Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007368.1 Hibiscus syriacus cultivar Beakdansim tig00019762_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: 423757
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 1 of 2
Found at i:3207 original size:11 final size:11
Alignment explanation
Indices: 3191--3217 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3181 TATTTTTTTC
3191 AAAAAAACAAA
1 AAAAAAACAAA
3202 AAAAAAACAAA
1 AAAAAAACAAA
3213 AAAAA
1 AAAAA
3218 GGCAAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:3249 original size:13 final size:11
Alignment explanation
Indices: 3198--3252 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 11
3188 TTCAAAAAAA
**
3198 CAAAAAAAAAA
1 CAAAAAAAAGG
3209 CAAAAAAAAGG
1 CAAAAAAAAGG
3220 CAAAGGAAAAAGG
1 CAAA--AAAAAGG
3233 CAAAAAAAAGAG
1 CAAAAAAAAG-G
3245 CCAAAAAA
1 -CAAAAAA
3253 GCCAAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
11 19 0.50
12 1 0.03
13 18 0.47
ACGTcount: A:0.75, C:0.11, G:0.15, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:8147 original size:11 final size:11
Alignment explanation
Indices: 8123--8166 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
8113 TTGGTGCTGG
8123 AAACAAGATAA
1 AAACAAGATAA
* *
8134 AAATAAGATTA
1 AAACAAGATAA
8145 AAACAAGATAA
1 AAACAAGATAA
8156 AGAA-AAGATAA
1 A-AACAAGATAA
8167 TGAATTGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 26 0.93
12 2 0.07
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:8151 original size:22 final size:22
Alignment explanation
Indices: 8123--8164 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
8113 TTGGTGCTGG
8123 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
8145 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
8165 AATGAATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:9856 original size:87 final size:86
Alignment explanation
Indices: 9704--9876 Score: 301
Period size: 87 Copynumber: 2.0 Consensus size: 86
9694 TTATAATATA
* *
9704 TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCCTGTTGTTTCCCGATCT
1 TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCATGTTGTTTCCCAATCT
9769 AGGAGAGACACCAAAATGCTAC
66 AGGAGAGACACC-AAATGCTAC
*
9791 TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCATGTTGTTTCTCAATCT
1 TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCATGTTGTTTCCCAATCT
*
9856 AGGAGAGACGCCAAATGCTAC
66 AGGAGAGACACCAAATGCTAC
9877 ACCTTGGATT
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 9 0.11
87 73 0.89
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (86 bp):
TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCATGTTGTTTCCCAATCT
AGGAGAGACACCAAATGCTAC
Found at i:10152 original size:22 final size:23
Alignment explanation
Indices: 10127--10178 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
10117 ATTTATAAGT
10127 TGGTGATAAAATAGGCGTGAT-A
1 TGGTGATAAAATAGGCGTGATAA
* *
10149 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAAAATAGGCGTGATAA
10172 TGGTGAT
1 TGGTGAT
10179 GGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
TGGTGATAAAATAGGCGTGATAA
Found at i:10160 original size:11 final size:11
Alignment explanation
Indices: 10144--10215 Score: 58
Period size: 11 Copynumber: 6.2 Consensus size: 11
10134 AAAATAGGCG
10144 TGATATGGTGA
1 TGATATGGTGA
*
10155 TGATATAGGCG-
1 TGATAT-GGTGA
10166 TGATAATGGTGA
1 TGAT-ATGGTGA
10178 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
10191 TGATATAGGCG-
1 TGATAT-GGTGA
10202 TGATAATGGTGA
1 TGAT-ATGGTGA
10214 TG
1 TG
10216 GACAGATTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
11 23 0.47
12 15 0.31
13 10 0.20
14 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:10169 original size:36 final size:38
Alignment explanation
Indices: 10129--10207 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 38
10119 TTATAAGTTG
10129 GTGATAAAATAGGCG-T-GA-TATGGTGATGATATAGGC
1 GTGATAAAAT-GGCGATGGACTATGGTGATGATATAGGC
*
10165 GTGAT--AATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAAAATGGCGATGGACTATGGTGATGATATAGGC
10201 GTGATAA
1 GTGATAA
10208 TGGTGATGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
33 3 0.08
34 4 0.11
35 2 0.05
36 28 0.76
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (38 bp):
GTGATAAAATGGCGATGGACTATGGTGATGATATAGGC
Found at i:10208 original size:36 final size:36
Alignment explanation
Indices: 10147--10218 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
10137 ATAGGCGTGA
10147 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
10183 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
10219 AGATTGTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.06, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:14651 original size:13 final size:12
Alignment explanation
Indices: 14632--14717 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
14622 AAATAGGCGT
14632 GATATGGTGATG
1 GATATGGTGATG
14644 GAATATGGTGAT-
1 G-ATATGGTGATG
*
14656 GATATAGGCG-T-
1 GATAT-GGTGATG
14667 GATAATGGTGATG
1 GAT-ATGGTGATG
14680 GACTATGGTGAT-
1 GA-TATGGTGATG
*
14692 GATATAGGCG-T-
1 GATAT-GGTGATG
14703 GATAATGGTGATG
1 GAT-ATGGTGATG
14716 GA
1 GA
14718 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:14687 original size:36 final size:36
Alignment explanation
Indices: 14614--14718 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
14604 ATTTATAAGT
* * *
14614 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
14649 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
14685 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
14719 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:16114 original size:15 final size:14
Alignment explanation
Indices: 16052--16115 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 14
16042 GAAAAAATTA
16052 AAGAAAGAAATGATT
1 AAGAAAGAAATGA-T
**
16067 AAGATGGAAAT-AT
1 AAGAAAGAAATGAT
16080 AA-ATAAGAAATGGAAT
1 AAGA-AAGAAAT-G-AT
16096 AAGAAAGGAAATGAT
1 AAGAAA-GAAATGAT
16111 AAGAA
1 AAGAA
16116 TTGAAATCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
12 1 0.03
13 8 0.21
14 1 0.03
15 16 0.41
16 7 0.18
17 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (14 bp):
AAGAAAGAAATGAT
Found at i:20389 original size:14 final size:14
Alignment explanation
Indices: 20370--20402 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20360 GTGCTTCCAA
20370 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
20384 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
20398 CTTTT
1 CTTTT
20403 TGAGTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:21357 original size:20 final size:21
Alignment explanation
Indices: 21317--21357 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
21307 TGCTTGAATG
21317 ATGCACATGGCAGTCTACTTGA
1 ATGCACATGG-AGTCTACTTGA
*
21339 ATGCACATGG-GTCTTCTTG
1 ATGCACATGGAGTCTACTTG
21358 CAAGGCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (21 bp):
ATGCACATGGAGTCTACTTGA
Found at i:28585 original size:23 final size:22
Alignment explanation
Indices: 28539--28585 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
28529 TGATGTAGGA
*
28539 GTCTTTTTCTTTTCTTTTTGTT
1 GTCTTTTTCTTTTCTCTTTGTT
28561 GTCTTCTTTCTTTTTCTCTTT-TT
1 GTCTT-TTTC-TTTTCTCTTTGTT
28584 GT
1 GT
28586 TGCTTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 8 0.36
24 9 0.41
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (22 bp):
GTCTTTTTCTTTTCTCTTTGTT
Found at i:35300 original size:11 final size:11
Alignment explanation
Indices: 35286--35341 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
35276 CTTTTTTGAA
35286 TTCTTTTTCTT
1 TTCTTTTTCTT
35297 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
35310 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
35323 TGTCTTTTTC-T
1 T-TCTTTTTCTT
35334 TTCTTTTT
1 TTCTTTTT
35342 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:35310 original size:19 final size:18
Alignment explanation
Indices: 35286--35341 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
35276 CTTTTTTGAA
35286 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
