Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 79 of 163
Found at i:21167684 original size:18 final size:17
Alignment explanation
Indices: 21167621--21167700 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 17
21167611 AATGGCACAC
*
21167621 AAATAAAT-AACAA-AT
1 AAATAAATAAAAAATAT
21167636 AAATAAAATAAAAAAT-T
1 AAAT-AAATAAAAAATAT
**
21167653 AAATAAAGGCAAAAATAT
1 AAATAAA-TAAAAAATAT
*
21167671 AAATAACAT-AAAAATAAA
1 AAATAA-ATAAAAAAT-AT
21167689 AAATAAATAAAA
1 AAATAAATAAAA
21167701 TAAAATAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
15 4 0.08
16 7 0.13
17 23 0.44
18 17 0.33
19 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.19
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:21167688 original size:61 final size:64
Alignment explanation
Indices: 21167586--21167709 Score: 164
Period size: 61 Copynumber: 2.0 Consensus size: 64
21167576 TAAAACATGT
* ** * *
21167586 AATTAAATAAAAGGCAAAAAATGTAAATGGCACACAAATAAATAACAAAT-AAATAAAATAAAA
1 AATTAAATAAAAGGCAAAAAATATAAATAACACAAAAATAAAAAACAAATAAAATAAAATAAAA
* *
21167649 AATTAAAT-AAAGGC-AAAAATATAAATAACATAAAAATAAAAAATAAATAAAATAAAATAAA
1 AATTAAATAAAAGGCAAAAAATATAAATAACACAAAAATAAAAAACAAATAAAATAAAATAAA
21167710 GGCAAGAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 27 0.51
62 18 0.34
63 8 0.15
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.19
Consensus pattern (64 bp):
AATTAAATAAAAGGCAAAAAATATAAATAACACAAAAATAAAAAACAAATAAAATAAAATAAAA
Found at i:21167699 original size:11 final size:11
Alignment explanation
Indices: 21167621--21167817 Score: 56
Period size: 11 Copynumber: 17.7 Consensus size: 11
21167611 AATGGCACAC
*
21167621 AAATAAATAAC
1 AAATAAATAAA
21167632 AAATAAAT--A
1 AAATAAATAAA
21167641 AAATAAA-AAA
1 AAATAAATAAA
*
21167651 TTAAATAAAGGCAAA
1 --AAATAAA--TAAA
21167666 AATATAAATAACA
1 AA-ATAAATAA-A
*
21167679 TAA-AAATAAA
1 AAATAAATAAA
21167689 AAATAAATAAA
1 AAATAAATAAA
*
21167700 ATA-AAATAAA
1 AAATAAATAAA
* * **
21167710 GGCAA-GAAT-GT
1 --AAATAAATAAA
21167721 AAATAACATAAA
1 AAATAA-ATAAA
* *
21167733 AAATGAATAAC
1 AAATAAATAAA
21167744 AAATAAAT---
1 AAATAAATAAA
*
21167752 AAATAGA-AAA
1 AAATAAATAAA
*
21167762 TAATAAATAAA
1 AAATAAATAAA
* **
21167773 AATTAAATACT
1 AAATAAATAAA
21167784 AAATAAACTATACA
1 AAATAAA-TA-A-A
21167798 AAATAATATAAA
1 AAATAA-ATAAA
*
21167810 GAATAAAT
1 AAATAAAT
21167818 GGGATCAAAT
Statistics
Matches: 135, Mismatches: 28, Indels: 46
0.65 0.13 0.22
Matches are distributed among these distances:
8 6 0.04
9 9 0.07
10 17 0.13
11 54 0.40
12 27 0.20
13 5 0.04
14 13 0.10
15 4 0.03
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:21167701 original size:50 final size:50
Alignment explanation
Indices: 21167621--21167734 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
21167611 AATGGCACAC
*
21167621 AAATAA-ATAACAAATAAATAAAATAAAAAATTAAATAAAGGCAAAAATAT
1 AAATAACATAA-AAATAAATAAAATAAAAAATAAAATAAAGGCAAAAATAT
* *
21167671 AAATAACATAAAAAT-AA-AAAATAAATAAAATAAAATAAAGGCAAGAATGT
1 AAATAACATAAAAATAAATAAAAT-AA-AAAATAAAATAAAGGCAAAAATAT
21167721 AAATAACATAAAAA
1 AAATAACATAAAAA
21167735 ATGAATAACA
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
48 5 0.09
49 4 0.07
50 45 0.78
51 4 0.07
ACGTcount: A:0.72, C:0.04, G:0.05, T:0.18
Consensus pattern (50 bp):
AAATAACATAAAAATAAATAAAATAAAAAATAAAATAAAGGCAAAAATAT
Found at i:21167768 original size:14 final size:14
Alignment explanation
Indices: 21167621--21167781 Score: 76
Period size: 15 Copynumber: 10.4 Consensus size: 14
21167611 AATGGCACAC
21167621 AAATAAATAACAAAT
1 AAATAAATAA-AAAT
21167636 AAATAAAATAAAAAATT
1 AAAT-AAAT-AAAAA-T
*
21167653 AAATAAAGGCAAAAATAT
1 AAATAAA---TAAAA-AT
21167671 AAATAACATAAAAAT
1 AAATAA-ATAAAAAT
*
21167686 AAA-AAATAAATA-
1 AAATAAATAAAAAT
*
21167698 AAATAAAATAAAGGCAAG
1 AAAT-AAATAAA---AAT
* *
21167716 AATGTAAATAACATAAA
1 AA-ATAAATAA-A-AAT
*
21167733 AAATGAATAACAAAT
1 AAATAAATAA-AAAT
21167748 AAATAAATAGAAAAT
1 AAATAAATA-AAAAT
21167763 -AATAAATAAAAATT
1 AAATAAATAAAAA-T
21167777 AAATA
1 AAATA
21167782 CTAAATAAAC
Statistics
Matches: 116, Mismatches: 11, Indels: 38
0.70 0.07 0.23
Matches are distributed among these distances:
12 3 0.03
13 10 0.09
14 18 0.16
15 27 0.23
16 23 0.20
17 12 0.10
18 19 0.16
19 4 0.03
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.20
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:21167780 original size:18 final size:18
Alignment explanation
Indices: 21167745--21167790 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
21167735 ATGAATAACA
*
21167745 AATAAATAAATAGAAAAT
1 AATAAATAAAAAGAAAAT
**
21167763 AATAAATAAAAATTAAAT
1 AATAAATAAAAAGAAAAT
*
21167781 ACTAAATAAA
1 AATAAATAAA
21167791 CTATACAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAATAAAAAGAAAAT
Found at i:21169201 original size:12 final size:13
Alignment explanation
Indices: 21169184--21169215 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
21169174 TTAATTTAGG
21169184 TTTATTTTA-TTA
1 TTTATTTTATTTA
21169196 TTTATTTTATTTA
1 TTTATTTTATTTA
21169209 TTTATTT
1 TTTATTT
21169216 ATATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:21169206 original size:17 final size:17
Alignment explanation
Indices: 21169184--21169217 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21169174 TTAATTTAGG
21169184 TTTATTT-TATTATTTAT
1 TTTATTTAT-TTATTTAT
21169201 TTTATTTATTTATTTAT
1 TTTATTTATTTATTTAT
21169218 ATAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTTATTTAT
Found at i:21170167 original size:99 final size:100
Alignment explanation
Indices: 21169762--21170710 Score: 1125
Period size: 99 Copynumber: 9.6 Consensus size: 100
21169752 TTCTAACTTA
* * * *
21169762 ACTCCATTCCATTACAACTTCAGTGGAGATTGAGATCTGTTAC-GATTAGTTTTAATCTG--CCC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTG-TTAGTTTTAATCCGATCCA
* * * * *
21169824 CT-CTATGACTTTAGGGGTATAGAATTTGATGTGCCTTC
65 CTGC-AT--CTTCAGGGATATAGGATTTGGTGTGGCTTC
* * * * *
21169862 AATCTATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTATTGTTAGTTTTAATCCGATTCAT
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCCGATCCAC
* * *
21169927 TACATCTTTAGGGATATAGGAGTTGGTGTGGCTTC
66 TGCATCTTCAGGGATATAGGATTTGGTGTGGCTTC
* * ** *
21169962 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATATTCTACTGTTAGTTTTAATCAAATCCAT
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCCGATCCAC
* *
21170027 TGCATCTTCAAGGATATAGGATTTGGTGTGACTTC
66 TGCATCTTCAGGGATATAGGATTTGGTGTGGCTTC
* *
21170062 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTGCTACTGTTAG-TTTAATCTGATCCAC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCCGATCCAC
*
21170126 TGCATCTTCAAGGATATAGGATTTGGTGTGGCTTC
66 TGCATCTTCAGGGATATAGGATTTGGTGTGGCTTC
* * * *
21170161 ACTCCATTTCACTACAACTTCAGTGGATATTGAGATCTGCTACTGTTAG-GTTAACCCGATCCAC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCCGATCCAC
* * * * *
21170225 TACATCTTCAGGGATATTGGAGTTAGTGTGGTTTC
66 TGCATCTTCAGGGATATAGGATTTGGTGTGGCTTC
* * * * * *
21170260 ACTCCATTCCACTGCAACTTCAGTGAAGATTGAGATCTACTACTATT-GTTTTAATCCAACCCAC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCCGATCCAC
* *
21170324 TGTAACTTCAAGGG-TATAGGATTTGGTGTGGCTTC
66 TGCATCTTC-AGGGATATAGGATTTGGTGTGGCTTC
* * * * *
21170359 ACTCCATTCCACTGCAATTTCAGTTGAGATTGAGATTTGCTACTGTTAGTTTT-ATTCGATCCAC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCCGATCCAC
*
21170423 TGTATCTTCAGGGATATAGGATTTGGTGTGGCTTC
66 TGCATCTTCAGGGATATAGGATTTGGTGTGGCTTC
** * * *
21170458 ACTTTATTCCACTACAACTTCAATGGAGATTGAGATCTACTATTGTTAG-TTTAA-CCAGATCCA
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCC-GATCCA
* * *
21170521 CTGCATCTTCAGGGATATAAGATTTAGTGTGGTTTC
65 CTGCATCTTCAGGGATATAGGATTTGGTGTGGCTTC
* * * * *
21170557 ACTCCGTTCCACTTCAACTTCAGTGGAGATTGAGATCTGCTACT-ATAGTTTTAATCCAACCCAC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCCGATCCAC
* *
21170621 TGCAACTTCAAGGG-TATAGGATTTGGTGTGGCATC
66 TGCATCTTC-AGGGATATAGGATTTGGTGTGGCTTC
* * *
21170656 ACTCCATTCCACTGCAACTTTAGTGGAGATTGAGATTTGCTACTGTT-GTTTTAAT
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAAT
21170711 TTGACCCACT
Statistics
Matches: 729, Mismatches: 106, Indels: 29
0.84 0.12 0.03
Matches are distributed among these distances:
98 12 0.02
99 485 0.67
100 226 0.31
101 1 0.00
102 4 0.01
103 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (100 bp):
ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCTACTGTTAGTTTTAATCCGATCCAC
TGCATCTTCAGGGATATAGGATTTGGTGTGGCTTC
Found at i:21170227 original size:52 final size:51
Alignment explanation
Indices: 21170069--21170243 Score: 132
Period size: 52 Copynumber: 3.5 Consensus size: 51
21170059 TTCACTCCAT
* * * *
21170069 TCCACTACAACTTCAGTGGAGATTGAGATTTGCTACTGTTAGTTTAATCTGA
1 TCCACTACAACTTCAGTGGATATTGAGA-TTGCTACTGTTAGGTTAACCCGA
* * * * ** *
21170121 TCCACTGCATCTTCA-AGGATATAG-GATT--TGGTG-T-GGCTTCACTCC-A
1 TCCACTACAACTTCAGTGGATATTGAGATTGCTACTGTTAGG-TTAAC-CCGA
*
21170167 TTTCACTACAACTTCAGTGGATATTGAGATCTGCTACTGTTAGGTTAACCCGA
1 -TCCACTACAACTTCAGTGGATATTGAGAT-TGCTACTGTTAGGTTAACCCGA
*
21170220 TCCACTACATCTTCAG-GGATATTG
1 TCCACTACAACTTCAGTGGATATTG
21170244 GAGTTAGTGT
Statistics
Matches: 91, Mismatches: 21, Indels: 23
0.67 0.16 0.17
Matches are distributed among these distances:
45 1 0.01
46 5 0.05
47 16 0.18
48 7 0.08
49 5 0.05
50 3 0.03
51 14 0.15
52 32 0.35
53 6 0.07
54 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (51 bp):
TCCACTACAACTTCAGTGGATATTGAGATTGCTACTGTTAGGTTAACCCGA
Found at i:21170281 original size:47 final size:46
Alignment explanation
Indices: 21170121--21170282 Score: 112
Period size: 47 Copynumber: 3.3 Consensus size: 46
21170111 TTTAATCTGA
* * * * * *
21170121 TCCACTGCATCTTCAAGGATATAGGATTTGGTGTGGCTTCACTCCAT
1 TCCACTACAACTTCAGGGATATTGGAGTTAGTGTGG-TTCACTCCAT
* * * *
21170168 TTCACTACAACTTCAGTGGATATTGAGATCTGCTACTGTTAGGTTAAC-CCGA-
1 TCCACTACAACTTCAG-GGATATTG-GA---GTTAGTG-T-GGTTCACTCC-AT
*
21170220 TCCACTACATCTTCAGGGATATTGGAGTTAGTGTGGTTTCACTCCAT
1 TCCACTACAACTTCAGGGATATTGGAGTTAGTGTGG-TTCACTCCAT
*
21170267 TCCACTGCAACTTCAG
1 TCCACTACAACTTCAG
21170283 TGAAGATTGA
Statistics
Matches: 87, Mismatches: 17, Indels: 22
0.69 0.13 0.17
Matches are distributed among these distances:
45 2 0.02
46 6 0.07
47 33 0.38
48 7 0.08
49 2 0.02
50 2 0.02
51 8 0.09
52 19 0.22
