Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 46 of 120
Found at i:12469063 original size:16 final size:16
Alignment explanation
Indices: 12469025--12469078 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
12469015 AAAATATAAT
12469025 TTAAAATA-ATTATT-A
1 TTAAAATATATT-TTAA
12469040 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
12469055 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
12469073 -TAAAAT
1 TTAAAAT
12469079 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.21
15 8 0.24
16 8 0.24
17 6 0.18
18 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:12469065 original size:18 final size:17
Alignment explanation
Indices: 12469044--12469078 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12469034 TTATTATTAA
*
12469044 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12469062 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12469079 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12469107 original size:120 final size:120
Alignment explanation
Indices: 12468963--12469293 Score: 626
Period size: 120 Copynumber: 2.8 Consensus size: 120
12468953 TTAAATATTA
* *
12468963 AATATTAAATATTCTTACATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
1 AATAATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
12469028 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT
66 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT
* *
12469083 AATAATAAATATTCTTGTGTGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
1 AATAATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
12469148 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT
66 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT
12469203 AATAATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
1 AATAATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
12469268 AAATAATTATTATTAAATATATTTTA
66 AAATAATTATTATTAAATATATTTTA
12469294 TAATCTACTT
Statistics
Matches: 205, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 205 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AATAATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT
Found at i:12469127 original size:61 final size:60
Alignment explanation
Indices: 12468963--12469249 Score: 212
Period size: 59 Copynumber: 4.8 Consensus size: 60
12468953 TTAAATATTA
* * * *
12468963 AATATTAAATATTCTTACATGAATTTACTAAAATCATAATATATAATACT-ATAAAA-T-AT
1 AATAATAAATATTCTTA-TTGAATTTACTAAAATCATAATATATAAT-TTAATAAAATTCTT
* * * * * ** * *
12469022 AAT-TTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT
1 AATAAT-AAAT-ATTCTTATTGAATTTACTAAAATCATAATATATAATTTAATAAAATTCTT
* * *
12469083 AATAATAAATATTCTTGTGTGAATTTACTAAAATCATAATATATAATACT-ATAAAA-T-AT
1 AATAATAAATATTCTTAT-TGAATTTACTAAAATCATAATATATAAT-TTAATAAAATTCTT
* * * * * ** * *
12469142 AAT-TTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT
1 AATAAT-AAAT-ATTCTTATTGAATTTACTAAAATCATAATATATAATTTAATAAAATTCTT
12469203 AATAATAAATATTCTTATATGAATTTACTAAAATCATAATATATAAT
1 AATAATAAATATTCTTAT-TGAATTTACTAAAATCATAATATATAAT
12469250 ACTATAAAAT
Statistics
Matches: 169, Mismatches: 44, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
58 5 0.03
59 69 0.41
60 28 0.17
61 64 0.38
62 3 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (60 bp):
AATAATAAATATTCTTATTGAATTTACTAAAATCATAATATATAATTTAATAAAATTCTT
Found at i:12469183 original size:16 final size:16
Alignment explanation
Indices: 12469145--12469198 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
12469135 AAAATATAAT
12469145 TTAAAATA-ATTATT-A
1 TTAAAATATATT-TTAA
12469160 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
12469175 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
12469193 -TAAAAT
1 TTAAAAT
12469199 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.21
15 8 0.24
16 8 0.24
17 6 0.18
18 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:12469185 original size:18 final size:17
Alignment explanation
Indices: 12469164--12469198 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12469154 TTATTATTAA
*
12469164 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12469182 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12469199 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12469210 original size:15 final size:16
Alignment explanation
Indices: 12469190--12469219 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12469180 ATATATAATT
12469190 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
12469205 TAATAAATATTCTTA
1 TAATAAATATTCTTA
12469220 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:12472484 original size:20 final size:20
Alignment explanation
Indices: 12472459--12472498 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12472449 CGTAAAACGA
*
12472459 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
12472479 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
12472499 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:12472488 original size:34 final size:35
Alignment explanation
Indices: 12472444--12472510 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12472434 CAGTAAAATG
*
12472444 TTTTCCGTAAAACGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAACGATTTACTGGAAAATATTTTAC
* *
12472478 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAACGATTTACTGGAAAATATTTT
12472511 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAACGATTTACTGGAAAATATTTTAC
Found at i:12474611 original size:25 final size:25
Alignment explanation
Indices: 12474572--12474623 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
12474562 AAAATGTCTG
12474572 CTGCTTAGAAGAGAATGGAAAATGT
1 CTGCTTAGAAGAGAATGGAAAATGT
12474597 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAATGGAAAATGT
12474622 CT
1 CT
12474624 TACCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (25 bp):
CTGCTTAGAAGAGAATGGAAAATGT
Found at i:12475021 original size:33 final size:33
Alignment explanation
Indices: 12474976--12475041 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
12474966 AAATTAAAAT
*
12474976 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
1 TTGTAGGTATATGCATAATTGAGCTAAAATTAA
*
12475009 TTGTTGGTATATGCATAATTGAGCTAAAATTAA
1 TTGTAGGTATATGCATAATTGAGCTAAAATTAA
12475042 AATTCCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (33 bp):
TTGTAGGTATATGCATAATTGAGCTAAAATTAA
Found at i:12475282 original size:19 final size:19
Alignment explanation
Indices: 12475255--12475291 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12475245 AACAAATTAA
*
12475255 TTGTTGGTATATGTAAAAT
1 TTGTAGGTATATGTAAAAT
12475274 TTGTAGGTATATGTAAAA
1 TTGTAGGTATATGTAAAA
12475292 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGTAGGTATATGTAAAAT
Found at i:12475522 original size:26 final size:27
Alignment explanation
Indices: 12475491--12475545 Score: 103
Period size: 26 Copynumber: 2.1 Consensus size: 27
12475481 CAGTATTTAA
12475491 TAATTAAATATATAATTTAATTA-TTT
1 TAATTAAATATATAATTTAATTAGTTT
12475517 TAATTAAATATATAATTTAATTAGTTT
1 TAATTAAATATATAATTTAATTAGTTT
12475544 TA
1 TA
12475546 TGAATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TAATTAAATATATAATTTAATTAGTTT
Found at i:12475551 original size:18 final size:18
Alignment explanation
Indices: 12475530--12475564 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12475520 TTAAATATAT
*
12475530 AATTTAATTAGTTTTATG
1 AATTTAAATAGTTTTATG
*
12475548 AATTTAAATATTTTTAT
1 AATTTAAATAGTTTTAT
12475565 TTTAACCAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
AATTTAAATAGTTTTATG
Found at i:12476190 original size:15 final size:15
Alignment explanation
Indices: 12476187--12476219 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
12476177 AAAATAGTAT
12476187 AAAATAGTATAAAAG
1 AAAATAGTATAAAAG
12476202 AAAATAGTATAAAAG
1 AAAATAGTATAAAAG
12476217 AAA
1 AAA
12476220 TGTTAATAAT
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:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (15 bp):
AAAATAGTATAAAAG
Found at i:12477409 original size:9 final size:9
Alignment explanation
Indices: 12477385--12477415 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12477375 ATTATGCCAT
12477385 TTCAAATGC
1 TTCAAATGC
12477394 TTC-AATGC
1 TTCAAATGC
12477402 TTCAAATGC
1 TTCAAATGC
12477411 TTCAA
1 TTCAA
12477416 CTGTAATCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (9 bp):
TTCAAATGC
Found at i:12483181 original size:35 final size:35
Alignment explanation
Indices: 12483120--12483223 Score: 165
Period size: 35 Copynumber: 3.0 Consensus size: 35
12483110 ATTTTTTAAA
* * *
12483120 TAGCACTAATATTAATTTTACT-ATTGAGTTTGAAT
