Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003161.1 Hibiscus syriacus cultivar Beakdansim tig00006653_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: 221518
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3802 original size:91 final size:91
Alignment explanation
Indices: 3647--3829 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 91
3637 CCTAGAACAC
*
3647 CCATGTGCCTTGCATATGACCAGACCCCATGTTCCTTGCATGTGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGACCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
* *
3712 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAATTCTCTCCCTATTCGACCAAG
** * * * * *
3738 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGACCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
3803 AAGAATTCTCTCCCTATTCGACCAAG
66 AAGAATTCTCTCCCTATTCGACCAAG
3829 C
1 C
3830 ATCAACTACC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGACCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
AAGAATTCTCTCCCTATTCGACCAAG
Found at i:5456 original size:35 final size:36
Alignment explanation
Indices: 5408--5476 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
5398 ATTTATAAGT
*
5408 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATAATATAGGCGTGAAAATGGTAATGGAATA
** *
5443 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAA
1 TGGTGATAATATAGGCGTGAAAATGGTAATGGAA
5477 GGTGGAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 17 0.59
36 12 0.41
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGAAAATGGTAATGGAATA
Found at i:10470 original size:17 final size:18
Alignment explanation
Indices: 10450--10483 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10440 ATATGAAAGA
*
10450 AAAGGAAATG-AGATAAT
1 AAAGAAAATGAAGATAAT
10467 AAAGAAAATGAAGATAA
1 AAAGAAAATGAAGATAA
10484 CTTACAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (18 bp):
AAAGAAAATGAAGATAAT
Found at i:10645 original size:14 final size:15
Alignment explanation
Indices: 10628--10656 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10618 TTGCTTTTGA
10628 TTTTC-TTCTTTTTC
1 TTTTCTTTCTTTTTC
10642 TTTTCTTTCTTTTTC
1 TTTTCTTTCTTTTTC
10657 ACTCCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:10703 original size:17 final size:17
Alignment explanation
Indices: 10681--10729 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
10671 GTAGGAGTCT
10681 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
10698 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
*
10716 TTTT-TTTTTGTTGT
1 TTTTCTTTTTCTTGT
10730 AGCACTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.24
17 13 0.45
18 9 0.31
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:11153 original size:35 final size:36
Alignment explanation
Indices: 11105--11188 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
11095 ATTTATAAGT
* * *
11105 TGGTGATAATATAGGCATG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCATGAAAATGGTAATGGAAGA
* * *
11140 TGGTGATGTTATAGGCATGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCATGAAAATGGTAATGGAAGA
11176 TGGTGATGA-ATAG
1 TGGTGATGATATAG
11189 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGAAAATGGTAATGGAAGA
Found at i:20073 original size:19 final size:18
Alignment explanation
Indices: 20051--20086 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20041 AAATTTTGGC
20051 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
20070 TTTTTTTGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
20087 TTTGCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:20076 original size:11 final size:11
Alignment explanation
Indices: 20062--20121 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
20052 TTTTTGGCTC
20062 TTTTTTTG-TT
1 TTTTTTTGTTT
***
20072 TTTTTGCCTTT
1 TTTTTTTGTTT
20083 TTTTTTTGCCTTT
1 TTTTTTTG--TTT
20096 TTTTTTTGTTT
1 TTTTTTTGTTT
20107 TTTTTTTGTTT
1 TTTTTTTGTTT
20118 TTTT
1 TTTT
20122 GAAAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
10 5 0.12
11 25 0.61
13 11 0.27
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:20088 original size:20 final size:20
Alignment explanation
Indices: 20051--20087 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20041 AAATTTTGGC
*
20051 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
20071 TTTTTTGCCT-TTTTTTT
1 TTTTTTGCCTCTTTTTTT
20088 TTGCCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:20121 original size:13 final size:13
Alignment explanation
Indices: 20070--20114 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
20060 TCTTTTTTTG
20070 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
20083 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
20096 TTTTTTTG--TTT
1 TTTTTTTGCCTTT
20107 TTTTTTTG
1 TTTTTTTG
20115 TTTTTTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.34
13 21 0.66
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:22589 original size:19 final size:19
Alignment explanation
Indices: 22565--22612 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
22555 TGACATGATT
22565 TTTAATGAAAAAATAAGAC
1 TTTAATGAAAAAATAAGAC
22584 TTTAATGAAAAAATAAGAC
1 TTTAATGAAAAAATAAGAC
22603 TTTAATGAAA
1 TTTAATGAAA
22613 CTACATGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.29
Consensus pattern (19 bp):
TTTAATGAAAAAATAAGAC
Found at i:25909 original size:23 final size:24
Alignment explanation
Indices: 25871--25923 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
25861 CTTTCTTTCT
25871 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
25895 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
25918 TTTCTT
1 TTTCTT
25924 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:29635 original size:18 final size:18
Alignment explanation
Indices: 29614--29650 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29604 CTAACATGTC
29614 TCTTCCATTCAACATCTT
1 TCTTCCATTCAACATCTT
29632 TCTTCCATTCAACATCTT
1 TCTTCCATTCAACATCTT
29650 T
1 T
29651 GTAGTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (18 bp):
TCTTCCATTCAACATCTT
Found at i:37245 original size:6 final size:6
Alignment explanation
Indices: 37234--37285 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
37224 CTTTTTGAAA
* *
37234 TCTTTT TCTTTT TCTTCTT T-TTCT TCTTTT TCTTTCT T-TTCT TCTTTT
1 TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT TCTTT-T TCTTTT TCTTTT
37282 TCTT
1 TCTT
37286 CTATTTGTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 4 0.11
6 29 0.76
7 5 0.13
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:37253 original size:9 final size:9
Alignment explanation
Indices: 37239--37305 Score: 84
Period size: 9 Copynumber: 7.2 Consensus size: 9
37229 TGAAATCTTT
37239 TTCTTTTTC
1 TTCTTTTTC
37248 TTCTTTTTC
1 TTCTTTTTC
37257 TTCTTTTTC
1 TTCTTTTTC
37266 TT-TCTTTTC
1 TTCT-TTTTC
37275 TTCTTTTTC
1 TTCTTTTTC
37284 TTCTATTTGTC
1 TTCT-TTT-TC
37295 TT-TTCTTTC
1 TTCTT-TTTC
37304 TT
1 TT
37306 TTTGCATTCC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
8 1 0.02
9 41 0.77
10 7 0.13
11 4 0.08
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.76
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:37273 original size:27 final size:30
Alignment explanation
Indices: 37237--37302 Score: 102
Period size: 27 Copynumber: 2.3 Consensus size: 30
37227 TTTGAAATCT
37237 TTTTCTTTTTCTTCTTTTTCTTCT-TTT-TC
1 TTTTC-TTTTCTTCTTTTTCTTCTATTTGTC
37266 -TTTCTTTTCTTCTTTTTCTTCTATTTGTC
1 TTTTCTTTTCTTCTTTTTCTTCTATTTGTC
37295 TTTTCTTT
1 TTTTCTTT
