Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009637.1 Hibiscus syriacus cultivar Beakdansim tig00117046_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 867493
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:253612 original size:3 final size:3
Alignment explanation
Indices: 253606--253630 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
253596 ATGATGATGA
253606 TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG T
253631 AGAGATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:255208 original size:12 final size:12
Alignment explanation
Indices: 255191--255231 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
255181 ATAAAATTTC
255191 AATTGCTTTCCT
1 AATTGCTTTCCT
255203 AATTGCTTTCCT
1 AATTGCTTTCCT
255215 AATTGCTTT-CT
1 AATTGCTTTCCT
255226 AATTGC
1 AATTGC
255232 CTTCAATTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.49
Consensus pattern (12 bp):
AATTGCTTTCCT
Found at i:272899 original size:17 final size:17
Alignment explanation
Indices: 272874--272913 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
272864 GTATGTTGTT
*
272874 CATTAAAGCATGCATTA
1 CATTTAAGCATGCATTA
* *
272891 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTA
272908 CATTTA
1 CATTTA
272914 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTA
Found at i:275164 original size:18 final size:18
Alignment explanation
Indices: 275141--275183 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
275131 GATACCCGAT
*
275141 TATGTGTTTCGAGTCATA
1 TATGTGATTCGAGTCATA
275159 TATGTGATTCGAGTCATA
1 TATGTGATTCGAGTCATA
275177 TATGTGA
1 TATGTGA
275184 ATGCCCGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (18 bp):
TATGTGATTCGAGTCATA
Found at i:276561 original size:18 final size:18
Alignment explanation
Indices: 276519--276564 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
276509 TAGTTTGATT
*
276519 AATGAAATAACATTTTTC
1 AATGAACTAACATTTTTC
276537 AATGAACTAAC-TTTATTC
1 AATGAACTAACATTT-TTC
276555 AATGAACTAA
1 AATGAACTAA
276565 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (18 bp):
AATGAACTAACATTTTTC
Found at i:276640 original size:17 final size:17
Alignment explanation
Indices: 276620--276661 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
276610 ACTACTTCCC
276620 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
276637 TAAATGTAATGCATGCT
1 TAAATGAAATACATGCT
*
276654 TTAATGAA
1 TAAATGAA
276662 CAACATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:278597 original size:38 final size:37
Alignment explanation
Indices: 278524--278869 Score: 222
Period size: 37 Copynumber: 9.4 Consensus size: 37
278514 CATTTACTTT
* * * *
278524 TATATTATATGTAT-TTTTCAAAAACGTTTAAAAAAAAC
1 TATATAATATATATATTTTCAAAAATGTTT--TAAAAAC
* *
278562 TATATAATATATATATTTTCTAAAATGTTTTAAAAAAAT
1 TATATAATATATATATTTTCAAAAATGTTTT--AAAAAC
* * *
278601 TATATATTATATATA-TTTCAAAAACGTTTTTCAAAAGC
1 TATATAATATATATATTTTCAAAAATG-TTTT-AAAAAC
278639 --TAT-ATA-ATATA---T---AAATGTTTTAAAAAC
1 TATATAATATATATATTTTCAAAAATGTTTTAAAAAC
* * * *
278666 TATATATTATATAAATTTTCAAAAATGTTTTCAAAAT
1 TATATAATATATATATTTTCAAAAATGTTTTAAAAAC
* *
278703 TATATATTATATA-AGTTTTC-AAAATGATTTTAAAAAT
1 TATATAATATATATA-TTTTCAAAAATG-TTTTAAAAAC
* ** *
278740 TATATAGTATATATATTTTTTAAAATGTTTTAAAAAT
1 TATATAATATATATATTTTCAAAAATGTTTTAAAAAC
*
278777 TATAT-AT-TATATAGTTTTCAAAAATATTTTAAAAAC
1 TATATAATATATATA-TTTTCAAAAATGTTTTAAAAAC
* * * * *
278813 TACATATTATATATGTATTTTTAAAAACCG-TTTACAAAC
1 T--ATATAATATATATATTTTCAAAAA-TGTTTTAAAAAC
278852 TATAATATATATATATAT
1 TAT-ATA-ATATATATAT
278870 ATAAATATAT
Statistics
Matches: 248, Mismatches: 34, Indels: 51
0.74 0.10 0.15
Matches are distributed among these distances:
27 5 0.02
28 4 0.02
29 7 0.03
30 2 0.01
31 4 0.02
32 1 0.00
34 6 0.02
35 8 0.03
36 30 0.12
37 73 0.29
38 38 0.15
39 65 0.26
40 5 0.02
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (37 bp):
TATATAATATATATATTTTCAAAAATGTTTTAAAAAC
Found at i:278612 original size:37 final size:35
Alignment explanation
Indices: 278524--278826 Score: 237
Period size: 37 Copynumber: 8.3 Consensus size: 35
278514 CATTTACTTT
* * *
278524 TATATTATATGTATTTTTCAAAAACGTTTAAAAAAAACTA
1 TATATTATA--TA-TTTTCAAAAATGTTT--TAAAAATTA
*
278564 TATAATATATATATTTTCTAAAATGTTTTAAAAAAATTA
1 TAT-AT-TATATATTTTCAAAAATGTTTT--AAAAATTA
* **
278603 TATATTATATATATTTCAAAAACGTTTTTCAAAAGCTA
1 TATATTATATAT-TTTCAAAAATG-TTTT-AAAAATTA
*
278641 TATA--ATATA---T---AAATGTTTTAAAAACTA
1 TATATTATATATTTTCAAAAATGTTTTAAAAATTA
*
278668 TATATTATATAAATTTTCAAAAATGTTTTCAAAATTA
1 TATATTATAT--ATTTTCAAAAATGTTTTAAAAATTA
278705 TATATTATATAAGTTTTC-AAAATGATTTTAAAAATTA
1 TATATTATAT-A-TTTTCAAAAATG-TTTTAAAAATTA
**
278742 TATAGTATATATATTTTTTAAAATGTTTTAAAAATTA
1 TATA-T-TATATATTTTCAAAAATGTTTTAAAAATTA
* *
278779 TATATTATATAGTTTTCAAAAATATTTTAAAAACTA
1 TATATTATATA-TTTTCAAAAATGTTTTAAAAATTA
*
278815 CATATTATATAT
1 TATATTATATAT
278827 GTATTTTTAA
Statistics
Matches: 221, Mismatches: 20, Indels: 49
0.76 0.07 0.17
Matches are distributed among these distances:
27 11 0.05
28 4 0.02
29 8 0.04
31 1 0.00
32 1 0.00
34 1 0.00
35 7 0.03
36 44 0.20
37 72 0.33
38 29 0.13
39 32 0.14
40 5 0.02
41 2 0.01
42 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATTATATATTTTCAAAAATGTTTTAAAAATTA
Found at i:278658 original size:29 final size:27
Alignment explanation
Indices: 278628--278690 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
278618 TCAAAAACGT
*
278628 TTTTCAAAAGCTATATAATATATAAATG
1 TTTT-AAAAACTATATAATATATAAATG
*
278656 TTTTAAAAACTATATATTATATAAAT-
1 TTTTAAAAACTATATAATATATAAATG
*
278682 TTTCAAAAA
1 TTTTAAAAA
278691 TGTTTTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 8 0.25
27 20 0.62
28 4 0.12
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (27 bp):
TTTTAAAAACTATATAATATATAAATG
Found at i:278677 original size:65 final size:65
Alignment explanation
Indices: 278584--278716 Score: 180
Period size: 65 Copynumber: 2.0 Consensus size: 65
278574 ATATTTTCTA
* *
278584 AAATGTTTTAAAAAAATTATATATTATATATA-TTTCAAAAACGTTTTTCAAAAGCTATATAATA
1 AAATGTTTT-AAAAAACTATATATTATATAAATTTTCAAAAACG-TTTTCAAAA-CTATATAATA
278648 TAT
63 TAT
* * *
278651 AAATGTTTT-AAAAACTATATATTATATAAATTTTCAAAAATGTTTTCAAAATTATATATTATAT
1 AAATGTTTTAAAAAACTATATATTATATAAATTTTCAAAAACGTTTTCAAAACTATATAATATAT
278715 AA
1 AA
278717 GTTTTCAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
64 13 0.22
65 28 0.47
66 10 0.17
67 9 0.15
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (65 bp):
AAATGTTTTAAAAAACTATATATTATATAAATTTTCAAAAACGTTTTCAAAACTATATAATATAT
Found at i:279650 original size:108 final size:108
Alignment explanation
Indices: 279481--279678 Score: 360
Period size: 108 Copynumber: 1.8 Consensus size: 108
279471 CTTAAACTCG
* * *
279481 AACTTGAACCTTAAATACATGAAAACATTGTACTGCATATTTTTAAAAAATTCAAGACATAAATG
1 AACTCGAACCTTAAATACATAAAAACATTGTACTGCATATTTTTAAAAAACTCAAGACATAAATG
279546 TTAATATTATTAATAATTTATTTTTAACTTGATTAAAGTCTCA
66 TTAATATTATTAATAATTTATTTTTAACTTGATTAAAGTCTCA
*
279589 AACTCGAACCTTAAATACATAAAAACATTGTACTGCATATTTTTGAAAAACTCAAGACATAAATG
1 AACTCGAACCTTAAATACATAAAAACATTGTACTGCATATTTTTAAAAAACTCAAGACATAAATG
279654 TTAATATTATTAATAATTTATTTTT
66 TTAATATTATTAATAATTTATTTTT
279679 TAAAAATAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 86 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (108 bp):
AACTCGAACCTTAAATACATAAAAACATTGTACTGCATATTTTTAAAAAACTCAAGACATAAATG
TTAATATTATTAATAATTTATTTTTAACTTGATTAAAGTCTCA
Found at i:287912 original size:23 final size:23
Alignment explanation
Indices: 287881--287996 Score: 151
Period size: 23 Copynumber: 5.0 Consensus size: 23
287871 AGTGCCACAT
* *
287881 ATTTGTCCCGAAAGACCACATAG
1 ATTTATCCCGAAGGACCACATAG
*
287904 ATTTATCCCGAAGGACCATATAG
1 ATTTATCCCGAAGGACCACATAG
* *
287927 GTTTGTCCCGAAGGACCACATAG
1 ATTTATCCCGAAGGACCACATAG
**
287950 GGTTATCCCGAAGGACCACATAG
1 ATTTATCCCGAAGGACCACATAG
**
287973 GGTTATCCCGAAGGACCACATAG
1 ATTTATCCCGAAGGACCACATAG
287996 A
1 A
287997 ACCCTCGATT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (23 bp):
ATTTATCCCGAAGGACCACATAG
Found at i:287933 original size:46 final size:46
Alignment explanation
Indices: 287875--287996 Score: 176
Period size: 46 Copynumber: 2.7 Consensus size: 46
287865 CACTGAAGTG
* *
287875 CCACATA--TTTGTCCCGAAAGACCACATAGATTTATCCCGAAGGA
1 CCACATAGGTTTGTCCCGAAGGACCACATAGAGTTATCCCGAAGGA
* *
287919 CCATATAGGTTTGTCCCGAAGGACCACATAGGGTTATCCCGAAGGA
1 CCACATAGGTTTGTCCCGAAGGACCACATAGAGTTATCCCGAAGGA
* *
287965 CCACATAGGGTTATCCCGAAGGACCACATAGA
1 CCACATAGGTTTGTCCCGAAGGACCACATAGA
287997 ACCCTCGATT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 6 0.09
46 62 0.91
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (46 bp):
CCACATAGGTTTGTCCCGAAGGACCACATAGAGTTATCCCGAAGGA
Found at i:288778 original size:20 final size:20
Alignment explanation
Indices: 288724--288778 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
288714 TTCAAGCTGA
*
288724 ATAGTATCGATACTCTACCC
1 ATAGTATCGATACTTTACCC
288744 ATAGTATCGATACTTTACCC
1 ATAGTATCGATACTTTACCC
288764 ATAGTATCGATACTT
1 ATAGTATCGATACTT
288779 CTCTTCTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (20 bp):
ATAGTATCGATACTTTACCC
Found at i:288877 original size:20 final size:20
Alignment explanation
Indices: 288852--288902 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
288842 TCAATTACAA
288852 TATCGATACCTTACTCTTGG
1 TATCGATACCTTACTCTTGG
288872 TATCGATACCTTACTCTTGG
1 TATCGATACCTTACTCTTGG
288892 TATCGATACCT
1 TATCGATACCT
288903 CCAGATCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (20 bp):
TATCGATACCTTACTCTTGG
Found at i:294167 original size:23 final size:23
Alignment explanation
Indices: 294124--294229 Score: 139
