Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 59 of 325
Found at i:21508046 original size:19 final size:19
Alignment explanation
Indices: 21507959--21508064 Score: 67
Period size: 21 Copynumber: 5.4 Consensus size: 19
21507949 AAATTTTATT
21507959 AAAATTAT-AAAATATTATA
1 AAAATTATAAAAATATT-TA
* * *
21507978 AAAATATAAAAAAATTTGTTT
1 AAAAT-TATAAAAATAT-TTA
21507999 AAAA-T-TAAAAATATATT-
1 AAAATTATAAAAATAT-TTA
* *
21508016 AGAATTCTTAAAAATATTTA
1 AAAATT-ATAAAAATATTTA
21508036 AAAATTATAAAAATAAATTTA
1 AAAATTATAAAAAT--ATTTA
21508057 AAATATTA
1 AAA-ATTA
21508065 AAACTGAAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
17 3 0.04
18 10 0.15
19 15 0.22
20 16 0.24
21 19 0.28
22 5 0.07
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTATAAAAATATTTA
Found at i:21508238 original size:19 final size:19
Alignment explanation
Indices: 21508216--21508264 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
21508206 TTTAATTTTT
*
21508216 TTATCAAACTAAAATTTCA
1 TTATCAAACTAAAAATTCA
*
21508235 TTATCCAAA-AAAAAATTCA
1 TTAT-CAAACTAAAAATTCA
*
21508254 TTATCTAACTA
1 TTATCAAACTA
21508265 TTAGCACATG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 4 0.17
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (19 bp):
TTATCAAACTAAAAATTCA
Found at i:21508678 original size:10 final size:9
Alignment explanation
Indices: 21508575--21508724 Score: 72
Period size: 9 Copynumber: 15.7 Consensus size: 9
21508565 TTAATAATTT
*
21508575 TTTTTATAG
1 TTTTTATAA
*
21508584 TTTTTATGA
1 TTTTTATAA
*
21508593 TTTTTACAGA
1 TTTTTATA-A
21508603 TTTTTAATACA
1 TTTTT-ATA-A
21508614 TTTTTATAAA
1 TTTTTAT-AA
*
21508624 ATTTTA-AA
1 TTTTTATAA
*
21508632 TATTTTAAATA
1 T-TTTTATA-A
*
21508643 TGTTTTATTA
1 T-TTTTATAA
21508653 TTTTTATAAA
1 TTTTTAT-AA
***
21508663 AAATTATAA
1 TTTTTATAA
*
21508672 TTTATTA-CA
1 TTT-TTATAA
21508681 TTTATTATAA
1 TTT-TTATAA
*
21508691 TATTTATAA
1 TTTTTATAA
21508700 GTTTTTATTAA
1 -TTTTTA-TAA
21508711 TTTTTAT-A
1 TTTTTATAA
21508719 TTTTTA
1 TTTTTA
21508725 ATATTCAATA
Statistics
Matches: 108, Mismatches: 22, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
8 9 0.08
9 41 0.38
10 39 0.36
11 19 0.18
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:21516649 original size:51 final size:51
Alignment explanation
Indices: 21516594--21516696 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
21516584 AATCTTATAC
21516594 ATGACATATCAACTCATATGTTCAATTATTCAAACTTACCAAAACAACCAT
1 ATGACATATCAACTCATATGTTCAATTATTCAAACTTACCAAAACAACCAT
21516645 ATGACATATCAACTCATATGTTCAATTATTCAAACTTACCAAAACAACCAT
1 ATGACATATCAACTCATATGTTCAATTATTCAAACTTACCAAAACAACCAT
21516696 A
1 A
21516697 CATATATGGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (51 bp):
ATGACATATCAACTCATATGTTCAATTATTCAAACTTACCAAAACAACCAT
Found at i:21517477 original size:25 final size:25
Alignment explanation
Indices: 21517443--21517506 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
21517433 TATCGAGCCA
21517443 TATAACGGGAAGCTTATTCGGGCTG
1 TATAACGGGAAGCTTATTCGGGCTG
21517468 TATAACGGGAAGCTTATTCGGGCTG
1 TATAACGGGAAGCTTATTCGGGCTG
21517493 TATAACGGGAAGCT
1 TATAACGGGAAGCT
21517507 CATAAGAGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (25 bp):
TATAACGGGAAGCTTATTCGGGCTG
Found at i:21517540 original size:24 final size:24
Alignment explanation
Indices: 21517494--21517541 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21517484 TTCGGGCTGT
* *
21517494 ATAACGGGAAGCTCATAAGAGCCA
1 ATAACGGGAAGCTCAGAAAAGCCA
* *
21517518 ATAACGGGTAGCTCCGAAAAGCCA
1 ATAACGGGAAGCTCAGAAAAGCCA
21517542 TTAATCGAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (24 bp):
ATAACGGGAAGCTCAGAAAAGCCA
Found at i:21519935 original size:8 final size:8
Alignment explanation
Indices: 21519922--21519947 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21519912 TAAGGTGAAA
21519922 AGATGGAT
1 AGATGGAT
21519930 AGATGGAT
1 AGATGGAT
21519938 AGATGGAT
1 AGATGGAT
21519946 AG
1 AG
21519948 GTGAACACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (8 bp):
AGATGGAT
Found at i:21520753 original size:19 final size:19
Alignment explanation
Indices: 21520708--21520753 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
21520698 ATTAACACAG
*
21520708 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
21520727 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
21520745 AATTAATAA
1 AATTAATAA
21520754 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:21520980 original size:10 final size:10
Alignment explanation
Indices: 21520967--21521001 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
21520957 AAGCTCGGTT
21520967 GAGCTCAAAC
1 GAGCTCAAAC
*
21520977 GAGCTGAAAC
1 GAGCTCAAAC
*
21520987 GAGCTCAAAT
1 GAGCTCAAAC
21520997 GAGCT
1 GAGCT
21521002 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:21521010 original size:20 final size:20
Alignment explanation
Indices: 21520964--21521011 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
21520954 AGTAAGCTCG
21520964 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
21520984 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
21521004 GTTGAGCT
1 GTTGAGCT
21521012 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:21522684 original size:18 final size:18
Alignment explanation
Indices: 21522659--21522704 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
21522649 TCTTTTTCGT
*
21522659 TCTCTTTTTCAATCTCAT
1 TCTCTTTTTCAATCTCAA
* *
21522677 TTTCTTTTTCACTCTCAA
1 TCTCTTTTTCAATCTCAA
21522695 TCTCTTTTTC
1 TCTCTTTTTC
21522705 TTTTTCTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (18 bp):
TCTCTTTTTCAATCTCAA
Found at i:21522694 original size:24 final size:24
Alignment explanation
Indices: 21522630--21522711 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
21522620 CTTGTTCACA
*
21522630 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
* * * * *
21522654 TTCGTTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCTTT
*
21522678 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
21522702 TTCTTTTTCT
1 TTCTTTTTCT
21522712 TTCTTTTCTC
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.11, C:0.27, G:0.01, T:0.61
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCTTT
Found at i:21522741 original size:42 final size:41
Alignment explanation
Indices: 21522707--21522791 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
21522697 TCTTTTTCTT
*
21522707 TTTCTTTCTTTTCTCGATTTCATTCAAGATTCTCTCATTTTC
1 TTTCTTTCTTCTCTCGATTTCATTCAAGATTCTCT-ATTTTC
* * *
21522749 TTTGTTTCTTCTCTCGATTTCATTCAAAATCCTCTCATTTTC
1 TTTCTTTCTTCTCTCGATTTCATTCAAGATTCTCT-ATTTTC
21522791 T
1 T
21522792 CTCATAATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.15, C:0.25, G:0.05, T:0.55
Consensus pattern (41 bp):
TTTCTTTCTTCTCTCGATTTCATTCAAGATTCTCTATTTTC
Found at i:21525025 original size:19 final size:19
Alignment explanation
Indices: 21524980--21525025 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
21524970 ATTAACACAG
*
21524980 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
21524999 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
21525017 AATTAATAA
1 AATTAATAA
21525026 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:21525252 original size:10 final size:10
Alignment explanation
Indices: 21525239--21525273 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
21525229 AAGCTCGGTT
21525239 GAGCTCAAAC
1 GAGCTCAAAC
*
21525249 GAGCTGAAAC
1 GAGCTCAAAC
*
21525259 GAGCTCAAAT
1 GAGCTCAAAC
21525269 GAGCT
1 GAGCT
21525274 GAGTTAAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:21525936 original size:14 final size:13
Alignment explanation
Indices: 21525916--21525947 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
21525906 AATATTTAAC
21525916 TTGTTCTTAATTA
1 TTGTTCTTAATTA
21525929 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
21525943 TTGTT
1 TTGTT
21525948 TTGATATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:21530704 original size:23 final size:23
Alignment explanation
Indices: 21530678--21530729 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
21530668 GTTAAATTTT
21530678 TCTTAAATATTATCACAAAATAA
1 TCTTAAATATTATCACAAAATAA
*
21530701 TCTTAAATATTATCACTAAATAA
1 TCTTAAATATTATCACAAAATAA
21530724 T-TTAAA
1 TCTTAAA
