Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 52 of 62
Found at i:12241466 original size:13 final size:12
Alignment explanation
Indices: 12241408--12241468 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 12
12241398 CTTTTTGAAC
12241408 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
12241421 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
*
12241434 TTCTGATTTTTTTTT
1 TTC---TTTTTTCTT
12241449 CTTCTTTTTGTCTT
1 -TTCTTTTT-TCTT
12241463 TTCTTT
1 TTCTTT
12241469 CTTTTTGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
12 3 0.08
13 23 0.57
14 3 0.08
15 4 0.10
16 7 0.17
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:12241473 original size:29 final size:29
Alignment explanation
Indices: 12241411--12241474 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
12241401 TTTGAACTTC
12241411 TCTTTTTCTTTTCTTTTCTTCTTTTCTGA
1 TCTTTTTCTTTTCTTTTCTTCTTTTCTGA
* *
12241440 T-TTTTTTTTCTTCTTTT-TGTCTTTTCT-T
1 TCTTTTTCTT-TTCTTTTCT-TCTTTTCTGA
12241468 TCTTTTT
1 TCTTTTT
12241475 GCATCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (29 bp):
TCTTTTTCTTTTCTTTTCTTCTTTTCTGA
Found at i:12241820 original size:12 final size:13
Alignment explanation
Indices: 12241796--12241828 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
12241786 TTGATGGTCT
12241796 TGATGGATGTTGA
1 TGATGGATGTTGA
12241809 TGATGG-TGTTGA
1 TGATGGATGTTGA
12241821 TGAATGGA
1 TG-ATGGA
12241829 AATGGTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.36
Consensus pattern (13 bp):
TGATGGATGTTGA
Found at i:12246515 original size:91 final size:91
Alignment explanation
Indices: 12246358--12246533 Score: 271
Period size: 91 Copynumber: 1.9 Consensus size: 91
12246348 CCTAGAACAC
* *
12246358 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATAGATCATTTAGGCGCCAATATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATAGATCATTTAGGCACCAAGATG
12246423 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * * *
12246449 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATAGATCATTTAGGCACCAAGATG
12246514 AAGAGTTCTCTCCCTATTCG
66 AAGAGTTCTCTCCCTATTCG
12246534 AAAAAGCATC
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATAGATCATTTAGGCACCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:12247409 original size:90 final size:91
Alignment explanation
Indices: 12247300--12247481 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
12247290 GGGAAATGAT
* *
12247300 GCTTGGCTGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
12247364 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * *
12247390 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
* **
12247455 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
12247481 G
1 G
12247482 GTGTTTTAGG
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 59 0.72
91 23 0.28
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:12250676 original size:22 final size:23
Alignment explanation
Indices: 12250651--12250696 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12250641 TTTTTCTTCC
12250651 TCTT-TGAGTGCTTTCAATTTCT
1 TCTTGTGAGTGCTTTCAATTTCT
* *
12250673 TCTTGTGAGTGCTTTGATTTTCT
1 TCTTGTGAGTGCTTTCAATTTCT
12250696 T
1 T
12250697 TGCTGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (23 bp):
TCTTGTGAGTGCTTTCAATTTCT
Found at i:12251590 original size:90 final size:91
Alignment explanation
Indices: 12251474--12251655 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
12251464 GGGAAATGAT
* *
12251474 GCTTGGTCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
12251538 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * *
12251564 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
* **
12251629 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
12251655 G
1 G
12251656 GTGTTCTAGG
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 59 0.72
91 23 0.28
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:12254583 original size:24 final size:21
Alignment explanation
Indices: 12254549--12254591 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
12254539 TCCACAAGAC
*
12254549 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
12254571 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
12254592 AGAATGTGCC
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:12256573 original size:91 final size:91
Alignment explanation
Indices: 12256418--12256594 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 91
12256408 CCTAGAACAC
12256418 CCATGTGCCTTGCATATGACCAACCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAACCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
12256483 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * * * * *
12256509 CCATGTGTTTTGCATGTGATCAGCCCCTATGTGCCTTGTATGTGGTTCATTTAGGGGCCAAGATG
1 CCATGTGCCTTGCATATGACCAACCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
12256574 AAGAGTTCTCTCCCTATTCGG
66 AAGAGTTCTCTCCCTATTCGG
12256595 AAAAGCATCA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.31
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAACCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:12260638 original size:19 final size:19
Alignment explanation
Indices: 12260611--12260649 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12260601 CCAATCGGCC
12260611 AAAAGCATGTACTTTCATT
1 AAAAGCATGTACTTTCATT
* *
12260630 AAAATCATGTATTTTCATT
1 AAAAGCATGTACTTTCATT
12260649 A
1 A
12260650 TAAAAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (19 bp):
AAAAGCATGTACTTTCATT
Found at i:12262098 original size:465 final size:461
Alignment explanation
Indices: 12261189--12262086 Score: 1448
Period size: 465 Copynumber: 1.9 Consensus size: 461
12261179 TTAAGTAGGA
12261189 GTGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGC
1 GTGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGC
* *
12261254 ACAAGTGAATGGCTCAAAACTGAATGGGTAAGGGTGGCAAACGTATGATTTAATAGGTAGGCTAT
66 ACAAGTGAATGGCTCAAAAC-GAATGGGTAAGGGTGGCAAACGTATGAGTGAATAGGTAGGCTAT
12261319 TTAATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGCGATGAAACAAAAAGGATG
130 TTAATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGCGATGAAACAAAAAGGATG
* *
12261384 GTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCGATGCTATAGAGAGAAAAGACCCA
195 GTTGTGAGGATAATATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGAAAAGACCCA
*
12261449 ATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATATGAACTAAG
260 ATCTTTATATTGTTTCTTCAAGGGGTGGTGATAAGTACTTTGACCCACTAGTTATATGAACTAAG
12261514 AACCAGAAGTATCAAGATGAAAGAAGAGGGTTGACGCCACAAGTATAAAATACTTGATAAGTCGA
325 AACCAGAAGTATCAAGATGAAAGAAGAGGGTTGACGCCACAAGTATAAAATACTTGATAAGTCGA
12261579 TAAAAAGTCACCAGGACTTAAGAAAGAGAATAATCTCACTTCAATTAAAATAAAAGGTCTGTTTA
390 TAAAAAGTCACCAGGACTTAAGAAAGAGAATAATCTCACTTCAATT-AAATAAAAGGTCTGTTTA
12261644 CAAATGGT
454 CAAATGGT
* * * **
12261652 GTGATTTAAGGTAATTTTACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTTT
1 GTGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGC
* *** *
12261717 ACTAGTGAATGGCTCAAGAA-G-ATAGGGTTAAGGGTGGTGGACGTATG-GTGAATAGGTGGGCT
66 ACAAGTGAATGGCTCAA-AACGAAT-GGG-TAAGGGTGGCAAACGTATGAGTGAATAGGTAGGCT
*
12261779 GTTT-A-AAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGTTATGGCGATGAAAC-A
128 ATTTAATAAATGAGAGATGGAAGCGGAAGATGATTG-AA-----ATGGTTATGGCGATGAAACAA
*
12261841 AAAGGATGGTTGTGAGGATAATATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCA
187 AAAGGATGGTTGTGAGGATAATATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGAA
*
12261906 AAGACCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGATAATTACTTTGACCCACTAGTTATAT
252 AAGACCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGATAAGTACTTTGACCCACTAGTTATAT
*
12261971 GAACTAGGAACCAGAAGTATCAAGATGAAAGAAGAGGGTTGACGCCACAAGTATAAATTATACTT
317 GAACTAAGAACCAGAAGTATCAAGATGAAAGAAGAGGGTTGACGCCACAAGTATAAA--ATACTT
* *