Period size: 23 Copynumber: 4.7 Consensus size: 23
294114 ATAATTTGCA
294124 CCAAAGTG-CCACATA--TTTGTC
1 CCAAAG-GACCACATAGGTTTGTC
*
294145 CCAAAGGACCATATAGGTTTGTC
1 CCAAAGGACCACATAGGTTTGTC
*
294168 CCGAAGGACCACATAGGTTTGTC
1 CCAAAGGACCACATAGGTTTGTC
294191 CCGAAA-GACCACATAGGTTTGTC
1 CC-AAAGGACCACATAGGTTTGTC
*
294214 CCGAAGGACCACATAG
1 CCAAAGGACCACATAG
294230 AACCCTCGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.01
21 12 0.16
22 2 0.03
23 58 0.77
24 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CCAAAGGACCACATAGGTTTGTC
Found at i:294201 original size:46 final size:45
Alignment explanation
Indices: 294132--294229 Score: 155
Period size: 46 Copynumber: 2.2 Consensus size: 45
294122 CACCAAAGTG
*
294132 CCACATA-TTTGTCCCAAAGGACCATATAGGTTTGTCCCGAAGGA
1 CCACATAGTTTGTCCCAAAGGACCACATAGGTTTGTCCCGAAGGA
294176 CCACATAGGTTTGTCCCGAAA-GACCACATAGGTTTGTCCCGAAGGA
1 CCACATA-GTTTGTCCC-AAAGGACCACATAGGTTTGTCCCGAAGGA
294222 CCACATAG
1 CCACATAG
294230 AACCCTCGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
44 7 0.14
45 1 0.02
46 39 0.78
47 3 0.06
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (45 bp):
CCACATAGTTTGTCCCAAAGGACCACATAGGTTTGTCCCGAAGGA
Found at i:297049 original size:3 final size:3
Alignment explanation
Indices: 297043--297091 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
297033 TTTTTAATAA
** *
297043 TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
297090 TA
1 TA
297092 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:301744 original size:21 final size:20
Alignment explanation
Indices: 301706--301745 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
301696 GATCAACATT
*
301706 TTTGCATCTGCATTTGCATC
1 TTTGCATCTGCATATGCATC
301726 TTTGCATCTTGCATATGCAT
1 TTTGCATC-TGCATATGCAT
301746 TTCATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTGCATCTGCATATGCATC
Found at i:303045 original size:11 final size:11
Alignment explanation
Indices: 303017--303046 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
303007 AAGAGCAAAG
303017 AGAAAAATCAA
1 AGAAAAATCAA
303028 AGCAAAAATCAA
1 AG-AAAAATCAA
303040 AGAAAAA
1 AGAAAAA
303047 GCAAGAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.73, C:0.10, G:0.10, T:0.07
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:304235 original size:4 final size:4
Alignment explanation
Indices: 304226--304263 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
304216 AAAAGTATAC
304226 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
304264 GATACATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 30 0.94
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:304255 original size:22 final size:20
Alignment explanation
Indices: 304226--304275 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
304216 AAAAGTATAC
304226 ACAT-ACATACATACATACAT
1 ACATAACATACATACAT-CAT
*
304246 ACATACACATACATACATGAT
1 ACATA-ACATACATACATCAT
304267 ACATAACAT
1 ACATAACAT
304276 TTGTATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 7 0.26
22 12 0.44
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (20 bp):
ACATAACATACATACATCAT
Found at i:304258 original size:26 final size:25
Alignment explanation
Indices: 304222--304271 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
304212 CGAGAAAAGT
304222 ATACACATACATACATACATACATAC
1 ATACACATACATACAT-CATACATAC
*
304248 ATACACATACATACATGATACATA
1 ATACACATACATACATCATACATA
304272 ACATTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (25 bp):
ATACACATACATACATCATACATAC
Found at i:304935 original size:101 final size:101
Alignment explanation
Indices: 304731--304965 Score: 282
Period size: 101 Copynumber: 2.3 Consensus size: 101
304721 TGAGGATTTT
** *
304731 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCTTGAGATACAAATTTTGAATTTGATTCACTAA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCTTGAGATACAAATTTAGAATTTGATTCACTAA
*
304796 AACAAAATTATCTCACCTTAGATTGTTGTTTCTTTC-
66 AACAAAATTATCTCACCTTAGATCGTTGTTTC-TTCA
* * *
304832 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTAGAATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTT-CC-TTGAGATACAAATTTAGAATTTGATTCAC-
* *
304897 TTAAACAAAGTTGATCTCA-CTTGAGATCG-T-TTTC-TCA
63 TAAAACAAAATT-ATCTCACCTT-AGATCGTTGTTTCTTCA
* *
304934 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
304966 TCTAAAAACA
Statistics
Matches: 116, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
101 31 0.27
102 30 0.26
103 30 0.26
104 14 0.12
105 11 0.09
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (101 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCTTGAGATACAAATTTAGAATTTGATTCACTAA
AACAAAATTATCTCACCTTAGATCGTTGTTTCTTCA
Found at i:304956 original size:36 final size:34
Alignment explanation
Indices: 304911--305029 Score: 114
Period size: 36 Copynumber: 3.4 Consensus size: 34
304901 ACAAAGTTGA
*
304911 TCTCACTTGAGATCGTTTTCTCAAAAACAAACTTTG
1 TCTCACTTGAGA-C-TTTTCTCAAAAACAAATTTTG
* *
304947 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGAC-TTTTCTC-AAAAACAAATTTTG
* * * *
304983 TCTCATTTGAGACTATATCT-TAAAGCAAATTTTG
1 TCTCACTTGAGACT-TTTCTCAAAAACAAATTTTG
*
305017 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
305030 ATCATTTTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 23 0.33
35 7 0.10
36 39 0.57
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (34 bp):
TCTCACTTGAGACTTTTCTCAAAAACAAATTTTG
Found at i:305017 original size:34 final size:36
Alignment explanation
Indices: 304929--305030 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
304919 GAGATCGTTT
* *
304929 TCTC-AAAAACAAACTTTGTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
** *
304964 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
*
305000 TCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
305031 TCATTTTCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.40
35 5 0.09
36 29 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
Found at i:305291 original size:25 final size:27
Alignment explanation
Indices: 305263--305320 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
305253 TTTGTCTCTC
305263 TTGAGA-CAATT-TTGTGAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAATCT
*** *
305288 TTGAGATTGTTTCTTTTGAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAATCT
305315 TTGAGA
1 TTGAGA
305321 ATTTCTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 6 0.22
26 2 0.07
27 19 0.70
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (27 bp):
TTGAGATCAATTCTTGTGAAAAAATCT
Found at i:305325 original size:25 final size:26
Alignment explanation
Indices: 305277--305363 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 26
305267 GACAATTTTG
*
305277 TGAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAAAAATCTTTGAGA-TATTTCTTT
305304 TGAAAAAATCTTTGAGA-ATTTCTTT
1 TGAAAAAATCTTTGAGATATTTCTTT
*
305329 TGAAACAAGAATCTTTGAGTCTATTTCTTT
1 TG-AA-AA-AATCTTTGAG-ATATTTCTTT
*
305359 GGAAA
1 TGAAA
305364 CAAAATTTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
25 9 0.17
26 2 0.04
27 19 0.37
28 11 0.21
29 2 0.04
30 9 0.17
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (26 bp):
TGAAAAAATCTTTGAGATATTTCTTT
Found at i:305437 original size:27 final size:28
Alignment explanation
Indices: 305401--305516 Score: 164
Period size: 29 Copynumber: 4.1 Consensus size: 28
305391 TTCTTTTGAA
*
305401 AAAAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAAAAATCTTTGAGTTTGTTCCTTTTG
305429 -AAAAAATCTTTGAGTTTGTTCCTTTTG
1 AAAAAAATCTTTGAGTTTGTTCCTTTTG
*
305456 AATAAAAATCTTGGAGTTTGTTCCTTTTG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
* *
305485 AATAAAAATCTTTGAG-TTGTTTCGTTTG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
305513 AAAA
1 AAAA
305517 TCTTTGAGTC
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
27 28 0.35
28 13 0.16
29 40 0.49
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (28 bp):
AAAAAAATCTTTGAGTTTGTTCCTTTTG
Found at i:305462 original size:29 final size:29
Alignment explanation
Indices: 305393--305502 Score: 170
Period size: 29 Copynumber: 3.8 Consensus size: 29
305383 AAGACAATTT
*
305393 CTTTTGAAAAAAAAATCTTTGAGTTTGTTC
1 CTTTTG-AATAAAAATCTTTGAGTTTGTTC
*
305423 CTCTTG-A-AAAAATCTTTGAGTTTGTTC
1 CTTTTGAATAAAAATCTTTGAGTTTGTTC
*
305450 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTGAATAAAAATCTTTGAGTTTGTTC
305479 CTTTTGAATAAAAATCTTTGAGTT
1 CTTTTGAATAAAAATCTTTGAGTT
305503 GTTTCGTTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
27 25 0.34
28 2 0.03
29 42 0.57
30 5 0.07
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (29 bp):
CTTTTGAATAAAAATCTTTGAGTTTGTTC
Found at i:305480 original size:56 final size:59
Alignment explanation
Indices: 305393--305516 Score: 175
Period size: 56 Copynumber: 2.2 Consensus size: 59
305383 AAGACAATTT
*
305393 CTTTTGAAAAAAAAATCTTTGAGTTTGTTCCTCTTG-A-AAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAAAATCTTGGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTTGTTC
* * *
305450 CTTTTG-AATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAAATCTTTGAG-TTGTTT
1 CTTTTGAAAAAAAAATCTTGGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTTGTTC
*
305507 CGTTTGAAAA
1 CTTTTGAAAA
305517 TCTTTGAGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
56 26 0.45
57 17 0.29
58 15 0.26
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (59 bp):
CTTTTGAAAAAAAAATCTTGGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTTGTTC
Found at i:305536 original size:24 final size:24
Alignment explanation
Indices: 305489--305539 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
305479 CTTTTGAATA
*
305489 AAAATCTTTGAGTTGTTTCGTTTG
1 AAAATCTTTGAGTTGTTTAGTTTG
*
305513 AAAATCTTTGAGTCT-TTTATTTTG
1 AAAATCTTTGAGT-TGTTTAGTTTG
305537 AAA
