Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 62 of 89
Found at i:14369680 original size:22 final size:22
Alignment explanation
Indices: 14369654--14369703 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
14369644 TGTATGGTTT
*
14369654 CAATATTGAGAGAAGAACGAGA
1 CAATATTGACAGAAGAACGAGA
14369676 CAATATTGACAGAAGAACGAGA
1 CAATATTGACAGAAGAACGAGA
14369698 CAATAT
1 CAATAT
14369704 GAACAACAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (22 bp):
CAATATTGACAGAAGAACGAGA
Found at i:14370175 original size:21 final size:21
Alignment explanation
Indices: 14370151--14370195 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
14370141 GTTTTAATAG
14370151 ATAAAGAATAACTTAGTATGA
1 ATAAAGAATAACTTAGTATGA
14370172 ATAAAGAATAACTTAGTATGA
1 ATAAAGAATAACTTAGTATGA
14370193 ATA
1 ATA
14370196 CATCTTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.29
Consensus pattern (21 bp):
ATAAAGAATAACTTAGTATGA
Found at i:14374732 original size:33 final size:33
Alignment explanation
Indices: 14374690--14374758 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
14374680 GTTGATGAAT
*
14374690 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
14374723 GAAGGATGATGTTATTGGCGTGATATGGTTATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
14374756 GAA
1 GAA
14374759 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:0.35, T:0.32
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:14374799 original size:36 final size:36
Alignment explanation
Indices: 14374729--14374841 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 36
14374719 AATGGAAGGA
* * *
14374729 TGATGTTATTGGCGTGAT-ATGGTTATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
14374764 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
** * *
14374800 TGATGATATAAACGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
14374836 TGATGA
1 TGATGA
14374842 AAATAGTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:14379257 original size:33 final size:33
Alignment explanation
Indices: 14379215--14379283 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
14379205 GTTGATGAAT
*
14379215 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
14379248 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
14379281 GAA
1 GAA
14379284 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:14379288 original size:13 final size:12
Alignment explanation
Indices: 14379269--14379365 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
14379259 TTATTGGCGT
14379269 GATATGGTGATG
1 GATATGGTGATG
14379281 GAATATGGTGAT-
1 G-ATATGGTGATG
*
14379293 GATATAGGCG-T-
1 GATAT-GGTGATG
14379304 GATAATGGTGATG
1 GAT-ATGGTGATG
14379317 GACTATGGTGAT-
1 GA-TATGGTGATG
*
14379329 GATATAGG-CAT-
1 GATAT-GGTGATG
*
14379340 GATAATGGAGATG
1 GAT-ATGGTGATG
14379353 GATTATGGTGATG
1 GA-TATGGTGATG
14379366 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:14379324 original size:36 final size:36
Alignment explanation
Indices: 14379254--14379366 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
14379244 AATGGAAGGA
* *
14379254 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
14379289 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
14379325 TGATGATATAGGCATGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
14379361 TGATGA
1 TGATGA
14379367 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:14382137 original size:17 final size:17
Alignment explanation
Indices: 14382117--14382149 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14382107 TTCTATTCTG
*
14382117 ATTTTTTTTCTTTTTGT
1 ATTTTCTTTCTTTTTGT
14382134 ATTTTCTTTCTTTTTG
1 ATTTTCTTTCTTTTTG
14382150 CACTCCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (17 bp):
ATTTTCTTTCTTTTTGT
Found at i:14382437 original size:19 final size:20
Alignment explanation
Indices: 14382409--14382448 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
14382399 GGATAATAAT
*
14382409 ATAAGTAATGAAATTAAATA
1 ATAAGTAATGAAATGAAATA
14382429 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
14382448 A
1 A
14382449 ATAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (20 bp):
ATAAGTAATGAAATGAAATA
Found at i:14387393 original size:19 final size:20
Alignment explanation
Indices: 14387343--14387385 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
14387333 GAAACCCCTT
*
14387343 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
14387363 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
14387382 TGAA
1 TGAA
14387386 GATGCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:14393001 original size:20 final size:19
Alignment explanation
Indices: 14392957--14393022 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 19
14392947 ACTTCTCTTT
* *
14392957 TTCTTTTCTTTTCTTGTTTTC
1 TTCTTTT-TTGTCTT-TTCTC
*
14392978 TTCTTTTTTGATTTTTTCTC
1 TTCTTTTTTG-TCTTTTCTC
14392998 TTC-TTTTTGTCTTTTCT-
1 TTCTTTTTTGTCTTTTCTC
14393015 TTCTTTTT
1 TTCTTTTT
14393023 GCACTCCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.08
18 11 0.28
19 6 0.15
20 9 0.23
21 10 0.26
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.77
Consensus pattern (19 bp):
TTCTTTTTTGTCTTTTCTC
Found at i:14393360 original size:11 final size:11
Alignment explanation
Indices: 14393344--14393388 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
14393334 TTGGTGCTGG
14393344 AAATAAGATAA
1 AAATAAGATAA
*
14393355 AAATAAGATTA
1 AAATAAGATAA
*
14393366 AAACAAGATAA
1 AAATAAGATAA
14393377 AGAA-AAGATAA
1 A-AATAAGATAA
14393388 A
1 A
14393389 TAAATTGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (11 bp):
AAATAAGATAA
Found at i:14402323 original size:11 final size:11
Alignment explanation
Indices: 14402309--14402378 Score: 79
Period size: 11 Copynumber: 6.4 Consensus size: 11
14402299 TTTTTTGAAA
*
14402309 TTTTGGTTTTT
1 TTTTGCTTTTT
14402320 TTTTGCTTTTT
1 TTTTGCTTTTT
*
14402331 TTGTGCCTTTTT
1 TTTTG-CTTTTT
**
14402343 TTTACCTTTTT
1 TTTTGCTTTTT
*
14402354 TTTTGCCTTTT
1 TTTTGCTTTTT
14402365 TTTTG-TTTTT
1 TTTTGCTTTTT
14402375 TTTT
1 TTTT
14402379 AAACAATAGC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
10 8 0.16
11 33 0.67
12 8 0.16
ACGTcount: A:0.01, C:0.10, G:0.10, T:0.79
Consensus pattern (11 bp):
TTTTGCTTTTT
Found at i:14402378 original size:23 final size:22
Alignment explanation
Indices: 14402316--14402377 Score: 88
Period size: 23 Copynumber: 2.8 Consensus size: 22
14402306 AAATTTTGGT
14402316 TTTTTTTTGCTTTTTTTGTGCC
1 TTTTTTTTGCTTTTTTTGTGCC
* *
14402338 TTTTTTTTACCTTTTTTTTTGCC
1 TTTTTTTT-GCTTTTTTTGTGCC
*
14402361 TTTTTTTTGTTTTTTTT
1 TTTTTTTTGCTTTTTTT
14402378 TAAACAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.02, C:0.11, G:0.08, T:0.79
Consensus pattern (22 bp):
TTTTTTTTGCTTTTTTTGTGCC
Found at i:14405172 original size:11 final size:11
Alignment explanation
Indices: 14405156--14405193 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
14405146 AAATTTTGGC
14405156 TTTTTTGGCTT
1 TTTTTTGGCTT
14405167 TTTTTTGGCTT
1 TTTTTTGGCTT
*
14405178 TTTTTTTGCTT
1 TTTTTTGGCTT
14405189 TTTTT
1 TTTTT
14405194 GTTTTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.08, G:0.13, T:0.79