12262036 GATAAGTTGATAAAAAGTCACCAGGACTTAAGGAAGAGAATAATCTCACTT
380 GATAAGTCGATAAAAAGTCACCAGGACTTAAGAAAGAGAATAATCTCACTT
12262087 TGATTAATAA
Statistics
Matches: 403, Mismatches: 21, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
460 29 0.07
461 5 0.01
462 19 0.05
463 92 0.23
464 2 0.00
465 182 0.45
466 19 0.05
467 55 0.14
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (461 bp):
GTGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGC
ACAAGTGAATGGCTCAAAACGAATGGGTAAGGGTGGCAAACGTATGAGTGAATAGGTAGGCTATT
TAATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGCGATGAAACAAAAAGGATGG
TTGTGAGGATAATATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGAAAAGACCCAA
TCTTTATATTGTTTCTTCAAGGGGTGGTGATAAGTACTTTGACCCACTAGTTATATGAACTAAGA
ACCAGAAGTATCAAGATGAAAGAAGAGGGTTGACGCCACAAGTATAAAATACTTGATAAGTCGAT
AAAAAGTCACCAGGACTTAAGAAAGAGAATAATCTCACTTCAATTAAATAAAAGGTCTGTTTACA
AATGGT
Found at i:12269148 original size:19 final size:21
Alignment explanation
Indices: 12269105--12269156 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
12269095 GAAACCCCTT
12269105 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
12269126 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
12269145 TGAAGATACATG
1 TGAAAATACATG
12269157 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:12278440 original size:19 final size:19
Alignment explanation
Indices: 12278418--12278476 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
12278408 TCTTTTTGAA
12278418 TTTCTTTTTCTTTTTTTCT
1 TTTCTTTTTCTTTTTTTCT
**
12278437 TTTCTTTTTCTGAATTTTCT
1 TTTCTTTTTCT-TTTTTTCT
12278457 TCTTCTTTTTGTCTTTTTTT
1 T-TTC-TTTT-TCTTTTTTT
12278477 TTTGTACTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.34
20 7 0.22
21 3 0.09
22 8 0.25
23 3 0.09
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTCTTTTTTTCT
Found at i:12278463 original size:34 final size:32
Alignment explanation
Indices: 12278406--12278480 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 32
12278396 CTTGGCTTGC
* *
12278406 TTTC-TTTTTGAATTTCTTTTTCTTTTTTTCT
1 TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
12278437 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTGTCT
12278471 TTT-TTTTTTG
1 TTTCTTTTTTG
12278481 TACTCCAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 4 0.10
32 6 0.15
33 9 0.23
34 20 0.51
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:12279217 original size:19 final size:20
Alignment explanation
Indices: 12279176--12279229 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
12279166 GAAACCCCTT
12279176 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGA-TTTTAAA
*
12279197 TGAAAATACATG-TTTTTAA
1 TGAAAATACATGATTTTAAA
*
12279216 TGAAGATACATGAT
1 TGAAAATACATGAT
12279230 ACGGGTCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 17 0.57
20 1 0.03
21 12 0.40
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:12300840 original size:24 final size:25
Alignment explanation
Indices: 12300805--12300859 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
12300795 ACTTGGAGCC
*
12300805 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
12300829 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
12300853 TCAAGTG
1 TCAAGTG
12300860 GCATAACTGT
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:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:12305525 original size:10 final size:10
Alignment explanation
Indices: 12305494--12305526 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
12305484 TGACATCAAG
12305494 TGTAGCTGAA
1 TGTAGCTGAA
*
12305504 TATAGCTGAA
1 TGTAGCTGAA
12305514 TGTAGCTGAA
1 TGTAGCTGAA
12305524 TGT
1 TGT
12305527 GTTGTTATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (10 bp):
TGTAGCTGAA
Found at i:12307793 original size:5 final size:5
Alignment explanation
Indices: 12307776--12307806 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
12307766 ACTCAAAAAG
*
12307776 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
12307807 GTAGTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:12312329 original size:24 final size:24
Alignment explanation
Indices: 12312296--12312346 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
12312286 ATCAACAAAG
*
12312296 AAATTGAAGCACTCCAAAAGAAGA
1 AAATTGAAGCACTCAAAAAGAAGA
*
12312320 AAATTTAAGCACTCAAAAAGAAGA
1 AAATTGAAGCACTCAAAAAGAAGA
12312344 AAA
1 AAA
12312347 GAAAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (24 bp):
AAATTGAAGCACTCAAAAAGAAGA
Found at i:12315240 original size:21 final size:21
Alignment explanation
Indices: 12315214--12315258 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
12315204 AGCGAAAGAA
12315214 AAAAAAATCAAAAAAGAAAAT
1 AAAAAAATCAAAAAAGAAAAT
* *
12315235 AAAAAAATCAACAAAGAAATT
1 AAAAAAATCAAAAAAGAAAAT
12315256 AAA
1 AAA
12315259 GCACTCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAAAAATCAAAAAAGAAAAT
Found at i:12315276 original size:23 final size:23
Alignment explanation
Indices: 12315248--12315300 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
12315238 AAAATCAACA
*
12315248 AAGAAATTAAAGCACTCCAAAAG
1 AAGAAATTAAAGCACTCAAAAAG
**
12315271 AAGAAAATTTCAGCACTCAAAAAG
1 AAG-AAATTAAAGCACTCAAAAAG
12315295 AAGAAA
1 AAGAAA
12315301 AGAAAGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.58, C:0.15, G:0.13, T:0.13
Consensus pattern (23 bp):
AAGAAATTAAAGCACTCAAAAAG
Found at i:12327393 original size:15 final size:16
Alignment explanation
Indices: 12327373--12327409 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
12327363 GATTAGAATA
12327373 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
12327388 AAATAAACGAAAGATG
1 AAATAAACAAAAGATG
12327404 AAATAA
1 AAATAA
12327410 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:12329735 original size:19 final size:20
Alignment explanation
Indices: 12329694--12329744 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
12329684 GAAACCCCTT
*
12329694 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
12329714 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
12329733 TGAAGATACATG
1 TGAAAATACATG
12329745 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:12333158 original size:11 final size:11
Alignment explanation
Indices: 12333144--12333199 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
12333134 TCTTTTTGAA
12333144 TTCTTTTTCTT
1 TTCTTTTTCTT
12333155 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
12333168 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
12333181 TGTCTTTTTC-T
1 T-TCTTTTTCTT
12333192 TTCTTTTT
1 TTCTTTTT
12333200 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:12333168 original size:19 final size:18
Alignment explanation
Indices: 12333144--12333199 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
12333134 TCTTTTTGAA
12333144 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
12333162 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
12333181 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
12333199 T
1 T
12333200 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:12333953 original size:19 final size:20
Alignment explanation
Indices: 12333912--12333962 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
12333902 GAAACCCCTT
*
12333912 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
12333932 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
12333951 TGAAGATACATG
1 TGAAAATACATG
12333963 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:12337375 original size:11 final size:11
Alignment explanation
Indices: 12337361--12337416 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
12337351 TCTTTTTGAA
12337361 TTCTTTTTCTT
1 TTCTTTTTCTT
12337372 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
12337385 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
12337398 TGTCTTTTTC-T
1 T-TCTTTTTCTT
12337409 TTCTTTTT