1 AAA
305540 CAAGTTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (24 bp):
AAAATCTTTGAGTTGTTTAGTTTG
Found at i:305683 original size:67 final size:65
Alignment explanation
Indices: 305513--305714 Score: 277
Period size: 66 Copynumber: 3.1 Consensus size: 65
305503 GTTTCGTTTG
* * * * * * *
305513 AAAATCTTTGAGTCT-TTTATTTTGAAAC-AAGTTTGTCTCTCTTGAGACAA-TT-TTGTGAAAA
1 AAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAA
305574 AAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAA-
305639 A
65 A
* *
305640 AAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAAATAATTTCTTTTGAAA
1 AAAATCTTTGAGTTTGTTTCTTTGGAAAC-AAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAA
305705 A
65 A
305706 AAAATCTTT
1 AAAATCTTT
305715 AAATCTGTTT
Statistics
Matches: 126, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
61 14 0.11
62 11 0.09
63 19 0.15
64 2 0.02
65 7 0.06
66 40 0.32
67 33 0.26
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (65 bp):
AAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAA
Found at i:305749 original size:67 final size:65
Alignment explanation
Indices: 305568--305749 Score: 226
Period size: 66 Copynumber: 2.7 Consensus size: 65
305558 GACAATTTTG
* *
305568 TGAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTG-TCTCTCTTAAGATAATTTCTT
1 TGAAAAAAAATCTTTGAGTTTGTTTCTTT-GAAAAAAATTTTGTTCTCTCTTAAAATAATTTCTT
305632 T
65 T
305633 TGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTT-TTCTCTCTTAAAATAATTTC
1 TGAAA-AAAAATCTTTGAGTTTGTTTCTTT-GAAA-AAAATTTTGTTCTCTCTTAAAATAATTTC
305697 TTT
63 TTT
* * * *
305700 TGAAAAAAAATCTTTAAATCTGTTTCTCTT-AAAATGAATTTTGTATCTCT
1 TGAAAAAAAATCTTTGAGTTTGTTTCT-TTGAAAA-AAATTTTGT-TCTCT
305750 TGAGACAGTT
Statistics
Matches: 104, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
64 1 0.01
65 14 0.13
66 49 0.47
67 40 0.38
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.46
Consensus pattern (65 bp):
TGAAAAAAAATCTTTGAGTTTGTTTCTTTGAAAAAAATTTTGTTCTCTCTTAAAATAATTTCTTT
Found at i:305965 original size:120 final size:118
Alignment explanation
Indices: 305827--306049 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 118
305817 TTAACAAAAT
* * *
305827 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAAA
305890 ACTAACTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGATC
64 A--AAC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
* ** **
305947 CATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
* * * *
306012 TCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 ACTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
306050 TCGAGACAAC
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
117 21 0.24
118 13 0.15
119 7 0.08
120 43 0.49
121 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (118 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
ACTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
Found at i:306074 original size:63 final size:63
Alignment explanation
Indices: 305948--306073 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
305938 GATGTGATCC
* *
305948 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
* * **
306011 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC-TCGAGACAACTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
306073 A
1 A
306074 AAAAACAGCT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 21 0.37
63 36 0.63
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
Found at i:306735 original size:28 final size:28
Alignment explanation
Indices: 306689--306767 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 28
306679 GAGACAGTTG
306689 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
306720 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
306748 CTTTTGAAACAAATCTTTGA
1 CTTTTGAAACAAATCTTTGA
306768 ATCAATTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
28 31 0.69
29 3 0.07
30 3 0.07
31 8 0.18
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.46
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:306776 original size:28 final size:28
Alignment explanation
Indices: 306723--306777 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
306713 CTTGTTTTTC
* **
306723 TTGAAACAAATCTTTGAGTCTGTTTCTT
1 TTGAAACAAATCTTTGAATCAATTTCTT
306751 TTGAAACAAATCTTTGAATCAATTTCT
1 TTGAAACAAATCTTTGAATCAATTTCT
306778 CCTGAAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (28 bp):
TTGAAACAAATCTTTGAATCAATTTCTT
Found at i:306783 original size:28 final size:28
Alignment explanation
Indices: 306724--306785 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
306714 TTGTTTTTCT
* ** **
306724 TGAAACAAATCTTTGAGTCTGTTTCTTT
1 TGAAACAAATCTTTGAATCAATTTCTCC
306752 TGAAACAAATCTTTGAATCAATTTCTCC
1 TGAAACAAATCTTTGAATCAATTTCTCC
306780 TGAAAC
1 TGAAAC
306786 CATGATCCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (28 bp):
TGAAACAAATCTTTGAATCAATTTCTCC
Found at i:307256 original size:130 final size:131
Alignment explanation
Indices: 306790--307263 Score: 573
Period size: 130 Copynumber: 3.6 Consensus size: 131
306780 TGAAACCATG
* *
306790 ATCCCTAAAGATGGCCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCT
1 ATCCCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACAGTGTCATCCCCTGACCAGATCTCCT
* *
306855 CATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTAT
66 CATCACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT
306920 C
131 C
** * * * *
306921 A--CCTTTAGATGGCCAGAAC-TCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCT
1 ATCCCTAAAGATGGCCAG-ACGTCCTCATCACGTAGGAACAGTGTCATCCCCTGACCAGATCTCC
* ** * * * *
306983 TCATCACGTATGAGCGGTAATCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTT
65 TCATCACGTAGGAGCCAT-GTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTT
307048 ATC
129 ATC
* * * * * *
307051 ACCACTCTTAAAGATGGCCAGCCGTCCCCATCACGTAGGAACCGTGTCATCACCTGACCAGAACT
1 ATC-C-C-TAAAGATGGCCAGACGTCCTCATCACGTAGGAACAGTGTCATCCCCTGACCAGATCT
* * * *
307116 CTTCATCACGTAAGAGCCATGTCAACC-T-GATAACCAGTCATCCTCATCACGTAGGAACCGTGT
63 CCTCATCACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGT
307179 TATC
128 TATC
* * *
307183 ATCCCTAAAGATGGCCAAGAAC-TCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTC
1 ATCCCTAAAGATGGCC-AG-ACGTCCTCATCACGTAGGAACAGTGTCATCCCCTGACCAGATCTC
307247 CTCATCACGTAGGAGCC
64 CTCATCACGTAGGAGCC
307264 GGGTCACCCT
Statistics
Matches: 287, Mismatches: 46, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
129 76 0.26
130 99 0.34
131 3 0.01
132 38 0.13
133 2 0.01
134 7 0.02
135 62 0.22
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACAGTGTCATCCCCTGACCAGATCTCCT
CATCACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT
C
Found at i:307273 original size:264 final size:263
Alignment explanation
Indices: 306795--307277 Score: 765
Period size: 264 Copynumber: 1.8 Consensus size: 263
306785 CCATGATCCC
* * * *
306795 TAAAGATGGCCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCA
1 TAAAGATGGCCAGCCGTCCCCATCACGTAGGAACCGTGTCATCACCTGACCAGAACTCCTCATCA
* * *
306860 TGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTATCACCT
66 CGTAAGAGCCATGTCAACCATAGATAACCAGCCATCCTCATCACGTAGAAACCGTGTTATCACCT
** *
306925 TTAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCTTCATCAC
131 AAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCATCAC
*
306990 GTATGAGCGGTAATCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCA
196 GTAGGAGCGG-AATCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCA
307055 CTCT
260 CTCT
*
307059 TAAAGATGGCCAGCCGTCCCCATCACGTAGGAACCGTGTCATCACCTGACCAGAACTCTTCATCA
1 TAAAGATGGCCAGCCGTCCCCATCACGTAGGAACCGTGTCATCACCTGACCAGAACTCCTCATCA
* *
307124 CGTAAGAGCCATGTCAACC-T-GATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCC
66 CGTAAGAGCCATGTCAACCATAGATAACCAGCCATCCTCATCACGTAGAAACCGTGTTATCA--C
307187 CTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCAT
129 CTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCAT
*
307252 CACGTAGGAGCCGG-GTCACCCTTAGA
193 CACGTAGGAG-CGGAATCACCCTTAGA
307278 CGACCAGACC
Statistics
Matches: 200, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
262 37 0.19
263 1 0.00
264 99 0.50
265 60 0.30
266 3 0.01
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (263 bp):
TAAAGATGGCCAGCCGTCCCCATCACGTAGGAACCGTGTCATCACCTGACCAGAACTCCTCATCA
CGTAAGAGCCATGTCAACCATAGATAACCAGCCATCCTCATCACGTAGAAACCGTGTTATCACCT
AAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCATCAC
GTAGGAGCGGAATCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCAC
TCT
Found at i:307472 original size:3 final size:3
Alignment explanation
Indices: 307466--307514 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
307456 CTTTTTTTAA
** *
307466 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
307513 TA
1 TA
307515 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:311517 original size:19 final size:19
Alignment explanation
Indices: 311483--311519 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
311473 TCTTTACTAT
* *
311483 TTTTTTTCCTTTTTTTTTA
1 TTTTTTTCCATCTTTTTTA
311502 TTTTTTTCCATCTTTTTT
1 TTTTTTTCCATCTTTTTT
311520 CTGTATGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTCCATCTTTTTTA
Found at i:315957 original size:21 final size:21
Alignment explanation
Indices: 315871--315960 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 21
315861 TCGAGGGTTC
* * *
315871 TATGTGGTCCTTCGGGATATA
1 TATGTGGTTCTTTGGAATATA
** *
315892 TATGTAATCCTTTGGAATATA
1 TATGTGGTTCTTTGGAATATA
* * * *
315913 TATGTGGTTCTTCGGGACACA
1 TATGTGGTTCTTTGGAATATA
*
315934 TATTTGGTTCTTTGGAATATA
1 TATGTGGTTCTTTGGAATATA
315955 TATGTG
1 TATGTG
315961 ATCCTTAAGG
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.42
Consensus pattern (21 bp):