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:14405547 original size:11 final size:11
Alignment explanation
Indices: 14405523--14405567 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
14405513 TTGGTGCTGG
14405523 AAACAAGATAA
1 AAACAAGATAA
* *
14405534 AAATAAGATTA
1 AAACAAGATAA
14405545 AAACAAGATAA
1 AAACAAGATAA
14405556 AGAA-AAGATAA
1 A-AACAAGATAA
14405567 A
1 A
14405568 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:14405551 original size:22 final size:22
Alignment explanation
Indices: 14405523--14405564 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
14405513 TTGGTGCTGG
14405523 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
14405545 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
14405565 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:14406808 original size:35 final size:36
Alignment explanation
Indices: 14406761--14406828 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
14406751 ATTTATAAGT
*
14406761 TGGTGATAATATAGGCATGA-CATGGTGATGGAATA
1 TGGTGATAATATAGGCATGATAATGGTGATGGAATA
* *
14406796 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCATGATAATGGTGATGGA
14406829 CAGATTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 18 0.62
36 11 0.38
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.29
Consensus pattern (36 bp):
TGGTGATAATATAGGCATGATAATGGTGATGGAATA
Found at i:14412302 original size:19 final size:20
Alignment explanation
Indices: 14412278--14412326 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
14412268 CGGCCAAGAG
14412278 CATGTATCTTCA-TTAAAA-T
1 CATGTAT-TTCATTTAAAAGT
14412297 CATGTATTTCCATTTAAAAGT
1 CATGTATTT-CATTTAAAAGT
14412318 CATGTATTT
1 CATGTATTT
14412327 TCAAAGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.07
19 9 0.33
20 6 0.22
21 10 0.37
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAGT
Found at i:14414436 original size:15 final size:16
Alignment explanation
Indices: 14414416--14414452 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
14414406 AAATGAAATA
14414416 AAGAAATAAAA-GGAT
1 AAGAAATAAAATGGAT
14414431 AAGAAATAAAATGGAT
1 AAGAAATAAAATGGAT
14414447 AGAGAA
1 A-AGAA
14414453 GTTATCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.14
Consensus pattern (16 bp):
AAGAAATAAAATGGAT
Found at i:14416292 original size:19 final size:20
Alignment explanation
Indices: 14416268--14416310 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
14416258 AGCATTTATC
*
14416268 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
14416287 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
14416307 TTCA
1 TTCA
14416311 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:14416714 original size:35 final size:36
Alignment explanation
Indices: 14416658--14416725 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
14416648 ATAACATCAC
* * *
14416658 CATCTTCCATATCACGTCTATATCATCATCATCTTT
1 CATCTTCCATATCACGCCTATATAATCACCATCTTT
*
14416694 CATCTT-CATTTCACGCCTATATAATCACCATC
1 CATCTTCCATATCACGCCTATATAATCACCATC
14416726 CCATTACCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 22 0.79
36 6 0.21
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.38
Consensus pattern (36 bp):
CATCTTCCATATCACGCCTATATAATCACCATCTTT
Found at i:14416880 original size:15 final size:15
Alignment explanation
Indices: 14416868--14416910 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
14416858 CATTTCTTTC
14416868 CATTTCCTTTCTTAT
1 CATTTCCTTTCTTAT
14416883 CATTTCCTTTCTTAT
1 CATTTCCTTTCTTAT
14416898 CATTTCCTTTCTT
1 CATTTCCTTTCTT
14416911 CTTCCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (15 bp):
CATTTCCTTTCTTAT
Found at i:14429554 original size:6 final size:6
Alignment explanation
Indices: 14429535--14429574 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
14429525 TGTAGGAGTC
*
14429535 TTTTC- TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
14429575 TGTTGCAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:14430300 original size:19 final size:20
Alignment explanation
Indices: 14430250--14430292 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
14430240 GAAACCATTT
*
14430250 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
14430270 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
14430289 TGAA
1 TGAA
14430293 GATGCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:14434870 original size:24 final size:25
Alignment explanation
Indices: 14434824--14434878 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
14434814 ACAGTTATGC
*
14434824 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
14434848 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
14434873 CA-TTGA
1 CACTTGA
14434879 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:14439075 original size:20 final size:20
Alignment explanation
Indices: 14439029--14439075 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
14439019 TTTGCTATTT
*
14439029 AAAAAAACAAAAAAAAGGTA
1 AAAAAAACAAAAAAAAGGCA
14439049 AAAAAAAC-AAAAAAAGGCA
1 AAAAAAACAAAAAAAAGGCA
14439068 AAAGAAAA
1 AAA-AAAA
14439076 ACAATAAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAGGCA
Found at i:14439084 original size:20 final size:21
Alignment explanation
Indices: 14439051--14439090 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
14439041 AAAAGGTAAA
*
14439051 AAAAACAAAAAAAGGCAAAAG
1 AAAAACAAAAAAAGCCAAAAG
*
14439072 AAAAAC-AATAAAGCCAAAA
1 AAAAACAAAAAAAGCCAAAA
14439091 TTTCAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.75, C:0.12, G:0.10, T:0.03
Consensus pattern (21 bp):
AAAAACAAAAAAAGCCAAAAG
Found at i:14440592 original size:12 final size:11
Alignment explanation
Indices: 14440546--14440600 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
14440536 GCTATTTTTT
*
14440546 AAAAAGAAAA-
1 AAAAAAAAAAG
* *
14440556 AACAAAAAAAC
1 AAAAAAAAAAG
14440567 AAAAAAAAAAG
1 AAAAAAAAAAG
14440578 AAAAAAAAAAGG
1 AAAAAAAAAA-G
14440590 AAAAGAAAAAA
1 AAAA-AAAAAA
14440601 TTTGAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
10 8 0.21
11 19 0.50
12 5 0.13
13 6 0.16
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:14446404 original size:19 final size:21
Alignment explanation
Indices: 14446380--14446425 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
14446370 CGGCCAAGAG
14446380 CATGTAACTTCA-TTAAAA-T
1 CATGTAACTTCATTTAAAAGT
**
14446399 CATGTATTTTCATTTAAAAGT
1 CATGTAACTTCATTTAAAAGT
14446420 CATGTA
1 CATGTA
14446426 TTTTCAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 6 0.26
21 7 0.30
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (21 bp):
CATGTAACTTCATTTAAAAGT
Found at i:14446424 original size:21 final size:19
Alignment explanation
Indices: 14446388--14446431 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 19
14446378 AGCATGTAAC
14446388 TTCATTAAAATCATGTATT
1 TTCATTAAAATCATGTATT
14446407 TTCATTTAAAAGTCATGTATT
1 TTCA-TTAAAA-TCATGTATT
14446428 TTCA
1 TTCA
14446432 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 6 0.26
21 13 0.57