37303 CTTTTTGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
27 18 0.53
28 7 0.21
29 2 0.06
30 7 0.21
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (30 bp):
TTTTCTTTTCTTCTTTTTCTTCTATTTGTC
Found at i:37304 original size:17 final size:16
Alignment explanation
Indices: 37261--37307 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
37251 TTTTTCTTCT
*
37261 TTTTCTTTCTTTTCTTC
1 TTTTCTTTCTTTT-GTC
37278 TTTT-TCTTCTATTTGTC
1 TTTTCT-TTCT-TTTGTC
37295 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
37308 TGCATTCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.15
17 18 0.69
18 4 0.15
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTCTTTCTTTTGTC
Found at i:37308 original size:27 final size:25
Alignment explanation
Indices: 37234--37308 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 25
37224 CTTTTTGAAA
37234 TCTTTTTCTTTT-TCTTC-TTTTTCT
1 TCTTTTTCTTTTCT-TTCTTTTTTCT
37258 TCTTTTTC-TTTCTTTTCTTCTTTTTCT
1 TCTTTTTCTTTTC-TTTC-T-TTTTTCT
37285 TCTATTTGTCTTTTCTTTCTTTTT
1 TCT-TTT-TCTTTTCTTTCTTTTT
37309 GCATTCCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
23 3 0.07
24 11 0.26
25 1 0.02
27 14 0.33
28 4 0.09
29 6 0.14
30 4 0.09
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.77
Consensus pattern (25 bp):
TCTTTTTCTTTTCTTTCTTTTTTCT
Found at i:45520 original size:28 final size:28
Alignment explanation
Indices: 45461--45526 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
45451 ACTTCTTTCT
* * *
45461 TTTCTTTTCTTCTTTTTGAGTGCTGGAT
1 TTTCTTTTCTTCTTTTGGAGTGCTGCAA
*
45489 TTTC-TTTCTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTTC-TTCTTTTGGAGTGCTGCAA
45517 TTTCTTTTCT
1 TTTCTTTTCT
45527 GATTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.12
28 24 0.75
29 4 0.12
ACGTcount: A:0.08, C:0.17, G:0.14, T:0.62
Consensus pattern (28 bp):
TTTCTTTTCTTCTTTTGGAGTGCTGCAA
Found at i:46455 original size:91 final size:91
Alignment explanation
Indices: 46300--46482 Score: 305
Period size: 91 Copynumber: 2.0 Consensus size: 91
46290 GGTAGTTGAT
46300 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
46365 GGGG-TGGATCACATGCAAAACACATG
66 GGGGCTGG-TCACATGCAAAACACATG
* *
46391 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
* **
46456 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
46482 G
1 G
46483 GTTTTCTAGG
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
91 83 0.97
92 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.20
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:47784 original size:12 final size:14
Alignment explanation
Indices: 47765--47798 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
47755 TATTTTTTTT
47765 CAAAAAAAA-AAGC
1 CAAAAAAAAGAAGC
47778 CAAAAAAAAGAAGC
1 CAAAAAAAAGAAGC
47792 CAAAAAA
1 CAAAAAA
47799 TCCAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAGAAGC
Found at i:52150 original size:12 final size:12
Alignment explanation
Indices: 52133--52160 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
52123 TTTAATCTTA
52133 TTTCTTACCTTG
1 TTTCTTACCTTG
52145 TTTCTTACCTTG
1 TTTCTTACCTTG
52157 TTTC
1 TTTC
52161 CAACACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.25, G:0.07, T:0.61
Consensus pattern (12 bp):
TTTCTTACCTTG
Found at i:54809 original size:36 final size:36
Alignment explanation
Indices: 54762--54863 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
54752 GATACAATCT
*
54762 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
54798 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
54834 TTCCACCACCA-TATCACGCCTATATTATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
54864 TCAACTTATA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 18 0.29
36 44 0.71
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:55350 original size:14 final size:15
Alignment explanation
Indices: 55316--55362 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
55306 AATTTGGAGT
55316 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
55331 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
55345 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
55362 G
1 G
55363 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:58903 original size:13 final size:11
Alignment explanation
Indices: 58862--58946 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
58852 ACAATCTGTC
58862 CATCACCATTAT
1 CATCACCA-TAT
*
58874 CA-CGCCTATAT
1 CATCACC-ATAT
58885 CATCACCATAGT
1 CATCACCATA-T
58897 CCATCACCATTAT
1 -CATCACCA-TAT
*
58910 CA-CGCCTATAT
1 CATCACC-ATAT
58921 CATCACCATATT
1 CATCACCATA-T
58933 CCATCACCATAT
1 -CATCACCATAT
58945 CA
1 CA
58947 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:58906 original size:36 final size:36
Alignment explanation
Indices: 58859--58963 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
58849 GATACAATCT
58859 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
58895 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
58931 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
58964 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:61769 original size:28 final size:28
Alignment explanation
Indices: 61710--61775 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
61700 ACTTCTTTCT
* * *
61710 TTTCTTTTCTTCTTTTTGAGTGCTGGAT
1 TTTCTTTTCTTCTTTTGGAGTGCTGCAA
*
61738 TTTC-TTTCTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTTC-TTCTTTTGGAGTGCTGCAA
61766 TTTCTTTTCT
1 TTTCTTTTCT
61776 GATTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.12
28 24 0.75
29 4 0.12
ACGTcount: A:0.08, C:0.17, G:0.14, T:0.62
Consensus pattern (28 bp):
TTTCTTTTCTTCTTTTGGAGTGCTGCAA
Found at i:68534 original size:8 final size:8
Alignment explanation
Indices: 68523--68580 Score: 73
Period size: 8 Copynumber: 7.0 Consensus size: 8
68513 TTTTTGGCTC
68523 TTTTTTTG
1 TTTTTTTG
68531 TTTTTTTG
1 TTTTTTTG
68539 TTTTTTTG
1 TTTTTTTG
*
68547 CCTTTTTT-
1 -TTTTTTTG
68555 TTTTTTTG
1 TTTTTTTG
68563 CCTTTTTTTG
1 --TTTTTTTG
68573 TTTTTTTG
1 TTTTTTTG
68581 AAAAAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 6 0.14
8 24 0.55
9 6 0.14
10 8 0.18
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:68544 original size:16 final size:17
Alignment explanation
Indices: 68523--68580 Score: 84
Period size: 16 Copynumber: 3.5 Consensus size: 17
68513 TTTTTGGCTC
68523 TTTTTTTG-TTTTTTTG
1 TTTTTTTGCTTTTTTTG
*
68539 TTTTTTTGCCTTTTTT-
1 TTTTTTTGCTTTTTTTG
68555 TTTTTTTGCCTTTTTTTG
1 TTTTTTTG-CTTTTTTTG
68573 TTTTTTTG
1 TTTTTTTG
68581 AAAAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 16 0.43
17 13 0.35
18 8 0.22
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (17 bp):
TTTTTTTGCTTTTTTTG
Found at i:73142 original size:14 final size:14
Alignment explanation
Indices: 73108--73158 Score: 75
Period size: 14 Copynumber: 3.5 Consensus size: 14
73098 AAATTTTGGC
*
73108 TTTTTTTGGCTCTTT
1 TTTTTTTGCCT-TTT
73123 TTTTTTTGCCTTTT
1 TTTTTTTGCCTTTT
73137 TTTTTTTGCCTTTT
1 TTTTTTTGCCTTTT
73151 TTGTTTTT
1 TT-TTTTT
73159 TTTTTTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 19 0.56
15 15 0.44
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (14 bp):
TTTTTTTGCCTTTT
Found at i:73162 original size:12 final size:12
Alignment explanation
Indices: 73120--73172 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
73110 TTTTTGGCTC
*
73120 TTTTTTTTTTGC
1 TTTTTTTTTTGT
*
73132 CTTTTTTTTT-T
1 TTTTTTTTTTGT
***
73143 TGCCTTTTTTGT
1 TTTTTTTTTTGT
73155 TTTTTTTTTTGT
1 TTTTTTTTTTGT
73167 TTTTTT
1 TTTTTT