53 6 0.07
54 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (46 bp):
TCCACTACAACTTCAGGGATATTGGAGTTAGTGTGGTTCACTCCAT
Found at i:21170731 original size:297 final size:297
Alignment explanation
Indices: 21169762--21170731 Score: 1309
Period size: 297 Copynumber: 3.3 Consensus size: 297
21169752 TTCTAACTTA
* * * * *
21169762 ACTCCATTCCATTACAACTTCAGTGGAGATTGAGATCTGTTAC-GATTAGTTTTAATCTGCCCCT
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTGCTACTG-TTAGTTTTAATCTGACCCA
* * * * * * *
21169826 CTATGACTTTAGGGGTATAGAATTTGATGTGCCTTCAATCTATTCCACTACAACTTCAGTGGAGA
65 CTATAACTTCAGGGATATAGGATTTGGTGTGGCTTCACTCTATTCCACTACAACTTCAGTGGAGA
* * * *
21169891 TTGAGATCTGCTATTGTTAGTTTTAATCCGATTCATTACATCTTTAGGGATATAGGAGTTGGTGT
130 TTGAGATCTGCTATTGTTAG-TTTAA-CCGATCCACTACATCTTCAGGGATATAGGAGTTAGTGT
* * * * *
21169956 GGCTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATATTCTACTGTTAGTTTTAATCAA
193 GGTTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTACTACT-ATAGTTTTAATCCA
* * * * *
21170021 ATCCATTGCATCTTCAAGGATATAGGATTTGGTGTGACTTC
257 ACCCACTGCAACTTCAAGGGTATAGGATTTGGTGTGGCTTC
*
21170062 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTGCTACTGTTAG-TTTAATCTGATCCAC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTGCTACTGTTAGTTTTAATCTGACCCAC
** * * * * *
21170126 TGCATCTTCAAGGATATAGGATTTGGTGTGGCTTCACTCCATTTCACTACAACTTCAGTGGATAT
66 TATAACTTCAGGGATATAGGATTTGGTGTGGCTTCACTCTATTCCACTACAACTTCAGTGGAGAT
* * *
21170191 TGAGATCTGCTACTGTTAGGTTAACCCGATCCACTACATCTTCAGGGATATTGGAGTTAGTGTGG
131 TGAGATCTGCTATTGTTAGTTTAA-CCGATCCACTACATCTTCAGGGATATAGGAGTTAGTGTGG
* * *
21170256 TTTCACTCCATTCCACTGCAACTTCAGTGAAGATTGAGATCTACTACTATTGTTTTAATCCAACC
195 TTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTACTACTATAGTTTTAATCCAACC
*
21170321 CACTGTAACTTCAAGGGTATAGGATTTGGTGTGGCTTC
260 CACTGCAACTTCAAGGGTATAGGATTTGGTGTGGCTTC
* * * * *
21170359 ACTCCATTCCACTGCAATTTCAGTTGAGATTGAGATTTGCTACTGTTAGTTTTATTC-GATCCAC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTGCTACTGTTAGTTTTAATCTGACCCAC
* * * *
21170423 TGTATCTTCAGGGATATAGGATTTGGTGTGGCTTCACTTTATTCCACTACAACTTCAATGGAGAT
66 TATAACTTCAGGGATATAGGATTTGGTGTGGCTTCACTCTATTCCACTACAACTTCAGTGGAGAT
* * * *
21170488 TGAGATCTACTATTGTTAGTTTAACCAGATCCACTGCATCTTCAGGGATATAAGATTTAGTGTGG
131 TGAGATCTGCTATTGTTAGTTTAACC-GATCCACTACATCTTCAGGGATATAGGAGTTAGTGTGG
* * *
21170553 TTTCACTCCGTTCCACTTCAACTTCAGTGGAGATTGAGATCTGCTACTATAGTTTTAATCCAACC
195 TTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTACTACTATAGTTTTAATCCAACC
*
21170618 CACTGCAACTTCAAGGGTATAGGATTTGGTGTGGCATC
260 CACTGCAACTTCAAGGGTATAGGATTTGGTGTGGCTTC
* * *
21170656 ACTCCATTCCACTGCAACTTTAGTGGAGATTGAGATTTGCTACTGTT-GTTTTAATTTGACCCAC
1 ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTGCTACTGTTAGTTTTAATCTGACCCAC
21170720 TATAACTTCAGG
66 TATAACTTCAGG
21170732 AAAATAGAAT
Statistics
Matches: 591, Mismatches: 75, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
296 9 0.02
297 368 0.62
298 88 0.15
299 81 0.14
300 44 0.07
301 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (297 bp):
ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTGCTACTGTTAGTTTTAATCTGACCCAC
TATAACTTCAGGGATATAGGATTTGGTGTGGCTTCACTCTATTCCACTACAACTTCAGTGGAGAT
TGAGATCTGCTATTGTTAGTTTAACCGATCCACTACATCTTCAGGGATATAGGAGTTAGTGTGGT
TTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTACTACTATAGTTTTAATCCAACCC
ACTGCAACTTCAAGGGTATAGGATTTGGTGTGGCTTC
Found at i:21171888 original size:5 final size:5
Alignment explanation
Indices: 21171819--21171901 Score: 62
Period size: 5 Copynumber: 16.0 Consensus size: 5
21171809 TCGGCCTCTC
* * * *
21171819 CTTTT CTTTTT CCTTTC CTTTC CTTTC CTTTC CTTTTCT CTTTCT CTTTT
1 CTTTT C-TTTT -CTTTT CTTTT CTTTT CTTTT C-TTT-T CTTT-T CTTTT
*
21171869 CTTTT CTTTT CTTTT CTTTT -TTCT -TTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
21171902 TTTGTGTGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
4 6 0.09
5 42 0.61
6 19 0.28
7 2 0.03
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (5 bp):
CTTTT
Found at i:21171894 original size:33 final size:33
Alignment explanation
Indices: 21171820--21171901 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
21171810 CGGCCTCTCC
*
21171820 TTTTCTTTTTCCTTTCCTTTCCTTTCCTTTCCTT
1 TTTTCTTTTT-CTTTTCTTTCCTTTCCTTTCCTT
* * * * *
21171854 TTCTCTTTCTCTTTTCTTTTCTTTTCTTTTCTT
1 TTTTCTTTTTCTTTTCTTTCCTTTCCTTTCCTT
21171887 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
21171902 TTTGTGTGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 32 0.80
34 8 0.20
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTCTTTTTCTTTTCTTTCCTTTCCTTTCCTT
Found at i:21171895 original size:6 final size:6
Alignment explanation
Indices: 21171847--21171902 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
21171837 TTTCCTTTCC
* *
21171847 TTTCCT TTTCTC TTTCTCT TTTC-T TTTC-T TTTC-T TTTCTTT TTTCTT
1 TTTCTT TTTCTT TTTCT-T TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT
21171894 TTTCTT TTT
1 TTTCTT TTT
21171903 TTGTGTGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
5 15 0.34
6 20 0.45
7 9 0.20
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:21173210 original size:65 final size:66
Alignment explanation
Indices: 21173124--21173312 Score: 184
Period size: 65 Copynumber: 2.8 Consensus size: 66
21173114 ATTCTATTCA
* * *
21173124 TTTCAAGATGCCCTTTGTGGGTTATCATCTTGACTTCTTTT-TTCTTTTCTTTTTT-TTTGTTTA
1 TTTCAAGATACCCTTTGTGGGTTATCATCTCGACCTCTTTTCTT-TTTTCTTTTTTGTTTGTTTA
21173187 GG
65 GG
* * *
21173189 TTTCAAGATACCTTTTTTGGGTTTTCATCTCGACCTCTTTTCTTTTTTCTTTTTTGTTTGTTTTT
1 TTTCAAGATACCCTTTGTGGGTTATCATCTCGACCTCTTTTCTTTTTTCTTTTTTGTTTG--TTT
***
21173254 TTA
64 AGG
* * * * * * *
21173257 TTTCAAGATGCCTTTTGTGGGTTTTTATCTCGATCATTTTTTCTTTTTCCTTTTTT
1 TTTCAAGATACCCTTTGTGGGTTATCATCTCGA-CCTCTTTTCTTTTTTCTTTTTT
21173313 TAGCCTCCTC
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 46 0.44
66 6 0.06
68 33 0.32
69 19 0.18
ACGTcount: A:0.11, C:0.16, G:0.13, T:0.61
Consensus pattern (66 bp):
TTTCAAGATACCCTTTGTGGGTTATCATCTCGACCTCTTTTCTTTTTTCTTTTTTGTTTGTTTAG
G
Found at i:21173281 original size:68 final size:69
Alignment explanation
Indices: 21173158--21173313 Score: 199
Period size: 68 Copynumber: 2.2 Consensus size: 69
21173148 TCATCTTGAC
* *
21173158 TTCTTTTTTCTTTTCTTTTTTTTTGTTTAGGTTTCAAGATACCTTTTTTGGGTTTTCATCTCGA-
1 TTCTTTTTTCTTTT-TTTTTGTTTGTTTA-GTTTCAAGATACCTTTTGTGGGTTTTCATCTCGAT
*
21173222 CCTCTT
64 CATCTT
* * *
21173228 TTCTTTTTTCTTTTTTGTTTGTTTTTTTA-TTTCAAGATGCCTTTTGTGGGTTTTTATCTCGATC
1 TTCTTTTTTCTTTTTT-TTTGTTTGTTTAGTTTCAAGATACCTTTTGTGGGTTTTCATCTCGATC
*
21173292 ATTTT
65 ATCTT
*
21173297 TTCTTTTTCCTTTTTTT
1 TTCTTTTTTCTTTTTTT
21173314 AGCCTCCTCT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
68 31 0.41
69 21 0.28
70 24 0.32
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.65
Consensus pattern (69 bp):
TTCTTTTTTCTTTTTTTTTGTTTGTTTAGTTTCAAGATACCTTTTGTGGGTTTTCATCTCGATCA
TCTT
Found at i:21174212 original size:14 final size:13
Alignment explanation
Indices: 21174188--21174231 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
21174178 TTTTATTAAT
*
21174188 TAATTAATGCATG
1 TAATAAATGCATG
21174201 TAATGAAATGCATTG
1 TAAT-AAATGCA-TG
21174216 CTAATAAATGCATG
1 -TAATAAATGCATG
21174230 TA
1 TA
21174232 TGCATATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 6 0.22
14 8 0.30
15 9 0.33
16 4 0.15
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (13 bp):
TAATAAATGCATG
Found at i:21181920 original size:21 final size:22
Alignment explanation
Indices: 21181864--21181920 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 22
21181854 GCACAAGATA
21181864 AAGAAGCAAGAAAAGGAGACAAAG
1 AAGAAG-AAGAAAAGGAGA-AAAG
* *
21181888 AAGAA-AAGGAAAAGTAG-AAGG
1 AAGAAGAA-GAAAAGGAGAAAAG
21181909 AAGAAGAAGAAA
1 AAGAAGAAGAAA
21181921 GTATTGCCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 12 0.41
22 4 0.14
23 8 0.28
24 5 0.17
ACGTcount: A:0.65, C:0.04, G:0.30, T:0.02
Consensus pattern (22 bp):
AAGAAGAAGAAAAGGAGAAAAG
Found at i:21194753 original size:17 final size:17
Alignment explanation
Indices: 21194733--21194771 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
21194723 TAAATGAAGG
*
21194733 TAAAAAT-ATAAATAGCA
1 TAAAAATAACAAATA-CA
21194750 TAAAAATAACAAATACA
1 TAAAAATAACAAATACA
21194767 TAAAA
1 TAAAA
21194772 TACATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAAAATAACAAATACA
Found at i:21194790 original size:27 final size:28
Alignment explanation
Indices: 21194736--21194799 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
21194726 ATGAAGGTAA
* *
21194736 AAATATAAATAGCATAAAAATAACAAA-T
1 AAATA-AAATAGCATAAAAAAAAAAAATT
*
21194764 ACATAAAATA-CATAAAAAAAATAAAATT
1 AAATAAAATAGCATAAAAAAAA-AAAATT
21194792 AAATAAAA
1 AAATAAAA
21194800 GCAAGAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 10 0.33
27 8 0.27
28 12 0.40
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (28 bp):
AAATAAAATAGCATAAAAAAAAAAAATT
Found at i:21194837 original size:17 final size:17
Alignment explanation
Indices: 21194817--21194917 Score: 77
Period size: 17 Copynumber: 6.1 Consensus size: 17
21194807 TGTGAATAGC
*
21194817 ATAAAAATGAATAATAA
1 ATAAAAATAAATAATAA
* * *
21194834 ATAATAATAAATGA-CA
1 ATAAAAATAAATAATAA
21194850 ATAAATAATAAATAATAA
1 ATAAA-AATAAATAATAA
* *
21194868 ATAATAATTAAATACTAA
1 ATAA-AAATAAATAATAA
*
21194886 AT-AAAAT-AAT-ACAA
1 ATAAAAATAAATAATAA
*
21194900 AT-AAAATAAAGAATAA
1 ATAAAAATAAATAATAA
21194916 AT
1 AT
21194918 GGGACCAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
14 9 0.14
15 5 0.08
16 13 0.20
17 20 0.31
18 17 0.26
19 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
ATAAAAATAAATAATAA
Found at i:21194838 original size:7 final size:7
Alignment explanation
Indices: 21194817--21194917 Score: 62
Period size: 7 Copynumber: 15.9 Consensus size: 7
21194807 TGTGAATAGC
21194817 ATAAA-A
1 ATAAATA
*
21194823 ATGAATA
1 ATAAATA
21194830 ATAAATA
1 ATAAATA
21194837 AT-AATA
1 ATAAATA
* *
21194843 A-ATGACA
1 ATA-AATA
21194850 ATAAATA
1 ATAAATA
21194857 ATAAATA
1 ATAAATA
21194864 ATAAATA
1 ATAAATA
21194871 AT-AAT-
1 ATAAATA
21194876 -TAAATA
1 ATAAATA
*
21194882 CTAAAT-
1 ATAAATA
21194888 A-AAATA
1 ATAAATA
*
21194894 ATACA-A
1 ATAAATA