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:14451576 original size:27 final size:27
Alignment explanation
Indices: 14451546--14451607 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
14451536 TGCAAAAGAA
14451546 AGAAAAGACA-AAAAGAAAAAAAAAATC
1 AGAAAAGA-AGAAAAGAAAAAAAAAATC
* * *
14451573 AGAATAGAAGAAAAGAAAAAGAAATTC
1 AGAAAAGAAGAAAAGAAAAAAAAAATC
14451600 A-AAAAGAA
1 AGAAAAGAA
14451608 AGCAATCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (27 bp):
AGAAAAGAAGAAAAGAAAAAAAAAATC
Found at i:14454068 original size:19 final size:17
Alignment explanation
Indices: 14454025--14454069 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
14454015 TATTATAACA
14454025 TATAGTGCACATCTTTAT
1 TATA-TGCACATCTTTAT
*
14454043 AATATGCACATCATTATAT
1 TATATGCACATC-TT-TAT
14454062 TATATGCA
1 TATATGCA
14454070 TTATATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 10 0.43
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (17 bp):
TATATGCACATCTTTAT
Found at i:14454898 original size:19 final size:20
Alignment explanation
Indices: 14454874--14454924 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
14454864 CGGCCAAGAG
* *
14454874 CATGTATCTTCATTAA-AAT
1 CATGTATTTTCATAAACAAT
14454893 CATGTATTTTCATAAACAAT
1 CATGTATTTTCATAAACAAT
14454913 CATGTATTTTCA
1 CATGTATTTTCA
14454925 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAACAAT
Found at i:14456283 original size:12 final size:12
Alignment explanation
Indices: 14456266--14456307 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
14456256 TTCACTTTTC
14456266 TTTTTCTTTGAA
1 TTTTTCTTTGAA
*
14456278 TTTTTC-TT--C
1 TTTTTCTTTGAA
14456287 TTTTTCTTTGAA
1 TTTTTCTTTGAA
14456299 TTTTTCTTT
1 TTTTTCTTT
14456308 CTTTTCCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.24
10 2 0.08
11 2 0.08
12 15 0.60
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTGAA
Found at i:14456313 original size:21 final size:22
Alignment explanation
Indices: 14456262--14456312 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 22
14456252 TTTCTTCACT
14456262 TTTCTTTTTCTTTGAATTTTTC
1 TTTCTTTTTCTTTGAATTTTTC
14456284 -TTCTTTTTCTTTGAATTTTTC
1 TTTCTTTTTCTTTGAATTTTTC
14456305 TTTCTTTT
1 TTTCTTTT
14456313 CCACTCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.08, C:0.14, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTCTTTTTCTTTGAATTTTTC
Found at i:14458599 original size:36 final size:35
Alignment explanation
Indices: 14458549--14458653 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 35
14458539 GATACAATAT
14458549 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCA-CATTATCACGCCTATATCATCACCATA
14458585 GTCCATCACTATTATCACGCCTATATCATCACCATA
1 GTCCATCAC-ATTATCACGCCTATATCATCACCATA
* * *
14458621 TTCCATCACCTTATCACGCCTATATTATCACCA
1 GTCCATCACATTATCACGCCTATATCATCACCA
14458654 ACTTCTAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 23 0.35
36 42 0.65
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (35 bp):
GTCCATCACATTATCACGCCTATATCATCACCATA
Found at i:14459067 original size:19 final size:20
Alignment explanation
Indices: 14459024--14459068 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
14459014 GTGCTACAAT
*
14459024 AAAAAACAACAAGAAAGAAG
1 AAAAAACAACAAGAAAGAAA
14459044 AAAAAA-AACAA-AAAGAAA
1 AAAAAACAACAAGAAAGAAA
14459062 ATAAAAA
1 A-AAAAA
14459069 GACTCCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.82, C:0.07, G:0.09, T:0.02
Consensus pattern (20 bp):
AAAAAACAACAAGAAAGAAA
Found at i:14459068 original size:18 final size:19
Alignment explanation
Indices: 14459024--14459060 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
14459014 GTGCTACAAT
14459024 AAAAAACAACAAGAAAGAAG
1 AAAAAA-AACAAGAAAGAAG
14459044 AAAAAAAACAA-AAAGAA
1 AAAAAAAACAAGAAAGAA
14459061 AATAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAAAACAAGAAAGAAG
Found at i:14459293 original size:16 final size:16
Alignment explanation
Indices: 14459274--14459312 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
14459264 TTTCTTACTA
14459274 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
* * *
14459290 TTTCATTTTTTTCTTG
1 TTTCATTTCTTTATTC
14459306 TTTCATT
1 TTTCATT
14459313 ACCATATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTCATTTCTTTATTC
Found at i:14459368 original size:16 final size:16
Alignment explanation
Indices: 14459347--14459390 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
14459337 TACCCTATCA
14459347 TAACCATTTCTATCCC
1 TAACCATTTCTATCCC
14459363 TAACCATTTCTATCCC
1 TAACCATTTCTATCCC
14459379 TAACCATTTCTA
1 TAACCATTTCTA
14459391 AACCGACGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.27, C:0.34, G:0.00, T:0.39
Consensus pattern (16 bp):
TAACCATTTCTATCCC
Found at i:14461278 original size:22 final size:22
Alignment explanation
Indices: 14461252--14461293 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
14461242 TATCATAACA
14461252 TTTGCATTCATTCATT-ATATGG
1 TTTGCA-TCATTCATTGATATGG
*
14461274 TTTGCATCATTGATTGATAT
1 TTTGCATCATTCATTGATAT
14461294 TCTAGCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (22 bp):
TTTGCATCATTCATTGATATGG
Found at i:14462637 original size:36 final size:36
Alignment explanation
Indices: 14462590--14462694 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
14462580 GATACAATCT
14462590 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
14462626 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
14462662 TTCCATCACC-TTATCACACCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
14462695 ACTTCTAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:14464554 original size:23 final size:23
Alignment explanation
Indices: 14464509--14464554 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
14464499 TTATACCTAT
*
14464509 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
14464532 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
14464555 TATATTATAC
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:14464625 original size:26 final size:25
Alignment explanation
Indices: 14464575--14464625 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
14464565 CTATAGTTAT
* *
14464575 TATGATAATAAGTTATCTATTTATA
1 TATGATAACAAGTTATCTATATATA
14464600 TATGATATACAAGTTAT-TATCATATA
1 TATGATA-ACAAGTTATCTAT-ATATA
14464626 CTATAGTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (25 bp):
TATGATAACAAGTTATCTATATATA
Found at i:14465895 original size:19 final size:20
Alignment explanation
Indices: 14465871--14465910 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
14465861 TATCCTTTCT
14465871 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
14465890 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
14465910 T
1 T
14465911 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:14466209 original size:13 final size:13
Alignment explanation
Indices: 14466177--14466250 Score: 62
Period size: 13 Copynumber: 5.8 Consensus size: 13
14466167 TTGGACTGCA
*
14466177 AAAAGAAAGAAAAT
1 AAAA-AAAGAAAAG
* *
14466191 ATAAAAAGAAGAG
1 AAAAAAAGAAAAG
**
14466204 -AAAAAA-ATCAG
1 AAAAAAAGAAAAG
*
14466215 AAAAGAAGAAAAG
1 AAAAAAAGAAAAG
