Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008660.1 Hibiscus syriacus cultivar Beakdansim tig00111657_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: 1057077
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 5
Found at i:547998 original size:20 final size:22
Alignment explanation
Indices: 547973--548013 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
547963 TGTTGTTTAT
547973 AGCCG-TTGGGGATG-TTTTTG
1 AGCCGTTTGGGGATGCTTTTTG
547993 AGCCGTTTGGGGATGCTTTTT
1 AGCCGTTTGGGGATGCTTTTT
548014 ATACTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.10, C:0.12, G:0.37, T:0.41
Consensus pattern (22 bp):
AGCCGTTTGGGGATGCTTTTTG
Found at i:548064 original size:21 final size:21
Alignment explanation
Indices: 548040--548082 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
548030 CCCAGAATAG
*
548040 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
548061 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
548082 A
1 A
548083 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:548144 original size:21 final size:21
Alignment explanation
Indices: 548118--548160 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
548108 CTGTTGAACA
548118 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
548139 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
548160 G
1 G
548161 ACATTATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:548219 original size:21 final size:21
Alignment explanation
Indices: 548194--548273 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
548184 AAAACCTGCA
548194 GGGGGTATCTGTACCCCCTGGG
1 GGGGGTATCTGTACCCCCT-GG
548216 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
548232 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
548252 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
548273 G
1 G
548274 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
20 3 0.06
21 19 0.38
22 13 0.26
ACGTcount: A:0.12, C:0.28, G:0.38, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:548237 original size:15 final size:15
Alignment explanation
Indices: 548217--548246 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
548207 CCCCCTGGGG
548217 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
548232 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
548247 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:548267 original size:36 final size:37
Alignment explanation
Indices: 548195--548267 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
548185 AAACCTGCAG
* *
548195 GGGGTATCTGTACCCCCTGGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
548232 GGGGTATCTGTACCCCCT-GGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
548268 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 16 0.47
37 18 0.53
ACGTcount: A:0.14, C:0.27, G:0.36, T:0.23
Consensus pattern (37 bp):
GGGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
Found at i:548395 original size:29 final size:31
Alignment explanation
Indices: 548363--548422 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
548353 AAACTTTGAA
548363 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
548392 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
548423 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:551150 original size:30 final size:34
Alignment explanation
Indices: 551114--551181 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
551104 CCTTACAAAC
*
551114 TCCCTAG-TTTTTC-CGGGCT-A-CTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
551144 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
551178 TCCC
1 TCCC
551182 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 7 0.21
31 5 0.15
32 6 0.18
33 1 0.03
34 14 0.42
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
Found at i:551422 original size:20 final size:22
Alignment explanation
Indices: 551397--551436 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
551387 TGTTGTTTAT
551397 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
551417 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
551437 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:551488 original size:21 final size:21
Alignment explanation
Indices: 551464--551506 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
551454 CCCAGAATAG
* *
551464 AGGGAATTGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
551485 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
551506 A
1 A
551507 ATATCCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:551623 original size:21 final size:21
Alignment explanation
Indices: 551597--551676 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
551587 AAATCCTGCA
*
551597 GGGGGGTATTTGTACCCCCTG
1 GGGGGGTATCTGTACCCCCTG
551618 GGGGGGTATCTGTA--CCC--
1 GGGGGGTATCTGTACCCCCTG
551635 --GGGGTATCTGTACCCCCTG
1 GGGGGGTATCTGTACCCCCTG
* *
551654 GGGGGGAATCTATACCCCCTG
1 GGGGGGTATCTGTACCCCCTG
551675 GG
1 GG
551677 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.12, C:0.26, G:0.38, T:0.24
Consensus pattern (21 bp):
GGGGGGTATCTGTACCCCCTG
Found at i:551640 original size:15 final size:15
Alignment explanation
Indices: 551620--551649 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
551610 ACCCCCTGGG
551620 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
551635 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
551650 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:551647 original size:36 final size:36
Alignment explanation
Indices: 551599--551670 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
551589 ATCCTGCAGG
* * *
551599 GGGGTATTTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
551635 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
551671 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.26, G:0.35, T:0.25
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:551798 original size:29 final size:31
Alignment explanation
Indices: 551766--551825 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
551756 AAACTTTGAA
551766 TAAATTCAATT-AAGTCCAAAAAT-ATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
551795 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
551826 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAATCATTTTG
Found at i:554371 original size:19 final size:20
Alignment explanation
Indices: 554324--554374 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
554314 GAAACCCCTT
**
554324 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
554344 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
554363 TGAAGATACATG
1 TGAAAATACATG
554375 CGCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:556655 original size:19 final size:18
Alignment explanation
Indices: 556631--556666 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
556621 CGGCCAAGAG
556631 CATGTATCTTCATTAAAAT
1 CATGTATCTTCA-TAAAAT
*
556650 CATGTATTTTCATAAAA
1 CATGTATCTTCATAAAA
556667 AAAATCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (18 bp):
CATGTATCTTCATAAAAT
Found at i:556667 original size:19 final size:20
Alignment explanation
Indices: 556631--556683 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
556621 CGGCCAAGAG
* *
556631 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
556650 CATGTATTTTCATAAAAAAAAT
1 CATGTATTTTCAT--AAAAAAT
556672 CATGTATTTTCA
1 CATGTATTTTCA
556684 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
22 17 0.59
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:559360 original size:19 final size:20
Alignment explanation
Indices: 559322--559364 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
559312 GAAACCCCTT
