Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006543.1 Hibiscus syriacus cultivar Beakdansim tig00015973_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: 104758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2206 original size:33 final size:33
Alignment explanation
Indices: 2159--2245 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
2149 ACAAAGTTTA
*
2159 CGAT-AATTGAAATACTT-AAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAT-CTTCCAAGTT
*
2191 TGATAAATTCAAATACTTAAAATCTTCCAAGTT
1 CGATAAATTCAAATACTTAAAATCTTCCAAGTT
2224 CGATAAATTCAAATACTTAAAA
1 CGATAAATTCAAATACTTAAAA
2246 ACGGTCAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
32 3 0.06
33 43 0.86
34 4 0.08
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAATCTTCCAAGTT
Found at i:2351 original size:22 final size:21
Alignment explanation
Indices: 2310--2360 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2300 TTAAACCCAT
*
2310 ACCGGTTTTTTTCGGATAAAA
1 ACCGGTTTTTTCCGGATAAAA
*
2331 ACCGGTTTTTTAACCGGTAAAAAA
1 ACCGGTTTTTT--CCGG-ATAAAA
2355 ACCGGT
1 ACCGGT
2361 CTAGGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.44
23 3 0.12
24 11 0.44
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (21 bp):
ACCGGTTTTTTCCGGATAAAA
Found at i:3481 original size:20 final size:20
Alignment explanation
Indices: 3452--3525 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
3442 GCAGCCTTCG
*
3452 TGCATGGATGCACAACATGA
1 TGCATCGATGCACAACATGA
* *
3472 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACA-ACATGA
* *
3493 TGCATCGATGCACAAAAGGA
1 TGCATCGATGCACAACATGA
3513 TGCATCGATGCAC
1 TGCATCGATGCAC
3526 TAATTGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 28 0.61
21 18 0.39
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAACATGA
Found at i:3495 original size:21 final size:21
Alignment explanation
Indices: 3443--3506 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
3433 CTAGCCATTG
*
3443 CAGCCTTCG-TGCATGGATGCA
1 CAGCCTT-GATGCATCGATGCA
* *
3464 CA-ACATGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
3484 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
3505 CA
1 CA
3507 AAAGGATGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 20 0.56
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (21 bp):
CAGCCTTGATGCATCGATGCA
Found at i:3503 original size:41 final size:41
Alignment explanation
Indices: 3443--3525 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
3433 CTAGCCATTG
* * *
3443 CAGCCTTCGTGCATGGATGCACAACATGATGCATCGATGCA
1 CAGCCTTCGTGCATCGATGCACAAAAGGATGCATCGATGCA
3484 CAGCCTT-GATGCATCGATGCACAAAAGGATGCATCGATGCA
1 CAGCCTTCG-TGCATCGATGCACAAAAGGATGCATCGATGCA
3525 C
1 C
3526 TAATTGCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (41 bp):
CAGCCTTCGTGCATCGATGCACAAAAGGATGCATCGATGCA
Found at i:3595 original size:21 final size:20
Alignment explanation
Indices: 3546--3624 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 20
3536 CGGTGTTTGA
3546 GTGCATGGATGCACT-AGTGCAG
1 GTGCATGGATGCACTGA-TG--G
3568 GTGCATGGATGCACTGATGG
1 GTGCATGGATGCACTGATGG
*
3588 GATGCATGGATGCACTGCAAGG
1 G-TGCATGGATGCACTG-ATGG
3610 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3625 TTGACACCCT
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
20 2 0.04
21 29 0.55
22 21 0.40
23 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGATGG
Found at i:3725 original size:29 final size:29
Alignment explanation
Indices: 3704--3761 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
3694 AAACTTTGAA
*
3704 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCAAAAAACA-TTTG
3733 TAAATTCAATTCAAGTCAAAAAATCATTT
1 TAAATTCAATTCAAGTCAAAAAA-CATTT
3762 TGCCTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCAAAAAACATTTG
Found at i:3755 original size:30 final size:30
Alignment explanation
Indices: 3704--3763 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
3694 AAACTTTGAA
*
3704 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCAAAAAATCATTTTG
3733 TAAATTCAATTCAAGTCAAAAAATCATTTTG
1 TAAATTCAATT-AAGTCAAAAAATCATTTTG
3764 CCTTAATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCAAAAAATCATTTTG
Found at i:6225 original size:16 final size:16
Alignment explanation
Indices: 6204--6236 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6194 TAATAAATAA
6204 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
6220 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
6236 A
1 A
6237 AATTTTTTTT