*
14466228 AAGAAAAGAAAAG
1 AAAAAAAGAAAAG
14466241 AAAAAAAGAA
1 AAAAAAAGAA
14466251 GTTCAAAAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
11 3 0.07
12 10 0.22
13 30 0.65
14 3 0.07
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:14466209 original size:29 final size:29
Alignment explanation
Indices: 14466176--14466251 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
14466166 ATTGGACTGC
*
14466176 AAAAAGAAAGAAAATATA-AAAAGAAGAGAA
1 AAAAAGAAAGAAAAGA-AGAAAAGAAGA-AA
**
14466206 AAAAA-TCAGAAAAGAAGAAAAGAAGAAA
1 AAAAAGAAAGAAAAGAAGAAAAGAAGAAA
14466234 AGAAAAGAAA-AAAAGAAG
1 A-AAAAGAAAGAAAAGAAG
14466252 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 4 0.11
29 28 0.74
30 6 0.16
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (29 bp):
AAAAAGAAAGAAAAGAAGAAAAGAAGAAA
Found at i:14466224 original size:8 final size:8
Alignment explanation
Indices: 14466213--14466237 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
14466203 GAAAAAAATC
14466213 AGAAAAGA
1 AGAAAAGA
14466221 AGAAAAGA
1 AGAAAAGA
14466229 AGAAAAGA
1 AGAAAAGA
14466237 A
1 A
14466238 AAGAAAAAAA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:14468984 original size:23 final size:23
Alignment explanation
Indices: 14468939--14468984 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
14468929 TTATACCTAT
*
14468939 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
14468962 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
14468985 TTATACCTAT
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:14470286 original size:19 final size:20
Alignment explanation
Indices: 14470262--14470301 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
14470252 TATCCTTTCT
14470262 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
14470281 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
14470301 T
1 T
14470302 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:14470650 original size:19 final size:20
Alignment explanation
Indices: 14470595--14470653 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
14470585 GAGTGCAAAA
14470595 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAG-AAAAGA-AAAAGAAG
*
14470617 AGAAA-AATCAG-AAAAGAAG
1 AGAAAGAA-AAGAAAAAGAAG
14470636 A-AAAGAAAAGAAAAAGAA
1 AGAAAGAAAAGAAAAAGAA
14470654 AATTCCTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 18 0.56
20 2 0.06
21 2 0.06
22 5 0.16
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAAGAAAAAGAAG
Found at i:14471941 original size:24 final size:24
Alignment explanation
Indices: 14471914--14471976 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
14471904 GTTCTTTGAC
*
14471914 GTTCCAACAGTTATGCCACTTAAA
1 GTTCCAAAAGTTATGCCACTTAAA
* * * *
14471938 GTTCAAAAAGATATGTCACTTGAA
1 GTTCCAAAAGTTATGCCACTTAAA
*
14471962 GTGCCAAAAGTTATG
1 GTTCCAAAAGTTATG
14471977 ATCATTGAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (24 bp):
GTTCCAAAAGTTATGCCACTTAAA
Found at i:14471992 original size:24 final size:24
Alignment explanation
Indices: 14471925--14471986 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
14471915 TTCCAACAGT
* * * *
14471925 TATGCCACTTAAAGTTCAAAAAGA
1 TATGTCACTTGAAGTGCCAAAAGA
*
14471949 TATGTCACTTGAAGTGCCAAAAGT
1 TATGTCACTTGAAGTGCCAAAAGA
14471973 TATGATCA-TTGAAG
1 TATG-TCACTTGAAG
14471987 CTCCAAGTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (24 bp):
TATGTCACTTGAAGTGCCAAAAGA
Found at i:14489520 original size:13 final size:13
Alignment explanation
Indices: 14489502--14489526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14489492 TTCTTTGTAT
14489502 TTTTCTTTCTTTG
1 TTTTCTTTCTTTG
14489515 TTTTCTTTCTTT
1 TTTTCTTTCTTT
14489527 AGATTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTCTTTCTTTG
Found at i:14491559 original size:19 final size:19
Alignment explanation
Indices: 14491524--14491578 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
14491514 CCATTCGGCC
* * *
14491524 AAAAGCATGTATCTTCATT
1 AAAATCATGTATTTTCATA
* *
14491543 TAAATCGTGTATTTTCATA
1 AAAATCATGTATTTTCATA
14491562 AAAATCATGTATTTTCA
1 AAAATCATGTATTTTCA
14491579 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (19 bp):
AAAATCATGTATTTTCATA
Found at i:14493689 original size:35 final size:35
Alignment explanation
Indices: 14493616--14493722 Score: 106
Period size: 35 Copynumber: 3.0 Consensus size: 35
14493606 AGATACTACC
* * *
14493616 TAAACATCAACATCTTCCATCTCCATTTTCACGCCTA
1 TAAA-ATCACCATCTTCCATCACCA-TTGCACGCCTA
* *
14493653 TAAAATCACCATCTTCCATTATCATTGCACGCCTA
1 TAAAATCACCATCTTCCATCACCATTGCACGCCTA
** * * *
14493688 TATCATTACCATCTTCTATCACCATTTCACGCCTA
1 TAAAATCACCATCTTCCATCACCATTGCACGCCTA
14493723 AATAACCACC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
35 38 0.66
36 16 0.28
37 4 0.07
ACGTcount: A:0.29, C:0.34, G:0.04, T:0.34
Consensus pattern (35 bp):
TAAAATCACCATCTTCCATCACCATTGCACGCCTA
Found at i:14497812 original size:17 final size:18
Alignment explanation
Indices: 14497790--14497866 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 18
14497780 AATTGGAGTG
14497790 CAAAAAGAAAGAAAAGA-
1 CAAAAAGAAAGAAAAGAT
14497807 CAAAAAGAAGAGAAAA-AT
1 CAAAAAGAA-AGAAAAGAT
14497825 CAGAAAAG-AAGAAAAGA-
1 CA-AAAAGAAAGAAAAGAT
* *
14497842 -AAAGAA-AAAGAGAAGTT
1 CAAA-AAGAAAGAAAAGAT
14497859 CAAAAAGA
1 CAAAAAGA
14497867 GAAAGCAAGC
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
15 2 0.04
16 10 0.20
17 18 0.37
18 14 0.29
19 5 0.10
ACGTcount: A:0.71, C:0.05, G:0.19, T:0.04
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAGAT
Found at i:14497813 original size:13 final size:12
Alignment explanation
Indices: 14497797--14497855 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 12
14497787 GTGCAAAAAG
14497797 AAAGAAAAGACAA
1 AAAGAAAAGA-AA
*
14497810 AAAGAAGAGAAA
1 AAAGAAAAGAAA
14497822 AATCAGAAAAGAAGA
1 AA--AGAAAAGAA-A
14497837 AAAGAAAAGAAA
1 AAAGAAAAGAAA
14497849 AAGAGAA
1 AA-AGAA
14497856 GTTCAAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.17
13 22 0.55
14 8 0.20
15 3 0.08
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:14497830 original size:27 final size:27
Alignment explanation
Indices: 14497799--14497850 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
14497789 GCAAAAAGAA
*
14497799 AGAAAAGACA-AAAAGAAGAGAAAAATC
1 AGAAAAGA-AGAAAAGAAAAGAAAAATC
14497826 AGAAAAGAAGAAAAGAAAAGAAAAA
1 AGAAAAGAAGAAAAGAAAAGAAAAA
14497851 GAGAAGTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (27 bp):
AGAAAAGAAGAAAAGAAAAGAAAAATC
Found at i:14497850 original size:19 final size:20
Alignment explanation
Indices: 14497795--14497852 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
14497785 GAGTGCAAAA
14497795 AGAAAGAAAAGACAAAAAGAAG
1 AGAAAGAAAAG--AAAAAGAAG
*
14497817 AGAAA-AATCAG-AAAAGAAG
1 AGAAAGAA-AAGAAAAAGAAG
14497836 A-AAAGAAAAGAAAAAGA
1 AGAAAGAAAAGAAAAAGA
14497853 GAAGTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 17 0.55
21 2 0.06
22 7 0.23
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAAGAAAAAGAAG
Found at i:14503987 original size:36 final size:35
Alignment explanation