TATGTGGTTCTTTGGAATATA
Found at i:315998 original size:21 final size:21
Alignment explanation
Indices: 315972--316029 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
315962 TCCTTAAGGA
*
315972 GTGGTCATTCGGGACATCTAT
1 GTGGTCCTTCGGGACATCTAT
* *
315993 GTGGTCCTTAGGAACATCTAT
1 GTGGTCCTTCGGGACATCTAT
*
316014 GTGGTCCTTCAGGACA
1 GTGGTCCTTCGGGACA
316030 AATTCTATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATCTAT
Found at i:321625 original size:21 final size:21
Alignment explanation
Indices: 321569--321626 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
321559 ATATGTAATC
321569 CTTTGGAACATATATGAGGTT
1 CTTTGGAACATATATGAGGTT
* * * **
321590 CTTCGGGACACATATTTGGTT
1 CTTTGGAACATATATGAGGTT
*
321611 CTTTGGAATATATATG
1 CTTTGGAACATATATG
321627 TGATCCTTAA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (21 bp):
CTTTGGAACATATATGAGGTT
Found at i:321665 original size:20 final size:21
Alignment explanation
Indices: 321640--321686 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
321630 TCCTTAAGGA
321640 GTGGTCATTCAG-ACATCTAT
1 GTGGTCATTCAGAACATCTAT
* *
321660 GTGGTCCTTCGGAACATCTAT
1 GTGGTCATTCAGAACATCTAT
321681 GTGGTC
1 GTGGTC
321687 CTTCGGGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (21 bp):
GTGGTCATTCAGAACATCTAT
Found at i:321678 original size:21 final size:21
Alignment explanation
Indices: 321652--321710 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
321642 GGTCATTCAG
321652 ACATCTATGTGGTCCTTCGGA
1 ACATCTATGTGGTCCTTCGGA
*
321673 ACATCTATGTGGTCCTTCGGG
1 ACATCTATGTGGTCCTTCGGA
*
321694 ACA--TATATGGTCCTTCG
1 ACATCTATGTGGTCCTTCG
321711 AGAAAAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.36
21 23 0.64
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.34
Consensus pattern (21 bp):
ACATCTATGTGGTCCTTCGGA
Found at i:331042 original size:24 final size:24
Alignment explanation
Indices: 331026--331072 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
331016 ATTTTATATA
331026 TAATAATATTATATATTTAATTAT
1 TAATAATATTATATATTTAATTAT
* *
331050 TAATAATTTTATATATTAAATTA
1 TAATAATATTATATATTTAATTA
331073 AACTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATAATATTATATATTTAATTAT
Found at i:333672 original size:23 final size:23
Alignment explanation
Indices: 333646--333695 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
333636 ATCAAGTAAA
333646 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
333669 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
333692 ATAA
1 ATAA
333696 AATAGGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:333701 original size:20 final size:21
Alignment explanation
Indices: 333655--333702 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 21
333645 AATAACAAAT
333655 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAA--TAA
333678 TAGGTAGCGCTTATATAA-AA
1 TAGGTAGCGCTTATATAATAA
333698 TAGGT
1 TAGGT
333703 TAATTACTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.28
23 18 0.72
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.33
Consensus pattern (21 bp):
TAGGTAGCGCTTATATAATAA
Found at i:333786 original size:23 final size:23
Alignment explanation
Indices: 333742--333786 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
333732 AACATATTAG
* * **
333742 GTAGCGTTTATTTAATGTAATAA
1 GTAGCGCTTATATAATAAAATAA
333765 GTAGCGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
333787 GGTTAATTAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAA
Found at i:333821 original size:87 final size:86
Alignment explanation
Indices: 333628--333864 Score: 343
Period size: 87 Copynumber: 2.8 Consensus size: 86
333618 CATTCAACCG
* * * *
333628 GAAATATTATCAAGTAAAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTAGCGC-T-TA
1 GAAAAATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATA
*
333691 TATAAAATAGGTTAATTACTG
66 TATAAAATAGGTTAATTACTA
* * *
333712 GAAAAATTATCAAGCACAATAACATATTAGGTAGCGTTTATTTAATGTAATAAGTAGCGCTTATA
1 GAAAAATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATA
333777 TAATAAAATAGGTTAATTACTA
66 T-ATAAAATAGGTTAATTACTA
* * * *
333799 GAAACATTATTAAGCACAATAACATATTAGGTAGTGCTTATATAATGTAATAGGTAACGCTTATA
1 GAAAAATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATA
333864 T
66 T
333865 TGACATATTC
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 53 0.39
85 1 0.01
86 3 0.02
87 78 0.58
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (86 bp):
GAAAAATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATA
TATAAAATAGGTTAATTACTA
Found at i:333985 original size:14 final size:14
Alignment explanation
Indices: 333917--333989 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
333907 ATTGCAAATT
333917 TATTTTAATAA-AA
1 TATTTTAATAATAA
** *
333930 TATAATAATCATAA
1 TATTTTAATAATAA
* * *
333944 TTTTTTATTTATAA
1 TATTTTAATAATAA
* *
333958 AATTATAGAT-ATAA
1 TATTTTA-ATAATAA
333972 TATTTTAATAATAA
1 TATTTTAATAATAA
333986 TATT
1 TATT
333990 GACATAGATA
Statistics
Matches: 43, Mismatches: 14, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
13 10 0.23
14 32 0.74
15 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:333985 original size:28 final size:28
Alignment explanation
Indices: 333917--333985 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
333907 ATTGCAAATT
*
333917 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
333944 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
333972 TATTTTAATAATAA
1 TATTTTAATAATAA
333986 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:334072 original size:24 final size:25
Alignment explanation
Indices: 334004--334072 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
333994 TAGATAATAT
*
334004 TAAATAA-ATTATTCTAATATT-TTAA
1 TAAATAATATTA-T-TATTATTGTTAA
334029 -AAATAATATTATTATT-TTGTTAA
1 TAAATAATATTATTATTATTGTTAA
334052 TAAATAATATTATT-TTATTGT
1 TAAATAATATTATTATTATTGT
334073 ATTTGATGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 9 0.23
24 24 0.62
25 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATAATATTATTATTATTGTTAA
Found at i:334454 original size:20 final size:20
Alignment explanation
Indices: 334420--334468 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
334410 CATTTTCGGT
*
334420 AAAACAGGT-AAAAAATAAC
1 AAAACCGGTAAAAAAATAAC
334439 AAAACCGGTAAAAAAATAAC
1 AAAACCGGTAAAAAAATAAC
*
334459 AAAATCGGTA
1 AAAACCGGTA
334469 GCGCTTTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAACCGGTAAAAAAATAAC
Found at i:334544 original size:92 final size:92
Alignment explanation
Indices: 334445--334739 Score: 486
Period size: 92 Copynumber: 3.2 Consensus size: 92
334435 TAACAAAACC
* *
334445 GGTAAAAAAATAACAAAATCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATAA
1 GGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTATAA
*
334510 AAAGGATCGATATTTTACAATATAACC
66 AAAGGATCGATATTTTACAATATAACA
334537 GGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTATAA
1 GGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTATAA
*
334602 AAAGGATCGATACTTTACAATATAACA
66 AAAGGATCGATATTTTACAATATAACA
* *
334629 GGTAAAAAAAATAACAAAACCGGTAGCGCTTTACATGATATATTGAAAGTATCGATTCTTTTATA
1 GGT-AAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTATA
*
334694 AAAAGGATAGATATTTT--AATATAACA
65 AAAAGGATCGATATTTTACAATATAACA
* *
334720 AGTAAAAAAATGACAAAACC
1 GGTAAAAAAATAACAAAACC
334740 AGTTTTATTA
Statistics
Matches: 192, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
90 16 0.08
91 11 0.06
92 91 0.47
93 74 0.39
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (92 bp):
GGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTATAA
AAAGGATCGATATTTTACAATATAACA
Found at i:338484 original size:183 final size:184
Alignment explanation
Indices: 337823--338537 Score: 1308
Period size: 184 Copynumber: 3.9 Consensus size: 184
337813 CCGCGTTACT
*
337823 TAAAGTATG-GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCCCATAAAACC
1 TAAAGTA-GCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACC
*
337887 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTT
65 GGTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTT
* * *
337952 TTTCAATCTACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACA
130 TTTCAATCGACACTTTTTGAAAAGGTATCGACACTGTTTTCATCCATTATGGACA
*
338007 TAAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAATCG
1 TAAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
338072 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
66 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
338137 TTCAATCGACACTTTTTGAAAAGGTATCGACACTGTTTTCATCCATTATGGACA
131 TTCAATCGACACTTTTTGAAAAGGTATCGACACTGTTTTCATCCATTATGGACA
*
338191 TAAAGTAGCGACACAATATTAAAAAGTCTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
1 TAAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
*
338256 GCATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
66 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
338321 TTCAATCGACACTTTTTGAAAAGGTATCGACACTGTTTTCATCCATT-TGGACA
131 TTCAATCGACACTTTTTGAAAAGGTATCGACACTGTTTTCATCCATTATGGACA
* *
338374 TAAAGTAGCGACACAATATTAAAAAATGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCA
1 TAAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
*
338439 GTATATCTATACCGATTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
66 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
338504 TTCAATCGACACTTTTTGAAAAGGTATCGACACT
131 TTCAATCGACACTTTTTGAAAAGGTATCGACACT
338538 TTATGCTGAT
Statistics
Matches: 516, Mismatches: 14, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
183 166 0.32
184 350 0.68
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (184 bp):
TAAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
TTCAATCGACACTTTTTGAAAAGGTATCGACACTGTTTTCATCCATTATGGACA