21530730 AATCAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
TCTTAAATATTATCACAAAATAA
Found at i:21531154 original size:5 final size:5
Alignment explanation
Indices: 21531144--21531169 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21531134 AAGATTCAAA
21531144 TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
21531170 GTAAGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:21533800 original size:27 final size:26
Alignment explanation
Indices: 21533744--21533802 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
21533734 TTTAGATCCT
* * *
21533744 TTAAAAGTTAGTATTTTTTTTTACTT
1 TTAAAAGTTAGAATTTTTTTTGACTA
21533770 TTAAAAGTTA-AATTTTTTTTGGACTCA
1 TTAAAAGTTAGAATTTTTTTT-GACT-A
21533797 TTAAAA
1 TTAAAA
21533803 ACTAGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.32
26 13 0.46
27 6 0.21
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (26 bp):
TTAAAAGTTAGAATTTTTTTTGACTA
Found at i:21534629 original size:20 final size:22
Alignment explanation
Indices: 21534589--21534630 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
21534579 ATTATTAAAA
*
21534589 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
21534611 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
21534631 CATTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:21534671 original size:15 final size:16
Alignment explanation
Indices: 21534643--21534673 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
21534633 TTTTTATTTC
21534643 AATAATAGATTTTAAA
1 AATAATAGATTTTAAA
21534659 AATAATA-ATTTTAAA
1 AATAATAGATTTTAAA
21534674 TAACATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AATAATAGATTTTAAA
Found at i:21534718 original size:14 final size:15
Alignment explanation
Indices: 21534696--21534772 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
21534686 CGATAATTGA
*
21534696 AAATA-TTTAATAGT
1 AAATATTTTAATAAT
21534710 -AATATTTTAATAAT
1 AAATATTTTAATAAT
*
21534724 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
21534743 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
21534758 AAATGTTTT-ATAAT
1 AAATATTTTAATAAT
21534772 A
1 A
21534773 TAAAAGTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.08
14 14 0.27
15 16 0.31
16 2 0.04
17 4 0.08
18 1 0.02
19 10 0.20
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:21535247 original size:14 final size:14
Alignment explanation
Indices: 21535225--21535263 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
21535215 TCAGAAAAAT
*
21535225 AAATTATTTTCTAG
1 AAATTATTTTCCAG
*
21535239 AAATCATTTTCCAG
1 AAATTATTTTCCAG
21535253 AAATTATTTTC
1 AAATTATTTTC
21535264 AGTGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (14 bp):
AAATTATTTTCCAG
Found at i:21542867 original size:13 final size:15
Alignment explanation
Indices: 21542839--21542871 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
21542829 GAGAGTAGAT
21542839 AAAAAAAAGGAGAAG
1 AAAAAAAAGGAGAAG
21542854 AAAAAAAA-GA-AAG
1 AAAAAAAAGGAGAAG
21542867 AAAAA
1 AAAAA
21542872 TATAGCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 2 0.11
15 8 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGGAGAAG
Found at i:21551753 original size:65 final size:65
Alignment explanation
Indices: 21551644--21551771 Score: 202
Period size: 65 Copynumber: 2.0 Consensus size: 65
21551634 CCCAAGCTAC
*
21551644 TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTGTAACTTTCTTCTCCT
1 TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTATAACTTTCTTCTCCT
* * * * *
21551709 TTTGCATTCATCAGCTGTCTCATCTCCTTTACAAACTTGTTTGGCTTCTATCACTTTTTTCTC
1 TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTATAACTTTCTTCTC
21551772 AATCATCTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.16, C:0.28, G:0.10, T:0.45
Consensus pattern (65 bp):
TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTATAACTTTCTTCTCCT
Found at i:21553303 original size:12 final size:12
Alignment explanation
Indices: 21553286--21553311 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21553276 TGGTAACTTT
21553286 AGTCATTGCTTG
1 AGTCATTGCTTG
21553298 AGTCATTGCTTG
1 AGTCATTGCTTG
21553310 AG
1 AG
21553312 AAACTTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.38
Consensus pattern (12 bp):
AGTCATTGCTTG
Found at i:21555296 original size:46 final size:44
Alignment explanation
Indices: 21555237--21555351 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
21555227 ACAGGACAGA
* *
21555237 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
21555283 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
21555327 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
21555352 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:21555332 original size:44 final size:45
Alignment explanation
Indices: 21555237--21555370 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
21555227 ACAGGACAGA
* *
21555237 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
21555283 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
21555327 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
21555371 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:21557436 original size:27 final size:27
Alignment explanation
Indices: 21557406--21557478 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
21557396 TGTCTTGATT
21557406 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
21557433 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
21557465 TTGTTGGATATTGA
1 TTGTTAGATATTGA
21557479 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:21557458 original size:32 final size:32
Alignment explanation
Indices: 21557419--21557479 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
21557409 TTAGATATTG
21557419 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
21557451 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
21557480 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:21558504 original size:22 final size:22
Alignment explanation
Indices: 21558474--21558518 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
21558464 ATTGTTGTTT
*
21558474 TCATGTGGTGTAATATTAGTTA
1 TCATATGGTGTAATATTAGTTA
21558496 TCATATGGTGTAATATTAGTTA
1 TCATATGGTGTAATATTAGTTA
21558518 T
1 T
21558519 GCACTTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (22 bp):
TCATATGGTGTAATATTAGTTA
Found at i:21558578 original size:68 final size:68
Alignment explanation
Indices: 21558438--21558581 Score: 200
Period size: 68 Copynumber: 2.1 Consensus size: 68
21558428 TAATGTGGTG
* * * *
21558438 TAATATTAGTTATGCACTTGGACAATATTGTTGTTTTCATGTGGTGTAATATTAGTTATCATATG
1 TAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATCATATA
*
21558503 GTG
66 GTA
* * *
21558506 TAATATTAGTTATGCACTTGGATAATGTTGTTGTTATCATGTGGTGTAATACTAATTATGCATTT
1 TAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTAT-CATAT
21558571 AG-A
65 AGTA
21558574 TAATATTA
1 TAATATTA
21558582 TTAATTTCTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 62 0.93
69 5 0.07
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (68 bp):
TAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATCATATA
GTA
Found at i:21558966 original size:15 final size:14
Alignment explanation
Indices: 21558936--21558994 Score: 75
Period size: 14 Copynumber: 4.2 Consensus size: 14
21558926 CCAGAAAAGT
21558936 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
21558950 AAATCATTTTTCAAG
1 AAATCA-TTTTCCAG
*
21558965 AAATTATTTTCCAG
1 AAATCATTTTCCAG
*
21558979 AAATTATTTTCC-G
1 AAATCATTTTCCAG
21558992 AAA
1 AAA
21558995 AATATTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
13 4 0.10
14 25 0.61
15 12 0.29
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:21558997 original size:29 final size:29
Alignment explanation
Indices: 21558936--21559002 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
21558926 CCAGAAAAGT
* *
21558936 AAATCATTTTCCAGAAATCATTTTTCAAG
1 AAATTATTTTCCAGAAATCATTTTCCAAG
*
21558965 AAATTATTTTCCAGAAATTATTTTCCGAA-
1 AAATTATTTTCCAGAAATCATTTTCC-AAG
21558994 AAA-TATTTT
1 AAATTATTTT
21559003 ACCTGCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 6 0.18
29 26 0.76
30 2 0.06
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (29 bp):
AAATTATTTTCCAGAAATCATTTTCCAAG
Found at i:21559000 original size:14 final size:14