Indices: 14503934--14504042 Score: 105
Period size: 35 Copynumber: 3.1 Consensus size: 35
14503924 TAAGATACTA
*
14503934 CCTA-AACATCACTATCTTCCATCTCCATTTTCACG
1 CCTATAACATCACCATCTTCCATCTCCA-TTTCACG
* **
14503969 CCTATAACATCACCATCTTCCAT-TACCATTGCTTG
1 CCTATAACATCACCATCTTCCATCT-CCATTTCACG
* * * * *
14504004 CCTATATCATTACCATATTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCTCCATTTCACG
14504039 CCTA
1 CCTA
14504043 AATAAACACC
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
35 39 0.66
36 20 0.34
ACGTcount: A:0.27, C:0.35, G:0.04, T:0.35
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCTCCATTTCACG
Found at i:14504895 original size:1 final size:1
Alignment explanation
Indices: 14504880--14504915 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
14504870 TCAAAGTGCT
* *
14504880 AAAACAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14504916 GAACTCCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14508858 original size:47 final size:45
Alignment explanation
Indices: 14508783--14508891 Score: 139
Period size: 47 Copynumber: 2.4 Consensus size: 45
14508773 TATAAAATCC
*
14508783 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * *
14508828 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
14508875 CTTGCCA-TTATTCCATA
1 CTTACCATTTATCCCATA
14508892 CCCATACACC
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
44 8 0.14
45 10 0.18
46 2 0.04
47 37 0.65
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:14514591 original size:2 final size:2
Alignment explanation
Indices: 14514584--14514619 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14514574 CACAAGTGAA
14514584 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
14514620 TTCATCTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14514654 original size:11 final size:11
Alignment explanation
Indices: 14514640--14514738 Score: 55
Period size: 11 Copynumber: 8.6 Consensus size: 11
14514630 ATTTTTTTCC
14514640 TCTTTTTCTTT
1 TCTTTTTCTTT
14514651 TC-TTTTCATTT
1 TCTTTTTC-TTT
14514662 TCTGTTTT-TTT
1 TCT-TTTTCTTT
14514673 TCTTTTT-TTCT
1 TCTTTTTCTT-T
**
14514684 TCCCTTTCTTT
1 TCTTTTTCTTT
14514695 T-TGTTTTCATCTT
1 TCT-TTTTC-T-TT
*
14514708 TCCTCTTTCTGTT
1 T-CTTTTTCT-TT
14514721 T-TTTTTCTATT
1 TCTTTTTCT-TT
14514732 TCTTTTT
1 TCTTTTT
14514739 TTCCTCTACG
Statistics
Matches: 69, Mismatches: 8, Indels: 21
0.70 0.08 0.21
Matches are distributed among these distances:
10 11 0.16
11 34 0.49
12 8 0.12
13 11 0.16
14 4 0.06
15 1 0.01
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:14514695 original size:22 final size:22
Alignment explanation
Indices: 14514644--14514732 Score: 63
Period size: 22 Copynumber: 3.8 Consensus size: 22
14514634 TTTTCCTCTT
**
14514644 TTTCTTTTCTTTTCATTTTCTG
1 TTTCTTTTCTTTTCATTTTCCC
* *
14514666 TTTTTTTTCTTTT-TTTCTTCCC
1 TTTCTTTTCTTTTCATT-TTCCC
*
14514688 TTTCTTTTTGTTTTCATCTTTCCTC
1 TTTC-TTTTCTTTTCAT-TTTCC-C
*
14514713 TTTCTGTTTTTTTTCTATTT
1 TTTCT-TTTCTTTTC-ATTT
14514733 CTTTTTTTCC
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
21 2 0.04
22 18 0.35
23 8 0.15
24 6 0.12
25 16 0.31
26 2 0.04
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTCTTTTCTTTTCATTTTCCC
Found at i:14522833 original size:19 final size:21
Alignment explanation
Indices: 14522809--14522852 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
14522799 AACATATATC
14522809 TTCA-TTAAAA-TCATGTATT
1 TTCATTTAAAAGTCATGTATT
14522828 TTCATTTAAAAGTCATGTATT
1 TTCATTTAAAAGTCATGTATT
14522849 TTCA
1 TTCA
14522853 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 6 0.26
21 13 0.57
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (21 bp):
TTCATTTAAAAGTCATGTATT
Found at i:14523560 original size:13 final size:13
Alignment explanation
Indices: 14523544--14523568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14523534 ATCAGAAAAA
14523544 AAAAGAAAAGAAG
1 AAAAGAAAAGAAG
14523557 AAAAGAAAAGAA
1 AAAAGAAAAGAA
14523569 AAAGTGAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAG
Found at i:14526918 original size:19 final size:21
Alignment explanation
Indices: 14526894--14526945 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
14526884 TGGCAAAGAG
*
14526894 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
14526913 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
14526934 CATGTATTTTCA
1 CATGTATTTTCA
14526946 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:14529428 original size:20 final size:20
Alignment explanation
Indices: 14529386--14529428 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
14529376 CCATTATTCC
* * *
14529386 ATAACCATATACCATGGAAA
1 ATAACCATAAACAATAGAAA
*
14529406 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGAAA
14529426 ATA
1 ATA
14529429 GCCCAATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.19, G:0.07, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGAAA
Found at i:14529612 original size:59 final size:58
Alignment explanation
Indices: 14529482--14529617 Score: 155
Period size: 59 Copynumber: 2.3 Consensus size: 58
14529472 ATAAGCACCG
* * * **
14529482 TAGTGCTATCCCGAGTATGACACATAAGGTCGTGTACACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCACACCATATACACTAGGTATCCTT
* *** *
14529541 AAGCACAGTCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCACACCATATACACTAGGTATCCTT
14529600 TAGTGTATTCCCGAATAT
1 TAGTGTA-TCCCGAATAT
14529618 CCAGCCTGCT
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
58 1 0.02
59 60 0.98
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCACACCATATACACTAGGTATCCTT
Found at i:14532154 original size:19 final size:21
Alignment explanation
Indices: 14532114--14532162 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
14532104 ACCCCTTTGC
14532114 AAATACATGATTTTTAAATGA
1 AAATACATGATTTTTAAATGA
*
14532135 AAATACATTA-TTTT-AATGA
1 AAATACATGATTTTTAAATGA
*
14532154 ATATACATG
1 AAATACATG
14532163 CTCTTGGCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.48
20 4 0.16
21 9 0.36
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (21 bp):
AAATACATGATTTTTAAATGA
Found at i:14540100 original size:12 final size:12
Alignment explanation
Indices: 14540085--14540120 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
14540075 AATACAAAAA
14540085 GAAGTGCAAAGT
1 GAAGTGCAAAGT
14540097 GAAGTGCAAAGT
1 GAAGTGCAAAGT
14540109 GAAGTGCAAAGT
1 GAAGTGCAAAGT
14540121 CAAAGAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.33, T:0.17
Consensus pattern (12 bp):
GAAGTGCAAAGT
Found at i:14542987 original size:11 final size:13
Alignment explanation
Indices: 14542955--14542989 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
14542945 TGGCCAAAGA
14542955 TGAAAAGGTATGT
1 TGAAAAGGTATGT
14542968 TGAAAAGGTATG-
1 TGAAAAGGTATGT
14542980 TG-AAAGGTAT
1 TGAAAAGGTAT
14542990 TTAGTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:14551313 original size:28 final size:26
Alignment explanation
Indices: 14551282--14551338 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
14551272 GAAAATCAGA
* *
14551282 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAAATCAAGCACT-CAAAAG-AAG
