Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 13 of 84
Found at i:2504982 original size:35 final size:35
Alignment explanation
Indices: 2504931--2505002 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
2504921 ATTATATATG
*
2504931 TGAAGTCAGTTGTAGGTTTATGCCCATAAAACATT
1 TGAAGTCAGTTATAGGTTTATGCCCATAAAACATT
*
2504966 TGAAGTCAGTTATAGGTTTATGCCTATAAAACATT
1 TGAAGTCAGTTATAGGTTTATGCCCATAAAACATT
2505001 TG
1 TG
2505003 GTTTATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (35 bp):
TGAAGTCAGTTATAGGTTTATGCCCATAAAACATT
Found at i:2505688 original size:41 final size:41
Alignment explanation
Indices: 2505578--2505718 Score: 165
Period size: 42 Copynumber: 3.4 Consensus size: 41
2505568 AAAGCTCTTC
** * * *
2505578 TAAACAGAGGCATAAACAACTTTGAAAAATAAAATGCTTCTC
1 TAAACAGAGGCA-CCACAACTTTGAAAAATAAATTGCTCCTT
*
2505620 TAAACAGAGGCACCACAACTTTGGAAAATTAAATTGCTCCTT
1 TAAACAGAGGCACCACAACTTT-GAAAAATAAATTGCTCCTT
* * * *
2505662 TAAATAGAGGCACCGCGACTTTGAAAAAATAAATTGCTCATT
1 TAAACAGAGGCACCACAACTTTG-AAAAATAAATTGCTCCTT
2505704 TAAACAGAGGCACCA
1 TAAACAGAGGCACCA
2505719 TTGCTCCTCT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 9 0.11
42 75 0.89
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (41 bp):
TAAACAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTT
Found at i:2505731 original size:24 final size:24
Alignment explanation
Indices: 2505694--2505742 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2505684 GAAAAAATAA
* *
2505694 ATTGCTCATTTAAACAGAGGCACC
1 ATTGCTCATCTAAACAGAAGCACC
*
2505718 ATTGCTCCTCTAAACAGAAGCACC
1 ATTGCTCATCTAAACAGAAGCACC
2505742 A
1 A
2505743 CGACTTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (24 bp):
ATTGCTCATCTAAACAGAAGCACC
Found at i:2505807 original size:107 final size:108
Alignment explanation
Indices: 2505612--2505826 Score: 306
Period size: 107 Copynumber: 2.0 Consensus size: 108
2505602 AAAAATAAAA
* * * * * * ** *
2505612 TGCTTCTCTAAACAGAGGCACCACAACTTTGGAAAATTAAATTGCTCCTTTAAATAGAGGCACCG
1 TGCTCCTCTAAACAGAAGCACCACAACTTTGAAAAATTAAATTGCTCATCTAAACAGAGAAACCA
*
2505677 CGACTTTGAAAAAATAAATTGCTCATTTAAACAGAGGCACCAT
66 CGACTTTGAAAAAATAAATTGCTCATCTAAACAGAGGCACCAT
*
2505720 TGCTCCTCTAAACAGAAGCACCACGACTTTGAAAAATT-AATTGCTCATCTAAACAGAGAAACCA
1 TGCTCCTCTAAACAGAAGCACCACAACTTTGAAAAATTAAATTGCTCATCTAAACAGAGAAACCA
* *
2505784 CGACTTTGAAAAAATAAATTGCTCCTCTAAATAGAGGCACCAT
66 CGACTTTGAAAAAATAAATTGCTCATCTAAACAGAGGCACCAT
2505827 GATTTTGAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
107 60 0.64
108 34 0.36
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (108 bp):
TGCTCCTCTAAACAGAAGCACCACAACTTTGAAAAATTAAATTGCTCATCTAAACAGAGAAACCA
CGACTTTGAAAAAATAAATTGCTCATCTAAACAGAGGCACCAT
Found at i:2505813 original size:42 final size:41
Alignment explanation
Indices: 2505718--2506084 Score: 417
Period size: 42 Copynumber: 9.0 Consensus size: 41
2505708 CAGAGGCACC
* *
2505718 ATTGCTCCTCTAAACAGAAGCACCACGACTTTGAAAAATTA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAA
* **
2505759 ATTGCTCATCTAAACAGAGAAACCACGACTTTGAAAAAATAA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAATAA
* * *
2505801 ATTGCTCCTCTAAATAGAGGCACCATGATTTTGAAAAAATAA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAATAA
* * *
2505843 ATTGCTCATCTAAATAGAGGCACCACGACTTTG------GA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAA
* * * *
2505878 A--GCTTCTTTAAACAGAGTCACCATGACTTTGAAAAAATAA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAATAA
* * * *
2505918 ATTGCTCCTTTAAACAGAGGCACCATGATTTTGGAAAATAA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAA
* *
2505959 ATTGCTCCTTTAAACAGAGGCACCATGACTTTGAAAAAATAA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAATAA
*
2506001 ATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAA
* *
2506042 AATGCTCCTCTAAACAGAGGCACCACAACTTTGGAAAAATAA
1 ATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAATAA
2506084 A
1 A
2506085 AAGCTCATCG
Statistics
Matches: 282, Mismatches: 32, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
33 24 0.09
35 2 0.01
40 2 0.01
41 107 0.38
42 147 0.52
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (41 bp):
ATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAA
Found at i:2505951 original size:75 final size:77
Alignment explanation
Indices: 2505720--2506084 Score: 322
Period size: 83 Copynumber: 4.5 Consensus size: 77
2505710 GAGGCACCAT
* * * * * **
2505720 TGCTCCTCTAAACAGAAGCACCACGACTTTG-AAAAATTAATTGCTCATCTAAACAGAGAAACCA
1 TGCTCCTTTAAACAGAGGCACCATGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCA
*
2505784 CGACTTTGAAAAAATAAA
66 CGACTTTG------GAAA
* * * * *
2505802 TTGCTCCTCTAAATAGAGGCACCATGATTTTGAAAAAATAAATTGCTCATCTAAATAGAGGCACC
1 -TGCTCCTTTAAACAGAGGCACCATGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACC
2505867 ACGACTTTGG-AA
65 ACGACTTTGGAAA
* * *
2505879 -GCTTCTTTAAACAGAGTCACCATGACTTTGAAAAAATAAATTGCTCCTTTAAACAGAGGCACCA
1 TGCTCCTTTAAACAGAGGCACCATGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCA
* *
2505943 TGATTTTGGAAAATAAA
66 CGACTTTGG-----AAA
2505960 TTGCTCCTTTAAACAGAGGCACCATGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACC
1 -TGCTCCTTTAAACAGAGGCACCATGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACC
* *
2506025 ACAACTTTGAAAAATAAAA
65 ACGACTTTG------GAAA
* ** *
2506044 TGCTCCTCTAAACAGAGGCACCACAACTTTGGAAAAATAAA
1 TGCTCCTTTAAACAGAGGCACCATGACTTTGAAAAAATAAA
2506085 AAGCTCATCG
Statistics
Matches: 237, Mismatches: 30, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
75 63 0.27
77 2 0.01
81 2 0.01
83 130 0.55
84 40 0.17
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (77 bp):
TGCTCCTTTAAACAGAGGCACCATGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCA
CGACTTTGGAAA
Found at i:2506560 original size:20 final size:21
Alignment explanation
Indices: 2506535--2506587 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
2506525 CACCTAAAAA
2506535 ATTCTCATTTGAAACTC-AAT
1 ATTCTCATTTGAAACTCAAAT
*
2506555 ATTCTCATTTGAAATTCAAAT
1 ATTCTCATTTGAAACTCAAAT
*
2506576 ATTCTTATTTGA
1 ATTCTCATTTGA
2506588 GATCAAGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (21 bp):
ATTCTCATTTGAAACTCAAAT
Found at i:2507755 original size:9 final size:8
Alignment explanation
Indices: 2507741--2507819 Score: 61
Period size: 8 Copynumber: 9.4 Consensus size: 8
2507731 AATATAAGTC
2507741 TTTCTTTT
1 TTTCTTTT
*
2507749 TTT-TCTT
1 TTTCTTTT
2507756 TTTCATCTTT
1 TTTC-T-TTT
* *
2507766 TTTCATTC
1 TTTCTTTT
2507774 TTTCATTTT
1 TTTC-TTTT
2507783 TTTCATTTT
1 TTTC-TTTT
*
2507792 TTTCTCTT
1 TTTCTTTT
2507800 TTTCATTTT
1 TTTC-TTTT
*
2507809 TTTATTTT
1 TTTCTTTT
2507817 TTT
1 TTT
2507820 TCATCTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
7 6 0.11
8 23 0.40
9 22 0.39
10 6 0.11
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTCTTTT
Found at i:2507766 original size:18 final size:19
Alignment explanation
Indices: 2507743--2507830 Score: 68
Period size: 18 Copynumber: 4.9 Consensus size: 19
2507733 TATAAGTCTT
2507743 TCTTTTTT-TTCTTTTTCA
1 TCTTTTTTATTCTTTTTCA
2507761 TCTTTTTTCATTC--TTTCA
1 TCTTTTTT-ATTCTTTTTCA
2507779 T-TTTTTTCATT-TTTTTC-
1 TCTTTTTT-ATTCTTTTTCA
*
2507796 TCTTTTTCATT-TTTTT-A
1 TCTTTTTTATTCTTTTTCA
*
2507813 TTTTTTTTCA-TCTTTTTC
1 TCTTTTTT-ATTCTTTTTC
2507831 CATCCATTAG
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
17 26 0.45
18 29 0.50
20 3 0.05
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTTTTTTATTCTTTTTCA
Found at i:2507792 original size:26 final size:26
Alignment explanation
Indices: 2507754--2507827 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 26
2507744 CTTTTTTTTC
2507754 TTTTTCATCTTTTTTCATTCTTTCATT
1 TTTTTCAT-TTTTTTCATTCTTTCATT
*
2507781 TTTTTCATTTTTTTC-TCTTTTTCATT
1 TTTTTCATTTTTTTCAT-TCTTTCATT
2507807 TTTTT-ATTTTTTTTCA-TCTTT
1 TTTTTCA-TTTTTTTCATTCTTT
2507828 TTCCATCCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.14
26 28 0.67
27 8 0.19
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTCATTTTTTTCATTCTTTCATT
Found at i:2507822 original size:44 final size:42
Alignment explanation
Indices: 2507741--2507830 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 42
2507731 AATATAAGTC
*
2507741 TTTCTTTTTTTTCTTTTTCATCTTTTTTCATTCTTTCATTTT
1 TTTCTTTTTTTTCTTTTTCATCTTTTTTCATTCTTTCATCTT
*
2507783 TTTCATTTTTTTCTCTTTTTCAT-TTTTTT-ATTTTTTTTCATCTT
1 TTTC-TTTTTTT-TCTTTTTCATCTTTTTTCA--TTCTTTCATCTT
2507827 TTTC
1 TTTC
2507831 CATCCATTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
42 5 0.12
43 13 0.31
44 24 0.57
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.77
Consensus pattern (42 bp):
TTTCTTTTTTTTCTTTTTCATCTTTTTTCATTCTTTCATCTT
Found at i:2507828 original size:9 final size:9
Alignment explanation
Indices: 2507752--2507830 Score: 74
Period size: 9 Copynumber: 8.9 Consensus size: 9
2507742 TTCTTTTTTT
2507752 TCTTTTTCA
1 TCTTTTTCA
2507761 TCTTTTTTCA
1 TC-TTTTTCA
*
2507771 T-TCTTTCA
1 TCTTTTTCA
*
2507779 TTTTTTTCA
1 TCTTTTTCA
*
2507788 TTTTTTTC-
1 TCTTTTTCA
2507796 TCTTTTTCA
1 TCTTTTTCA
*
2507805 T-TTTTTTA
1 TCTTTTTCA
*
2507813 TTTTTTTTCA
1 -TCTTTTTCA
2507823 TCTTTTTC
1 TCTTTTTC
2507831 CATCCATTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
8 20 0.34
9 25 0.42
10 14 0.24
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (9 bp):
TCTTTTTCA
Found at i:2508230 original size:24 final size:24
Alignment explanation
Indices: 2508184--2508231 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2508174 TTGTTTGTGG
* *
2508184 CATTTTTCTTTTCAATCTTTCTTT
1 CATTTTACTTTTCAATCTCTCTTT
**
2508208 CATTTTACTTTTCTTTCTCTCTTT
1 CATTTTACTTTTCAATCTCTCTTT
2508232 GAGACCTTTT
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:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (24 bp):
CATTTTACTTTTCAATCTCTCTTT
Found at i:2511340 original size:21 final size:21
Alignment explanation
Indices: 2511302--2511346 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2511292 TTAATTAAAT
*
2511302 ATAAGTATTAAAACCAAATCA
1 ATAAGTATTAAAAACAAATCA
*
2511323 ATAAGTA-TAATAAACAAATTA
1 ATAAGTATTAA-AAACAAATCA
2511344 ATA
1 ATA
2511347 TTAAACTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAGTATTAAAAACAAATCA
Found at i:2516024 original size:16 final size:17
Alignment explanation
Indices: 2515999--2516032 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2515989 AATAAGTAAA
2515999 ATAATATTTT-TTATTT
1 ATAATATTTTGTTATTT
*
2516015 ATAATGTTTTGTTATTT
1 ATAATATTTTGTTATTT
2516032 A
1 A
2516033 ATTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
ATAATATTTTGTTATTT
Found at i:2518731 original size:30 final size:30
Alignment explanation
Indices: 2518697--2518757 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2518687 AAAAGGCAAT
*
2518697 TATAACTTCTTCCATGATAAAATTAATGCA
1 TATAACTTCTTCCATAATAAAATTAATGCA
*
2518727 TATAACTTCTTCCATAATAAGATTAATGCA
1 TATAACTTCTTCCATAATAAAATTAATGCA
2518757 T
1 T
2518758 CTTTTGTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (30 bp):
TATAACTTCTTCCATAATAAAATTAATGCA
Found at i:2522665 original size:25 final size:26