73173 GAAAAAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 6 0.19
12 25 0.81
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:74761 original size:15 final size:16
Alignment explanation
Indices: 74741--74777 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
74731 GATTAGAATA
74741 AAATAAACGGAAGAT-
1 AAATAAACGGAAGATG
74756 AAATAAACGGAAGATG
1 AAATAAACGGAAGATG
74772 AAATAA
1 AAATAA
74778 GATAATAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.62, C:0.05, G:0.19, T:0.14
Consensus pattern (16 bp):
AAATAAACGGAAGATG
Found at i:75771 original size:18 final size:18
Alignment explanation
Indices: 75748--75807 Score: 81
Period size: 15 Copynumber: 3.4 Consensus size: 18
75738 TATTTTTTTT
75748 CAAAAAAACAAAAAAAGG
1 CAAAAAAACAAAAAAAGG
75766 C--AAAAA-AAAAAAAGG
1 CAAAAAAACAAAAAAAGG
75781 CAAAAAAACAAAAAAAGAG
1 CAAAAAAACAAAAAAAG-G
75800 CCAAAAAA
1 -CAAAAAA
75808 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.27
16 5 0.14
17 5 0.14
18 9 0.24
19 1 0.03
20 7 0.19
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (18 bp):
CAAAAAAACAAAAAAAGG
Found at i:75814 original size:20 final size:20
Alignment explanation
Indices: 75770--75807 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
75760 AAAAGGCAAA
*
75770 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
75790 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
75808 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:80267 original size:8 final size:8
Alignment explanation
Indices: 80254--80287 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
80244 TTTTTTTTTT
80254 CAAAAAAA
1 CAAAAAAA
80262 CAAAAAAA
1 CAAAAAAA
80270 GGCAAAAAAA
1 --CAAAAAAA
80280 CAAAAAAA
1 CAAAAAAA
80288 GAGCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:80279 original size:19 final size:20
Alignment explanation
Indices: 80254--80298 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 20
80244 TTTTTTTTTT
80254 CAAAAAAACAAAAAAAG-G-
1 CAAAAAAACAAAAAAAGAGC
80272 CAAAAAAACAAAAAAAGAGC
1 CAAAAAAACAAAAAAAGAGC
80292 CAAAAAA
1 CAAAAAA
80299 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 17 0.68
19 1 0.04
20 7 0.28
ACGTcount: A:0.78, C:0.13, G:0.09, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAGAGC
Found at i:85336 original size:14 final size:14
Alignment explanation
Indices: 85317--85359 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
85307 ATAAGATATT
85317 ATCTTTCCATCACC
1 ATCTTTCCATCACC
85331 ATCTTTCCATCACC
1 ATCTTTCCATCACC
* *
85345 AT-TCTCTATCACC
1 ATCTTTCCATCACC
85358 AT
1 AT
85360 TCACTCCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (14 bp):
ATCTTTCCATCACC
Found at i:85357 original size:13 final size:13
Alignment explanation
Indices: 85322--85361 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
85312 ATATTATCTT
*
85322 TCCATCACCATCTT
1 TCCATCACCAT-TC
85336 TCCATCACCATTC
1 TCCATCACCATTC
*
85349 TCTATCACCATTC
1 TCCATCACCATTC
85362 ACTCCTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (13 bp):
TCCATCACCATTC
Found at i:85817 original size:16 final size:15
Alignment explanation
Indices: 85769--85820 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
85759 CAAAAGCAAC
*
85769 AAAAAGAGAAAAAAG
1 AAAAAGAAAAAAAAG
*
85784 AAAGAAG-AAAAACA-
1 AAA-AAGAAAAAAAAG
85798 AAAAAGAAAAGAAAAG
1 AAAAAGAAAA-AAAAG
85814 AAAAAGA
1 AAAAAGA
85821 CTCCTACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 11 0.37
16 10 0.33
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:88218 original size:16 final size:16
Alignment explanation
Indices: 88184--88230 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
88174 ATAACATCTC
*
88184 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
88200 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
88215 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
88228 TAT
1 TAT
88231 TTCCAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:88232 original size:12 final size:13
Alignment explanation
Indices: 88205--88233 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
88195 TTTCTTATCC
88205 TTTCATTTCTTTA
1 TTTCATTTCTTTA
88218 TTTCATTTC-TTA
1 TTTCATTTCTTTA
88230 TTTC
1 TTTC
88234 CAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:90755 original size:11 final size:12
Alignment explanation
Indices: 90725--90759 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
90715 TTAAGTGCTG
90725 GAAACAAGATAA
1 GAAACAAGATAA
*
90737 GAAACAAGATTA
1 GAAACAAGATAA
90749 G-AACAAGATAA
1 GAAACAAGATAA
90760 ACAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.63, C:0.09, G:0.17, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:95646 original size:35 final size:36
Alignment explanation
Indices: 95598--95681 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
95588 ATTTATAAGT
* * *
95598 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
* * *
95633 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
95669 TGGTGATGA-ATAG
1 TGGTGATGATATAG
95682 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
Found at i:98858 original size:20 final size:20
Alignment explanation
Indices: 98833--98879 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
98823 AAACTTCTGA
*
98833 CTTGGCTTATTGATGTAGGT
1 CTTGGCCTATTGATGTAGGT
98853 CTTGGCCTATTGATGTAGGT
1 CTTGGCCTATTGATGTAGGT
98873 CTTGGCC
1 CTTGGCC
98880 AGTCCTGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.40
Consensus pattern (20 bp):
CTTGGCCTATTGATGTAGGT
Found at i:100698 original size:17 final size:18
Alignment explanation
Indices: 100673--100706 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
100663 AGATGAAAGA
*
100673 AAAGGAAATG-AGATAAT
1 AAAGAAAATGAAGATAAT
100690 AAAGAAAATGAAGATAA
1 AAAGAAAATGAAGATAA
100707 CTTACAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (18 bp):
AAAGAAAATGAAGATAAT
Found at i:101370 original size:35 final size:36
Alignment explanation
Indices: 101322--101405 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
101312 ATTTATAAGT
* * *
101322 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
* * *
101357 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
101393 TGGTGATGA-ATAG
1 TGGTGATGATATAG
101406 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
Found at i:106476 original size:16 final size:16
Alignment explanation
Indices: 106442--106488 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
106432 ATAACATCTC
*
106442 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
106458 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
106473 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
106486 TAT
1 TAT
106489 TTCCAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:106490 original size:12 final size:13
Alignment explanation
Indices: 106463--106491 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
106453 TTTCTTATCC
106463 TTTCATTTCTTTA
1 TTTCATTTCTTTA
106476 TTTCATTTC-TTA
1 TTTCATTTCTTTA
106488 TTTC
1 TTTC
106492 CAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:110054 original size:25 final size:25
Alignment explanation
Indices: 110026--110084 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
110016 CCTACTTTGA
110026 TATCATTTCTTTCCATTTCATTTCT
1 TATCATTTCTTTCCATTTCATTTCT
* *
110051 TATCTTTTCTTTCCATTTCCTTTCT
1 TATCATTTCTTTCCATTTCATTTCT
110076 TATCATTTC
1 TATCATTTC
110085 CATTCTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (25 bp):
TATCATTTCTTTCCATTTCATTTCT
Found at i:110631 original size:33 final size:33
