Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 9 of 144
Found at i:2057390 original size:2 final size:2
Alignment explanation
Indices: 2057355--2057379 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2057345 ACTCAAAGTT
2057355 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2057380 TCTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2064874 original size:17 final size:19
Alignment explanation
Indices: 2064844--2064884 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
2064834 ACATTTATCT
2064844 CTATTTTCATTTTA-TTAAA
1 CTATTTTCA-TTTACTTAAA
2064863 CTATTTTC-TTTACTTAAA
1 CTATTTTCATTTACTTAAA
2064881 -TATT
1 CTATT
2064885 AAAATTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.38
18 5 0.24
19 8 0.38
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (19 bp):
CTATTTTCATTTACTTAAA
Found at i:2068174 original size:19 final size:19
Alignment explanation
Indices: 2068150--2068187 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2068140 AACATCAACC
2068150 ACACTGTTGTAAGTTCAAA
1 ACACTGTTGTAAGTTCAAA
2068169 ACACTGTTGTAAGTTCAAA
1 ACACTGTTGTAAGTTCAAA
2068188 TTAACTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
ACACTGTTGTAAGTTCAAA
Found at i:2069433 original size:33 final size:32
Alignment explanation
Indices: 2069389--2069474 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 32
2069379 GTCTTGGGAG
*
2069389 ACTCTA-TCTATGTTTACTGTCCTATCAGACT
1 ACTCTATTCTATGTTTACTGTCCTACCAGACT
* *
2069420 ATCTCTATTCTATGTTTACTATCCTACCGGACT
1 A-CTCTATTCTATGTTTACTGTCCTACCAGACT
* *
2069453 A-TCTATTCTGTGTTTATTGTCC
1 ACTCTATTCTATGTTTACTGTCC
2069475 CAATGGATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 19 0.40
32 5 0.11
33 23 0.49
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.45
Consensus pattern (32 bp):
ACTCTATTCTATGTTTACTGTCCTACCAGACT
Found at i:2069676 original size:58 final size:58
Alignment explanation
Indices: 2069607--2069719 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
2069597 TACTTGGATG
*
2069607 CCATAACATCTTTCA-TCTATGGTCTTACACCGTATACCTCATACATTATACCATGCCA
1 CCATAACATCTTTCATTC-ATGGTCTTACACCATATACCTCATACATTATACCATGCCA
* * * * *
2069665 CCATTACATCTTTCATTCATGGTCTTAGACCATATACCTTATACCTTGTACCATG
1 CCATAACATCTTTCATTCATGGTCTTACACCATATACCTCATACATTATACCATG
2069720 TTGTTATGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 46 0.96
59 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.35
Consensus pattern (58 bp):
CCATAACATCTTTCATTCATGGTCTTACACCATATACCTCATACATTATACCATGCCA
Found at i:2078581 original size:4 final size:4
Alignment explanation
Indices: 2078572--2078599 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2078562 TTAAACTAAG
2078572 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
2078600 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:2080005 original size:23 final size:22
Alignment explanation
Indices: 2079954--2080005 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
2079944 CCTCGTCTTT
*
2079954 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
2079976 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
2079999 TTCTTTT
1 TTCTTTT
2080006 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:2080020 original size:18 final size:18
Alignment explanation
Indices: 2079999--2080037 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2079989 TTTCTTCAAC
* *
2079999 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
2080017 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
2080035 TTC
1 TTC
2080038 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:2082638 original size:3 final size:3
Alignment explanation
Indices: 2082630--2082657 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2082620 NNNNNNNNNN
2082630 GCT GCT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT G
2082658 ATGGTGCCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.36, T:0.32
Consensus pattern (3 bp):
GCT
Found at i:2091853 original size:15 final size:16
Alignment explanation
Indices: 2091830--2091864 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2091820 TAGTCACTAT
2091830 TAGTCACTAAAA-TTA
1 TAGTCACTAAAATTTA
*
2091845 TAGTGACTAAAATTTA
1 TAGTCACTAAAATTTA
2091861 TAGT
1 TAGT
2091865 TTTCTTGATT
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:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (16 bp):
TAGTCACTAAAATTTA
Found at i:2104278 original size:13 final size:13
Alignment explanation
Indices: 2104260--2104285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2104250 ACTTTACGCA
2104260 AACAAATGGTTTT
1 AACAAATGGTTTT
2104273 AACAAATGGTTTT
1 AACAAATGGTTTT
2104286 TGGAAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AACAAATGGTTTT
Found at i:2107265 original size:12 final size:12
Alignment explanation
Indices: 2107226--2107282 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
2107216 GAACAAATAT
*
2107226 AGATGCAATTTC
1 AGATGCAATGTC
* * *
2107238 ATATACAAAGTC
1 AGATGCAATGTC
*
2107250 AGATGCAATTTC
1 AGATGCAATGTC
* *
2107262 AGATACAAAGTC
1 AGATGCAATGTC
2107274 AGATGCAAT
1 AGATGCAAT
2107283 ATCAACTACA
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (12 bp):
AGATGCAATGTC
Found at i:2107301 original size:24 final size:24
Alignment explanation
Indices: 2107226--2107282 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
2107216 GAACAAATAT
*
2107226 AGATGCAATTTCATATACAAAGTC
1 AGATGCAATTTCAGATACAAAGTC
2107250 AGATGCAATTTCAGATACAAAGTC
1 AGATGCAATTTCAGATACAAAGTC
2107274 AGATGCAAT
1 AGATGCAAT
2107283 ATCAACTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (24 bp):
AGATGCAATTTCAGATACAAAGTC
Found at i:2114042 original size:127 final size:124
Alignment explanation
Indices: 2113790--2114089 Score: 334
Period size: 127 Copynumber: 2.4 Consensus size: 124
2113780 ACTTGATTTG
* * * *
2113790 GGATGGACGATTTTGCTTCAAGGGTCTTCTA-AGCTTGATATTGAAGAATGGGTTTTATCTTCTT
1 GGATGGAAGATTCTGCTTCAAGGGTCTTTTAGA-CTTGATCTTGAAGAATGGGTTTTATCTTCTT
* * * *
2113854 TGAGTTGGTGCAACTAAATCGGAAAAAGCTTTTATCCAAGGTTATTTGAGACTTGATCTT
65 TGAGTTGGTGCAACTAAATCGGAAAAAGCTTTTAACCAAGGGTATTTGAAACTTGACCTT
* *
2113914 GGATGGAAGATTCTGCTTCAAGGGTCTTTTAGACTTGATCCTGAAGAATGGGTTTTTATCTTTTT
1 GGATGGAAGATTCTGCTTCAAGGGTCTTTTAGACTTGATCTTGAAGAATGGG-TTTTATC-TTCT
* * * * ** *
2113979 TTTATGTTGGTGTAACTAGATTGGGGAAAGCTTTTAACCAAGGGTCTTTGAAACTTGACCTT
64 TTGA-GTTGGTGCAACTAAATCGGAAAAAGCTTTTAACCAAGGGTATTTGAAACTTGACCTT
* * * * * * *
2114041 GGATTGATGATTC-ACTTCAAAGGCCTTTTAGGCTTGATCTTTAAGAATG
1 GGATGGAAGATTCTGCTTCAAGGGTCTTTTAGACTTGATCTTGAAGAATG
2114090 AATTTAGCCT
Statistics
Matches: 147, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
124 45 0.31
125 8 0.05
126 36 0.24
127 58 0.39
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (124 bp):
GGATGGAAGATTCTGCTTCAAGGGTCTTTTAGACTTGATCTTGAAGAATGGGTTTTATCTTCTTT
GAGTTGGTGCAACTAAATCGGAAAAAGCTTTTAACCAAGGGTATTTGAAACTTGACCTT
Found at i:2120560 original size:56 final size:56
Alignment explanation
Indices: 2120487--2120596 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
2120477 TGAAACTAAC
* *
2120487 TCCTATATATCAAGAGTACACCAAAACAGCAAACAAGAGTAAAGAAATTTGAAATA
1 TCCTATATATCAAGAGTACACCAAAACAGAAAACAAAAGTAAAGAAATTTGAAATA
* * *
2120543 TCCTATATATCAGGAGTACATCAAAATAGAAAACAAAAGTAAAGAAATTTGAAA
1 TCCTATATATCAAGAGTACACCAAAACAGAAAACAAAAGTAAAGAAATTTGAAA
2120597 CACAAACAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.53, C:0.14, G:0.13, T:0.21
Consensus pattern (56 bp):
TCCTATATATCAAGAGTACACCAAAACAGAAAACAAAAGTAAAGAAATTTGAAATA
Found at i:2127199 original size:8 final size:8
Alignment explanation
Indices: 2127186--2127223 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
2127176 AAGATTTATA
2127186 AAAAAAAT
1 AAAAAAAT
2127194 AAAAAAAT
1 AAAAAAAT
2127202 -AAAAAAT
1 AAAAAAAT
2127209 GAAATAAAAT
1 -AAA-AAAAT
2127219 AAAAA
1 AAAAA
2127224 TGAATAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.26
8 10 0.37
9 5 0.19
10 5 0.19
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:2127229 original size:15 final size:15
Alignment explanation
Indices: 2127188--2127244 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
2127178 GATTTATAAA
*
2127188 AAAAAT-AAAAAAAT
1 AAAAATGAATAAAAT
2127202 AAAAAATGAAATAAAAT
1 -AAAAATG-AATAAAAT
**
2127219 AAAAATGAATAACTT
1 AAAAATGAATAAAAT
*
2127234 AAAAATTAATA
1 AAAAATGAATA
2127245 CCTACGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 22 0.61
16 7 0.19
17 7 0.19
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (15 bp):
AAAAATGAATAAAAT
Found at i:2127238 original size:16 final size:17
Alignment explanation
Indices: 2127187--2127227 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
2127177 AGATTTATAA
2127187 AAAAAAT-AAA-AAAAT
1 AAAAAATGAAATAAAAT
2127202 AAAAAATGAAATAAAAT
1 AAAAAATGAAATAAAAT
2127219 -AAAAATGAA
1 AAAAAATGAA
2127228 TAACTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.29
16 12 0.50
17 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAAAATGAAATAAAAT
Found at i:2129345 original size:44 final size:44
Alignment explanation
Indices: 2129297--2129562 Score: 134
Period size: 44 Copynumber: 6.1 Consensus size: 44
2129287 AACGTCAGAT
*
2129297 AGATAAGATCTATTATTTTAATCCGCTCCACTGCAACTTCAGGG
1 AGATAAGATCTATTATTTTAATCTGCTCCACTGCAACTTCAGGG
* *** * * ** *
2129341 AGATAGGAT-TACTGGCTTCAATCTGCTCCACTACTGCCT-AGGG
1 AGATAAGATCTA-TTATTTTAATCTGCTCCACTGCAACTTCAGGG
* *** * * **
2129384 GGATAAGATCTGCCATCTTAGATCTGCTCCACTACTGCTT-AGGG
1 AGATAAGATCTATTATTTTA-ATCTGCTCCACTGCAACTTCAGGG
* * ** *
2129428 AGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGG
1 AGATAAGATCTATTATT-TT-AATCTGCTCCACTGCAACTTCAGGG
* ** * * *
2129474 AGATAAGAACTGA-TA---CGATCTACTCTACTGCAACTTCAGAG
1 AGATAAGATCT-ATTATTTTAATCTGCTCCACTGCAACTTCAGGG
* * *
2129515 AGATAAGATCCT-TTATTTTAATCCGCTCTACTGCAACTTCAAGG
1 AGATAAGAT-CTATTATTTTAATCTGCTCCACTGCAACTTCAGGG
