Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 158 of 199
Found at i:47103537 original size:11 final size:12
Alignment explanation
Indices: 47103521--47103549 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
47103511 GGACACACGG
47103521 CCGTGTCCA-AC
1 CCGTGTCCATAC
47103532 CCGTGTCCATAC
1 CCGTGTCCATAC
47103544 CCGTGT
1 CCGTGT
47103550 AACTTCTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.14, C:0.41, G:0.21, T:0.24
Consensus pattern (12 bp):
CCGTGTCCATAC
Found at i:47105970 original size:50 final size:50
Alignment explanation
Indices: 47105848--47106183 Score: 397
Period size: 50 Copynumber: 6.7 Consensus size: 50
47105838 ATATGGGTAA
* * *
47105848 AGAGATCCCATGTAAGACCATGTCTGGTACATGGCATTGGCATCATTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGATG
* * *
47105901 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTCGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* **
47105951 AGAGGTCCCATGTAAGACCATGTATGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
47106001 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
47106051 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
47106101 AGAACTCCCATGTAAGATCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* **
47106150 AAACATCCCATGTAAGACCATGTCTGGGACATGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGG
47106184 TTTTGACATG
Statistics
Matches: 247, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
48 1 0.00
49 31 0.13
50 177 0.72
53 38 0.15
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:47107637 original size:25 final size:25
Alignment explanation
Indices: 47107596--47107675 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
47107586 GGAAATTCAA
47107596 GAGAGCC-AATATCGGGAAGCTCGT
1 GAGAGCCAAATATCGGGAAGCTCGT
* *
47107620 GAGAGCCAAATATCGGGATGCTCAT
1 GAGAGCCAAATATCGGGAAGCTCGT
* ** *
47107645 AAGAGATAAATAACGGGAAGCTCGT
1 GAGAGCCAAATATCGGGAAGCTCGT
47107670 GAGAGC
1 GAGAGC
47107676 TATGGTGTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 7 0.16
25 38 0.84
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.16
Consensus pattern (25 bp):
GAGAGCCAAATATCGGGAAGCTCGT
Found at i:47109750 original size:2 final size:2
Alignment explanation
Indices: 47109743--47109768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47109733 NNNNNNNNNN
47109743 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
47109769 AATATTTATG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47121563 original size:26 final size:25
Alignment explanation
Indices: 47121511--47121564 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
47121501 TTATTATTAT
* *
47121511 TATATTTTCTATACATATACATTCA
1 TATATTTTATATACATATACATGCA
47121536 TATATTTTATATATCATAT-CTATGCA
1 TATATTTTATATA-CATATAC-ATGCA
47121562 TAT
1 TAT
47121565 TTAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (25 bp):
TATATTTTATATACATATACATGCA
Found at i:47122769 original size:16 final size:17
Alignment explanation
Indices: 47122748--47122779 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47122738 TAATAACAAT
47122748 AATTTAATCAT-AAAAA
1 AATTTAATCATCAAAAA
47122764 AATTTAATCATCAAAA
1 AATTTAATCATCAAAA
47122780 TACCATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTTAATCATCAAAAA
Found at i:47129775 original size:24 final size:26
Alignment explanation
Indices: 47129748--47129805 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
47129738 TTTATTAGTT
47129748 TATCAAAAATCA-ACTAC-TC-AAAAC
1 TATCAAAAATCACA-TACATCAAAAAC
47129772 TATCAAAAA-CACATACATCAAAAAC
1 TATCAAAAATCACATACATCAAAAAC
47129797 T-TCAAAAAT
1 TATCAAAAAT
47129806 TATTCTCCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 5 0.17
24 19 0.63
25 6 0.20
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.21
Consensus pattern (26 bp):
TATCAAAAATCACATACATCAAAAAC
Found at i:47130739 original size:14 final size:14
Alignment explanation
Indices: 47130720--47130746 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47130710 CATGATAAAA
47130720 TAAAATACAAGTGG
1 TAAAATACAAGTGG
47130734 TAAAATACAAGTG
1 TAAAATACAAGTG
47130747 TGCAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAAATACAAGTGG
Found at i:47132417 original size:43 final size:43
Alignment explanation
Indices: 47132361--47132444 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
47132351 CTTCCTTGTT
* * * *
47132361 ATACCTTGTGTAATATGCTTCGCGAACTTTATAGTGCACCTTG
1 ATACCTTATGTAATAGGCTTCACGAACCTTATAGTGCACCTTG
* * *
47132404 ATACCTTATGTAATGGGCTTCACGGACCTTATAGTGTACCT
1 ATACCTTATGTAATAGGCTTCACGAACCTTATAGTGCACCT
47132445 CACGAACTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (43 bp):
ATACCTTATGTAATAGGCTTCACGAACCTTATAGTGCACCTTG
Found at i:47134728 original size:2 final size:2
Alignment explanation
Indices: 47134721--47134752 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47134711 TTCCAGTTTC
47134721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47134753 GTCTATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47138609 original size:14 final size:14
Alignment explanation
Indices: 47138590--47138625 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
47138580 TTGTTTCACT
* *
47138590 GAAAATTATTTTTG
1 GAAAATGATTTCTG
47138604 GAAAATGATTTCTG
1 GAAAATGATTTCTG
47138618 GAAAATGA
1 GAAAATGA
47138626 CTTACTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:47142378 original size:20 final size:21
Alignment explanation
Indices: 47142355--47142401 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
47142345 AAAAAAATGT
47142355 AAAAGTTTATAAAAAT-CAT-A
1 AAAAGTTTAT-AAAATGCATCA
*
47142375 AAAAATTTATAAAATGCATCA
1 AAAAGTTTATAAAATGCATCA
47142396 AAAAGT
1 AAAAGT
47142402 CCCTTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 12 0.52
21 6 0.26
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (21 bp):
AAAAGTTTATAAAATGCATCA
Found at i:47142798 original size:10 final size:10
Alignment explanation
Indices: 47142785--47142883 Score: 59
Period size: 9 Copynumber: 10.4 Consensus size: 10
47142775 CTTTATAAAA
47142785 TTTTATATA-
1 TTTTATATAT
*
47142794 TTTT-TACAT
1 TTTTATATAT
*
47142803 TTCTATATA-
1 TTTTATATAT
47142812 TTTTATA-AT
1 TTTTATATAT
* *
47142821 TTTTTTACGAT
1 TTTTATA-TAT
*
47142832 TTTTATAAAT
1 TTTTATATAT
*
47142842 TTTTACA-AT
1 TTTTATATAT
47142851 TTTT-TATAT
1 TTTTATATAT
* *
47142860 TTTTTTACGAT
1 TTTTATA-TAT
47142871 TTTTATAT-T
1 TTTTATATAT
47142880 TTTT
1 TTTT
47142884 TGTAATTTTC
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
8 5 0.07
9 36 0.51
10 13 0.19
11 16 0.23
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATATAT
Found at i:47142837 original size:20 final size:20
Alignment explanation
Indices: 47142715--47142884 Score: 101
Period size: 20 Copynumber: 8.8 Consensus size: 20
47142705 TGGTACGATA
47142715 ATTTTTATAATTTTTTTTACG
1 ATTTTTATAA-TTTTTTTACG
**
47142736 AAATTTAT-A-TTTTTTAC-
1 ATTTTTATAATTTTTTTACG
* *
47142753 ATTTTGTATAATTTTCTTATG
1 ATTTT-TATAATTTTTTTACG
* * * *
47142774 A-CTTTATAAAATTTTATA-T
1 ATTTTTAT-AATTTTTTTACG
* * * *
47142793 ATTTTTA-CATTTCTATA-T
1 ATTTTTATAATTTTTTTACG
47142811 A-TTTTATAATTTTTTTACG
1 ATTTTTATAATTTTTTTACG
* *
47142830 ATTTTTATAA-ATTTTTACA
1 ATTTTTATAATTTTTTTACG
47142849 ATTTTT-TATATTTTTTTACG
1 ATTTTTATA-ATTTTTTTACG
47142869 ATTTTTAT-ATTTTTTT
1 ATTTTTATAATTTTTTT
47142885 GTAATTTTCG
Statistics
Matches: 114, Mismatches: 23, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
17 8 0.07
18 29 0.25
19 28 0.25
20 41 0.36
21 8 0.07
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTTTTATAATTTTTTTACG
Found at i:47142884 original size:19 final size:19
Alignment explanation
Indices: 47142812--47142884 Score: 101
Period size: 19 Copynumber: 3.7 Consensus size: 19
47142802 TTTCTATATA
47142812 TTTTATAATTTTTTTACGAT
1 TTTTAT-ATTTTTTTACGAT
** *
47142832 TTTTATAAATTTTTACAATT
1 TTTTATATTTTTTTACGA-T
47142852 TTTTATATTTTTTTACGAT
1 TTTTATATTTTTTTACGAT
47142871 TTTTATATTTTTTT
1 TTTTATATTTTTTT
47142885 GTAATTTTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 24 0.52
20 22 0.48
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTATATTTTTTTACGAT
Found at i:47143100 original size:88 final size:87
Alignment explanation
Indices: 47143001--47143185 Score: 219
Period size: 87 Copynumber: 2.1 Consensus size: 87
47142991 AGCAGGGGTA
*
47143001 TAATTGCTTTTTTGGAAAAAGTTTGAAGGTATTTTTGATGCATTTTGAAAGTTCAAGTACCCAAT
1 TAATTGCTTTTTT-GAAAAAGTTTGAAGGTATTTTTGATGCATTTTGAAAGTTCAAGTACCCAAA
47143066 TGAGTGCAAAACAAATATGGGCT
65 TGAGTGCAAAACAAATATGGGCT
* ** * * * * * * *
47143089 TAATTGTTTTTTTTTAAAGGTTTGAGGGTTTTTTTGGTGTATTTTGAAAGTTTAAGTACCTAAAT
1 TAATTGCTTTTTTGAAAAAGTTTGAAGGTATTTTTGATGCATTTTGAAAGTTCAAGTACCCAAAT
* *
47143154 GAGTGCAAAAGAAAACAAT-GGCT
66 GAGTGCAAAA-CAAA-TATGGGCT
