Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 62 of 93
Found at i:23615114 original size:25 final size:24
Alignment explanation
Indices: 23615086--23615146 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
23615076 TGGACTTCTC
23615086 CCATTTCTT-TTTAATTGGACCATGT
1 CCATTT-TTCTTT-ATTGGACCATGT
*
23615111 CCATTTTTCCTTTATTGGACCATAT
1 CCATTTTT-CTTTATTGGACCATGT
*
23615136 CTATTTTTCTT
1 CCATTTTTCTT
23615147 GCTTGTTGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 5 0.16
25 24 0.75
26 3 0.09
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.52
Consensus pattern (24 bp):
CCATTTTTCTTTATTGGACCATGT
Found at i:23615192 original size:5 final size:5
Alignment explanation
Indices: 23615178--23615223 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
23615168 TTCCTTGTTA
* *
23615178 TTTTC TTTTC CTTTC TTTTC TTTTC TTTTC TTTT- ATTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
23615224 CTCTCCCACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 7 0.19
5 29 0.81
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:23615635 original size:34 final size:34
Alignment explanation
Indices: 23615539--23615621 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
23615529 ACACTTTTTG
*
23615539 GCCTCCAAAACCAGCAGAAAAATGGCACTTTCCA
1 GCCTCCAAAACCAGCAGAAAAATGGCTCTTTCCA
* *
23615573 GCCTCCAAAACTAGCAGAAAAATGGCTCTTTTCA
1 GCCTCCAAAACCAGCAGAAAAATGGCTCTTTCCA
23615607 GCCTCCAAAACCAGC
1 GCCTCCAAAACCAGC
23615622 CCTTAAATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.17
Consensus pattern (34 bp):
GCCTCCAAAACCAGCAGAAAAATGGCTCTTTCCA
Found at i:23620200 original size:11 final size:11
Alignment explanation
Indices: 23620184--23620213 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
23620174 ATAACTTTTG
23620184 GGTTTAAAGTT
1 GGTTTAAAGTT
23620195 GGTTTAAAGTT
1 GGTTTAAAGTT
*
23620206 GTTTTAAA
1 GGTTTAAA
23620214 TTTATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (11 bp):
GGTTTAAAGTT
Found at i:23624305 original size:19 final size:19
Alignment explanation
Indices: 23624277--23624314 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
23624267 CTATTTGACT
*
23624277 TATTGGAGTATGATTTGAG
1 TATTGCAGTATGATTTGAG
23624296 TATTGCAGTATGATTTGAG
1 TATTGCAGTATGATTTGAG
23624315 GTTAAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGCAGTATGATTTGAG
Found at i:23627607 original size:17 final size:16
Alignment explanation
Indices: 23627569--23627607 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
23627559 TCTTCTCATT
*
23627569 TTTTTTCCTTCCTTTC
1 TTTTTTCCTACCTTTC
*
23627585 TCTTTTCCTACCTCTTC
1 TTTTTTCCTACCT-TTC
23627602 TTTTTT
1 TTTTTT
23627608 TACTTCTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTCCTACCTTTC
Found at i:23628493 original size:12 final size:13
Alignment explanation
Indices: 23628472--23628501 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
23628462 GATAAAAAAC
23628472 TCCAACCAAAATT
1 TCCAACCAAAATT
23628485 TCCAA-CAAAATT
1 TCCAACCAAAATT
23628497 TCCAA
1 TCCAA
23628502 TGGATTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (13 bp):
TCCAACCAAAATT
Found at i:23629754 original size:32 final size:33
Alignment explanation
Indices: 23629717--23629783 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 33
23629707 ATACAACTTT
*
23629717 ATGTATATGAGTTAAT-ATATATGTTTATATAC
1 ATGTATATGAGTTAATAATATATGTTTACATAC
23629749 ATGTATATGAGTTAATACATATATGTTTACATAC
1 ATGTATATGAGTTAATA-ATATATGTTTACATAC
23629783 A
1 A
23629784 ACTTTATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 16 0.50
34 16 0.50
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (33 bp):
ATGTATATGAGTTAATAATATATGTTTACATAC
Found at i:23629869 original size:155 final size:151
Alignment explanation
Indices: 23629667--23630113 Score: 744
Period size: 145 Copynumber: 3.0 Consensus size: 151
23629657 AGTTAAGTTA
* *
23629667 ATATATATGTATGTATATGTTTACATACATATATGTATGCATACAACTTTATGTATATGAGTTAA
1 ATATATATGTATGTATATG-TTAAATACATATATGTATGCATACAACTTGATGTATATGAGTTAA
*
23629732 TATATATGTTTATATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATATAACT
65 TATATATGTTTACATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATATAACT
23629797 TTATAACTAAGTTAATACATATATAT
130 TTATAACTAAGTTAAT--AT-TA-AT
*
23629823 ATATATATGTATGTATATGTTAAATACATATATTTATGCATACAACTTGATGTATATGAGTTAAT
1 ATATATATGTATGTATATGTTAAATACATATATGTATGCATACAACTTGATGTATATGAGTTAAT
* *
23629888 ATATATGTTTACATACATGTGTATGAGTTAATACATATATGTTTATATACAACTTTATATAACTT
66 ATATATGTTTACATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATATAACTT
23629953 TATAACTAAG------TTAAT
131 TATAACTAAGTTAATATTAAT
23629968 ATATATATGTATGTATATGTTAAATACATATATGTATGCATACAACTTGATGTATATGAGTTAAT
1 ATATATATGTATGTATATGTTAAATACATATATGTATGCATACAACTTGATGTATATGAGTTAAT
23630033 ATATATGTTTACATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATATAACTT
66 ATATATGTTTACATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATATAACTT
*
23630098 TATAATTAAGTTAATA
131 TATAACTAAGTTAATA
23630114 NNNNNNNNNN
Statistics
Matches: 275, Mismatches: 10, Indels: 17
0.91 0.03 0.06
Matches are distributed among these distances:
145 138 0.50
146 2 0.01
147 1 0.00
155 115 0.42
156 19 0.07
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (151 bp):
ATATATATGTATGTATATGTTAAATACATATATGTATGCATACAACTTGATGTATATGAGTTAAT
ATATATGTTTACATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATATAACTT
TATAACTAAGTTAATATTAAT
Found at i:23629926 original size:34 final size:33
Alignment explanation
Indices: 23629872--23630083 Score: 139
Period size: 34 Copynumber: 6.0 Consensus size: 33
23629862 ATACAACTTG
23629872 ATGTATATGAGTTAAT-ATATATGTTTACATAC
1 ATGTATATGAGTTAATAATATATGTTTACATAC
* *
23629904 ATGTGTATGAGTTAATACATATATGTTTATATAC
1 ATGTATATGAGTTAATA-ATATATGTTTACATAC
* * * * * *
23629938 AACTTTATATAACTTTATAACTA-A-GTTAATATATAT
1 -A-TGTATATGAGTTAATAA-TATATGTT--TACATAC
23629974 ATGTATGTAT-ATGTTAAATACATATATGTATGCATACA-AC
1 ATGTA--TATGA-GTT-AATA-ATATATGT-T---TACATAC
23630014 TTGATGTATATGAGTTAAT-ATATATGTTTACATAC
1 ---ATGTATATGAGTTAATAATATATGTTTACATAC
23630049 ATGTATATGAGTTAATACATATATGTTTACATAC
1 ATGTATATGAGTTAATA-ATATATGTTTACATAC
23630083 A
1 A
23630084 ACTTTATATA
Statistics
Matches: 143, Mismatches: 14, Indels: 44
0.71 0.07 0.22
Matches are distributed among these distances:
32 31 0.22
34 42 0.29
35 7 0.05
36 24 0.17
37 6 0.04
38 10 0.07
39 2 0.01
40 5 0.03
41 10 0.07
42 1 0.01
43 5 0.03
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (33 bp):
ATGTATATGAGTTAATAATATATGTTTACATAC
Found at i:23630057 original size:18 final size:16
Alignment explanation
Indices: 23630033--23630083 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
23630023 ATGAGTTAAT
23630033 ATATATGTTTACATAC
1 ATATATGTTTACATAC
*
23630049 ATGTATATGAGTTA-ATAC
1 A--TATATG-TTTACATAC
23630067 ATATATGTTTACATAC
1 ATATATGTTTACATAC
23630083 A
1 A
23630084 ACTTTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
18 11 0.38
19 3 0.10
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (16 bp):
ATATATGTTTACATAC
Found at i:23638426 original size:18 final size:18
Alignment explanation
Indices: 23638405--23638440 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
23638395 TCTTGATGAA
*
23638405 AACATAGCTCTTAAGAGT
1 AACACAGCTCTTAAGAGT
23638423 AACACAGCTCTTAAGAGT
1 AACACAGCTCTTAAGAGT
23638441 TTGAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (18 bp):
AACACAGCTCTTAAGAGT
Found at i:23647234 original size:18 final size:18
Alignment explanation
Indices: 23647211--23647245 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23647201 ACAAAAAGGG
*
23647211 GGAGTAGAATGGGTGCAA
1 GGAGTAGAATAGGTGCAA
23647229 GGAGTAGAATAGGTGCA
1 GGAGTAGAATAGGTGCA
23647246 GGAACTAGAG
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:0.34, C:0.06, G:0.43, T:0.17
Consensus pattern (18 bp):
GGAGTAGAATAGGTGCAA
Found at i:23649571 original size:30 final size:31
Alignment explanation
Indices: 23649537--23649600 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
23649527 AACAGAAGTG
*
23649537 TCCGTTGGAAC-CAAGTTTCCAAC-AAAATTT
1 TCCGTTGAAACAC-AGTTTCCAACGAAAATTT
* *
23649567 TCCGTTGAAACACTGTTTCTAACGAAAATTT
1 TCCGTTGAAACACAGTTTCCAACGAAAATTT
23649598 TCC
1 TCC
23649601 CCCTGAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (31 bp):
TCCGTTGAAACACAGTTTCCAACGAAAATTT
Found at i:23649682 original size:29 final size:28
Alignment explanation
Indices: 23649640--23649736 Score: 105
Period size: 28 Copynumber: 3.6 Consensus size: 28
23649630 CGTTGGAAAT
*
23649640 TTCCAATG-AATTTTCTTTTTGCATTGCA
1 TTCCAACGAAATTTTCTTTTTGCATTG-A
* * *
23649668 TTCCAACGAAATTTTC-TTTGGAAAT--
1 TTCCAACGAAATTTTCTTTTTGCATTGA
23649693 TTCCAAC-AAATTTTCTTTTTGCATTGTA
1 TTCCAACGAAATTTTCTTTTTGCATTG-A
23649721 TTCCAACGAAATTTTC
1 TTCCAACGAAATTTTC
23649737 GTTGGAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
24 8 0.14
25 13 0.23
28 20 0.36
29 15 0.27
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (28 bp):
TTCCAACGAAATTTTCTTTTTGCATTGA
Found at i:23649703 original size:24 final size:25
Alignment explanation
Indices: 23649614--23649753 Score: 95
Period size: 25 Copynumber: 5.4 Consensus size: 25
23649604 TGAATTCTCT
* * *
23649614 TTTCCAATGAAAATTTCGTTGGAAA
1 TTTCCAACGAAATTTTCTTTGGAAA
* * * *
23649639 TTTCCAATG-AATTTTCTTTTTGCAT
1 TTTCCAACGAAATTTTC-TTTGGAAA
23649664 TGCATTCCAACGAAATTTTCTTTGGAAA
1 T---TTCCAACGAAATTTTCTTTGGAAA
* **
23649692 TTTCCAAC-AAATTTTCTTTTTGCATTG
1 TTTCCAACGAAATTTTC--TTTGGA-AA
*
23649719 TATTCCAACGAAATTTTCGTTGGAAA
1 T-TTCCAACGAAATTTTCTTTGGAAA
23649745 TTTCCAACG
1 TTTCCAACG
23649754 GATTTTTAAT
Statistics
Matches: 89, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
24 14 0.16
25 29 0.33
26 6 0.07
27 5 0.06
28 20 0.22
29 15 0.17
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (25 bp):
TTTCCAACGAAATTTTCTTTGGAAA
Found at i:23649759 original size:53 final size:53
Alignment explanation
Indices: 23649615--23649759 Score: 227
Period size: 53 Copynumber: 2.7 Consensus size: 53
23649605 GAATTCTCTT
* * *
23649615 TTCCAATGAAAATTTCGTTGGAAATTTCCAATGAATTTTCTTTTTGCATTGCA