Alignment explanation
Indices: 2522629--2522680 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
2522619 TATAATGATA
2522629 TTTATATTTATAAATATTTTAT-TAT
1 TTTATATTTATAAATATTTTATATAT
*
2522654 TTTAT-TTGTATAATTATTTTATATAT
1 TTTATATT-TATAAATATTTTATATAT
2522680 T
1 T
2522681 GTACCCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 2 0.08
25 18 0.75
26 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTATATTTATAAATATTTTATATAT
Found at i:2531134 original size:3 final size:3
Alignment explanation
Indices: 2531126--2531166 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2531116 ATCGATTTTG
2531126 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2531167 GTAGACACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2532248 original size:22 final size:20
Alignment explanation
Indices: 2532197--2532248 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
2532187 ATGAATAAAT
*
2532197 AAAATAAAAAACAAAACTAA
1 AAAATATAAAACAAAACTAA
* *
2532217 AATAAAATAAAATAAAGACCTAA
1 AA-AATATAAAACAAA-A-CTAA
2532240 AAAATATAA
1 AAAATATAA
2532249 TATGCAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 10 0.40
22 7 0.28
23 6 0.24
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (20 bp):
AAAATATAAAACAAAACTAA
Found at i:2532380 original size:14 final size:14
Alignment explanation
Indices: 2532363--2532403 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2532353 TATTTTTTAC
2532363 TAAATAAATAATAA
1 TAAATAAATAATAA
*
2532377 TAAATAAATGATAAA
1 TAAATAAATAAT-AA
2532392 TAAA-AAA-AATAA
1 TAAATAAATAATAA
2532404 ATTGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 2 0.08
13 2 0.08
14 14 0.58
15 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
TAAATAAATAATAA
Found at i:2532390 original size:21 final size:20
Alignment explanation
Indices: 2532366--2532405 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2532356 TTTTTACTAA
*
2532366 ATAAATAATAATAAATAAATG
1 ATAAATAA-AAAAAATAAATG
2532387 ATAAATAAAAAAAATAAAT
1 ATAAATAAAAAAAATAAAT
2532406 TGTTTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
ATAAATAAAAAAAATAAATG
Found at i:2532392 original size:11 final size:11
Alignment explanation
Indices: 2532365--2532405 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
2532355 TTTTTTACTA
2532365 AATAAAT-AAT
1 AATAAATAAAT
2532375 AATAAATAAAT
1 AATAAATAAAT
*
2532386 GATAAATAAA-
1 AATAAATAAAT
2532396 AA-AAATAAAT
1 AATAAATAAAT
2532406 TGTTTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 7 0.26
10 8 0.30
11 12 0.44
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:2544779 original size:40 final size:40
Alignment explanation
Indices: 2544724--2544938 Score: 161
Period size: 40 Copynumber: 5.5 Consensus size: 40
2544714 CATCTCAGAT
* * *
2544724 TTTTAACATTTAAAGTTTGTTACCTTTGGTTAAAGAAGCC
1 TTTTAATATTTAAAGTTTGTTACCTCTGGTGAAAGAAGCC
* * * *
2544764 TTTTAGTATTTAAAGTTTGTTGCCTCTGGTGAGAGGAGCC
1 TTTTAATATTTAAAGTTTGTTACCTCTGGTGAAAGAAGCC
* * * *
2544804 TTTTAATATTTAAAGTTTGTTGCCTCTTGTGATAGGAG-C
1 TTTTAATATTTAAAGTTTGTTACCTCTGGTGAAAGAAGCC
*** * * * * *
2544843 TTTCTAA-ATTTAAAGTCCATTGCCTGTGGTGAGAGGAGTC
1 TTT-TAATATTTAAAGTTTGTTACCTCTGGTGAAAGAAGCC
* * * *
2544883 TTTTGA-ATTTAAAGTTTGTTGCCTCTGGTCAAA-AGAGCT
1 TTTTAATATTTAAAGTTTGTTACCTCTGGTGAAAGA-AGCC
*
2544922 TTTTGA-ATTTAAAGTTT
1 TTTTAATATTTAAAGTTT
2544939 CATAGCCTCT
Statistics
Matches: 146, Mismatches: 26, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
39 71 0.49
40 75 0.51
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (40 bp):
TTTTAATATTTAAAGTTTGTTACCTCTGGTGAAAGAAGCC
Found at i:2544873 original size:79 final size:78
Alignment explanation
Indices: 2544724--2544971 Score: 223
Period size: 79 Copynumber: 3.1 Consensus size: 78
2544714 CATCTCAGAT
* * * * ***
2544724 TTTTAACATTTAAAGTTTGTTACCTTTGGT-TAAAGAAGCCTTT-TAGTATTTAAAGTTTGTTGC
1 TTTTAA-ATTTAAAGTTTGTTGCCTCTGGTCAAAAG-AG-CTTTCTA-AATTTAAAGTCCATTGC
2544787 CTCTGGTGAGAGGAGCC
62 CTCTGGTGAGAGGAGCC
* * * * *
2544804 TTTTAATATTTAAAGTTTGTTGCCTCTTGTGATAGGAGCTTTCTAAATTTAAAGTCCATTGCCTG
1 TTTTAA-ATTTAAAGTTTGTTGCCTCTGGTCAAAAGAGCTTTCTAAATTTAAAGTCCATTGCCTC
*
2544869 TGGTGAGAGGAGTC
65 TGGTGAGAGGAGCC
* * * * *
2544883 TTTTGAATTTAAAGTTTGTTGCCTCTGGTCAAAAGAGCTTTTTGAATTTAAAGTTTCATAGCCTC
1 TTTTAAATTTAAAGTTTGTTGCCTCTGGTCAAAAGAGCTTTCTAAATTTAAAG-TCCATTGCCTC
* * *
2544948 TGTTTAAAGGAG-C
65 TGGTGAGAGGAGCC
2544961 TTTTCAAATTT
1 TTTT-AAATTT
2544972 TCTTTAAAAA
Statistics
Matches: 137, Mismatches: 27, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
78 46 0.34
79 59 0.43
80 30 0.22
81 2 0.01
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (78 bp):
TTTTAAATTTAAAGTTTGTTGCCTCTGGTCAAAAGAGCTTTCTAAATTTAAAGTCCATTGCCTCT
GGTGAGAGGAGCC
Found at i:2544971 original size:40 final size:40
Alignment explanation
Indices: 2544771--2544971 Score: 146
Period size: 39 Copynumber: 5.1 Consensus size: 40
2544761 GCCTTTTAGT
* * *
2544771 ATTTAAAGTTT-GTTGCCTCTGGTGAGAGGAGCCTTTT-AA
1 ATTTAAAGTTTCATTGCCTCTGGTCAAAGGAG-CTTTTCAA
* * * *
2544810 TATTTAAAGTTT-GTTGCCTCTTGTGATAGGAGC-TTTCTAA
1 -ATTTAAAGTTTCATTGCCTCTGGTCAAAGGAGCTTTTC-AA
* * * * *
2544850 ATTTAAAG-TCCATTGCCTGTGGTGAGAGGAGTCTTTT-GA
1 ATTTAAAGTTTCATTGCCTCTGGTCAAAGGAG-CTTTTCAA
* * **
2544889 ATTTAAAGTTT-GTTGCCTCTGGTCAAAAGAGCTTTTTGA
1 ATTTAAAGTTTCATTGCCTCTGGTCAAAGGAGCTTTTCAA
* * *
2544928 ATTTAAAGTTTCATAGCCTCTGTTTAAAGGAGCTTTTCAA
1 ATTTAAAGTTTCATTGCCTCTGGTCAAAGGAGCTTTTCAA
2544968 ATTT
1 ATTT
2544972 TCTTTAAAAA
Statistics
Matches: 132, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
38 9 0.07
39 62 0.47
40 58 0.44
41 3 0.02
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (40 bp):
ATTTAAAGTTTCATTGCCTCTGGTCAAAGGAGCTTTTCAA
Found at i:2546094 original size:16 final size:15
Alignment explanation
Indices: 2546059--2546088 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2546049 TTTTATGATG
2546059 TTATTGTTAGTTTTA
1 TTATTGTTAGTTTTA
2546074 TTATTGTT-GTTTTA
1 TTATTGTTAGTTTTA
2546088 T
1 T
2546089 ATTATTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (15 bp):
TTATTGTTAGTTTTA
Found at i:2546132 original size:13 final size:13
Alignment explanation
Indices: 2546114--2546156 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2546104 AACTTTTTAG
2546114 AAATAAATAAATA
1 AAATAAATAAATA
2546127 AAATAAA-AAACTA
1 AAATAAATAAA-TA
2546140 AAATAAAATAAAATA
1 AAAT-AAAT-AAATA
2546155 AA
1 AA
2546157 GACCTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 13 0.50
14 3 0.12
15 4 0.15
16 3 0.12
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:2546151 original size:23 final size:22
Alignment explanation
Indices: 2546118--2546165 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
2546108 TTTTAGAAAT
2546118 AAATAAATAAAATAAAAAACTA
1 AAATAAATAAAATAAAAAACTA
* *
2546140 AAATAAAATAAAATAAAGACCTA
1 AAAT-AAATAAAATAAAAAACTA
2546163 AAA
1 AAA
2546166 AATATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (22 bp):
AAATAAATAAAATAAAAAACTA
Found at i:2546318 original size:13 final size:13
Alignment explanation
Indices: 2546287--2546330 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
2546277 TAATTTTTGC
2546287 TAAATAAATAATAA
1 TAAATAAA-AATAA
*
2546301 TAAATAAAAATGA
1 TAAATAAAAATAA
2546314 TAAATAAAAA-AA
1 TAAATAAAAATAA
2546326 TAAAT
1 TAAAT
2546331 TTTTTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 6 0.21
13 14 0.50
14 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
TAAATAAAAATAA
Found at i:2549192 original size:78 final size:79
Alignment explanation
Indices: 2549093--2549243 Score: 277
Period size: 78 Copynumber: 1.9 Consensus size: 79
2549083 ACTAAAATTA
*
2549093 AAAATAAAATTTATTTAAAATTTTAAAATTTTAATTCTAAAAGTATTAAAAGTGATTGTCCAAAC
1 AAAATAAAATTTATTTAAAATTTTAAAACTTTAATTCTAAAAGTATTAAAAGTGATTGTCCAAAC
2549158 TATCCTTATTATGT
66 TATCCTTATTATGT
*
2549172 AAAATTAAA-TTATTTAAAATTTTAAAACTTTAATTCTAAAAGTATTAAAAGTGATTGTCCAAAC
1 AAAATAAAATTTATTTAAAATTTTAAAACTTTAATTCTAAAAGTATTAAAAGTGATTGTCCAAAC
2549236 TATCCTTA
66 TATCCTTA
2549244 CTAAATGTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
78 62 0.89
79 8 0.11
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (79 bp):
AAAATAAAATTTATTTAAAATTTTAAAACTTTAATTCTAAAAGTATTAAAAGTGATTGTCCAAAC
TATCCTTATTATGT
Found at i:2550041 original size:14 final size:17
Alignment explanation
Indices: 2550009--2550041 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2549999 GATCTAACAT
2550009 AAATTATTCTAAGTAAA
1 AAATTATTCTAAGTAAA
2550026 AAATTA-TC-AAGTAAA
1 AAATTATTCTAAGTAAA
2550041 A
1 A
2550042 TAAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
AAATTATTCTAAGTAAA
Found at i:2550523 original size:539 final size:534
Alignment explanation
Indices: 2549166--2550652 Score: 2033
Period size: 539 Copynumber: 2.8 Consensus size: 534
2549156 ACTATCCTTA
*
2549166 TTATGTAAAATTAAATTATTTAAAATTTTAAAACTTTAATTCTAAAAGTATTAAAAGTGATTGTC
1 TTATGTAAAATTAAATTATTTAAAATTTTAAAATTTTAATTCT-AAAGTATTAAAAGTGATTG-C
* *
2549231 C-AAACTATCCTTACTAAATGTTTTTATATGAATTTTTTATTATTAGACTCTTTCCTTTTATAAT
64 CTAAAATATCCTTACT-AATGTTTTTATATGAATTTTTTATTATTAGACTCTTTCTTTTTATAAT
**
2549295 TAGGGTAAAAAAAATACTAAAAGTGATTGATTAAAATACTCTTAATAAAATTTTAATTTAAAAAA
128 TAGACTAAAAAAAATACTAAAAGTGATTGATTAAAATACTCTTAATAAAATTTTAATTTAAAAAA
** * *
2549360 TATTAAAAAATGATTGATCAAAATGCCATTAGCAATTTTTTTAGAAATTTTCATTTAAATGACTT
193 TATT-AAAAATGATTGATCAAAATATCATTAGTAATTTTTTTAGAAATTTTAATTTAAATGACTT
*
2549425 TTTTTATTA--A-ATTCTTTTAATAAGTAAAATGATTTTTCACATTAAATAATCT-TGGTGGTTG
257 TTTTTATTATTAGATTCTTTTTATAAGTAAAATGATTTTTCACATTAAATAATCTAT-GTGGTTG
*
2549486 AATGATCTAACGTAAATTATTCTAAGT-AAAAATTATCAAGTAAACTAAAATTAATTATTTTTGG
321 AATGATCTAACGTAAATTATTCTAAGTAAAAAATTATCAAGTAAAATAAAATTAATTATTTTTGG
* * * ***
2549550 TCAATTCTATT-AA--TAATGA----A--TGA---CA------TAAA-TATCCCTATAAATTTTT
386 TGAATTCT-TTCAAGGTAA-GATTTTATTTTATTTTATTTTTTTAAATTATGTATATAAATTTTT
* * *
2549596 AAATTAACGAATTGATCCTTAAATATGGATCAATTTTATTAATTTATTTAAATTTAATTTAAATA
449 AAATTAACAAATTGATACTTAAATATGGATCAATTTTATTAATTCATTTAAATTTAATTTAAATA
2549661 AACTAAAATTAAAAATAGAGT
514 AACTAAAATTAAAAATAGAGT
*
2549682 TTATGTAAAATTAAATTATTTAAAATTTT--AATTTT-A----AAAGTATTAAAAGTGATTGTCT
1 TTATGTAAAATTAAATTATTTAAAATTTTAAAATTTTAATTCTAAAGTATTAAAAGTGATTGCCT
* *
2549740 AAGATATCCTTACTGAATGTTTTTATATGAATTTTTTATTATTAGACTCTTTCTTTTTGTAATTA
66 AAAATATCCTTACT-AATGTTTTTATATGAATTTTTTATTATTAGACTCTTTCTTTTTATAATTA
*
2549805 -AGCTAAAAAAAATACTAAAAGTGATTGATTAAAATACTTTTAATAAAATTTTAATTTAAAAAA-
130 GA-CTAAAAAAAATACTAAAAGTGATTGATTAAAATACTCTTAATAAAATTTTAATTTAAAAAAT
* *
2549868 AATAAAAATGATTGATCAAATTATCATTAGTAATTTTTTTAGAAATTTTAATTTAAAATGACTTT
194 ATTAAAAATGATTGATCAAAATATCATTAGTAATTTTTTTAGAAATTTTAATTT-AAATGACTTT
*
2549933 TTTTATTATTAGACTCTTTTTATAAGTAAAAT-ATTTTTTCACATTAAATAATCTATGTGGTTGA
258 TTTTATTATTAGATTCTTTTTATAAGTAAAATGA-TTTTTCACATTAAATAATCTATGTGGTTGA
* * *
2549997 ATGATCTAACATAAATTATTCTAAGTAAAAAATTATCAAGTAAAATAAAATTAATTTTTTTTTTG
322 ATGATCTAACGTAAATTATTCTAAGTAAAAAATTATCAAGTAAAATAAAATTAA-TTATTTTTGG
*
2550062 TGATTTCTTTCAAGGTAAGATTTTATTTTATTTTATTTTTTTAAATTATGTATATTAAA-TTTTA