47143177 TAATTGCTT
1 TAATTGCTT
47143186 CTTCTTCTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
87 52 0.64
88 27 0.33
89 2 0.02
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (87 bp):
TAATTGCTTTTTTGAAAAAGTTTGAAGGTATTTTTGATGCATTTTGAAAGTTCAAGTACCCAAAT
GAGTGCAAAACAAATATGGGCT
Found at i:47165600 original size:30 final size:30
Alignment explanation
Indices: 47165557--47165615 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
47165547 CTTAACAAGC
47165557 AAATGCCTCTAAAATAATAACAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
* *
47165587 AAATGTCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
47165616 CAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:47171337 original size:32 final size:32
Alignment explanation
Indices: 47171296--47171368 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
47171286 AATGATATTA
47171296 GATATTGAATTTATTATGTTTTAAGCTTGTTG
1 GATATTGAATTTATTATGTTTTAAGCTTGTTG
47171328 GATATTGAATTTATTATGTTTTAAGCTTGTTG
1 GATATTGAATTTATTATGTTTTAAGCTTGTTG
47171360 GATATTGAA
1 GATATTGAA
47171369 ATGATTGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (32 bp):
GATATTGAATTTATTATGTTTTAAGCTTGTTG
Found at i:47171536 original size:48 final size:48
Alignment explanation
Indices: 47171468--47171560 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
47171458 CATCTTTTTC
47171468 TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTATTT
1 TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTATTT
* *
47171516 TTGAAATTCTAGTAGAGGAGGCCAAGAGAGGAGATAAGCCTTCTA
1 TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTA
47171561 ATACTTTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (48 bp):
TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTATTT
Found at i:47172666 original size:14 final size:14
Alignment explanation
Indices: 47172647--47172686 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
47172637 TTTTAAAAAA
47172647 ATAAATTATTTTTC
1 ATAAATTATTTTTC
47172661 ATAAATTATTTTTC
1 ATAAATTATTTTTC
* *
47172675 AGAAAATATTTT
1 ATAAATTATTTT
47172687 AGTTACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (14 bp):
ATAAATTATTTTTC
Found at i:47188824 original size:21 final size:21
Alignment explanation
Indices: 47188798--47188846 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
47188788 CAGTGGGGGA
*
47188798 GAGATTAGTTACTGA-AGCGGT
1 GAGATTAGATACT-ATAGCGGT
*
47188819 GAGATTGGATACTATAGCGGT
1 GAGATTAGATACTATAGCGGT
47188840 GAGATTA
1 GAGATTA
47188847 AAAACAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.31, C:0.08, G:0.33, T:0.29
Consensus pattern (21 bp):
GAGATTAGATACTATAGCGGT
Found at i:47191532 original size:23 final size:22
Alignment explanation
Indices: 47191481--47191537 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
47191471 GGTCTTCATA
*
47191481 TTTTTCGTTTTAAGTAATTTAAT
1 TTTTTC-TTTTAAGTAATTTAAC
47191504 TGTTTTCTTTTATA-TAATTTTAAC
1 T-TTTTCTTTTA-AGTAA-TTTAAC
*
47191528 TTTTTTTTTT
1 TTTTTCTTTT
47191538 CATTCTCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTTCTTTTAAGTAATTTAAC
Found at i:47191533 original size:24 final size:22
Alignment explanation
Indices: 47191481--47191537 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
47191471 GGTCTTCATA
47191481 TTTTTCGTTTTAAGTAATTTAAT
1 TTTTTC-TTTTAAGTAATTTAAT
47191504 TGTTTTCTTTTATA-TAATTTTAACT
1 T-TTTTCTTTTA-AGTAA-TTTAA-T
47191529 TTTTT-TTTT
1 TTTTTCTTTT
47191538 CATTCTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
23 13 0.43
24 15 0.50
25 2 0.07
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTTCTTTTAAGTAATTTAAT
Found at i:47193048 original size:23 final size:23
Alignment explanation
Indices: 47193018--47193065 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
47193008 CAAAACGATG
* *
47193018 AAATCTTAGTA-ACATTTTATTTT
1 AAATCTTAATATA-ATTATATTTT
47193041 AAATCTTAATATAATTATATTTT
1 AAATCTTAATATAATTATATTTT
47193064 AA
1 AA
47193066 TAGTATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATCTTAATATAATTATATTTT
Found at i:47193394 original size:23 final size:23
Alignment explanation
Indices: 47193368--47193412 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
47193358 ATAAAAGAAT
*
47193368 TTATTGGTAATTA-TTAAAAAGTG
1 TTATTAGT-ATTATTTAAAAAGTG
*
47193391 TTATTAGTTTTATTTAAAAAGT
1 TTATTAGTATTATTTAAAAAGT
47193413 AAAAGACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (23 bp):
TTATTAGTATTATTTAAAAAGTG
Found at i:47203955 original size:31 final size:29
Alignment explanation
Indices: 47203913--47203972 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
47203903 ACTAAGTTAC
*
47203913 TTAACTTTCGAAAAATA-ACATATCAATCA
1 TTAACTTTCG-AAAATAGACAAATCAATCA
47203942 TTAACATTATCGAAAATAGACAAATCAATCA
1 TTAAC-TT-TCGAAAATAGACAAATCAATCA
47203973 CCCATTAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 5 0.19
30 8 0.30
31 14 0.52
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (29 bp):
TTAACTTTCGAAAATAGACAAATCAATCA
Found at i:47204116 original size:28 final size:29
Alignment explanation
Indices: 47204079--47204143 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
47204069 TCATCCTTCC
47204079 TTTTCTATTTTTT-AATAAATGGCCCAATA
1 TTTT-TATTTTTTGAATAAATGGCCCAATA
* *
47204108 TTTTTATTTTTTGCATAAATGGCCTAATA
1 TTTTTATTTTTTGAATAAATGGCCCAATA
*
47204137 TGTTTAT
1 TTTTTAT
47204144 GCTTCTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (29 bp):
TTTTTATTTTTTGAATAAATGGCCCAATA
Found at i:47210061 original size:16 final size:17
Alignment explanation
Indices: 47210026--47210064 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
47210016 ATTTATGAAA
47210026 TATAAATTTTAATTACT
1 TATAAATTTTAATTACT
* *
47210043 TATAATTTTTAA-TATT
1 TATAAATTTTAATTACT
47210059 TATAAA
1 TATAAA
47210065 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TATAAATTTTAATTACT
Found at i:47210802 original size:90 final size:89
Alignment explanation
Indices: 47210642--47210858 Score: 219
Period size: 90 Copynumber: 2.4 Consensus size: 89
47210632 GGACTATCTT
* * * * * *
47210642 AAAAAGCCCTTAAACTTTTTTCAAAAAAAAATAATTAAACCTCTCTTTTTTTACACTCAATTGAG
1 AAAAAGCCCTCAAACTTTCTTCAAAAAAAAACAATTAAACCCCTATTTTTTTACACTCAATTGAA
47210707 CATTTGAA-TTTTCAAAATGCATCG
66 CATTTGAACTTTT-AAAATGCATCG
* * *
47210731 AAAAAGCCCTCAAAC-TTCTTCAAAAATAAAAGCAATTAAGCCCCTATTTTTTTTCACTTAATTG
1 AAAAAGCCCTCAAACTTTCTTCAAAAA-AAAA-CAATTAAACCCCTATTTTTTTACACTCAATTG
* * **
47210795 AATATTTGAACTTTTAAAATACATAAAA
64 AACATTTGAACTTTTAAAATGCAT--CG
*
47210823 AAAAAGACCCTCAAAATTT-TTC--AAAAAAACAATTAA
1 AAAAAG-CCCTCAAACTTTCTTCAAAAAAAAACAATTAA
47210859 GCCTAAGCTC
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
88 10 0.09
89 25 0.23
90 46 0.43
91 7 0.07
92 6 0.06
93 11 0.10
94 2 0.02
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.33
Consensus pattern (89 bp):
AAAAAGCCCTCAAACTTTCTTCAAAAAAAAACAATTAAACCCCTATTTTTTTACACTCAATTGAA
CATTTGAACTTTTAAAATGCATCG
Found at i:47210916 original size:18 final size:19
Alignment explanation
Indices: 47210895--47210945 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
47210885 AAAATTAATA
47210895 AAAAATAATAAATTTT-AG
1 AAAAATAATAAATTTTAAG
* *
47210913 AAAAATTATTAAATTTTAAT
1 AAAAA-TAATAAATTTTAAG
47210933 AAAAAT-ATAAATT
1 AAAAATAATAAATT
47210946 ATTATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.39
19 11 0.39
20 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATAATAAATTTTAAG
Found at i:47210936 original size:19 final size:19
Alignment explanation
Indices: 47210889--47210945 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
47210879 TAGAAAAAAA
*
47210889 TTAATAAAAAATAATAAATT
1 TTAAT-AAAAATATTAAATT
*
47210909 TTAGA-AAAATTATTAAATT
1 TTA-ATAAAAATATTAAATT
47210928 TTAATAAAAATA-TAAATT
1 TTAATAAAAATATTAAATT
47210946 ATTATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.22
19 21 0.66
20 3 0.09
21 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TTAATAAAAATATTAAATT
Found at i:47210952 original size:18 final size:17
Alignment explanation
Indices: 47210895--47210980 Score: 66
Period size: 19 Copynumber: 4.6 Consensus size: 17
47210885 AAAATTAATA
*
47210895 AAAAATAATAAATTTTAG
1 AAAAAT-ATAAATTTTAT
47210913 AAAAATTATTAAATTTTAAT
1 AAAAA-TA-TAAATTTT-AT
47210933 AAAAATATAAATTATTAT
1 AAAAATATAAATT-TTAT
* *
47210951 -AAATTATAATTTTTTTAT
1 AAAAATATAA--ATTTTAT
47210969 AAAAATCATAAA
1 AAAAAT-ATAAA
47210981 AAATAAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
17 8 0.15
18 18 0.33
19 19 0.35
20 10 0.18
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
AAAAATATAAATTTTAT
Found at i:47211249 original size:59 final size:58
Alignment explanation
Indices: 47211171--47211318 Score: 167
Period size: 58 Copynumber: 2.5 Consensus size: 58
47211161 AATTACGAAA
* * *