1 TTCTTTTT
12337417 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:12337385 original size:19 final size:18
Alignment explanation
Indices: 12337361--12337416 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
12337351 TCTTTTTGAA
12337361 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
12337379 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
12337398 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
12337416 T
1 T
12337417 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:12338167 original size:19 final size:20
Alignment explanation
Indices: 12338126--12338176 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
12338116 GAAACCCCTT
*
12338126 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
12338146 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
12338165 TGAAGATACATG
1 TGAAAATACATG
12338177 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:12342405 original size:15 final size:16
Alignment explanation
Indices: 12342385--12342421 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
12342375 GAATAGAATA
12342385 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
12342400 AAATAAACGAAAGATG
1 AAATAAACAAAAGATG
12342416 AAATAA
1 AAATAA
12342422 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:12350825 original size:35 final size:36
Alignment explanation
Indices: 12350769--12350836 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
12350759 ATACAATCTG
12350769 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
12350805 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
12350837 ACTTCTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:12353275 original size:24 final size:19
Alignment explanation
Indices: 12353215--12353262 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
12353205 TACAAATACC
12353215 TTGCATCAAGTTCAGAGCA
1 TTGCATCAAGTTCAGAGCA
12353234 TTGCATCAAGTTCAGAGCA
1 TTGCATCAAGTTCAGAGCA
12353253 TTGCATCAAG
1 TTGCATCAAG
12353263 CGGTAATCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (19 bp):
TTGCATCAAGTTCAGAGCA
Found at i:12375144 original size:19 final size:20
Alignment explanation
Indices: 12375097--12375146 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
12375087 GAAACCCCTT
* *
12375097 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATGTTTAA
12375117 TGAAAATACATGA-GTTTAA
1 TGAAAATACATGATGTTTAA
*
12375136 TGAAGATACAT
1 TGAAAATACAT
12375147 TCTCTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATGTTTAA
Found at i:12378551 original size:5 final size:5
Alignment explanation
Indices: 12378532--12378584 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
12378522 TTTGAAATCT
* * *
12378532 TTTTC TTTTC -CTTC TTTTC TCTTC TTTTC TTCTTT TTTTC TTTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC
12378581 TTTT
1 TTTT
12378585 TGCACTCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 7 0.18
5 28 0.72
6 4 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:12378585 original size:10 final size:9
Alignment explanation
Indices: 12378533--12378584 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
12378523 TTGAAATCTT
12378533 TTTCTTTTC
1 TTTCTTTTC
*
12378542 CTTCTTTTC
1 TTTCTTTTC
12378551 TCTTCTTTTC
1 T-TTCTTTTC
12378561 -TTCTTTT-
1 TTTCTTTTC
12378568 TTTCTTTTC
1 TTTCTTTTC
12378577 TTTCTTTT
1 TTTCTTTT
12378585 TGCACTCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 14 0.37
9 16 0.42
10 8 0.21
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:12379341 original size:19 final size:20
Alignment explanation
Indices: 12379299--12379350 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
12379289 GAAACCCCTT
*
12379299 TGAAAATACATGATTTTTTGA
1 TGAAAATACATGA-TTTTTAA
12379320 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
12379339 TGAAGATACATG
1 TGAAAATACATG
12379351 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:12395188 original size:11 final size:11
Alignment explanation
Indices: 12395158--12395193 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
12395148 TTTTTTTGCC
**
12395158 TTTTTTTGACT
1 TTTTTTTGTTT
12395169 TTTTTTTGTTT
1 TTTTTTTGTTT
12395180 TTTTTTTGTTT
1 TTTTTTTGTTT
12395191 TTT
1 TTT
12395194 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:12408374 original size:9 final size:9
Alignment explanation
Indices: 12408362--12408393 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
12408352 TTTTTTGAAA
12408362 TTTTGGCTT
1 TTTTGGCTT
12408371 TTTTGGCTTT
1 TTTTGGC-TT
12408381 TTTTGGCTT
1 TTTTGGCTT
12408390 TTTT
1 TTTT
12408394 TTTGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.00, C:0.09, G:0.19, T:0.72
Consensus pattern (9 bp):
TTTTGGCTT
Found at i:12408397 original size:12 final size:10
Alignment explanation
Indices: 12408362--12408394 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
12408352 TTTTTTGAAA
12408362 TTTTGGC-TT
1 TTTTGGCTTT
12408371 TTTTGGCTTT
1 TTTTGGCTTT
12408381 TTTTGGCTTT
1 TTTTGGCTTT
12408391 TTTT
1 TTTT
12408395 TTGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.00, C:0.09, G:0.18, T:0.73
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:12412816 original size:24 final size:21
Alignment explanation
Indices: 12412781--12412823 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
12412771 GGCTCATTCT
*
12412781 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
12412804 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
12412824 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:12414043 original size:15 final size:15
Alignment explanation
Indices: 12414017--12414052 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12414007 GCGCTTCAAC
12414017 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
12414031 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
*
12414046 TTTTTTG
1 TTCTTTG
12414053 AGTGCTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:12414094 original size:28 final size:27
Alignment explanation
Indices: 12414040--12414097 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
12414030 TTTCTTTGCT
* * *
12414040 TTTCTTTTTTTTGAGTGCTGGATTTTC
1 TTTCTTTTTTTGGAGTGCTGCAATTTC
*
12414067 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTCTTT-TTTTGGAGTGCTGCAATTTC
12414095 TTT
1 TTT
12414098 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.09, C:0.14, G:0.16, T:0.62
Consensus pattern (27 bp):
TTTCTTTTTTTGGAGTGCTGCAATTTC
Found at i:12427263 original size:13 final size:12
Alignment explanation
Indices: 12427238--12427297 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 12
12427228 CTTGGCTTGC
12427238 TTTCTCTTTTTCT
1 TTTCT-TTTTTCT
12427251 TTTCTTTTCTTCT
1 TTTCTTTT-TTCT
12427264 TTTCTGATTTTTCT
1 TTTCT--TTTTTCT
*
12427278 CTTCTTTTTGTCT
1 TTTCTTTTT-TCT
12427291 TTTCTTT
1 TTTCTTT
12427298 CTTTTTGCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.17
13 23 0.56
14 8 0.20
15 3 0.07
ACGTcount: A:0.02, C:0.20, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:12427301 original size:17 final size:18
Alignment explanation
Indices: 12427253--12427304 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
12427243 CTTTTTCTTT
12427253 TCTTTTC-TTCTTTTCTGA
1 TCTTTTCTTTCTTTT-TGA
12427271 T-TTTTCTCTTCTTTTTG-
1 TCTTTTCT-TTCTTTTTGA
12427288 TCTTTTCTTTCTTTTTG
1 TCTTTTCTTTCTTTTTG
12427305 CACTCCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 15 0.48
18 9 0.29
19 7 0.23
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.73
Consensus pattern (18 bp):
TCTTTTCTTTCTTTTTGA
Found at i:12427302 original size:27 final size:27
Alignment explanation
Indices: 12427244--12427295 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
12427234 TTGCTTTCTC
*
12427244 TTTTTCTTTTCTTTTCTTCTTTTCTGA
1 TTTTTCTCTTCTTTTCTTCTTTTCTGA
12427271 TTTTTCTCTTCTTTT-TGTCTTTTCT
1 TTTTTCTCTTCTTTTCT-TCTTTTCT
12427296 TTCTTTTTGC