21194900 AT-AA-A
1 ATAAATA
*
21194905 ATAAAGA
1 ATAAATA
21194912 ATAAAT
1 ATAAAT
21194918 GGGACCAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
4 1 0.01
5 11 0.15
6 18 0.24
7 43 0.58
8 1 0.01
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (7 bp):
ATAAATA
Found at i:21194839 original size:10 final size:10
Alignment explanation
Indices: 21194817--21194894 Score: 63
Period size: 10 Copynumber: 7.7 Consensus size: 10
21194807 TGTGAATAGC
21194817 ATAA-AAATGA
1 ATAATAAAT-A
21194827 ATAATAAATA
1 ATAATAAATA
*
21194837 ATAATAAATG
1 ATAATAAATA
*
21194847 ACAATAAATA
1 ATAATAAATA
21194857 ATAA-ATAATAA
1 ATAATA-AAT-A
*
21194868 ATAATAATTAA
1 ATAATAAAT-A
*
21194879 ATACTAAATA
1 ATAATAAATA
21194889 A-AATAA
1 ATAATAA
21194895 TACAAATAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
9 5 0.09
10 30 0.54
11 20 0.36
12 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (10 bp):
ATAATAAATA
Found at i:21194917 original size:11 final size:10
Alignment explanation
Indices: 21194829--21194917 Score: 58
Period size: 10 Copynumber: 8.7 Consensus size: 10
21194819 AAAAATGAAT
*
21194829 AATAAATAAT
1 AATAAATAAA
* *
21194839 AATAAATGAC
1 AATAAATAAA
21194849 AATAAATAATA
1 AATAAATAA-A
21194860 AAT-AATAAA
1 AATAAATAAA
*
21194869 TAATAATTAAA
1 -AATAAATAAA
*
21194880 TACTAAAT-AA
1 -AATAAATAAA
*
21194890 AAT-AATACA
1 AATAAATAAA
21194899 AATAAAATAAA
1 AAT-AAATAAA
21194910 GAATAAAT
1 -AATAAAT
21194918 GGGACCAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
8 3 0.05
9 7 0.11
10 26 0.42
11 23 0.37
12 3 0.05
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (10 bp):
AATAAATAAA
Found at i:21195420 original size:36 final size:36
Alignment explanation
Indices: 21195349--21195424 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
21195339 AACGGAGTCA
* *
21195349 TTTTGGGGCCTATGCAATTAGGCCAAAATAGCGTCG
1 TTTTGAGGCCTATGCAATTAGGCCAAAAGAGCGTCG
*
21195385 TTTTGAGGCCTATGCAATTAGGCCAAGACGA-CGTCG
1 TTTTGAGGCCTATGCAATTAGGCCAA-AAGAGCGTCG
21195421 TTTT
1 TTTT
21195425 AAAGGCTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (36 bp):
TTTTGAGGCCTATGCAATTAGGCCAAAAGAGCGTCG
Found at i:21203002 original size:20 final size:20
Alignment explanation
Indices: 21202966--21203015 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
21202956 TCATTAAGAT
*
21202966 TTAATTAACCACTTTTA-ATC
1 TTAATTAAACACTTTTATA-C
21202986 TTAATTAAAC-CTATTTATAC
1 TTAATTAAACACT-TTTATAC
21203006 TTAATATAAA
1 TTAAT-TAAA
21203016 TCATGCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACACTTTTATAC
Found at i:21207641 original size:20 final size:20
Alignment explanation
Indices: 21207605--21207654 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
21207595 TCATTAAGAT
*
21207605 TTAATTAACCACTTTTA-ATC
1 TTAATTAAACACTTTTATA-C
21207625 TTAATTAAAC-CTATTTATAC
1 TTAATTAAACACT-TTTATAC
21207645 TTAATATAAA
1 TTAAT-TAAA
21207655 TCATGCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACACTTTTATAC
Found at i:21218385 original size:17 final size:17
Alignment explanation
Indices: 21218363--21218402 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
21218353 TTGTAGTATA
*
21218363 ATTGTCCCTGCATTTTT
1 ATTGTCACTGCATTTTT
21218380 ATTGTCACTGCATTTTT
1 ATTGTCACTGCATTTTT
21218397 ATTGTC
1 ATTGTC
21218403 GCTACATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.20, G:0.12, T:0.53
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Found at i:21222938 original size:17 final size:17
Alignment explanation
Indices: 21222918--21222975 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
21222908 TAATTGTCCC
*
21222918 TGCATTTTTATTGCCAT
1 TGCATTTTTATTGTCAT
21222935 TGCATTTTTATTGTCAT
1 TGCATTTTTATTGTCAT
* **
21222952 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
21222969 TGCATTT
1 TGCATTT
21222976 CCAAAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:21254413 original size:18 final size:18
Alignment explanation
Indices: 21254386--21254428 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
21254376 TACATATATA
*
21254386 TTTTTCTTCTTTTCCCCT
1 TTTTTTTTCTTTTCCCCT
* *
21254404 TTTTTTTTCTTTTTCTCT
1 TTTTTTTTCTTTTCCCCT
21254422 TTTTTTT
1 TTTTTTT
21254429 ATGTGACTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTTCTTTTCCCCT
Found at i:21255488 original size:13 final size:14
Alignment explanation
Indices: 21255461--21255494 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
21255451 TTCTCTTCTT
21255461 TCTTCTTTTTCTTCC
1 TCTTC-TTTTCTTCC
21255476 TCTTCTTTT-TTCC
1 TCTTCTTTTCTTCC
21255489 TCTTCT
1 TCTTCT
21255495 ATCTCCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 4 0.21
15 5 0.26
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
TCTTCTTTTCTTCC
Found at i:21255494 original size:22 final size:22
Alignment explanation
Indices: 21255453--21255494 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21255443 TCAGGTCCTT
* *
21255453 CTCTTCTTTCTTCTTTTTCTTC
1 CTCTTCTTTCTTCCTCTTCTTC
*
21255475 CTCTTCTTTTTTCCTCTTCT
1 CTCTTCTTTCTTCCTCTTCT
21255495 ATCTCCACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
CTCTTCTTTCTTCCTCTTCTTC
Found at i:21266775 original size:13 final size:14
Alignment explanation
Indices: 21266757--21266789 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
21266747 GTTTGAAAGC
21266757 ATAAAAA-ATAAAA
1 ATAAAAATATAAAA
21266770 ATAAAAATATAAAA
1 ATAAAAATATAAAA
21266784 ATAAAA
1 ATAAAA
21266790 TAAAATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
ATAAAAATATAAAA
Found at i:21267790 original size:15 final size:15
Alignment explanation
Indices: 21267767--21267823 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
21267757 AAAAACAAAC
*
21267767 TAAACTATAAATGTA
1 TAAAATATAAATGTA
* *
21267782 TAAAATATAAAGGAA
1 TAAAATATAAATGTA
*
21267797 CTAAACTATAAATGTA
1 -TAAAATATAAATGTA
21267813 TAAAATATAAA
1 TAAAATATAAA
21267824 GGAAATTACT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 22 0.65
16 12 0.35
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (15 bp):
TAAAATATAAATGTA
Found at i:21267799 original size:31 final size:31
Alignment explanation
Indices: 21267764--21267827 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
21267754 TTAAAAAACA
21267764 AACTAAACTATAAATGTATAAAATATAAAGG
1 AACTAAACTATAAATGTATAAAATATAAAGG
21267795 AACTAAACTATAAATGTATAAAATATAAAGG
1 AACTAAACTATAAATGTATAAAATATAAAGG
21267826 AA
1 AA
21267828 ATTACTCGAT
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:0.59, C:0.06, G:0.09, T:0.25
Consensus pattern (31 bp):
AACTAAACTATAAATGTATAAAATATAAAGG
Found at i:21268611 original size:32 final size:33
Alignment explanation
Indices: 21268559--21268632 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 33
21268549 TTTCTTTCTC
21268559 TTTTCTTTTCTTTTTTTTTTGTATTTTTACTCA
1 TTTTCTTTTCTTTTTTTTTTGTATTTTTACTCA
21268592 TTTTCTTTTC-TTTTTTTTTGTATTTTTACTCA
1 TTTTCTTTTCTTTTTTTTTTGTATTTTTACTCA
21268624 TTTTCTTTT
1 TTTTCTTTT
21268633 TTGTTCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 31 0.76
33 10 0.24
ACGTcount: A:0.08, C:0.12, G:0.03, T:0.77
Consensus pattern (33 bp):
TTTTCTTTTCTTTTTTTTTTGTATTTTTACTCA
Found at i:21291607 original size:408 final size:408
Alignment explanation
Indices: 21290852--21291666 Score: 1504
Period size: 408 Copynumber: 2.0 Consensus size: 408
21290842 AAATCTTCAT
*
21290852 AGTTCTAAAATTATTCATTGAATTGACTATTACTGATACTTGACCACTAGGTACCGGTAGAAGTC
1 AGTTCTAAAATTATTCATTGAATTGACTATTACCGATACTTGACCACTAGGTACCGGTAGAAGTC
21290917 CCCTAAAATATTAGAAATTCCATTTCTACCCTTGATAAAAATTGTGTCATGTTTAGATATTGTTT
66 CCCTAAAATATTAGAAATTCCATTTCTACCCTTGATAAAAATTGTGTCATGTTTAGATATTGTTT
*
21290982 TAAACTGGGAGAAATGATTTTTGTATTAATTAAATATACGAATAGTCGAATAATTATAAAGGATG
131 TAAACTGGGAGAAAGGATTTTTGTATTAATTAAATATACGAATAGTCGAATAATTATAAAGGATG
* *
21291047 AATAGTGAAAAATGAATAGTAAATACCAGAATTCTAATCGGTGATGGTGTACGAAATTTAGGTGT
196 AACAGTGAAAAATGAATAGTAAATACCAAAATTCTAATCGGTGATGGTGTACGAAATTTAGGTGT
*
21291112 TACATTTAGTGGTATCAGAACTTTCGATTTAGCCATTTCTTGGACAGCTATTGTTATATTAAATA
261 TACATTTAGTGGTATCAGAACTTTCGATTTAGCCATTTCTTGGACAGCTATTATTATATTAAATA
21291177 ATTTCAGAGTACATGCCATATGAACCTGTGATAATGTGATACAGATGAATCTGATCTAACCATAG
326 ATTTCAGAGTACATGCCATATGAACCTGTGATAATGTGATACAGATGAATCTGATCTAACCATAG
* *
21291242 TTTTTGTAAATAAGGTAC
391 CTTTTGCAAATAAGGTAC
21291260 AGTTCTAAAATTATTCATTGAATTGACTATTACCGATACTTGACCACTAGGTACCGGTAGAAGTC
1 AGTTCTAAAATTATTCATTGAATTGACTATTACCGATACTTGACCACTAGGTACCGGTAGAAGTC
** *
21291325 TTCTAAAATGTTAGAAATTCCATTTCTACCCTTGATAAAAATTGTGTCATGTTTAGATATTGTTT
66 CCCTAAAATATTAGAAATTCCATTTCTACCCTTGATAAAAATTGTGTCATGTTTAGATATTGTTT
* *
21291390 TAAATTGGGAGAAAGGATTTTTGTATTAATTAAATATACGAATAGTCGAATAATTGTAAAGGATG
131 TAAACTGGGAGAAAGGATTTTTGTATTAATTAAATATACGAATAGTCGAATAATTATAAAGGATG
21291455 AACAGTGAAAAATGAATAGTAAATACCAAAATTCTAATCGGTGATGGTGTACGAAATTTAGGTGT
196 AACAGTGAAAAATGAATAGTAAATACCAAAATTCTAATCGGTGATGGTGTACGAAATTTAGGTGT
* *
21291520 TACATTTAGTGGTATCAGAGCTTTCGATTTAGCCGTTTCTTGGACAGCTATTATTATATTAAATA
261 TACATTTAGTGGTATCAGAACTTTCGATTTAGCCATTTCTTGGACAGCTATTATTATATTAAATA
21291585 ATTTCAGAGTACATGCCATATGAACCTGTGATAATGTGATACAGATGAATCTGATCTAACCATAG
326 ATTTCAGAGTACATGCCATATGAACCTGTGATAATGTGATACAGATGAATCTGATCTAACCATAG
21291650 CTTTTGCAAATAAGGTA
391 CTTTTGCAAATAAGGTA
21291667 AAAATGCCTG
Statistics
Matches: 393, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
408 393 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (408 bp):
AGTTCTAAAATTATTCATTGAATTGACTATTACCGATACTTGACCACTAGGTACCGGTAGAAGTC
CCCTAAAATATTAGAAATTCCATTTCTACCCTTGATAAAAATTGTGTCATGTTTAGATATTGTTT
TAAACTGGGAGAAAGGATTTTTGTATTAATTAAATATACGAATAGTCGAATAATTATAAAGGATG
AACAGTGAAAAATGAATAGTAAATACCAAAATTCTAATCGGTGATGGTGTACGAAATTTAGGTGT
TACATTTAGTGGTATCAGAACTTTCGATTTAGCCATTTCTTGGACAGCTATTATTATATTAAATA
ATTTCAGAGTACATGCCATATGAACCTGTGATAATGTGATACAGATGAATCTGATCTAACCATAG
CTTTTGCAAATAAGGTAC
Found at i:21311414 original size:18 final size:18
Alignment explanation
Indices: 21311388--21311441 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
21311378 ATGCATAGCA
* *
21311388 TTTAGTTGTCATTACATT
1 TTTATTTGTCACTACATT
*
21311406 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTACATT
* *
21311423 TTTATTTGTTAGTACATT
1 TTTATTTGTCACTACATT
21311441 T
1 T
21311442 GCATTGTAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTATTTGTCACTACATT
Found at i:21311440 original size:17 final size:17
Alignment explanation
Indices: 21311388--21311441 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
21311378 ATGCATAGCA
* *
21311388 TTTAGTTGTCATTACATT
1 TTTATTTGTCACTACA-T
*
21311406 TTTATTTGTCACTGCAT
1 TTTATTTGTCACTACAT
* *
21311423 TTTATTTGTTAGTACAT
1 TTTATTTGTCACTACAT
21311440 TT
1 TT
21311442 GCATTGTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.57
Consensus pattern (17 bp):
TTTATTTGTCACTACAT
Found at i:21324660 original size:20 final size:20
Alignment explanation
Indices: 21324623--21324660 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21324613 CAACAATTAC
*
21324623 AAGTCTTTAAATAAAAAACA
1 AAGTCTTTAAAAAAAAAACA
21324643 AAGTC-TTAAAAAATAAAA
1 AAGTCTTTAAAAAA-AAAA
21324661 TTCAATCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (20 bp):
AAGTCTTTAAAAAAAAAACA
Found at i:21339495 original size:25 final size:26
Alignment explanation
Indices: 21339444--21339505 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
21339434 CATGATTTTC
21339444 TTCTTCTTTTTTGTTTCTTACTCATTT
1 TTCTT-TTTTTTGTTTCTTACTCATTT
*
21339471 TTCTTTTTTATT-TTTTTTACT-ATTT
1 TTCTTTTTT-TTGTTTCTTACTCATTT
* *
21339496 CTCTATTTTT
1 TTCTTTTTTT
21339506 GTCTAGACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.03
25 11 0.35
26 12 0.39
27 7 0.23
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.74
Consensus pattern (26 bp):
TTCTTTTTTTTGTTTCTTACTCATTT
Found at i:21351227 original size:15 final size:15
Alignment explanation
Indices: 21351193--21351232 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
21351183 TGACCAGATG
*
21351193 AAAGAGAAGGAAGAG
1 AAAGAGAAGGAAGAA
*
21351208 GAAGAGAAGGAAGAA
1 AAAGAGAAGGAAGAA
21351223 AAAGAAGAAG
1 AAAG-AGAAG
21351233 AGAGTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGGAAGAA
Found at i:21365093 original size:20 final size:20
Alignment explanation
Indices: 21365043--21365090 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 20
21365033 GTCTTAAACA
21365043 AAAAATAAATACGAAAGAAAT
1 AAAAA-AAATACGAAAGAAAT
21365064 AAAAAAAATACG-AA-AAAT
1 AAAAAAAATACGAAAGAAAT
21365082 AAAATAAAA
1 AAAA-AAAA
21365091 ATAAAAACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.31
19 6 0.23
20 7 0.27
21 5 0.19
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.12
Consensus pattern (20 bp):
AAAAAAAATACGAAAGAAAT
Found at i:21384468 original size:24 final size:24
Alignment explanation
Indices: 21384435--21384489 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
21384425 GTTAAGAGTA
21384435 AAAATTGTCAGTGCAAATGTAATAT
1 AAAA-TGTCAGTGCAAATGTAATAT
*
21384460 AAAATGTCAGTGCAGATGTAATAT
1 AAAATGTCAGTGCAAATGTAATAT
21384484 AAAATG
1 AAAATG
21384490 AATTGATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.29
Consensus pattern (24 bp):
AAAATGTCAGTGCAAATGTAATAT
Found at i:21385959 original size:18 final size:19
Alignment explanation
Indices: 21385931--21385966 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
21385921 CAATTATATA
21385931 TATATATTTTTTTTCTTTT
1 TATATATTTTTTTTCTTTT
21385950 TATA-ATTTTTTTTCTTT
1 TATATATTTTTTTTCTTT
21385967 ATTTCTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (19 bp):
TATATATTTTTTTTCTTTT
Found at i:21386625 original size:17 final size:17
Alignment explanation
Indices: 21386582--21386625 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
21386572 AACTATGAAA
* *
21386582 ACAAATAAAATGCAGGG
1 ACAAAAAAAATGCAAGG
* *
21386599 ACAATAAAAATGCAATG
1 ACAAAAAAAATGCAAGG
21386616 ACAAAAAAAA
1 ACAAAAAAAA
21386626 AGCATGCAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.64, C:0.11, G:0.14, T:0.11
Consensus pattern (17 bp):
ACAAAAAAAATGCAAGG
Found at i:21397644 original size:14 final size:15
Alignment explanation
Indices: 21397619--21397652 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21397609 GGGGAAGAAA
21397619 AAAATAAAAATAAAC
1 AAAATAAAAATAAAC
*
21397634 AAAAT-AAAATAAAT
1 AAAATAAAAATAAAC
21397648 AAAAT
1 AAAAT
21397653 CGTATCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAAATAAAC
Found at i:21417339 original size:10 final size:10
Alignment explanation
Indices: 21417324--21417358 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
21417314 GGAAAATTAG
21417324 AAAAAGAAAA
1 AAAAAGAAAA
21417334 AAAAAGAAAA
1 AAAAAGAAAA
*
21417344 GAAAAGAAGAA
1 AAAAAGAA-AA
21417355 AAAA
1 AAAA
21417359 TGTTTACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:21419707 original size:16 final size:16
Alignment explanation
Indices: 21419686--21419716 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21419676 ATAATATGAA
21419686 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
21419702 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
21419717 GGATCCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:21420547 original size:26 final size:26
Alignment explanation
Indices: 21420518--21420567 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
21420508 ACAATTCTGG
*
21420518 GCGAAAATTTTGGACACGTTCATGCA
1 GCGAAAATTCTGGACACGTTCATGCA
* *
21420544 GCGACAATTCTGGACATGTTCATG
1 GCGAAAATTCTGGACACGTTCATG
21420568 TAGCAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (26 bp):
GCGAAAATTCTGGACACGTTCATGCA
Found at i:21421528 original size:34 final size:34
Alignment explanation
Indices: 21421485--21421554 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
21421475 TGACAAATGG
* *
21421485 AAATGCAATGATAACGCAAATGCAGTGACAATTA
1 AAATGCAATGACAAAGCAAATGCAGTGACAATTA
* **
21421519 AAATGCAATGACAAAGGAAATGTGGTGACAATTA
1 AAATGCAATGACAAAGCAAATGCAGTGACAATTA
21421553 AA
1 AA
21421555 TTACAACTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAAAGCAAATGCAGTGACAATTA
Found at i:21421539 original size:17 final size:17
Alignment explanation
Indices: 21421468--21421540 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
21421458 CATTATCCTT
*
21421468 AATGCATTGACAAATGGA
1 AATGCAATGACAAA-GGA
* * *
21421486 AATGCAATGATAACGCA
1 AATGCAATGACAAAGGA
* ***
21421503 AATGCAGTGACAATTAA
1 AATGCAATGACAAAGGA
21421520 AATGCAATGACAAAGGA
1 AATGCAATGACAAAGGA
21421537 AATG
1 AATG
21421541 TGGTGACAAT
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
17 31 0.74
18 11 0.26
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (17 bp):
AATGCAATGACAAAGGA
Found at i:21423848 original size:16 final size:16
Alignment explanation
Indices: 21423827--21423857 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21423817 ATAATGTGAA
21423827 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
21423843 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
21423858 GGATCCACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:21424737 original size:26 final size:26
Alignment explanation
Indices: 21424677--21424730 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
21424667 ATTTTAGGTG
*
21424677 CAATTCTAGACACGTTCATGCAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
*
21424703 CAATTCTGGACATGTTCATGCAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
21424729 CA
1 CA
21424731 TTCCTGGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (26 bp):
CAATTCTGGACACGTTCATGCAGCGA
Found at i:21424776 original size:37 final size:37
Alignment explanation
Indices: 21424717--21424821 Score: 97
Period size: 37 Copynumber: 2.8 Consensus size: 37
21424707 TCTGGACATG
* * * *
21424717 TTCATGCAGCGACATTCCTGGGTGCAAT-TGAAGAATA
1 TTCATACAGCGATAGTCTTGGGTGCAATCTGAA-AATA
* * *
21424754 CTT-ATGCAGCGATGGTCTTGGGTGCATTCTGAAAATA
1 -TTCATACAGCGATAGTCTTGGGTGCAATCTGAAAATA
* *
21424791 TTCATACGGCGATAGTTTTGGGTGCAATCTG
1 TTCATACAGCGATAGTCTTGGGTGCAATCTG
21424822 GAAGTGCTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
36 2 0.04
37 47 0.85
38 6 0.11
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (37 bp):
TTCATACAGCGATAGTCTTGGGTGCAATCTGAAAATA
Found at i:21426214 original size:16 final size:14
Alignment explanation
Indices: 21426185--21426219 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
21426175 TTAAATTTTG
21426185 TTATTTTCTTTATT
1 TTATTTTCTTTATT
21426199 TTATTATTCTTTTATT
1 TTATT-TTC-TTTATT
21426215 TTATT
1 TTATT
21426220 CTTATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 3 0.16
16 11 0.58
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTTCTTTATT
Found at i:21427879 original size:29 final size:26
Alignment explanation
Indices: 21427855--21427935 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 26
21427845 TATTATTTCA
21427855 AAAAACATAATTTTAATAATTTTATATTTT
1 AAAAA-ATAATTTTAATAA-TTT-TA-TTT
* *
21427885 AAAAAATAATTTAAAAAAATTTATATTT
1 AAAAAATAATTT-TAATAATTT-TATTT
*
21427913 TAAAAATAATTTTAATAATTTTA
1 AAAAAATAATTTTAATAATTTTA
21427936 AAATATTTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.04
27 7 0.16
28 14 0.31
29 13 0.29
30 9 0.20
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
AAAAAATAATTTTAATAATTTTATTT
Found at i:21427917 original size:28 final size:29
Alignment explanation
Indices: 21427855--21427924 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
21427845 TATTATTTCA
* * *
21427855 AAAAACATAATTTTAATAATTTTATATTTT
1 AAAAA-ATAATTTAAAAAAATTTATATTTT
21427885 AAAAAATAATTTAAAAAAATTTATATTTT
1 AAAAAATAATTTAAAAAAATTTATATTTT
21427914 -AAAAATAATTT
1 AAAAAATAATTT
21427925 TAATAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 11 0.30
29 21 0.57
30 5 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAAAATAATTTAAAAAAATTTATATTTT
Found at i:21429590 original size:4 final size:4
Alignment explanation
Indices: 21429581--21429606 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
21429571 TCCTTTTTGC
21429581 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
21429607 TATATCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:21431561 original size:27 final size:28
Alignment explanation
Indices: 21431527--21431671 Score: 116
Period size: 27 Copynumber: 5.3 Consensus size: 28
21431517 ATATTGAATT
*
21431527 AAAAGCCTTTGTGGCCTAACATGAAG-G
1 AAAAGCCTTTGTGGCGTAACATGAAGAG
* * * * * *
21431554 AAATGCCTTGGTAGTGTAACAAGAAG-C
1 AAAAGCCTTTGTGGCGTAACATGAAGAG
* * *
21431581 AAAAGCCTTGGTGGCGTAATATGAAGAA
1 AAAAGCCTTTGTGGCGTAACATGAAGAG
* *
21431609 AAAAGCCCTTGTGGCGTATCATGAAGAG
1 AAAAGCCTTTGTGGCGTAACATGAAGAG
* * * * *