Alignment explanation
Indices: 21558936--21559002 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
21558926 CCAGAAAAGT
21558936 AAATCATTTTCCAG-
1 AAAT-ATTTTCCAGA
*
21558950 AAATCATTTTTCAAGA
1 AAAT-A-TTTTCCAGA
*
21558966 AATTATTTTCCAGA
1 AAATATTTTCCAGA
*
21558980 AATTATTTTCC-GAA
1 AAATATTTTCCAG-A
21558994 AAATATTTT
1 AAATATTTT
21559003 ACCTGCAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
13 1 0.02
14 34 0.74
15 8 0.17
16 3 0.07
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (14 bp):
AAATATTTTCCAGA
Found at i:21559652 original size:21 final size:20
Alignment explanation
Indices: 21559626--21559664 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21559616 TGTAACAAAT
21559626 ATATTATAAATTTTTTTCCAA
1 ATATTAT-AATTTTTTTCCAA
*
21559647 ATATTATGATTTTTTTCC
1 ATATTATAATTTTTTTCC
21559665 CTTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (20 bp):
ATATTATAATTTTTTTCCAA
Found at i:21562079 original size:42 final size:42
Alignment explanation
Indices: 21562013--21562096 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
21562003 AGGTAAACAA
*
21562013 AATTAGCCTTAACTTTACACATTTTATCAATTTAGTCTTACT
1 AATTAGCCTCAACTTTACACATTTTATCAATTTAGTCTTACT
* *
21562055 AATTAGCCTCAACTTTATATATTTTATCAATTTAGTCTTACT
1 AATTAGCCTCAACTTTACACATTTTATCAATTTAGTCTTACT
21562097 TCTTAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (42 bp):
AATTAGCCTCAACTTTACACATTTTATCAATTTAGTCTTACT
Found at i:21565485 original size:26 final size:28
Alignment explanation
Indices: 21565426--21565486 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
21565416 TAATTTTCGG
*
21565426 TTAAATTTAAATTAACTCGGTTAATTGA
1 TTAAATTTAAATTAACTCGGTTAATTAA
* * *
21565454 TCAAATTT-AATTAA-TTGGTTAGTTAA
1 TTAAATTTAAATTAACTCGGTTAATTAA
21565480 TTAAATT
1 TTAAATT
21565487 AATCGAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 15 0.54
27 6 0.21
28 7 0.25
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (28 bp):
TTAAATTTAAATTAACTCGGTTAATTAA
Found at i:21565859 original size:16 final size:16
Alignment explanation
Indices: 21565822--21565860 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
21565812 CACCTAATGA
21565822 AATTTTAATTTTTTAT
1 AATTTTAATTTTTTAT
21565838 AA-TTT-ATATTTTTAT
1 AATTTTAAT-TTTTTAT
21565853 AATTTTAA
1 AATTTTAA
21565861 AGAATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.10
15 12 0.60
16 5 0.25
17 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTTTAATTTTTTAT
Found at i:21568068 original size:6 final size:6
Alignment explanation
Indices: 21568057--21568081 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21568047 CGCTATACGC
21568057 TCCCCT TCCCCT TCCCCT TCCCCT T
1 TCCCCT TCCCCT TCCCCT TCCCCT T
21568082 ACATTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCCCT
Found at i:21571176 original size:35 final size:35
Alignment explanation
Indices: 21571136--21571205 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
21571126 ATAATATTTC
*
21571136 ATGATAATAATCTTCATATCATATAAATAACATTA
1 ATGATAATAATCATCATATCATATAAATAACATTA
21571171 ATGATAATAATCATCATATCATATAAATAACATTA
1 ATGATAATAATCATCATATCATATAAATAACATTA
21571206 TATTACTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (35 bp):
ATGATAATAATCATCATATCATATAAATAACATTA
Found at i:21571208 original size:19 final size:19
Alignment explanation
Indices: 21571151--21571208 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
21571141 AATAATCTTC
21571151 ATATCATATAAATAACATT
1 ATATCATATAAATAACATT
* *
21571170 A-AT--GAT-AATAATCATC
1 ATATCATATAAATAA-CATT
21571186 ATATCATATAAATAACATT
1 ATATCATATAAATAACATT
21571205 ATAT
1 ATAT
21571209 TACTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 5 0.17
16 6 0.20
17 2 0.07
18 2 0.07
19 10 0.33
20 5 0.17
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATCATATAAATAACATT
Found at i:21574215 original size:37 final size:37
Alignment explanation
Indices: 21574165--21574241 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
21574155 GAATAGTATA
21574165 TATGCAGGAGTCAGCATAGAACTCACTTGATTCTCAC
1 TATGCAGGAGTCAGCATAGAACTCACTTGATTCTCAC
* * *
21574202 TATGCATGAGTCAGTATAGAATTCACTTGATTCTCAC
1 TATGCAGGAGTCAGCATAGAACTCACTTGATTCTCAC
21574239 TAT
1 TAT
21574242 CGGTAATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (37 bp):
TATGCAGGAGTCAGCATAGAACTCACTTGATTCTCAC
Found at i:21579383 original size:52 final size:48
Alignment explanation
Indices: 21579321--21579513 Score: 196
Period size: 47 Copynumber: 4.0 Consensus size: 48
21579311 GAAATGTGAT
* * *
21579321 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATTTGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
21579373 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * *
21579420 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * *
21579466 ATCCGTATAAGACCATGGCTGGGCTATGGCCTCG-GTATGTGATATGTG
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAG--TGTGATATGTG
21579514 ACTATGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
46 27 0.22
47 53 0.43
48 11 0.09
50 1 0.01
51 1 0.01
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:21590586 original size:5 final size:5
Alignment explanation
Indices: 21590576--21590617 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
21590566 TGCTGGCAAC
21590576 TGTTT TGTTT TGTTT TGTTT T-TCGTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGT--TT TGTTT TGTTT TGTTT T
21590618 TCGACTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.03
5 29 0.85
6 3 0.09
7 1 0.03
ACGTcount: A:0.00, C:0.02, G:0.19, T:0.79
Consensus pattern (5 bp):
TGTTT
Found at i:21590604 original size:21 final size:21
Alignment explanation
Indices: 21590579--21590620 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
21590569 TGGCAACTGT
21590579 TTTGTTTTGTTTTGTTTTTCG
1 TTTGTTTTGTTTTGTTTTTCG
21590600 TTTGTTTTGTTTTGTTTTTCG
1 TTTGTTTTGTTTTGTTTTTCG
21590621 ACTTGAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.05, G:0.19, T:0.76
Consensus pattern (21 bp):
TTTGTTTTGTTTTGTTTTTCG
Found at i:21596121 original size:22 final size:22
Alignment explanation
Indices: 21596081--21596122 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21596071 TTAACAGTGT
**
21596081 AAATAAACAATTTTTTTAATAA
1 AAATAAACAATTTACTTAATAA
21596103 AAATAAACAATTTACTTAAT
1 AAATAAACAATTTACTTAAT
21596123 TTTTAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATAAACAATTTACTTAATAA
Found at i:21604121 original size:16 final size:16
Alignment explanation
Indices: 21604052--21604119 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
21604042 TTTGGTTCGC
21604052 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
21604068 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
21604084 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
21604100 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
21604116 TGTA
1 TGTA
21604120 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:21604154 original size:45 final size:44
Alignment explanation
Indices: 21604100--21604194 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
21604090 GGATTAGAGG
* *
21604100 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
21604145 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
21604189 TGTAAT
1 TGTAAT
21604195 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:21604505 original size:124 final size:127
Alignment explanation
Indices: 21604275--21604505 Score: 396
Period size: 124 Copynumber: 1.8 Consensus size: 127
21604265 ATGATTATTG
21604275 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
21604340 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTAGCAGAAATTTGTTTTGGTAAA
64 ACATAATTACTATTAAATATATTTTAATTAAAATATATAATTAGCAGAAATTTGTTTTGGTAAA
*
21604404 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
21604466 ATAATTACTATTAAATATATTTTAATTAAAATATATAATT
66 ATAATTACTATTAAATATATTTTAATTAAAATATATAATT
21604506 TAATAAAATT
Statistics
Matches: 99, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
124 70 0.71
125 1 0.01
128 23 0.23
129 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (127 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTACTATTAAATATATTTTAATTAAAATATATAATTAGCAGAAATTTGTTTTGGTAAA
Found at i:21604507 original size:18 final size:17
Alignment explanation
