Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003887.1 Hibiscus syriacus cultivar Beakdansim tig00008394_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: 95509
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1168 original size:3 final size:3
Alignment explanation
Indices: 1155--1198 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
1145 TAAATACACT
*
1155 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1199 TTTTTAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 1 0.03
3 33 0.89
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1497 original size:104 final size:103
Alignment explanation
Indices: 1321--1611 Score: 316
Period size: 103 Copynumber: 2.7 Consensus size: 103
1311 TCGTTAGATT
* * * *
1321 GAACAAGTTCTTCTCATTATGAACTTCTTTTTTCTCGTGGATGAGTTCTTCTCATTATGAACTCT
1 GAAC-AGTTCTTCTCATTATGAA---CTTTCTCCT-TTGGACGAGTTCTTCTCATTATGAACTCT
* * * *
1386 TTTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTTAGAAA-
61 TCTGGAAATGTTGATCCAAATCCATCTGCGGT-GAATTAGAAAG
*
1429 GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGACGAG-TCTTCTCATTATGAACTCTTCT
1 GAACA-GTTCTTCTCATTATGAACTTTCTCCTTT-GGACGAGTTCTTCTCATTATGAACTCTTCT
* * ** * *
1493 GGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGAAAG
64 GGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAAG
* *
1533 GAACAGTTCTTCTCATTATGAACTTTCTCCTTTTGATGAGTTCTTCTCATTATGAACTCTTCATT
1 GAACAGTTCTTCTCATTATGAACTTTCTCCTTTGGACGAGTTCTTCTCATTATGAACTCTTC--T
*
1598 GGAAATGTCGATCC
64 GGAAATGTTGATCC
1612 TCAAGCGAGG
Statistics
Matches: 156, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
102 5 0.03
103 56 0.36
104 49 0.31
105 25 0.16
107 1 0.01
108 20 0.13
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (103 bp):
GAACAGTTCTTCTCATTATGAACTTTCTCCTTTGGACGAGTTCTTCTCATTATGAACTCTTCTGG
AAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAAG
Found at i:1580 original size:103 final size:105
Alignment explanation
Indices: 1359--1611 Score: 325
Period size: 103 Copynumber: 2.4 Consensus size: 105
1349 TTTTTCTCGT
* * * *
1359 GGATGAGTTCTTCTCATTATGAACTCTTTTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGTGGAATT
*
1424 AGAAAGAACATGTTTTTCTCATTATGAACTTTCTCCTTTA
66 AGAAAGAACATGTTCTTCTCATTATGAACTTTCTCCTTTA
* * * ** *
1464 GGACGAG-TCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCATCTGTGGT-GAATT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGTGGAATT
*
1527 TGAAAGGAACA-GTTCTTCTCATTATGAACTTTCTCCTTT-
66 AGAAA-GAACATGTTCTTCTCATTATGAACTTTCTCCTTTA
* *
1566 TGATGAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTCGATCC
1 GGATGAGTTCTTCTCATTATGAACTCTTC--TGGAAATGTTGATCC
1612 TCAAGCGAGG
Statistics
Matches: 127, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
102 5 0.04
103 56 0.44
104 48 0.38
105 18 0.14
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (105 bp):
GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGTGGAATT
AGAAAGAACATGTTCTTCTCATTATGAACTTTCTCCTTTA
Found at i:1924 original size:217 final size:216
Alignment explanation
Indices: 1533--1955 Score: 590
Period size: 217 Copynumber: 2.0 Consensus size: 216
1523 AATTTGAAAG
* *
1533 GAACAGTTCTTCTCATTATGAACTTTCTCCTTTTGATGAGTTCTTCTCATTATGAACTCTTCATT
1 GAACAGTTCTTCTCATTATGAACTTTCTCCTTTGGATGAGTTCTTCTCATTATGAACTCTTCACT
* * * * * *
1598 GGAAATGTCGATCCTCAAGCGAGGCGTCACTGATTCGAAATCGTGAATCAGTGATAGGTCAAAAA
66 GAAAATATCAATCCTCAAGCGAGGCGTCACTGATTCGAAATCATAAATCAGTGATAAGTCAAAAA
* *
1663 ACTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATG-ACTCTCCAT
131 ACTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAACTCTCCAT
1727 TGAAAATGTTGATGCGAATTT
196 TGAAAATGTTGATGCGAATTT
1748 GAACAAGTTCTTCTCATTATGAAC-TTCTTCCTCGTTGGATGAGTTCTTCTCATTATG-ACTC-T
1 GAAC-AGTTCTTCTCATTATGAACTTTC-TCCT--TTGGATGAGTTCTTCTCATTATGAACTCTT
*
1810 C-CTGAAAATATCAATCCCTCAAGCGA-GTGTCACTGATTC-AAATGCATAAATCGAGTGATAAG
62 CACTGAAAATATCAAT-CCTCAAGCGAGGCGTCACTGATTCGAAAT-CATAAATC-AGTGATAAG
* * *
1872 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTATGAA
124 TC-AAAAAACTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAA
*
1937 CTCTCCATTGGAAATGTTG
188 CTCTCCATTGAAAATGTTG
1956 GTTCACCTCC
Statistics
Matches: 184, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
214 4 0.02
215 35 0.19
216 45 0.24
217 59 0.32
218 41 0.22
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (216 bp):
GAACAGTTCTTCTCATTATGAACTTTCTCCTTTGGATGAGTTCTTCTCATTATGAACTCTTCACT
GAAAATATCAATCCTCAAGCGAGGCGTCACTGATTCGAAATCATAAATCAGTGATAAGTCAAAAA
ACTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAACTCTCCAT
TGAAAATGTTGATGCGAATTT
Found at i:2821 original size:8 final size:8
Alignment explanation
Indices: 2819--2875 Score: 66
Period size: 8 Copynumber: 7.4 Consensus size: 8
2809 TATTTTTTCA
2819 TTTC-TTT
1 TTTCATTT
2826 TTTCA-TT
1 TTTCATTT
2833 TTTCATTT
1 TTTCATTT
**
2841 TTTTTTTT
1 TTTCATTT
2849 TTTCATTT
1 TTTCATTT
2857 TTTCA-TT
1 TTTCATTT
2864 TTTCATCTT
1 TTTCAT-TT
2873 TTT
1 TTT
2876 ATGTTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
7 18 0.43
8 19 0.45
9 5 0.12
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTCATTT
Found at i:2828 original size:19 final size:19
Alignment explanation
Indices: 2800--2856 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
2790 AACCCTCCTT
*
2800 TTTCTCTTTTATTTTTTCA
1 TTTCTTTTTTATTTTTTCA
2819 TTTCTTTTTTCA-TTTTTCA
1 TTTCTTTTTT-ATTTTTTCA
2838 -TT-TTTTTT-TTTTTTCA
1 TTTCTTTTTTATTTTTTCA
2854 TTT
1 TTT
2857 TTTCATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 7 0.21
17 8 0.24
18 2 0.06
19 16 0.47
20 1 0.03
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCTTTTTTATTTTTTCA
Found at i:2834 original size:6 final size:7
Alignment explanation
Indices: 2819--2874 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