2129559 AGAT
1 AGAT
2129563 CCACTACTGC
Statistics
Matches: 164, Mismatches: 46, Indels: 24
0.70 0.20 0.10
Matches are distributed among these distances:
41 30 0.18
42 2 0.01
43 15 0.09
44 86 0.52
45 16 0.10
46 15 0.09
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
AGATAAGATCTATTATTTTAATCTGCTCCACTGCAACTTCAGGG
Found at i:2129630 original size:151 final size:151
Alignment explanation
Indices: 2129411--2129693 Score: 557
Period size: 151 Copynumber: 1.9 Consensus size: 151
2129401 TTAGATCTGC
2129411 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
2129476 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
66 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
2129541 TCTACTGCAACTTCAAGGAGA
131 TCTACTGCAACTTCAAGGAGA
2129562 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
*
2129627 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
66 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
2129692 TC
131 TC
2129694 CACTACTGCT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 131 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (151 bp):
TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
TCTACTGCAACTTCAAGGAGA
Found at i:2129656 original size:41 final size:41
Alignment explanation
Indices: 2129606--2130107 Score: 136
Period size: 41 Copynumber: 11.7 Consensus size: 41
2129596 CTTCGGTCTG
2129606 CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
1 CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
* * * * ** * *
2129647 CTCTACTGCAACTTCAGAGAGATAAGATCTTTTA--TTTTA
1 CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
* * * * * * * *
2129686 ATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTG
1 CTCCACTGCA--AC--CTCAGGGAGATAAGAACTG--A---TACGATCTA
2129736 CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
1 CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
* * * * * *** *
2129777 CTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCTG
1 CTCCACTGCAACCTCAGGGAGATAAGAAC--TGA-TACGATCTA
* * * * * *
2129821 CTCCACTGCAACTTCAGGGAGATAGGATTACTGGTTTCAATCTG
1 CTCCACTGCAACCTCAGGGAGATAAGA--ACT-GATACGATCTA
* ** * ** * *
2129865 CTCCACTAC-TGCTTAGGGAGATAAGATTTGTAATTTTTC-AGCCTA
1 CTCCACTGCAACCTCAGGGAGATAAGAACTG--A---TACGA-TCTA
* *
2129910 CTCCACTGCAACTTCAGGGAGATAAG-ACTTGATGCGATCTA
1 CTCCACTGCAACCTCAGGGAGATAAGAAC-TGATACGATCTA
* * * * ** * *
2129951 CTCTACTGCAACTTCAGAGAGATAAGATCTTTTA--TTTTA
1 CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
* * * * * * * *
2129990 ATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTG
1 CTCCACTGCA--AC--CTCAGGGAGATAAGAACTG--A---TACGATCTA
2130040 CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
1 CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
* * *
2130081 CTCTACTGCAACTTCAGAGAGATAAGA
1 CTCCACTGCAACCTCAGGGAGATAAGA
2130108 TCTTTTATTT
Statistics
Matches: 326, Mismatches: 97, Indels: 76
0.65 0.19 0.15
Matches are distributed among these distances:
39 18 0.06
40 1 0.00
41 125 0.38
42 2 0.01
43 44 0.13
44 50 0.15
45 13 0.04
46 49 0.15
48 6 0.02
50 18 0.06
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (41 bp):
CTCCACTGCAACCTCAGGGAGATAAGAACTGATACGATCTA
Found at i:2129795 original size:130 final size:130
Alignment explanation
Indices: 2129562--2129827 Score: 523
Period size: 130 Copynumber: 2.0 Consensus size: 130
2129552 TTCAAGGAGA
2129562 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
2129627 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
66 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
2129692 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
*
2129757 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCTGC
66 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
2129822 TCCACT
1 TCCACT
2129828 GCAACTTCAG
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 135 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (130 bp):
TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
Found at i:2129870 original size:174 final size:174
Alignment explanation
Indices: 2129685--2130001 Score: 537
Period size: 174 Copynumber: 1.8 Consensus size: 174
2129675 CTTTTATTTT
* * *
2129685 AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCT
1 AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCAGCCTACTCCACTGCAACCT
2129750 CAGGGAGATAAGAAC-TGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTT
66 CAGGGAGATAAG-ACTTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTT
*
2129814 TAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTACTGGTTTC
130 TAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTGGTTTC
* * * *
2129859 AATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTTCAGCCTACTCCACTGCAACTT
1 AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCAGCCTACTCCACTGCAACCT
*
2129924 CAGGGAGATAAGACTTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTT
66 CAGGGAGATAAGACTTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTT
2129989 AATCCGCTCCACT
131 AATCCGCTCCACT
2130002 ACTGCTTAGG
Statistics
Matches: 133, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
173 2 0.02
174 131 0.98
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (174 bp):
AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCAGCCTACTCCACTGCAACCT
CAGGGAGATAAGACTTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTT
AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTGGTTTC
Found at i:2130002 original size:130 final size:130
Alignment explanation
Indices: 2129774--2130163 Score: 523
Period size: 130 Copynumber: 3.0 Consensus size: 130
2129764 CTGATACGAT
* * * *** * * *
2129774 CTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCTGCTCCACTGCAACTTCAGG
1 CTACTCCACTGCAACTTCAGGGAGATAAGA-C-TTGA-TACGATCTACTCTACTGCAACTTCAGA
* * ** * * * *
2129839 GAGATAGGAT-TACTGGTTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTT
63 GAGATAAGATCT-TTTATTTTAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTT
2129903 CAGC
127 CAGC
*
2129907 CTACTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGCAACTTCAGAGAG
1 CTACTCCACTGCAACTTCAGGGAGATAAGACTTGATACGATCTACTCTACTGCAACTTCAGAGAG
* *
2129972 ATAAGATCTTTTATTTTAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGT
66 ATAAGATCTTTTATTTTAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCAGC
* *
2130037 CTGCTCCACTGCAACCTCAGGGAGATAAGAAC-TGATACGATCTACTCTACTGCAACTTCAGAGA
1 CTACTCCACTGCAACTTCAGGGAGATAAG-ACTTGATACGATCTACTCTACTGCAACTTCAGAGA
2130101 GATAAGATCTTTTATTTTAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTC
65 GATAAGATCTTTTATTTTAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTC
2130164 GGTCTATAAT
Statistics
Matches: 233, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
130 198 0.85
131 6 0.03
132 1 0.00
133 28 0.12
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (130 bp):
CTACTCCACTGCAACTTCAGGGAGATAAGACTTGATACGATCTACTCTACTGCAACTTCAGAGAG
ATAAGATCTTTTATTTTAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCAGC
Found at i:2130111 original size:304 final size:304
Alignment explanation
Indices: 2129562--2130131 Score: 1052
Period size: 304 Copynumber: 1.9 Consensus size: 304
2129552 TTCAAGGAGA
* * *
2129562 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCAGCCTACTCCACTGCAACCTCAGGGAG
2129627 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
66 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
2129692 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
131 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
*
2129757 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCTGC
196 ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
2129822 TCCACTGCAACTTCAGGGAGATAGGATTACTGGTTTCAATCTGC
261 TCCACTGCAACTTCAGGGAGATAGGATTACTGGTTTCAATCTGC
* * *
2129866 TCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTTCAGCCTACTCCACTGCAACTTCAGGGAG
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCAGCCTACTCCACTGCAACCTCAGGGAG
*
2129931 ATAAG-ACTTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCG
66 ATAAGAAC-TGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCG
2129995 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGA
130 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGA
2130060 GATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCG
195 GATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCG
2130125 CTCCACT
260 CTCCACT
2130132 ACTGCTTAGG
Statistics
Matches: 257, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
303 2 0.01
304 255 0.99
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (304 bp):
TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCAGCCTACTCCACTGCAACCTCAGGGAG
ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAG
ATAAGAACTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGC
TCCACTGCAACTTCAGGGAGATAGGATTACTGGTTTCAATCTGC
Found at i:2130164 original size:130 final size:130
Alignment explanation
Indices: 2129859--2130169 Score: 534
Period size: 130 Copynumber: 2.4 Consensus size: 130
2129849 TACTGGTTTC
* * * * * *
2129859 AATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTTCAGCCTACTCCACTGCAACTT
1 AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTACTCCACTGCAACCT
*
2129924 CAGGGAGATAAGACTTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTT
66 CAGGGAGATAAGACTTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTT
*
2129989 AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCT
1 AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTACTCCACTGCAACCT
2130054 CAGGGAGATAAGAAC-TGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTT
66 CAGGGAGATAAG-ACTTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTT
2130118 T
130 T
2130119 AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTA
1 AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTA
2130170 TAATTCTTCA