Indices: 21604480--21604514 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21604470 TTACTATTAA
*
21604480 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21604498 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21604515 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21604544 original size:124 final size:125
Alignment explanation
Indices: 21604288--21604673 Score: 390
Period size: 124 Copynumber: 3.0 Consensus size: 125
21604278 TTGTTATTTA
*
21604288 AATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAAACATAATTATTAT
1 AATTTTAATAAGATTA---ATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTAT
* ** ** ** * *
21604353 TTAATATATTTTAATTAAAATATATAA-TTAGCAGAAATT-TGTTTTGGTAAATTATT-TTATTT
63 TAAATATATTTTAATTAAAATATATAATTTAATA-AAATTCT-TAATAATTAA-TATTCTTATAT
*
21604415 A
125 G
*
21604416 AATTTTAATAAGATTAA-TATCAATAATAAATAATTTAATCATATTTAAACATAATTACTATTAA
1 AATTTTAATAAGATTAATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAA
21604480 ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATG
66 ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATG
* * * * * * * * **
21604540 AA-TTTACTCAA-ACCATAATTATTATTAAATATGATACTGTAA-AATATAAAATAACATAATTA
1 AATTTTAAT-AAGA--TTAATTATCAAT-AATA-AATAATTTAATCATAT-TTA-AACATAATTA
* *
21604602 TTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
59 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
21604667 TG
124 TG
21604669 AATTT
1 AATTT
21604674 ACTCAAATCA
Statistics
Matches: 221, Mismatches: 25, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
123 10 0.05
124 87 0.39
125 9 0.04
126 5 0.02
127 8 0.04
128 24 0.11
129 76 0.34
130 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (125 bp):
AATTTTAATAAGATTAATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAA
ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATG
Found at i:21604630 original size:18 final size:17
Alignment explanation
Indices: 21604609--21604643 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21604599 TTATTATTAA
21604609 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
21604627 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
21604644 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:21604706 original size:17 final size:16
Alignment explanation
Indices: 21604684--21604730 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
21604674 ACTCAAATCA
21604684 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
21604701 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
21604715 TAAATATATGATTTAA
1 T-AATATATGATTTAA
21604731 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:21604731 original size:17 final size:17
Alignment explanation
Indices: 21604703--21604736 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21604693 ATTATAACTA
*
21604703 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
21604720 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
21604737 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:21604879 original size:93 final size:91
Alignment explanation
Indices: 21604769--21604962 Score: 284
Period size: 92 Copynumber: 2.1 Consensus size: 91
21604759 GATTATAGTT
* *
21604769 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTA-ATATAATTAT-ATAATAATATATAATTTC
* *
21604832 ATAAAATTCTTGATAATAAAAATTTTCTTA
63 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
21604862 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAGTGATATATAATTTCATA
1 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
21604927 AAATTCTTAATAATAAAATGTTCTTA
66 AAATTCTTAATAATAAAATGTTCTTA
21604953 TATGAATTTA
1 TATGAATTTA
21604963 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 21 0.23
92 40 0.43
93 29 0.31
94 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
AAATTCTTAATAATAAAATGTTCTTA
Found at i:21606373 original size:11 final size:11
Alignment explanation
Indices: 21606359--21606385 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21606349 AAAAATCAAT
21606359 ACAAAAGTTTC
1 ACAAAAGTTTC
21606370 ACAAAAGTTTC
1 ACAAAAGTTTC
21606381 ACAAA
1 ACAAA
21606386 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:21616650 original size:92 final size:93
Alignment explanation
Indices: 21616525--21616719 Score: 288
Period size: 92 Copynumber: 2.1 Consensus size: 93
21616515 TTGATTTTAG
* *
21616525 TAAATTCATATAAGAACATTTTAATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATT
1 TAAATTCATATAAGAAAATTTTAATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATT
*
21616589 ATAT-TAAT-ATTAATTATTTTAAATTGTA
65 ATATGTAATAATT-ATTATTTTAAATTATA
* * *
21616617 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAATTTTAATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
21616682 TATGTAATAATTATTATTTTAAATTATA
66 TATGTAATAATTATTATTTTAAATTATA
*
21616710 CAAATTCATA
1 TAAATTCATA
21616720 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 60 0.65
93 30 0.32
94 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (93 bp):
TAAATTCATATAAGAAAATTTTAATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
TATGTAATAATTATTATTTTAAATTATA
Found at i:21616767 original size:48 final size:52
Alignment explanation
Indices: 21616697--21616795 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
21616687 AATAATTATT
21616697 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
21616745 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
21616796 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:21616777 original size:17 final size:17
Alignment explanation
Indices: 21616752--21616785 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21616742 ATAATTTTAA
*
21616752 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
21616769 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
21616786 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:21616802 original size:17 final size:16
Alignment explanation
Indices: 21616757--21616804 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
21616747 TTTAAATTTT
21616757 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
21616774 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
21616788 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
21616805 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:21616938 original size:126 final size:128
Alignment explanation
Indices: 21616792--21617021 Score: 385
Period size: 126 Copynumber: 1.8 Consensus size: 128
21616782 ATATTAGTTA
*
21616792 TAATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAA-TATTAAGAATTTTATTAAAT
* *
21616857 TATATATTTTAATT-TATTAT-TTTAATAATAATTATGTTATTTATATTTTACAGTATCATATT
65 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTATATTTTACAGTATCATATT
*
21616919 TAATAATA-ATTATGGTTTGAGTAAATTCATATAAGAATATTAATATTAAGAATTTTATTAAATT
1 TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATATTAAGAATTTTATTAAATT
*
21616983 ATATATTTTAATTAAAATATATTTAATAGTAATTATGTT
66 ATATATTTTAATTAAAATATATTTAATAATAATTATGTT
21617022 TAAATATGAT
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
125 34 0.35
126 38 0.40
127 24 0.25
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (128 bp):
TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATATTAAGAATTTTATTAAATT
ATATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTATATTTTACAGTATCATATT
Found at i:21616996 original size:18 final size:17
Alignment explanation
Indices: 21616970--21617004 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21616960 AATATTAAGA
*
21616970 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
21616987 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
21617005 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:21617120 original size:124 final size:127
Alignment explanation
Indices: 21616979--21617209 Score: 396
Period size: 124 Copynumber: 1.8 Consensus size: 127
21616969 AATTTTATTA
* *
21616979 AATTATATATTTTAATTAAAATATATTTAATAGTAATTATGTTTAAATATGATTAAATTATTTAT
1 AATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTAT
21617044 TATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTACCAAAACAAATTTCTGCT
66 TATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTACCAAAACAAATTTCTGCT
21617103 AATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTAT
1 AATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTAT
*
21617168 TTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 TATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
21617210 CAATAATCAT
Statistics
Matches: 99, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
124 69 0.70
125 2 0.02
128 23 0.23
129 5 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (127 bp):
AATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTAT
TATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTACCAAAACAAATTTCTGCT
Found at i:21617339 original size:44 final size:45
Alignment explanation
Indices: 21617290--21617384 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
21617280 TTACACCTCT
* *
21617290 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
21617334 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
21617379 ATTACA
1 ATTACA
21617385 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:21617384 original size:16 final size:16
Alignment explanation
Indices: 21617365--21617416 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
21617355 GATTTGCTAT
* *
21617365 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
21617381 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21617397 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21617413 TACA
1 TACA
21617417 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:21619708 original size:8 final size:8
Alignment explanation
Indices: 21619666--21619690 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21619656 ATATAGACTA
21619666 AATAAAAT
1 AATAAAAT
21619674 AATAAAAT
1 AATAAAAT
21619682 AATAAAAT
1 AATAAAAT
21619690 A
1 A
21619691 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:21619714 original size:29 final size:31
Alignment explanation
Indices: 21619663--21619735 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
21619653 TATATATAGA
*
21619663 CTAAATAAAATAATAAAATAATAA-AA-TAT
1 CTAATTAAAATAATAAAATAATAATAATTAT
* *
21619692 CTTATTAAAAT-ATTAAATAAATAATAATTAT
1 CTAATTAAAATAATAAAAT-AATAATAATTAT
21619723 CTAATT-AAATAAT
1 CTAATTAAAATAAT
21619736 TATAAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 6 0.17
29 14 0.39
30 6 0.17
31 10 0.28
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (31 bp):
CTAATTAAAATAATAAAATAATAATAATTAT
Found at i:21619740 original size:29 final size:30
Alignment explanation
Indices: 21619670--21619741 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 30
21619660 AGACTAAATA
*
21619670 AAATAA-TA-AAATAATAAAATATCTTATT
1 AAATAATTATAAATAATAAAATATCTAATT
*
21619698 AAA-ATATTAAATAAATAAT-AATTATCTAATT
1 AAATA-ATT--ATAAATAATAAAATATCTAATT
21619729 AAATAATTATAAA
1 AAATAATTATAAA
21619742 ATATCACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
27 1 0.03
28 4 0.11
29 6 0.17
31 17 0.47
32 8 0.22
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATAATTATAAATAATAAAATATCTAATT
Found at i:21623716 original size:16 final size:17
Alignment explanation
Indices: 21623685--21623717 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21623675 TTCATAAGTA
21623685 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
21623702 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
21623718 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:21624251 original size:138 final size:138
Alignment explanation
Indices: 21623998--21624261 Score: 411
Period size: 138 Copynumber: 1.9 Consensus size: 138
21623988 TTATCTTTAA
* ** * *
21623998 CATGATGCCATAGTGTCTTTCAATTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
** *
21624063 TCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCA
21624128 TTTCCCGT
131 TTTCCCGT
* * *
21624136 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
* *
21624201 TCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTA
66 TCAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTA
21624262 CACATTTCAT
Statistics
Matches: 113, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 113 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (138 bp):
CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCA
TTTCCCGT
Found at i:21624276 original size:46 final size:46
Alignment explanation
Indices: 21623998--21624271 Score: 370
Period size: 46 Copynumber: 6.0 Consensus size: 46
21623988 TTATCTTTAA
* * * **
21623998 CATGATGCCATAGTGTCTTTCAATTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
*
21624044 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * **
21624090 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* **
21624136 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
21624182 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
21624228 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
21624272 ATCAGAGAGC
Statistics
Matches: 209, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 205 0.98
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:21628299 original size:46 final size:44
Alignment explanation
Indices: 21628195--21628302 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
21628185 TGTCTTTGAC
** * * *
21628195 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
21628239 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
21628285 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
21628303 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:21635588 original size:46 final size:44
Alignment explanation
Indices: 21635484--21635591 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
21635474 TGTCTTTGAC
** * * *
21635484 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
21635528 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
21635574 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
21635592 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:21638238 original size:28 final size:28
Alignment explanation
Indices: 21638184--21638245 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
21638174 AACATGCCAA
*
21638184 ATACTTATAAAAAATTAATCATCATAAC
1 ATACTTATAAAAAACTAATCATCATAAC
*
21638212 -TACTTATAACCAAACTAATTCA-CATAAC
1 ATACTTATAA-AAAACTAA-TCATCATAAC
21638240 ATACTT
1 ATACTT
21638246 GAAGTATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 9 0.31
28 12 0.41
29 8 0.28
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (28 bp):
ATACTTATAAAAAACTAATCATCATAAC
Found at i:21638705 original size:38 final size:39
Alignment explanation
Indices: 21638649--21638735 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 39
21638639 TTACACCAGT
* * *
21638649 ACAATGCCTGTTAGGCACAAAGCCCGAAT-ATCACCTGC
1 ACAAAGCCTGCTAGGCACAAAGCCCGAATAATCACCGGC
* * *
21638687 ACAAAGCCTGCTAGGCACATAGCCTGAATAATTACCGGC
1 ACAAAGCCTGCTAGGCACAAAGCCCGAATAATCACCGGC
*
21638726 ACACAGCCTG
1 ACAAAGCCTG
21638736 AATAATCACC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 25 0.61
39 16 0.39
ACGTcount: A:0.32, C:0.31, G:0.20, T:0.17
Consensus pattern (39 bp):
ACAAAGCCTGCTAGGCACAAAGCCCGAATAATCACCGGC
Found at i:21638733 original size:23 final size:23
Alignment explanation
Indices: 21638700--21638751 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
21638690 AAGCCTGCTA
* *
21638700 GGCACATAGCCTGAATAATTACC
1 GGCACACAGCCTGAATAATCACC
21638723 GGCACACAGCCTGAATAATCACC
1 GGCACACAGCCTGAATAATCACC
*
21638746 GACACA
1 GGCACA
21638752 TAACATGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.15
Consensus pattern (23 bp):
GGCACACAGCCTGAATAATCACC
Found at i:21638779 original size:62 final size:61
Alignment explanation
Indices: 21638662--21638785 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 61
21638652 ATGCCTGTTA
* ** *
21638662 GGCACAAAGCCCGAATATCACCTGCACAAAGCCTGCTAGGCACATAGCCTGAATAATTACC
1 GGCACAAAGCCCGAATATCACCTGCACAAAGCATGCTAGGCACATAGCCCAAATAATCACC
* *
21638723 GGCACACAGCCTGAATAATCACC-GACACATAA-CATGCTAGGCACATAGCCCAAATAATCACC
1 GGCACAAAGCCCGAAT-ATCACCTG-CACA-AAGCATGCTAGGCACATAGCCCAAATAATCACC
21638785 G
1 G
21638786 ACACTTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
61 15 0.28
62 37 0.69
63 2 0.04
ACGTcount: A:0.36, C:0.31, G:0.17, T:0.15
Consensus pattern (61 bp):
GGCACAAAGCCCGAATATCACCTGCACAAAGCATGCTAGGCACATAGCCCAAATAATCACC
Found at i:21641550 original size:33 final size:33
Alignment explanation
Indices: 21641513--21641576 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