1 TTCCAACGAAATTTTCGTTGGAAATTTCCAACGAATTTTCTTTTTGCATTGCA
* * *
23649668 TTCCAACGAAATTTTCTTTGGAAATTTCCAACAAATTTTCTTTTTGCATTGTA
1 TTCCAACGAAATTTTCGTTGGAAATTTCCAACGAATTTTCTTTTTGCATTGCA
*
23649721 TTCCAACGAAATTTTCGTTGGAAATTTCCAACGGATTTT
1 TTCCAACGAAATTTTCGTTGGAAATTTCCAACGAATTTT
23649760 TAATGTGAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 83 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (53 bp):
TTCCAACGAAATTTTCGTTGGAAATTTCCAACGAATTTTCTTTTTGCATTGCA
Found at i:23652516 original size:23 final size:24
Alignment explanation
Indices: 23652485--23652541 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
23652475 GGGTTTAACT
*
23652485 TTGCATGACTGA-TTGATAAGTCA
1 TTGCGTGACTGAGTTGATAAGTCA
** *
23652508 TTGCGTGACT-AGTTTCTATGTCA
1 TTGCGTGACTGAGTTGATAAGTCA
23652531 TTGCGTGACTG
1 TTGCGTGACTG
23652542 GTTTCTAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.39
Consensus pattern (24 bp):
TTGCGTGACTGAGTTGATAAGTCA
Found at i:23652545 original size:23 final size:23
Alignment explanation
Indices: 23652504--23652548 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
23652494 TGATTGATAA
23652504 GTCATTGCGTGACTAGTTTCTAT
1 GTCATTGCGTGACTAGTTTCTAT
*
23652527 GTCATTGCGTGACTGGTTTCTA
1 GTCATTGCGTGACTAGTTTCTA
23652549 GGTTACTACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (23 bp):
GTCATTGCGTGACTAGTTTCTAT
Found at i:23652560 original size:23 final size:23
Alignment explanation
Indices: 23652511--23652561 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
23652501 TAAGTCATTG
* * *
23652511 CGTGACTAGTTTCTATGTCATTG
1 CGTGACTAGTTTCTAGGTCACTA
* *
23652534 CGTGACTGGTTTCTAGGTTACTA
1 CGTGACTAGTTTCTAGGTCACTA
23652557 CGTGA
1 CGTGA
23652562 ATACTGTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (23 bp):
CGTGACTAGTTTCTAGGTCACTA
Found at i:23654211 original size:18 final size:19
Alignment explanation
Indices: 23654173--23654212 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
23654163 AAAGTGAAAT
* *
23654173 TATAAATATTTGAATATAA
1 TATAAATATTTCAATAAAA
23654192 TATAAATA-TTCAATAAAA
1 TATAAATATTTCAATAAAA
23654210 TAT
1 TAT
23654213 TCTATTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
TATAAATATTTCAATAAAA
Found at i:23657394 original size:24 final size:24
Alignment explanation
Indices: 23657361--23657407 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
23657351 TTGAAGCTGT
*
23657361 TCATGGTGCTTCTCCTGCTACTCA
1 TCATGGTGCTACTCCTGCTACTCA
* *
23657385 TCATGTTGCTACTCCTTCTACTC
1 TCATGGTGCTACTCCTGCTACTC
23657408 CCCCTCCTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.34, G:0.13, T:0.40
Consensus pattern (24 bp):
TCATGGTGCTACTCCTGCTACTCA
Found at i:23657614 original size:24 final size:24
Alignment explanation
Indices: 23657587--23657634 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
23657577 CATGTAGATA
*
23657587 TAGTCAATACAGTTGGAGATCCAG
1 TAGTCAATACAGTTGGAAATCCAG
**
23657611 TAGTCAATGTAGTTGGAAATCCAG
1 TAGTCAATACAGTTGGAAATCCAG
23657635 CGGGTGATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (24 bp):
TAGTCAATACAGTTGGAAATCCAG
Found at i:23657678 original size:45 final size:45
Alignment explanation
Indices: 23657614--23657723 Score: 184
Period size: 45 Copynumber: 2.4 Consensus size: 45
23657604 GATCCAGTAG
* *
23657614 TCAATGTAGTTGGAAATCCAGCGGGTGATGCAGATGCAAATGCAA
1 TCAATGCAGTTGGAAATCCAGCGGGCGATGCAGATGCAAATGCAA
*
23657659 TCAATGCAGTTGGAAATCCAGCGGGCGATGCAGATGCAAATGCAG
1 TCAATGCAGTTGGAAATCCAGCGGGCGATGCAGATGCAAATGCAA
*
23657704 TCAATGCAGTTGGAGATCCA
1 TCAATGCAGTTGGAAATCCA
23657724 ATAGTCAATG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (45 bp):
TCAATGCAGTTGGAAATCCAGCGGGCGATGCAGATGCAAATGCAA
Found at i:23657731 original size:24 final size:24
Alignment explanation
Indices: 23657702--23657749 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
23657692 ATGCAAATGC
* *
23657702 AGTCAATGCAGTTGGAGATCCAAT
1 AGTCAATGCAATTAGAGATCCAAT
23657726 AGTCAATGCAATTAGAGATCCAAT
1 AGTCAATGCAATTAGAGATCCAAT
23657750 GGGCGATTCA
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:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (24 bp):
AGTCAATGCAATTAGAGATCCAAT
Found at i:23659413 original size:26 final size:26
Alignment explanation
Indices: 23659384--23659435 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
23659374 AACATTATTC
*
23659384 TGTATCATTTCCATATTATTCTTTGT
1 TGTATCATTTACATATTATTCTTTGT
*
23659410 TGTATTATTTACATATTATTCTTTGT
1 TGTATCATTTACATATTATTCTTTGT
23659436 ATTCATTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.08, T:0.60
Consensus pattern (26 bp):
TGTATCATTTACATATTATTCTTTGT
Found at i:23659435 original size:23 final size:23
Alignment explanation
Indices: 23659377--23659438 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 23
23659367 TAACATTAAC
* *
23659377 ATTATTC--TGTATCATTTCCAT
1 ATTATTCTTTGTATTATTTACAT
23659398 ATTATTCTTTGTTGTATTATTTACAT
1 ATTATTC--T-TTGTATTATTTACAT
23659424 ATTATTCTTTGTATT
1 ATTATTCTTTGTATT
23659439 CATTCATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
21 7 0.21
23 7 0.21
24 1 0.03
26 19 0.56
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (23 bp):
ATTATTCTTTGTATTATTTACAT
Found at i:23663053 original size:77 final size:78
Alignment explanation
Indices: 23662962--23663126 Score: 233
Period size: 78 Copynumber: 2.1 Consensus size: 78
23662952 TGAGAGAGAT
* * * *
23662962 ATCTTGTGTTTTAGATTTGCTTGTCCCCTAGTCAC-GCACTCATTTTGCTTCATTGTATTGGTCA
1 ATCTTGTGTTTTAGATATGCTTGTCCCCCAATCACACCACTCATTTTGCTTCATTGTATTGGTCA
* *
23663026 CAGCTGCTGCAAC
66 CAACTACTGCAAC
* * *
23663039 ATCTTGTGTTTTAGATATGCTTGTCCCCCAATCACACCAGTCATTTTGCTTCGTTGTTTTGGTCA
1 ATCTTGTGTTTTAGATATGCTTGTCCCCCAATCACACCACTCATTTTGCTTCATTGTATTGGTCA
23663104 CAACTACTGCAAC
66 CAACTACTGCAAC
*
23663117 ATCATGTGTT
1 ATCTTGTGTT
23663127 GCAAATATCA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 32 0.42
78 45 0.58
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (78 bp):
ATCTTGTGTTTTAGATATGCTTGTCCCCCAATCACACCACTCATTTTGCTTCATTGTATTGGTCA
CAACTACTGCAAC
Found at i:23666600 original size:22 final size:22
Alignment explanation
Indices: 23666568--23666615 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23666558 CACCACTCTA
*
23666568 GCAATACATAACAA-CAGGTCAC
1 GCAATACATAAAAACCA-GTCAC
*
23666590 GCAATATATAAAAACCAGTCAC
1 GCAATACATAAAAACCAGTCAC
23666612 GCAA
1 GCAA
23666616 GCCTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.15
Consensus pattern (22 bp):
GCAATACATAAAAACCAGTCAC
Found at i:23666771 original size:112 final size:111
Alignment explanation
Indices: 23666477--23667003 Score: 716
Period size: 112 Copynumber: 4.7 Consensus size: 111
23666467 ATCACGTAAC
*
23666477 ATATAAAAACCAGTCACACAAGCCTAAAAAACTACTGAACAAAATCCTCAAAACAACACATGAAT
1 ATATAAAAACCAGTCACACAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAAT
* * *
23666542 TGCACAAGTCACGTGCCACCACTCTAGCAATACATAACAACAGGTCACGCAAT
66 TGCACAAGTCACGCGCCACCACTCT--C---GC-T-ACAACAGGTAACGCAAT
* **
23666595 ATATAAAAACCAGTCACGCAAGCCTAAAAAACTACTGAACAAAAGAATCAAAACAACACATGAAT
1 ATATAAAAACCAGTCACACAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAAT
*
23666660 TGCACAAGTCACGCGCCACCACTCTCGCTACAATAGGTAACGCAAT
66 TGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAAT
* * *
23666706 ATATAAAAACCAATCACGCACAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACGTGAA
1 ATATAAAAACCAGTCACACA-AGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAA
* * *
23666771 TTGCACAAGTCATGCGCCACTACTCTCGCTACAACAGGTAATGCAAT
65 TTGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAAT
* * * **
23666818 ATATAAAAACCAGT--CACATGCCTAAAAAACTACTGAACAAAAGCCTCTAAATAACACACAAAT
1 ATATAAAAACCAGTCACACAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAAT
* *
23666881 TGCACAAGTCACGCACCACCACTCTCCCTACAACAGGTAACGCAAT
66 TGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAAT
* * * * *
23666927 ATATAAAAACCAGTCATACACTGCCTAAAAAACTACTGAATAGAAGTCTCAAAACAACACATGAA
1 ATATAAAAACCAGTCACACA-AGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAA
*
23666992 TTGCATAAGTCA
65 TTGCACAAGTCA
23667004 GTCACGCACC
Statistics
Matches: 367, Mismatches: 38, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
109 94 0.26
110 3 0.01
111 37 0.10
112 146 0.40
113 1 0.00
116 1 0.00
118 85 0.23
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.17
Consensus pattern (111 bp):
ATATAAAAACCAGTCACACAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAAT
TGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAAT
Found at i:23666921 original size:221 final size:226
Alignment explanation
Indices: 23666477--23667003 Score: 742
Period size: 221 Copynumber: 2.3 Consensus size: 226
23666467 ATCACGTAAC
*
23666477 ATATAAAAACCAGTCACACA-AGCCTAAAAAACTACTGAACAAAATCCTCAAAACAACACATGAA
1 ATATAAAAACCAGTCACACACAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAA
* *
23666541 TTGCACAAGTCACGTGCCACCACTCTAGCAATACATAACAACAGGTCACGCAATATATAAAAACC
66 TTGCACAAGTCACGCGCCACCACTCTA-C-A-ACATAACAACAGGTAACGCAATATATAAAAACC
**
23666606 AGTCACGCAAGCCTAAAAAACTACTGAACAAAAGAATCAAAACAACACATGAATTGCACAAGTCA
128 AGTCAC-CAAGCCTAAAAAACTACTGAACAAAAGAATCAAAACAACACACAAATTGCACAAGTCA
* * *
23666671 CGCGCCACCACTCTCGCTACAATAGGTAACGCAAT
192 CGCACCACCACTCTCCCTACAACAGGTAACGCAAT
* * *
23666706 ATATAAAAACCAATCACGCACAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACGTGAA
1 ATATAAAAACCAGTCACACACAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAA
* * * *
23666771 TTGCACAAGTCATGCGCCACTACTCT-C-GC-T-ACAACAGGTAATGCAATATATAAAAACCAGT
66 TTGCACAAGTCACGCGCCACCACTCTACAACATAACAACAGGTAACGCAATATATAAAAACCAGT
* ** * *
23666832 CA-CATGCCTAAAAAACTACTGAACAAAAGCCTCTAAATAACACACAAATTGCACAAGTCACGCA
131 CACCAAGCCTAAAAAACTACTGAACAAAAGAATCAAAACAACACACAAATTGCACAAGTCACGCA
23666896 CCACCACTCTCCCTACAACAGGTAACGCAAT
196 CCACCACTCTCCCTACAACAGGTAACGCAAT
* * * * *
23666927 ATATAAAAACCAGTCATACACTGCCTAAAAAACTACTGAATAGAAGTCTCAAAACAACACATGAA
1 ATATAAAAACCAGTCACACACAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAA
*
23666992 TTGCATAAGTCA
66 TTGCACAAGTCA
23667004 GTCACGCACC
Statistics
Matches: 268, Mismatches: 29, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
