Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002108.1 Hibiscus syriacus cultivar Beakdansim tig00004313_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: 131245
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:699 original size:10 final size:10
Alignment explanation
Indices: 664--701 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
654 CCACATACAA
664 CTATATGATC
1 CTATATGATC
*
674 CTAAATGCAT-
1 CTATATG-ATC
684 CTATATGATC
1 CTATATGATC
694 CTATATGA
1 CTATATGA
702 GCTTTTAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (10 bp):
CTATATGATC
Found at i:3495 original size:35 final size:35
Alignment explanation
Indices: 3433--3567 Score: 159
Period size: 35 Copynumber: 3.8 Consensus size: 35
3423 TAAGAAGAAT
* * *
3433 GAAAGAAAGCATCGACACTCTCTATTCAAGTGAAC
1 GAAAGGAAGCATCGACACTTTCGATTCAAGTGAAC
* * *
3468 GGAATGAAGCATC-ATCACTTTCGATTCAAGAAGAAC
1 GAAAGGAAGCATCGA-CACTTTCGATTCAAG-TGAAC
3504 GAAAGGAAGCATCGACACTTTCGATTCAAGTGAAC
1 GAAAGGAAGCATCGACACTTTCGATTCAAGTGAAC
3539 GAAAGGATA-CATC-AGCACTTTCGATTCAA
1 GAAAGGA-AGCATCGA-CACTTTCGATTCAA
3568 TTATTCATCT
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
34 2 0.02
35 52 0.60
36 31 0.36
37 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (35 bp):
GAAAGGAAGCATCGACACTTTCGATTCAAGTGAAC
Found at i:3515 original size:71 final size:71
Alignment explanation
Indices: 3424--3567 Score: 209
Period size: 71 Copynumber: 2.0 Consensus size: 71
3414 GAAGGTGAAT
* * * * *
3424 AAGAAGAATGAAAGAAAGCATCGACACTCTCTATTCAAGTGAACGGAATGA-AGCATCATCACTT
1 AAGAAGAACGAAAGAAAGCATCGACACTCTCGATTCAAGTGAACGAAAGGATA-CATCAGCACTT
3488 TCGATTC
65 TCGATTC
* *
3495 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGAAAGGATACATCAGCACTTT
1 AAGAAGAACGAAAGAAAGCATCGACACTCTCGATTCAAGTGAACGAAAGGATACATCAGCACTTT
3560 CGATTC
66 CGATTC
3566 AA
1 AA
3568 TTATTCATCT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 64 0.98
72 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (71 bp):
AAGAAGAACGAAAGAAAGCATCGACACTCTCGATTCAAGTGAACGAAAGGATACATCAGCACTTT
CGATTC
Found at i:4236 original size:36 final size:36
Alignment explanation
Indices: 4182--4514 Score: 316
Period size: 36 Copynumber: 9.2 Consensus size: 36
4172 AGATTAAAAC
* *
4182 TTGAATCAAAAGTGTCGATGCTTCATTCCATTCGAT
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCGAT
* * *
4218 TTGAATCGAAAATATCGATGCTTCCTTCCGTTCGAT
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCGAT
* * *
4254 TCGAATCGAAAGTGTCGACGCTTCCTTCCGTTCGAT
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCGAT
* ** * *
4290 TCGAATCGAAAGTGTCGATGCTTCCCCTCCGTTCAAC
1 TTGAATCGAAAGTGTCGATGCTT-CATTCCGTTCGAT
* ** * * *
4327 TTGAATCGGAAGTACCGATGCTTCTTTCTGTTCG-C
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCGAT
* *
4362 TTGAATC-AGAAGTG-CTGATGCTTCATTTCATTCGAT
1 TTGAATCGA-AAGTGTC-GATGCTTCATTCCGTTCGAT
* *
4398 TTGCATCGAAAGTGTCGATGCTTCATTTCGTTCGAT
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCGAT
* * *
4434 TTGAATCGGAAGTGCCGATGCTTCCA-TCCGTTCGAC
1 TTGAATCGAAAGTGTCGATGCTT-CATTCCGTTCGAT
* ** *
4470 TTGAATC-AGAAGTGTTGATGCTTCCCTCCGTTCGAC
1 TTGAATCGA-AAGTGTCGATGCTTCATTCCGTTCGAT
4506 TTGAATCGA
1 TTGAATCGA
4515 TGCAAAATTT
Statistics
Matches: 248, Mismatches: 39, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.00
35 27 0.11
36 186 0.75
37 34 0.14
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (36 bp):
TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCGAT
Found at i:4492 original size:180 final size:179
Alignment explanation
Indices: 4181--4513 Score: 483
Period size: 180 Copynumber: 1.9 Consensus size: 179
4171 GAGATTAAAA
*
4181 CTTGAATCAAAAGTGTCGATGCTTCATTCCATTCGATTTGAATCGAAAATATCGATGCTTCCTTC
1 CTTGAATCAAAAGTGTCGATGCTTCATTCCATTCGATTTGAATCGAAAATATCGATGCTTCATTC
* *
4246 CGTTCGATTCGAATCGAAAGTGTCGACGCTTCCTTCCGTTCGATTCGAATCGAAAGTGTCGATGC
66 CGTTCGATTCGAATCGAAAGTGCCGACGCTTCCATCCGTTCGATTCGAATCGAAAGTGTCGATGC
4311 TTCCCCTCCGTTCAACTTGAATCGGAAGTACCGATGCTTCTTTCTGTTCG
131 TT-CCCTCCGTTCAACTTGAATCGGAAGTACCGATGCTTCTTTCTGTTCG
* * * * *
4361 CTTGAATCAGAAGTG-CTGATGCTTCATTTCATTCGATTTGCATCGAAAGTGTCGATGCTTCATT
1 CTTGAATCAAAAGTGTC-GATGCTTCATTCCATTCGATTTGAATCGAAAATATCGATGCTTCATT
* * * * *
4425 TCGTTCGATTTGAATCGGAAGTGCCGATGCTTCCATCCGTTCGACTT-GAATC-AGAAGTGTTGA
65 CCGTTCGATTCGAATCGAAAGTGCCGACGCTTCCATCCGTTCGA-TTCGAATCGA-AAGTGTCGA
*
4488 TGCTTCCCTCCGTTCGACTTGAATCG
128 TGCTTCCCTCCGTTCAACTTGAATCG
4514 ATGCAAAATT
Statistics
Matches: 136, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
179 22 0.16
180 112 0.82
181 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (179 bp):
CTTGAATCAAAAGTGTCGATGCTTCATTCCATTCGATTTGAATCGAAAATATCGATGCTTCATTC
CGTTCGATTCGAATCGAAAGTGCCGACGCTTCCATCCGTTCGATTCGAATCGAAAGTGTCGATGC
TTCCCTCCGTTCAACTTGAATCGGAAGTACCGATGCTTCTTTCTGTTCG
Found at i:29076 original size:6 final size:6
Alignment explanation
Indices: 29055--29092 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
29045 GCTCGGTATA
*
29055 GGGA-T GGGATT AGGATT GGGATT GGGATT GGGATT GGG
1 GGGATT GGGATT GGGATT GGGATT GGGATT GGGATT GGG
29093 GTTTGAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.18, C:0.00, G:0.53, T:0.29
Consensus pattern (6 bp):
GGGATT
Found at i:30137 original size:17 final size:16
Alignment explanation
Indices: 30083--30138 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
30073 TTTTAATTAT
*
30083 TAAAGTAAA-AAAA-A
1 TAAATTAAAGAAAATA
30097 TAAATT-AAGAAAATA
