Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 25 of 26
Found at i:4358859 original size:49 final size:49
Alignment explanation
Indices: 4358759--4358859 Score: 143
Period size: 49 Copynumber: 2.1 Consensus size: 49
4358749 TTTCTTGTTT
* *
4358759 ATTATATCCAAACAACCAAATATTATAATACCTAGTTCTTGTTTATTTC
1 ATTATATCCAAACAACCAAATATTATAATACCTAGTTCTCGTTTATATC
*
4358808 ATTATATCCAATCAACCAAATATTATAATACCTA-TTAC-CGTTTCATATC
1 ATTATATCCAAACAACCAAATATTATAATACCTAGTT-CTCGTTT-ATATC
4358857 ATT
1 ATT
4358860 CTCATCAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
48 6 0.13
49 41 0.87
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (49 bp):
ATTATATCCAAACAACCAAATATTATAATACCTAGTTCTCGTTTATATC
Found at i:4359458 original size:29 final size:28
Alignment explanation
Indices: 4359407--4359461 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
4359397 AGATAGAAAC
**
4359407 CTCCATATCTTTTTACGGGCTAAGATCT
1 CTCCATATCTTTTTAAAGGCTAAGATCT
*
4359435 CTCCCTATCTTTTTCAAAGGCTAAGAT
1 CTCCATATCTTTTT-AAAGGCTAAGAT
4359462 AGAACCTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (28 bp):
CTCCATATCTTTTTAAAGGCTAAGATCT
Found at i:4359941 original size:22 final size:22
Alignment explanation
Indices: 4359910--4359966 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
4359900 ATGTATAGTG
* *
4359910 ATGAATAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCAATAC
* *
4359932 ATGAACAGTGATGTTTCAATAT
1 ATGAACAGTGATGTATCAATAC
4359954 ATGAACAGTGATG
1 ATGAACAGTGATG
4359967 AACAGTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.32
Consensus pattern (22 bp):
ATGAACAGTGATGTATCAATAC
Found at i:4360018 original size:13 final size:13
Alignment explanation
Indices: 4360000--4360024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4359990 CTCTAATTTT
4360000 ATGTATCGATACA
1 ATGTATCGATACA
4360013 ATGTATCGATAC
1 ATGTATCGATAC
4360025 TAAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4360237 original size:19 final size:20
Alignment explanation
Indices: 4360200--4360238 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4360190 TCATATCTCT
**
4360200 AAAACATCTTTGATTATTAG
1 AAAACATCTTTGACAATTAG
4360220 AAAACAT-TTTGACAATTAG
1 AAAACATCTTTGACAATTAG
4360239 TTTTAGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAACATCTTTGACAATTAG
Found at i:4361827 original size:13 final size:13
Alignment explanation
Indices: 4361806--4361844 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4361796 TATACTGAAG
4361806 CAATGTATCGATA
1 CAATGTATCGATA
*
4361819 CATTGTATCGATA
1 CAATGTATCGATA
4361832 CAATGTATCGATA
1 CAATGTATCGATA
4361845 TAAACTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:4363162 original size:21 final size:22
Alignment explanation
Indices: 4363108--4363162 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
4363098 TTATTAGTTT
4363108 ACTCA-TCATTTTCATTTTGCA
1 ACTCATTCATTTTCATTTTGCA
4363129 ACTCATTTC-TTTTC-TTTT-CAA
1 ACTCA-TTCATTTTCATTTTGC-A
4363150 ACTCATTCATTTT
1 ACTCATTCATTTT
4363163 TTCTTGTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.13
21 19 0.63
22 5 0.17
23 2 0.07
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.53
Consensus pattern (22 bp):
ACTCATTCATTTTCATTTTGCA
Found at i:4364810 original size:36 final size:32
Alignment explanation
Indices: 4364728--4364822 Score: 115
Period size: 36 Copynumber: 2.9 Consensus size: 32
4364718 CCTTACAACA
4364728 CTATC-TTTC-AAGGCTAAGATAGAAACC-TCC
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTTCC
*
4364758 CTATCTTTTCACAGGCTAAGATAGAACCTATTTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACC---TTCC
4364793 CTATCTTTTTCAAAGGCTAAGATAGAACCT
1 CTATC-TTTTCAAAGGCTAAGATAGAACCT
4364823 CTCAATCACT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
30 5 0.09
31 8 0.14
32 12 0.21
33 1 0.02
35 8 0.14
36 22 0.39
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (32 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTTCC
Found at i:4365290 original size:22 final size:22
Alignment explanation
Indices: 4365263--4365341 Score: 149
Period size: 22 Copynumber: 3.6 Consensus size: 22
4365253 ATGTATAGTA
4365263 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
*
4365285 ATGAACAATGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
4365307 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
4365329 ATGAACAGTGATG
1 ATGAACAGTGATG
4365342 AACAGTATTG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:4366209 original size:23 final size:23
Alignment explanation
Indices: 4366183--4366227 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4366173 AATGCATCTT
4366183 GTTCCCCTTCAAGGAGAGAGATG
1 GTTCCCCTTCAAGGAGAGAGATG
*
4366206 GTTCTCCTTCAAGGAGAGAGAT
1 GTTCCCCTTCAAGGAGAGAGAT
4366228 TATATATATA
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:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (23 bp):
GTTCCCCTTCAAGGAGAGAGATG
Found at i:4367400 original size:11 final size:11
Alignment explanation
Indices: 4367377--4367415 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
4367367 AGGCTTTTGA
4367377 TTATTTAAAATT
1 TTATTT-AAATT
4367389 TTATTTAAA-T
1 TTATTTAAATT
*
4367399 TTAATTAAATT
1 TTATTTAAATT
4367410 TTATTT
1 TTATTT
4367416 TAGATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.38
11 9 0.38
12 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTAAATT
Found at i:4367449 original size:24 final size:25
Alignment explanation
Indices: 4367403--4367453 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4367393 TTAAATTTAA
4367403 TTAAATTTTATTTTAGATAAAAAAT
1 TTAAATTTTATTTTAGATAAAAAAT
4367428 TTAAATTTTATTTTAGATAAAAAAT
1 TTAAATTTTATTTTAGATAAAAAAT
4367453 T
1 T
4367454 ATATTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TTAAATTTTATTTTAGATAAAAAAT
Found at i:4368052 original size:13 final size:13
Alignment explanation
Indices: 4368018--4368098 Score: 69
Period size: 13 Copynumber: 6.0 Consensus size: 13
4368008 TATAAAATTA
4368018 TTTAATATATTATAT
1 TTTAA-ATA-TATAT
4368033 TTT-AATATATAT
1 TTTAAATATATAT
4368045 TTTAAATATAT-T
1 TTTAAATATATAT
4368057 TTTAAAATATTATAT
1 TTT-AAATA-TATAT
*
4368072 TTATAAATAATAAAT
1 TT-TAAAT-ATATAT
*
4368087 TATAAATA-ATAT
1 TTTAAATATATAT
4368099 AATATTCTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
12 15 0.26
13 16 0.28
14 9 0.16
15 15 0.26
16 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAAATATATAT
Found at i:4368055 original size:11 final size:11
Alignment explanation
Indices: 4368028--4368067 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
4368018 TTTAATATAT
4368028 TATATTTTAATA
1 TATATTTTAA-A
4368040 TATATTTTAAA
1 TATATTTTAAA
4368051 TATATTTTTAAA
1 TATA-TTTTAAA
4368063 -ATATT
1 TATATT
4368068 ATATTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.07
11 8 0.30
12 17 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATTTTAAA
Found at i:4368115 original size:39 final size:40
Alignment explanation
Indices: 4368066--4368166 Score: 104
Period size: 39 Copynumber: 2.6 Consensus size: 40
4368056 TTTTAAAATA
4368066 TTATATTTATAAATAATAA-AT-TATAAATAATATAATATTC
1 TTATATTTATAAATAATAATATAT-TAAA-AATATAATATTC
** *
4368106 TTAT-TTTATATTTAATAATATATTAAAAATATAATAAAT-
1 TTATATTTATAAATAATAATATATTAAAAATATAAT-ATTC
*
4368145 TTATATATATAAAT-ATAATATA
1 TTATATTTATAAATAATAATATA
4368167 AAATATTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
39 32 0.63
40 18 0.35
41 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (40 bp):
TTATATTTATAAATAATAATATATTAAAAATATAATATTC
Found at i:4368721 original size:18 final size:18
Alignment explanation
Indices: 4368698--4368732 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4368688 AGTTTTTTAT
4368698 TTTTTATATTTTT-AATTG
1 TTTTTA-ATTTTTCAATTG
4368716 TTTTTAATTTTTCAATT
1 TTTTTAATTTTTCAATT
