Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008923.1 Hibiscus syriacus cultivar Beakdansim tig00112227_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: 468757
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 3
Found at i:10604 original size:20 final size:20
Alignment explanation
Indices: 10575--10631 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
10565 TTAGAGTAAA
10575 GGTTTTGAAACCCCTTGGTT
1 GGTTTTGAAACCCCTTGGTT
* *
10595 GGTTTCGAAACCCCTGGGTT
1 GGTTTTGAAACCCCTTGGTT
*
10615 AGTTTTGAAACCCCTTG
1 GGTTTTGAAACCCCTTG
10632 TCCAGAATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (20 bp):
GGTTTTGAAACCCCTTGGTT
Found at i:16031 original size:19 final size:20
Alignment explanation
Indices: 15988--16035 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
15978 TCTAAATCCT
*
15988 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
16008 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
16027 TTTTCAAAA
1 TTTTCAAAA
16036 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:21011 original size:91 final size:91
Alignment explanation
Indices: 20877--21059 Score: 312
Period size: 91 Copynumber: 2.0 Consensus size: 91
20867 CTCACATTGC
* *
20877 AATGCTACTGTATTACTGCATTTTCCTTAAGTTTCTAGATGCTACTTCGCCCGGACTCGGATTGA
1 AATGCTACTGTATTACTACATTTTCCTTAAGTTTCTAGATGCTACGTCGCCCGGACTCGGATTGA
*
20942 GTGTTGGATATGTTTTTGCATCAGGG
66 GTGTTGGATATGTTTATGCATCAGGG
* *
20968 AATGCTACTGTATTACTACATTTTTCTTAAGTTTCTAGTTGCTACGTCGCCCGGACTCGGATTGA
1 AATGCTACTGTATTACTACATTTTCCTTAAGTTTCTAGATGCTACGTCGCCCGGACTCGGATTGA
*
21033 GTTTTGGATATGTTTATGCATCAGGG
66 GTGTTGGATATGTTTATGCATCAGGG
21059 A
1 A
21060 CCCTGAACTG
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (91 bp):
AATGCTACTGTATTACTACATTTTCCTTAAGTTTCTAGATGCTACGTCGCCCGGACTCGGATTGA
GTGTTGGATATGTTTATGCATCAGGG
Found at i:37186 original size:19 final size:19
Alignment explanation
Indices: 37146--37187 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
37136 CGGGTCGGTT
* *
37146 CGGTTCGGACCGGTCAACC
1 CGGTTCAGACCGGTCAAAC
*
37165 CGGTTCAGACCGGTTAAAC
1 CGGTTCAGACCGGTCAAAC
37184 CGGT
1 CGGT
37188 CAAATCGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (19 bp):
CGGTTCAGACCGGTCAAAC
Found at i:39678 original size:31 final size:31
Alignment explanation
Indices: 39643--39713 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
39633 GTAAAGTGAC
* *
39643 TTTTGTCATAAATCGATAACATTAATGACCA
1 TTTTGTCACAAATCAATAACATTAATGACCA
* * * *
39674 TTTTGTTACAAATTAATAACGTTAGTGACCA
1 TTTTGTCACAAATCAATAACATTAATGACCA
*
39705 ATTTGTCAC
1 TTTTGTCAC
39714 TTTTAAAACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (31 bp):
TTTTGTCACAAATCAATAACATTAATGACCA
Found at i:47276 original size:200 final size:196
Alignment explanation
Indices: 46714--47277 Score: 566
Period size: 200 Copynumber: 2.9 Consensus size: 196
46704 TACCCAAGTC
* * * * * * * *
46714 TCGATACTTTTGTGTAAGGTATCGAAACTTTTAAGACGTTTCATTTTTTCATTTCTTTTCAATTC
1 TCGATACATATGTGTAAGGTATCGATAC-TTT-ATACATTTCCTTTTTCCATTTCTTTTAAATTC
* * * * *
46779 CTAAATTATCGATACTATGGTACATATACTTATAAAAGTAT---TA-ATATCGTCAACATATCTG
64 CTAAAGTATCGATACTTTGATACATATACTTATAAAAGTATCGATACAAAT-GTCAACATTTC-G
* * * * * * *
46840 GTAGCGCTTTACCGGTTTTTTCAAATTGAAACTGATTTTTTCAAATTTCAACCTGTTATATTTTC
127 GTAGCTCTTTACCGGTTTTCTCAAATTGAAACTGGTTTTGTCAAACTTCAACATGTTATATTGTC
46905 ATGTA
192 ATGTA
* * ** * *
46910 TCGATACATATGTCTAAGGTATCGATACTTTAT--A-TGCGCTATTATTGTAATTCGTTTAAATT
1 TCGATACATATGTGTAAGGTATCGATACTTTATACATTTC-CT-TT-TTCCATTTCTTTTAAATT
* * * *
46972 CCTAAAGTATCGATGCTTTGATGCATATATTTATAAAAGTATCGATACAAATGTCAACCATTCCG
63 CCTAAAGTATCGATACTTTGATACATATACTTATAAAAGTATCGATACAAATGTCAA-CATTTCG
* * *
47037 ATATCTCTTTACCGGTTTTGTCAAATTGAAACTGGTTTTGTCAAACTTCAACATGTTATATTGTC
127 GTAGCTCTTTACCGGTTTTCTCAAATTGAAACTGGTTTTGTCAAACTTCAACATGTTATATTGTC
47102 ATGTA
192 ATGTA
*
47107 TCGATACATGTGTGTAAGGTATCGATACTTTCGATACATTTTCCTTTTTCCATTTCTTTTAAATT
1 TCGATACATATGTGTAAGGTATCGATACTTT--ATACA-TTTCCTTTTTCCATTTCTTTTAAATT
* * * * *
47172 CCTACAGTACCGATACTTTGATACATATACTTATAAACGTATCGATACAAATTTCAATAATTTCG
63 CCTAAAGTATCGATACTTTGATACATATACTTATAAAAGTATCGATACAAATGTCAA-CATTTCG
* * * ** *
47237 GTAGCTCTTTACTGATTTTCTCAGATTTCAACCGGTTTTGT
127 GTAGCTCTTTACCGGTTTTCTCAAATTGAAACTGGTTTTGT
47278 TAATTTTTAA
Statistics
Matches: 297, Mismatches: 57, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
191 2 0.01
192 1 0.00
193 2 0.01
194 50 0.17
195 3 0.01
196 24 0.08
197 98 0.33
198 7 0.02
199 2 0.01
200 101 0.34
201 3 0.01
202 2 0.01
203 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (196 bp):
TCGATACATATGTGTAAGGTATCGATACTTTATACATTTCCTTTTTCCATTTCTTTTAAATTCCT
AAAGTATCGATACTTTGATACATATACTTATAAAAGTATCGATACAAATGTCAACATTTCGGTAG
CTCTTTACCGGTTTTCTCAAATTGAAACTGGTTTTGTCAAACTTCAACATGTTATATTGTCATGT
A
Found at i:50675 original size:3 final size:3
Alignment explanation
Indices: 50662--50768 Score: 83
Period size: 3 Copynumber: 36.3 Consensus size: 3
50652 AAACATAAGC
* * * * *
50662 AAT ATT AAT AAT AAT AAT ACT AAT AAT AAT TAT AAT TAT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * * * *
50710 TAT AAT TGT TAT AAT AAT AAT AAT TAT TAT AAT -AT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
50757 TAT AAT -AT AAT A
1 AAT AAT AAT AAT A
50769 TTTATAACCC
Statistics
Matches: 80, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
2 4 0.05
3 76 0.95
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (3 bp):
AAT
Found at i:51009 original size:53 final size:53
Alignment explanation
Indices: 50925--51159 Score: 330
Period size: 53 Copynumber: 4.4 Consensus size: 53
50915 CTCTTATTTG
* *
50925 AACAATCTTC-GACC-AGCGGGTTCGCTCCCTCTTGCTTCAGGCAGTAGAATTCA
1 AACAATCTTCTG-CCTA-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
* *
50978 AACTATCTTTTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
* * * *
51031 AACAATCTTCTGCCTACGGATTCGCTCTCTATTGCTTCAGGGAGTAGAACTCG
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
* * *
51084 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTAGTGAGTAGAACTCG
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
*
51137 AACAATCTTCTGCCTATGGGTTC
1 AACAATCTTCTGCCTACGGGTTC
51160 ACTTCACTAT
Statistics
Matches: 164, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
53 162 0.99
54 2 0.01
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (53 bp):
AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
Found at i:51577 original size:41 final size:42
Alignment explanation
Indices: 51515--51605 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
51505 ACTCTTCTGA
* * *
51515 GAAAG-CTT-AAAATGGCTCAAAGGACTT-ATCATCTTGCTC
1 GAAAGACTTAAAAATGACCCAAAGGACTTCATCATCATGCTC
*
51554 GAAAGACTTAAAAATGACCCAAAGGATTTCATCATCATGCTC
1 GAAAGACTTAAAAATGACCCAAAGGACTTCATCATCATGCTC
51596 GAAAGACTTA
1 GAAAGACTTA
51606 CTGATGGATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 5 0.11
40 3 0.07
41 16 0.36
42 21 0.47
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (42 bp):
GAAAGACTTAAAAATGACCCAAAGGACTTCATCATCATGCTC
Found at i:51698 original size:42 final size:41
Alignment explanation
Indices: 51652--51855 Score: 168
Period size: 42 Copynumber: 5.0 Consensus size: 41
51642 TACCAATTAC
51652 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATAGG
1 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGAT-GG
* *
51694 CCGAAAGATTTCATCATCATGCTCGAAAGACTTACTGATGG
1 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
*** * * * * ** **
51735 --GTTTGCTTCACTACTCTTC-TG-T-G-AAGGCTTACAAATTAC
1 CCGAAGGATT---TAATCATCATGCTCGAAAGACTTACTGA-TGG
51774 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
51815 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATG
1 -CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
51856 ACCCGAAAGA
Statistics
Matches: 123, Mismatches: 28, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
38 15 0.12
39 8 0.07
40 2 0.02
41 10 0.08
42 88 0.72
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:51700 original size:20 final size:22
Alignment explanation
Indices: 51667--51732 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
51657 GGATTTAATC
*
51667 ATCATGCTCGAAAGACTTACTG
1 ATCAGGCTCGAAAGACTTACTG
* *
51689 AT-AGGC-CGAAAGA-TTTCATC
1 ATCAGGCTCGAAAGACTTAC-TG
*
51709 ATCATGCTCGAAAGACTTACTG
1 ATCAGGCTCGAAAGACTTACTG
51731 AT
1 AT
51733 GGGTTTGCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 6 0.18
22 12 0.35
23 3 0.09
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (22 bp):
ATCAGGCTCGAAAGACTTACTG
Found at i:51709 original size:122 final size:121
Alignment explanation
Indices: 51534--51855 Score: 477
Period size: 122 Copynumber: 2.6 Consensus size: 121
51524 AAATGGCTCA
* * *** *
51534 AAGGACTT-ATCATCTTGCTCGAAAGACTTAAAAATGACCCAAAGGATTTCATCATCATGCTCGA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAA-GATTTCATCATCATGCTCGA
*
51598 AAGACTTACTGATGGATTTGCTTCACTACTCTT-TGGTGAAGGCTTACCAATTACCCG
65 AAGACTTACTGATGGATTTGCTTCACTACTCTTCT-GTGAAGGCTTACAAATTACCCG
*
51655 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATAGGCCGAAAGATTTCATCATCATGCTCGA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGAT-GGCCCAAAGATTTCATCATCATGCTCGA
*
51720 AAGACTTACTGATGGGTTTGCTTCACTACTCTTCTGTGAAGGCTTACAAATTACCCG
65 AAGACTTACTGATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTACAAATTACCCG
* * *
51777 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTAAGCATCATGCTCGA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC-AAAGATTTCATCATCATGCTCGA
*
51842 AAGACTTATTGATG
65 AAGACTTACTGATG
51856 ACCCGAAAGA
Statistics
Matches: 183, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