Statistics
Matches: 171, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
130 169 0.99
131 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (130 bp):
AATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTACTCCACTGCAACCT
CAGGGAGATAAGACTTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTT
Found at i:2130582 original size:9 final size:9
Alignment explanation
Indices: 2130568--2130652 Score: 134
Period size: 9 Copynumber: 9.4 Consensus size: 9
2130558 GTAGTGATTC
2130568 AATTCGGTT
1 AATTCGGTT
*
2130577 AATTCGGGT
1 AATTCGGTT
*
2130586 AATTCGATT
1 AATTCGGTT
2130595 AATTCGGTT
1 AATTCGGTT
2130604 AATTCGGTT
1 AATTCGGTT
2130613 AATTCGGTT
1 AATTCGGTT
*
2130622 AATTCGGGT
1 AATTCGGTT
2130631 AATTCGGTT
1 AATTCGGTT
*
2130640 AATTCAGTT
1 AATTCGGTT
2130649 AATT
1 AATT
2130653 TTTAACCAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:2132150 original size:42 final size:42
Alignment explanation
Indices: 2132101--2132209 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
2132091 AGATCGTCAT
* **
2132101 ATGCCCCAATCTAATCAAAATTTGAA-CTGTTCAGATCACCTC
1 ATGCCCCATTCTAATCAAAATTTGAACCACTT-AGATCACCTC
* **
2132143 ATGCCCCATTCTGATCAACTTTTGAACCACTTAGATCACCTC
1 ATGCCCCATTCTAATCAAAATTTGAACCACTTAGATCACCTC
* *
2132185 ATGCCCCGTTCTAATCAATATTTGA
1 ATGCCCCATTCTAATCAAAATTTGA
2132210 GCCGTCCTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 53 0.95
43 3 0.05
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.31
Consensus pattern (42 bp):
ATGCCCCATTCTAATCAAAATTTGAACCACTTAGATCACCTC
Found at i:2144765 original size:5 final size:5
Alignment explanation
Indices: 2144755--2144795 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
2144745 AGATTTATAA
*
2144755 AAAAT AAAAT AAAAAT AAAAT AAAAAT GAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT -AAAAT AAAAT AAAAT AAAA
2144796 ATGAATAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 22 0.69
6 10 0.31
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:2144776 original size:16 final size:17
Alignment explanation
Indices: 2144755--2144797 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2144745 AGATTTATAA
2144755 AAAAT-AAAATAAAAAT
1 AAAATAAAAATAAAAAT
*
2144771 AAAATAAAAAT-GAAAT
1 AAAATAAAAATAAAAAT
2144787 AAAATAAAAAT
1 AAAATAAAAAT
2144798 GAATAACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAATAAAAATAAAAAT
Found at i:2144797 original size:11 final size:11
Alignment explanation
Indices: 2144754--2144795 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
2144744 AAGATTTATA
2144754 AAAAATAAAAT
1 AAAAATAAAAT
2144765 AAAAATAAAAT
1 AAAAATAAAAT
*
2144776 AAAAATGAAAT
1 AAAAATAAAAT
2144787 -AAAATAAAA
1 AAAAATAAAA
2144796 ATGAATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2144798 original size:16 final size:16
Alignment explanation
Indices: 2144767--2144800 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2144757 AATAAAATAA
2144767 AAATAAAATAAAAATG
1 AAATAAAATAAAAATG
2144783 AAATAAAATAAAAATG
1 AAATAAAATAAAAATG
2144799 AA
1 AA
2144801 TAACTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATAAAATAAAAATG
Found at i:2144802 original size:15 final size:15
Alignment explanation
Indices: 2144768--2144817 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2144758 ATAAAATAAA
2144768 AATAAAATAAAAATG
1 AATAAAATAAAAATG
2144783 AAATAAAATAAAAATG
1 -AATAAAATAAAAATG
** *
2144799 AATAACTTAAAAATT
1 AATAAAATAAAAATG
2144814 AATA
1 AATA
2144818 TCTACGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 16 0.52
16 15 0.48
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (15 bp):
AATAAAATAAAAATG
Found at i:2146527 original size:17 final size:17
Alignment explanation
Indices: 2146491--2146530 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2146481 GCCTTCACTA
*
2146491 TTATTTTTTATTTGGCT
1 TTATTTTTTATTTGGAT
**
2146508 TTATTTTTTATTTTTAT
1 TTATTTTTTATTTGGAT
2146525 TTATTT
1 TTATTT
2146531 GTTTTTCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.78
Consensus pattern (17 bp):
TTATTTTTTATTTGGAT
Found at i:2147620 original size:31 final size:31
Alignment explanation
Indices: 2147582--2147640 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2147572 AATTATACAC
*
2147582 ATGAAACTTTGATTGTGATTCAAATGTATAT
1 ATGAAACTTTAATTGTGATTCAAATGTATAT
* *
2147613 ATGAAACTTTAATTTTGATTCAATTGTA
1 ATGAAACTTTAATTGTGATTCAAATGTA
2147641 CACATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (31 bp):
ATGAAACTTTAATTGTGATTCAAATGTATAT
Found at i:2148037 original size:21 final size:21
Alignment explanation
Indices: 2148013--2148057 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2148003 AAATAGTTAA
2148013 AATTT-ATGGTTTAAAAAATAT
1 AATTTAAT-GTTTAAAAAATAT
* *
2148034 AATTTAATGTTTAACAAATTT
1 AATTTAATGTTTAAAAAATAT
2148055 AAT
1 AAT
2148058 ATTTTTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (21 bp):
AATTTAATGTTTAAAAAATAT
Found at i:2148138 original size:16 final size:16
Alignment explanation
Indices: 2148117--2148170 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
2148107 TTTGGTTCGT
2148117 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
*
2148133 TGTAATTGAATAGAGC
1 TGTAATGGAATAGAGC
* *
2148149 TATAATGGAATAGAAC
1 TGTAATGGAATAGAGC
2148165 TGTAAT
1 TGTAAT
2148171 AGTAATTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:2148446 original size:37 final size:37
Alignment explanation
Indices: 2148337--2148463 Score: 115
Period size: 37 Copynumber: 3.6 Consensus size: 37
2148327 GTTATTAAAT
* *
2148337 TTTAATAAAATTATTAATATAA--A-TAATAA-ATAA
1 TTTAATAAAATTCTTAATATAATTATTATTAATATAA
* * *
2148370 TTTAATCATATT-TTAACATAATTATTATTAAATATAA
1 TTTAATAAAATTCTTAATATAATTATTATT-AATATAA
*
2148407 TTTAATAAAATTCTTAATATAATTATTCTT-ATATGAA
1 TTTAATAAAATTCTTAATATAATTATTATTAATAT-AA
* *
2148444 TTTACTAAAA-TCATAATATA
1 TTTAATAAAATTCTTAATATA
2148464 TAATAATATA
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
32 8 0.10
33 10 0.13
34 1 0.01
35 3 0.04
36 15 0.19
37 25 0.32
38 15 0.19
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.45
Consensus pattern (37 bp):
TTTAATAAAATTCTTAATATAATTATTATTAATATAA
Found at i:2152889 original size:19 final size:20
Alignment explanation
Indices: 2152843--2152894 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
2152833 AAAGAAAAAA
* *
2152843 ATTTTAATTTTCCTATTATT
1 ATTTTATTTTTACTATTATT
2152863 ATTATTTATTTTTACTATT-TT
1 A-T-TTTATTTTTACTATTATT
2152884 ATTTTATTTTT
1 ATTTTATTTTT
2152895 GTAGGAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 9 0.32
20 2 0.07
21 4 0.14
22 13 0.46
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTATTTTTACTATTATT
Found at i:2157340 original size:29 final size:30
Alignment explanation
Indices: 2157307--2157365 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
2157297 TATGGTTTAA
2157307 TGTGCAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* * *
2157336 TGTGCAATTTTATATATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
2157366 GCTCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:2158754 original size:64 final size:65
Alignment explanation
Indices: 2158630--2158763 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 65
2158620 ATTTTATGCC
* * *
2158630 AAAATCATGGTAGATTAGTGGTCCTCAAATTTATTTTCATTTAATATTAAAATTAACGTAATTTG
1 AAAATCATGGTAGATTAGTGGTCCTC--A-GTATTTTCATTTAATATCAAAATTAACGTAACTTG
2158695 TGG
63 TGG
* *
2158698 AAAATTATGGTAGATTAGTGGTCCTC-GTATTTTCATTTAATATCAAATTTAACGTAACTTGTGG
1 AAAATCATGGTAGATTAGTGGTCCTCAGTATTTTCATTTAATATCAAAATTAACGTAACTTGTGG
2158762 AA
1 AA
2158764 CCTAAGTTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
64 36 0.59
68 25 0.41
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (65 bp):
AAAATCATGGTAGATTAGTGGTCCTCAGTATTTTCATTTAATATCAAAATTAACGTAACTTGTGG
Found at i:2158858 original size:43 final size:42
Alignment explanation
Indices: 2158725--2158858 Score: 101
Period size: 41 Copynumber: 3.1 Consensus size: 42
2158715 GTGGTCCTCG
*
2158725 TATTTTCATTTAATATCAAATTTAACGTAACTTGTGGAACCTA
1 TATTTTCATTTAATATCAAAATTAACGTAACTTGT-GAACCTA
* * * ** * ** * **
2158768 -A-GTTGATTTTATGCCAAAATCATGGTAAATTTGTGGTCCTCA
1 TATTTTCATTTAATATCAAAATTAACGT-AACTTGTGAACCT-A
*
2158810 AATTTTCATTTAATATCAAAATTAACGTAACTTGTGAAACCTA
1 TATTTTCATTTAATATCAAAATTAACGTAACTTGTG-AACCTA
2158853 TATTTT
1 TATTTT
2158859 TATAGAAGAA
Statistics
Matches: 62, Mismatches: 24, Indels: 10
0.65 0.25 0.10
Matches are distributed among these distances:
41 20 0.32
42 8 0.13
43 14 0.23
44 20 0.32
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (42 bp):
TATTTTCATTTAATATCAAAATTAACGTAACTTGTGAACCTA
Found at i:2159449 original size:18 final size:19
Alignment explanation
Indices: 2159424--2159463 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2159414 AGATTCAGAG
2159424 TAAAAAAATCGCCTAAGGT
1 TAAAAAAATCGCCTAAGGT
2159443 TAAAAAAATCGCCTAAGGT
1 TAAAAAAATCGCCTAAGGT
2159462 TA
1 TA
2159464 CGCGATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (19 bp):
TAAAAAAATCGCCTAAGGT
Found at i:2169332 original size:40 final size:40
Alignment explanation
Indices: 2169274--2169364 Score: 148
Period size: 40 Copynumber: 2.2 Consensus size: 40
2169264 GTGAATAAAT
*
2169274 AAATAAATAAACATCAAGTAAAGCAATAATAAT-AACAAAGA
1 AAATAGAT-AACATCAAGTAAAGCAATAATAATGAA-AAAGA
2169315 AAATAGATAACATCAAGTAAAGCAATAATAATGAAAAAGA
1 AAATAGATAACATCAAGTAAAGCAATAATAATGAAAAAGA
2169355 AAATAGATAA
1 AAATAGATAA
2169365 AAATTATAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 39 0.81
41 9 0.19
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.18
Consensus pattern (40 bp):
AAATAGATAACATCAAGTAAAGCAATAATAATGAAAAAGA
Found at i:2169415 original size:23 final size:22
Alignment explanation
Indices: 2169375--2169418 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
2169365 AAATTATAAA
*
2169375 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
