Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004201.1 Hibiscus syriacus cultivar Beakdansim tig00009193_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: 111037
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4406 original size:20 final size:20
Alignment explanation
Indices: 4377--4415 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4367 ATTTCACCAC
*
4377 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
4397 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
4416 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:18024 original size:32 final size:32
Alignment explanation
Indices: 17988--18055 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
17978 CCATCAATAG
* *
17988 TGAAAGAAT-GATGTTGTTGTTGCCACCGACGA
1 TGAAAGAATGGA-GATGTTGTTGCCACAGACGA
*
18020 TGAAAGAATGGAGATGTTGTTGCCACAGACGG
1 TGAAAGAATGGAGATGTTGTTGCCACAGACGA
18052 TGAA
1 TGAA
18056 CAAGAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (32 bp):
TGAAAGAATGGAGATGTTGTTGCCACAGACGA
Found at i:18391 original size:21 final size:21
Alignment explanation
Indices: 18366--18405 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18356 AGAAATATTA
*
18366 AAAAACATTAATATTTTAGGT
1 AAAAACAATAATATTTTAGGT
*
18387 AAAAATAATAATATTTTAG
1 AAAAACAATAATATTTTAG
18406 ATAATCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAAACAATAATATTTTAGGT
Found at i:19092 original size:31 final size:32
Alignment explanation
Indices: 19049--19121 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
19039 TTAACATGTG
* *
19049 GTGACCACATCTTAATT-AAATAAATACGAAA
1 GTGACCATATCTTAATTAAAATAAAAACGAAA
19080 GTGACCATATCTTAATTAAAATAAAAACGAAA
1 GTGACCATATCTTAATTAAAATAAAAACGAAA
*
19112 GTGATCATAT
1 GTGACCATAT
19122 ATTATTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 16 0.42
32 22 0.58
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (32 bp):
GTGACCATATCTTAATTAAAATAAAAACGAAA
Found at i:30433 original size:19 final size:19
Alignment explanation
Indices: 30409--30446 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
30399 TCTTGAACTG
30409 TTTCATT-CATTAATCTTCA
1 TTTCATTGC-TTAATCTTCA
30428 TTTCATTGCTTAATCTTCA
1 TTTCATTGCTTAATCTTCA
30447 ATGAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTCATTGCTTAATCTTCA
Found at i:34024 original size:23 final size:23
Alignment explanation
Indices: 33990--34054 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
33980 CACCACAGCT
* *
33990 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
34013 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
34036 CGTAGAAATGCACCAAAGT
1 CGTAGAAATGCACCGAAGT
34055 ACCATATAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:34999 original size:2 final size:2
Alignment explanation
Indices: 34992--35019 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34982 ATCTTACGTT
34992 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35020 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:35024 original size:2 final size:2
Alignment explanation
Indices: 35019--35050 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35009 ACACACACAC
35019 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
35051 CAATGGTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39002 original size:23 final size:23
Alignment explanation
Indices: 38966--39034 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
38956 CACCACAGCT
* *
38966 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
38989 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
39012 CGTAGAAATGCACCAAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
39035 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:39967 original size:2 final size:2
Alignment explanation
Indices: 39960--40047 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
39950 ACGTTTGCAC
**
39960 AT AT AT AT AT GG 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
40002 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
40044 AT AT
1 AT AT
40048 CAATGGTTTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43638 original size:23 final size:23
Alignment explanation
Indices: 43612--43680 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
43602 CACCACAGCT
*
43612 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
43635 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
43658 CGTAGAAATACACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
43681 TATTAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:44609 original size:2 final size:2
Alignment explanation
Indices: 44604--44661 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
44594 ACGTTCACAC
**
44604 AT AT AT AT AT GG 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
44646 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
44662 CAATGGTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48591 original size:23 final size:23
Alignment explanation
Indices: 48565--48633 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
48555 CACCACAGCT
* *
48565 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
48588 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
48611 CGTAGAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
48634 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:49565 original size:2 final size:2
Alignment explanation
Indices: 49560--49599 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
49550 TCACACACAC
*
49560 AT AT AT AT AT AT AT AT AT AT GT 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
49600 CAATGGTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52162 original size:21 final size:20
Alignment explanation
Indices: 52136--52190 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
52126 TATATCTAAA
*
52136 TTGAAATCCATAACAACAAAC
1 TTGAAATCCATAA-AAAAAAC
52157 TTGAAATCCATATAAAAAAAC