*
559322 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
559342 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
559361 TGAA
1 TGAA
559365 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:561171 original size:14 final size:13
Alignment explanation
Indices: 561136--561166 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
561126 TAGGAGTCTT
561136 TTCTTTGTTTTTC
1 TTCTTTGTTTTTC
561149 TTCTTTGTTTTTC
1 TTCTTTGTTTTTC
561162 -TCTTT
1 TTCTTT
561167 TTGTTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.77
Consensus pattern (13 bp):
TTCTTTGTTTTTC
Found at i:561510 original size:35 final size:35
Alignment explanation
Indices: 561465--561580 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
561455 TGGTAAGGGA
* *
561465 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
* *
561500 ATGGTGATGATATAGGCATGCAATGGTGATGGAAA
1 ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
* *
561535 ATAGTGATGTTATAGGCATGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCATG-AAATGGTGATGGAAG
561571 ATGGTGATGA
1 ATGGTGATGA
561581 ACAGATAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
35 49 0.70
36 21 0.30
ACGTcount: A:0.34, C:0.03, G:0.35, T:0.27
Consensus pattern (35 bp):
ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
Found at i:562947 original size:13 final size:13
Alignment explanation
Indices: 562929--562958 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
562919 GTCATAACCC
562929 GACCCGACCCGTT
1 GACCCGACCCGTT
562942 GACCCGACCCGTT
1 GACCCGACCCGTT
562955 GACC
1 GACC
562959 GTTGACCAAC
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:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:563893 original size:36 final size:35
Alignment explanation
Indices: 563800--563910 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
563790 TTGGTGGTTA
* ** *
563800 TATAGGTGTGAAATGGTGATAAAAGATGGTAATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
563835 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
563870 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
563906 T-TAGG
1 TATAGG
563911 TAGTATCTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 43 0.64
36 24 0.36
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.30
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:570429 original size:21 final size:20
Alignment explanation
Indices: 570369--570440 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
570359 TGGCCAAGAG
*
570369 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
570388 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
570408 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTT-AAAAT
570429 CATGTATTTTCA
1 CATGTATTTTCA
570441 AAAAGATTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 11 0.22
20 22 0.44
21 17 0.34
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:572740 original size:30 final size:31
Alignment explanation
Indices: 572688--572747 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
572678 CTTAGCTTTA
**
572688 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
572718 TATTATGTTTTCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
572748 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:0.08, T:0.57
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:575352 original size:16 final size:16
Alignment explanation
Indices: 575331--575362 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
575321 TAGTTAGCTC
575331 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
575347 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
575363 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:576801 original size:9 final size:8
Alignment explanation
Indices: 576786--576847 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 8
576776 ATTGGAGTGC
576786 AAAAAGAA
1 AAAAAGAA
576794 AGAAAAGACA
1 A-AAAAGA-A
*
576804 AAAGAGAA
1 AAAAAGAA
*
576812 AAATCAGAA
1 AAA-AAGAA
576821 AAAAAGAA
1 AAAAAGAA
*
576829 AAGAAA-AG
1 AA-AAAGAA
576837 AAAAAGAA
1 AAAAAGAA
576845 AAA
1 AAA
576848 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
7 3 0.07
8 18 0.41
9 21 0.48
10 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:576825 original size:35 final size:33
Alignment explanation
Indices: 576786--576860 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 33
576776 ATTGGAGTGC
576786 AAAAAG-AAAGAAAAGACAAAAGAGAAAAATCAGAA
1 AAAAAGAAAAGAAAAGA-AAAAGA-AAAAATCA-AA
*
576821 AAAAAGAAAAGAAAAGAAAAAGAAAAATTCAAA
1 AAAAAGAAAAGAAAAGAAAAAGAAAAAATCAAA
576854 AAGAAAG
1 AA-AAAG
576861 CAAGCCAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 4 0.11
34 11 0.30
35 12 0.32
36 10 0.27
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (33 bp):
AAAAAGAAAAGAAAAGAAAAAGAAAAAATCAAA
Found at i:576838 original size:18 final size:18
Alignment explanation
Indices: 576786--576841 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
576776 ATTGGAGTGC
576786 AAAAAG-AAAGAAAAGACA
1 AAAAAGAAAAGAAAAGA-A
* **
576804 AAAGAGAAAA-ATCAGAA
1 AAAAAGAAAAGAAAAGAA
576821 AAAAAGAAAAGAAAAGAA
1 AAAAAGAAAAGAAAAGAA
576839 AAA
1 AAA
576842 GAAAAATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 10 0.33
18 17 0.57
19 3 0.10
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAGAA
Found at i:576846 original size:16 final size:16
Alignment explanation
Indices: 576786--576846 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 16
576776 ATTGGAGTGC
576786 AAAAAG-AAAGAAAAG
1 AAAAAGAAAAGAAAAG
*
576801 ACAAAAGAGAAA-AATCAGAA
1 A-AAAAGA-AAAGAA--A-AG
576821 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
576837 AAAAAGAAAA
1 AAAAAGAAAA
576847 ATTCAAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 1 0.03
16 16 0.43
17 3 0.08
18 6 0.16
19 9 0.24
20 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:576846 original size:24 final size:25
Alignment explanation
Indices: 576786--576847 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 25
576776 ATTGGAGTGC
576786 AAAAAGAAAGAAAAGACAAAAGAGAAA
1 AAAAAGAAA-AAAAGA-AAAAGAGAAA
**
576813 AATCAGAAAAAAAG-AAAAGA-AAA
1 AAAAAGAAAAAAAGAAAAAGAGAAA
576836 GAAAAAGAAAAA
1 -AAAAAGAAAAA
576848 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 3 0.10
24 15 0.50
26 5 0.17
27 7 0.23
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAAGAAAAAAAGAAAAAGAGAAA
Found at i:581381 original size:8 final size:8
Alignment explanation
Indices: 581352--581395 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
581342 TTGGAGTGTA
581352 AAAAGAAAG
1 AAAAG-AAG
*
581361 AAAAG-AT
1 AAAAGAAG
581368 AAAAGAAG
1 AAAAGAAG
581376 AAAAGAAG
1 AAAAGAAG
581384 AAAAGAAG
1 AAAAGAAG
581392 AAAA
1 AAAA
581396 AAATAGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 6 0.19
8 21 0.66
9 5 0.16
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:584307 original size:23 final size:23
Alignment explanation
Indices: 584262--584307 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
584252 TTATACCTAT
*
584262 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
584285 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
584308 TATTATACTT
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:586452 original size:216 final size:213
Alignment explanation
Indices: 586037--586468 Score: 803
Period size: 216 Copynumber: 2.0 Consensus size: 213
586027 TTGATCCTAA
586037 ATTCCTAGATTGTTATCTAGTGGGTTGAAGACACTATCACCACCCCAAGCAAGTTTGTGAAGACC
1 ATTCCTAGATTGTTATCTAGTGGGTTGAAGACACTATCACCACCCCAAGCAAGTTTGTGAAGACC
586102 GGGATTGTGCTCTTAGCACTATTTCATCTTTGGCGTGTTTGAGATCAACATCACCACCATTGCCA
66 GGGATTGTGCTCTTAGCACTATTTCATCTTTGGCGTGTTTGAGATCAACATCACCACCATTGCCA