35304 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
35323 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
35341 T
1 T
35342 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:37494 original size:9 final size:9
Alignment explanation
Indices: 37472--37511 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
37462 TTGATGGTCT
*
37472 TGTTGGATGA
1 TGTT-GATGG
37482 TGTTGATGG
1 TGTTGATGG
37491 TGTTGATGG
1 TGTTGATGG
37500 TGTTGATGG
1 TGTTGATGG
37509 TGT
1 TGT
37512 AATGGAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 25 0.86
10 4 0.14
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.45
Consensus pattern (9 bp):
TGTTGATGG
Found at i:38278 original size:16 final size:16
Alignment explanation
Indices: 38254--38286 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38244 TGTTTGAGCT
*
38254 ACTTTGGACATATTTG
1 ACTTAGGACATATTTG
38270 ACTTAGGACATATTTG
1 ACTTAGGACATATTTG
38286 A
1 A
38287 AGCGTCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (16 bp):
ACTTAGGACATATTTG
Found at i:42572 original size:6 final size:6
Alignment explanation
Indices: 42561--42621 Score: 50
Period size: 6 Copynumber: 9.2 Consensus size: 6
42551 TCTTTTTGAA
* *
42561 TTTCTT TTTCTTT TCTTCTT TTTCTT TTTCTGAAT TTTCTT CTTCTT TTTGTCT
1 TTTCTT TTTC-TT T-TTCTT TTTCTT TTTCT---T TTTCTT TTTCTT TTTCT-T
42615 TTTCTT T
1 TTTCTT T
42622 CTTTTTGTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
6 25 0.56
7 11 0.24
8 3 0.07
9 6 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:42607 original size:35 final size:32
Alignment explanation
Indices: 42549--42621 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 32
42539 CTTGGCTTGC
*
42549 TTTC-TTTTTGAATTTCTTTTTCTTTTCT-TCTT
1 TTTCTTTTTTGAATTTCTTCTTCTTTT-TGTC-T
42581 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTGTCT
42615 TTTCTTT
1 TTTCTTT
42622 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
32 4 0.11
33 4 0.11
34 13 0.36
35 15 0.42
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:47735 original size:22 final size:23
Alignment explanation
Indices: 47710--47752 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
47700 CTTTTTGAAA
*
47710 TTCT-ATTTTTTTTTCTTTTTTT
1 TTCTGATTTCTTTTTCTTTTTTT
47732 TTCTGATTTCTTTTTCTTTTT
1 TTCTGATTTCTTTTTCTTTTT
47753 GTCTTTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (23 bp):
TTCTGATTTCTTTTTCTTTTTTT
Found at i:47742 original size:29 final size:30
Alignment explanation
Indices: 47688--47758 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
47678 TTTTCCTTGG
47688 CTTTTTTCTTTTCTTTTTGAAATTCTATTT
1 CTTTTTTCTTTTCTTTTTGAAATTCTATTT
* * *
47718 -TTTTTTCTTTTTTTTTCTG-ATTTCTTTTT
1 CTTTTTTCTTTTCTTTT-TGAAATTCTATTT
47747 CTTTTTGTCTTT
1 CTTTTT-TCTTT
47759 GAACTCATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 23 0.66
30 7 0.20
31 5 0.14
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (30 bp):
CTTTTTTCTTTTCTTTTTGAAATTCTATTT
Found at i:57706 original size:11 final size:11
Alignment explanation
Indices: 57682--57726 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
57672 TTAGTGCTGG
57682 AAACAAGATAA
1 AAACAAGATAA
* *
57693 AAATAAGATTA
1 AAACAAGATAA
57704 AAACAAGATAA
1 AAACAAGATAA
57715 ACAA-AAGATAA
1 A-AACAAGATAA
57726 A
1 A
57727 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:57710 original size:22 final size:22
Alignment explanation
Indices: 57682--57723 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
57672 TTAGTGCTGG
57682 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAACAA-AAGATTA
57704 AAACAAGATAAACAAAAGAT
1 AAACAAGATAAACAAAAGAT
57724 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAACAAAAGATTA
Found at i:64490 original size:2 final size:2
Alignment explanation
Indices: 64479--64518 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
64469 TAACTATAGG
64479 TA TA -A TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
64519 GAAAATAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66867 original size:133 final size:133
Alignment explanation
Indices: 66629--66895 Score: 516
Period size: 133 Copynumber: 2.0 Consensus size: 133
66619 TACATATCAT
*
66629 TTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGTTATATGATATTC
1 TTCTTAGGATATTATTATCACATGTTTCCATTTATCATTTATGAATACCATGTTATATGATATTC
*
66694 ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
66 ATGCATACAACATAGACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
66759 TTA
131 TTA
66762 TTCTTAGGATATTATTATCACATGTTTCCATTTATCATTTATGAATACCATGTTATATGATATTC
1 TTCTTAGGATATTATTATCACATGTTTCCATTTATCATTTATGAATACCATGTTATATGATATTC
66827 ATGCATACAACATAGACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
66 ATGCATACAACATAGACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
66892 TTA
131 TTA
66895 T
1 T
66896 AATCATATTA
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 132 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (133 bp):
TTCTTAGGATATTATTATCACATGTTTCCATTTATCATTTATGAATACCATGTTATATGATATTC
ATGCATACAACATAGACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
TTA
Found at i:69330 original size:19 final size:19
Alignment explanation
Indices: 69264--69331 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
69254 CCTTGGCTTG
*
69264 CTTTCTCTTTG-ATTTTTT
1 CTTTCTTTTTGCATTTTTT
*
69282 -TTTCTTTTCTGAATTTTTT
1 CTTTCTTTT-TGCATTTTTT
*
69301 C-TTCTTTTTGCCTTTTTT
1 CTTTCTTTTTGCATTTTTT
69319 CTTTCTTTTTGCA
1 CTTTCTTTTTGCA
69332 CTCCAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
17 7 0.17
18 11 0.26
19 24 0.57
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.71
Consensus pattern (19 bp):
CTTTCTTTTTGCATTTTTT
Found at i:73889 original size:18 final size:19
Alignment explanation
Indices: 73866--73901 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
73856 GCTTTCTCTT
73866 TGAA-TTTTTTTTCTTTTC
1 TGAATTTTTTTTTCTTTTC
73884 TGAATTTTTTTTTCTTTT
1 TGAATTTTTTTTTCTTTT
73902 TGTCTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.11, C:0.08, G:0.06, T:0.75
Consensus pattern (19 bp):
TGAATTTTTTTTTCTTTTC
Found at i:85562 original size:12 final size:12
Alignment explanation
Indices: 85547--85577 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
85537 AAATTTTGGC
*
85547 TTTTTTGGCTTT
1 TTTTTTGCCTTT
85559 TTTTTTGCCTTT
1 TTTTTTGCCTTT
85571 TTTTTTG
1 TTTTTTG
85578 AAAAAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.13, T:0.77
Consensus pattern (12 bp):
TTTTTTGCCTTT
Found at i:90578 original size:24 final size:24
Alignment explanation
Indices: 90551--90596 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
90541 TACTATTTGA
*
90551 ATTCTGTTATAATACTTGACCTGG
1 ATTCTGATATAATACTTGACCTGG
*
90575 ATTCTGATATGATACTTGACCT
1 ATTCTGATATAATACTTGACCT
90597 AAATTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (24 bp):
ATTCTGATATAATACTTGACCTGG
Found at i:93681 original size:24 final size:24
Alignment explanation
Indices: 93640--93717 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
93630 ATTTACTATT
* * *
93640 TGAATTATGTTATAATACTTGACC
1 TGAATTCTGATATGATACTTGACC
93664 TGAATTCTGATATGATACTTGACC
1 TGAATTCTGATATGATACTTGACC
*
93688 TGGATTCTGATATGATACTTGACC
1 TGAATTCTGATATGATACTTGACC
93712 TGAATT
1 TGAATT
93718 ATGTTTTGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACC
Found at i:94475 original size:159 final size:158
Alignment explanation
Indices: 94183--94500 Score: 609
Period size: 159 Copynumber: 2.0 Consensus size: 158
94173 GCACGTTCTT
*
94183 TAACATCATTTGGTAGTTATGTATTTCTGAGCTTTTGAAGCTCACTACTCACCATTCCAGGTTAA
1 TAACATCATCTGGTAGTTATGTATTTCTGAGCTTTTGAAGCTCACTACTCACCATTCCAGGTTAA
*
94248 AATAATTTTACCAGTGCAGCTATTGGCTTCAGTAAGGTAGTTATGTATTTCTGTTTTATTTTTGC
66 AATAATTTTACCAGTGCAGCTATTGGCTTCAGTAAGGTAGTTATGTATTTCTGTTTTATTTTTAC
94313 ATACTGATAAATCATTTTATAAGTTACA
131 ATACTGATAAATCATTTTATAAGTTACA
94341 TAACATCATCTGGTAGTTATGTATTTCTGAGCTTTCTGAAGCTCACTACTCACCATTCCAGGTTA
1 TAACATCATCTGGTAGTTATGTATTTCTGAGCTTT-TGAAGCTCACTACTCACCATTCCAGGTTA
94406 AAATAATTTTACCAGTGCAGCTATTGGCTTCAGTAAGGTAGTTATGTATTTCTGTTTTATTTTTA