2809 TATTTTTTCA
*
2819 TTTCTTT
1 TTTCATT
2826 TTTCATT
1 TTTCATT
2833 TTTCA-T
1 TTTCATT
2839 TTT--TT
1 TTTCATT
2844 TTT--TT
1 TTTCATT
2849 TTTCATTT
1 TTTCA-TT
2857 TTTCATT
1 TTTCATT
2864 TTTCATCT
1 TTTCAT-T
2872 TTT
1 TTT
2875 TATGTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
5 9 0.21
6 4 0.09
7 19 0.44
8 11 0.26
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTCATT
Found at i:2844 original size:16 final size:16
Alignment explanation
Indices: 2823--2875 Score: 72
Period size: 15 Copynumber: 3.3 Consensus size: 16
2813 TTTTCATTTC
2823 TTTTTTCATTTTTCAT
1 TTTTTTCATTTTTCAT
**
2839 TTTTTTTTTTTTTCA-
1 TTTTTTCATTTTTCAT
2854 TTTTTTCATTTTTCAT
1 TTTTTTCATTTTTCAT
2870 CTTTTT
1 -TTTTT
2876 ATGTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 13 0.42
16 13 0.42
17 5 0.16
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCATTTTTCAT
Found at i:2882 original size:16 final size:14
Alignment explanation
Indices: 2819--2882 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 14
2809 TATTTTTTCA
2819 TTTC-TTTTTTCATT
1 TTTCATTTTTT-ATT
*
2833 TTTCATTTTTTTTTTT
1 TTTCA--TTTTTTATT
2849 TTTCATTTTTTCATT
1 TTTCATTTTTT-ATT
2864 TTTCATCTTTTTATGT
1 TTTCAT-TTTTTAT-T
2880 TTT
1 TTT
2883 TTTTCTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
14 10 0.24
15 10 0.24
16 16 0.38
17 6 0.14
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTCATTTTTTATT
Found at i:14584 original size:24 final size:24
Alignment explanation
Indices: 14557--14602 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
14547 AATGGAACAT
14557 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
14581 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
14603 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:15170 original size:2 final size:2
Alignment explanation
Indices: 15163--15195 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15153 GACACATTAA
15163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15196 CACGTTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15180 original size:49 final size:47
Alignment explanation
Indices: 14969--15178 Score: 348
Period size: 47 Copynumber: 4.4 Consensus size: 47
14959 CTAAGACACA
* *
14969 TTAAACAAATATATGTATATGAACAAAGAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
15016 TTAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
15063 TTAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
**
15110 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACACA
1 TTAAAC-AA-ATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
* *
15159 TTAAATATATATATATATAT
1 TTAAACAAATATATATATAT
15179 ATATATATAT
Statistics
Matches: 155, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
47 110 0.71
48 3 0.02
49 42 0.27
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (47 bp):
TTAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
Found at i:15759 original size:15 final size:15
Alignment explanation
Indices: 15739--15771 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
15729 TAGTGTGACT
15739 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
15754 AAAATAAAATACTTA
1 AAAATAAAATACTTA
15769 AAA
1 AAA
15772 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:17134 original size:3 final size:3
Alignment explanation
Indices: 17119--17164 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
17109 TAAATACACT
* *
17119 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17165 TTTTTTAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:19823 original size:31 final size:31
Alignment explanation
Indices: 19788--19864 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
19778 AACTACATAC
*
19788 AATATCATTTAAATAGTTAAATGGTTTAATT
1 AATATCATTTAAATAGTTAAATGATTTAATT
* *
19819 AATATCGTTTAAATAGTTAAATGATTTGATT
1 AATATCATTTAAATAGTTAAATGATTTAATT
* *
19850 AACATTATTTAAATA
1 AATATCATTTAAATA
19865 AAATTGTGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (31 bp):
AATATCATTTAAATAGTTAAATGATTTAATT
Found at i:28479 original size:47 final size:47
Alignment explanation
Indices: 28421--28514 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
28411 AGATTCTTTG
28421 CATAGAACTCAATTGAGAAGCAATATATATGATTTATTCTTCAGAAA
1 CATAGAACTCAATTGAGAAGCAATATATATGATTTATTCTTCAGAAA
*
28468 CATATAACTCAATTGAGAAGCAATATATATGATTTATTCTTCAGAAA
1 CATAGAACTCAATTGAGAAGCAATATATATGATTTATTCTTCAGAAA
28515 GATGCATACT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (47 bp):
CATAGAACTCAATTGAGAAGCAATATATATGATTTATTCTTCAGAAA
Found at i:32987 original size:2 final size:2
Alignment explanation
Indices: 32980--33004 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32970 GGAGAAGGAT
32980 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
33005 TTGAAGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33321 original size:39 final size:39
Alignment explanation
Indices: 33277--33353 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
33267 CCCTCCATCC
* *
33277 AGCAGCCCCTCCACACATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACACATCAGTTCCAACAGCTTCCAGCG
* *
33316 AGCAGCCCCTCCACGCATCAGTTGCAACAGCTTCCAGC
1 AGCAGCCCCTCCACACATCAGTTCCAACAGCTTCCAGC
33354 ACTGCCAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.23, C:0.43, G:0.17, T:0.17
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAGTTCCAACAGCTTCCAGCG
Found at i:34463 original size:3 final size:3
Alignment explanation
Indices: 34449--34511 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
34439 TTATTTGCAA
* * *
34449 TAT TAT TTT TAT TAT TAT TATT TAT TGT T-T TAAT TAT TAT T-T CAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TAT TAT TAT
34494 TAT TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