221 151 0.56
223 31 0.12
224 1 0.00
225 1 0.00
228 1 0.00
229 18 0.07
230 65 0.24
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.17
Consensus pattern (226 bp):
ATATAAAAACCAGTCACACACAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAA
TTGCACAAGTCACGCGCCACCACTCTACAACATAACAACAGGTAACGCAATATATAAAAACCAGT
CACCAAGCCTAAAAAACTACTGAACAAAAGAATCAAAACAACACACAAATTGCACAAGTCACGCA
CCACCACTCTCCCTACAACAGGTAACGCAAT
Found at i:23668407 original size:48 final size:47
Alignment explanation
Indices: 23668346--23668580 Score: 149
Period size: 48 Copynumber: 5.2 Consensus size: 47
23668336 AGGTGGCTAA
23668346 AGTCACGTAATGCCTACAAATAGGTCACACAATGCTCAACAAATATTC
1 AGTCACGTAATGCCTACAAATA-GTCACACAATGCTCAACAAATATTC
* * *
23668394 AGTCACGTTATG-C--C---T-GTCACGCAACGCTCAACAAATATTC
1 AGTCACGTAATGCCTACAAATAGTCACACAATGCTCAACAAATATTC
* * * * * *
23668434 AGTCACGTAATACCTATAAAGAACTCACACAATACTCAACAAATATTT
1 AGTCACGTAATGCCTACAAA-TAGTCACACAATGCTCAACAAATATTC
* * * *
23668482 AGTCACGTATTG-C--C---T-GTCACGCAACT-CTCAGCAAATATTT
1 AGTCACGTAATGCCTACAAATAGTCACACAA-TGCTCAACAAATATTC
* * * * ** *
23668522 AGTAACGTAATGCCTATAAAGAACTCACGTAATACTCAACAAATATTC
1 AGTCACGTAATGCCTACAAA-TAGTCACACAATGCTCAACAAATATTC
23668570 AGTCACGTAAT
1 AGTCACGTAAT
23668581 ATTTAAGCAC
Statistics
Matches: 141, Mismatches: 28, Indels: 36
0.69 0.14 0.18
Matches are distributed among these distances:
40 63 0.45
41 3 0.02
42 1 0.01
45 1 0.01
47 3 0.02
48 70 0.50
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.26
Consensus pattern (47 bp):
AGTCACGTAATGCCTACAAATAGTCACACAATGCTCAACAAATATTC
Found at i:23668424 original size:40 final size:40
Alignment explanation
Indices: 23668369--23668536 Score: 147
Period size: 40 Copynumber: 4.0 Consensus size: 40
23668359 CTACAAATAG
* *
23668369 GTCACACAATGCTCAACAAATATTCAGTCACGTTATGCCT
1 GTCACACAACGCTCAACAAATATTCAGTCACGTAATGCCT
* *
23668409 GTCACGCAACGCTCAACAAATATTCAGTCACGTAATACCTAT
1 GTCACACAACGCTCAACAAATATTCAGTCACGTAATGCC--T
** * *
23668451 AAAGAACTCACACAATACTCAACAAATATTTAGTCACGTATTGCCT
1 ---G---TCACACAACGCTCAACAAATATTCAGTCACGTAATGCCT
* * * * *
23668497 GTCACGCAACTCTCAGCAAATATTTAGTAACGTAATGCCT
1 GTCACACAACGCTCAACAAATATTCAGTCACGTAATGCCT
23668537 ATAAAGAACT
Statistics
Matches: 104, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
40 68 0.65
42 1 0.01
43 1 0.01
45 1 0.01
46 1 0.01
48 32 0.31
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (40 bp):
GTCACACAACGCTCAACAAATATTCAGTCACGTAATGCCT
Found at i:23668496 original size:88 final size:89
Alignment explanation
Indices: 23668346--23668578 Score: 335
Period size: 88 Copynumber: 2.6 Consensus size: 89
23668336 AGGTGGCTAA
* * ** *
23668346 AGTCACGTAATGCCTACAAATAGGTCACACAATGCTCAACAAATATTCAGTCACGT-TATGCCTG
1 AGTCACGTAATGCCTATAAAGAACTCACACAATACTCAACAAATATTCAGTCACGTATATGCCTG
23668410 TCACGCAACGCTCAACAAATATTC
66 TCACGCAACGCTCAACAAATATTC
* *
23668434 AGTCACGTAATACCTATAAAGAACTCACACAATACTCAACAAATATTTAGTCACGTAT-TGCCTG
1 AGTCACGTAATGCCTATAAAGAACTCACACAATACTCAACAAATATTCAGTCACGTATATGCCTG
* * *
23668498 TCACGCAACTCTCAGCAAATATTT
66 TCACGCAACGCTCAACAAATATTC
* **
23668522 AGTAACGTAATGCCTATAAAGAACTCACGTAATACTCAACAAATATTCAGTCACGTA
1 AGTCACGTAATGCCTATAAAGAACTCACACAATACTCAACAAATATTCAGTCACGTA
23668579 ATATTTAAGC
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
88 128 0.99
89 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (89 bp):
AGTCACGTAATGCCTATAAAGAACTCACACAATACTCAACAAATATTCAGTCACGTATATGCCTG
TCACGCAACGCTCAACAAATATTC
Found at i:23677023 original size:2 final size:2
Alignment explanation
Indices: 23677016--23677048 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
23677006 CTGCCTGATT
23677016 TA TA TA TA 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 TA TA TA TA T
23677049 TTGTCTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23678933 original size:61 final size:60
Alignment explanation
Indices: 23678818--23678935 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
23678808 CATTTAAGCA
* *
23678818 TTTTAAGCATTTTGGAGTAGTTTTTGATATATGAAGAAAACCTTTGAGCGTTTTGAGTAT
1 TTTTAAGCATTTTGGAGTAGTTTTTGATATATGAAGAAAACCTTTGAACATTTTGAGTAT
* *
23678878 TTTTAAGCATTTTGGAGT-GATTTTTTATATATGAAGAAAAACTTTTGAACATTTTGAG
1 TTTTAAGCATTTTGGAGTAG-TTTTTGATATATGAAG-AAAACCTTTGAACATTTTGAG
23678936 CATCCTTTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 1 0.02
60 33 0.63
61 18 0.35
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (60 bp):
TTTTAAGCATTTTGGAGTAGTTTTTGATATATGAAGAAAACCTTTGAACATTTTGAGTAT
Found at i:23679154 original size:23 final size:23
Alignment explanation
Indices: 23679143--23679226 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
23679133 TGGTTGATAT
23679143 GGCATTGCGTGACTTGTTATTAA
1 GGCATTGCGTGACTTGTTATTAA
*
23679166 GGCATTGCGTGACTTGTTAGTAA
1 GGCATTGCGTGACTTGTTATTAA
* * * *
23679189 GGTATTGCGTTACTAGTTAGTAA
1 GGCATTGCGTGACTTGTTATTAA
*
23679212 GGCATTGTGTGACTT
1 GGCATTGCGTGACTT
23679227 AGGCATTGCT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (23 bp):
GGCATTGCGTGACTTGTTATTAA
Found at i:23679276 original size:22 final size:22
Alignment explanation
Indices: 23679237--23679308 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
23679227 AGGCATTGCT
* *
23679237 TAAAAATCAATCATGCAATGTC
1 TAAAAACCAATCACGCAATGTC
* *
23679259 TAAAAACCAGTCACGCAATGCC
1 TAAAAACCAATCACGCAATGTC
* **
23679281 T-AAAACTAATCACATAATGTC
1 TAAAAACCAATCACGCAATGTC
23679302 TAAAAAC
1 TAAAAAC
23679309 TAGTCACATA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 16 0.40
22 24 0.60
ACGTcount: A:0.47, C:0.22, G:0.08, T:0.22
Consensus pattern (22 bp):
TAAAAACCAATCACGCAATGTC
Found at i:23679310 original size:22 final size:22
Alignment explanation
Indices: 23679253--23679321 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
23679243 TCAATCATGC
* **
23679253 AATGTCTAAAAACCAGTCACGC
1 AATGTCTAAAAACTAGTCACAT
* *
23679275 AATGCCT-AAAACTAATCACAT
1 AATGTCTAAAAACTAGTCACAT
23679296 AATGTCTAAAAACTAGTCACAT
1 AATGTCTAAAAACTAGTCACAT
23679318 AATG
1 AATG
23679322 ATTAAGTCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 16 0.41
22 23 0.59
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (22 bp):
AATGTCTAAAAACTAGTCACAT
Found at i:23680087 original size:19 final size:20
Alignment explanation
Indices: 23680063--23680100 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23680053 CTTTAATCCC
23680063 TTTTAAACT-TTTTTATTTA
1 TTTTAAACTATTTTTATTTA
*
23680082 TTTTAAATTATTTTTATTT
1 TTTTAAACTATTTTTATTT
23680101 GTTATATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTAAACTATTTTTATTTA
Found at i:23681273 original size:62 final size:62
Alignment explanation
Indices: 23681176--23681297 Score: 226
Period size: 62 Copynumber: 2.0 Consensus size: 62
23681166 GTCAATCTCT
*
23681176 CATTTGGAACCTTTGTGATTGACCGTTCCACTATTATGAGTTAACATTTATGCATTGTGTAA
1 CATTTGGAACCTTTGTGATTGACCATTCCACTATTATGAGTTAACATTTATGCATTGTGTAA
*
23681238 CATTTGGAACCTTTGTGATTGACCATTCCACTATTATGAGTTAACATTTATGCGTTGTGT
1 CATTTGGAACCTTTGTGATTGACCATTCCACTATTATGAGTTAACATTTATGCATTGTGT
23681298 GATTTTACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (62 bp):
CATTTGGAACCTTTGTGATTGACCATTCCACTATTATGAGTTAACATTTATGCATTGTGTAA
Found at i:23684791 original size:24 final size:25
Alignment explanation
Indices: 23684755--23684817 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
23684745 GTCAGCCCAT
* *
23684755 TTTTTAT-TTTTTTTAAAAAAATCA
1 TTTTTATAATTTTATAAAAAAATCA
* *
23684779 TTTTTATAATTTTATAATAAAATTA
1 TTTTTATAATTTTATAAAAAAATCA
*
23684804 -TTTTATGATTTTAT
1 TTTTTATAATTTTAT
23684818 TTATAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTTATAATTTTATAAAAAAATCA
Found at i:23686400 original size:22 final size:22
Alignment explanation
Indices: 23686368--23686429 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
23686358 AATAGAATGT
*
23686368 TTCTCATTGCAGCGAGAATGCA
1 TTCTCACTGCAGCGAGAATGCA
** *
23686390 TTCTGGCTGCAGCAAGAATGCA
1 TTCTCACTGCAGCGAGAATGCA
*
23686412 TTTTCACTGCAGCGAGAA
1 TTCTCACTGCAGCGAGAA
23686430 CCAAACTGGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (22 bp):
TTCTCACTGCAGCGAGAATGCA
Found at i:23688642 original size:42 final size:43
Alignment explanation
Indices: 23688483--23688642 Score: 182
Period size: 43 Copynumber: 3.7 Consensus size: 43
23688473 TTCCCAACTC
* * * * *
23688483 ATGCGCACTCCCTACTAGCACAT-GGCTAGGTCATC-ACTGGGTT
1 ATGCGCACTCCCTACTCGCACATAGCCGA-GTCAGCAAC-GGATT
* * * *
23688526 ATGCGCACTCCCTACTCGCACATAACCGAGTCATCATCGGCTT
1 ATGCGCACTCCCTACTCGCACATAGCCGAGTCAGCAACGGATT
23688569 ATGCGCACTCCCTACTCGCACATAGCCGAGTCAGCAACGGATT
1 ATGCGCACTCCCTACTCGCACATAGCCGAGTCAGCAACGGATT
* *
23688612 ATGTGCACT-CCTACTCGCACATAGCTGAGTC
1 ATGCGCACTCCCTACTCGCACATAGCCGAGTC
23688643 CACATCAACA
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
42 21 0.20
43 79 0.77
44 3 0.03
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAGCCGAGTCAGCAACGGATT
Found at i:23697385 original size:35 final size:35
Alignment explanation
Indices: 23697290--23697397 Score: 144
Period size: 35 Copynumber: 3.1 Consensus size: 35
23697280 CTTACTCAGC
* ***
23697290 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
1 TCATGTGCACTCCCTACACGAACATTTCAATATCA
*
23697325 TCATGTGCACTCCCTACACGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGAACATTTCAATATCA
* * *
23697360 TCATGTGCACTTCTTACATGAACATTTCAATATCA
1 TCATGTGCACTCCCTACACGAACATTTCAATATCA
23697395 TCA
1 TCA
23697398 CACGCACTTC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGAACATTTCAATATCA
Found at i:23713374 original size:43 final size:43
Alignment explanation
Indices: 23713295--23713402 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
23713285 CACTCTTTAT
* * *
23713295 TCGCACATAGCTGGGTCATCATCGGCTTACGCGCACTCCCTAC-
1 TCGCACATAGCTGGGTCATCATCAGCTCACACGCACTCCC-ACA
* * * *
23713338 TCGCACATAGCCGAGTCATCATCAGCTCATATGCACTCCCACA
1 TCGCACATAGCTGGGTCATCATCAGCTCACACGCACTCCCACA
*
23713381 TTGCACATAGCTGGGTCATCAT
1 TCGCACATAGCTGGGTCATCAT
23713403 TATCACACAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 2 0.04
43 52 0.96
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (43 bp):