21641503 AAGACTATAT
* *
21641513 CTGGGATATGGCACCACGA-GTGTAAGACCATGG
1 CTGGGACATGGCAACAC-ACGTGTAAGACCATGG
* *
21641546 CTGGGCCATGGCAATACACGTGTAAGACCAT
1 CTGGGACATGGCAACACACGTGTAAGACCAT
21641577 AGTTGGACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (33 bp):
CTGGGACATGGCAACACACGTGTAAGACCATGG
Found at i:21641788 original size:46 final size:46
Alignment explanation
Indices: 21641699--21641818 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 46
21641689 TCAAATGTGA
* * * *
21641699 AAGACCATGGTTGAAAGATACAATGACAATATGACAAGGAATGAAT
1 AAGACCATGGTTGAAAGATACAATGGCAACACGACAAGAAATGAAT
* * *
21641745 AAGACTATGGTTGAAAGATACCATGGCAACACGAC-AGAAAATGAGT
1 AAGACCATGGTTGAAAGATACAATGGCAACACGACAAG-AAATGAAT
* * *
21641791 AAGACCATAGTTGAAAGACACTATGGCA
1 AAGACCATGGTTGAAAGATACAATGGCA
21641819 TCATGTTGAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
45 2 0.03
46 60 0.97
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (46 bp):
AAGACCATGGTTGAAAGATACAATGGCAACACGACAAGAAATGAAT
Found at i:21641947 original size:13 final size:13
Alignment explanation
Indices: 21641906--21641948 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
21641896 ATCGATGATG
*
21641906 AATGGTTATATGA
1 AATGGTTGTATGA
* **
21641919 ATTGGTTGTACAA
1 AATGGTTGTATGA
21641932 AATGGTTGTATGA
1 AATGGTTGTATGA
21641945 AATG
1 AATG
21641949 TTTACAAGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (13 bp):
AATGGTTGTATGA
Found at i:21641963 original size:26 final size:26
Alignment explanation
Indices: 21641906--21641987 Score: 71
Period size: 26 Copynumber: 3.1 Consensus size: 26
21641896 ATCGATGATG
*
21641906 AATGGTTATATGAATTGGTTGTACAA
1 AATGGTTATATGAAATGGTTGTACAA
*
21641932 AATGGTTGTATGAAAT-GTT-TACAA
1 AATGGTTATATGAAATGGTTGTACAA
* *
21641956 GAATTGGTCATATGGAAAT-ATATGTACAA
1 -AA-TGGTTATAT-GAAATGGT-TGTACAA
21641985 AAT
1 AAT
21641988 AGTTGCATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.11
25 5 0.11
26 21 0.46
27 7 0.15
28 3 0.07
29 5 0.11
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (26 bp):
AATGGTTATATGAAATGGTTGTACAA
Found at i:21649516 original size:46 final size:46
Alignment explanation
Indices: 21649382--21649598 Score: 183
Period size: 46 Copynumber: 4.6 Consensus size: 46
21649372 TTTGTGTGCT
** * *
21649382 AGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACG-AGAGC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCAACGAGACGTAAATC
* ** *
21649428 TAGTGTAAGACATGTCTGAGACATGCATCGGCGTCGTA-ATGTAAATC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCAACG-AGACGTAAATC
* *
21649475 AGTGTAAGACATGTCTGGGACATGCATCAGCAACGAGATGT--ATC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCAACGAGACGTAAATC
* * **
21649519 AGTGTAAGACCATGTTTGGGACGTGACATCGGC-ACGGAGACGTGAGAGCC
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCAAC-GAGACGT-A-AATC
21649569 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
21649599 AACTTAATGG
Statistics
Matches: 141, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
44 12 0.09
45 16 0.11
46 59 0.42
47 26 0.18
50 27 0.19
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCAACGAGACGTAAATC
Found at i:21649646 original size:97 final size:94
Alignment explanation
Indices: 21649474--21649649 Score: 221
Period size: 97 Copynumber: 1.8 Consensus size: 94
21649464 TAATGTAAAT
* * * *
21649474 CAGTGTAAGACATGTCTGGGACATGCATCAGCAACGAGATGTATCAGTGTAAGACCATGTTTGGG
1 CAGTGTAAGACATGTCTGGGACATGCATCAACAACGAGATGTACCAATGTAAGACCATGTCTGGG
*
21649539 ACGTGACATCGGCACGGAGACGTGAGAGC
66 ACATGACATCGGCACGGAGACGTGAGAGC
*
21649568 CAGTGTAAGACCATGTCTGGGACATGGCATCAACTTAATG-GATG-AGCCAATGTAAGACCATGT
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCAAC--AACGAGATGTA-CCAATGTAAGACCATGT
* *
21649631 CTGGGATATGGCATCGGCA
61 CTGGGACATGACATCGGCA
21649650 TTACACCCCA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
94 10 0.14
95 14 0.20
96 8 0.12
97 34 0.49
98 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (94 bp):
CAGTGTAAGACATGTCTGGGACATGCATCAACAACGAGATGTACCAATGTAAGACCATGTCTGGG
ACATGACATCGGCACGGAGACGTGAGAGC
Found at i:21651739 original size:18 final size:18
Alignment explanation
Indices: 21651699--21651739 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21651689 TCGGTAATTT
*
21651699 TAAATTTTACAAATTTAA
1 TAAATGTTACAAATTTAA
* *
21651717 GAAATGTTACAAATTTTA
1 TAAATGTTACAAATTTAA
21651735 TAAAT
1 TAAAT
21651740 CATCTTTGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
TAAATGTTACAAATTTAA
Found at i:21654721 original size:22 final size:22
Alignment explanation
Indices: 21654682--21654727 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
21654672 TAATCATATA
*
21654682 ATAAATTATTAATATAATTAAT
1 ATAAATTATTAATATAATAAAT
* * *
21654704 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
21654726 AT
1 AT
21654728 TTTAATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:21654762 original size:16 final size:16
Alignment explanation
Indices: 21654730--21654776 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
21654720 ATAAATATTT
**
21654730 TAATTTTATTTAATAA
1 TAATTTTAAATAATAA
21654746 TAAATTTTAAA-AATAA
1 T-AATTTTAAATAATAA
21654762 TAATTTTAAATAATA
1 TAATTTTAAATAATA
21654777 TTCATCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 9 0.33
16 11 0.41
17 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTTAAATAATAA
Found at i:21655349 original size:20 final size:21
Alignment explanation
Indices: 21655324--21655374 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
21655314 CATCTAAACA
21655324 TAAAAAAATATTAATT-TTTT
1 TAAAAAAATATTAATTATTTT
21655344 TAAAAAAATA--AATTATTTT
1 TAAAAAAATATTAATTATTTT
* *
21655363 TCAAAAATTATT
1 TAAAAAAATATT
21655375 TTTAGTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 10 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAAAATATTAATTATTTT
Found at i:21655357 original size:18 final size:20
Alignment explanation
Indices: 21655324--21655369 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
21655314 CATCTAAACA
21655324 TAAAAAAATATTAATT-TTTT
1 TAAAAAAATA-TAATTATTTT
21655344 TAAAAAAATA-AATTATTTT
1 TAAAAAAATATAATTATTTT
21655363 TCAAAAA
1 T-AAAAA
21655370 TTATTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.17
19 5 0.21
20 15 0.62
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAAAATATAATTATTTT
Found at i:21660325 original size:46 final size:46
Alignment explanation
Indices: 21660273--21660361 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
21660263 AACTCTAGTG
21660273 TTTATGCATTTAGATATACATGTACACACACAAATATATATATATT
1 TTTATGCATTTAGATATACATGTACACACACAAATATATATATATT
*
21660319 TTTATGCATTTATATATACATGTACACACACAAATATATATAT
1 TTTATGCATTTAGATATACATGTACACACACAAATATATATAT
21660362 GTTTGATGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (46 bp):
TTTATGCATTTAGATATACATGTACACACACAAATATATATATATT
Found at i:21670775 original size:51 final size:51
Alignment explanation
Indices: 21670699--21670797 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
21670689 AAAAAAAATT
*
21670699 ATGTGAATTCAAATATTAGAATGCATTCTAAAATATATATAAATTTCAATC
1 ATGTGAATTCAAATATTAGAATGCATCCTAAAATATATATAAATTTCAATC
*
21670750 ATGTGAATTCAAATGTTAGAATGCATCCTAAAATATATATAAATTTCA
1 ATGTGAATTCAAATATTAGAATGCATCCTAAAATATATATAAATTTCA
21670798 GTCGGGAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (51 bp):
ATGTGAATTCAAATATTAGAATGCATCCTAAAATATATATAAATTTCAATC
Found at i:21670943 original size:28 final size:28
Alignment explanation
Indices: 21670903--21670961 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
21670893 GCTCTCTCAG
21670903 CTTGATTCGATGCTAGTAGTCATACAAT
1 CTTGATTCGATGCTAGTAGTCATACAAT
21670931 CTTGATTCGATGCTAGTAGTCATACAAT
1 CTTGATTCGATGCTAGTAGTCATACAAT
21670959 CTT
1 CTT
21670962 TGCAAGTCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (28 bp):
CTTGATTCGATGCTAGTAGTCATACAAT
Found at i:21672088 original size:21 final size:21
Alignment explanation
Indices: 21672047--21672088 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21672037 GAAAGTGGCT
**
21672047 TTATTTATTCTGTAAGTAATA
1 TTATTTATTCTGTAAAAAATA
21672068 TTATTTAATTC-GTAAAAAATA
1 TTATTT-ATTCTGTAAAAAATA
21672089 ATTTTAAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (21 bp):
TTATTTATTCTGTAAAAAATA