121 11 0.06
122 165 0.90
123 7 0.04
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (121 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGATTTCATCATCATGCTCGAA
AGACTTACTGATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTACAAATTACCCG
Found at i:51723 original size:22 final size:21
Alignment explanation
Indices: 51653--51723 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
51643 ACCAATTACC
*
51653 CGAAGGATTTAATCATCATGCT
1 CGAAAGATTT-ATCATCATGCT
* * *
51675 CGAAAGACTTACTGAT-AGGC-
1 CGAAAGATTTA-TCATCATGCT
51695 CGAAAGATTTCATCATCATGCT
1 CGAAAGATTT-ATCATCATGCT
51717 CGAAAGA
1 CGAAAGA
51724 CTTACTGATG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 12 0.32
21 8 0.21
22 18 0.47
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
CGAAAGATTTATCATCATGCT
Found at i:56323 original size:13 final size:13
Alignment explanation
Indices: 56295--56334 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
56285 AAATACATGC
56295 AATGCAAATG-AA
1 AATGCAAATGCAA
*
56307 AATGAAAATGCAA
1 AATGCAAATGCAA
*
56320 AATGCAAATACAA
1 AATGCAAATGCAA
56333 AA
1 AA
56335 GGTGTCATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.15
Consensus pattern (13 bp):
AATGCAAATGCAA
Found at i:62192 original size:3 final size:3
Alignment explanation
Indices: 62173--62267 Score: 68
Period size: 3 Copynumber: 32.0 Consensus size: 3
62163 CAATAAAAAC
* * * * *
62173 ATA ATCA ATA TTA ATA ATA ATA CTA ATA ATA ATT ATA ATT ATA ATT
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
62219 GTT ATA ATA ATA ATA GTT ATA AT- ATA ATA TTA ATA ATT ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
62265 ATA
1 ATA
62268 TTTATAACCC
Statistics
Matches: 69, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.90
4 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:62246 original size:20 final size:20
Alignment explanation
Indices: 62179--62267 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
62169 AAACATAATC
* *
62179 AATATTAATAATAATACTAAT
1 AATA-TAATAATAATAATTAT
* * *
62200 AATAATTATAATTATAATTGT
1 AAT-ATAATAATAATAATTAT
*
62221 --TATAATAATAATAGTTAT
1 AATATAATAATAATAATTAT
*
62239 AATATAATATTAATAATTAT
1 AATATAATAATAATAATTAT
62259 AATATAATA
1 AATATAATA
62268 TTTATAACCC
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
18 13 0.24
19 1 0.02
20 25 0.46
21 14 0.26
22 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (20 bp):
AATATAATAATAATAATTAT
Found at i:66728 original size:8 final size:10
Alignment explanation
Indices: 66697--66723 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
66687 TGTTATAAAC
66697 ATAAGTATAT
1 ATAAGTATAT
66707 ATAAGTATAT
1 ATAAGTATAT
66717 ATAAGTA
1 ATAAGTA
66724 AATAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (10 bp):
ATAAGTATAT
Found at i:67597 original size:32 final size:34
Alignment explanation
Indices: 67556--67633 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
67546 TTTAAATAGT
*
67556 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
*
67588 TATTATTTTTT-TATTAAATAATATTTATATAAT
1 TATTATTTTTTATATTAAATAATATTTATATAAA
67621 TATTATTTATTTA
1 TATTATTT-TTTA
67634 GAATTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 4 0.10
32 14 0.35
33 19 0.47
34 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:67607 original size:18 final size:19
Alignment explanation
Indices: 67578--67613 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
67568 TATTAATATA
*
67578 TTTATGTAAATATTATTTT
1 TTTATGTAAATAATATTTT
67597 TTTAT-TAAATAATATTT
1 TTTATGTAAATAATATTT
67614 ATATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTATGTAAATAATATTTT
Found at i:67793 original size:17 final size:17
Alignment explanation
Indices: 67771--67824 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
67761 AATGTTAATA
67771 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
67788 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
67805 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
67822 TTT
1 TTT
67825 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:82343 original size:7 final size:7
Alignment explanation
Indices: 82331--82392 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
82321 TATGTGATAA
82331 GGTTTAG
1 GGTTTAG
82338 GGTTTAG
1 GGTTTAG
*
82345 AGTTTAG
1 GGTTTAG
* *
82352 GTTTTAT
1 GGTTTAG
*
82359 AGTTTAG
1 GGTTTAG
*
82366 AGTTTAG
1 GGTTTAG
* *
82373 GATTTAA
1 GGTTTAG
82380 GGTTTAG
1 GGTTTAG
*
82387 AGTTTA
1 GGTTTA
82393 TGTGATATGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (7 bp):
GGTTTAG
Found at i:82363 original size:21 final size:21
Alignment explanation
Indices: 82333--82392 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
82323 TGTGATAAGG
* *
82333 TTTAGGGTTTAGAGTTTAGGT
1 TTTAAGGTTTAGAGTTTAGGA
82354 TTTATA-GTTTAGAGTTTAGGA
1 TTTA-AGGTTTAGAGTTTAGGA
82375 TTTAAGGTTTAGAGTTTA
1 TTTAAGGTTTAGAGTTTA
82393 TGTGATATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (21 bp):
TTTAAGGTTTAGAGTTTAGGA
Found at i:82404 original size:28 final size:28
Alignment explanation
Indices: 82373--82452 Score: 133
Period size: 28 Copynumber: 2.9 Consensus size: 28
82363 TAGAGTTTAG
82373 GATTTAAGGTTTAGAGTTTATGTGATAT
1 GATTTAAGGTTTAGAGTTTATGTGATAT
*
82401 GATTTAAGATTTAGAGTTTATGTGATAT
1 GATTTAAGGTTTAGAGTTTATGTGATAT
* *
82429 GATTTAGGGTTTAGGGTTTATGTG
1 GATTTAAGGTTTAGAGTTTATGTG
82453 TTAAGAGTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (28 bp):
GATTTAAGGTTTAGAGTTTATGTGATAT
Found at i:82441 original size:7 final size:7
Alignment explanation
Indices: 82431--82483 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
82421 TGTGATATGA
82431 TTTAGGG
1 TTTAGGG
82438 TTTAGGG
1 TTTAGGG
*
82445 TTTATGTG
1 TTTA-GGG
* *
82453 TTAAGAG
1 TTTAGGG
*
82460 -TTAGAG
1 TTTAGGG
82466 TTTAGGG
1 TTTAGGG
82473 TTTAGGG
1 TTTAGGG
82480 TTTA
1 TTTA
82484 AGTTACGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 5 0.13
7 29 0.74
8 5 0.13
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:82463 original size:28 final size:28
Alignment explanation
Indices: 82373--82476 Score: 127
Period size: 28 Copynumber: 3.7 Consensus size: 28
82363 TAGAGTTTAG
*
82373 GATTTAAGGTTTAGAGTTTATGTGATAT
1 GATTTAGGGTTTAGAGTTTATGTGATAT
* *
82401 GATTTAAGATTTAGAGTTTATGTGATAT
1 GATTTAGGGTTTAGAGTTTATGTGATAT
* * *
82429 GATTTAGGGTTTAGGGTTTATGTGTTAA
1 GATTTAGGGTTTAGAGTTTATGTGATAT
* * *
82457 GAGTTAGAGTTTAGGGTTTA
1 GATTTAGGGTTTAGAGTTTA
82477 GGGTTTAAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (28 bp):
GATTTAGGGTTTAGAGTTTATGTGATAT
Found at i:85664 original size:11 final size:11
Alignment explanation
Indices: 85618--85691 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
85608 GAGTTTGAGT
*
85618 TCGAGCTTGAA
1 TCGAGCTTCAA
* *
85629 TCAAGCTTGAA
1 TCGAGCTTCAA
85640 TCGAGC-TCAAAA
1 TCGAGCTTC--AA
85652 TCGAGCTTCAA
1 TCGAGCTTCAA
* *
85663 TCGAGCTTGAG
1 TCGAGCTTCAA
85674 TCTTGAGCTTCAA
1 TC--GAGCTTCAA
85687 TCGAG
1 TCGAG
85692 GTCTTGAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
10 1 0.02
11 31 0.61
12 8 0.16
13 11 0.22
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:97119 original size:7 final size:7
Alignment explanation
Indices: 97107--97133 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
97097 TTTGAGAGTT
97107 GGGAGAC
1 GGGAGAC
97114 GGGAGAC
1 GGGAGAC
97121 GGGAGAC
1 GGGAGAC
97128 GGGAGA
1 GGGAGA
97134 TGAGAGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.59, T:0.00
Consensus pattern (7 bp):
GGGAGAC
Found at i:98679 original size:29 final size:29
Alignment explanation
Indices: 98626--98682 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
98616 TCAAAGCATT
*
98626 TATTTAAAAAATAATAAAAATAAAATTTC
1 TATTTAAAAAATAATAAAAAAAAAATTTC
98655 TATTT-AAAAAT-ATCAAAATAAAAAATTT
1 TATTTAAAAAATAAT-AAAA-AAAAAATTT
98683 AATGACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 2 0.08
28 10 0.40
29 13 0.52
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (29 bp):
TATTTAAAAAATAATAAAAAAAAAATTTC
Found at i:99096 original size:118 final size:118
Alignment explanation
Indices: 98888--99632 Score: 1332
Period size: 118 Copynumber: 6.3 Consensus size: 118
98878 GTATCGTACA
* * * *
98888 AAACAAACGCCATTGATAATTAAGAAAGAAGATTATTATCAATAAAGATTTTGAATTCGACTACC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
*
98953 ACCATTTTCCTCTAAACCAAACATAAATATCTTCTGTAAATCAAATACACTTT
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
99006 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
* *
99071 ACCACTTTCCTCTAAACCAAACATAAAAATATTCTGTAAATCAAATACACTTT
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
*
99124 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCATC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
*
99189 ACCATTTTCTTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
99242 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
99307 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
*
99360 AAACAAGCGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGA-C-CC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
*
99423 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTT
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
* *
99476 AAACAAACGACATTGATAAATAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCCCC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
* **
99541 ACCACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTT
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
99594 AAACAAACGACATTGATAATTAAGAAAGATGATTATTAT
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTAT
99633 TCGACCACCA
Statistics