65 AAATAATTTTACCAGTGCAGCTATTGGCTTCAGTAAGGTAGTTATGTATTTCTGTTTTATTTTTA
94471 CATACTGATAAATCATTTTATAAGTTACA
130 CATACTGATAAATCATTTTATAAGTTACA
94500 T
1 T
94501 TTTTTAATAA
Statistics
Matches: 157, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
158 34 0.22
159 123 0.78
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (158 bp):
TAACATCATCTGGTAGTTATGTATTTCTGAGCTTTTGAAGCTCACTACTCACCATTCCAGGTTAA
AATAATTTTACCAGTGCAGCTATTGGCTTCAGTAAGGTAGTTATGTATTTCTGTTTTATTTTTAC
ATACTGATAAATCATTTTATAAGTTACA
Found at i:98274 original size:24 final size:24
Alignment explanation
Indices: 98242--98300 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
98232 TATGTTGTAG
*
98242 TACTTGACCTGGATTCTGATCTGA
1 TACTTGACCTGGATTCTGATATGA
98266 TACTTGACCTGGATTCTGATATGA
1 TACTTGACCTGGATTCTGATATGA
*
98290 TACATGACCTG
1 TACTTGACCTG
98301 AATTATGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (24 bp):
TACTTGACCTGGATTCTGATATGA
Found at i:98314 original size:24 final size:24
Alignment explanation
Indices: 98242--98307 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
98232 TATGTTGTAG
* * *
98242 TACTTGACCTGGATTCTGATCTGA
1 TACTTGACCTGAATTATGATATGA
* *
98266 TACTTGACCTGGATTCTGATATGA
1 TACTTGACCTGAATTATGATATGA
*
98290 TACATGACCTGAATTATG
1 TACTTGACCTGAATTATG
98308 TTTTGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (24 bp):
TACTTGACCTGAATTATGATATGA
Found at i:102845 original size:24 final size:24
Alignment explanation
Indices: 102759--102845 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
102749 ATTTATAATT
*
102759 TGAATTATG-TTTAATACTTGACC
1 TGAATTATGATTTGATACTTGACC
*
102782 T-ATATTATGATCTGATACTTGACC
1 TGA-ATTATGATTTGATACTTGACC
* * * *
102806 TGGATTCTGATATGATACTTGATC
1 TGAATTATGATTTGATACTTGACC
*
102830 TGAATTATGTTTTGAT
1 TGAATTATGATTTGAT
102846 TTTTGATATA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.02
23 7 0.14
24 43 0.84
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (24 bp):
TGAATTATGATTTGATACTTGACC
Found at i:104441 original size:22 final size:22
Alignment explanation
Indices: 104411--104462 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
104401 AACCTTACTC
104411 TTTC-TAAAAGTTTGTAAAATA
1 TTTCTTAAAAGTTTGTAAAATA
*
104432 TTTCTTAAAATTTTGTAAAATA
1 TTTCTTAAAAGTTTGTAAAATA
104454 TTTCTTAAA
1 TTTCTTAAA
104463 TTTTACACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (22 bp):
TTTCTTAAAAGTTTGTAAAATA
Found at i:104442 original size:12 final size:12
Alignment explanation
Indices: 104425--104462 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
104415 TAAAAGTTTG
104425 TAAAATATTTCT
1 TAAAATATTTCT
*
104437 TAAAAT-TTT-G
1 TAAAATATTTCT
104447 TAAAATATTTCT
1 TAAAATATTTCT
104459 TAAA
1 TAAA
104463 TTTTACACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.27
11 6 0.27
12 10 0.45
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (12 bp):
TAAAATATTTCT
Found at i:108544 original size:24 final size:24
Alignment explanation
Indices: 108517--108587 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
108507 AAACATAATT
108517 CAGGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* * * *
108541 CAGGTCATGTATTAGATCAGAATT
1 CAGGTCAAGTATCATATCAGAATC
* *
108565 CAGG-GAAGGTATCATAACAGAAT
1 CAGGTCAA-GTATCATATCAGAAT
108588 TCAAATCGGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:137921 original size:82 final size:80
Alignment explanation
Indices: 137785--138128 Score: 485
Period size: 82 Copynumber: 4.2 Consensus size: 80
137775 CCTTACAGAC
* * ** *
137785 CTAAGGATATC-TTGGGTAGGGCCCAAGACATATCCTTAGGTTGGTTTCATTTGCTGTGTGCATA
1 CTAAGGATACCTTTGGGTA-GACCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCATA
137849 AGGTAACCCTACGGAT
65 AGGTAACCCTACGGAT
* * *
137865 CTAAGCATACCTTTGGGTAGACCCAAGGTATATATCCTTAGGTTGGTTTCCGTTGCTGTGTGTAT
1 CTAAGGATACCTTTGGGTAGACCCAAGG--TATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCAT
137930 AAGGTAACCCTACGGAT
64 AAGGTAACCCTACGGAT
* *
137947 CTAAGGATACCTTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTATGTGCGTAA
1 CTAAGGATACCTTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCATAA
*
138012 GGTAACACTACGGAT
66 GGTAACCCTACGGAT
* * * *
138027 CTAAGGATACCCTTGGGTATACCCAAGGTATATCCTTAGGTTGGTTTACTTTTTGCTGTGTGCTT
1 CTAAGGATACCTTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTT-C-CTTTGCTGTGTGCAT
138092 AAGGTAACCCTACGGAT
64 AAGGTAACCCTACGGAT
138109 CTAAGGATATCC-TTGGGTAG
1 CTAAGGATA-CCTTTGGGTAG
138129 GCCATAAGCC
Statistics
Matches: 237, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
80 108 0.46
81 8 0.03
82 119 0.50
83 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (80 bp):
CTAAGGATACCTTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCATAA
GGTAACCCTACGGAT
Found at i:138053 original size:162 final size:161
Alignment explanation
Indices: 137785--138128 Score: 496
Period size: 162 Copynumber: 2.1 Consensus size: 161
137775 CCTTACAGAC
* * *
137785 CTAAGGATATCTTGGGTAGGGCCCAAGACATATCCTTAGGTTGGTTTCATTTGCTGTGTGCATAA
1 CTAAGGATACCTTGGGTA-GACCCAAGACATATCCTTAGGTTGGTTTCATTTGCTATGTGCATAA
* *
137850 GGTAACCCTACGGATCTAAGCATACCTTTGGGTAGACCCAAGGTATATATCCTTAGGTTGGTTT-
65 GGTAACACTACGGATCTAAGCATACCCTTGGGTAGACCCAAGG--TATATCCTTAGGTTGGTTTA
137914 C-CGTTGCTGTGTG-TATAAGGTAACCCTACGGAT
128 CTCGTTGCTGTGTGCT-TAAGGTAACCCTACGGAT
** * *
137947 CTAAGGATACCTTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTATGTGCGTAA
1 CTAAGGATACC-TTGGGTAGACCCAAGACATATCCTTAGGTTGGTTTCATTTGCTATGTGCATAA
* *
138012 GGTAACACTACGGATCTAAGGATACCCTTGGGTATACCCAAGGTATATCCTTAGGTTGGTTTACT
65 GGTAACACTACGGATCTAAGCATACCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTTACT
**
138077 TTTTGCTGTGTGCTTAAGGTAACCCTACGGAT
130 CGTTGCTGTGTGCTTAAGGTAACCCTACGGAT
138109 CTAAGGATATCCTTGGGTAG
1 CTAAGGATA-CCTTGGGTAG
138129 GCCATAAGCC
Statistics
Matches: 164, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
160 19 0.12
161 1 0.01
162 134 0.82
163 10 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (161 bp):
CTAAGGATACCTTGGGTAGACCCAAGACATATCCTTAGGTTGGTTTCATTTGCTATGTGCATAAG
GTAACACTACGGATCTAAGCATACCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTTACTC
GTTGCTGTGTGCTTAAGGTAACCCTACGGAT
Found at i:139636 original size:11 final size:11
Alignment explanation
Indices: 139620--139657 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
139610 TTTATCATCG
*
139620 TCCCTCCTTTT
1 TCCCTCCTCTT
139631 TCCCTCCTCTT
1 TCCCTCCTCTT
*
139642 TCTCTCC-CTT
1 TCCCTCCTCTT
139652 TCCCTC
1 TCCCTC
139658 AAACCAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
TCCCTCCTCTT
Found at i:141321 original size:31 final size:31
Alignment explanation
Indices: 141284--141343 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
141274 GGTCAACGTC
141284 GGTCAACGGGTCAGGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCAGGTCAACGGGTCGGGTCA
*
141315 GGTCAACGGGTCGGGTCAACGGGTCGGGT
1 GGTCAACGGGTCAGGTCAACGGGTCGGGT
141344 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCAGGTCAACGGGTCGGGTCA
Found at i:141340 original size:13 final size:13
Alignment explanation
Indices: 141284--141343 Score: 66
Period size: 13 Copynumber: 4.2 Consensus size: 13
141274 GGTCAACGTC
*
141284 GGTCAACGGGTCA
1 GGTCAACGGGTCG
141297 GGTCAACGGGTCGGG
1 GGTCAACGGGTC--G
141312 TCAGGTCAACGGGTCG
1 ---GGTCAACGGGTCG
141328 GGTCAACGGGTCG
1 GGTCAACGGGTCG
141341 GGT
1 GGT
141344 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
13 28 0.68
16 1 0.02
18 12 0.29
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:141343 original size:18 final size:18
Alignment explanation
Indices: 141290--141332 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
141280 CGTCGGTCAA
141290 CGGGTCAGGTCAACGGGT
1 CGGGTCAGGTCAACGGGT
141308 CGGGTCAGGTCAACGGGT
1 CGGGTCAGGTCAACGGGT
141326 CGGGTCA
1 CGGGTCA
141333 ACGGGTCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.23, G:0.44, T:0.16
Consensus pattern (18 bp):
CGGGTCAGGTCAACGGGT
Found at i:141393 original size:9 final size:10
Alignment explanation
Indices: 141348--141393 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