1 TTGAAATCCATA-AAAAAAAC
52178 TTGAAATCCATAA
1 TTGAAATCCATAA
52191 TAATAAATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (20 bp):
TTGAAATCCATAAAAAAAAC
Found at i:53157 original size:26 final size:27
Alignment explanation
Indices: 53121--53189 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
53111 TTAATAAAAT
*
53121 ATTTATCTAAAAATAA-TTAAAATATATA
1 ATTTAT-TAAAAATAAGATAAAATAT-TA
* *
53149 ATTTA-TAAAAGTAAGATAAAATATTT
1 ATTTATTAAAAATAAGATAAAATATTA
53175 ATTTATTTAAAAATA
1 ATTTA-TTAAAAATA
53190 TCAAAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 14 0.41
27 8 0.24
28 12 0.35
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (27 bp):
ATTTATTAAAAATAAGATAAAATATTA
Found at i:53282 original size:144 final size:140
Alignment explanation
Indices: 52998--53276 Score: 346
Period size: 144 Copynumber: 1.9 Consensus size: 140
52988 TAATTTTATG
* * * * *
52998 AAAATATATTAATTTAAATATAAATAAGATATTTATTTATTTAGAAATATCACAAAATGGCTTCT
1 AAAATATATTAATTTAAAAATAAATAAAATATTTATTTATTTAAAAATATCAAAAAATGGCATCT
* * * *
53063 AGGTGCTTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTATC
66 AGGTGCTTTAAGACAGCCCCTTTCTTAATATTAAAAAATAAATAAACATGAATAAAATAATTATC
53128 TAAAAATAATT
131 -AAAAATAATT
53139 AAAATATA-TAATTTATAAAAGTAAGATAAAATATTTATTTATTTAAAAATATCAAAAAATGGAC
1 AAAATATATTAATTTA-AAAA-TAA-ATAAAATATTTATTTATTTAAAAATATCAAAAAATGG-C
* * * * *
53203 ATCTAGTTGCTTTAAGACTGCCCCTTTCTTAATATTGAAAACTAAATTGAAAACATGATTAAAAT
62 ATCTAGGTGCTTTAAGACAGCCCCTTTCTTAATATTAAAAAATAAA-T--AAACATGAATAAAAT
53268 AATT-TCAAA
124 AATTATCAAA
53277 GTAATTTATA
Statistics
Matches: 117, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
140 7 0.06
141 11 0.09
142 3 0.03
143 34 0.29
144 41 0.35
145 4 0.03
146 2 0.02
147 15 0.13
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37
Consensus pattern (140 bp):
AAAATATATTAATTTAAAAATAAATAAAATATTTATTTATTTAAAAATATCAAAAAATGGCATCT
AGGTGCTTTAAGACAGCCCCTTTCTTAATATTAAAAAATAAATAAACATGAATAAAATAATTATC
AAAAATAATT
Found at i:54728 original size:3 final size:3
Alignment explanation
Indices: 54720--54789 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
54710 TGTAATTATT
* * *
54720 TAA TAA TAA -AA -AA TATA TATA TAA TAA TAA TTA TTA TAA TTA TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
54765 TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TA
54790 TTCAAATAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
2 8 0.14
3 41 0.71
4 9 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:54764 original size:18 final size:18
Alignment explanation
Indices: 54712--54768 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
54702 ATGATATTTG
54712 TAATTATT-TAATAATAA
1 TAATTATTATAATAATAA
* *
54729 AAAATA-TATATATAATAA
1 TAATTATTATA-ATAATAA
*
54747 TAATTATTATAATTATAA
1 TAATTATTATAATAATAA
54765 TAAT
1 TAAT
54769 AATAATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.03
17 6 0.19
18 21 0.66
19 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTATTATAATAATAA
Found at i:55170 original size:122 final size:124
Alignment explanation
Indices: 55024--55676 Score: 688
Period size: 122 Copynumber: 5.4 Consensus size: 124
55014 GTTGAACAAA
*
55024 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-CTTCTGGAAATGCTGATACTGA
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTC-TCTGGAAATGCTGATACTGA
* *
55087 TCTATCTCCTTCTGTGATAGAATCAAAC-AAAGGTTGAACAAGTTCATCTCATTATGAAC
65 TCTATCTCATTCTGTGATAGAATCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * *
55146 TTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTACGAACTTTCTCTGGAAA---AG-T--TG--
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATACTGAT
** * *
55202 --ATC-CATTGAGTAAT-GAATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
66 CTATCTCATTCTGTGATAGAA-TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * * * * *
55258 TTCTTATTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTGTCTCTGGAAAGGTTGATACTGAT
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATACTGAT
* * * ** *
55323 TTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
66 CTATCTCATTCTGTGATAGAATCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * *
55382 TTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAATGCTGGTAATG-
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGG-AAATGCTGATACTGA
** * * *
55445 -CTAATC-CATTGGGTGAT-GAATTAAAGCAAAAAGTTGAACAAGTTCTTCTCATTGTGAAC
65 TCT-ATCTCATTCTGTGATAGAATCAAA-CAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * * * * **
55504 TTCTTC-TCCTTTTTCAGATGAGTTCTTCTTATTATGAACACT-TCTGGAAATGTTGATGTTGAT
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATACTGAT
** * ** *
55567 CTATCTGTTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
66 CTATCTCATTCTGTGATAGAATCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
55626 TTCTTCTTCCTT-TTCAAATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAA
55677 AGTTGATCCA
Statistics
Matches: 435, Mismatches: 69, Indels: 53
0.78 0.12 0.10
Matches are distributed among these distances:
110 3 0.01
111 13 0.03
112 41 0.09
113 37 0.09
116 3 0.01
117 1 0.00
118 1 0.00
119 3 0.01
120 10 0.02
121 15 0.03
122 184 0.42
123 62 0.14
124 60 0.14
125 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (124 bp):
TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATACTGAT
CTATCTCATTCTGTGATAGAATCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:55649 original size:244 final size:234
Alignment explanation
Indices: 55024--55704 Score: 961
Period size: 244 Copynumber: 2.9 Consensus size: 234
55014 GTTGAACAAA
* *
55024 TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGCTGATACTGATC
1 TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-ACTTCTGGAAATGTTGATACTGATC
* ** * *
55089 TATCTCCTTCTGTGATAGAATCAAAC-AAAGGTTGAACAAGTTCATCTCATTATGAACTTCTTCT