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:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTTCTCTTCTTTTCTTCTTTTCTGA
Found at i:12437648 original size:14 final size:14
Alignment explanation
Indices: 12437629--12437670 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
12437619 GTCTTTTTCT
12437629 TTTCTTTTTTGTTG
1 TTTCTTTTTTGTTG
* *
12437643 TTTCTTCTTTCTTG
1 TTTCTTTTTTGTTG
*
12437657 TTGC-TTTTTGTTG
1 TTTCTTTTTTGTTG
12437670 T
1 T
12437671 AGCACTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.00, C:0.12, G:0.14, T:0.74
Consensus pattern (14 bp):
TTTCTTTTTTGTTG
Found at i:12437883 original size:16 final size:16
Alignment explanation
Indices: 12437862--12437895 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12437852 ATGAAAGAAG
12437862 AAAGGAAAT-GATAAGA
1 AAAGGAAATAGAT-AGA
12437878 AAAGGAAATAGATAGA
1 AAAGGAAATAGATAGA
12437894 AA
1 AA
12437896 TGTTATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (16 bp):
AAAGGAAATAGATAGA
Found at i:12449241 original size:157 final size:156
Alignment explanation
Indices: 12448974--12449288 Score: 573
Period size: 157 Copynumber: 2.0 Consensus size: 156
12448964 TGATCTTTTA
12448974 AACAGCACCAGGAGTATTATCTTCACCAAACGATATGTCTCTCCCATTCAAGGACATATGATGGT
1 AACAGCACCAGGAGTATTATCTTCACCAAACGATATGTCTCTCCCATTCAAGGACATATGATGGT
12449039 TCCCAACATTTTGTCCTCCCATAAAAGGACGTGAAGTTACCAGAATTGAAGCC-ATAGTTTCAAC
66 TCCCAACATTTTGTCCTCCCATAAAAGGACGTGAAGTTACCAGAATTGAAGCCAATAGTTTCAAC
12449103 A-TTT-TGTGAAGCATTTATTGGAGG
131 ATTTTGTGTGAAGCATTTATTGGAGG
12449127 AACAGCACCAAGGAGTTATTATCTTCACCAAACGATATGTCTCTCCCATTCAAAGGACATATGAT
1 AACAGCACC-AGGAG-TATTATCTTCACCAAACGATATGTCTCTCCCATTC-AAGGACATATGAT
12449192 GGTTCCCAAACATTTTGTCCTCCCATAAAAGGACGTGAAGTTACCAGAATTGAAGCCAATAGTTT
63 GGTTCCC-AACATTTTGTCCTCCCATAAAAGGACGTGAAGTTACCAGAATTGAAGCCAATAGTTT
12449257 CAACATTTTGTGTGAAGCATTTATTGGAGG
127 CAACATTTTGTGTGAAGCATTTATTGGAGG
12449287 AA
1 AA
12449289 AACATAAGGA
Statistics
Matches: 155, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
153 9 0.06
154 5 0.03
155 35 0.23
156 20 0.13
157 49 0.32
158 12 0.08
159 3 0.02
160 22 0.14
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (156 bp):
AACAGCACCAGGAGTATTATCTTCACCAAACGATATGTCTCTCCCATTCAAGGACATATGATGGT
TCCCAACATTTTGTCCTCCCATAAAAGGACGTGAAGTTACCAGAATTGAAGCCAATAGTTTCAAC
ATTTTGTGTGAAGCATTTATTGGAGG
Found at i:12455705 original size:24 final size:21
Alignment explanation
Indices: 12455670--12455712 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
12455660 GGCTCATTCT
*
12455670 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
12455693 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
12455713 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:12457624 original size:20 final size:22
Alignment explanation
Indices: 12457595--12457634 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
12457585 GGGAGAGCTT
12457595 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
12457615 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
12457635 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:12461333 original size:20 final size:22
Alignment explanation
Indices: 12461304--12461343 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
12461294 GGGAGAGCTT
12461304 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
12461324 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
12461344 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:12463114 original size:90 final size:91
Alignment explanation
Indices: 12462998--12463179 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
12462988 GGGAAATGAT
* *
12462998 GCTTGGCCGAATAGGGAGAGAGCTCTTCATATTGGCGCCTAGATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
12463062 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * * *
12463088 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACTTGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
* **
12463153 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
12463179 G
1 G
12463180 GTGTTCTAGG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 58 0.72
91 23 0.28
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:12466244 original size:22 final size:22
Alignment explanation
Indices: 12466216--12466258 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12466206 TTTCTTCCTT
*
12466216 TTTGAGTTCTTTCAATTTCTTC
1 TTTGAGTGCTTTCAATTTCTTC
* *
12466238 TTTGAGTGCTTTGATTTTCTT
1 TTTGAGTGCTTTCAATTTCTT
12466259 TGCTGGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (22 bp):
TTTGAGTGCTTTCAATTTCTTC
Found at i:12467139 original size:90 final size:91
Alignment explanation
Indices: 12467023--12467195 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 91
12467013 GGGAAATCAT
* *
12467023 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATCCAAGGCACATG
*
12467087 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* *
12467113 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATCCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATCCAAGGCACATG
*
12467178 GGGGCTGGTCATATGCAA
66 GGGGCTGGTCACATGCAA
12467196 GGCTCATGGG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 60 0.79
91 16 0.21
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATCCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:12470694 original size:90 final size:91
Alignment explanation
Indices: 12470540--12470721 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
12470530 CCTAGAACAC
* *
12470540 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTCGCATGAGGATCATTTAGGTGCCAAGATG
*
12470605 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * *
12470631 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTCGCATGTGGTTTATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTCGCATGAGGATCATTTAGGTGCCAAGATG
12470695 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
12470721 C
1 C
12470722 ATCATTTCCC
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 63 0.77
91 19 0.23
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTCGCATGAGGATCATTTAGGTGCCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:12477715 original size:28 final size:25
Alignment explanation
Indices: 12477684--12477739 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
12477674 GAAAATCAGA
*
12477684 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAA-TCAAGCACT-CAAAAG-AAG
*
12477712 AAAGAAATCCAGCACTCAAAAGAAG
1 AAAGAAATCAAGCACTCAAAAGAAG
12477737 AAA
1 AAA
12477740 AAGCAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 6 0.23
26 6 0.23
27 7 0.27
28 7 0.27
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.09
Consensus pattern (25 bp):
AAAGAAATCAAGCACTCAAAAGAAG
Found at i:12482900 original size:90 final size:91
Alignment explanation
Indices: 12482746--12482927 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
12482736 CCTAGAACAC
*
12482746 CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTACCTTGCATGAGGATCATTTAGGCGCCAAGATG
* *
12482811 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGACCAAG
** * * * * *
12482837 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTACCTTGCATGAGGATCATTTAGGCGCCAAGATG
12482901 AAGAGCTCTCTCCCTATTCGACCAAG
66 AAGAGCTCTCTCCCTATTCGACCAAG
12482927 C
1 C
12482928 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 62 0.77
91 19 0.23
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTACCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCGACCAAG
Found at i:12486657 original size:24 final size:21
Alignment explanation
Indices: 12486622--12486664 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
12486612 GGCTCATTCT
*
12486622 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
12486645 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
12486665 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:12496112 original size:19 final size:20