*
14551310 AAAGAAAATCCAGCACTCAAAAGAAG
1 AAAGAAAATCAAGCACTCAAAAGAAG
14551336 AAA
1 AAA
14551339 AAGCAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 6 0.23
28 14 0.54
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.09
Consensus pattern (26 bp):
AAAGAAAATCAAGCACTCAAAAGAAG
Found at i:14552364 original size:105 final size:105
Alignment explanation
Indices: 14552202--14552726 Score: 756
Period size: 105 Copynumber: 5.0 Consensus size: 105
14552192 ATATCGTGCT
* * *
14552202 ACTCAAGACAACACAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
14552267 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
14552307 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGACAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
14552372 ATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
14552412 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
14552477 ATTTCAGAGCCAATTTCAACTTCCCAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
14552517 ACTCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAAC-A-AAGTT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
14552578 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * * *
14552617 ACTCGAGACAGCACAAGCTCAACTTCACGGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCC
* * * *
14552682 AAATCCAG-GACCAATTTCAACTTCACGGCGGAGGATATTGG
65 AATTTCAGAG-CCAATTTCAACTTCACAGCGAAGGATATTGG
14552723 ACTC
1 ACTC
14552727 GGAACAATAT
Statistics
Matches: 379, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
100 78 0.21
101 1 0.00
102 2 0.01
103 8 0.02
104 2 0.01
105 252 0.66
106 36 0.09
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:14554422 original size:15 final size:15
Alignment explanation
Indices: 14554398--14554428 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14554388 TTAAATATAT
*
14554398 TATGTTTTATTATTA
1 TATGTATTATTATTA
14554413 TATGTATTATTATTA
1 TATGTATTATTATTA
14554428 T
1 T
14554429 TATATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TATGTATTATTATTA
Found at i:14554555 original size:2 final size:2
Alignment explanation
Indices: 14554550--14554582 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14554540 TTTTTTTTTG
14554550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14554583 TATTCTTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14554718 original size:2 final size:2
Alignment explanation
Indices: 14554705--14554749 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
14554695 TTCATTTTAT
*
14554705 TA TA TT 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
14554747 TA T
1 TA T
14554750 CATTTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:14555376 original size:28 final size:29
Alignment explanation
Indices: 14555345--14555400 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
14555335 TTTGTTTTGC
14555345 AGGACA-ATTCAAGAGA-CATATCTTTTCA
1 AGGACAGATTCAAGA-ATCATATCTTTTCA
*
14555373 AGGAGATGATTCAAGAATCATATCTTTT
1 AGGACA-GATTCAAGAATCATATCTTTT
14555401 GGAGGACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.21
29 1 0.04
30 18 0.75
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (29 bp):
AGGACAGATTCAAGAATCATATCTTTTCA
Found at i:14557344 original size:19 final size:21
Alignment explanation
Indices: 14557320--14557371 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
14557310 CGGCCAAGAG
*
14557320 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
14557339 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
14557360 CATGTATTTTCA
1 CATGTATTTTCA
14557372 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:14559002 original size:8 final size:8
Alignment explanation
Indices: 14558989--14559059 Score: 74
Period size: 8 Copynumber: 8.9 Consensus size: 8
14558979 TGAATTTCTT
*
14558989 TTCTTTTA
1 TTCTTTTC
14558997 TTCTTTTC
1 TTCTTTTC
14559005 TTCTTTTC
1 TTCTTTTC
14559013 TTCTTTTC
1 TTCTTTTC
*
14559021 TGACTTTTTC
1 T-TC-TTTTC
*
14559031 TTCTTTTT
1 TTCTTTTC
14559039 TTC-TTT-
1 TTCTTTTC
14559045 TTCTTTTC
1 TTCTTTTC
*
14559053 TTATTTT
1 TTCTTTT
14559060 GCACTCCAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
6 3 0.06
7 6 0.11
8 37 0.69
9 2 0.04
10 6 0.11
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:14559010 original size:21 final size:22
Alignment explanation
Indices: 14558984--14559059 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 22
14558974 TCTTTTGAAT
*
14558984 TTCTTTTCTT-TTATTCTTTTC
1 TTCTTTTCTTCTTTTTCTTTTC
14559005 TTCTTTTCTTCTTTTCTGACTTTTTC
1 TTCTTTTCTTCTTTT-T--C-TTTTC
*
14559031 TTCTTTTTTTCTTTTTCTTTTC
1 TTCTTTTCTTCTTTTTCTTTTC
*
14559053 TTATTTT
1 TTCTTTT
14559060 GCACTCCAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 10 0.21
22 14 0.30
23 2 0.04
25 2 0.04
26 19 0.40
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (22 bp):
TTCTTTTCTTCTTTTTCTTTTC
Found at i:14559046 original size:18 final size:18
Alignment explanation
Indices: 14559000--14559046 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
14558990 TCTTTTATTC
14559000 TTTTCTTCTTTTCTTCTTT
1 TTTTCTT-TTTTCTTCTTT
**
14559019 TCTGAC-TTTTTCTTCTTT
1 T-TTTCTTTTTTCTTCTTT
14559037 TTTTCTTTTT
1 TTTTCTTTTT
14559047 CTTTTCTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 5
0.71 0.13 0.16
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 2 0.09
20 2 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTTTCTTCTTT
Found at i:14562992 original size:11 final size:13
Alignment explanation
Indices: 14562960--14562989 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14562950 TGGCCAAAGA
14562960 TGAAAAGGTATGT
1 TGAAAAGGTATGT
14562973 TGAAAAGGTATG-
1 TGAAAAGGTATGT
14562985 TGAAA
1 TGAAA
14562990 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:14565626 original size:20 final size:20
Alignment explanation
Indices: 14565601--14565640 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
14565591 CTATCATAAG
14565601 CATTCATTCACATGTTAGTA
1 CATTCATTCACATGTTAGTA
14565621 CATTCATTCACATGTTAGTA
1 CATTCATTCACATGTTAGTA
14565641 TAAATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (20 bp):
CATTCATTCACATGTTAGTA
Found at i:14567520 original size:15 final size:15
Alignment explanation
Indices: 14567509--14567537 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14567499 ACTCAAAAAG
14567509 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
14567524 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
14567538 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:14568783 original size:24 final size:21
Alignment explanation
Indices: 14568749--14568791 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
14568739 TCCCCAAGAC
*
14568749 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
14568771 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
14568792 AGAATATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:14581828 original size:16 final size:17
Alignment explanation
Indices: 14581804--14581844 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
14581794 AAACTCGTTG
*
14581804 TTTTGCTTT-CAACTTC
1 TTTTTCTTTGCAACTTC
*