Found at i:339619 original size:32 final size:33
Alignment explanation
Indices: 339557--339643 Score: 115
Period size: 32 Copynumber: 2.7 Consensus size: 33
339547 ATGACATCGA
* *
339557 CTTCCTTCCTCC-TCATTTCTTCCATCTCTTCTT
1 CTTCC-TCCTCCATCTTTTCTTCCATATCTTCTT
*
339590 CTTCCT-CTCCATCTTTTCTTTCATATCTTCTT
1 CTTCCTCCTCCATCTTTTCTTCCATATCTTCTT
*
339622 CTTCCTCCTCCCTCTTTTCTTC
1 CTTCCTCCTCCATCTTTTCTTC
339644 TTCATATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 4 0.09
32 25 0.53
33 18 0.38
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.53
Consensus pattern (33 bp):
CTTCCTCCTCCATCTTTTCTTCCATATCTTCTT
Found at i:339867 original size:33 final size:33
Alignment explanation
Indices: 339830--339895 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
339820 CATCTTAAGA
*
339830 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
339863 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
339896 CAATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:339954 original size:21 final size:21
Alignment explanation
Indices: 339929--339991 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
339919 CCCCTTATGC
* *
339929 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
339950 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
339971 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
339992 TTTGATTGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:340096 original size:15 final size:15
Alignment explanation
Indices: 340076--340108 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
340066 ACTCTGTTTT
*
340076 CCCTCACCGTCGTCC
1 CCCTCACCGTCATCC
340091 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
340106 CCC
1 CCC
340109 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.64, G:0.09, T:0.18
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:341840 original size:20 final size:19
Alignment explanation
Indices: 341794--341840 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
341784 TCCGGTAGCG
*
341794 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
341813 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
341834 TTTTACC
1 TTTTACC
341841 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:342031 original size:20 final size:19
Alignment explanation
Indices: 341976--342022 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
341966 TCCGGTAGCG
341976 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
341995 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
342016 TTTTACC
1 TTTTACC
342023 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:342130 original size:182 final size:180
Alignment explanation
Indices: 341761--342234 Score: 750
Period size: 182 Copynumber: 2.6 Consensus size: 180
341751 CGTACTTACG
*
341761 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
341826 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTTTAAAGTATCGACACTTT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCAATACA--TTTTTTTAAAGTATCGACACTTT
* *
341891 ATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGCGATCCCTATAT
129 ATAGGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTGCGATCCCTATAT
341943 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
342008 TATCATATTTTTACCTGTTATATCGTTGTGGATTAATACATTTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCAATACATTTTTTTAAAGTATCGACACTTTAT
* * *
342073 AGGCGCTAAAACTGATTCTTTTTTAAATTAACGAAGTGTCGATCCTTATATT
131 AGGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTG-CGATCCCTATA-T
* * ** * * **
342125 AAAGTACCGACACTTTAAATATATTTGGTACCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
342190 TGTCATAGTTTTACCTGTTATATCGTTGTGGATCAATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCAATACATTTTT
342235 AATTTGGATC
Statistics
Matches: 271, Mismatches: 19, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
180 59 0.22
181 10 0.04
182 202 0.75
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCAATACATTTTTTTAAAGTATCGACACTTTAT
AGGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTGCGATCCCTATAT
Found at i:342738 original size:24 final size:24
Alignment explanation
Indices: 342701--342749 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
342691 AAATTACATT
*
342701 AAAATTCTAAAGATGT-AAAATTAC
1 AAAATTCGAAAGAT-TAAAAATTAC
*
342725 AAAATTCGATAGATTAAAAATTAC
1 AAAATTCGAAAGATTAAAAATTAC
342749 A
1 A
342750 TCATCAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (24 bp):
AAAATTCGAAAGATTAAAAATTAC
Found at i:342845 original size:20 final size:20
Alignment explanation
Indices: 342822--342861 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
342812 GTATTGCCTG
342822 TTGATTCATCCTTATTCCCT
1 TTGATTCATCCTTATTCCCT
342842 TTGATTCATCCTTATTCCCT
1 TTGATTCATCCTTATTCCCT
342862 ACCGTAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.05, T:0.50
Consensus pattern (20 bp):
TTGATTCATCCTTATTCCCT
Found at i:347365 original size:15 final size:15
Alignment explanation
Indices: 347345--347375 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
347335 GGGACTGGTC
*
347345 TGGCTTGGCTTGGCA
1 TGGCTTGGCATGGCA
347360 TGGCTTGGCATGGCA
1 TGGCTTGGCATGGCA
347375 T
1 T
347376 AGGGAATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.39, T:0.32
Consensus pattern (15 bp):
TGGCTTGGCATGGCA
Found at i:347892 original size:17 final size:18
Alignment explanation
Indices: 347862--347903 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
347852 AAGGTAAAAA
*
347862 TATTT-TTTATTATAT-T
1 TATTTATTTAATATATAT
347878 TATTTATTTAATATATAT
1 TATTTATTTAATATATAT
347896 TA-TTATTT
1 TATTTATTT
347904 TATTATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 15 0.65
18 3 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTATTTAATATATAT
Found at i:349746 original size:23 final size:23
Alignment explanation
Indices: 349712--349798 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
349702 ACATATTATA
349712 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
349735 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
349758 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTACGGTG-C--AATTCTACG
349783 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
349799 ATTTATATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 2 0.04
25 16 0.31
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:352076 original size:31 final size:31
Alignment explanation
Indices: 352041--352104 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
352031 TAAAAGCCCT
352041 GTTAGAAGTTATGTAAATCGAAGCAGAAAAA
1 GTTAGAAGTTATGTAAATCGAAGCAGAAAAA
352072 GTTAGAAGTTATGTAAATCGAAGCAGAAAAA
1 GTTAGAAGTTATGTAAATCGAAGCAGAAAAA
352103 GT
1 GT
352105 ATTTGAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.23
Consensus pattern (31 bp):
GTTAGAAGTTATGTAAATCGAAGCAGAAAAA
Found at i:364225 original size:56 final size:58
Alignment explanation
Indices: 364163--364270 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
364153 GCAAATGTAA
* * *
364163 TGAATTGTGAAC-TTTTTATTT-AT-TTTGTTTCTTAA-TGTTTTTATTATTTAATTGTT
1 TGAATTGT-AACGTTTGTATTTAATGTTTGTAT-TTAATTATTTTTATTATTTAATTGTT
364219 TGAATTGTAACGTTTGTATTTAATGTTTGTATTTAATTATTTTTATTATTTA
1 TGAATTGTAACGTTTGTATTTAATGTTTGTATTTAATTATTTTTATTATTTA
364271 GTTTGTAATG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
55 3 0.07
56 16 0.36
57 6 0.13
58 20 0.44
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.62
Consensus pattern (58 bp):
TGAATTGTAACGTTTGTATTTAATGTTTGTATTTAATTATTTTTATTATTTAATTGTT
Found at i:364248 original size:13 final size:13
Alignment explanation
Indices: 364207--364255 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
364197 ATGTTTTTAT
364207 TATTTAATTGTTTG
1 TATTTAA-TGTTTG
* *
364221 AATTGTAACGTTTG
1 TATT-TAATGTTTG
364235 TATTTAATGTTTG
1 TATTTAATGTTTG
364248 TATTTAAT
1 TATTTAAT
364256 TATTTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 16 0.53
14 11 0.37
15 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (13 bp):
TATTTAATGTTTG
Found at i:367908 original size:15 final size:15
Alignment explanation
Indices: 367888--367919 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
367878 CCGATTTCCA
*
367888 GGTAATAATTGAAGG
1 GGTAATAATTCAAGG
367903 GGTAATAATTCAAGG
1 GGTAATAATTCAAGG
367918 GG
1 GG
367920 GACTAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.34, T:0.25
Consensus pattern (15 bp):
GGTAATAATTCAAGG
Found at i:368344 original size:21 final size:21
Alignment explanation
Indices: 368320--368362 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
368310 TTATTAAAAT
*
368320 AAATATTTAAATTATTTTTTA
1 AAATATCTAAATTATTTTTTA
* *
368341 AAATCTCTAATTTATTTTTTA
1 AAATATCTAAATTATTTTTTA
368362 A
1 A
368363 TTAAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATCTAAATTATTTTTTA
Found at i:369048 original size:28 final size:28
Alignment explanation
Indices: 369003--369062 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
368993 AACAACGTTA
* *
369003 AATAATCAATGATCATTTTGTAACTTTT
1 AATAATCAATAATCATTTTATAACTTTT
* *
369031 AATAATCGATAATTATTTTATAACTTTT
1 AATAATCAATAATCATTTTATAACTTTT
369059 AATA
1 AATA
369063 GTCTGAGACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (28 bp):
AATAATCAATAATCATTTTATAACTTTT
Found at i:370178 original size:33 final size:33
Alignment explanation
Indices: 370106--370181 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
370096 TTATAAGTTG
*
370106 ATTATAAATACTTAATAGATCAATCTAATATTA
1 ATTATATATACTTAATAGATCAATCTAATATTA
370139 ATTATATATACTTAATAGATCAATCTAATATTA
1 ATTATATATACTTAATAGATCAATCTAATATTA
370172 ATTATATATA
1 ATTATATATA
370182 AAGAATTAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (33 bp):
ATTATATATACTTAATAGATCAATCTAATATTA
Found at i:374317 original size:45 final size:44