141338 TCGGGTTGTG
141348 ACCGGT-AAA
1 ACCGGTCAAA
141357 ACCGGTCAAA
1 ACCGGTCAAA
* *
141367 ACAGTTCTAAA
1 ACCGGTC-AAA
141378 ACCGGTC-AA
1 ACCGGTCAAA
141387 ACCGGTC
1 ACCGGTC
141394 GCTTTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 15 0.48
10 8 0.26
11 8 0.26
ACGTcount: A:0.37, C:0.28, G:0.20, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:147187 original size:18 final size:18
Alignment explanation
Indices: 147164--147198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
147154 TTCCATCCGG
*
147164 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
147182 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
147199 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:148520 original size:13 final size:13
Alignment explanation
Indices: 148502--148544 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
148492 GGTAAACAGT
148502 GGTCAACGGGTCG
1 GGTCAACGGGTCG
148515 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
148528 GGTTAACGGGTCG
1 GGTCAACGGGTCG
148541 GGTC
1 GGTC
148545 GGGTTATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.14, C:0.21, G:0.47, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:156354 original size:7 final size:7
Alignment explanation
Indices: 156342--156385 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
156332 GTCAAAGGAA
156342 GTCAACG
1 GTCAACG
156349 GTCAACG
1 GTCAACG
*
156356 GTC-ACA
1 GTCAACG
156362 GTCAACG
1 GTCAACG
*
156369 ATCAACG
1 GTCAACG
156376 GTCAACG
1 GTCAACG
156383 GTC
1 GTC
156386 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:156366 original size:20 final size:20
Alignment explanation
Indices: 156341--156379 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
156331 GGTCAAAGGA
*
156341 AGTCAACGGTCAACGGTCAC
1 AGTCAACGATCAACGGTCAC
156361 AGTCAACGATCAACGGTCA
1 AGTCAACGATCAACGGTCA
156380 ACGGTCGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.15
Consensus pattern (20 bp):
AGTCAACGATCAACGGTCAC
Found at i:163614 original size:14 final size:14
Alignment explanation
Indices: 163579--163612 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
163569 CAACGGTCGG
*
163579 GTCGGGTCGGGTCA
1 GTCGGGTCGAGTCA
163593 GTCGGGTCGAGTCA
1 GTCGGGTCGAGTCA
163607 GATCGG
1 G-TCGG
163613 TCAAACCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.12, C:0.21, G:0.47, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGAGTCA
Found at i:163639 original size:10 final size:9
Alignment explanation
Indices: 163610--163681 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
163600 CGAGTCAGAT
163610 CGGTCAAAC
1 CGGTCAAAC
**
163619 CGGTTTGAAC
1 CGG-TCAAAC
163629 CGGTCGAAAC
1 CGGTC-AAAC
*
163639 CGGTTAAAC
1 CGGTCAAAC
*
163648 CGATCAGAAC
1 CGGTCA-AAC
*
163658 CGGTTGAAAAC
1 CGG-T-CAAAC
163669 CGGTCAAAC
1 CGGTCAAAC
163678 CGGT
1 CGGT
163682 TTCCAGCCCT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
9 20 0.42
10 20 0.42
11 7 0.15
12 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:163648 original size:19 final size:18
Alignment explanation
Indices: 163610--163682 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 18
163600 CGAGTCAGAT
*
163610 CGGTCAAACCGGTTTGAAC
1 CGGTCAAACCGG-TTAAAC
163629 CGGTCGAAACCGGTTAAAC
1 CGGTC-AAACCGGTTAAAC
*
163648 CGATCAGAACCGGTTGAAAAC
1 CGGTCA-AACCGGTT--AAAC
163669 CGGTCAAACCGGTT
1 CGGTCAAACCGGTT
163683 TCCAGCCCTC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 1 0.02
19 22 0.47
20 15 0.32
21 9 0.19
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (18 bp):
CGGTCAAACCGGTTAAAC
Found at i:166408 original size:24 final size:24
Alignment explanation
Indices: 166398--166512 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
166388 CACAATTCAC
* * *
166398 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
166422 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
166446 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
166470 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
166494 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
166513 ATCAAATCGA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:166529 original size:72 final size:71
Alignment explanation
Indices: 166378--166529 Score: 182
Period size: 72 Copynumber: 2.1 Consensus size: 71
166368 GGATATATCA
* *
166378 AAAATCAAATCACAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
1 AAAATCAGATCACAATCCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
*
166443 CAAGTC
66 CAAATC
* * * * *
166449 AAGTATCAGATCAGAATCCATGTC-AGATATCATATCAGAATCCATGTCAAGTATCAGATCAGAA
1 AA-AATCAGATCACAATCCACGTCAAG-TATCATATCAAAATCCAGGTCAAGTATCAGATCAG-A
166513 AT-CAAATC
63 ATCCAAATC
166521 GAAAATCAG
1 -AAAATCAG
166530 GTAAAATATT
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
71 4 0.06
72 59 0.87
73 5 0.07
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (71 bp):
AAAATCAGATCACAATCCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
CAAATC
Found at i:172518 original size:46 final size:46
Alignment explanation
Indices: 172393--172640 Score: 394
Period size: 46 Copynumber: 5.4 Consensus size: 46
172383 TATAAAATCT
* * *
172393 CTTACCATTTA-TACCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTTCCATAAGCTCGTAAGCTTATTTTATCAATATA
*
172438 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT-ATTTCCATAAGCTCGTAAGCTTATTTTATCAATATA
* *
172485 CTTACCATTTATTTCCATAAGCTCGTAATCTTATTTTATCAATGTA
1 CTTACCATTTATTTCCATAAGCTCGTAAGCTTATTTTATCAATATA
172531 CTTACCATTTATTTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTTATTTCCATAAGCTCGTAAGCTTATTTTATCAATATA
*
172577 CTTACCATTTATTTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTTCCATAAGCTCGTAAGCTTATTTTATCAATATA
*
172623 CTTGCCA-TTA-TTCCATAA
1 CTTACCATTTATTTCCATAA
172641 CCATATACCA
Statistics
Matches: 191, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
44 8 0.04
45 13 0.07
46 129 0.68
47 41 0.21
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.41
Consensus pattern (46 bp):
CTTACCATTTATTTCCATAAGCTCGTAAGCTTATTTTATCAATATA
Found at i:174547 original size:21 final size:20
Alignment explanation
Indices: 174521--174561 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
174511 AAATAGTATT
174521 TTCAAACATTTTATAACATTC
1 TTCAAA-ATTTTATAACATTC
* *
174542 TTCAAATTTTTGTAACATTC
1 TTCAAAATTTTATAACATTC
174562 CAATTCGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.46
Consensus pattern (20 bp):
TTCAAAATTTTATAACATTC
Found at i:178759 original size:28 final size:28
Alignment explanation
Indices: 178719--178773 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
178709 CCATTGTTGG
*
178719 ACCTCCAATAAATTTTCTCATTTTCTTAT
1 ACCTCCAATAAATTTCCTCA-TTTCTTAT
178748 ACCT-CAATAAATTTCCTCATTTCTTA
1 ACCTCCAATAAATTTCCTCATTTCTTA
178774 AATTTTACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.28
28 14 0.56
29 4 0.16
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.45
Consensus pattern (28 bp):
ACCTCCAATAAATTTCCTCATTTCTTAT
Found at i:182910 original size:2 final size:2
Alignment explanation
Indices: 182903--182939 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
182893 CTTTTAATTG
182903 AT AT 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 AT AT A
182940 ATTTGAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:192538 original size:13 final size:13
Alignment explanation
Indices: 192520--192573 Score: 78
Period size: 13 Copynumber: 4.4 Consensus size: 13
192510 CGACCCGTTT
192520 ACCCGTTTACCCG
1 ACCCGTTTACCCG
192533 ACCCGTTTACCCG
1 ACCCGTTTACCCG
192546 ACCCG---ACCCG
1 ACCCGTTTACCCG
*
192556 ACCCGTTGACCCG
1 ACCCGTTTACCCG
192569 ACCCG
1 ACCCG
192574 ACTCGTTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.26
13 28 0.74
ACGTcount: A:0.17, C:0.50, G:0.19, T:0.15
Consensus pattern (13 bp):
ACCCGTTTACCCG
Found at i:192558 original size:23 final size:23
Alignment explanation
Indices: 192528--192575 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
192518 TTACCCGTTT
*
192528 ACCCGACCCGTTTACCCGACCCG
1 ACCCGACCCGTTGACCCGACCCG
192551 ACCCGACCCGTTGACCCGACCCG