14581820 TTTTTCTTTGCAATTTC
1 TTTTTCTTTGCAACTTC
14581837 -TTTTCTTT
1 TTTTTCTTT
14581845 TTCTTTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.10, C:0.20, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTTCTTTGCAACTTC
Found at i:14582806 original size:24 final size:24
Alignment explanation
Indices: 14582766--14582812 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
14582756 CAGCCTTGTG
* *
14582766 CATAGGATAAAGGTTGATCATGTC
1 CATAGGATAAAGATTGAGCATGTC
*
14582790 CATAGGATGAAGATTGAGCATGT
1 CATAGGATAAAGATTGAGCATGT
14582813 GCATCACCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (24 bp):
CATAGGATAAAGATTGAGCATGTC
Found at i:14583089 original size:20 final size:20
Alignment explanation
Indices: 14583051--14583091 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
14583041 GGGTAATAAT
*
14583051 ATAAGTAATGAAAGGAAATA
1 ATAAGTAATGAAAGAAAATA
14583071 ATAAG-AATGAAATGAAAATA
1 ATAAGTAATGAAA-GAAAATA
14583091 A
1 A
14583092 AGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAGAAAATA
Found at i:14589388 original size:30 final size:33
Alignment explanation
Indices: 14589352--14589412 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
14589342 AATGATTAAG
14589352 ATGGAAAT-ATAA-ATAA-GAAATGGA-AGAAGA
1 ATGGAAATGATAAGA-AAGGAAATGGATAGAAGA
14589382 ATGGAAATGATAAGAAAGGAAATGGATAGAA
1 ATGGAAATGATAAGAAAGGAAATGGATAGAA
14589413 ATGTTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 6 0.22
32 9 0.33
33 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.16
Consensus pattern (33 bp):
ATGGAAATGATAAGAAAGGAAATGGATAGAAGA
Found at i:14590023 original size:19 final size:20
Alignment explanation
Indices: 14589982--14590024 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
14589972 GAAACTCCTT
*
14589982 TGAAAACACATGATTTCTAA
1 TGAAAACACATAATTTCTAA
*
14590002 TGAAAATACATAATTT-TAA
1 TGAAAACACATAATTTCTAA
14590021 TGAA
1 TGAA
14590025 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTCTAA
Found at i:14598263 original size:35 final size:36
Alignment explanation
Indices: 14598173--14598273 Score: 159
Period size: 36 Copynumber: 2.8 Consensus size: 36
14598163 CAATATGTCA
* *
14598173 ATCACCATTATTACGCCTATATCATCACTATAGTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCC
*
14598209 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCC
*
14598245 ATCACCA-TATCACGCCTATATTATCACCA
1 ATCACCATTATCACGCCTATATCATCACCA
14598274 ACTTATAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 21 0.34
36 40 0.66
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.31
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATAGTCC
Found at i:14598755 original size:11 final size:11
Alignment explanation
Indices: 14598717--14598756 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
14598707 AGTGCCAAAG
*
14598717 AAAGAAATGAA
1 AAAGAAAAGAA
14598728 AAAG--AAGAA
1 AAAGAAAAGAA
14598737 AAAGAAAAGAA
1 AAAGAAAAGAA
14598748 AAAGAAAAG
1 AAAGAAAAG
14598757 TGAAGAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:14598995 original size:15 final size:16
Alignment explanation
Indices: 14598977--14599010 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
14598967 TCTTTCTACC
14598977 CTAT-CATAACCATTT
1 CTATCCATAACCATTT
*
14598992 CTATCCCTAACCATTT
1 CTATCCATAACCATTT
14599008 CTA
1 CTA
14599011 AACCGACGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (16 bp):
CTATCCATAACCATTT
Found at i:14604837 original size:19 final size:21
Alignment explanation
Indices: 14604813--14604863 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
14604803 GTCCAAGATA
*
14604813 ATGTATCTTCA-TTAAAA-TC
1 ATGTATTTTCATTTAAAAGTC
14604832 ATGTATTTTCATTTAAAAGTC
1 ATGTATTTTCATTTAAAAGTC
14604853 ATGTATTTTCA
1 ATGTATTTTCA
14604864 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 6 0.21
21 13 0.45
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTTAAAAGTC
Found at i:14605490 original size:13 final size:11
Alignment explanation
Indices: 14605468--14605533 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
14605458 TATCACGCCT
14605468 ATATCATCACC
1 ATATCATCACC
14605479 ATAGTCCATCACC
1 ATA-T-CATCACC
*
14605492 ATTATCA-CGCC
1 A-TATCATCACC
14605503 TATATCATCACC
1 -ATATCATCACC
14605515 ATATTCCATCACC
1 ATA-T-CATCACC
14605528 ATATCA
1 ATATCA
14605534 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:14605495 original size:36 final size:36
Alignment explanation
Indices: 14605454--14605542 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
14605444 TGAAGATTCG
14605454 CCATTATCACGCCTATATCATCACCATAGTCCATCA
1 CCATTATCACGCCTATATCATCACCATAGTCCATCA
*
14605490 CCATTATCACGCCTATATCATCACCATATTCCATCA
1 CCATTATCACGCCTATATCATCACCATAGTCCATCA
14605526 CCA-TATCACGCCTATAT
1 CCATTATCACGCCTATAT
14605543 TATCTCCAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 14 0.27
36 38 0.73
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
CCATTATCACGCCTATATCATCACCATAGTCCATCA
Found at i:14609685 original size:23 final size:25
Alignment explanation
Indices: 14609630--14609686 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
14609620 CAACTTTTCT
*
14609630 TTCTTTT-TTCTTCTTTTGAGTGTT
1 TTCTTTTCTTCTTCTTTTGAGTGTC
*
14609654 TTCAATTTCTTCTT-TTTTGAGTG-C
1 TTC-TTTTCTTCTTCTTTTGAGTGTC
14609678 TTCTTTTCT
1 TTCTTTTCT
14609687 GATTTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 12 0.43
26 5 0.18
ACGTcount: A:0.07, C:0.16, G:0.11, T:0.67
Consensus pattern (25 bp):
TTCTTTTCTTCTTCTTTTGAGTGTC
Found at i:14613067 original size:17 final size:17
Alignment explanation
Indices: 14613042--14613075 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14613032 TCGGCTTAAA
*
14613042 AAATGGTTAGGGTATAG
1 AAATAGTTAGGGTATAG
*
14613059 AAATAGTTATGGTATAG
1 AAATAGTTAGGGTATAG
14613076 GGGTAGGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (17 bp):
AAATAGTTAGGGTATAG
Found at i:14629828 original size:19 final size:21
Alignment explanation
Indices: 14629785--14629836 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
14629775 GAAACCCCTT
14629785 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
14629806 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
14629825 TGAAGATACATG
1 TGAAAATACATG
14629837 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:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:14632892 original size:26 final size:29
Alignment explanation
Indices: 14632863--14632924 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
14632853 TGGTAGAGCA
*
14632863 CTTTTCTTTGCTTGTTTTC-TC-TTT-TT
1 CTTTTCTTTGCTTCTTTTCTTCTTTTCTT
* *
14632889 CTTTTATTTTCTTCTTTTCTTCTTTTCTT
1 CTTTTCTTTGCTTCTTTTCTTCTTTTCTT
14632918 CTTTTCT
1 CTTTTCT
14632925 CTTCTTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 16 0.55
27 2 0.07
28 3 0.10
29 8 0.28
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (29 bp):
CTTTTCTTTGCTTCTTTTCTTCTTTTCTT
Found at i:14632906 original size:8 final size:8
Alignment explanation
Indices: 14632895--14632924 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
14632885 TTTTCTTTTA
14632895 TTTTCTTC
1 TTTTCTTC
14632903 TTTTCTTC
1 TTTTCTTC