47211171 TTTATATTTCTTTACATTTTGTATAATTTTCTTATGA-CTTTAT-AAAATTTTATAATTTT
1 TTTATATTTCTATACA-TTT-TATAATTTT-TTATGATCTTTATAAAAAATTTACAATTTT
* *
47211230 TTTATATTTCTATATATTTTATAATTTTTTATGATTTTTATAAAAAATTTACAATTTT
1 TTTATATTTCTATACATTTTATAATTTTTTATGATCTTTATAAAAAATTTACAATTTT
* *
47211288 TTTATATTT-TTTACGATTTTTATATTTTTTT
1 TTTATATTTCTATAC-A-TTTTATAATTTTTT
47211319 TCTAATTTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
56 6 0.08
57 17 0.22
58 27 0.35
59 27 0.35
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.64
Consensus pattern (58 bp):
TTTATATTTCTATACATTTTATAATTTTTTATGATCTTTATAAAAAATTTACAATTTT
Found at i:47211300 original size:20 final size:19
Alignment explanation
Indices: 47211277--47211329 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
47211267 TTATAAAAAA
*
47211277 TTTACAATTTTTTTATATTT
1 TTTACAATTTTTATAT-TTT
*
47211297 TTTACGATTTTTATATTTT
1 TTTACAATTTTTATATTTT
*
47211316 TTTTCTAATTTTTA
1 TTTAC-AATTTTTA
47211330 ATAAAACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTACAATTTTTATATTTT
Found at i:47211344 original size:58 final size:57
Alignment explanation
Indices: 47211171--47211356 Score: 143
Period size: 57 Copynumber: 3.2 Consensus size: 57
47211161 AATTACGAAA
* * * **
47211171 TTTATATTTCTTTACAT-TTTGTATAATTTTCTTATGA-CTTTATAAAATTTTATAATTTT
1 TTTATATTT-TTTAGATATTT-TATAATTTT-TTATAATTTTTATAAAAAATT-TAATTTT
* * *
47211230 TTTATA-TTTCTATATATTTTATAATTTTTTATGATTTTTATAAAAAATTTACAATTTT
1 TTTATATTTTTTAGATATTTTATAATTTTTTATAATTTTTATAAAAAATTT--AATTTT
* * *
47211288 TTTATATTTTTTACGAT-TTTTATATTTTTTTTCTAATTTTTA-ATAAAACTTTAA-TTT
1 TTTATATTTTTTA-GATATTTTATA-ATTTTTTATAATTTTTATA-AAAAATTTAATTTT
47211345 TTTAT-TTTTTTA
1 TTTATATTTTTTA
47211357 TTAAAATTTA
Statistics
Matches: 108, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
56 14 0.13
57 33 0.31
58 19 0.18
59 19 0.18
60 23 0.21
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (57 bp):
TTTATATTTTTTAGATATTTTATAATTTTTTATAATTTTTATAAAAAATTTAATTTT
Found at i:47211353 original size:26 final size:27
Alignment explanation
Indices: 47211315--47211368 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
47211305 TTTTATATTT
47211315 TTTTTCTA-ATTTTTAATAAAACTTTAA
1 TTTTTCTATATTTTTAATAAAA-TTTAA
* *
47211342 TTTTT-TATTTTTTTATTAAAATTTAA
1 TTTTTCTATATTTTTAATAAAATTTAA
47211368 T
1 T
47211369 AATATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTTTCTATATTTTTAATAAAATTTAA
Found at i:47211367 original size:37 final size:38
Alignment explanation
Indices: 47211303--47211394 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 38
47211293 ATTTTTTACG
**
47211303 ATTTTTATATTTTTTT-TCTAATTTTTAATAAAACTTTA-
1 ATTTTT-TATTTTTTTATCTAAAATTTAATAAAA-TTTAT
*
47211341 ATTTTTTATTTTTTTAT-TAAAATTTAATAATATTTAT
1 ATTTTTTATTTTTTTATCTAAAATTTAATAAAATTTAT
*
47211378 ATCTTTTATTTATTTTA
1 ATTTTTTATTT-TTTTA
47211395 ATTTTTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 4 0.09
37 31 0.66
38 12 0.26
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (38 bp):
ATTTTTTATTTTTTTATCTAAAATTTAATAAAATTTAT
Found at i:47211412 original size:20 final size:21
Alignment explanation
Indices: 47211387--47211427 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
47211377 TATCTTTTAT
*
47211387 TTATTT-TAATTTTTTATAAA
1 TTATTTCTAATTTTTAATAAA
47211407 TTATTTCTAATTTTTAATAAA
1 TTATTTCTAATTTTTAATAAA
47211428 AGCAGGGGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTCTAATTTTTAATAAA
Found at i:47211589 original size:89 final size:91
Alignment explanation
Indices: 47211434--47211605 Score: 231
Period size: 89 Copynumber: 1.9 Consensus size: 91
47211424 TAAAAGCAGG
* *
47211434 GGCTTAATTGCTTTTTTTGAAAAAAATTTGAGGGTCTTTTTGATACATTTTAAAAATTCAAGTAC
1 GGCTTAATTGCTTTTTTTGAAAAAAATTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATAC
*
47211499 CCAATTGAGTGCAAAAAAAAAGTATA
66 CCAAATGAGTGCAAAAAAAAAGTATA
** * * * * *
47211525 GGCTTAATTG-TTTTTTTG-AAAAGGTTTGAGAGTCTTTTTTATGCATTTTGAAAGTTTAAATAC
1 GGCTTAATTGCTTTTTTTGAAAAAAATTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATAC
*
47211588 CCAAATGATTGCAAAAAA
66 CCAAATGAGTGCAAAAAA
47211606 GAAAAAACAA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
89 52 0.74
90 8 0.11
91 10 0.14
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (91 bp):
GGCTTAATTGCTTTTTTTGAAAAAAATTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATAC
CCAAATGAGTGCAAAAAAAAAGTATA
Found at i:47214014 original size:2 final size:2
Alignment explanation
Indices: 47214009--47214055 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
47213999 TTTTGTTTAA
47214009 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47214051 AT AT A
1 AT AT A
47214056 CTTTTGAGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47214864 original size:17 final size:17
Alignment explanation
Indices: 47214844--47214888 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
47214834 TATTACTAGA
47214844 AATTTTTAATTATAAAT
1 AATTTTTAATTATAAAT
** *
47214861 AATTTAAAATAATAAAT
1 AATTTTTAATTATAAAT
47214878 AATTTTTAATT
1 AATTTTTAATT
47214889 TTTAATTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTTAATTATAAAT
Found at i:47215849 original size:11 final size:11
Alignment explanation
Indices: 47215833--47215858 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47215823 AACCAACACC
47215833 AAAAAATTAAA
1 AAAAAATTAAA
47215844 AAAAAATTAAA
1 AAAAAATTAAA
47215855 AAAA
1 AAAA
47215859 TTACTCGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:47231275 original size:191 final size:195
Alignment explanation
Indices: 47230943--47231331 Score: 642
Period size: 191 Copynumber: 2.0 Consensus size: 195
47230933 TATTTAGATT
*
47230943 ATAAAAGTTATTTAATTCTAGCATTTGAGTACACCAAAACTTGCATACTAGTTAAATGATTACTT
1 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTG---ACTAG-TAAATGATTACTT
* * *
47231008 AAATGGTAGTGTCTTGAGAAGGGCATGTTGGTTCTTTTACAGAAGCAACTTCACTTACTGTTTCT
62 AAATGGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCT
47231073 TAAGCAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTC
127 TAAGCAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTC
47231138 AGGA
192 AGGA
*
47231142 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTG-C-A-T-AATGCTTACTTAAAT
1 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTGACTAGTAAATGATTACTTAAAT
* *
47231203 GGTGGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTGCCGGTTCTTAAG
66 GGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCTTAAG
*
47231268 CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAATTCCAGATGGCCAATTTCAGG
131 CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTCAGG
47231332 GATTCCATTT
Statistics
Matches: 182, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
191 137 0.75
192 1 0.01
194 1 0.01
195 1 0.01
199 42 0.23
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (195 bp):
ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTGACTAGTAAATGATTACTTAAAT
GGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCTTAAG
CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTCAGGA
Found at i:47232813 original size:28 final size:28
Alignment explanation
Indices: 47232773--47232830 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
47232763 ATGTAGGGGG
47232773 TTAAAATGTTTTTACATGAAATCCTTTC
1 TTAAAATGTTTTTACATGAAATCCTTTC
47232801 TTAAAATGTTTTTACATGAAATCCTTTC
1 TTAAAATGTTTTTACATGAAATCCTTTC
47232829 TT
1 TT
47232831 TCCTCTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (28 bp):
TTAAAATGTTTTTACATGAAATCCTTTC
Found at i:47237835 original size:115 final size:113
Alignment explanation
Indices: 47237671--47237880 Score: 269
Period size: 115 Copynumber: 1.8 Consensus size: 113
47237661 GCACCAGAGG
* * ** * *
47237671 CATTTAAAATTTTTTTTTTGGATGCTGGCCAATAGATGGCCGGTACCAAGTACATTTTTCGGCTC
1 CATTTAAAATTTTTTTCTTGGATGCTGGCCAATAAATGGCCGACACCAAGTACATCTTTCAGCTC
*
47237736 CCAAGAAACTTTTTTTTTTTACTTTGGGACACTAACGGCCTGCACTAGTGT
66 CCAAG--AC-ATTTTTTTTTACTTTGGGACACTAACGGCCTGCACTAGTGT
* * *
47237787 CATTTAAAATTTTTTTCTTGG-TGCTGGCCAGTAAATGGTCGACACCAAGTCCATCTTTCAGCTC
1 CATTTAAAATTTTTTTCTTGGATGCTGGCCAATAAATGGCCGACACCAAGTACATCTTTCAGCTC
** *
47237851 TTAAGGCATTTTTTTTTACTTTGGGACACT
66 CCAAGACATTTTTTTTTACTTTGGGACACT
47237881 GATGGCCCGC
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
112 22 0.27
113 1 0.01
115 38 0.47
116 20 0.25
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (113 bp):
CATTTAAAATTTTTTTCTTGGATGCTGGCCAATAAATGGCCGACACCAAGTACATCTTTCAGCTC
CCAAGACATTTTTTTTTACTTTGGGACACTAACGGCCTGCACTAGTGT
Found at i:47237989 original size:58 final size:58
Alignment explanation
Indices: 47237857--47237995 Score: 145
Period size: 58 Copynumber: 2.4 Consensus size: 58
47237847 GCTCTTAAGG
* * * * * * *
47237857 CATTTTTTTTTACTTTGGGACACTGATGGCCCGCACCACCTTTTTCGGGTCCCAAAAA