386 TGAATTCTTTCAAGGTAAGATTTTATTTTATTTTATTTTTTTAAATTATGTATA-TAAATTTTTA
* * *
2550126 AATTAACAAATTTATACTTAAATATGTAT-AACTTTTATTAATTCATTTAAATTTAATTTAAATC
450 AATTAACAAATTGATACTTAAATATGGATCAA-TTTTATTAATTCATTTAAATTTAATTTAAATA
*
2550190 GACTAAAATTAAAAATAGAGT
514 AACTAAAATTAAAAATAGAGT
* *
2550211 TTATGTAAAATTAAATTTTTTTTAAAATTTTAAAATTTTAATTCTAAGAGCATTAAAAGTGATTG
1 TTATGTAAAATTAAA--TTATTTAAAATTTTAAAATTTTAATTCTAA-AGTATTAAAAGTGATTG
* *
2550276 CCTAAAATATCCTTACTAATTGTTTTTATATAAATTTTTTATTATTGGACTCTTTCTTTTTATAA
63 CCTAAAATATCCTTACTAA-TGTTTTTATATGAATTTTTTATTATTAGACTCTTTCTTTTTATAA
*
2550341 TTAGACT-AAAAAAATATTAAAAGTGATTGATTAAAATACTCTTAATAAAATTTTAATTTAAAAA
127 TTAGACTAAAAAAAATACTAAAAGTGATTGATTAAAATACTCTTAATAAAATTTTAATTTAAAAA
* * * *
2550405 ATGTTAAAAGTGATTGATCAAAACATCATTAGTAATTTTTTTAGAAATTTTAATTTAAATGAAAT
192 ATATTAAAAATGATTGATCAAAATATCATTAGTAATTTTTTTAGAAATTTTAATTTAAATG-ACT
* * * * *
2550470 TTTTTTATTATTAGATTCTTTTTATAAGTAAAATGATCTTTCACATCAAATAATCCAAGTGGTTA
256 TTTTTTATTATTAGATTCTTTTTATAAGTAAAATGATTTTTCACATTAAATAATCTATGTGGTTG
* * * * * *
2550535 AATGATCTAATGTGAATTATTCTAAGTAAAAAACTATTAAGTGAAATAAAATTAATTGTTTTTGG
321 AATGATCTAACGTAAATTATTCTAAGTAAAAAATTATCAAGTAAAATAAAATTAATTATTTTTGG
*
2550600 TGAATTCTTTCAAGGTAAGATTTTATTTTATTTTATTTTTTAAAATTATGTAT
386 TGAATTCTTTCAAGGTAAGATTTTATTTTATTTTATTTTTTTAAATTATGTAT
2550653 TTATATAACA
Statistics
Matches: 858, Mismatches: 67, Indels: 70
0.86 0.07 0.07
Matches are distributed among these distances:
506 46 0.05
507 21 0.02
508 138 0.16
509 2 0.00
510 71 0.08
511 29 0.03
512 16 0.02
513 3 0.00
514 8 0.01
516 29 0.03
517 1 0.00
519 2 0.00
522 1 0.00
528 6 0.01
529 100 0.12
530 4 0.00
531 13 0.02
533 6 0.01
534 1 0.00
538 124 0.14
539 235 0.27
540 2 0.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (534 bp):
TTATGTAAAATTAAATTATTTAAAATTTTAAAATTTTAATTCTAAAGTATTAAAAGTGATTGCCT
AAAATATCCTTACTAATGTTTTTATATGAATTTTTTATTATTAGACTCTTTCTTTTTATAATTAG
ACTAAAAAAAATACTAAAAGTGATTGATTAAAATACTCTTAATAAAATTTTAATTTAAAAAATAT
TAAAAATGATTGATCAAAATATCATTAGTAATTTTTTTAGAAATTTTAATTTAAATGACTTTTTT
TATTATTAGATTCTTTTTATAAGTAAAATGATTTTTCACATTAAATAATCTATGTGGTTGAATGA
TCTAACGTAAATTATTCTAAGTAAAAAATTATCAAGTAAAATAAAATTAATTATTTTTGGTGAAT
TCTTTCAAGGTAAGATTTTATTTTATTTTATTTTTTTAAATTATGTATATAAATTTTTAAATTAA
CAAATTGATACTTAAATATGGATCAATTTTATTAATTCATTTAAATTTAATTTAAATAAACTAAA
ATTAAAAATAGAGT
Found at i:2552451 original size:148 final size:148
Alignment explanation
Indices: 2552173--2552448 Score: 365
Period size: 148 Copynumber: 1.9 Consensus size: 148
2552163 GACCATTTAT
*
2552173 AATATTTTTTACTCTTTCCAAATGAAGAAGTTAATTGACATCAAAATATCAAAAAAGTCATTTTA
1 AATATTATTTACTCTTTCCAAATGAAGAAGTTAATTGACATCAAAATATCAAAAAAGTCATTTTA
* * * *
2552238 AATAATGGTAATAAGAATGAAGTAACAATTAAAAATATACTATCTTTTCATGTAGTAGAAGAAAT
66 AATAATGGTAATAAGAATGAAGCAACAATTAAAAATATACTAGCTTTTCATGTAGTAAAAAAAAT
2552303 TTTTTATAGAGAATGCGA
131 TTTTTATAGAGAATGCGA
** * * * * * *
2552321 AATATTATTTACTCTTTTTAAATGGAGAATTTGATTGGCATCAAAATATCAAAAAAGTTATTTTG
1 AATATTATTTACTCTTTCCAAATGAAGAAGTTAATTGACATCAAAATATCAAAAAAGTCATTTTA
** * * ** *
2552386 AATGGTGGTAATTAGAATGAAGCAACAATTAAAAATAT-CTAGGTTTTTGTTTAGTAAAAAAAA
66 AATAATGGTAATAAGAATGAAGCAACAATTAAAAATATACTAGCTTTTCATGTAGTAAAAAAAA
2552449 ATTATGAAGA
Statistics
Matches: 108, Mismatches: 20, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
147 18 0.17
148 90 0.83
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (148 bp):
AATATTATTTACTCTTTCCAAATGAAGAAGTTAATTGACATCAAAATATCAAAAAAGTCATTTTA
AATAATGGTAATAAGAATGAAGCAACAATTAAAAATATACTAGCTTTTCATGTAGTAAAAAAAAT
TTTTTATAGAGAATGCGA
Found at i:2553160 original size:22 final size:22
Alignment explanation
Indices: 2553135--2553195 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
2553125 AATTTAGTAG
2553135 TAAATTAATGATAACTTAATAA
1 TAAATTAATGATAACTTAATAA
* * * *
2553157 TAAATGAACGATAA-TGTAGTGA
1 TAAATTAATGATAACT-TAATAA
2553179 TAAA-TAATTGATAACTT
1 TAAATTAA-TGATAACTT
2553196 TTAGTAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
21 3 0.10
22 26 0.87
23 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.34
Consensus pattern (22 bp):
TAAATTAATGATAACTTAATAA
Found at i:2553342 original size:22 final size:22
Alignment explanation
Indices: 2553317--2553396 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 22
2553307 AAAAAATAAG
* *
2553317 TGATAATTTAGTAGTTAATTAT
1 TGATAATTTAATAGTTAATTAA
* * * *
2553339 TGATAACTTAGTA-ATAATCAA
1 TGATAATTTAATAGTTAATTAA
* *
2553360 TGATAATTTAATAGTAAATTAG
1 TGATAATTTAATAGTTAATTAA
*
2553382 TAATAATTTAATAGT
1 TGATAATTTAATAGT
2553397 ATATCAAATT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 16 0.35
22 30 0.65
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (22 bp):
TGATAATTTAATAGTTAATTAA
Found at i:2553456 original size:22 final size:22
Alignment explanation
Indices: 2553431--2553473 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2553421 TAATTGATAG
2553431 TAAATCAA-TGATAAATTAGTAA
1 TAAAT-AATTGATAAATTAGTAA
*
2553453 TAAATAATTGATAATTTAGTA
1 TAAATAATTGATAAATTAGTA
2553474 GTTAATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (22 bp):
TAAATAATTGATAAATTAGTAA
Found at i:2553567 original size:22 final size:21
Alignment explanation
Indices: 2553528--2553614 Score: 61
Period size: 22 Copynumber: 4.0 Consensus size: 21
2553518 TAAATAATTT
* * *
2553528 ATAACATAATAGTTAATCTATA
1 ATAACTTAATAATAAATC-ATA
*
2553550 ATAACTTAATAATAAATCATGC
1 ATAACTTAATAATAAATCAT-A
2553572 ATAA-TCTAAT-ATAAATCAGTA
1 ATAACT-TAATAATAAATCA-TA
* * *
2553593 ATAACTTGATCATGAATCATA
1 ATAACTTAATAATAAATCATA
2553614 A
1 A
2553615 ATAATTTAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
21 21 0.40
22 32 0.60
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (21 bp):
ATAACTTAATAATAAATCATA
Found at i:2553877 original size:33 final size:33
Alignment explanation
Indices: 2553838--2553909 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
2553828 AGTTAATCAT
* * * *
2553838 TGATAACTTTTTAGTAAATTATCAGTAACTTAA
1 TGATAACTTTATAATAAATCATCAATAACTTAA
*
2553871 TTATAACTTTATAATAAATCATCAATAACTTAA
1 TGATAACTTTATAATAAATCATCAATAACTTAA
2553904 TGATAA
1 TGATAA
2553910 ATCACCAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (33 bp):
TGATAACTTTATAATAAATCATCAATAACTTAA
Found at i:2553985 original size:22 final size:22
Alignment explanation
Indices: 2553873--2553985 Score: 99
Period size: 22 Copynumber: 5.2 Consensus size: 22
2553863 TAACTTAATT
* *
2553873 ATAACTTTATAATAAATCA-TC
1 ATAACTTAATGATAAATCATTC
*
2553894 AATAACTTAATGATAAATCA-CC
1 -ATAACTTAATGATAAATCATTC
* * *
2553916 AACAATTTAAT-AGAAATCATTC
1 -ATAACTTAATGATAAATCATTC
* *
2553938 ACAACTTAATGATAAAT-ATTTT
1 ATAACTTAATGATAAATCA-TTC
2553960 ATAACTTAATGATAAATCATTC
1 ATAACTTAATGATAAATCATTC
2553982 ATAA
1 ATAA
2553986 AATAAAAGTA
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
21 17 0.23
22 57 0.76
23 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (22 bp):
ATAACTTAATGATAAATCATTC
Found at i:2554031 original size:22 final size:22
Alignment explanation
Indices: 2554003--2554044 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2553993 GTAAATATCA
*
2554003 TTGATAATTTAGTAGTAAATCT
1 TTGATAATTTAGTAATAAATCT
2554025 TTGATAATTTAGTAATAAAT
1 TTGATAATTTAGTAATAAAT
2554045 AACTGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (22 bp):
TTGATAATTTAGTAATAAATCT
Found at i:2554051 original size:22 final size:22
Alignment explanation
Indices: 2554004--2554053 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2553994 TAAATATCAT
* ***
2554004 TGATAATTTAGTAGTAAATCTT
1 TGATAATTTAGTAATAAATAAC
2554026 TGATAATTTAGTAATAAATAAC
1 TGATAATTTAGTAATAAATAAC
2554048 TGATAA
1 TGATAA
2554054 ATTAATTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (22 bp):
TGATAATTTAGTAATAAATAAC
Found at i:2554390 original size:22 final size:22
Alignment explanation
Indices: 2554365--2554616 Score: 77
Period size: 22 Copynumber: 11.7 Consensus size: 22
2554355 ACTTAACAAA
*
2554365 AAATCAATTATAACTTAATAGT
1 AAATCAATGATAACTTAATAGT
* *
2554387 AAATTAGTGATAACTTAATAGT
1 AAATCAATGATAACTTAATAGT
* * * * *
2554409 AATTAAAT-CTCAATTTAGTAGT
1 AAATCAATGAT-AACTTAATAGT
* * * *
2554431 -AGTTAATTGATAAATTTAGTAGT
1 AAATCAA-TGAT-AACTTAATAGT
* * *
2554454 AAAT-TATAAATAATTTAATAGT
1 AAATCAAT-GATAACTTAATAGT
*
2554476 AAATCAATGATAATTTAATAGT
1 AAATCAATGATAACTTAATAGT
** * *
2554498 TTAT-ATTGA-AA-TCTAAAAGT
1 AAATCAATGATAACT-TAATAGT
2554518 AAATCAAT-ATAACTTAGTAGTAGT
1 AAATCAATGATAACTTA--A-TAGT
* *
2554542 TAATC-ATCAATAACTTAATAGT
1 AAATCAAT-GATAACTTAATAGT
2554564 ---T-AA--ATAACTTAATAGT
1 AAATCAATGATAACTTAATAGT
* *
2554580 AAAT-TATGGATAATTTAATA-T
1 AAATCAAT-GATAACTTAATAGT
*
2554601 AAATTAATGATAACTT
1 AAATCAATGATAACTT
2554617 GATTATGAAT
Statistics
Matches: 175, Mismatches: 32, Indels: 47
0.69 0.13 0.19
Matches are distributed among these distances:
16 13 0.07
19 5 0.03
20 11 0.06
21 27 0.15
22 81 0.46
23 21 0.12
24 9 0.05
25 8 0.05
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (22 bp):
AAATCAATGATAACTTAATAGT
Found at i:2554464 original size:19 final size:20
Alignment explanation
Indices: 2554427--2554464 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2554417 CTCAATTTAG
*
2554427 TAGTAGTTAATTGATAAATT
1 TAGTAGTAAATTGATAAATT
2554447 TAGTAGTAAATT-ATAAAT
1 TAGTAGTAAATTGATAAAT
2554465 AATTTAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (20 bp):
TAGTAGTAAATTGATAAATT
Found at i:2554571 original size:16 final size:15
Alignment explanation
Indices: 2554550--2554583 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
2554540 GTTAATCATC
2554550 AATAACTTAATAGTTA
1 AATAACTTAATAG-TA
2554566 AATAACTTAATAGTA
1 AATAACTTAATAGTA
2554581 AAT
1 AAT
2554584 TATGGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
AATAACTTAATAGTA
Found at i:2554612 original size:21 final size:22
Alignment explanation
Indices: 2554567--2554616 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
2554557 TAATAGTTAA
2554567 ATAACTTAATAGTAAATTATGG
1 ATAACTTAATAGTAAATTATGG
*
2554589 ATAATTTAATA-TAAATTAAT-G
1 ATAACTTAATAGTAAATT-ATGG
2554610 ATAACTT
1 ATAACTT
2554617 GATTATGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTATGG
Found at i:2554742 original size:22 final size:22
Alignment explanation
Indices: 2554676--2554765 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 22
2554666 TAAATCAAAA
* *
2554676 AATA-AATAGTAAATTAATGAT
1 AATATAATAGTAAATCATTGAT
* * * *
2554697 AACAAAATAATAAATGCA-TAAT
1 AATATAATAGTAAAT-CATTGAT
2554719 AATATAATAGTAAATCATTGAT
1 AATATAATAGTAAATCATTGAT
* *
2554741 AAT-TTATATGTAAATTATTGAT
1 AATATAATA-GTAAATCATTGAT
2554763 AAT
1 AAT
2554766 TTAGTTGTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
21 9 0.16
22 45 0.82
23 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (22 bp):
AATATAATAGTAAATCATTGAT
Found at i:2554766 original size:22 final size:22
Alignment explanation
Indices: 2554728--2554779 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2554718 TAATATAATA
*
2554728 GTAAATCATTGATAATTTA-TAT