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:6328 original size:10 final size:10
Alignment explanation
Indices: 6313--6338 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6303 AAACGAACAT
6313 GAACATAAAC
1 GAACATAAAC
6323 GAACATAAAC
1 GAACATAAAC
6333 GAACAT
1 GAACAT
6339 GAACATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:8379 original size:16 final size:18
Alignment explanation
Indices: 8358--8402 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
8348 AACATTACCA
8358 GTAATCTTATT-CCA-TG
1 GTAATCTTATTCCCACTG
8374 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
8394 GTAATCTTA
1 GTAATCTTA
8403 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 3 0.12
20 10 0.40
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:9281 original size:21 final size:21
Alignment explanation
Indices: 9257--9296 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9247 AGAAATGTTA
*
9257 AAAAACATTAATATTTTAGAT
1 AAAAACAATAATATTTTAGAT
*
9278 AAAAATAATAATATTTTAG
1 AAAAACAATAATATTTTAG
9297 GTAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAACAATAATATTTTAGAT
Found at i:22907 original size:22 final size:21
Alignment explanation
Indices: 22873--22914 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
22863 CTAAAATCCC
* *
22873 TAAAAATATAAAAGTAAAAGG
1 TAAAAAAATAAAAGGAAAAGG
22894 TAAAAAAATCAAAAGGAAAAG
1 TAAAAAAAT-AAAAGGAAAAG
22915 TGGAGAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (21 bp):
TAAAAAAATAAAAGGAAAAGG
Found at i:23733 original size:22 final size:22
Alignment explanation
Indices: 23705--23749 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
23695 ACTATGATTC
23705 CTCTACCACTTCATCAATACAT
1 CTCTACCACTTCATCAATACAT
23727 CTCTACCACTTCATCAATACAT
1 CTCTACCACTTCATCAATACAT
23749 C
1 C
23750 CAGCTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (22 bp):
CTCTACCACTTCATCAATACAT
Found at i:27268 original size:30 final size:30
Alignment explanation
Indices: 27234--27324 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
27224 TATTCTAAAC
27234 TTGATATCAATACAAAATAGCATTATGAAA
1 TTGATATCAATACAAAATAGCATTATGAAA
* * * * * * *
27264 TTGATATCTACT-CTAGATCG-GTTCTAAAA
1 TTGATATC-AATACAAAATAGCATTATGAAA
27293 TTGATATCAATACAAAATAGCATTATGAAA
1 TTGATATCAATACAAAATAGCATTATGAAA
27323 TT
1 TT
27325 TTAAAGTTTT
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
28 2 0.05
29 19 0.43
30 21 0.48
31 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (30 bp):
TTGATATCAATACAAAATAGCATTATGAAA
Found at i:43713 original size:21 final size:21
Alignment explanation
Indices: 43666--43713 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
43656 ACCGATACGA
* *
43666 TGCTGATATGGCACTTCACGG
1 TGCTGACATGGCACTACACGG
* * *
43687 TTCTGACATGGCAGTACATGG
1 TGCTGACATGGCACTACACGG
43708 TGCTGA
1 TGCTGA
43714 AGTGGTAGTC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (21 bp):
TGCTGACATGGCACTACACGG
Found at i:44455 original size:17 final size:17
Alignment explanation
Indices: 44430--44463 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44420 ATTTCAATGA
*
44430 AAATAAAATAGTAAATT
1 AAATAAAATAATAAATT
*
44447 AAATTAAATAATAAATT
1 AAATAAAATAATAAATT
44464 TTAAAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATAAAATAATAAATT
Found at i:46687 original size:13 final size:13
Alignment explanation
Indices: 46650--46689 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
46640 TCGATATTGA
46650 AAAATAAATA-TT
1 AAAATAAATATTT
*
46662 AAAATAATTTATTT
1 AAAATAA-ATATTT
46676 AAAATAAATATTT
1 AAAATAAATATTT
46689 A
1 A
46690 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:48049 original size:3 final size:3
Alignment explanation
Indices: 48041--48121 Score: 135
Period size: 3 Copynumber: 27.0 Consensus size: 3
48031 TTAATATATT
* *
48041 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48089 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48122 ATAAATCAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:48416 original size:16 final size:17
Alignment explanation
Indices: 48394--48434 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
48384 TATGAACTTT
48394 CTCTTCTTCA-GATGAA
1 CTCTTCTTCATGATGAA
* *
48410 TTCTTC-TCATTATGAA
1 CTCTTCTTCATGATGAA
48426 CTCTTCTTC
1 CTCTTCTTC
48435 TTCATATGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 3 0.15
16 15 0.75
17 2 0.10
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.46
Consensus pattern (17 bp):
CTCTTCTTCATGATGAA
Found at i:48434 original size:19 final size:19
Alignment explanation