Alignment explanation
Indices: 12496055--12496104 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
12496045 ATAATGGGTT
*
12496055 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
12496074 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
12496094 TAAG-AATGAAA
1 TAAGTAATGAAA
12496105 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:12496567 original size:19 final size:21
Alignment explanation
Indices: 12496524--12496575 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
12496514 GAAACCCCTT
12496524 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
12496545 TGAAAATATATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
12496564 TGAAGATACATG
1 TGAAAATACATG
12496576 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:12499579 original size:26 final size:25
Alignment explanation
Indices: 12499528--12499587 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
12499518 CTTGGCTTGC
**
12499528 TTTCTTTTTGAATTTTTTCTTTTTT
1 TTTCTTTTTGAATTTTTTCTCCTTT
12499553 TTTCTTTTCTG-ATTTTTCTCTCCTTT
1 TTTCTTTT-TGAATTTTT-TCTCCTTT
*
12499579 TGTCTTTTT
1 TTTCTTTTT
12499588 CATTCTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 15 0.50
26 15 0.50
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (25 bp):
TTTCTTTTTGAATTTTTTCTCCTTT
Found at i:12499901 original size:19 final size:20
Alignment explanation
Indices: 12499844--12499893 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
12499834 ATAATGGGTT
*
12499844 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
12499863 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
12499883 TAAG-AATGAAA
1 TAAGTAATGAAA
12499894 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:12503813 original size:23 final size:25
Alignment explanation
Indices: 12503787--12503841 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
12503777 AAATCCATCA
12503787 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
12503810 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
12503835 AAGAAAA
1 AAGAAAA
12503842 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:12507886 original size:19 final size:20
Alignment explanation
Indices: 12507845--12507895 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
12507835 GAAACCCCTT
*
12507845 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
12507865 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
12507884 TGAAGATACATG
1 TGAAAATACATG
12507896 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:12511646 original size:17 final size:18
Alignment explanation
Indices: 12511623--12511664 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
12511613 TTTTTTTCAA
12511623 AAAAAAACAAAAAAAGG-C
1 AAAAAAAC-AAAAAAGGCC
12511641 AAAAAAACAAAAAAGGCC
1 AAAAAAACAAAAAAGGCC
12511659 AAAAAA
1 AAAAAA
12511665 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.79, C:0.12, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAGGCC
Found at i:12511646 original size:18 final size:17
Alignment explanation
Indices: 12511623--12511664 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
12511613 TTTTTTTCAA
12511623 AAAAAAACAAAAAAAGGC
1 AAAAAAAC-AAAAAAGGC
12511641 AAAAAAACAAAAAAGGC
1 AAAAAAACAAAAAAGGC
*
12511658 CAAAAAA
1 AAAAAAA
12511665 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.79, C:0.12, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAAGGC
Found at i:12519464 original size:11 final size:11
Alignment explanation
Indices: 12519442--12519521 Score: 65
Period size: 11 Copynumber: 6.7 Consensus size: 11
12519432 TTTGAGAATT
12519442 TGGTGATGATA
1 TGGTGATGATA
12519453 TAGGTG-TGATA
1 T-GGTGATGATA
12519464 TGGTGATGGACTA
1 TGGTGAT-GA-TA
12519477 TGGTGATGATA
1 TGGTGATGATA
12519488 TAGGTG-TGATAA
1 T-GGTGATGAT-A
*
12519500 TGGAAGATGGATTA
1 TGG-TGAT-GA-TA
12519514 TGGTGATG
1 TGGTGATG
12519522 GAAATAGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
10 4 0.07
11 17 0.30
12 16 0.28
13 13 0.23
14 6 0.11
15 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.38, T:0.34
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:12519470 original size:22 final size:22
Alignment explanation
Indices: 12519442--12519521 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 22
12519432 TTTGAGAATT
12519442 TGGTGATGATATAGGTG-TGATA
1 TGGTGATGATAT-GGTGATGATA
12519464 TGGTGATGGACTATGGTGATGATA
1 TGGTGAT-GA-TATGGTGATGATA
*
12519488 TAGGTG-TGATAATGGAAGATGGATTA
1 T-GGTGATGAT-ATGG-TGAT-GA-TA
12519514 TGGTGATG
1 TGGTGATG
12519522 GAAATAGTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
22 8 0.17
23 12 0.25
24 13 0.27
25 10 0.21
26 5 0.10
ACGTcount: A:0.28, C:0.01, G:0.38, T:0.34
Consensus pattern (22 bp):
TGGTGATGATATGGTGATGATA
Found at i:12519488 original size:35 final size:37
Alignment explanation
Indices: 12519442--12519521 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
12519432 TTTGAGAATT
*
12519442 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
*
12519477 TGGTGATGATATAGGTGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
12519514 TGGTGATG
1 TGGTGATG
12519522 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.01, G:0.38, T:0.34
Consensus pattern (37 bp):
TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
Found at i:12519523 original size:13 final size:13
Alignment explanation
Indices: 12519462--12519523 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
12519452 ATAGGTGTGA
*
12519462 TATGGTGATGGAC
1 TATGGTGATGGAT
12519475 TATGGTGAT-GA-
1 TATGGTGATGGAT
12519486 TATAGGTG-T-GAT
1 TAT-GGTGATGGAT
* *
12519498 AATGGAAGATGGAT
1 TATGG-TGATGGAT
12519512 TATGGTGATGGA
1 TATGGTGATGGA
12519524 AATAGTATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
11 8 0.20
12 9 0.22
13 16 0.40
14 7 0.17
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.32
Consensus pattern (13 bp):
TATGGTGATGGAT
Found at i:12523531 original size:17 final size:17
Alignment explanation
Indices: 12523509--12523551 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
12523499 GTAGCAGTCT
12523509 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
12523526 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
12523544 TTTT-TTTT
1 TTTTCTTTT
12523552 ATTGTAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:12523951 original size:11 final size:11
Alignment explanation
Indices: 12523929--12523975 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
12523919 TTTGAGAATT
12523929 TGGTGATGATA
1 TGGTGATGATA
12523940 TAGGTG-TGATA
1 T-GGTGATGATA
12523951 TGGTGATGGACTA
1 TGGTGAT-GA-TA
12523964 TGGTGATGATA
1 TGGTGATGATA
12523975 T
1 T
12523976 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:12523957 original size:22 final size:24
Alignment explanation
Indices: 12523929--12523975 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
12523919 TTTGAGAATT
12523929 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
12523951 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
12523975 T
1 T
12523976 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:12523975 original size:35 final size:37
Alignment explanation
Indices: 12523929--12524008 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
12523919 TTTGAGAATT
* **
12523929 TGGTGATGATATAGGTGTGAT-AT-GGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATAGAAGATGGACTA
*
12523964 TGGTGATGATATAGGCGTGATAATAGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATAGAAGATGGACTA
12524001 TGGTGATG
1 TGGTGATG
12524009 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 2 0.05
37 17 0.44
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATAGAAGATGGACTA
Found at i:12525519 original size:35 final size:36
Alignment explanation
Indices: 12525432--12525519 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
12525422 TACAATCTGT
*
12525432 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