34512 TATAAAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
2 5 0.10
3 40 0.80
4 5 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:34467 original size:33 final size:33
Alignment explanation
Indices: 34430--34512 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 33
34420 TTATTTCCTT
34430 TTATTTTCATTATTTGCAA-TATTATTT-TTATTA
1 TTATTTT-ATTATTT-CAATTATTATTTATTATTA
* *
34463 TTATTATTTATTGTTTTAATTATTATTTCATTATTA
1 TTA-T-TTTATTATTTCAATTATTATTT-ATTATTA
34499 TTATTTTATTATTT
1 TTATTTTATTATTT
34513 ATAAAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
33 5 0.12
34 24 0.57
35 4 0.10
36 9 0.21
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (33 bp):
TTATTTTATTATTTCAATTATTATTTATTATTA
Found at i:34474 original size:22 final size:22
Alignment explanation
Indices: 34449--34514 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
34439 TTATTTGCAA
34449 TATTATTTTTATTATTATTATT
1 TATTATTTTTATTATTATTATT
*
34471 TATT-GTTTTA--ATTATTATT
1 TATTATTTTTATTATTATTATT
*
34490 TCATTATTATTATT-TTATTATT
1 T-ATTATTTTTATTATTATTATT
34512 TAT
1 TAT
34515 AAAAATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 10 0.27
20 3 0.08
21 11 0.30
22 13 0.35
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTATTTTTATTATTATTATT
Found at i:34500 original size:14 final size:14
Alignment explanation
Indices: 34481--34511 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34471 TATTGTTTTA
34481 ATTATTATTTCATT
1 ATTATTATTTCATT
*
34495 ATTATTATTTTATT
1 ATTATTATTTCATT
34509 ATT
1 ATT
34512 TATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTATTATTTCATT
Found at i:34840 original size:17 final size:17
Alignment explanation
Indices: 34818--34855 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
34808 ATATTTTATT
34818 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
34835 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
34852 TATA
1 TATA
34856 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:37055 original size:15 final size:15
Alignment explanation
Indices: 37019--37057 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
37009 AATTTACATT
37019 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
37033 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
37048 TTTGCATTTG
1 TTTACATTTG
37058 TATTTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:41842 original size:20 final size:21
Alignment explanation
Indices: 41758--41840 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
41748 AACAGAACCC
*
41758 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATTCCCCT
** *
41779 GTGGGGGGAATCGGTTCCCCTT
1 CAGGGGGGAATCGATTCCCC-T
* * *
41801 CAAAGGAGGAATCGGTT-CCCT
1 C-AGGGGGGAATCGATTCCCCT
41822 CAGGGGGGAATCGATTCCC
1 CAGGGGGGAATCGATTCCC
41841 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 12 0.25
21 20 0.42
22 4 0.08
23 12 0.25
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
CAGGGGGGAATCGATTCCCCT
Found at i:49629 original size:2 final size:2
Alignment explanation
Indices: 49622--49649 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
49612 TTATCCTTTA
49622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49650 CCTTTGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52406 original size:95 final size:94
Alignment explanation
Indices: 52243--52500 Score: 326
Period size: 95 Copynumber: 2.8 Consensus size: 94
52233 GTTCTCAGAA
* * * * *
52243 TAGAAACAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATTTGGTTTGGT
1 TAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
* * *
52308 ATGAACCACAGAATCAGTTATTGAACATGG
66 ATGAACCACAGAACCAATCATTGAA-ATGG
52338 TAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
1 TAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
* *
52403 ATGAACCACAGAACCAATCATTGAATTTG
66 ATGAACCACAGAACCAATCATTGAAATGG
* * * * *
52432 -A-AAGATGAATG-TGCTC-ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTG
1 TAGAA-AT-AAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
52493 GTATGAAC
64 GTATGAAC
52501 TCCAAAATAA
Statistics
Matches: 146, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
92 53 0.36
93 6 0.04
94 5 0.03
95 82 0.56
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (94 bp):
TAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
ATGAACCACAGAACCAATCATTGAAATGG
Found at i:52487 original size:92 final size:92
Alignment explanation
Indices: 52265--52541 Score: 335
Period size: 92 Copynumber: 3.0 Consensus size: 92
52255 GACCCAATAG
* * * *
52265 CATCTTCTGAAAGTGTTCTTTGAGTTATCTGATTTGGTTTGGTATGAACCACAGAATCAGTTATT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAATCAATCATT
* * * * * *
52330 GAACATGGTAGAA-AT-AAGGAGGCCCAATAG
66 GAA-TTTG-A-AAGATGAATG-TGCTC-ATAA
*
52360 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAATCAATCATT
52425 GAATTTGAAAGATGAATGTGCTCATAA
66 GAATTTGAAAGATGAATGTGCTCATAA
* * *
52452 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTC-CAAAATAAATCAT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAC-CACAGAATCAATCAT
* *
52516 TGGATTTGAAAGATGAATTTGCTCAT
65 TGAATTTGAAAGATGAATGTGCTCAT
52542 GGTAGAAATA
Statistics
Matches: 162, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
92 87 0.54
93 7 0.04
94 5 0.03
95 63 0.39
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (92 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAATCAATCATT
GAATTTGAAAGATGAATGTGCTCATAA
Found at i:52652 original size:114 final size:114
Alignment explanation
Indices: 52452--52874 Score: 686
Period size: 114 Copynumber: 3.7 Consensus size: 114
52442 GTGCTCATAA
*
52452 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATAAATCATT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATT
52517 GGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCCCAATAG
66 GGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCCCAATAG
52566 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATT
*
52631 GGATTTGAAAGATAAATTTGCTCATGGTAGAAATAAGGAGGCCCAATAG
66 GGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCCCAATAG
52680 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATT
* * * * * *
52745 GGATTTGAAAGATGAATTTGCTCATAGTACAAATAAAGAGACCCGATAA
66 GGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCCCAATAG
* * * * * *
52794 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGATAGGAAC-CACAGAACCAATCAT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTC-CAAAATCAATCAT
* *
52858 TGGAATTAAAAGATGAA
65 TGGATTTGAAAGATGAA
52875 CTGCATGATC
Statistics
Matches: 291, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 1 0.00
114 290 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (114 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATT
GGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCCCAATAG
Found at i:55432 original size:22 final size:22
Alignment explanation
Indices: 55401--55455 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
55391 ATCTACACTC
55401 TTCAAAGATGATAGACTCCT-TT
1 TTCAAAGATGATAGA-TCCTCTT
* *
55423 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATCCTCTT
55445 TTCAAAGATGA
1 TTCAAAGATGA
55456 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATCCTCTT
Found at i:56402 original size:77 final size:73
Alignment explanation
Indices: 56303--56552 Score: 315
Period size: 73 Copynumber: 3.4 Consensus size: 73
56293 CTATTTCCCA
* * * *
56303 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGA--TCTT--A
*
56368 AACCCTCAGGGT
62 AAGCCTCAGGGT
* *
56380 CATCTATAAGACCTACAGTGCATGATG-TTCTCAAAAAGCCTTC-ATAAGCTTTTTGATCTTATA
1 CATCTATAAGACCTACAGTGCATGATGTTTC-CAAAAAGCCTTCGA-GAGCTTTTTGATCTTAAA
56443 GCCTCAGGGT
64 GCCTCAGGGT
* * *
56453 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTATAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
*
56518 CTTAGGGT
66 CTCAGGGT
* *
56526 CATCTATAAGCCCTACAGTGCAAGATG
1 CATCTATAAGACCTACAGTGCATGATG
56553 ATAAGACCTC
Statistics
Matches: 153, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
73 98 0.64
74 2 0.01
75 3 0.02
76 4 0.03
77 46 0.30
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (73 bp):
CATCTATAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:56811 original size:112 final size:114
Alignment explanation
Indices: 56608--57041 Score: 396
Period size: 123 Copynumber: 3.6 Consensus size: 114
56598 CAATATTTCC
*
56608 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGGAA-AAGTTCATAATGAGAAGAACT
1 AGAA-AGTTCATAATGAGAAGAACTTATCTGAAGAGGAA-GAAGAAGTTCATAATGAGAAGAACT
* * *
56672 TGTTCAACCTTTTGCTCAAATTCATCAC-CCGATGGAT-CAGCGTTGCCAG
64 TGTTCAACCTTTTGCTCAAATTCATCACACAGATAGATACAACGTTGCCAG
*
56721 AGAAAGTTCATAATGAGAAGAATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGA-TT
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA-ACTT
* * * *
56785 GTTCAACCTTTTGCAT-GAA-TCTATCACAGAAAGAGATAGATCAACACCAACTTTTCCAG
65 GTTCAACCTTTTGC-TCAAATTC-ATCAC----ACAGATAGAT----A-CAACGTTGCCAG
* *
56844 AGAAAGTTCATAATGAGAAGAGCTTATCTGAAGAGGAAGATGAAGTTCATAATGAGAAGAACTTG
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * * * * *
56909 TTCAACCTTTTGCTCGACTCCATTTCCAAAAAGAGATAGAGCAGCAGAGCTATTTCCAG
66 TTCAACCTTTTGCTCAAATTCA--T-C--ACACAGATAGA-TA-CA-A-C-GTTGCCAG
* * *
56968 -GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTT
1 AG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
57032 GTTCAACCTT
65 GTTCAACCTT
57042 GCATTGATTC
Statistics
Matches: 270, Mismatches: 23, Indels: 45
0.80 0.07 0.13
Matches are distributed among these distances:
111 5 0.02
112 73 0.27
113 6 0.02
117 6 0.02
121 3 0.01
122 3 0.01
123 87 0.32
124 84 0.31
125 1 0.00
126 1 0.00
128 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (114 bp):
AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCTCAAATTCATCACACAGATAGATACAACGTTGCCAG
Found at i:57006 original size:124 final size:123
Alignment explanation
Indices: 56717--57041 Score: 444
Period size: 124 Copynumber: 2.6 Consensus size: 123
56707 ATCAGCGTTG
*
56717 CCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAG
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA-
* *
56782 A-TTGTTCAACCTTTTGCATGAATCTATCACAGAAAGAGATAGATCAACACCAACTTTT
65 ACTTGTTCAACCTTTTGCATGAATCTATCACAAAAAGAGATAGAGCAACACCAACTTTT
* *
56840 CCAGAGAAAGTTCATAATGAGAAGAGCTTATCTGAAGAGGAAGATGAAGTTCATAATGAGAAGAA
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
* * * * *
56905 CTTGTTCAACCTTTTGC-TCGACTCCATTTC-CAAAAAGAGATAGAGCAGCA-GAGCTATTT
66 CTTGTTCAACCTTTTGCAT-GAAT-C-TATCACAAAAAGAGATAGAGCAACACCAACT-TTT
* * *
56964 CCAG-GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGA
1 CCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
57028 ACTTGTTCAACCTT
65 ACTTGTTCAACCTT
57042 GCATTGATTC
Statistics
Matches: 181, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
122 2 0.01
123 84 0.46
124 92 0.51
125 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (123 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGCATGAATCTATCACAAAAAGAGATAGAGCAACACCAACTTTT
Found at i:57288 original size:138 final size:139
Alignment explanation
Indices: 56960--57315 Score: 459
Period size: 139 Copynumber: 2.6 Consensus size: 139
56950 CAGCAGAGCT
*
56960 ATTTCCAG-GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAG
1 ATTTCCAGAG-GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
* * * * * *
57024 AAGAACTTGTTCAACCTTGCATTGATTCATCTCCTATGGAATTGAATGAAAGAAGAACCTCATTT
65 AAGAATTTGTTCAACCTTACATTAATTCATCACATATGGAATTGAATCAAAGAAGAACCTCATTT
* *
57089 GAGGATCAAT
130 GAAGATCAAC
* * * *
