 7 0.12
41 20 0.34
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAATTATTACTTCGGATTAAGCCG
Found at i:27997681 original size:32 final size:32
Alignment explanation
Indices: 27997636--27997729 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 32
27997626 TAATTAATAA
**
27997636 TTTTAATAA-TAATAATCATCTAAT-AAATATC
1 TTTTAATAATTAATAAT-AAATAATAAAATATC
*
27997667 TTTTATTAATTAATAATAAATAATAAAATATC
1 TTTTAATAATTAATAATAAATAATAAAATATC
*
27997699 TTTTCACTAATT-ATACATAAATAATACAAAT
1 TTTT-AATAATTAATA-ATAAATAATA-AAAT
27997730 GTGCTTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
31 13 0.24
32 21 0.39
33 16 0.30
34 4 0.07
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTTAATAATTAATAATAAATAATAAAATATC
Found at i:27997719 original size:33 final size:32
Alignment explanation
Indices: 27997656--27997729 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
27997646 AATAATCATC
*
27997656 TAAT-AAATATCTTTTATTAATTAATAATAAA
1 TAATAAAATATCTTTTACTAATTAATAATAAA
27997687 TAATAAAATATCTTTTCACTAATT-ATACATAAA
1 TAATAAAATATCTTTT-ACTAATTAATA-ATAAA
27997720 TAATACAAAT
1 TAATA-AAAT
27997730 GTGCTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 4 0.11
32 14 0.37
33 16 0.42
34 4 0.11
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (32 bp):
TAATAAAATATCTTTTACTAATTAATAATAAA
Found at i:28004016 original size:15 final size:14
Alignment explanation
Indices: 28003998--28004028 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
28003988 TTAATTTATT
28003998 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
28004013 TAATAATAATCTAA
1 TAATAATAATCTAA
28004027 TA
1 TA
28004029 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:28004039 original size:21 final size:20
Alignment explanation
Indices: 28004015--28004083 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
28004005 AATGCTAATA
28004015 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
28004036 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
28004055 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
28004076 ATAATAAT
1 ATAATAAT
28004084 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:28006854 original size:25 final size:25
Alignment explanation
Indices: 28006819--28006869 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
28006809 TAGCCGAAGT
*
28006819 AAAGCGGTACCCAGTACCTCATCGA
1 AAAGCGATACCCAGTACCTCATCGA
28006844 AAAGCGATACCCAGTACCTCATCGA
1 AAAGCGATACCCAGTACCTCATCGA
28006869 A
1 A
28006870 TCTATCCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.31, G:0.18, T:0.16
Consensus pattern (25 bp):
AAAGCGATACCCAGTACCTCATCGA
Found at i:28008043 original size:15 final size:15
Alignment explanation
Indices: 28008023--28008055 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28008013 CTTCATATCT
28008023 ATTTGTTTTATTTTA
1 ATTTGTTTTATTTTA
28008038 ATTTGTTTTATTTTA
1 ATTTGTTTTATTTTA
28008053 ATT
1 ATT
28008056 AATTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (15 bp):
ATTTGTTTTATTTTA
Found at i:28008255 original size:33 final size:32
Alignment explanation
Indices: 28008192--28008267 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
28008182 AATAATCATC
28008192 TAAT-AAATATCTTTTACTAATTAATAATAAA
1 TAATAAAATATCTTTTACTAATTAATAATAAA
* *
28008223 TAATAAAATATTTTTTCGCTAATT-ATACATAAA
1 TAATAAAATATCTTTT-ACTAATTAATA-ATAAA
28008256 TAATACAAATAT
1 TAATA-AAATAT
28008268 ATTTATTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 4 0.10
32 13 0.33
33 16 0.41
34 6 0.15
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (32 bp):
TAATAAAATATCTTTTACTAATTAATAATAAA
Found at i:28008279 original size:33 final size:31
Alignment explanation
Indices: 28008192--28008284 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 31
28008182 AATAATCATC
*
28008192 TAAT-AAATATCTTTTACTAATTAATAATAAA
1 TAATAAAATAT-TTTTTCTAATTAATAATAAA
28008223 TAATAAAATATTTTTTCGCTAATT-ATACATAAA
1 TAATAAAATATTTTTT--CTAATTAATA-ATAAA
28008256 TAATACAAATATATTTATT-TAATTTAATA
1 TAATA-AAATAT-TTT-TTCTAA-TTAATA
28008285 CACTTGTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
31 8 0.15
32 9 0.17
33 19 0.37
34 8 0.15
35 6 0.12
36 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44
Consensus pattern (31 bp):
TAATAAAATATTTTTTCTAATTAATAATAAA
Found at i:28010251 original size:19 final size:19
Alignment explanation