*
586167 TTTCATCATCAACATCATCCATCGCTTCCATCAATTCCGCAGCCCATCTCTATCTTTTTTTATTT
131 TTTCATCATCAACATCATCCATCGCTTCCATCAATTCCGCAGCCCATCTCTATCTTTTATTATTT
586232 AATTCATTCTTATTATTT
196 AATTCATTCTTATTATTT
586250 ATTCCTAGATTGTTATCTAGTGGGTTGAAGACACTATCACCACCCCTCAAGCAAGTTTGTGAAGA
1 ATTCCTAGATTGTTATCTAGTGGGTTGAAGACACTATCACCA-CCC-CAAGCAAGTTTGTGAAGA
586315 CCGGGATTGTGCTCCTTAGCACTATTTCATCTTTGGCGTGTTTGAGATACAACATCACCACCATT
64 CCGGGATTGTGCT-CTTAGCACTATTTCATCTTTGGCGTGTTTGAGAT-CAACATCACCACCATT
*
586380 GCCATTTCATCATCAACATCATCCATCGCTTCCATCAATTCCGCCG-CCATCTCTATCTTTTATT
127 GCCATTTCATCATCAACATCATCCATCGCTTCCATCAATTCCGCAGCCCATCTCTATCTTTTATT
586444 ATTTAATTCATTCTTATTATTT
192 ATTTAATTCATTCTTATTATTT
586466 ATT
1 ATT
586469 TCATTACTTA
Statistics
Matches: 213, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
213 42 0.20
214 3 0.01
215 31 0.15
216 76 0.36
217 61 0.29
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (213 bp):
ATTCCTAGATTGTTATCTAGTGGGTTGAAGACACTATCACCACCCCAAGCAAGTTTGTGAAGACC
GGGATTGTGCTCTTAGCACTATTTCATCTTTGGCGTGTTTGAGATCAACATCACCACCATTGCCA
TTTCATCATCAACATCATCCATCGCTTCCATCAATTCCGCAGCCCATCTCTATCTTTTATTATTT
AATTCATTCTTATTATTT
Found at i:586462 original size:18 final size:19
Alignment explanation
Indices: 586439--586479 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
586429 TCTCTATCTT
586439 TTATTATTTAATTCATT-C
1 TTATTATTTAATTCATTAC
*
586457 TTATTATTTATTTCATTAC
1 TTATTATTTAATTCATTAC
586476 TTAT
1 TTAT
586480 ATTATCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTATTTAATTCATTAC
Found at i:587685 original size:19 final size:16
Alignment explanation
Indices: 587661--587705 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 16
587651 GGAGTGCAAA
587661 AAGAAAGAAAAGTCAAAAG
1 AAGAAA-AAAAG--AAAAG
*
587680 AAGAAAAGAAGAAAAG
1 AAGAAAAAAAGAAAAG
587696 AAGAAAAAAA
1 AAGAAAAAAA
587706 AAGATTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 14 0.58
18 4 0.17
19 6 0.25
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (16 bp):
AAGAAAAAAAGAAAAG
Found at i:587688 original size:8 final size:8
Alignment explanation
Indices: 587675--587702 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
587665 AAGAAAAGTC
587675 AAAAGAAG
1 AAAAGAAG
587683 AAAAGAAG
1 AAAAGAAG
587691 AAAAGAAG
1 AAAAGAAG
587699 AAAA
1 AAAA
587703 AAAAAGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:590690 original size:21 final size:23
Alignment explanation
Indices: 590666--590709 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
590656 TTATACCTAT
*
590666 AGATA-TTA-TTTCATATGTATA
1 AGATAGTTATTTTCATATATATA
590687 AGATAGTTATTTTCATATATATA
1 AGATAGTTATTTTCATATATATA
590710 TTATACCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATAGTTATTTTCATATATATA
Found at i:592621 original size:19 final size:20
Alignment explanation
Indices: 592582--592633 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
592572 GAAACCCCTT
592582 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
592603 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
592622 TGAAGATACATG
1 TGAAAATACATG
592634 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:594234 original size:27 final size:27
Alignment explanation
Indices: 594201--594254 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
594191 CATTCGAAAC
594201 ATCAAAGAAAAAATCTGTAATTACATG
1 ATCAAAGAAAAAATCTGTAATTACATG
594228 ATCAAAGAAAAAATCTGTAATTACATG
1 ATCAAAGAAAAAATCTGTAATTACATG
594255 TTTAGAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (27 bp):
ATCAAAGAAAAAATCTGTAATTACATG
Found at i:595934 original size:18 final size:19
Alignment explanation
Indices: 595913--595957 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
595903 CTTAGCTTGC
595913 TTTCTTTT-TGAATTTTT-T
1 TTTCTTTTCTG-ATTTTTCT
595931 TTTCTTTTCTGATTTTTCT
1 TTTCTTTTCTGATTTTTCT
*
595950 CTTCTTTT
1 TTTCTTTT
595958 GCCTTTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTCTTTTCTGATTTTTCT
Found at i:596734 original size:19 final size:20
Alignment explanation
Indices: 596693--596743 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
596683 TAAACCCCTT
*
596693 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
596713 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
596732 TGAAGATACATG
1 TGAAAATACATG
596744 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:600872 original size:36 final size:36
Alignment explanation
Indices: 600825--600956 Score: 210
Period size: 36 Copynumber: 3.7 Consensus size: 36
600815 GATACAATCT
600825 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
600861 GTCCATCACCATTATCACGCCTTTATCATCACTATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
600897 GTCCATCTCCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
600933 TTCCACCACCATTATCACGCCTAT
1 GTCCATCACCATTATCACGCCTAT
600957 TTATCAACTT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 86 1.00
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:600931 original size:23 final size:24
Alignment explanation
Indices: 600828--600931 Score: 85
Period size: 23 Copynumber: 4.4 Consensus size: 24
600818 ACAATCTGTC
*
600828 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACCTATAT
600851 CATCACCA-TAGTCCATCACC-ATTAT
1 CATCACCATTA-T-CATCACCTA-TAT
* *
600876 CA-CGCCTTTATCATCA-CTATAGT
1 CATCACCATTATCATCACCTATA-T
*
600899 CCATCTCCATTATCA-CACCTATAT
1 -CATCACCATTATCATCACCTATAT
600923 CATCACCAT
1 CATCACCAT
600932 ATTCCACCAC
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
22 5 0.08
23 24 0.37
24 12 0.18
25 24 0.37
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.31
Consensus pattern (24 bp):
CATCACCATTATCATCACCTATAT
Found at i:601438 original size:14 final size:15
Alignment explanation
Indices: 601404--601450 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
601394 AATTTGGAGT
601404 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
601419 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
601433 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
601450 G
1 G
601451 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:604917 original size:23 final size:24
Alignment explanation
Indices: 604889--604992 Score: 76
Period size: 25 Copynumber: 4.4 Consensus size: 24
604879 ACAATCTGTC
604889 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCCTATAT
*
604912 CATCACCA-TAGTCCATCACC-ATTAT
1 CATCACCATTA-T-CATCGCCTA-TAT
* * *
604937 CA-CGCCTTTATCATC-ACTATAGT
1 CATCACCATTATCATCGCCTATA-T
*
604960 CCATCTCCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCGCCTATAT
604984 CATCACCAT
1 CATCACCAT
604993 ATTCCTCCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
22 5 0.08
23 23 0.37
24 11 0.17
25 24 0.38
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.31
Consensus pattern (24 bp):
CATCACCATTATCATCGCCTATAT
Found at i:604933 original size:36 final size:36
Alignment explanation
Indices: 604886--605027 Score: 223
Period size: 36 Copynumber: 3.9 Consensus size: 36
604876 GATACAATCT
604886 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
604922 GTCCATCACCATTATCACGCCTTTATCATCACTATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
604958 GTCCATCTCCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
604994 TTCC-TCCACCATTATCACGCCTATATTATCACCA
1 GTCCAT-CACCATTATCACGCCTATATCATCACCA
605028 ACTTATAATT
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 1 0.01
36 96 0.99
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:608893 original size:12 final size:12
Alignment explanation
Indices: 608876--608902 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
608866 TGTTGATAAA
608876 ACTCTATTAACT
1 ACTCTATTAACT