Alignment explanation
Indices: 110594--110662 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
110584 TTTGATGAAT
*
110594 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
110627 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
110660 GAA
1 GAA
110663 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:115121 original size:33 final size:35
Alignment explanation
Indices: 115077--115157 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
115067 ATGGTGATGA
* * *
115077 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGG-TGATGATATAGGCGTGAT
115111 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
115146 AATGGTGATGGA
1 AATGGTGATGGA
115158 CAGATTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 9 0.22
34 1 0.03
35 18 0.45
36 12 0.30
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:118972 original size:2 final size:2
Alignment explanation
Indices: 118965--119011 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
118955 TAGTTATTTC
118965 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
119007 AT AT A
1 AT AT A
119012 GTTATTATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:121116 original size:26 final size:26
Alignment explanation
Indices: 121080--121150 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
121070 CTAAATGAAC
* *
121080 CATATACAAGGCTCATGGGGGCTGGT
1 CATATACAAGGCACATGGGGGCTGAT
*
121106 CATATGCAAGGCACATGGGGGCTGAT
1 CATATACAAGGCACATGGGGGCTGAT
*
121132 CATATACAAAGCACATGGG
1 CATATACAAGGCACATGGG
121151 TGTTCTAGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.20
Consensus pattern (26 bp):
CATATACAAGGCACATGGGGGCTGAT
Found at i:127437 original size:12 final size:12
Alignment explanation
Indices: 127398--127430 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
127388 TTTTTTTAGC
127398 TTTTTTTTGCCT
1 TTTTTTTTGCCT
127410 TTTTTTTTGCCT
1 TTTTTTTTGCCT
127422 TTTTTTTTG
1 TTTTTTTTG
127431 TTTTTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGCCT
Found at i:130372 original size:20 final size:19
Alignment explanation
Indices: 130343--130381 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
130333 CATCATTTTT
*
130343 TTTGGAGTGATCGTGAGGA
1 TTTGGAGTGATCGTAAGGA
130362 TTTGTGAGTGATCGTAAGGA
1 TTTG-GAGTGATCGTAAGGA
130382 ATCCATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.23, C:0.05, G:0.38, T:0.33
Consensus pattern (19 bp):
TTTGGAGTGATCGTAAGGA
Found at i:134372 original size:27 final size:27
Alignment explanation
Indices: 134338--134394 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
134328 TTTCTTTGCT
* *
134338 TTTCTTCTTTTTGAATGC-TGAATTTC
1 TTTCTTCTTTTGGAATGCTTCAATTTC
*
134364 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTTGGAATGCTTCAATTTC
134392 TTT
1 TTT
134395 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 12 0.46
28 10 0.38
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (27 bp):
TTTCTTCTTTTGGAATGCTTCAATTTC
Found at i:135225 original size:26 final size:26
Alignment explanation
Indices: 135195--135265 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
135185 CTAAATGAAC
* *
135195 CATATCCAAGGCACATGGGGGCTGAT
1 CATATGCAAGGCACATGGGGGATGAT
135221 CATATGCAAGGCACATGGGGGATGAT
1 CATATGCAAGGCACATGGGGGATGAT
*
135247 CATATGCAAAGCACATGGG
1 CATATGCAAGGCACATGGG
135266 TGTTCTAGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (26 bp):
CATATGCAAGGCACATGGGGGATGAT
Found at i:136565 original size:9 final size:9
Alignment explanation
Indices: 136551--136609 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
136541 TGGAGTAAAA
136551 AAAAGAAAG
1 AAAAGAAAG
136560 AAAAGATAA-
1 AAAAGA-AAG
136569 AAAAG-AAG
1 AAAAGAAAG
*
136577 AAAAAAAAG
1 AAAAGAAAG
136586 AAAAG-AAG
1 AAAAGAAAG
*
136594 AAAA-TAAG
1 AAAAGAAAG
136602 AAAAGAAA
1 AAAAGAAA
136610 AAGAATAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
7 2 0.05
8 18 0.43
9 20 0.48
10 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:136577 original size:17 final size:16
Alignment explanation
Indices: 136547--136608 Score: 70
Period size: 17 Copynumber: 3.7 Consensus size: 16
136537 AATTTGGAGT
136547 AAAAAAAAGAAAGAAAA
1 AAAAAAAAG-AAGAAAA
*
136564 GATAAAAAAGAAGAAAA
1 -AAAAAAAAGAAGAAAA
136581 AAAAGAAAAGAAGAAAA
1 AAAA-AAAAGAAGAAAA
* *
136598 TAAGAAAAGAA
1 AAAAAAAAGAA
136609 AAAGAATAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.26
17 21 0.54
18 8 0.21
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGAAGAAAA
Found at i:136577 original size:21 final size:20
Alignment explanation
Indices: 136547--136611 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
136537 AATTTGGAGT
136547 AAAAAA-AAGAAAGAAAAGA
1 AAAAAAGAAGAAAGAAAAGA
*
136566 TAAAAAAGAAGAAAAAAAAGA
1 -AAAAAAGAAGAAAGAAAAGA
* *
136587 AAAGAAGAAAATAAGAAAAGA
1 AAAAAAGAAGA-AAGAAAAGA
136608 AAAA
1 AAAA
136612 GAATAGAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 15 0.39
21 23 0.61
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (20 bp):
AAAAAAGAAGAAAGAAAAGA
Found at i:136580 original size:8 final size:8
Alignment explanation
Indices: 136551--136608 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
136541 TGGAGTAAAA
136551 AAAAGAAAG
1 AAAAG-AAG
*
136560 AAAAGATAA
1 AAAAGA-AG
136569 AAAAGAAG
1 AAAAGAAG
*
136577 AAAAAAAAG
1 -AAAAGAAG
136586 AAAAGAAG
1 AAAAGAAG
*
136594 AAAATAAG
1 AAAAGAAG
136602 AAAAGAA
1 AAAAGAA
136609 AAAGAATAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
8 22 0.54
9 19 0.46
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (8 bp):
AAAAGAAG
Found at i:136581 original size:30 final size:28
Alignment explanation
Indices: 136547--136619 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 28
136537 AATTTGGAGT
136547 AAAAAAAAGAAAGAAAAGATAAAAAAGAA
1 AAAAAAAAGAAAGAAAAGA-AAAAAAGAA
* *
136576 GAAAAAAAAGAAA-AGAAGAAAATAAGAA
1 -AAAAAAAAGAAAGAAAAGAAAAAAAGAA
*
136604 AAGAAAAAGAATAGAA
1 AAAAAAAAGAA-AGAA
136620 TTTCAAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 10 0.27
28 9 0.24
29 6 0.16
30 12 0.32
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (28 bp):
AAAAAAAAGAAAGAAAAGAAAAAAAGAA
Found at i:136616 original size:17 final size:16
Alignment explanation
Indices: 136547--136616 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
136537 AATTTGGAGT
136547 AAAAAA-AAG-AAAG-
1 AAAAAATAAGAAAAGA
*
136560 AAAAGATAA-AAAAGA
1 AAAAAATAAGAAAAGA
*
136575 AGAAAAAAAAGAAAAGA
1 A-AAAAATAAGAAAAGA
*
136592 AGAAAATAAGAAAAGA
1 AAAAAATAAGAAAAGA
136608 AAAAGAATA
1 AAAA-AATA
136617 GAATTTCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 5 0.11
14 6 0.13
15 1 0.02
16 22 0.49
17 11 0.24
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAAATAAGAAAAGA
Found at i:139525 original size:30 final size:31
Alignment explanation
Indices: 139474--139532 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
139464 TTAGCTTTAA
*
139474 ATTATGTTTACATACGTTTTAGAT-TCATTT
1 ATTATGTTTACATACGATTTAGATATCATTT
*
139504 ATTATGTTTGCATATC-ATTTAGATATCAT
1 ATTATGTTTACATA-CGATTTAGATATCAT
139533 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (31 bp):
ATTATGTTTACATACGATTTAGATATCATTT
Found at i:140431 original size:19 final size:21
Alignment explanation
Indices: 140407--140457 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
140397 GGCCAAGAGT
*
140407 ATGTATCTTCA-TT-AAAATC
1 ATGTATTTTCATTTAAAAATC
140426 ATGTATTTTCATTTAAAAATC
1 ATGTATTTTCATTTAAAAATC
140447 ATGTATTTTCA
1 ATGTATTTTCA
140458 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 10 0.34