1 TAGCACCAATTTTAAATTTA-TAATTGAGTTTGAAT
12483155 TAGCACCAATTTTAAATTTATAATTGAGTTTGAAT
1 TAGCACCAATTTTAAATTTATAATTGAGTTTGAAT
12483190 TAGCACCAATTTTAAATTTATAATTGAGTTTGAA
1 TAGCACCAATTTTAAATTTATAATTGAGTTTGAA
12483224 CCCAATTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
34 1 0.02
35 64 0.98
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (35 bp):
TAGCACCAATTTTAAATTTATAATTGAGTTTGAAT
Found at i:12486150 original size:24 final size:24
Alignment explanation
Indices: 12486115--12486162 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
12486105 GACAAGTGGC
*
12486115 ATGTTGTGGTCAAGCCACTGAATA
1 ATGTTGTAGTCAAGCCACTGAATA
*
12486139 ATGTTGTAGTCAAGCCATTGAATA
1 ATGTTGTAGTCAAGCCACTGAATA
12486163 TTGCAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (24 bp):
ATGTTGTAGTCAAGCCACTGAATA
Found at i:12495911 original size:28 final size:28
Alignment explanation
Indices: 12495871--12495935 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
12495861 AAAAGCACAT
*
12495871 CACTTTTCTGCTTCAGGAAGAACGCTTA
1 CACTTTTCTGCTTCAGGAAGAACGCTCA
12495899 CACTTTTCTGCTTCAGGAAGAACGCTCA
1 CACTTTTCTGCTTCAGGAAGAACGCTCA
12495927 CACTTTTCT
1 CACTTTTCT
12495936 AGAAAAATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (28 bp):
CACTTTTCTGCTTCAGGAAGAACGCTCA
Found at i:12501524 original size:11 final size:12
Alignment explanation
Indices: 12501486--12501529 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
12501476 CTCTTAACTC
*
12501486 TTTTTTTAAATA
1 TTTTTTAAAATA
* *
12501498 ATTTTAAAAATA
1 TTTTTTAAAATA
12501510 TTTTTTAAAAT-
1 TTTTTTAAAATA
12501521 TTTTTTAAA
1 TTTTTTAAA
12501530 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:12503194 original size:14 final size:14
Alignment explanation
Indices: 12503175--12503207 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12503165 GACTCTGTCA
12503175 CAAGTCCTATTTCG
1 CAAGTCCTATTTCG
*
12503189 CAAGTCTTATTTCG
1 CAAGTCCTATTTCG
12503203 CAAGT
1 CAAGT
12503208 GTACACGATA
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:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (14 bp):
CAAGTCCTATTTCG
Found at i:12505990 original size:125 final size:124
Alignment explanation
Indices: 12505808--12506185 Score: 578
Period size: 125 Copynumber: 3.0 Consensus size: 124
12505798 CCCAAACATG
* * * *
12505808 CTACTGTAGCAAAAACGCGTCTACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCACGTCCACGAGGGTGCGATTTT-ACAAATTCTTCTCAAATAGCATCCTG
*
12505873 CTAGAAGCGATTTTATAGTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
12505933 CTACTGTAGCAAAAGCACGTCCACGAGGGTGCGATTTTACAAATTCTTCTCAGAATAGCATCCTG
1 CTACTGTAGCAAAAGCACGTCCACGAGGGTGCGATTTTACAAATTCTTCTCA-AATAGCATCCTG
*
12505998 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* *
12506058 CTACTGTAGCAAAAGCGA-GTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAACATCCTG
1 CTACTGTAGCAAAAGC-ACGTCCACGAGGGTGCGATTTTACAAATTCTTCTCAAATAGCATCCTG
* * * *** *
12506122 CTAGAAGCGATTTTATACTGTTTGATTAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGAC
12506183 CTA
1 CTA
12506186 AAAACCCTAA
Statistics
Matches: 234, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
124 60 0.26
125 173 0.74
126 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCACGTCCACGAGGGTGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:12510428 original size:13 final size:13
Alignment explanation
Indices: 12510410--12510435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12510400 TTAAGGCCAC
12510410 TTTTTTATTATGT
1 TTTTTTATTATGT
12510423 TTTTTTATTATGT
1 TTTTTTATTATGT
12510436 ATTGCATGAC
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTTTTATTATGT
Found at i:12510774 original size:6 final size:6
Alignment explanation
Indices: 12510756--12510785 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
12510746 TTCTGAAAAT
12510756 ATTTTC TATTTTC ATTTTC ATTTTC ATTTT
1 ATTTTC -ATTTTC ATTTTC ATTTTC ATTTT
12510786 TAGAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTC
Found at i:12524602 original size:11 final size:11
Alignment explanation
Indices: 12524586--12524612 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12524576 TAGAAATTAG
12524586 TTTGTGAAACT
1 TTTGTGAAACT
12524597 TTTGTGAAACT
1 TTTGTGAAACT
12524608 TTTGT
1 TTTGT
12524613 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:12525488 original size:93 final size:92
Alignment explanation
Indices: 12525356--12525550 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
12525346 TTGATTTTAG
* *
12525356 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
12525420 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
12525448 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
12525513 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
12525541 CAAATTCATA
1 TAAATTCATA
12525551 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:12525608 original size:17 final size:17
Alignment explanation
Indices: 12525583--12525616 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12525573 ATAATTTTAA
*
12525583 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
12525600 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
12525617 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:12525618 original size:15 final size:16
Alignment explanation
Indices: 12525583--12525621 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
12525573 ATAATTTTAA
*
12525583 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
12525600 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
12525615 ATTTAAT
1 ATTTAAT
12525622 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:12525625 original size:17 final size:18
Alignment explanation
Indices: 12525587--12525626 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
12525577 TTTTAAATTT
*
12525587 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
12525605 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
12525621 TATTAA
1 TATTAA
12525627 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:12525741 original size:15 final size:15
Alignment explanation
Indices: 12525717--12525840 Score: 64
Period size: 15 Copynumber: 8.1 Consensus size: 15
12525707 ATTAAATTAC
12525717 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
12525731 ATATATTTAATAATA
1 ATATATTTAATTATA
12525746 AT-TATATTAATT-T-
1 ATATAT-TTAATTATA
* *
12525759 ATAT-TTTACAGTATC
1 ATATATTTA-ATTATA
*
12525774 ATATATTATGATTTGAGTAA
1 ATATATT-T-AATT-A-T-A
*
12525794 ATTCATATTAAATTAT-
1 A-T-ATATTTAATTATA
12525810 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
12525824 ATATATTTAATAATA
1 ATATATTTAATTATA
12525839 AT
1 AT
12525841 TATGTTTAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 31
0.67 0.08 0.25
Matches are distributed among these distances:
12 3 0.04
13 13 0.15
14 16 0.19
15 32 0.38
16 3 0.04
17 2 0.02
18 3 0.04
19 2 0.02
20 4 0.05
21 1 0.01
22 5 0.06
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:12525748 original size:120 final size:119
Alignment explanation
Indices: 12525582--12525800 Score: 338
Period size: 120 Copynumber: 1.8 Consensus size: 119
12525572 AATAATTTTA
* *
12525582 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTAT-TTGAAATTT-TCTTT
1 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATATT--AATTTATATTT
*
12525645 TATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
64 TACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
12525701 AATTTTATTAAATTACATAT-TTTAATTATAAT-ATATTTAATAATAATTATATTAATTTATATT
1 AATTTTATTAAA-T-CATATATTTAATTA-AATCATATTTAATAATAATTATATTAATTTATATT
12525764 TTACAGTATCATATATTATGATTTGAGTAAATTCATA
63 TTACAGTATCATATATTATGATTTGAGTAAATTCATA
12525801 TTAAATTATA
Statistics
Matches: 92, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
119 17 0.18
120 65 0.71
121 10 0.11
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATATTAATTTATATTTTA
CAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
Found at i:12525829 original size:16 final size:16
Alignment explanation
Indices: 12525808--12525849 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12525798 ATATTAAATT
*
12525808 ATATATTTTAATTATA
1 ATATATTTTAATAATA
12525824 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
12525839 AT-TATGTTTAA
1 ATATAT-TTTAA
12525850 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:12525957 original size:154 final size:156
Alignment explanation
Indices: 12525799--12526096 Score: 546
Period size: 154 Copynumber: 1.9 Consensus size: 156
12525789 AGTAAATTCA
*
12525799 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
12525864 TTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