21431637 AAAGGCCTTTATGGTGCAGCATGAA-AG
1 AAAAGCCTTTGTGGCGTAACATGAAGAG
21431664 AAAAGCCT
1 AAAAGCCT
21431672 CTACGGCAAA
Statistics
Matches: 92, Mismatches: 25, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
27 50 0.54
28 42 0.46
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (28 bp):
AAAAGCCTTTGTGGCGTAACATGAAGAG
Found at i:21435389 original size:403 final size:403
Alignment explanation
Indices: 21434642--21435540 Score: 1654
Period size: 403 Copynumber: 2.2 Consensus size: 403
21434632 AAGCCACTTA
*
21434642 TTCACAAAGTAAAAACCTTTATCACTAATAATAGCTCTTGGTGTCTCAAACCGTGTAAACACATG
1 TTCACAAAGTAAAAACCTTCATCACTAATAATAGCTCTTGGTGTCTCAAACCGTGTAAACACATG
*
21434707 CTTATGTAGGAATCGCATGACTACCTTCACATCATTTGTAGGGTATGCTTCAGCTTCAACCAACA
66 CTTATGTAGGAATCGCATGACTACCTTCACATCATTTATAGGGTATGCTTCAGCTTCAACCAACA
*
21434772 TGGATACATAGTCGACAACAACTAAGATGTACTTGTTCCCATACGAAGAAGGAAACGAGCCTAGA
131 TGGATACATAGTCCACAACAACTAAGATGTACTTGTTCCCATACGAAGAAGGAAACGAGCCTAGA
* *
21434837 AAGTTAATGCCCCACATGTCGAACAATTCAACTTCTAATATGTTTGTCAAGGGCATCTCGTTCCT
196 AAGTCAACGCCCCACATGTCGAACAATTCAACTTCTAATATGTTTGTCAAGGGCATCTCGTTCCT
21434902 CCTTGATATATTTCCAGTCCTTTGGCATCTACCACAATTCTTCAAATATGCATAAGCATCTTTAA
261 CCTTGATATATTTCCAGTCCTTTGGCATCTACCACAATTCTTCAAATATGCATAAGCATCTTTAA
21434967 ATACTGTAGGCCAAAAGCATTTGATCACCTCCGAACGTACTCCTGTTCGATGTAGGTTTTTGGCT
326 ATACTGTAGGCCAAAAGCATTTGATCACCTCCGAACGTACTCCTGTTCGATGTAGGTTTTTGGCT
21435032 TCCGCAAGTATAC
391 TCCGCAAGTATAC
*
21435045 TTCACAAAGTAAAAACCTTCATCACTAATAATAGCTCTTGGTGTGTCAAACCGTGTAAACACATG
1 TTCACAAAGTAAAAACCTTCATCACTAATAATAGCTCTTGGTGTCTCAAACCGTGTAAACACATG
* * *
21435110 CTTATGTAGGAAACGCATGACTACCTTCACATCATTTATAGGGTATGCTTCAGCTTCAACTAACG
66 CTTATGTAGGAATCGCATGACTACCTTCACATCATTTATAGGGTATGCTTCAGCTTCAACCAACA
** * *
21435175 TGGATACATAGTCCACGGCAACTAAGATGTACTTGTTCCCATACGAAGAAGGAAACGGGCCTTGA
131 TGGATACATAGTCCACAACAACTAAGATGTACTTGTTCCCATACGAAGAAGGAAACGAGCCTAGA
*
21435240 AAGTCAACGCCCCATATGTCGAACAATTCAACTTCTAATATGTTTGTCAAGGGCATCTCGTTCCT
196 AAGTCAACGCCCCACATGTCGAACAATTCAACTTCTAATATGTTTGTCAAGGGCATCTCGTTCCT
*
21435305 CCTTGATATATTTCCAGTCCTTTGGCATCTATCACAATTCTTCAAATATGCATAAGCATCTTTAA
261 CCTTGATATATTTCCAGTCCTTTGGCATCTACCACAATTCTTCAAATATGCATAAGCATCTTTAA
21435370 ATACTGTAGGCCAAAAGCATTTGATCACCTCCGAACGTACTCCTGTTCGATGTAGGTTTTTGGCT
326 ATACTGTAGGCCAAAAGCATTTGATCACCTCCGAACGTACTCCTGTTCGATGTAGGTTTTTGGCT
*
21435435 TCCTCAAGTATAC
391 TCCGCAAGTATAC
21435448 TTCACAAAGTAAAAACCTTCATCACTAATAATAGCTCTTGGTGTCTCAAACCGTGTAAACACATG
1 TTCACAAAGTAAAAACCTTCATCACTAATAATAGCTCTTGGTGTCTCAAACCGTGTAAACACATG
21435513 CTTATGTAGGAATCGCATGACTACCTTC
66 CTTATGTAGGAATCGCATGACTACCTTC
21435541 CTTTGCCCAA
Statistics
Matches: 478, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
403 478 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (403 bp):
TTCACAAAGTAAAAACCTTCATCACTAATAATAGCTCTTGGTGTCTCAAACCGTGTAAACACATG
CTTATGTAGGAATCGCATGACTACCTTCACATCATTTATAGGGTATGCTTCAGCTTCAACCAACA
TGGATACATAGTCCACAACAACTAAGATGTACTTGTTCCCATACGAAGAAGGAAACGAGCCTAGA
AAGTCAACGCCCCACATGTCGAACAATTCAACTTCTAATATGTTTGTCAAGGGCATCTCGTTCCT
CCTTGATATATTTCCAGTCCTTTGGCATCTACCACAATTCTTCAAATATGCATAAGCATCTTTAA
ATACTGTAGGCCAAAAGCATTTGATCACCTCCGAACGTACTCCTGTTCGATGTAGGTTTTTGGCT
TCCGCAAGTATAC
Found at i:21449136 original size:7 final size:7
Alignment explanation
Indices: 21449124--21449162 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
21449114 TAACACTGGT
21449124 TGGGACA
1 TGGGACA
21449131 TGGGACA
1 TGGGACA
21449138 TGGGACA
1 TGGGACA
*
21449145 TGGGACC
1 TGGGACA
21449152 TGGGACA
1 TGGGACA
21449159 -GGGA
1 TGGGA
21449163 AGGGAAGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.26, C:0.15, G:0.46, T:0.13
Consensus pattern (7 bp):
TGGGACA
Found at i:21452830 original size:36 final size:36
Alignment explanation
Indices: 21452699--21452820 Score: 183
Period size: 36 Copynumber: 3.4 Consensus size: 36
21452689 TGTATCTCAA
* * *
21452699 ACAACCTCTTCAAGTTTCCTAGT-ATTTCAGCTCAT
1 ACAAGCTCTTCAAGTTTCCTAGTAAATTCAGCTCTT
* *
21452734 ACGAGCTCTTCAAGTTTCTTAGTAAATTCAGCTCTT
1 ACAAGCTCTTCAAGTTTCCTAGTAAATTCAGCTCTT
*
21452770 AAAAGCTCTTCAAGTTTCCTAGTAAATTCAGCTCTT
1 ACAAGCTCTTCAAGTTTCCTAGTAAATTCAGCTCTT
21452806 ACAAGCTCTTCAAGT
1 ACAAGCTCTTCAAGT
21452821 CTCTCAGTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 20 0.26
36 57 0.74
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (36 bp):
ACAAGCTCTTCAAGTTTCCTAGTAAATTCAGCTCTT
Found at i:21460628 original size:21 final size:22
Alignment explanation
Indices: 21460597--21460655 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
21460587 ATGAAGGAGC
21460597 AAGAGAAGAAGAGAAA-CAAGAA
1 AAGA-AAGAAGAGAAAGCAAGAA
*
21460619 AAGAAAGAAG-GAAAGGAAGAA
1 AAGAAAGAAGAGAAAGCAAGAA
* * *
21460640 GAGAAGGAAGATAAAG
1 AAGAAAGAAGAGAAAG
21460656 AAAGCATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 19 0.61
22 8 0.26
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (22 bp):
AAGAAAGAAGAGAAAGCAAGAA
Found at i:21461079 original size:17 final size:17
Alignment explanation
Indices: 21461053--21461097 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
21461043 GCATGCATTT
21461053 ATTTTAATTGTCAT-TGC
1 ATTTTAATTGTC-TCTGC
*
21461070 ATTTTTATTGTCTCTGC
1 ATTTTAATTGTCTCTGC
*
21461087 ATTTTATTTGT
1 ATTTTAATTGT
21461098 TTTAGCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (17 bp):
ATTTTAATTGTCTCTGC
Found at i:21461708 original size:12 final size:10
Alignment explanation
Indices: 21461678--21461712 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
21461668 TCAGTCACAT
21461678 AAAAAAAAGA
1 AAAAAAAAGA
21461688 AAAAAAAAGA
1 AAAAAAAAGA
21461698 GAAAAAGAAAGA
1 -AAAAA-AAAGA
21461710 AAA
1 AAA
21461713 GTTGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.43
11 8 0.35
12 5 0.22
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:21461712 original size:17 final size:18
Alignment explanation
Indices: 21461681--21461728 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
21461671 GTCACATAAA
*
21461681 AAAAAGAAAAAAAAAG-AG
1 AAAAAG-AAAGAAAAGTAG
*
21461699 AAAAAGAAAGAAAAGTTG
1 AAAAAGAAAGAAAAGTAG
21461717 AAAAA-AAAGAAA
1 AAAAAGAAAGAAA
21461729 GAATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAGAAAAGTAG
Found at i:21484967 original size:5 final size:5
Alignment explanation
Indices: 21484957--21485038 Score: 121
Period size: 5 Copynumber: 16.2 Consensus size: 5
21484947 GGTTCGAACC
*
21484957 AGAAA AGAAA AG-AA AGAAA AGAAA AGAAA AGAAA AGAAAAA AGAAA AGGAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AG--AAA AGAAA AGAAA
*
21485008 AGAAA GGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
21485039 TATCCTCACA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
4 4 0.06
5 61 0.87
7 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:21485009 original size:37 final size:36
Alignment explanation
Indices: 21484959--21485033 Score: 132
Period size: 37 Copynumber: 2.1 Consensus size: 36
21484949 TTCGAACCAG
21484959 AAAAGAAAAGAAAGAAAAGAAAAGAAAAGAAAAGAA
1 AAAAGAAAAGAAAGAAAAGAAAAGAAAAGAAAAGAA
*
21484995 AAAAGAAAAGGAAAGAAAGGAAAAGAAAAGAAAAGAA
1 AAAAGAAAA-GAAAGAAAAGAAAAGAAAAGAAAAGAA
21485032 AA
1 AA
21485034 GAAAATATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 9 0.24
37 28 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (36 bp):
AAAAGAAAAGAAAGAAAAGAAAAGAAAAGAAAAGAA
Found at i:21485018 original size:42 final size:41
Alignment explanation
Indices: 21484957--21485038 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 41
21484947 GGTTCGAACC
21484957 AGAAAAGAAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAA
1 AGAAAAGAAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAA
*
21484998 AGAAAAGGAAAGAAAGGAAAAGAAAAGAAAAGAAAAGAAAA
1 AGAAAAGAAAAGAAA-GAAAAGAAAAGAAAAGAAAAGAAAA
21485039 TATCCTCACA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 14 0.36
42 25 0.64
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (41 bp):
AGAAAAGAAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAA
Found at i:21487726 original size:24 final size:24
Alignment explanation
Indices: 21487672--21487726 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
21487662 TAATAATTCT
21487672 CTTTGAGTTTTTCTTCAAGAATTG
1 CTTTGAGTTTTTCTTCAAGAATTG
**
21487696 CTCTTGAGTTTTT-TTTTAGAAGTTG
1 CT-TTGAGTTTTTCTTCAAGAA-TTG
21487721 CTTTGA
1 CTTTGA
21487727 TAGTCTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (24 bp):
CTTTGAGTTTTTCTTCAAGAATTG
Found at i:21493276 original size:24 final size:24
Alignment explanation
Indices: 21493244--21493295 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
21493234 TAATGGGTTG
21493244 GATGCATCTACCAGATCTGGATTA
1 GATGCATCTACCAGATCTGGATTA
21493268 GATGCATCTACCAGATCTGGATTA
1 GATGCATCTACCAGATCTGGATTA
21493292 GATG
1 GATG
21493296 GTGTCGCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (24 bp):
GATGCATCTACCAGATCTGGATTA
Found at i:21498202 original size:21 final size:20
Alignment explanation
Indices: 21498176--21498228 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 20
21498166 CAACCCACGG
21498176 ATATTTTTTTTTCTTTTTCTC
1 ATATTTTTTTTT-TTTTTCTC
21498197 ATATTTTTCTTTTTTTTTCTC
1 ATATTTTT-TTTTTTTTTCTC
21498218 -TACTTTTTTTT
1 ATA-TTTTTTTT
21498229 ATCACTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.17
21 21 0.70
22 4 0.13
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.77
Consensus pattern (20 bp):
ATATTTTTTTTTTTTTTCTC
Found at i:21498226 original size:14 final size:13
Alignment explanation
Indices: 21498207--21498240 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
21498197 ATATTTTTCT
*
21498207 TTTTTTTTCTCTAC
1 TTTTTTTTATC-AC
21498221 TTTTTTTTATCAC
1 TTTTTTTTATCAC
21498234 TTTTTTT
1 TTTTTTT
21498241 GCAGGAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTATCAC
Found at i:21501094 original size:24 final size:25
Alignment explanation
Indices: 21501070--21501117 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
21501060 AAACAACTTC
21501070 TAAAAAAAAACTC-AAGAGCAATTCT
1 TAAAAAAAAACTCAAAGAG-AATTCT
* *
21501095 TGAAGAAAAACTCAAAGAGAATT
1 TAAAAAAAAACTCAAAGAGAATT
21501118 ATTATTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (25 bp):
TAAAAAAAAACTCAAAGAGAATTCT
Found at i:21511192 original size:23 final size:24