20 2 0.07
21 17 0.59
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTTAAAAATC
Found at i:141318 original size:12 final size:12
Alignment explanation
Indices: 141257--141321 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
141247 TATTTTTTTT
141257 CAAAAAAAAA--
1 CAAAAAAAAAGG
141267 CAAAAAAAAAGG
1 CAAAAAAAAAGG
141279 CAAAAAAAAAGG
1 CAAAAAAAAAGG
**
141291 CAAAAAAAAAAA
1 CAAAAAAAAAGG
*
141303 CAAAAAAAAAGC
1 CAAAAAAAAAGG
141315 CAAAAAA
1 CAAAAAA
141322 GCCAAAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
10 10 0.20
12 39 0.80
ACGTcount: A:0.82, C:0.11, G:0.08, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAGG
Found at i:146754 original size:578 final size:578
Alignment explanation
Indices: 145659--146817 Score: 1960
Period size: 578 Copynumber: 2.0 Consensus size: 578
145649 AGCTACATTG
* *
145659 GAGCTAAATGGAGCATGTAACAGCAAGGAGACTCACATAAGAACGCTTAGGAGAGCATAAGGACC
1 GAGCTAAATGGAGCATGTAACAACAAGGAGACTCACATAAGAACGCTTAAGAGAGCATAAGGACC
*
145724 CATTGGTGAAAAGTTATCCGGAGGCCCGTGAGCTCATAGCTGGATTGAGCTGAAGATTTGAGCTA
66 CATTGGTGAAAAGTTATCCGAAGGCCCGTGAGCTCATAGCTGGATTGAGCTGAAGATTTGAGCTA
* *
145789 CAAGATACCCTCATTTCAGTTGGGGAGCTGCACCATCATCATCACCACTTAAGACACTTCAAAAA
131 CAAGATACCCTCATTTCAGCTGGGGAGCTGCACCATCATCATCACCACTTAAGACACTTAAAAAA
* * **
145854 TGTCCTAAGTTAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTTTCACCTCAAGAGGTACCT
196 TATCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCACCTCAAGAGGTACCT
* * *
145919 TTTGAAAAGGAGTTGCCCTAATGATCAGCATGCTACAAGTCACCTAAGGCCAGCTCAACTCCAGC
261 TTTGAAAAGGAGCTGCCCTAACGATCACCATGCTACAAGTCACCTAAGGCCAGCTCAACTCCAGC
** * * *
145984 TCATTCACACCTGAAGTAGTTCAAATATGAAGGGTCACCTTTTTCAAACAATGTGACCTTTCATG
326 TCATTCACACCCAAAGTAGCTCAAACATGAAGGGTCACCTTTTTCAAACAATGTAACCTTTCATG
* *
146049 AATAATGCTGCCCATGAAGATACCTTTTCATCTAGGAGCACGCTGGTGAAGAGATTGCAACCATT
391 AATAATACTGCCCATAAAGATACCTTTTCATCTAGGAGCACGCTGGTGAAGAGATTGCAACCATT
146114 GGAGGCTTGAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGACCACAACACATGCCA
456 GGAGGCTTGAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGACCACAACACATGCCA
* *
146179 TGCACGTGAGAGCCTTTGGTGCCAAACATGAGAAGGCACATCACCATTCGGCCAAGGA
521 TGCACATGAGAGCCTTTGGCGCCAAACATGAGAAGGCACATCACCATTCGGCCAAGGA
* * *
146237 GAGCTAATTGGAGCATGTAACAACAAGGAGACTCACATAGGAACTCTTAAGAGAGCATAAGGACC
1 GAGCTAAATGGAGCATGTAACAACAAGGAGACTCACATAAGAACGCTTAAGAGAGCATAAGGACC
* *
146302 CATTGGTGACACGTTATCCGAAGGCCCGTGAGCTCATAGCTGGATTGAGCTGAAGATTTGAGCTA
66 CATTGGTGAAAAGTTATCCGAAGGCCCGTGAGCTCATAGCTGGATTGAGCTGAAGATTTGAGCTA
*
146367 CAAGATGCCCTCATTTCAGCTGGGGAGCTGCACCATCATCATCACCACTTAAGACACTTAAAAAA
131 CAAGATACCCTCATTTCAGCTGGGGAGCTGCACCATCATCATCACCACTTAAGACACTTAAAAAA
*
146432 TATCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGTGAATAGTTGCCACCTCAAGAGGTACCT
196 TATCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCACCTCAAGAGGTACCT
* * * *
146497 TTTTATAAGGAGCTGCCCTAACGATCACCATGCTACAAGTCACCTAAGGCTAGCTCACCTCCAGC
261 TTTGAAAAGGAGCTGCCCTAACGATCACCATGCTACAAGTCACCTAAGGCCAGCTCAACTCCAGC
*
146562 TCATTCACACCCAAAGTAGCTCAAACATGAAGGGTCACCTTTTTCAAACATTGTAACCTTTCATG
326 TCATTCACACCCAAAGTAGCTCAAACATGAAGGGTCACCTTTTTCAAACAATGTAACCTTTCATG
* * *
146627 AATAATACTGCCCATAAAGATGA-TTTTTCATCTAGGAGCACGTTGGTGAAGAGATTGTAACCAT
391 AATAATACTGCCCATAAAGAT-ACCTTTTCATCTAGGAGCACGCTGGTGAAGAGATTGCAACCAT
* *
146691 TGGAGGCTTGAATCACCAAGGGACATGAGATAGATCTCCATGCCTATTCGACCACAACACATGCC
455 TGGAGGCTTGAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGACCACAACACATGCC
146756 ATGCACATGAGAGCCTTTGGCGCCAAACATGAGAAGGCACATCACCATTCGGCCAAGGA
520 ATGCACATGAGAGCCTTTGGCGCCAAACATGAGAAGGCACATCACCATTCGGCCAAGGA
146815 GAG
1 GAG
146818 AAAAATGGCA
Statistics
Matches: 542, Mismatches: 38, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
578 541 1.00
579 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (578 bp):
GAGCTAAATGGAGCATGTAACAACAAGGAGACTCACATAAGAACGCTTAAGAGAGCATAAGGACC
CATTGGTGAAAAGTTATCCGAAGGCCCGTGAGCTCATAGCTGGATTGAGCTGAAGATTTGAGCTA
CAAGATACCCTCATTTCAGCTGGGGAGCTGCACCATCATCATCACCACTTAAGACACTTAAAAAA
TATCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCACCTCAAGAGGTACCT
TTTGAAAAGGAGCTGCCCTAACGATCACCATGCTACAAGTCACCTAAGGCCAGCTCAACTCCAGC
TCATTCACACCCAAAGTAGCTCAAACATGAAGGGTCACCTTTTTCAAACAATGTAACCTTTCATG
AATAATACTGCCCATAAAGATACCTTTTCATCTAGGAGCACGCTGGTGAAGAGATTGCAACCATT
GGAGGCTTGAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGACCACAACACATGCCA
TGCACATGAGAGCCTTTGGCGCCAAACATGAGAAGGCACATCACCATTCGGCCAAGGA
Found at i:154346 original size:23 final size:23
Alignment explanation
Indices: 154301--154346 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
154291 TTATACCTAT
*
154301 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
154324 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
154347 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:156311 original size:91 final size:91
Alignment explanation
Indices: 156136--156313 Score: 207
Period size: 91 Copynumber: 2.0 Consensus size: 91
156126 CCTAGAACAC
* * *
156136 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCATCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATATGGATCATTTAGGCACCAAGATG
** *
156201 AGGAGTTCTCTCCCTATTCGGCAAAG
66 AGGACATCTATCCCTATTCGGCAAAG
** * * * *
156227 CCATGTGTTTTGCATGTGATCAGCCCCCATGTACCTTGCATATGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATATGGATCATTTAGGCACCAAGATG
*
156292 AATGGCCATCTAT-CC-ATTCGGC
66 -A-GGACATCTATCCCTATTCGGC
156314 CAATCACCAT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
91 63 0.88
92 3 0.04
93 6 0.08
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATATGGATCATTTAGGCACCAAGATG
AGGACATCTATCCCTATTCGGCAAAG
Found at i:161972 original size:19 final size:21
Alignment explanation
Indices: 161929--161980 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
161919 GAAACCCCTT
161929 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
161950 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
161969 TGAAGATACATG
1 TGAAAATACATG
161981 CTCTTGGGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:165189 original size:8 final size:8
Alignment explanation
Indices: 165176--165200 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
165166 ACTTTTTCTT
165176 TTCTTTTC
1 TTCTTTTC
165184 TTCTTTTC
1 TTCTTTTC
165192 TTCTTTTC
1 TTCTTTTC
165200 T
1 T
165201 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:165594 original size:20 final size:21
Alignment explanation
Indices: 165556--165594 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
165546 TGATGGTCTT
*
165556 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGTTGACGATGAA
*
165577 ATGAA-GATGTTGGCGATG
1 ATGAAGGATGTTGACGATG
165595 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGTTGACGATGAA
Found at i:165974 original size:19 final size:21
Alignment explanation
Indices: 165931--165974 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
165921 GAAACCCCTT
165931 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
165952 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
165971 TGAA
1 TGAA
165975 GATAGATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 13 0.57
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:171518 original size:22 final size:21
Alignment explanation
Indices: 171491--171539 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
171481 ATGGTTGCGG
171491 AATTGATGGTCTTGATGGATGA
1 AATTGATGGTCTTGAT-GATGA
*
171513 TATTGATGGTCTTGATGATGA