TCGCACATAGCTGGGTCATCATCAGCTCACACGCACTCCCACA
Found at i:23720010 original size:14 final size:14
Alignment explanation
Indices: 23719993--23720035 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
23719983 TTAACTCACC
23719993 TAAAATAACTAATT
1 TAAAATAACTAATT
* *
23720007 TAAAATAATTAA-A
1 TAAAATAACTAATT
23720020 TAAAATATACTAATT
1 TAAAATA-ACTAATT
23720035 T
1 T
23720036 CTATGCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 7 0.30
14 15 0.65
15 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAATAACTAATT
Found at i:23723145 original size:13 final size:13
Alignment explanation
Indices: 23723127--23723151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23723117 AGAGAAATTG
23723127 TGATTTTATAAAA
1 TGATTTTATAAAA
23723140 TGATTTTATAAA
1 TGATTTTATAAA
23723152 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:23730509 original size:5 final size:4
Alignment explanation
Indices: 23730484--23730533 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
23730474 TTTCTCCCTT
*
23730484 TTTC TTTC TTTC TTTC TTTCC TTTCC TTTC TCT- TTTC -TTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTT-C TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
23730532 TT
1 TT
23730534 CCCCTTTCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 5 0.12
4 27 0.66
5 9 0.22
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:23730530 original size:32 final size:36
Alignment explanation
Indices: 23730483--23730553 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 36
23730473 ATTTCTCCCT
*
23730483 TTTTCTTTCTTTCTTTCTT-TCCTTTC-CTTT-CTC
1 TTTTCTTTCTTTCTTTCTTCCCCTTTCTCTTTCCTC
23730516 TTTTC-TTCTTTCTTTCTTCCCCTTTCTCTTTCCTC
1 TTTTCTTTCTTTCTTTCTTCCCCTTTCTCTTTCCTC
23730551 TTT
1 TTT
23730554 GGCTATGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.38
33 11 0.32
34 4 0.12
35 6 0.18
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTTCTTTCTTTCTTTCTTCCCCTTTCTCTTTCCTC
Found at i:23730539 original size:28 final size:29
Alignment explanation
Indices: 23730478--23730546 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
23730468 CCCTCATTTC
*
23730478 TCCCTTTTTC-TTTCTTTCTTTCTTTCCT
1 TCCCTTTCTCTTTTCTTTCTTTCTTTCCT
*
23730506 TTCCTTTCTCTTTTC-TTCTTTCTTT-CT
1 TCCCTTTCTCTTTTCTTTCTTTCTTTCCT
23730533 TCCCCTTTCTCTTT
1 T-CCCTTTCTCTTT
23730547 CCTCTTTGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 29 0.81
29 4 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (29 bp):
TCCCTTTCTCTTTTCTTTCTTTCTTTCCT
Found at i:23742590 original size:19 final size:19
Alignment explanation
Indices: 23742566--23742603 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23742556 ACATTTGACT
23742566 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
23742585 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
23742604 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:23744995 original size:17 final size:17
Alignment explanation
Indices: 23744965--23744997 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23744955 TTCTTGATAA
23744965 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
23744982 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
23744998 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:23745239 original size:29 final size:28
Alignment explanation
Indices: 23745161--23745306 Score: 172
Period size: 29 Copynumber: 5.1 Consensus size: 28
23745151 TTAAGACAAA
*
23745161 AAAATATTTTATCTTGTCTAAATTGAGAC
1 AAAATATTTT-TCTTGTCTAAATTAAGAC
*
23745190 -AAATATGTTTTCTTGACTAAATTAAGAC
1 AAAATAT-TTTTCTTGTCTAAATTAAGAC
*
23745218 AAAATATTTTTCTTGTCTTAAATTAAGGC
1 AAAATATTTTTCTTGTC-TAAATTAAGAC
*
23745247 AAACATA-TTTTCTTATCTAAATTAAGACCC
1 AAA-ATATTTTTCTTGTCTAAATTAAGA--C
*
23745277 AACATA-TTTTCTTGTCTAAATTAAGAC
1 AAAATATTTTTCTTGTCTAAATTAAGAC
23745304 AAA
1 AAA
23745307 CATGTCAAAT
Statistics
Matches: 102, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.03
28 40 0.39
29 53 0.52
30 6 0.06
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (28 bp):
AAAATATTTTTCTTGTCTAAATTAAGAC
Found at i:23745240 original size:57 final size:57
Alignment explanation
Indices: 23745161--23745311 Score: 200
Period size: 57 Copynumber: 2.6 Consensus size: 57
23745151 TTAAGACAAA
* *
23745161 AAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGA-CTAAATTAAGA-C
1 AAAATATTTT-TCTTGTCTAAATTAAGACAAACATGTTTTCTT-ATCTAAATTAAGACC
* *
23745218 AAAATATTTTTCTTGTCTTAAATTAAGGCAAACATATTTTCTTATCTAAATTAAGACCC
1 AAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTATCTAAATTAAGA-CC
*
23745277 AACATA-TTTTCTTGTCTAAATTAAGACAAACATGT
1 AAAATATTTTTCTTGTCTAAATTAAGACAAACATGT
23745312 CAAATCTGCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
56 8 0.10
57 59 0.71
58 10 0.12
59 6 0.07
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (57 bp):
AAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTAAATTAAGACC
Found at i:23751223 original size:19 final size:19
Alignment explanation
Indices: 23751175--23751222 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
23751165 TTAATATTTT
23751175 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
*
23751194 AATATTATTTTATT-TTAA
1 AATATTATTTTATTCATAA
23751212 AATATTATTTT
1 AATATTATTTT
23751223 TGCCTGTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:23752615 original size:21 final size:21
Alignment explanation
Indices: 23752589--23752676 Score: 122
Period size: 21 Copynumber: 4.1 Consensus size: 21
23752579 TAAATGGAGA
* * *
23752589 CATCAGTCATTATCATAAATG
1 CATCAGTCTTTGTCATGAATG
*
23752610 CATCAGTCTTTGTTATGAATG
1 CATCAGTCTTTGTCATGAATG
23752631 CATCAGTCTTTGTCATGAATG
1 CATCAGTCTTTGTCATGAATG
*
23752652 CATCAGTCTTTGTTATGAATTG
1 CATCAGTCTTTGTCATGAA-TG
23752674 CAT
1 CAT
23752677 GAACATATCC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
21 55 0.92
22 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (21 bp):
CATCAGTCTTTGTCATGAATG
Found at i:23752652 original size:42 final size:43
Alignment explanation
Indices: 23752589--23752676 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 43
23752579 TAAATGGAGA
23752589 CATCAGTCATTATCATAAATGCATCAGTCTTTGTTATGAA-TG
1 CATCAGTCATTATCATAAATGCATCAGTCTTTGTTATGAATTG
* * *
23752631 CATCAGTCTTTGTCATGAATGCATCAGTCTTTGTTATGAATTG
1 CATCAGTCATTATCATAAATGCATCAGTCTTTGTTATGAATTG
23752674 CAT
1 CAT
23752677 GAACATATCC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 37 0.88
43 5 0.12
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (43 bp):
CATCAGTCATTATCATAAATGCATCAGTCTTTGTTATGAATTG
Found at i:23756439 original size:39 final size:39
Alignment explanation
Indices: 23756384--23756475 Score: 130
Period size: 39 Copynumber: 2.4 Consensus size: 39
23756374 CAAGATTCAA
* * *
23756384 TCTCGCTGCAATGAAATTGTAACCTAGAAATAGAAGGTT
1 TCTCGCTGCAACGAAATTGTAACCCAGAAATAGAAAGTT
* *
23756423 TCTCGCTGCAGCGAAATTGTATCCCAGAAATAGAAAGTT
1 TCTCGCTGCAACGAAATTGTAACCCAGAAATAGAAAGTT
*
23756462 TCTCGCTACAACGA
1 TCTCGCTGCAACGA
23756476 GAATAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (39 bp):
TCTCGCTGCAACGAAATTGTAACCCAGAAATAGAAAGTT
Found at i:23756937 original size:43 final size:43
Alignment explanation
Indices: 23756863--23756981 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
23756853 TCACCAGCTC
* * * **
23756863 ATGCGCACTCCCTACTCGTACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATC-CTCGACTT
* * *
23756906 ATGCGTACTCCCTACTGGCACATAACCGGGTCATCCTCGACTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCCTCGACTT
* *
23756949 ATGCGCACTCCTTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCA
23756982 ATGTCATTAC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 1 0.02
43 61 0.98
ACGTcount: A:0.20, C:0.34, G:0.21, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCCTCGACTT
Found at i:23757013 original size:2 final size:2
Alignment explanation
Indices: 23756999--23757081 Score: 134
Period size: 2 Copynumber: 41.5 Consensus size: 2
23756989 TACACAACAG
23756999 TA TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23757041 TA TA TA TA TA -A NTA TA 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 TA TA TA TA TA TA TA TA T
23757082 CAACACAATG
Statistics
Matches: 77, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 73 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23762325 original size:20 final size:21
Alignment explanation
Indices: 23762302--23762346 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
23762292 ACCCAAAAAT
23762302 AGAAAGT-TTCTCGCT-CAGCG
1 AGAAAGTATT-TCGCTGCAGCG
*
23762322 AGAATGTATTTCGCTGCAGCG
1 AGAAAGTATTTCGCTGCAGCG
23762343 AGAA
1 AGAA
23762347 GCTACAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (21 bp):
AGAAAGTATTTCGCTGCAGCG
Found at i:23770113 original size:60 final size:60
Alignment explanation
Indices: 23770020--23770165 Score: 193
Period size: 60 Copynumber: 2.4 Consensus size: 60
23770010 TAGGAGACCA
* * * * *
23770020 AAACAGAAAGTTTTTCGCTACAGCGAGATTCAATCTCATTACAGCGAAATTGTAACCCAC
1 AAACAGAAAGTTTCTCGCTGCAGCGAAATTCAATCTCACTACAGCGAAATTGCAACCCAC
** * * * *
23770080 AAACAGAAAGTTTCTCAATGCAGCGAAATTCAATCTCCCTGCAGCGAAATTGCAACCTAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAAATTCAATCTCACTACAGCGAAATTGCAACCCAC
23770140 AAACAGAAAGTTTCTCGCTGCAGCGA
1 AAACAGAAAGTTTCTCGCTGCAGCGA
23770166 GAATGTATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (60 bp):
AAACAGAAAGTTTCTCGCTGCAGCGAAATTCAATCTCACTACAGCGAAATTGCAACCCAC
Found at i:23770182 original size:60 final size:59
Alignment explanation
Indices: 23770020--23770188 Score: 171
Period size: 60 Copynumber: 2.8 Consensus size: 59
23770010 TAGGAGACCA
* * * * *
23770020 AAACAGAAAGTTTTTCGCTACAGCGAG-ATTCAATCTCATTACAGCGAAATTGTAACCCAC
1 AAACAGAAAGTTTCTCGCTGCAGCGAGAATT--ATCTCACTGCAGCGAAATTGCAACCCAC
** * * *
23770080 AAACAGAAAGTTTCTCAATGCAGCGA-AATTCAATCTCCCTGCAGCGAAATTGCAACCTAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAGAATT--ATCTCACTGCAGCGAAATTGCAACCCAC
* *
23770140 AAACAGAAAGTTTCTCGCTGCAGCGAGAATGTATTTCGCTGCAGCGAAA
1 AAACAGAAAGTTTCTCGCTGCAGCGAGAAT-TATCTCACTGCAGCGAAA
23770189 AGCTACAGTG
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
60 88 0.96
61 3 0.03