Indices: 48410--48467 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
48400 TTCAGATGAA
48410 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
**
48429 TTCTTCTTCA-TATG-ACGAG
1 TTCTTC-TCATTATGAAC-TC
*
48448 TTCTTCTGATTATGAACTC
1 TTCTTCTCATTATGAACTC
48467 T
1 T
48468 ATCTGGCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
18 4 0.13
19 21 0.70
20 5 0.17
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.47
Consensus pattern (19 bp):
TTCTTCTCATTATGAACTC
Found at i:48452 original size:38 final size:36
Alignment explanation
Indices: 48375--48467 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 36
48365 TTGAATAAGC
* *
48375 TCTTCTTATTATGAACTTTCTCTTCTTCAGATGAAT
1 TCTTCTCATTATGAACTCTCTCTTCTTCAGATGAAT
*
48411 TCTTCTCATTATGAACTCT-TCTTCTTCATATGACGAGT
1 TCTTCTCATTATGAACTCTCTCTTCTTCAGATGA--A-T
*
48449 TCTTCTGATTATGAACTCT
1 TCTTCTCATTATGAACTCT
48468 ATCTGGCAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
35 13 0.26
36 17 0.34
37 1 0.02
38 19 0.38
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.47
Consensus pattern (36 bp):
TCTTCTCATTATGAACTCTCTCTTCTTCAGATGAAT
Found at i:48586 original size:113 final size:113
Alignment explanation
Indices: 48408--49065 Score: 866
Period size: 113 Copynumber: 5.9 Consensus size: 113
48398 TCTTCAGATG
* * * * *
48408 AATTCTTCTCATTATGAAC-TCTTCTT-CTTCAT-ATGACGAGTTCTTCTGATTATGAACTCTAT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTTATTATGAACTTTCT
* * * * * *
48470 CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACA
65 CTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACA
*
48519 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
* *
48584 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGGGTTAAACA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTAAAC-AAAA-GGTTGAACA
* * * * * *
48634 AGTTC-T-TCA-GATGAAC-T-TTCTT-TTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
**** * * * * *
48693 TGGCGCTGCTGATCCATCAAATGATGAATTCAAACAAAGGGTTAAACA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACA
* * **
48741 AGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTAAC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
* * * *
48806 TGGAAAGGCTGATCCATCAAGTAATGGATTTGAGCAAAAGGTTGAACA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACA
48854 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
*
48919 TGGAAAAGCTGATCCATCAAGTGATGGATTTAAACATAAGGTTGAACA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACA
* *
48967 AATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
49032 TGGAAAAGCTGATCCATCAAGTGATGGATTTAAA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTAAA
49066 TCTTTGCTAA
Statistics
Matches: 478, Mismatches: 58, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
107 14 0.03
108 4 0.01
109 64 0.13
110 11 0.02
111 21 0.04
112 17 0.04
113 329 0.69
114 6 0.01
115 12 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
TGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACA
Found at i:48715 original size:222 final size:226
Alignment explanation
Indices: 48408--49062 Score: 914
Period size: 222 Copynumber: 2.9 Consensus size: 226
48398 TCTTCAGATG
* * * * *
48408 AATTCTTCTCATTATGAAC-TCTTCTT-CTTCAT-ATGACGAGTTCTTCTGATTATGAACTCTAT
1 AATTCTTCTCATGATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATGAACTCTCT
* *
48470 CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
65 CTGGCAATGCTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
*
48535 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCA
130 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCA
48600 TCAAGTGATGGATTTGAACAAAAAGGGTTAAACA
195 TCAAGTGATGGATTTGAAC-AAAA-GGTTAAACA
* * *
48634 AGTTC-T-TCA-GATGAAC-T-TTCTT-TTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTT
1 AATTCTTCTCATGATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTC
** * * * *
48693 TGGCGCTGCTGATCCATCAAATGATGAATTCAAACAAAGGGTTAAACAAGTTCTTCTCATTATGA
66 TGGCAATGCTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGA
* ** *
48758 ACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTAACTGGAAAGGCTGATCCAT
131 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCAT
* * *
48823 CAAGTAATGGATTTGAGCAAAAGGTTGAACA
196 CAAGTGATGGATTTGAACAAAAGGTTAAACA
* * *
48854 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
1 AATTCTTCTCATGATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTC
* * * * *
48919 TGGAAAAGCTGATCCATCAAGTGATGGATTTAAACATAAGGTTGAACAAATTCTTCTCATTATGA
66 TGGCAATGCTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGA
* *
48984 ATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCAT
131 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCAT
49049 CAAGTGATGGATTT
196 CAAGTGATGGATTT
49063 AAATCTTTGC
Statistics
Matches: 374, Mismatches: 48, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
220 12 0.03
221 5 0.01
222 170 0.45
223 14 0.04
224 4 0.01
225 6 0.02
226 163 0.44
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (226 bp):
AATTCTTCTCATGATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTC
TGGCAATGCTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCAT
CAAGTGATGGATTTGAACAAAAGGTTAAACA
Found at i:50033 original size:82 final size:82
Alignment explanation
Indices: 49896--50542 Score: 1037
Period size: 82 Copynumber: 7.9 Consensus size: 82
49886 TTGGGGTTCA
* *
49896 TACCAAACCAGATCAGATAACTCAAAGCACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
49961 AAATTCAATAACTGTTT
66 AAATTCAATAACTGTTT
*
49978 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
50043 AAATTCAATAACTGTTT
66 AAATTCAATAACTGTTT
* *
50060 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
50125 AAATTCAATAACTGTTT
66 AAATTCAATAACTGTTT
*
50142 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
* * * *
50207 AATTTCAATGATTGGTTC
66 AAATTCAATAACT-GTTT
* *
50225 TGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
50290 AAATTCAATAACTGGTTT
66 AAATTCAATAACT-GTTT
* * *
50308 TACCAAACCATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAGTACATTCATCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
* * *
50373 -AATTCAATGATTGGTT
66 AAATTCAATAACTGTTT
* *
50389 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCAAATTCATCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
* *
50454 AAATTCAATGATTGGTTT
66 AAATTCAATAACT-GTTT
* *
50472 TGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
50537 -AATTCA
66 AAATTCA
50543 TGTTTGGACT
Statistics
Matches: 531, Mismatches: 31, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
81 63 0.12
82 262 0.49
83 206 0.39
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (82 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
AAATTCAATAACTGTTT
Found at i:50379 original size:247 final size:247
Alignment explanation
Indices: 49896--50542 Score: 1075
Period size: 247 Copynumber: 2.6 Consensus size: 247
49886 TTGGGGTTCA
*
49896 TACCAAACCAGATCAGATAACTCAAAGCACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCC
* * *
49961 AAATTCAATAACT-GTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
66 AAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
*
50025 TGAGCAAATTCATCTTCCAAATTCAATAACTGTTTTACCAAACCAGATCAGATAACTCAAAGAAC
131 TGAGCAAATTCATCTTTCAAATTCAATAACTGTTTTACCAAACCAGATCAGATAACTCAAAGAAC
* * *
50090 ACTTCCAGAAGATGTTATGAGCACATTCATCTTTCAAATTCAATAACTGTTT
196 ACTTCCAGAAGATGCTATAAGCACATTCATCTTTCAAATTCAATAACTGGTT
* *
50142 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCC
* *
50207 AATTTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
66 AAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* *
50272 TGAGCACATTCATCTTTCAAATTCAATAACTGGTTTTACCAAACCATATCAGATAACTCAAAGAA
131 TGAGCAAATTCATCTTTCAAATTCAATAACT-GTTTTACCAAACCAGATCAGATAACTCAAAGAA
* * * *
50337 CACTTCCAGAAGATGCTATAAGTACATTCATC-TTCCAATTCAATGATTGGTT
195 CACTTCCAGAAGATGCTATAAGCACATTCATCTTTCAAATTCAATAACTGGTT
*
50389 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCAAATTCATCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCC
50454 AAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
66 AAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* *
50519 TGAGCATATTCATC-TTCCAATTCA
131 TGAGCAAATTCATCTTTCAAATTCA
50543 TGTTTGGACT
Statistics
Matches: 374, Mismatches: 25, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
246 81 0.22
247 232 0.62
248 61 0.16
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (247 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCC
AAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
TGAGCAAATTCATCTTTCAAATTCAATAACTGTTTTACCAAACCAGATCAGATAACTCAAAGAAC
ACTTCCAGAAGATGCTATAAGCACATTCATCTTTCAAATTCAATAACTGGTT
Found at i:51691 original size:10 final size:10
Alignment explanation
Indices: 51676--51724 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
51666 TGACCCCCCC
51676 TTTTTCTTCT
1 TTTTTCTTCT
*
51686 TTTTTCTTTT
1 TTTTTCTTCT
51696 TTTTTCTTTTCT
1 TTTTTC--TTCT
*
51708 TTCTTTTTTCT
1 TT-TTTCTTCT
51719 TTTTTC
1 TTTTTC
51725 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 18 0.56