1 TAAATTAAAGAAAATA
*
30112 TAAAGTTAAAGAAAACTT
1 TAAA-TTAAAGAAAA-TA
30130 TAAATTAAA
1 TAAATTAAA
30139 AGGGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 2 0.06
14 9 0.26
15 5 0.14
16 2 0.06
17 12 0.34
18 5 0.14
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (16 bp):
TAAATTAAAGAAAATA
Found at i:31271 original size:21 final size:19
Alignment explanation
Indices: 31240--31278 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
31230 TAGATAAATA
*
31240 AATAAATAAAATTAATAAC
1 AATAAATAAAATAAATAAC
31259 AATAGAATAAAAATAAATAA
1 AATA-AAT-AAAATAAATAA
31279 TATTAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
AATAAATAAAATAAATAAC
Found at i:31305 original size:34 final size:31
Alignment explanation
Indices: 31233--31305 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
31223 AATGAAATAG
*
31233 ATAAATAAATAAATAAAATTAATAACAATAGA
1 ATAAA-AAATAAATAAAATTAATAACAATAAA
* *
31265 AT-AAAAATAAATAATATTAATATATAATAAAA
1 ATAAAAAATAAATAAAATTAATA-ACAAT-AAA
31297 ACTAAAAAA
1 A-TAAAAAA
31306 ATAACATGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 17 0.50
31 6 0.18
32 5 0.15
33 1 0.03
34 5 0.15
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (31 bp):
ATAAAAAATAAATAAAATTAATAACAATAAA
Found at i:31516 original size:37 final size:37
Alignment explanation
Indices: 31356--31693 Score: 242
Period size: 37 Copynumber: 8.9 Consensus size: 37
31346 AAAAAAATCA
* * *
31356 TTTTTTAAAACTATATATTACATATGATTTCAAAAATT-
1 TTTTTCAAAACTATATA--ATATATGTTTTCAAAAATTG
*
31394 ATTTTCGAAAA-TATATAATATATATGTTTTCAAAAATTG
1 TTTTTC-AAAACTATAT-A-ATATATGTTTTCAAAAATTG
* * * * *
31433 CTTTCCAAAACCATA-ATATATATGTTCTC---AATTT
1 TTTTTCAAAACTATATA-ATATATGTTTTCAAAAATTG
* * *
31467 TTTTTCAAAACTATATAATACACGTTCTCAAAAATTG
1 TTTTTCAAAACTATATAATATATGTTTTCAAAAATTG
** * *
31504 TTTTTCGCAACTATATAATATATGTTTTTAAAAAAATTA
1 TTTTTCAAAACTATATAATATATG-TTTT-CAAAAATTG
31543 TTTTTCAAAACTATATAATATATGTTTTCAAAAATGTG
1 TTTTTCAAAACTATATAATATATGTTTTCAAAAAT-TG
* * *
31581 TTTTCTAAAAAAACTATATATTATATGTTTTCAAAATTATATT
1 TTTT-T--CAAAACTATATAATATATGTTTTCAAAA--AT-TG
* * *
31624 TTTTTTAAAACTATATAATATACGTTTTCTAAAAAATG
1 TTTTTCAAAACTATATAATATATGTTTTC-AAAAATTG
* * *
31662 -TTTTCAAAACCT-TATATTATACGTTTTTAAAA
1 TTTTTCAAAA-CTATATAATATATGTTTTCAAAA
31694 CATGTACTAT
Statistics
Matches: 244, Mismatches: 38, Indels: 38
0.76 0.12 0.12
Matches are distributed among these distances:
34 26 0.11
35 1 0.00
36 4 0.02
37 65 0.27
38 46 0.19
39 43 0.18
40 21 0.09
41 30 0.12
42 1 0.00
43 7 0.03
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTTCAAAACTATATAATATATGTTTTCAAAAATTG
Found at i:31600 original size:41 final size:40
Alignment explanation
Indices: 31512--31658 Score: 154
Period size: 41 Copynumber: 3.6 Consensus size: 40
31502 TGTTTTTCGC
* * *
31512 AACTATATAATATATGTTTTTAAAAAAATTATTTTT--CAA
1 AACTATATAATATATGTTTTCAAAAATA-TATTTTTAAAAA
* *
31551 AACTATATAATATATGTTTTCAAAAATGTGTTTTCTAAAAA
1 AACTATATAATATATGTTTTCAAAAATATATTTT-TAAAAA
* * ***
31592 AACTATATATTATATGTTTTCAAAATTATATTTTTTTTAA
1 AACTATATAATATATGTTTTCAAAAATATATTTTTAAAAA
*
31632 AACTATATAATATACGTTTTCTAAAAA
1 AACTATATAATATATGTTTTC-AAAAA
31659 ATGTTTTCAA
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
38 5 0.06
39 26 0.29
40 22 0.25
41 36 0.40
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (40 bp):
AACTATATAATATATGTTTTCAAAAATATATTTTTAAAAA
Found at i:31712 original size:81 final size:79
Alignment explanation
Indices: 31473--31714 Score: 187
Period size: 81 Copynumber: 3.1 Consensus size: 79
31463 ATTTTTTTTC
* * ** * *
31473 AAAACTATATAATACACGTTCTCAAAAAT-TGTTTTTC--GCAACTATATAATATATGTTTTTAA
1 AAAACTATATAATATACGTTTTCAAAAATATG-TTTTCAAAAAACTATATATTATACG-TTTTAA
* *
31535 AAA-AAT-TAT-TTTT
64 AAATTATATATACTTT
* * * *
31548 CAAAACTATATAATATATGTTTTCAAAAATGTGTTTTCTAAAAAAACTATATATTATATGTTTTC
1 -AAAACTATATAATATACGTTTTCAAAAATATGTTTTC--AAAAAACTATATATTATACGTTTTA
* **
31613 AAAATTATATTTTTTTT
63 AAAATTATATATACTTT
*
31630 AAAACTATATAATATACGTTTTCTAAAAA-ATGTTTTC-AAAACCT-TATATTATACGTTTTTAA
1 AAAACTATATAATATACGTTTTC-AAAAATATGTTTTCAAAAAACTATATATTATACG-TTTTAA
31692 AACATGTACTATATACTTT
64 AA-AT-TA-TATATACTTT
31711 AAAA
1 AAAA
31715 AAACTACATT
Statistics
Matches: 136, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
76 31 0.23
77 12 0.09
78 13 0.10
79 10 0.07
80 19 0.14
81 42 0.31
82 9 0.07
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (79 bp):
AAAACTATATAATATACGTTTTCAAAAATATGTTTTCAAAAAACTATATATTATACGTTTTAAAA
ATTATATATACTTT
Found at i:32648 original size:2 final size:2
Alignment explanation
Indices: 32641--32678 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
32631 ACATATGAAA
*
32641 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32679 TACATATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35803 original size:36 final size:36
Alignment explanation
Indices: 35739--35895 Score: 181
Period size: 36 Copynumber: 4.3 Consensus size: 36
35729 AACATATACA
** *
35739 TTTTGAAAACAATTTTTGTAAAATATATATTATATAG
1 TTTTGAAAACGGTTTTAG-AAAATATATATTATATAG
*
35776 TTTTGAAAACGGTTTAAGAAAATATATATATTATATAG
1 TTTTGAAAACGGTTTTAG-AAA-ATATATATTATATAG
*** * *
35814 TTTTGAAAATATTTTTTGAAAGTATATATTATATAG
1 TTTTGAAAACGGTTTTAGAAAATATATATTATATAG
*
35850 TTTTGAAAACGGTTTTAGAAAATATATATAATAT-G
1 TTTTGAAAACGGTTTTAGAAAATATATATTATATAG
35885 ATTTTGAAAAC
1 -TTTTGAAAAC
35896 ATATTTTTGA
Statistics
Matches: 101, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