2169397 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
2169419 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:2169443 original size:31 final size:30
Alignment explanation
Indices: 2169366--2169447 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 30
2169356 AATAGATAAA
*
2169366 AATTATAAAATATAAAA-ATATATATATGT
1 AATTATAAAAAATAAAATATATATATATGT
* *
2169395 ACA-TAT--AAGA-AAAATATATATGTATGT
1 A-ATTATAAAAAATAAAATATATATATATGT
2169422 GAATTATAAAAAATAAAATATATATA
1 -AATTATAAAAAATAAAATATATATA
2169448 AATATACATA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
26 4 0.10
27 15 0.36
28 4 0.10
29 4 0.10
30 4 0.10
31 11 0.26
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (30 bp):
AATTATAAAAAATAAAATATATATATATGT
Found at i:2169445 original size:66 final size:67
Alignment explanation
Indices: 2169361--2169489 Score: 156
Period size: 66 Copynumber: 1.9 Consensus size: 67
2169351 AAGAAAATAG
* * *
2169361 ATAAAAATTATAAAATATAAAAATATATATA-TGTACATA-TAAGAAAAATATATATGTATGTGA
1 ATAAAAAATATAAAATATAAAAATATACATATTGTA-ATAGTAAGAAAAATATATAAGTATGTGA
2169424 ATT
65 ATT
* * *
2169427 ATAAAAAATA-AAATATATATAAATATACATATTTTAATATGTAAGAAATATATATAAGTATGT
1 ATAAAAAATATAAA-ATATAAAAATATACATATTGTAATA-GTAAGAAAAATATATAAGTATGT
2169490 ATATAAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
65 3 0.06
66 27 0.51
67 3 0.06
68 20 0.38
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (67 bp):
ATAAAAAATATAAAATATAAAAATATACATATTGTAATAGTAAGAAAAATATATAAGTATGTGAA
TT
Found at i:2169551 original size:36 final size:36
Alignment explanation
Indices: 2169511--2169586 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
2169501 TGAAACATAG
*
2169511 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
2169547 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
2169584 AAA
1 AAA
2169587 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:2169929 original size:23 final size:21
Alignment explanation
Indices: 2169890--2169932 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
2169880 AAATTAAAAA
*
2169890 TATACAAATCAATAAAATAAT
1 TATACAAATCAACAAAATAAT
2169911 TATACACAGATCAACAAAATAA
1 TATACA-A-ATCAACAAAATAA
2169933 GAACAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.23
Consensus pattern (21 bp):
TATACAAATCAACAAAATAAT
Found at i:2170152 original size:22 final size:21
Alignment explanation
Indices: 2170127--2170195 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
2170117 TACAAATTAA
*
2170127 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATT-CAATATCAT
*
2170149 ATCTTCTAAGATTGAATATCAT
1 ATC-TCTAAGATTCAATATCAT
2170171 A--TCTAAGATTGCATATATCAT
1 ATCTCTAAGATT-CA-ATATCAT
2170192 ATCT
1 ATCT
2170196 AAGATTGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 9 0.23
20 1 0.03
21 8 0.21
22 11 0.28
23 10 0.26
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (21 bp):
ATCTCTAAGATTCAATATCAT
Found at i:2170190 original size:21 final size:20
Alignment explanation
Indices: 2170153--2170208 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 20
2170143 AATCATATCT
2170153 TCTAAGATTGA-ATATCATA
1 TCTAAGATTGATATATCATA
2170172 TCTAAGATTGCATATATCATA
1 TCTAAGATTG-ATATATCATA
2170193 TCTAAGATTG-TATATC
1 TCTAAGATTGATATATC
2170209 CTTGAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.46
20 1 0.03
21 18 0.51
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (20 bp):
TCTAAGATTGATATATCATA
Found at i:2170535 original size:29 final size:28
Alignment explanation
Indices: 2170493--2170562 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
2170483 GAGCAATCCC
* *
2170493 TAAAATCTCCAAAATCAGAAATCCTAAACA
1 TAAAATCCCCAAAATCA-AAACCCT-AACA
*
2170523 -AAAATCCCCAAAATCAAAACCCTTACA
1 TAAAATCCCCAAAATCAAAACCCTAACA
2170550 TAAAATCCCCAAA
1 TAAAATCCCCAAA
2170563 TTCGACCACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 18 0.50
29 15 0.42
ACGTcount: A:0.53, C:0.29, G:0.01, T:0.17
Consensus pattern (28 bp):
TAAAATCCCCAAAATCAAAACCCTAACA
Found at i:2170577 original size:23 final size:23
Alignment explanation
Indices: 2170551--2170595 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2170541 ACCCTTACAT
2170551 AAAATCCCCAAATTCGACCACCC
1 AAAATCCCCAAATTCGACCACCC
*
2170574 AAAATCCCCAAATTCGATCACC
1 AAAATCCCCAAATTCGACCACC
2170596 TTAAGCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.40, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAATCCCCAAATTCGACCACCC
Found at i:2170970 original size:38 final size:38
Alignment explanation
Indices: 2170927--2171048 Score: 226
Period size: 38 Copynumber: 3.2 Consensus size: 38
2170917 GAAATGATAT
2170927 ATTTTAATAATTTTATATTTCAAAAAAATAATATAATA
1 ATTTTAATAATTTTATATTTCAAAAAAATAATATAATA
2170965 ATTTTAATAATTTTATATTTCAAAAAAATAATATAATA
1 ATTTTAATAATTTTATATTTCAAAAAAATAATATAATA
*
2171003 ATTTTAATAATTTTATATTTCAAAAAAATAATTTTAATA
1 ATTTTAATAATTTTATATTTCAAAAAAATAA-TATAATA
2171042 ATTTTAA
1 ATTTTAA
2171049 AATCATTTAC
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
38 69 0.84
39 13 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (38 bp):
ATTTTAATAATTTTATATTTCAAAAAAATAATATAATA
Found at i:2177402 original size:17 final size:17
Alignment explanation
Indices: 2177389--2177421 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2177379 TCATTTGGCG
*
2177389 AACTCTAGGTTTTGACA
1 AACTCTAGGGTTTGACA
2177406 AACTCTAGGGTTTGAC
1 AACTCTAGGGTTTGAC
2177422 GGATTGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (17 bp):
AACTCTAGGGTTTGACA
Found at i:2181018 original size:20 final size:20
Alignment explanation
Indices: 2180993--2181031 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2180983 GTTTGATTTC
2180993 TTAAAAGAC-TTTTAACTTGG
1 TTAAAA-ACATTTTAACTTGG
*
2181013 TTAAAATCATTTTAACTTG
1 TTAAAAACATTTTAACTTG
2181032 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (20 bp):
TTAAAAACATTTTAACTTGG
Found at i:2181679 original size:20 final size:20
Alignment explanation
Indices: 2181605--2181679 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
2181595 TATACTTTTT
2181605 TTAACATTAA-TTAATCTTAA
1 TTAACA-TAAGTTAATCTTAA
* * *
2181625 TTAA-TTAAACTAAATCTTAA
1 TTAACAT-AAGTTAATCTTAA
2181645 TTAAC-T-AGTCATAATCTTAA
1 TTAACATAAGT--TAATCTTAA
2181665 TTAACATAAGTTAAT
1 TTAACATAAGTTAAT
2181680 GGGAACATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
19 2 0.05
20 35 0.80
21 1 0.02
22 3 0.07
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (20 bp):
TTAACATAAGTTAATCTTAA
Found at i:2193710 original size:30 final size:30
Alignment explanation
Indices: 2193674--2193734 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2193664 GGAAAAGATC
2193674 TGGCCATGATACGCATGTCAAAGTCTCAAG
1 TGGCCATGATACGCATGTCAAAGTCTCAAG
*
2193704 TGGCCATGATACGCTTGTCAAAGTCTCAAG
1 TGGCCATGATACGCATGTCAAAGTCTCAAG
2193734 T
1 T
2193735 CTTGGAATTG
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:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (30 bp):
TGGCCATGATACGCATGTCAAAGTCTCAAG
Found at i:2195939 original size:30 final size:30
Alignment explanation
Indices: 2195903--2195971 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2195893 AATATGATAT
* **
2195903 TCACACAAGCTGACAGTATATCAGGGTTGC
1 TCACACAAGCTGACAGTATAACAGAATTGC
* *
2195933 TCACACAAACTGACATTATAACAGAATTGC
1 TCACACAAGCTGACAGTATAACAGAATTGC
*
2195963 TCAAACAAG
1 TCACACAAG
2195972 TTGAAATTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (30 bp):
TCACACAAGCTGACAGTATAACAGAATTGC
Found at i:2197294 original size:25 final size:22
Alignment explanation
Indices: 2197254--2197332 Score: 63
Period size: 25 Copynumber: 3.4 Consensus size: 22
2197244 AATAAAAAAG
*
2197254 ATATAAATAAGTAAATAATATTA
1 ATATAAATAAGCAAAT-ATATTA
2197277 ATATATAATAAGACAAATATATTTAAA
1 ATATA-AATAAG-CAAATATA-TT--A
* *
2197304 ATTTAAATAAGTAAATATA--A
1 ATATAAATAAGCAAATATATTA
2197324 ATATAAATA
1 ATATAAATA
2197333 TAAATATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
20 9 0.19
23 5 0.11
24 9 0.19
25 13 0.28
26 6 0.13
27 5 0.11
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATAAATAAGCAAATATATTA
Found at i:2197324 original size:6 final size:6
Alignment explanation
Indices: 2197315--2197347 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2197305 TTTAAATAAG
2197315 TAAATA TAAATA TAAATA TAAATA TAAATA TAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAA
2197348 TAATAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATA
Found at i:2197353 original size:12 final size:12
Alignment explanation
Indices: 2197309--2197365 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
2197299 TTAAAATTTA
2197309 AATAAGTAAATAT
1 AATAA-TAAATAT
2197322 AA-ATATAAATAT
1 AATA-ATAAATAT
2197334 AA-ATATAAATAT
1 AATA-ATAAATAT
2197346 AATAAT-AATGAT
1 AATAATAAAT-AT
2197358 AATAATAA
1 AATAATAA
2197366 TAATAACATC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.08
12 32 0.80
13 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:2197353 original size:18 final size:18
Alignment explanation
Indices: 2197309--2197371 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
2197299 TTAAAATTTA
2197309 AATAAGTAAATATAAATAT
1 AATAA-TAAATATAAATAT
2197328 AA-ATATAAATATAAATAT
1 AATA-ATAAATATAAATAT
2197346 AATAAT-AATGAT-AATAAT
1 AATAATAAAT-ATAAAT-AT
2197364 AATAATAA
1 AATAATAA
2197372 CATCAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.15
18 28 0.72
19 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AATAATAAATATAAATAT
Found at i:2198149 original size:19 final size:18
Alignment explanation
Indices: 2198141--2198179 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2198131 TGAATCTTTG
2198141 TTCTTTTTTTAAATCGGT
1 TTCTTTTTTTAAATCGGT
*
2198159 TTCTTTTTTTTAAATCAGT
1 TTC-TTTTTTTAAATCGGT
2198178 TT
1 TT
2198180 TTTCTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (18 bp):
TTCTTTTTTTAAATCGGT
Found at i:2200642 original size:3 final size:3