62 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (59 bp):
AAACAGAAAGTTTCTCGCTGCAGCGAGAATTATCTCACTGCAGCGAAATTGCAACCCAC
Found at i:23770585 original size:43 final size:43
Alignment explanation
Indices: 23770534--23770652 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
23770524 TCACCAGCTC
** * **
23770534 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGACTT
* *
23770577 ATGTGCACTCCCTACTTGCACATAACCGGGTCATCCTCGACTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
* * *
23770620 ATGCACACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
23770653 ATATAATTGC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
42 1 0.02
43 62 0.98
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
Found at i:23772638 original size:21 final size:21
Alignment explanation
Indices: 23772614--23772654 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23772604 TTTTTCCAAA
23772614 ATCTAAATATATCGATACATG
1 ATCTAAATATATCGATACATG
* *
23772635 ATCTAAATGTATTGATACAT
1 ATCTAAATATATCGATACAT
23772655 TTTGTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (21 bp):
ATCTAAATATATCGATACATG
Found at i:23773710 original size:68 final size:68
Alignment explanation
Indices: 23773601--23773750 Score: 178
Period size: 68 Copynumber: 2.2 Consensus size: 68
23773591 CATGTTTGGT
* * ** * *
23773601 ATGATAAATGGCATAAGATTGTGTATATAATGTAAATTCCATGTATCA-TATGAGATGATTAAAT
1 ATGATGAATGCCATAAGATTGTGTATATAATACAAATTCCATATA-CAGTACGAGATGATTAAAT
23773665 ATGC
65 ATGC
** *
23773669 ATGATGAATGCCATAAGATTGTGTATA-AGATACATTTTCCATATACAGTACGAGATGATTAAGT
1 ATGATGAATGCCATAAGATTGTGTATATA-ATACAAATTCCATATACAGTACGAGATGATTAAAT
23773733 ATGC
65 ATGC
*
23773737 ATGATGATTGCCAT
1 ATGATGAATGCCAT
23773751 GAAAAAGTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
67 3 0.04
68 67 0.96
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (68 bp):
ATGATGAATGCCATAAGATTGTGTATATAATACAAATTCCATATACAGTACGAGATGATTAAATA
TGC
Found at i:23773780 original size:68 final size:65
Alignment explanation
Indices: 23773626--23773798 Score: 161
Period size: 68 Copynumber: 2.6 Consensus size: 65
23773616 AGATTGTGTA
* * * * * * *
23773626 TATAATGTAAATTCCATGTATCATATGAGATGATTAAATATGCATGATGAATGCCATAAGATTGT
1 TATAATGTAAATTTCATATA-CATACGAGATGATTAAGTATGCATGATGAATGCCATAAAAGTAT
23773691 G
65 G
* *
23773692 TATAA-GATACATTTTCCATATACAGTACGAGATGATTAAGTATGCATGATGATTGCCATGAAAA
1 TATAATG-TA-AATTT-CATATACA-TACGAGATGATTAAGTATGCATGATGAATGCCAT--AAA
23773756 AGTATG
60 AGTATG
* *
23773762 TATAATGTAGATTTCATATAC-TACTAAGATGATTAAG
1 TATAATGTAAATTTCATATACATAC-GAGATGATTAAG
23773799 CATGTACGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
65 1 0.01
66 10 0.11
67 16 0.18
68 43 0.49
69 3 0.03
70 13 0.15
71 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (65 bp):
TATAATGTAAATTTCATATACATACGAGATGATTAAGTATGCATGATGAATGCCATAAAAGTATG
Found at i:23776664 original size:177 final size:177
Alignment explanation
Indices: 23776464--23776817 Score: 611
Period size: 177 Copynumber: 2.0 Consensus size: 177
23776454 TTTTGTGTGT
*
23776464 AATGTTTCTTGCATTTTTCTTTTTCTTATATATTTTTTGGGTTTAAAAAGTTGGTGCAAATGAAT
1 AATGTTTCTTGCATTTTTCTTTTTCTTATATATTTTTTGGGTTTAAAAAGTTGGTGAAAATGAAT
* * * * *
23776529 GTATAGGATTCTAAACAATTATGAATATGAAATGCTCTTTCACTTTGTACTCATAACCGTAACAA
66 GCATAGGATTATAAACAACTATGAATATGAAATGCTCTCTCACTTTGTACTCATAACCGTAAAAA
*
23776594 CTTTTGTGTATATATATTTCTATAAACAC-TTCATTCAAGATCTTTTA
131 CTTTTGTGGATATATATTTCTATAAACACTTTC-TTCAAGATCTTTTA
*
23776641 AATGTTTCTTGCATTTTTCTTTTTCTTATTTATTTTTTGGGTTTAAAAAGTTGGTGAAAATGAAT
1 AATGTTTCTTGCATTTTTCTTTTTCTTATATATTTTTTGGGTTTAAAAAGTTGGTGAAAATGAAT
*
23776706 GCATAGGATTATAAACAACTATGAATATGAAATGCTCTCTCACTTTGTACTCATAACTGTAAAAA
66 GCATAGGATTATAAACAACTATGAATATGAAATGCTCTCTCACTTTGTACTCATAACCGTAAAAA
23776771 CTTTTGTGGATATATATTTCTATAAACACTTTCTTCAAGATCTTTTA
131 CTTTTGTGGATATATATTTCTATAAACACTTTCTTCAAGATCTTTTA
23776818 TTTGACTCGA
Statistics
Matches: 167, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
177 164 0.98
178 3 0.02
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (177 bp):
AATGTTTCTTGCATTTTTCTTTTTCTTATATATTTTTTGGGTTTAAAAAGTTGGTGAAAATGAAT
GCATAGGATTATAAACAACTATGAATATGAAATGCTCTCTCACTTTGTACTCATAACCGTAAAAA
CTTTTGTGGATATATATTTCTATAAACACTTTCTTCAAGATCTTTTA
Found at i:23780112 original size:21 final size:21
Alignment explanation
Indices: 23780070--23780108 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
23780060 CTCTCCCATC
*
23780070 TCTTCCTCATCTTCTCTCTCT
1 TCTTCCTCATCTTCTATCTCT
*
23780091 TCTTCCTC-TCTTTTATCT
1 TCTTCCTCATCTTCTATCT
23780109 TCTTTCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.56
Consensus pattern (21 bp):
TCTTCCTCATCTTCTATCTCT
Found at i:23780308 original size:12 final size:12
Alignment explanation
Indices: 23780291--23780315 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23780281 CCTCCTTTTC
23780291 AACATCATCCTT
1 AACATCATCCTT
23780303 AACATCATCCTT
1 AACATCATCCTT
23780315 A
1 A
23780316 TTCATCGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (12 bp):
AACATCATCCTT
Found at i:23781990 original size:32 final size:31
Alignment explanation
Indices: 23781948--23782022 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
23781938 ATCACTAAAA
*
23781948 TTATATAAAAAATAAATTTTATACTTATTAGT
1 TTATAAAAAAAATAAATTTT-TACTTATTAGT
* *
23781980 TTAT-AAAAAAATAAGTTTTTATTTATTAGT
1 TTATAAAAAAAATAAATTTTTACTTATTAGT
*
23782010 TCATAAAAAAAAT
1 TTATAAAAAAAAT
23782023 TGATTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 13 0.34
31 21 0.55
32 4 0.11
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (31 bp):
TTATAAAAAAAATAAATTTTTACTTATTAGT
Found at i:23781992 original size:31 final size:30
Alignment explanation
Indices: 23781948--23782020 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
23781938 ATCACTAAAA
23781948 TTATATAAAAAATAAATTTTATACTTATTAGT
1 TTATA-AAAAAATAAATTTT-TACTTATTAGT
* *
23781980 TTATAAAAAAATAAGTTTTTATTTATTAGT
1 TTATAAAAAAATAAATTTTTACTTATTAGT
*
23782010 TCATAAAAAAA
1 TTATAAAAAAA
23782021 ATTGATTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 20 0.53
31 13 0.34
32 5 0.13
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (30 bp):
TTATAAAAAAATAAATTTTTACTTATTAGT
Found at i:23790889 original size:12 final size:12
Alignment explanation
Indices: 23790872--23790896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23790862 AAGAAAATGA
23790872 AATATTTTATTT
1 AATATTTTATTT
23790884 AATATTTTATTT
1 AATATTTTATTT
23790896 A
1 A
23790897 GTTTGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATATTTTATTT
Found at i:23792361 original size:60 final size:60
Alignment explanation
Indices: 23792268--23792446 Score: 236
Period size: 60 Copynumber: 3.0 Consensus size: 60
23792258 ATATTTGATT
* * * *
23792268 GTAAAAGGGGACCTGAAGCCTCGATTCATATTGGGTGGCGTGGGCAATTCCCACGAGTAA
1 GTAAAGGGGGACCTAAAGCCCCGATTCATATTGGGTGGCGTGGGCAGTTCCCACGAGTAA
* * *
23792328 GTAAAGGGGGACCTAAAGCCCCGATTCACATTGGGTGGCATGGGCAGTTCCCACGAGTAG
1 GTAAAGGGGGACCTAAAGCCCCGATTCATATTGGGTGGCGTGGGCAGTTCCCACGAGTAA
* * *
23792388 GTAAAGGGGGACCCGAAA-CCCCGATTTATATAT-GGTGGCGTGGGCAGTTCCTACGAGTA
1 GTAAAGGGGGA-CCTAAAGCCCCGATTCATAT-TGGGTGGCGTGGGCAGTTCCCACGAGTA
23792447 GGTGATGATG
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
60 99 0.94
61 6 0.06
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (60 bp):
GTAAAGGGGGACCTAAAGCCCCGATTCATATTGGGTGGCGTGGGCAGTTCCCACGAGTAA
Found at i:23798163 original size:19 final size:19
Alignment explanation
Indices: 23798141--23798178 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23798131 CCATTTGACT
23798141 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
23798160 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
23798179 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:23809687 original size:2 final size:2
Alignment explanation
Indices: 23809675--23809706 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
23809665 ACCATATACC
*
23809675 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23809707 CAATCATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23809808 original size:42 final size:42
Alignment explanation
Indices: 23809747--23809908 Score: 207
Period size: 42 Copynumber: 3.9 Consensus size: 42
23809737 CAGCTCATAT
* **
23809747 GCATCGGCTTATGTGCACTCCCACTCGCACATAGTTGGGTTA
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGGTTA
* * * *
23809789 GCATTGGCCTATGCGCACTCCCACTCCCACGTAGCCGGGTTA
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGGTTA
* * * *
23809831 GCATCGGTTTATGTGCACTCCCACTCGCATATAGCCGGGTCA
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGGTTA
* *
23809873 GCATCGGCTTATGCACACTCCTACTCGCACATAGCC
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCC
23809909 AGGTAAATAT
Statistics
Matches: 100, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.19, C:0.34, G:0.22, T:0.25
Consensus pattern (42 bp):
GCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGGTTA
Found at i:23811345 original size:22 final size:22
Alignment explanation
Indices: 23811326--23811374 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
23811316 TTGATGAATG
23811326 AAGTCTTGAGACCTATTGAAAA
1 AAGTCTTGAGACCTATTGAAAA
* * *
23811348 AAGTCTTGTGACCTACTAAAAA
1 AAGTCTTGAGACCTATTGAAAA
23811370 AAGTC
1 AAGTC
23811375 GCAAGGCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (22 bp):
AAGTCTTGAGACCTATTGAAAA
Found at i:23822803 original size:2 final size:2
Alignment explanation
Indices: 23822798--23822830 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
23822788 TATATATATA
*
23822798 TG TG TG TG TG TG TT TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
23822831 ATGTTTGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:23824879 original size:62 final size:62
Alignment explanation
Indices: 23824806--23825079 Score: 302
Period size: 62 Copynumber: 4.4 Consensus size: 62
23824796 TTTCTCGCTA
* * * *
23824806 CGGCGAGAATCAATTTGGTTGCGACGAGAACAGTGACTCTCAAGATAAAAAGTTTGTCG-CAG
1 CGGCGAAAATCAATTTGGCTGCGACGAGAACAGTGACTCTTAAGATAAAAAGTTTCTCGTC-G
* * * *
23824868 CGGCGAAAATCAATTTGGCTACAACGAGAATAGTGACTCTTAAGATAGAAAGTTTCTCGTCG