Alignment explanation
Indices: 21511166--21511212 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
21511156 ACAATTCATT
21511166 TTTATCTTA-ATTTGC-TCTGACAA
1 TTTATCTTATATTTGCGT-TGACAA
*
21511189 TTTATTTTATATTTGCGTTGACAA
1 TTTATCTTATATTTGCGTTGACAA
21511213 ATTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTATCTTATATTTGCGTTGACAA
Found at i:21521746 original size:24 final size:23
Alignment explanation
Indices: 21521709--21521755 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
21521699 ACAATTCATT
21521709 TTTATCTTAATTTGC-TCTGACAA
1 TTTATCTTAATTTGCGT-TGACAA
*
21521732 TTTATTTTATATTTGCGTTGACAA
1 TTTATCTTA-ATTTGCGTTGACAA
21521756 ATTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.51
Consensus pattern (23 bp):
TTTATCTTAATTTGCGTTGACAA
Found at i:21523661 original size:37 final size:37
Alignment explanation
Indices: 21523480--21523663 Score: 251
Period size: 37 Copynumber: 4.9 Consensus size: 37
21523470 CTTGAATCAT
* *
21523480 CGGCACAAAGGCCTGCAAGGCACATAGCCCGAAAACAC
1 CGGCACAAA-GCCTGCTAGGCACATAGCCCGAATACAC
* *
21523518 CGACACAAAGCCTGCTAGGCACATAGCCCAAATACAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATACAC
* * *
21523555 CGGCATAAAGCCTGCTAGGCATATAGCCCGAATACAT
1 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATACAC
* *
21523592 CGGCACAAAGCTTGCTAGGCACATAGCTCGAATACAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATACAC
* * *
21523629 CAGCACAAAGCTTGCTAGGCATATAGCCCGAATAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATAC
21523664 TTAGATGCAA
Statistics
Matches: 129, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
37 121 0.94
38 8 0.06
ACGTcount: A:0.35, C:0.31, G:0.21, T:0.14
Consensus pattern (37 bp):
CGGCACAAAGCCTGCTAGGCACATAGCCCGAATACAC
Found at i:21527163 original size:5 final size:5
Alignment explanation
Indices: 21527153--21527215 Score: 90
Period size: 5 Copynumber: 12.6 Consensus size: 5
21527143 GGTTCAAACC
* * * *
21527153 AGAAA AGAAA AGAGA AGAAA AGAAA AGAAA AGAAA GGAAA GGAAA AGAGA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
21527203 AGAAA AGAAA AGA
1 AGAAA AGAAA AGA
21527216 TATCCTCACA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 52 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:21530867 original size:19 final size:18
Alignment explanation
Indices: 21530824--21530868 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
21530814 AGAGTGTGAG
*
21530824 AAAAGAGATCGAAATTGA
1 AAAAGAAATCGAAATTGA
21530842 AAAAGAAATCGAGAA-TGA
1 AAAAGAAATCGA-AATTGA
21530860 AGAAAGAAA
1 A-AAAGAAA
21530869 AGAAAGAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.62, C:0.04, G:0.22, T:0.11
Consensus pattern (18 bp):
AAAAGAAATCGAAATTGA
Found at i:21532274 original size:17 final size:17
Alignment explanation
Indices: 21532254--21532286 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21532244 TTTAAGGACT
21532254 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
21532271 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
21532287 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:21532560 original size:50 final size:50
Alignment explanation
Indices: 21532493--21532636 Score: 157
Period size: 50 Copynumber: 2.8 Consensus size: 50
21532483 ACTCTGATGA
* *
21532493 TTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAGTAACTTACATG
1 TTAGTTAAATTTGCATCATAAATAATGACATGCATTAAGTAACTCACATG
* ** * *
21532543 TTAGTTAAATATGCATCATAAATCCT-ATCATGCATTATGTAACTCCCATG
1 TTAGTTAAATTTGCATCATAAATAATGA-CATGCATTAAGTAACTCACATG
* *
21532593 TTAGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATTTAGTAA
1 TTAGTTAAA-TTTGCATCA-TAAAT-AATGACATGCATTAAGTAA
21532637 TCCATTAGTT
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 50 0.66
51 8 0.11
52 17 0.22
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (50 bp):
TTAGTTAAATTTGCATCATAAATAATGACATGCATTAAGTAACTCACATG
Found at i:21537871 original size:81 final size:81
Alignment explanation
Indices: 21537779--21538041 Score: 517
Period size: 81 Copynumber: 3.2 Consensus size: 81
21537769 TGTTTATATC
21537779 TTTAATTATGTCCTGCATTAAGTGTTTTGCATTTAATTAAATCATTCATAAAAGCATCTCCTATG
1 TTTAATTATGTCCTGCATTAAGTGTTTTGCATTTAATTAAATCATTCATAAAAGCATCTCCTATG
21537844 TTTATTAAGATTGTGA
66 TTTATTAAGATTGTGA
21537860 TTTAATTATGTCCTGCATTAAGTGTTTTGCATTTAATTAAATCATTCATAAAAGCATCTCCTATG
1 TTTAATTATGTCCTGCATTAAGTGTTTTGCATTTAATTAAATCATTCATAAAAGCATCTCCTATG
21537925 TTTATTAAGATTGTGA
66 TTTATTAAGATTGTGA
21537941 TTTAATTATGTCCTGCATTAAGTGTTTTGCATTTAATTAAATCATTCATAAAAGCATCTCCTATG
1 TTTAATTATGTCCTGCATTAAGTGTTTTGCATTTAATTAAATCATTCATAAAAGCATCTCCTATG
21538006 TTTATTAAGATTGTGA
66 TTTATTAAGATTGTGA
*
21538022 TTTAATTATGTCATGCATTA
1 TTTAATTATGTCCTGCATTA
21538042 TTAATCTACA
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 181 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (81 bp):
TTTAATTATGTCCTGCATTAAGTGTTTTGCATTTAATTAAATCATTCATAAAAGCATCTCCTATG
TTTATTAAGATTGTGA
Found at i:21538155 original size:47 final size:49
Alignment explanation
Indices: 21538093--21538190 Score: 112
Period size: 50 Copynumber: 2.0 Consensus size: 49
21538083 GTGCATTATG
* * *
21538093 TAATGACATCCATTAACT-C-T-GATGATTAGTTAAATTTGCATCATAAA
1 TAATGACATCAATTAACTACTTACATG-TTAGTTAAATATGCATCATAAA
* *
21538140 TAATGACATGAATTAAGTAACTTACATGTTAGTTAAATATGCATCATAAA
1 TAATGACATCAATTAACT-ACTTACATGTTAGTTAAATATGCATCATAAA
21538190 T
1 T
21538191 CCTATCATGC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
47 15 0.36
49 1 0.02
50 23 0.55
51 3 0.07
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (49 bp):
TAATGACATCAATTAACTACTTACATGTTAGTTAAATATGCATCATAAA
Found at i:21538233 original size:50 final size:50
Alignment explanation
Indices: 21538118--21538243 Score: 148
Period size: 50 Copynumber: 2.5 Consensus size: 50
21538108 ACTCTGATGA
* *
21538118 TTAGTTAAATTTGCATCATAAATAATGACATGAATTAAGTAACTTACATG
1 TTAGTTAAATTTGCATCATAAATCATGACATGAATTAAGTAACTCACATG
* * * * *
21538168 TTAGTTAAATATGCATCATAAATCCT-ATCATGCA-TATGTAACTCCCATG
1 TTAGTTAAATTTGCATCATAAATCATGA-CATGAATTAAGTAACTCACATG
21538217 TTAGTTAAAGTTTGCATCATTAAATCA
1 TTAGTTAAA-TTTGCATCA-TAAATCA
21538244 AGTCATCCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
49 22 0.34
50 36 0.56
51 6 0.09
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (50 bp):
TTAGTTAAATTTGCATCATAAATCATGACATGAATTAAGTAACTCACATG
Found at i:21539566 original size:21 final size:21
Alignment explanation
Indices: 21539520--21539566 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
21539510 TCGAAGTTTG
**
21539520 AAAAAAAGAAAAAAATCGAAT
1 AAAAAAAGAAAAAAAAAGAAT
*
21539541 TAAAAAAGAAAAAAAGAAGAA-
1 AAAAAAAGAAAAAAA-AAGAAT
21539562 AAAAA
1 AAAAA
21539567 TTCGAGTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAGAAT
Found at i:21539975 original size:16 final size:16
Alignment explanation
Indices: 21539954--21539989 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
21539944 ATCCTTTGTT
21539954 GAAAATCATGTCTGAA
1 GAAAATCATGTCTGAA
*
21539970 GAAAATCTTGTCTGAA
1 GAAAATCATGTCTGAA
21539986 GAAA
1 GAAA
21539990 GGCTACAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (16 bp):
GAAAATCATGTCTGAA
Found at i:21540451 original size:22 final size:22
Alignment explanation
Indices: 21540428--21540528 Score: 68
Period size: 22 Copynumber: 4.5 Consensus size: 22
21540418 AACTAGTGAG
*
21540428 GAAATTGAAAAGGAAAGAAAAG
1 GAAATTGAAAAGGAAAGAAAAA
*
21540450 GAGAATGTGTAAA--AAAGAAAAA
1 GA-AAT-TGAAAAGGAAAGAAAAA
*
21540472 GAAGA-TG-AAAGAGATATTGAAAAA
1 GAA-ATTGAAAAG-GA-A-AGAAAAA
*
21540496 -AAATTGTGAAAGGAAAGAAAAA
1 GAAATTG-AAAAGGAAAGAAAAA
21540518 GAAATTGAAAA
1 GAAATTGAAAA
21540529 AAGAATGAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 24
0.68 0.05 0.26
Matches are distributed among these distances:
19 3 0.05
20 2 0.03
21 1 0.02
22 24 0.39
23 15 0.24
24 13 0.21
25 4 0.06
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (22 bp):
GAAATTGAAAAGGAAAGAAAAA
Found at i:21542024 original size:17 final size:17
Alignment explanation
Indices: 21542004--21542036 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21541994 TTTAAGGACT
21542004 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
21542021 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
21542037 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:21542315 original size:50 final size:51
Alignment explanation
Indices: 21542231--21542367 Score: 145
Period size: 50 Copynumber: 2.7 Consensus size: 51
21542221 TGACATCCAT
* * *
21542231 TAACTCTCATGATTAATT-AAGTTTGCATCATAAATAATGA-CATGCATTAAG
1 TAACTCACATG-TTAGTTAAAGTATGCATCATAAATAAT-ATCATGCATTAAG
* ** *
21542282 TAACTTACATGTTAGTTAAA-TATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAAGTATGCATCATAAATAATATCATGCATTAAG
* *
21542332 TAACTCCCATGTTAGTTAAAGTTTGCATCATTAAAT
1 TAACTCACATGTTAGTTAAAGTATGCATCA-TAAAT
21542368 CAAGTCATCC
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
49 1 0.01
50 47 0.65
51 19 0.26
52 5 0.07
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (51 bp):
TAACTCACATGTTAGTTAAAGTATGCATCATAAATAATATCATGCATTAAG
Found at i:21546466 original size:17 final size:17
Alignment explanation
Indices: 21546431--21546471 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
21546421 AGTAAATTAC
21546431 TAAAA-AAATTAATACA
1 TAAAATAAATTAATACA
21546447 TAAAATAAATTCAATA-A
1 TAAAATAAATT-AATACA
21546464 T-AAATAAA
1 TAAAATAAA
21546472 ACGAGATGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.52
17 7 0.30
18 4 0.17
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAATAAATTAATACA
Found at i:21548944 original size:25 final size:25
Alignment explanation
Indices: 21548914--21548961 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
21548904 CTTTGTCTGG
21548914 GCTCGTAT-GAGCTAACCCTATCTAA
1 GCTCGTATAG-GCTAACCCTATCTAA
21548939 GCTCGTATAGGCTAACCCTATCT
1 GCTCGTATAGGCTAACCCTATCT
21548962 GAAAGACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (25 bp):
GCTCGTATAGGCTAACCCTATCTAA
Found at i:21551567 original size:9 final size:9
Alignment explanation
Indices: 21551553--21551577 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21551543 AAGTGTTTTC
21551553 TTGTTATTT
1 TTGTTATTT
21551562 TTGTTATTT
1 TTGTTATTT
21551571 TTGTTAT
1 TTGTTAT