Alignment explanation
Indices: 374240--374327 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 44
374230 GGATTATTTA
*
374240 TTGGTATGTCTCTTATTTTCACTTGATTCCCCTATGGCATTTTT
1 TTGGTATGGCTCTTATTTTCACTTGATTCCCCTATGGCATTTTT
374284 TTGGTATGGCTCTTATTTTTCACTTGATTCCCCTATGGCATTTT
1 TTGGTATGGCTCTTA-TTTTCACTTGATTCCCCTATGGCATTTT
374328 CATTTGATAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 14 0.33
45 28 0.67
ACGTcount: A:0.14, C:0.20, G:0.15, T:0.51
Consensus pattern (44 bp):
TTGGTATGGCTCTTATTTTCACTTGATTCCCCTATGGCATTTTT
Found at i:383822 original size:18 final size:17
Alignment explanation
Indices: 383801--383843 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
383791 ATATATACAT
383801 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
383819 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
383836 ATAA-AATA
1 ATAATAATA
383844 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:384251 original size:37 final size:37
Alignment explanation
Indices: 384201--384305 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
384191 GTGCTTGTGG
* * * *
384201 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
384238 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
384275 ATCTTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
384306 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:385152 original size:105 final size:105
Alignment explanation
Indices: 384848--385472 Score: 929
Period size: 105 Copynumber: 6.0 Consensus size: 105
384838 GCATTGTTCC
* * ** *
384848 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
384912 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
384954 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGCCAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
385014 CAACGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
385054 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
385119 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
385159 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
385224 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
385264 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
385329 AATCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
385369 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * *
385434 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
385473 CCGATTGTCA
Statistics
Matches: 480, Mismatches: 32, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
100 83 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 304 0.63
106 80 0.17
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:385725 original size:36 final size:36
Alignment explanation
Indices: 385678--385753 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
385668 TGTTTGGAGA
* * *
385678 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
385714 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
385750 GAAA
1 GAAA
385754 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:385864 original size:104 final size:101
Alignment explanation
Indices: 385653--385866 Score: 338
Period size: 104 Copynumber: 2.1 Consensus size: 101
385643 TTCGTTAAAT
*
385653 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAA
1 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAA
* * *
385718 CTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 CTATCTCAAGAGAGAAAAAATTAATTTCAAGGGAAA
* *
385754 TGTTTTCAATGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTATTTCGAGGG
1 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-ATTTCAAGGG
*
385819 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
63 AAACTATCTCAAGAGAGAAAAAATTAATTTCAAGGGAAA
385858 TGTTTTCAA
1 TGTTTTCAA
385867 GAGAAACTGT
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 48 0.47
103 3 0.03
104 52 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (101 bp):
TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAA
CTATCTCAAGAGAGAAAAAATTAATTTCAAGGGAAA
Found at i:386044 original size:36 final size:36
Alignment explanation
Indices: 385991--386098 Score: 101
Period size: 36 Copynumber: 3.0 Consensus size: 36
385981 GTGAAAACGG
* *
385991 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
** * * ** *
386027 TCTTTAGTGAAATAAATCTTCTTTCGAGAAAAACAG
1 TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
* *
386063 TCTCAAGTGAGACAAAGT-ATGTTTTAAGAAAAACAA
1 TCTCAAGTGAAACAAA-TCTTGTTTTAAGAAAAACAA
386099 ATTTGAGTGA
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
36 52 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (36 bp):
TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
Found at i:386108 original size:72 final size:74
Alignment explanation
Indices: 385953--386113 Score: 204
Period size: 72 Copynumber: 2.2 Consensus size: 74
385943 AAAAATAGCA
* * *
385953 TTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAATCTTGTTTTAA
1 TTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATCATGTTTTAA
386018 GAAAAACAATC
64 GAAAAACAATC
* *
386029 TTTAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAG
1 TTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAA-TCATGTTTTAAG
386091 AAAAACAAAT-
65 AAAAAC-AATC
*
386101 TTGAGTGAGATAA
1 TTGAGTGAAATAA
386114 TCATCTGCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
72 47 0.62
73 15 0.20
75 4 0.05
76 10 0.13
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (74 bp):
TTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATCATGTTTTAAGA
AAAACAATC
Found at i:387555 original size:183 final size:183
Alignment explanation
Indices: 387247--387783 Score: 977
Period size: 183 Copynumber: 2.9 Consensus size: 183
387237 ATCAGGTTTA
*
387247 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * **
387312 GCCAAGTGTCCGAGCAATATCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
387376 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
387430 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
387495 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
387560 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTCTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
387613 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
387678 GCCAAGTGTCCGAACAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
387743 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
387784 CGGATTTAAT
Statistics
Matches: 342, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 341 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:391842 original size:21 final size:21
Alignment explanation
Indices: 391818--391873 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
391808 AAAAAAGAAA
* *
391818 AATATATATATATATATATAT
1 AATATATATATATAAATAAAT
391839 AATATATATATATAAATAAAT
1 AATATATATATATAAATAAAT
**
391860 AAGCTATATATATA
1 AATATATATATATA
391874 CACCAAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATATATATATAAATAAAT
Found at i:391872 original size:2 final size:2
Alignment explanation
Indices: 391819--391852 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
391809 AAAAAGAAAA
391819 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
391853 AATAAATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:392310 original size:19 final size:18
Alignment explanation
Indices: 392277--392313 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
392267 ATATATATAT
*
392277 ATATATAATAATAATAAA
1 ATATATAAAAATAATAAA
392295 ATATAGTAAAAATAATAAA
1 ATATA-TAAAAATAATAAA
392314 TAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
ATATATAAAAATAATAAA
Found at i:392370 original size:18 final size:17
Alignment explanation
Indices: 392349--392391 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
392339 ATATATACAT
392349 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
392367 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
392384 ATAA-AATA
1 ATAATAATA
392392 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:392392 original size:62 final size:60
Alignment explanation
Indices: 392265--392392 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 60
392255 AATATTAAAG
*
392265 AAATATATATATATATATAATAATAATAAAATATAGTAAAAATAATAAATAAAAATAATT
1 AAATATATATATATATATAATAATAATAAAATATAGTAAAAATAATAAATAAAAATAATA
*
392325 TAATATATATATATATAT-ATACAT-ATAATAATA-A-TAACATGAATAATAAA-AATAAATGAA
1 AAATATATATATATATATAATA-ATAATAA-AATATAGTAA-A--AATAATAAATAA-AAAT-AA
392385 TA
59 TA
392387 AAATAT
1 AAATAT
392393 CCATATAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
58 3 0.05
59 9 0.16
60 25 0.43
61 13 0.22
62 8 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (60 bp):
AAATATATATATATATATAATAATAATAAAATATAGTAAAAATAATAAATAAAAATAATA
Found at i:392399 original size:62 final size:64
Alignment explanation
Indices: 392267--392399 Score: 141
Period size: 66 Copynumber: 2.1 Consensus size: 64
392257 TATTAAAGAA
* *
392267 ATATATATATATATATAATAATAATAAAATATAGTAAAAATAATAAATAAAAATAATTTAATATA
1 ATATATATATATACATAATAATAATAAAACATAGTAAAAATAATAAATAAAAATAA--TAATATA
*
392332 T
64 C
*
392333 ATATATATATATACAT-ATAATAATAATAACAT-G-AATAATAA-AAATAAATGAATAA-AATAT
1 ATATATATATATACATAATAATAATAA-AACATAGTAAAAATAATAAATAAA--AATAATAATAT
*
392393 CC
63 AC
392395 ATATA
1 ATATA
392400 ATAAATAAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
62 10 0.17
63 7 0.12
64 7 0.12
65 16 0.27
66 19 0.32
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (64 bp):
ATATATATATATACATAATAATAATAAAACATAGTAAAAATAATAAATAAAAATAATAATATAC
Found at i:401087 original size:160 final size:164
Alignment explanation
Indices: 400823--401147 Score: 622
Period size: 160 Copynumber: 2.0 Consensus size: 164
400813 GCACCTATCA
400823 ACAAAATGGATTTGTTGAGAGAAAAAATCGAACTTTAGAAGAAATGGCTAGAACCATGCTTTGTG