1 GTAAATTATTGATAATTTAGT-T
2554750 GTAAATTATTGATAATTTAGTT
1 GTAAATTATTGATAATTTAGTT
2554772 GTAAATTA
1 GTAAATTA
2554780 GTCAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (22 bp):
GTAAATTATTGATAATTTAGTT
Found at i:2554824 original size:22 final size:22
Alignment explanation
Indices: 2554799--2554977 Score: 161
Period size: 22 Copynumber: 8.1 Consensus size: 22
2554789 TAATATCTTT
*
2554799 ATAGTAAATCA-TCATTAAATTA
1 ATAGTAAATCATTCA-TAATTTA
2554821 ATAGTAAATCAGTT-ATAACTTTA
1 ATAGTAAATCA-TTCATAA-TTTA
* *
2554844 TTA-CAAATCATT-AGTAATTTA
1 ATAGTAAATCATTCA-TAATTTA
* *
2554865 ATAGTAAATCATTAACAATTTA
1 ATAGTAAATCATTCATAATTTA
*
2554887 ATAATAAATCATTCATAATTTA
1 ATAGTAAATCATTCATAATTTA
* * *
2554909 GTACTAAATCATTCATAAGTTA
1 ATAGTAAATCATTCATAATTTA
*
2554931 ATAGTAAATCAAT-ACTAATTTA
1 ATAGTAAATCATTCA-TAATTTA
* * *
2554953 GTAATAAATCATTGATAATTTA
1 ATAGTAAATCATTCATAATTTA
2554975 ATA
1 ATA
2554978 ATATATCACT
Statistics
Matches: 129, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
21 10 0.08
22 110 0.85
23 8 0.06
24 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (22 bp):
ATAGTAAATCATTCATAATTTA
Found at i:2554876 original size:66 final size:66
Alignment explanation
Indices: 2554799--2554974 Score: 182
Period size: 66 Copynumber: 2.7 Consensus size: 66
2554789 TAATATCTTT
** * *
2554799 ATAGTAAATCATCATTAAATTAATAGTAAATCAGTT-ATAACTTTATTAC-AAATCATT-AGTAA
1 ATAGTAAATCATCAACAAATTAATAATAAATCA-TTCATAA-TTTAGTACTAAATCATTCA-TAA
*
2554861 TTTA
63 GTTA
* *
2554865 ATAGTAAATCATTAACAATTTAATAATAAATCATTCATAATTTAGTACTAAATCATTCATAAGTT
1 ATAGTAAATCATCAACAAATTAATAATAAATCATTCATAATTTAGTACTAAATCATTCATAAGTT
2554930 A
66 A
* * *
2554931 ATAGTAAATCA--ATACTAATTTAGTAATAAATCATTGATAATTTA
1 ATAGTAAATCATCA-AC-AAATTAATAATAAATCATTCATAATTTA
2554975 ATAATATATC
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
64 1 0.01
65 11 0.11
66 83 0.86
67 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (66 bp):
ATAGTAAATCATCAACAAATTAATAATAAATCATTCATAATTTAGTACTAAATCATTCATAAGTT
A
Found at i:2555002 original size:66 final size:66
Alignment explanation
Indices: 2554862--2555005 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 66
2554852 CATTAGTAAT
* * * *
2554862 TTAATAGTAAATCATTAACAATTTAATAATAAATCATTCATAATTTAGTACTAAATCATTCATAA
1 TTAATAGTAAATCAATAACAATTTAATAATAAATCATTCATAATTTAATAATAAATCACTCATAA
2554927 G
66 G
* * * *
2554928 TTAATAGTAAATCAAT-ACTAATTTAGTAATAAATCATTGATAATTTAATAATATATCACTGAT-
1 TTAATAGTAAATCAATAAC-AATTTAATAATAAATCATTCATAATTTAATAATAAATCACTCATA
2554991 AG
65 AG
*
2554993 CTTAGTAGTAAAT
1 -TTAATAGTAAAT
2555006 TGTTGATAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 4 0.06
66 63 0.94
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (66 bp):
TTAATAGTAAATCAATAACAATTTAATAATAAATCATTCATAATTTAATAATAAATCACTCATAA
G
Found at i:2555005 original size:44 final size:43
Alignment explanation
Indices: 2554822--2555005 Score: 156
Period size: 44 Copynumber: 4.2 Consensus size: 43
2554812 ATTAAATTAA
* * * *
2554822 TAGTAAATCAGTT-ATAACTTT-ATTACAAATCATTAGTAATTTAA
1 TAGTAAATCA-TTAATAA-TTTAATAATAAATCAATA-TAATTTAG
* *
2554866 TAGTAAATCATTAACAATTTAATAATAAATCATTCATAATTTAG
1 TAGTAAATCATTAATAATTTAATAATAAATCAAT-ATAATTTAG
* * * *
2554910 TACTAAATCATTCATAAGTTAATAGTAAATCAATACTAATTTAG
1 TAGTAAATCATTAATAATTTAATAATAAATCAATA-TAATTTAG
* * * * **
2554954 TAATAAATCATTGATAATTTAATAATATATCACTGATAGCTTAG
1 TAGTAAATCATTAATAATTTAATAATAAATCAAT-ATAATTTAG
2554998 TAGTAAAT
1 TAGTAAAT
2555006 TGTTGATAGT
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
43 6 0.05
44 108 0.93
45 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (43 bp):
TAGTAAATCATTAATAATTTAATAATAAATCAATATAATTTAG
Found at i:2555440 original size:20 final size:21
Alignment explanation
Indices: 2555393--2555442 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2555383 AACGATTACG
* *
2555393 AAAATTGTATCGAAAGTTATT
1 AAAATTTTATCAAAAGTTATT
2555414 AAAATTTTATCAAAAGTTA-T
1 AAAATTTTATCAAAAGTTATT
*
2555434 CAAATTTTA
1 AAAATTTTA
2555443 CATATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
AAAATTTTATCAAAAGTTATT
Found at i:2556561 original size:26 final size:28
Alignment explanation
Indices: 2556508--2556561 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
2556498 AGACATTATT
*
2556508 ATATAAATTAAAATTATTTTAATTTTAAA
1 ATATAAATTAAAA-TATTTTAATATTAAA
2556537 ATAT-AATTAAAA-ATTTTAATATTAA
1 ATATAAATTAAAATATTTTAATATTAA
2556562 TAGAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 12 0.50
28 8 0.33
29 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATAAATTAAAATATTTTAATATTAAA
Found at i:2556568 original size:19 final size:20
Alignment explanation
Indices: 2556528--2556572 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
2556518 AAATTATTTT
2556528 AATTTTAAAATATAATTAAA
1 AATTTTAAAATATAATTAAA
*
2556548 AATTTTAATAT-TAA-TAGAA
1 AATTTTAAAATATAATTA-AA
2556567 AATTTT
1 AATTTT
2556573 TCATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTTTAAAATATAATTAAA
Found at i:2556570 original size:26 final size:27
Alignment explanation
Indices: 2556512--2556570 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
2556502 ATTATTATAT
* *
2556512 AAATTAAAATTATTTTAATTTTAAAATA
1 AAATTAAAA-TATTTTAATATTAAAAGA
* *
2556540 TAATTAAAA-ATTTTAATATTAATAGA
1 AAATTAAAATATTTTAATATTAAAAGA
2556566 AAATT
1 AAATT
2556571 TTTCATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 18 0.69
28 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAATTAAAATATTTTAATATTAAAAGA
Found at i:2565577 original size:2 final size:2
Alignment explanation
Indices: 2565570--2565615 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2565560 GAAAGAAAGA
2565570 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2565612 AG AG
1 AG AG
2565616 GACGAAGATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2570703 original size:30 final size:30
Alignment explanation
Indices: 2570667--2570727 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2570657 TGTATTCATG
*
2570667 TTGCTTTTTATATTGCAATGAAATTATACT
1 TTGCTTTTTATATTACAATGAAATTATACT
2570697 TTGCTTTTTATATTACAATGAAATTATACT
1 TTGCTTTTTATATTACAATGAAATTATACT
2570727 T
1 T
2570728 ACTTTTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (30 bp):
TTGCTTTTTATATTACAATGAAATTATACT
Found at i:2572089 original size:8 final size:7
Alignment explanation
Indices: 2572067--2572184 Score: 56
Period size: 7 Copynumber: 15.3 Consensus size: 7
2572057 AACCACTCAC
2572067 CCTAAAA
1 CCTAAAA
2572074 CCCTTAAAA
1 -CC-TAAAA
2572083 CTCTAAAA
1 C-CTAAAA
2572091 CCTCAAAA
1 CCT-AAAA
2572099 CCTTAAAA
1 CC-TAAAA
*
2572107 CTTAAAAAA
1 CCT--AAAA
*
2572116 TCTAAAA
1 CCTAAAA
*
2572123 TCCTAAAC
1 -CCTAAAA
*
2572131 CCTAAAC
1 CCTAAAA
*
2572138 CCTAAAC
1 CCTAAAA
2572145 CCTAAATA
1 CCTAAA-A
* *
2572153 CTTAAGA
1 CCTAAAA
*
2572160 CCCAAAA
1 CCTAAAA
2572167 CCTTCAAAA
1 CC-T-AAAA
*
2572176 CCCAAAA
1 CCTAAAA
2572183 CC
1 CC
2572185 CCAAATACTT
Statistics
Matches: 87, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
7 40 0.46
8 29 0.33
9 18 0.21
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.19
Consensus pattern (7 bp):
CCTAAAA
Found at i:2572129 original size:24 final size:25
Alignment explanation
Indices: 2572068--2572122 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
2572058 ACCACTCACC
**
2572068 CTAAAACCCTTAAAACTCTAAAACCT
1 CTAAAA-CCTTAAAACTCTAAAAAAT
2572094 C-AAAACCTTAAAACT-TAAAAAAT
1 CTAAAACCTTAAAACTCTAAAAAAT
2572117 CTAAAA
1 CTAAAA
2572123 TCCTAAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 7 0.27
24 14 0.54
25 4 0.15
26 1 0.04
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.22
Consensus pattern (25 bp):
CTAAAACCTTAAAACTCTAAAAAAT
Found at i:2572215 original size:39 final size:39
Alignment explanation
Indices: 2572118--2572215 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 39
2572108 TTAAAAAATC
* * *
2572118 TAAAATCCTAAACCC-T-AAACCCTAAACCCTAAATACT
1 TAAAACCCTAAACCCTTAAAACCCAAAACCCCAAATACT
* *
2572155 TAAGACCC-AAAACCTTCAAAACCCAAAACCCCAAATACT
1 TAAAACCCTAAACCCTT-AAAACCCAAAACCCCAAATACT
*
2572194 TAAAACCCTACACCCTTAAAAC
1 TAAAACCCTAAACCCTTAAAAC
2572216 TCCATGGCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
36 5 0.10
37 7 0.14
39 31 0.63
40 6 0.12
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.17
Consensus pattern (39 bp):
TAAAACCCTAAACCCTTAAAACCCAAAACCCCAAATACT
Found at i:2572393 original size:1 final size:1
Alignment explanation
Indices: 2572389--2572438 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
2572379 ATGAGAAGAG
* ** * *
2572389 AAAAAAAAAAAAAAAAGAAAAAAAAAGGAAAAAAAAAAGAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2572439 TGAAAGAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:2572409 original size:11 final size:11
Alignment explanation
Indices: 2572389--2572443 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
2572379 ATGAGAAGAG
2572389 AAAAAA-AAAA
1 AAAAAAGAAAA
2572399 AAAAAAGAAAA
1 AAAAAAGAAAA
*
2572410 AAAAAGGAAAA
1 AAAAAAGAAAA
2572421 AAAAAAGAAAA
1 AAAAAAGAAAA
2572432 GAAAAAATGAAA
1 -AAAAAA-GAAA
2572444 GAATGAGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
10 6 0.15
11 24 0.60
12 6 0.15
13 4 0.10
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:2572409 original size:12 final size:12
Alignment explanation
Indices: 2572389--2572443 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
2572379 ATGAGAAGAG
2572389 AAAAA-AAAAAA
1 AAAAAGAAAAAA
2572400 AAAAAG--AAAA
1 AAAAAGAAAAAA
*
2572410 AAAAAGGAAAAA
1 AAAAAGAAAAAA
2572422 AAAAAGAAAAGAA
1 AAAAAGAAAA-AA
*
2572435 AAAATGAAA
1 AAAAAGAAA
2572444 GAATGAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 10 0.26
11 5 0.13
12 13 0.34
13 10 0.26
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:2572444 original size:12 final size:12
Alignment explanation
Indices: 2572384--2572446 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 12
2572374 GAAAAATGAG
2572384 AAGAGAAAAAA-A
1 AAGA-AAAAAAGA
2572396 AA-AAAAAAAGA
1 AAGAAAAAAAGA
*
2572407 AA-AAAAAAGGA
1 AAGAAAAAAAGA
2572418 AA-AAAAAAAGAA
1 AAGAAAAAAAG-A
*
2572430 AAGAAAAAATGA
1 AAGAAAAAAAGA
2572442 AAGAA
1 AAGAA
2572447 TGAGAAAATG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
10 6 0.13
11 21 0.47
12 11 0.24
13 7 0.16
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:2572444 original size:17 final size:17
Alignment explanation
Indices: 2572388--2572477 Score: 60
Period size: 17 Copynumber: 5.3 Consensus size: 17
2572378 AATGAGAAGA
* *
2572388 GAAAAAAAAAAAAAAAA
1 GAAAAAAAAGAAAAAAT
2572405 GAAAAAAAAAGGAAAAAA-
1 G-AAAAAAAA-GAAAAAAT
2572423 -AAAAGAAAAGAAAAAAT
1 GAAAA-AAAAGAAAAAAT
* * *
2572440 G-AAAGAATGAGAAAAT
1 GAAAAAAAAGAAAAAAT
* * *
2572456 GTAAAAGAAGAGAAAAT
1 GAAAAAAAAGAAAAAAT
2572473 GAAAA
1 GAAAA
2572478 CTCAAATTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
16 21 0.36
17 24 0.41
18 8 0.14
19 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (17 bp):
GAAAAAAAAGAAAAAAT
Found at i:2572462 original size:18 final size:16
Alignment explanation