35 1 0.01
36 52 0.51
37 20 0.20
38 28 0.28
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACGGTTTTAGAAAATATATATTATATAG
Found at i:35803 original size:38 final size:38
Alignment explanation
Indices: 35739--35937 Score: 176
Period size: 36 Copynumber: 5.2 Consensus size: 38
35729 AACATATACA
** * *
35739 TTTTGAAAACAATTTTTGTAAA-ATATATATTATATAG
1 TTTTGAAAACGGTTTTAGAAAATATATATATTATATAG
*
35776 TTTTGAAAACGGTTTAAGAAAATATATATATTATATAG
1 TTTTGAAAACGGTTTTAGAAAATATATATATTATATAG
*** * *
35814 TTTTGAAAATATTTTTTG-AAA-GTATATATTATATAG
1 TTTTGAAAACGGTTTTAGAAAATATATATATTATATAG
35850 TTTTGAAAACGGTTTTAGAAAATATATATA--ATAT-G
1 TTTTGAAAACGGTTTTAGAAAATATATATATTATATAG
** *
35885 ATTTTGAAAACATATTTTTGAAAATGTATATAATATATATATAG
1 -TTTTGAAAAC-GGTTTTAGAAAA--TATAT-ATAT-TATATAG
*
35929 TTTTTAAAA
1 TTTTGAAAA
35938 TAATTTTTTC
Statistics
Matches: 130, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
35 1 0.01
36 42 0.32
37 32 0.25
38 34 0.26
39 5 0.04
40 3 0.02
43 12 0.09
44 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (38 bp):
TTTTGAAAACGGTTTTAGAAAATATATATATTATATAG
Found at i:35803 original size:67 final size:68
Alignment explanation
Indices: 35671--35803 Score: 153
Period size: 69 Copynumber: 2.0 Consensus size: 68
35661 ATAGTATAGT
* * **
35671 TTTTGAAAATATTTTTGAAAAAAATATAATATATGGTTTTTAAAAAACGATTTTTGAAAACATAT
1 TTTTGAAAAAATTTTTGAAAAAAATATAATATATAGTTTTTAAAAAACGATTTAAGAAAACATAT
35736 ACA
66 ACA
* * * * * *
35739 TTTTGAAAACAATTTTTGTAAAATATATATTATATAG-TTTT-GAAAACGGTTTAAGAAAATATA
1 TTTTGAAAA-AATTTTTGAAAAAAATATAATATATAGTTTTTAAAAAACGATTTAAGAAAACATA
35802 TA
65 TA
35804 TATTATATAG
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
67 19 0.35
68 13 0.24
69 22 0.41
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.41
Consensus pattern (68 bp):
TTTTGAAAAAATTTTTGAAAAAAATATAATATATAGTTTTTAAAAAACGATTTAAGAAAACATAT
ACA
Found at i:35845 original size:74 final size:73
Alignment explanation
Indices: 35738--35923 Score: 261
Period size: 74 Copynumber: 2.5 Consensus size: 73
35728 AAACATATAC
*
35738 ATTTTGAAAACAATTTTTGTAAAA-TATATATTATATAGTTTTGAAAACGGTTTAAGAAAATATA
1 ATTTTGAAAACATTTTTTG-AAAAGTATATATTATATAGTTTTGAAAACGGTTTAAGAAAATATA
35802 TATATTATAT-
65 TATA--ATATG
* *
35812 AGTTTTGAAAATATTTTTTG-AAAGTATATATTATATAGTTTTGAAAACGGTTTTAGAAAATATA
1 A-TTTTGAAAACATTTTTTGAAAAGTATATATTATATAGTTTTGAAAACGGTTTAAGAAAATATA
35876 TATAATATG
65 TATAATATG
*
35885 ATTTTGAAAACATATTTTTGAAAATGTATATAATATATA
1 ATTTTGAAAACAT-TTTTTGAAAA-GTATATATTATATA
35924 TATAGTTTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
72 15 0.15
73 10 0.10
74 47 0.47
75 29 0.29
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (73 bp):
ATTTTGAAAACATTTTTTGAAAAGTATATATTATATAGTTTTGAAAACGGTTTAAGAAAATATAT
ATAATATG
Found at i:36116 original size:21 final size:21
Alignment explanation
Indices: 36090--36130 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
36080 AACATACAGT
36090 TTTTTAAAAATGATTTTTTGG
1 TTTTTAAAAATGATTTTTTGG
36111 TTTTTAAAAATGATTTTTTG
1 TTTTTAAAAATGATTTTTTG
36131 AAAACATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (21 bp):
TTTTTAAAAATGATTTTTTGG
Found at i:36210 original size:25 final size:24
Alignment explanation
Indices: 36181--36239 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
36171 CATATTATTA
*
36181 TTTTATTTTATTTTC-TATTTTCCAT
1 TTTTATTTTATTTACTTATTTT--AT
*
36206 TTTTATTTCATTTACTTATTTTAT
1 TTTTATTTTATTTACTTATTTTAT
36230 TTCTTATTTT
1 TT-TTATTTT
36240 CAGTCCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 4 0.14
25 19 0.66
26 6 0.21
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTTACTTATTTTAT
Found at i:36237 original size:12 final size:11
Alignment explanation
Indices: 36181--36239 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 11
36171 CATATTATTA
36181 TTTTATTTTAT
1 TTTTATTTTAT
36192 TTTCTATTTTCCAT
1 TTT-TATTTT--AT
*
36206 TTTTATTTCAT
1 TTTTATTTTAT
36217 TTACTTATTTTAT
1 TT--TTATTTTAT
36230 TTCTTATTTT
1 TT-TTATTTT
36240 CAGTCCAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
11 7 0.17
12 14 0.34
13 15 0.37
14 5 0.12
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:37383 original size:23 final size:24
Alignment explanation
Indices: 37337--37383 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
37327 TCTTATTTTA
**
37337 TTTTATTTTTTCCTACTTTTTTTCT
1 TTTTATTTTTT-CTACTTACTTTCT
37362 TTTTATTTTTT-TACTTACTTTC
1 TTTTATTTTTTCTACTTACTTTC
37384 AAAATCTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTATTTTTTCTACTTACTTTCT
Found at i:37475 original size:4 final size:4
Alignment explanation
Indices: 37455--37488 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
37445 CTTCACTCTT
*
37455 TTTA -TTA TTTA TCTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
37489 TAAAACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:37684 original size:13 final size:13
Alignment explanation
Indices: 37666--37695 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
37656 TTGAATCAGG
37666 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
37679 TTTTAATTTTTAA
1 TTTTAAATTTTAA
37692 TTTT
1 TTTT
37696 CGTAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:39437 original size:13 final size:13
Alignment explanation
Indices: 39419--39443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39409 TTTTCCCAAC
39419 CCTAAAACCCTTA
1 CCTAAAACCCTTA
39432 CCTAAAACCCTT
1 CCTAAAACCCTT