4368733 TGCCTCGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTAATTTTTCAATTG
Found at i:4369766 original size:26 final size:26
Alignment explanation
Indices: 4369727--4369777 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4369717 TTGTTCTTGT
4369727 AAAGAAAATAATAACTTTA-AAATAA
1 AAAGAAAATAATAACTTTATAAATAA
* *
4369752 AAAGAAAAATTATAATTTTATAAATA
1 AAAG-AAAATAATAACTTTATAAATA
4369778 TAATATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 13 0.59
27 5 0.23
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (26 bp):
AAAGAAAATAATAACTTTATAAATAA
Found at i:4370903 original size:3 final size:3
Alignment explanation
Indices: 4370895--4370929 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
4370885 GAACCAAGTT
*
4370895 TTC TTC TTC -TC TTC TTC GTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4370930 ATTTTTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:4371515 original size:3 final size:3
Alignment explanation
Indices: 4371502--4371537 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
4371492 TGTGATTTTG
*
4371502 ATT ATT AATT ATT ATT ATT ACT ATT ATT ATT ATT AT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4371538 AAAAAGAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:4372369 original size:21 final size:22
Alignment explanation
Indices: 4372319--4372370 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
4372309 AATAGGAGCG
* *
4372319 TTTGTAACATTTTAATCTAATA
1 TTTGTAAAATTTAAATCTAATA
**
4372341 -TTAAAAAATTTAAAT-TAATA
1 TTTGTAAAATTTAAATCTAATA
4372361 TTTGTAAAAT
1 TTTGTAAAAT
4372371 ATTTTTATAG
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTGTAAAATTTAAATCTAATA
Found at i:4372801 original size:18 final size:19
Alignment explanation
Indices: 4372778--4372823 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
4372768 ACCATTTTGT
4372778 GTAATCATAGTTGT-ATCA
1 GTAATCATAGTTGTAATCA
*
4372796 GTAATCATATTTGTAATCA
1 GTAATCATAGTTGTAATCA
4372815 -TATATCATA
1 GTA-ATCATA
4372824 CAATAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (19 bp):
GTAATCATAGTTGTAATCA
Found at i:4373921 original size:28 final size:25
Alignment explanation
Indices: 4373889--4373945 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 25
4373879 TATTTAAAAG
* *
4373889 TATTTTTAATATAATTATAAAAATATAA
1 TATTTTAAATAT-A-TAAAAAAATAT-A
4373917 TATTTTAAATATATAAAAAAATATA
1 TATTTTAAATATATAAAAAAATATA
4373942 TATT
1 TATT
4373946 AACATCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 5 0.19
26 10 0.37
27 1 0.04
28 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATTTTAAATATATAAAAAAATATA
Found at i:4374274 original size:22 final size:22
Alignment explanation
Indices: 4374246--4374311 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
4374236 TTATAAAAAG
4374246 TTAATTAAATTAATATCTTAAA
1 TTAATTAAATTAATATCTTAAA
4374268 TTAATTATATATTAAT-T-TT-AA
1 TTAATTA-A-ATTAATATCTTAAA
*
4374289 -TACATATAAATTAATATCATAAA
1 TTA-AT-TAAATTAATATCTTAAA
4374312 GTATTTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
20 8 0.22
21 6 0.17
22 12 0.33
23 4 0.11
24 6 0.17
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATTAAATTAATATCTTAAA
Found at i:4374503 original size:19 final size:20
Alignment explanation
Indices: 4374461--4374502 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4374451 AATTAATCAC
*
4374461 TTTTAAAAATAATTATTTAA
1 TTTTAAAAATAATTACTTAA
*
4374481 TTTTAAAAA-ATTTACTT-A
1 TTTTAAAAATAATTACTTAA
4374499 TTTT
1 TTTT
4374503 TTTTACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 6 0.30
20 9 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAAAATAATTACTTAA
Found at i:4376481 original size:1 final size:1
Alignment explanation
Indices: 4376470--4376501 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
4376460 ATTTTACCTG
*
4376470 AAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4376502 CCTCCAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:4379990 original size:8 final size:8