66 TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
12525927 AAATTTATGCTAATTATTAAGAATTT
131 AAATTTATGCTAATTATTAAGAATTT
12525953 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
*
12526018 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAA
66 TTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
*
12526083 CAAATTTTTGCTAA
130 CAAATTTATGCTAA
12526097 GGGTATTCTA
Statistics
Matches: 138, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 76 0.55
155 2 0.01
157 60 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (156 bp):
TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
AAATTTATGCTAATTATTAAGAATTT
Found at i:12525977 original size:18 final size:17
Alignment explanation
Indices: 12525949--12525983 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12525939 ATTATTAAGA
*
12525949 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12525966 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12525984 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12526237 original size:16 final size:16
Alignment explanation
Indices: 12526216--12526254 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12526206 TTGATTTGCT
*
12526216 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
12526232 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
12526248 ATTACAC
1 ATTACAC
12526255 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:12526255 original size:16 final size:16
Alignment explanation
Indices: 12526229--12526285 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
12526219 ACACAGCTTT
* *
12526229 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
12526245 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
12526261 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
12526277 TCCAATACA
1 TCCAATACA
12526286 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:12544768 original size:13 final size:13
Alignment explanation
Indices: 12544750--12544774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12544740 AATGAGACAT
12544750 TTGAAATGAATAC
1 TTGAAATGAATAC
12544763 TTGAAATGAATA
1 TTGAAATGAATA
12544775 TGTGATGGTT
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:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAAATGAATAC
Found at i:12548940 original size:27 final size:27
Alignment explanation
Indices: 12548922--12549308 Score: 452
Period size: 27 Copynumber: 14.3 Consensus size: 27
12548912 GGTATAACAC
12548922 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
12548949 TCATTTTACCCTATCGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
12548976 TCATTCTACCCTATTGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
12549003 TCATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
12549030 TCATTTTACCTTATGGGGGTATCTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
12549057 TCATTTTACCCTATAGGGGTATTCCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
** *
12549084 TCATTTTACCCTATAAGGGTA-TTCTGA
1 TCATTTTACCCTATGGGGGTATTTC-GG
* * *
12549111 TCATTCTACCCTATGAGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
* **
12549138 TCATTTCACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCGG
12549165 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
12549192 TTATTTTACCCTATAGAGGTATTTCTG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
12549219 TTATTTTATCTTATAGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * **
12549246 TCATTTTACCCTACGAGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
12549273 TCATTCTACCCTATGAGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
12549300 TCATTTTAC
1 TCATTTTAC
12549309 TCGATGGAGT
Statistics
Matches: 308, Mismatches: 50, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 2 0.01
27 303 0.98
28 3 0.01
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:12551855 original size:28 final size:27
Alignment explanation
Indices: 12551812--12551898 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 27
12551802 CAGCGACAGT
12551812 ACAGTGTGGGCTTTAGCCCAATACAATA
1 ACAGTGTGGGC-TTAGCCCAATACAATA
12551840 ACAGTGTGGGACTTAGCCCAATACAGA-A
1 ACAGTGTGGG-CTTAGCCCAATACA-ATA
* *
12551868 TCAGTGTGGGCCTTAGCCCAATACAGTA
1 ACAGTGTGGG-CTTAGCCCAATACAATA
12551896 ACA
1 ACA
12551899 ATGCAGTGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
28 50 0.96
29 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (27 bp):
ACAGTGTGGGCTTAGCCCAATACAATA
Found at i:12552312 original size:27 final size:27
Alignment explanation
Indices: 12552282--12552340 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
12552272 ATCTCCTAAG
*
12552282 GGTATAACAATCATTTTACCCTATGGA
1 GGTATAACAATCATTTTACCCAATGGA
** * *
12552309 GGTATCTCAGTCATTTTACCCAATGGG
1 GGTATAACAATCATTTTACCCAATGGA
12552336 GGTAT
1 GGTAT
12552341 TTCGGTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTATAACAATCATTTTACCCAATGGA
Found at i:12552355 original size:27 final size:27
Alignment explanation
Indices: 12552292--12552684 Score: 358
Period size: 27 Copynumber: 14.5 Consensus size: 27
12552282 GGTATAACAA
* * *
12552292 TCATTTTACCCTATGGAGGTATCTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
12552319 TCATTTTACCCAATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
12552346 TTATTCTACCCAATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
12552373 TCATTTCATCCTATGAGGGTATCTT-AG
1 TCATTTTACCCTATGGGGGTAT-TTCGG
* * * *
12552400 TCATTTTACCCTATAGAGATATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
**
12552427 TCATTTTACCCTATGGGGGTATTTTAG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
12552454 TTATTTTACTCAATGGGGGGTA-TTCTGG
1 TCATTTTACCCTAT-GGGGGTATTTC-GG
* * * *
12552482 TTATTCTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
12552509 TCATTTTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
12552536 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * * *
12552563 TCATTCTATCCTGTGGAGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
12552590 TCATTTTACCTTATGAGAGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
12552617 TCATTTTATCTTATGGGAGTGTTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
12552644 TCACTTTACCCTATGGAGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
12552671 TCATTTTATCCTAT
1 TCATTTTACCCTAT
12552685 AAATAGGCCT
Statistics
Matches: 293, Mismatches: 68, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
26 2 0.01
27 267 0.91
28 24 0.08
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:12556921 original size:18 final size:18
Alignment explanation
Indices: 12556881--12556914 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12556871 CCATGTGGTC
12556881 TGCCCGTGTGGGCCCACA
1 TGCCCGTGTGGGCCCACA
12556899 TGCCCGTGT-GGCCCAC
1 TGCCCGTGTGGGCCCAC
12556915 TCGGCCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.09, C:0.41, G:0.32, T:0.18
Consensus pattern (18 bp):
TGCCCGTGTGGGCCCACA
Found at i:12560081 original size:26 final size:26
Alignment explanation
Indices: 12560026--12560100 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
12560016 AGCTGGCCAT
* * *
12560026 ATCAGGAAACTC-CAGAGAACCATTA
1 ATCAGGAAGCTCACAAAGAGCCATTA
*
12560051 ATCAGGAAGCTCACAAAGAGCCTTTA
1 ATCAGGAAGCTCACAAAGAGCCATTA
12560077 ATCAGGAAGCTCACAAAGAGCCAT
1 ATCAGGAAGCTCACAAAGAGCCAT
12560101 ATAACGGGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 11 0.25
26 33 0.75
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (26 bp):
ATCAGGAAGCTCACAAAGAGCCATTA
Found at i:12560587 original size:5 final size:5
Alignment explanation
Indices: 12560577--12560601 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12560567 TACAATTCCT
12560577 ATTCA ATTCA ATTCA ATTCA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA
12560602 CACCCTAGGC
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:12568027 original size:12 final size:12
Alignment explanation
Indices: 12568010--12568044 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
12568000 TTTCGAATCA
12568010 CACATAGTTTGG
1 CACATAGTTTGG
12568022 CACATAGTTTGG
1 CACATAGTTTGG
*
12568034 CACACAGTTTG
1 CACATAGTTTG
12568045 ATGACACAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (12 bp):
CACATAGTTTGG
Found at i:12569487 original size:18 final size:18
Alignment explanation
Indices: 12569460--12569501 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
12569450 ATTTCAAGTT
*
12569460 GGTTATGTTAAAGGTTTC
1 GGTTACGTTAAAGGTTTC
12569478 GGTTACGTTAAAGGTTTC
1 GGTTACGTTAAAGGTTTC
*
12569496 AGTTAC
1 GGTTAC
12569502 ATGAGAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (18 bp):
GGTTACGTTAAAGGTTTC
Found at i:12571821 original size:24 final size:24