1 ACCCGACCCGTTGACCCGACCCG
192574 AC
1 AC
192576 TCGTTGACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.52, G:0.19, T:0.10
Consensus pattern (23 bp):
ACCCGACCCGTTGACCCGACCCG
Found at i:192566 original size:18 final size:18
Alignment explanation
Indices: 192545--192584 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
192535 CCGTTTACCC
192545 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
192563 GACCCGACCCGACTCGTT
1 GACCCGACCCGACCCGTT
192581 GACC
1 GACC
192585 GTTGACCGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:192734 original size:16 final size:16
Alignment explanation
Indices: 192713--192745 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
192703 GACCTCCTTT
192713 GACCAGAACTTTGACC
1 GACCAGAACTTTGACC
192729 GACCAGAACTTTGACC
1 GACCAGAACTTTGACC
192745 G
1 G
192746 CTATATTAAA
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:0.30, C:0.30, G:0.21, T:0.18
Consensus pattern (16 bp):
GACCAGAACTTTGACC
Found at i:204295 original size:31 final size:31
Alignment explanation
Indices: 204259--204320 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
204249 TGAACCGGGT
* *
204259 TTGACCGGTCACGACCCGTTTACCCGACCCG
1 TTGACCGGACACGACCCGTTGACCCGACCCG
* *
204290 TTGACCTGACCCGACCCGTTGACCCGACCCG
1 TTGACCGGACACGACCCGTTGACCCGACCCG
204321 ACCCGTTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.18
Consensus pattern (31 bp):
TTGACCGGACACGACCCGTTGACCCGACCCG
Found at i:204303 original size:18 final size:18
Alignment explanation
Indices: 204280--204331 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
204270 CGACCCGTTT
*
204280 ACCCGACCCGTTGACCTG
1 ACCCGACCCGTTGACCCG
204298 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
204316 ACCCGACCCGTTGACC
1 ACCCGACCCGTTGACC
204332 GTTGATCGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:204331 original size:13 final size:13
Alignment explanation
Indices: 204296--204320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
204286 CCCGTTGACC
204296 TGACCCGACCCGT
1 TGACCCGACCCGT
204309 TGACCCGACCCG
1 TGACCCGACCCG
204321 ACCCGTTGAC
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:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:204400 original size:29 final size:29
Alignment explanation
Indices: 204343--204405 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
204333 TTGATCGGTA
* *** *
204343 CTATTCTGGGAATTAATTCGGTTTTGGTG
1 CTATTATGGGAATTAATTCGAAATGGGTG
204372 CTATTATGGGAATTAATTCGAAATGGGTG
1 CTATTATGGGAATTAATTCGAAATGGGTG
204401 CTATT
1 CTATT
204406 TTGGTAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (29 bp):
CTATTATGGGAATTAATTCGAAATGGGTG
Found at i:204491 original size:10 final size:12
Alignment explanation
Indices: 204467--204498 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
204457 TGTTGACCTC
204467 CTTTGACCAGAA
1 CTTTGACCAGAA
204479 CTTTGACC-G-A
1 CTTTGACCAGAA
204489 CTTTGACCAG
1 CTTTGACCAG
204499 CTATTAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.47
11 2 0.11
12 8 0.42
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (12 bp):
CTTTGACCAGAA
Found at i:207390 original size:13 final size:13
Alignment explanation
Indices: 207374--207423 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
207364 CCCGACCCGA
*
207374 CCCGTTTACCCAT
1 CCCGTTGACCCAT
207387 CCCGTTGACCCGA-
1 CCCGTTGACCC-AT
207400 CCCGTTGACCC-T
1 CCCGTTGACCCAT
207412 ACCCGTTGACCC
1 -CCCGTTGACCC
207424 GTTGACCGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 32 0.97
14 1 0.03
ACGTcount: A:0.14, C:0.48, G:0.16, T:0.22
Consensus pattern (13 bp):
CCCGTTGACCCAT
Found at i:207400 original size:26 final size:26
Alignment explanation
Indices: 207367--207424 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
207357 AACCCGACCC
*
207367 GACCCGACCCGTTTACCC-ATCCCGTT
1 GACCCGACCCGTTGACCCTA-CCCGTT
207393 GACCCGACCCGTTGACCCTACCCGTT
1 GACCCGACCCGTTGACCCTACCCGTT
207419 GACCCG
1 GACCCG
207425 TTGACCGGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.19
Consensus pattern (26 bp):
GACCCGACCCGTTGACCCTACCCGTT
Found at i:209930 original size:24 final size:24
Alignment explanation
Indices: 209903--210018 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
209893 TTCGATTTGA
209903 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
209927 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
* *
209951 ATTTTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
209975 ATTCTGATCTAATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
209999 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
210019 CTGATTTATG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:235590 original size:7 final size:7
Alignment explanation
Indices: 235578--235612 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
235568 TTTACTACTT
235578 CTTTATG
1 CTTTATG
235585 CTTTATG
1 CTTTATG
*
235592 ATTTATG
1 CTTTATG
*
235599 ATTTATG
1 CTTTATG
235606 CTTTATG
1 CTTTATG
235613 GGACATGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (7 bp):
CTTTATG
Found at i:236020 original size:21 final size:21
Alignment explanation
Indices: 235994--236047 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
235984 ACTACATATG
235994 TGCTTAAGAAATGCTAGATTT
1 TGCTTAAGAAATGCTAGATTT
* *
236015 TGCTTACGAAATTCTAGATTT
1 TGCTTAAGAAATGCTAGATTT
*
236036 TGCTTATGAAAT
1 TGCTTAAGAAAT
236048 ACGAATAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (21 bp):
TGCTTAAGAAATGCTAGATTT
Found at i:237829 original size:43 final size:42
Alignment explanation
Indices: 237763--237856 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 42
237753 GGGCCTTACT
* *
237763 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTATACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCT-GGAAACCTACACATTA
*
237806 TGGTTTGTTGGTGGGTGTATGGTTCTGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGAAACCTACACATTA
237848 TGGTGTGTT
1 TGGTGTGTT
237857 CGGTTGGAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 22 0.47
43 25 0.53
ACGTcount: A:0.16, C:0.10, G:0.35, T:0.39
Consensus pattern (42 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGAAACCTACACATTA
Found at i:240989 original size:21 final size:19
Alignment explanation
Indices: 240965--241007 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
240955 AACCTTACTC
240965 TTTCTAAAATCTTGTAAAATA
1 TTTCTAAAAT-TT-TAAAATA
* *
240986 TTTCTTAAATTTTACAATA
1 TTTCTAAAATTTTAAAATA
241005 TTT
1 TTT
241008 TCAAAATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTCTAAAATTTTAAAATA
Found at i:242842 original size:21 final size:19
Alignment explanation
Indices: 242818--242860 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
242808 AACCTTACTC
242818 TTTCTAAAATCTTGTAAAATA
1 TTTCTAAAAT-TT-TAAAATA
* *
242839 TTTCTTAAATTTTACAATA
1 TTTCTAAAATTTTAAAATA
242858 TTT
1 TTT
242861 TCAAAATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTCTAAAATTTTAAAATA
Found at i:244692 original size:21 final size:19
Alignment explanation
Indices: 244668--244710 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
244658 AACCTTACTC
244668 TTTCTAAAATCTTGTAAAATA
1 TTTCTAAAAT-TT-TAAAATA
* *
244689 TTTCTTAAATTTTACAATA
1 TTTCTAAAATTTTAAAATA
244708 TTT
1 TTT
244711 TCAAAATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTCTAAAATTTTAAAATA
Found at i:246167 original size:21 final size:21
Alignment explanation
Indices: 246143--246196 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
246133 ACTACAGATG
*
246143 TGCTTAAGAAATGCTAGATTT
1 TGCTTACGAAATGCTAGATTT
246164 TGCTTACGAAATGCTAGATTT
1 TGCTTACGAAATGCTAGATTT
246185 TGCTTACGAAAT
1 TGCTTACGAAAT
246197 ACGAATAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (21 bp):
TGCTTACGAAATGCTAGATTT
Found at i:247860 original size:20 final size:19
Alignment explanation
Indices: 247826--247872 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
247816 GAATATTTTA
247826 TCTGATTTTCAATTTGAAT
1 TCTGATTTTCAATTTGAAT
*
247845 TCTGATATTTCGATTTGAAT
1 TCTGAT-TTTCAATTTGAAT
247865 TCTGATTT
1 TCTGATTT
247873 GATACTTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (19 bp):