1 CATTTTTTTTTATTTTGGGACACCGATGGCCCGCACCAACTTTATCAGATCCAAAAAA
* ** * *
47237915 TATTTTTTTTGGTTTTGGGACACCGATGGCCGGCACCAACTTTATCAGAT-TAAAAAA
1 CATTTTTTTTTATTTTGGGACACCGATGGCCCGCACCAACTTTATCAGATCCAAAAAA
*
47237972 CATTTTTTTCTTATTTTGGAACAC
1 CATTTTTTT-TTATTTTGGGACAC
47237996 TAATAGCCGA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
57 13 0.20
58 51 0.80
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (58 bp):
CATTTTTTTTTATTTTGGGACACCGATGGCCCGCACCAACTTTATCAGATCCAAAAAA
Found at i:47241328 original size:15 final size:16
Alignment explanation
Indices: 47241295--47241334 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
47241285 AAGATAATTT
*
47241295 AAATGAAATGAGAAAA
1 AAATTAAATGAGAAAA
47241311 AAATTAAATGAGAAAA
1 AAATTAAATGAGAAAA
47241327 AAA-TAAAT
1 AAATTAAAT
47241335 TTAAATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (16 bp):
AAATTAAATGAGAAAA
Found at i:47241338 original size:21 final size:21
Alignment explanation
Indices: 47241243--47241363 Score: 83
Period size: 21 Copynumber: 5.7 Consensus size: 21
47241233 GATGAAATAT
47241243 ATAAA-TTAATATG-GAAAAAA
1 ATAAATTTAA-ATGAGAAAAAA
* *
47241263 CATAAATTAAAATGGAAAAAAAA
1 -ATAAATTTAAAT-GAGAAAAAA
*
47241286 AGATAATTTAAATGA-AATGAGAAA
1 ATA-AATTTAAATGAGAA--A-AAA
47241310 A-AAA-TTAAATGAGAAAAAA
1 ATAAATTTAAATGAGAAAAAA
47241329 ATAAATTTAAAT-AGAAAAAA
1 ATAAATTTAAATGAGAAAAAA
* *
47241349 AGATAATTTAGATGA
1 ATA-AATTTAAATGA
47241364 AATGGAAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
19 4 0.05
20 14 0.17
21 31 0.38
22 13 0.16
23 16 0.20
24 4 0.05
ACGTcount: A:0.64, C:0.01, G:0.12, T:0.23
Consensus pattern (21 bp):
ATAAATTTAAATGAGAAAAAA
Found at i:47241356 original size:63 final size:65
Alignment explanation
Indices: 47241245--47241377 Score: 184
Period size: 63 Copynumber: 2.1 Consensus size: 65
47241235 TGAAATATAT
47241245 AAATTAATATGGAAAAAACATAAATTAAAATGGAAAAAAAAAGATAATTTAAATGAAATGAGAAA
1 AAATTAATATGGAAAAAACATAAATTAAAAT-GAAAAAAAAAGATAATTTAAATGAAATG-GAAA
47241310 -A
64 TA
* * *
47241311 AAATTAA-ATGAGAAAAAA-ATAAATTTAAAT-AGAAAAAAAGATAATTTAGATGAAATGGAAAT
1 AAATTAATATG-GAAAAAACATAAATTAAAATGAAAAAAAAAGATAATTTAAATGAAATGGAAAT
47241373 A
65 A
47241374 AAAT
1 AAAT
47241378 GAAAAAAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
62 4 0.06
63 30 0.48
65 14 0.23
66 14 0.23
ACGTcount: A:0.65, C:0.01, G:0.12, T:0.23
Consensus pattern (65 bp):
AAATTAATATGGAAAAAACATAAATTAAAATGAAAAAAAAAGATAATTTAAATGAAATGGAAATA
Found at i:47241777 original size:5 final size:5
Alignment explanation
Indices: 47241767--47241866 Score: 74
Period size: 5 Copynumber: 18.4 Consensus size: 5
47241757 AAAAAAAATT
* *
47241767 AATGA AATGA AATGTTA AATGA ATATGA AATGA AATGTA ATTTGT AATGA
1 AATGA AATGA AATG--A AATGA A-ATGA AATGA AATG-A A-ATGA AATGA
* * * *
47241817 ATATGA AATGA AATGA AATGA ATTTGT AATGA TTATGA AATGG AATGA
1 A-ATGA AATGA AATGA AATGA A-ATGA AATGA -AATGA AATGA AATGA
47241865 AA
1 AA
47241867 GTTTAAAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
5 48 0.64
6 20 0.27
7 7 0.09
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (5 bp):
AATGA
Found at i:47241799 original size:11 final size:10
Alignment explanation
Indices: 47241767--47241866 Score: 74
Period size: 11 Copynumber: 9.2 Consensus size: 10
47241757 AAAAAAAATT
47241767 AATGAAATGA
1 AATGAAATGA
47241777 AATGTTAAATGA
1 AATG--AAATGA
47241789 ATATGAAATGA
1 A-ATGAAATGA
* *
47241800 AATGTAATTTGT
1 AATG-AA-ATGA
47241812 AATGAATATGA
1 AATGAA-ATGA
47241823 AATGAAATGA
1 AATGAAATGA
* *
47241833 AATGAATTTGT
1 AATGAA-ATGA
*
47241844 AATGATTATGA
1 AATGA-AATGA
*
47241855 AATGGAATGA
1 AATGAAATGA
47241865 AA
1 AA
47241867 GTTTAAAAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
10 23 0.32
11 33 0.46
12 13 0.18
13 3 0.04
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (10 bp):
AATGAAATGA
Found at i:47241799 original size:28 final size:29
Alignment explanation
Indices: 47241767--47241866 Score: 114
Period size: 28 Copynumber: 3.4 Consensus size: 29
47241757 AAAAAAAATT
47241767 AATGAAATGAAATGTT-AAATGAATATGA
1 AATGAAATGAAATGTTGAAATGAATATGA
* *
47241795 AATGAAATGTAAT-TTGTAATGAATATGA
1 AATGAAATGAAATGTTGAAATGAATATGA
* *
47241823 AATGAAATGAAATGAATTTGTAATGATTATGA
1 AATGAAATGAAATG---TTGAAATGAATATGA
*
47241855 AATGGAATGAAA
1 AATGAAATGAAA
47241867 GTTTAAAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
27 2 0.03
28 35 0.56
32 25 0.40
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (29 bp):
AATGAAATGAAATGTTGAAATGAATATGA
Found at i:47241846 original size:32 final size:33
Alignment explanation
Indices: 47241785--47241866 Score: 130
Period size: 32 Copynumber: 2.5 Consensus size: 33
47241775 GAAATGTTAA
47241785 ATGAATATGAAATGAAATGTAATTTGTAATGAAT
1 ATGAA-ATGAAATGAAATGTAATTTGTAATGAAT
*
47241819 ATGAAATGAAATGAAATG-AATTTGTAATGATT
1 ATGAAATGAAATGAAATGTAATTTGTAATGAAT
*
47241851 ATGAAATGGAATGAAA
1 ATGAAATGAAATGAAA
47241867 GTTTAAAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 28 0.61
33 13 0.28
34 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.32
Consensus pattern (33 bp):
ATGAAATGAAATGAAATGTAATTTGTAATGAAT
Found at i:47241913 original size:18 final size:17
Alignment explanation
Indices: 47241892--47241925 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
47241882 AATTATAAAT
47241892 TGAAATGAAAACAAAAAC
1 TGAAATGAAAA-AAAAAC
47241910 TGAAATGAAAAAAAAA
1 TGAAATGAAAAAAAAA
47241926 TTAATATCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.12
Consensus pattern (17 bp):
TGAAATGAAAAAAAAAC
Found at i:47241984 original size:21 final size:20
Alignment explanation
Indices: 47241959--47241997 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
47241949 AATATGAAAA
47241959 AAATTGAAATGAGAAAAAATT
1 AAATTGAAATG-GAAAAAATT
*
47241980 AAATTTAAATGGAAAAAA
1 AAATTGAAATGGAAAAAA
47241998 AGATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (20 bp):
AAATTGAAATGGAAAAAATT
Found at i:47241998 original size:21 final size:21
Alignment explanation
Indices: 47241955--47242011 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
47241945 TATTAATATG
*
47241955 AAAA-AAATTGAAAT-GAGAA
1 AAAAGAAATTTAAATGGAGAA
*
47241974 AAAATTAAATTTAAATGGA-AA
1 AAAA-GAAATTTAAATGGAGAA
47241995 AAAAGATAATTTAAATG
1 AAAAGA-AATTTAAATG
47242012 AAATGGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 4 0.12
20 1 0.03
21 25 0.78
22 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (21 bp):
AAAAGAAATTTAAATGGAGAA
Found at i:47242449 original size:6 final size:6
Alignment explanation
Indices: 47242438--47242469 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
47242428 CACTCGATGG
*
47242438 ATCCTA ATCCTA ATTCTA ATCCTA ATCCTA AT
1 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA AT
47242470 ATTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (6 bp):
ATCCTA
Found at i:47244803 original size:89 final size:90
Alignment explanation
Indices: 47244709--47244918 Score: 262
Period size: 90 Copynumber: 2.3 Consensus size: 90
47244699 ATTCTTGAAT
* * * * *
47244709 ATTAATATACAAAAATATAAAATTTAAAC-AAAAATAATATG-CATTAAATTAAATTTAAACACC
1 ATTAATACACAAAAATATAAAATTCAAACTAAAAATAACA-GAAACTAAATTAAATTTAAACACC
*
47244772 CAAAAAACTATAAACAGATGGGTAAA
65 CAAAAAACTAAAAACAGATGGGTAAA
* * * * *
47244798 TTTAATACACAAAAATTTTAAATTCAAACTACATATAACAGAAACTAAATTAAATTTAAACACCC
1 ATTAATACACAAAAATATAAAATTCAAACTAAAAATAACAGAAACTAAATTAAATTTAAACACCC
*
47244863 AACAAACTAAAAACAGATGGGTAAA
66 AAAAAACTAAAAACAGATGGGTAAA
* * *
47244888 ATTAATACACGAAAATTTTAAATTCAAACTA
1 ATTAATACACAAAAATATAAAATTCAAACTA
47244919 CATATAATAC
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
89 25 0.24
90 80 0.76
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (90 bp):
ATTAATACACAAAAATATAAAATTCAAACTAAAAATAACAGAAACTAAATTAAATTTAAACACCC
AAAAAACTAAAAACAGATGGGTAAA
Found at i:47244861 original size:90 final size:90
Alignment explanation
Indices: 47244753--47244925 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 90
47244743 TAATATGCAT
* *
47244753 TAAATTAAATTTAAACACCCAAAAAACTATAAACAGATGGGTAAATTTAATACACAAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
47244818 AATTCAAACTACATATAACAGAAAC
66 AATTCAAACTACATATAACAGAAAC
* *
47244843 TAAATTAAATTTAAACACCCAACAAACTAAAAACAGATGGGTAAAATTAATACACGAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
47244908 AATTCAAACTACATATAA
66 AATTCAAACTACATATAA
47244926 TACCGGCTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.25
Consensus pattern (90 bp):
TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
AATTCAAACTACATATAACAGAAAC
Found at i:47244967 original size:90 final size:90
Alignment explanation
Indices: 47244753--47244945 Score: 305
Period size: 90 Copynumber: 2.1 Consensus size: 90
47244743 TAATATGCAT