65 TATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
*
55153 TCCTCTTCAGATAAGTTCTTCTCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGA
130 TCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGA
*
55218 ATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
195 ATTCAAACAAAAAGTTAAACAAGTTCTTCTCATTATGAAC
* * ** *
55258 TTCTTATTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTGTCTCTGGAAAGGTTGATACTGAT
1 TTCTT-CTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGGAAATGTTGATACTGAT
*
55323 TTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
64 CTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
55388 TTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAATGCTGGTAATGCTAATCCA
129 TTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-----GT--TG---ATCCA
* * * *
55453 TTGGGTGATGAATT-AAAGCAAAAAGTTGAACAAGTTCTTCTCATTGTGAAC
184 TTGAGTAATGAATTCAAA-CAAAAAGTTAAACAAGTTCTTCTCATTATGAAC
* * **
55504 TTCTTCTCCTTTTTCAGATGAGTTCTTCTTATTATGAACACTTCTGGAAATGTTGATGTTGATCT
1 TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATACTGATCT
**
55569 ATCTGTTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT
66 ATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT
* * * *
55634 CCTTTTCAAATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTGATGGA
131 CCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAA
55699 TTCAAA
196 TTCAAA
55705 TCTTGCTAAA
Statistics
Matches: 398, Mismatches: 34, Indels: 29
0.86 0.07 0.06
Matches are distributed among these distances:
234 23 0.06
235 77 0.19
236 80 0.20
237 2 0.01
239 2 0.01
241 2 0.01
243 2 0.01
244 124 0.31
245 34 0.09
246 52 0.13
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (234 bp):
TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATACTGATCT
ATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT
CCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAA
TTCAAACAAAAAGTTAAACAAGTTCTTCTCATTATGAAC
Found at i:58713 original size:16 final size:16
Alignment explanation
Indices: 58692--58724 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58682 AAGGTGACTT
58692 TCTCAAATTCTTTCAC
1 TCTCAAATTCTTTCAC
58708 TCTCAAATTCTTTCAC
1 TCTCAAATTCTTTCAC
58724 T
1 T
58725 AATTCGAGAG
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:0.24, C:0.30, G:0.00, T:0.45
Consensus pattern (16 bp):
TCTCAAATTCTTTCAC
Found at i:64633 original size:16 final size:16
Alignment explanation
Indices: 64614--64647 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
64604 TGCAATGAAT
*
64614 AATGAATGTGTGCAAA
1 AATGAATGTATGCAAA
64630 AATGAATGTATGCAAA
1 AATGAATGTATGCAAA
64646 AA
1 AA
64648 GGTATTGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.24
Consensus pattern (16 bp):
AATGAATGTATGCAAA
Found at i:67862 original size:24 final size:24
Alignment explanation
Indices: 67801--67862 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
67791 ATTTAATAAC
67801 TGAAAATAA-AATA-AAACATTAA
1 TGAAAATAATAATATAAACATTAA
*
67823 T-AAAATAATATATATAAATATT-A
1 TGAAAATAATA-ATATAAACATTAA
67846 TGAAAATAATAAGTATA
1 TGAAAATAATAA-TATA
67863 TATAAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 7 0.21
22 2 0.06
23 6 0.18
24 19 0.56
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (24 bp):
TGAAAATAATAATATAAACATTAA
Found at i:67877 original size:28 final size:27
Alignment explanation
Indices: 67826--67879 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
67816 ACATTAATAA
*
67826 AATAATATATATAAATATTATGAAAAT
1 AATAATATATATAAAAATTATGAAAAT
*
67853 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAATTATGAAAA
67880 GAAAGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AATAATATATATAAAAATTATGAAAAT
Found at i:68487 original size:18 final size:18
Alignment explanation
Indices: 68464--68519 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
68454 CTCCTTTCTT
68464 AATATTAAAAAATAATTA
1 AATATTAAAAAATAATTA
68482 AATATTAATAAAAT-ATT-
1 AATATTAA-AAAATAATTA
68499 --TATCT-AAAAATAATTA
1 AATAT-TAAAAAATAATTA
68515 AATAT
1 AATAT
68520 ATAATTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 5 0.16
15 7 0.22
16 1 0.03
18 14 0.44
19 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATTAAAAAATAATTA
Found at i:70014 original size:3 final size:3
Alignment explanation
Indices: 70006--70061 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
69996 TGTAATTATT
* *
70006 TAA TAA TAA TGA TAA AAA TATA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
70051 T-A TAAA TAA TA
1 TAA T-AA TAA TA
70062 TTCAAATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.80
4 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:70034 original size:22 final size:22
Alignment explanation
Indices: 70006--70047 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
69996 TGTAATTATT
*
70006 TAATAATAATGATAAAAATATA
1 TAATAATAATAATAAAAATATA
*
70028 TAATAATAATAATAATAATA
1 TAATAATAATAATAAAAATA
70048 AAATATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATAAAAATATA
Found at i:70040 original size:25 final size:26
Alignment explanation
Indices: 70006--70061 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 26
69996 TGTAATTATT
*
70006 TAATAATAATGATAAAAATATATAATAA
1 TAATAATAATAAT-AAAATATA-AATAA
70034 TAATAATAATAATAAAATATAAATAA
1 TAATAATAATAATAAAATATAAATAA
70060 TA
1 TA
70062 TTCAAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 7 0.26
27 8 0.30
28 12 0.44
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (26 bp):
TAATAATAATAATAAAATATAAATAA
Found at i:70075 original size:25 final size:27
Alignment explanation
Indices: 70006--70075 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
69996 TGTAATTATT
70006 TAATAATAATGATAAAAATATATAATAA
1 TAATAATAATGA-AAAAATATATAATAA
70034 TAATAATAAT-AATAAAATATA-AATAA
1 TAATAATAATGAA-AAAATATATAATAA
* *
70060 TATTCA-AATGAAAAAA
1 TAATAATAATGAAAAAA