Indices: 28010227--28010266 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28010217 AATTTTAAAA
28010227 TAAATTTAAT-ATTAATTCT
1 TAAATTTAATAATT-ATTCT
*
28010246 TAAATTTGATAATTATTCT
1 TAAATTTAATAATTATTCT
28010265 TA
1 TA
28010267 CACAAGGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (19 bp):
TAAATTTAATAATTATTCT
Found at i:28013461 original size:21 final size:21
Alignment explanation
Indices: 28013420--28013461 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28013410 TTAACTGCTT
**
28013420 AATTGCATTTTTATATTTTGA
1 AATTGCATTTTTATAAATTGA
28013441 AATTAGCATTTTTA-AAATTGA
1 AATT-GCATTTTTATAAATTGA
28013462 CATATAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (21 bp):
AATTGCATTTTTATAAATTGA
Found at i:28019075 original size:17 final size:17
Alignment explanation
Indices: 28019053--28019091 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28019043 TCTAAGTTTA
28019053 ATTTTTTTATATTTTCT
1 ATTTTTTTATATTTTCT
* *
28019070 ATTTTTTTCTTTTTTCT
1 ATTTTTTTATATTTTCT
28019087 -TTTTT
1 ATTTTT
28019092 GATAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (17 bp):
ATTTTTTTATATTTTCT
Found at i:28023499 original size:21 final size:22
Alignment explanation
Indices: 28023460--28023508 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
28023450 TACTATTTAG
* * *
28023460 TATATTTTAAATTCTAATATAC
1 TATATTTAAAATTCGAATAAAC
*
28023482 TATATTTAAAATT-GAATAAAT
1 TATATTTAAAATTCGAATAAAC
28023503 TATATT
1 TATATT
28023509 AGTATCATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATTTAAAATTCGAATAAAC
Found at i:28023848 original size:7 final size:7
Alignment explanation
Indices: 28023836--28023861 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28023826 AACTGGAATA
28023836 TTAAATC
1 TTAAATC
28023843 TTAAATC
1 TTAAATC
28023850 TTAAATC
1 TTAAATC
28023857 TTAAA
1 TTAAA
28023862 CCTTGAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATC
Found at i:28026074 original size:23 final size:23
Alignment explanation
Indices: 28026048--28026095 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
28026038 AGGTTTGAAG
28026048 TTGGAACCTATTATTTGCAATCC
1 TTGGAACCTATTATTTGCAATCC
28026071 TTGGAACCTATTATTTGCAATCC
1 TTGGAACCTATTATTTGCAATCC
28026094 TT
1 TT
28026096 TTATGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (23 bp):
TTGGAACCTATTATTTGCAATCC
Found at i:28029070 original size:13 final size:13
Alignment explanation
Indices: 28029054--28029129 Score: 102
Period size: 13 Copynumber: 5.8 Consensus size: 13
28029044 TTTAAACCAA
28029054 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
28029067 ACTTTTTC-AAAGT
1 AC-TTTTCAAAAGT
*
28029080 ACTTTTTC-ATAGT
1 AC-TTTTCAAAAGT
28029093 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
*
28029106 ACTTTTCAAAAGC
1 ACTTTTCAAAAGT
28029119 ACTTTTCAAAA
1 ACTTTTCAAAA
28029130 ACATTGCCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
12 5 0.09
13 48 0.83
14 5 0.09
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:28031481 original size:19 final size:18
Alignment explanation
Indices: 28031459--28031507 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
28031449 TTAGTGATTT
*
28031459 TTAAAAAAATTAATTTTAA
1 TTAAAAAAATTAA-ATTAA
*
28031478 TTAAGTAAAATTAAATTAA
1 TTAA-AAAAATTAAATTAA
28031497 TTAAAATAAAT
1 TTAAAA-AAAT
28031508 GTGATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TTAAAAAAATTAAATTAA
Found at i:28039870 original size:5 final size:5
Alignment explanation
Indices: 28039849--28039901 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
28039839 TGTTAAAATA
* *
28039849 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
28039897 TATAT
1 TATAT
28039902 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:28039880 original size:10 final size:9
Alignment explanation
Indices: 28039846--28039902 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
28039836 ATGTGTTAAA
28039846 ATATATATT
1 ATATATATT
*
28039855 AAAT-TATT
1 ATATATATT
28039863 AT-TATATT
1 ATATATATT
28039871 ATAGTATATT
1 ATA-TATATT
28039881 ATAT-TA-T
1 ATATATATT
28039888 ATATTATATT
1 ATA-TATATT
28039898 ATATA
1 ATATA
28039903 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:28039892 original size:12 final size:12
Alignment explanation
Indices: 28039847--28039902 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
28039837 TGTGTTAAAA
*
28039847 TATATATTAAAT
1 TATATATTATAT
28039859 TAT-TATTATATT
1 TATATATTATA-T