608888 ACTCTATTAACT
1 ACTCTATTAACT
608900 ACT
1 ACT
608903 TAAGAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (12 bp):
ACTCTATTAACT
Found at i:614106 original size:24 final size:24
Alignment explanation
Indices: 614079--614138 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
614069 CGAACTATTC
*
614079 TTTCGCTTCAATTGAGCTGAAATT
1 TTTCGCTTCAATTGAGCTCAAATT
614103 TTTCGCTTCAATTGAGCTCAAATT
1 TTTCGCTTCAATTGAGCTCAAATT
**
614127 TTAGGCTTCAAT
1 TTTCGCTTCAAT
614139 CGAACTTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (24 bp):
TTTCGCTTCAATTGAGCTCAAATT
Found at i:614425 original size:20 final size:20
Alignment explanation
Indices: 614379--614438 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
614369 ACCAGTTTTG
*
614379 CCGGTTTTCAGCCGGTTCAAC
1 CCGGTTTTCAGCCGGTTC-TC
*
614400 CCGGTTTTCAGCCGGTTCTT
1 CCGGTTTTCAGCCGGTTCTC
*
614420 CCGGTTCTTTA-CCGGTTCT
1 CCGGTT-TTCAGCCGGTTCT
614439 GTGCTAATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.08, C:0.32, G:0.23, T:0.37
Consensus pattern (20 bp):
CCGGTTTTCAGCCGGTTCTC
Found at i:614896 original size:23 final size:25
Alignment explanation
Indices: 614850--614903 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 25
614840 TTTCTTTCGT
*
614850 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTGGAGTGCTTTCAA
614875 TTTCTT-CTTTTGGAGTGC-TTCAA
1 TTTCTTCCTTTTGGAGTGCTTTCAA
614898 TTTCTT
1 TTTCTT
614904 TTATGATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 11 0.39
24 11 0.39
25 6 0.21
ACGTcount: A:0.11, C:0.19, G:0.13, T:0.57
Consensus pattern (25 bp):
TTTCTTCCTTTTGGAGTGCTTTCAA
Found at i:623454 original size:37 final size:35
Alignment explanation
Indices: 623378--623456 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 35
623368 TTTGAGAATT
**
623378 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATATGAAGATGGACTA
*
623413 TGGTGATGATATAGGCGTGATAATGAAAGATGGATTA
1 TGGTGATGATATAGGCGTGAT-ATG-AAGATGGACTA
623450 TGGTGAT
1 TGGTGAT
623457 AGAAATAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGAAGATGGACTA
Found at i:628667 original size:17 final size:18
Alignment explanation
Indices: 628645--628683 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
628635 GTAGGAGTCT
628645 TTTTCTT-TTCTCTT-TTG
1 TTTTCTTCTT-TCTTGTTG
628662 TTTTCTTCTTTCTTGTTG
1 TTTTCTTCTTTCTTGTTG
628680 TTTT
1 TTTT
628684 TTTGTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTTCTTCTTTCTTGTTG
Found at i:629115 original size:35 final size:37
Alignment explanation
Indices: 629067--629147 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
629057 TTTGAGAATT
* *
629067 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGGTATAGGCGTGATAATGGAAGATGGACTA
*
629102 TGGTGATGGTATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGGTATAGGCGTGATAATGGAAGATGGACTA
629139 TGGTGATGG
1 TGGTGATGG
629148 AAATAGTATC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.49
36 4 0.10
37 17 0.41
ACGTcount: A:0.26, C:0.04, G:0.40, T:0.31
Consensus pattern (37 bp):
TGGTGATGGTATAGGCGTGATAATGGAAGATGGACTA
Found at i:633880 original size:13 final size:11
Alignment explanation
Indices: 633837--633891 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
633827 ATTGGAGTGC
633837 AAAAAG-AAAG
1 AAAAAGAAAAG
633847 AAAAAGAGAAA-
1 AAAAAGA-AAAG
**
633858 AATCAGAAAAG
1 AAAAAGAAAAG
633869 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
633882 AAAAAGAAAA
1 AAAAAGAAAA
633892 ATTCAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 9 0.25
11 14 0.39
12 5 0.14
13 8 0.22
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:633901 original size:33 final size:34
Alignment explanation
Indices: 633838--633903 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
633828 TTGGAGTGCA
633838 AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
1 AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
*
633872 AAAAGAAAAGAAAAAGA-AAAATTCA-AAAAGAA
1 AAAAG-AAAGAAAAAGAGAAAAATCAGAAAAGAA
633904 AGCAAGCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.23
34 12 0.40
35 11 0.37
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.05
Consensus pattern (34 bp):
AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
Found at i:638120 original size:19 final size:20
Alignment explanation
Indices: 638096--638135 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
638086 TATCCCATCC
638096 TTATTTCATTTAATT-CTTA
1 TTATTTCATTTAATTACTTA
* *
638115 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTAATTACTTA
638135 T
1 T
638136 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTAATTACTTA
Found at i:641451 original size:16 final size:17
Alignment explanation
Indices: 641429--641466 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
641419 CTATCATTTC
641429 CTTATTTCATATCATTA
1 CTTATTTCATATCATTA
* *
641446 -TTATTTCTTTTCATTA
1 CTTATTTCATATCATTA
641462 CTTAT
1 CTTAT
641467 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.61
Consensus pattern (17 bp):
CTTATTTCATATCATTA
Found at i:641758 original size:17 final size:17
Alignment explanation
Indices: 641721--641758 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
641711 TTGGAGTGCA
*
641721 AAAAGAAAGAAAAAGAG
1 AAAAGAAAGAAAAAGAC
641738 AAAAGAAGAGAAAAA-AC
1 AAAAGAA-AGAAAAAGAC
641755 AAAA
1 AAAA
641759 AAAAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAAAAAGAC
Found at i:641759 original size:18 final size:18
Alignment explanation
Indices: 641719--641759 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
641709 AATTGGAGTG
641719 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAAGAAAAAGA
*
641737 -GAAAAGAAGAGAAAAA-A
1 CAAAAAGAA-AGAAAAAGA
641754 CAAAAA
1 CAAAAA
641760 AAAATCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAAGA
Found at i:643016 original size:23 final size:23
Alignment explanation
Indices: 642971--643016 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
642961 TTATACCTAT
*
642971 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
642994 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
643017 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:644659 original size:8 final size:8
Alignment explanation
Indices: 644630--644681 Score: 79
Period size: 8 Copynumber: 6.5 Consensus size: 8
644620 TTGGAGTGAA
644630 AAAAGAAAG
1 AAAAG-AAG
*
644639 AAAAG-AC
1 AAAAGAAG
644646 AAAAGAAG
1 AAAAGAAG
644654 AAAAGAAG
1 AAAAGAAG
644662 AAAAGAAG
1 AAAAGAAG
644670 AAAAGAAG
1 AAAAGAAG
644678 AAAA
1 AAAA
644682 AAAAAGATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
7 6 0.15
8 29 0.73
9 5 0.12
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:667986 original size:168 final size:168
Alignment explanation
Indices: 667708--668046 Score: 646
Period size: 168 Copynumber: 2.0 Consensus size: 168
667698 ACTCCAAAAA
667708 AAATGATGATGCTCCACTCAACGCTGGTGTTTGCACTCGGGAATATAAATTGGCCTTTTCAATTC
1 AAATGATGATGCTCCACTCAACGCTGGTGTTTGCACTCGGGAATATAAATTGGCCTTTTCAATTC
667773 CCCTTCTGATCTCACACACTCGATTAGCCTTTTTCCACTCGTTCCTCTCTTGTAAAGTTCTTAAA
66 CCCTTCTGATCTCACACACTCGATTAGCCTTTTTCCACTCGTTCCTCTCTTGTAAAGTTCTTAAA
667838 TGAACAACTCGAGACC-TTC-AGTGTTATGGACATCAACT
131 TGAACAACTCGAGACCTTTCAAGTG-T-TGGACATCAACT
667876 AAATGATGATGCTCCACTCAACGCTGGTGTTTGCACTCGGGAATATAAATTGGCCTTTTCAATTC
1 AAATGATGATGCTCCACTCAACGCTGGTGTTTGCACTCGGGAATATAAATTGGCCTTTTCAATTC
667941 CCCTTCTGATCTCACACACTCGATTAGCCTTTTTCCACTCGTTCCTCTCTTGTAAAGTTCTTAAA
66 CCCTTCTGATCTCACACACTCGATTAGCCTTTTTCCACTCGTTCCTCTCTTGTAAAGTTCTTAAA
668006 TGAACAACTCGAGACCTTTCAAGTGTTGGACATCAACT
131 TGAACAACTCGAGACCTTTCAAGTGTTGGACATCAACT
668044 AAA
1 AAA
668047 AATTCGTTAG
Statistics