* * *
12525468 TCATCACCATAGTCCATCATCA-TATCATGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
12525503 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
12525520 TTCCATTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 27 0.59
36 19 0.41
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:12525917 original size:17 final size:17
Alignment explanation
Indices: 12525895--12525927 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12525885 AAAAAGAGAA
12525895 AAAG-AAAGAAGAAAAAT
1 AAAGAAAAGAA-AAAAAT
12525912 AAAGAAAAGAAAAAAA
1 AAAGAAAAGAAAAAAA
12525928 CTCCTACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAGAAAAGAAAAAAAT
Found at i:12529324 original size:19 final size:20
Alignment explanation
Indices: 12529300--12529346 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
12529290 CAAGAGCATT
*
12529300 TATTTTCATT-AAAATTATG
1 TATTTTCATTAAAAATCATG
12529319 TATTTTCATTAAAAATCATG
1 TATTTTCATTAAAAATCATG
*
12529339 TGTTTTCA
1 TATTTTCA
12529347 AAGGGGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (20 bp):
TATTTTCATTAAAAATCATG
Found at i:12534262 original size:7 final size:6
Alignment explanation
Indices: 12534218--12534261 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
12534208 GTTGTAGGAG
* * *
12534218 TCTTTT TCTTTC TCTTTT TGTTTT TCTCATT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCT-TTT TCTTTT TCTTTT T
12534262 TTTGTTTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:12534603 original size:15 final size:16
Alignment explanation
Indices: 12534552--12534604 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
12534542 AGATAGTGAA
12534552 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
12534569 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
12534586 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
12534601 ATAA
1 ATAA
12534605 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:12534815 original size:13 final size:12
Alignment explanation
Indices: 12534797--12534832 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
12534787 GTAGGAGTCC
12534797 TTTTCTTTTTTGT
1 TTTTCTTTTTT-T
12534810 TTTTCTTCTTTTT
1 TTTTCTT-TTTTT
12534823 TTTTCTTTTT
1 TTTTCTTTTT
12534833 GTTGCTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 15 0.68
14 4 0.18
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:12538566 original size:4 final size:5
Alignment explanation
Indices: 12538538--12538563 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12538528 ACTCAAAAAG
12538538 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
12538564 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:12539743 original size:25 final size:25
Alignment explanation
Indices: 12539707--12539757 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
12539697 TCACTTCAAG
* *
12539707 TTGAAGATTCAAGAAACATGTCTTT
1 TTGAAGAATCAAGAAACATGACTTT
* *
12539732 TTGAAGAATCAATAAACGTGACTTT
1 TTGAAGAATCAAGAAACATGACTTT
12539757 T
1 T
12539758 GGTGATCCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (25 bp):
TTGAAGAATCAAGAAACATGACTTT
Found at i:12543263 original size:13 final size:11
Alignment explanation
Indices: 12543243--12543341 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
12543233 AATATAGGCG
12543243 TGATATGGTGA
1 TGATATGGTGA
12543254 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
12543267 TGATATAGGCG-
1 TGATAT-GGTGA
12543278 TGATAATGGTGA
1 TGAT-ATGGTGA
12543290 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
12543303 TGATATAGGCG-
1 TGATAT-GGTGA
12543314 TGATAATGGTGA
1 TGAT-ATGGTGA
*
12543326 TGGAAGATGGTGA
1 T-G-ATATGGTGA
12543339 TGA
1 TGA
12543342 ACAGATTGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
11 23 0.32
12 17 0.24
13 29 0.41
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:12543299 original size:36 final size:36
Alignment explanation
Indices: 12543226--12543341 Score: 198
Period size: 36 Copynumber: 3.2 Consensus size: 36
12543216 ATTTATAAGT
*
12543226 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
12543261 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
12543297 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
12543333 TGGTGATGA
1 TGGTGATGA
12543342 ACAGATTGTA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 20 0.26
36 56 0.74
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:12548415 original size:21 final size:20
Alignment explanation
Indices: 12548389--12548438 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
12548379 GTGCTACAAC
* *
12548389 AAAAAAGCAACAAGAAAGAAG
1 AAAAAAGAAACAA-AAAGAAA
*
12548410 AAAAAATAAACAAAAAGAAA
1 AAAAAAGAAACAAAAAGAAA
12548430 AGAAAAAGA
1 A-AAAAAGA
12548439 CTCCTACAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAAGAAACAAAAAGAAA
Found at i:12554164 original size:230 final size:230
Alignment explanation
Indices: 12553761--12554221 Score: 850
Period size: 230 Copynumber: 2.0 Consensus size: 230
12553751 ATCCATTATC
12553761 ACTTGAAGGATCATTCTACAACACTTCCGCAACCCTTCTTTCATAACTATTCTATCCATTTCAAT
1 ACTTGAAGGATCATTCTACAACACTTCCGCAACCCTTCTTTCATAACTATTCTATCCATTTCAAT
12553826 TCTTTCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTGCAGATTACT
66 TCTTTCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTGCAGATTACT
*
12553891 TTTCAATTCAAGGTGTAGCATTTGGTGTCTCTCCTAGATCGGGAAATAATAAGGTTGCCATCTTC
131 TTTCAATTCAAGGTGTAGCATTTGGTGTCTCTCCTAGATCGGGAAATAACAAGGTTGCCATCTTC
* *
12553956 TCTATTATTGAAGAAGCCTGGTTAGCCTTACATCA
196 TCCATTATTGAAGAAGCCTGGTCAGCCTTACATCA
* * *
12553991 ACTTGAAGGATCATTCTACAACACTTCTGCAGCCCTTCTTTGATAACTATTCTATCCATTTCAAT
1 ACTTGAAGGATCATTCTACAACACTTCCGCAACCCTTCTTTCATAACTATTCTATCCATTTCAAT
12554056 TCTTTCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTGCAGATTACT
66 TCTTTCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTGCAGATTACT
*
12554121 TTTCAATTCAAGGTGTAGCATTTGGTGTCTCTCCTAGATCGGGAAATAACAAGGTTGCCATCTTT
131 TTTCAATTCAAGGTGTAGCATTTGGTGTCTCTCCTAGATCGGGAAATAACAAGGTTGCCATCTTC
*
12554186 TCCATTATTGAAGAAGCCTGGTCAGCCTTATATCA
196 TCCATTATTGAAGAAGCCTGGTCAGCCTTACATCA
12554221 A
1 A
12554222 GCGGTAATAA
Statistics
Matches: 223, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
230 223 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (230 bp):
ACTTGAAGGATCATTCTACAACACTTCCGCAACCCTTCTTTCATAACTATTCTATCCATTTCAAT
TCTTTCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTGCAGATTACT
TTTCAATTCAAGGTGTAGCATTTGGTGTCTCTCCTAGATCGGGAAATAACAAGGTTGCCATCTTC
TCCATTATTGAAGAAGCCTGGTCAGCCTTACATCA
Found at i:12554312 original size:20 final size:20
Alignment explanation
Indices: 12554276--12554314 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12554266 TAAAAAAAGC
*
12554276 AACAAGAAAGAAGGAAAAAA
1 AACAAGAAAGAAAGAAAAAA
12554296 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAG-AAAGAAAAA
12554315 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (20 bp):
AACAAGAAAGAAAGAAAAAA
Found at i:12554557 original size:12 final size:12
Alignment explanation
Indices: 12554540--12554583 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
12554530 ATTTCATTTC
12554540 CTTTTCTTTCAT
1 CTTTTCTTTCAT
12554552 CTTTTCTTTCAT
1 CTTTTCTTTCAT
12554564 CTTTTCTTT-AT
1 CTTTTCTTTCAT
12554575 CCTTTTCTT
1 -CTTTTCTT
12554584 AACCTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 2 0.06
12 29 0.94
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (12 bp):
CTTTTCTTTCAT
Found at i:12561055 original size:11 final size:11
Alignment explanation
Indices: 12560986--12561057 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 11
12560976 ACAATCTGTC
12560986 CATCACCATTAT
1 CATCACCA-TAT
*
12560998 CA-CGCCTATAT
1 CATCACC-ATAT
12561009 CATCACCATAGT
1 CATCACCATA-T
12561021 CCATCACCAT-T
1 -CATCACCATAT
12561032 -ATCACGTCTATAT
1 CATCAC--C-ATAT
12561045 CATCACCATAT
1 CATCACCATAT
12561056 CA
1 CA