TCTGATTTTCAATTTGAAT
Found at i:247891 original size:24 final size:24
Alignment explanation
Indices: 247863--247973 Score: 152
Period size: 24 Copynumber: 4.6 Consensus size: 24
247853 TTCGATTTGA
*
247863 ATTCTGATTTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
247887 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
247911 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
247935 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
247959 ATTTTGATATGATAC
1 ATTCTGATATGATAC
247974 CTAACATGAA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:247950 original size:72 final size:73
Alignment explanation
Indices: 247845--247981 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 73
247835 CAATTTGAAT
* * * * * *
247845 TCTGATATTTCGATTTGAATTCTGATTTGATACTTGACATGGATTCTGATCTGATATCTGACATG
1 TCTGATACTTCGACTTGAATTCTGATATGATACTTGACATGGATTCTGATATGATACCTAACATG
247910 GATTCTGA
66 GATTCTGA
* * *
247918 TCTGATACTT-GACTTGGATTCTGATATGATACTTGACCTGGATTTTGATATGATACCTAACATG
1 TCTGATACTTCGACTTGAATTCTGATATGATACTTGACATGGATTCTGATATGATACCTAACATG
247982 AATTATGTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
72 46 0.84
73 9 0.16
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (73 bp):
TCTGATACTTCGACTTGAATTCTGATATGATACTTGACATGGATTCTGATATGATACCTAACATG
GATTCTGA
Found at i:248165 original size:43 final size:43
Alignment explanation
Indices: 248099--248191 Score: 150
Period size: 43 Copynumber: 2.2 Consensus size: 43
248089 GCCTTACTTG
* * *
248099 GTGTATTGGTGGGTGTATGGTTCTGGGGAACCTATACATTATA
1 GTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTATA
*
248142 GTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTATG
1 GTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTATA
248185 GTGTGTT
1 GTGTGTT
248192 CGGTTGGAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.18, C:0.10, G:0.34, T:0.38
Consensus pattern (43 bp):
GTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTATA
Found at i:256963 original size:20 final size:19
Alignment explanation
Indices: 256927--256970 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
256917 GAACGCTGGA
*
256927 AACCGGTTTTGACCGGTTT
1 AACCGATTTTGACCGGTTT
256946 AACCGATTTTGAACCGGTTT
1 AACCGATTTTG-ACCGGTTT
*
256966 GACCG
1 AACCG
256971 GTCACGACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (19 bp):
AACCGATTTTGACCGGTTT
Found at i:257004 original size:16 final size:18
Alignment explanation
Indices: 256975--257026 Score: 72
Period size: 16 Copynumber: 3.0 Consensus size: 18
256965 TGACCGGTCA
*
256975 CGACCCGTTTACCCGACC
1 CGACCAGTTTACCCGACC
256993 CGA-CAG-TTACCCGACC
1 CGACCAGTTTACCCGACC
*
257009 CGACCCGTTTACCCGACC
1 CGACCAGTTTACCCGACC
257027 ATTGACCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 13 0.43
17 4 0.13
18 13 0.43
ACGTcount: A:0.19, C:0.48, G:0.17, T:0.15
Consensus pattern (18 bp):
CGACCAGTTTACCCGACC
Found at i:257113 original size:29 final size:28
Alignment explanation
Indices: 257051--257173 Score: 106
Period size: 29 Copynumber: 4.4 Consensus size: 28
257041 GACCGTTGAC
***
257051 TGGTGCTATTCTGGGAATTAATTCAGTTT
1 TGGTGCTATTCTGGGAATTAATTC-GAAA
257080 TGGTGCTATTCTGGGAATTAATTCGAAA
1 TGGTGCTATTCTGGGAATTAATTCGAAA
* * * *
257108 TGGGTGCTATTTTAGTAATT-TTTCGAAA
1 T-GGTGCTATTCTGGGAATTAATTCGAAA
** * *
257136 -AATGATATTTTGGGAATTAATTCGAAAA
1 TGGTGCTATTCTGGGAATTAATTCG-AAA
257164 TGGTGCTATT
1 TGGTGCTATT
257174 TGTGTAAAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
26 13 0.18
27 4 0.05
28 12 0.16
29 45 0.61
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (28 bp):
TGGTGCTATTCTGGGAATTAATTCGAAA
Found at i:264231 original size:18 final size:17
Alignment explanation
Indices: 264208--264258 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
264198 CGGTCACGAC
264208 CCGTTTACCCGACCCGA
1 CCGTTTACCCGACCCGA
264225 CCAGTTTACCCGACCCGA
1 CC-GTTTACCCGACCCGA
*
264243 CCGTTGACCCGACCCG
1 CCGTTTACCCGACCCG
264259 TTGATCGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (17 bp):
CCGTTTACCCGACCCGA
Found at i:264333 original size:29 final size:29
Alignment explanation
Indices: 264272--264338 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
264262 ATCGTTGACT
*** *
264272 GGTGCTATTCTGGGAATTAATCCGGTTTT
1 GGTGCTATTCTGGGAATTAATCCGAAATG
*
264301 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATCCGAAATG
264330 GGTGCTATT
1 GGTGCTATT
264339 TTAGTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATCCGAAATG
Found at i:267953 original size:24 final size:24
Alignment explanation
Indices: 267926--267997 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
267916 GTAAACGGAT
*
267926 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
*
267950 ATATCAGATAA-CAGAACAGAATCC
1 ATATCAGA-AATCAGAACAGAATTC
267974 ATATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
267997 A
1 A
267998 GGTAACGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.05
23 13 0.30
24 26 0.60
25 2 0.05
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:268012 original size:47 final size:48
Alignment explanation
Indices: 267926--268018 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 48
267916 GTAAACGGAT
*
267926 ATATCAGAAATCAAAACAGAATTCATATCAGATAACAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTCATAACAGATAACAGAACAGAATCC
* *
267974 ATATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATATCAGAAATCAAAACAGAATTCA--TAACAGATAACAGAACAGAAT
268019 TCAATTCGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
47 29 0.73
48 8 0.20
49 3 0.08
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.19
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCATAACAGATAACAGAACAGAATCC
Found at i:269259 original size:24 final size:24
Alignment explanation
Indices: 269221--269290 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
269211 CAAAACAGAG
* *
269221 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
269245 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
269269 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
269291 CTATTTATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:270031 original size:29 final size:28
Alignment explanation
Indices: 270000--270142 Score: 103
Period size: 29 Copynumber: 5.0 Consensus size: 28
269990 ATAGAACCCT
*
270000 TTTTTAAATAATTACCAAAATAGCACCA
1 TTTTGAAATAATTACCAAAATAGCACCA
*
270028 TTTTCAAATTAATT-CTCAAAATAGCACCAA
1 TTTTGAAA-TAATTAC-CAAAATAGCACC-A
* * * * * *
270058 TTTCGAATTAATTCCCAGAATATCA-CT
1 TTTTGAAATAATTACCAAAATAGCACCA
*
270085 TTTTCGATA-AATTACCAAAATAGCACCCCA
1 TTTT-GAAATAATTACCAAAATAGCA--CCA
* * *
270115 TTTTGAATTAATTTCCAGAATAGCACCA
1 TTTTGAAATAATTACCAAAATAGCACCA
270143 AAACTGAATT
Statistics
Matches: 88, Mismatches: 18, Indels: 18
0.71 0.15 0.15
Matches are distributed among these distances:
27 16 0.18
28 14 0.16
29 32 0.36
30 26 0.30
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (28 bp):
TTTTGAAATAATTACCAAAATAGCACCA
Found at i:270152 original size:86 final size:85
Alignment explanation
Indices: 270009--270170 Score: 204
Period size: 86 Copynumber: 1.9 Consensus size: 85
269999 TTTTTTAAAT
**
270009 AATTACCAAAATAGCACCATTTTCAAATTAATTCTCAAAATAGCACCAATTTCGAATTAATTCCC
1 AATTACCAAAATAGCACCATTTTCAAATTAATTCTCAAAATAGCACCAAACTCGAATTAATTCCC
* *
270074 AGAATATCACTTTTTCGATA
66 AAAATAGCACTTTTTCGATA
* * *
270094 AATTACCAAAATAGCACCCCATTTT-GAATTAATT-TCCAGAATAGCACCAAAACT-GAATTGAT
1 AATTACCAAAATAGCA--CCATTTTCAAATTAATTCT-CAAAATAGCACC-AAACTCGAATTAAT
270156 TCCCAAAATAGCACT
62 TCCCAAAATAGCACT
270171 GGTCAACGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
85 17 0.26
86 39 0.59
87 10 0.15
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (85 bp):
AATTACCAAAATAGCACCATTTTCAAATTAATTCTCAAAATAGCACCAAACTCGAATTAATTCCC
AAAATAGCACTTTTTCGATA
Found at i:270203 original size:13 final size:13
Alignment explanation
Indices: 270178--270214 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
270168 ACTGGTCAAC
270178 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
270190 GGTCAACGGGTCG