1 AATTGATGGTCTTGATGATGA
171534 AATTGA
1 AATTGA
171540 GATGGTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (21 bp):
AATTGATGGTCTTGATGATGA
Found at i:175356 original size:19 final size:21
Alignment explanation
Indices: 175313--175364 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
175303 GAAATCCCTT
175313 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
175334 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
175353 TGAAGATACATG
1 TGAAAATACATG
175365 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:176260 original size:19 final size:21
Alignment explanation
Indices: 176217--176266 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
176207 GAAACCCCTT
176217 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
176238 TGAAACTACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
176257 TGAAGATACA
1 TGAAAATACA
176267 AGCTCTTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 4 0.15
21 12 0.46
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:176484 original size:903 final size:901
Alignment explanation
Indices: 174698--176511 Score: 2809
Period size: 903 Copynumber: 2.0 Consensus size: 901
174688 TCACAAGTTC
* *
174698 TGATGTAAGGCGAATCTACACGCTTTGATGGAAGAGAGTAGATAGCCTTATTGTGTCCCGATCTA
1 TGATGTAAGGCCAATCTACACGCTTTGATGGAAGAGAGTAGATAACCTTATTGTGTCCCGATCTA
* *
174763 GGATTGACAAGTACTGATGTCCTTGAATTTATAAGTTTGGGCTGCAAAATAAGATAAAAAAAGAA
66 GGATTGACAAGTACTGATGTCCTTGAATTTATAAGCTTGGGCTACAAAATAAGATAAAAAAAGAA
*
174828 TGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAAATAAATAATAAGAATGA
131 TGATTAATAATGGAATTAAGAAAGGGGATAATAATATAAGTAATG-----AAATAATAAGAATGA
*
174893 AATGAAATAAATAAAGGATAGAGATGGCTGCGGAATTGATGGAAGAGATGGATGATGTTGATGAT
191 AATG-AAT-AAT-AA-GATAGAGATGGCTGCGGAATTGATGGAAGAGATGGATGATGTGGATGAT
* *
174958 GAAATGGCAATGGTGGTGATGTTGTATCTCAAACACGCCAAAGAGGAAACTATGATATGAAGCAC
252 GAAATGGCAATGGTGGTGATGTTGTATCCCAAACACGCCAAAGAGGAAACTATGATAAGAAGCAC
*
175023 AATCTCGGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAAT
317 AATCCCGGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAAT
* * *
175088 CTAGAAATTTAGGAATCAAGATGGAAGGAATGACGCCACAAGTATAGAAACTATACTTGTTTAAT
382 CTAGAAATTTAGGAATCAAGATGGAAAGAATGACACCACAAGTATAGAAACTATACTTGCTTAAT
*
175153 CGATAAATTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTATATTTTATATAAGAGATG
447 CGATAAAGTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTATATTTTATATAAGAGATG
* * * *
175218 AGATGCTTACAAATGAAATGGCTAAGCCTATTTATAGTTTCAAAGGGTTTAGGCATAATAGGTAC
512 AGATGCATACAAATGAAATGCCAAAGCCTATTTATAGTTTCAAAGGGTTTAGGCAGAATAGGTAC
*
175283 ATGATGGTTCGACTATGCATGAAATCCCTTTGAAAATACATGACTTTTAAATGAAAATACATGAT
577 ATGATGGTTCGACTATGCATGAAACCCCTTTGAAAATACATGACTTTTAAATGAAAATACATGAT
*
175348 TTTAATGAAGATACATGCTCTTGGCCGAATAGTAAGGTGTTGGTTCGGCCTAAGGATGTTTTGAA
642 TTTAATGAAGATACAAGCTCTTGGCCGAATAGTAAGGTGTTGGTTCGGCCTAAGGATGTTTTGAA
**
175413 TGCTTTTGGAAGTCATTTGGGTGCCAAAATGGAGAGGAATAAGTCTTTGGCCGAATAGGAAGCAT
707 TGCTTTTGGAAGTCATTTGGGCACCAAAATGGAGAGGAATAAGTCTTTGGCCGAATAGGAAGCAT
* *
175478 CCCTTGGTGTTTTGGCACCTATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCACATGGC
772 CCCTTGGTGTTTTGACACCTATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCAAATGGC
175543 AGCCTACTTGAACGCACATGGGTCTTCTAGCAAGGCTTTGGTGAGGTTGAAACCATAGGATAATG
837 AGCCTACTTGAACGCACATGGGTCTTCTAGCAAGGCTTTGGTGAGGTTGAAACCATAGGATAATG
*
175608 TGATGTAAGGCCAATCTACACGCTTTGGT-G-AGAAGAGTAGATAACCTTATTGTGTCCCGATCT
1 TGATGTAAGGCCAATCTACACGCTTTGATGGAAG-AGAGTAGATAACCTTATTGTGTCCCGATCT
*
175671 AGGATTGACAAGTACTGATGTCCTTGAATTTATAAGCTTGGGCTACAAAATAAGATAAGAAAAGG
65 AGGATTGACAAGTACTGATGTCCTTGAATTTATAAGCTTGGGCTACAAAATAAGATAA-AAAAAG
* * * * *
175736 AAATAAGATTAATGATGGAATTAAGAAA-TGGATGATAATATAAGTAATG-GA-AATGA-AAT-A
129 -AAT--GATTAATAATGGAATTAAGAAAGGGGATAATAATATAAGTAATGAAATAATAAGAATGA
* * *
175796 AA-G-AT-AT-A-ATAGAGATGGCTGTGGAATTGATGGATTGATGGATGTTGTTGATGATGGGAA
191 AATGAATAATAAGATAGAGATGGCTGCGGAATTGATGGA-AGA--GATG--GATGATG-T-GG-A
* *
175856 TGATGAAAATGG-AGATGGTGGTGAT-TTGTATCCCAAACACGCCAAAGATGAAA-TAGTGCTAA
248 TGATG-AAATGGCA-ATGGTGGTGATGTTGTATCCCAAACACGCCAAAGAGGAAACTA-TGATAA
* *
175918 GGAGCACAATCCCTGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGA
310 GAAGCACAATCCCGGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGA
* * *
175983 TATCAATCTAGGAATTTTGGAATCAAGATGGAAAGAATGACACCACAAGTATATG-AATTATACT
375 TATCAATCTAGAAATTTAGGAATCAAGATGGAAAGAATGACACCACAAGTATA-GAAACTATACT
*
176047 TGCTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTATGTTTTATAT
439 TGCTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTATATTTTATAT
176112 AAGAGATGAGATAAG-ATACAAATGAAATGCCAAAGCCTATTTATAGTTTTCAAAGGGTTTAGGC
504 AAGAGATGAGAT--GCATACAAATGAAATGCCAAAGCCTATTTATAG-TTTCAAAGGGTTTAGGC
* * *
176176 CGAATAGGTACATGATGGTTCGGCTATGCCTGAAACCCCTTTGAAAATACATGACTTTTAAATGA
566 AGAATAGGTACATGATGGTTCGACTATGCATGAAACCCCTTTGAAAATACATGACTTTTAAATGA
*
176241 AACTACATGATTTTAATGAAGATACAAGCTCTTGGCCGAATAGTAA-GTGTTGGTTCGGCCTAAG
631 AAATACATGATTTTAATGAAGATACAAGCTCTTGGCCGAATAGTAAGGTGTTGGTTCGGCCTAAG
176305 GATGTTTTGAATGCTTTTGGAAGTCATTTGGGCACCAAAATGGAGAGGAATAAGTCTTTGGCCGA
696 GATGTTTTGAATGCTTTTGGAAGTCATTTGGGCACCAAAATGGAGAGGAATAAGTCTTTGGCCGA
*
176370 ATAGGAAGCATCCCTTGGTGTTTTGACGCCTATTTGATGTCACATGGAGTGCACATGCTTGAATG
761 ATAGGAAGCATCCCTTGGTGTTTTGACACCTATTTGATGTCACATGGAGTGCACATGCTTGAATG
* *
176435 ATGCAAATGGCAGCCTACTTGAATGCACATGGGTCTTCTTGCAAGGCTTTGGTGAGGTTGAAACC
826 ATGCAAATGGCAGCCTACTTGAACGCACATGGGTCTTCTAGCAAGGCTTTGGTGAGGTTGAAACC
176500 ATAGGATAATG
891 ATAGGATAATG
176511 T
1 T
176512 CTTGAAGTCC
Statistics
Matches: 836, Mismatches: 48, Indels: 47
0.90 0.05 0.05
Matches are distributed among these distances:
894 25 0.03
895 2 0.00
896 1 0.00
897 4 0.00
898 2 0.00
899 6 0.01
900 3 0.00
901 3 0.00
902 231 0.28
903 267 0.32
904 125 0.15
905 4 0.00
906 1 0.00
908 2 0.00
909 86 0.10
910 32 0.04
911 3 0.00
912 19 0.02
913 20 0.02
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (901 bp):
TGATGTAAGGCCAATCTACACGCTTTGATGGAAGAGAGTAGATAACCTTATTGTGTCCCGATCTA
GGATTGACAAGTACTGATGTCCTTGAATTTATAAGCTTGGGCTACAAAATAAGATAAAAAAAGAA
TGATTAATAATGGAATTAAGAAAGGGGATAATAATATAAGTAATGAAATAATAAGAATGAAATGA
ATAATAAGATAGAGATGGCTGCGGAATTGATGGAAGAGATGGATGATGTGGATGATGAAATGGCA
ATGGTGGTGATGTTGTATCCCAAACACGCCAAAGAGGAAACTATGATAAGAAGCACAATCCCGGT
CTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATCTAGAAATT
TAGGAATCAAGATGGAAAGAATGACACCACAAGTATAGAAACTATACTTGCTTAATCGATAAAGT
TCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTATATTTTATATAAGAGATGAGATGCATA
CAAATGAAATGCCAAAGCCTATTTATAGTTTCAAAGGGTTTAGGCAGAATAGGTACATGATGGTT
CGACTATGCATGAAACCCCTTTGAAAATACATGACTTTTAAATGAAAATACATGATTTTAATGAA
GATACAAGCTCTTGGCCGAATAGTAAGGTGTTGGTTCGGCCTAAGGATGTTTTGAATGCTTTTGG
AAGTCATTTGGGCACCAAAATGGAGAGGAATAAGTCTTTGGCCGAATAGGAAGCATCCCTTGGTG
TTTTGACACCTATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCAAATGGCAGCCTACTT
GAACGCACATGGGTCTTCTAGCAAGGCTTTGGTGAGGTTGAAACCATAGGATAATG
Found at i:179506 original size:19 final size:20
Alignment explanation
Indices: 179484--179528 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
179474 TTTGAACTTC
179484 TCTTTTTCTT-TTCTTT-TCT
1 TCTTTTTCTTATT-TTTCTCT
179503 TC-TTTTCTTATTTTTCTCT
1 TCTTTTTCTTATTTTTCTCT
179522 TCTTTTT
1 TCTTTTT
179529 GCACTCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 10 0.43
19 9 0.39
20 4 0.17
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (20 bp):
TCTTTTTCTTATTTTTCTCT