Matches: 169, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
168 161 0.95
169 4 0.02
170 4 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (168 bp):
AAATGATGATGCTCCACTCAACGCTGGTGTTTGCACTCGGGAATATAAATTGGCCTTTTCAATTC
CCCTTCTGATCTCACACACTCGATTAGCCTTTTTCCACTCGTTCCTCTCTTGTAAAGTTCTTAAA
TGAACAACTCGAGACCTTTCAAGTGTTGGACATCAACT
Found at i:674055 original size:21 final size:20
Alignment explanation
Indices: 674029--674075 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
674019 TCGTTTGCAA
674029 TTTTTTTGAAATTTTGGATTT
1 TTTTTTTGAAATTTTGG-TTT
***
674050 TTTTTTTGTTTTTTTGGTTT
1 TTTTTTTGAAATTTTGGTTT
674070 TTTTTT
1 TTTTTT
674076 GCCTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.09, C:0.00, G:0.13, T:0.79
Consensus pattern (20 bp):
TTTTTTTGAAATTTTGGTTT
Found at i:674061 original size:9 final size:10
Alignment explanation
Indices: 674049--674096 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
674039 ATTTTGGATT
674049 TTTTTTTTG-
1 TTTTTTTTGC
* *
674058 TTTTTTTGGT
1 TTTTTTTTGC
674068 TTTTTTTTGC
1 TTTTTTTTGC
*
674078 CTTTTTTTGCC
1 TTTTTTTTG-C
674089 TTTTTTTT
1 TTTTTTTT
674097 ATTTTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.81
Consensus pattern (10 bp):
TTTTTTTTGC
Found at i:674061 original size:10 final size:10
Alignment explanation
Indices: 674048--674103 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
674038 AATTTTGGAT
674048 TTTTTTTTTG
1 TTTTTTTTTG
*
674058 -TTTTTTTGG
1 TTTTTTTTTG
674067 TTTTTTTTTG
1 TTTTTTTTTG
**
674077 CCTTTTTTTG
1 TTTTTTTTTG
* *
674087 CCTTTTTTTTA
1 -TTTTTTTTTG
674098 TTTTTT
1 TTTTTT
674104 ATTTAAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 8 0.22
10 21 0.57
11 8 0.22
ACGTcount: A:0.02, C:0.07, G:0.09, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:674082 original size:11 final size:11
Alignment explanation
Indices: 674058--674096 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
674048 TTTTTTTTTG
**
674058 TTTTTTTGGTT
1 TTTTTTTGCCT
674069 TTTTTTTGCC-
1 TTTTTTTGCCT
674079 TTTTTTTGCCT
1 TTTTTTTGCCT
674090 TTTTTTT
1 TTTTTTT
674097 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.79
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:674082 original size:21 final size:19
Alignment explanation
Indices: 674048--674103 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
674038 AATTTTGGAT
*
674048 TTTTTTTTTGTTTTTTTGG
1 TTTTTTTTTGTTTTTTTGC
674067 TTTTTTTTTGCCTTTTTTTGC
1 TTTTTTTTTG--TTTTTTTGC
* *
674088 CTTTTTTTTATTTTTT
1 TTTTTTTTTGTTTTTT
674104 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.02, C:0.07, G:0.09, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTTTGC
Found at i:677682 original size:426 final size:426
Alignment explanation
Indices: 676889--678027 Score: 2239
Period size: 426 Copynumber: 2.7 Consensus size: 426
676879 TAGTTATGAT
676889 AATGGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATT
1 AATGGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATT
676954 ATGAACCACATATTTATATCTTATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTT
66 ATGAACCACATATTTATATCTTATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTT
677019 CGGCCACATCATGGGAGCTGATTTAAAGCTAGAATTGAAGTCAATGAGCTAGGAAACCTTACATA
131 CGGCCACATCATGGGAGCTGATTTAAAGCTAGAATTGAAGTCAATGAGCTAGGAAACCTTACATA
677084 GGATGACTTGGGAGATCATGAAGAACAAATGGTGAAAAGTTGTCAGCTGACCCTCGAGCTCATAG
196 GGATGACTTGGGAGATCATGAAGAACAAATGGTGAAAAGTTGTCAGCTGACCCTCGAGCTCATAG
*
677149 CTCACTTGAGTTGGACTTTTGAGCTAGCTAGAGACTTCATTTCAGCTGGAGAGTTGCACCATCAT
261 CTCACTTGAGCTGGACTTTTGAGCTAGCTAGAGACTTCATTTCAGCTGGAGAGTTGCACCATCAT
*
677214 CTTCACCACACAGAGCACTACAAATATGGTCTAGGTCAAATTTTGTGAATTCGTACCTTTTCGCG
326 CTTCACCACACAGAGCACTACAAATACGGTCTAGGTCAAATTTTGTGAATTCGTACCTTTTCGCG
677279 AAGAGTTGCCAATCCGAGAAGTGACTCATAACTATG
391 AAGAGTTGCCAATCCGAGAAGTGACTCATAACTATG
677315 AATGGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATT
1 AATGGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATT
677380 ATGAACCACATATTTATATCTTATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTT
66 ATGAACCACATATTTATATCTTATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTT
677445 CGGCCACATCATGGGAGCTGATTTAAAGCTAGAATTGAAGTCAATGAGCTAGGAAACCTTACATA
131 CGGCCACATCATGGGAGCTGATTTAAAGCTAGAATTGAAGTCAATGAGCTAGGAAACCTTACATA
677510 GGATGACTTGGGAGATCATGAAGAACAAATGGTGAAAAGTTGTCAGCTGACCCTCGAGCTCATAG
196 GGATGACTTGGGAGATCATGAAGAACAAATGGTGAAAAGTTGTCAGCTGACCCTCGAGCTCATAG
677575 CTCACTTGAGCTGGACTTTTGAGCTAGCTAGAGACTTCATTTCAGCTGGAGAGTTGCACCATCAT
261 CTCACTTGAGCTGGACTTTTGAGCTAGCTAGAGACTTCATTTCAGCTGGAGAGTTGCACCATCAT
677640 CTTCACCACACAGAGCACTACAAATACGGTCTAGGTCAAATTTTGTGAATTCGTACCTTTTCGCG
326 CTTCACCACACAGAGCACTACAAATACGGTCTAGGTCAAATTTTGTGAATTCGTACCTTTTCGCG
677705 AAGAGTTGCCAATCCGAGAAGTGACTCATAACTATG
391 AAGAGTTGCCAATCCGAGAAGTGACTCATAACTATG
677741 AATGGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATT
1 AATGGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATT
677806 ATGAA-CACATATTTATATCTTATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTT
66 ATGAACCACATATTTATATCTTATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTT
677870 CGGCCACATCATGGGAGCTGATTTAAAGCTAGAATTGAAGTCAATGAGCTA-GAAACCTTACATA
131 CGGCCACATCATGGGAGCTGATTTAAAGCTAGAATTGAAGTCAATGAGCTAGGAAACCTTACATA
677934 GGATGACTTGGGAGATCATGAAGAACAAATGGTGAAAAG-TGTCAGCTGACCCTCGAGCTCATAG
196 GGATGACTTGGGAGATCATGAAGAACAAATGGTGAAAAGTTGTCAGCTGACCCTCGAGCTCATAG
677998 CTCACTTGAGCTGGACTTTTGAGCTAGCTA
261 CTCACTTGAGCTGGACTTTTGAGCTAGCTA
678028 CTTCGCATTG
Statistics
Matches: 711, Mismatches: 2, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
423 55 0.08
424 52 0.07
425 110 0.15
426 494 0.69
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (426 bp):
AATGGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATT
ATGAACCACATATTTATATCTTATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTT
CGGCCACATCATGGGAGCTGATTTAAAGCTAGAATTGAAGTCAATGAGCTAGGAAACCTTACATA
GGATGACTTGGGAGATCATGAAGAACAAATGGTGAAAAGTTGTCAGCTGACCCTCGAGCTCATAG
CTCACTTGAGCTGGACTTTTGAGCTAGCTAGAGACTTCATTTCAGCTGGAGAGTTGCACCATCAT
CTTCACCACACAGAGCACTACAAATACGGTCTAGGTCAAATTTTGTGAATTCGTACCTTTTCGCG
AAGAGTTGCCAATCCGAGAAGTGACTCATAACTATG
Found at i:679373 original size:33 final size:33
Alignment explanation
Indices: 679294--679397 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
679284 ATACAATCTG
* *
679294 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
679330 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
679363 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
679396 TC
1 TC
679398 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:683841 original size:33 final size:33
Alignment explanation
Indices: 683762--683865 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
683752 ATACAATCTG
* *
683762 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
683798 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
683831 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
683864 TC
1 TC
683866 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:684843 original size:5 final size:5
Alignment explanation
Indices: 684835--684887 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
684825 GACTTTTCTT
684835 TTTTC TTTTC TTTT- TTTTC TTTT- TTTTC TTCTT- TTTGTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTT-TC TTTTC TTTTC
684884 TTTT
1 TTTT
684888 TGTACTCCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 9 0.21
5 29 0.67
6 5 0.12
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:684849 original size:12 final size:12
Alignment explanation
Indices: 684817--684882 Score: 68