Alignment explanation
Indices: 2200627--2200668 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2200617 ATTATGTTAT
*
2200627 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2200669 GAAAGGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2201925 original size:24 final size:26
Alignment explanation
Indices: 2201898--2201956 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
2201888 TGAGAAATGA
2201898 AATATGAAAT-AGTAT-ATTGTTGTG
1 AATATGAAATAAGTATGATTGTTGTG
* *
2201922 AATATGAATTGAATTATGATTGTTGTG
1 AATATGAAAT-AAGTATGATTGTTGTG
2201949 AATATGAA
1 AATATGAA
2201957 TTGAATTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 9 0.30
26 4 0.13
27 17 0.57
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (26 bp):
AATATGAAATAAGTATGATTGTTGTG
Found at i:2201951 original size:27 final size:27
Alignment explanation
Indices: 2201913--2201967 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2201903 GAAATAGTAT
2201913 ATTGTTGTGAATATGAATTGAATTATG
1 ATTGTTGTGAATATGAATTGAATTATG
2201940 ATTGTTGTGAATATGAATTGAATTATG
1 ATTGTTGTGAATATGAATTGAATTATG
2201967 A
1 A
2201968 GAAATGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.44
Consensus pattern (27 bp):
ATTGTTGTGAATATGAATTGAATTATG
Found at i:2201993 original size:20 final size:19
Alignment explanation
Indices: 2201964--2202003 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
2201954 GAATTGAATT
2201964 ATGAGAAATGAGATATGAA
1 ATGAGAAATGAGATATGAA
*
2201983 ATGATGAAATGAGATGTGAA
1 ATGA-GAAATGAGATATGAA
2202003 A
1 A
2202004 CTTGAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.23
Consensus pattern (19 bp):
ATGAGAAATGAGATATGAA
Found at i:2209285 original size:19 final size:19
Alignment explanation
Indices: 2209261--2209297 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2209251 TTTCAAAAAA
2209261 TAAAAC-ATAAAAATGATTT
1 TAAAACTATAAAAA-GATTT
2209280 TAAAACTATAAAAAGATT
1 TAAAACTATAAAAAGATT
2209298 CTCAAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAACTATAAAAAGATTT
Found at i:2209692 original size:18 final size:19
Alignment explanation
Indices: 2209652--2209716 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
2209642 TATTAGAATC
*
2209652 TTTTATATTTTTAAAAATA
1 TTTTTTATTTTTAAAAATA
*
2209671 TTTTTTATTTTTAAAGAGT-
1 TTTTTTATTTTTAAA-AATA
* *
2209690 TTTTTATTTTTTTAAATATA
1 TTTTT-TATTTTTAAAAATA
2209710 TTTTTTA
1 TTTTTTA
2209717 AAACTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTTTATTTTTAAAAATA
Found at i:2209974 original size:21 final size:21
Alignment explanation
Indices: 2209943--2209982 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2209933 GATTTTTATA
*
2209943 ATTTTTCAATATTTTTATTTTT
1 ATTTTTCAATA-ATTTATTTTT
2209965 ATTTTT-AATAATTTATTT
1 ATTTTTCAATAATTTATTT
2209983 GCTTTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTTCAATAATTTATTTTT
Found at i:2210834 original size:40 final size:40
Alignment explanation
Indices: 2210766--2210884 Score: 170
Period size: 40 Copynumber: 3.0 Consensus size: 40
2210756 ACCAAAAATT
2210766 TATTTTAAAAATTAAAATAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAATTAAAAAAAGTATTTTAAAAA
2210809 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
** *
2210849 -AAATTAAAATTAAAAAAAAT-AAAAAAGTATTTTAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAA
2210885 GTTAAAAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
38 16 0.22
39 17 0.23
40 25 0.34
41 3 0.04
42 6 0.08
43 6 0.08
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:2210861 original size:16 final size:15
Alignment explanation
Indices: 2210824--2210872 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
2210814 TAAAATTAAA
*
2210824 AAAATTAAAAAAAGT
1 AAAATTAAAAAAAAT
**
2210839 -ATTTTAAAAAAAATT
1 AAAATTAAAAAAAA-T
2210854 AAAATTAAAAAAAAT
1 AAAATTAAAAAAAAT
2210869 AAAA
1 AAAA
2210873 AAGTATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 10 0.37
15 6 0.22
16 11 0.41
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAATTAAAAAAAAT
Found at i:2211619 original size:42 final size:42
Alignment explanation
Indices: 2211564--2211647 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
2211554 TACAAAGTGT
2211564 ATTGACATCTAAATATT-ATTATAATTTAATTTAGATTTATTA
1 ATTGACATCTAAAT-TTAATTATAATTTAATTTAGATTTATTA
* *
2211606 ATTGACATTTAAATTTAATTATAATTTAATTTAGGTTTATTA
1 ATTGACATCTAAATTTAATTATAATTTAATTTAGATTTATTA
2211648 GACTTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (42 bp):
ATTGACATCTAAATTTAATTATAATTTAATTTAGATTTATTA
Found at i:2212321 original size:25 final size:25
Alignment explanation
Indices: 2212280--2212332 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2212270 ACAAATCTTG
* **
2212280 TAATATATATTTTTAAATTTTAAAA
1 TAATATATATTTATAAATTAAAAAA
2212305 TAATAT-TATTTAATAAATTAAAAAA
1 TAATATATATTT-ATAAATTAAAAAA
2212330 TAA
1 TAA
2212333 GTACGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAATATATATTTATAAATTAAAAAA
Found at i:2214777 original size:42 final size:42
Alignment explanation
Indices: 2214730--2214843 Score: 228
Period size: 42 Copynumber: 2.7 Consensus size: 42
2214720 TGTTTTAATG
2214730 AATTTAATTTAATATTTATCTAGATATTAATATGAGATATTA
1 AATTTAATTTAATATTTATCTAGATATTAATATGAGATATTA
2214772 AATTTAATTTAATATTTATCTAGATATTAATATGAGATATTA
1 AATTTAATTTAATATTTATCTAGATATTAATATGAGATATTA
2214814 AATTTAATTTAATATTTATCTAGATATTAA
1 AATTTAATTTAATATTTATCTAGATATTAA
2214844 ATTTAATTTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (42 bp):
AATTTAATTTAATATTTATCTAGATATTAATATGAGATATTA
Found at i:2214826 original size:24 final size:25
Alignment explanation
Indices: 2214798--2214855 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
2214788 TATCTAGATA
2214798 TTAATAT-GAGATATTAAATTTAAT
1 TTAATATCGAGATATTAAATTTAAT
*
2214822 TTAATATTTATCTAGATATTAAATTTAAT
1 TT-A-A--TATCGAGATATTAAATTTAAT
2214851 TTAAT
1 TTAAT
2214856 GTTTATCTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
24 2 0.07
25 2 0.07
26 1 0.04
27 1 0.04
28 4 0.14
29 18 0.64
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (25 bp):
TTAATATCGAGATATTAAATTTAAT
Found at i:2214844 original size:29 final size:29
Alignment explanation
Indices: 2214806--2214876 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
2214796 TATTAATATG
2214806 AGATATTAAATTTAATTTAATATTTATCT
1 AGATATTAAATTTAATTTAATATTTATCT
*
2214835 AGATATTAAATTTAATTTAATGTTTATCT
1 AGATATTAAATTTAATTTAATATTTATCT
*
2214864 AGATAAT-AATTTA
1 AGATATTAAATTTA
2214877 TTAATTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (29 bp):
AGATATTAAATTTAATTTAATATTTATCT
Found at i:2218272 original size:23 final size:23
Alignment explanation
Indices: 2218241--2218292 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
2218231 TAAGATATCT
*
2218241 ATATATAAATTATAAATAA-ATAA
1 ATAT-TAAATTAAAAATAATATAA
2218264 AGTATTAAATTAAAAATAATATAA
1 A-TATTAAATTAAAAATAATATAA
2218288 ATATT
1 ATATT
2218293 TTCAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATTAAATTAAAAATAATATAA
Found at i:2221946 original size:7 final size:6
Alignment explanation
Indices: 2221925--2221982 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
2221915 TAAGTTTCCA
* ** ** *
2221925 AAAATG AAAATG AAAATG GAAATG GGAATG GGAATG GAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
*
2221973 AAAACG AAAA
1 AAAATG AAAA
2221983 CTTGCAATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.59, C:0.02, G:0.26, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:2221954 original size:18 final size:18
Alignment explanation
Indices: 2221926--2221976 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2221916 AAGTTTCCAA
2221926 AAATGAAAATGAAAATGG
1 AAATGAAAATGAAAATGG
** **
2221944 AAATGGGAATGGGAATGG
1 AAATGAAAATGAAAATGG
2221962 AAATGAAAATGAAAA
1 AAATGAAAATGAAAA
2221977 CGAAAACTTG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (18 bp):
AAATGAAAATGAAAATGG
Found at i:2225170 original size:27 final size:28
Alignment explanation
Indices: 2225118--2225176 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
2225108 AGAAAAATTT
*
2225118 TAAAATTAATATATAAAGCGACTAAAAA
1 TAAAATTAATATATAAAGCAACTAAAAA
*
2225146 TAAAA-TAATATATAAA-TAACTTAAAAA
1 TAAAATTAATATATAAAGCAAC-TAAAAA
2225173 TAAA
1 TAAA
2225177 TCATTTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 21 0.75
28 5 0.18
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.27
Consensus pattern (28 bp):
TAAAATTAATATATAAAGCAACTAAAAA
Found at i:2225258 original size:15 final size:16
Alignment explanation
Indices: 2225240--2225280 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2225230 AAGATGAATT
2225240 TTTAAAATAAATCA-A
1 TTTAAAATAAATCACA
*
2225255 TTTAAGGAT-AATCACA
1 TTTAA-AATAAATCACA
2225271 TTTAAAATAA
1 TTTAAAATAA
2225281 CATATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (16 bp):
TTTAAAATAAATCACA
Found at i:2225854 original size:15 final size:14
Alignment explanation
Indices: 2225815--2225854 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
2225805 GCATATAGAG
2225815 AAAAAATAGAGAGAA
1 AAAAAATA-AGAGAA
2225830 AAAAAA-AAGAGAA
1 AAAAAATAAGAGAA
2225843 AAAAAACTAAGA
1 AAAAAA-TAAGA
2225855 AAACCAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.52
14 1 0.04
15 10 0.43
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAAAATAAGAGAA
Found at i:2225857 original size:13 final size:13
Alignment explanation
Indices: 2225811--2225848 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2225801 TTTCGCATAT
* *
2225811 AGAGAAAAAATAG
1 AGAGAAAAAAAAA
2225824 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
2225837 AGAGAAAAAAAA
1 AGAGAAAAAAAA
2225849 CTAAGAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (13 bp):
AGAGAAAAAAAAA
Found at i:2232160 original size:31 final size:31
Alignment explanation
Indices: 2232124--2232182 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2232114 GGATAATTTC