21551578 AGAAATGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (9 bp):
TTGTTATTT
Found at i:21569388 original size:17 final size:17
Alignment explanation
Indices: 21569366--21569404 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
21569356 ATAATTGTCC
21569366 CTGCATTTTTATTCTCA
1 CTGCATTTTTATTCTCA
*
21569383 CTGCA-TTTTATTGTCA
1 CTGCATTTTTATTCTCA
21569399 CTGCAT
1 CTGCAT
21569405 CTACATTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.18, C:0.23, G:0.10, T:0.49
Consensus pattern (17 bp):
CTGCATTTTTATTCTCA
Found at i:21570008 original size:9 final size:9
Alignment explanation
Indices: 21569996--21570021 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21569986 TCGAATTATT
21569996 CGAATAAAC
1 CGAATAAAC
21570005 CGAATAAAC
1 CGAATAAAC
21570014 CGAATAAA
1 CGAATAAA
21570022 ACTATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (9 bp):
CGAATAAAC
Found at i:21591852 original size:19 final size:18
Alignment explanation
Indices: 21591832--21591870 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
21591822 AATATAAATA
21591832 AAATT-TAAATTTAATAAT
1 AAATTGTAAA-TTAATAAT
21591850 AAATTGTAAATTAATAA-
1 AAATTGTAAATTAATAAT
21591867 AAAT
1 AAAT
21591871 AAATGAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATTGTAAATTAATAAT
Found at i:21601762 original size:37 final size:37
Alignment explanation
Indices: 21601712--21601914 Score: 275
Period size: 37 Copynumber: 5.5 Consensus size: 37
21601702 CACAAAGGCC
*
21601712 TGCTAGGCACATAGCCCGAATACACTAGCACGAAGCT
1 TGCTAGGCACATAGCCCGAATACACTGGCACGAAGCT
* * *
21601749 TGCTAGGCACATAGCCCAAATACACTGGCATGAAGCC
1 TGCTAGGCACATAGCCCGAATACACTGGCACGAAGCT
**
21601786 TGCTAGGCACATAGCCCGAATACACCAGCACG-AGCT
1 TGCTAGGCACATAGCCCGAATACACTGGCACGAAGCT
* **
21601822 TGCTAGGCACGTAGCCCGAATACTTTGGCACGAAGCT
1 TGCTAGGCACATAGCCCGAATACACTGGCACGAAGCT
* *
21601859 TGCTAGGCACAAAGCCCGAATACACCGGCACGAAGCCT
1 TGCTAGGCACATAGCCCGAATACACTGGCACGAAG-CT
*
21601897 AG-TAGGCACATAGCCCGA
1 TGCTAGGCACATAGCCCGA
21601915 TTTACTTGAA
Statistics
Matches: 143, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
36 30 0.21
37 110 0.77
38 3 0.02
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.15
Consensus pattern (37 bp):
TGCTAGGCACATAGCCCGAATACACTGGCACGAAGCT
Found at i:21601857 original size:73 final size:74
Alignment explanation
Indices: 21601700--21601914 Score: 299
Period size: 73 Copynumber: 2.9 Consensus size: 74
21601690 TCCAATCATC
* *
21601700 GGCACAAAGGCCTGCTAGGCACATAGCCCGAATACACTAGCACGAAGCTTGCTAGGCACATAGCC
1 GGCACGAA-GCCTGCTAGGCACATAGCCCGAATACACCAGCACGAAGCTTGCTAGGCACATAGCC
*
21601765 CAAATACACT
65 CGAATACACT
* *
21601775 GGCATGAAGCCTGCTAGGCACATAGCCCGAATACACCAGCACG-AGCTTGCTAGGCACGTAGCCC
1 GGCACGAAGCCTGCTAGGCACATAGCCCGAATACACCAGCACGAAGCTTGCTAGGCACATAGCCC
**
21601839 GAATACTTT
66 GAATACACT
* * * *
21601848 GGCACGAAGCTTGCTAGGCACAAAGCCCGAATACACCGGCACGAAGCCTAG-TAGGCACATAGCC
1 GGCACGAAGCCTGCTAGGCACATAGCCCGAATACACCAGCACGAAG-CTTGCTAGGCACATAGCC
21601912 CGA
65 CGA
21601915 TTTACTTGAA
Statistics
Matches: 125, Mismatches: 13, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
73 65 0.52
74 51 0.41
75 9 0.07
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (74 bp):
GGCACGAAGCCTGCTAGGCACATAGCCCGAATACACCAGCACGAAGCTTGCTAGGCACATAGCCC
GAATACACT
Found at i:21601859 original size:110 final size:110
Alignment explanation
Indices: 21601712--21601914 Score: 318
Period size: 110 Copynumber: 1.8 Consensus size: 110
21601702 CACAAAGGCC
* *
21601712 TGCTAGGCACATAGCCCGAATACACTAGCACGAAGCTTGCTAGGCACATAGCCCAAATACACTGG
1 TGCTAGGCACATAGCCCGAATACACTAGCACGAAGCTTGCTAGGCACAAAGCCCAAATACACCGG
*
21601777 CATGAAGCCT-GCTAGGCACATAGCCCGAATACACCAGCACGAGCT
66 CACGAAGCCTAG-TAGGCACATAGCCCGAATACACCAGCACGAGCT
* ** * *
21601822 TGCTAGGCACGTAGCCCGAATACTTTGGCACGAAGCTTGCTAGGCACAAAGCCCGAATACACCGG
1 TGCTAGGCACATAGCCCGAATACACTAGCACGAAGCTTGCTAGGCACAAAGCCCAAATACACCGG
21601887 CACGAAGCCTAGTAGGCACATAGCCCGA
66 CACGAAGCCTAGTAGGCACATAGCCCGA
21601915 TTTACTTGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
110 83 0.99
111 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.15
Consensus pattern (110 bp):
TGCTAGGCACATAGCCCGAATACACTAGCACGAAGCTTGCTAGGCACAAAGCCCAAATACACCGG
CACGAAGCCTAGTAGGCACATAGCCCGAATACACCAGCACGAGCT
Found at i:21612643 original size:17 final size:18
Alignment explanation
Indices: 21612604--21612647 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21612594 ATGCATATCA
* *
21612604 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
21612622 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTGCATT
21612639 TTTATTTGT
1 TTTATTTGT
21612648 TAGTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:21615645 original size:491 final size:491
Alignment explanation
Indices: 21614723--21615705 Score: 1957
Period size: 491 Copynumber: 2.0 Consensus size: 491
21614713 CGTTAAATTT
21614723 ATTTATTTTAATATTTACGATGTCGTTAGCATCGTATTGAAATTTGGTTATAGAATTTCAATGTC
1 ATTTATTTTAATATTTACGATGTCGTTAGCATCGTATTGAAATTTGGTTATAGAATTTCAATGTC
21614788 TGGATAGTTAATTGAATAGAAAGGATTGTAAAAATTACAAAAGTAGAAATTGTTTTAGAAAGATC
66 TGGATAGTTAATTGAATAGAAAGGATTGTAAAAATTACAAAAGTAGAAATTGTTTTAGAAAGATC
21614853 AAATAGGCAAATTAACCCATAGCATTTTACTAAGTGGATTAGCATGAGATATGTTGATTATAAGA
131 AAATAGGCAAATTAACCCATAGCATTTTACTAAGTGGATTAGCATGAGATATGTTGATTATAAGA
21614918 AAGATTATTTAAGGCTAAGTAAGTGGTTAATTAAGTTAATTAAGAAAGTCTAAATATTCACAAAA
196 AAGATTATTTAAGGCTAAGTAAGTGGTTAATTAAGTTAATTAAGAAAGTCTAAATATTCACAAAA
21614983 TTGCCCTTTAGTATATAAAGGAAATTAAAAGAAGAAAAATAGAAATTTTCACTTGTTTCTTCTTT
261 TTGCCCTTTAGTATATAAAGGAAATTAAAAGAAGAAAAATAGAAATTTTCACTTGTTTCTTCTTT
21615048 TCTACACGGCAAGAGCAAGAGGAGTTAGGGTTTTACATCCCAAAGTTTGAGCTTTGATTTGAGTA
326 TCTACACGGCAAGAGCAAGAGGAGTTAGGGTTTTACATCCCAAAGTTTGAGCTTTGATTTGAGTA
21615113 AGCAAATGTTAACCGCTTTTAGTTATTTTTATGTTTTTTAGTTCGTATTAGCTCAATCTAGCTAA
391 AGCAAATGTTAACCGCTTTTAGTTATTTTTATGTTTTTTAGTTCGTATTAGCTCAATCTAGCTAA
21615178 TCTAAGGACCAATTTTGAATCTGTCAAATGTTATGA
456 TCTAAGGACCAATTTTGAATCTGTCAAATGTTATGA
21615214 ATTTATTTTAATATTTACGATGTCGTTAGCATCGTATTGAAATTTGGTTATAGAATTTCAATGTC
1 ATTTATTTTAATATTTACGATGTCGTTAGCATCGTATTGAAATTTGGTTATAGAATTTCAATGTC
21615279 TGGATAGTTAATTGAATAGAAAGGATTGTAAAAATTACAAAAGTAGAAATTGTTTTAGAAAGATC
66 TGGATAGTTAATTGAATAGAAAGGATTGTAAAAATTACAAAAGTAGAAATTGTTTTAGAAAGATC
21615344 AAATAGGCAAATTAACCCATAGCATTTTACTAAGTGGATTAGCATGAGATATGTTGATTATAAGA
131 AAATAGGCAAATTAACCCATAGCATTTTACTAAGTGGATTAGCATGAGATATGTTGATTATAAGA
21615409 AAGATTATTTAAGGCTAAGTAAGTGGTTAATTAAGTTAATTAAGAAAGTCTAAATATTCACAAAA
196 AAGATTATTTAAGGCTAAGTAAGTGGTTAATTAAGTTAATTAAGAAAGTCTAAATATTCACAAAA
21615474 TTGCCCTTTAGTATATAAAGGAAATTAAAAGAAGAAAAATAGAAATTTTCACTTGTTTCTTCTTT
261 TTGCCCTTTAGTATATAAAGGAAATTAAAAGAAGAAAAATAGAAATTTTCACTTGTTTCTTCTTT
21615539 TCTACACGGCAAGAGCAAGAGGAGTTAGGGTTTTACATCCCAAAGTTTGAGCTTTGATTTGAGTA
326 TCTACACGGCAAGAGCAAGAGGAGTTAGGGTTTTACATCCCAAAGTTTGAGCTTTGATTTGAGTA
*
21615604 AGCAAATGTTAACCGCTTTTAGTTATTTTTATGTTTTTTAGTTCGTATTAGCTCAATCTAGTTAA
391 AGCAAATGTTAACCGCTTTTAGTTATTTTTATGTTTTTTAGTTCGTATTAGCTCAATCTAGCTAA
21615669 TCTAAGGACCAATTTTGAATCTGTCAAATGTTATGA
456 TCTAAGGACCAATTTTGAATCTGTCAAATGTTATGA
21615705 A
1 A
21615706 ACTTGCCATT
Statistics
Matches: 491, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
491 491 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (491 bp):
ATTTATTTTAATATTTACGATGTCGTTAGCATCGTATTGAAATTTGGTTATAGAATTTCAATGTC
TGGATAGTTAATTGAATAGAAAGGATTGTAAAAATTACAAAAGTAGAAATTGTTTTAGAAAGATC
AAATAGGCAAATTAACCCATAGCATTTTACTAAGTGGATTAGCATGAGATATGTTGATTATAAGA
AAGATTATTTAAGGCTAAGTAAGTGGTTAATTAAGTTAATTAAGAAAGTCTAAATATTCACAAAA
TTGCCCTTTAGTATATAAAGGAAATTAAAAGAAGAAAAATAGAAATTTTCACTTGTTTCTTCTTT
TCTACACGGCAAGAGCAAGAGGAGTTAGGGTTTTACATCCCAAAGTTTGAGCTTTGATTTGAGTA
AGCAAATGTTAACCGCTTTTAGTTATTTTTATGTTTTTTAGTTCGTATTAGCTCAATCTAGCTAA
TCTAAGGACCAATTTTGAATCTGTCAAATGTTATGA
Found at i:21632298 original size:19 final size:20
Alignment explanation
Indices: 21632251--21632298 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
21632241 TTGATAATTC
21632251 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
21632269 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
21632288 TTAATTATTAT
1 TTAATTATTAT
21632299 CAAAAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:21632330 original size:155 final size:148
Alignment explanation
Indices: 21632175--21632460 Score: 358
Period size: 148 Copynumber: 1.9 Consensus size: 148
21632165 AATATTTTTA
** * * *
21632175 AAACAGCCAAAAATAAAGTTTTATTTATTTATTTAAATTATCTATTTTA-TTTCCTTTTTCAAAA
1 AAACAGCCAAAAATAAA--TAAATTT-TTTATTTAAATT-T-AATGTTATTTTCATTTTTC-AAA
* *
21632239 TTTTGATAATTCTTAATATTAAATTATAAATTAAATTTTATAATTTATATTAATTATTATCAAAA
60 TTTTGATAATTATTAATATT-AATTATAAATTAAATTTTATAAATTATATTAATTATTATCAAAA
21632304 GTTTGAATTGAGATTTGTTTTCTTT
124 GTTTGAATTGAGATTTGTTTTCTTT
**** ** * * *
21632329 AAACTTTTAAATTTAAATAAATTTTTTATTTGAATTTAATGTTATTTTTATTTTTCGAATTTTGA
1 AAACAGCCAAAAATAAATAAATTTTTTATTTAAATTTAATGTTATTTTCATTTTTCAAATTTTGA
21632394 TAATTATTAATATTAATTATAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTTGAA
66 TAATTATTAATATTAATTATAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTTGAA
21632459 TT
131 TT
21632461 AAGAGTTTTC
Statistics
Matches: 115, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
148 52 0.45
149 26 0.23
150 10 0.09
151 11 0.10
152 5 0.04
154 11 0.10
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (148 bp):
AAACAGCCAAAAATAAATAAATTTTTTATTTAAATTTAATGTTATTTTCATTTTTCAAATTTTGA
TAATTATTAATATTAATTATAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTTGAA
TTGAGATTTGTTTTCTTT
Found at i:21632514 original size:110 final size:106
Alignment explanation
Indices: 21632373--21632682 Score: 423
Period size: 110 Copynumber: 2.9 Consensus size: 106
21632363 TTTAATGTTA
*
21632373 TTTTTATTTTTCGAATTTTGATAATTATTAATATTAATTATAAATTAAATTTTATAAATTATATT
1 TTTTTATTTTTCAAATTTTGATAATTATTAATATTAATTATAAATTAAATTTTAT-AATT-TATT
21632438 AATTATTATCAAAAGTTTGAATTAAGAGTTTTC-ATTTAAATGT
64 AATTATTATCAAAAGTTTGAATTAAGA-TTTTCTATTTAAATGT
* *
21632481 TTTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAAATATAAATTAAATTTTATAATTCGTA
1 TTT-TTATTTTTCAAA-TTTTGATAATTATTAATATTAATTATAAATTAAATTTTATAATT--TA
* *
21632546 TTAATTATTAACAAGAGTTTGAAATT-AGATTTTCTTATTTAAA---