Matches: 605, Mismatches: 20, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
116 112 0.19
117 2 0.00
118 491 0.81
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (118 bp):
AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
Found at i:99301 original size:236 final size:236
Alignment explanation
Indices: 98888--99814 Score: 1559
Period size: 236 Copynumber: 4.0 Consensus size: 236
98878 GTATCGTACA
* * * *
98888 AAACAAACGCCATTGATAATTAAGAAAGAAGATTATTATCAATAAAGATTTTGAATTCGACTACC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
*
98953 ACCATTTTCCTCTAAACCAAACATAAATATCTTCTGTAAATCAAATACACTTTAAACAAACGACA
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTAAACAAACGACA
99018 TTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACCACTTTCCTC
131 TTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACCACTTTCCTC
* *
99083 TAAACCAAACATAAAAATATTCTGTAAATCAAATACACTTT
196 TAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTT
*
99124 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCATC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
*
99189 ACCATTTTCTTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTAAACAAACGACA
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTAAACAAACGACA
*
99254 TTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACCATTTTCCTC
131 TTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACCACTTTCCTC
*
99319 TAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTT
196 TAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTT
*
99360 AAACAAGCGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGA-C-CC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
*
99423 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTTAAACAAACGACA
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTAAACAAACGACA
* *
99488 TTGATAAATAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCCCCACCACTTTCCTC
131 TTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACCACTTTCCTC
*
99553 TAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTT
196 TAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTT
99594 AAACAAACGACATTGATAATTAAGAAAGATG------A--T-T----A--TT--ATTCGACCACC
1 AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
99642 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTAAACAAACGACA
66 ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTAAACAAACGACA
* *
99707 TTGATAATTAAAAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACCATTTTCCTC
131 TTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACCACTTTCCTC
99772 TAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTT
196 TAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTT
99813 AA
1 AA
99815 CAAGACCCTC
Statistics
Matches: 664, Mismatches: 25, Indels: 21
0.94 0.04 0.03
Matches are distributed among these distances:
217 6 0.01
218 1 0.00
219 171 0.26
221 1 0.00
225 1 0.00
226 1 0.00
228 1 0.00
234 195 0.29
235 1 0.00
236 286 0.43
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (236 bp):
AAACAAACGACATTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACC
ACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTAAACAAACGACA
TTGATAATTAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACCACTTTCCTC
TAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTT
Found at i:99705 original size:101 final size:101
Alignment explanation
Indices: 99530--99733 Score: 363
Period size: 101 Copynumber: 2.0 Consensus size: 101
99520 AAGATTTTGA
*
99530 ATTCGACCCCCACCACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTTA
1 ATTCGACCACCACCACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTTA
*
99595 AACAAACGACATTGATAATTAAGAAAGATGATTATT
66 AACAAACGACATTGATAATTAAAAAAGATGATTATT
* **
99631 ATTCGACCACCACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTA
1 ATTCGACCACCACCACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTTA
99696 AACAAACGACATTGATAATTAAAAAAGATGATTATT
66 AACAAACGACATTGATAATTAAAAAAGATGATTATT
99732 AT
1 AT
99734 CTATAAAGAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.28
Consensus pattern (101 bp):
ATTCGACCACCACCACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTTA
AACAAACGACATTGATAATTAAAAAAGATGATTATT
Found at i:99801 original size:219 final size:217
Alignment explanation
Indices: 99414--99814 Score: 730
Period size: 219 Copynumber: 1.8 Consensus size: 217
99404 AAGATTTTGA
99414 ATTCGACCCACCATTTTCCTCTAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTTAAA
1 ATTCGACCCACCATTTTCCTCTAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTTAAA
* *
99479 CAAACGACATTGATAAATAAGAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCCCCACC
66 CAAACGACATTGATAAATAAAAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACC
99544 ACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTTAAACAAACGACATTG
131 ACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTTAAACAAACGACATTG
99609 ATAATTAAGAAAGATGATTATT
196 ATAATTAAGAAAGATGATTATT
*
99631 ATTCGACCACCACCATTTTCCTCTAAACCAAACATAAAAATCTTCTGTAAATCAAATACACTTTA
1 ATTCGA-C-CCACCATTTTCCTCTAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTTA
*
99696 AACAAACGACATTGATAATTAAAAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCA
64 AACAAACGACATTGATAAATAAAAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCA
* *
99761 CCATTTTCCTCTAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTTAA
129 CCACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTTAA
99815 CAAGACCCTC
Statistics
Matches: 176, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
217 6 0.03
218 1 0.01
219 169 0.96
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (217 bp):
ATTCGACCCACCATTTTCCTCTAAACCAAACATAAAAATCTTCTATAAATCAAATACACTTTAAA
CAAACGACATTGATAAATAAAAAAGATGATTATTATCTATAAAGATTTTGAATTCGACCACCACC
ACTTTCCTCTAAACCAAACATAAAAATCTTCAATAAATCAAATACACTTTAAACAAACGACATTG
ATAATTAAGAAAGATGATTATT
Found at i:116156 original size:21 final size:21
Alignment explanation
Indices: 116130--116169 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
116120 AATCTATAAA
116130 CAAATCACAATATTAAAATGT
1 CAAATCACAATATTAAAATGT
* *
116151 CAAATCTCAATATTCAAAT
1 CAAATCACAATATTAAAAT
116170 TACAATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (21 bp):
CAAATCACAATATTAAAATGT
Found at i:116263 original size:75 final size:75
Alignment explanation
Indices: 116076--116268 Score: 188
Period size: 75 Copynumber: 2.6 Consensus size: 75
116066 TAAATAAAGT
* * * ** * *
116076 CAAATATCAAGACTCGAATCACTGTATTAAGTTTAGAACAATAAAATCTATAAACAAATCACAAT
1 CAAATCTCAAGACTCAAAGCACAATATTAAGTATAGAAAAATAAAATCTATAAACAAATCACAAT
*
116141 ATTAAAATGT
66 ATTAAAATGA
* * ** * * * * * *
116151 CAAATCTCAATATTCAAATTACAATATCAATTCTAGAATAATAAAATCTATAATCAAATCATAAT
1 CAAATCTCAAGACTCAAAGCACAATATTAAGTATAGAAAAATAAAATCTATAAACAAATCACAAT
*
116216 ATTAAAGTGA
66 ATTAAAATGA
* * *
116226 CAAATCTTAAGACTGAAAGCATAATATTAAGTATAGAAAAATA
1 CAAATCTCAAGACTCAAAGCACAATATTAAGTATAGAAAAATA
116269 TTAAACAACA
Statistics
Matches: 92, Mismatches: 26, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
75 92 1.00
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (75 bp):
CAAATCTCAAGACTCAAAGCACAATATTAAGTATAGAAAAATAAAATCTATAAACAAATCACAAT
ATTAAAATGA
Found at i:118582 original size:18 final size:20
Alignment explanation
Indices: 118549--118586 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
118539 AACATGGAAA
118549 TTTTCGCAACGCGAATTTCG
1 TTTTCGCAACGCGAATTTCG
118569 TTTTCGC-A-GCGAATTTCG
1 TTTTCGCAACGCGAATTTCG
118587 CAACATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (20 bp):
TTTTCGCAACGCGAATTTCG
Found at i:118646 original size:20 final size:20
Alignment explanation
Indices: 118621--118674 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
118611 AACACAACTA
118621 TCGCAACGCGAATTTCGTTC
1 TCGCAACGCGAATTTCGTTC
* *
118641 TCGCAATGCGAATTTCGTTT
1 TCGCAACGCGAATTTCGTTC
* *
118661 TTGCAACGCTAATT
1 TCGCAACGCGAATT
118675 ACCGATATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (20 bp):
TCGCAACGCGAATTTCGTTC
Found at i:118683 original size:77 final size:71
Alignment explanation
Indices: 118552--118800 Score: 309
Period size: 77 Copynumber: 3.5 Consensus size: 71
118542 ATGGAAATTT
*
118552 TCGCAACGCGAATTTCGTTTTCGC-A-GCGAATTTC-GCAACATTAATTACCGATATAGGTAAAC
1 TCGCAACGCGAATTTCG-TTTCGCAATGCGAATTTCGGCAACACTAATTACCGATATAGGTAAAC
118614 ACAACTA
65 ACAACTA
*
118621 TCGCAACGCGAATTTCGTTCTCGCAATGCGAATTTCGTTTTTGCAACGCTAATTACCGATATAGG
1 TCGCAACGCGAATTTCGTT-TCGCAATGCGAATTTCG-----GCAACACTAATTACCGATATAGG
118686 TAAACACAACTA
60 TAAACACAACTA
* * *
118698 TCGCAACGCGAATTTCATTT-TC---GCGAATTTC-GCAACACTAATTACTGATATAGGTAAACA
1 TCGCAACGCGAATTTCGTTTCGCAATGCGAATTTCGGCAACACTAATTACCGATATAGGTAAACA
118758 CAACTA
66 CAACTA
118764 TCGCAACGCGAATTTCGTTTTCGCAACT-CGAATTTCG
1 TCGCAACGCGAATTTCG-TTTCGCAA-TGCGAATTTCG
118801 CAAATCGAAT
Statistics
Matches: 156, Mismatches: 8, Indels: 29
0.81 0.04 0.15
Matches are distributed among these distances:
66 49 0.31
67 3 0.02
68 3 0.02
69 21 0.13
70 1 0.01
71 17 0.11
72 9 0.06
75 1 0.01
76 1 0.01
77 51 0.33
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (71 bp):
TCGCAACGCGAATTTCGTTTCGCAATGCGAATTTCGGCAACACTAATTACCGATATAGGTAAACA
CAACTA
Found at i:118769 original size:66 final size:66
Alignment explanation
Indices: 118663--118787 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 66
118653 TTTCGTTTTT
*
118663 GCAACGCTAATTACCGATATAGGTAAACACAACTATCGCAACGCGAATTTCATTTTCGCGAATTT
1 GCAACACTAATTACCGATATAGGTAAACACAACTATCGCAACGCGAATTTCATTTTCGCGAATTT
118728 C
66 C
* *
118729 GCAACACTAATTACTGATATAGGTAAACACAACTATCGCAACGCGAATTTCGTTTTCGC