Alignment explanation
Indices: 4379977--4380001 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4379967 ATAAAACTTG
4379977 ATTTTAAA
1 ATTTTAAA
4379985 ATTTTAAA
1 ATTTTAAA
4379993 ATTTTAAA
1 ATTTTAAA
4380001 A
1 A
4380002 AACTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:4380680 original size:27 final size:27
Alignment explanation
Indices: 4380627--4380682 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
4380617 AAATATAGAA
* *
4380627 AATATTTATAAATATTACATAATTTAT
1 AATATTTATAAATAATACAAAATTTAT
*
4380654 AATATTTTTAAATAATA-AAAATATTAT
1 AATATTTATAAATAATACAAAAT-TTAT
4380681 AA
1 AA
4380683 AAAAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AATATTTATAAATAATACAAAATTTAT
Found at i:4380840 original size:24 final size:24
Alignment explanation
Indices: 4380804--4380855 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4380794 AACATATAAA
*
4380804 TTTTTTTTCTTCTTT-TCTTCTTTC
1 TTTTTTTTCTTCTTTCT-TTATTTC
4380828 TTTTTGTTT-TTCTTTCTTTATTTC
1 TTTTT-TTTCTTCTTTCTTTATTTC
4380852 TTTT
1 TTTT
4380856 CCACCACGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (24 bp):
TTTTTTTTCTTCTTTCTTTATTTC
Found at i:4380842 original size:16 final size:15
Alignment explanation
Indices: 4380804--4380856 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
4380794 AACATATAAA
*
4380804 TTTTT-TTTCTTCTT
1 TTTTTCTTTCTTTTT
*
4380818 TTCTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
4380833 GTTTTTCTTTCTTTATT
1 -TTTTTCTTTCTTT-TT
4380850 TCTTTTC
1 T-TTTTC
4380857 CACCACGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 4 0.12
15 8 0.25
16 13 0.41
17 7 0.22
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTCTTTTT
Found at i:4381498 original size:23 final size:21
Alignment explanation
Indices: 4381462--4381505 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4381452 CAACATAAAT
*
4381462 AAAAAATAATTAAAACATTATA
1 AAAAAATAAAT-AAACATTATA
4381484 AAAAAATAACATAAACATTATA
1 AAAAAATAA-ATAAACATTATA
4381506 CGAATATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAAATAAATAAACATTATA
Found at i:4381732 original size:13 final size:13
Alignment explanation
Indices: 4381714--4381742 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4381704 TATTTTCAAT
4381714 AATAAAAAATATA
1 AATAAAAAATATA
4381727 AAT-AAAAATATA
1 AATAAAAAATATA
4381739 AATA
1 AATA
4381743 CTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAAAAATATA
Found at i:4381801 original size:14 final size:14
Alignment explanation
Indices: 4381761--4381803 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
4381751 TTTTTCTCCC
4381761 ATATATAAAATAAA
1 ATATATAAAATAAA
* *
4381775 ATATA-CATA-AAA
1 ATATATAAAATAAA
4381787 ATATATAAAATAAA
1 ATATATAAAATAAA
4381801 ATA
1 ATA
4381804 AATTATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
ATATATAAAATAAA
Found at i:4381856 original size:34 final size:35
Alignment explanation
Indices: 4381773--4381861 Score: 85
Period size: 37 Copynumber: 2.5 Consensus size: 35
4381763 ATATAAAATA
4381773 AAATATACATAAAAATATATAAAATAAAATAAATTATT
1 AAATATA-A-AAAAATATATAAAATAAAAT-AATTATT
* *
4381811 -AATATTTAAAAAATATATAAAAATATAAT-ATT-TT
1 AAATA-TAAAAAAATATAT-AAAATAAAATAATTATT
*
4381845 AAATATAAAAAATTATA
1 AAATATAAAAAAATATA
4381862 AATGCAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
34 12 0.27
35 7 0.16
36 10 0.23
37 14 0.32
38 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATATAAAAAAATATATAAAATAAAATAATTATT
Found at i:4382143 original size:19 final size:19
Alignment explanation
Indices: 4382063--4382146 Score: 66
Period size: 19 Copynumber: 4.2 Consensus size: 19
4382053 CTCATTTTAG
4382063 ATATATTTAAAATAGATATATAA
1 ATATA-TTAAAAT--ATA-ATAA
*
4382086 A-ATATTAAAACATAATATA
1 ATATATTAAAATATAATA-A
4382105 A-ATATTATACGAATAT-ATAA
1 ATATATTA-A--AATATAATAA
4382125 ATATATTAAAATATAATAA
1 ATATATTAAAATATAATAA