Found at i:180281 original size:19 final size:21
Alignment explanation
Indices: 180238--180289 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
180228 GAAACCCCTT
180238 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
180259 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
180278 TGAAGATACATG
1 TGAAAATACATG
180290 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:182289 original size:912 final size:912
Alignment explanation
Indices: 180527--182352 Score: 3348
Period size: 912 Copynumber: 2.0 Consensus size: 912
180517 CAACCATAGG
180527 ATAATGTCTTGAAGTCCATGGAATGAAGATGGCAGCAACTAGGCGTGACTTGGCTTCCAACATGC
1 ATAATGTCTTGAAGTCCATGGAATGAAGATGGCAGCAACTAGGCGTGACTTGGCTTCCAACATGC
*
180592 ATCTAGGTGTCATGGTCTTCAATGGGCAGCAACTTGTCATGAAAGGTCACATTTGTGGAAGGTAA
66 ATCTAGGTGTCATGGTATTCAATGGGCAGCAACTTGTCATGAAAGGTCACATTTGTGGAAGGTAA
* * *
180657 CCTTTCATCATTTGAGCTAGTTCCCATTTGTATGAGCTGAAGATAAGCTGGTCATAGGTGAATTA
131 CCTTTCATCATTTGAGCTACTTCCCATGTGTATGAGATGAAGATAAGCTGGTCATAGGTGAATTA
*
180722 CATGAAGATGAGTCTTTGGCCAGCTCCTTGTGAAAAGACACCTCTTGGAATGGCAACTCTTCACG
196 CATGAAGATGAGGCTTTGGCCAGCTCCTTGTGAAAAGACACCTCTTGGAATGGCAACTCTTCACG
*
180787 AAAAGGTACGAATCCACAAAAATTGACTTATACCATATTTGAAGTACTCTATGTGGTGGTGATGA
261 AAAAGGTACGAATCCACAAAAATTGACTTAGACCATATTTGAAGTACTCTATGTGGTGGTGATGA
* *
180852 TGGTGCAACTCTCCAGCTGAAATGAGGTCTCTATCTAGCTCAAAAGTCTAGCTCAAGTGAGCTAT
326 TGGTGCAACTCTCCAGCTGAAATGAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTAT
*
180917 GAGCTCGGGGGTCAGCTGACAACTTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATG
391 GAGCTCAGGGGTCAGCTGACAACTTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATG
180982 AAAGTTTTCCTAGCTCCTTATCATTAGTTAAGCTCAAATATATCTCCCAAGTGTTGGCCGAATAT
456 AAAGTTTTCCTAGCTCCTTATCATTAGTTAAGCTCAAATATATCTCCCAAGTGTTGGCCGAATAT
*
181047 GCCTACATGCATAACATAAAGAAATAAACTAAGTATATAAACTATATAATGCATATAATATAATG
521 GCCTACATGCATAACATAAAGAAATAAACTAAGCATATAAACTATATAATGCATATAATATAATG
*
181112 ATGTGCATATTATAAAGATGTGAACTATACGTTATAATAATAATTTATGCATCATATGATAATGA
586 ATGTGCATATTATAAAGATGTGAACTATACGTTATAATAATAATTCATGCATCATATGATAATGA
181177 ATGAATATTAATATTATAACTATAGATTATATACATGAATATCAATCAATGATGCAAACCATAGG
651 ATGAATATTAATATTATAACTATAGATTATATACATGAATATCAATCAATGATGCAAACCATAGG
*
181242 ATATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGTATGCTCA
716 ATATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCAAATATGCAAATGTATGCTCA
* * * *
181307 TAATAATATATATAGTGCGTAAATCAGTAAATATAATATAATGTATGGTATAACTCCCTTATATT
781 TAATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATT
*
181372 GAGTTTGATGGTTCTTCAATGATGTAAGTATGCCATGCAGAAAGTTGGTGCTAAACAGGATCACT
846 GAGTTTGATGGTTCTTCAATGATGTAAGTATGCCATGCAGAAAGTTGGTGCTAAACAGGATCACA
181437 TC
911 TC
*
181439 ATAATGTCTTGAAGTCCATGGAATGAAGATTGCAGCAACTAGGCGTGACTTGGCTTCCAACATGC
1 ATAATGTCTTGAAGTCCATGGAATGAAGATGGCAGCAACTAGGCGTGACTTGGCTTCCAACATGC
*
181504 ATCTAGGTGTCATGGTATTCAATGGGCAGTAACTTGTCATGAAAGGTCACATTTGTGGAAGGTAA
66 ATCTAGGTGTCATGGTATTCAATGGGCAGCAACTTGTCATGAAAGGTCACATTTGTGGAAGGTAA
*
181569 CCTTTCATCATTTGAGCTACTTCCCATGTGTATGAGATGAAGATGAGCTGGTCATAGGTGAATTA
131 CCTTTCATCATTTGAGCTACTTCCCATGTGTATGAGATGAAGATAAGCTGGTCATAGGTGAATTA
* *
181634 CATGAAGATGAGGCTTTGGCCAGCTCCTTGTGAAAAGGCACCTCTTGGAATGGCAACTCTTCGCG
196 CATGAAGATGAGGCTTTGGCCAGCTCCTTGTGAAAAGACACCTCTTGGAATGGCAACTCTTCACG
* * *
181699 AAAAGGTACGAATCCACAAAAATTGACTTAGACTATATTTGAAGTACTCTGTGTTGTGGTGATGA
261 AAAAGGTACGAATCCACAAAAATTGACTTAGACCATATTTGAAGTACTCTATGTGGTGGTGATGA
181764 TGGTGCAACTCTCCAGCTGAAATGAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTAT
326 TGGTGCAACTCTCCAGCTGAAATGAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTAT
*
181829 GAGCTCAGGGGTCAGCTGGCAACTTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATG
391 GAGCTCAGGGGTCAGCTGACAACTTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATG
* *
181894 AAAGTTTTCCTAGCTCCTTATCATTATTTAAGCTCAAATATAGT-TTCCAAGTGTTGGCCGAATA
456 AAAGTTTTCCTAGCTCCTTATCATTAGTTAAGCTCAAATATA-TCTCCCAAGTGTTGGCCGAATA
*
181958 TGCCTACATGCATAACATAAAGAAATAAACTAAGCATATAAACTATATAATGCATATAATATATT
520 TGCCTACATGCATAACATAAAGAAATAAACTAAGCATATAAACTATATAATGCATATAATATAAT
182023 GATGTGCATATTATAAAGATGTGAACTATACGTTATAATAATAATTCATGCATCATATGATAATG
585 GATGTGCATATTATAAAGATGTGAACTATACGTTATAATAATAATTCATGCATCATATGATAATG
*
182088 AATGAATATTAATATTATAACTATATATTATATACATGAATATCAATCAATGATGCAAACCATAG
650 AATGAATATTAATATTATAACTATAGATTATATACATGAATATCAATCAATGATGCAAACCATAG
182153 GATATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCAAATATGCAAATGTATGCTC
715 GATATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCAAATATGCAAATGTATGCTC
182218 ATAATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATAT
780 ATAATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATAT
* *
182283 TGAGTTTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCAC
845 TGAGTTTGATGGTTCTTCAATGATGTAAGTATGCCATGCAGAAAGTTGGTGCTAAACAGGATCAC
182348 ATC
910 ATC
182351 AT
1 AT
182353 CATCCCCTTC
Statistics
Matches: 881, Mismatches: 32, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
912 880 1.00
913 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (912 bp):
ATAATGTCTTGAAGTCCATGGAATGAAGATGGCAGCAACTAGGCGTGACTTGGCTTCCAACATGC
ATCTAGGTGTCATGGTATTCAATGGGCAGCAACTTGTCATGAAAGGTCACATTTGTGGAAGGTAA
CCTTTCATCATTTGAGCTACTTCCCATGTGTATGAGATGAAGATAAGCTGGTCATAGGTGAATTA
CATGAAGATGAGGCTTTGGCCAGCTCCTTGTGAAAAGACACCTCTTGGAATGGCAACTCTTCACG
AAAAGGTACGAATCCACAAAAATTGACTTAGACCATATTTGAAGTACTCTATGTGGTGGTGATGA
TGGTGCAACTCTCCAGCTGAAATGAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTAT
GAGCTCAGGGGTCAGCTGACAACTTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATG
AAAGTTTTCCTAGCTCCTTATCATTAGTTAAGCTCAAATATATCTCCCAAGTGTTGGCCGAATAT
GCCTACATGCATAACATAAAGAAATAAACTAAGCATATAAACTATATAATGCATATAATATAATG
ATGTGCATATTATAAAGATGTGAACTATACGTTATAATAATAATTCATGCATCATATGATAATGA
ATGAATATTAATATTATAACTATAGATTATATACATGAATATCAATCAATGATGCAAACCATAGG
ATATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCAAATATGCAAATGTATGCTCA
TAATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATT
GAGTTTGATGGTTCTTCAATGATGTAAGTATGCCATGCAGAAAGTTGGTGCTAAACAGGATCACA
TC
Found at i:183966 original size:11 final size:11
Alignment explanation
Indices: 183942--183986 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
183932 TTGGTGCTGG
183942 AAACAAGATAA
1 AAACAAGATAA
* *
183953 AAATAAGATTA
1 AAACAAGATAA
183964 AAACAAGATAA
1 AAACAAGATAA
183975 AGAA-AAGATAA
1 A-AACAAGATAA
183986 A
1 A
183987 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:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:183970 original size:22 final size:22
Alignment explanation
Indices: 183942--183983 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
183932 TTGGTGCTGG
183942 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
183964 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
183984 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:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:188186 original size:10 final size:10
Alignment explanation
Indices: 188171--188196 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
188161 AAAATTTGGC
188171 TTTTTTTTGT
1 TTTTTTTTGT
188181 TTTTTTTTGT
1 TTTTTTTTGT
188191 TTTTTT
1 TTTTTT
188197 GAAAAAAATA
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:188539 original size:11 final size:11
Alignment explanation
Indices: 188515--188559 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
188505 TTAGTGCTGG