**
2232124 TTAACCATTCACATCCCACTAAGTCCCATAA
1 TTAACCACCCACATCCCACTAAGTCCCATAA
*
2232155 TTAACCACCCACATCCCTCTAAGTCCCA
1 TTAACCACCCACATCCCACTAAGTCCCA
2232183 CAGATAACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.41, G:0.03, T:0.24
Consensus pattern (31 bp):
TTAACCACCCACATCCCACTAAGTCCCATAA
Found at i:2232191 original size:31 final size:31
Alignment explanation
Indices: 2232124--2232193 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
2232114 GGATAATTTC
** *
2232124 TTAACCATTCACATCCCACTAAGTCCCATAA
1 TTAACCACCCACATCCCACTAAGTCCCACAA
*
2232155 TTAACCACCCACATCCCTCTAAGTCCCACAGA
1 TTAACCACCCACATCCCACTAAGTCCCACA-A
2232187 -TAACCAC
1 TTAACCAC
2232194 TCACCAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.40, G:0.04, T:0.21
Consensus pattern (31 bp):
TTAACCACCCACATCCCACTAAGTCCCACAA
Found at i:2234047 original size:54 final size:54
Alignment explanation
Indices: 2233965--2234074 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
2233955 CTCTTCTTCC
2233965 CTACACTACTCGACCCCCACTTCTTCACTAAGGGAAGCTTTCCCTTTTAATTTT
1 CTACACTACTCGACCCCCACTTCTTCACTAAGGGAAGCTTTCCCTTTTAATTTT
**
2234019 CTACACTACTCGACCTTCACTTCTTCACTAAGGGAAGCTTTCCCTTTTAATTTT
1 CTACACTACTCGACCCCCACTTCTTCACTAAGGGAAGCTTTCCCTTTTAATTTT
2234073 CT
1 CT
2234075 TGCCATTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.22, C:0.32, G:0.09, T:0.37
Consensus pattern (54 bp):
CTACACTACTCGACCCCCACTTCTTCACTAAGGGAAGCTTTCCCTTTTAATTTT
Found at i:2234551 original size:12 final size:12
Alignment explanation
Indices: 2234534--2234559 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2234524 AAAAACAGGC
2234534 TTTTAGCGGCGT
1 TTTTAGCGGCGT
2234546 TTTTAGCGGCGT
1 TTTTAGCGGCGT
2234558 TT
1 TT
2234560 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:2235119 original size:114 final size:114
Alignment explanation
Indices: 2234628--2235115 Score: 806
Period size: 114 Copynumber: 4.3 Consensus size: 114
2234618 AAAATAACCA
* * *
2234628 TTAGTGGCGTTTTT-GAGAAAGCGCCAC-AAAAAACCTAAGCCCAACGACGTCGTTTCTCGAGCT
1 TTAGCGGCGTTTTTGGA-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCTCGAGCT
2234691 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
2234741 TTAGCGGCGTTTTTGCAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTCTCGAGCTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCTCGAGCTT
2234806 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
2234855 TTAGCGGCGTTTTTGCAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTT-TATGAGCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCT-CGAGCT
*
2234919 TTCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
2234969 TTAGCGGCGTTTGTGGGAAAGCGCCGCAAAAAAACCTAAGCCCCACGACGCCGTTT-TCTGAGCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCTC-GAGCT
*
2235033 TT-AGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
2235082 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAA
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAA
2235116 ACCTCGAGCT
Statistics
Matches: 356, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
113 100 0.28
114 256 0.72
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCTCGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:2235746 original size:21 final size:22
Alignment explanation
Indices: 2235711--2235761 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2235701 ATTATGAAGT
* *
2235711 AGGAATTATGGTTTAAGGGTT-
1 AGGATTTAAGGTTTAAGGGTTA
* *
2235732 GGGATTTAAGGTTTAGGGGTTA
1 AGGATTTAAGGTTTAAGGGTTA
2235754 AGGATTTA
1 AGGATTTA
2235762 GGGGTTAGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.37
Consensus pattern (22 bp):
AGGATTTAAGGTTTAAGGGTTA
Found at i:2235763 original size:15 final size:14
Alignment explanation
Indices: 2235737--2235784 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
2235727 GGGTTGGGAT
2235737 TTAAGGTTTAGGGG
1 TTAAGGTTTAGGGG
2235751 TTAAGGATTTAGGGG
1 TTAAGG-TTTAGGGG
*
2235766 TTAGATGTTT-GGGG
1 TTA-AGGTTTAGGGG
2235780 TTAAG
1 TTAAG
2235785 AGTTAGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 1 0.03
14 13 0.43
15 14 0.47
16 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.38
Consensus pattern (14 bp):
TTAAGGTTTAGGGG
Found at i:2236620 original size:147 final size:147
Alignment explanation
Indices: 2236346--2236865 Score: 821
Period size: 147 Copynumber: 3.5 Consensus size: 147
2236336 ATTTTATAAA
* * *
2236346 AAATCAATTTATAAAAAATAAAATAAAAAAATTTTAGCATAGCAAAACGGTGTTATTTTGTTCAA
1 AAATCAATTTAT--AAAA-AAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCAA
*** **
2236411 AATGAAATAGCGGCGTTTTTA-CGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTT
63 AATGAAA-A---AAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTT
2236475 TTCCAGAAAAATGCCGCAAAGAAT
124 TTCCAGAAAAATGCCGCAAAGAAT
* *
2236499 AAATCAATTTATAAAAAAAATAAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAAT
1 AAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAAT
2236564 GAAAAAAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGA
66 GAAAAAAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGA
2236629 AAAATGCCGCAAAGAAT
131 AAAATGCCGCAAAGAAT
* *
2236646 AAATCAATTTATAAAAAAAATAAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAAT
1 AAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAAT
*
2236711 GAAAAAAATTTGCGGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGA
66 GAAAAAAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGA
2236776 AAAATGCCGCAAAGAAT
131 AAAATGCCGCAAAGAAT
* *
2236793 AAATCAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAAC-G-GTCGTTTTGTTCAAAAT
1 AAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAAT
2236856 GAAAAAAATT
66 GAAAAAAATT
2236866 AGGTAAGCAA
Statistics
Matches: 351, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
145 26 0.07
146 5 0.01
147 255 0.73
149 1 0.00
150 48 0.14
151 4 0.01
153 12 0.03
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (147 bp):
AAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAAT
GAAAAAAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGA
AAAATGCCGCAAAGAAT
Found at i:2236874 original size:117 final size:119
Alignment explanation
Indices: 2236749--2236984 Score: 422
Period size: 117 Copynumber: 2.0 Consensus size: 119
2236739 GCGCCGCTAA
2236749 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
*
2236814 AAAAAAAATTTAGAATAGCAAAAC-G-GTCGTTTTGTTCAAAATGAAAAAAATT
66 AAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATT
2236866 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
** *
2236931 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATT
66 AAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATT
2236985 TGCAGCGTTT
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
117 86 0.76
118 1 0.01
119 26 0.23
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (119 bp):
AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
AAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATT
Found at i:2237042 original size:147 final size:147
Alignment explanation
Indices: 2236866--2237318 Score: 807
Period size: 147 Copynumber: 3.1 Consensus size: 147
2236856 GAAAAAAATT
* * * *
2236866 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGTGTTTTTCAGAAAAACGCTGCAAAGAATAAATCAATTTATAAAAAAAAT
2236931 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
66 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
2236996 ATAAGAAGCGCCGCTAA
131 ATAAGAAGCGCCGCTAA
*
2237013 AGGTAAGCAATAGCGGTGTTTTTCAGAAAAACGCTGCAAAGAATAAATTAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGTGTTTTTCAGAAAAACGCTGCAAAGAATAAATCAATTTATAAAAAAAAT
2237078 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
66 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
2237143 ATAAGAAGCGCCGCTAA
131 ATAAGAAGCGCCGCTAA
2237160 AGGTAAGCAATAGCGGTGTTTTTCAGAAAAACGCTGCAAAGAATAAATCAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGTGTTTTTCAGAAAAACGCTGCAAAGAATAAATCAATTTATAAAAAAAAT
* * * *
2237225 AAAAAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGTTTT
66 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
*
2237290 TTAAGAAGCGCCGCTAA
131 ATAAGAAGCGCCGCTAA
*
2237307 AGATAAGCAATA
1 AGGTAAGCAATA
2237319 CCAGCGTCAC
Statistics
Matches: 294, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 294 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (147 bp):
AGGTAAGCAATAGCGGTGTTTTTCAGAAAAACGCTGCAAAGAATAAATCAATTTATAAAAAAAAT
AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
ATAAGAAGCGCCGCTAA
Found at i:2237072 original size:264 final size:266
Alignment explanation
Indices: 2236602--2237131 Score: 956
Period size: 264 Copynumber: 2.0 Consensus size: 266
2236592 GCGCCGCTAA
2236602 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
*
2236667 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCGGCGTTTT
66 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
*
2236732 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAAT
131 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAACGCCGCAAAGAATAAAT
*
2236797 CAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAAC-G-GTCGTTTTGTTCAAAATGAAA
196 CAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
2236860 AAAATT
261 AAAATT
2236866 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
2236931 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
66 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
* * *
2236996 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGTGTTTTTCAGAAAAACGCTGCAAAGAATAAAT
131 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAACGCCGCAAAGAATAAAT
* ** *
2237061 TAATTTATAAAAAAAATAAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAA
196 CAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
2237126 AAAATT
261 AAAATT
2237132 TGCAGCGTTT
Statistics
Matches: 254, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