1 CGGCGAAAATCAATTTGGCTGCGACGAGAACAGTGACTCTTAAGATAAAAAGTTTCTCGTCG
* * * * *
23824930 CAGTGAAAATCAATTTGGCTG-TAGCGAGAACAATGACTCTTAAGATGAAAAGTTTCTCGTCG
1 CGGCGAAAATCAATTTGGCTGCGA-CGAGAACAGTGACTCTTAAGATAAAAAGTTTCTCGTCG
* * * * **
23824992 TGGCGAAAATCAATTTGGCTGCTG-TGAGAACAGTGACTCTTAAGACAGAAAGTTTCTCACCG
1 CGGCGAAAATCAATTTGGCTGC-GACGAGAACAGTGACTCTTAAGATAAAAAGTTTCTCGTCG
***
23825054 TAACGAAAATCAATTTGGCTGCGACG
1 CGGCGAAAATCAATTTGGCTGCGACG
23825080 GGTGTTGGTC
Statistics
Matches: 177, Mismatches: 30, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
61 2 0.01
62 174 0.98
63 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (62 bp):
CGGCGAAAATCAATTTGGCTGCGACGAGAACAGTGACTCTTAAGATAAAAAGTTTCTCGTCG
Found at i:23825449 original size:67 final size:66
Alignment explanation
Indices: 23825332--23825509 Score: 223
Period size: 67 Copynumber: 2.7 Consensus size: 66
23825322 TACCAGGTTT
* * * *
23825332 AACCAAAACCTTTCATAATAGTTTTTACTGGGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 AACCACAACCTTTCACAATGGTTTTT-CTGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
23825397 TC
65 TC
* * *
23825399 AATCACAACCTTTCACAATGGTTTTTCGTGGGCTCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
1 AACCACAACCTTTCACAATGGTTTTTC-TGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
23825464 TC
65 TC
* * *
23825466 AACCACAACC-TACAACAATGGTTTTTCACGAGATCAACCAAAAC
1 AACCACAACCTTTC-ACAATGGTTTTTC-TGGGATCAACCAAAAC
23825510 TCAACAACTA
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
66 3 0.03
67 93 0.97
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.27
Consensus pattern (66 bp):
AACCACAACCTTTCACAATGGTTTTTCTGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCT
C
Found at i:23825465 original size:32 final size:32
Alignment explanation
Indices: 23825365--23825477 Score: 111
Period size: 32 Copynumber: 3.4 Consensus size: 32
23825355 TTTACTGGGA
* *
23825365 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
* * ***
23825397 TCAATCACAACCTTTCACAA-TGGTTTTTCGTGGGC
1 TCAACCAAAACC--T-A-AAGTGGTTTTTCAAAGGC
23825432 TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
*
23825464 TCAACCACAACCTA
1 TCAACCAAAACCTA
23825478 CAACAATGGT
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
31 2 0.03
32 35 0.56
33 1 0.02
35 23 0.37
36 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (32 bp):
TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
Found at i:23827222 original size:35 final size:35
Alignment explanation
Indices: 23827143--23827305 Score: 157
Period size: 35 Copynumber: 4.6 Consensus size: 35
23827133 AACCTAGCTT
* *
23827143 ATGCACACTCCCACACCGCACATA-GCTAATGTCATC
1 ATGCGCACTCCCACACCGCACA-AGGC-AATATCATC
*
23827179 ATGTGCACTCCCACACCGCACAAGGCAATATCATC
1 ATGCGCACTCCCACACCGCACAAGGCAATATCATC
**** * *
23827214 ATGCGCACTCCCACACCGCACCTCACCATCACCATC
1 ATGCGCACTCCCACACCGCACAAGGCAAT-ATCATC
* ** * *
23827250 ATGTGCACTCTTACACTGCACACGGCAATATCATC
1 ATGCGCACTCCCACACCGCACAAGGCAATATCATC
*
23827285 ATGCGCACTCCCACATCGCAC
1 ATGCGCACTCCCACACCGCAC
23827306 CTCACCATCA
Statistics
Matches: 100, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
35 53 0.53
36 47 0.47
ACGTcount: A:0.28, C:0.41, G:0.12, T:0.18
Consensus pattern (35 bp):
ATGCGCACTCCCACACCGCACAAGGCAATATCATC
Found at i:23827339 original size:71 final size:71
Alignment explanation
Indices: 23827175--23827342 Score: 257
Period size: 71 Copynumber: 2.4 Consensus size: 71
23827165 TAGCTAATGT
* *
23827175 CATCATGTGCACTCCCACACCGCACAAGGCAATATCATCATGCGCACTCCCACACCGCACCTCAC
1 CATCATGTGCACTTCCACACTGCACAAGGCAATATCATCATGCGCACTCCCACACCGCACCTCAC
23827240 CATCAC
66 CATCAC
* * *
23827246 CATCATGTGCAC-TCTTACACTGCACACGGCAATATCATCATGCGCACTCCCACATCGCACCTCA
1 CATCATGTGCACTTC-CACACTGCACAAGGCAATATCATCATGCGCACTCCCACACCGCACCTCA
23827310 CCATCAC
65 CCATCAC
* *
23827317 CGTCATGTGCACTTCCATACTGCACA
1 CATCATGTGCACTTCCACACTGCACA
23827343 TGCACAGTTG
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
70 1 0.01
71 84 0.97
72 2 0.02
ACGTcount: A:0.27, C:0.42, G:0.12, T:0.20
Consensus pattern (71 bp):
CATCATGTGCACTTCCACACTGCACAAGGCAATATCATCATGCGCACTCCCACACCGCACCTCAC
CATCAC
Found at i:23833743 original size:69 final size:74
Alignment explanation
Indices: 23833641--23833829 Score: 196
Period size: 77 Copynumber: 2.6 Consensus size: 74
23833631 AAGAAAGTTT
* *
23833641 AATGCTATCACATAACTTTA-GAATTTTCTTTTAAAATAGGAAAC-TA-T-TTC-CAATGAATT-
1 AATGCTATC-CTTAATTTTAGGAA-TTTCTTTTAAAATAGGAAACATACTATTCTCAATGAATTA
23833700 TCTC-AAATTAA
64 TC-CAAAATTAA
* **
23833711 AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGGAAACAATTTACTATTCTTTATGAATT
1 AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAATAGGAAAC-A--TACTATTCTCAATGAATT
23833776 ATCCAAAATTAA
63 ATCCAAAATTAA
* *
23833788 AATTCTATCCTTAATTTTAGGAATTGC-TTTAAAAGTAGGAAA
1 AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAA-TAGGAAA
23833830 TAATTTCTTA
Statistics
Matches: 100, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
69 27 0.27
70 12 0.12
73 2 0.02
74 1 0.01
75 3 0.03
76 14 0.14
77 41 0.41
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (74 bp):
AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAATAGGAAACATACTATTCTCAATGAATTATC
CAAAATTAA
Found at i:23833796 original size:77 final size:77
Alignment explanation
Indices: 23833704--23833867 Score: 251
Period size: 77 Copynumber: 2.1 Consensus size: 77
23833694 TGAATTTCTC
* *
23833704 AAATTAAAATGCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGGAAACAATTTAC-TATTCTT
1 AAATTAAAATGCTATCCTTAATTTTAGGAATTGCTTTAAAAGTAGGAAACAATTT-CTTATTCTT
*
23833768 TATGAATTA-TCCA
65 TATGAATCACT-CA
* *
23833781 AAATTAAAATTCTATCCTTAATTTTAGGAATTGCTTTAAAAGTAGGAAATAATTTCTTATTCTTT
1 AAATTAAAATGCTATCCTTAATTTTAGGAATTGCTTTAAAAGTAGGAAACAATTTCTTATTCTTT
23833846 ATGAATCACTCA
66 ATGAATCACTCA
23833858 AAATTAAAAT
1 AAATTAAAAT
23833868 AGGTGACATT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
76 1 0.01
77 78 0.98
78 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.41
Consensus pattern (77 bp):
AAATTAAAATGCTATCCTTAATTTTAGGAATTGCTTTAAAAGTAGGAAACAATTTCTTATTCTTT
ATGAATCACTCA
Found at i:23835252 original size:20 final size:20
Alignment explanation
Indices: 23835207--23835244 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
23835197 TTTTGGCCCC
23835207 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
23835227 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
23835245 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:23849032 original size:49 final size:52
Alignment explanation
Indices: 23848976--23849171 Score: 231
Period size: 55 Copynumber: 3.7 Consensus size: 52
23848966 TAACAGTGCG
* *
23848976 TGTGCGGTGTGGGAGTGCACATGCTAG-TGAT-AAC-GG-G-TGATTCCAGCTA
1 TGTGCGGTGTGGGAGTGCACATG--AGCTGATGACCGGGAGATGATTCCAACTA
23849025 TGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTAGATGATGATTCCAACTA
1 TGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGG--GA-GATGATTCCAACTA
* *
23849080 TGTACGGTGTGGGAGTGCACATGAGTTGATGACCGGTGGATGATGATTCCAACTA
1 TGTGCGGTGTGGGAGTGCACATGAGCTGATGACC-G-GGA-GATGATTCCAACTA
*
23849135 TGTGCGGTGTGGGAGTGCACATGAGCTAATGAGCCGG
1 TGTGCGGTGTGGGAGTGCACATGAGCTGATGA-CCGG
23849172 TAGTTGTATA
Statistics
Matches: 129, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
47 2 0.02
48 4 0.03
49 25 0.19
50 1 0.01
52 1 0.01
54 2 0.02
55 90 0.70
56 3 0.02
57 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.26
Consensus pattern (52 bp):
TGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGGAGATGATTCCAACTA
Found at i:23849074 original size:55 final size:55
Alignment explanation
Indices: 23849013--23849174 Score: 270
Period size: 55 Copynumber: 2.9 Consensus size: 55
23849003 TGATAACGGG
*
23849013 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTAGATGA
1 TGATTCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTAGATGA
* * *
23849068 TGATTCCAACTATGTACGGTGTGGGAGTGCACATGAGTTGATGACCGGTGGATGA
1 TGATTCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTAGATGA
*
23849123 TGATTCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTAATGAGCCGGTAG
1 TGATTCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTGATGA-CCGGTAG
23849175 TTGTATACAT
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 92 0.94
56 6 0.06
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (55 bp):
TGATTCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTAGATGA
Found at i:23854344 original size:11 final size:11
Alignment explanation
Indices: 23854330--23854359 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
23854320 AATAATATTT
23854330 TATTAATAAAA
1 TATTAATAAAA
*
23854341 TATTATTAAAA
1 TATTAATAAAA
23854352 TATTAATA
1 TATTAATA
23854360 TTTAGCCGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:23861060 original size:13 final size:13
Alignment explanation
Indices: 23861042--23861066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23861032 TTCCAAAAAA
23861042 TTTATAAAATCAG
1 TTTATAAAATCAG
23861055 TTTATAAAATCA
1 TTTATAAAATCA
23861067 TAATTTCTCC
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:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTATAAAATCAG
Found at i:23865322 original size:21 final size:23
Alignment explanation
Indices: 23865296--23865343 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
23865286 TCCTAGGTGG
*
23865296 AAAAATTCAAGGGAA-AAGT-AT
1 AAAAATTCAAGGAAACAAGTGAT
23865317 AAAAATTCAAGGAAACAAGTGAT
1 AAAAATTCAAGGAAACAAGTGAT
23865340 AAAA
1 AAAA
23865344 GGTAAGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.58
22 4 0.17
23 6 0.25
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (23 bp):
AAAAATTCAAGGAAACAAGTGAT
Found at i:23869965 original size:15 final size:16
Alignment explanation
Indices: 23869945--23869987 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
23869935 ACATTAAATT
*
23869945 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
23869960 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
23869977 AAAATAACTAA
1 AAAATAACTAA
23869988 AAATAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:23874614 original size:20 final size:20