Alignment explanation
Indices: 12571775--12571821 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
12571765 TTTTTTCTTA
* * *
12571775 TTTTTAGATTAGGTTTTCCTTTTC
1 TTTTTAGACTAGATTTTACTTTTC
*
12571799 TTTTTAGACTAGATTTTATTTTT
1 TTTTTAGACTAGATTTTACTTTT
12571822 TGTTGTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTTTAGACTAGATTTTACTTTTC
Found at i:12572684 original size:7 final size:7
Alignment explanation
Indices: 12572676--12572714 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
12572666 AAAGAGAAAG
*
12572676 TTTAAAG
1 TTTAAAA
12572683 TTTAAAA
1 TTTAAAA
12572690 TTTAAAA
1 TTTAAAA
12572697 TTTAAAA
1 TTTAAAA
12572704 TTTAAAA
1 TTTAAAA
12572711 TTTA
1 TTTA
12572715 TGGATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:12584940 original size:23 final size:25
Alignment explanation
Indices: 12584908--12584955 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
12584898 ACTATAAATA
*
12584908 CTCATTTAAC-AATT-AACATTTCT
1 CTCATATAACTAATTAAACATTTCT
12584931 CTCATATAACTAATTAAACATTTCT
1 CTCATATAACTAATTAAACATTTCT
12584956 TAGCAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
24 4 0.18
25 9 0.41
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.42
Consensus pattern (25 bp):
CTCATATAACTAATTAAACATTTCT
Found at i:12585185 original size:23 final size:23
Alignment explanation
Indices: 12585159--12585280 Score: 192
Period size: 23 Copynumber: 5.3 Consensus size: 23
12585149 ATAAGTGCCA
12585159 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12585182 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
12585205 CACTGAAATGTAGCCGAAGCGAC
1 CACTGATATGTAGCCGAAGCTAC
*
12585228 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12585251 CACTGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
12585274 CACTGAT
1 CACTGAT
12585281 CAATAACACT
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
22 1 0.01
23 88 0.99
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12585230 original size:46 final size:46
Alignment explanation
Indices: 12585159--12585280 Score: 217
Period size: 46 Copynumber: 2.7 Consensus size: 46
12585149 ATAAGTGCCA
*
12585159 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
*
12585205 CACTGAAATGTAGCCGAAGCGACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
*
12585251 CACTGAATTGTAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
12585281 CAATAACACT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
Found at i:12598491 original size:29 final size:30
Alignment explanation
Indices: 12598437--12598515 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
12598427 TTTGAACCAT
* * *
12598437 AATTAAAGTTTAATGTGTATAATTG-CATCA
1 AATTAAAG-TTCATGTATACAATTGACATCA
*
12598467 AATTAAAGTTCATGTATACAATTGCACATTA
1 AATTAAAGTTCATGTATACAATTG-ACATCA
* *
12598498 AACTAAAATTCATGTATA
1 AATTAAAGTTCATGTATA
12598516 ATTTTGAGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.32
30 8 0.20
31 20 0.49
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (30 bp):
AATTAAAGTTCATGTATACAATTGACATCA
Found at i:12599416 original size:8 final size:8
Alignment explanation
Indices: 12599403--12599429 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12599393 AATGTCTTAA
12599403 AAAATTTT
1 AAAATTTT
12599411 AAAATTTT
1 AAAATTTT
12599419 AAAATTTT
1 AAAATTTT
12599427 AAA
1 AAA
12599430 TCTTTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAAATTTT
Found at i:12601549 original size:28 final size:28
Alignment explanation
Indices: 12601517--12601572 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
12601507 TAGTCCAAAT
12601517 TTGGAGATAACTAAATTCAGACCTACAA
1 TTGGAGATAACTAAATTCAGACCTACAA
12601545 TTGGAGATAACTAAATTCAGACCTACAA
1 TTGGAGATAACTAAATTCAGACCTACAA
12601573 GGAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (28 bp):
TTGGAGATAACTAAATTCAGACCTACAA
Found at i:12601944 original size:19 final size:18
Alignment explanation
Indices: 12601906--12601954 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
12601896 TAAAAAAATC
*
12601906 AATAAAATTTATAATTTTT
1 AATAAAA-TTATAATATTT
12601925 AATAAAATTATAATAATTT
1 AATAAAATTATAAT-ATTT
12601944 -AT-AAATTATAA
1 AATAAAATTATAA
12601955 AAATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.32
18 9 0.32
19 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAAAATTATAATATTT
Found at i:12602210 original size:8 final size:8
Alignment explanation
Indices: 12602199--12602256 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 8
12602189 TTTTATAATA
12602199 TTTTCTAT
1 TTTTCTAT
12602207 TTTT-TAT
1 TTTTCTAT
12602214 ACTTTTCTAT
1 --TTTTCTAT
12602224 TTTTCTATT
1 TTTTCTA-T
*
12602233 TTTTATAT
1 TTTTCTAT
*
12602241 TTTTATAT
1 TTTTCTAT
12602249 TTTT-TAT
1 TTTTCTAT
12602256 T
1 T
12602257 AATATTTAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
7 7 0.16
8 24 0.53
9 11 0.24
10 3 0.07
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCTAT
Found at i:12602219 original size:17 final size:16
Alignment explanation
Indices: 12602196--12602256 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
12602186 AAATTTTATA
12602196 ATATTTTCTATTTTTT
1 ATATTTTCTATTTTTT
12602212 ATACTTTTCTATTTTTCT
1 ATA-TTTTCTATTTTT-T
12602230 AT-TTTT-TATATTTTT
1 ATATTTTCTAT-TTTTT
*
12602245 ATATTTTTTATT
1 ATATTTTCTATT
12602257 AATATTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.15
16 16 0.40
17 15 0.38
18 3 0.08
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (16 bp):
ATATTTTCTATTTTTT
Found at i:12602227 original size:25 final size:25
Alignment explanation
Indices: 12602189--12602256 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
12602179 TTTTTTCAAA
12602189 TTTTATAATATTTTCTATTTTTTATAC
1 TTTTAT-AT-TTTTCTATTTTTTATAC
* *
12602216 TTTTCTATTTTTCTATTTTTTATAT
1 TTTTATATTTTTCTATTTTTTATAC
12602241 TTTTATATTTTT-TATT
1 TTTTATATTTTTCTATT
12602257 AATATTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.11
25 27 0.71
26 2 0.05
27 5 0.13
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTATATTTTTCTATTTTTTATAC
Found at i:12602254 original size:9 final size:9
Alignment explanation
Indices: 12602189--12602308 Score: 79
Period size: 9 Copynumber: 13.4 Consensus size: 9
12602179 TTTTTTCAAA
*
12602189 TTTTATAATA
1 TTTTAT-ATT
*
12602199 TTTTCTATT
1 TTTTATATT
*
12602208 TTTTATA-C
1 TTTTATATT
*
12602216 TTTTCTA-T
1 TTTTATATT
*
12602224 TTTTCTATT
1 TTTTATATT
12602233 TTTTATA-T
1 TTTTATATT
12602241 TTTTATATT
1 TTTTATATT
*
12602250 TTTTATTAATA
1 TTTTA-T-ATT
*
12602261 TTTAATATT
1 TTTTATATT
**
12602270 TTTTATAAC
1 TTTTATATT
12602279 TTTTAT-TT
1 TTTTATATT
12602287 ATTTT-TATT
1 -TTTTATATT
*
12602296 TTTTATCTT
1 TTTTATATT
12602305 TTTT
1 TTTT
12602309 TGTCACATGT
Statistics
Matches: 87, Mismatches: 16, Indels: 15
0.74 0.14 0.13
Matches are distributed among these distances:
8 26 0.30
9 48 0.55
10 7 0.08
11 6 0.07
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:12602289 original size:20 final size:19
Alignment explanation
Indices: 12602229--12602292 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
12602219 TCTATTTTTC
12602229 TATTTTTTAT-ATTTT-TA
1 TATTTTTTATAATTTTATA
12602246 TATTTTTTATTAATATTTA-A
1 TATTTTTTA-TAAT-TTTATA
*
12602266 TATTTTTTATAACTTTTATT
1 TATTTTTTATAA-TTTTATA
12602286 TATTTTT
1 TATTTTT
12602293 ATTTTTTATC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 9 0.22
18 1 0.03
19 9 0.22
20 21 0.52
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTTATAATTTTATA
Found at i:12602301 original size:17 final size:16
Alignment explanation
Indices: 12602199--12602309 Score: 69
Period size: 17 Copynumber: 6.4 Consensus size: 16
12602189 TTTTATAATA
* *
12602199 TTTTCTATTTTTTATAC
1 TTTTTTATTTTTTAT-T
*
12602216 TTTTCTATTTTTCTATT
1 TTTTTTATTTTT-TATT
*
12602233 TTTTATATTTTTATATT
1 TTTTTTATTTTT-TATT
*
12602250 TTTTATTAATATTTAATATT
1 TTTT-TT-AT-TTT-TTATT
* **
12602270 TTTTATAACTTTTATT
1 TTTTTTATTTTTTATT
12602286 TATTTTTATTTTTTATCT
1 T-TTTTTATTTTTTAT-T
12602304 TTTTTT
1 TTTTTT
12602310 GTCACATGTC
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
16 5 0.07
17 49 0.65
18 7 0.09
19 3 0.04
20 11 0.15
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTATTTTTTATT
Found at i:12604942 original size:2 final size:2
Alignment explanation
Indices: 12604935--12604959 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12604925 AAATCTAATT
12604935 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12604960 TCTTTTTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12610646 original size:59 final size:59
Alignment explanation
Indices: 12610513--12610676 Score: 201