39444 TTCTTCTACA
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:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (13 bp):
CCTAAAACCCTTA
Found at i:40170 original size:189 final size:189
Alignment explanation
Indices: 39850--40230 Score: 753
Period size: 189 Copynumber: 2.0 Consensus size: 189
39840 CAATGGTTAG
39850 GTGCTTATCCACACTTCATCTTTGACAAGGTTCGAAATTCCAGAGATATACCATGAAAAAAAAAT
1 GTGCTTATCCACACTTCATCTTTGACAAGGTTCGAAATTCCAGAGATATACCATGAAAAAAAAAT
39915 TACGGTGGAGGTTGGTGGAAGATTCGGTTGAGGATGGGAAAGAAGGGCAATTTTAACATATTATA
66 TACGGTGGAGGTTGGTGGAAGATTCGGTTGAGGATGGGAAAGAAGGGCAATTTTAACATATTATA
39980 TGTTTTATTTTTAAATTGATTTTCATTTATTCAAATAAAAAAAATAAAAAAAAGATTAT
131 TGTTTTATTTTTAAATTGATTTTCATTTATTCAAATAAAAAAAATAAAAAAAAGATTAT
40039 GTGCTTATCCACACTTCATCTTTGACAAGGTTCGAAATTCCAGAGATATACCATGAAAAAAAAAT
1 GTGCTTATCCACACTTCATCTTTGACAAGGTTCGAAATTCCAGAGATATACCATGAAAAAAAAAT
40104 TACGGTGGAGGTTGGTGGAAGATTCGGTTGAGGATGGGAAAGAAGGGCAATTTTAACATATTATA
66 TACGGTGGAGGTTGGTGGAAGATTCGGTTGAGGATGGGAAAGAAGGGCAATTTTAACATATTATA
*
40169 TGTTTTATTTTTAAATTGATTTTCATTTATTCAAATAAAAAAAATTAAAAAAAGATTAT
131 TGTTTTATTTTTAAATTGATTTTCATTTATTCAAATAAAAAAAATAAAAAAAAGATTAT
40228 GTG
1 GTG
40231 ACATATTTTT
Statistics
Matches: 191, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 191 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (189 bp):
GTGCTTATCCACACTTCATCTTTGACAAGGTTCGAAATTCCAGAGATATACCATGAAAAAAAAAT
TACGGTGGAGGTTGGTGGAAGATTCGGTTGAGGATGGGAAAGAAGGGCAATTTTAACATATTATA
TGTTTTATTTTTAAATTGATTTTCATTTATTCAAATAAAAAAAATAAAAAAAAGATTAT
Found at i:44721 original size:15 final size:15
Alignment explanation
Indices: 44701--44731 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44691 TCGAAATATC
44701 AAAATGTTTTCAACA
1 AAAATGTTTTCAACA
44716 AAAATGTTTTCAACA
1 AAAATGTTTTCAACA
44731 A
1 A
44732 TCTCCCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (15 bp):
AAAATGTTTTCAACA
Found at i:44853 original size:16 final size:16
Alignment explanation
Indices: 44832--44864 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44822 CTCATTTATC
44832 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
44848 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
44864 A
1 A
44865 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:47197 original size:20 final size:21
Alignment explanation
Indices: 47122--47205 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 21
47112 ACAGAACCCC
* *
47122 ATGGGGGTATCGATTCCC-CT
1 ATGGGGGGATCGATTCCCTCA
* *
47142 GTGGGGGGAATCGGTTCCCCTTCA
1 ATGGGGGG-ATCGATT-CCC-TCA
* * *
47166 AAGGGGGAATCGGTTCCCTC-
1 ATGGGGGGATCGATTCCCTCA
47186 ATGGGGGGATCGATTCCCTC
1 ATGGGGGGATCGATTCCCTC
47206 TGCACAAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
20 23 0.46
21 8 0.16
22 6 0.12
23 7 0.14
24 6 0.12
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (21 bp):
ATGGGGGGATCGATTCCCTCA
Found at i:51286 original size:117 final size:117
Alignment explanation
Indices: 51058--51287 Score: 277
Period size: 117 Copynumber: 2.0 Consensus size: 117
51048 AAGCTTATCT
* *
51058 TTTAAATTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAGAGTTCTAAATCCTTCTT
1 TTTAAATTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTT
* * *
51123 CAAGATTTCATTTTGATTTTCAAAATCCATTTTCATTTCTAGAAGAAGTTTG
66 CAACATTTCATTTTGATTTTCAAAATCCATTTTAATTTCTAAAAGAAGTTTG
* * * * * *
51175 TTTAATTTGAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCATT-T
1 TTTAAATTGAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT
* * **
51238 CTCAACATTTCATTTTGATTTTCCAAGTCTGTTTTAACTTTC-AAAAGAAG
65 -TCAACATTTCATTTTGATTTTCAAAATCCATTTTAA-TTTCTAAAAGAAG
51288 ATCATTTTTA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
116 2 0.02
117 89 0.94
118 4 0.04
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
TTTAAATTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTT
CAACATTTCATTTTGATTTTCAAAATCCATTTTAATTTCTAAAAGAAGTTTG
Found at i:54956 original size:21 final size:22
Alignment explanation
Indices: 54918--54966 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
54908 TTTATTTAAG
*
54918 AATTTTTGCCGGTAATTTC-AA
1 AATTTTTGCAGGTAATTTCGAA
* *
54939 AATTTTTGTAGGTGATTTCGAA
1 AATTTTTGCAGGTAATTTCGAA
*
54961 TATTTT
1 AATTTT
54967 ATCTTTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (22 bp):
AATTTTTGCAGGTAATTTCGAA
Found at i:55285 original size:21 final size:21
Alignment explanation
Indices: 55247--55292 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
55237 AACTGCATTG
* *
55247 TTTCATAATGTTTTTTGGTGA
1 TTTCATAAAGTTTTTTGGGGA
55268 TTTCA-AAAGTTTTGTTGGGGA
1 TTTCATAAAGTTTT-TTGGGGA
55289 TTTC
1 TTTC
55293 GAATCTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.52
Consensus pattern (21 bp):
TTTCATAAAGTTTTTTGGGGA
Found at i:55294 original size:168 final size:165
Alignment explanation
Indices: 54757--55428 Score: 624
Period size: 167 Copynumber: 4.0 Consensus size: 165
54747 ATCTTAGATT
* * * * ** * * * *
54757 TTTTTCCCGGTGATTTCAAAAATCTTGTCGTTGCTTTTGAATCTTCTATTTTCTTTCTTCAAGAG
1 TTTTTACCGGTGATTTCAAAATTTTTGTAGGAGATTTCGAATCTTCTATCTTCTTTCTTGAAGAG
* *
54822 AGATTTCAAAAGATTTTTTATCTAAGCTTGTATACTGATTA--GAACGATCTTGGATTACTTGTT
66 AGATCTCAAAAGATTTTTTATCTAAGCTTGTATACTGATTACCGAACGATCTTGGATTACTGGTT
* **
54885 CGAGAATTTATTTTCTTAACTGTTTTATTTAAGAA
131 CGAGAATTTATTTTCTCAACTGCATTATTTAAGAA
* * * * *
54920 TTTTTGCCGGTAATTTCAAAATTTTTGTAGGTGATTTCGAATATTTTATCTT-TATTCTTGAAGA