1 GCAACACTAATTACCGATATAGGTAAACACAACTATCGCAACGCGAATTTCATTTTCGC
118788 AACTCGAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (66 bp):
GCAACACTAATTACCGATATAGGTAAACACAACTATCGCAACGCGAATTTCATTTTCGCGAATTT
C
Found at i:118801 original size:14 final size:14
Alignment explanation
Indices: 118782--118811 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
118772 CGAATTTCGT
*
118782 TTTCGCAACTCGAA
1 TTTCGCAAATCGAA
118796 TTTCGCAAATCGAA
1 TTTCGCAAATCGAA
118810 TT
1 TT
118812 CGCCAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (14 bp):
TTTCGCAAATCGAA
Found at i:120387 original size:41 final size:41
Alignment explanation
Indices: 120321--120402 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
120311 ACCAACGGTG
* * * *
120321 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
1 CTGAACATTGATACACAAATATACCAAAGATGAAATGATAA
120362 CTGAACATTGATACACAAATATACCAAAGATGAAATGATAA
1 CTGAACATTGATACACAAATATACCAAAGATGAAATGATAA
120403 GTATTCACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (41 bp):
CTGAACATTGATACACAAATATACCAAAGATGAAATGATAA
Found at i:120548 original size:18 final size:18
Alignment explanation
Indices: 120520--120572 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
120510 TTTTGTAATT
*
120520 ATATGATAACTGTAAATC
1 ATATAATAACTGTAAATC
* *
120538 ATCTAATAACTGAAAATC
1 ATATAATAACTGTAAATC
*
120556 ATATGATAACTGTAAAT
1 ATATAATAACTGTAAAT
120573 ATTTAGAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.32
Consensus pattern (18 bp):
ATATAATAACTGTAAATC
Found at i:123426 original size:29 final size:30
Alignment explanation
Indices: 123338--123426 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
123328 TAAAATCTAT
* * * *
123338 AACTTTTAAAAATTACATTTTTGGTCCCTA
1 AACTTTCAAAAATTTCATTTTTAGTCACTA
*
123368 AACTTTTC-AAACTTT-ATTCTTTAG-CTACTA
1 AAC-TTTCAAAAATTTCATT-TTTAGTC-ACTA
123398 AACTTTCAAAAATTTCA-TTTTAGTCACTA
1 AACTTTCAAAAATTTCATTTTTAGTCACTA
123427 GTCAAAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
29 17 0.36
30 26 0.55
31 4 0.09
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.44
Consensus pattern (30 bp):
AACTTTCAAAAATTTCATTTTTAGTCACTA
Found at i:127242 original size:30 final size:31
Alignment explanation
Indices: 127199--127267 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
127189 AAAAGCCTTA
* * * * *
127199 GAAAAATTTGGGGACC-ATTCTATAATTTTT
1 GAAAAGTTAGGGGACCAATTCAACAATTTTG
127229 GAAAAGTTAGGGGACCAATTCAACAATTTTG
1 GAAAAGTTAGGGGACCAATTCAACAATTTTG
127260 GAAAAGTT
1 GAAAAGTT
127268 GTGAATGGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (31 bp):
GAAAAGTTAGGGGACCAATTCAACAATTTTG
Found at i:128109 original size:21 final size:21
Alignment explanation
Indices: 128085--128165 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
128075 GATATTGTAA
*
128085 TAGTACTTTGTGTACTTGGAG
1 TAGTACTTTGTGTACTTGAAG
**
128106 TAGTACTTTACGTACTATCGTAAG
1 TAGTACTTTGTGTACT-T-G-AAG
128130 -AGTACTTTGTGTACTT-ATAG
1 TAGTACTTTGTGTACTTGA-AG
*
128150 TAATACTTTGTGTACT
1 TAGTACTTTGTGTACT
128166 ATGGCACTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 28 0.57
22 2 0.04
23 14 0.29
24 2 0.04
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (21 bp):
TAGTACTTTGTGTACTTGAAG
Found at i:128157 original size:44 final size:44
Alignment explanation
Indices: 128081--128167 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
128071 TTATGATATT
* * *
128081 GTAATAGTACTTTGTGTACTTGGAGTAGTACTTTACGTACTATC
1 GTAAGAGTACTTTGTGTACTTAGAGTAATACTTTACGTACTATC
* **
128125 GTAAGAGTACTTTGTGTACTTATAGTAATACTTTGTGTACTAT
1 GTAAGAGTACTTTGTGTACTTAGAGTAATACTTTACGTACTAT
128168 GGCACTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (44 bp):
GTAAGAGTACTTTGTGTACTTAGAGTAATACTTTACGTACTATC
Found at i:128588 original size:33 final size:33
Alignment explanation
Indices: 128546--128614 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
128536 TATTGTTTAA
* *
128546 CAGGTTATTTGATGAAAATTTGACTTATCAAGT
1 CAGGTTATTTAATGAAAACTTGACTTATCAAGT
128579 CAGGTTATTTAATGAAAACTTGACTTATCAAGT
1 CAGGTTATTTAATGAAAACTTGACTTATCAAGT
128612 CAG
1 CAG
128615 AGCAAGTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
CAGGTTATTTAATGAAAACTTGACTTATCAAGT
Found at i:136183 original size:21 final size:21
Alignment explanation
Indices: 136159--136219 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
136149 AACTTTGAAA
136159 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
136180 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
136194 AAATGATTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
136215 AAATG
1 AAATG
136220 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:136197 original size:35 final size:36
Alignment explanation
Indices: 136124--136268 Score: 174
Period size: 35 Copynumber: 4.1 Consensus size: 36
136114 TGAAATTATT
* **
136124 AAAATGGTTTTC-AAGTTTGGT-AA-CTAACTTTGAA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-A
136158 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
*
136193 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
* * *
136229 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
136265 AAAA
1 AAAA
136269 ATGATAATGA
Statistics
Matches: 99, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
34 12 0.12
35 43 0.43
36 15 0.15
37 29 0.29
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.42
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
Found at i:140809 original size:21 final size:21
Alignment explanation
Indices: 140785--140845 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
140775 AACTTTGAAA
140785 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
140806 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
140820 AAATGATTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
140841 AAATG
1 AAATG
140846 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:140876 original size:37 final size:37
Alignment explanation
Indices: 140777--140895 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 37
140767 TGGTAACCAA
*
140777 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GATTTTCAAAGTTTGGTAAATGTTT
140814 CTTTG-AAAAT-GATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
* *
140849 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
*
140886 -GTTGAAAAAT
1 CTTTGAAAAAT
140896 GATAATGGGA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
35 29 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
Found at i:144884 original size:3 final size:3
Alignment explanation
Indices: 144876--144936 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
144866 ATATAATTTA
* *
144876 TAT TAT TA- TAT TAT TATT TAT TAT ATAT TAT ATAT TTT TAT TAT TAA
1 TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT -TAT TAT TAT TAT TAT
144923 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
144937 CAAACAGACC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 39 0.78
4 9 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:144896 original size:20 final size:19
Alignment explanation
Indices: 144871--144932 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
144861 TATTTATATA
144871 ATTTATATTATTATATTATT
1 ATTT-TATTATTATATTATT
144891 A-TTTATTA-TATATTATAT
1 ATTTTATTATTATATTAT-T
144909 ATTTTTATTATTAATATTATT
1 A-TTTTATTATT-ATATTATT
144930 ATT
1 ATT
144933 ATTACAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 8 0.22
18 7 0.19
19 2 0.05
20 10 0.27
21 3 0.08
22 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTATTATTATATTATT
Found at i:144920 original size:9 final size:9
Alignment explanation
Indices: 144860--144929 Score: 64
Period size: 9 Copynumber: 8.6 Consensus size: 9
144850 TGTCCCGGTT
144860 TTATTTATA
1 TTATTTATA
*
144869 TAATTTATA
1 TTATTTATA
144878 TTA-TTATA
1 TTATTTATA
144886 TTA-TTAT-
1 TTATTTATA
144893 TTA-TTATA
1 TTATTTATA
144901 -TA-TTATA
1 TTATTTATA
*
144908 -TATTTTTA
1 TTATTTATA
*
144916 TTATTAATA
1 TTATTTATA
144925 TTATT
1 TTATT
144930 ATTATTACAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
7 16 0.30
8 16 0.30
9 21 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTATTTATA
Found at i:144930 original size:9 final size:8
Alignment explanation
Indices: 144873--144936 Score: 71
Period size: 8 Copynumber: 8.0 Consensus size: 8
144863 TTTATATAAT
144873 TTATATTA
1 TTATATTA
144881 TTATATTA
1 TTATATTA
144889 TTAT-TTA
1 TTATATTA
144896 TTATA-TA
1 TTATATTA
144903 TTATA-TA
1 TTATATTA
*
144910 TTTTTATTA
1 -TTATATTA
144919 TTAATATTA
1 TT-ATATTA
144928 TTATTATTA
1 TTA-TATTA
144937 CAAACAGACC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
7 16 0.33
8 19 0.39
9 14 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATATTA
Found at i:146343 original size:31 final size:31
Alignment explanation
Indices: 146308--146382 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 31
146298 TTATTATAGT
* *
146308 TATTATTTA-AACTTTATATATATATTTAAAA
1 TATTATTTATAA-TATATATATATATATAAAA
146339 TATTATTATTATAATATATATATATATATAAAA
1 TATTA-T-TTATAATATATATATATATATAAAA
146372 TATTTATTTAT
1 TA-TTATTTAT
146383 TTATTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 5 0.13
32 5 0.13
33 23 0.61
34 5 0.13
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
TATTATTTATAATATATATATATATATAAAA
Found at i:147149 original size:28 final size:28
Alignment explanation
Indices: 147129--147185 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
147119 TTTCGAAATT
*
147129 TATATATATATTTATTATTTTCATAATA
1 TATATATATATATATTATTTTCATAATA
147157 TATATATATATATATTATTTT-ATTAATA
1 TATATATATATATATTATTTTCA-TAATA
147185 T
1 T
147186 TTCATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATATATATATATTATTTTCATAATA
Found at i:151800 original size:2 final size:2
Alignment explanation
Indices: 151793--151834 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
151783 TTAACCTTTA
151793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
151835 CATTTGTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152134 original size:1 final size:1
Alignment explanation
Indices: 152130--152278 Score: 136
Period size: 1 Copynumber: 149.0 Consensus size: 1
152120 GGAAAAAAGG
* * * * * * *
152130 AAAAAAAAGAAAAAAAAGAAAAGAAAAAAAAAAAAGAAAAAAGAAAAAAAAAAAGAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
152195 AAGAAAAAAGAAAAAAGAAAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
152260 AAAGAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAA
152279 TTGAATCAAG
Statistics
Matches: 112, Mismatches: 36, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 112 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:152169 original size:44 final size:44
Alignment explanation
Indices: 152114--152277 Score: 227
Period size: 44 Copynumber: 3.8 Consensus size: 44
152104 TATACTCATA
152114 AAAAAAGGAAAAAAGGAAAAAAAAGAAAAAAAAGAAAAGAAAAAA-
1 AAAAAA-GAAAAAA-GAAAAAAAAGAAAAAAAAGAAAAGAAAAAAG
*
152159 AAAAAAGAAAAAAG---AAAAA-AAAAAAGA-AAAAGAAAAAAG
1 AAAAAAGAAAAAAGAAAAAAAAGAAAAAAAAGAAAAGAAAAAAG
152198 AAAAAAGAAAAAAGAAAAAAAAGAAAAAAGAA-AAAAGAAAAAAG
1 AAAAAAGAAAAAAGAAAAAAAAGAAAAAA-AAGAAAAGAAAAAAG
152242 AAAAAAGAAAAAAG-AAAAAAAGAAAAAAAAAGAAAA
1 AAAAAAGAAAAAAGAAAAAAAAG-AAAAAAAAGAAAA
152278 ATTGAATCAA
Statistics
Matches: 109, Mismatches: 2, Indels: 17
0.85 0.02 0.13
Matches are distributed among these distances:
38 11 0.10
39 21 0.19
40 5 0.05
42 5 0.05
43 17 0.16
44 44 0.40
45 6 0.06
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (44 bp):
AAAAAAGAAAAAAGAAAAAAAAGAAAAAAAAGAAAAGAAAAAAG
Found at i:152180 original size:37 final size:36
Alignment explanation
Indices: 152122--152272 Score: 207
Period size: 37 Copynumber: 4.1 Consensus size: 36
152112 TAAAAAAAGG
* *
152122 AAAAAAGGAAAAAA-AAGAAAAAAAAGAAAAGAAAAA
1 AAAAAAAGAAAAAAGAA-AAAAAAAAAAAAAGAAAAA
152158 AAAAAAAGAAAAAAGAAAAAAAAAAAGAAAAAGAAAAA
1 AAAAAAAGAAAAAAG-AAAAAAAAAA-AAAAAGAAAAA
*
152196 AGAAAAAAGAAAAAAGAAAAAAAAGAAAAAAGAAAAA
1 A-AAAAAAGAAAAAAGAAAAAAAAAAAAAAAGAAAAA
*
152233 AGAAAAAAGAAAAAAG-AAAAAAGAAAAAAAGAAAAA
1 A-AAAAAAGAAAAAAGAAAAAAAAAAAAAAAGAAAAA
152269 AAAA
1 AAAA
152273 GAAAAATTGA
Statistics
Matches: 106, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
35 3 0.03
36 32 0.30
37 35 0.33
38 22 0.21
39 14 0.13
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (36 bp):
AAAAAAAGAAAAAAGAAAAAAAAAAAAAAAGAAAAA
Found at i:152278 original size:7 final size:7
Alignment explanation
Indices: 152132--152269 Score: 205
Period size: 7 Copynumber: 19.9 Consensus size: 7
152122 AAAAAAGGAA
152132 AAAAAAG
1 AAAAAAG
152139 AAAAAA-
1 AAAAAAG
152145 AAGAAAAG
1 AA-AAAAG
152153 AAAAAA-
1 AAAAAAG
152159 AAAAAAG
1 AAAAAAG
152166 AAAAAAG
1 AAAAAAG
152173 -AAAAA-
1 AAAAAAG
152178 AAAAAAG
1 AAAAAAG
152185 -AAAAAG
1 AAAAAAG
152191 AAAAAAG
1 AAAAAAG
152198 AAAAAAG
1 AAAAAAG
152205 AAAAAAG
1 AAAAAAG
152212 AAAAAAAAG
1 --AAAAAAG
152221 AAAAAAG
1 AAAAAAG
152228 AAAAAAG
1 AAAAAAG
152235 AAAAAAG
1 AAAAAAG
152242 AAAAAAG
1 AAAAAAG
152249 AAAAAAG
1 AAAAAAG
152256 AAAAAAAG
1 -AAAAAAG
152264 AAAAAA
1 AAAAAA
152270 AAAGAAAAAT
Statistics
Matches: 122, Mismatches: 0, Indels: 18
0.87 0.00 0.13
Matches are distributed among these distances:
6 24 0.20
7 82 0.67
8 9 0.07
9 7 0.06
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:156803 original size:54 final size:54
Alignment explanation
Indices: 156721--156878 Score: 193
Period size: 54 Copynumber: 3.0 Consensus size: 54
156711 TGATTGAGAA
* *
156721 ATCTGAGTAGAAGCCAGAGAAAAGGATGAATGTGTTGTCAAAT-TCTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGT-TTTACGAAC
*
156775 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTT----AC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
156825 ATCTGAGCAGAAACCACATG-AGATGATGCATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
156879 CAGTTATTCT
Statistics
Matches: 90, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
50 43 0.48
51 1 0.01
54 45 0.50
55 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:156858 original size:50 final size:50
Alignment explanation
Indices: 156721--156874 Score: 168
Period size: 50 Copynumber: 3.0 Consensus size: 50
156711 TGATTGAGAA
* * *
156721 ATCTGAGTAGAAGCCAGAGAAAAGGATGAATGTGTTGTCAAAT-TCTTTACGAAC
1 ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGT-TTT----AC
* *
156775 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
1 ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * *
156825 ATCTGAGCAGAAACCACATG-AGATGATGCATGTGTTGTCAAATGTTTTAC
1 ATCTGAGCAGAAACCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTAC
156875 GAACCAGTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
50 45 0.50
51 1 0.01
54 43 0.48
55 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (50 bp):
ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:157286 original size:44 final size:44
Alignment explanation
Indices: 157231--157329 Score: 171
Period size: 44 Copynumber: 2.2 Consensus size: 44
157221 ATCTACATTC
*
157231 TTCAAAGATGATAGATTCTATCTTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTATCTTCAAAGATGAAAGATTCTCTT
* *
157275 TTTAAAGATGATAGATTCTATTTTCAAAGATGAAAGATTCTCTT
1 TTCAAAGATGATAGATTCTATCTTCAAAGATGAAAGATTCTCTT
157319 TTCAAAGATGA
1 TTCAAAGATGA
157330 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (44 bp):
TTCAAAGATGATAGATTCTATCTTCAAAGATGAAAGATTCTCTT
Found at i:157332 original size:22 final size:22
Alignment explanation
Indices: 157231--157329 Score: 153
Period size: 22 Copynumber: 4.5 Consensus size: 22
157221 ATCTACATTC
*
157231 TTCAAAGATGATAGATTCTATC
1 TTCAAAGATGATAGATTCTATT
*
157253 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTATT
*
157275 TTTAAAGATGATAGATTCTATT
1 TTCAAAGATGATAGATTCTATT
* *
157297 TTCAAAGATGAAAGATTCTCTT
1 TTCAAAGATGATAGATTCTATT
157319 TTCAAAGATGA
1 TTCAAAGATGA
157330 AAGCTTTATT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTATT
Found at i:158134 original size:76 final size:76
Alignment explanation
Indices: 158008--158239 Score: 421
Period size: 76 Copynumber: 3.1 Consensus size: 76
157998 CTATTTCTCA
158008 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
158073 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
158084 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
158149 AGCCTTAGGGT
66 AGCCTTAGGGT
158160 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
158225 AACCTTCA-GGT
66 AGCCTT-AGGGT
158236 CATC
1 CATC
158240 AGCATTTCCA
Statistics
Matches: 150, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
76 149 0.99
77 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:158384 original size:113 final size:113
Alignment explanation
Indices: 158252--158774 Score: 811
Period size: 113 Copynumber: 4.7 Consensus size: 113
158242 CATTTCCAGA
* *
158252 AGAGTTCATAATGGGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTAT
* *
158317 TTAACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGT
66 TCAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGGT
158365 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTAT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTAT
*
158430 TCAACCTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGT
66 TCAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGGT
* * *
158478 AGAGTTCATAATGACAATAACTCATCTGAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTTAT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTAT
* * *
158543 TCAACATTTCGCTTGAATTCATCATTCGATTGATCAACATTACCAGGT
66 TCAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGGT
* * *
158591 AGAGTCCATAATAAGAAGAACTCATCTGAAG-A-GAAGAAGAAGTTCATAATGAGAAGAATTTAT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTAT
* * * * *
158654 TCAACTTTTTGCTTGATTTCATCATTCGATGGATCAATATTGCCAGGA
66 TCAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGGT
* * *
158702 AGAGTTCATAATAAGAAGAACTCATCTGAAG-AGG-AGAAGAAGTTCATAATGAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTAT
*
158765 TCAGCCTTTT
66 TCAACCTTTT
158775 TCATGACTCT
Statistics
Matches: 382, Mismatches: 27, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
111 138 0.36
112 2 0.01
113 242 0.63
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTAT
TCAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGGT
Found at i:159114 original size:3 final size:3
Alignment explanation
Indices: 159106--159192 Score: 113
Period size: 3 Copynumber: 28.7 Consensus size: 3
159096 GTTTTATTTA
159106 TAT TAT TAT TAT TAT TA- TAT TAT TATT TAT TAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT TAT TAT
* * * *
159152 TAA AAT TAT TAT TAA TAT TAT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
159193 CAAACATGCC
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.03
3 65 0.89
4 6 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:160590 original size:28 final size:28
Alignment explanation
Indices: 160536--160590 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
160526 TTATTAGTTT
* *
160536 TTATTATTTTTACTTTCATTTATTATAG
1 TTATTATTTTAACTTTCATATATTATAG
160564 TTATTATTTTAACTTT-ATATATATATA
1 TTATTATTTTAACTTTCATATAT-TATA
160591 TTTAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (28 bp):
TTATTATTTTAACTTTCATATATTATAG
Found at i:160635 original size:28 final size:28
Alignment explanation
Indices: 160578--160631 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