Period size: 59 Copynumber: 2.8 Consensus size: 59
12610503 TTTAATATTA
* * *
12610513 TATATTATGATTTTTATT-AATTCATATTTTAAAAATAATTATATTAAGAATGTTATTAAAT
1 TATA-TATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAGAATATTATTAAAT
*
12610574 TATATATTA-TTTTATTAAATTATATTTAATAATAATTATGTTAA-AATATTATTAAAT
1 TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAGAATATTATTAAAT
* *
12610631 TATATCATTATTTTTAGTAAATTATATTTAGTAATAATCT-TATTAA
1 TATAT-ATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAA
12610677 AATTTAATAA
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
57 17 0.18
58 22 0.24
59 40 0.43
60 9 0.10
61 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (59 bp):
TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAGAATATTATTAAAT
Found at i:12610878 original size:16 final size:16
Alignment explanation
Indices: 12610857--12610897 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
12610847 ATTACAGTTC
* *
12610857 TATTCCATTGCAGCTA
1 TATTCCATTACAGCCA
*
12610873 TATTCCATTACAGCCC
1 TATTCCATTACAGCCA
12610889 TATTCCATT
1 TATTCCATT
12610898 CACCCCAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.39
Consensus pattern (16 bp):
TATTCCATTACAGCCA
Found at i:12611160 original size:14 final size:15
Alignment explanation
Indices: 12611140--12611184 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
12611130 GTAGTGATTT
12611140 TATCTATAATATATA
1 TATCTATAATATATA
*
12611155 -ATCTATATTATATA
1 TATCTATAATATATA
*
12611169 TATATAT-ATATATA
1 TATCTATAATATATA
12611183 TA
1 TA
12611185 CACGAGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
TATCTATAATATATA
Found at i:12611168 original size:2 final size:2
Alignment explanation
Indices: 12611144--12611184 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
12611134 TGATTTTATC
*
12611144 TA TA -A TA TA TA -A TC TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12611183 TA
1 TA
12611185 CACGAGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12611264 original size:23 final size:23
Alignment explanation
Indices: 12611238--12611375 Score: 72
Period size: 23 Copynumber: 5.9 Consensus size: 23
12611228 TTTTCACCAT
12611238 ATTATTAATTTACATTTAAAATA
1 ATTATTAATTTACATTTAAAATA
* * *
12611261 ATTATAATATTTA-ATTTAGAATT
1 ATTATTA-ATTTACATTTAAAATA
** **
12611284 ATTAGTTAA-AAATCACGTAAAATA
1 ATTA-TTAATTTA-CATTTAAAATA
* *
12611308 A-AAGTGATAATTATACATTTAAAAAA
1 ATTA-T--TAATT-TACATTTAAAATA
12611334 ATTA-TAATTTACATTTAAAAATA
1 ATTATTAATTTACATTT-AAAATA
*
12611357 ATTA-TAATTTA-ATATAAAA
1 ATTATTAATTTACATTTAAAA
12611376 GTATGGTAAT
Statistics
Matches: 86, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
21 4 0.05
22 11 0.13
23 43 0.50
24 14 0.16
25 3 0.03
26 9 0.10
27 2 0.02
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTATTAATTTACATTTAAAATA
Found at i:12611346 original size:22 final size:23
Alignment explanation
Indices: 12611314--12611415 Score: 99
Period size: 23 Copynumber: 4.6 Consensus size: 23
12611304 AATAAAAGTG
12611314 ATAATTATACATTTAAAAA-AATT
1 ATAATT-TACATTTAAAAATAATT
12611337 ATAATTTACATTTAAAAATAATT
1 ATAATTTACATTTAAAAATAATT
* * *
12611360 ATAATTTA-ATATAAAAGT-ATG
1 ATAATTTACATTTAAAAATAATT
*
12611381 GTAA-TTACATATATAAAAATAA-T
1 ATAATTTACAT-T-TAAAAATAATT
12611404 ATAATTTA-ATTT
1 ATAATTTACATTT
12611416 GCAATTATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.05
21 8 0.12
22 21 0.32
23 29 0.45
24 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (23 bp):
ATAATTTACATTTAAAAATAATT
Found at i:12616054 original size:51 final size:51
Alignment explanation
Indices: 12615940--12616199 Score: 383
Period size: 51 Copynumber: 5.3 Consensus size: 51
12615930 CTTACGTATG
* * *
12615940 ATCACTTATCACTTGTCCCTGATCAAATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
12615990 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
12616041 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC-T
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
12616091 -T-A----TCACTTGTCACTGATCAGATAAGTGTAGTTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
12616136 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
12616187 ATCACTTGTCACT
1 ATCACTTGTCACT
12616200 GATCAGAAGT
Statistics
Matches: 188, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
44 38 0.20
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 35 0.19
51 110 0.59
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:12616128 original size:95 final size:95
Alignment explanation
Indices: 12615940--12616206 Score: 392
Period size: 95 Copynumber: 2.7 Consensus size: 95
12615930 CTTACGTATG
* * *
12615940 ATCACTTATCACTTGTCCCTGATCAAATAAGTGTAGCT-AAGCTACCACTTATCACTTGCCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC-T-T-A--T--CACTT
12616004 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
59 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
12616041 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTG
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTG
* * *
12616106 ATCAGATAAGTGTAGTTGAAGCTATCACTT
66 ATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
12616136 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTGTCACTG
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTG
12616201 ATCAGA
66 ATCAGA
12616207 AGTATTCAAA
Statistics
Matches: 157, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
95 108 0.69
97 1 0.01
99 1 0.01
100 1 0.01
101 36 0.23
102 10 0.06
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (95 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTG
ATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:12623225 original size:3 final size:3
Alignment explanation
Indices: 12623217--12623247 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12623207 CTTGGTCCAA
12623217 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12623248 AAAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:12624148 original size:3 final size:3
Alignment explanation
Indices: 12624140--12624171 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12624130 GAAAGAAAAG
12624140 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12624172 AGGCAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12628795 original size:17 final size:17
Alignment explanation
Indices: 12628773--12628805 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12628763 CACTAACATG
*
12628773 AAAATGTAATGACAATA
1 AAAATGGAATGACAATA
12628790 AAAATGGAATGACAAT
1 AAAATGGAATGACAAT
12628806 GTGTACTTAT
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:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (17 bp):
AAAATGGAATGACAATA
Found at i:12629247 original size:21 final size:21
Alignment explanation
Indices: 12629223--12629273 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
12629213 TCATCTTCAG
* * *
12629223 CAACTTCTTTTTCTTCAGCAA
1 CAACTTCCTCTTCTGCAGCAA
*
12629244 CAACTTCCTCTTCTGCAGCAG
1 CAACTTCCTCTTCTGCAGCAA
12629265 CAACTTCCT
1 CAACTTCCT
12629274 TCTTAACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (21 bp):
CAACTTCCTCTTCTGCAGCAA
Found at i:12635731 original size:16 final size:16
Alignment explanation
Indices: 12635707--12635747 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
12635697 GTTCGCTTAT
*
12635707 TGGATTAGAGGCATAA
1 TGGAATAGAGGCATAA
**
12635723 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCATAA
12635739 TGGAATAGA
1 TGGAATAGA
12635748 TGTGTAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCATAA
Found at i:12635752 original size:16 final size:16
Alignment explanation
Indices: 12635720--12635755 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
12635710 ATTAGAGGCA
12635720 TAATGGAATAGAGGTG
1 TAATGGAATAGAGGTG
*
12635736 TAATGGAATAGATGTG
1 TAATGGAATAGAGGTG
12635752 TAAT
1 TAAT
12635756 AGCAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGGTG
Found at i:12635800 original size:45 final size:44
Alignment explanation
Indices: 12635734--12635824 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
12635724 GGAATAGAGG
* *
12635734 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
12635779 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
12635823 TG
1 TG
12635825 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:12637925 original size:16 final size:17
Alignment explanation
Indices: 12637904--12637936 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12637894 ATTTCCCCCT
12637904 ACTTTCTCACTT-TATC
1 ACTTTCTCACTTATATC
12637920 ACTTTCTCACTTATATC
1 ACTTTCTCACTTATATC
12637937 TGAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.48
Consensus pattern (17 bp):
ACTTTCTCACTTATATC