4382144 ATA
1 ATA
4382147 AATAAATAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
18 8 0.15
19 18 0.34
20 4 0.08
21 15 0.28
22 7 0.13
23 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATATTAAAATATAATAA
Found at i:4382905 original size:27 final size:27
Alignment explanation
Indices: 4382874--4382931 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
4382864 TTAAATATTA
* *
4382874 ATTTTTTATG-AAATTCATTAATTAAT
1 ATTTTTTTTGTAAATACATTAATTAAT
**
4382900 ATTTTTTTTGTTCATACATTAATTAAT
1 ATTTTTTTTGTAAATACATTAATTAAT
4382927 ATTTT
1 ATTTT
4382932 AATTATAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (27 bp):
ATTTTTTTTGTAAATACATTAATTAAT
Found at i:4383176 original size:20 final size:22
Alignment explanation
Indices: 4383153--4383195 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
4383143 AATTAACAAC
4383153 ATTTAAA-GTAAAAAT-ATGTT
1 ATTTAAATGTAAAAATAATGTT
*
4383173 ATTTAAATTTAAAAATAATGTT
1 ATTTAAATGTAAAAATAATGTT
4383195 A
1 A
4383196 AGACTGGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 7 0.35
22 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
ATTTAAATGTAAAAATAATGTT
Found at i:4385958 original size:16 final size:16
Alignment explanation
Indices: 4385939--4385972 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4385929 GAATAGGATA
*
4385939 AATTTTAAATTATTTT
1 AATTTTAAATTATCTT
4385955 AATTTTAAATTATCTT
1 AATTTTAAATTATCTT
4385971 AA
1 AA
4385973 ATTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTTAAATTATCTT
Found at i:4386264 original size:29 final size:30
Alignment explanation
Indices: 4386207--4386265 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
4386197 ATAAATAATT
* *
4386207 AAAATATTACATAAAATATGATATGATAAA
1 AAAATATTAAATAAAATATAATATGATAAA
4386237 AAAATA-TAAATAAAATATAAATAT-ATAAA
1 AAAATATTAAATAAAATAT-AATATGATAAA
4386266 TATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAATATTAAATAAAATATAATATGATAAA
Found at i:4386281 original size:18 final size:18
Alignment explanation
Indices: 4386241--4386327 Score: 65
Period size: 17 Copynumber: 4.9 Consensus size: 18
4386231 GATAAAAAAA
* * *
4386241 TATAAATAAAATATAAATA
1 TATAAATATATTA-AAATT
*
4386260 TATAAATATTTTAAAATT
1 TATAAATATATTAAAATT
*
4386278 TATATATA-ATTAAAA-T
1 TATAAATATATTAAAATT
* *
4386294 TATCAACATATTAAAATT
1 TATAAATATATTAAAATT
4386312 TATATAA-ATA-TAAAAT
1 TATA-AATATATTAAAAT
4386328 ATATTAAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
16 6 0.11
17 19 0.35
18 18 0.33
19 12 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAAATATATTAAAATT
Found at i:4386290 original size:17 final size:16
Alignment explanation
Indices: 4386270--4386364 Score: 62
Period size: 17 Copynumber: 6.1 Consensus size: 16
4386260 TATAAATATT
4386270 TTAAAATTTATATATAA
1 TTAAAATTTATATA-AA
4386287 TTAAAA-TTATCA-ACATA
1 TTAAAATTTAT-ATA-A-A
4386304 TTAAAATTTATATAAA
1 TTAAAATTTATATAAA
*
4386320 TATAAAATATAT-TAAA
1 T-TAAAATTTATATAAA
*
4386336 TT-TAA-TTATAATAAA
1 TTAAAATTTAT-ATAAA
4386351 -TAAAA--TATATAAA
1 TTAAAATTTATATAAA
4386364 T
1 T
4386365 ATAATATAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
13 8 0.12
14 6 0.09
15 7 0.11
16 13 0.20
17 25 0.39
18 5 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAATTTATATAAA
Found at i:4386373 original size:11 final size:11
Alignment explanation
Indices: 4386313--4386385 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
4386303 ATTAAAATTT
4386313 ATATAAATATA
1 ATATAAATATA
* *
4386324 AAATATAT-TAA
1 ATATAAATAT-A
* *
4386335 ATTTAATTATA
1 ATATAAATATA
4386346 ATAAATAAA-AT-
1 AT--ATAAATATA
4386357 ATATAAATATA
1 ATATAAATATA
4386368 ATATAAATATA
1 ATATAAATATA
4386379 ATATAAA
1 ATATAAA
4386386 CGTATTAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 34 0.71
12 3 0.06
13 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAATATA
Found at i:4386384 original size:22 final size:21
Alignment explanation