Indices: 2572430--2572477 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
2572420 AAAAAAAGAA
*
2572430 AAGAAAAAATG-AAAG
1 AAGAGAAAATGAAAAG
2572445 AATGAGAAAATGTAAAAG
1 AA-GAGAAAATG-AAAAG
2572463 AAGAGAAAATGAAAA
1 AAGAGAAAATGAAAA
2572478 CTCAAATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
17 9 0.31
18 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (16 bp):
AAGAGAAAATGAAAAG
Found at i:2573672 original size:25 final size:24
Alignment explanation
Indices: 2573627--2573901 Score: 182
Period size: 25 Copynumber: 11.6 Consensus size: 24
2573617 TTTAAGTCTT
2573627 AAATGAGAATC-TTAAGATGTTTTC
1 AAATGAGAATCTTTAAGA-GTTTTC
* *
2573651 AGATGAAAATCTTTAAGATGTTTTC
1 AAATGAGAATCTTTAAGA-GTTTTC
* * *
2573676 AGATGAGAGTCTTT--GAGTCTT-
1 AAATGAGAATCTTTAAGAGTTTTC
*
2573697 AAATGAGAATCTTTAAGAGGTTTTT
1 AAATGAGAATCTTTAAGA-GTTTTC
* *
2573722 AAATGAGAACCTTT--GAGTCTT-
1 AAATGAGAATCTTTAAGAGTTTTC
*
2573743 AAATGAAAATCTTTAAGAGGTTTTC
1 AAATGAGAATCTTTAAGA-GTTTTC
* *
2573768 AAATGAGAATCTTT--GAATCTT-
1 AAATGAGAATCTTTAAGAGTTTTC
* *
2573789 AAATGAAAATCTTTAAGACGTTTTG
1 AAATGAGAATCTTTAAGA-GTTTTC
* * * *
2573814 AAATAATAACCTTT--GAGTCTT-
1 AAATGAGAATCTTTAAGAGTTTTC
2573835 AAATGAGAATCTTTAAGACGTTTTC
1 AAATGAGAATCTTTAAGA-GTTTTC
* *
2573860 AAATGAAAATATTTGAATTTTGAG-TTTC
1 AAATGAGAATCTTT-AA----GAGTTTTC
2573888 AAATGAGAATCTTT
1 AAATGAGAATCTTT
2573902 GAGGTGTGAA
Statistics
Matches: 198, Mismatches: 31, Indels: 40
0.74 0.12 0.15
Matches are distributed among these distances:
21 48 0.24
22 15 0.08
23 16 0.08
24 24 0.12
25 74 0.37
26 2 0.01
28 16 0.08
29 1 0.01
30 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (24 bp):
AAATGAGAATCTTTAAGAGTTTTC
Found at i:2573774 original size:92 final size:92
Alignment explanation
Indices: 2573653--2573877 Score: 333
Period size: 92 Copynumber: 2.4 Consensus size: 92
2573643 ATGTTTTCAG
* * * * * *
2573653 ATGAAAATCTTTAAGATGTTTTCAGATGAGAGTCTTTGAGTCTTAAATGAGAATCTTTAAGAGGT
1 ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAATCTTAAATGAAAATCTTTAAGACGT
* *
2573718 TTTTAAATGAGAACCTTTGAGTCTTAA
66 TTTGAAATAAGAACCTTTGAGTCTTAA
*
2573745 ATGAAAATCTTTAAGAGGTTTTCAAATGAGAATCTTTGAATCTTAAATGAAAATCTTTAAGACGT
1 ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAATCTTAAATGAAAATCTTTAAGACGT
*
2573810 TTTGAAATAATAACCTTTGAGTCTTAA
66 TTTGAAATAAGAACCTTTGAGTCTTAA
* * *
2573837 ATGAGAATCTTTAAGACGTTTTCAAATGAAAATATTTGAAT
1 ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAAT
2573878 TTTGAGTTTC
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 120 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (92 bp):
ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAATCTTAAATGAAAATCTTTAAGACGT
TTTGAAATAAGAACCTTTGAGTCTTAA
Found at i:2573875 original size:46 final size:46
Alignment explanation
Indices: 2573653--2573875 Score: 302
Period size: 46 Copynumber: 4.8 Consensus size: 46
2573643 ATGTTTTCAG
* * *
2573653 ATGAAAATCTTTAAGATGTTTTCAGATGAGAGTCTTTGAGTCTTAA
1 ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTCTTAA
* * * *
2573699 ATGAGAATCTTTAAGAGGTTTTTAAATGAGAACCTTTGAGTCTTAA
1 ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTCTTAA
* *
2573745 ATGAAAATCTTTAAGAGGTTTTCAAATGAGAATCTTTGAATCTTAA
1 ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTCTTAA
* * * *
2573791 ATGAAAATCTTTAAGACGTTTTGAAATAATAACCTTTGAGTCTTAA
1 ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTCTTAA
* * *
2573837 ATGAGAATCTTTAAGACGTTTTCAAATGAAAATATTTGA
1 ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGA
2573876 ATTTTGAGTT
Statistics
Matches: 155, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 155 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (46 bp):
ATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTCTTAA
Found at i:2574455 original size:41 final size:41
Alignment explanation
Indices: 2574327--2574676 Score: 313
Period size: 42 Copynumber: 8.2 Consensus size: 41
2574317 CAAGGAACCT
* * ** *
2574327 TTTATTTTTCAAAGTTGTAATGCCTCTGTTTAGAGGAGCAT
1 TTTATTTTTCAAAATTATGGTGCCTCTGTTTAGAGGAGCAA
* * *
2574368 TTTATTTTTCAAAAGTAGTGGTGCCTCTATTTAGAGGAGCAT
1 TTTATTTTTCAAAATTA-TGGTGCCTCTGTTTAGAGGAGCAA
* * *
2574410 TTTATTTTTCAAAATTATGGTGCCTCTGTTTAAAAGAGTAA
1 TTTATTTTTCAAAATTATGGTGCCTCTGTTTAGAGGAGCAA
* * *
2574451 TTTATTTTTCAAAGTTTTGGTTGCCCCTGTTTAGAGGAGCAA
1 TTTATTTTTCAAAATTATGG-TGCCTCTGTTTAGAGGAGCAA
* * * *
2574493 TTTATTTTTTAAAAGTTGTGGTACCTCTGTTTAGATGAGCAA
1 TTTATTTTTCAAAA-TTATGGTGCCTCTGTTTAGAGGAGCAA
* * * *
2574535 TTTATTTTTCAAAGTTTCAAAGTTGTGGTGCCTCTATTTGGAAGAGCAA
1 TTTATTTTTC--A-----AAA-TTATGGTGCCTCTGTTTAGAGGAGCAA
* * * * *
2574584 TTTATTTTACAAAGTTATAGTGCCTCTGTTTAGAAGAGCATT
1 TTTATTTTTCAAAATTATGGTGCCTCTGTTTAGAGGAGCA-A
* * * *
2574626 TTTATTTTTTAAAGTTATGGTGCTTCTGTTTAGAGGAGCAT
1 TTTATTTTTCAAAATTATGGTGCCTCTGTTTAGAGGAGCAA
2574667 TTTATTTTTC
1 TTTATTTTTC
2574677 TCAAAGTCGT
Statistics
Matches: 256, Mismatches: 42, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
41 83 0.32
42 130 0.51
43 5 0.02
44 1 0.00
47 1 0.00
49 36 0.14
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (41 bp):
TTTATTTTTCAAAATTATGGTGCCTCTGTTTAGAGGAGCAA
Found at i:2574484 original size:83 final size:82
Alignment explanation
Indices: 2574326--2574676 Score: 342
Period size: 83 Copynumber: 4.1 Consensus size: 82
2574316 TCAAGGAACC
* * * * * **
2574326 TTTTATTTTTCAAAGTTGTAATGCCTCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTAGTGGTG
1 TTTTATTTTTCAAAATTATAGTGCCTCTGTTTAGAAGAGCAATTTATTTTTC-AAAGTTTTGGTG
2574391 CCTCTATTTAGAGGAGCA
65 CCTCTATTTAGAGGAGCA
* * *
2574409 TTTTATTTTTCAAAATTATGGTGCCTCTGTTTAAAAGAGTAATTTATTTTTCAAAGTTTTGGTTG
1 TTTTATTTTTCAAAATTATAGTGCCTCTGTTTAGAAGAGCAATTTATTTTTCAAAGTTTTGG-TG
* *
2574474 CCCCTGTTTAGAGGAGCA
65 CCTCTATTTAGAGGAGCA
* * * * * *
2574492 ATTTATTTTTTAAAAGTTGTGGTACCTCTGTTTAGATGAGCAATTTATTTTTCAAAGTTTCAAAG
1 TTTTATTTTTCAAAA-TTATAGTGCCTCTGTTTAGAAGAGCAATTTATTTTTCAAAG--T-----
* *
2574557 TTGTGGTGCCTCTATTTGGAAGAGCA
58 TT-TGGTGCCTCTATTTAGAGGAGCA
* * * * * *
2574583 ATTTATTTTACAAAGTTATAGTGCCTCTGTTTAGAAGAGCATTTTTATTTTTTAAAGTTATGGTG
1 TTTTATTTTTCAAAATTATAGTGCCTCTGTTTAGAAGAGCA-ATTTATTTTTCAAAGTTTTGGTG
* *
2574648 CTTCTGTTTAGAGGAGCA
65 CCTCTATTTAGAGGAGCA
2574666 TTTTATTTTTC
1 TTTTATTTTTC
2574677 TCAAAGTCGT
Statistics
Matches: 218, Mismatches: 39, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
82 8 0.04
83 103 0.47
84 37 0.17
86 1 0.00
89 1 0.00
90 22 0.10
91 43 0.20
92 3 0.01
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (82 bp):
TTTTATTTTTCAAAATTATAGTGCCTCTGTTTAGAAGAGCAATTTATTTTTCAAAGTTTTGGTGC
CTCTATTTAGAGGAGCA
Found at i:2574582 original size:49 final size:49
Alignment explanation
Indices: 2574504--2574599 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
2574494 TTATTTTTTA
* * *
2574504 AAAGTTGTGGTACCTCTGTTTAGATGAGCAATTTATTTTTCAAAGTTTC
1 AAAGTTGTGGTACCTCTATTTAGAAGAGCAATTTATTTTACAAAGTTTC
* *
2574553 AAAGTTGTGGTGCCTCTATTTGGAAGAGCAATTTATTTTACAAAGTT
1 AAAGTTGTGGTACCTCTATTTAGAAGAGCAATTTATTTTACAAAGTT
2574600 ATAGTGCCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (49 bp):
AAAGTTGTGGTACCTCTATTTAGAAGAGCAATTTATTTTACAAAGTTTC
Found at i:2574657 original size:174 final size:176
Alignment explanation
Indices: 2574374--2574702 Score: 448
Period size: 174 Copynumber: 1.9 Consensus size: 176
2574364 GCATTTTATT
* * * *
2574374 TTTCAAAAGTAGTGGTGCCTCTATTTAGAGGAGCATTTTATTTTTCAAAATTATGGTGCCTCTGT
1 TTTCAAAAGTAGTGGTGCCTCTATTTAGAAGAGCAATTTATTTTACAAAATTATAGTGCCTCTGT
* *
2574439 TTAAAAGAGTAATTTATTTTTCAAAGTTTTGGTTGCCCCTGTTTAGAGGAGCAATTTATTTTT-T
66 TTAAAAGAGCAATTTATTTTTCAAAGTTATGGTTGCCCCTGTTTAGAGGAGCAATTTATTTTTCT
* *
2574503 AAAAGTTGTGGTACCTCTGTTTAGATGAGCAATTTATTTTTCAAAG
131 AAAAGTCGTGGAACCTCTGTTTAGATGAGCAATTTATTTTTCAAAG
* * *
2574549 TTTC-AAAGTTGTGGTGCCTCTATTTGGAAGAGCAATTTATTTTACAAAGTTATAGTGCCTCTGT
1 TTTCAAAAGTAGTGGTGCCTCTATTTAGAAGAGCAATTTATTTTACAAAATTATAGTGCCTCTGT
* * * ** *
2574613 TTAGAAGAGCATTTTTATTTTTTAAAGTTATGG-TGCTTCTGTTTAGAGGAGCATTTTATTTTTC
66 TTAAAAGAGCA-ATTTATTTTTCAAAGTTATGGTTGCCCCTGTTTAGAGGAGCAATTTATTTTTC
* * *
2574677 TCAAAGTCGTTGAATCTCTGTTTAGA
130 TAAAAGTCGTGGAACCTCTGTTTAGA
2574703 GGAACTTTGT
Statistics
Matches: 132, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
174 89 0.67
175 43 0.33
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (176 bp):
TTTCAAAAGTAGTGGTGCCTCTATTTAGAAGAGCAATTTATTTTACAAAATTATAGTGCCTCTGT
TTAAAAGAGCAATTTATTTTTCAAAGTTATGGTTGCCCCTGTTTAGAGGAGCAATTTATTTTTCT
AAAAGTCGTGGAACCTCTGTTTAGATGAGCAATTTATTTTTCAAAG
Found at i:2576095 original size:11 final size:11
Alignment explanation
Indices: 2576081--2576121 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2576071 AATTTTTAAA
2576081 AAATATAAAAT
1 AAATATAAAAT
2576092 AAATATAAAAT
1 AAATATAAAAT
*
2576103 AAATTTTAAGAAT
1 AAA-TATAA-AAT
2576116 AAATAT
1 AAATAT
2576122 TAATTATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 14 0.54
12 6 0.23
13 6 0.23
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:2577183 original size:23 final size:23
Alignment explanation
Indices: 2577143--2577207 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
2577133 TGTTATGACA
*
2577143 CCTTAAATACTCAAAACCCTAAAC
1 CCTTAAA-ACCCAAAACCCTAAAC
*
2577167 CCTTAAAACCCAAAACCCTAAAT
1 CCTTAAAACCCAAAACCCTAAAC
* *
2577190 ACTCAAAACCCTAAAACC
1 CCTTAAAACCC-AAAACC
2577208 TTTAAAACCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 23 0.64
24 13 0.36
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (23 bp):
CCTTAAAACCCAAAACCCTAAAC
Found at i:2577200 original size:39 final size:40
Alignment explanation
Indices: 2577146--2577253 Score: 148
Period size: 39 Copynumber: 2.8 Consensus size: 40
2577136 TATGACACCT
2577146 TAAATACTCAAAACCCT-AAACCCTTAAAACCCAAAACCC
1 TAAATACTCAAAACCCTAAAACCCTTAAAACCCAAAACCC
* * *
2577185 TAAATACTCAAAACCCTAAAACCTTTAAAACCCTAAACCT
1 TAAATACTCAAAACCCTAAAACCCTTAAAACCCAAAACCC
* * *
2577225 TAAACACTTAAAA-CCTAAAACCCTAAAAA
1 TAAATACTCAAAACCCTAAAACCCTTAAAA
2577254 TATAAACCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 31 0.51
40 30 0.49
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.19
Consensus pattern (40 bp):
TAAATACTCAAAACCCTAAAACCCTTAAAACCCAAAACCC
Found at i:2577253 original size:16 final size:15
Alignment explanation
Indices: 2577163--2577252 Score: 85
Period size: 16 Copynumber: 5.7 Consensus size: 15
2577153 TCAAAACCCT
*
2577163 AAACCCTTAAAACCCA
1 AAACCC-TAAAACCTA
2577179 AAACCCTAAATA-CTCA
1 AAACCCTAAA-ACCT-A
2577195 AAACCCTAAAACCTTTA
1 AAACCCTAAAACC--TA
*
2577212 AAACCCT-AAACCTT
1 AAACCCTAAAACCTA
*
2577226 AAACACTTAAAACCTA
1 AAAC-CCTAAAACCTA
2577242 AAACCCTAAAA
1 AAACCCTAAAA
2577253 ATATAAACCT
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.08
15 14 0.23
16 34 0.55
17 8 0.13
18 1 0.02
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (15 bp):
AAACCCTAAAACCTA
Found at i:2577259 original size:23 final size:23
Alignment explanation
Indices: 2577163--2577252 Score: 71
Period size: 23 Copynumber: 3.8 Consensus size: 23
2577153 TCAAAACCCT
*
2577163 AAACCCTTAAAACCC-AAAACCCTA