28039871 ATAGTATATTATAT
1 -TA-TATATTATAT
28039885 TATATATTATAT
1 TATATATTATAT
28039897 TATATA
1 TATATA
28039903 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:28041240 original size:18 final size:19
Alignment explanation
Indices: 28041219--28041257 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28041209 ATATATAGAT
28041219 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
28041237 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
28041256 AT
1 AT
28041258 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:28041542 original size:41 final size:38
Alignment explanation
Indices: 28041494--28041595 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 38
28041484 TCGACCTCGA
*
28041494 GTCGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAG
1 GTCGATGAGACACTGGGTGTCAAC--T-TTACTTCGGATAG
* ** * *
28041534 ATTCGATGAGGTACTGGGTATCAACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCAACTTTACTTCGGATAG
*
28041573 GCCGATGAGACACTGGGTGTCAA
1 GTCGATGAGACACTGGGTGTCAA
28041596 ATATTGCTTC
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
38 18 0.37
39 11 0.22
40 1 0.02
41 17 0.35
42 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (38 bp):
GTCGATGAGACACTGGGTGTCAACTTTACTTCGGATAG
Found at i:28041606 original size:39 final size:39
Alignment explanation
Indices: 28041496--28041630 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 39
28041486 GACCTCGAGT
* * * *
28041496 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** * * *
28041537 CGATGAGGTACTGGGTATCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
28041575 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
28041614 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
28041631 CCATATTGGT
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
38 19 0.25
39 35 0.47
40 4 0.05
41 17 0.23
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:28041774 original size:18 final size:19
Alignment explanation
Indices: 28041753--28041793 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
28041743 AATGAAATGA
28041753 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
28041771 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
28041790 GAAA
1 GAAA
28041794 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:28049975 original size:19 final size:20
Alignment explanation
Indices: 28049932--28049976 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
28049922 TTGGTCACTT
*
28049932 ATTTTAGTCACTCAATTTCC
1 ATTTTAGTCACTCAATTTAC
28049952 ATTTTAGTCACT-AATTTAC
1 ATTTTAGTCACTCAATTTAC
*
28049971 TTTTTA
1 ATTTTA
28049977 AAGATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTTAGTCACTCAATTTAC
Found at i:28056917 original size:167 final size:168
Alignment explanation
Indices: 28056617--28056919 Score: 482
Period size: 167 Copynumber: 1.8 Consensus size: 168
28056607 ATAGATAATC
* * * * *
28056617 AAGAAAAGTTGTTCAGTATTCATCACTGTTTCATTTCAGCTATCTAATGAAGTTCCAGTTCCAAC
1 AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAAGTTCCAATTCCAAC
* * *
28056682 ACAGATGAATGAATGATTGTCTAATTAACAGGTGCTAGTTCAAGAACAATGACTTCCAATTATTA
66 ACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTATTA
28056747 CCCAATATTTAACGTTTCATTTCAGCAATTTGTAAACA
131 CCCAATATTTAACGTTTCATTTCAGCAATTTGTAAACA
*
28056785 AAGAAAA-CTGTTCAATATTCATCAATGTTTCATTTCAGCAATTTAATGAAGTTCCAATTCCAAC
1 AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAAGTTCCAATTCCAAC
* * * *
28056849 ACAGATCAATGAATGATTGTGTAATTAACAGCTGCTAGTTCAAGAACAATAACTTTCATTTTTTA
66 ACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTATTA
28056914 CCCAAT
131 CCCAAT
28056920 CTTTCAAGCA
Statistics
Matches: 122, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
167 115 0.94
168 7 0.06
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (168 bp):
AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAAGTTCCAATTCCAAC
ACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTATTA
CCCAATATTTAACGTTTCATTTCAGCAATTTGTAAACA
Found at i:28059080 original size:43 final size:42
Alignment explanation
Indices: 28059032--28059120 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 42
28059022 GTCGAATATG
28059032 ATAGGAGAAGACAACTTATATTAGTAGGAGGTCTAAATAGTT
1 ATAGGAGAAGACAACTTATATTAGTAGGAGGTCTAAATAGTT
* *
28059074 CATAGGAGAAGACAACTTATGTTAGTAGGTGGTCTAAATAGTT
1 -ATAGGAGAAGACAACTTATATTAGTAGGAGGTCTAAATAGTT
28059117 ATAG