Alignment explanation
Indices: 23874589--23874632 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
23874579 CATTTCCTAA
23874589 GCTCCAATCCAATCCAAATG
1 GCTCCAATCCAATCCAAATG
23874609 GCTCCAATCCAATCCAAATG
1 GCTCCAATCCAATCCAAATG
23874629 GCTC
1 GCTC
23874633 TAAAAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.36, G:0.11, T:0.20
Consensus pattern (20 bp):
GCTCCAATCCAATCCAAATG
Found at i:23877064 original size:36 final size:37
Alignment explanation
Indices: 23877016--23877087 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
23877006 ATTGAAAAGA
23877016 TTCAATACAATGCATTCT-ATGGATC-AAGCACAACCT
1 TTCAATACAATGCATTCTCATGG-TCAAAGCACAACCT
* *
23877052 TTCAATATAATGCCTTCTCATGGTCAAAGCACAACC
1 TTCAATACAATGCATTCTCATGGTCAAAGCACAACC
23877088 ACTCTACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (37 bp):
TTCAATACAATGCATTCTCATGGTCAAAGCACAACCT
Found at i:23887192 original size:43 final size:43
Alignment explanation
Indices: 23887134--23887260 Score: 157
Period size: 43 Copynumber: 3.0 Consensus size: 43
23887124 TGTGATAATA
* *
23887134 ATGATCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
1 ATGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
* ** *
23887177 ATGACCCAATTATGTGCGGTGTGGGAGTGCACATGAATTAATG
1 ATGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
** *
23887220 ATGACCCGGCTATGTGCGAGT-AGGGAGTGCACATGAGCTGA
1 ATGACCCAACTATGTGCG-GTGTGGGAGTGCACATGAGCTGA
23887261 GTGTGGCGGG
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
43 68 0.97
44 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (43 bp):
ATGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
Found at i:23893992 original size:63 final size:63
Alignment explanation
Indices: 23893911--23894047 Score: 220
Period size: 63 Copynumber: 2.2 Consensus size: 63
23893901 TCGGGTCGTG
* * *
23893911 ACATGCACGGTTGCAATTGTCACAACATTGTCATTCAACCAGCATGTGCACTGTCCACTCTGC
1 ACATGCACGGTCGCAATTGTCACAACATTGTCATTCAACCAGCATGTGCACTGCCCACTATGC
* * *
23893974 ACATGCACGGTCGTAATTGTCACAACATTGTCATTCAATCGGCATGTGCACTGCCCACTATGC
1 ACATGCACGGTCGCAATTGTCACAACATTGTCATTCAACCAGCATGTGCACTGCCCACTATGC
23894037 ACATGCACGGT
1 ACATGCACGGT
23894048 TACATCAATT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (63 bp):
ACATGCACGGTCGCAATTGTCACAACATTGTCATTCAACCAGCATGTGCACTGCCCACTATGC
Found at i:23894686 original size:23 final size:23
Alignment explanation
Indices: 23894640--23894687 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23894630 TTTCTAAATA
* *
23894640 ATTTCCACCCAAATCCATCTTAT
1 ATTTCCACACAAATCCATCATAT
23894663 ATTTCCACACATAATCCA-CATAT
1 ATTTCCACACA-AATCCATCATAT
23894686 AT
1 AT
23894688 GGTAGCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTTCCACACAAATCCATCATAT
Found at i:23911204 original size:2 final size:2
Alignment explanation
Indices: 23911197--23911268 Score: 99
Period size: 2 Copynumber: 36.0 Consensus size: 2
23911187 GCACTTGTTG
* * * * *
23911197 AT AT AT AT AT AT AT AT AT AT GT GT GT GT GT 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
23911239 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
23911269 NATAAGCAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23911323 original size:2 final size:2
Alignment explanation
Indices: 23911312--23911353 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
23911302 GTTGTTTGTG
*
23911312 TA TA -A TA TA TA TA TA TA TA TA TA AA TA TA TA TA T- 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
23911352 TA
1 TA
23911354 ATGCTTGAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23913177 original size:35 final size:35
Alignment explanation
Indices: 23913138--23913246 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
23913128 GTTGATCCCG
*
23913138 TGAAAAACCATTGTTGTAGGTTGTGGTTAAGCCTT
1 TGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTT
* * * **
23913173 TGAAAAATCACT-TTG--GGTTTTGGTTGAGCCCA
1 TGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTT
23913205 TGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTT
1 TGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTT
23913240 TGAAAAA
1 TGAAAAA
23913247 TCACTTTGGG
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
32 23 0.38
33 3 0.05
34 3 0.05
35 31 0.52
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.35
Consensus pattern (35 bp):
TGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTT
Found at i:23913196 original size:67 final size:67
Alignment explanation
Indices: 23913118--23913258 Score: 255
Period size: 67 Copynumber: 2.1 Consensus size: 67
23913108 AAGTTAATTG
* *
23913118 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTGTAGGTTGTGGTTAAGCCTTTGAAAAATCA
1 TTGGGTTTTGGTTGAGCCCATGAAAAACCATTGTTGTAGGTTGTGGTTAAGCCTTTGAAAAATCA
23913183 CT
66 CT
*
23913185 TTGGGTTTTGGTTGAGCCCATGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAATCA
1 TTGGGTTTTGGTTGAGCCCATGAAAAACCATTGTTGTAGGTTGTGGTTAAGCCTTTGAAAAATCA
23913250 CT
66 CT
23913252 TTGGGTT
1 TTGGGTT
23913259 ATAATTGATC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.38
Consensus pattern (67 bp):
TTGGGTTTTGGTTGAGCCCATGAAAAACCATTGTTGTAGGTTGTGGTTAAGCCTTTGAAAAATCA
CT
Found at i:23913209 original size:32 final size:33
Alignment explanation
Indices: 23913116--23913258 Score: 128
Period size: 35 Copynumber: 4.3 Consensus size: 33
23913106 AAAAGTTAAT
* * * *
23913116 TGTTGGGTTTTGGTTGATCCCGTGAAAAACCAT
1 TGTTGGGTTGTGGTTGAGCCCTTGAAAAACCAC
* * *
23913149 TGTTGTAGGTTGTGGTTAAGCCTTTGAAAAATCAC
1 TGTTG--GGTTGTGGTTGAGCCCTTGAAAAACCAC
* * *
23913184 T-TTGGGTTTTGGTTGAGCCCATGAAAAACCAT
1 TGTTGGGTTGTGGTTGAGCCCTTGAAAAACCAC
* *
23913216 TGTTGTAGGTTGTGGTTGAGCCTTTGAAAAATCAC
1 TGTTG--GGTTGTGGTTGAGCCCTTGAAAAACCAC
23913251 T-TTGGGTT
1 TGTTGGGTT
23913259 ATAATTGATC
Statistics
Matches: 87, Mismatches: 18, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
32 27 0.31
33 8 0.09
34 6 0.07
35 46 0.53
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (33 bp):
TGTTGGGTTGTGGTTGAGCCCTTGAAAAACCAC
Found at i:23920624 original size:17 final size:17
Alignment explanation
Indices: 23920602--23920636 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
23920592 AAGTAAAATA
23920602 AACACACACTAAGGGGG
1 AACACACACTAAGGGGG
*
23920619 AACACACACTTAGGGGG
1 AACACACACTAAGGGGG
23920636 A
1 A
23920637 GCAATCCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.29, T:0.09
Consensus pattern (17 bp):
AACACACACTAAGGGGG
Found at i:23921566 original size:35 final size:35
Alignment explanation
Indices: 23921521--23921637 Score: 107
Period size: 35 Copynumber: 3.4 Consensus size: 35
23921511 TTAGTTGTTG
* *
23921521 GGTTTTGGTTGATCTCATTAAAAACCATTGTTGTA
1 GGTTATGGTTGAGCTCATTAAAAACCATTGTTGTA
* * *
23921556 GGTTATGGTTGAGC-CTTTGAAAAACTACT-TTG--
1 GGTTATGGTTGAGCTCATT-AAAAACCATTGTTGTA
* * * * *
23921588 GGTTTTGGTTAAGCTCGTGAAAAACCATTGTTTTA
1 GGTTATGGTTGAGCTCATTAAAAACCATTGTTGTA
23921623 GGTTATGGTTGAGCT
1 GGTTATGGTTGAGCT
23921638 TTTGAAAACC
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
32 20 0.32
33 4 0.06
34 6 0.10
35 33 0.52
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (35 bp):
GGTTATGGTTGAGCTCATTAAAAACCATTGTTGTA
Found at i:23921597 original size:67 final size:67
Alignment explanation
Indices: 23921518--23921685 Score: 212
Period size: 67 Copynumber: 2.5 Consensus size: 67
23921508 AAATTAGTTG
*
23921518 TTGGGTTTTGGTTGATCTCATTAAAAACCATTGTTGTAGGTTATGGTTGAGCCTTTGAAAAACTA
1 TTGGGTTTTGGTTGATCTCATTAAAAACCATTGTTGTAGGTTATGGTTGAGCCTTTGAAAAACCA
23921583 CT
66 CT
* * * * * * *
23921585 TTGGGTTTTGGTTAAGCTCGTGAAAAACCATTGTTTTAGGTTATGGTTGAGCTTTTGAAAACCCA
1 TTGGGTTTTGGTTGATCTCATTAAAAACCATTGTTGTAGGTTATGGTTGAGCCTTTGAAAAACCA
*
23921650 TT
66 CT
* * *
23921652 TTGGGTTTTAGTTGATCCCGA-TAAAAACTATTGT
1 TTGGGTTTTGGTTGATCTC-ATTAAAAACCATTGT
23921686 GAAAGGTTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 84 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (67 bp):
TTGGGTTTTGGTTGATCTCATTAAAAACCATTGTTGTAGGTTATGGTTGAGCCTTTGAAAAACCA
CT
Found at i:23921644 original size:35 final size:35
Alignment explanation
Indices: 23921540--23921651 Score: 113
Period size: 35 Copynumber: 3.3 Consensus size: 35
23921530 TGATCTCATT
* *
23921540 AAAAACCATTGTTGTAGGTTATGGTTGAGCCTTTG
1 AAAAACCATTGTTTTAGGTTATGGTTGAGCTTTTG
** * * * **
23921575 AAAAA-C--TACTTTGGGTTTTGGTTAAGCTCGTG
1 AAAAACCATTGTTTTAGGTTATGGTTGAGCTTTTG
23921607 AAAAACCATTGTTTTAGGTTATGGTTGAGCTTTTG
1 AAAAACCATTGTTTTAGGTTATGGTTGAGCTTTTG
*
23921642 AAAACCCATT
1 AAAAACCATT
23921652 TTGGGTTTTA
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
32 22 0.39
33 1 0.02
34 1 0.02
35 33 0.58
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (35 bp):
AAAAACCATTGTTTTAGGTTATGGTTGAGCTTTTG
Found at i:23929918 original size:39 final size:39
Alignment explanation
Indices: 23929862--23929941 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
23929852 TCGCTGTAGT
23929862 GAAATTGTAACCCAGAAACAAAAAGTTTCTCACTACAGC
1 GAAATTGTAACCCAGAAACAAAAAGTTTCTCACTACAGC
* *
23929901 GAAATTGTAACCTAGAAACAAAAAGTTTCTCACTGCAGC
1 GAAATTGTAACCCAGAAACAAAAAGTTTCTCACTACAGC
23929940 GA
1 GA
23929942 GAAGCTACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (39 bp):
GAAATTGTAACCCAGAAACAAAAAGTTTCTCACTACAGC
Found at i:23930339 original size:43 final size:44
Alignment explanation
Indices: 23930287--23930404 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 44
23930277 TCACCAGCTC
* * **
23930287 ATGCACACTCCCTACTCGCACATGGCTGGA-TCATCATCGGGTT
1 ATGCGCACTCCCTACTCGCACATAGCTGGAGTCATCATCGACTT
* * *
23930330 ATGCGCACTCCCTACTCGCACATAAC-CGAGTCATCCTCGACTT
1 ATGCGCACTCCCTACTCGCACATAGCTGGAGTCATCATCGACTT
23930373 ATGCGCACTCCCTACTCGCACATAGCT-GAGTC
1 ATGCGCACTCCCTACTCGCACATAGCTGGAGTC
23930405 TATGTCATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
42 2 0.03
43 63 0.97
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (44 bp):
ATGCGCACTCCCTACTCGCACATAGCTGGAGTCATCATCGACTT
Found at i:23937431 original size:43 final size:43
Alignment explanation
Indices: 23937380--23937489 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 43
23937370 TCACCAGCTC
* ** * * *