264 227 0.89
265 1 0.00
266 26 0.10
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (266 bp):
AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAACGCCGCAAAGAATAAAT
CAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
AAAATT
Found at i:2237217 original size:411 final size:413
Alignment explanation
Indices: 2236455--2237275 Score: 1520
Period size: 411 Copynumber: 2.0 Consensus size: 413
2236445 GCGCCGCTAA
2236455 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
2236520 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
66 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
*
2236585 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAAT
131 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAACGCCGCAAAGAATAAAT
2236650 CAATTTATAAAAAAAATAAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAA
196 CAATTTATAAAAAAAATAAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAA
*
2236715 AAAATTTGCGGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAA
261 AAAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAA
*
2236780 TGCCGCAAAGAATAAATCAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAAC-G-GTCG
326 CGCCGCAAAGAATAAATCAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCG
2236843 TTTTGTTCAAAATGAAAAAAATT
391 TTTTGTTCAAAATGAAAAAAATT
2236866 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
1 AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
2236931 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
66 AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
* * *
2236996 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGTGTTTTTCAGAAAAACGCTGCAAAGAATAAAT
131 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAACGCCGCAAAGAATAAAT
*
2237061 TAATTTATAAAAAAAATAAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAA
196 CAATTTATAAAAAAAATAAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAA
* *
2237126 AAAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGTGTTTTTCAGAAAAA
261 AAAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAA
* **
2237191 CGCTGCAAAGAATAAATCAATTTATAAAAAAAATAAAAAATTTTTAGAATAGCAAAACGGCGTCG
326 CGCCGCAAAGAATAAATCAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCG
2237256 TTTTGTTCAAAATGAAAAAA
391 TTTTGTTCAAAATGAAAAAA
2237276 TTTTGCGGCG
Statistics
Matches: 396, Mismatches: 12, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
411 371 0.94
412 1 0.00
413 24 0.06
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (413 bp):
AGGTAAGCAATAGCGGCGTTTTCCAGAAAAATGCCGCAAAGAATAAATCAATTTATAAAAAAAAT
AAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTGCAGCGTTTT
ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAACGCCGCAAAGAATAAAT
CAATTTATAAAAAAAATAAAAAATTTTTAGAATAGTAAAACGGCGTCATTTTGTTCAAAATGAAA
AAAATTTGCAGCGTTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCAGAAAAA
CGCCGCAAAGAATAAATCAATTTATAAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCG
TTTTGTTCAAAATGAAAAAAATT
Found at i:2240470 original size:15 final size:13
Alignment explanation
Indices: 2240437--2240473 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
2240427 CATACATATA
2240437 TTTATATATGCTT
1 TTTATATATGCTT
2240450 TTTATATATGCTT
1 TTTATATATGCTT
2240463 TTTATATATGC
1 TTTATATATGC
2240474 CTCTACATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.59
Consensus pattern (13 bp):
TTTATATATGCTT
Found at i:2240928 original size:24 final size:23
Alignment explanation
Indices: 2240844--2240935 Score: 107
Period size: 23 Copynumber: 4.0 Consensus size: 23
2240834 GAAATTTGAT
* *
2240844 AGTGCTGTAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTATTTA
2240867 AGTGCTGCAAATTGAAGTATTT-
1 AGTGCTGCAAATTGAAGTATTTA
*
2240889 AGTTGCTGGAAATTGAGATGT-TTTA
1 AG-TGCTGCAAATTGA-A-GTATTTA
*
2240914 AGTGCTGCAAGTTGAAGTATTT
1 AGTGCTGCAAATTGAAGTATTT
2240936 TGCACAACCA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
22 4 0.07
23 36 0.61
24 15 0.25
25 4 0.07
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.38
Consensus pattern (23 bp):
AGTGCTGCAAATTGAAGTATTTA
Found at i:2240929 original size:47 final size:46
Alignment explanation
Indices: 2240846--2240935 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 46
2240836 AATTTGATAG
*
2240846 TGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGT
1 TGCTGGAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGT
*
2240892 TGCTGGAAATTG-AGATGTTTTAAGTGCTGCAAGTTGAAGTATTT
1 TGCTGGAAATTGAAG-TG-TTTAAGTGCTGCAAATTGAAGTATTT
2240936 TGCACAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
45 2 0.05
46 13 0.32
47 25 0.62
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.39
Consensus pattern (46 bp):
TGCTGGAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGT
Found at i:2241721 original size:43 final size:42
Alignment explanation
Indices: 2241673--2241901 Score: 253
Period size: 43 Copynumber: 5.4 Consensus size: 42
2241663 GTTTTTTGAG
* * * *
2241673 AAAGCGTCGCTAAAGGTCTTGTTTTTTAGCGGCACTTT-AGGAA
1 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGC-GTTTGA-GAA
* *
2241716 AAAGCGCCGCTAAAGGTCTTAGTTTTTAGCGGCGTTTGAGAGA
1 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGAGA-A
* * *
2241759 AAAGTGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAAA
1 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGAG-AA
* * * * *
2241802 AAAGCGCTGCTAAAGGTCTTGGTCTTTAGTGGCGTTGGGGGA
1 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGAGAA
* *
2241844 AAAGCGCCGCTAAAGATCTTGGTCTTTAGCGGCGTTTGTGGAA
1 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTG-AGAA
*
2241887 AAAGTGCCGCTAAAG
1 AAAGCGCCGCTAAAG
2241902 TTAGCGACGA
Statistics
Matches: 160, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
42 40 0.25
43 119 0.74
44 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGAGAA
Found at i:2241870 original size:85 final size:85
Alignment explanation
Indices: 2241673--2241901 Score: 291
Period size: 86 Copynumber: 2.7 Consensus size: 85
2241663 GTTTTTTGAG
* * *
2241673 AAAGCGTCGCTAAAGGTCTTGTTTTTTAGCGGCACTTTAG-GAAAAAGCGCCGCTAAAGGTCTTA
1 AAAGCGTCGCTAAAGGTCTTGGTCTTTAGCGGC-GTTT-GTGAAAAAGCGCCGCTAAAGGTCTTA
*
2241737 GTTTTTAGCGGCGTTTGAGAGA
64 GTCTTTAGCGGCGTTTGAGAGA
* * *
2241759 AAAGTGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCTGCTAAAGGTCTTGG
1 AAAGCGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTG-AAAAAGCGCCGCTAAAGGTCTTAG
* * *
2241824 TCTTTAGTGGCG-TTGGGGGA
65 TCTTTAGCGGCGTTTGAGAGA
* * *
2241844 AAAGCGCCGCTAAAGATCTTGGTCTTTAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAG
1 AAAGCGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAG
2241902 TTAGCGACGA
Statistics
Matches: 125, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 61 0.49
86 63 0.50
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (85 bp):
AAAGCGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCTTAGT
CTTTAGCGGCGTTTGAGAGA
Found at i:2242902 original size:5 final size:6
Alignment explanation
Indices: 2242886--2242910 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2242876 ATAAAAATTT
2242886 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
2242911 TTATCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:2243091 original size:10 final size:10
Alignment explanation
Indices: 2243076--2243265 Score: 53
Period size: 10 Copynumber: 19.8 Consensus size: 10
2243066 TTTAAATGAT
2243076 TTTTTATATA
1 TTTTTATATA
*
2243086 TTTTTATAAA
1 TTTTTATATA
* *
2243096 ATTTTAAATA
1 TTTTTATATA
*
2243106 TTTTAAATATA
1 TTTT-TATATA
*
2243117 TTTTTATTAAA
1 TTTTTA-TATA
*
2243128 TTTGTA-A-A
1 TTTTTATATA
** *
2243136 TTTTTGCAAA
1 TTTTTATATA
*
2243146 TTATTATA-A
1 TTTTTATATA
2243155 -TTTTATA-A
1 TTTTTATATA
*
2243163 TTTTTAT-GA
1 TTTTTATATA
*
2243172 TTTTCATAT-
1 TTTTTATATA
*
2243181 GTTTTA-ATGA
1 TTTTTATAT-A
* *
2243191 TTGTTAT-GA
1 TTTTTATATA
*
2243200 TTATTATA-A
1 TTTTTATATA
* *
2243209 CTTTTA-AGA
1 TTTTTATATA
2243218 TTTTTATATA
1 TTTTTATATA
* *
2243228 ATTTTATAAA
1 TTTTTATATA
* *
2243238 ATTTTAAATA
1 TTTTTATATA
2243248 TGTTTTAT-TA
1 T-TTTTATATA
*
2243258 ATTTTATA
1 TTTTTATA
2243266 AAATTTATAA
Statistics
Matches: 130, Mismatches: 35, Indels: 30
0.67 0.18 0.15
Matches are distributed among these distances:
8 15 0.12
9 44 0.34
10 50 0.38
11 21 0.16
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (10 bp):
TTTTTATATA
Found at i:2243116 original size:31 final size:31
Alignment explanation
Indices: 2243066--2243140 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
2243056 ATTTTAGGGG
**
2243066 TTTAAATGATTTTTTATATATTTTTATAAAAT
1 TTTAAAT-ATTTTAAATATATTTTTATAAAAT
*
2243098 TTTAAATATTTTAAATATATTTTTATTAAAT
1 TTTAAATATTTTAAATATATTTTTATAAAAT
2243129 TTGTAAAT-TTTT
1 TT-TAAATATTTT
2243141 GCAAATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 27 0.69
32 12 0.31
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTAAATATTTTAAATATATTTTTATAAAAT
Found at i:2243119 original size:20 final size:21
Alignment explanation
Indices: 2243066--2243120 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
2243056 ATTTTAGGGG
* *
2243066 TTTAAATGATTTTTTATATATT
1 TTTAAAT-ATATTTTAAATATT
2243088 TTTATAA-A-ATTTTAAATA-T
1 TTTA-AATATATTTTAAATATT
2243107 TTTAAATATATTTT
1 TTTAAATATATTTT
2243121 TATTAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.07
19 6 0.21
20 13 0.46
21 1 0.04
22 4 0.14
23 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAAATATATTTTAAATATT
Found at i:2243167 original size:9 final size:9
Alignment explanation
Indices: 2243076--2243281 Score: 66
Period size: 9 Copynumber: 21.7 Consensus size: 9
2243066 TTTAAATGAT
2243076 TTTTTATATA
1 TTTTTATA-A
2243086 TTTTTATAAA
1 TTTTTAT-AA
*
2243096 ATTTTA-AA
1 TTTTTATAA
2243104 TATTTTAAATATA
1 T-TTTT--ATA-A
2243117 TTTTTATTAAA
1 TTTTTA-T-AA
*
2243128 TTTGTA-AA
1 TTTTTATAA