11 6 0.19
12 5 0.16
13 3 0.09
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:51694 original size:7 final size:7
Alignment explanation
Indices: 51677--51724 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
51667 GACCCCCCCT
51677 TTTTCTTC
1 TTTT-TTC
51685 TTTTTTC
1 TTTTTTC
51692 TTTTTT-
1 TTTTTTC
*
51698 TTTCTT-
1 TTTTTTC
*
51704 TTCTTTC
1 TTTTTTC
51711 TTTTTTC
1 TTTTTTC
51718 TTTTTTC
1 TTTTTTC
51725 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 9 0.26
7 22 0.63
8 4 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:62389 original size:28 final size:27
Alignment explanation
Indices: 62317--62403 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 27
62307 CTTTGACAGA
*
62317 AAAATAATAA-TGAAATA-AAATACTTG
1 AAAATAATAAGT-AAATATAAATATTTG
* *
62343 CAAATAA-AATGAAACATATAAATATTATG
1 AAAATAATAA-GTAA-ATATAAATATT-TG
*
62372 AAAATAATAAGTAAATATAAAAATTTTG
1 AAAATAATAAGTAAATATAAATA-TTTG
62400 AAAA
1 AAAA
62404 GAAAAGAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
25 2 0.04
26 8 0.17
27 3 0.06
28 20 0.42
29 13 0.27
30 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (27 bp):
AAAATAATAAGTAAATATAAATATTTG
Found at i:63120 original size:13 final size:13
Alignment explanation
Indices: 63064--63103 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
63054 TCGATATTGA
63064 AAAATAAATA-TT
1 AAAATAAATATTT
*
63076 AAAATAATTTATTT
1 AAAATAA-ATATTT
63090 AAAATAAATATTT
1 AAAATAAATATTT
63103 A
1 A
63104 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:63134 original size:17 final size:17
Alignment explanation
Indices: 63077--63124 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
63067 ATAAATATTA
63077 AAATAATTTATTTAAAAT
1 AAAT-ATTTATTTAAAAT
63095 AAATATTTATTTAAAAT
1 AAATATTTATTTAAAAT
63112 AAATATTTATTTA
1 AAATATTTATTTA
63125 TTATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATATTTATTTAAAAT
Found at i:64349 original size:16 final size:16
Alignment explanation
Indices: 64328--64369 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
64318 ACCGTTGGCT
64328 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
64344 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
64360 GAGGCGGCTG
1 GAGGCGGCTG
64370 CGGCGCTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.57, T:0.07
Consensus pattern (16 bp):
GAGGCGGCTGGAGGCA
Found at i:64492 original size:12 final size:11
Alignment explanation
Indices: 64474--64563 Score: 78
Period size: 9 Copynumber: 9.1 Consensus size: 11
64464 TTATATATAT
64474 ATTTAAT-AT-
1 ATTTAATAATA
64483 ATTTAATAATA
1 ATTTAATAATA
64494 A--TAATAATA
1 ATTTAATAATA
64503 A--TAATAATA
1 ATTTAATAATA
64512 A-TT-ATAATA
1 ATTTAATAATA
64521 ATTATAATAATA
1 ATT-TAATAATA
64533 A--TAATAATA
1 ATTTAATAATA
64542 ATTATAATAATA
1 ATT-TAATAATA
64554 A--TAATAATA
1 ATTTAATAATA
64563 A
1 A
64564 ATAAATCAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 18
0.80 0.00 0.20
Matches are distributed among these distances:
9 50 0.69
10 4 0.06
11 2 0.03
12 16 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:64494 original size:3 final size:3
Alignment explanation
Indices: 64486--64563 Score: 129
Period size: 3 Copynumber: 26.0 Consensus size: 3
64476 TTAATATATT
* *
64486 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
64534 TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
64564 ATAAATCAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:65058 original size:28 final size:28
Alignment explanation
Indices: 65027--65081 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
65017 TTTTAACATA
65027 TGATCAGTTCACAAACATTAAACAAATC
1 TGATCAGTTCACAAACATTAAACAAATC
*
65055 TGATCAGTTCACAAATATTAAACAAAT
1 TGATCAGTTCACAAACATTAAACAAAT
65082 TTGTTCATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.27
Consensus pattern (28 bp):
TGATCAGTTCACAAACATTAAACAAATC
Found at i:65990 original size:24 final size:24
Alignment explanation
Indices: 65961--66104 Score: 68
Period size: 24 Copynumber: 6.0 Consensus size: 24
65951 ATATATATCA
65961 ATATTTTAAAATAATTAAAATAAT
1 ATATTTTAAAATAATTAAAATAAT
* **
65985 ATATTTTATATTAATATATTCATAATTTTT
1 ATATTTTA-A--AATA-ATT-A-AAATAAT
*
66015 ATTATTTCT-AAATGATTAAAATAAT
1 A-TATTT-TAAAATAATTAAAATAAT
* * **
66040 ATATTTTATAATAATT--TATTGT
1 ATATTTTAAAATAATTAAAATAAT
66062 A-ATTTT--AATAATT-AAATAAT
1 ATATTTTAAAATAATTAAAATAAT
* * *
66082 ATATTTTAACATTATAAAAATAA
1 ATATTTTAAAATAATTAAAATAA
66105 AAATATTAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
19 7 0.08