Found at i:12639520 original size:47 final size:46
Alignment explanation
Indices: 12639457--12639681 Score: 184
Period size: 47 Copynumber: 4.9 Consensus size: 46
12639447 TATTTAATAT
*
12639457 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAA
1 TAATT-TTTGAAATTATATAAATTCATATAAGAAAATTTATTATCAA
* * * *
12639504 TAATTTTATGAAATTATATATCATT-AT-TAA-ATTATATTTAATATTAA
1 TAATTTT-TGAAATTATATA-AATTCATATAAGA--AAATTTATTATCAA
*
12639551 TTA-TTTT-AAATTATATAAATTCATATAAGAAAATTTATTATCAA
1 TAATTTTTGAAATTATATAAATTCATATAAGAAAATTTATTATCAA
* **
12639595 GAATTTTATGAAATTATAT--ATT-AT-T-ATTAAATTATATTTAAT-AA
1 TAATTTT-TGAAATTATATAAATTCATATAAGAAAATT-TA-TT-ATCAA
* *
12639639 TAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTA
1 TAATT-TTTGAAATTATATAAATTCATATAAGAAAATTTATTA
12639682 GGTATAATTA
Statistics
Matches: 140, Mismatches: 19, Indels: 39
0.71 0.10 0.20
Matches are distributed among these distances:
42 6 0.04
43 6 0.04
44 43 0.31
45 15 0.11
46 14 0.10
47 44 0.31
48 6 0.04
49 6 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (46 bp):
TAATTTTTGAAATTATATAAATTCATATAAGAAAATTTATTATCAA
Found at i:12639621 original size:101 final size:92
Alignment explanation
Indices: 12639567--12639758 Score: 174
Period size: 101 Copynumber: 2.0 Consensus size: 92
12639557 TAAATTATAT
*
12639567 AAATTCATATAAGAAAATTTATTATCAAGAATT-TTATGA--AATTATATATTATTATTAAATTA
1 AAATTCATATAAGAAAATTTATTAGCAAGAATTATT-TGATTAATTATATA-TATTATTAAATTA
* *
12639629 TATTTAATAATAATTATTTTAAATTATAC
64 TATTTAATATTAATTATTTTAAATTATAT
** * * *
12639658 AAATTCATATAAGAAAATTTATTAGGTATAATTATTTTAAATTTTATTAAATCATATATTTTAAT
1 AAATTCATATAAGAAAATTTATTAGCAAGAATTA-TTT-GA-TTAATT--AT-ATATA--TT-AT
* *
12639723 TAAAATATATTTAATATTAATTATTTCAAATTATAT
57 TAAATTATATTTAATATTAATTATTTTAAATTATAT
12639759 TTTATAGTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
91 29 0.37
92 1 0.01
93 3 0.04
96 3 0.04
98 4 0.05
99 3 0.04
100 2 0.03
101 34 0.43
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (92 bp):
AAATTCATATAAGAAAATTTATTAGCAAGAATTATTTGATTAATTATATATATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATAT
Found at i:12639700 original size:91 final size:91
Alignment explanation
Indices: 12639423--12639681 Score: 482
Period size: 91 Copynumber: 2.8 Consensus size: 91
12639413 TTAAATGTAT
12639423 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
12639488 GAAAATTTATTATCAATAATTTTATG
66 GAAAATTTATTATCAATAATTTTATG
12639514 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
*
12639579 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAATAATTTTATG
* * *
12639605 AAATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
12639670 GAAAATTTATTA
66 GAAAATTTATTA
12639682 GGTATAATTA
Statistics
Matches: 164, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 164 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (91 bp):
AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
GAAAATTTATTATCAATAATTTTATG
Found at i:12639852 original size:16 final size:16
Alignment explanation
Indices: 12639831--12639876 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12639821 TTATTAAATT
12639831 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
12639847 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
12639862 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
12639877 CTATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:12639854 original size:221 final size:225
Alignment explanation
Indices: 12639566--12639973 Score: 571
Period size: 221 Copynumber: 1.8 Consensus size: 225
12639556 TTAAATTATA
*
12639566 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTGATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
* * *
12639631 TTTAATAATAATTATTTTAAATTATAC-AAATTCAT-A-TAAGAAAATT-TATTAG-GTA-TAAT
66 TTTAATAATAATTATGTTAAATTAT-CTAAATT-ATGATTAAGAAAATTATATAAGAATATTAAT
** *
12639690 TATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATT
129 TATTAAAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
12639755 ATATTTTATAGTATCATATATTATGATTTTAG
194 ATATTTTATAGTATCATATATTATGATTTTAG
* * *
12639787 TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATT-TTAATTATAA-TA
1 TAAATTCATATAAGAAAATTGATTATCAAGAATTTTATGAAATTATATATTATT-ATTA-AATTA
* * *
12639850 TATTTAATAATAATTATGTTAAATTATCTATATTATGATTTGAGTAAATTCATATAAGAATATTA
64 TATTTAATAATAATTATGTTAAATTATCTAAATTATGA-TTAAGAAAATT-ATATAAGAATATTA
* *
12639915 ATTATTAAAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
127 ATTATTAAAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT
12639974 GTTTAAATAT
Statistics
Matches: 162, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
220 5 0.03
221 84 0.52
222 2 0.01
223 8 0.05
225 5 0.03
226 2 0.01
227 56 0.35
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (225 bp):
TAAATTCATATAAGAAAATTGATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
TTTAATAATAATTATGTTAAATTATCTAAATTATGATTAAGAAAATTATATAAGAATATTAATTA
TTAAAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTAT
ATTTTATAGTATCATATATTATGATTTTAG
Found at i:12639883 original size:107 final size:109
Alignment explanation
Indices: 12639766--12639981 Score: 391
Period size: 107 Copynumber: 2.0 Consensus size: 109
12639756 TATTTTATAG
* * *
12639766 TATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAAATTTTATTAAATT
12639831 ATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
66 ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
12639874 TATC-TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAAATTTTATTAAATT
1 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAAATTTTATTAAATT
12639938 ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
66 ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
12639982 ATGATTAAAT
Statistics
Matches: 104, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
107 94 0.90
108 10 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (109 bp):
TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAAATTTTATTAAATT
ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
Found at i:12639959 original size:16 final size:16
Alignment explanation
Indices: 12639938--12639979 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12639928 TTATTAAATT
*
12639938 ATATATTTTAATTATA
1 ATATATTTTAATAATA
12639954 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
12639969 AT-TATGTTTAA
1 ATATAT-TTTAA
12639980 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:12639964 original size:15 final size:15
Alignment explanation
Indices: 12639929--12639970 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12639919 TTAAAAATTT
*
12639929 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12639943 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12639957 TATTTAATAATAAT
1 TATTTAATTATAAT
12639971 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12640156 original size:39 final size:40
Alignment explanation
Indices: 12640113--12640217 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
12640103 TTCCATTATG
12640113 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
12640152 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
12640197 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
12640218 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:12640211 original size:45 final size:44
Alignment explanation
Indices: 12640111--12640220 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
12640101 TTTTCCATTA
12640111 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
12640150 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
12640195 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
12640221 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:12640220 original size:16 final size:16
Alignment explanation
Indices: 12640201--12640252 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
12640191 GATTTGCTAT
* *
12640201 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
12640217 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12640233 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12640249 TACA
1 TACA
12640253 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12645622 original size:23 final size:23
Alignment explanation
Indices: 12645583--12645645 Score: 94
Period size: 23 Copynumber: 2.7 Consensus size: 23
12645573 TGTACTGACT
12645583 AACAAATCAAGAACAATTTCCAG
1 AACAAATCAAGAACAATTTCCAG
12645606 CAGAC-AATCAA-AACAATTTCCAG
1 -A-ACAAATCAAGAACAATTTCCAG
12645629 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
12645646 ATCAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.06
22 7 0.19
23 18 0.50
24 7 0.19