Period size: 12 Copynumber: 5.7 Consensus size: 12
684807 CTTAGCTTGC
**
684817 TTTCTTTTGACT
1 TTTCTTTTTTCT
684829 TTTCTTTTTTCT
1 TTTCTTTTTTCT
684841 TTTC--TTTT-T
1 TTTCTTTTTTCT
684850 TTTCTTTTTT-T
1 TTTCTTTTTTCT
684861 TCTTCTTTTTGTCT
1 T-TTCTTTTT-TCT
684875 TTTCTTTT
1 TTTCTTTT
684883 CTTTTTGTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
9 5 0.11
10 4 0.09
11 6 0.13
12 22 0.47
13 8 0.17
14 2 0.04
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:684854 original size:21 final size:21
Alignment explanation
Indices: 684828--684888 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
684818 TTCTTTTGAC
684828 TTTTCTTTTTTCTTTTCTTTT
1 TTTTCTTTTTTCTTTTCTTTT
684849 TTTTCTTTTTT-TTCTTC-TTT
1 TTTTCTTTTTTCTT-TTCTTTT
*
684869 TTGTC--TTTTCTTTTCTTTT
1 TTTTCTTTTTTCTTTTCTTTT
684888 T
1 T
684889 GTACTCCAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.19
19 6 0.17
20 9 0.25
21 14 0.39
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.84
Consensus pattern (21 bp):
TTTTCTTTTTTCTTTTCTTTT
Found at i:684890 original size:18 final size:17
Alignment explanation
Indices: 684817--684888 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 17
684807 CTTAGCTTGC
684817 TTTCTTTTGACTTTTCTTT
1 TTTCTTTT--CTTTTCTTT
684836 TTTCTTTTCTTTT-TTT
1 TTTCTTTTCTTTTCTTT
684852 TCTT-TTTT-TTCTTCTTT
1 T-TTCTTTTCTT-TTCTTT
684869 TTGTCTTTTCTTTTCTTT
1 TT-TCTTTTCTTTTCTTT
684887 TT
1 TT
684889 GTACTCCAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.04
16 11 0.23
17 12 0.26
18 12 0.26
19 10 0.21
ACGTcount: A:0.01, C:0.15, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTCTTTTCTTTTCTTT
Found at i:685859 original size:22 final size:22
Alignment explanation
Indices: 685831--685876 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
685821 TTTTCTTTTA
*
685831 TTTTTGAGTTCTTTCAATTTCT
1 TTTTTGAGTGCTTTCAATTTCT
* *
685853 TTTTTGAGTGCTTTGATTTTCT
1 TTTTTGAGTGCTTTCAATTTCT
685875 TT
1 TT
685877 GTTGGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.65
Consensus pattern (22 bp):
TTTTTGAGTGCTTTCAATTTCT
Found at i:686573 original size:19 final size:20
Alignment explanation
Indices: 686526--686576 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
686516 GAAACCCCTT
**
686526 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
686546 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
686565 TGAAGATACATG
1 TGAAAATACATG
686577 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:690231 original size:26 final size:28
Alignment explanation
Indices: 690178--690233 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
690168 ATTTCTTCTT
* * *
690178 TTCTTCCTTTTTGAGTGCTTGATTTTTC
1 TTCTTCCTTTTGGAGTGCTTCATATTTC
690206 TTCTT-CTTTTGGAGTGCTTCA-ATTTC
1 TTCTTCCTTTTGGAGTGCTTCATATTTC
690232 TT
1 TT
690234 TTGTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 14 0.56
28 5 0.20
ACGTcount: A:0.09, C:0.18, G:0.14, T:0.59
Consensus pattern (28 bp):
TTCTTCCTTTTGGAGTGCTTCATATTTC
Found at i:698154 original size:32 final size:33
Alignment explanation
Indices: 698118--698184 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
698108 AGGTTAAGAA
*
698118 AAAGAATAAAGTAAT-AAA-AATAAGAAAAGATG
1 AAAGAATAAAGAAATGAAATAATAAGAAAA-ATG
* *
698150 AAAGAATAAGGAAATGAAATAGTAAGAAAAATG
1 AAAGAATAAAGAAATGAAATAATAAGAAAAATG
698183 AA
1 AA
698185 GATAACTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 13 0.43
33 8 0.27
34 9 0.30
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (33 bp):
AAAGAATAAAGAAATGAAATAATAAGAAAAATG
Found at i:698296 original size:6 final size:6
Alignment explanation
Indices: 698285--698310 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
698275 TGTAATATGC
698285 TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT
698311 CTTTTGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:700019 original size:22 final size:22
Alignment explanation
Indices: 699979--700020 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
699969 AAATATATGG
*
699979 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
700001 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
700021 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:702799 original size:27 final size:28
Alignment explanation
Indices: 702764--702830 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
702754 CTTTTCTTTT
* *
702764 ATTTGCTTTTCTTCTTTTTGAATGC-TGA
1 ATTT-CTTTTCTTCTTTTGGAATGCTTCA
*
702792 ATTTC-TTTCTTTCTTTTGGAGTGCTTCA
1 ATTTCTTTTC-TTCTTTTGGAATGCTTCA
702820 ATTTCTTTTCT
1 ATTTCTTTTCT
702831 GATTTTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.12
27 13 0.39
28 12 0.36
29 4 0.12
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (28 bp):
ATTTCTTTTCTTCTTTTGGAATGCTTCA
Found at i:705030 original size:13 final size:12
Alignment explanation
Indices: 705000--705042 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
704990 TTCAAAAAAA
*
705000 CAAAAAAAAA-A
1 CAAAAAAAAAGG
705011 C-AAAAAAAAGG
1 CAAAAAAAAAGG
705022 CAAAGAAAAAAGG
1 CAAA-AAAAAAGG
705035 CAAAAAAA
1 CAAAAAAA
705043 CAAAAAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 6 0.21
13 12 0.43
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAGG
Found at i:705050 original size:11 final size:11
Alignment explanation
Indices: 704993--705042 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
704983 TATTTTTTTC
704993 AAAAAAACAAA
1 AAAAAAACAAA
705004 AAAAAAACAAA
1 AAAAAAACAAA
**
705015 AAAAAGGCAAA
1 AAAAAAACAAA
*
705026 GAAAAAAGGCAAA
1 -AAAAAA-ACAAA
705039 AAAA
1 AAAA
705043 CAAAAAAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 20 0.59
12 9 0.26
13 5 0.15
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:710630 original size:19 final size:19
Alignment explanation
Indices: 710601--710663 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
710591 AAAAATAAGA
*
710601 AGAAATGAGAGTTGAAAA-
1 AGAATTGAGAGTTGAAAAG
710619 AGACATTGAGAGTATTGAAAAG
1 AGA-ATTGAGAG--TTGAAAAG
710641 AGAATTGAGAG-TGAAAATG
1 AGAATTGAGAGTTGAAAA-G
710660 AGAA
1 AGAA
710664 CATTGAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 9 0.23
19 12 0.31
21 15 0.38
22 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.29, T:0.19
Consensus pattern (19 bp):
AGAATTGAGAGTTGAAAAG
Found at i:711873 original size:17 final size:16
Alignment explanation
Indices: 711832--711903 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 16
711822 ATTCAAGCAT
711832 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
*
711849 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
*
711867 CTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
711884 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
711901 CTA
1 CTA
711904 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
16 1 0.02
17 29 0.62
18 17 0.36
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:715684 original size:19 final size:19
Alignment explanation
Indices: 715655--715711 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
715645 AAAAAGAAGA
*
715655 AGAAATGAGAGTTGAAAA-
1 AGAATTGAGAGTTGAAAAG
715673 AGACATTGAGAGTATTGAAAAG
1 AGA-ATTGAGAG--TTGAAAAG
715695 AGAATTGAGAG-TGAAAA
1 AGAATTGAGAGTTGAAAA
715712 TGAGCACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 9 0.26
19 7 0.21
21 15 0.44
22 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.28, T:0.19
Consensus pattern (19 bp):
AGAATTGAGAGTTGAAAAG
Found at i:715690 original size:21 final size:21
Alignment explanation
Indices: 715666--715706 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
715656 GAAATGAGAG
715666 TTGAAAA-AGACATTGAGAGTA
1 TTGAAAAGAGA-ATTGAGAGTA
715687 TTGAAAAGAGAATTGAGAGT