14632911 TTTTCTTC
1 TTTTCTTC
14632919 TTTTCT
1 TTTTCT
14632925 CTTCTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCTTC
Found at i:14632927 original size:26 final size:26
Alignment explanation
Indices: 14632877--14632932 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
14632867 TCTTTGCTTG
*
14632877 TTTTCTCTTTTTCTTTTATTTTCTTC
1 TTTTCTCTTTTTCTTTTATTCTCTTC
14632903 TTTTCT-TCTTTTCTTCTT-TTCTCTTC
1 TTTTCTCT-TTTTCTT-TTATTCTCTTC
14632929 TTTT
1 TTTT
14632933 TGCACTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 1 0.04
26 24 0.89
27 2 0.07
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTCTCTTTTTCTTTTATTCTCTTC
Found at i:14632929 original size:21 final size:20
Alignment explanation
Indices: 14632866--14632930 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
14632856 TAGAGCACTT
* *
14632866 TTCTTTGCTTGTTTTCTCTTT
1 TTCTTTTCTT-TTTTCTCTTC
* *
14632887 TTCTTTTATTTTCTTCTTTTC
1 TTCTTTTCTTTT-TTCTCTTC
14632908 TTCTTTTCTTCTTTTCTCTTC
1 TTCTTTTCTT-TTTTCTCTTC
14632929 TT
1 TT
14632931 TTTGCACTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.02, C:0.22, G:0.03, T:0.74
Consensus pattern (20 bp):
TTCTTTTCTTTTTTCTCTTC
Found at i:14633669 original size:19 final size:21
Alignment explanation
Indices: 14633626--14633677 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
14633616 GAAAGCCCTT
14633626 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
14633647 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
14633666 TGAAGATACATG
1 TGAAAATACATG
14633678 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:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:14650332 original size:24 final size:24
Alignment explanation
Indices: 14650305--14650356 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
14650295 ACATGTTTTT
14650305 GAACTTCAAGTGGCATAATTGTTG
1 GAACTTCAAGTGGCATAATTGTTG
14650329 GAACTTCAAGTGGCATAATTGTTG
1 GAACTTCAAGTGGCATAATTGTTG
14650353 GAAC
1 GAAC
14650357 GAAAAATGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (24 bp):
GAACTTCAAGTGGCATAATTGTTG
Found at i:14653332 original size:28 final size:28
Alignment explanation
Indices: 14653300--14653357 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
14653290 AATATCATAT
14653300 AACATGGTATTCATAAATGATAAATGGA
1 AACATGGTATTCATAAATGATAAATGGA
14653328 AACATGGTATTCATAAATGATAAATGGA
1 AACATGGTATTCATAAATGATAAATGGA
14653356 AA
1 AA
14653358 AATGATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (28 bp):
AACATGGTATTCATAAATGATAAATGGA
Found at i:14653995 original size:19 final size:19
Alignment explanation
Indices: 14653971--14654012 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
14653961 ATCCTTTCTT
14653971 TATTTCATTTCATT-CTTAA
1 TATTTCATTTCATTACTT-A
14653990 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
14654009 TATT
1 TATT
14654013 ATTATCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:14658078 original size:19 final size:19
Alignment explanation
Indices: 14658054--14658095 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
14658044 ATCCTTTCTT
14658054 TATTTCATTTCATT-CTTAA
1 TATTTCATTTCATTACTT-A
14658073 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
14658092 TATT
1 TATT
14658096 ATTATCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:14662397 original size:24 final size:24
Alignment explanation
Indices: 14662351--14662397 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
14662341 AGAAAATAAG
**
14662351 CACTCAAAAAGAAGAAATTGAAAA
1 CACTCAAAAAGAAGAAAAAGAAAA
14662375 CACTC-AAAAGAAGAAAAAAGAAA
1 CACTCAAAAAGAAG-AAAAAGAAA
14662398 GAAAAGTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.66, C:0.13, G:0.13, T:0.09
Consensus pattern (24 bp):
CACTCAAAAAGAAGAAAAAGAAAA
Found at i:14664979 original size:21 final size:22
Alignment explanation
Indices: 14664954--14665007 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
14664944 GAATTGTTGA
*
14664954 TGAGTGCTTCCAA-CTTTTTTT
1 TGAGTGCTTCCAATCTTCTTTT
*
14664975 TGAGTGCTTTCAATTTCTTCTTTT
1 TGAGTGCTTCCAA--TCTTCTTTT
14664999 TGAGTGCTT
1 TGAGTGCTT
14665008 ATTTTCTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.43
24 16 0.57
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.54
Consensus pattern (22 bp):
TGAGTGCTTCCAATCTTCTTTT
Found at i:14665020 original size:22 final size:24
Alignment explanation
Indices: 14664971--14665021 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
14664961 TTCCAACTTT
**
14664971 TTTTTGAGTGCTTTCAATTTCTTC
1 TTTTTGAGTGCTTTCAATTTCTGA
*
14664995 TTTTTGAGTGC-TT-ATTTTCTGA
1 TTTTTGAGTGCTTTCAATTTCTGA
14665017 TTTTT
1 TTTTT
14665022 TCTTGCTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 2 0.08
24 11 0.46
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.63
Consensus pattern (24 bp):
TTTTTGAGTGCTTTCAATTTCTGA
Found at i:14667917 original size:13 final size:13
Alignment explanation
Indices: 14667899--14667928 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
14667889 TCATTTAGGC
14667899 GCCAAGATGAAGA
1 GCCAAGATGAAGA
14667912 GCCAAGATGAAGA
1 GCCAAGATGAAGA
14667925 GCCA
1 GCCA
14667929 TTTAACCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.30, T:0.07
Consensus pattern (13 bp):
GCCAAGATGAAGA
Found at i:14675090 original size:17 final size:17
Alignment explanation
Indices: 14675062--14675097 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
14675052 GTGCTTCAAC
14675062 TTCTTTCTTTTCTT-TT
1 TTCTTTCTTTTCTTCTT
14675078 TTCTTTGCTTTTCTTCTT
1 TTCTTT-CTTTTCTTCTT
14675096 TT
1 TT
14675098 TGAGTGCTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 8 0.44
18 4 0.22
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (17 bp):
TTCTTTCTTTTCTTCTT
Found at i:14693840 original size:22 final size:22
Alignment explanation
Indices: 14693790--14693841 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
14693780 GAAAAATCAG
14693790 AAAAGAAATTGAAGCACTCCTAA
1 AAAAGAAATTGAAGCACT-CTAA
*
14693813 AGAAGAAATTGAAAGCACT-TAA
1 AAAAGAAATTG-AAGCACTCTAA
14693835 AAAAGAA
1 AAAAGAA
14693842 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 10 0.38
24 7 0.27
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (22 bp):
AAAAGAAATTGAAGCACTCTAA
Found at i:14701949 original size:19 final size:22
Alignment explanation
Indices: 14701904--14701950 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
14701894 GCGTCAGAGG
*
14701904 GGTATCGATACCACTATTTAGT
1 GGTATCGATACCACTATTGAGT
*
14701926 CGTATCGATACCA-T-TTGA-T
1 GGTATCGATACCACTATTGAGT
14701945 GGTATC
1 GGTATC
14701951 AGTACCATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 1 0.05
22 12 0.55
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (22 bp):
GGTATCGATACCACTATTGAGT
Found at i:14706409 original size:18 final size:19
Alignment explanation
Indices: 14706375--14706410 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
14706365 AATATTCTCA
14706375 CAAAGAGTTTGTATTTATC
1 CAAAGAGTTTGTATTTATC
*
14706394 CAAAGGGTTT-TATTTAT
1 CAAAGAGTTTGTATTTAT
14706411 AATGGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (19 bp):
CAAAGAGTTTGTATTTATC
Done.