25 2 0.06
ACGTcount: A:0.54, C:0.22, G:0.08, T:0.16
Consensus pattern (23 bp):
AACAAATCAAGAACAATTTCCAG
Found at i:12649983 original size:14 final size:14
Alignment explanation
Indices: 12649959--12649991 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12649949 ATGCAAGTAA
12649959 AAAAAAGCTATTTT
1 AAAAAAGCTATTTT
12649973 AGAAAAA-CTATTTT
1 A-AAAAAGCTATTTT
12649987 AAAAA
1 AAAAA
12649992 GCAGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (14 bp):
AAAAAAGCTATTTT
Found at i:12659901 original size:22 final size:22
Alignment explanation
Indices: 12659876--12659918 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12659866 GGAAACCTGT
*
12659876 AAAAAATG-AAAAGAAAACAAG
1 AAAAAAAGCAAAAGAAAACAAG
* *
12659897 AAAAATAGCAAAATAAAACAAG
1 AAAAAAAGCAAAAGAAAACAAG
12659919 TTTTGAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.74, C:0.07, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAAAAGCAAAAGAAAACAAG
Found at i:12668680 original size:25 final size:25
Alignment explanation
Indices: 12668652--12668721 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
12668642 GAGTTTAGCG
*
12668652 TGCTCTCTGATTAGTAGCACATCAA
1 TGCTCTCTGATTAATAGCACATCAA
* * *
12668677 TGCTCTCTGATTATTAGCACGTCAG
1 TGCTCTCTGATTAATAGCACATCAA
*
12668702 TACTCTCTGATTAATAGCAC
1 TGCTCTCTGATTAATAGCAC
12668722 GCTCTTTGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (25 bp):
TGCTCTCTGATTAATAGCACATCAA
Found at i:12668731 original size:19 final size:19
Alignment explanation
Indices: 12668704--12668741 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12668694 CACGTCAGTA
12668704 CTCTCTGATTAATAGCACG
1 CTCTCTGATTAATAGCACG
* *
12668723 CTCTTTGATTACTAGCACG
1 CTCTCTGATTAATAGCACG
12668742 TTAGTGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (19 bp):
CTCTCTGATTAATAGCACG
Found at i:12668732 original size:44 final size:44
Alignment explanation
Indices: 12668678--12668765 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
12668668 GCACATCAAT
* *
12668678 GCTCTCTGATTATTAGCACGTCAGTACTCTCTGATTAATAGCAC
1 GCTCTCTGATTACTAGCACGTCAGTACTCTCCGATTAATAGCAC
* * * *
12668722 GCTCTTTGATTACTAGCACGTTAGTGCTCTCCGATTATTAGCAC
1 GCTCTCTGATTACTAGCACGTCAGTACTCTCCGATTAATAGCAC
12668766 ATTGGTGCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (44 bp):
GCTCTCTGATTACTAGCACGTCAGTACTCTCCGATTAATAGCAC
Found at i:12668787 original size:22 final size:22
Alignment explanation
Indices: 12668735--12668821 Score: 86
Period size: 22 Copynumber: 3.8 Consensus size: 22
12668725 CTTTGATTAC
*
12668735 TAGCACGTTAGTGCTCTCCGATTAT
1 TAGCACATTAGTGCTCTCCG--T-T
*
12668760 TAGCACATTGGTGCTCTCCGTT
1 TAGCACATTAGTGCTCTCCGTT
* *
12668782 TAGCACATCT-GTGCTCTCTGTA
1 TAGCACAT-TAGTGCTCTCCGTT
*
12668804 TAGCACTTTAGTGCTCTC
1 TAGCACATTAGTGCTCTC
12668822 TATTTAATAG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
21 1 0.02
22 34 0.62
23 2 0.04
25 18 0.33
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCCGTT
Found at i:12669093 original size:13 final size:12
Alignment explanation
Indices: 12669075--12669115 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
12669065 GGGTTATAAG
12669075 GAAAAGAAATAGT
1 GAAAAGAAA-AGT
12669088 GAAAAGAAAAGT
1 GAAAAGAAAAGT
*
12669100 GAGAA-AAAAGT
1 GAAAAGAAAAGT
12669111 GAAAA
1 GAAAA
12669116 TTCCCGGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.38
12 7 0.27
13 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.10
Consensus pattern (12 bp):
GAAAAGAAAAGT
Found at i:12682654 original size:30 final size:30
Alignment explanation
Indices: 12682618--12682678 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
12682608 AACAAGGGCA
12682618 AACTTCCTAATTCTTAAACCAAAAAACTCT
1 AACTTCCTAATTCTTAAACCAAAAAACTCT
*
12682648 AACTTCCTAATTCTTAAACCAACAAACTCT
1 AACTTCCTAATTCTTAAACCAAAAAACTCT
12682678 A
1 A
12682679 TCATAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.30
Consensus pattern (30 bp):
AACTTCCTAATTCTTAAACCAAAAAACTCT
Found at i:12696304 original size:24 final size:25
Alignment explanation
Indices: 12696277--12696332 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
12696267 GGTTTAGAAG
*
12696277 CAGGAGCA-GAGGGAGGTTGTGGAA
1 CAGGAGCAGGAGGGAGGTCGTGGAA
*
12696301 CAGGAG-AGGGGGGAGGTCGTGGAA
1 CAGGAGCAGGAGGGAGGTCGTGGAA
12696325 CAGGAGCA
1 CAGGAGCA
12696333 TCCCTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 1 0.04
24 26 0.93
25 1 0.04
ACGTcount: A:0.29, C:0.11, G:0.52, T:0.09
Consensus pattern (25 bp):
CAGGAGCAGGAGGGAGGTCGTGGAA
Found at i:12700048 original size:7 final size:7
Alignment explanation
Indices: 12700036--12700064 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
12700026 AAAACAAAAC
12700036 GAGAGAA
1 GAGAGAA
12700043 GAGAGAA
1 GAGAGAA
12700050 GAGAGAA
1 GAGAGAA
12700057 GAGA-AA
1 GAGAGAA
12700063 GA
1 GA
12700065 AAAAAGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
GAGAGAA
Found at i:12704858 original size:31 final size:29
Alignment explanation
Indices: 12704789--12704862 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
12704779 ACAAAATAAT
**
12704789 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGGCA
*
12704818 AACATAAGTGACTAAAATGTAACATGAGGCA
1 AACATAAGTGACTAAAACGTAACAT--GGCA
*
12704849 AACAAAAGTGACTA
1 AACATAAGTGACTA
12704863 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGGCA
Found at i:12708375 original size:15 final size:16
Alignment explanation
Indices: 12708348--12708385 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
12708338 ATAGCTTATT
12708348 AAAAAATGTAAAATGA-
1 AAAAAATGTAAAA-GAC
12708364 AAAAAATG-AAAAGAC
1 AAAAAATGTAAAAGAC
12708379 AAAAAAT
1 AAAAAAT
12708386 CATAACTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 8 0.38
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAAAATGTAAAAGAC
Found at i:12710689 original size:25 final size:26
Alignment explanation
Indices: 12710660--12710720 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
12710650 TTTCTCACAC
*
12710660 CAATTTTATCTC-AATAAAATTTTGA
1 CAATTTTACCTCTAATAAAATTTTGA
*
12710685 CAATTTTACCTCTAGTAAAATTTTGA
1 CAATTTTACCTCTAATAAAATTTTGA
*
12710711 CGATTTTACC
1 CAATTTTACC
12710721 CCCGATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (26 bp):
CAATTTTACCTCTAATAAAATTTTGA
Found at i:12710729 original size:26 final size:25
Alignment explanation
Indices: 12710673--12710733 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
12710663 TTTTATCTCA
* *
12710673 ATAAAATTTTGACAATTTTACCTCT
1 ATAAAATTTTGACAATTTTACCCCG
*
12710698 AGTAAAATTTTGACGATTTTACCCCCG
1 A-TAAAATTTTGACAATTTTA-CCCCG
12710725 ATAAAATTT
1 ATAAAATTT
12710734 CGAGAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.03
26 26 0.84
27 4 0.13
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (25 bp):
ATAAAATTTTGACAATTTTACCCCG
Found at i:12714797 original size:62 final size:58
Alignment explanation
Indices: 12714706--12714838 Score: 160
Period size: 62 Copynumber: 2.2 Consensus size: 58
12714696 TTCAAAAATA
* * * * *
12714706 ATATTATTTTAAT-AATTTAATATTAAATTTTATTTTATTTTTATCTTGTAGATAAATATT
1 ATATTATTTTAATAAACTTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATT
*
12714766 CTATTATTTTAATAAGACTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
1 ATATTATTTTAATAA-ACTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
*
12714825 ATATTAATTTAATA
1 ATATTATTTTAATA
12714839 TTAAAGTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
59 22 0.35
60 13 0.21
61 2 0.03
62 26 0.41
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (58 bp):
ATATTATTTTAATAAACTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
Found at i:12718594 original size:13 final size:13
Alignment explanation
Indices: 12718576--12718609 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
12718566 TTTTGGTTTT
12718576 TCATAATTGTCCA
1 TCATAATTGTCCA
12718589 TCATAATTGTCCA
1 TCATAATTGTCCA
12718602 TCATAATT
1 TCATAATT
12718610 CAGTTCAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (13 bp):
TCATAATTGTCCA
Found at i:12719517 original size:2 final size:2
Alignment explanation
Indices: 12719512--12719537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12719502 GTAGTAGCTT
12719512 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
12719538 AGAGTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12722680 original size:18 final size:18
Alignment explanation
Indices: 12722653--12722687 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12722643 TTCATGAGGT
*
12722653 TGTGGTTGTGGTTGTGAC
1 TGTGGCTGTGGTTGTGAC
12722671 TGTGGCTGTGGTTGTGA
1 TGTGGCTGTGGTTGTGA
12722688 GGTTCTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.46, T:0.43