1 ACAAAATGGATTTGTTGAGAGAAAAAATCGAACTTTAGAAGAAATGGCTAGAACCATGCTTTGTG
400888 AAAACAATTTGCCTAAATATTTTTAGGCGGAAGCCACAAATACCGCTTG-T-TGTTATTAACCGA
66 AAAACAATTTGCCTAAATATTTTTAGGCGGAAGCCACAAATACCGCTTGTTATGTTATTAACCGA
400951 GTAATGATTA-ACCTATTTTAAAG-AAATTCCAT
131 GTAATGATTAGACCTATTTTAAAGAAAATTCCAT
400983 ACAAAATGGATTTGTTGAGAGAAAAAATCGAACTTTAGAAGAAATGGCTAGAACCATGCTTTGTG
1 ACAAAATGGATTTGTTGAGAGAAAAAATCGAACTTTAGAAGAAATGGCTAGAACCATGCTTTGTG
401048 AAAACAATTTGCCTAAATATTTTTAGGCGGAAGCCACAAATACCGCTTGTTATGTTATTAACCGA
66 AAAACAATTTGCCTAAATATTTTTAGGCGGAAGCCACAAATACCGCTTGTTATGTTATTAACCGA
401113 GTAATGATTAGACCTATTTTAAAGAAAATTCCAT
131 GTAATGATTAGACCTATTTTAAAGAAAATTCCAT
401147 A
1 A
401148 TGAAATTTTC
Statistics
Matches: 161, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
160 114 0.71
161 1 0.01
162 23 0.14
163 13 0.08
164 10 0.06
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (164 bp):
ACAAAATGGATTTGTTGAGAGAAAAAATCGAACTTTAGAAGAAATGGCTAGAACCATGCTTTGTG
AAAACAATTTGCCTAAATATTTTTAGGCGGAAGCCACAAATACCGCTTGTTATGTTATTAACCGA
GTAATGATTAGACCTATTTTAAAGAAAATTCCAT
Found at i:406004 original size:18 final size:18
Alignment explanation
Indices: 405981--406034 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
405971 GAATTTTAAG
405981 ATTTTATATTTGATTCAA
1 ATTTTATATTTGATTCAA
*
405999 ATTTTATATTTAATTCAA
1 ATTTTATATTTGATTCAA
*
406017 ATTTTATATTCGATTCAA
1 ATTTTATATTTGATTCAA
406035 TTATTCGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (18 bp):
ATTTTATATTTGATTCAA
Found at i:406455 original size:43 final size:44
Alignment explanation
Indices: 406389--406480 Score: 127
Period size: 42 Copynumber: 2.1 Consensus size: 44
406379 TTAAGGTACT
*
406389 GATACTACTTTCAATAGTAGTATCGATACCCCCATGGA-CAATATC
1 GATACTACTTACAATAGTAGTATCGATA-CCCC-TGGACCAATATC
*
406434 GATACTAC-TACAA-AGTAGTATCGATACCCCTTGACCAATATC
1 GATACTACTTACAATAGTAGTATCGATACCCCTGGACCAATATC
406476 GATAC
1 GATAC
406481 CATTGGGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 3 0.07
42 16 0.36
43 13 0.30
44 4 0.09
45 8 0.18
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (44 bp):
GATACTACTTACAATAGTAGTATCGATACCCCTGGACCAATATC
Found at i:408703 original size:36 final size:36
Alignment explanation
Indices: 408661--408772 Score: 165
Period size: 35 Copynumber: 3.2 Consensus size: 36
408651 TACTATATGT
408661 TCATCACCATCTTCCATCACCATTGTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGTCACGCCTATA
*
408697 TCATCACCATCTTCCATCACCATTG-CACGCTTATA
1 TCATCACCATCTTCCATCACCATTGTCACGCCTATA
* ** *
408732 TCAACACCATCTTTTATCACCATT-TCACGCCTATG
1 TCATCACCATCTTCCATCACCATTGTCACGCCTATA
408767 TCATCA
1 TCATCA
408773 TCATTCCTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 43 0.63
36 25 0.37
ACGTcount: A:0.26, C:0.37, G:0.05, T:0.32
Consensus pattern (36 bp):
TCATCACCATCTTCCATCACCATTGTCACGCCTATA
Found at i:412850 original size:13 final size:13
Alignment explanation
Indices: 412832--412856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
412822 TTTTGTTATT
412832 TTTTGATTTTTGG
1 TTTTGATTTTTGG
412845 TTTTGATTTTTG
1 TTTTGATTTTTG
412857 TTATTTTATT
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:0.08, C:0.00, G:0.20, T:0.72
Consensus pattern (13 bp):
TTTTGATTTTTGG
Found at i:412971 original size:15 final size:17
Alignment explanation
Indices: 412953--412984 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
412943 CATAATATAA
412953 TAAATT-CAA-ATAGAT
1 TAAATTGCAAGATAGAT
412968 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
412985 AAAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:413615 original size:20 final size:20
Alignment explanation
Indices: 413590--413636 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
413580 ACTGCACTCG
*
413590 TTTTTTCAAGATGCAAAATA
1 TTTTTTAAAGATGCAAAATA
*
413610 TTTTTTAAAGTTGCAAAATA
1 TTTTTTAAAGATGCAAAATA
413630 TTTTTTA
1 TTTTTTA
413637 CCAAATCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTTTTAAAGATGCAAAATA
Found at i:415834 original size:15 final size:17
Alignment explanation
Indices: 415803--415834 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
415793 ATGTATTTTT
415803 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
415820 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
415835 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:415978 original size:20 final size:20
Alignment explanation
Indices: 415929--415969 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
415919 AAAGAAAAGG
*
415929 AAAAGAAAAGAAAATAACAA
1 AAAAGAAAAAAAAATAACAA
*
415949 AAAAGTAAAAAAAATAA-AA
1 AAAAGAAAAAAAAATAACAA
415968 AA
1 AA
415970 TCAGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAAAAAATAACAA
Found at i:415987 original size:20 final size:18
Alignment explanation
Indices: 415939--415991 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
415929 AAAAGAAAAG
*
415939 AAAATAACAAAAAAGTAA
1 AAAATAACAAAAAAATAA
*
415957 AAAA-AA-TAAAAAATCAGA
1 AAAATAACAAAAAAAT-A-A
415975 AAAATAACAAAAAAATA
1 AAAATAACAAAAAAATA
415992 TAATATGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 6 0.21
17 3 0.11
18 9 0.32
19 3 0.11
20 7 0.25
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (18 bp):
AAAATAACAAAAAAATAA
Found at i:417742 original size:18 final size:18
Alignment explanation
Indices: 417711--417745 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
417701 GAAGAAGACT
*
417711 AAAAATAATGAAACGAAG
1 AAAAACAATGAAACGAAG
*
417729 AAAAACAATTAAACGAA
1 AAAAACAATGAAACGAA
417746 CCCGAGGAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAACAATGAAACGAAG
Found at i:418359 original size:25 final size:25
Alignment explanation
Indices: 418312--418358 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
418302 GTCACAAAAT
* *
418312 AATAAATTATGATAATAATAAAAGA
1 AATAAAGTATGATAACAATAAAAGA
418337 AATAAAGTAT-ATAACAATAAAA
1 AATAAAGTATGATAACAATAAAA
418359 AAAAGTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (25 bp):
AATAAAGTATGATAACAATAAAAGA
Found at i:421628 original size:961 final size:966
Alignment explanation
Indices: 419758--421687 Score: 3343
Period size: 961 Copynumber: 2.0 Consensus size: 966
419748 AGCATGATTA
*
419758 AGATTGCGTGCTATGTGAATGTGACATGCTTGCATTACATGTATGTGATGTACATTATGTGTTAT
1 AGATTGCGTGCTATGGGAATGTGACATGCTTGCATTACATGTATGTGATGTACATTATGTGTTAT
419823 GATAATGATTTATGAAAACAATACAAGAATATTATCTGAGTTACTGATTATTAACTTCTAAGATT
66 GATAATGATTTATGAAAACAATACAAGAATATTATCTGAGTTACTGATTATTAACTTCTAAGATT
419888 TCATGCATATGTAATATAAGTTATAAGATGAGAAAACATATATTTATATGTATATGAGAAGATAT
131 TCATGCATATGTAATATAAGTTATAAGATGAGAAAACATATATTTATATG-ATATGAGAAGATAT
*
419953 AGGAACAAGAAATAAGTCAAGTAATAAAGGAATATGAAATTGTATGAAATGTAACATAAGCTCTG
195 AGGAACAAGAAATAAGTCAAGTAATAAAGGAATATAAAATTGTATGAAATGTAACATAAGCTCTG
* * *
420018 TGATAAAGTCATAAGGAATGAAATAAACATGTGACCTAGGTTGTAAGTTAAAGCATTATTTGATA
260 TGATAAAGTCATAAGGAATGAAAAAAACATGTGACCTAGGTTATAAGTTAAAGAATTATTTGATA
420083 TAAGTAATTGTGATCATAAGATAATCAAGTATAGGTTATATTATATGGTATAAGGGTTTATATAA
325 TAAGTAATTGTGATCATAAGATAATCAAGTATAGGTTATATTATATGGTATAAGGGTTTATATAA
420148 GAAAAGGTTATAAGACTTTAGGAGAATAGTATGTAAATTAGGGTGCATAAATAAATGATGATACC
390 GAAAAGGTTATAAGACTTTAGGAGAATAGTATGTAAATTAGGGTGCATAAATAAATGATGATACC
420213 AAATTATAAGTTAAGTGTTTATAGAAGAATATATTTAAAAGAACTATGATATAGGAGTCATGTGA
455 AAATTATAAGTTAAGTGTTTATAGAAGAATATATTTAAAAGAACTATGATATAGGAGTCATGTGA
420278 CATGAAGCTAGATAAATGGATTAATTTAGTATATAAATTATGTTATGATATAGATTAAATGATCA
520 CATGAAGCTAGATAAATGGATTAATTTAGTATATAAATTATGTTATGATATAGATTAAATGATCA
420343 ATATAAATGCAAGATAGTATAATAAATTATATGAATTGATATAATCAATTATGTGAAAAGAAAAG
585 ATATAAATGCAAGATAGTATAATAAATTATATGAATTGA-ATAATCAATTATGTGAAAAGAAAAG
420408 AAAAGTGAGTTAAGATAAGTATTGACTTATAGGATAAATGAGATTATATGAACATATAGTATACC
649 AAAAGTGAGTTAAGATAAGTATTGACTTATAGGATAAATGAGATTATATGAACATATAGTATACC
420473 TTCATGAAAGATTTAGGTGTTATATTTTAGGTATGAAAATGATATATATGTAAGTGAATTATGTG
714 TTCATGAAAGATTTAGGTGTTATATTTTAGGTATGAAAATGATATATATGTAAGTGAATTATGTG
420538 ATTATGTGACTATGGGTGAAATGGAGTAAACTATGTAATTATAAAATATATGAATATATGTATAT
779 ATTATGTGACTATGGGTGAAATGGAGTAAACTATGTAATTATAAAATATATGAATATATGTATAT
*
420603 AAAATAGTCACGGACTATTGAGCTATATGAAATCAAATGAGAATGTTATGATAAGAAGTATAAGA
844 AAAATAGTCACGGACTATTAAGCTATATGAAATCAAATGAGAATGTTATGATAAGAAGTATAAGA
420668 GTATATGTTT-TGAG-AAA-ATAAGAATAAGTTATAAGACATGTGATATGTGATTTAT
909 GTATATGTTTATGAGAAAATATAAGAATAAGTTATAAGACATGTGATATGTGATTTAT
* * *
420723 AGATTGCGTGCTATGGGAATGTGACATGCTTGCATTAC-TGTTATGTGTGTGTGCATTTTGTGTT
1 AGATTGCGTGCTATGGGAATGTGACATGCTTGCATTACATG-TATGTG-ATGTACATTATGTG-T
420787 ATATGATAATGATTTATG-AAACAATACAAG-A-ATTATCTGAGTTACTGATTATTAACTTCTAA
63 -TATGATAATGATTTATGAAAACAATACAAGAATATTATCTGAGTTACTGATTATTAACTTCTAA
*
420849 GATTTCATGCATATGTAATATAAGTTATAAGATGAGAAATC-TATATTTATA-G-TATGAGAAGA
127 GATTTCATGCATATGTAATATAAGTTATAAGATGAGAAAACATATATTTATATGATATGAGAAGA
* *
420911 TATAGGAACAAGAAATAAGTCAAGTAATAAGGGAATATAAAATTGTATGAAATGTGACA-AAGCT
192 TATAGGAACAAGAAATAAGTCAAGTAATAAAGGAATATAAAATTGTATGAAATGTAACATAAGCT
*
420975 GTGTGATAAAGTCATAAGGAAT-AAAAAAACATGTGACCTAGGTTATAAGTTAAAGAATTATTTG
257 CTGTGATAAAGTCATAAGGAATGAAAAAAACATGTGACCTAGGTTATAAGTTAAAGAATTATTTG
*
421039 ATATAAGTAATTGTGATCATAAGATAATCAAGTATATGTTATA-TATATGGTATAAGGGTTTATA
322 ATATAAGTAATTGTGATCATAAGATAATCAAGTATAGGTTATATTATATGGTATAAGGGTTTATA
421103 T-AGAAAAGGTTATAAGACTTTAGGAGAATAGTATGTAAATTAGGGTGCATAAATATAAATGATG
387 TAAGAAAAGGTTATAAGACTTTAGGAGAATAGTATGTAAATTAGGGTGCAT-AA-ATAAATGATG
*
421167 ATACCAAATTATAAGTTAAGTGTTTATAGAAGAACTATATTTAAAAGAAATTATGATATAGGAGT
450 ATACCAAATTATAAGTTAAGTGTTTATAGAAGAA-TATATTTAAAAG-AACTATGATATAGGAGT
421232 CATGTGACATGAAGCTAGATAAATGGATTAATTTAGTATATAAATTATGTTATGATATAGATTAA
513 CATGTGACATGAAGCTAGATAAATGGATTAATTTAGTATATAAATTATGTTATGATATAGATTAA