Found at i:21692819 original size:21 final size:22
Alignment explanation
Indices: 21692795--21692847 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
21692785 ATTGTAATAA
*
21692795 TAAATTTTTA-TATT-ATATACT
1 TAAATTTTAAGTATTCATATA-T
*
21692816 TAAATATTAAGTATTCATATAT
1 TAAATTTTAAGTATTCATATAT
21692838 TAATATTTTA
1 TAA-ATTTTA
21692848 TGCATATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.31
22 8 0.31
23 10 0.38
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAATTTTAAGTATTCATATAT
Found at i:21695107 original size:222 final size:222
Alignment explanation
Indices: 21694721--21695159 Score: 869
Period size: 222 Copynumber: 2.0 Consensus size: 222
21694711 CATACGCCCG
21694721 TGTGGTGTCGACATATTCATTTTTCAGCTTTCACCGATTCTCGTTTTCTGTGTTTTCGGGTACAC
1 TGTGGTGTCGACATATTCATTTTTCAGCTTTCACCGATTCTCGTTTTCTGTGTTTTCGGGTACAC
21694786 ACCTGGAATTGTTAGAAGCTAATCTGAACTCCGAGCACTCATGAACCTAAATATTTATAAATTTA
66 ACCTGGAATTGTTAGAAGCTAATCTGAACTCCGAGCACTCATGAACCTAAATATTTATAAATTTA
21694851 TATTCGATTAATCGCTTAGAAACTGAATTCATCTAATCCCAAAACAAGGTAACTAGCTTTCGAGT
131 TATTCGATTAATCGCTTAGAAACTGAATTCATCTAATCCCAAAACAAGGTAACTAGCTTTCGAGT
21694916 GATAAGCTAGTACCTTCTATCGCTTTT
196 GATAAGCTAGTACCTTCTATCGCTTTT
21694943 TGTGGTGTCGACATATTCATTTTTCAGCTTTCACCGATTCTCGTTTTCTGTGTTTTCGGGTACAC
1 TGTGGTGTCGACATATTCATTTTTCAGCTTTCACCGATTCTCGTTTTCTGTGTTTTCGGGTACAC
21695008 ACCTGGAATTGTTAGAAGCTAATCTGAACTCCGAGCACTCATGAACCTAAATATTTATAAATTTA
66 ACCTGGAATTGTTAGAAGCTAATCTGAACTCCGAGCACTCATGAACCTAAATATTTATAAATTTA
*
21695073 TATTCGATTAATCGCTTAGAAACTGAATTCATCTAATCCTAAAACAAGGTAACTAGCTTTCGAGT
131 TATTCGATTAATCGCTTAGAAACTGAATTCATCTAATCCCAAAACAAGGTAACTAGCTTTCGAGT
21695138 GATAAGCTAGTACCTTCTATCG
196 GATAAGCTAGTACCTTCTATCG
21695160 ATTAGCAAAA
Statistics
Matches: 216, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 216 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (222 bp):
TGTGGTGTCGACATATTCATTTTTCAGCTTTCACCGATTCTCGTTTTCTGTGTTTTCGGGTACAC
ACCTGGAATTGTTAGAAGCTAATCTGAACTCCGAGCACTCATGAACCTAAATATTTATAAATTTA
TATTCGATTAATCGCTTAGAAACTGAATTCATCTAATCCCAAAACAAGGTAACTAGCTTTCGAGT
GATAAGCTAGTACCTTCTATCGCTTTT
Found at i:21698673 original size:21 final size:21
Alignment explanation
Indices: 21698634--21698673 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21698624 ATTATCTAAA
**
21698634 TTTAATTAATCATGTTTTAGT
1 TTTAATTAATCATAATTTAGT
*
21698655 TTTAATTAATCTTAATTTA
1 TTTAATTAATCATAATTTA
21698674 CTAAATTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTAATTAATCATAATTTAGT
Found at i:21705913 original size:3 final size:3
Alignment explanation
Indices: 21705907--21705933 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21705897 GCTGCTAAGC
21705907 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
21705934 ATGATAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21706099 original size:11 final size:11
Alignment explanation
Indices: 21706085--21706109 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21706075 TTTACAATTT
21706085 TTTAAAATATA
1 TTTAAAATATA
21706096 TTTAAAATATA
1 TTTAAAATATA
21706107 TTT
1 TTT
21706110 TTTAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATATA
Found at i:21710865 original size:18 final size:16
Alignment explanation
Indices: 21710833--21710866 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
21710823 AGCCACAAAT
21710833 AAAAAAAAAGAGAGCA
1 AAAAAAAAAGAGAGCA
21710849 AAAACAAAAAGATGAGCA
1 AAAA-AAAAAGA-GAGCA
21710867 TGAAAGAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.71, C:0.09, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAGAGCA
Found at i:21717154 original size:16 final size:17
Alignment explanation
Indices: 21717123--21717155 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21717113 TTCATAAGTA
21717123 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
21717140 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
21717156 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:21717501 original size:46 final size:46
Alignment explanation
Indices: 21717441--21717714 Score: 358
Period size: 46 Copynumber: 6.0 Consensus size: 46
21717431 TTTGACATGA
* * * * *
21717441 TGCCATAGTGTCTTTCAACTATGGTCTTATTAATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTAA-TTTCATATCAGGT
* * * *
21717487 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTAATTTCATATCAGGT
* *
21717533 TGCCATGGTATCTTTCAACAATGGTCTTATTCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTAATTTCATATCAGGT
*
21717579 TGCCATGGTATCTTTCAACCATGGTCTTA-CACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTA-ATTTCATATCAGGT
* *
21717625 TGCCATGCTATCTTTCAACCATGGTCTTA-CACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTA-ATTTCATATCAGGT
21717671 TGCCATGGTATCTTTCAACCATGGTCTTA-TACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTATTA-ATTTCATATCAG
21717715 AGAGCATACT
Statistics
Matches: 210, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 4 0.02
46 206 0.98
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTAATTTCATATCAGGT
Found at i:21717598 original size:92 final size:92
Alignment explanation
Indices: 21717441--21717713 Score: 395
Period size: 92 Copynumber: 3.0 Consensus size: 92
21717431 TTTGACATGA
* * * * * *
21717441 TGCCATAGTGTCTTTCAACTATGGTCTTATTAATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACAATGGTCTTATTCA-TTTCATATCAGGTTGCCATGGTATCTTTCAA
* *
21717505 CCATGGTCTTATTCATTTCATGTCACGC
65 CCATGGTCTTATACATTTCATATCACGC
21717533 TGCCATGGTATCTTTCAACAATGGTCTTATTCATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACAATGGTCTTATTCATTTCATATCAGGTTGCCATGGTATCTTTCAAC
* * *
21717598 CATGGTCTTACACATTTCATATCAGGT
66 CATGGTCTTATACATTTCATATCACGC
* * **
21717625 TGCCATGCTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACAATGGTCTTATTCATTTCATATCAGGTTGCCATGGTATCTTTCAAC
21717690 CATGGTCTTATACATTTCATATCA
66 CATGGTCTTATACATTTCATATCA
21717714 GAGAGCATAC
Statistics
Matches: 164, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
91 4 0.02
92 160 0.98
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACAATGGTCTTATTCATTTCATATCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTATACATTTCATATCACGC
Found at i:21721134 original size:36 final size:35
Alignment explanation
Indices: 21721068--21721135 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
21721058 AAAATAGAAA
* *
21721068 AAAATTGTAAATTTTTTATAAAAGTCATAAAATAT
1 AAAATTGTAAATTTTATATAAAAATCATAAAATAT
*
21721103 AAAATTGTAAAATTTTATA-AGAAAATTATAAAA
1 AAAATTGT-AAATTTTATATA-AAAATCATAAAA
21721136 AAATGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 9 0.32
36 19 0.68
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (35 bp):
AAAATTGTAAATTTTATATAAAAATCATAAAATAT
Found at i:21721166 original size:10 final size:9
Alignment explanation
Indices: 21721124--21721179 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
21721114 ATTTTATAAG
21721124 AAAATTATAAA
1 AAAATTAT--A
*
21721135 AAAATGTAAA
1 AAAAT-TATA
*
21721145 AAAAATAT-
1 AAAATTATA
21721153 AAAATTCATA
1 AAAATT-ATA
21721163 AAAATTATA
1 AAAATTATA
21721172 AAAATTAT
1 AAAATTAT
21721180 CATACCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 5 0.13
9 15 0.39
10 11 0.29
11 5 0.13
12 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:21721381 original size:20 final size:19
Alignment explanation
Indices: 21721348--21721402 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
21721338 TTGAAAGGCC
21721348 TTTTTGATGCATTTTTATAAA
1 TTTTT-ATG-ATTTTTATAAA
21721369 TTTTTAATGATTTTTATAAA
1 TTTTT-ATGATTTTTATAAA
*
21721389 ATTTTATG-TTTTTA
1 TTTTTATGATTTTTA
21721403 ATTTTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 6 0.19
19 3 0.09
20 15 0.47
21 8 0.25
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTTTATGATTTTTATAAA
Found at i:21721475 original size:29 final size:30
Alignment explanation
Indices: 21721413--21721475 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
21721403 ATTTTAATTT
*
21721413 TTTTAATAAAATTTAAATATTTTTTTATAT
1 TTTTAATAAAATTTAAATATTTTTTTATAC
*
21721443 TTTTATTAAAATTT-AATA-TTTTTTATAAC
1 TTTTAATAAAATTTAAATATTTTTTTAT-AC
21721472 TTTT
1 TTTT
21721476 TTTTTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 8 0.27
29 9 0.30
30 13 0.43
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTAATAAAATTTAAATATTTTTTTATAC