* *
47244753 TAAATTAAATTTAAACACCCAAAAAACTATAAACAGATGGGTAAATTTAATACACAAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
*
47244818 AATTCAAACTACATATAACAGAAAC
66 AATTCAAACTACATATAACACAAAC
* *
47244843 TAAATTAAATTTAAACACCCAACAAACTAAAAACAGATGGGTAAAATTAATACACGAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
* ***
47244908 AATTCAAACTACATATAATACCGGC
66 AATTCAAACTACATATAACACAAAC
47244933 TAAATTAAATTTA
1 TAAATTAAATTTA
47244946 CAGATACAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 94 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (90 bp):
TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
AATTCAAACTACATATAACACAAAC
Found at i:47245971 original size:111 final size:111
Alignment explanation
Indices: 47245660--47245987 Score: 453
Period size: 111 Copynumber: 2.9 Consensus size: 111
47245650 CCAAAAAAGG
* * *
47245660 TGGTGCCGGACATCAGTGTCCCAAAGTAAAAAAAAAGTGCCTTAGGAGCCGAAAAATGTACTTGG
1 TGGTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGTGCCTTGGGAGCCGGAAAATGTACTTGG
* * *
47245725 TGCCGGCTAGCTGCTGGCC-GACACCCAAAATATTTCTTTAAATGACAC
66 TGCCGGCCATCTACTGGCCAG-CACCCAAAAT-TTT-TTTAAATGACAC
* *
47245773 TGGTGTCGGCCATCAGTGTACCAAAGTAAAAAAAAAAGTGCCTTGGGAGCC-GAAACATGTACTT
1 TGGTGCCGGCCATCAGTGTCCCAAAGT-AAAAAAAAAGTGCCTTGGGAGCCGGAAA-ATGTACTT
*
47245837 GGTGCCGACCATCTACTGGCCAGCACCCAAAATTTTTTTAAATGACAC
64 GGTGCCGGCCATCTACTGGCCAGCACCCAAAATTTTTTTAAATGACAC
* * *
47245885 TGGTGCCGGCCATCAGTGTCCCAAAGTAAAATAAAAGTTCATTGGGAGCCGGAAAATGTACTTGG
1 TGGTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGTGCCTTGGGAGCCGGAAAATGTACTTGG
* * *
47245950 TGCTGGCCATCTATTGACCAGCACCCAAAATTATTTTT
66 TGCCGGCCATCTACTGGCCAGCACCCAAAATT-TTTTT
47245988 TTAAAATGCC
Statistics
Matches: 192, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
111 58 0.30
112 46 0.24
113 30 0.16
114 57 0.30
115 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (111 bp):
TGGTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGTGCCTTGGGAGCCGGAAAATGTACTTGG
TGCCGGCCATCTACTGGCCAGCACCCAAAATTTTTTTAAATGACAC
Found at i:47249427 original size:17 final size:17
Alignment explanation
Indices: 47249405--47249444 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
47249395 GCTTATAGAC
47249405 CCAAAAGAATTTGGGTA
1 CCAAAAGAATTTGGGTA
47249422 CCAAAAGAATTTGGGTA
1 CCAAAAGAATTTGGGTA
47249439 CCAAAA
1 CCAAAA
47249445 ATCAAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (17 bp):
CCAAAAGAATTTGGGTA
Found at i:47251499 original size:26 final size:26
Alignment explanation
Indices: 47251450--47251499 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
47251440 AAGTTTAATT
* **
47251450 AATTTTATATTTAAATAATTTAATAA
1 AATTATATATTTAAATAAGATAATAA
47251476 AATTATATATTTAAATAAGATAAT
1 AATTATATATTTAAATAAGATAAT
47251500 TGATCAGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AATTATATATTTAAATAAGATAATAA
Found at i:47251499 original size:31 final size:30
Alignment explanation
Indices: 47251412--47251500 Score: 73
Period size: 31 Copynumber: 3.0 Consensus size: 30
47251402 TTTAATTTAA
*
47251412 TTAATAAAATTACATACTTAAATGAAGA-AAGT
1 TTAATAAAATTATATA-TTAAAT-AAGATAA-T
* *
47251444 TTAAT-TAATTTTATATT---TAA-ATAAT
1 TTAATAAAATTATATATTAAATAAGATAAT
47251469 TTAATAAAATTATATATTTAAATAAGATAAT
1 TTAATAAAATTATATA-TTAAATAAGATAAT
47251500 T
1 T
47251501 GATCAGCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
25 7 0.16
26 12 0.27
27 3 0.07
30 5 0.11
31 13 0.29
32 5 0.11
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (30 bp):
TTAATAAAATTATATATTAAATAAGATAAT
Found at i:47254960 original size:5 final size:5
Alignment explanation
Indices: 47254950--47254982 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
47254940 GAAAATTTTT
47254950 GATTC GATTC GATTC GATTC GATTC GATTC GAT
1 GATTC GATTC GATTC GATTC GATTC GATTC GAT
47254983 CGAATGCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
GATTC
Found at i:47262865 original size:19 final size:20
Alignment explanation
Indices: 47262838--47262876 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
47262828 TATGTGCTAT
*
47262838 AAATTACATAATAT-ATATA
1 AAATAACATAATATAATATA
47262857 AAATAACATAATATAATATA
1 AAATAACATAATATAATATA
47262877 TTATACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAACATAATATAATATA
Found at i:47264858 original size:26 final size:25
Alignment explanation
Indices: 47264818--47264866 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
47264808 AAGTTTAATT
*
47264818 AATTTATATTTAAATAAGTTAATAA
1 AATTTATATTTAAATAAGATAATAA
47264843 AATTATATATTTAAATAAGATAAT
1 AATT-TATATTTAAATAAGATAAT
47264867 TTATTAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AATTTATATTTAAATAAGATAATAA
Found at i:47266110 original size:16 final size:16
Alignment explanation
Indices: 47266091--47266123 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
47266081 TCCCAAAATT
47266091 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
*
47266107 AAAAGAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
47266123 A
1 A
47266124 GTAAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:47277446 original size:19 final size:20
Alignment explanation
Indices: 47277410--47277451 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
47277400 AAAATAATAA
*
47277410 TATTATTTTGATATTATTTT
1 TATTATTTTGATAATATTTT
*
47277430 TATTTTTTTG-TAATATTTT
1 TATTATTTTGATAATATTTT
47277449 TAT
1 TAT
47277452 AAAACACCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TATTATTTTGATAATATTTT
Found at i:47279073 original size:22 final size:20
Alignment explanation
Indices: 47279034--47279084 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
47279024 AATAAAAAAA
*
47279034 TGCTATTTTTTTTGTTTTCT
1 TGCTATTTTTTTTATTTTCT
*
47279054 TGCTATTTTTTTTAAATTTTGT
1 TGCTATTTTTTTT--ATTTTCT
47279076 TGCTATTTT
1 TGCTATTTT
47279085 CTTCTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 13 0.48
22 14 0.52
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.71
Consensus pattern (20 bp):
TGCTATTTTTTTTATTTTCT
Found at i:47280699 original size:40 final size:41
Alignment explanation
Indices: 47280653--47280735 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
47280643 AATTCATTAC
* * *
47280653 TTTAGTAATTTCACAGTTCAATGCAGTACACA-TAACAATA
1 TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
* *
47280693 TTTAGTAACTTCACAATTCAATTCAGTACTCAGAAACAATA
1 TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
47280734 TT
1 TT
47280736 CAGTTCAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 28 0.76
41 9 0.24
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (41 bp):
TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
Found at i:47283053 original size:12 final size:12
Alignment explanation
Indices: 47283036--47283083 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 12
47283026 AATTAAAGTA
47283036 AAATAATATTTT
1 AAATAATATTTT
*
47283048 AAATAAT-TATT
1 AAATAATATTTT
*
47283059 -AATAATATTAT
1 AAATAATATTTT
47283070 AAA-AATA-TTT
1 AAATAATATTTT
47283080 AAAT
1 AAAT
47283084 GTTCTTGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
10 11 0.38
11 9 0.31
12 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:47284470 original size:31 final size:30
Alignment explanation
Indices: 47284415--47284473 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
47284405 GTAAATACTC
***
47284415 AAAATTTGAAGGGTTAAAGTGTAAATATAA
1 AAAATTTGAAGGACCAAAGTGTAAATATAA
47284445 AAAATTTGAAGGACCAATAGTGTAAATAT
1 AAAATTTGAAGGACCAA-AGTGTAAATAT
47284474 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (30 bp):
AAAATTTGAAGGACCAAAGTGTAAATATAA
Found at i:47285662 original size:21 final size:21
Alignment explanation
Indices: 47285636--47285729 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 21
47285626 TTTTACTTTT
**
47285636 TGTTTAGCTTTTACGAGCTTC
1 TGTTTAGCTCATACGAGCTTC
* * *
47285657 TGTTTAACTCATATGAGTTTC
1 TGTTTAGCTCATACGAGCTTC
* * ** **
47285678 CGTTCAGCTTTTTTGAGCTTC
1 TGTTTAGCTCATACGAGCTTC
* *
47285699 TGTTTACCTCATACGAGTTTC
1 TGTTTAGCTCATACGAGCTTC
*
47285720 CGTTTAGCTC
1 TGTTTAGCTC
47285730 CTTTGAGCTT
Statistics
Matches: 51, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (21 bp):
TGTTTAGCTCATACGAGCTTC
Found at i:47285688 original size:42 final size:42
Alignment explanation
Indices: 47285637--47285828 Score: 190
Period size: 42 Copynumber: 4.6 Consensus size: 42
47285627 TTTACTTTTT
*
47285637 GTTTAGCTTTTACGAGCTTCTGTTTAACTCATATGAGTTTCC
1 GTTTAGCTTTTATGAGCTTCTGTTTAACTCATATGAGTTTCC
* * * *
47285679 GTTCAGCTTTTTTGAGCTTCTGTTTACCTCATACGAGTTTCC
1 GTTTAGCTTTTATGAGCTTCTGTTTAACTCATATGAGTTTCC
* * * * *
47285721 GTTTAGCTCCTT-TGAGCTTCTATTTAAACT-TTATGGGTTTTC
1 GTTTAGCT-TTTATGAGCTTCTGTTT-AACTCATATGAGTTTCC
* * * * * * *