160568 TATTTTAACT
* * *
160578 TTATATATATATATTTAAAATATTATTA
1 TTATAAATATATATTAAAAATAATATTA
160606 TTATAAATATATA-TAAAAATAATATT
1 TTATAAATATATATTAAAAATAATATT
160632 TATTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTATAAATATATATTAAAAATAATATTA
Found at i:164601 original size:37 final size:36
Alignment explanation
Indices: 164542--164661 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
164532 ATCCCATTAT
* *
164542 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
164577 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
164614 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
164649 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
164662 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 8 0.10
37 34 0.44
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:164617 original size:21 final size:20
Alignment explanation
Indices: 164590--164653 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
164580 TTTTTCAAAG
164590 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
164610 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
164625 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
164645 AAATCATTT
1 AAA-CATTT
164654 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:168749 original size:16 final size:16
Alignment explanation
Indices: 168725--168756 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
168715 TATCGCCGAT
*
168725 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
168741 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
168757 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:169227 original size:37 final size:36
Alignment explanation
Indices: 169162--169283 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
169152 TTATCCCATT
* *
169162 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTG-AAA
* *
169198 ATTATTTTTCAAAGAAATATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
169234 ACCA-TTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
169269 ATCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
169284 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 33 0.44
36 14 0.19
37 28 0.37
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:169240 original size:21 final size:20
Alignment explanation
Indices: 169216--169275 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
169206 TCAAAGAAAT
169216 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAA-C
*
169237 ATTT-TCAAA----G-AAAC
1 ATTTACCAAACTTTGAAAAC
169251 ATTTACCAAACTTTGAAAATC
1 ATTTACCAAACTTTGAAAA-C
169272 ATTT
1 ATTT
169276 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.33
Consensus pattern (20 bp):
ATTTACCAAACTTTGAAAAC
Found at i:172568 original size:20 final size:20
Alignment explanation
Indices: 172543--172580 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
172533 CTTGTGAAGG
172543 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
172563 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
172581 CCATATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:172622 original size:18 final size:18
Alignment explanation
Indices: 172599--172671 Score: 137
Period size: 18 Copynumber: 4.1 Consensus size: 18
172589 AATGCATTTT
172599 ATGCATCGATGCACTACC
1 ATGCATCGATGCACTACC
172617 ATGCATCGATGCACTACC
1 ATGCATCGATGCACTACC
172635 ATGCATCGATGCACTACC
1 ATGCATCGATGCACTACC
*
172653 ATGCATCGATGTACTACC
1 ATGCATCGATGCACTACC
172671 A
1 A
172672 GGTTTCATGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (18 bp):
ATGCATCGATGCACTACC
Found at i:172638 original size:10 final size:10
Alignment explanation
Indices: 172607--172657 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
172597 TTATGCATCG
172607 ATGCACTACC
1 ATGCACTACC
*
172617 ATGCA-T-CG
1 ATGCACTACC
172625 ATGCACTACC
1 ATGCACTACC
*
172635 ATGCA-T-CG
1 ATGCACTACC
172643 ATGCACTACC
1 ATGCACTACC
172653 ATGCA
1 ATGCA
172658 TCGATGTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
8 12 0.36
9 4 0.12
10 17 0.52
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (10 bp):
ATGCACTACC
Found at i:173890 original size:21 final size:21
Alignment explanation
Indices: 173864--173912 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
173854 TCAAATGCCA
173864 AGGAGATGTGGGTTAAGCTTG
1 AGGAGATGTGGGTTAAGCTTG
173885 AGGAGATGTGGGTTAAGCTTG
1 AGGAGATGTGGGTTAAGCTTG
173906 AGGAGAT
1 AGGAGAT
173913 CTATAGAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.04, G:0.43, T:0.27
Consensus pattern (21 bp):
AGGAGATGTGGGTTAAGCTTG
Found at i:178264 original size:45 final size:44
Alignment explanation
Indices: 178189--178282 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 44
178179 TTGTGCATAA
*
178189 TGCATCAATACACTATGAAAGTGCATCGATGCA-TCCCTTTGAATG
1 TGCATCAATACACTATGAAAGTGCACCGATGCACT-CC-TTGAATG
*
178234 TGCATCGATACA-TCATG-AAGATGCACCGATGCACTCCTTGAATG
1 TGCATCAATACACT-ATGAAAG-TGCACCGATGCACTCCTTGAATG
178278 TGCAT
1 TGCAT
178283 TGATGCACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
44 16 0.36
45 27 0.61
46 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
TGCATCAATACACTATGAAAGTGCACCGATGCACTCCTTGAATG
Found at i:178815 original size:13 final size:14
Alignment explanation
Indices: 178788--178816 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
178778 CTATATATAT
178788 TATTATTTCTCAAA
1 TATTATTTCTCAAA
178802 TATTATTT-TCAAA
1 TATTATTTCTCAAA
178815 TA
1 TA
178817 GTTTTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTATTTCTCAAA
Found at i:181340 original size:24 final size:23
Alignment explanation
Indices: 181293--181351 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
181283 TTGTGCATAA
181293 TGCATCGATACA--CTATGAAAG
1 TGCATCGATACATCCTATGAAAG
* *
181314 TGCATCGATACATCCCTTTGAATG
1 TGCATCGATACAT-CCTATGAAAG
181338 TGCATCGATACATC
1 TGCATCGATACATC
181352 ATTAAGATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.36
23 1 0.03
24 20 0.61
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (23 bp):
TGCATCGATACATCCTATGAAAG
Found at i:184215 original size:64 final size:63
Alignment explanation
Indices: 184080--184234 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 63
184070 CACTCACCAT
* * *
184080 ATCGAATGCATTTTATGCATCGATGCACGGTAGTGCATCGATGCACTCAGGTTTCATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACAGTAATGCATCGAGGCACTCAGGTTTCATGAAAAC
* *
184143 ATCTAATGCATTTTATGCATCGATGCACAG-ACCATGCATCGAGGCACTCAGGCTTGT-TTG-AA
1 ATCGAATGCATTTTATGCATCGATGCACAGTA--ATGCATCGAGGCACTCAGG-TT-TCATGAAA
*
184205 GC
62 AC
*
184207 ATCGAATGCATTTTATGCATTGATGCAC
1 ATCGAATGCATTTTATGCATCGATGCAC
184235 TCTTAGTGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 28 0.35
64 46 0.57
65 4 0.05
66 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACAGTAATGCATCGAGGCACTCAGGTTTCATGAAAAC
Found at i:188332 original size:15 final size:17
Alignment explanation
Indices: 188312--188346 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
188302 TAGTCCTCTT
188312 TTCTTCTTT-TTA-TTC
1 TTCTTCTTTGTTAGTTC
188327 TTCTTCTTTGTTAGTTC
1 TTCTTCTTTGTTAGTTC
188344 TTC
1 TTC
188347 ACAAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 3 0.17
17 6 0.33
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.69
Consensus pattern (17 bp):
TTCTTCTTTGTTAGTTC
Found at i:189758 original size:21 final size:22
Alignment explanation
Indices: 189734--189774 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
189724 ACATATGATG
189734 TAAAATAA-AATATTTACAACA
1 TAAAATAACAATATTTACAACA
*
189755 TAAAATAACATTATTTACAA
1 TAAAATAACAATATTTACAA
189775 TATATGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAACAATATTTACAACA
Found at i:190018 original size:26 final size:28
Alignment explanation
Indices: 189989--190043 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
189979 GAATACTAAA
*
189989 GGACCAAAATA-AAAAAT-GAATCTTAG
1 GGACCAAAATACAAAAATAGAAGCTTAG
*
190015 GGACTAAAATAGCAAAAATAGAAGCTTAG
1 GGACCAAAATA-CAAAAATAGAAGCTTAG
190044 AGGAATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
28 6 0.25
29 8 0.33
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (28 bp):
GGACCAAAATACAAAAATAGAAGCTTAG
Found at i:190082 original size:29 final size:30
Alignment explanation
Indices: 190000--190082 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 30
189990 GACCAAAATA
*
190000 AAAAAT-GAATCTTAGGGACTAAAA-TAGC
1 AAAAATAGAATCTTGGGGACTAAAACTAGC
* * * *
190028 AAAAATAGAAGCTTAGAGGAAT-AAACT-GG
1 AAAAATAGAATCTT-GGGGACTAAAACTAGC
*
190057 TAAAATAGAATCTTGGGGACTAAAAC
1 AAAAATAGAATCTTGGGGACTAAAAC
190083 AGAAGAAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
28 11 0.26
29 26 0.62
30 5 0.12
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.20
Consensus pattern (30 bp):
AAAAATAGAATCTTGGGGACTAAAACTAGC
Found at i:191659 original size:3 final size:3
Alignment explanation
Indices: 191651--191698 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
191641 ACAAAATTTG
*
191651 TAA TAA TAA TAT TAA TAA -AA TAA TAA TAA TAA TAA TAA -AA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
191696 TAA
1 TAA
191699 AATTATATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:191674 original size:17 final size:17
Alignment explanation
Indices: 191652--191701 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
191642 CAAAATTTGT
*
191652 AATAATAATATTAATAA
1 AATAATAATAATAATAA
191669 AATAATAATAATAAT--
1 AATAATAATAATAATAA
191684 AATAA-AATAA-AATAA
1 AATAATAATAATAATAA
191699 AAT
1 AAT
191702 TATATAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 8 0.27
17 14 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:191676 original size:20 final size:20