1 TTTTTACCGGTGATTTCAAAATTTTTGTAGGAGATTTCGAATCTTCTATCTTCT-TTCTTGAAG-
* * * * * * * *
54984 AAATTATCTTAAAAGATTTTTGATCAAAACTTGTATACTGATTACCGAACGATCTTGGGTTACTA
64 AGA-GATCTCAAAAGATTTTTTATCTAAGCTTGTATACTGATTACCGAACGATCTTGGATTACTG
* * * * *
55049 GTTCGGGAGTTTATTTTCTTAACTTCATTATTTAAAAA
128 GTTCGAGAATTTATTTTCTCAACTGCATTATTTAAGAA
* * * *
55087 TTTTTACCGGTGGTTTCCAAATTTTTG-CGAGAGATTTCGAATCTTTTATCTTCTTTCTTGAAGA
1 TTTTTACCGGTGATTTCAAAATTTTTGTAG-GAGATTTCGAATCTTCTATCTTCTTTCTTGAAGA
*
55151 GAAAGATCTCAAAAGATTTTTTTATCTAAGCTTGCT-TACTGATTACCTAACGATCTTGGATTAC
65 G--AGATCTCAAAAGA-TTTTTTATCTAAGCTTG-TATACTGATTACCGAACGATCTTGGATTAC
* * * *
55215 TGGTTTC-AAAATTTATTTTCTCAACTGCATTGTTTCATAA
126 TGG-TTCGAGAATTTATTTTCTCAACTGCATTATTTAAGAA
** * * * * *
55255 TGTTTT-TTGGTGATTTCAAAAGTTTTGTTGGGGATTTCGAATCTTCTAGTTTTTTTTCTTGAAG
1 T-TTTTACCGGTGATTTCAAAATTTTTGTAGGAGATTTCGAATCTTCTA-TCTTCTTTCTTGAAG
* * * * * * *
55319 AGAGATGTCAAAAATATTTTTTACCTAAGTTTTTATACTGATTACCGAACAATATTGTG-TTACT
64 AGAGATCTC-AAAAGATTTTTTATCTAAGCTTGTATACTGATTACCGAACGATCTTG-GATTACT
* *
55383 GGTTCTG-GAATTTGTTTCCTCAACTGCATTATTTAAGAA
127 GGTTC-GAGAATTTATTTTCTCAACTGCATTATTTAAGAA
55422 TGTTTTA
1 T-TTTTA
55429 TGGGGAATTT
Statistics
Matches: 413, Mismatches: 75, Indels: 37
0.79 0.14 0.07
Matches are distributed among these distances:
162 1 0.00
163 49 0.12
164 2 0.00
165 34 0.08
166 6 0.01
167 189 0.46
168 108 0.26
169 24 0.06
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (165 bp):
TTTTTACCGGTGATTTCAAAATTTTTGTAGGAGATTTCGAATCTTCTATCTTCTTTCTTGAAGAG
AGATCTCAAAAGATTTTTTATCTAAGCTTGTATACTGATTACCGAACGATCTTGGATTACTGGTT
CGAGAATTTATTTTCTCAACTGCATTATTTAAGAA
Found at i:71348 original size:19 final size:20
Alignment explanation
Indices: 71324--71361 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
71314 GGAAGCAAGT
71324 GAAAGAC-AGAGAAAATGGA
1 GAAAGACAAGAGAAAATGGA
*
71343 GAAAGACAAGGGAAAATGG
1 GAAAGACAAGAGAAAATGG
71362 CAAAATGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.55, C:0.05, G:0.34, T:0.05
Consensus pattern (20 bp):
GAAAGACAAGAGAAAATGGA
Found at i:72028 original size:4 final size:4
Alignment explanation
Indices: 72019--72210 Score: 120
Period size: 4 Copynumber: 45.8 Consensus size: 4
72009 GACGGGAATT
* * *
72019 TTTA TTTA TTTA -TTA TTTT TTTA TTTA TTTCAAA TTTA TGTA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT---A TTTA TTTA TTTA TTTA
* **
72069 TTTCAAA TTTA TTTG TTTA TTTA TTTA TTT- TAGA TTTA TTTA TTTA TTTCA
1 TTT---A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A
* * ** *
72120 CTTGAA TTTA TTTT TTTA TTTA TTTA TTTA GATA TTTCGAA ATTA TTTA
1 -TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT---A TTTA TTTA
* ** *
72169 TTTG TTT- TGAA ATTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
72211 GAATGAATAT
Statistics
Matches: 144, Mismatches: 29, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
3 5 0.03
4 122 0.85
5 3 0.02
6 3 0.02
7 11 0.08
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:72043 original size:15 final size:16
Alignment explanation
Indices: 72018--72147 Score: 72
Period size: 15 Copynumber: 7.9 Consensus size: 16
72008 TGACGGGAAT
72018 TTTTATTTATTTATTA
1 TTTTATTTATTTATTA
72034 TTTT-TTTATTTATT-
1 TTTTATTTATTTATTA
*** *
72048 TCAAATTTATGTATTCA
1 TTTTATTTATTTATT-A
72065 -TTTATTTCAAATTTATT-
1 TTTTATTT---ATTTATTA
72082 TGTTTATTTATTTATT-
1 T-TTTATTTATTTATTA
**
72098 TTAGATTTATTTATTTA
1 TTTTATTTATTTA-TTA
* * *
72115 TTTCACTTGAATTTATTT
1 TTTTA-TT-TATTTATTA
72133 TTTTATTTATTTATT
1 TTTTATTTATTTATT
72148 TAGATATTTC
Statistics
Matches: 86, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
14 1 0.01
15 29 0.34
16 25 0.29
17 5 0.06
18 8 0.09
19 18 0.21
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTATTTATTTATTA
Found at i:72055 original size:19 final size:19
Alignment explanation
Indices: 72017--72090 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
72007 CTGACGGGAA
*
72017 TTTTTATTTATTT-ATTATT
1 TTTTTATTTATTTCA-AATT
72036 TTTTTATTTATTTCAAATT
1 TTTTTATTTATTTCAAATT
72055 TATGTATTCATTTATTTCAAATT
1 T-T-T-TT-ATTTATTTCAAATT
* *
72078 TATTTGTTTATTT
1 TTTTTATTTATTT
72091 ATTTATTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 24 0.51
20 4 0.09
21 2 0.04
22 2 0.04
23 15 0.32
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTATTTATTTCAAATT
Found at i:72057 original size:23 final size:23
Alignment explanation
Indices: 72017--72144 Score: 106
Period size: 23 Copynumber: 5.6 Consensus size: 23
72007 CTGACGGGAA
72017 TTTTTATTTATTT---A-TTATT
1 TTTTTATTTATTTCAAATTTATT
*
72036 TTTTTATTTATTTCAAATTTATG
1 TTTTTATTTATTTCAAATTTATT
* *
72059 TATTCATTTATTTCAAATTTATT
1 TTTTTATTTATTTCAAATTTATT
* *
72082 TGTTTATTTATTT--ATTTTAGATT
1 TTTTTATTTATTTCAAATTT--ATT
*
72105 TATTTATTTATTTCACTTGAATTTATT
1 TTTTTATTTATTTCA----AATTTATT
72132 TTTTTATTTATTT
1 TTTTTATTTATTT
72145 ATTTAGATAT
Statistics
Matches: 87, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
19 13 0.15
21 4 0.05
22 1 0.01
23 50 0.57
27 15 0.17
29 4 0.05
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (23 bp):
TTTTTATTTATTTCAAATTTATT
Found at i:72068 original size:27 final size:27
Alignment explanation
Indices: 72026--72210 Score: 102
Period size: 27 Copynumber: 6.9 Consensus size: 27
72016 ATTTTTATTT
*
72026 ATTTA-TTATTTTTTTATTTATTTC-A
1 ATTTATTTATTTATTTATTTATTTCAA
* *
72051 A---ATTTATGTATTCATTTATTTCAA
1 ATTTATTTATTTATTTATTTATTTCAA
* * *
72075 ATTTATTTGTTTATTTATTTATTTTAG