1 ATAG
28059121 TCTAAAGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 4 0.09
43 40 0.91
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (42 bp):
ATAGGAGAAGACAACTTATATTAGTAGGAGGTCTAAATAGTT
Found at i:28062150 original size:18 final size:18
Alignment explanation
Indices: 28062117--28062175 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
28062107 TAAATAAAGG
28062117 TACTGAATAA-TGGACTGC
1 TACTGAATAACT-GACTGC
*
28062135 TACTGAATAACTGACTGT
1 TACTGAATAACTGACTGC
* * * *
28062153 TATTGGATCACTGATTGC
1 TACTGAATAACTGACTGC
28062171 TACTG
1 TACTG
28062176 CGTAAAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 32 0.97
19 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (18 bp):
TACTGAATAACTGACTGC
Found at i:28062232 original size:18 final size:19
Alignment explanation
Indices: 28062188--28062235 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
28062178 TAAAAAATTT
28062188 GTTACTGAATAATTGATTA
1 GTTACTGAATAATTGATTA
*
28062207 -TTACTGAATAATTTA-TA
1 GTTACTGAATAATTGATTA
*
28062224 GTTAGTGAATAA
1 GTTACTGAATAA
28062236 CTAACTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.42
Consensus pattern (19 bp):
GTTACTGAATAATTGATTA
Found at i:28067707 original size:43 final size:43
Alignment explanation
Indices: 28067659--28067824 Score: 140
Period size: 43 Copynumber: 3.9 Consensus size: 43
28067649 GTTATCGAGA
* * *
28067659 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT
* * * * *
28067702 TGTGATTACGTGTAAGACCATGTCTGAGACATTGGCGTCGTTAA
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCG-TAT
* * * * * * *
28067746 T-CGATTTCGTATAAGACCCTATTTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT
* *
28067787 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 -TGTGATTACATGTAAGACCATATCTGGGACATTGGCAT
28067825 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 24, Indels: 7
0.76 0.19 0.06
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 85 0.89
44 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT
Found at i:28070730 original size:16 final size:16
Alignment explanation
Indices: 28070709--28070748 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
28070699 TTTTCATGCG
28070709 AGCTTACTAAGCGTAA
1 AGCTTACTAAGCGTAA
28070725 AGCTTACTAAGCGTAA
1 AGCTTACTAAGCGTAA
28070741 AGCTTACT
1 AGCTTACT
28070749 TCCTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (16 bp):
AGCTTACTAAGCGTAA
Found at i:28073694 original size:68 final size:68
Alignment explanation
Indices: 28073582--28073723 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 68
28073572 TAGTTAGGCC
* * * *
28073582 GTGTGTCCCCTGCACCTTAATTTTGAGAAATAGAATGCTTAAAATTGAGCACACGGGCAGAGACA
1 GTGTGTCCCCTGCACCCTAATTTTAAGAAATAGAATGCTCAAAATTGAGCACACAGGCAGAGACA
28073647 CGG
66 CGG
28073650 GTGTGTCCCCTGCACCCTAATTTTAAGAAATAGAATGCTCAAAATTGAGCACACAGGCAGAGACA
1 GTGTGTCCCCTGCACCCTAATTTTAAGAAATAGAATGCTCAAAATTGAGCACACAGGCAGAGACA
28073715 CGG
66 CGG
28073718 GTGTGT
1 GTGTGT
28073724 GTCTCAACCG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (68 bp):
GTGTGTCCCCTGCACCCTAATTTTAAGAAATAGAATGCTCAAAATTGAGCACACAGGCAGAGACA
CGG
Found at i:28075686 original size:36 final size:36
Alignment explanation
Indices: 28075617--28075687 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
28075607 TGTCGGGGAG
* *
28075617 TGTTGGGCACACCCATTTGTCGATTGTATCGACCAA
1 TGTTGGGCACACCCATTTGTCGATTATACCGACCAA
* * *
28075653 TGTTGGGCACATCTATTTGTCGGTTATACCGACCA
1 TGTTGGGCACACCCATTTGTCGATTATACCGACCA
28075688 GTGTAGGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (36 bp):
TGTTGGGCACACCCATTTGTCGATTATACCGACCAA
Found at i:28077944 original size:17 final size:17
Alignment explanation
Indices: 28077911--28077945 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28077901 AATGGATTTG
*
28077911 TAAATTTTGAGATATAA
1 TAAATTTTGAGAGATAA
*
28077928 TAAATTTTGTGAGATAA
1 TAAATTTTGAGAGATAA
28077945 T
1 T
28077946 GTCAGAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
TAAATTTTGAGAGATAA
Found at i:28079534 original size:23 final size:23
Alignment explanation
Indices: 28079508--28079552 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28079498 TGGGTATGTG
*
28079508 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
28079531 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
28079553 TTGAGTTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Done.