20 4 0.05
21 10 0.11
22 4 0.05
23 5 0.06
24 25 0.28
25 6 0.07
26 1 0.01
27 7 0.08
28 6 0.07
29 1 0.01
30 6 0.07
31 5 0.06
32 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (24 bp):
ATATTTTAAAATAATTAAAATAAT
Found at i:66131 original size:2 final size:2
Alignment explanation
Indices: 66124--66159 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
66114 AAGTCTGATT
66124 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66160 CCGGGTCGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70684 original size:12 final size:12
Alignment explanation
Indices: 70648--70691 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
70638 AGAACAAAAA
*
70648 GAAAAACTTAAA
1 GAAAAACTTAAT
70660 G-AAAACTTAAT
1 GAAAAACTTAAT
*
70671 GAAAAACTTGAT
1 GAAAAACTTAAT
*
70683 GATAAACTT
1 GAAAAACTT
70692 GATTGCCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (12 bp):
GAAAAACTTAAT
Found at i:71813 original size:15 final size:14
Alignment explanation
Indices: 71777--71815 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
71767 CACAATTTTG
71777 TTTCTTTTGTTTCT
1 TTTCTTTTGTTTCT
*
71791 TTTCCTTTTTTTATCT
1 TTT-CTTTTGTT-TCT
71807 TTTCTTTTG
1 TTTCTTTTG
71816 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 12 0.57
16 6 0.29
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (14 bp):
TTTCTTTTGTTTCT
Found at i:77259 original size:3 final size:3
Alignment explanation
Indices: 77251--77284 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
77241 ATCACCAACT
*
77251 TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
77285 GCATCACCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:82219 original size:2 final size:2
Alignment explanation
Indices: 82212--82275 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
82202 GTCTACAAGA
82212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82254 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
82276 GCGTGTTTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93318 original size:17 final size:17
Alignment explanation
Indices: 93296--93432 Score: 159
Period size: 17 Copynumber: 7.9 Consensus size: 17
93286 ATTCTAAATG
93296 TTTACAGTTATCAGATA
1 TTTACAGTTATCAGATA
*
93313 TTTACAATTATCAGATGA
1 TTTACAGTTATCAGAT-A
*
93331 TTTTCAGTTATCAGATA
1 TTTACAGTTATCAGATA
*
93348 TTTGCAGTTATCAGATGA
1 TTTACAGTTATCAGAT-A
** *
93366 TTTTTAGTTATCATATA
1 TTTACAGTTATCAGATA
*
93383 TTTACAGTTATTAGATGA
1 TTTACAGTTATCAGAT-A
*
93401 -TTACAGTTATTAGATA
1 TTTACAGTTATCAGATA
93417 TTTTACAGTTATCAGA
1 -TTTACAGTTATCAGA
93433 CGTAGATTAA
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.01
17 59 0.57
18 43 0.42
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:93339 original size:35 final size:35
Alignment explanation
Indices: 93300--93432 Score: 187
Period size: 35 Copynumber: 3.8 Consensus size: 35
93290 TAAATGTTTA
*
93300 CAGTTATCAGATATTTACAATTATCAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
*
93335 CAGTTATCAGATATTTGCAGTTATCAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
* * * *
93370 TAGTTATCATATATTTACAGTTATTAGATGA-TTA
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
*
93404 CAGTTATTAGATATTTTACAGTTATCAGA
1 CAGTTATCAGATA-TTTACAGTTATCAGA
93433 CGTAGATTAA
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 12 0.14
35 74 0.86
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (35 bp):
CAGTTATCAGATATTTACAGTTATCAGATGATTTT
Found at i:93357 original size:52 final size:51
Alignment explanation
Indices: 93297--93432 Score: 157
Period size: 52 Copynumber: 2.6 Consensus size: 51
93287 TTCTAAATGT
* *
93297 TTACAGTTATCAGATATTTACAATTATCAGATGATTTTCAGTTATCAGAT-A
1 TTACAGTTATCAGATATTTACAGTTATCAGAT-ATTTACAGTTATCAGATGA
* ** * *
93348 TTTGCAGTTATCAGATGATTTTTAGTTATCATATATTTACAGTTATTAGATGA
1 -TTACAGTTATCAGAT-ATTTACAGTTATCAGATATTTACAGTTATCAGATGA
*
93401 TTACAGTTATTAGATATTTTACAGTTATCAGA
1 TTACAGTTATCAGATA-TTTACAGTTATCAGA
93433 CGTAGATTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
51 1 0.01
52 54 0.78
53 14 0.20
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (51 bp):
TTACAGTTATCAGATATTTACAGTTATCAGATATTTACAGTTATCAGATGA
Found at i:98823 original size:23 final size:22
Alignment explanation
Indices: 98793--98872 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 22
98783 ACACTAGATA
98793 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * * *
98816 GTGCATCGATACA-CCATAAAG
1 GTGCATCGATGCATCCTTGAAT
*
98837 GTGCA-CTGATGCATTCATTGAAT
1 GTGCATC-GATGCA-TCCTTGAAT
*
98860 GTGCACCGATGCA