12561058 CGCCTATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
9 5 0.10
11 19 0.39
12 10 0.20
13 10 0.20
14 5 0.10
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:12561056 original size:22 final size:23
Alignment explanation
Indices: 12561022--12561074 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
12561012 CACCATAGTC
*
12561022 CATCACCATTATCACGTCTATAT
1 CATCACCATTATCACGCCTATAT
12561045 CATCACCA-TATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
*
12561067 TATCACCA
1 CATCACCA
12561075 ACTTATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCACGCCTATAT
Found at i:12561072 original size:36 final size:36
Alignment explanation
Indices: 12560983--12561054 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
12560973 GATACAATCT
12560983 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
12561019 GTCCATCACCATTATCACGTCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
12561055 TCACGCCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.35, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:12561708 original size:30 final size:31
Alignment explanation
Indices: 12561669--12561728 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
12561659 CTTAGCTTTA
**
12561669 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
12561699 TATTTTGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
12561729 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:12562592 original size:19 final size:20
Alignment explanation
Indices: 12562568--12562618 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
12562558 CGGCCAAGAG
* *
12562568 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
12562587 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
12562607 CATGTATTTTCA
1 CATGTATTTTCA
12562619 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:12563415 original size:13 final size:12
Alignment explanation
Indices: 12563396--12563460 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
12563386 ATATAGGCGT
12563396 GATATGGTGATG
1 GATATGGTGATG
12563408 GAATATGGTGAT-
1 G-ATATGGTGATG
*
12563420 GATATAGGCG-T-
1 GATAT-GGTGATG
12563431 GATAATGGTGATG
1 GAT-ATGGTGATG
12563444 GACTATGGTGAT-
1 GA-TATGGTGATG
12563456 GATAT
1 GATAT
12563461 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:12563451 original size:36 final size:36
Alignment explanation
Indices: 12563378--12563479 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
12563368 ATTTAGAAGT
*
12563378 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
12563413 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
12563449 TGGTGATGATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
12563480 AACAGATTGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:12565850 original size:6 final size:6
Alignment explanation
Indices: 12565839--12565877 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
12565829 GATGTAGGAG
*
12565839 TCTTTT TCTTTT TCCTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
12565878 TGTTGCAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:12569095 original size:13 final size:13
Alignment explanation
Indices: 12569073--12569102 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12569063 ACTAAACACC
12569073 TTTC-ACATACCT
1 TTTCAACATACCT
12569085 TTTCAACATACCT
1 TTTCAACATACCT
12569098 TTTCA
1 TTTCA
12569103 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:12571920 original size:28 final size:25
Alignment explanation
Indices: 12571865--12571920 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
12571855 TTCTTTGCTT
**
12571865 TTTCTTCTTTTGAGTGCTGGATTTC
1 TTTCTTCTTTTGAGTGCTCAATTTC
12571890 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGC-TCAATTTC
12571918 TTT
1 TTT
12571921 TTTGATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 7 0.27
27 6 0.23
28 9 0.35
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (25 bp):
TTTCTTCTTTTGAGTGCTCAATTTC
Found at i:12572855 original size:90 final size:93
Alignment explanation
Indices: 12572715--12572883 Score: 236
Period size: 90 Copynumber: 1.8 Consensus size: 93
12572705 TGGCCGAATA
* *
12572715 AAGAGAAAGCTCTTCATCTTGGCGCCTAAATAAACCACATACAAGGCACAT-GGGGCTGTTCACA
1 AAGAGAAAGCTCTTCATCTTGGCACCTAAATAAACCACATACAAGGCACATGGGGGCTGGTCACA
12572779 TGCAAAACACATGGCTTGACTGAATAAG
66 TGCAAAACACATGGCTTGACTGAATAAG
* * * * *
12572807 AAGAG-AA-CTCTTCATCTTGGCACCTAAATGATCCTCATGCAAGGCACATGGGGGCTGGTCATA
1 AAGAGAAAGCTCTTCATCTTGGCACCTAAATAAACCACATACAAGGCACATGGGGGCTGGTCACA
**
12572870 TGCAAGGCACATGG
66 TGCAAAACACATGG
12572884 GTGTTCTAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
90 37 0.55
91 25 0.37
92 5 0.07
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (93 bp):
AAGAGAAAGCTCTTCATCTTGGCACCTAAATAAACCACATACAAGGCACATGGGGGCTGGTCACA
TGCAAAACACATGGCTTGACTGAATAAG
Found at i:12574676 original size:90 final size:91
Alignment explanation
Indices: 12574560--12574732 Score: 267
Period size: 90 Copynumber: 1.9 Consensus size: 91
12574550 GGGAAATGAT
*
12574560 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
*
12574624 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
** * * *
12574650 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
*
12574715 GGGGCTGGTCATATGCAA
66 GGGGCTGGTCACATGCAA
12574733 GGCATATGGG
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 58 0.78
91 16 0.22
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:12578165 original size:28 final size:25
Alignment explanation
Indices: 12578110--12578165 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
12578100 TTCTTTGCTT
**
12578110 TTTCTTCTTTTGAGTGTTGGATTTC
1 TTTCTTCTTTTGAGTGTTCAATTTC
12578135 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTG-TTCAATTTC
12578163 TTT
1 TTT
12578166 TCAGATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 7 0.27
27 5 0.19
28 10 0.38
ACGTcount: A:0.09, C:0.14, G:0.16, T:0.61
Consensus pattern (25 bp):
TTTCTTCTTTTGAGTGTTCAATTTC
Found at i:12579103 original size:90 final size:91
Alignment explanation
Indices: 12578950--12579131 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 91
12578940 GGGAAATGAT
*
12578950 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGGGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGGGCCTAAATAAACCACATGCAAGGCACATG
*
12579014 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* ** * * *
12579040 GCTTGGCTGAATAGGGAGAGAACTCTTCATCTTGGTTCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGGGCCTAAATAAACCACATGCAAGGCACATG
* **
12579105 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
12579131 G
1 G
12579132 GTGTTCTAGG
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 57 0.71
91 23 0.29
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGGGCCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:12590421 original size:13 final size:12
Alignment explanation
Indices: 12590403--12590432 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
12590393 TGGCCAAAGA
12590403 TGAAAAGGTATG
1 TGAAAAGGTATG
12590415 TTGAAAAGGTATG
1 -TGAAAAGGTATG
12590428 TGAAA
1 TGAAA
12590433 GGGTTTAGTA
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 (12 bp):
TGAAAAGGTATG
Found at i:12596504 original size:10 final size:12
Alignment explanation
Indices: 12596471--12596509 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
12596461 GGTCTTCTCA
12596471 ACTC-CTCAGCT
1 ACTCTCTCAGCT
12596482 ACTCTCTCAGCT
1 ACTCTCTCAGCT
12596494 ACT-TC-CAGCT
1 ACTCTCTCAGCT
12596504 AC-CTCT
1 ACTCTCT
12596510 AGTCCACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.18, C:0.44, G:0.08, T:0.31
Consensus pattern (12 bp):
ACTCTCTCAGCT
Found at i:12598062 original size:24 final size:21
Alignment explanation
Indices: 12598027--12598069 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
12598017 GGCACATTCT
*
12598027 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