47285763 GTTAAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCT
1 GTTTAGCTTTTATGAGCTTCTGTTTAACTCATATGAGTTTCC
*
47285805 GTTTAGCTTTCATGAGCTTCTGTT
1 GTTTAGCTTTTATGAGCTTCTGTT
47285829 CAGCCTCCGG
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
41 6 0.05
42 113 0.91
43 5 0.04
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (42 bp):
GTTTAGCTTTTATGAGCTTCTGTTTAACTCATATGAGTTTCC
Found at i:47285795 original size:21 final size:21
Alignment explanation
Indices: 47285771--47285830 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
47285761 TCGTTAAGCT
47285771 CTTATGAGCTTCTGTTCAACC
1 CTTATGAGCTTCTGTTCAACC
* * * *
47285792 CTTATGGGTTTCTGTT-TAGC
1 CTTATGAGCTTCTGTTCAACC
*
47285812 TTTCATGAGCTTCTGTTCA
1 CTT-ATGAGCTTCTGTTCA
47285831 GCCTCCGGGC
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (21 bp):
CTTATGAGCTTCTGTTCAACC
Found at i:47285963 original size:2 final size:2
Alignment explanation
Indices: 47285956--47285983 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47285946 ATGTATTATG
47285956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47285984 CAATATCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47287700 original size:41 final size:39
Alignment explanation
Indices: 47287581--47287716 Score: 114
Period size: 41 Copynumber: 3.5 Consensus size: 39
47287571 ACCAGTTTGG
* ** * *
47287581 CACCCAGTGCCTTATCGAATAATTTGAAGCAATAATTTGA
1 CACCCAGTGCCTCATCGAATAATCCGAAG-AGTAAATTGA
* * ** *
47287621 CACTCAGTGTCTCATCGGCTAAACCG-A-AGTAAATTGA
1 CACCCAGTGCCTCATCGAATAATCCGAAGAGTAAATTGA
47287658 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAG-AGTAAATTGA
* * *
47287699 CATCTAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
47287717 CTCAAAGTCA
Statistics
Matches: 74, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 23 0.31
38 6 0.08
39 2 0.03
40 18 0.24
41 25 0.34
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGAGTAAATTGA
Found at i:47287909 original size:24 final size:24
Alignment explanation
Indices: 47287872--47287918 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
47287862 TATATATACC
47287872 AATTCAATCAATA-TAAATTCAATA
1 AATTCAATCAATATTAAA-TCAATA
47287896 AATTC-ATCACATATTAAATCAAT
1 AATTCAATCA-ATATTAAATCAAT
47287919 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCAATCAATATTAAATCAATA
Found at i:47288656 original size:21 final size:20
Alignment explanation
Indices: 47288619--47288659 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
47288609 TTTCGTTTGG
47288619 CTTTCTCTATTTC-TTTCTTT
1 CTTT-TCTATTTCTTTTCTTT
47288639 CTTTTCTATTTCTATTTCTTT
1 CTTTTCTATTTCT-TTTCTTT
47288660 TTCTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
CTTTTCTATTTCTTTTCTTT
Found at i:47288710 original size:5 final size:5
Alignment explanation
Indices: 47288700--47288862 Score: 310
Period size: 5 Copynumber: 32.8 Consensus size: 5
47288690 TTTGTTTTAT
*
47288700 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA CATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
47288750 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
47288800 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
47288850 TATAA TAT-A TATA
1 TATAA TATAA TATA
47288863 CTTAAATGTT
Statistics
Matches: 155, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
4 4 0.03
5 151 0.97
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:47297389 original size:7 final size:7
Alignment explanation
Indices: 47297379--47297466 Score: 85
Period size: 7 Copynumber: 12.4 Consensus size: 7
47297369 AAAAATTCAA
47297379 AAAAATC
1 AAAAATC
47297386 AAAAATC
1 AAAAATC
47297393 AAAAATC
1 AAAAATC
47297400 AAAAATC
1 AAAAATC
47297407 AAAAAATC
1 -AAAAATC
47297415 AAAAAAAATC
1 ---AAAAATC
47297425 AAAAAATC
1 -AAAAATC
*
47297433 -AAAA-G
1 AAAAATC
47297438 AAAAA-C
1 AAAAATC
47297444 AAAAAT-
1 AAAAATC
*
47297450 AAAAATA
1 AAAAATC
47297457 AAAAATC
1 AAAAATC
47297464 AAA
1 AAA
47297467 TTCAAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
6 19 0.26
7 30 0.42
8 15 0.21
10 8 0.11
ACGTcount: A:0.77, C:0.10, G:0.01, T:0.11
Consensus pattern (7 bp):
AAAAATC
Found at i:47297449 original size:18 final size:19
Alignment explanation
Indices: 47297377--47297466 Score: 89
Period size: 18 Copynumber: 4.6 Consensus size: 19
47297367 AAAAAAATTC
47297377 AAAAAAATC-AAAAATCAAA
1 AAAAAAATCAAAAAATC-AA
47297396 AATCAAAAATCAAAAAATC-A
1 AA--AAAAATCAAAAAATCAA
47297416 AAAAAAATCAAAAAATCAA
1 AAAAAAATCAAAAAATCAA
*
47297435 AAGAAAAA-C-AAAAATAAAA
1 AA-AAAAATCAAAAAAT-CAA
47297454 ATAAAAAATCAAA
1 A-AAAAAATCAAA
47297467 TTCAAAAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
18 21 0.34
19 14 0.23
20 10 0.16
21 9 0.15
22 7 0.11
ACGTcount: A:0.78, C:0.10, G:0.01, T:0.11
Consensus pattern (19 bp):
AAAAAAATCAAAAAATCAA
Found at i:47297453 original size:5 final size:6
Alignment explanation
Indices: 47297379--47297460 Score: 51
Period size: 6 Copynumber: 12.8 Consensus size: 6
47297369 AAAAATTCAA
*
47297379 AAAAAT CAAAAAT CAAAAAT CAAAAAT CAAAAA- ATCAAA- AAAAAT CAAAAAAT
1 AAAAAT -AAAAAT -AAAAAT -AAAAAT -AAAAAT A-AAAAT AAAAAT --AAAAAT
* * *
47297432 CAAAAG AAAAAC AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
47297461 ATCAAATTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
5 4 0.06
6 28 0.44
7 26 0.41
8 6 0.09
ACGTcount: A:0.78, C:0.10, G:0.01, T:0.11
Consensus pattern (6 bp):
AAAAAT
Found at i:47297460 original size:39 final size:40
Alignment explanation
Indices: 47297377--47297466 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
47297367 AAAAAAATTC
**
47297377 AAAAAAATC-AAAAATCAAAAATCAAAAATCAAAAAATCA
1 AAAAAAATCAAAAAATCAAAAATCAAAAATCAAAAAAAAA
*
47297416 AAAAAAATCAAAAAATC-AAAA-GAAAAA-CAAAAATAAAA
1 AAAAAAATCAAAAAATCAAAAATCAAAAATCAAAAA-AAAA
47297454 ATAAAAAATCAAA
1 A-AAAAAATCAAA
47297467 TTCAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
37 6 0.13
38 8 0.18
39 24 0.53
40 7 0.16
ACGTcount: A:0.78, C:0.10, G:0.01, T:0.11
Consensus pattern (40 bp):
AAAAAAATCAAAAAATCAAAAATCAAAAATCAAAAAAAAA
Found at i:47298351 original size:10 final size:10
Alignment explanation
Indices: 47298333--47298367 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
47298323 TGAGTCAAAC
47298333 AAAAAAAATG
1 AAAAAAAATG
**
47298343 ATGAAAAATG
1 AAAAAAAATG
47298353 AAAAAAAATG
1 AAAAAAAATG
47298363 AAAAA
1 AAAAA
47298368 GTAAAAATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:47299783 original size:43 final size:43
Alignment explanation
Indices: 47299650--47299872 Score: 152
Period size: 43 Copynumber: 5.2 Consensus size: 43
47299640 AAAACAAGCA
47299650 TTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATC
1 TTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATC
* * * * * * * * * *
47299693 TTACCTTC-CTGCATTAACAGCGAAGCAGATCAAA-AA-CAAAGCC
1 TTGCCTTCATTG-GTT-ACAGTGGAGCTGGTTAAAGAAGCAGA-TC
*
47299736 TTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATC
1 TTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATC
* * * * * ** * *
47299779 TTGCCTTC-CTGCGTTAACAGCGAAGCAGATCGAA-AA-CAAAGCC
1 TTGCCTTCATTG-GTT-ACAGTGGAGCTGGTTAAAGAAGCAGA-TC
* *
47299822 TTACCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATC
1 TTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATC
47299865 TTGCCTTC
1 TTGCCTTC
47299873 CTGCATTAAC
Statistics
Matches: 125, Mismatches: 43, Indels: 24
0.65 0.22 0.12
Matches are distributed among these distances:
42 33 0.26
43 58 0.46
44 34 0.27
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (43 bp):
TTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATC
Found at i:47299912 original size:43 final size:43
Alignment explanation
Indices: 47299864--47300087 Score: 129
Period size: 43 Copynumber: 5.2 Consensus size: 43
47299854 AGAAGCAGAT
47299864 CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGC
** * * ** * * * * * *
47299907 CTTGCCTTTAT-TAGTT-GCAGTGGAGCTGGTCAAAGATAGCATA-T
1 CTTGCCTTCCTGCA-TTAACAACGAAGCAGATCGAA-A-A-CAAAGC
47299951 CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGC
* * * * * * * *
47299994 CTTGCCTTCATTG-GTT-GCAATGGAGCTAG-TTGAAGATAGCAGA-T
1 CTTGCCTTC-CTGCATTAACAACGAAGC-AGATCGAA-A-A-CAAAGC
*
47300038 CTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGC
47300081 CTTGCCT
1 CTTGCCT
47300088 CCACCGNNNN
Statistics
Matches: 126, Mismatches: 39, Indels: 32
0.64 0.20 0.16
Matches are distributed among these distances:
42 29 0.23
43 37 0.29
44 31 0.25
45 29 0.23
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGC
Found at i:47299995 original size:87 final size:86
Alignment explanation
Indices: 47299596--47300087 Score: 797
Period size: 86 Copynumber: 5.7 Consensus size: 86
47299586 CAGATCAGTG
* * *
47299596 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGCATTGCCTTCAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTCAT
*
47299660 TGGTTACAGTGGAGCTGGTTA
66 TGGTTGCAGTGGAGCTGGTTA
* * *
47299681 AAGAAGCAGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTTCAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTCAT
47299746 TGGTTGCAGTGGAGCTGGTTA
66 TGGTTGCAGTGGAGCTGGTTA
* * *
47299767 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTACCTTCAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTCAT
47299832 TGGTTGCAGTGGAGCTGGTTA
66 TGGTTGCAGTGGAGCTGGTTA
*
47299853 AAGAAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTTAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTCAT
* *
47299918 TAGTTGCAGTGGAGCTGGTCA
66 TGGTTGCAGTGGAGCTGGTTA
*
47299939 AAGATAGCATATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
1 AAGA-AGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
* * *
47300004 TTGGTTGCAATGGAGCTAGTTG
65 TTGGTTGCAGTGGAGCTGGTTA
*
47300026 AAGATAGCAGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCT
1 AAGA-AGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCT
47300088 CCACCGNNNN
Statistics
Matches: 381, Mismatches: 24, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
85 46 0.12
86 200 0.52
87 135 0.35
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (86 bp):
AAGAAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTTCAT
TGGTTGCAGTGGAGCTGGTTA
Found at i:47302290 original size:3 final size:3
Alignment explanation
Indices: 47302282--47302325 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
47302272 TGTTTACTAA
47302282 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
47302326 ACTCTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:47302460 original size:51 final size:49
Alignment explanation
Indices: 47302351--47302463 Score: 122
Period size: 51 Copynumber: 2.3 Consensus size: 49
47302341 AAATTCTTGT
**
47302351 TATATA-TTTATATATACAAACGCATACTTTTTATAATATATATGTATA
1 TATATATTTTATATATACAAACGCATACTTTTTATAATATATAAATATA
* * ** *
47302399 CATATTTTTTATATATACTTACGTACATACTTTTTAT-TTATTATAAATATA
1 TATATATTTTATATATACAAACG--CATACTTTTTATAATA-TATAAATATA
47302450 TATATATTTTATAT
1 TATATATTTTATAT
47302464 TTCATATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
48 4 0.08
49 14 0.27
50 2 0.04
51 32 0.62
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (49 bp):
TATATATTTTATATATACAAACGCATACTTTTTATAATATATAAATATA
Found at i:47307113 original size:22 final size:21
Alignment explanation
Indices: 47307078--47307135 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
47307068 AAAGGGTATC
* * *
47307078 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAAAT
47307099 TACAAAATCATATCTTCTAAAAT
1 TAC-AAATCATATC-TCTAAAAT
* *
47307122 TGCATATCATATCT
1 TACAAATCATATCT
47307136 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Found at i:47322170 original size:120 final size:119
Alignment explanation
Indices: 47322040--47322437 Score: 613
Period size: 120 Copynumber: 3.4 Consensus size: 119
47322030 AATTATTTTA
* * *
47322040 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTT-AAATTATATTTT
* *
47322105 ATAGTATCATATATTTTGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
47322160 AATTTTATTAAATTATATATTTTTAATTATAATATATTTAATAATAATTA--T--GTTA-A----
1 AATTTTATTAAATTATATA-TTTTAATTATAATATATTTAATAATAATTATTTAAATTATATTTT
*
47322216 AT--TATC-TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
47322268 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATCATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT-TTAAATTATATTTT
47322333 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
47322388 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
47322438 GTTTAAATAT
Statistics
Matches: 253, Mismatches: 11, Indels: 28
0.87 0.04 0.10
Matches are distributed among these distances:
107 29 0.11
108 62 0.25
109 4 0.02
110 1 0.00
111 2 0.01
112 3 0.01
113 1 0.00
115 1 0.00
116 3 0.01
117 2 0.01
119 5 0.02
120 112 0.44
121 28 0.11
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTAAATTATATTTTA
TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:47322185 original size:15 final size:16
Alignment explanation
Indices: 47322167--47322220 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
47322157 AAGAATTTTA
47322167 TTAAATTAT-ATAT-T
1 TTAAATTATAATATAT
*
47322181 TTTAATTATAATATAT
1 TTAAATTATAATATAT
*
47322197 TT-AATAATAAT-TAT
1 TTAAATTATAATATAT
47322211 GTTAAATTAT
1 -TTAAATTAT
47322221 CTATATTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.33
15 14 0.42
16 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTATAATATAT
Found at i:47322327 original size:228 final size:222
Alignment explanation
Indices: 47321930--47322445 Score: 731
Period size: 228 Copynumber: 2.3 Consensus size: 222
47321920 NNNNNNNTTT
* * * *
47321930 ATTATCAAGAATTTTATGAAATTATATATTATT-ATTA-AATTATATTTAATAATAATTATTTTA
1 ATTATTAAGAATTTTATTAAATTATATATTTTTAATTATAA-TATATTTAATAATAATTATGTTA
* * *
47321993 AATTATACAAATTCATATAAGAAAATTTATTAGTTATAATTATTTTAAATTTTATTAAATCATAT
65 AATTATACAAATTCATATAAGAAAATTTATAAGATATAATTATTTAAAATTTTATTAAATCATAT
* * *
47322058 ATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGTATCATATATTTTG
130 ATTTTAATTAAAATATATTTAATAATAATCATTTCAAATTATATTTTATAGTATCATATATTATG
*
47322123 ATTTTAGTAAATTCATATAAGAATATTG
195 ATTTGAGTAAATTCATATAAGAATATTG
47322151 ATTATTAAGAATTTTATTAAATTATATATTTTTAATTATAATATATTTAATAATAATTATGTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTTAATTATAATATATTTAATAATAATTATGTTAA
* * *
47322216 ATTAT-CTATATT-ATGATTTGAGTAAATTCATATAAGAATATTAATTA-TTAAGAATTTTATTA
66 ATTATAC-AAATTCAT-A--TAAGAAAATT--TATAAG-ATA-TAATTATTTAA-AATTTTATTA
* *
47322278 AATTATATATTTTAATTATAATATATTTAATAATAATCATGTT-AAATTATATTTTATAGTATCA
122 AATCATATATTTTAATTAAAATATATTTAATAATAATCAT-TTCAAATTATATTTTATAGTATCA
47322342 TATATTATGATTTGAGTAAATTCATATAAGAATATTG
186 TATATTATGATTTGAGTAAATTCATATAAGAATATTG
47322379 ATTATTAAGAATTTTATTAAATTATATA-TTTTAATTATAATATATTTAATAATAATTATGTTTA
1 ATTATTAAGAATTTTATTAAATTATATATTTTTAATTATAATATATTTAATAATAATTATG-TTA
47322443 AAT
65 AAT
47322446 ATGATTAAAT
Statistics
Matches: 266, Mismatches: 16, Indels: 19
0.88 0.05 0.06
Matches are distributed among these distances:
221 33 0.12
222 37 0.14
223 2 0.01
224 8 0.03
226 5 0.02
227 37 0.14
228 142 0.53
229 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (222 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTTAATTATAATATATTTAATAATAATTATGTTAA
ATTATACAAATTCATATAAGAAAATTTATAAGATATAATTATTTAAAATTTTATTAAATCATATA
TTTTAATTAAAATATATTTAATAATAATCATTTCAAATTATATTTTATAGTATCATATATTATGA
TTTGAGTAAATTCATATAAGAATATTG
Found at i:47322423 original size:16 final size:16
Alignment explanation
Indices: 47322402--47322443 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
47322392 TTATTAAATT
*
47322402 ATATATTTTAATTATA
1 ATATATTTTAATAATA
47322418 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
47322433 AT-TATGTTTAA
1 ATATAT-TTTAA
47322444 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:47322428 original size:15 final size:15
Alignment explanation
Indices: 47322393--47322434 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
47322383 TTAAGAATTT
*
47322393 TATTAAATTAT-ATA
1 TATTTAATTATAATA
47322407 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
47322421 TATTTAATAATAAT
1 TATTTAATTATAAT
47322435 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:47322678 original size:16 final size:16
Alignment explanation
Indices: 47322657--47322689 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
47322647 TTGATTTGCT
*
47322657 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
47322673 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
47322689 A
1 A
47322690 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:47326404 original size:5 final size:5
Alignment explanation
Indices: 47326394--47326440 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
47326384 ACCTGTCCAT
* *
47326394 GGGCC GGGCC GGGCC GGGTTC GGGCC GGGCC GGGTTC GGGCC GGGCC
1 GGGCC GGGCC GGGCC GGG-CC GGGCC GGGCC GGG-CC GGGCC GGGCC
47326441 CACAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 28 0.78
6 8 0.22
ACGTcount: A:0.00, C:0.34, G:0.57, T:0.09
Consensus pattern (5 bp):
GGGCC
Found at i:47326419 original size:11 final size:10
Alignment explanation
Indices: 47326394--47326440 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
47326384 ACCTGTCCAT
47326394 GGGCCGGGCC
1 GGGCCGGGCC
*
47326404 GGGCCGGGTTC
1 GGGCCGGG-CC
47326415 GGGCCGGGCC
1 GGGCCGGGCC
*
47326425 GGGTTCGGGCC
1 GGG-CCGGGCC
47326436 GGGCC
1 GGGCC
47326441 CACAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 13 0.42
11 18 0.58
ACGTcount: A:0.00, C:0.34, G:0.57, T:0.09
Consensus pattern (10 bp):
GGGCCGGGCC