Indices: 4386313--4386385 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 21
4386303 ATTAAAATTT
4386313 ATATAAATATAAAAT-ATATTAA
1 ATAT-AATATAAAATAATA-TAA
* *
4386335 ATTTAAT-TATAATAA-ATAA
1 ATATAATATAAAATAATATAA
4386354 A-AT-ATATAAATATAATATAA
1 ATATAATATAAA-ATAATATAA
4386374 ATATAATATAAA
1 ATATAATATAAA
4386386 CGTATTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
17 2 0.05
18 4 0.10
19 8 0.20
20 11 0.27
21 6 0.15
22 10 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAATATAAAATAATATAA
Found at i:4386449 original size:6 final size:6
Alignment explanation
Indices: 4386437--4386471 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4386427 ACACGAGAAA
* *
4386437 GGGGAG GGAGAG GGGGAG GGGGAG GGGGAA GGGGA
1 GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG GGGGA
4386472 AAATATTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (6 bp):
GGGGAG
Found at i:4387062 original size:2 final size:2
Alignment explanation
Indices: 4387050--4387096 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
4387040 AATACCAGAT
* *
4387050 TA TA TA CA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4387092 GA TA T
1 TA TA T
4387097 TAGCATTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4387172 original size:18 final size:18
Alignment explanation
Indices: 4387149--4387195 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
4387139 GAATAACTAT
*
4387149 TAAAATAAAATATAGATA
1 TAAAATAAAATATAAATA
4387167 TAAAAT--AATATAAATA
1 TAAAATAAAATATAAATA
*
4387183 TAATA-AAAATATA
1 TAAAATAAAATATA
4387196 TGAATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 13 0.52
17 6 0.24
18 6 0.24
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAAATAAAATATAAATA
Found at i:4387178 original size:16 final size:17
Alignment explanation
Indices: 4387155--4387195 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
4387145 CTATTAAAAT
*
4387155 AAAATATAGATATAA-A
1 AAAATATAAATATAATA
*
4387171 ATAATATAAATATAATA
1 AAAATATAAATATAATA
4387188 AAAATATA
1 AAAATATA
4387196 TGAATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATATAAATATAATA
Found at i:4387187 original size:11 final size:11
Alignment explanation
Indices: 4387152--4387195 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
4387142 TAACTATTAA
4387152 AATA-AAATAT
1 AATATAAATAT
4387162 AGATATAAA-AT
1 A-ATATAAATAT
4387173 AATATAAATAT
1 AATATAAATAT
*
4387184 AATAAAAATAT
1 AATATAAATAT
4387195 A
1 A
4387196 TGAATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 8 0.27
11 19 0.63
12 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AATATAAATAT
Found at i:4387205 original size:19 final size:20
Alignment explanation
Indices: 4387152--4387193 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
4387142 TAACTATTAA
4387152 AATA-AAATATAGATATAAAAT
1 AATATAAATATA-ATA-AAAAT
4387173 AATATAAATATAATAAAAAT
1 AATATAAATATAATAAAAAT
4387193 A
1 A
4387194 TATGAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 7 0.35
22 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AATATAAATATAATAAAAAT
Found at i:4391018 original size:19 final size:20
Alignment explanation
Indices: 4390980--4391025 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
4390970 GGATTGAATT
4390980 TAAAT-TAATAAAAATAATA
1 TAAATATAATAAAAATAATA
*
4390999 TAAATATAATAAATAT-ATA
1 TAAATATAATAAAAATAATA
4391018 TAAATATA
1 TAAATATA
4391026 TCAAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATATAATAAAAATAATA
Found at i:4391032 original size:10 final size:10
Alignment explanation
Indices: 4390991--4391026 Score: 58
Period size: 9 Copynumber: 3.8 Consensus size: 10
4390981 AAATTAATAA
4390991 AAATA-ATAT
1 AAATATATAT
4391000 AAATATA-AT
1 AAATATATAT
4391009 AAATATATAT
1 AAATATATAT
4391019 AAATATAT
1 AAATATAT
4391027 CAAAATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 14 0.56
10 11 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATATATAT
Found at i:4392718 original size:68 final size:69
Alignment explanation
Indices: 4392639--4392789 Score: 250
Period size: 68 Copynumber: 2.2 Consensus size: 69
4392629 TCAGAGGAAT
4392639 GGGGTTGGAGTATTTCCGACAATGATAATTTAGACAAAATAAGACTTAAATTTTGAT-AGTTTAA
1 GGGGTTGGAGTATTTCCGACAATGATAATTTAGACAAAATAAGACTTAAATTTTGATGAGTTTAA
4392703 AAAC
66 AAAC
* * *
4392707 GGGGTTGGAGTATCTCCGACAATGATAATTTAGATAAAATAAGATTTAAATTTTGATGAGTTTAA
1 GGGGTTGGAGTATTTCCGACAATGATAATTTAGACAAAATAAGACTTAAATTTTGATGAGTTTAA
*
4392772 AAAT
66 AAAC
*
4392776 GAGGTTGGAGTATT
1 GGGGTTGGAGTATT
4392790 CTCTTGGAAG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 54 0.71
69 22 0.29
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.34
Consensus pattern (69 bp):
GGGGTTGGAGTATTTCCGACAATGATAATTTAGACAAAATAAGACTTAAATTTTGATGAGTTTAA
AAAC
Found at i:4392857 original size:97 final size:96
Alignment explanation
Indices: 4392707--4393684 Score: 1191
Period size: 97 Copynumber: 10.1 Consensus size: 96
4392697 GTTTAAAAAC
* ** * * *
4392707 GGGGTTGGAGTATCTCCGACAATGATAATTTAGA--TAAAATAAGATTTAAATTTTGATGAGTTT
1 GGGGTTGGAGTGTCTCCGATGATGACAATTTA-ACCGAAAATAAGATTTAAATTTTGATAAGTTT
* * *
4392770 AAAAATGAGGTTGGAGTATTCTCTTGGAAGAAT
65 AAAAACGAGGTTGGAGTA-TCCCTTGGAGGAAT
4392803 GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
1 GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
**
4392868 AAAACGAGGTTGGAGTATCCCCTCAGAGGAAT
66 AAAACGAGGTTGGAGTAT-CCCTTGGAGGAAT
** * * *
4392900 GAAGTTGGAGTATCTCCAATGATAACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
1 GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
* * * *
4392965 AAAACGGGGTTGGAGTATTCCATCGGAAGAAT
66 AAAACGAGGTTGGAGTA-TCCCTTGGAGGAAT
*
4392997 GGGGTTGGAGTGTCCCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
1 GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
* *
4393062 AAAACGGGGTTGGAGTATCCCCTCGGAGGAAT
66 AAAACGAGGTTGGAGTAT-CCCTTGGAGGAAT
* * *
4393094 GGGGTTGGAGTGTCCCCGATGATGACAATTTAACTGAAAATAAGATTTAAATTTTGATACGTTTA
1 GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
* *
4393159 AAAACG-GAGTTGAAGTATCCCCTCGGAGGAAT
66 AAAACGAG-GTTGGAGTAT-CCCTTGGAGGAAT
*** * * * *
4393191 AAAGTTGGAATGTCCCCGATGATGACAATTTAACCAAAAATAAGATTTAAATTTTAATAAGTTTA
1 GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
* *
4393256 AAAACGAGGTTGGAGTATCTCTTCAGAGGAAT
66 AAAACGAGGTTGGAGTATCCCTT-GGAGGAAT
* * * *
4393288 GAGGTTAGAGTGTCTCCGATTATGATAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
1 GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
* * *
4393353 AAAACGGGGTTGGAGTATCCCCTCGAAGGAAT
66 AAAACGAGGTTGGAGTAT-CCCTTGGAGGAAT
* **
4393385 GGGGTTGGAGTGTCCCCGATGATGGTAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
1 GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
4393450 AAAAC-AGGATTGGAGTATCCCTTCGGAGGAAT
66 AAAACGAGG-TTGGAGTATCCCTT-GGAGGAAT
* * * *
4393482 GGGGTTGAAGTGTCTCC-ATTGATTACAATTTAACTGAAAATAAGATTTAAATTTTGATATGTTT
1 GGGGTTGGAGTGTCTCCGA-TGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTT
*
4393546 -AAAACG-GAGTTGGAGTATCCCTTTAGAGGAAT
65 AAAAACGAG-GTTGGAGTATCCC-TTGGAGGAAT
* * * * * *
4393578 GAGGTTTGAGTGT-TCCCGATGATGATAATTTAATCG-AAATAATATTTAAATTTTTATAAGTTT
1 GGGGTTGGAGTGTCT-CCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTT
* * *
4393641 AAAAAAGGGGTTGGAGTATCCCTTCGGAAGAAT
65 AAAAACGAGGTTGGAGTATCCCTT-GGAGGAAT
*
4393674 AGGGTTGGAGT
1 GGGGTTGGAGT
4393685 ATCCCCTCGG
Statistics
Matches: 773, Mismatches: 89, Indels: 40
0.86 0.10 0.04
Matches are distributed among these distances:
95 28 0.04
96 123 0.16
97 617 0.80
98 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (96 bp):
GGGGTTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTA
AAAACGAGGTTGGAGTATCCCTTGGAGGAAT
Found at i:4393269 original size:291 final size:289
Alignment explanation
Indices: 4392742--4393690 Score: 1336