12598050 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
12598070 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:12599354 original size:24 final size:23
Alignment explanation
Indices: 12599326--12599385 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
12599316 ACTTTTCTTT
12599326 CTTTCTTTTTCTTCTTTTTGAGTG
1 CTTTCTTTTTCTTC-TTTTGAGTG
** *
12599350 CTTTCAATTTCTTCTTTTGAGTT
1 CTTTCTTTTTCTTCTTTTGAGTG
12599373 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
12599386 TACTGATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.08, C:0.17, G:0.08, T:0.67
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:12599371 original size:23 final size:24
Alignment explanation
Indices: 12599333--12599385 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
12599323 TTTCTTTCTT
12599333 TTTCTTCTTTTTGAGTGCTTTCAA
1 TTTCTTCTTTTTGAGTGCTTTCAA
* * *
12599357 TTTCTTC-TTTTGAGTTCTTTTAT
1 TTTCTTCTTTTTGAGTGCTTTCAA
12599380 TTTCTT
1 TTTCTT
12599386 TACTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.09, C:0.15, G:0.09, T:0.66
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGCTTTCAA
Found at i:12603433 original size:24 final size:23
Alignment explanation
Indices: 12603405--12603464 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
12603395 AATTTTCTTT
12603405 CTTTCTTTTTCTTCTTTTCGAGTG
1 CTTTCTTTTTCTTCTTTT-GAGTG
**
12603429 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTCTTTTGAGTG
12603452 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
12603465 TACTGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.08, C:0.18, G:0.10, T:0.63
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:12603454 original size:23 final size:24
Alignment explanation
Indices: 12603412--12603464 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
12603402 TTTCTTTCTT
12603412 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
12603436 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
12603459 TTTCTT
1 TTTCTT
12603465 TACTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:12606890 original size:15 final size:15
Alignment explanation
Indices: 12606838--12606878 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
12606828 GTTGTAGGAG
12606838 TCTTTTTTT-TTCTAT
1 TCTTTTTTTCTTCT-T
*
12606853 T-TTGTTTTCTTCTT
1 TCTTTTTTTCTTCTT
12606867 TCTTTTTTTCTT
1 TCTTTTTTTCTT
12606879 TTTGTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (15 bp):
TCTTTTTTTCTTCTT
Found at i:12607274 original size:33 final size:33
Alignment explanation
Indices: 12607232--12607300 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
12607222 GTTGATGAAT
*
12607232 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
12607265 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
12607298 GAA
1 GAA
12607301 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:12607305 original size:13 final size:12
Alignment explanation
Indices: 12607286--12607382 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
12607276 TTATTGGCGT
12607286 GATATGGTGATG
1 GATATGGTGATG
12607298 GAATATGGTGAT-
1 G-ATATGGTGATG
*
12607310 GATATAGGCG-T-
1 GATAT-GGTGATG
12607321 GATAATGGTGATG
1 GAT-ATGGTGATG
12607334 GACTATGGTGAT-
1 GA-TATGGTGATG
*
12607346 GATATAGGCG-T-
1 GATAT-GGTGATG
*
12607357 GATAATGGAGATG
1 GAT-ATGGTGATG
12607370 GATTATGGTGATG
1 GA-TATGGTGATG
12607383 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:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:12607341 original size:36 final size:36
Alignment explanation
Indices: 12607271--12607383 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
12607261 AATGGAAGGA
* *
12607271 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
12607306 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
12607342 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
12607378 TGATGA
1 TGATGA
12607384 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:12610834 original size:20 final size:18
Alignment explanation
Indices: 12610778--12610834 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 18
12610768 CTTGGCTTGC
12610778 TTTC-TCTTTTTCTTTTCT
1 TTTCTTCTTTTTCTTTT-T
12610796 TTTCTTC-TTTTCTGATTTT
1 TTTCTTCTTTTTCT--TTTT
12610815 TTCTCTTCTTTTGTCTTTTT
1 TT-TCTTCTTTT-TCTTTTT
12610835 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
18 10 0.30
19 5 0.15
20 12 0.36
21 3 0.09
22 3 0.09
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTCTTCTTTTTCTTTTT
Found at i:12610894 original size:10 final size:11
Alignment explanation
Indices: 12610870--12610894 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12610860 TGTAGGAGTC
12610870 TTTTCTTCTGT
1 TTTTCTTCTGT
12610881 TTTTCTTCTGT
1 TTTTCTTCTGT
12610892 TTT
1 TTT
12610895 GCACGCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTCTTCTGT
Found at i:12614846 original size:5 final size:5
Alignment explanation
Indices: 12614838--12614887 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
12614828 TGCTTTCTCT
*
12614838 TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TGATT- TTTTC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC T-TTTC TTTTC TTTTC
12614884 TTTT
1 TTTT
12614888 GTCTTTTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 2 0.05
5 31 0.79
6 6 0.15
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:12614856 original size:8 final size:8
Alignment explanation
Indices: 12614845--12614885 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
12614835 TCTTTTTCTT
12614845 TTCTTTTC
1 TTCTTTTC
12614853 TTCTTTTC
1 TTCTTTTC
12614861 TTCTTTTC
1 TTCTTTTC
**
12614869 TGATTTT-
1 TTCTTTTC
12614876 TTCTTTTC
1 TTCTTTTC
12614884 TT
1 TT
12614886 TTGTCTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 5 0.18
8 23 0.82
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:12614859 original size:18 final size:18
Alignment explanation
Indices: 12614838--12614904 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 18
12614828 TGCTTTCTCT
12614838 TTTTCTTTTCTTTTCTTC
1 TTTTCTTTTCTTTTCTTC
*
12614856 TTTTC--TTCTTTTCTGATT
1 TTTTCTTTTCTTTTCT--TC
*
12614874 TTTTCTTTTCTTTT-GTC
1 TTTTCTTTTCTTTTCTTC
12614891 TTTT-TCTTTCTTTT
1 TTTTCT-TTTCTTTT
12614905 TGCACTCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
16 10 0.24
17 13 0.32
18 11 0.27
20 7 0.17
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTTC
Found at i:12614906 original size:18 final size:19
Alignment explanation
Indices: 12614835--12614904 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 19
12614825 GCTTGCTTTC
12614835 TCTTTTTCTTTTCTTTTCT-
1 TCTTTTTC-TTTCTTTTCTG
12614854 TC-TTTTC-TTCTTTTCTG
1 TCTTTTTCTTTCTTTTCTG
12614871 AT-TTTTTCTTT-TCTTT-TG
1 -TCTTTTTCTTTCT-TTTCTG
12614889 TCTTTTTCTTTCTTTT
1 TCTTTTTCTTTCTTTT
12614905 TGCACTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
16 9 0.20
17 1 0.02
18 26 0.59
19 8 0.18
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (19 bp):
TCTTTTTCTTTCTTTTCTG
Found at i:12617619 original size:36 final size:36
Alignment explanation
Indices: 12617550--12617737 Score: 306
Period size: 36 Copynumber: 5.2 Consensus size: 36
12617540 ATACTATTTC
* *
12617550 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAGTCCATC-ACCATTATCACGCCTATAT
*
12617587 CATCACCATAGTCCATCACCATTATCATGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
12617623 CATCATCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
12617659 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
12617695 CATCACCATATTCCATCACCA-TATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
12617730 TATCACCA
1 CATCACCA
12617738 ACTTATAAAT
Statistics
Matches: 143, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
35 21 0.15
36 106 0.74
37 16 0.11
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.30
Consensus pattern (36 bp):
CATCACCATAGTCCATCACCATTATCACGCCTATAT
Done.