Found at i:47326419 original size:16 final size:16
Alignment explanation
Indices: 47326398--47326440 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
47326388 GTCCATGGGC
47326398 CGGGCCGGGCCGGGTT
1 CGGGCCGGGCCGGGTT
47326414 CGGGCCGGGCCGGGTT
1 CGGGCCGGGCCGGGTT
47326430 CGGGCCGGGCC
1 CGGGCCGGGCC
47326441 CACAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.00, C:0.35, G:0.56, T:0.09
Consensus pattern (16 bp):
CGGGCCGGGCCGGGTT
Found at i:47326580 original size:22 final size:23
Alignment explanation
Indices: 47326527--47326582 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
47326517 CCCGTTTTTA
* * *
47326527 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
47326550 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
47326572 ATTAAAATTAA
1 ATTAAAATTAA
47326583 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:47326595 original size:16 final size:16
Alignment explanation
Indices: 47326558--47326597 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
47326548 TTAATAAAAT
* *
47326558 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
47326574 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
47326590 TAAAATTA
1 TAAAATTA
47326598 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:47326676 original size:59 final size:59
Alignment explanation
Indices: 47326600--47326747 Score: 253
Period size: 59 Copynumber: 2.5 Consensus size: 59
47326590 TAAAATTATC
* *
47326600 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
*
47326658 AAATTATCAAATTATTAATTTTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
*
47326717 AATTTATCAAATTATTAATTGTATTAATTGT
1 AAATTATCAAATTATTAATTGTATTAATTGT
47326748 ATTAATTGTT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 7 0.08
59 77 0.92
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
Found at i:47326741 original size:9 final size:9
Alignment explanation
Indices: 47326729--47326756 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
47326719 TTTATCAAAT
47326729 TATTAATTG
1 TATTAATTG
47326738 TATTAATTG
1 TATTAATTG
47326747 TATTAATTG
1 TATTAATTG
47326756 T
1 T
47326757 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:47326893 original size:22 final size:23
Alignment explanation
Indices: 47326851--47326896 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
47326841 GTTAATAAAC
*
47326851 TTAAAATAAAAAACTATTATATT
1 TTAAAATAAAAAAATATTATATT
47326874 TTAAAATAAAAAAATA-TATATT
1 TTAAAATAAAAAAATATTATATT
47326896 T
1 T
47326897 AATATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTAAAATAAAAAAATATTATATT
Found at i:47336672 original size:22 final size:22
Alignment explanation
Indices: 47336647--47336688 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
47336637 TTCCGCTATA
*
47336647 AAGAGGGAAAAAGAGAAGGAAG
1 AAGAAGGAAAAAGAGAAGGAAG
* *
47336669 AAGAAGGAGAAGGAGAAGGA
1 AAGAAGGAAAAAGAGAAGGA
47336689 GAAAAACAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (22 bp):
AAGAAGGAAAAAGAGAAGGAAG
Found at i:47342113 original size:18 final size:19
Alignment explanation
Indices: 47342077--47342123 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
47342067 AAATGTAAAA
*
47342077 AAAAAGCATAAAATTTATT
1 AAAAAGCATAAAATATATT
*
47342096 AAAAAGTATAAAA-ATATT
1 AAAAAGCATAAAATATATT
*
47342114 AAAAATCATA
1 AAAAAGCATA
47342124 TCTAATAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAAAGCATAAAATATATT
Found at i:47346686 original size:2 final size:2
Alignment explanation
Indices: 47346681--47346705 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47346671 TCTCTCTCTC
47346681 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
47346706 TTGTTCATTG
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:47347193 original size:2 final size:2
Alignment explanation
Indices: 47347186--47347222 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
47347176 TATTAAGTTC
*
47347186 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47347223 TTGGATAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:47349184 original size:3 final size:3
Alignment explanation
Indices: 47349176--47349203 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47349166 TAGAGGCCTG
47349176 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
47349204 TCACATTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:47350187 original size:17 final size:17
Alignment explanation
Indices: 47350165--47350198 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47350155 ATCCTTGTAT
47350165 AAGAAAATAAGCAAATA
1 AAGAAAATAAGCAAATA
* *
47350182 AAGAAACTAAGGAAATA
1 AAGAAAATAAGCAAATA
47350199 GAAATATGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.12
Consensus pattern (17 bp):
AAGAAAATAAGCAAATA
Found at i:47352773 original size:30 final size:30
Alignment explanation
Indices: 47352732--47352822 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
47352722 TATATAAAGC
*
47352732 TTAAGTGATATGATAAATTCTGTAGTGCTG
1 TTAAGTCATATGATAAATTCTGTAGTGCTG
47352762 TTAAGTCATATGATAAATTCTGTAGTGCTG
1 TTAAGTCATATGATAAATTCTGTAGTGCTG
47352792 TTAAGTCATATGATAAATTCTGTAGTGCTG
1 TTAAGTCATATGATAAATTCTGTAGTGCTG
47352822 T
1 T
47352823 CTAGTTTATC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.41
Consensus pattern (30 bp):
TTAAGTCATATGATAAATTCTGTAGTGCTG
Found at i:47353536 original size:2 final size:2
Alignment explanation
Indices: 47353531--47353565 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
47353521 AAAAGAAGGA
47353531 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
47353566 CAGGTGCCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47356128 original size:140 final size:140
Alignment explanation
Indices: 47355876--47356156 Score: 463
Period size: 140 Copynumber: 2.0 Consensus size: 140
47355866 TGGAATTTTC
* *
47355876 ATTAGTTCTGAAATTTCAATTTTGCGTAGCCCTATAATATTATGGTATCTATGTATCCATATCCA
1 ATTAGTTCTGAAATTTCAATTTTGCATAGCCCTATAATATTATGGTATCCATGTATCCATATCCA
*
47355941 GCTCTCACACTCTTCATAGCCTACTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTTGG
66 GCTCTCACACTCTTCATAGCCTACTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTAGG
47356006 ATCAAATCTA
131 ATCAAATCTA
* * * * *
47356016 ATTAGTTCTGAAATTTCAATTTTGTATAGTCCTATCATATTATGGTATCCATGTATCCTTATTCA
1 ATTAGTTCTGAAATTTCAATTTTGCATAGCCCTATAATATTATGGTATCCATGTATCCATATCCA
* * *
47356081 GCTCTCAGACTTTTCATAGCCTTCTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTAGG
66 GCTCTCACACTCTTCATAGCCTACTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTAGG
47356146 ATCAAATCTA
131 ATCAAATCTA
47356156 A
1 A
47356157 ACCATAACCT
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
140 130 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (140 bp):
ATTAGTTCTGAAATTTCAATTTTGCATAGCCCTATAATATTATGGTATCCATGTATCCATATCCA
GCTCTCACACTCTTCATAGCCTACTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTAGG
ATCAAATCTA
Found at i:47359789 original size:14 final size:16
Alignment explanation
Indices: 47359764--47359795 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
47359754 GTTTTTTATA
47359764 AAAAATAGATAAT-TT
1 AAAAATAGATAATATT
47359779 AAAAATA-ATAATATT
1 AAAAATAGATAATATT
47359794 AA
1 AA
47359796 TATAACCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAAATAGATAATATT
Found at i:47360369 original size:17 final size:17
Alignment explanation
Indices: 47360336--47360373 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
47360326 CATGTCACAT
*
47360336 AATTAAAAAATTTTAAA
1 AATTAAAAAATTATAAA
47360353 AATT-AAAAATTAATAAA
1 AATTAAAAAATT-ATAAA
47360370 AATT
1 AATT
47360374 CTAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTAAAAAATTATAAA
Found at i:47360457 original size:11 final size:12
Alignment explanation
Indices: 47360430--47360456 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
47360420 AGACATATGC
47360430 AAAATTATAAAA
1 AAAATTATAAAA
47360442 AAAATTATAAAA
1 AAAATTATAAAA
47360454 AAA
1 AAA
47360457 TAAAATTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:47360820 original size:3 final size:3
Alignment explanation
Indices: 47360812--47360871 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
47360802 TAGGCAGTAA
* * * *
47360812 AAG AAG AAG AAG AAG AAG AAT AAA AAG AAG -AG GAG GAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
47360859 ACG AAG GAG AAG A
1 AAG AAG AAG AAG A
47360872 GAAAAAATAG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.62, C:0.02, G:0.35, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:47364614 original size:3 final size:3
Alignment explanation
Indices: 47364608--47364649 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
47364598 CTTTTATTCT
47364608 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
47364650 TACTTAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.