62 TTAATTATTATCAAAAGTTTG-AATTAAGATTTTC-TATTTAAATGT
*
21632589 TTTTTATTTTTCAAAATTTTGATAATTTTTAATATTAATTATAAATTAAATTTTATAATTTATTA
1 TTTTTATTTTTC-AAATTTTGATAATTATTAATATTAATTATAAATTAAATTTTATAATTTATTA
* *
21632654 ATTATTATCCAAAGTTTGAATTAGGATTT
65 ATTATTATCAAAAGTTTGAATTAAGATTT
21632683 GTTTTAAATA
Statistics
Matches: 182, Mismatches: 12, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
104 4 0.02
105 25 0.14
107 51 0.28
108 9 0.05
109 20 0.11
110 62 0.34
111 11 0.06
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (106 bp):
TTTTTATTTTTCAAATTTTGATAATTATTAATATTAATTATAAATTAAATTTTATAATTTATTAA
TTATTATCAAAAGTTTGAATTAAGATTTTCTATTTAAATGT
Found at i:21632716 original size:17 final size:17
Alignment explanation
Indices: 21632696--21632730 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21632686 TTAAATATTT
21632696 TTGAGTTTAAATAAAAA
1 TTGAGTTTAAATAAAAA
* *
21632713 TTGAGTTTGAATTAAAA
1 TTGAGTTTAAATAAAAA
21632730 T
1 T
21632731 AAAATTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (17 bp):
TTGAGTTTAAATAAAAA
Found at i:21634189 original size:24 final size:24
Alignment explanation
Indices: 21634157--21634205 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
21634147 GATTTTGTTA
21634157 AAGAAGAAGAAGATC-CTGAGGAAG
1 AAGAAGAAGAAGATCTC-GAGGAAG
21634181 AAGAAGAAGAAGATCTCGAGGAAG
1 AAGAAGAAGAAGATCTCGAGGAAG
21634205 A
1 A
21634206 TCCTGTGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.51, C:0.08, G:0.33, T:0.08
Consensus pattern (24 bp):
AAGAAGAAGAAGATCTCGAGGAAG
Found at i:21644518 original size:37 final size:37
Alignment explanation
Indices: 21644467--21644663 Score: 279
Period size: 37 Copynumber: 5.3 Consensus size: 37
21644457 CAGCACAAAG
*
21644467 GCCTGCTAGGCACATAGCCTGAAAACACCGGCACGAA
1 GCCTGCTAGGCACATAGCCCGAAAACACCGGCACGAA
* *
21644504 ACCTGCTAGGCACATAGCCC-AAATACACCGGCACGAG
1 GCCTGCTAGGCACATAGCCCGAAA-ACACCGGCACGAA
* * * * *
21644541 GCATGCTAGGCAAATAGCCCGAACACACCGACACGAG
1 GCCTGCTAGGCACATAGCCCGAAAACACCGGCACGAA
*
21644578 GCCTGCTAGGCACATAGCCCGAATACACCGGCACGAA
1 GCCTGCTAGGCACATAGCCCGAAAACACCGGCACGAA
* *
21644615 GCTTGCTAGGCACATAGCCCGAATACACCGGCACGAA
1 GCCTGCTAGGCACATAGCCCGAAAACACCGGCACGAA
21644652 GCCTGCTAGGCA
1 GCCTGCTAGGCA
21644664 TATAACCTAA
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
36 3 0.02
37 138 0.97
38 2 0.01
ACGTcount: A:0.31, C:0.34, G:0.24, T:0.11
Consensus pattern (37 bp):
GCCTGCTAGGCACATAGCCCGAAAACACCGGCACGAA
Found at i:21651626 original size:29 final size:29
Alignment explanation
Indices: 21651589--21651668 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
21651579 TTGTCTTAGA
*
21651589 TTATATTTTAGTCACTTATGTTTAAAATG
1 TTATATTTTAGTAACTTATGTTTAAAATG
* * *
21651618 TTATGTTTTAGTAACTTATGTATGAAATG
1 TTATATTTTAGTAACTTATGTTTAAAATG
* *
21651647 TTATATTTTAGTTATTTATGTT
1 TTATATTTTAGTAACTTATGTT
21651669 ATTGTTTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (29 bp):
TTATATTTTAGTAACTTATGTTTAAAATG
Found at i:21667631 original size:27 final size:27
Alignment explanation
Indices: 21667593--21667646 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21667583 CTCAACGGTA
21667593 AGAAAAACAAAATAATTAGCTTGGTTG
1 AGAAAAACAAAATAATTAGCTTGGTTG
21667620 AGAAAAACAAAATAATTAGCTTGGTTG
1 AGAAAAACAAAATAATTAGCTTGGTTG
21667647 TGAATTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (27 bp):
AGAAAAACAAAATAATTAGCTTGGTTG
Found at i:21669066 original size:31 final size:31
Alignment explanation
Indices: 21669007--21669073 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
21668997 TTTCAATTTA
*
21669007 GTCACTAATGTTTTACATCATTTTTATTTCG
1 GTCACTAATGTTTTACATCATTTCTATTTCG
* * * *
21669038 GTCACTCATGTTTTAGATCGTTTCTATTTTG
1 GTCACTAATGTTTTACATCATTTCTATTTCG
21669069 GTCAC
1 GTCAC
21669074 ATGCTTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.49
Consensus pattern (31 bp):
GTCACTAATGTTTTACATCATTTCTATTTCG
Found at i:21670032 original size:27 final size:27
Alignment explanation
Indices: 21669989--21670063 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
21669979 TGTTGATCCA
* *
21669989 GATTTCCCATATCAGATAGTTCTTAG-G
1 GATTTCCCACATTAGATAGTTCTT-GCG
*
21670016 GATTTCCCACATTAGATAGTCCTTGCG
1 GATTTCCCACATTAGATAGTTCTTGCG
* * *
21670043 GACTTCCCACAATAGGTAGTT
1 GATTTCCCACATTAGATAGTT
21670064 TTTGTAGACT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (27 bp):
GATTTCCCACATTAGATAGTTCTTGCG
Found at i:21671330 original size:40 final size:40
Alignment explanation
Indices: 21671271--21671503 Score: 324
Period size: 40 Copynumber: 5.8 Consensus size: 40
21671261 TATTTTGAAT
21671271 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTA
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTA
* * *
21671311 AAATTCAAGCTACGGCTTAGCAGGCTATGAGCCGGTGTTG
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTA
* * * * *
21671351 AATTTCAAGCTACGGCTTAGCAAGCTATGAGTCGGTGTTA
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTA
* *
21671391 AAATTCAAGCTACGACTTAGCAGGCTAAGAGCC-AGTGTTG
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGA-TGTTA
*
21671431 AAATTCAAGCTACGATTTAGCAGGCTATGAGCCGATGTTA
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTA
* * *
21671471 AAACTCAAGCTACGGCTTACCAGGCTATGAGCC
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCC
21671504 AGTGTTGAAA
Statistics
Matches: 170, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
40 169 0.99
41 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (40 bp):
AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTA
Found at i:21671410 original size:80 final size:80
Alignment explanation
Indices: 21671271--21671515 Score: 391
Period size: 80 Copynumber: 3.1 Consensus size: 80
21671261 TATTTTGAAT
21671271 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTAAAATTCAAGCTACGGCTTAGCAGGC
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTAAAATTCAAGCTACGGCTTAGCAGGC
*
21671336 TATGAGCCGGTGTTG
66 TATGAGCCAGTGTTG
* * * * * *
21671351 AATTTCAAGCTACGGCTTAGCAAGCTATGAGTCGGTGTTAAAATTCAAGCTACGACTTAGCAGGC
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTAAAATTCAAGCTACGGCTTAGCAGGC
*
21671416 TAAGAGCCAGTGTTG
66 TATGAGCCAGTGTTG
* * *
21671431 AAATTCAAGCTACGATTTAGCAGGCTATGAGCCGATGTTAAAACTCAAGCTACGGCTTACCAGGC
1 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTAAAATTCAAGCTACGGCTTAGCAGGC
21671496 TATGAGCCAGTGTTG
66 TATGAGCCAGTGTTG
21671511 AAATT
1 AAATT
21671516 TGATGGTACT
Statistics
Matches: 147, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 147 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (80 bp):
AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTAAAATTCAAGCTACGGCTTAGCAGGC
TATGAGCCAGTGTTG
Found at i:21671484 original size:120 final size:120
Alignment explanation
Indices: 21671271--21671515 Score: 357
Period size: 120 Copynumber: 2.0 Consensus size: 120
21671261 TATTTTGAAT
* *
21671271 AAATTCAAGCTACGACTTAGCAGGCTATGAGCCGATGTTAAAATTCAAGCTACGGCTTAGCAGGC
1 AAATTCAAGCTACGACTTAGCAGGCTAAGAGCCGATGTTAAAATTCAAGCTACGACTTAGCAGGC
* * ** * * *
21671336 TATGAGCCGGTGTTGAATTTCAAGCTACGGCTTAGCAAGCTATGAGTCGGTGTTA
66 TATGAGCCGATGTTAAAACTCAAGCTACGGCTTACCAAGCTATGAGCCAGTGTTA
* *
21671391 AAATTCAAGCTACGACTTAGCAGGCTAAGAGCC-AGTGTTGAAATTCAAGCTACGATTTAGCAGG
1 AAATTCAAGCTACGACTTAGCAGGCTAAGAGCCGA-TGTTAAAATTCAAGCTACGACTTAGCAGG
* *
21671455 CTATGAGCCGATGTTAAAACTCAAGCTACGGCTTACCAGGCTATGAGCCAGTGTTG
65 CTATGAGCCGATGTTAAAACTCAAGCTACGGCTTACCAAGCTATGAGCCAGTGTTA
21671511 AAATT
1 AAATT
21671516 TGATGGTACT
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
119 1 0.01
120 110 0.99
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (120 bp):
AAATTCAAGCTACGACTTAGCAGGCTAAGAGCCGATGTTAAAATTCAAGCTACGACTTAGCAGGC
TATGAGCCGATGTTAAAACTCAAGCTACGGCTTACCAAGCTATGAGCCAGTGTTA
Found at i:21671837 original size:37 final size:37
Alignment explanation
Indices: 21671790--21671887 Score: 119
Period size: 37 Copynumber: 2.6 Consensus size: 37
21671780 GCAATTTTAA
21671790 TCCAGAATTGCGCCC-AAACATGTCG-CTGCATGAGCACT
1 TCCAG-ATTGCGCCCAAAAC-TGTCGTC-GCATGAGCACT
*
21671828 TCTAGATTGCGCCCAAAACTGTCGTCGCATGAGCACT
1 TCCAGATTGCGCCCAAAACTGTCGTCGCATGAGCACT
***
21671865 TCCAGATTTAACCCAAAACTGTC
1 TCCAGATTGCGCCCAAAACTGTC
21671888 CCCACAGGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
37 44 0.83
38 9 0.17
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
TCCAGATTGCGCCCAAAACTGTCGTCGCATGAGCACT
Found at i:21672006 original size:37 final size:37
Alignment explanation
Indices: 21671912--21672006 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 37
21671902 TCCGGAATGT
*
21671912 ACCCAAGACTGTCGCTGCATAAATATTCTTCAAATTGC
1 ACCC-AGAATGTCGCTGCATAAATATTCTTCAAATTGC
* * **
21671950 ATCCAGAACTATCATTGCATAAATATTCTTC-AATTGC
1 ACCCAGAA-TGTCGCTGCATAAATATTCTTCAAATTGC
21671987 ACCCAGGAATGTCGCTGCAT
1 ACCCA-GAATGTCGCTGCAT
21672007 GAACATGTAC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 21 0.46
38 25 0.54
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (37 bp):
ACCCAGAATGTCGCTGCATAAATATTCTTCAAATTGC
Found at i:21672029 original size:26 final size:26
Alignment explanation
Indices: 21672000--21672050 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
21671990 CAGGAATGTC
21672000 GCTGCATGAACATGTACAGAATTGTT
1 GCTGCATGAACATGTACAGAATTGTT
* *
21672026 GCTGCATGAACGTGTCCAGAATTGT
1 GCTGCATGAACATGTACAGAATTGT
21672051 GCCTAGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (26 bp):
GCTGCATGAACATGTACAGAATTGTT
Found at i:21677388 original size:14 final size:14
Alignment explanation
Indices: 21677369--21677404 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
21677359 GAAAAGTAAT
*
21677369 TCATTTTCCGGAAA
1 TCATTTTCCGAAAA
21677383 TCATTTTCCGAAAA
1 TCATTTTCCGAAAA
*
21677397 CCATTTTC
1 TCATTTTC
21677405 AGTCAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (14 bp):
TCATTTTCCGAAAA
Found at i:21679124 original size:17 final size:17
Alignment explanation
Indices: 21679102--21679141 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
21679092 GCGTGAAAAA
*
21679102 CCCAAAACAAAAATAAT
1 CCCAAAACAAAAACAAT
*
21679119 CCCAAAGCAAAAACAAT
1 CCCAAAACAAAAACAAT
21679136 CCCAAA
1 CCCAAA
21679142 CCATAGTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.60, C:0.30, G:0.03, T:0.07
Consensus pattern (17 bp):
CCCAAAACAAAAACAAT
Done.