70076 ACGAGTATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.18
26 12 0.32
27 9 0.24
28 10 0.26
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
TAATAATAATGAAAAAATATATAATAA
Found at i:72915 original size:16 final size:16
Alignment explanation
Indices: 72874--72916 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
72864 CAATTAGTAA
*
72874 TTAGCGGTTAGAAATG
1 TTAGCGGTTAGAAAAG
**
72890 TTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
72906 TTAGCGGTTAG
1 TTAGCGGTTAG
72917 TAGAGTCCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:73127 original size:4 final size:4
Alignment explanation
Indices: 73118--73151 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
73108 TATTAGAAAC
73118 AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
73152 AATGGTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:73154 original size:127 final size:127
Alignment explanation
Indices: 72912--73152 Score: 335
Period size: 127 Copynumber: 1.9 Consensus size: 127
72902 AAAGTTAGCG
* * *
72912 GTTAGTAGAGTCCGAATCATAATAATGTGGATCATACCTCGGATCGGGTCACCACAAGGTCGAAT
1 GTTAGTAGAGTCCGAATCATAATAATGAGGATCATACCCCGGATCGAGTCACCACAAGGTCGAAT
* * *** *
72977 CAAACATTATAAATAATAAATAAATAAATAATGGTTAGAATGCAATAAAATAAAAGTCAGTA
66 CAAACATTAGAAACAATAAATAAATAAATAATAAATAGAATGAAATAAAATAAAAGTCAGTA
73039 GTTAGTAGAGTCCGAA-CAATAATAATGAGGATCATACCCCGGATCGAGTCACCACAAGGTCGAA
1 GTTAGTAGAGTCCGAATC-ATAATAATGAGGATCATACCCCGGATCGAGTCACCACAAGGTCGAA
** *
73103 TTGAATATTAGAAACAATAAATAAATAAATAAATAAATA-AAT-AAATAAAA
65 TCAAACATTAGAAACAATAAATAAATAAAT-AATAAATAGAATGAAATAAAA
73153 ATGGTTAAAG
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
126 8 0.08
127 87 0.87
128 5 0.05
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (127 bp):
GTTAGTAGAGTCCGAATCATAATAATGAGGATCATACCCCGGATCGAGTCACCACAAGGTCGAAT
CAAACATTAGAAACAATAAATAAATAAATAATAAATAGAATGAAATAAAATAAAAGTCAGTA
Found at i:73171 original size:146 final size:146
Alignment explanation
Indices: 72985--73281 Score: 420
Period size: 146 Copynumber: 2.0 Consensus size: 146
72975 ATCAAACATT
*
72985 ATAAATAATAAATAAATAAATAATGGTTAGAATGCAATAAAATAAAAGTCAGTAGTTAGTAGAGT
1 ATAAATAATAAATAAATAAATAATGGTTAGAATGCAATAAAATAAAAGTCAGTAGTTAGCAGAGT
** * * * *
73050 CCGAACAATAATAATGAGGATCATACCCCGGATC-GAGTCACCACAAGGTCGAATTGAATATTAG
66 CCGAACAATAATAATGAGGATCATACCCAAGATCTG-GTCACCACAAGGTCAAATCGAAAAATAG
73114 AAACAATAAATAAATAA
130 AAACAATAAATAAATAA
** *
73131 ATAAATAAATAAATAAATAAA-AATGGTTA-AAGTGTGATAAAATAAAAGTTAGTAGTTAGCAGA
1 ATAAAT-AATAAATAAATAAATAATGGTTAGAA-TGCAATAAAATAAAAGTCAGTAGTTAGCAGA
* * *
73194 GTCTGAACCATAATAATGCGGATCATACCCAAGATCTGGTCACCACAAGGTCAAATCGAAAAATA
64 GTCCGAACAATAATAATGAGGATCATACCCAAGATCTGGTCACCACAAGGTCAAATCGAAAAATA
*
73259 GAAACCATAAATAAATAA
129 GAAACAATAAATAAATAA
73277 ATAAA
1 ATAAA
73282 CAATGGTTAG
Statistics
Matches: 134, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
145 2 0.01
146 117 0.87
147 15 0.11
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (146 bp):
ATAAATAATAAATAAATAAATAATGGTTAGAATGCAATAAAATAAAAGTCAGTAGTTAGCAGAGT
CCGAACAATAATAATGAGGATCATACCCAAGATCTGGTCACCACAAGGTCAAATCGAAAAATAGA
AACAATAAATAAATAA
Found at i:73319 original size:29 final size:29
Alignment explanation
Indices: 73282--73351 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
73272 AATAAATAAA
*
73282 CAATGGTTAGAATGCAATAAAATAAAAGT
1 CAATAGTTAGAATGCAATAAAATAAAAGT
*
73311 CAGTAGTTA-ATATGCAATAAAATAAAAGT
1 CAATAGTTAGA-ATGCAATAAAATAAAAGT
*
73340 TAATAGTTAGAA
1 CAATAGTTAGAA
73352 ATAAATAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 33 0.94
30 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (29 bp):
CAATAGTTAGAATGCAATAAAATAAAAGT
Found at i:73358 original size:29 final size:29
Alignment explanation
Indices: 73282--73359 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
73272 AATAAATAAA
* * *
73282 CAATGGTTAGAATGCAATAAAATAAAAGT
1 CAATAGTTAAAATGAAATAAAATAAAAGT
* * *
73311 CAGTAGTTAATATGCAATAAAATAAAAGT
1 CAATAGTTAAAATGAAATAAAATAAAAGT
*
73340 TAATAGTTAGAAAT-AAATAA
1 CAATAGTTA-AAATGAAATAA
73360 CACAGCAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 37 0.93
30 3 0.08
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (29 bp):
CAATAGTTAAAATGAAATAAAATAAAAGT
Found at i:74489 original size:122 final size:123
Alignment explanation
Indices: 74283--74600 Score: 442
Period size: 122 Copynumber: 2.6 Consensus size: 123
74273 GTTCCTCCAT
* * * *
74283 GTTGAGGATGTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACATTACTGATACATGTTG
1 GTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACACTGCTCATACATGTTG
* ** * * *
74348 AAGAGTT-CTGGTTGCTTTCAGGTAAATTGTTTGCTGAAGATGACACTATTCCTTCTC
66 AAGAGTTACTAGCCGCTTTCAAGTAAATTGTTTACTGAAGATGACACTATTCATTCTC
* *
74405 GTTGAGGAAGTCGGGTCAATCTTGAGATAATTTGGTGTTGAAGACTACACTGCTCATACATGTTG
1 GTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACACTGCTCATACATGTTG
*
74470 AAGAGTTAC-AGCCGTTTTCAAGTAAATTGTTTACTGAAGATGACACTATTCATTCTC
66 AAGAGTTACTAGCCGCTTTCAAGTAAATTGTTTACTGAAGATGACACTATTCATTCTC
* * * * * *
74527 GTTGAGGAAGTCGGGTCAATCTGGAGATAATTTTGTTATTGAAGACGACACTGCTCATCCACGAT
1 GTTGAGGAAGTCGGGTCAATCTGGAGATAA-TTTGGTGTTGAAGACAACACTGCTCATACATGTT
74592 GAAGAGTTA
65 GAAGAGTTA
74601 TAGTCATTTT
Statistics
Matches: 174, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
122 136 0.78
123 38 0.22
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (123 bp):
GTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACACTGCTCATACATGTTG
AAGAGTTACTAGCCGCTTTCAAGTAAATTGTTTACTGAAGATGACACTATTCATTCTC
Found at i:74874 original size:137 final size:137
Alignment explanation
Indices: 74623--75032 Score: 502
Period size: 137 Copynumber: 3.0 Consensus size: 137
74613 GGTAATTTTG
* * * * * *
74623 GAGACAACACGGTTCCTATGTGATGAGGAAATCTGGTTATCTAAAGGTGACGCTG-CTCCTATGT