1 GGTCAACGGGTCG
270203 GGTCAACGGGTC
1 GGTCAACGGGTC
270215 ATGACCGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:270232 original size:9 final size:10
Alignment explanation
Indices: 270218--270262 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
270208 ACGGGTCATG
270218 ACCGGTC-AA
1 ACCGGTCAAA
270227 ACCGGTCAAA
1 ACCGGTCAAA
270237 ACCGGTTCAAA
1 ACCGG-TCAAA
*
270248 ACCGGT-TAA
1 ACCGGTCAAA
270257 ACCGGT
1 ACCGGT
270263 TTCCAGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 15 0.45
10 8 0.24
11 10 0.30
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:270248 original size:11 final size:11
Alignment explanation
Indices: 270225--270263 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
270215 ATGACCGGTC
270225 AAACCGG-TCA
1 AAACCGGTTCA
270235 AAACCGGTTCA
1 AAACCGGTTCA
270246 AAACCGGTT--
1 AAACCGGTTCA
270255 AAACCGGTT
1 AAACCGGTT
270264 TCCAGATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.32
10 7 0.25
11 12 0.43
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:276540 original size:24 final size:24
Alignment explanation
Indices: 276502--276571 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
276492 CAAAACAGAG
* *
276502 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
276526 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
276550 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
276572 CTATTTATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:277415 original size:29 final size:29
Alignment explanation
Indices: 277269--277449 Score: 129
Period size: 29 Copynumber: 6.3 Consensus size: 29
277259 CATTGTACAC
** * *
277269 AAATAGCA-CCATTTTTAAATAATTACCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
*
277297 AAATAGCA-CCATTTTC-ACATTAATTCTCA
1 AAATAGCACCCA-TTTCGA-ATTAATTCCCA
*
277326 AAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
* * ** ** *
277355 GAATATCA-CTTTTTC-AAAAAATTACCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
277382 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
* * * ***
277411 TAATAGAACCAAAACCGAATTAATTCCCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
*
277440 GAATAGCACC
1 AAATAGCACC
277450 GGTCAACGGT
Statistics
Matches: 119, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
27 15 0.13
28 22 0.18
29 79 0.66
30 3 0.03
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCATTTCGAATTAATTCCCA
Found at i:277432 original size:85 final size:84
Alignment explanation
Indices: 277280--277444 Score: 226
Period size: 85 Copynumber: 2.0 Consensus size: 84
277270 AATAGCACCA
* * * ***
277280 TTTTTAAATAATTACCAAAATAGCACCATTTTCACATTAATTCTCAAAATAGCACCAATTTCGAA
1 TTTTTAAAAAATTACCAAAATAGCACCATTTTCACATTAATTCCCAAAATAGAACCAAAACCGAA
277345 TTAATTCCCAGAATATCAC
66 TTAATTCCCAGAATATCAC
*
277364 TTTTTCAAAAAATTACCAAAATAGCACCCA-TTTCGA-ATTAATTCCCATAATAGAACCAAAACC
1 TTTTT-AAAAAATTACCAAAATAGCA-CCATTTTC-ACATTAATTCCCAAAATAGAACCAAAACC
277427 GAATTAATTCCCAGAATA
63 GAATTAATTCCCAGAATA
277445 GCACCGGTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
84 5 0.07
85 62 0.87
86 4 0.06
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.30
Consensus pattern (84 bp):
TTTTTAAAAAATTACCAAAATAGCACCATTTTCACATTAATTCCCAAAATAGAACCAAAACCGAA
TTAATTCCCAGAATATCAC
Found at i:277490 original size:13 final size:13
Alignment explanation
Indices: 277472--277504 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
277462 ACGGTCGGGT
277472 CGGGTCAGGTCAA
1 CGGGTCAGGTCAA
*
277485 CGGGTCGGGTCAA
1 CGGGTCAGGTCAA
277498 CGGGTCA
1 CGGGTCA
277505 TGACAGGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.15
Consensus pattern (13 bp):
CGGGTCAGGTCAA
Found at i:285345 original size:17 final size:18
Alignment explanation
Indices: 285314--285347 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
285304 TCAAAAGGAC
*
285314 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
285332 TGAA-TAAATAATAAGA
1 TGAAGTAAATAATAAGA
285348 CCGGATGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:290580 original size:250 final size:250
Alignment explanation
Indices: 290131--290630 Score: 919
Period size: 250 Copynumber: 2.0 Consensus size: 250
290121 GACTCTGAAT
290131 GAGAAAGTACTTTGAGGATTTGTACTTAACTCGATTAAGTACGAATTTGATTGTTAAGATCCTGA
1 GAGAAAGTACTTTGAGGATTTGTACTTAACTCGATTAAGTACGAATTTGATTGTTAAGATCCTGA
* *
290196 CTTAGTGCAGAAAATTCTTGATATTCCATTGGTAAAAATTTGAGATGGCACTTGACCCGAAAATA
66 CTTAGTGCAGAAAATTCTTGATATTCCATTGGTAAAAATCTGAGAAGGCACTTGACCCGAAAATA
290261 TCCGAGTTACGAGTAAATACCTGAAGAACAATTTATCGGGGTGCTCTTTTATCAGAATTATTCGA
131 TCCGAGTTACGAGTAAATACCTGAAGAACAATTTATCGGGGTGCTCTTTTATCAGAATTATTCGA
290326 AGGGACTAAAATAGATGATAAATTGGAATTAAATAATAAGACAAGATGAAAGAAA
196 AGGGACTAAAATAGATGATAAATTGGAATTAAATAATAAGACAAGATGAAAGAAA
290381 GAGAAAGTACTTTGAGGATTTGTACTTAACTCGATTAAGTACGAATTTGATTGTTAAGATCCTGA
1 GAGAAAGTACTTTGAGGATTTGTACTTAACTCGATTAAGTACGAATTTGATTGTTAAGATCCTGA
* *
290446 CTTAGTGCAGAAAATTCTTGATATTCCGTTGGTAAAAATCTGAGAAGGCACTTGGCCCGAAAATA
66 CTTAGTGCAGAAAATTCTTGATATTCCATTGGTAAAAATCTGAGAAGGCACTTGACCCGAAAATA
* * *
290511 TCCGAGTTACGAGTAAATACCTGAAGAATAATTTATCGGGGTGCTCTTTTATCAGAATTGTTTGA
131 TCCGAGTTACGAGTAAATACCTGAAGAACAATTTATCGGGGTGCTCTTTTATCAGAATTATTCGA
* *
290576 AGGGACTGAAATAGATGATAAATTGGAATTAAATAATAAGACAGGATGAAAGAAA
196 AGGGACTAAAATAGATGATAAATTGGAATTAAATAATAAGACAAGATGAAAGAAA
290631 ATGATTGAAA
Statistics
Matches: 241, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
250 241 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (250 bp):
GAGAAAGTACTTTGAGGATTTGTACTTAACTCGATTAAGTACGAATTTGATTGTTAAGATCCTGA
CTTAGTGCAGAAAATTCTTGATATTCCATTGGTAAAAATCTGAGAAGGCACTTGACCCGAAAATA
TCCGAGTTACGAGTAAATACCTGAAGAACAATTTATCGGGGTGCTCTTTTATCAGAATTATTCGA
AGGGACTAAAATAGATGATAAATTGGAATTAAATAATAAGACAAGATGAAAGAAA
Found at i:290845 original size:162 final size:163
Alignment explanation
Indices: 290572--290897 Score: 645
Period size: 162 Copynumber: 2.0 Consensus size: 163
290562 TCAGAATTGT
290572 TTGAAGGGACTGAAATAGATGATAAATTGGAATTAAATAATAAGACAGGATGAAAGAAAATGATT
1 TTGAAGGGACTGAAATAGATGATAAATTGGAATTAAATAATAAGACAGGATGAAAGAAAATGATT
290637 GAAATACATTGGATTTGTAGAATGACCAGAATACCCCTGTAATGGAAATAACCCAAGAATATCAC
66 GAAATACATTGGATTTGTAGAATGACCAGAATACCCCTGTAATGGAAATAACCCAAGAATATCAC
290702 CAAGCTAAGGAATGATTGGATATCCTCGAGCTC
131 CAAGCTAAGGAATGATTGGATATCCTCGAGCTC
290735 TTGAA-GGACTGAAATAGATGATAAATTGGAATTAAATAATAAGACAGGATGAAAGAAAATGATT
1 TTGAAGGGACTGAAATAGATGATAAATTGGAATTAAATAATAAGACAGGATGAAAGAAAATGATT
290799 GAAATACATTGGATTTGTAGAATGACCAGAATACCCCTGTAATGGAAATAACCCAAGAATATCAC
66 GAAATACATTGGATTTGTAGAATGACCAGAATACCCCTGTAATGGAAATAACCCAAGAATATCAC
290864 CAAGCTAAGGAATGATTGGATATCCTCGAGCTC
131 CAAGCTAAGGAATGATTGGATATCCTCGAGCTC
290897 T
1 T
290898 GAAATGAATG
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 158 0.97
163 5 0.03
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (163 bp):
TTGAAGGGACTGAAATAGATGATAAATTGGAATTAAATAATAAGACAGGATGAAAGAAAATGATT
GAAATACATTGGATTTGTAGAATGACCAGAATACCCCTGTAATGGAAATAACCCAAGAATATCAC
CAAGCTAAGGAATGATTGGATATCCTCGAGCTC
Found at i:291909 original size:24 final size:23
Alignment explanation
Indices: 291882--291957 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 23
291872 TACCTGATTT
*
291882 TTGATTTGATTTCTGATCTAATAC
1 TTGATTTGA-TTCTGATCTGATAC
**
291906 TTGACATGAATTCTGATCTGATAC
1 TTGATTTG-ATTCTGATCTGATAC
* *
291930 TTGACTTGGATTCTGATATGATAC
1 TTGA-TTTGATTCTGATCTGATAC
291954 TTGA
1 TTGA
291958 CCTGGATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 41 0.95
25 2 0.05
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (23 bp):
TTGATTTGATTCTGATCTGATAC
Found at i:291958 original size:24 final size:24
Alignment explanation
Indices: 291892--291982 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 24
291882 TTGATTTGAT
* * *
291892 TTCTGATCTAATACTTGACATGAA
1 TTCTGATATGATACTTGACATGGA
* *
291916 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
*
291940 TTCTGATATGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
* *
291964 TTTTGATATGACACTTGAC
1 TTCTGATATGATACTTGAC