1 AAACCC-TAAAACCCTAAAA-CTTA
*
2577187 AATACTC-AAAACCCTAAAACCTTTA
1 AA-ACCCTAAAACCCTAAAA-C-TTA
*
2577212 AAACCCT-AAACCTTAAACACTTA
1 AAACCCTAAAACCCTAAA-ACTTA
2577235 AAA-CCTAAAACCCTAAAA
1 AAACCCTAAAACCCTAAAA
2577253 ATATAAACCT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
22 4 0.07
23 22 0.40
24 21 0.38
25 8 0.15
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (23 bp):
AAACCCTAAAACCCTAAAACTTA
Found at i:2578326 original size:497 final size:496
Alignment explanation
Indices: 2577389--2578371 Score: 1567
Period size: 497 Copynumber: 2.0 Consensus size: 496
2577379 CAAAACCCCA
* * *
2577389 AAAACCATCTTAAAATTCTAAGGATACGTATGAAAATCTCTTGTGAAATAATTTGTTCCTGAATG
1 AAAACCATCCTAAAATTCTAAAGATACGTATGAAAATCTCTTGTGAAATAATTTGTTCATGAATG
* * *
2577454 CCGCTTAGAAAATGGGGTATATAAGAAATTTTATTTCACCAAGTTTTTTTTACAAGTCCTTAAGT
66 CCGCCTAGAAAATGGGGTATATAAGAAATTTTATTTCACCAAGTTTTTTGTACAAGTCCTTAACT
* * * *
2577519 TGCAACAATAATGCGATTAAATAAAAAAATTAAAAAATGAGATTTTAAATATAAATAGTCACACC
131 TGCAACAAAAATACAATTAAATAAAAAAATTAAAAAATGAGATTTTAAATATAAATAGCCACACC
* * * *
2577584 TAATCTCAGTCTAGAGGTTAAAGGGTCTAGGTGATCTCATTATATTTAAAAACCCAAACTTAAAA
196 TAATCTCAGCCTAAAGGTTAAAGGGTCTAGATGATCTCACTATATTTAAAAACCCAAACTTAAAA
* *
2577649 TGGCATTTCATCATCATGCACATCATCCATTGGCATATATGCACTTATGGATCATTACTCTCATT
261 TGGCATCTCATCATCATGCACATCATCCATTGGCACATATGCACTTATGGATCATTACTCTCATT
2577714 CATTACGCATGTCTATACCTTTTACAATTTTTTCTTAGTTAGTTGTAGTATAATTAGTTTTTACA
326 CATTACGCATGTCTATACCTTTTACAATTTTTTCTTAGTTAGTTGTAGTATAATTAGTTTTTACA
*
2577779 TAAGATGTTTTTGTAAAAAACATTATTCAAAAATAAATTTTTAAATAAATTAAAAATAACATTCT
391 TAAGATGTTTTTGTAAAAAACATTATTCAAAAATAAATTTCTAAATAAATTAAAAATAACATTCT
*
2577844 -AAAGGAAATAATT-TTTGATACTCTGCCTAGAACCCATACCC
456 GAAA-GAAATAATTATTAG-TACTCTGCCTAGAACCCATACCC
*
2577885 AAAACCATCCTAGAATTCTAAAGATACGTATGAAAATCTCTTGTGAAATAATTTGTTCATGAATG
1 AAAACCATCCTAAAATTCTAAAGATACGTATGAAAATCTCTTGTGAAATAATTTGTTCATGAATG
* * **
2577950 CTGCCTAGAAAATGGGGTATATAGGAAATTTTATTTCATTAAGTTTTTTGTACAAGTCCTTAACT
66 CCGCCTAGAAAATGGGGTATATAAGAAATTTTATTTCACCAAGTTTTTTGTACAAGTCCTTAACT
*
2578015 TGCAACAAAAATACAATTAAATAAAAAAATTAAAAAAATGAGATTTTAAATATAAATAGCCGCAC
131 TGCAACAAAAATACAATTAAATAAAAAAATT-AAAAAATGAGATTTTAAATATAAATAGCCACAC
** * * *
2578080 CTAATCTTTGCCTAAAGGTTGAAGGGTCTAGATGGTCTCACTATATTTAAGAAA-CCGAACTTAA
195 CTAATCTCAGCCTAAAGGTTAAAGGGTCTAGATGATCTCACTATATTTAA-AAACCCAAACTTAA
*
2578144 AATGGCATCTCATCATCATGCACATCATCCATTGGCACATATGCACTTATGGATTATTACTCTCA
259 AATGGCATCTCATCATCATGCACATCATCCATTGGCACATATGCACTTATGGATCATTACTCTCA
* *
2578209 TTCATTACGCATGTTTATACCTTTTACAATTTTTTCTTAGTTAGTTGTAGTATAATTAGTTTTTG
324 TTCATTACGCATGTCTATACCTTTTACAATTTTTTCTTAGTTAGTTGTAGTATAATTAGTTTTTA
* * * *
2578274 CATAAGATGTTTTTGTGAAAAACATTATTCAAAAATAGATTTCTATATAAATTAAAAATAATATT
389 CATAAGATGTTTTTGTAAAAAACATTATTCAAAAATAAATTTCTAAATAAATTAAAAATAACATT
* *
2578339 TTGAAAGAAATAATTATTAGTACTCTGTCTAGA
454 CTGAAAGAAATAATTATTAGTACTCTGCCTAGA
2578372 TATTGAGGAG
Statistics
Matches: 445, Mismatches: 38, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
496 147 0.33
497 289 0.65
498 9 0.02
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (496 bp):
AAAACCATCCTAAAATTCTAAAGATACGTATGAAAATCTCTTGTGAAATAATTTGTTCATGAATG
CCGCCTAGAAAATGGGGTATATAAGAAATTTTATTTCACCAAGTTTTTTGTACAAGTCCTTAACT
TGCAACAAAAATACAATTAAATAAAAAAATTAAAAAATGAGATTTTAAATATAAATAGCCACACC
TAATCTCAGCCTAAAGGTTAAAGGGTCTAGATGATCTCACTATATTTAAAAACCCAAACTTAAAA
TGGCATCTCATCATCATGCACATCATCCATTGGCACATATGCACTTATGGATCATTACTCTCATT
CATTACGCATGTCTATACCTTTTACAATTTTTTCTTAGTTAGTTGTAGTATAATTAGTTTTTACA
TAAGATGTTTTTGTAAAAAACATTATTCAAAAATAAATTTCTAAATAAATTAAAAATAACATTCT
GAAAGAAATAATTATTAGTACTCTGCCTAGAACCCATACCC
Found at i:2578762 original size:23 final size:24
Alignment explanation
Indices: 2578722--2578776 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
2578712 TCTAATTTTA
* *
2578722 TTTTTCATAAATTATAAA-TTATT
1 TTTTTAATAAATTATAAACATATT
2578745 TTTTTAATAAACTT-TAAACATATT
1 TTTTTAATAAA-TTATAAACATATT
*
2578769 TTTATAAT
1 TTTTTAAT
2578777 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTTAATAAATTATAAACATATT
Found at i:2583112 original size:19 final size:19
Alignment explanation
Indices: 2583081--2583146 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
2583071 GATTTGAATT
2583081 TAAAT-AATAATATTAAATA
1 TAAATAAAT-ATATTAAATA
*
2583100 TAAATAAATATA-TAAACA
1 TAAATAAATATATTAAATA
*
2583118 -AATTATAATAT-TATAAATA
1 TAAATA-AATATAT-TAAATA
2583137 TAAAATAAAT
1 T-AAATAAAT
2583147 TAATACACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
17 4 0.11
18 10 0.27
19 13 0.35
20 6 0.16
21 4 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATAAATATATTAAATA
Found at i:2583122 original size:27 final size:25
Alignment explanation
Indices: 2583092--2583149 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
2583082 AAATAATAAT
2583092 ATTAAATATAAATAAATATATAAACAA
1 ATTAAATAT-AATAAATATA-AAACAA
* *
2583119 ATTATAATATTATAAATATAAAATAA
1 ATTA-AATATAATAAATATAAAACAA
2583145 ATTAA
1 ATTAA
2583150 TACACAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 1 0.04
26 9 0.32
27 13 0.46
28 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
ATTAAATATAATAAATATAAAACAA
Found at i:2583143 original size:38 final size:38
Alignment explanation
Indices: 2583084--2583159 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
2583074 TTGAATTTAA
2583084 ATAATAATATTAAATATAAATAAA-TATATAAACAAATT
1 ATAATAATATTAAATATAAATAAATTA-ATAAACAAATT
* *
2583122 ATAATATTA-TAAATATAAAATAAATTAATACACAAATT
1 ATAATAATATTAAATAT-AAATAAATTAATAAACAAATT
2583160 TCTAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 7 0.21
38 25 0.74
39 2 0.06
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (38 bp):
ATAATAATATTAAATATAAATAAATTAATAAACAAATT
Found at i:2586736 original size:28 final size:28
Alignment explanation
Indices: 2586705--2586767 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
2586695 TTTGTTAAAA
*
2586705 AAAAATTTTCAAACACTTGCATTGATGT
1 AAAAATTCTCAAACACTTGCATTGATGT
* *
2586733 AAAAATTCTCAAATACTTGTATTGATGT
1 AAAAATTCTCAAACACTTGCATTGATGT
2586761 AAAAATT
1 AAAAATT
2586768 ATGGATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.37
Consensus pattern (28 bp):
AAAAATTCTCAAACACTTGCATTGATGT
Found at i:2588744 original size:21 final size:21
Alignment explanation
Indices: 2588720--2588769 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2588710 AAATTACTTG
2588720 TGAAGAAGTGGCTGTTACAGT
1 TGAAGAAGTGGCTGTTACAGT
2588741 TGAAGAAGTGGCTGTTACAGT
1 TGAAGAAGTGGCTGTTACAGT
2588762 TGAAGAAG
1 TGAAGAAG
2588770 AGAGAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.34, T:0.26
Consensus pattern (21 bp):
TGAAGAAGTGGCTGTTACAGT
Found at i:2588792 original size:13 final size:15
Alignment explanation
Indices: 2588764--2588795 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
2588754 GTTACAGTTG
2588764 AAGAAGAGAGAAGAA
1 AAGAAGAGAGAAGAA
2588779 AAGAAG-GA-AAGAA
1 AAGAAGAGAGAAGAA
2588792 AAGA
1 AAGA
2588796 GAGTGGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAGAAGAA
Found at i:2596344 original size:2 final size:2
Alignment explanation
Indices: 2596337--2596366 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2596327 GAATTATGGG
2596337 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
2596367 CTTGAAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2599841 original size:233 final size:233
Alignment explanation
Indices: 2599434--2599897 Score: 741
Period size: 233 Copynumber: 2.0 Consensus size: 233
2599424 TAGCCAATTG
* *
2599434 AAATAATTGGGCCAATCCTTGATAGTCTCAAACAGAATAACAGGTCAAGAATAAGAACCAAGCTA
1 AAATAATTGGGCCAATCCTTGATAGTCTCAAACAGAATAACAGATCAAGAAAAAGAACCAAGCTA
* * * * **
2599499 ACAACTCCAGAGTTCAAAATATGCATTATACACAGTTTGTAGTGATGTGACTTGGGCAAATTGAT
66 ACAACTCCAGAGTTCAAAATATACATTATACACAGATTGTAGAGATGTAACTTGGGCAAATCCAT
**
2599564 AAAGACTCAACACAAATCCAACAAGACAAGGCCAATAGGGAAGCTTGAGCTGAACCTTTAATACT
131 AAAGACTCAACACAAATCCAACAAGACAAGGCCAATAGGGAAGCTCAAGCTGAACCTTTAATACT
2599629 TTAGGGGGAAATTGAGGGCAGAGTCAAAACTCCAACTC
196 TTAGGGGGAAATTGAGGGCAGAGTCAAAACTCCAACTC
* **
2599667 AAATAATTGGGCCAATCCTTGATAGTCTCAAGCAGAATAACAGATCAAGAAAAAGAACTGAGCTA
1 AAATAATTGGGCCAATCCTTGATAGTCTCAAACAGAATAACAGATCAAGAAAAAGAACCAAGCTA
* * *
2599732 ACAATTCCAGAGTTCAAAATATACATTGTACACAGATTGTAGAGATGTAACTTGGGCAAGTCCA-
66 ACAACTCCAGAGTTCAAAATATACATTATACACAGATTGTAGAGATGTAACTTGGGCAAATCCAT
* *
2599796 ACAAGACTCAACTCAAATCCAACATGACAAGGCCAATAGGGAAGCTCAAGCTGAACCTTTAATAC
131 A-AAGACTCAACACAAATCCAACAAGACAAGGCCAATAGGGAAGCTCAAGCTGAACCTTTAATAC
*
2599861 TTTAGGGGGAAATTGAGGGCAGAGTCCAAACTCCAAC
195 TTTAGGGGGAAATTGAGGGCAGAGTCAAAACTCCAAC
2599898 ACATAAATAC
Statistics
Matches: 211, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
232 1 0.00
233 210 1.00
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (233 bp):
AAATAATTGGGCCAATCCTTGATAGTCTCAAACAGAATAACAGATCAAGAAAAAGAACCAAGCTA
ACAACTCCAGAGTTCAAAATATACATTATACACAGATTGTAGAGATGTAACTTGGGCAAATCCAT
AAAGACTCAACACAAATCCAACAAGACAAGGCCAATAGGGAAGCTCAAGCTGAACCTTTAATACT
TTAGGGGGAAATTGAGGGCAGAGTCAAAACTCCAACTC
Found at i:2603727 original size:16 final size:16
Alignment explanation
Indices: 2603690--2603724 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2603680 ATAAGATTTT
2603690 ATAATTATATAATAAA
1 ATAATTATATAATAAA
*
2603706 ATAATTA-ATAATTAA
1 ATAATTATATAATAAA
2603721 ATAA
1 ATAA
2603725 ATTTTATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATTATATAATAAA
Found at i:2605407 original size:16 final size:17
Alignment explanation
Indices: 2605386--2605418 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2605376 TGAATTTTGA
2605386 ATTTTTTA-AATATTTT
1 ATTTTTTATAATATTTT
2605402 ATTTTTTATAATATTTT
1 ATTTTTTATAATATTTT
2605419 TTATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTTATAATATTTT
Found at i:2627605 original size:28 final size:27
Alignment explanation
Indices: 2627511--2627606 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 27
2627501 TAAAACTGTT
2627511 ATTT-TATTTAAAAATTTTTTATATTTT-
1 ATTTATATTTAAAAA-TTTTTA-ATTTTA
* **
2627538 A-TTATATTCAAATAAACATTTAATTTTA
1 ATTTATATT-TAA-AAATTTTTAATTTTA
* *
2627566 ATTTAAACTTAAAAATTTTTAATCTTTA
1 ATTTATATTTAAAAATTTTTAAT-TTTA
2627594 ATTTATATTTAAA
1 ATTTATATTTAAA
2627607 TGAATATTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
26 2 0.04
27 19 0.36
28 24 0.45
29 8 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTATATTTAAAAATTTTTAATTTTA
Found at i:2632752 original size:60 final size:60
Alignment explanation
Indices: 2632675--2633096 Score: 448
Period size: 60 Copynumber: 7.0 Consensus size: 60
2632665 AATTTCGAGG
* * *
2632675 AAAATTAATACTTTCAACTTTTCCTAAAAAAAAAAATTTATTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAATTTTTTTGAAAATTTATTTTTAAGA
*
2632735 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAACTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAA--TTTTTTTGAAAATTTATTTTTAAGA
** *
2632797 AAAATTGATACTTTCAACCTTTTTTTTAAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAA-C-TTTTCCTAAAAAAAAAATTTTTTTGAAAATTTATTTTTAAGA