1 GAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGAAG-TGACTCCTACGT
* * * * * * *
74687 AATGAGGAGATATGGTCGGTAGATGAAACTATTCCTACGTGAAGAGGACGTCTGGCCATCTTTAG
65 GATGAGGAGATTTTGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTAG
74752 GGATAATA
130 GGATAATA
* *
74760 GAGATAACACGGTTCCTACGTGATGAGGAAGTTTGGCTATCTAAGGGTGAAGTGACTCCTACGTG
1 GAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGAAGTGACTCCTACGTG
* * * * *
74825 ACGAGGAGATTTTGTTGGTGGATGACACTGTTCCTACGTGATGAGGACGTTTGGTCATCATTAGG
66 ATGAGGAGATTTTGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTAGG
*
74890 GATAATG
131 GATAATA
** * * *
74897 GAGATAACACAATTCCTACATGATGAGGAAGTCTGGTTATCTAAGGGTGACACT-ACTTCTACGT
1 GAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGA-AGTGACTCCTACGT
* * * *
74961 GATGAGGAGA-TCTGCTCAGTGGATGACATTGTTCCTACCTGATGAGGACGTCTGGCCATCTTTA
65 GATGAGGAGATTTTG-TCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
75025 GGGATAAT
129 GGGATAAT
75033 TTGTTTCAAG
Statistics
Matches: 233, Mismatches: 37, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
136 5 0.02
137 226 0.97
138 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (137 bp):
GAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGAAGTGACTCCTACGTG
ATGAGGAGATTTTGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTAGG
GATAATA
Found at i:75156 original size:67 final size:67
Alignment explanation
Indices: 75034--75292 Score: 367
Period size: 67 Copynumber: 3.9 Consensus size: 67
75024 AGGGATAATT
* * * *
75034 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTCCAAGAGAAACAATCTCAATGTTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATGTTTT
75099 TA
66 TA
* * * * * * *
75101 TGTTTCGAGATAAATTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAATAATCTCAAAG-ATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATGTTTT
75165 TA
66 TA
* * *
75167 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAATCTCAATGTTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATGTTTT
75232 TA
66 TA
* *
75234 TGTTTCGAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAACAATCTCAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAA
75293 AGAGATGGAA
Statistics
Matches: 167, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
66 56 0.34
67 111 0.66
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATGTTTT
TA
Found at i:75158 original size:36 final size:34
Alignment explanation
Indices: 75118--75225 Score: 84
Period size: 36 Copynumber: 3.2 Consensus size: 34
75108 AGATAAATTG
75118 TCTCAAGAGAAACAAAATTTGTTTCAAGGGAAATAA
1 TCTCAAGAG-AAC-AAATTTGTTTCAAGGGAAATAA
* *
75154 TCTCAA-AG----ATTTATGTTTCAAGAGAAACT-A
1 TCTCAAGAGAACAAATT-TGTTTCAAGGGAAA-TAA
* *
75184 TCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAA
1 TCTCAAGAGA-AC-AAATTTGTTTCAAGGGAAATAA
75220 TCTCAA
1 TCTCAA
75226 TGTTTTTATG
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
29 3 0.05
30 20 0.36
31 3 0.05
35 2 0.04
36 25 0.45
37 3 0.05
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.27
Consensus pattern (34 bp):
TCTCAAGAGAACAAATTTGTTTCAAGGGAAATAA
Found at i:75272 original size:133 final size:133
Alignment explanation
Indices: 75034--75295 Score: 418
Period size: 133 Copynumber: 2.0 Consensus size: 133
75024 AGGGATAATT
* *
75034 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTCCAAGAGAAACAATCTCAATGTTTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTCCAAGAGAAACAATCTCAATGTTTT
* * *
75099 TATGTTTCGAGATAAATTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAATAATCTCAAAGAT
66 TATGTTTCGAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT
75164 TTA
131 TTA
* * *
75167 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAG-GAAAACAATCTCAATGTTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTCCAAGAG-AAACAATCTCAATGTTT
* *
75231 TTATGTTTCGAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAACAATCTCAAAGA
65 TTATGTTTCGAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAACAATCTCAAAGA
75296 GATGGAATTT
Statistics
Matches: 118, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
132 1 0.01
133 117 0.99
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (133 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTCCAAGAGAAACAATCTCAATGTTTT
TATGTTTCGAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT
TTA
Found at i:75284 original size:36 final size:35
Alignment explanation
Indices: 75234--75309 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
75224 AATGTTTTTA
* **
75234 TGTTTCGAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACAATCTCAA-AGAGACGAAATT
* * *
75270 TGTTTCAAGGGAAACAATCTCAAAGAGATGGAATT
1 TGTTTCAAGAGAAACAATCTCAAAGAGACGAAATT
75305 TGTTT
1 TGTTT
75310 TGAGGAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 15 0.44
36 19 0.56
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAACAATCTCAAAGAGACGAAATT
Found at i:75365 original size:102 final size:103
Alignment explanation
Indices: 75167--75412 Score: 243
Period size: 102 Copynumber: 2.4 Consensus size: 103
75157 CAAAGATTTA
* * **
75167 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAATCTCAATGTTTT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAATATCAATGTTCG
* * *
75232 TATGTTTCGAGAGAAACTGTCTCAAGAGAGACGAAA-TT
66 TATGCTTCAAGAGAAACTATCTCAAGAGAGAC-AAAGTT
* * * **
75270 TGTTTCAAGGGAAACAATCTCAA-AGAGATGGAATTTGTTTTGAGGAAAAACAATATCAAATGTT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACGAAATTTGTTTCAAGG-AAAACAATATC-AATGTT
*
75334 CGTAT-CTT-AAGA-AAGACTATCTCAAGTGAGACAAAGTT
64 CGTATGCTTCAAGAGAA-ACTATCTCAAGAGAGACAAAGTT
** ** *
75372 TGTTTTGAGAGAAACTGTCTCAAGCGAGAC-AATATTTGTTT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACGAA-ATTTGTTT
75413 TTAGAGAAAA
Statistics
Matches: 116, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
101 5 0.04
102 57 0.49
103 45 0.39
104 9 0.08