1 GTGCATCGATGCA
98873 CTCTGCTATG
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.02
21 15 0.34
23 27 0.61
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:98858 original size:44 final size:43
Alignment explanation
Indices: 98774--98869 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 43
98764 TTGTGCATAA
* * *
98774 TGCATCGATACACTAGATAGTGCATCGATGCATCCCTTGAATG
1 TGCATCGATACACCAGAAAGTGCATCGATGCATCCATTGAATG
* *
98817 TGCATCGATACACCATAAAGGTGCA-CTGATGCATTCATTGAATG
1 TGCATCGATACACCAGAAA-GTGCATC-GATGCATCCATTGAATG
*
98861 TGCACCGAT
1 TGCATCGAT
98870 GCACTCTGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 17 0.38
44 28 0.62
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (43 bp):
TGCATCGATACACCAGAAAGTGCATCGATGCATCCATTGAATG
Found at i:99277 original size:9 final size:10
Alignment explanation
Indices: 99247--99276 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
99237 AAAACACAAG
*
99247 ATTTTTCAAA
1 ATTTTTGAAA
99257 ATTTTTGAAA
1 ATTTTTGAAA
99267 ATTTTTGAAA
1 ATTTTTGAAA
99277 TAAAAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (10 bp):
ATTTTTGAAA
Found at i:99309 original size:13 final size:13
Alignment explanation
Indices: 99291--99315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
99281 AATATCATTA
99291 TTTTGATTTAATG
1 TTTTGATTTAATG
99304 TTTTGATTTAAT
1 TTTTGATTTAAT
99316 TGTATTTATG
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTTGATTTAATG
Found at i:100838 original size:2 final size:2
Alignment explanation
Indices: 100831--100855 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
100821 ATTGAACTTA
100831 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 A
100856 GTTTTTGCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:102492 original size:31 final size:31
Alignment explanation
Indices: 102457--102515 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
102447 TAAACTTAAA
* * *
102457 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
102488 AGTTTTACAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
102516 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:102646 original size:31 final size:32
Alignment explanation
Indices: 102610--102801 Score: 189
Period size: 31 Copynumber: 6.8 Consensus size: 32
102600 CAATCCATAT
102610 TTTAAAATAAATCAATCCATACAAAT-AATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
102641 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
102663 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
102695 TTT-AAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
102726 TAT-AAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
102747 TTTAAAAT-AATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
102778 TTTAAAATAAATCAATCCATACAA
1 TTTAAAATAAATCAATCCATACAA
102802 CTACAATAAT
Statistics
Matches: 135, Mismatches: 4, Indels: 43
0.74 0.02 0.24
Matches are distributed among these distances:
21 9 0.07
22 22 0.16
23 3 0.02
24 1 0.01
25 5 0.04
26 1 0.01
27 4 0.03
28 2 0.01
29 1 0.01
30 4 0.03
31 66 0.49
32 17 0.13
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:102673 original size:53 final size:52
Alignment explanation
Indices: 102538--102911 Score: 292
Period size: 53 Copynumber: 7.3 Consensus size: 52
102528 AATAATAAAT
*
102538 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAACTACA
1 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATA-A
102591 -A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAA
1 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAA
102638 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAA
1 -TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAAT-AA
** * * * ** *
102692 TTATTT-AAATAAATCAATCCATACTAATAAATTATATAAATAAAT-C-AATCCA
1 -TATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACAAAT-AA
*
102744 TATTTTAAAAT-AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA
1 TA-TTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATACAAATA-A
102807 -A--T--AATAAATCAATCCATATTTTAAAATAAATCAAT-C---C--AT-A
1 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAA
* *
102847 T-TTTAAAAT-AATCAATTCATATTTT-AAATAAATCAATCCATACTAATAAA
1 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAAT-AA
102897 TTATTTAAAATAAAT
1 -TATTTAAAATAAAT
102912 TATTTAAAAA
Statistics
Matches: 260, Mismatches: 22, Indels: 78
0.72 0.06 0.22
Matches are distributed among these distances:
40 1 0.00
42 14 0.05
43 16 0.06
44 4 0.02
46 1 0.00
47 2 0.01
48 61 0.23
49 2 0.01
50 3 0.01
51 4 0.02
52 25 0.10