188515 AAACAAGATAA
1 AAACAAGATAA
* *
188526 AAATAAGATTA
1 AAACAAGATAA
188537 AAACAAGATAA
1 AAACAAGATAA
188548 AGAA-AAGATAA
1 A-AACAAGATAA
188559 A
1 A
188560 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:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:188543 original size:22 final size:22
Alignment explanation
Indices: 188515--188556 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
188505 TTAGTGCTGG
188515 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
188537 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
188557 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:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:190887 original size:19 final size:20
Alignment explanation
Indices: 190846--190897 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
190836 AACCCCTTTA
190846 AAAATACATGACTTTTAAATG
1 AAAATACATGA-TTTTAAATG
190867 AAAATACATGATTTT-AATG
1 AAAATACATGATTTTAAATG
*
190886 AAGATACATGAT
1 AAAATACATGAT
190898 CTTGGCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 15 0.50
20 4 0.13
21 11 0.37
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (20 bp):
AAAATACATGATTTTAAATG
Found at i:192278 original size:12 final size:14
Alignment explanation
Indices: 192260--192291 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
192250 ATAGGTTAGG
192260 GTAGAAA-GGAAAA
1 GTAGAAATGGAAAA
192273 -TAGAAATGGAAAA
1 GTAGAAATGGAAAA
192286 GTAGAA
1 GTAGAA
192292 GAAAAGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.12
Consensus pattern (14 bp):
GTAGAAATGGAAAA
Found at i:192559 original size:17 final size:17
Alignment explanation
Indices: 192533--192567 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
192523 CTTATTTCCT
192533 TCTTTTCTTTCCTTTTG
1 TCTTTTCTTTCCTTTTG
*
192550 TCTTTTCTTTCTTTTTG
1 TCTTTTCTTTCCTTTTG
192567 T
1 T
192568 ACTCTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.74
Consensus pattern (17 bp):
TCTTTTCTTTCCTTTTG
Found at i:195212 original size:25 final size:24
Alignment explanation
Indices: 195184--195230 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
195174 CAACAAAAGC
*
195184 AACAAACAGAAAAAGAAAGAAGAAA
1 AACAAAAAGAAAAAGAAA-AAGAAA
*
195209 AACAAAAAGAGAAAGAAAAAGA
1 AACAAAAAGAAAAAGAAAAAGA
195231 CTCCTACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGAAAAAGAAAAAGAAA
Found at i:195223 original size:6 final size:6
Alignment explanation
Indices: 195191--195230 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
195181 AGCAACAAAC
* *
195191 AGAAAA AGAAAGA AGAAAA ACAAAA AGAGAA AGAAAA AGA
1 AGAAAA AGAAA-A AGAAAA AGAAAA AGAAAA AGAAAA AGA
195231 CTCCTACAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:199301 original size:30 final size:30
Alignment explanation
Indices: 199265--199325 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
199255 AAACAACATG
199265 TTTGCCAACTTCTCTATTATTAAAGAAGCC
1 TTTGCCAACTTCTCTATTATTAAAGAAGCC
199295 TTTGCCAACTTCTCTATTATTAAAGAAGCC
1 TTTGCCAACTTCTCTATTATTAAAGAAGCC
199325 T
1 T
199326 GGTTAGCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (30 bp):
TTTGCCAACTTCTCTATTATTAAAGAAGCC
Found at i:201006 original size:22 final size:21
Alignment explanation
Indices: 200980--201020 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
200970 GGCTGCGGAA
*
200980 TTGATAGTCTTGATGGATGATG
1 TTGATAGTATTGAT-GATGATG
*
201002 TTGATGGTATTGATGATGA
1 TTGATAGTATTGATGATGA
201021 AATGGAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.24, C:0.02, G:0.32, T:0.41
Consensus pattern (21 bp):
TTGATAGTATTGATGATGATG
Found at i:207803 original size:19 final size:20
Alignment explanation
Indices: 207762--207812 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
207752 GAAACCCCTT
* *
207762 TGAAAATACATTATTTTTGA
1 TGAAAATACATGATTTTTAA
207782 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
207801 TGAAGATACATG
1 TGAAAATACATG
207813 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:208135 original size:201 final size:201
Alignment explanation
Indices: 207790--208193 Score: 799
Period size: 201 Copynumber: 2.0 Consensus size: 201
207780 GATGAAAATA
207790 CATGATTTTAATGAAGATACATGCTCTTGGCCGAATAGTTATGTGTTGGTTCGGCCCTAAGGATG
1 CATGATTTTAATGAAGATACATGCTCTTGGCCGAATAGTTATGTGTTGGTTCGGCCCTAAGGATG
207855 ATTTGAATGCATTTGGAAGTTATTTGGGCGCCAAAATGGAGAGGAAGGAGTCTTTGGCCGAATAG
66 ATTTGAATGCATTTGGAAGTTATTTGGGCGCCAAAATGGAGAGGAAGGAGTCTTTGGCCGAATAG
207920 GAAGCATCCCTTGGTGTTTTGGCGCCTATTTGATGTCACATGGAGTGCACATGCTTGAATGATGC
131 GAAGCATCCCTTGGTGTTTTGGCGCCTATTTGATGTCACATGGAGTGCACATGCTTGAATGATGC
207985 ACATGG
196 ACATGG
*
207991 CATGATTTTAATGAAGATACATGCTCTTGGCCGAATGGTTATGTGTTGGTTCGGCCCTAAGGATG
1 CATGATTTTAATGAAGATACATGCTCTTGGCCGAATAGTTATGTGTTGGTTCGGCCCTAAGGATG
208056 ATTTGAATGCATTTGGAAGTTATTTGGGCGCCAAAATGGAGAGGAAGGAGTCTTTGGCCGAATAG
66 ATTTGAATGCATTTGGAAGTTATTTGGGCGCCAAAATGGAGAGGAAGGAGTCTTTGGCCGAATAG
208121 GAAGCATCCCTTGGTGTTTTGGCGCCTATTTGATGTCACATGGAGTGCACATGCTTGAATGATGC
131 GAAGCATCCCTTGGTGTTTTGGCGCCTATTTGATGTCACATGGAGTGCACATGCTTGAATGATGC
208186 ACATGG
196 ACATGG
208192 CA
1 CA
208194 GCCTACTTGA
Statistics
Matches: 202, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 202 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (201 bp):
CATGATTTTAATGAAGATACATGCTCTTGGCCGAATAGTTATGTGTTGGTTCGGCCCTAAGGATG
ATTTGAATGCATTTGGAAGTTATTTGGGCGCCAAAATGGAGAGGAAGGAGTCTTTGGCCGAATAG
GAAGCATCCCTTGGTGTTTTGGCGCCTATTTGATGTCACATGGAGTGCACATGCTTGAATGATGC
ACATGG
Found at i:209045 original size:22 final size:20
Alignment explanation
Indices: 209000--209045 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
208990 AAGTAAAGAT
209000 GTGAAAATATATGTTATGAA
1 GTGAAAATATATGTTATGAA
209020 -TGAAAATCATATAG-TATGCAA
1 GTGAAAAT-ATAT-GTTATG-AA
209041 GTGAA
1 GTGAA
209046 TGATATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.32
20 8 0.36
21 3 0.14
22 4 0.18
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (20 bp):
GTGAAAATATATGTTATGAA
Found at i:209324 original size:16 final size:16
Alignment explanation
Indices: 209290--209338 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
209280 GTAAGTTATC
* * *
209290 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
209306 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
209322 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
209339 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:213332 original size:10 final size:9
Alignment explanation
Indices: 213312--213350 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
213302 CCAACAGTCA
213312 AAAAG-AAG
1 AAAAGAAAG
213320 AAAAGCAAAG
1 AAAAG-AAAG
213330 AAAAGAAAAG
1 AAAAG-AAAG
213340 AAAAGAAAG
1 AAAAGAAAG
213349 AA
1 AA
213351 GTTGAAGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 5 0.18
9 6 0.21
10 17 0.61
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:213334 original size:5 final size:5
Alignment explanation
Indices: 213317--213347 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
213307 AGTCAAAAAG
*
213317 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
213348 GAAGTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:215941 original size:15 final size:15
Alignment explanation
Indices: 215917--215952 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
215907 TTTGATAACT
*
215917 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
215932 ATTCTTTCCATTTCA
1 ATTCTTTCCATTTCA
*
215947 TTTCTT
1 ATTCTT
215953 AATTACTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Done.