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (103 bp):
TGTTTCAAGAGAAACAATCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAATATCAATGTTCG
TATGCTTCAAGAGAAACTATCTCAAGAGAGACAAAGTT
Found at i:75438 original size:38 final size:36
Alignment explanation
Indices: 75353--75461 Score: 114
Period size: 36 Copynumber: 2.9 Consensus size: 36
75343 AGAAAGACTA
*
75353 TCTCAAGTGAGACAAAGTTTGTTTTGAGAGAAACTG
1 TCTCAAGCGAGACAAAGTTTGTTTTGAGAGAAACTG
*
75389 TCTCAAGCGAGACAATA-TTTGTTTTTAGAGAAAACTTG
1 TCTCAAGCGAGACAA-AGTTTGTTTTGAGAG-AAAC-TG
* * *
75427 TCTCTAA-CGAGACGACACTTTGTTTCGAGAGAAAC
1 TCTC-AAGCGAGAC-AAAGTTTGTTTTGAGAGAAAC
75462 AATCTCAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
36 26 0.42
37 5 0.08
38 17 0.27
39 14 0.23
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (36 bp):
TCTCAAGCGAGACAAAGTTTGTTTTGAGAGAAACTG
Found at i:77946 original size:20 final size:18
Alignment explanation
Indices: 77913--77968 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
77903 GTGCTTCTTG
*
77913 TCTTTTTTTCTTTCTTATT
1 TCTTTTTTTTTTTCTT-TT
77932 TCTTTATTTTTTTTCTCTTT
1 TCTTT-TTTTTTTTCT-TTT
*
77952 GCTTTTTTTCTTTTCTT
1 TCTTTTTTT-TTTTCTT
77969 CTTTTCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 10 0.31
20 21 0.66
21 1 0.03
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (18 bp):
TCTTTTTTTTTTTCTTTT
Found at i:77957 original size:13 final size:13
Alignment explanation
Indices: 77941--77984 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
77931 TTCTTTATTT
77941 TTTTTCTCTTTGC
1 TTTTTCTCTTTGC
* *
77954 TTTTTTTCTTTTC
1 TTTTTCTCTTTGC
77967 TTCTTTTCTCTTTGC
1 -T-TTTTCTCTTTGC
77982 TTT
1 TTT
77985 GATTTAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 13 0.52
14 2 0.08
15 10 0.40
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTTTCTCTTTGC
Found at i:77957 original size:15 final size:15
Alignment explanation
Indices: 77939--77984 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
77929 ATTTCTTTAT
77939 TTTTTTTCTCTTTGC
1 TTTTTTTCTCTTTGC
77954 TTTTTTTCT-TTT-C
1 TTTTTTTCTCTTTGC
*
77967 TTCTTTTCTCTTTGC
1 TTTTTTTCTCTTTGC
77982 TTT
1 TTT
77985 GATTTAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
15 12 0.44
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTCTTTGC
Found at i:82356 original size:130 final size:130
Alignment explanation
Indices: 82060--82457 Score: 524
Period size: 130 Copynumber: 3.1 Consensus size: 130
82050 GTTGTTAGAC
** * *
82060 AAGTTAGCGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCAAATCAGGTCACTACA
1 AAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCAGATCAGGTCACCACA
* *
82125 AGGTAGAATCAAATATTAG--A-AATAAATAAAT--A-AACAATGGTTAGAATGCAATAAAATAA
66 AGGTCGAATCGAATATTAGAAACAATAAATAAATAAATAACAATGGTTAGAATGCAATAAAATAA
* * * * *
82184 AAGTAAATAGTTAGCCGAGTCTC-AACCATAATAATGTGGATCATACCCTAGATCGGGTCACCAC
1 AAGTTAGTAGTTAGCAGAGTC-CGAACCATAATAATGTGGATCATACCCCAGATCAGGTCACCAC
*
82248 AAGGTCGAATCGAATATTAGAAACAATAAATAAATAAATAACAATGATTA-AAGTGCAATAAAAT
65 AAGGTCGAATCGAATATTAGAAACAATAAATAAATAAATAACAATGGTTAGAA-TGCAATAAAAT
82312 AA
129 AA
** * *
82314 AAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCAGATCATACCCCGGATCTGGTCACCACA
1 AAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCAGATCAGGTCACCACA
* * * *
82379 AGGTCGAATCGAAAAATAGAAACCATAAATAAATAAATAAACAATGGTTAGAATGCAATAAAGTA
66 AGGTCGAATCGAATATTAGAAACAATAAATAAATAAAT-AACAATGGTTAGAATGCAATAAAATA
82444 A
130 A
*
82445 AAGTCAGTAGTTA
1 AAGTTAGTAGTTA
82458 ATATGCAATA
Statistics
Matches: 237, Mismatches: 26, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
124 71 0.30
125 1 0.00
126 1 0.00
127 11 0.05
129 4 0.02
130 113 0.48
131 34 0.14
132 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.22
Consensus pattern (130 bp):
AAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCAGATCAGGTCACCACA
AGGTCGAATCGAATATTAGAAACAATAAATAAATAAATAACAATGGTTAGAATGCAATAAAATAA
Found at i:82457 original size:29 final size:29
Alignment explanation
Indices: 82425--82489 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
82415 ATAAACAATG
*
82425 GTTAGAATGCAAT-AAAGTAAAAGTCAGTA
1 GTTAGAATGCAATAAAAG-AAAAATCAGTA
*
82454 GTTA-ATATGCAATAAAAGAAAAATTAGTA
1 GTTAGA-ATGCAATAAAAGAAAAATCAGTA
82483 GTTAGAA
1 GTTAGAA
82490 ATAAATAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 1 0.03
29 25 0.81
30 5 0.16
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (29 bp):
GTTAGAATGCAATAAAAGAAAAATCAGTA
Found at i:83566 original size:42 final size:42
Alignment explanation
Indices: 83510--83615 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 42
83500 TGTAAAAACG
* * * *
83510 CTATTGCGGTGTTTATTACAAAAATACCACTAATGTAAATGA
1 CTATTGCGGCGTTTATTACAAAAAAACCACTAAAGTAAATAA
* * **
83552 CTATTACGGCGTTTA-TA-AAAAAAATCACTAAAGTGCATAA
1 CTATTGCGGCGTTTATTACAAAAAAACCACTAAAGTAAATAA
*
83592 CTATTGTGGCGTTTATTACAAAAA
1 CTATTGCGGCGTTTATTACAAAAA
83616 CGCTGCTAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
40 30 0.58
41 4 0.08
42 18 0.35
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (42 bp):
CTATTGCGGCGTTTATTACAAAAAAACCACTAAAGTAAATAA
Found at i:83595 original size:108 final size:108
Alignment explanation
Indices: 83404--83606 Score: 273
Period size: 108 Copynumber: 1.9 Consensus size: 108
83394 GGATTGCACA
* * * **
83404 ATTGCGGCGTTTATTACAAAAACACAGCTAAAGTACATGATTATTGCGGCGTTTATAAAAAATGC
1 ATTGCGGCGTTTATTACAAAAACACAGCTAAAGTAAATGACTATTACGGCGTTTATAAAAAAAAC
** *
83469 CGTTAAAATGCATGACTATTGTGGCGTTTACTGTAAAAACGCT
66 CACTAAAATGCATAACTATTGTGGCGTTTACTGTAAAAACGCT
* * *
83512 ATTGCGGTGTTTATTACAAAAATACCA-CTAATGTAAATGACTATTACGGCGTTTATAAAAAAAA
1 ATTGCGGCGTTTATTACAAAAACA-CAGCTAAAGTAAATGACTATTACGGCGTTTATAAAAAAAA
* *
83576 TCACTAAAGTGCATAACTATTGTGGCGTTTA
65 CCACTAAAATGCATAACTATTGTGGCGTTTA
83607 TTACAAAAAC
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