Consensus pattern (18 bp):
TGTGGCTGTGGTTGTGAC
Found at i:12727362 original size:24 final size:24
Alignment explanation
Indices: 12727299--12727365 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
12727289 TTTAATTTTT
* **
12727299 AAAAATAAAAATTATGAAAAAATA
1 AAAAATAAAAATAATTCAAAAATA
***
12727323 AAAAATCTTTAA-AATTCAAAAATA
1 AAAAAT-AAAAATAATTCAAAAATA
12727347 AAAAATAAAAATAATTCAA
1 AAAAATAAAAATAATTCAA
12727366 TGTTAACTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
23 2 0.06
24 28 0.88
25 2 0.06
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.24
Consensus pattern (24 bp):
AAAAATAAAAATAATTCAAAAATA
Found at i:12727831 original size:24 final size:24
Alignment explanation
Indices: 12727791--12727841 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
12727781 ATTTTAAAAA
*
12727791 TAATTATAAATTCTTTTCATTTTT
1 TAATTATAAATTCTTTTCATATTT
* *
12727815 TAATTTTAAATAT-TTTTTATATTT
1 TAATTATAAAT-TCTTTTCATATTT
12727839 TAA
1 TAA
12727842 AATATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TAATTATAAATTCTTTTCATATTT
Found at i:12727838 original size:18 final size:18
Alignment explanation
Indices: 12727809--12727852 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
12727799 AATTCTTTTC
12727809 ATTTTTTAATTTT-AAAT
1 ATTTTTTAATTTTAAAAT
12727826 ATTTTTTATATTTTAAAAT
1 ATTTTTTA-ATTTTAAAAT
12727845 ATATTTTT
1 AT-TTTTT
12727853 TAAAAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 5 0.21
19 6 0.25
20 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTAATTTTAAAAT
Found at i:12732895 original size:62 final size:61
Alignment explanation
Indices: 12732774--12732895 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 61
12732764 TATATTTGTA
** ****
12732774 CAATATATTTTTATATTATTTTATTTAATAAAATAAAAGTTTTTTTGAATATTTTAATAGT
1 CAATATATTTTTATATTATTTTATTTAATAAAATAAAAGTTCGTTTGAATAAGGCAATAGT
12732835 CAAT-TATTTTTATATT-TTATCCTATTTAATAAAATAAAAGTTCGTTTGAATAAGGCAATAG
1 CAATATATTTTTATATTATT-T--TATTTAATAAAATAAAAGTTCGTTTGAATAAGGCAATAG
12732896 AAATAATGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 4 0.08
62 33 0.63
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (61 bp):
CAATATATTTTTATATTATTTTATTTAATAAAATAAAAGTTCGTTTGAATAAGGCAATAGT
Found at i:12735960 original size:15 final size:16
Alignment explanation
Indices: 12735940--12735969 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12735930 GTACTACAAG
12735940 ATTATTTT-TTTAAAA
1 ATTATTTTATTTAAAA
12735955 ATTATTTTATTTAAA
1 ATTATTTTATTTAAA
12735970 TATCTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTTTATTTAAAA
Found at i:12736350 original size:22 final size:22
Alignment explanation
Indices: 12736325--12736508 Score: 224
Period size: 22 Copynumber: 8.1 Consensus size: 22
12736315 CTCTCTGATA
* * *
12736325 TTTAGCACGTCAGTGCTTTCTG
1 TTTAGCACATCTGTGCTCTCTG
12736347 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCTGTGCTCTCTG
* *
12736369 ATATTTAGCACGTCAGTGCTCTCTG
1 ---TTTAGCACATCTGTGCTCTCTG
* *
12736394 TTTAGCAAATTTGTGCTCTCTG
1 TTTAGCACATCTGTGCTCTCTG
** *
12736416 ATTATTAGCATGTCAGTGCTCTCTG
1 --T-TTAGCACATCTGTGCTCTCTG
12736441 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCTGTGCTCTCTG
12736463 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCTGTGCTCTCTG
12736485 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCTGTGCTCTCTG
12736507 TT
1 TT
12736509 CATTAGTGCA
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
22 101 0.72
23 1 0.01
24 1 0.01
25 37 0.26
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (22 bp):
TTTAGCACATCTGTGCTCTCTG
Found at i:12736383 original size:47 final size:46
Alignment explanation
Indices: 12736314--12736506 Score: 291
Period size: 47 Copynumber: 4.2 Consensus size: 46
12736304 ACTCTAGCGC
*
12736314 GCTCTCTGATATTTAGCACGTCAGTGCTTTCTGTTTAGCACATCTGT
1 GCTCTCTGAT-TTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
* *
12736361 GCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCAAATTTGT
1 GCTCTCTGAT-TTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
*
12736408 GCTCTCTGATTATTAGCATGTCAGTGCTCTCTGTTTAGCACATCTGT
1 GCTCTCTGATT-TTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
* *
12736455 GCTCTCTG--TTTAGCACATCTGTGCTCTCTGTTTAGCACATCTGT
1 GCTCTCTGATTTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
12736499 GCTCTCTG
1 GCTCTCTG
12736507 TTCATTAGTG
Statistics
Matches: 136, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
44 40 0.29
45 1 0.01
46 1 0.01
47 94 0.69
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
Found at i:12736457 original size:69 final size:66
Alignment explanation
Indices: 12736337--12736508 Score: 209
Period size: 69 Copynumber: 2.5 Consensus size: 66
12736327 TAGCACGTCA
* * *
12736337 GTGCTTTCTGTTTAGCACATCTGTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCAA
1 GTGCTCTCTGTTTAGCACATCAGTGCTCTCTG---TTTAGCACATCAGTGCTCTCTGTTTAGCAA
*
12736402 ATTT
63 ATCT
** * *
12736406 GTGCTCTCTGATTATTAGCATGTCAGTGCTCTCTGTTTAGCACATCTGTGCTCTCTGTTTAGCAC
1 GTGCTCTCTG--T-TTAGCACATCAGTGCTCTCTGTTTAGCACATCAGTGCTCTCTGTTTAGCAA
12736471 ATCT
63 ATCT
*
12736475 GTGCTCTCTGTTTAGCACATCTGTGCTCTCTGTT
1 GTGCTCTCTGTTTAGCACATCAGTGCTCTCTGTT
12736509 CATTAGTGCA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
66 20 0.22
67 1 0.01
69 49 0.55
71 1 0.01
72 18 0.20
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (66 bp):
GTGCTCTCTGTTTAGCACATCAGTGCTCTCTGTTTAGCACATCAGTGCTCTCTGTTTAGCAAATC
T
Found at i:12743390 original size:21 final size:21
Alignment explanation
Indices: 12743364--12743411 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
12743354 ATTTTCTAAA
12743364 ACCACTTGACCTCAGGGTCTT
1 ACCACTTGACCTCAGGGTCTT
* *
12743385 ACCACTTGACCTTAGGGTTTT
1 ACCACTTGACCTCAGGGTCTT
12743406 ACCACT
1 ACCACT
12743412 CGAACTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (21 bp):
ACCACTTGACCTCAGGGTCTT
Found at i:12743419 original size:21 final size:21
Alignment explanation
Indices: 12743377--12743419 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12743367 ACTTGACCTC
* *
12743377 AGGGTCTTACCACTTGACCTT
1 AGGGTCTTACCACTCGAACTT
*
12743398 AGGGTTTTACCACTCGAACTT
1 AGGGTCTTACCACTCGAACTT
12743419 A
1 A
12743420 AAAATCGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (21 bp):
AGGGTCTTACCACTCGAACTT
Found at i:12745283 original size:126 final size:126
Alignment explanation
Indices: 12745053--12745567 Score: 764
Period size: 126 Copynumber: 4.1 Consensus size: 126
12745043 GCCAAGCACG
* * *
12745053 AACTACTGTAGAAAAAGAGCGTCCACGTTGGAGCTTTTTTCAGTAATTTTACTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* * *
12745118 TGCTTGAAGCGTTTTTGACACTATTTTTTCGGAACCGTCTTCTCAAAATTATTTTTTCAGG
66 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTCAGA
* *
12745179 AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAGTTTTGTTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
*
12745244 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAATTTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTCAGA
* * * * *
12745305 AACTACTATAAAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATACTTTTGCTGACAGTGCATAC
1 AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* * * *
12745370 TGCTTGAAGCGTTTTTAAGATTATTTTTTCAGAA-CTGTCTTCTAAAAATTA-TTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATC-GTCTTCTCAAAATTATTTTTTCAGA
* * **
12745430 AATTACTATAGAAAAAAGAATGTCCACGTAGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATC
1 AACTACTGTAG-AAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATC
* * *
12745495 CTGCTTGAAACGTTTTTGTCACTATTTTTTCAGAATCGTCTTCTCAAAATTAATTTTTCAGA
65 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTCAGA
*
12745557 AACTATTGTAG
1 AACTACTGTAG
12745568 GAGAAAAAAC
Statistics
Matches: 349, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
125 19 0.05
126 312 0.89
127 18 0.05
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTCAGA
Found at i:12745710 original size:34 final size:32
Alignment explanation
Indices: 12745665--12745771 Score: 117
Period size: 34 Copynumber: 3.2 Consensus size: 32
12745655 ATTATTTTCA
12745665 AAAAATCCTAAACCTTAATTTAATTAATTTTCTT
1 AAAAA-CCTAAACC-TAATTTAATTAATTTTCTT
*
12745699 AAAAACTCTAAACCCTAATTTAATTAATTTACTT
1 AAAAAC-CTAAA-CCTAATTTAATTAATTTTCTT
* *
12745733 AGAAACCTTAAAACCTAAATTAATTAA-TTTCTTT
1 AAAAACC-T-AAACCTAATTTAATTAATTTTC-TT
12745767 AAAAA
1 AAAAA
12745772 AAATTCTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
33 5 0.08
34 53 0.84
35 5 0.08
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (32 bp):
AAAAACCTAAACCTAATTTAATTAATTTTCTT
Done.