Found at i:21722540 original size:3 final size:3
Alignment explanation
Indices: 21722532--21722587 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
21722522 AAAATAGTAA
* * * *
21722532 AAG AAG AAG AAG AA- AAG AAG ATG AAA AAC AAG TAG AAG AAG AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21722578 AAG AAG AAG A
1 AAG AAG AAG A
21722588 GAGACGCGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.66, C:0.02, G:0.29, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:21722588 original size:11 final size:11
Alignment explanation
Indices: 21722532--21722589 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
21722522 AAAATAGTAA
21722532 AAGAAGAAGAAG
1 AAGAAGAAG-AG
21722544 AA-AAGAAGATG
1 AAGAAGAAGA-G
* *
21722555 AAAAACAAGTAG
1 AAGAAGAAG-AG
21722567 AAGAAGAAGAG
1 AAGAAGAAGAG
21722578 AAGAAGAAGAG
1 AAGAAGAAGAG
21722589 A
1 A
21722590 GACGCGAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 1 0.03
11 23 0.57
12 15 0.38
13 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.29, T:0.03
Consensus pattern (11 bp):
AAGAAGAAGAG
Found at i:21724161 original size:26 final size:27
Alignment explanation
Indices: 21724126--21724191 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 27
21724116 TAATTTTATC
21724126 TATATACATACGTATATA-TATT-AAAA
1 TATATACATA-GTATATAGTATTAAAAA
* *
21724152 TATAAACATAATA-ATAGTATTAAAAA
1 TATATACATAGTATATAGTATTAAAAA
21724178 TATATACATAGTAT
1 TATATACATAGTAT
21724192 TAAAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
24 3 0.09
25 6 0.18
26 24 0.73
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (27 bp):
TATATACATAGTATATAGTATTAAAAA
Found at i:21724190 original size:20 final size:20
Alignment explanation
Indices: 21724165--21724207 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
21724155 AAACATAATA
21724165 ATAGTATTAAAAATATATAC
1 ATAGTATTAAAAATATATAC
21724185 ATAGTATTAAAAATATATAC
1 ATAGTATTAAAAATATATAC
21724205 ATA
1 ATA
21724208 ATATATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
ATAGTATTAAAAATATATAC
Found at i:21724207 original size:46 final size:46
Alignment explanation
Indices: 21724143--21724243 Score: 127
Period size: 46 Copynumber: 2.2 Consensus size: 46
21724133 ATACGTATAT
*
21724143 ATATT-AAAATATAAACATAATA-ATA-GTATTAAAAATATATACATA
1 ATATTAAAAATATAAACATAATATATACATATTAAAAATA-ATA-ATA
* * *
21724188 GTATTAAAAATATATACATAATATATACATATTAGAAATAATAATA
1 ATATTAAAAATATAAACATAATATATACATATTAAAAATAATAATA
21724234 ATATTAAAAA
1 ATATTAAAAA
21724244 CAACTATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
45 4 0.08
46 28 0.58
47 6 0.12
48 10 0.21
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (46 bp):
ATATTAAAAATATAAACATAATATATACATATTAAAAATAATAATA
Found at i:21724212 original size:11 final size:11
Alignment explanation
Indices: 21724176--21724218 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
21724166 TAGTATTAAA
21724176 AATATATACAT
1 AATATATACAT
* *
21724187 AGTAT-TA-AA
1 AATATATACAT
21724196 AATATATACAT
1 AATATATACAT
21724207 AATATATACAT
1 AATATATACAT
21724218 A
1 A
21724219 TTAGAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
11 17 0.65
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (11 bp):
AATATATACAT
Found at i:21724301 original size:46 final size:45
Alignment explanation
Indices: 21724139--21724301 Score: 103
Period size: 45 Copynumber: 3.6 Consensus size: 45
21724129 ATACATACGT
* *
21724139 ATATATATTAAAATATAAACATAATAATAGTATTA-A-AAATATATAC
1 ATATATATTAAAA-ACATACATAATAATAGTA-TACATAAATATA-AC
* * * *
21724185 ATA-GTATT-AAAA-ATATATACATAATA-TATACATATTAGAAATAAT
1 ATATATATTAAAAACATACATA-ATAATAGTATACATA--A-ATATAAC
*
21724230 A-ATAATATTAAAAACA-AC-TATTAATAGTACTACATAAATATACAC
1 ATAT-ATATTAAAAACATACATAATAATAGTA-TACATAAATATA-AC
21724275 ATATATATTAAAAA-ATACATAATAATA
1 ATATATATTAAAAACATACATAATAATA
21724302 TTAAAAATAC
Statistics
Matches: 90, Mismatches: 11, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
41 2 0.02
42 8 0.09
43 8 0.09
44 9 0.10
45 27 0.30
46 24 0.27
47 11 0.12
48 1 0.01
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (45 bp):
ATATATATTAAAAACATACATAATAATAGTATACATAAATATAAC
Found at i:21724302 original size:20 final size:20
Alignment explanation
Indices: 21724223--21724322 Score: 64
Period size: 20 Copynumber: 4.8 Consensus size: 20
21724213 TACATATTAG
21724223 AAATA-ATAATAATATTAAA
1 AAATACATAATAATATTAAA
* *
21724242 AACA-ACTATTAATAGTACTACATA
1 AA-ATAC-A-TAATAATATTA-A-A
*
21724266 AATATACA-CATATATATTAAA
1 AA-ATACATAATA-ATATTAAA
21724287 AAATACATAATAATATT-AA
1 AAATACATAATAATATTAAA
*
21724306 AAATACGTACATAATAT
1 AAATACATA-ATAATAT
21724323 ATATACATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
19 13 0.21
20 18 0.29
21 7 0.11
22 13 0.21
23 5 0.08
24 5 0.08
25 2 0.03
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATACATAATAATATTAAA
Found at i:21724320 original size:23 final size:21
Alignment explanation
Indices: 21724275--21724326 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
21724265 AAATATACAC
21724275 ATATATATTAAAAAATACATA
1 ATATATATTAAAAAATACATA
21724296 ATA-ATATTAAAAATACGTACATA
1 ATATATATTAAAAA-A--TACATA
21724319 ATATATAT
1 ATATATAT
21724327 ACATATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.37
21 4 0.15
23 9 0.33
24 4 0.15
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATATATTAAAAAATACATA
Found at i:21724377 original size:25 final size:27
Alignment explanation
Indices: 21724334--21724388 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
21724324 TATACATATA
21724334 ATATAGTTATTAAAAAATACACACAAT
1 ATATAGTTATTAAAAAATACACACAAT
* *
21724361 ATATAG-TATT-AAGAATATACACAAT
1 ATATAGTTATTAAAAAATACACACAAT
21724386 ATA
1 ATA
21724389 CACAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 16 0.62
26 4 0.15
27 6 0.23
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (27 bp):
ATATAGTTATTAAAAAATACACACAAT
Found at i:21724419 original size:14 final size:15
Alignment explanation
Indices: 21724397--21724430 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21724387 TACACAATAT
*
21724397 ATATGGTATT-AAAA
1 ATATAGTATTAAAAA
21724411 ATATAGTATTAAAAA
1 ATATAGTATTAAAAA
21724426 ATATA
1 ATATA
21724431 CATATAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (15 bp):
ATATAGTATTAAAAA
Found at i:21724470 original size:3 final size:3
Alignment explanation
Indices: 21724450--21724514 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
21724440 ATTGATTAAA
* * * *
21724450 AAT AAT ACT AAT ACT AAT AAT AGT AAT AAT AA- AAT ACT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
21724495 AAT AGAT -AT AGT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AA
21724515 GAACGTATAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 4 0.08
3 39 0.81
4 5 0.10
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21724495 original size:15 final size:15
Alignment explanation
Indices: 21724450--21724514 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
21724440 ATTGATTAAA
*
21724450 AATAATACTAATACT
1 AATAATACTAATAAT
*
21724465 AATAATAGTAATAAT
1 AATAATACTAATAAT
21724480 AA-AATACTAATAAAT
1 AATAATACTAAT-AAT
*
21724495 AATAGATA-TAGTAAT
1 AATA-ATACTAATAAT
21724510 AATAA
1 AATAA
21724515 GAACGTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.21
15 27 0.63
16 4 0.09
17 3 0.07
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (15 bp):
AATAATACTAATAAT
Found at i:21724889 original size:3 final size:3
Alignment explanation
Indices: 21724862--21724997 Score: 50
Period size: 3 Copynumber: 45.0 Consensus size: 3
21724852 GAATATATAC
* * * * * *
21724862 ATA AT- ATA ATA TTA AGA AAA ATA ATA ATA ACA A-A AAA ACTA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* * * * *
21724906 ATA ATA CTA TATA AT- ATA TATA AGTA TTA AGTA AAA ATA ATA CTA ATG
1 ATA ATA ATA -ATA ATA ATA -ATA A-TA ATA A-TA ATA ATA ATA ATA ATA
* *
21724954 CTA ATAA ATA ATA A-A TATA ATA ATA ATA GTA ATA A-A AT- ATA ATA
1 ATA AT-A ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21724998 GTATACATAT
Statistics
Matches: 97, Mismatches: 23, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
2 11 0.11
3 71 0.73
4 15 0.15
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Done.