53 69 0.27
54 23 0.09
56 1 0.00
57 4 0.02
58 9 0.03
59 1 0.00
60 2 0.01
61 13 0.05
62 2 0.01
63 3 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (52 bp):
TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAA
Found at i:102683 original size:22 final size:22
Alignment explanation
Indices: 102540--102630 Score: 119
Period size: 22 Copynumber: 4.0 Consensus size: 22
102530 TAATAAATTA
102540 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
102562 TTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCAT---AT
**
102587 TACAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATAT
102610 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
102631 CAAATAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
22 36 0.61
23 4 0.07
25 4 0.07
26 15 0.25
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:102692 original size:22 final size:22
Alignment explanation
Indices: 102643--102691 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
102633 AATAATTATT
***
102643 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATAAAA
102665 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
102688 TAAA
1 TAAA
102692 TTATTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:102721 original size:84 final size:84
Alignment explanation
Indices: 102614--102911 Score: 360
Period size: 84 Copynumber: 3.5 Consensus size: 84
102604 CCATATTTTA
*
102614 AAATAAATCAATCCATACAAAT-AATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA
1 AAATAAATCAATCCATACTAATAAATTATTT-AAATAAATCAATCCATATTTTAAAATAAATCAA
102678 TCCATACAAATAAATTATTT
65 TCCATACAAATAAATTATTT
*
102698 AAATAAATCAATCCATACTAATAAATTATATAAATAAATCAATCCATATTTTAAAAT-AATCAAT
1 AAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAAT
*
102762 CCATACTAATAAATTATTT
66 CCATACAAATAAATTATTT
*
102781 AAAATAAATCAATCCATAC-AACTACA--A--T-AATAAATCAATCCATATTTTAAAATAAATCA
1 -AAATAAATCAATCCATACTAA-TAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCA
*
102840 ATCCATATTTTAAAATAATCAATTCATATTTT
64 ATCCATA----CAAAT-A--AA-T--TA-TTT
102872 AAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 AAATAAATCAATCCATACTAATAAATTATTT-AAATAAAT
102912 TATTTAAAAA
Statistics
Matches: 185, Mismatches: 7, Indels: 32
0.83 0.03 0.14
Matches are distributed among these distances:
79 25 0.14
80 13 0.07
82 1 0.01
83 27 0.15
84 71 0.38
85 8 0.04
87 2 0.01
88 1 0.01
90 23 0.12
91 5 0.03
92 1 0.01
94 1 0.01
96 7 0.04
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (84 bp):
AAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAAT
CCATACAAATAAATTATTT
Found at i:102775 original size:21 final size:21
Alignment explanation
Indices: 102727--102775 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
102717 AATAAATTAT
*
102727 ATAAATAAATCAATCCATATT
1 ATAAATAAATCAATCCATATA
*
102748 TTAAA-ATAATCAATCCATACTA
1 ATAAATA-AATCAATCCATA-TA
102770 ATAAAT
1 ATAAAT
102776 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATAAATCAATCCATATA
Found at i:102861 original size:21 final size:22
Alignment explanation
Indices: 102809--102948 Score: 140
Period size: 22 Copynumber: 6.3 Consensus size: 22
102799 CAACTACAAT
102809 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
102831 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
102853 AAT-AATCAATTCATATTTT-A
1 AATAAATCAATCCATATTTTAA
**
102873 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * ** *
102896 ATTATTTAAAATAAATTATTTAAA
1 AATAAAT-CAATCCA-TATTTTAA
*
102920 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
102942 AATAAAT
1 AATAAAT
102949 TATTTAAAAT
Statistics
Matches: 92, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.04
21 26 0.28
22 40 0.43
23 9 0.10
24 11 0.12
25 2 0.02
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:102910 original size:14 final size:15
Alignment explanation
Indices: 102891--102926 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
102881 AATCCATACT
102891 AATAAATTATTT-AA
1 AATAAATTATTTAAA
102905 AATAAATTATTTAAA
1 AATAAATTATTTAAA
102920 AATAAAT
1 AATAAAT
102927 CAATCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATAAATTATTTAAA
Found at i:104390 original size:21 final size:21
Alignment explanation
Indices: 104364--104405 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
104354 TATCAGACTT
104364 TATTTCAAAA-TACAAAAATGA
1 TATTTCAAAATTA-AAAAATGA
104385 TATTTCAAAATTAAAAAATGA
1 TATTTCAAAATTAAAAAATGA
104406 AAATAGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (21 bp):
TATTTCAAAATTAAAAAATGA
Done.