2243136 TTTTTGCA-AA
1 TTTTT--ATAA
*
2243146 TTATTATAA
1 TTTTTATAA
2243155 -TTTTATAA
1 TTTTTATAA
*
2243163 TTTTTATGA
1 TTTTTATAA
*
2243172 TTTTCAT-A
1 TTTTTATAA
*
2243180 TGTTTTAATGA
1 T-TTTT-ATAA
* *
2243191 TTGTTATGA
1 TTTTTATAA
*
2243200 TTATTATAA
1 TTTTTATAA
*
2243209 CTTTTA-AGA
1 TTTTTATA-A
2243218 TTTTTATATA
1 TTTTTATA-A
*
2243228 ATTTTATAAA
1 TTTTTAT-AA
* *
2243238 ATTTTAAATA
1 TTTTTATA-A
2243248 TGTTTTATTAA
1 T-TTTTA-TAA
2243259 -TTTTATAA
1 TTTTTATAA
**
2243267 AATTTATAA
1 TTTTTATAA
2243276 TTTTTA
1 TTTTTA
2243282 GTTTTTAATA
Statistics
Matches: 151, Mismatches: 23, Indels: 45
0.69 0.11 0.21
Matches are distributed among these distances:
8 22 0.15
9 60 0.40
10 42 0.28
11 18 0.12
12 7 0.05
13 2 0.01
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:2243213 original size:28 final size:27
Alignment explanation
Indices: 2243145--2243224 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
2243135 ATTTTTGCAA
*
2243145 ATTATTATAATTTT-ATAATTTTTATG
1 ATTATTATAATTTTAATGATTTTTATG
* *
2243171 ATT-TTCATATGTTTTAATGATTGTTATG
1 ATTATT-ATA-ATTTTAATGATTTTTATG
2243199 ATTATTATAACTTTTAA-GATTTTTAT
1 ATTATTATAA-TTTTAATGATTTTTAT
2243225 ATAATTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
25 2 0.05
26 6 0.14
27 12 0.27
28 22 0.50
29 2 0.05
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (27 bp):
ATTATTATAATTTTAATGATTTTTATG
Found at i:2243968 original size:87 final size:88
Alignment explanation
Indices: 2243802--2244016 Score: 276
Period size: 87 Copynumber: 2.5 Consensus size: 88
2243792 TTAATGGTGT
* *
2243802 AAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATCAAGCCCCTCAAATTTTTTTACACTTAATTG
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCT--AATTTTTTTACACTCAATTG
2243866 AGCACTTGAACTTTCAAAATGCATC
64 AGCACTTGAACTTTCAAAATGCATC
* * * * *
2243891 AAAAAGACCCTCAAACTTCTTCAAAAAAAGTAATTAAGTCCCT-TTTTTTTTCCACTCAATTGAG
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTAATTTTTTTACACTCAATTGAG
* * *
2243955 TATTTGAATTTTCAAAATGCATC
66 CACTTGAACTTTCAAAATGCATC
* *
2243978 ACAAAGA-CCTCAAAATTTTTCAAAAAAA-CAATTAAGCCC
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCC
2244017 ATGCTCTTAT
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
85 9 0.08
86 19 0.17
87 44 0.40
89 6 0.05
90 32 0.29
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.30
Consensus pattern (88 bp):
AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTAATTTTTTTACACTCAATTGAG
CACTTGAACTTTCAAAATGCATC
Found at i:2244066 original size:19 final size:18
Alignment explanation
Indices: 2244034--2244104 Score: 85
Period size: 19 Copynumber: 4.0 Consensus size: 18
2244024 TATTAAAAAG
2244034 TAAAAAATAA-TAAATTT
1 TAAAAAATAATTAAATTT
*
2244051 TAGAAAAATAATTAAAATT
1 TA-AAAAATAATTAAATTT
2244070 T--AAAATAATTAAATTT
1 TAAAAAATAATTAAATTT
*
2244086 TATAAAATTAATTAAATTT
1 TA-AAAAATAATTAAATTT
2244105 ATTAAAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 15 0.33
17 2 0.04
18 8 0.17
19 21 0.46
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
TAAAAAATAATTAAATTT
Found at i:2244098 original size:35 final size:34
Alignment explanation
Indices: 2244037--2244122 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 34
2244027 TAAAAAGTAA
2244037 AAAATAA-TAAATTTTAGAAAAATAATTAAAATTT
1 AAAATAATTAAATTTTAGAAAAATAATT-AAATTT
* *
2244071 AAAATAATTAAATTTTATAAAATTAATTAAATTT
1 AAAATAATTAAATTTTAGAAAAATAATTAAATTT
2244105 ATTAAA-AATTAGAATTTT
1 A--AAATAATTA-AATTTT
2244123 TTTTATAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 14 0.30
35 23 0.50
36 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (34 bp):
AAAATAATTAAATTTTAGAAAAATAATTAAATTT
Found at i:2244110 original size:19 final size:17
Alignment explanation
Indices: 2244037--2244123 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 17
2244027 TAAAAAGTAA
*
2244037 AAAATAA-TAAATTTTAGA
1 AAAATAATTAAATTTT--T
*
2244055 AAAATAATTAAA-ATTT
1 AAAATAATTAAATTTTT
2244071 AAAATAATTAAATTTTAT
1 AAAATAATTAAATTTT-T
2244089 AAAATTAATTAAATTTATT
1 AAAA-TAATTAAATTT-TT
2244108 -AAA-AATTAGAATTTTT
1 AAAATAATTA-AATTTTT
2244124 TTTATAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
16 19 0.32
17 7 0.12
18 17 0.28
19 16 0.27
20 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATAATTAAATTTTT
Found at i:2244148 original size:16 final size:16
Alignment explanation
Indices: 2244127--2244157 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2244117 AATTTTTTTT
2244127 ATAAAAATCGTAAAAA
1 ATAAAAATCGTAAAAA
*
2244143 ATAAAAATTGTAAAA
1 ATAAAAATCGTAAAA
2244158 TTTTATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (16 bp):
ATAAAAATCGTAAAAA
Found at i:2245708 original size:283 final size:282
Alignment explanation
Indices: 2245164--2245713 Score: 940
Period size: 283 Copynumber: 1.9 Consensus size: 282
2245154 TGGGTTTCCC
2245164 TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGGAAG
1 TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGGAAG
* *
2245229 AAGATGAACTTGTGGGTCAAAGTTGAGATACAGTTAGTAATTTATCTCTGAATTTGCCTAGTTTT
66 AAGATAAACTTGTGGGTCAAAGTTGAGATACAGTTAGTAATTTATCTCTGAATTTGCCTAGTTGT
* * *
2245294 AAAGCTGAGTTATGGAGTGCTAAAGATTTATATAACTGTTTTGTTTTCAATGTTGTTACTGATAG
131 AAAGCTGAGCTATGGAGCGCTAAAGATTTATATAACTGTTCTGTTTTCAATGTTGTTACTGATAG
2245359 TTTTGCTATTTGCTCCACTTTCTTGAGAAATTGCTATGAGTAAATATCTTATTTGACCAAAAAAA
196 TTTTGCTATTTGCTCCACTTTCTTGAGAAATTGCTATGAGTAAATATCTTATTTGACC-AAAAAA
2245424 AAAAAAAGAGAAATTGCTAAAGA
260 AAAAAAAGAGAAATTGCTAAAGA
*
2245447 TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGTAAG
1 TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGGAAG
* *
2245512 AAGATAAACTTGTGGGTCAAAGTTGAGATACAGTTAGTAATTTATCTTTGAATTTGTCTAGTTGT
66 AAGATAAACTTGTGGGTCAAAGTTGAGATACAGTTAGTAATTTATCTCTGAATTTGCCTAGTTGT
* *
2245577 GAAGCTGAGCTATTGAGCGCTAAAGATTTATATAACTGTTCTGTTTTCAATGTTGTTACTGATAG
131 AAAGCTGAGCTATGGAGCGCTAAAGATTTATATAACTGTTCTGTTTTCAATGTTGTTACTGATAG
* * *
2245642 TTTTGCTCTTTGCTTTCCTCTTTCTT-ACGAAATTGCTATGAGTAAATATTTTATTTGACCAAAA
196 TTTTGCTATTTGC--TCCACTTTCTTGA-GAAATTGCTATGAGTAAATATCTTATTTGACCAAAA
2245706 AAAAAAAA
258 AAAAAAAA
2245714 TGGACACATT
Statistics
Matches: 251, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
283 197 0.78
284 13 0.05
285 41 0.16
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (282 bp):
TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGGAAG
AAGATAAACTTGTGGGTCAAAGTTGAGATACAGTTAGTAATTTATCTCTGAATTTGCCTAGTTGT
AAAGCTGAGCTATGGAGCGCTAAAGATTTATATAACTGTTCTGTTTTCAATGTTGTTACTGATAG
TTTTGCTATTTGCTCCACTTTCTTGAGAAATTGCTATGAGTAAATATCTTATTTGACCAAAAAAA
AAAAAAGAGAAATTGCTAAAGA
Found at i:2248384 original size:2 final size:2
Alignment explanation
Indices: 2248377--2248416 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2248367 ATTGTCCCAA
2248377 TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2248417 ATCGCTATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2255023 original size:19 final size:19
Alignment explanation
Indices: 2254999--2255036 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2254989 TGAGGTTAGA
* *
2254999 GGATCAACTTTTGGTGTCG
1 GGATCAACTCTTAGTGTCG
2255018 GGATCAACTCTTAGTGTCG
1 GGATCAACTCTTAGTGTCG
2255037 TATTAAGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.34
Consensus pattern (19 bp):
GGATCAACTCTTAGTGTCG
Found at i:2258023 original size:40 final size:39
Alignment explanation
Indices: 2257951--2258038 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 39
2257941 CAGACAGAAA
* *
2257951 CTCATAAGAGCTAATCCAACTGAAATATGCCAAACAAAAG
1 CTCATAAGAGCTAATCCAACTGAAACACGCC-AACAAAAG
** *
2257991 CTCATAAGAGCTGGTCC-ACTCGAAACACGCCAACATAAG
1 CTCATAAGAGCTAATCCAACT-GAAACACGCCAACAAAAG
2258030 CTCATAAGA
1 CTCATAAGA
2258039 TGTAACACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 19 0.45
40 23 0.55
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (39 bp):
CTCATAAGAGCTAATCCAACTGAAACACGCCAACAAAAG
Found at i:2264965 original size:21 final size:21
Alignment explanation
Indices: 2264932--2264991 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
2264922 GAAACACGCC
*
2264932 AACAGAAGTTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * *
2264953 AATAGAAGCTCATAAAAACTG
1 AACAGAAGCTCATAAGAGCTG
*
2264974 AACAAAAGCTCATAAGAG
1 AACAGAAGCTCATAAGAG
2264992 TTGATCCACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:2268466 original size:35 final size:35
Alignment explanation
Indices: 2268427--2268571 Score: 105
Period size: 35 Copynumber: 4.1 Consensus size: 35
2268417 TTTCTCTTGC
*
2268427 AAGCCTCCGCCATGTGTTGGGAGCAAGATCTCTCT
1 AAGCCTCCGCCATGTGTTGGGAGCAAGACCTCTCT
* * * * *
2268462 AAGCCTCTGTCATGTGTTGGAAGTAAGACCTCTTAT
1 AAGCCTCCGCCATGTGTTGGGAGCAAGACCTC-TCT
* * * * * *
2268498 AAGCCTCCCCCTTTGTGCTGGGAGTAGGACCTCCCAT
1 AAGCCTCCGCC-ATGTGTTGGGAGCAAGACCTCTC-T
* * *
2268535 AAGCC-CC-CTATGTGTTGGGAGCAGGACCCCTCAT
1 AAGCCTCCGCCATGTGTTGGGAGCAAGACCTCTC-T
2268569 AAG
1 AAG
2268572 TGCCCTCCAT
Statistics
Matches: 86, Mismatches: 21, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
34 23 0.27
35 28 0.33
36 12 0.14
37 23 0.27
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (35 bp):
AAGCCTCCGCCATGTGTTGGGAGCAAGACCTCTCT
Found at i:2268554 original size:34 final size:34
Alignment explanation
Indices: 2268504--2268607 Score: 104
Period size: 34 Copynumber: 3.0 Consensus size: 34
2268494 TTATAAGCCT
* * *
2268504 CCCCCTTTGTGCTGGGAGTAGGACCTCCCATAAG
1 CCCCCTATGTGTTGGGAGCAGGACCTCCCATAAG
2268538 CCCCCTATGTGTTGGGAGCAGGACC-CCTCATAAGTG
1 CCCCCTATGTGTTGGGAGCAGGACCTCC-CATAA--G
* * *
2268574 CCCTCC-ATATATTAGGAGCAGGACCTCCCATAAG
1 CCC-CCTATGTGTTGGGAGCAGGACCTCCCATAAG
2268608 TATCTCCTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
33 2 0.03
34 28 0.47
36 25 0.42
37 4 0.07
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (34 bp):
CCCCCTATGTGTTGGGAGCAGGACCTCCCATAAG
Done.