57099 ATTTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAAAGAAGTTCATAATAAGC
1 ATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
* * ** *
57164 AGAATTTGTTCAACCTTACCTTAATTCATCACATATGGAGTTGAATCAACA-AA-TCCCTCTTTT
66 AGAATTTGTTCAACCTTACATTAATTCATCACATATGGAATTGAATCAA-AGAAGAACCTCATTT
*
57227 GAAGATCAGC
130 GAAGATCAAC
* *
57237 ATTTCCAGAAGG-AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAGTTCATAATGAG
1 ATTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
*
57301 AAGAGTTTGTTCAAC
65 AAGAATTTGTTCAAC
57316 TTTTTGCTAG
Statistics
Matches: 188, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
138 82 0.44
139 104 0.55
140 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (139 bp):
ATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTACATTAATTCATCACATATGGAATTGAATCAAAGAAGAACCTCATTTG
AAGATCAAC
Found at i:57608 original size:39 final size:39
Alignment explanation
Indices: 57564--57640 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
57554 CCATCCATCC
* *
57564 AGCAGCCCCTCCACACATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACACATCAGTTCCAACAGCTTCCAGCG
* *
57603 AGCAGCCCCTCCACGCATCAGTTGCAACAGCTTCCAGC
1 AGCAGCCCCTCCACACATCAGTTCCAACAGCTTCCAGC
57641 ACTGCCAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.23, C:0.43, G:0.17, T:0.17
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAGTTCCAACAGCTTCCAGCG
Found at i:58734 original size:12 final size:11
Alignment explanation
Indices: 58717--58791 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
58707 TTATTTCCTT
58717 TTATTTTAATCA
1 TTATTTTAAT-A
*
58729 TTATTTGCAATA
1 TTATTT-TAATA
*
58741 TTATTTTATTA
1 TTATTTTAATA
**
58752 TTATTATTTTTA
1 TTATT-TTAATA
*
58764 TTGTTTTAATTA
1 TTATTTTAA-TA
* *
58776 TTATTTCATTA
1 TTATTTTAATA
58787 TTATT
1 TTATT
58792 ATTTTATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
11 17 0.34
12 30 0.60
13 3 0.06
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:58752 original size:3 final size:3
Alignment explanation
Indices: 58739--58802 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
58729 TTATTTGCAA
* *
58739 TAT TAT T-T TAT TAT TAT TAT TTT TAT TGT T-T TAAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
*
58782 CAT TAT TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
58803 TATAAAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
2 7 0.14
3 42 0.82
4 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:58758 original size:14 final size:15
Alignment explanation
Indices: 58739--58802 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 15
58729 TTATTTGCAA
58739 TATTATT-TTATTAT
1 TATTATTATTATTAT
* *
58753 TATTATTTTTATTGT
1 TATTATTATTATTAT
58768 T-TTAATTATTATT-T
1 TATT-ATTATTATTAT
*
58782 CATTATTATTATT-T
1 TATTATTATTATTAT
58796 TATTATT
1 TATTATT
58803 TATAAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
14 26 0.60
15 17 0.40
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (15 bp):
TATTATTATTATTAT
Found at i:59005 original size:115 final size:115
Alignment explanation
Indices: 58878--59100 Score: 258
Period size: 114 Copynumber: 1.9 Consensus size: 115
58868 CATAAATTAC
* * *
58878 TTTTAATAATTATGTTTTAATATATATTTATTTA-TTTTTCAATAT-TAAGAAATG-GCAGTCTT
1 TTTTAATAATTATATTTT-A-AT-TATTTATTTATTTTTTCAATATCGAAGAAAAGAGCAGTCTT
* *
58940 AAAATAACT-GAATGTCTATTTTCTGATATTTTTAAATAAATAAATATCCTATTG
63 AAAACAACTAGAA-GTC-ATTTTCTGATATTTCTAAATAAATAAATATCCTATTG
* * * *
58994 TTTTAA-AATTATATTTTAATTGTTTATTTATTTTTTTAATATCGAAGAAAAGAGCTGTCTTAAG
1 TTTTAATAATTATATTTTAATTATTTATTTATTTTTTCAATATCGAAGAAAAGAGCAGTCTTAAA
* * *
59058 GCACCTAGAAGTCCTTTTCTGATATTTCTAAATAAATAAATAT
66 ACAACTAGAAGTCATTTTCTGATATTTCTAAATAAATAAATAT
59101 TTTATTTATA
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
112 9 0.10
113 12 0.13
114 36 0.40
115 25 0.27
116 9 0.10
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (115 bp):
TTTTAATAATTATATTTTAATTATTTATTTATTTTTTCAATATCGAAGAAAAGAGCAGTCTTAAA
ACAACTAGAAGTCATTTTCTGATATTTCTAAATAAATAAATATCCTATTG
Found at i:59129 original size:17 final size:17
Alignment explanation
Indices: 59107--59144 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
59097 ATATTTTATT
59107 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
59124 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
59141 TATA
1 TATA
59145 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:64561 original size:14 final size:14
Alignment explanation
Indices: 64542--64574 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
64532 ACCATACCAC
*
64542 TAAAAATATTCATA
1 TAAAAATATTCACA
64556 TAAAAATATTCACA
1 TAAAAATATTCACA
64570 TAAAA
1 TAAAA
64575 CAGCTCCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAATATTCACA
Found at i:66057 original size:14 final size:14
Alignment explanation
Indices: 66038--66070 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
66028 GTGATCGCAA
66038 TGACTAAATAATTT
1 TGACTAAATAATTT
66052 TGACTAAATAATTT
1 TGACTAAATAATTT
66066 TGACT
1 TGACT
66071 GTGTGCGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (14 bp):
TGACTAAATAATTT
Found at i:68583 original size:21 final size:21
Alignment explanation
Indices: 68524--68586 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 21
68514 ACGTAATTAT
*
68524 TTTTTAATATTATGTATATATATA
1 TTTTTACTATTAT-T-T-TATATA
68548 TTTTT-C-ATTTAATTTTATATA
1 TTTTTACTA-TT-ATTTTATATA
68569 TTTTTACTATTATTTTAT
1 TTTTTACTATTATTTTAT
68587 TCTCTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
21 18 0.53
22 5 0.15
23 4 0.12
24 7 0.21
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTACTATTATTTTATATA
Found at i:68807 original size:11 final size:11
Alignment explanation
Indices: 68791--68820 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
68781 CTTTTTCGTC
68791 TTAGCATTTAT