1 TTGAAAAGAGAATTGAGAGT
715707 GAAAATGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.24
Consensus pattern (21 bp):
TTGAAAAGAGAATTGAGAGTA
Found at i:716954 original size:17 final size:17
Alignment explanation
Indices: 716885--716956 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
716875 ATTCATGCAT
*
716885 CTAGTTCATTGAATAAA
1 CTAGTTCATTTAATAAA
* *
716902 GTTAGTTGA-TTAATTAAA
1 -CTAGTTCATTTAA-TAAA
716920 CTAGTTCATTT-ATCAAA
1 CTAGTTCATTTAAT-AAA
716937 CTAGTTCATTTAATAAA
1 CTAGTTCATTTAATAAA
716954 CTA
1 CTA
716957 ACTCTTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
16 1 0.02
17 30 0.67
18 14 0.31
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTTAATAAA
Found at i:720842 original size:27 final size:28
Alignment explanation
Indices: 720780--720843 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
720770 CCTTGGATTG
* *
720780 CTTTCTTTTTCTTTTCTTTTCTTCTTTT
1 CTTTCTTTTTCTATTCTTTTCGTCTTTT
**
720808 C-TGATTTTTCTATTCTTTT-GTCTTTT
1 CTTTCTTTTTCTATTCTTTTCGTCTTTT
720834 CTTTCTTTTT
1 CTTTCTTTTT
720844 GCACTCCAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 7 0.24
27 21 0.72
28 1 0.03
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (28 bp):
CTTTCTTTTTCTATTCTTTTCGTCTTTT
Found at i:722438 original size:21 final size:22
Alignment explanation
Indices: 722399--722447 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
722389 CTATAGGTAT
*
722399 TATATATATATGAAAATAACTC
1 TATATACATATGAAAATAACTC
* *
722421 TTTATACATATG-AAATAAGTC
1 TATATACATATGAAAATAACTC
722442 TATATA
1 TATATA
722448 GGTATAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (22 bp):
TATATACATATGAAAATAACTC
Found at i:735224 original size:26 final size:26
Alignment explanation
Indices: 735182--735240 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
735172 CTTGGCTTGC
735182 TTTTC-TCTTTTTGGAATCTTT-TTCT
1 TTTTCTTCTTTTTGGAAT-TTTCTTCT
735207 TTTTCTTCTTTTAT-GAATTTTCTTCT
1 TTTTCTTCTTTT-TGGAATTTTCTTCT
735233 TTTGTCTT
1 TTT-TCTT
735241 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 8 0.27
26 17 0.57
27 5 0.17
ACGTcount: A:0.08, C:0.15, G:0.07, T:0.69
Consensus pattern (26 bp):
TTTTCTTCTTTTTGGAATTTTCTTCT
Found at i:740604 original size:30 final size:31
Alignment explanation
Indices: 740568--740627 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
740558 CTTAGCTTTA
**
740568 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
740598 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
740628 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:741536 original size:19 final size:21
Alignment explanation
Indices: 741512--741557 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
741502 CGGCCAAGAG
741512 CATGTATCTTCA-TT-AAAAT
1 CATGTATCTTCATTTAAAAAT
*
741531 CATGTATTTTCATTTAAAAAT
1 CATGTATCTTCATTTAAAAAT
741552 CATGTA
1 CATGTA
741558 ATTTCAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.46
20 2 0.08
21 11 0.46
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAAT
Found at i:741552 original size:21 final size:19
Alignment explanation
Indices: 741512--741563 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
741502 CGGCCAAGAG
*
741512 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
741531 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
*
741552 CATGTAATTTCA
1 CATGTATTTTCA
741564 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:744771 original size:30 final size:31
Alignment explanation
Indices: 744735--744794 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
744725 CTTAGCTTTA
**
744735 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
744765 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
744795 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:745688 original size:21 final size:19
Alignment explanation
Indices: 745648--745697 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 19
745638 CGGCCAAGAG
*
745648 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
745667 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
745688 CATGTATTTT
1 CATGTATTTT
745698 TAAAGGGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 11 0.39
20 2 0.07
21 15 0.54
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:746648 original size:11 final size:11
Alignment explanation
Indices: 746632--746661 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
746622 ATGGTGTGAA
746632 TGAGCTGGTGG
1 TGAGCTGGTGG
746643 TGAGCTGGTGG
1 TGAGCTGGTGG
746654 TGAGCTGG
1 TGAGCTGG
746662 CCTTAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.53, T:0.27
Consensus pattern (11 bp):
TGAGCTGGTGG
Found at i:750090 original size:27 final size:26
Alignment explanation
Indices: 750058--750108 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
750048 GATTGCTTTC
*
750058 TTTTTCTTTTCTTTTCTTCTTTTCTGA
1 TTTTTCTATTCTTTT-TTCTTTTCTGA
750085 TTTTTCTATTCTTTTTTCTTTTCT
1 TTTTTCTATTCTTTTTTCTTTTCT
750109 TTCTTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTTTCTATTCTTTTTTCTTTTCTGA
Found at i:765463 original size:26 final size:27
Alignment explanation
Indices: 765426--765485 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
765416 CTTGGCTTGC
*
765426 TTTTC-TCTTTTTTTGAATCTTT-TTCT
1 TTTTCTTCTTTTTATGAAT-TTTATTCT
765452 TTTTCTTC-TTTTATGAATTTTATTCT
1 TTTTCTTCTTTTTATGAATTTTATTCT
765478 TTTGTCTT
1 TTT-TCTT
765486 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 21 0.70
27 6 0.20
ACGTcount: A:0.10, C:0.13, G:0.05, T:0.72
Consensus pattern (27 bp):
TTTTCTTCTTTTTATGAATTTTATTCT
Found at i:771580 original size:19 final size:21
Alignment explanation
Indices: 771556--771601 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
771546 CGGCCAAGAG
771556 CATGTATCTTCA-TT-AAAAT
1 CATGTATCTTCATTTAAAAAT
*
771575 CATGTATTTTCATTTAAAAAT
1 CATGTATCTTCATTTAAAAAT
771596 CATGTA
1 CATGTA
771602 ATTTCAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.46
20 2 0.08
21 11 0.46
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAAT
Found at i:771596 original size:21 final size:19
Alignment explanation
Indices: 771556--771607 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
771546 CGGCCAAGAG
*
771556 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
771575 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
*
771596 CATGTAATTTCA
1 CATGTATTTTCA
771608 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:774785 original size:30 final size:31
Alignment explanation
Indices: 774749--774808 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
774739 CTTAGCTTTA
**
774749 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
774779 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
774809 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:775737 original size:21 final size:19
Alignment explanation
Indices: 775697--775746 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 19
775687 CGGCCAAGAG
*
775697 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
775716 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
775737 CATGTATTTT
1 CATGTATTTT
775747 TAAAGGGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 11 0.39
20 2 0.07
21 15 0.54
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:779149 original size:7 final size:6
Alignment explanation
Indices: 779130--779165 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
779120 GTGTTGCAAC
*
779130 AAAAAC AAAAAG AAAGAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAA
779166 AACTCCTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:779433 original size:17 final size:17
Alignment explanation
Indices: 779411--779443 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