* * * ** *
2632859 AAAATTGATACTTTCAACTTTTCCT--CAAAAATATTTTTTTAGAAACTTTAATTTCGAA-T
1 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAATTTTTTT-GAAAATTT-ATTTTTAAGA
* * * * *
2632918 AAAATTGATACTTTTAACTTTTTCTCAAAAAAACATTTTTTTGAATATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAATTTTTTTGAAAATTTATTTTTAAGA
* * * * * *
2632978 AAAATTGATACTTTTAATTTTTTCC---CAAAAATATTTTTTTGAAAAGCTTATTTTCAAGA
1 AAAATTGATACTTTCAA-CTTTTCCTAAAAAAAAAATTTTTTTGAAAA-TTTATTTTTAAGA
* * * * *
2633037 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTTG-AATTTTA-TTTAAAGA
1 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAATTTTTTTGAAAATTTATTTTTAAGA
2633094 AAA
1 AAA
2633097 TAAAATAAAA
Statistics
Matches: 307, Mismatches: 42, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
57 10 0.03
58 38 0.12
59 65 0.21
60 80 0.26
61 19 0.06
62 80 0.26
63 1 0.00
64 14 0.05
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (60 bp):
AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAATTTTTTTGAAAATTTATTTTTAAGA
Found at i:2632924 original size:59 final size:58
Alignment explanation
Indices: 2632675--2633076 Score: 439
Period size: 59 Copynumber: 6.7 Consensus size: 58
2632665 AATTTCGAGG
* * * *
2632675 AAAATTAATACTTTCAACTTTTCCTAAAAAAAAAAATTTATTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCT--CAAAAAAATTTTTTTGAAAATTTATTTTTAAGA
* *
2632735 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAACTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCT--CAAAAAAA--TTTTTTTGAAAATTTATTTTTAAGA
** *
2632797 AAAATTGATACTTTCAACCTTTTTTTTAAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAA-C-TTTTCCT-CAAAAAAA-TTTTTTTGAAAATTTATTTTTAAGA
* * ** *
2632859 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAACTTTAATTTCGAA-T
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTT-GAAAATTT-ATTTTTAAGA
* * *
2632918 AAAATTGATACTTTTAACTTTTTCTCAAAAAAACATTTTTTTGAATATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAAA-ATTTTTTTGAAAATTTATTTTTAAGA
* * * * *
2632978 AAAATTGATACTTTTAATTTTTTCC-CAAAAATATTTTTTTGAAAAGCTTATTTTCAAGA
1 AAAATTGATACTTTCAA-CTTTTCCTCAAAAAAATTTTTTTGAAAA-TTTATTTTTAAGA
*
2633037 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTT
2633077 TGAATTTTAT
Statistics
Matches: 298, Mismatches: 32, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
58 25 0.08
59 90 0.30
60 74 0.25
61 14 0.05
62 80 0.27
63 10 0.03
64 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGAAAATTTATTTTTAAGA
Found at i:2633110 original size:7 final size:7
Alignment explanation
Indices: 2633098--2633127 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2633088 TAAAGAAAAT
2633098 AAAATAA
1 AAAATAA
2633105 AAAATAA
1 AAAATAA
2633112 AAAAT-A
1 AAAATAA
2633118 AAAATAA
1 AAAATAA
2633125 AAA
1 AAA
2633128 GTATTAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:2633120 original size:13 final size:12
Alignment explanation
Indices: 2633093--2633127 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2633083 TTATTTAAAG
*
2633093 AAAATAAAATAA
1 AAAATAAAAAAA
2633105 AAAATAAAAAATA
1 AAAATAAAAAA-A
2633118 AAAATAAAAA
1 AAAATAAAAA
2633128 GTATTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAATAAAAAAA
Found at i:2636864 original size:59 final size:57
Alignment explanation
Indices: 2636708--2637198 Score: 421
Period size: 59 Copynumber: 8.1 Consensus size: 57
2636698 TTTAATTTCG
* ** *
2636708 AGAAAAATTGATACTTTCAACTTTTCTTAAAAAAAAAAAACTTTATTGAAAATTTATTTTTA
1 AGAAAAATTGATACTTTCAACTTTTC-T----CAAAAAATTTTTTTTGAAAATTTATTTTTA
* *
2636770 AGGAAAATTGATACTTTCAACTTTTTTTCAAAAAAAACCTTTTTTTTGAAAATTTATTTTTTA
1 AGAAAAATTGATACTTTCAAC-TTTTCTC--AAAAAA--TTTTTTTTGAAAATTTA-TTTTTA
* **
2636833 A-AAAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTTTGGAAACTTTAATTTCGAGGAA
1 AGAAAAATTGATACTTTCAACTTTTCTCAAAAAAT-TTTTTTT-GAAAATTT-ATTT----TTA
* *
2636896 ATTTGATAAAATTGATACTTTCAACTTTTCTTCAAAAAAATATTTTTTAAAAATTTATTTTTA
1 A---GA-AAAATTGATACTTTCAACTTTTC-TC-AAAAAATTTTTTTTGAAAATTTATTTTTA
* * * * * * **
2636959 AGAAAAATTGATACTTTCAATTTTTCCTTAAAAATATTTTCTTGGAAACTTTAATTTCG
1 AGAAAAATTGATACTTTCAACTTTT-CTCAAAAA-ATTTTTTTTGAAAATTTATTTTTA
*
2637018 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTTGAAGATTTATTTTTA
1 AGAAAAATTGATACTTTCAACTTTT-CTC-AAAAAA-TTTTTTTTGAAAATTTATTTTTA
* * * * *
2637078 AGGAAAATTGATATTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAAGCTTATTTTCA
1 AGAAAAATTGATACTTTCAACTTTTCTCAAAAAAT-TTTTTTTGAAAA-TTTATTTTTA
* * *
2637137 AGAAAAATTGATACTTTCAACTTTCCTCAAAAATATTTTTTTTG-AATTTTA-TTTAA
1 AGAAAAATTGATACTTTCAACTTTTCTCAAAAA-ATTTTTTTTGAAAATTTATTTTTA
2637193 AGAAAA
1 AGAAAA
2637199 TAAAATAAAA
Statistics
Matches: 354, Mismatches: 48, Indels: 60
0.77 0.10 0.13
Matches are distributed among these distances:
56 10 0.03
57 5 0.01
58 30 0.08
59 130 0.37
60 56 0.16
61 6 0.02
62 53 0.15
63 15 0.04
67 5 0.01
68 29 0.08
69 8 0.02
70 7 0.02
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (57 bp):
AGAAAAATTGATACTTTCAACTTTTCTCAAAAAATTTTTTTTGAAAATTTATTTTTA
Found at i:2636915 original size:68 final size:67
Alignment explanation
Indices: 2636835--2637030 Score: 198
Period size: 68 Copynumber: 3.0 Consensus size: 67
2636825 ATTTTTTAAA
*
2636835 AAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTTTGGAAACTTTAATTTCGAGGAAATTT
1 AAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTTTGGAAACTTTAATTTCGA-GAAAATT
2636900 GAT
65 GAT
* * **
2636903 AAAATTGATACTTTCAACTTTTCTTCAAAAAA-ATATTTTTT-AAAAATTT-ATTT----TTAA-
1 AAAATTGATACTTTCAACTTTTC-TCAAAAAATAT-TTTTTTGGAAACTTTAATTTCGAGAAAAT
2636960 -GA-
64 TGAT
* * *
2636962 AAAATTGATACTTTCAATTTTTC-CTTAAAAATATTTTCTTGGAAACTTTAATTTCGAGAAAAAT
1 AAAATTGATACTTTCAACTTTTCTC-AAAAAATATTTTTTTGGAAACTTTAATTTCGAG-AAAAT
2637026 TGAT
64 TGAT
2637030 A
1 A
2637031 CTTTCAACTT
Statistics
Matches: 102, Mismatches: 12, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
57 1 0.01
58 10 0.10
59 30 0.29
60 6 0.06
62 1 0.01
65 2 0.02
67 6 0.06
68 32 0.31
69 14 0.14
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (67 bp):
AAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTTTGGAAACTTTAATTTCGAGAAAATTG
AT
Found at i:2637204 original size:119 final size:116
Alignment explanation
Indices: 2636903--2637198 Score: 393
Period size: 119 Copynumber: 2.5 Consensus size: 116
2636893 GAAATTTGAT
* **
2636903 AAAATTGATACTTTCAACTTTTCTTCAAAAAAATATTTTTTAAAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAAT-TTTTTTTGAAATTTATTTTTAAGAAAAATT
* *
2636968 GATACTTTCAATTTTTCCTTAAAAATATTTTCTTGGAAACTTTAATTTCGAGA
65 GATACTTTCAATTTTTCC-TAAAAATATTTTCTTGAAAACTTTAATTTCAAGA
*
2637021 AAAATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTTGAAGATTTATTTTTAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAA-TTTTTTTTGAA-ATTTATTTTTAAGAAAAAT
* * *
2637086 TGATATTTTCAACTTTTCTCC-AAAAATATTTTTTTGAAAAGC-TTATTTTCAAGA
64 TGATACTTTCAA-TTTT-TCCTAAAAATATTTTCTTGAAAA-CTTTAATTTCAAGA
* * *
2637140 AAAATTGATACTTTCAAC-TTTCCTCAAAAATATTTTTTTTGAATTTTA-TTTAAAGAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAATTTATTTTTAAGAAAA
2637199 TAAAATAAAA
Statistics
Matches: 160, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
115 9 0.06
116 4 0.03
117 11 0.07
118 53 0.33
119 75 0.47
120 5 0.03
121 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAATTTATTTTTAAGAAAAATTG
ATACTTTCAATTTTTCCTAAAAATATTTTCTTGAAAACTTTAATTTCAAGA
Found at i:2637286 original size:17 final size:16
Alignment explanation
Indices: 2637264--2637311 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
2637254 TAATCTAATG
2637264 AATAAATAATAATAAAA
1 AATAAATAA-AATAAAA
2637281 AATAAATAAAATAAAA
1 AATAAATAAAATAAAA
2637297 AATGAAA-AAAA-AAAA
1 AAT-AAATAAAATAAAA
2637312 CCTGAAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.13
16 14 0.47
17 12 0.40
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (16 bp):
AATAAATAAAATAAAA
Found at i:2638222 original size:12 final size:13
Alignment explanation
Indices: 2638207--2638266 Score: 65
Period size: 12 Copynumber: 4.7 Consensus size: 13
2638197 AAATTATTTT
2638207 TTTAATTT-TATA
1 TTTAATTTATATA
2638219 TTTAATTATATATA
1 TTTAATT-TATATA
2638233 TTT--TTATATATA
1 TTTAATT-TATATA
2638245 TTTAATTT-TATA
1 TTTAATTTATATA
2638257 TTTATATTTA
1 TTTA-ATTTA
2638267 AAATAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
12 27 0.64
13 6 0.14
14 9 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTAATTTATATA
Found at i:2638239 original size:22 final size:22
Alignment explanation
Indices: 2638212--2638267 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2638202 ATTTTTTTAA
2638212 TTTTATATTTAATT-ATATATAT
1 TTTTATATTTAATTAAT-TATAT
* * *
2638234 TTTTATATATATTTAATTTTAT
1 TTTTATATTTAATTAATTATAT
*
2638256 ATTTATATTTAA
1 TTTTATATTTAA
2638268 AATAATATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATATTTAATTAATTATAT
Found at i:2638244 original size:16 final size:16
Alignment explanation
Indices: 2638225--2638263 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2638215 TATATTTAAT
*
2638225 TATATATATTTTTATA
1 TATATATAATTTTATA
*
2638241 TATATTTAATTTTATA
1 TATATATAATTTTATA
*
2638257 TTTATAT
1 TATATAT
2638264 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATATAATTTTATA
Found at i:2638601 original size:24 final size:23
Alignment explanation
Indices: 2638528--2638683 Score: 72
Period size: 24 Copynumber: 6.6 Consensus size: 23
2638518 AAATTAATCA
* * *
2638528 AAATAAAAAGATAAATATATTAAT
1 AAATAAAAAAATAGATA-AATAAT
* * *
2638552 AGATAACAAAAA-AAATAATTAGAT
1 AAATAA-AAAAATAGATAAATA-AT
2638576 AAATAAAAGAAATAGATAAATAAT
1 AAATAAAA-AAATAGATAAATAAT
* *
2638600 AATAAAAAATAAAAGCAGATAAATAAT
1 -A-AATAAA-AAAA-TAGATAAATAAT
**
2638627 AAA-AATATTAATAGAT-AA-AA-
1 AAATAA-AAAAATAGATAAATAAT
*
2638647 AAATAAAAAAATATATTAAATAAT
1 AAATAAAAAAATAGA-TAAATAAT
2638671 AAA-AATAAAAATA
1 AAATAA-AAAAATA
2638684 AAAACCCATT
Statistics
Matches: 104, Mismatches: 13, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
20 9 0.09
21 5 0.05
22 4 0.04
23 14 0.13
24 36 0.35
25 15 0.14
26 9 0.09
27 12 0.12
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (23 bp):
AAATAAAAAAATAGATAAATAAT
Found at i:2638628 original size:30 final size:30
Alignment explanation
Indices: 2638576--2638659 Score: 73
Period size: 30 Copynumber: 2.7 Consensus size: 30
2638566 ATAATTAGAT
* *
2638576 AAATAAAAGAAATAGATAAATAATAATAAA
1 AAATAAAAGAAATAAATAAATAAAAATAAA
*
2638606 AAATAAAAGCAGATAAAT-AATAAAAATATTAA
1 AAATAAAAG-AAATAAATAAATAAAAATA--AA
* *
2638638 TAGATAAAA-AAATAAAAAAATA
1 -AAATAAAAGAAATAAATAAATA
2638660 TATTAAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
30 18 0.42
31 12 0.28
32 6 0.14
33 7 0.16
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (30 bp):
AAATAAAAGAAATAAATAAATAAAAATAAA
Found at i:2638672 original size:28 final size:27
Alignment explanation
Indices: 2638620--2638675 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
2638610 AAAAGCAGAT
*
2638620 AAATAATAAAAATATTAATAGATAAAA
1 AAATAAAAAAAATATTAATAGATAAAA
2638647 AAATAAAAAAATATATTAAATA-ATAAAA