1 TTAGCATTTAT
68802 TTAGCATTTAT
1 TTAGCATTTAT
*
68813 TTATCATT
1 TTAGCATT
68821 CTTTCACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (11 bp):
TTAGCATTTAT
Found at i:68932 original size:31 final size:31
Alignment explanation
Indices: 68875--68936 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
68865 ATGTTATCAT
*
68875 CTTTCTTCATTTTTTATTTATTTTTATCTTTA
1 CTTTCTTCATTTTTTATTTATCTTTAT-TTTA
68907 CTTT-TTCATTCTTTTATTT-TCTTTATTTTA
1 CTTTCTTCATT-TTTTATTTATCTTTATTTTA
68937 TATTACTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 4 0.14
31 12 0.43
32 12 0.43
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.73
Consensus pattern (31 bp):
CTTTCTTCATTTTTTATTTATCTTTATTTTA
Found at i:69920 original size:14 final size:16
Alignment explanation
Indices: 69901--69932 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
69891 TCCTTTACCA
69901 TTTATTT-TTT-TATT
1 TTTATTTATTTCTATT
69915 TTTATTTATTTCTATT
1 TTTATTTATTTCTATT
69931 TT
1 TT
69933 ATTAACCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTATTTATTTCTATT
Found at i:72265 original size:387 final size:387
Alignment explanation
Indices: 71551--72327 Score: 1518
Period size: 387 Copynumber: 2.0 Consensus size: 387
71541 GTCAAGGATA
71551 ACGCCAAATTGAAGGTAACCTCTGAATACTGGAAAGACGAAGCTCATAGCCTGAAAAGGAAGTTT
1 ACGCCAAATTGAAGGTAACCTCTGAATACTGGAAAGACGAAGCTCATAGCCTGAAAAGGAAGTTT
*
71616 GAGGGGCCTGATGAGAAAGCTTGGAAGGAACAGATGAAGATTGCCCAAAGACGCTTGGCAGATAG
66 GAGGGGCCTGATGAGAAAGCTTGGAAGGAAAAGATGAAGATTGCCCAAAGACGCTTGGCAGATAG
*
71681 TCAATATCAGAACCAGTGCTTGAGAGTTCGGGTAGCTGACTTAGAAAAACAGCATGAGAAAGATG
131 TCAATATCAGAACCAGCGCTTGAGAGTTCGGGTAGCTGACTTAGAAAAACAGCATGAGAAAGATG
71746 GCAAGACAATAGCTGAGTTAGAGGCTATTGTAGATGGGTTCAAGAGGCAAGCAAACGAGCTTCAG
196 GCAAGACAATAGCTGAGTTAGAGGCTATTGTAGATGGGTTCAAGAGGCAAGCAAACGAGCTTCAG
71811 ATGGTGCCCTTCGACAGAGGATTACAATGGCATTTTCGTTGGGAGCAAGCACAACGAAGGGTGAG
261 ATGGTGCCCTTCGACAGAGGATTACAATGGCATTTTCGTTGGGAGCAAGCACAACGAAGGGTGAG
71876 GGCCCGAGATGCAACCATCCGAGATTTCCTAGATCAAGTGCAAAAAGTAGCCCGTCATCTTC
326 GGCCCGAGATGCAACCATCCGAGATTTCCTAGATCAAGTGCAAAAAGTAGCCCGTCATCTTC
71938 ACGCCAAATTGAAGGTAACCTCTGAATACTGGAAAGACGAAGCTCATAGCCTGAAAAGGAAGTTT
1 ACGCCAAATTGAAGGTAACCTCTGAATACTGGAAAGACGAAGCTCATAGCCTGAAAAGGAAGTTT
*
72003 GAGGGGCCTGATGAGAAAGCTTGGAAGGAAAAGATGAAGATTGCCCAAATACGCTTGGCAGATAG
66 GAGGGGCCTGATGAGAAAGCTTGGAAGGAAAAGATGAAGATTGCCCAAAGACGCTTGGCAGATAG
72068 TCAATATCAGAACCAGCGCTTGAGAGTTCGGGTAGCTGACTTAGAAAAACAGCATGAGAAAGATG
131 TCAATATCAGAACCAGCGCTTGAGAGTTCGGGTAGCTGACTTAGAAAAACAGCATGAGAAAGATG
72133 GCAAGACAATAGCTGAGTTAGAGGCTATTGTAGATGGGTTCAAGAGGCAAGCAAACGAGCTTCAG
196 GCAAGACAATAGCTGAGTTAGAGGCTATTGTAGATGGGTTCAAGAGGCAAGCAAACGAGCTTCAG
*
72198 ATGGTGCCCTTCGACGGAGGATTACAATGGCATTTTCGTTGGGAGCAAGCACAACGAAGGGTGAG
261 ATGGTGCCCTTCGACAGAGGATTACAATGGCATTTTCGTTGGGAGCAAGCACAACGAAGGGTGAG
72263 GGCCCGAGATGCAACCATCCGAGATTTCCTAGATCAAGTGCAAAAAGTAGCCCGTCATCTTC
326 GGCCCGAGATGCAACCATCCGAGATTTCCTAGATCAAGTGCAAAAAGTAGCCCGTCATCTTC
72325 ACG
1 ACG
72328 GCCTAGCAAG
Statistics
Matches: 386, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
387 386 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (387 bp):
ACGCCAAATTGAAGGTAACCTCTGAATACTGGAAAGACGAAGCTCATAGCCTGAAAAGGAAGTTT
GAGGGGCCTGATGAGAAAGCTTGGAAGGAAAAGATGAAGATTGCCCAAAGACGCTTGGCAGATAG
TCAATATCAGAACCAGCGCTTGAGAGTTCGGGTAGCTGACTTAGAAAAACAGCATGAGAAAGATG
GCAAGACAATAGCTGAGTTAGAGGCTATTGTAGATGGGTTCAAGAGGCAAGCAAACGAGCTTCAG
ATGGTGCCCTTCGACAGAGGATTACAATGGCATTTTCGTTGGGAGCAAGCACAACGAAGGGTGAG
GGCCCGAGATGCAACCATCCGAGATTTCCTAGATCAAGTGCAAAAAGTAGCCCGTCATCTTC
Found at i:72609 original size:15 final size:15
Alignment explanation
Indices: 72591--72619 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
72581 ATATTTCAAG
72591 TTTTTATTTTTTTTA
1 TTTTTATTTTTTTTA
72606 TTTTTATTTTTTTT
1 TTTTTATTTTTTTT
72620 TACATTCGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Found at i:79640 original size:6 final size:6
Alignment explanation
Indices: 79625--79669 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
79615 AAGTTGGAAA
79625 AAAAAC -AAAAC AAAAAC AAAAAC AAAAA- AACAAA- AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AA-AAAC AAAAAC AAAAA
79670 GAGAAAAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:79647 original size:17 final size:17
Alignment explanation
Indices: 79622--79669 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
79612 CTTAAGTTGG
79622 AAAAAAAACAAAACAAA-
1 AAAAAAAACAAAA-AAAC
*
79639 AACAAAAACAAAAAAAC
1 AAAAAAAACAAAAAAAC
79656 AAAAAAAACAAAAA
1 AAAAAAAACAAAAA
79670 GAGAAAAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 3 0.11
17 25 0.89
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAAAAAC
Found at i:79652 original size:25 final size:23
Alignment explanation
Indices: 79623--79678 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
79613 TTAAGTTGGA
79623 AAAAAAACAAAACAAAAACAAAAAC
1 AAAAAAAC-AAA-AAAAACAAAAAC
*
79648 AAAAAAACAAAAAAAACAAAAAG
1 AAAAAAACAAAAAAAACAAAAAC
*
79671 AGAAAAAC
1 AAAAAAAC
79679 GTTTAGGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 18 0.62
24 3 0.10
25 8 0.28
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (23 bp):
AAAAAAACAAAAAAAACAAAAAC
Found at i:79654 original size:20 final size:20
Alignment explanation
Indices: 79622--79669 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
79612 CTTAAGTTGG
79622 AAAAAAAACAAAACAAAAAC
1 AAAAAAAACAAAACAAAAAC
79642 AAAAACAAA-AAAACAAAAA-
1 AAAAA-AAACAAAACAAAAAC
79661 AAACAAAAA
1 AAA-AAAAA
79670 GAGAAAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.23
20 17 0.65
21 3 0.12
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAACAAAAAC
Found at i:79676 original size:17 final size:16
Alignment explanation