1 ATTTATTTATTTATTTATTTATTTCAA
* *
72102 ATTTATTTATTTATTTCACTTGAATTT-ATTT
1 ATTTATTTATTTATTT-A-TT-TATTTCA--A
* **
72133 TTTTATTTATTTATTTAGATATTTCGAA
1 ATTTATTTATTTATTTATTTATTTC-AA
* *
72161 A-TTATTTATTTGTTTTGAAATTATTT---
1 ATTTATTTATTT-ATTT--ATTTATTTCAA
72187 ATTTATTTATTTATTTATTTATTT
1 ATTTATTTATTTATTTATTTATTT
72211 GAATGAATAT
Statistics
Matches: 122, Mismatches: 22, Indels: 33
0.69 0.12 0.19
Matches are distributed among these distances:
22 1 0.01
23 16 0.13
24 9 0.07
25 1 0.01
26 4 0.03
27 53 0.43
28 8 0.07
29 3 0.02
30 12 0.10
31 15 0.12
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.66
Consensus pattern (27 bp):
ATTTATTTATTTATTTATTTATTTCAA
Found at i:72166 original size:23 final size:20
Alignment explanation
Indices: 72139--72191 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 20
72129 ATTTTTTTAT
72139 TTATTTATTTAGATATTTCGAAA
1 TTATTTATTTAG-T-TTT-GAAA
72162 TTATTTATTT-GTTTTGAAA
1 TTATTTATTTAGTTTTGAAA
72181 TTATTTATTTA
1 TTATTTATTTA
72192 TTTATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 1 0.03
22 1 0.03
23 10 0.34
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (20 bp):
TTATTTATTTAGTTTTGAAA
Found at i:72166 original size:54 final size:49
Alignment explanation
Indices: 72026--72203 Score: 146
Period size: 50 Copynumber: 3.5 Consensus size: 49
72016 ATTTTTATTT
* * * * *
72026 ATTTA-TTATTTTTTTATTTATTTCAAATTT-ATGTATTCATTT-ATTTCAA
1 ATTTATTTATTTATTTATTTATTT-AGATTTAAT-TATTTATTTCACTT-GA
* *
72075 ATTTATTTGTTTATTTATTTATTTTAGATTTATTTATTTATTTCACTTGA
1 ATTTATTTATTTATTTATTTA-TTTAGATTTAATTATTTATTTCACTTGA
* ***
72125 ATTTATTTTTTTATTTATTTATTTAGATATTTCGAAATTATTTATTTGTTTTGA
1 ATTTATTTATTTATTTATTTATTTAG--ATTT---AATTATTTATTTCACTTGA
*
72179 AATTATTTATTTATTTATTTATTTA
1 ATTTATTTATTTATTTATTTATTTA
72204 TTTATTTGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
49 10 0.09
50 47 0.44
51 11 0.10
54 38 0.36
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.65
Consensus pattern (49 bp):
ATTTATTTATTTATTTATTTATTTAGATTTAATTATTTATTTCACTTGA
Found at i:72210 original size:54 final size:56
Alignment explanation
Indices: 72075--72212 Score: 156
Period size: 54 Copynumber: 2.5 Consensus size: 56
72065 TTTATTTCAA
* * * * *
72075 ATTTATTTGTTTATTTATTTATTTTAGATTTATTTATTTATTTCACTTGAATTTATTT
1 ATTTATTTATTTATTTATTTATTTGAGAATTATTTATTTAGTT--CTTGAAATTATTT
* **
72133 TTTTATTTATTTATTTAGATATTTCGA-AATTATTTATTT-GTT-TTGAAATTATTT
1 ATTTATTTATTTATTTATTTATTT-GAGAATTATTTATTTAGTTCTTGAAATTATTT
72187 ATTTATTTATTTATTTATTTATTTGA
1 ATTTATTTATTTATTTATTTATTTGA
72213 ATGAATATGA
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
53 2 0.03
54 32 0.47
57 2 0.03
58 31 0.46
59 1 0.01
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (56 bp):
ATTTATTTATTTATTTATTTATTTGAGAATTATTTATTTAGTTCTTGAAATTATTT
Found at i:74210 original size:23 final size:23
Alignment explanation
Indices: 74182--74232 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
74172 TAAATTTGTA
74182 ATTTTTTTAGTT-ATTCGAACTAC
1 ATTTTTTTAGTTAATT-GAACTAC
*
74205 ATTTTTTTAGTTAATTGAACTAT
1 ATTTTTTTAGTTAATTGAACTAC
74228 ATTTT
1 ATTTT
74233 CTTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (23 bp):
ATTTTTTTAGTTAATTGAACTAC
Found at i:74326 original size:17 final size:17
Alignment explanation
Indices: 74281--74331 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
74271 TGTTTTTTAA
*
74281 AATTTGTTTAAATTATT
1 AATTTCTTTAAATTATT
**
74298 AATCAACTTTAAATTATT
1 AAT-TTCTTTAAATTATT
*
74316 AATTTCTTTAAGTTAT
1 AATTTCTTTAAATTAT
74332 CATTGAACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTCTTTAAATTATT
Found at i:77737 original size:33 final size:33
Alignment explanation
Indices: 77700--77762 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
77690 TTATAAATCT
*
77700 TAAACCTCAAACCATATACCCTATAACCTACCC
1 TAAACCTCAAACCATATACCATATAACCTACCC
* *
77733 TAAACCTCAAATCATATATCATATAACCTA
1 TAAACCTCAAACCATATACCATATAACCTA
77763 AACTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (33 bp):
TAAACCTCAAACCATATACCATATAACCTACCC
Found at i:77778 original size:14 final size:14
Alignment explanation
Indices: 77759--77808 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
77749 TATCATATAA
77759 CCTAAACTTTAAAT
1 CCTAAACTTTAAAT
*
77773 CCTAAAGC-TTAAGT
1 CCTAAA-CTTTAAAT
* *
77787 CTTAAACCTTAAAT
1 CCTAAACTTTAAAT
77801 CCTAAACT
1 CCTAAACT
77809 CTAACCTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (14 bp):
CCTAAACTTTAAAT
Found at i:85779 original size:22 final size:23
Alignment explanation
Indices: 85738--85781 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
85728 ACACCGCCGG
*
85738 GTGATTTTTAACAAAGGGGGGGA
1 GTGATTTTCAACAAAGGGGGGGA
85761 GTGATTTTCAACAAAGGGGGG
1 GTGATTTTCAACAAAGGGGGG
85782 CACAATTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.39, T:0.25
Consensus pattern (23 bp):
GTGATTTTCAACAAAGGGGGGGA
Found at i:103062 original size:610 final size:618
Alignment explanation
Indices: 102135--103898 Score: 2160
Period size: 610 Copynumber: 2.8 Consensus size: 618
102125 GGTTATTTCT
*
102135 TTCAATCTATTGTTTCACCTATATGACAAATATTAA-CCTTTCACATTTTGCAGTTAGACTTTCA
1 TTCAATCTATTGTTTCACCTATATGACAAAT-TTAAGCCTTTCACGTTTTGCAGTTAGACTTTCA
* * *
102199 GGCGATGAAAGTTGTACATCTGTGCAGCCATGTCAACAGCTTGGTGAAAACAATGAGGTTAGTGT
65 GGCAATGGAAGTAGTACATCTGTGCAGCCATGTCAACAGCTTGGTGAAAACAATGAGGTTA-TGT
* * * * * **
102264 TTGTTCTATATTCTGTATTAATATCAAAATTAACCTTTAGCCTTTTTTCA-TTTGACAACATTTC