108 79 0.98
109 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (108 bp):
ATTGCGGCGTTTATTACAAAAACACAGCTAAAGTAAATGACTATTACGGCGTTTATAAAAAAAAC
CACTAAAATGCATAACTATTGTGGCGTTTACTGTAAAAACGCT
Found at i:89436 original size:3 final size:3
Alignment explanation
Indices: 89428--89457 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
89418 GTAAAGAAAA
89428 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
89458 CCTGTATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:90159 original size:5 final size:5
Alignment explanation
Indices: 90149--90177 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
90139 AATTAGGTCC
90149 TAATT TAATT TAATT TAATT TAATT TAAT
1 TAATT TAATT TAATT TAATT TAATT TAAT
90178 AAATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:90558 original size:2 final size:2
Alignment explanation
Indices: 90547--90602 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
90537 AGAAATCAAT
90547 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
90588 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
90603 TAATGATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90931 original size:20 final size:18
Alignment explanation
Indices: 90885--90956 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 18
90875 AATTTAATTT
* *
90885 TAAATATAATTTCATATA
1 TAAATATAATTTAATAAA
*
90903 TATATATAATCATTAATAAA
1 TAAATATAAT--TTAATAAA
90923 TAAATATAA---AATAAA
1 TAAATATAATTTAATAAA
*
90938 TAAATTTAATTTAA-AAA
1 TAAATATAATTTAATAAA
90955 TA
1 TA
90957 TTAAAATCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 14 0.32
17 5 0.11
18 11 0.25
20 14 0.32
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATATAATTTAATAAA
Found at i:90955 original size:28 final size:27
Alignment explanation
Indices: 90924--90987 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
90914 ATTAATAAAT
90924 AAATATAAAATAAATAAATTTAATT-TAA
1 AAATATAAAAT-AATAAA-TTAATTATAA
*
90952 AAATATTAAAATCATAAATTAATTATAA
1 AAATA-TAAAATAATAAATTAATTATAA
90980 ATAATATA
1 A-AATATA
90988 TTAGATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.19
28 16 0.50
29 10 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATATAAAATAATAAATTAATTATAA
Found at i:91119 original size:17 final size:17
Alignment explanation
Indices: 91097--91133 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
91087 AAATATATTT
91097 TAATTGATCTTGATTAC
1 TAATTGATCTTGATTAC
*
91114 TAATTGATCTTGGTTAC
1 TAATTGATCTTGATTAC
91131 TAA
1 TAA
91134 ATAATCTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (17 bp):
TAATTGATCTTGATTAC
Found at i:91140 original size:17 final size:17
Alignment explanation
Indices: 91103--91143 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
91093 ATTTTAATTG
* * *
91103 ATCTTGATTACTAATTG
1 ATCTTGGTTACTAAATA
91120 ATCTTGGTTACTAAATA
1 ATCTTGGTTACTAAATA
91137 ATCTTGG
1 ATCTTGG
91144 GTTCAAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (17 bp):
ATCTTGGTTACTAAATA
Found at i:93292 original size:28 final size:26
Alignment explanation
Indices: 93261--93313 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
93251 TTCTTACATA
*
93261 AATTTTATTTAAAAATATAAAAATATTG
1 AATTTGATTTAAAAA-AT-AAAATATTG
*
93289 AATTTGATTTTAAAAATAAAATATT
1 AATTTGATTTAAAAAATAAAATATT
93314 AAACTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 2 0.09
28 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
AATTTGATTTAAAAAATAAAATATTG
Found at i:93602 original size:2 final size:2
Alignment explanation
Indices: 93595--93627 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
93585 AACATTTTAA
93595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93628 GATTTTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93644 original size:52 final size:51
Alignment explanation
Indices: 93562--93666 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 51
93552 TTTTTTGAAA
* * * *
93562 ATATCTATTATATAGTTTTTGAAAACATTTT-AAATATATATATATATATAT
1 ATATATATTATATAGATTTTGAAAACATTTTGAAAAAAATATATA-ATATAT
* *
93613 ATATATATATATATAGATTTTGAAAATATTTTGAAAAAAATATGTAATATAT
1 ATATATAT-TATATAGATTTTGAAAACATTTTGAAAAAAATATATAATATAT
93665 AT
1 AT
93667 TTTTTGAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 7 0.15
52 29 0.63
53 10 0.22
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (51 bp):
ATATATATTATATAGATTTTGAAAACATTTTGAAAAAAATATATAATATAT
Found at i:93701 original size:38 final size:39
Alignment explanation
Indices: 93609--93706 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 39
93599 ATATATATAT
* *
93609 ATATATATATATATATATAGATTTTGAAAATATTTTGAA
1 ATATATATATATATATATATATTTTGAAAACATTTTGAA
* * * *
93648 AAAAATATGTA-ATATATATTTTTTGAAAACATTTT-AA
1 ATATATATATATATATATATATTTTGAAAACATTTTGAA
93685 ATATATATATATATATATATAT
1 ATATATATATATATATATATAT
93707 ATATAGTTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
37 10 0.21
38 30 0.62
39 8 0.17
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (39 bp):
ATATATATATATATATATATATTTTGAAAACATTTTGAA
Found at i:93730 original size:2 final size:2
Alignment explanation
Indices: 93685--93711 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
93675 AACATTTTAA
93685 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 A
93712 GTTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:102006 original size:17 final size:17
Alignment explanation
Indices: 101986--102043 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
101976 TCTTATTTCA
101986 TTTCTTTTGAATTCAAT
1 TTTCTTTTGAATTCAAT
*
102003 TTTC-TTT-CATTCAATACT
1 TTTCTTTTGAATTC-A-A-T
*
102021 TTTCTTTTGAATTGAAT
1 TTTCTTTTGAATTCAAT
102038 TTTCTT
1 TTTCTT
102044 CATTCAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 4 0.12
16 4 0.12
17 12 0.36
18 6 0.18
19 4 0.12
20 3 0.09
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTCTTTTGAATTCAAT
Found at i:102051 original size:34 final size:35
Alignment explanation
Indices: 101986--102055 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
101976 TCTTATTTCA
101986 TTTCTTTTGAATTCAATTTTCTTTCATTCAATACT
1 TTTCTTTTGAATTCAATTTTCTTTCATTCAATACT
*
102021 TTTCTTTTGAATTGAATTTTC-TTCATTCAATACT
1 TTTCTTTTGAATTCAATTTTCTTTCATTCAATACT
102055 T
1 T
102056 CGTTTTATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 14 0.41
35 20 0.59
ACGTcount: A:0.23, C:0.16, G:0.04, T:0.57
Consensus pattern (35 bp):
TTTCTTTTGAATTCAATTTTCTTTCATTCAATACT
Found at i:103369 original size:48 final size:48
Alignment explanation
Indices: 103284--103380 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 48
103274 TTTCTTTTAT
*
103284 TGACTTTCCAGAATGTTTGTCATATACTTTGTTCATTTTTCCTTATAAA
1 TGACTTTCCAGAATGTTTGTCATATACTCTGTTCA-TTTTCCTTATAAA
103333 TGACTTTCCAGAATGTTT-TCATATACTCTGTTCATTTTCCTTATAAA
1 TGACTTTCCAGAATGTTTGTCATATACTCTGTTCATTTTCCTTATAAA
103380 T
1 T
103381 AAATATGGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 14 0.30
48 15 0.32
49 18 0.38
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (48 bp):
TGACTTTCCAGAATGTTTGTCATATACTCTGTTCATTTTCCTTATAAA
Found at i:103998 original size:107 final size:107
Alignment explanation
Indices: 103837--104036 Score: 314
Period size: 107 Copynumber: 1.9 Consensus size: 107
103827 TATTGAACTC
*
103837 ATTTACAAGATTGGATTCCAACTTCACAACGAAGGACATCCCATTCAAAGCTCAACTTCACA-TC
1 ATTTACAAGATTGGATTCCAACTTCACAACGAAGGACATCCAATTCAAAGCTCAACTTCACAGT-
*
103901 GAATGAGCCACCATA-ATTTCAACTTCACAACGAAAACAATGCA
65 GAAGGAGCCACC-TACATTTCAACTTCACAACGAAAACAATGCA
** *
103944 ATTTACAAGATTGGATTTGAACTTCACAACGAAGGACATCCAATTCAAATCTCAACTTCACAGTG
1 ATTTACAAGATTGGATTCCAACTTCACAACGAAGGACATCCAATTCAAAGCTCAACTTCACAGTG
104009 AAGGAGCCACCTACGATTTCAACTTCAC
66 AAGGAGCCACCTAC-ATTTCAACTTCAC
104037 GAAGAAGTAT
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
106 2 0.02
107 69 0.81
108 14 0.16
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (107 bp):
ATTTACAAGATTGGATTCCAACTTCACAACGAAGGACATCCAATTCAAAGCTCAACTTCACAGTG
AAGGAGCCACCTACATTTCAACTTCACAACGAAAACAATGCA
Found at i:104639 original size:2 final size:2
Alignment explanation
Indices: 104632--104672 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
104622 TTAATAAATA
104632 AT AT 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 AT AT A
104673 AAACGTTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:104767 original size:37 final size:37
Alignment explanation
Indices: 104650--104977 Score: 402
Period size: 37 Copynumber: 8.9 Consensus size: 37
104640 ATATATATAT
* * *
104650 ATATATATATATATATA-TATAT-AAAACGTTTTGAAAA
1 ATATATATA-ATATATAGTTTTTGAAAACATTTTG-AAA
*
104687 CATATATATAATATATAGCTTTTT--AAATATTTTGAAA
1 -ATATATATAATATATAG-TTTTTGAAAACATTTTGAAA
* *
104724 ATATATATAATATATAATCTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
* *
104761 GCATATATATAATATATAGTTTTTGAAGATATTTTGAAA
1 --ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
104800 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
104837 ATATATAT--TATATAGTTTTTGAAAACATTTTGAAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTG-AAA
*
104873 TATATATATAATATATAGTTTTTGAAAATATTTTGAAA
1 -ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
* * *
104911 AAATATGTAATATATTGTTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
* *
104948 ATATATAT--TATATAGTTTTTAAAAATATTT
1 ATATATATAATATATAGTTTTTGAAAACATTT
104978 ATATATTATA
Statistics
Matches: 257, Mismatches: 23, Indels: 23
0.85 0.08 0.08
Matches are distributed among these distances:
35 47 0.18
36 19 0.07
37 112 0.44
38 20 0.08
39 59 0.23
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
Found at i:104806 original size:76 final size:74
Alignment explanation
Indices: 104648--104977 Score: 386
Period size: 76 Copynumber: 4.4 Consensus size: 74
104638 ATATATATAT
* * *
104648 ATATATATATATATATATATATAT-AAAACGTTTTGAAAACATATATATAATATATAGCTTTTT-
1 ATATATATA-ATATATA-ATTTTTGAAAACATTTTG-AAA-ATATATATAATATATAG-TTTTTG
*
104711 -AAATATTTTGAAA
61 AAAACATTTTGAAA
* *
104724 ATATATATAATATATAATCTTTGAAAACATTTTGAAAGCATATATATAATATATAGTTTTTGAAG
1 ATATATATAATATATAATTTTTGAAAACATTTTGAAA--ATATATATAATATATAGTTTTTGAAA
*
104789 ATATTTTGAAA
64 ACATTTTGAAA
*
104800 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATAT--TATATAGTTTTTGAAAAC
1 ATATATATAATATATAATTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
104863 ATTTTGAAAA
66 ATTTTG-AAA
* * * * *
104873 TATATATATAATATATAGTTTTTGAAAATATTTTGAAAAAATATGTAATATATTGTTTTTGAAAA
1 -ATATATATAATATATAATTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAA
104938 CATTTTGAAA
65 CATTTTGAAA
* * *
104948 ATATATAT--TATATAGTTTTTAAAAATATTT
1 ATATATATAATATATAATTTTTGAAAACATTT
104978 ATATATTATA
Statistics
Matches: 233, Mismatches: 13, Indels: 20
0.88 0.05 0.08
Matches are distributed among these distances:
72 43 0.18
73 3 0.01
74 70 0.30
75 38 0.16
76 79 0.34
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (74 bp):
ATATATATAATATATAATTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
ATTTTGAAA
Found at i:104967 original size:24 final size:21
Alignment explanation
Indices: 104940--104982 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
104930 TTTGAAAACA
*
104940 TTTTGAAAATATATATTATATAG
1 TTTTTAAAA-ATAT-TTATATAG
104963 TTTTTAAAAATATTTATATA
1 TTTTTAAAAATATTTATATA
104983 TTATATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTTAAAAATATTTATATAG
Found at i:106395 original size:15 final size:17
Alignment explanation
Indices: 106352--106393 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
106342 TGCAATTGAC
106352 ATTTTTTATTTA-ATTG
1 ATTTTTTATTTACATTG
*
106368 ACTTTTTATTTACATT-
1 ATTTTTTATTTACATTG
106384 ATTTTTTATT
1 ATTTTTTATT
106394 ACTTTGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTTTTTATTTACATTG
Done.