779401 ATCTTACCTT
*
779411 TACCATATCCATTTCTA
1 TACCATAACCATTTCTA
779428 TACCATAACCATTTCT
1 TACCATAACCATTTCT
779444 TTTAGCCGAC
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:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:782119 original size:15 final size:17
Alignment explanation
Indices: 782099--782139 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
782089 ATTTTCTTAC
782099 TATTTCATTTCTTTT-T
1 TATTTCATTTCTTTTGT
782115 T-TTTCA--TCTTTTGT
1 TATTTCATTTCTTTTGT
782129 TATTTCATTTC
1 TATTTCATTTC
782140 CTTATCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
13 6 0.29
14 2 0.10
15 10 0.48
16 1 0.05
17 2 0.10
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (17 bp):
TATTTCATTTCTTTTGT
Found at i:782182 original size:26 final size:26
Alignment explanation
Indices: 782153--782242 Score: 153
Period size: 26 Copynumber: 3.5 Consensus size: 26
782143 ATCCATTTCT
*
782153 TAACCTTTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
*
782179 TAACCATTTCTATCCTATCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
*
782205 TAAACATTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
782231 TAACCATTTCTA
1 TAACCATTTCTA
782243 GACCCTAACC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (26 bp):
TAACCATTTCTATCCTACCCCTATCA
Found at i:786308 original size:36 final size:35
Alignment explanation
Indices: 786257--786367 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
786247 TAAGATACTA
786257 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * * *
786292 CCTATAACATCACCATCCTCCATTACCATTGCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * *
786327 CC-ATTATCATTACCATCTTCTATCACCATTTCACG
1 CCTA-TAACATCACCATCTTCCATCACCATTTCACG
*
786362 CTTATA
1 CCTATA
786368 TAACCACCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
34 1 0.02
35 38 0.62
36 22 0.36
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:788280 original size:40 final size:40
Alignment explanation
Indices: 788225--788306 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
788215 ACCAAAACAC
788225 CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
1 CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
788265 CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
1 CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
788305 CA
1 CA
788307 TTTTGGTACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (40 bp):
CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
Found at i:794276 original size:11 final size:11
Alignment explanation
Indices: 794262--794315 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
794252 CTCTTTTGAA
*
794262 TTTCTTTTTGT
1 TTTCTTTTTCT
794273 TTTCTTTTT-T
1 TTTCTTTTTCT
**
794283 TTTCTGATTCT
1 TTTCTTTTTCT
794294 TTGGTCTTTTTCT
1 TT--TCTTTTTCT
794307 TTTCTTTTT
1 TTTCTTTTT
794316 ACACTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 8 0.22
11 19 0.53
13 9 0.25
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:809004 original size:47 final size:47
Alignment explanation
Indices: 808928--809018 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
808918 TCATTACTGA
* * *
808928 TGTAAGGTACTTGTACCTTATCGATTGATTGTGGATCTAGGAAGTGG
1 TGTAAGGCACTTGTACCTTATCAACTGATTGTGGATCTAGGAAGTGG
808975 TGTAAGGCACTTGTACCTTATCAACTGATTGTGGATCTAGGAAG
1 TGTAAGGCACTTGTACCTTATCAACTGATTGTGGATCTAGGAAG
809019 GAAGAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (47 bp):
TGTAAGGCACTTGTACCTTATCAACTGATTGTGGATCTAGGAAGTGG
Found at i:812282 original size:27 final size:28
Alignment explanation
Indices: 812232--812294 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
812222 AGAAAATCAT
812232 AAAAGAAATTGAAGCACTTCAAAAGAA-
1 AAAAGAAATTGAAGCACTTCAAAAGAAG
*
812259 AGAAAGAAATT-CAGCA-TTCAAAAAGAAG
1 A-AAAGAAATTGAAGCACTTC-AAAAGAAG
812287 AAAAGAAA
1 AAAAGAAA
812295 AGAAAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 19 0.59
28 10 0.31
ACGTcount: A:0.62, C:0.10, G:0.16, T:0.13
Consensus pattern (28 bp):
AAAAGAAATTGAAGCACTTCAAAAGAAG
Found at i:812314 original size:4 final size:5
Alignment explanation
Indices: 812284--812313 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
812274 ATTCAAAAAG
812284 AAGAA AAGAA AAGAA AAGAA AAG-A AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
812314 GTTGAAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:814001 original size:13 final size:11
Alignment explanation
Indices: 813957--814041 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
813947 ACAATCTGTC
813957 CATCACCATCAT
1 CATCACCAT-AT
*
813969 CA-CGCCTATAT
1 CATCACC-ATAT
*
813980 CATCGCCATAGT
1 CATCACCATA-T
813992 CCATCACCATTAT
1 -CATCACCA-TAT
*
814005 CA-CGCCTATAT
1 CATCACC-ATAT
814016 CATCACCATATT
1 CATCACCATA-T
814028 CCATCACCATAT
1 -CATCACCATAT
814040 CA
1 CA
814042 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 23 0.38
12 17 0.28
13 18 0.30
14 2 0.03
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.27
Consensus pattern (11 bp):
CATCACCATAT
Found at i:814001 original size:36 final size:35
Alignment explanation
Indices: 813954--814058 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 35
813944 GATACAATCT
*
813954 GTCCATCACCATCATCACGCCTATATCATCGCCATA
1 GTCCATCACCAT-ATCACGCCTATATCATCACCATA
813990 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCA-TATCACGCCTATATCATCACCATA
* *
814026 TTCCATCACCATATCACGCCTATATTATCACCA
1 GTCCATCACCATATCACGCCTATATCATCACCA
814059 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 21 0.32
36 43 0.66
37 1 0.02
ACGTcount: A:0.30, C:0.37, G:0.06, T:0.28
Consensus pattern (35 bp):
GTCCATCACCATATCACGCCTATATCATCACCATA
Found at i:815561 original size:14 final size:15
Alignment explanation
Indices: 815537--815565 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
815527 AGATATTTCT
815537 GCATATGGACAGCTG
1 GCATATGGACAGCTG
815552 GCAT-TGGACAGCTG
1 GCATATGGACAGCTG
815566 TCTCTGCACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (15 bp):
GCATATGGACAGCTG
Found at i:822981 original size:20 final size:20
Alignment explanation
Indices: 822956--822993 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
822946 TTTTTCTTTA
822956 TCTTTCATTATTAA-TTTTTC
1 TCTTTCATT-TTAACTTTTTC
822976 TCTTTCATTTTAACTTTT
1 TCTTTCATTTTAACTTTT
822994 ACCTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (20 bp):
TCTTTCATTTTAACTTTTTC
Found at i:822999 original size:19 final size:19
Alignment explanation
Indices: 822952--822999 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
822942 TAACTTTTTC
*
822952 TTTATCTTTCATTATTAAT
1 TTTACCTTTCATTATTAAT
*
822971 TTTTCTCTTTCATT-TTAACT
1 TTTAC-CTTTCATTATTAA-T
822991 TTTACCTTT
1 TTTACCTTT
823000 TCTCTTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTACCTTTCATTATTAAT
Found at i:828732 original size:21 final size:19
Alignment explanation
Indices: 828698--828744 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
828688 AAAGGGGCAA
*
828698 CTTTTTTCTATTTT-TTTGT
1 CTTTTTTATATTTTCTTT-T
828717 CCTTTTTTATATTTTTCTTTT
1 -CTTTTTTATA-TTTTCTTTT
828738 CTTTTTT
1 CTTTTTT
828745 GATAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 16 0.67
21 5 0.21
22 3 0.12
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.79
Consensus pattern (19 bp):
CTTTTTTATATTTTCTTTT
Found at i:828762 original size:13 final size:13
Alignment explanation
Indices: 828746--828777 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
828736 TTCTTTTTTG
828746 ATAATAAATAATA
1 ATAATAAATAATA
*
828759 ATAATTAATAATA
1 ATAATAAATAATA
828772 ATAATA
1 ATAATA
828778 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATAAATAATA
Done.