129 CTGTTCTACATTCTGTATTAATGTCAAAATTGACCATTAGCCTTTTTTCACCCTGACAACATTTC
*
102328 TTGCCCTCTCTAGGACTCACTGGATCTGCTGGTATCACATAAGCATGTTGATCCAAGTGATAACA
194 TTGCCCTCTCTAGGACTCACTGGATCTGCTGGTATCACATAAGCATGTTGATTCAAGTGATAACA
* * * *
102393 ATCAGGGTCATCAGGTACGAATATCACCCATTTATTGGATCAGGGTTGTAAGATTTATATATATG
259 ATCAGGGTCTTCAGGTACGAGTATGACCCATTTCTTGGATCAGGGTTGTAAGATTTATATATATG
* *
102458 CGATGCATTTTTGGGATGGTTTTGAGAGAAATATGGCTTGGTTTCCAAATTAGATACCTGAAAGC
324 CGATGCATTTTTGGGATGGTTTTGACAGAAATATGGTTTGGTTTCCAAATTAGATACCTGAAAGC
* * * *
102523 TTTCATGGGACTGAAAATATTCACGACGATTCAACTGAGTCAAATAATGTGGTTACTGAGCATCT
389 TTTCCTGGGACTGAAAATATTCACGAGGATTCAAGTGAGTCAAATAATGTGGTTGCTGAGCATCT
* *
102588 TGATCTTAATTCACATGAAACAGGTCTGGTTTAGAATCTCAACTTTTATATTACAAACCACAATC
454 TGATCCTAATTCACATGAAACAGGTCTGGTTTAGAAACTCAAC-TTTATATTACAAACCACAATC
*
102653 ATGAAACATGTTACAAC-TTACCATTTCTCCTGTATTTGCAAACTAGATAACGACCTATCATATA
518 ATGAAACATATTACAACTTTACCATTTCTCCTGTATTTGCAAACTAGATAACGACCTATCATATA
*
102717 -T-A-T-TTTG-TT-G-A-TTGGGATTTCTTTCTCC
583 TTCATTATTTGTTTGGAAGTTGGGATTTCCTTCTCC
* * * * * * *
102745 TTCAGTCTATTGTTTCACCTATATGAAAAATTTAAGCCTTTAACGTCTTGTAGCTAGACTCTCAG
1 TTCAATCTATTGTTTCACCTATATGACAAATTTAAGCCTTTCACGTTTTGCAGTTAGACTTTCAG
* * * * ** *
102810 GCAATGGAAGTAGTGCATCTTTGAAGCCATGTCAACAACTTGGTGAAAATGACGAGGTT-TGTCT
66 GCAATGGAAGTAGTACATCTGTGCAGCCATGTCAACAGCTTGGTGAAAACAATGAGGTTATGTCT
** * * *
102874 CGATTCCGCATTCTGTATTAATGTCAAAATTGACCGTTAGCCTTTTTTTTACCCTG-CAACATTC
131 -G-TTCTACATTCTGTATTAATGTCAAAATTGACCATTAGCC-TTTTTTCACCCTGACAACATTT
* * * *
102938 CTTGCCCTCTCTAGGACTCACTGTATCTACTGGTAACACATAAGCATGTTGATTCAAGTGACAAC
193 CTTGCCCTCTCTAGGACTCACTGGATCTGCTGGTATCACATAAGCATGTTGATTCAAGTGATAAC
* *
103003 AATCAGGGTCTTCAGCTACGAGTATGACCCATTTCTT-GATCAGGGTTGTAAGATTTATATTTAT
258 AATCAGGGTCTTCAGGTACGAGTATGACCCATTTCTTGGATCAGGGTTGTAAGATTTATATATAT
* * *
103067 GCGATGTA-TTTTGGGATGGTTTTGACAGAAATGTGGTTTGGTTTCCAAATTAGATACCTAAAAG
323 GCGATGCATTTTTGGGATGGTTTTGACAGAAATATGGTTTGGTTTCCAAATTAGATACCTGAAAG
*
103131 CTTTCCTGGGACTGAAAATATTCACGAGGATTCAAGTGAGTCAAATAATGTGGTTGTTGAGCATC
388 CTTTCCTGGGACTGAAAATATTCACGAGGATTCAAGTGAGTCAAATAATGTGGTTGCTGAGCATC
* * *
103196 TTGATCCTGATTCACATGAAACAAGTATGGTTTAGAAACTCTAA----ATATTACAAACCACAAT
453 TTGATCCTAATTCACATGAAACAGGTCTGGTTTAGAAACTC-AACTTTATATTACAAACCACAAT
* *
103257 CATGAAACATATTACATCTTATAGTCCCCTTGTTACCATTTCTCATG-AGTTTGCAAACTTGATA
517 CATGAAACATATT--A-C--A-A-----C-T-TTACCATTTCTCCTGTA-TTTGCAAACTAGATA
* ** *
103321 ACGGCCTATCATATATGTTC-TGCATATTTGTTTGAGAAAAGGGGGGTGTATTTCCTTCCCC
568 ACGACCTATCATATA--TTCAT---TATTTGTTTG-G--AA-GTTGG-G-ATTTCCTTCTCC
* * * *
103382 TT-GATCTATT-CTTCACC-ATAAGACAAATTTAAGCCTTTCACATTTTGCAGTTAGACTTTCAG
1 TTCAATCTATTGTTTCACCTATATGACAAATTTAAGCCTTTCACGTTTTGCAGTTAGACTTTCAG
* * **
103444 GCAATGGAAGTAGTACATTTGTGCAGCCATGTAAACAGCTTGGTGAAAACGTTGAGGTTAGTGTC
66 GCAATGGAAGTAGTACATCTGTGCAGCCATGTCAACAGCTTGGTGAAAACAATGAGGTTA-TGTC
* **** *
103509 CGTTCTACATTCTGTATTAATGTCAAAATTGACCATTAGCC-TCCCCCCCCCTTTGACAACATTT
130 TGTTCTACATTCTGTATTAATGTCAAAATTGACCATTAGCCTTTTTTCACCC--TGACAACATTT
* ** * *
103573 CTTGCCCTCTCTAGGACTCACTGGATTTTTTGGTATCACATATGCATGTTGATTCAAGTGACAAC
193 CTTGCCCTCTCTAGGACTCACTGGATCTGCTGGTATCACATAAGCATGTTGATTCAAGTGATAAC
* *
103638 AATCAGGGT-TGTCAGCTACGAGTATGACCCATTTCTTGGATCAGGGTTGTAAGATTTATATACA
258 AATCAGGGTCT-TCAGGTACGAGTATGACCCATTTCTTGGATCAGGGTTGTAAGATTTATATATA
* *
103702 TGCGATGCATTTTTGGGATGGTTCTGACAGAAATATGATTTGGTTTCCAAATTAGATACCTGAAA
322 TGCGATGCATTTTTGGGATGGTTTTGACAGAAATATGGTTTGGTTTCCAAATTAGATACCTGAAA
* * * *
103767 GCTTTCCTGGGACTGAAAATATTCACGAGTATTTGAA-TGAGTCAAATAATGTGATTGCTGAGCG
387 GCTTTCCTGGGACTGAAAATATTCACGAGGA-TTCAAGTGAGTCAAATAATGTGGTTGCTGAGCA
* *
103831 TCTTGATCCTAATTCACATGAAACATGTCTGGTTTAGAAACTCGACTCTTATATTACAAACCACA
451 TCTTGATCCTAATTCACATGAAACAGGTCTGGTTTAGAAACTCAACT-TTATATTACAAACCACA
103896 ATC
515 ATC
103899 TATTATTTCA
Statistics
Matches: 984, Mismatches: 116, Indels: 77
0.84 0.10 0.07
Matches are distributed among these distances:
605 29 0.03
607 1 0.00
608 5 0.01
609 153 0.16
610 170 0.17
611 107 0.11
612 2 0.00
616 1 0.00
618 1 0.00
619 42 0.04
622 1 0.00
626 1 0.00
627 4 0.00
628 2 0.00
630 1 0.00
632 4 0.00
633 1 0.00
634 126 0.13
635 110 0.11
636 44 0.04
637 157 0.16
638 4 0.00
641 18 0.02
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (618 bp):
TTCAATCTATTGTTTCACCTATATGACAAATTTAAGCCTTTCACGTTTTGCAGTTAGACTTTCAG
GCAATGGAAGTAGTACATCTGTGCAGCCATGTCAACAGCTTGGTGAAAACAATGAGGTTATGTCT
GTTCTACATTCTGTATTAATGTCAAAATTGACCATTAGCCTTTTTTCACCCTGACAACATTTCTT
GCCCTCTCTAGGACTCACTGGATCTGCTGGTATCACATAAGCATGTTGATTCAAGTGATAACAAT
CAGGGTCTTCAGGTACGAGTATGACCCATTTCTTGGATCAGGGTTGTAAGATTTATATATATGCG
ATGCATTTTTGGGATGGTTTTGACAGAAATATGGTTTGGTTTCCAAATTAGATACCTGAAAGCTT
TCCTGGGACTGAAAATATTCACGAGGATTCAAGTGAGTCAAATAATGTGGTTGCTGAGCATCTTG
ATCCTAATTCACATGAAACAGGTCTGGTTTAGAAACTCAACTTTATATTACAAACCACAATCATG
AAACATATTACAACTTTACCATTTCTCCTGTATTTGCAAACTAGATAACGACCTATCATATATTC
ATTATTTGTTTGGAAGTTGGGATTTCCTTCTCC
Found at i:108254 original size:4 final size:4
Alignment explanation
Indices: 108245--108271 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
108235 TTCATCATCA
108245 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
108272 GCCCCACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:120898 original size:14 final size:15
Alignment explanation
Indices: 120879--120907 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