1 AAATAAAAAAA-ATATT-AATAGATAAAA
2638675 A
1 A
2638676 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.38
28 12 0.46
29 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (27 bp):
AAATAAAAAAAATATTAATAGATAAAA
Found at i:2638674 original size:26 final size:26
Alignment explanation
Indices: 2638620--2638681 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
2638610 AAAAGCAGAT
*
2638620 AAATAATAAAAATATTAATAGATAAAA
1 AAATAA-AAAAATATTAATAAATAAAA
*
2638647 AAATAAAAAAATA-TATTAAATAATAA
1 AAATAAAAAAATATTAATAAATAA-AA
2638673 AAATAAAAA
1 AAATAAAAA
2638682 TAAAAACCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 8 0.25
26 18 0.56
27 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (26 bp):
AAATAAAAAAATATTAATAAATAAAA
Found at i:2639069 original size:25 final size:26
Alignment explanation
Indices: 2639041--2639099 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
2639031 TAACATCATT
*
2639041 TATAAAATTAAAA-ATTAA-ATTATAA
1 TATAAAA-AAAAACATTAATATTATAA
2639066 TATAAAAAAAAACATTAATTATTATAA
1 TATAAAAAAAAACATTAA-TATTATAA
*
2639093 TTTAAAA
1 TATAAAA
2639100 GTCAATCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 12 0.41
27 13 0.45
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TATAAAAAAAAACATTAATATTATAA
Found at i:2642556 original size:3 final size:3
Alignment explanation
Indices: 2642542--2642585 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2642532 AATTCTCGTG
* **
2642542 TAA TAT TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2642586 TTGGTTTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2642611 original size:17 final size:17
Alignment explanation
Indices: 2642591--2642639 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
2642581 TAATATTGGT
2642591 TTAATTAAAATTAAAAA
1 TTAATTAAAATTAAAAA
2642608 TTAATT--AATTAAAAA
1 TTAATTAAAATTAAAAA
* * *
2642623 ATAAATAAATTTAAAAA
1 TTAATTAAAATTAAAAA
2642640 AAAAAACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.48
17 14 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAATTAAAATTAAAAA
Found at i:2642624 original size:16 final size:16
Alignment explanation
Indices: 2642598--2642640 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2642588 GGTTTAATTA
*
2642598 AAATT-AAAAATTAAT
1 AAATTAAAAAATAAAT
*
2642613 TAATTAAAAAATAAAT
1 AAATTAAAAAATAAAT
2642629 AAATTTAAAAAA
1 AAA-TTAAAAAA
2642641 AAAAACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 8 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTAAAAAATAAAT
Found at i:2642636 original size:21 final size:21
Alignment explanation
Indices: 2642590--2642636 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
2642580 ATAATATTGG
*
2642590 TTTAATTAAAATTAAAAATTAA
1 TTTAATTAAAA-TAAAAATAAA
2642612 -TTAATTAAAA-AATAAATAAA
1 TTTAATTAAAATAA-AAATAAA
2642632 TTTAA
1 TTTAA
2642637 AAAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 6 0.27
21 14 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAATTAAAATAAAAATAAA
Found at i:2643893 original size:3 final size:3
Alignment explanation
Indices: 2643887--2643943 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
2643877 ATTATTAAAA
* * *
2643887 AAT AAT AAT AAT AAT AAT AAG ATT AAT AAAT AA- AAA AACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA-T AAT AAT
2643933 AAT AAT AAT AA
1 AAT AAT AAT AA
2643944 AATTTCATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2644099 original size:16 final size:15
Alignment explanation
Indices: 2644074--2644117 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
2644064 AATTAAAATC
2644074 AAAACCTAAAATTTT
1 AAAACCTAAAATTTT
*
2644089 AAAATCCTAAAAATTT
1 AAAA-CCTAAAATTTT
2644105 AAAACCTTAAAAT
1 AAAACC-TAAAAT
2644118 CAAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAACCTAAAATTTT
Found at i:2650218 original size:37 final size:37
Alignment explanation
Indices: 2650168--2650241 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2650158 TAATTTTTTT
2650168 TATTGGATTGAGAGTATAGCTCAAAAAGTGGAAACAA
1 TATTGGATTGAGAGTATAGCTCAAAAAGTGGAAACAA
2650205 TATTGGATTGAGAGTATAGCTCAAAAAGTGGAAACAA
1 TATTGGATTGAGAGTATAGCTCAAAAAGTGGAAACAA
2650242 AAATTAACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (37 bp):
TATTGGATTGAGAGTATAGCTCAAAAAGTGGAAACAA
Found at i:2652658 original size:24 final size:23
Alignment explanation
Indices: 2652630--2652684 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
2652620 TAAAAATAAT
2652630 AAAAATTATTATAACTGTA-ATTGA
1 AAAAATTATTATAA-T-TACATTGA
*
2652654 AAAAATAATTATAATTACGATTGA
1 AAAAATTATTATAATTAC-ATTGA
2652678 AAAAATT
1 AAAAATT
2652685 TAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 1 0.04
24 24 0.89
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.35
Consensus pattern (23 bp):
AAAAATTATTATAATTACATTGA
Found at i:2675846 original size:2 final size:2
Alignment explanation
Indices: 2675835--2675870 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2675825 TATATGTTGT
*
2675835 TA TA -A TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2675871 TAAATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2679637 original size:21 final size:21
Alignment explanation
Indices: 2679594--2679639 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2679584 GAAAACATTA
*
2679594 TTTGTTGTTCTGCAAATAATC
1 TTTGTTGTTCTGCAAACAATC
* *
2679615 TTTGTTGTTCTGCAAGCACTC
1 TTTGTTGTTCTGCAAACAATC
2679636 TTTG
1 TTTG
2679640 AATTCAGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (21 bp):
TTTGTTGTTCTGCAAACAATC
Found at i:2680095 original size:546 final size:546
Alignment explanation
Indices: 2679063--2680671 Score: 3155
Period size: 546 Copynumber: 2.9 Consensus size: 546
2679053 TTTGTTGATG
*
2679063 ATAATCTTTGTTGTTCTGCAAGCACTCTTTGAATTCAGAACATAGACTTATTACACATGCTAAGA
1 ATAATCTTTGTTGTTCTGCAAGCACTCTTTGAATTCAGAACATAGACTTATTACACATGCTAAAA
2679128 CGTAGAAATACAGAAAACATTAAAGAAGCACAGCATGTGCAGGGAAAACACAAAAATTATTACAT
66 CGTAGAAATACAGAAAACATTAAAGAAGCACAGCATGTGCAGGGAAAACACAAAAATTATTACAT
2679193 TTGATGAACACACCACATTAGACTTCAATAATGCAGCAATGTTTGTTGATTAAAAATTGAATGTC
131 TTGATGAACACACCACATTAGACTTCAATAATGCAGCAATGTTTGTTGATTAAAAATTGAATGTC
2679258 ATTTGACTCATTCCAGCCACTGGAACAATTAATCACATCTGGAAAAACTACATAGTTATCGACCA
196 ATTTGACTCATTCCAGCCACTGGAACAATTAATCACATCTGGAAAAACTACATAGTTATCGACCA
2679323 GCCACGTAGGGCTTGTACTAACATTCTTCTTGATTTTTCGTTAAGGGATTTGCACATACAATTGG
261 GCCACGTAGGGCTTGTACTAACATTCTTCTTGATTTTTCGTTAAGGGATTTGCACATACAATTGG
*
2679388 TGAAAATTTGGCTCACTTCTGTAACCTAGCTCCCAGACAGCAGATCTGAAAGAATAGAGACCAAT
326 TGAAAATTTGGCTCACTTCTGTAACCTAGCTCCCAGACAGCAGATCTGAAAGACTAGAGACCAAT
2679453 AGTTCTATACTTATATTGACTATTGGATAACTCAGTAAGTTCCAAGACAAACCAGGTCCATACTT
391 AGTTCTATACTTATATTGACTATTGGATAACTCAGTAAGTTCCAAGACAAACCAGGTCCATACTT
2679518 AGGCAAAGTAAATGTCCTTATATTCTTCAACAAAACTCATTTTCACAACAAGTCTCCAAAAATAC
456 AGGCAAAGTAAATGTCCTTATATTCTTCAACAAAACTCATTTTCACAACAAGTCTCCAAAAATAC
2679583 AGAAAACATTATTTGTTGTTCTGCAA
521 AGAAAACATTATTTGTTGTTCTGCAA
2679609 ATAATCTTTGTTGTTCTGCAAGCACTCTTTGAATTCAGAACATAGACTTATTACACATGCTAAAA
1 ATAATCTTTGTTGTTCTGCAAGCACTCTTTGAATTCAGAACATAGACTTATTACACATGCTAAAA
* *
2679674 CGTAGAAATACAGAAAACATTAAAGAAGCACAGTATGTGCAGGGAAAACACAAAAATAATTACAT
66 CGTAGAAATACAGAAAACATTAAAGAAGCACAGCATGTGCAGGGAAAACACAAAAATTATTACAT
2679739 TTGATGAACACACCACATTAGACTTCAATAATGCAGCAATGTTTGTTGATTAAAAATTGAATGTC
131 TTGATGAACACACCACATTAGACTTCAATAATGCAGCAATGTTTGTTGATTAAAAATTGAATGTC
*
2679804 ATTTGACTCATTCCAGCCACTGGAACAATTAATCACATCTGGAAAAACTACATAGTTATAGACCA
196 ATTTGACTCATTCCAGCCACTGGAACAATTAATCACATCTGGAAAAACTACATAGTTATCGACCA
2679869 GCCACGTAGGGCTTGTACTAACATTCTTCTTGATTTTTCGTTAAGGGATTTGCACATACAATTGG
261 GCCACGTAGGGCTTGTACTAACATTCTTCTTGATTTTTCGTTAAGGGATTTGCACATACAATTGG
2679934 TGAAAATTTGGCTCACTTCTGTAACCTAGCTCCCAGACAGCAGATCTGAAAGACTAGAGACCAAT
326 TGAAAATTTGGCTCACTTCTGTAACCTAGCTCCCAGACAGCAGATCTGAAAGACTAGAGACCAAT
2679999 AGTTCTATACTTATATTGACTATTGGATAACTCAGTAAGTTCCAAGACAAACCAGGTCCATACTT
391 AGTTCTATACTTATATTGACTATTGGATAACTCAGTAAGTTCCAAGACAAACCAGGTCCATACTT
2680064 AGGCAAAGTAAATGTCCTTATATTCTTCAACAAAACTCATTTTCACAACAAGTCTCCAAAAATAC
456 AGGCAAAGTAAATGTCCTTATATTCTTCAACAAAACTCATTTTCACAACAAGTCTCCAAAAATAC
2680129 AGAAAACATTATTTGTTGTTCTGCAA
521 AGAAAACATTATTTGTTGTTCTGCAA
2680155 ATAATCTTTGTTGTTCTGCAAGCACTCTTTGAATTCAGAACATAGACTTATTACACATGCTAAAA
1 ATAATCTTTGTTGTTCTGCAAGCACTCTTTGAATTCAGAACATAGACTTATTACACATGCTAAAA
2680220 CGTAGAAATACAGAAAACATTAAAGAAGCACAGCATGTGCAGGGAAAACACAAAAATTATTACAT
66 CGTAGAAATACAGAAAACATTAAAGAAGCACAGCATGTGCAGGGAAAACACAAAAATTATTACAT
2680285 TTGATGAACACACCACATTAGACTTCAATAATGCAGCAATGTTTGTTGATTAAAAATTGAATGTC
131 TTGATGAACACACCACATTAGACTTCAATAATGCAGCAATGTTTGTTGATTAAAAATTGAATGTC
*
2680350 ATTTGACTCATTCCAGCCACTGGAACGATTAATCACATCTGGAAAAACTACATAGTTATCGACCA
196 ATTTGACTCATTCCAGCCACTGGAACAATTAATCACATCTGGAAAAACTACATAGTTATCGACCA
2680415 GCCACGTAGGGCTTGTACTAACATTCTTCTTGATTTTTCGTTAAGGGATTTGCACATACAATTGG
261 GCCACGTAGGGCTTGTACTAACATTCTTCTTGATTTTTCGTTAAGGGATTTGCACATACAATTGG
*
2680480 TGAAAATTTGGCTCACTTCTGTAACCTAGCTCCCAGACAGCAGATCTGAAAGACTAGAGACCAAC
326 TGAAAATTTGGCTCACTTCTGTAACCTAGCTCCCAGACAGCAGATCTGAAAGACTAGAGACCAAT
2680545 AGTTCTATACTTATATTGACTATTGGATAACTCAGTAAGTTCCAAGACAAACCAGGTCCATACTT
391 AGTTCTATACTTATATTGACTATTGGATAACTCAGTAAGTTCCAAGACAAACCAGGTCCATACTT
2680610 AGGCAAAGTAAATGTCCTTATATTCTTCAACAAAACTCATTTTCACAACAAGTCTCCAAAAA
456 AGGCAAAGTAAATGTCCTTATATTCTTCAACAAAACTCATTTTCACAACAAGTCTCCAAAAA
2680672 CTCACCTGCT
Statistics
Matches: 1053, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
546 1053 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (546 bp):
ATAATCTTTGTTGTTCTGCAAGCACTCTTTGAATTCAGAACATAGACTTATTACACATGCTAAAA
CGTAGAAATACAGAAAACATTAAAGAAGCACAGCATGTGCAGGGAAAACACAAAAATTATTACAT
TTGATGAACACACCACATTAGACTTCAATAATGCAGCAATGTTTGTTGATTAAAAATTGAATGTC
ATTTGACTCATTCCAGCCACTGGAACAATTAATCACATCTGGAAAAACTACATAGTTATCGACCA
GCCACGTAGGGCTTGTACTAACATTCTTCTTGATTTTTCGTTAAGGGATTTGCACATACAATTGG
TGAAAATTTGGCTCACTTCTGTAACCTAGCTCCCAGACAGCAGATCTGAAAGACTAGAGACCAAT
AGTTCTATACTTATATTGACTATTGGATAACTCAGTAAGTTCCAAGACAAACCAGGTCCATACTT
AGGCAAAGTAAATGTCCTTATATTCTTCAACAAAACTCATTTTCACAACAAGTCTCCAAAAATAC
AGAAAACATTATTTGTTGTTCTGCAA
Found at i:2680183 original size:21 final size:21
Alignment explanation
Indices: 2680140--2680185 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2680130 GAAAACATTA
*
2680140 TTTGTTGTTCTGCAAATAATC
1 TTTGTTGTTCTGCAAACAATC
* *
2680161 TTTGTTGTTCTGCAAGCACTC
1 TTTGTTGTTCTGCAAACAATC
2680182 TTTG
1 TTTG
2680186 AATTCAGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (21 bp):
TTTGTTGTTCTGCAAACAATC
Found at i:2683188 original size:16 final size:17
Alignment explanation
Indices: 2683149--2683194 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
2683139 AATTTATTAA
*
2683149 TTAATATAAT-ATTTATT
1 TTAA-ATAATGATTAATT
*
2683166 TTTAAT-ATGATTAATT
1 TTAAATAATGATTAATT
2683182 TTAAATAATGATT
1 TTAAATAATGATT
2683195 TGTAACGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.08
16 13 0.54
17 9 0.38
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAAATAATGATTAATT
Done.