421297 ATGATCAATATAAATGCAAGATAGTATAATAAATTATATGAA-TG-AT-AT-AATTATGTGAAAA
578 ATGATCAATATAAATGCAAGATAGTATAATAAATTATATGAATTGAATAATCAATTATGTGAAAA
421358 GAAAAGAAAAGTGAGTTAAGATAAGTA-TGACTTATAGGATAAAATGAGATTATATGAACATATA
643 GAAAAGAAAAGTGAGTTAAGATAAGTATTGACTTATAGGAT-AAATGAGATTATATGAACATATA
421422 GTA-A-C-T-ATGAGGAAGATTTA-GTGGTTATATGATTTAGGTATGAAAATGATATATATGTAA
707 GTATACCTTCATGA--AAGATTTAGGT-GTTATAT--TTTAGGTATGAAAATGATATATATGTAA
421482 GTGAATTA-GTGATTATGTGACTATGGGTGAAATGGAGTAAACTATGTAATTATAAAATATATGA
767 GTGAATTATGTGATTATGTGACTATGGGTGAAATGGAGTAAACTATGTAATTATAAAATATATGA
421546 ATATATGTATATAAAATAAGTCACGTGACTATTAAGCTATATGAAATCAAATGATAAGAATGTTA
832 ATATATGTATATAAAAT-AGTCACG-GACTATTAAGCTATATGAAATCAAATG---AGAATGTTA
*
421611 TGATAAGAAGTTATAAGAGTATCTGTTTATGAGAAAATATAAGAATAAGTTATAAGACATGTGAT
892 TGATAAGAAG-TATAAGAGTATATGTTTATGAGAAAATATAAGAATAAGTTATAAGACATGTGAT
421676 ATGTGATTTAT
956 ATGTGATTTAT
421687 A
1 A
421688 TGGAATTGTT
Statistics
Matches: 926, Mismatches: 16, Indels: 47
0.94 0.02 0.05
Matches are distributed among these distances:
952 4 0.00
953 3 0.00
954 16 0.02
955 87 0.09
956 109 0.12
957 77 0.08
958 26 0.03
959 125 0.13
960 59 0.06
961 205 0.22
962 4 0.00
963 4 0.00
964 51 0.06
965 114 0.12
966 12 0.01
967 13 0.01
968 17 0.02
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (966 bp):
AGATTGCGTGCTATGGGAATGTGACATGCTTGCATTACATGTATGTGATGTACATTATGTGTTAT
GATAATGATTTATGAAAACAATACAAGAATATTATCTGAGTTACTGATTATTAACTTCTAAGATT
TCATGCATATGTAATATAAGTTATAAGATGAGAAAACATATATTTATATGATATGAGAAGATATA
GGAACAAGAAATAAGTCAAGTAATAAAGGAATATAAAATTGTATGAAATGTAACATAAGCTCTGT
GATAAAGTCATAAGGAATGAAAAAAACATGTGACCTAGGTTATAAGTTAAAGAATTATTTGATAT
AAGTAATTGTGATCATAAGATAATCAAGTATAGGTTATATTATATGGTATAAGGGTTTATATAAG
AAAAGGTTATAAGACTTTAGGAGAATAGTATGTAAATTAGGGTGCATAAATAAATGATGATACCA
AATTATAAGTTAAGTGTTTATAGAAGAATATATTTAAAAGAACTATGATATAGGAGTCATGTGAC
ATGAAGCTAGATAAATGGATTAATTTAGTATATAAATTATGTTATGATATAGATTAAATGATCAA
TATAAATGCAAGATAGTATAATAAATTATATGAATTGAATAATCAATTATGTGAAAAGAAAAGAA
AAGTGAGTTAAGATAAGTATTGACTTATAGGATAAATGAGATTATATGAACATATAGTATACCTT
CATGAAAGATTTAGGTGTTATATTTTAGGTATGAAAATGATATATATGTAAGTGAATTATGTGAT
TATGTGACTATGGGTGAAATGGAGTAAACTATGTAATTATAAAATATATGAATATATGTATATAA
AATAGTCACGGACTATTAAGCTATATGAAATCAAATGAGAATGTTATGATAAGAAGTATAAGAGT
ATATGTTTATGAGAAAATATAAGAATAAGTTATAAGACATGTGATATGTGATTTAT
Found at i:421982 original size:18 final size:18
Alignment explanation
Indices: 421938--422011 Score: 103
Period size: 18 Copynumber: 3.9 Consensus size: 18
421928 AGGGATTATC
*
421938 AGTGGTCCTTTGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
421958 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
421977 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
421995 AGTGGTCCTTAGGGACA
1 AGTGGTCCTTCGGGACA
422012 AATTTCAGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
18 34 0.67
19 2 0.04
21 15 0.29
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:423141 original size:21 final size:21
Alignment explanation
Indices: 423117--423161 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
423107 TGAATTTTTA
423117 CTACAATTCTTTCTGTAAATT
1 CTACAATTCTTTCTGTAAATT
*
423138 CTACAATTCTTTTTGTAAATT
1 CTACAATTCTTTCTGTAAATT
423159 CTA
1 CTA
423162 TCCTAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (21 bp):
CTACAATTCTTTCTGTAAATT
Found at i:423275 original size:17 final size:15
Alignment explanation
Indices: 423253--423287 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
423243 ATACATCTAA
423253 TAATTTTATATAATATT
1 TAATTTTA-ATAA-ATT
423270 TAATTTTAATAAATT
1 TAATTTTAATAAATT
423285 TAA
1 TAA
423288 AATAGGGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 4 0.22
17 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTTTAATAAATT
Found at i:424631 original size:30 final size:29
Alignment explanation
Indices: 424596--424682 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
424586 TTAGCATTAA
424596 AAATATATTTTATTTTTATATTAACTTATT
1 AAATATATTTTATTTTTAT-TTAACTTATT
* * *
424626 AAATATATTTTATTATTATTTTAACCTA-A
1 AAATATATTTTATTTTTA-TTTAACTTATT
*
424655 AAATATA-TTTATTTTTATCTAACTTATT
1 AAATATATTTTATTTTTATTTAACTTATT
424683 TTTTTTGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 7 0.15
28 9 0.19
29 7 0.15
30 24 0.50
31 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (29 bp):
AAATATATTTTATTTTTATTTAACTTATT
Found at i:426088 original size:17 final size:17
Alignment explanation
Indices: 426066--426103 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
426056 ACCAATTCAA
426066 CATCATATTCATCCTTG
1 CATCATATTCATCCTTG
426083 CATCATATTCATCCTTG
1 CATCATATTCATCCTTG
426100 CATC
1 CATC
426104 TCCAACCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.39
Consensus pattern (17 bp):
CATCATATTCATCCTTG
Found at i:426225 original size:25 final size:28
Alignment explanation
Indices: 426178--426229 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
426168 ATGATGATTA
426178 TATTCATAATATATGATTCATATCTTATT
1 TATTCATAATATATGATTCATAT-TTATT
426207 TATT-ATAATATA-GA-T-ATATTTAT
1 TATTCATAATATATGATTCATATTTAT
426230 ATACATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 4 0.17
25 4 0.17
26 1 0.04
27 2 0.09
28 8 0.35
29 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (28 bp):
TATTCATAATATATGATTCATATTTATT
Found at i:427307 original size:54 final size:50
Alignment explanation
Indices: 427235--427348 Score: 138
Period size: 54 Copynumber: 2.2 Consensus size: 50
427225 ATTGCACCGA
** *
427235 AGTGTCGAAATGGAAATTCACAAACTTATTATGAATTCCATGGATTGCACACAT
1 AGTGTCGAAATGGAAATTCACAAACACATTAT-AA--CCATGG-TTACACACAT
* * *
427289 AGTGTCGAAATGGTAATTCATAAACACATTATAACCATGGTTACACATAT
1 AGTGTCGAAATGGAAATTCACAAACACATTATAACCATGGTTACACACAT
427339 AGTGTCGAAA
1 AGTGTCGAAA
427349 ATACACCATT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
50 18 0.33
51 6 0.11
53 2 0.04
54 28 0.52
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (50 bp):
AGTGTCGAAATGGAAATTCACAAACACATTATAACCATGGTTACACACAT
Found at i:438888 original size:21 final size:22
Alignment explanation
Indices: 438844--438888 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
438834 GCACTCATGG
*
438844 AAAGCAAGCCTAACTGCTCATC
1 AAAGCAAGCCTAACTGCGCATC
* *
438866 AAAGCCAG-CTAACTGCGCTTC
1 AAAGCAAGCCTAACTGCGCATC
438887 AA
1 AA
438889 CGTCTAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.36, C:0.31, G:0.16, T:0.18
Consensus pattern (22 bp):
AAAGCAAGCCTAACTGCGCATC
Found at i:439140 original size:20 final size:19
Alignment explanation
Indices: 439115--439178 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
439105 AAAATGCTAA
439115 AGTGTATCGATACACTCTGC
1 AGTGTATCGATACAC-CTGC
439135 AGTGTATAC-ATACA-CTG-
1 AGTGTAT-CGATACACCTGC
*
439152 -GTGTACCGATACACCCTGC
1 AGTGTATCGATACA-CCTGC
439171 AGTGTATC
1 AGTGTATC
439179 CACACCCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 1 0.03
16 10 0.28
18 6 0.17
20 18 0.50
21 1 0.03
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (19 bp):
AGTGTATCGATACACCTGC
Found at i:439239 original size:20 final size:20
Alignment explanation
Indices: 439214--439253 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
439204 TGAATGTAAT
*
439214 TAGTGTA-CCGATACAGTCTG
1 TAGTGTATCC-ATACACTCTG
439234 TAGTGTATCCATACACTCTG
1 TAGTGTATCCATACACTCTG
439254 GCTGCAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (20 bp):
TAGTGTATCCATACACTCTG
Found at i:439400 original size:20 final size:22
Alignment explanation
Indices: 439362--439401 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
439352 GTTTTGTAGA
439362 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
439384 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
439402 AGATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:439670 original size:33 final size:33
Alignment explanation
Indices: 439624--439687 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
439614 AGGGGTTTTT
*
439624 GGTTCTAGCTTAGCCTACT-AAAAACTAGGGAAA
1 GGTTCTAGCTTAGCCCA-TGAAAAACTAGGGAAA
*
439657 GGTTCTAGTTTAGCCCATGAAAAACTAGGGA
1 GGTTCTAGCTTAGCCCATGAAAAACTAGGGA
439688 GTTTGTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (33 bp):
GGTTCTAGCTTAGCCCATGAAAAACTAGGGAAA
Found at i:441569 original size:43 final size:44
Alignment explanation
Indices: 441521--441623 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 44
441511 TAAACATCAT
*
441521 AAAAGGTCGATATATATAACAACATTTTTAGA-ATAAACGCCGC
1 AAAAGGTCGATATATATAACAACATTTTTAGATACAAACGCCGC
* * * ** *
441564 TAAAGGTC-AGATCTATAACGGCATTTTTGGATACAAACGCCGC
1 AAAAGGTCGATATATATAACAACATTTTTAGATACAAACGCCGC
*
441607 AAAAGGTCAGATCTATA
1 AAAAGGTC-GATATATA
441624 GCGATATTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
42 18 0.39
43 24 0.52
45 4 0.09
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (44 bp):
AAAAGGTCGATATATATAACAACATTTTTAGATACAAACGCCGC
Found at i:441633 original size:43 final size:43
Alignment explanation
Indices: 441555--441734 Score: 213
Period size: 43 Copynumber: 4.2 Consensus size: 43
441545 TTTTTAGAAT
* * *
441555 AAACGCCGCTAAAGGTCAGATCTATAACGGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGTATTTTTGGATAC
*
441598 AAACGCCGCAAAAGGTCAGATCTATAGCGATATTTTTGGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGTATTTTTGGATAC
**
441640 AAACATCGCAAAAGGTCAGATCTATAGCGGCGT-TTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGC-G-GTATTTTTGGATAC
* * * **
441684 AAACGCCACAAAAGGTCAGCTCTATAGCTGCGTTTTT-GATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGTATTTTTGGATAC
*
441726 AAAAGCCGC
1 AAACGCCGC
441735 TATATATGCA
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
42 41 0.35
43 50 0.42
44 27 0.23
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGTATTTTTGGATAC
Done.