Indices: 79621--79677 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
79611 TCTTAAGTTG
79621 GAAAAAAAACAAAACAA
1 GAAAAAAAACAAAA-AA
79638 -AAACAAAAACAAAAAAA
1 GAAA-AAAAAC-AAAAAA
*
79655 CAAAAAAAACAAAAAGA
1 GAAAAAAAACAAAAA-A
79672 GAAAAA
1 GAAAAA
79678 CGTTTAGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 8 0.23
17 20 0.57
18 7 0.20
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (16 bp):
GAAAAAAAACAAAAAA
Found at i:79737 original size:10 final size:9
Alignment explanation
Indices: 79715--79753 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 9
79705 CCCTAAATTG
79715 AAGAAAAAA
1 AAGAAAAAA
79724 AAGAAAAGAA
1 AAGAAAA-AA
79734 AAGAGAAAAA
1 AAGA-AAAAA
79744 AAGAACAAAA
1 AAGAA-AAAA
79754 GAGAGAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 16 0.59
11 3 0.11
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:79744 original size:20 final size:20
Alignment explanation
Indices: 79715--79762 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
79705 CCCTAAATTG
79715 AAGA-AAAAAAAGAA-AAGAA
1 AAGAGAAAAAAAGAACAA-AA
79734 AAGAGAAAAAAAGAACAAAA
1 AAGAGAAAAAAAGAACAAAA
*
79754 GAGAGAAAA
1 AAGAGAAAA
79763 CAATGGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 20 0.77
21 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
AAGAGAAAAAAAGAACAAAA
Found at i:80696 original size:105 final size:105
Alignment explanation
Indices: 80509--81281 Score: 1426
Period size: 105 Copynumber: 7.4 Consensus size: 105
80499 AGGTTTTACC
*
80509 CAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
80574 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
80614 CAGAGCCAATCTT-AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAAT-TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * *
80678 GATGAAGGGACCGTTGGTTGTCAACAAATATTTCTCAAATT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
80719 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
80784 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
80824 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA-TCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
80888 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
80928 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
80993 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
81033 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
81098 ATGAAGGGACCGCTGGTTGTCAAC-AACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
81137 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
81202 ACGAAGGGATCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
81242 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
81282 GGAACAATAC
Statistics
Matches: 647, Mismatches: 17, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
104 205 0.32
105 441 0.68
106 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:80993 original size:209 final size:210
Alignment explanation
Indices: 80509--81281 Score: 1435
Period size: 209 Copynumber: 3.7 Consensus size: 210
80499 AGGTTTTACC
*
80509 CAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
80574 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATCTT-AACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT-TTCAACTTCACAAC
*
80638 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGTTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAAC
*
80703 AAATATTTCTCAAATT
195 AAACATTTCTCAAATT
80719 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
80784 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
* *
80849 AAGGATATTGGA-TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACA
*
80913 AACATTTCTCAATTT
196 AACATTTCTCAAATT
80928 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
80993 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGTCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
81058 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAAC-
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACA
81122 AACATTTCTCAAATT
196 AACATTTCTCAAATT
81137 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
81202 ACGAAGGGATCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
81267 AAGGATATTGGACTC
131 AAGGATATTGGACTC
81282 GGAACAATAC
Statistics
Matches: 548, Mismatches: 13, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
209 361 0.66
210 187 0.34
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (210 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACA
AACATTTCTCAAATT
Found at i:81079 original size:314 final size:314
Alignment explanation
Indices: 80509--81281 Score: 1433
Period size: 314 Copynumber: 2.5 Consensus size: 314
80499 AGGTTTTACC
*
80509 CAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
80574 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATCTT-AACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAAT-TTCAACTTCACAAC
* *
80638 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGTTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
*
80703 AAATATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
195 AAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
80768 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
260 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACATTTCTCAAATT
*
80824 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA-TCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
80888 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
80953 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
81018 AACATTTCTCAAATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
196 AACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
*
81083 AAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAACATTTCTCAAATT
261 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACATTTCTCAAATT
81137 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
81202 ACGAAGGGATCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
81267 AAGGATATTGGACTC
131 AAGGATATTGGACTC
81282 GGAACAATAC
Statistics
Matches: 446, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
313 54 0.12
314 356 0.80
315 36 0.08
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (314 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACATTTCTCAAATT
Found at i:82776 original size:22 final size:22
Alignment explanation
Indices: 82726--82805 Score: 53
Period size: 21 Copynumber: 3.8 Consensus size: 22
82716 TTTCTATTTG
* * *
82726 TATATTTTTATTTGTTACGTAT-
1 TATATTTTTA-ATATTATGTATA
82748 TAT-TTTTTAATATTATGTATA
1 TATATTTTTAATATTATGTATA
* *
82769 TATA-TTTTCAT-TTAAT-TTTA
1 TATATTTTTAATATT-ATGTATA
*
82789 TATATTTTTACTATTAT
1 TATATTTTTAATATTAT
82806 ATTTATTCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
20 17 0.37
21 24 0.52
22 5 0.11
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (22 bp):
TATATTTTTAATATTATGTATA
Found at i:82810 original size:22 final size:21
Alignment explanation
Indices: 82751--82811 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
82741 TACGTATTAT
* *
82751 TTTTTAATATTATGTATATATA
1 TTTTT-ATATTATATTTATATA
*
82773 TTTTCAT-TTA-ATTTTATATA
1 TTTTTATATTATA-TTTATATA
82793 TTTTTACTATTATATTTAT
1 TTTTTA-TATTATATTTAT
82812 TCTCTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
20 15 0.48
21 3 0.10
22 12 0.39
23 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTATATTATATTTATATA
Found at i:82883 original size:24 final size:25
Alignment explanation
Indices: 82837--82888 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
82827 TATTCGTTTG
* *
82837 TATTATATATTTTATTACTATT-AT
1 TATTATATATTATATCACTATTAAT
82861 TATTATATATTATACTCAC-ATTAAT
1 TATTATATATTATA-TCACTATTAAT
82886 TAT
1 TAT
82889 ATCTACCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATATATTATATCACTATTAAT
Found at i:83142 original size:36 final size:35
Alignment explanation
Indices: 83080--83151 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 35
83070 TGTTATCATC
*
83080 TTTCTTCATTTTATTTATTTATTTTTATCTTTACTT
1 TTTCTTCATTTTATTTATTTATTTTTAT-ATTACTT
*
83116 TTTCATTC-TTTTATTTTCTTTA-TTTTATATTACTT
1 TTTC-TTCATTTTA-TTTATTTATTTTTATATTACTT
83151 T
1 T
83152 CTTTATTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 7 0.22
36 15 0.47
37 10 0.31
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (35 bp):
TTTCTTCATTTTATTTATTTATTTTTATATTACTT
Found at i:84649 original size:21 final size:21
Alignment explanation
Indices: 84623--84690 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
84613 GATTTACATA
84623 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
84644 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
84665 CTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
84686 TTCGC
1 TTCGC
84691 GTTAAGAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:85515 original size:16 final size:15
Alignment explanation
Indices: 85494--85525 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
85484 CGCCGCAGCG
85494 CCTCCTCTTGCTTCTT
1 CCTCCTCTT-CTTCTT
85510 CCTCCTCTTCTTCTT
1 CCTCCTCTTCTTCTT
85525 C
1 C
85526 AGCTTCCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (15 bp):
CCTCCTCTTCTTCTT
Found at i:86764 original size:42 final size:41
Alignment explanation
Indices: 86649--86845 Score: 152
Period size: 42 Copynumber: 4.8 Consensus size: 41
86639 AATTGATACT
* ** * * *
86649 TTAGCGGCGTTTTTAGTACAAACGCTGCAATAGAGTTG-ACA
1 TTAGCGGCGTTTATACCACAAACGCCGCAATAG-GTGGTAAA
* * * *
86690 TATAGCGGCGTTTTTACAAAAAATGCCGCAATAGGGTGGTAAA
1 T-TAGCGGCGTTTATACCACAAACGCCGCAATA-GGTGGTAAA
* *
86733 TTAGCGGCGTTTATACCACAAACGCCACAATA-GT-ATAAA
1 TTAGCGGCGTTTATACCACAAACGCCGCAATAGGTGGTAAA
* * *
86772 TTTTGCGGCGATTGA-GCCA-AAACGCCGCAATAGAGTGGTAAA
1 -TTAGCGGCG-TTTATACCACAAACGCCGCAATAG-GTGGTAAA
* *
86814 TTCGTGGCGTTTATACCACAAACGCCGCAATA
1 TTAGCGGCGTTTATACCACAAACGCCGCAATA
86846 TATTACACAT
Statistics
Matches: 124, Mismatches: 22, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
39 16 0.13
40 16 0.13
41 16 0.13
42 72 0.58
43 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (41 bp):
TTAGCGGCGTTTATACCACAAACGCCGCAATAGGTGGTAAA
Found at i:86945 original size:41 final size:40
Alignment explanation
Indices: 86886--87025 Score: 185
Period size: 41 Copynumber: 3.5 Consensus size: 40
86876 AACGCCGCAA
* *
86886 TAATCAATAGTGGTGTTTTTAGACAAACGCCATAATAGTG
1 TAATCAATAGTGGCGTTTTTAGACAAACGCCACAATAGTG
* * * *
86926 TTAATCAATAATGGCGTTTTTAGAAAAACGCCGCAATAG-A
1 -TAATCAATAGTGGCGTTTTTAGACAAACGCCACAATAGTG
*
86966 TAATCAATAGTGGCGTTTTTTA-ACAAACGCCAGAATAGTG
1 TAATCAATAGTGGCG-TTTTTAGACAAACGCCACAATAGTG
87006 TAATCAATAGTGGCGTTTTT
1 TAATCAATAGTGGCGTTTTT
87026 TTTTATAAAC
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 32 0.37
40 21 0.24
41 33 0.38
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (40 bp):
TAATCAATAGTGGCGTTTTTAGACAAACGCCACAATAGTG
Found at i:86981 original size:39 final size:38
Alignment explanation
Indices: 86885--87025 Score: 158
Period size: 39 Copynumber: 3.6 Consensus size: 38
86875 AAACGCCGCA
* *
86885 ATAATCAATAGTGGTGTTTTTAGACAAACGCCATAATAGTG
1 ATAATCAATAGTGGCGTTTTTAGACAAACGCC-GAATA--G
* * *
86926 TTAATCAATAATGGCGTTTTTAGAAAAACGCCGCAATAG
1 ATAATCAATAGTGGCGTTTTTAGACAAACGCCG-AATAG
86965 ATAATCAATAGTGGCGTTTTTTA-ACAAACGCCAGAATAG
1 ATAATCAATAGTGGCG-TTTTTAGACAAACGCC-GAATAG
*
87004 TGTAATCAATAGTGGCGTTTTT
1 -ATAATCAATAGTGGCGTTTTT
87026 TTTTATAAAC
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
39 33 0.38
40 22 0.25
41 32 0.37
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (38 bp):
ATAATCAATAGTGGCGTTTTTAGACAAACGCCGAATAG
Done.