291983 GTGAATTATG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:291994 original size:24 final size:24
Alignment explanation
Indices: 291892--291999 Score: 108
Period size: 24 Copynumber: 4.5 Consensus size: 24
291882 TTGATTTGAT
* *
291892 TTCTGATCTAATACTTGACATGAA
1 TTCTGATATGATACTTGACATGAA
* * *
291916 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGAA
* *
291940 TTCTGATATGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGAA
* * *
291964 TTTTGATATGACACTTGACGTGAA
1 TTCTGATATGATACTTGACATGAA
* *
291988 TTATGATGTGAT
1 TTCTGATATGAT
292000 TTTTGATATA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGAA
Found at i:293812 original size:24 final size:24
Alignment explanation
Indices: 293785--293892 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
293775 TATATCAAAA
* * *
293785 ATCAAATCATAATTCACGTCAAGT
1 ATCAAATCAGAATCCAAGTCAAGT
* *
293809 ATCAAATCAAAATCCAGGTCAAGT
1 ATCAAATCAGAATCCAAGTCAAGT
* *
293833 ATTATATCAGAATCCAAGTCAAGT
1 ATCAAATCAGAATCCAAGTCAAGT
*
293857 ATCATATCAGAATCCATA-TCAAGT
1 ATCAAATCAGAATCCA-AGTCAAGT
*
293881 ATCAGATCAGAA
1 ATCAAATCAGAA
293893 ATCAAATCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
24 73 0.99
25 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (24 bp):
ATCAAATCAGAATCCAAGTCAAGT
Found at i:298041 original size:24 final size:24
Alignment explanation
Indices: 297937--298021 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
297927 ATTTGATTTT
*
297937 TGATCTGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
* * *
297961 TGATCTGATACTTAACTTGGATTC
1 TGATATGATACTTGACATGGATTC
* *
297985 TGATATGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTC
298009 TGATATGATACTT
1 TGATATGATACTT
298022 TACGTGAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:327835 original size:11 final size:13
Alignment explanation
Indices: 327803--327832 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
327793 TGGCCAAAGA
327803 TGAAAAGGTATGT
1 TGAAAAGGTATGT
327816 TGAAAAGGTATG-
1 TGAAAAGGTATGT
327828 TGAAA
1 TGAAA
327833 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:329439 original size:49 final size:50
Alignment explanation
Indices: 329379--329480 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 50
329369 AAGCACATGA
*
329379 CCAGCCCATCATCCAATGCACATGGGTGCA-CACAAGGCTTCCTAGAACCC
1 CCAGCCCATCATCCAATGCACATGGG-GCACCACAAGGCTTCCTAGAACAC
329429 CCAG-CCATCATCCAATGCACATGGGGCACCACAAGGCTTCCTAGAACAC
1 CCAGCCCATCATCCAATGCACATGGGGCACCACAAGGCTTCCTAGAACAC
329478 CCA
1 CCA
329481 TGTGCCGTGC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
48 3 0.06
49 43 0.86
50 4 0.08
ACGTcount: A:0.29, C:0.38, G:0.18, T:0.15
Consensus pattern (50 bp):
CCAGCCCATCATCCAATGCACATGGGGCACCACAAGGCTTCCTAGAACAC
Found at i:349187 original size:18 final size:18
Alignment explanation
Indices: 349164--349216 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
349154 AGACCGGTCA
349164 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
349182 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
349200 CGACCCGA-TCGTTGACC
1 CGACCCGACCCGTTGACC
349217 GTTGATCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 8 0.24
18 26 0.76
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:356475 original size:13 final size:14
Alignment explanation
Indices: 356457--356493 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
356447 ACCGGGCACG
356457 ACCCGACCCGTT-T
1 ACCCGACCCGTTGT
356470 ACCCGACCCGTTGT
1 ACCCGACCCGTTGT
356484 -CCCGACCCGT
1 ACCCGACCCGT
356494 AAACCTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 22 0.96
14 1 0.04
ACGTcount: A:0.14, C:0.49, G:0.19, T:0.19
Consensus pattern (14 bp):
ACCCGACCCGTTGT
Found at i:356566 original size:29 final size:29
Alignment explanation
Indices: 356522--356602 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
356512 GACTGTTGAC
356522 CGGTGCTATATC-GGTAAATAATTTAGTTT
1 CGGTGCTAT-TCTGGTAAATAATTTAGTTT
* *
356551 TGGTGCTATTCTGGTAAATAATTTCGTTT
1 CGGTGCTATTCTGGTAAATAATTTAGTTT
*
356580 CGGTGCTATTCTGGTAATTAATT
1 CGGTGCTATTCTGGTAAATAATT
356603 CGAAATGGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
28 2 0.04
29 45 0.96
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.44
Consensus pattern (29 bp):
CGGTGCTATTCTGGTAAATAATTTAGTTT
Found at i:356613 original size:29 final size:29
Alignment explanation
Indices: 356552--356628 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
356542 ATTTAGTTTT
* **
356552 GGTGCTATTCTGGTAAATAATTTCGTTTC
1 GGTGCTATTCTGGTAATTAATTTCGAATC
*
356581 GGTGCTATTCTGGTAATTAA-TTCGAAATG
1 GGTGCTATTCTGGTAATTAATTTCG-AATC
*
356610 GGTGCTATTTTGGTAATTA
1 GGTGCTATTCTGGTAATTA
356629 TTTTAAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 4 0.10
29 38 0.90
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGTAATTAATTTCGAATC
Found at i:356647 original size:28 final size:29
Alignment explanation
Indices: 356581--356647 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
356571 ATTTCGTTTC
* **
356581 GGTGCTATTCTGGTAATTAATTCGAAATG
1 GGTGCTATTTTGGTAATTAATTCGAAAAA
**
356610 GGTGCTATTTTGGTAATT-ATTTTAAAAA
1 GGTGCTATTTTGGTAATTAATTCGAAAAA
356638 GGTGCTATTT
1 GGTGCTATTT
356648 GTGTAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTCGAAAAA
Found at i:368383 original size:19 final size:19
Alignment explanation
Indices: 368359--368410 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
368349 TTCAACTGGT
368359 TTTGACCGGTCCGAACCGG
1 TTTGACCGGTCCGAACCGG
*
368378 TTTGACCGGTCTGAACCGG
1 TTTGACCGGTCCGAACCGG
368397 TTTGACCGGTCCGA
1 TTTGACCGGTCCGA
368411 CCCGACCGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.15, C:0.29, G:0.31, T:0.25
Consensus pattern (19 bp):
TTTGACCGGTCCGAACCGG
Found at i:368444 original size:17 final size:17
Alignment explanation
Indices: 368407--368470 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
368397 TTTGACCGGT
**
368407 CCGACCCGACCGACCGAC
1 CCGACCCGACCG-TTGAC
368425 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
368442 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
368459 CCGACCCGACCG
1 CCGACCCGACCG
368471 GACCGGACCG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.19, C:0.52, G:0.23, T:0.06
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:368480 original size:5 final size:5
Alignment explanation
Indices: 368407--368479 Score: 60
Period size: 5 Copynumber: 14.2 Consensus size: 5
368397 TTTGACCGGT
* *
368407 CCGAC CCGA- CCGA- CCGAC CCGAC CCGAC CGTTGAC CCGAC CCGAC CGTTGAC
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC C--CGAC
* *
368459 CCGAC CCGAC CGGAC CGGAC C
1 CCGAC CCGAC CCGAC CCGAC C
368480 GTTAACCGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
4 8 0.14
5 42 0.72
7 8 0.14
ACGTcount: A:0.19, C:0.51, G:0.25, T:0.05
Consensus pattern (5 bp):
CCGAC
Found at i:387678 original size:19 final size:19
Alignment explanation
Indices: 387654--387692 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
387644 TTGAACCGGT
387654 CTGACCCGACCCGACCCGA
1 CTGACCCGACCCGACCCGA
*
387673 CTGACCCGATCCGACCCGA
1 CTGACCCGACCCGACCCGA
387692 C
1 C
387693 CATTAACCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.51, G:0.21, T:0.08
Consensus pattern (19 bp):
CTGACCCGACCCGACCCGA
Found at i:387710 original size:5 final size:5
Alignment explanation
Indices: 387656--387693 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
387646 GAACCGGTCT
* *
387656 GACCC GACCC GACCC GA-CT GACCC GATCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
387694 ATTAACCCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 3 0.11
5 25 0.89
ACGTcount: A:0.21, C:0.53, G:0.21, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:387728 original size:14 final size:14
Alignment explanation
Indices: 387709--387735 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
387699 CCCGACCCGA
387709 CCTTTGACCGTTGC
1 CCTTTGACCGTTGC
387723 CCTTTGACCGTTG
1 CCTTTGACCGTTG
387736 ACCGTGACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.33, G:0.22, T:0.37
Consensus pattern (14 bp):
CCTTTGACCGTTGC
Done.