Alignment explanation
Indices: 191651--191703 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
191641 ACAAAATTTG
191651 TAATAATAATATTAATAAAA
1 TAATAATAATATTAATAAAA
*
191671 TAATAATAATAATAATAAAA
1 TAATAATAATATTAATAAAA
*
191691 TAA-AATAAAATTA
1 TAATAATAATATTA
191704 TATAGAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATAATAATATTAATAAAA
Found at i:191925 original size:43 final size:40
Alignment explanation
Indices: 191861--191972 Score: 120
Period size: 40 Copynumber: 2.7 Consensus size: 40
191851 TGTTGGGGAC
* *
191861 GACACTGCTCATACGCGATGAAGAGTTCGGGTCGTCTAAGG-G-T
1 GACACGGCTCATACGTGATGAAGAGTTC---TCGTC--AGGAGAT
* * *
191904 GACACGGCTCCTACGTGATGAAGAGATCTGGTCAGGAGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTCGTCAGGAGAT
191944 GACACGGCTCATACGTGATGAAGAGTTCT
1 GACACGGCTCATACGTGATGAAGAGTTCT
191973 GGCCATCTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
38 3 0.05
39 1 0.02
40 32 0.53
43 24 0.40
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (40 bp):
GACACGGCTCATACGTGATGAAGAGTTCTCGTCAGGAGAT
Found at i:192298 original size:64 final size:64
Alignment explanation
Indices: 192188--192327 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 64
192178 CAAAGATGGT
*
192188 AAATTTTGTTTTCAAAGAAACAAACTCAAAGATTTTTCTTAAAAGAAACTATCTCAAAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTC-TAAAAGAAACTATCTCAAAAGAGACA
* * * * * * *
192253 AAATTTTGTTTCCCAAAGAAACATATTCAATGATTTTTC-AAAAGAAATTGTCTCAAGATAGACA
1 AAATTTTGTTT-CCAAAGAAACAAACTCAAAGATTTTTCTAAAAGAAACTATCTCAAAAGAGACA
*
192317 AAACTTTGTTT
1 AAATTTTGTTT
192328 TTCAGAAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 31 0.48
65 11 0.17
66 23 0.35
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (64 bp):
AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTAAAAGAAACTATCTCAAAAGAGACA
Found at i:192567 original size:31 final size:31
Alignment explanation
Indices: 192507--192567 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
192497 AAGGGAAATG
*
192507 ACTCAAAGATGGTTTTATTTCAAGAGAAACAA
1 ACTCAAAGAT-GTTTGATTTCAAGAGAAACAA
*
192539 ACTCAAAGAT-TTTGATTTTCTAGAGAAAC
1 ACTCAAAGATGTTTGA-TTTCAAGAGAAAC
192568 TGCCTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 12 0.46
32 10 0.38
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (31 bp):
ACTCAAAGATGTTTGATTTCAAGAGAAACAA
Found at i:192910 original size:38 final size:38
Alignment explanation
Indices: 192834--192912 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
192824 CGAGACAATT
*
192834 TTTTTTTAAGAAAACTGTCTCAAGTGAGAGAAAGTTTG
1 TTTTTTTAAGAAAACTGTCTCAAGTGAGAGAAACTTTG
* **
192872 TTTTTTTGAGAAAAC-GATCTCAAGTGAGATCAACTTTG
1 TTTTTTTAAGAAAACTG-TCTCAAGTGAGAGAAACTTTG
192910 TTT
1 TTT
192913 AATGTGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (38 bp):
TTTTTTTAAGAAAACTGTCTCAAGTGAGAGAAACTTTG
Found at i:193002 original size:105 final size:104
Alignment explanation
Indices: 192880--193186 Score: 301
Period size: 103 Copynumber: 3.0 Consensus size: 104
192870 TGTTTTTTTG
* *
192880 AGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAATAAATTTGAAATTTGTATTCTCA
1 AGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTTGAAATTTGTATTCTCA
*
192945 AAGGAAAAATGTCTCAAACGAGACAGAA-TTGTTTTGAA
66 AAGGAAAAATGTCTCAAGCGAGACAGAATTTGTTTTGAA
* * *
192983 AGAAATAACAATCTCAAGTGATAT-AATTTTGTTTCAA-GT-ACAACAAATTT-AAATTTTTATT
1 AG-AA-AACAATCTCAAGTGAGATCAACTTTGTTT-AATGTGA-AACAAATTTGAAATTTGTATT
* ***
193044 -TCATA-GAAAAATGTCTCAAGCGAGAC-GAAGTTTGTTTTTTTTT
62 CTCAAAGGAAAAATGTCTCAAGCGAGACAGAA-TTTG--TTTTGAA
* ** * * *
193087 AGAAAGCGGTCTCGAA-TGAGATCAACTTTGTTTATTGTGAAACAAATTTGAATTTTGCA-TCTC
1 AGAAAACAATCTC-AAGTGAGATCAACTTTGTTTAATGTGAAACAAATTTGAAATTTGTATTCTC
* * *
193150 AAAGGAAACATGTCTCAAGTGAGACAAAATTTGTTTT
65 AAAGGAAAAATGTCTCAAGCGAGACAGAATTTGTTTT
193187 TCAAAAGAAG
Statistics
Matches: 165, Mismatches: 23, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
100 3 0.02
101 20 0.12
102 19 0.12
103 42 0.25
104 38 0.23
105 41 0.25
106 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (104 bp):
AGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTTGAAATTTGTATTCTCA
AAGGAAAAATGTCTCAAGCGAGACAGAATTTGTTTTGAA
Found at i:193529 original size:4 final size:4
Alignment explanation
Indices: 193522--193573 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
193512 TTTATATATA
* *
193522 ATGT ATGT ATG- -TGT ATAT ATGT TTGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
193568 ATGT AT
1 ATGT AT
193574 TGATGTTTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
4 40 0.95
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
ATGT
Found at i:194753 original size:23 final size:20
Alignment explanation
Indices: 194727--194776 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 20
194717 GTCAAGGGAC
*
194727 TCTTTGTCTTTGTGCTTTTGTCT
1 TCTTTGTCTTT-TGCTATT-T-T
*
194750 TCTTTTTCTTTTGCTATTTT
1 TCTTTGTCTTTTGCTATTTT
194770 TCTTTGT
1 TCTTTGT
194777 ACTCTGCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 6 0.25
23 10 0.42
ACGTcount: A:0.02, C:0.16, G:0.12, T:0.70
Consensus pattern (20 bp):
TCTTTGTCTTTTGCTATTTT
Found at i:198499 original size:21 final size:22
Alignment explanation
Indices: 198475--198515 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
198465 ACATATGATG
198475 TAAAATAA-AATATTTACAACA
1 TAAAATAACAATATTTACAACA
*
198496 TAAAATAACATTATTTACAA
1 TAAAATAACAATATTTACAA
198516 TATATGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAACAATATTTACAACA
Found at i:198767 original size:29 final size:27
Alignment explanation
Indices: 198666--198818 Score: 85
Period size: 29 Copynumber: 5.4 Consensus size: 27
198656 TAAACCTAAA
*
198666 GACTAAAATAGCAAAATCAGGAAT-TTAGG
1 GACTAAAATAG-AAAA--AAGAATCTTAGG
* * * *
198695 GACTAAAACAATAAAAATAGAATACTAAAG
1 GACTAAAA-TAGAAAAA-AGAAT-CTTAGG
* *
198725 GACCAAAATA-AAAAATGAATCTTAGG
1 GACTAAAATAGAAAAAAGAATCTTAGG
*
198751 GACTAAAATAGCAAAAACAGAAGCTTAGAG
1 GACTAAAATAG-AAAAA-AGAATCTTAG-G
* * * * *
198781 GAATAAACTGGTAAAATAGAATCTTGGG
1 GACTAAAATAG-AAAAAAGAATCTTAGG
198809 GACTAAAATA
1 GACTAAAATA
198819 AAAGAAACTT
Statistics
Matches: 93, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
26 13 0.14
27 5 0.05
28 22 0.24
29 29 0.31
30 24 0.26
ACGTcount: A:0.53, C:0.10, G:0.18, T:0.19
Consensus pattern (27 bp):
GACTAAAATAGAAAAAAGAATCTTAGG
Found at i:200384 original size:3 final size:3
Alignment explanation
Indices: 200376--200410 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
200366 ACAAAATTTG
*
200376 TAA TAA TAA TAT TAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
200411 ATTAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:200399 original size:17 final size:17
Alignment explanation
Indices: 200377--200420 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
200367 CAAAATTTGT
*
200377 AATAATAATATTAATAA
1 AATAATAATAATAATAA
200394 AATAATAATAATAATAA
1 AATAATAATAATAATAA
*
200411 ATTAA-AATAA
1 AATAATAATAA
200421 AATTATATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:205293 original size:130 final size:131
Alignment explanation
Indices: 205024--205368 Score: 445
Period size: 130 Copynumber: 2.6 Consensus size: 131
205014 AGTTCGGGTG
* * *
205024 ATCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACTGCTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACAC-GCTCATACG
* * * *
205089 TGAT---GCGTTCTTGGCCATCTTTAGGAAGTGTGATAACCGATTCCTACGCGATGAGGACGGCT
64 TGATGAAGAGTTC-TGGCCATCTTTAAGAAGGGCGATAACCGATTCCTACGCGATGAGGACGGCT
205151 GGTT
128 GGTT
* * * *
205155 ATCTAGGGGTGACAAGGCTCCTACGCGATGAGGAGATCTAGTCAGGGATGA-ACGACTCATATGT
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACG-CTCATACGT
* * *
205219 GATGAAGAGTTCTGGCCATCTTTAAGAAGGGCGATAA-CGGTTCCTACGTGATGAGGACGTCTGG
65 GATGAAGAGTTCTGGCCATCTTTAAGAAGGGCGATAACCGATTCCTACGCGATGAGGACGGCTGG
205283 TT
130 TT
*
205285 ATCTAGGGGTGACGCGGCTCCTACGTGATGA-GAGA--TGGTCAGGAGATGACACGGCTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGG-GATGACAC-GCTCATACG
205347 TGATGAAGAGTTCTGGCCATCT
64 TGATGAAGAGTTCTGGCCATCT
205369 CTAGGGATAT
Statistics
Matches: 188, Mismatches: 19, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
127 7 0.04
128 6 0.03
129 48 0.26
130 63 0.34
131 59 0.31
132 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (131 bp):
ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACGCTCATACGTG
ATGAAGAGTTCTGGCCATCTTTAAGAAGGGCGATAACCGATTCCTACGCGATGAGGACGGCTGGT
T
Found at i:205714 original size:29 final size:31
Alignment explanation
Indices: 205652--205883 Score: 103
Period size: 29 Copynumber: 8.0 Consensus size: 31
205642 AGACAAAAAC
205652 TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
1 TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
**
205683 TTTG-GTTTCAAAAGAAA-TGACTCAAAGAT
1 TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
* ** * *
205712 TTTTTCACGAATTGTCTTAAG--AGAAA--CAAA-AC
1 TTTGT---G--TT-TCAAAAGAAACAAACTCAAAGAT
*
205744 TTTG-G-TTCAAAAGAAACAGACTCAAA-A-
1 TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
*
205771 ---AT-TTTCAAAAGAAAC-AACTCAAAGAT
1 TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
* * * *
205797 TTT-TATTTCAAAAGAAAC-AACTCACATAC
1 TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
* *
205826 TTT-TATTTCAAAAGAAAC-AACTCACAGA-
1 TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
* *
205854 CTT-TGTTTCAAGAGAAACAAACTCAAAGAT
1 TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
205884 AGGTTTTGTT
Statistics
Matches: 156, Mismatches: 23, Indels: 45
0.70 0.10 0.20
Matches are distributed among these distances:
24 12 0.08
25 14 0.09
26 3 0.02
28 22 0.14
29 70 0.45
30 13 0.08
31 4 0.03
32 4 0.03
33 5 0.03
34 1 0.01
35 3 0.02
36 5 0.03
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (31 bp):
TTTGTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:205798 original size:24 final size:25
Alignment explanation
Indices: 205749--205799 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
205739 AAAACTTTGG
205749 TTCAAAAGAAACAGACTCAAAAATT
1 TTCAAAAGAAACAGACTCAAAAATT
*
205774 TTCAAAAGAAACA-ACTCAAAGATT
1 TTCAAAAGAAACAGACTCAAAAATT
205798 TT
1 TT
205800 TATTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (25 bp):
TTCAAAAGAAACAGACTCAAAAATT
Found at i:205800 original size:25 final size:26
Alignment explanation
Indices: 205749--205883 Score: 112
Period size: 29 Copynumber: 4.9 Consensus size: 26
205739 AAAACTTTGG
*
205749 TTCAAAAGAAACAGACTCAAA-AAT-T
1 TTCAAAAGAAACA-ACTCAAAGATTAT
205774 TTCAAAAGAAACAACTCAAAGATTTTTAT
1 TTCAAAAGAAACAACTCAAAGA---TTAT
**
205803 TTCAAAAGAAACAACTCACATACTTTTAT
1 TTCAAAAGAAACAACTCA-A-A-GATTAT
* *
205832 TTCAAAAGAAACAACTCACAGACTTTGT
1 TTCAAAAGAAACAACTCAAAGA--TTAT
*
205860 TTCAAGAGAAACAAACTCAAAGAT
1 TTCAAAAGAAAC-AACTCAAAGAT
205884 AGGTTTTGTT
Statistics
Matches: 90, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
24 7 0.08
25 14 0.16
27 2 0.02
28 15 0.17
29 50 0.56
30 1 0.01
31 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (26 bp):
TTCAAAAGAAACAACTCAAAGATTAT
Found at i:205871 original size:28 final size:28
Alignment explanation
Indices: 205773--205878 Score: 140
Period size: 29 Copynumber: 3.7 Consensus size: 28
205763 ACTCAAAAAT
* *
205773 TTTCAAAAGAAACAACTCAAAGATTTTTA
1 TTTCAAAAGAAACAACTCACAGA-CTTTA
*
205802 TTTCAAAAGAAACAACTCACATACTTTTA
1 TTTCAAAAGAAACAACTCACAGAC-TTTA
*
205831 TTTCAAAAGAAACAACTCACAGACTTTG
1 TTTCAAAAGAAACAACTCACAGACTTTA
*
205859 TTTCAAGAGAAACAAACTCA
1 TTTCAAAAGAAAC-AACTCA
205879 AAGATAGGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 15 0.22
29 54 0.78
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (28 bp):
TTTCAAAAGAAACAACTCACAGACTTTA
Found at i:205921 original size:29 final size:31
Alignment explanation
Indices: 205773--205932 Score: 97
Period size: 29 Copynumber: 5.4 Consensus size: 31
205763 ACTCAAAAAT
* * *
205773 TTTCAAAAGAAAC-AACTCAAAGAT-TTTTA
1 TTTCAAGAGAAACAAACTCAAAGATAGTTTG
* * * *
205802 TTTCAAAAGAAAC-AACTC--ACATACTTTTA
1 TTTCAAGAGAAACAAACTCAAAGATA-GTTTG
* * *
205831 TTTCAAAAGAAAC-AACTCACAG--ACTTTG
1 TTTCAAGAGAAACAAACTCAAAGATAGTTTG
205859 TTTCAAGAGAAACAAACTCAAAGATAGGTTTTG
1 TTTCAAGAGAAACAAACTCAAAGATA-G-TTTG
* * *
205892 TTTCAAGGGAAACAATCTTAAAGAT-G-TTG
1 TTTCAAGAGAAACAAACTCAAAGATAGTTTG
*
205921 TTTTAAGAGAAA
1 TTTCAAGAGAAA
205933 TTGTCTTAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
27 3 0.03
28 15 0.14
29 63 0.57
31 3 0.03
33 26 0.24
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.29
Consensus pattern (31 bp):
TTTCAAGAGAAACAAACTCAAAGATAGTTTG
Found at i:206066 original size:62 final size:63
Alignment explanation
Indices: 205983--206109 Score: 188
Period size: 62 Copynumber: 2.0 Consensus size: 63
205973 TTAAAGATTT
* * *
205983 TTCTTCAAAAGGAACTGTCTCAAAAGTGACAAAATTTTGTT-TCCAAA-GAACATACTCAAAGA
1 TTCTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTAT-CAAATAAACATACTCAAAGA
206045 TTCTTCAAAAGAAAC-GTTCTCAAAAGAGACAAAATTTTGTTATCAAATAAACATACTCAAAGA
1 TTCTTCAAAAGAAACTG-TCTCAAAAGAGACAAAATTTTGTTATCAAATAAACATACTCAAAGA
206108 TT
1 TT
206110 TTTTCATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
61 1 0.02
62 41 0.69
63 17 0.29
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (63 bp):
TTCTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTATCAAATAAACATACTCAAAGA
Found at i:206234 original size:30 final size:31
Alignment explanation
Indices: 206180--206238 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
206170 GAGACAAAGT
206180 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
*
206211 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
206239 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:206394 original size:36 final size:36
Alignment explanation
Indices: 206275--206384 Score: 168
Period size: 36 Copynumber: 3.1 Consensus size: 36
206265 ATAATTTGGA
*
206275 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * *
206311 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
*
206347 AAATTGTCTCAAGCGAGACAACGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
206382 AAA
1 AAA
206385 ACGATCTCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 6 0.09
36 60 0.91
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:222154 original size:39 final size:39
Alignment explanation
Indices: 222089--222166 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
222079 TCAGTAGTCC
* *
222089 TGTTTTAATCTATATTATCTATATTATTGTTGTTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGTTGCTTTAAT
* *
222128 TGTTTTAATCTATGTTATGTAGATTATTGTTGCTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGTTGCTTTAAT
222167 CTATGTTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (39 bp):
TGTTTTAATCTATATTATCTAGATTATTGTTGCTTTAAT
Found at i:222178 original size:39 final size:39
Alignment explanation
Indices: 222093--222184 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
222083 TAGTCCTGTT
* * * *
222093 TTAATCTATATTATCTATATTATTGTTGTTTTAATTGTT
1 TTAATCTATATTATCTAGATTATTGTTGCTTTAATTATG
* *
222132 TTAATCTATGTTATGTAGATTATTGTTGCTTTAATCTATG
1 TTAATCTATATTATCTAGATTATTGTTGCTTTAAT-TATG
*
222172 TT-ATCTAGATTAT
1 TTAATCTATATTAT
222185 TAAGAGAGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 40 0.91
40 4 0.09
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.57
Consensus pattern (39 bp):
TTAATCTATATTATCTAGATTATTGTTGCTTTAATTATG
Found at i:248625 original size:47 final size:49
Alignment explanation
Indices: 248536--248647 Score: 142
Period size: 49 Copynumber: 2.3 Consensus size: 49
248526 AGATGCACGT
* *
248536 ATGTAAGTATATATTTATTGTTAGGCTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTATTGTTAGGCTGGGAGATGTA-ATACTTACACCG
248585 A-GTAAGTATGTGTTTATT-TTAGGCTGAGAGAGATGT-ATACTTACACCG
1 ATGTAAGTATGTGTTTATTGTTAGGCTG-G-GAGATGTAATACTTACACCG
*
248633 ATATAAGTATGTGTT
1 ATGTAAGTATGTGTT
248648 AATTATTACA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
47 19 0.34
48 17 0.30
49 20 0.36
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (49 bp):
ATGTAAGTATGTGTTTATTGTTAGGCTGGGAGATGTAATACTTACACCG
Found at i:248641 original size:49 final size:47
Alignment explanation
Indices: 248539--248647 Score: 132
Period size: 47 Copynumber: 2.3 Consensus size: 47
248529 TGCACGTATG
* * *
248539 TAAGTATATATTTATTGTTAGGCTGGGAGATGTACATACTTACACCAG
1 TAAGTATGTGTTTATTGTTAGGCTGGGAGATGTA-ATACTTACACCAA
248587 TAAGTATGTGTTTATT-TTAGGCTGAGAGAGATGT-ATACTTACACCGATA
1 TAAGTATGTGTTTATTGTTAGGCTG-G-GAGATGTAATACTTACACC-A-A
248636 TAAGTATGTGTT
1 TAAGTATGTGTT
248648 AATTATTACA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
47 19 0.35
48 16 0.30
49 19 0.35
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (47 bp):
TAAGTATGTGTTTATTGTTAGGCTGGGAGATGTAATACTTACACCAA
Found at i:248973 original size:15 final size:15
Alignment explanation
Indices: 248953--248982 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
248943 TTACACGTAA
248953 ATATACAAAAGGAAT
1 ATATACAAAAGGAAT
248968 ATATACAAAAGGAAT
1 ATATACAAAAGGAAT
248983 GATTATTTTG
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:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (15 bp):
ATATACAAAAGGAAT
Found at i:250977 original size:13 final size:14
Alignment explanation
Indices: 250959--250987 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
250949 ACAAAATATT
250959 CAAAATATAT-GTG
1 CAAAATATATAGTG
250972 CAAAATATATAGTG
1 CAAAATATATAGTG
250986 CA
1 CA
250988 TGGTAATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (14 bp):
CAAAATATATAGTG
Found at i:259181 original size:14 final size:14
Alignment explanation
Indices: 259158--259188 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
259148 ATTATTTAAA
259158 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
259172 TTATTTGAATTTAT
1 TTATTAGAATTTAT
259186 TTA
1 TTA
259189 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:262500 original size:49 final size:50
Alignment explanation
Indices: 262427--262548 Score: 174
Period size: 49 Copynumber: 2.5 Consensus size: 50
262417 AGATGCACGT
* * *
262427 ATGTAAGTATATATTTATTGTTAGGCTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
262476 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
262526 ATATAAGTATGTGTTAATTGTTA
1 ATGTAAGTATGTGTTTATTGTTA
262549 CACTTTTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 44 0.69
50 20 0.31
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.40
Consensus pattern (50 bp):
ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
Found at i:262879 original size:15 final size:15
Alignment explanation
Indices: 262859--262889 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
262849 CACGTGTAAT
262859 TATATACAAAAGGAA
1 TATATACAAAAGGAA
262874 TATATACAAAAGGAA
1 TATATACAAAAGGAA
262889 T
1 T
262890 GATTATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (15 bp):
TATATACAAAAGGAA
Found at i:263611 original size:18 final size:20
Alignment explanation
Indices: 263580--263616 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
263570 GCTTTATAAT
263580 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
263600 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
263617 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Done.