120869 TCTTAAGTCG
120879 TTATTATT-TAAAAT
1 TTATTATTATAAAAT
120893 TTATTATTATAAAAT
1 TTATTATTATAAAAT
120908 ATATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTATTATAAAAT
Found at i:121214 original size:15 final size:15
Alignment explanation
Indices: 121194--121225 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
121184 AGTGTGGAAA
121194 AACACTCCCCTTTCT
1 AACACTCCCCTTTCT
*
121209 AACACTTCCCTTTCT
1 AACACTCCCCTTTCT
121224 AA
1 AA
121226 AAATCCAAGT
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:0.25, C:0.41, G:0.00, T:0.34
Consensus pattern (15 bp):
AACACTCCCCTTTCT
Found at i:122115 original size:21 final size:21
Alignment explanation
Indices: 122089--122129 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
122079 ATTAACTTAT
* *
122089 TTTAAAAATATTTTATTTTAA
1 TTTAAAAATAATATATTTTAA
122110 TTTAAAAATAATATATTTTA
1 TTTAAAAATAATATATTTTA
122130 TTCTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAAATAATATATTTTAA
Found at i:122241 original size:27 final size:26
Alignment explanation
Indices: 122119--122244 Score: 71
Period size: 29 Copynumber: 4.6 Consensus size: 26
122109 ATTTAAAAAT
* *
122119 AATATATTTTATTCTAATTTAATTTTTA
1 AATATATTTTATTCT--TTAAATTATTA
* *
122147 AATAT-TTTAATATTATTTTAACTT-TTA
1 AATATATTT--TATT-CTTTAAATTATTA
* *
122174 AATTATATGTTTA-TC-TTAATTTACTA
1 AA-TATAT-TTTATTCTTTAAATTATTA
*
122200 AATATATAGATTATTACTTTAAATTATTA
1 AATATAT--TTTATT-CTTTAAATTATTA
122229 AATATATTTTATTCTT
1 AATATATTTTATTCTT
122245 ATCTTAACTT
Statistics
Matches: 77, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
25 11 0.14
26 11 0.14
27 15 0.19
28 16 0.21
29 21 0.27
30 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (26 bp):
AATATATTTTATTCTTTAAATTATTA
Found at i:122307 original size:22 final size:22
Alignment explanation
Indices: 122263--122358 Score: 93
Period size: 22 Copynumber: 4.1 Consensus size: 22
122253 TTCAAAATAT
*
122263 TTAACATAAAAATATATTTTAAA
1 TTAAAATAAAAATAT-TTTTAAA
*
122286 TTAAAATACAAATATTTTTAAA
1 TTAAAATAAAAATATTTTTAAA
* *
122308 TTAAATTATTAAAAAGTCTTTAATAAA
1 TTAAA--A-TAAAAA-TATTT-TTAAA
*
122335 TTAATATAAAAATATTTTTAAA
1 TTAAAATAAAAATATTTTTAAA
122357 TT
1 TT
122359 TAATATATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
22 18 0.30
23 17 0.28
24 7 0.12
25 6 0.10
26 4 0.07
27 8 0.13
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (22 bp):
TTAAAATAAAAATATTTTTAAA
Found at i:122361 original size:23 final size:23
Alignment explanation
Indices: 122261--122365 Score: 97
Period size: 23 Copynumber: 4.4 Consensus size: 23
122251 ACTTCAAAAT
*
122261 ATTTAACATAAAAATATATTTTAA
1 ATTTAATATAAAAATAT-TTTTAA
* *
122285 A-TTAAAATACAAATATTTTTAA
1 ATTTAATATAAAAATATTTTTAA
* * *
122307 ATTAAATTATTAAAAAGTCTTTAATAA
1 ATTTAA-TA-TAAAAA-TATTT-TTAA
122334 A-TTAATATAAAAATATTTTTAA
1 ATTTAATATAAAAATATTTTTAA
122356 ATTTAATATA
1 ATTTAATATA
122366 TATTAAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
22 11 0.17
23 28 0.43
24 8 0.12
25 7 0.11
26 7 0.11
27 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (23 bp):
ATTTAATATAAAAATATTTTTAA
Found at i:123366 original size:20 final size:20
Alignment explanation
Indices: 123317--123478 Score: 114
Period size: 20 Copynumber: 8.0 Consensus size: 20
123307 AAAATGACCA
*
123317 ACAAAATCGCAACGCGATAT
1 ACAAAATCGCAACGCGATTT
*
123337 -CAAAACCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* * * **
123356 AGAAAAGCGCAACGTTGA-AA
1 ACAAAATCGCAACG-CGATTT
* *
123376 AGAAGATCGCAACGCGATCTT
1 ACAAAATCGCAACGCGAT-TT
*
123397 CCAAGAATCGCAACGCGATCTT
1 ACAA-AATCGCAACGCGAT-TT
* *
123419 CCAAGAATCGCAACGCGATTA
1 ACAA-AATCGCAACGCGATTT
*
123440 AGAAAATCGCAACGCGA-TT
1 ACAAAATCGCAACGCGATTT
* *
123459 CCAAGAATCGCAATGCGATT
1 ACAA-AATCGCAACGCGATT
123479 CAGAAAATGA
Statistics
Matches: 113, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
19 22 0.19
20 48 0.42
21 8 0.07
22 35 0.31
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
ACAAAATCGCAACGCGATTT
Found at i:123409 original size:22 final size:21
Alignment explanation
Indices: 123381--123478 Score: 128
Period size: 22 Copynumber: 4.7 Consensus size: 21
123371 TGAAAAGAAG
123381 ATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGAT-TTCCAAGA
123403 ATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGAT-TTCCAAGA
***
123425 ATCGCAACGCGATTAAGAA-A
1 ATCGCAACGCGATTTCCAAGA
123445 ATCGCAACGCGA-TTCCAAGA
1 ATCGCAACGCGATTTCCAAGA
*
123465 ATCGCAATGCGATT
1 ATCGCAACGCGATT
123479 CAGAAAATGA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 25 0.37
21 4 0.06
22 35 0.52
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAAGA
Found at i:123461 original size:40 final size:40
Alignment explanation
Indices: 123319--123486 Score: 153
Period size: 40 Copynumber: 4.1 Consensus size: 40
123309 AATGACCAAC
*
123319 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTTAG
* * **** **
123358 AAAAGCGCAACGTTGAAAAGAAG-ATCGCAACGCGATCTTCC
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT-TTAG
*
123399 AAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTTAG
* *
123442 AAAATCGCAACGCGATTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
123482 AAAAT
1 AAAAT
123487 GAGTAAATTC
Statistics
Matches: 102, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
39 11 0.11
40 44 0.43
41 6 0.06
42 22 0.22
43 6 0.06
44 13 0.13
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
Done.