23937380 ATGCGCACTCCCTACTCGCACATGGCTAGGTCATCATCGGGTT
1 ATGCGCACTCCCTACTCGAACATAACCAAGTCATCATCGGCTT
* * *
23937423 ATGTGCACTCCCTACTCGTACATAACCAAGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGAACATAACCAAGTCATCATCGGCTT
23937466 ATGCGCACTCCCTACTCGAACATA
1 ATGCGCACTCCCTACTCGAACATA
23937490 GCCGAGTCTA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGAACATAACCAAGTCATCATCGGCTT
Found at i:23939119 original size:11 final size:11
Alignment explanation
Indices: 23939086--23939122 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23939076 GATCAGTTGG
23939086 AAGAAATGAGA
1 AAGAAATGAGA
*
23939097 AAGGAA--AGA
1 AAGAAATGAGA
23939106 AAGAAATGAGA
1 AAGAAATGAGA
23939117 AAGAAA
1 AAGAAA
23939123 AAGAGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (11 bp):
AAGAAATGAGA
Found at i:23944429 original size:15 final size:15
Alignment explanation
Indices: 23944409--23944439 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
23944399 TTGCGTGTTT
23944409 TGTTGCAATTTTTGG
1 TGTTGCAATTTTTGG
23944424 TGTTGCAATTTTTGG
1 TGTTGCAATTTTTGG
23944439 T
1 T
23944440 TTTTATTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.06, G:0.26, T:0.55
Consensus pattern (15 bp):
TGTTGCAATTTTTGG
Found at i:23944626 original size:26 final size:26
Alignment explanation
Indices: 23944597--23944936 Score: 314
Period size: 26 Copynumber: 14.0 Consensus size: 26
23944587 TTTGTGCTTG
* *
23944597 GTTTTTGATAAGGTATTGTGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
23944623 GTTTTTGATAAGTCATTGCGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
23944649 GTTTCTGATAAGGCATTGCGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
23944675 G---TTGAT-AGGCATTGCGTAACT-
1 GTTTTTGATAAGGCATTGCGTGACTA
** * *
23944696 GACTTTG----GGTATTACGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
23944718 GTTTTTGATAAGGCATTGCATGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
23944744 GTTTCTGATAAGGCATTGCGTGACT-
1 GTTTTTGATAAGGCATTGCGTGACTA
* *
23944769 -TACTTTG---A-GAATTGCGTGACTA
1 GT-TTTTGATAAGGCATTGCGTGACTA
*
23944791 GTTTTTGATAAGGCATTGCATGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
* *
23944817 GTTTCTGATAAGGCATTACGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
23944843 G---TTGATAA-GCATTGCGTGACT-
1 GTTTTTGATAAGGCATTGCGTGACTA
**
23944864 G-ACTT--T-AGGCATTGCGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
23944886 GTTTTTGATAAGGCATTGCATGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
* *
23944912 GTTTCTGATAAGGCATTGTGTGACT
1 GTTTTTGATAAGGCATTGCGTGACT
23944937 TACTTTAGGA
Statistics
Matches: 257, Mismatches: 34, Indels: 46
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.00
21 39 0.15
22 37 0.14
23 15 0.06
24 4 0.02
25 5 0.02
26 156 0.61
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (26 bp):
GTTTTTGATAAGGCATTGCGTGACTA
Found at i:23944894 original size:168 final size:167
Alignment explanation
Indices: 23944611--23945079 Score: 609
Period size: 168 Copynumber: 2.8 Consensus size: 167
23944601 TTGATAAGGT
*
23944611 ATTGTGTGACTAGTTTTTGATAAGTCATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAG
1 ATTGCGTGACTAGTTTTTGATAAGTCATTGC-TGACTAGTTTCTGATAAGGCATTGCGTGACTAG
* * * * *
23944676 TTGATAGGCATTGCGTAACTGACTTTGGGTATTACGTGACTAGTTTTTGATAAGGCATTGCATGA
65 TTGATAAGCATTGCGTGACTGACTTTAGGCATTGCGTGACTAGTTTTTGATAAGGCATTGCATGA
23944741 CTAGTTTCTGATAAGGCATTGCGTGACTTACTTT-GAGA
130 CTAGTTTCTGATAAGGCATTGCGTGACTTACTTTAG-GA
* *
23944779 ATTGCGTGACTAGTTTTTGATAAGGCATTGCATGACTAGTTTCTGATAAGGCATTACGTGACTAG
1 ATTGCGTGACTAGTTTTTGATAAGTCATTGC-TGACTAGTTTCTGATAAGGCATTGCGTGACTAG
23944844 TTGATAAGCATTGCGTGACTGACTTTAGGCATTGCGTGACTAGTTTTTGATAAGGCATTGCATGA
65 TTGATAAGCATTGCGTGACTGACTTTAGGCATTGCGTGACTAGTTTTTGATAAGGCATTGCATGA
*
23944909 CTAGTTTCTGATAAGGCATTGTGTGACTTACTTTAGGA
130 CTAGTTTCTGATAAGGCATTGCGTGACTTACTTTAGGA
* ** * *
23944947 ATTGCATGACT-GACTTTG-TGAA-TTA-TG-TGACTAGTTTTTGATAAGGCATTGCGTGACTAG
1 ATTGCGTGACTAGTTTTTGAT-AAGTCATTGCTGACTAGTTTCTGATAAGGCATTGCGTGACTAG
* *
23945007 TTTCTGATAAGGCATTGCATGACT-AGTTGATAGGCATTGCGTGAC---TTTTT-ATTAAGGCAT
65 --T-TGATAA-GCATTGCGTGACTGACTT--TAGGCATTGCGTGACTAGTTTTTGA-TAAGGCAT
*
23945067 TGCGTGACTAGTT
123 TGCATGACTAGTT
23945080 AGTAAAGAAT
Statistics
Matches: 272, Mismatches: 20, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
163 31 0.11
164 1 0.00
165 28 0.10
166 11 0.04
167 19 0.07
168 181 0.67
169 1 0.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (167 bp):
ATTGCGTGACTAGTTTTTGATAAGTCATTGCTGACTAGTTTCTGATAAGGCATTGCGTGACTAGT
TGATAAGCATTGCGTGACTGACTTTAGGCATTGCGTGACTAGTTTTTGATAAGGCATTGCATGAC
TAGTTTCTGATAAGGCATTGCGTGACTTACTTTAGGA
Found at i:23945064 original size:45 final size:48
Alignment explanation
Indices: 23944601--23945079 Score: 226
Period size: 47 Copynumber: 10.0 Consensus size: 48
23944591 TGCTTGGTTT
* * * * *
23944601 TTGATAAGGTATTGTGTGACTAGTTTTTGATAAGTCATTGCGTGACTAG
1 TTGATAAGGCATTGCGTGACTA-TTTCTGATAAGGCATTGCATGACTAG
* * * *
23944650 TTTCTGATAAGGCATTGCGTGACTA-GT-TGAT-AGGCATTGCGTAACTGAC
1 --T-TGATAAGGCATTGCGTGACTATTTCTGATAAGGCATTGCATGACT-AG
* * * *
23944699 TT--T-GGGTATTACGTGACTAGTTTTTGATAAGGCATTGCATGACTAG
1 TTGATAAGGCATTGCGTGACTA-TTTCTGATAAGGCATTGCATGACTAG
* * *
23944745 TTTCTGATAAGGCATTGCGTGACTTACTT-TG---A-GAATTGCGTGACTAG
1 --T-TGATAAGGCATTGCGTGAC-TATTTCTGATAAGGCATTGCATGACTAG
* * *
23944792 TTTTTGATAAGGCATTGCATGACTAGTTTCTGATAAGGCATTACGTGACTAG
1 ---TTGATAAGGCATTGCGTGACTA-TTTCTGATAAGGCATTGCATGACTAG
* *
23944844 TTGATAA-GCATTGCGTGACTGA---CT--TTAGGCATTGCGTGACTAG
1 TTGATAAGGCATTGCGTGACT-ATTTCTGATAAGGCATTGCATGACTAG
* ** *
23944887 TTTTTGATAAGGCATTGCATGACTAGTTTCTGATAAGGCATTGTGTGACTTAC
1 ---TTGATAAGGCATTGCGTGACTA-TTTCTGATAAGGCATTGCATGAC-TAG
* * * **
23944940 TT--T-AGGAATTGCATGACTGACTT-TG-TGAA-TTA-TG--TGACTAG
1 TTGATAAGGCATTGCGTGACT-ATTTCTGAT-AAGGCATTGCATGACTAG
23944981 TTTTTGATAAGGCATTGCGTGACTAGTTTCTGATAAGGCATTGCATGACTAG
1 ---TTGATAAGGCATTGCGTGACTA-TTTCTGATAAGGCATTGCATGACTAG
*
23945033 TTGAT-AGGCATTGCGTGACT-TTT-T-ATTAAGGCATTGCGTGACTAG
1 TTGATAAGGCATTGCGTGACTATTTCTGA-TAAGGCATTGCATGACTAG
23945078 TT
1 TT
23945080 AGTAAAGAAT
Statistics
Matches: 339, Mismatches: 41, Indels: 102
0.70 0.09 0.21
Matches are distributed among these distances:
41 2 0.01
42 4 0.01
43 30 0.09
44 6 0.02
45 26 0.08
46 25 0.07
47 90 0.27
48 53 0.16
49 21 0.06
50 7 0.02
51 5 0.01
52 66 0.19
53 4 0.01
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (48 bp):
TTGATAAGGCATTGCGTGACTATTTCTGATAAGGCATTGCATGACTAG
Found at i:23945068 original size:23 final size:23
Alignment explanation
Indices: 23944599--23945076 Score: 202
Period size: 26 Copynumber: 20.0 Consensus size: 23
23944589 TGTGCTTGGT
* *
23944599 TTTTGATAAGGTATTGTGTGACTA
1 TTTT-ATAAGGCATTGCGTGACTA
*
23944623 GTTTTTGATAAGTCATTGCGTGACTA
1 --TTTT-ATAAGGCATTGCGTGACTA
23944649 GTTTCTGATAAGGCATTGCGTGACTA
1 -TTT-T-ATAAGGCATTGCGTGACTA
* * *
23944675 GTTGAT-AGGCATTGCGTAACTGA
1 TTTTATAAGGCATTGCGTGACT-A
* * * *
23944698 -CTT-T-GGGTATTACGTGACTA
1 TTTTATAAGGCATTGCGTGACTA
*
23944718 GTTTTTGATAAGGCATTGCATGACTA
1 --TTTT-ATAAGGCATTGCGTGACTA
23944744 GTTTCTGATAAGGCATTGCGTGACT-
1 -TTT-T-ATAAGGCATTGCGTGACTA
* * *
23944769 TACTT-TGA-GAATTGCGTGACTA
1 T-TTTATAAGGCATTGCGTGACTA
*
23944791 GTTTTTGATAAGGCATTGCATGACTA
1 --TTTT-ATAAGGCATTGCGTGACTA
*
23944817 GTTTCTGATAAGGCATTACGTGACTA
1 -TTT-T-ATAAGGCATTGCGTGACTA
* *
23944843 GTTGATAA-GCATTGCGTGACTGA
1 TTTTATAAGGCATTGCGTGACT-A
*
23944866 -CTT-T-AGGCATTGCGTGACTA
1 TTTTATAAGGCATTGCGTGACTA
*
23944886 GTTTTTGATAAGGCATTGCATGACTA
1 --TTTT-ATAAGGCATTGCGTGACTA
*
23944912 GTTTCTGATAAGGCATTGTGTGACT-
1 -TTT-T-ATAAGGCATTGCGTGACTA
* * *
23944937 TACTT-T-AGGAATTGCATGACTGA
1 T-TTTATAAGGCATTGCGTGACT-A
* * * **
23944960 CTTTGT---GAATTATGTGACTA
1 TTTTATAAGGCATTGCGTGACTA
23944980 GTTTTTGATAAGGCATTGCGTGACTA
1 --TTTT-ATAAGGCATTGCGTGACTA
*
23945006 GTTTCTGATAAGGCATTGCATGACTA
1 -TTT-T-ATAAGGCATTGCGTGACTA
* *
23945032 GTTGAT-AGGCATTGCGTGACT-
1 TTTTATAAGGCATTGCGTGACTA
23945053 TTTTATTAAGGCATTGCGTGACTA
1 TTTTA-TAAGGCATTGCGTGACTA
23945077 GTTAGTAAAG
Statistics
Matches: 350, Mismatches: 62, Indels: 82
0.71 0.13 0.17
Matches are distributed among these distances:
20 4 0.01
21 63 0.18
22 51 0.15
23 33 0.09
24 5 0.01
25 27 0.08
26 167 0.48
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (23 bp):
TTTTATAAGGCATTGCGTGACTA
Found at i:23945912 original size:71 final size:70
Alignment explanation
Indices: 23945745--23945913 Score: 161
Period size: 71 Copynumber: 2.4 Consensus size: 70
23945735 CACATTAATG
**
23945745 TATAC-ATAT-AAAATGTA-TTAAGAAATAAAAATAAAATATTATCTTCTAAAGAAAAAATTTAA
1 TATACAATATAAAAAT-TATTTAA-AAATAAAAATAAAATATTATCTTCTAAAGAAAAAATGAAA
23945807 AATAAAA
64 AATAAAA
* * * *
23945814 TGTACAATATAAGAAATTATATTAAAAATAAAAATAAAATA-TATACTTGT-AATAAGAAATGAA
1 TATACAATATAA-AAATTAT-TTAAAAATAAAAATAAAATATTAT-CTTCTAAAGAAAAAATGAA
23945877 AAATAAAA
63 AAATAAAA
*
23945885 TATATTTAAT-TAAAAATATATTTAAAAAT
1 TATA--CAATATAAAAAT-TATTTAAAAAT
23945914 GACATTATAT
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
69 4 0.05
70 4 0.05
71 38 0.46
72 30 0.36
73 7 0.08
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (70 bp):
TATACAATATAAAAATTATTTAAAAATAAAAATAAAATATTATCTTCTAAAGAAAAAATGAAAAA
TAAAA
Found at i:23946119 original size:15 final size:15
Alignment explanation
Indices: 23946099--23946159 Score: 104
Period size: 15 Copynumber: 4.1 Consensus size: 15
23946089 TGTTATCTTC
23946099 CCTGCAATCACATTA
1 CCTGCAATCACATTA
23946114 CCTGCAATCACATTA
1 CCTGCAATCACATTA
23946129 CCTGCAATCACATTA
1 CCTGCAATCACATTA
**
23946144 CCTATAATCACATTA
1 CCTGCAATCACATTA
23946159 C
1 C
23946160 ATTGTAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.28
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:23948220 original size:17 final size:17
Alignment explanation
Indices: 23948200--23948240 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
23948190 AAAACAATAG
23948200 AAAATA-AAATGAAAAAC
1 AAAATAGAAA-GAAAAAC
23948217 AAAATAGAAAGAAAAAC
1 AAAATAGAAAGAAAAAC
23948234 AATAATA
1 AA-AATA
23948241 CCTTAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (17 bp):
AAAATAGAAAGAAAAAC
Done.