Period size: 291 Copynumber: 3.3 Consensus size: 289
4392732 TAATTTAGAT
* * * * * *
4392742 AAAATAAGATTTAAATTTTGATGAGTTTAAAAATGAGGTTGGAGTATTCTCTTGGAAGAATGGGG
1 AAAATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATCCCCTCGGAAGAATGGGG
*
4392807 TTGGAGTGTCTCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTAAAAA
66 TTGGAGTGTCCCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTAAAAA
* * *
4392872 C-GAGGTTGGAGTATCCCCTCAGAGGAATGAAGTTGGAGTATCTCCAATGATAACAATTTAACCG
131 CGGA-GTTGGAGTATCCCCTCGGAGGAATGAAGTTGGAATGTCTCC-ATGATAACAATTTAACCG
* * * *
4392936 AAAATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATTCCATCGGAAGAATGGGG
194 AAAATAAGATTTAAATTTTGATAAGTTTAAAAAC-GGGTTGGAGTATTCCTTCAGAGGAATGAGG
* *
4393001 TTGGAGTGTCCCCGATGATGACAATTTAACCG
258 TTAGAGTGTCCCCGATGATGATAATTTAACCG
*
4393033 AAAATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGG
1 AAAATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATCCCCTCGGAAGAATGGGG
* *
4393098 TTGGAGTGTCCCCGATGATGACAATTTAACTGAAAATAAGATTTAAATTTTGATACGTTTAAAAA
66 TTGGAGTGTCCCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTAAAAA
* * * * *
4393163 CGGAGTTGAAGTATCCCCTCGGAGGAATAAAGTTGGAATGTCCCCGATGATGACAATTTAACCAA
131 CGGAGTTGGAGTATCCCCTCGGAGGAATGAAGTTGGAATGTCTCC-ATGATAACAATTTAACCGA
*
4393228 AAATAAGATTTAAATTTTAATAAGTTTAAAAACGAGGTTGGAGTA-TCTCTTCAGAGGAATGAGG
195 AAATAAGATTTAAATTTTGATAAGTTTAAAAACG-GGTTGGAGTATTC-CTTCAGAGGAATGAGG
* *
4393292 TTAGAGTGTCTCCGATTATGATAATTTAACCG
258 TTAGAGTGTCCCCGATGATGATAATTTAACCG
4393324 AAAATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATCCCCTC-GAAGGAATGGG
1 AAAATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATCCCCTCGGAA-GAATGGG
**
4393388 GTTGGAGTGTCCCCGATGATGGTAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTAAAA
65 GTTGGAGTGTCCCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTAAAA
* ** *
4393453 ACAGGA-TTGGAGTATCCCTTCGGAGGAATGGGGTT-GAAGTGTCTCCATTGATTACAATTTAAC
130 AC-GGAGTTGGAGTATCCCCTCGGAGGAATGAAGTTGGAA-TGTCTCCA-TGATAACAATTTAAC
* * * *
4393516 TGAAAATAAGATTTAAATTTTGATATGTTT-AAAACGGAGTTGGAGTATCCCTTTAGAGGAATGA
192 CGAAAATAAGATTTAAATTTTGATAAGTTTAAAAACGG-GTTGGAGTATTCCTTCAGAGGAATGA
* * *
4393580 GGTTTGAGTGTTCCCGATGATGATAATTTAATCG
256 GGTTAGAGTGTCCCCGATGATGATAATTTAACCG
* * * * *
4393614 -AAATAATATTTAAATTTTTATAAGTTTAAAAAAGGGGTTGGAGTATCCCTTCGGAAGAATAGGG
1 AAAATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATCCCCTCGGAAGAATGGGG
*
4393678 TTGGAGTATCCCC
66 TTGGAGTGTCCCC
4393691 TCGGAAGAAT
Statistics
Matches: 591, Mismatches: 57, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
289 68 0.12
290 69 0.12
291 449 0.76
292 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (289 bp):
AAAATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATCCCCTCGGAAGAATGGGG
TTGGAGTGTCCCCGATGATGACAATTTAACCGAAAATAAGATTTAAATTTTGATAAGTTTAAAAA
CGGAGTTGGAGTATCCCCTCGGAGGAATGAAGTTGGAATGTCTCCATGATAACAATTTAACCGAA
AATAAGATTTAAATTTTGATAAGTTTAAAAACGGGTTGGAGTATTCCTTCAGAGGAATGAGGTTA
GAGTGTCCCCGATGATGATAATTTAACCG
Found at i:4393685 original size:27 final size:27
Alignment explanation
Indices: 4393648--4393711 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
4393638 TTTAAAAAAG
*
4393648 GGGTTGGAGTATCCCTTCGGAAGAATA
1 GGGTTGGAGTATCCCCTCGGAAGAATA
4393675 GGGTTGGAGTATCCCCTCGGAAGAATA
1 GGGTTGGAGTATCCCCTCGGAAGAATA
4393702 GGGTTGGAGT
1 GGGTTGGAGT
4393712 GTCCTCGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.25
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCTCGGAAGAATA
Found at i:4393783 original size:124 final size:122
Alignment explanation
Indices: 4393554--4393808 Score: 327
Period size: 124 Copynumber: 2.1 Consensus size: 122
4393544 TTAAAACGGA
* * * * * * *
4393554 GTTGGAGTATCCCTTTAGAGGAATGAGGTTTGAGTGTTCCCGATGATGATAATTTAATCGAAATA
1 GTTGGAGTATCCCCTCAGAAGAATGAGGTTGGAGTGTTCCCGATGATAACAATTTAACCGAAATA
* * *
4393619 ATATTTAAATTTTTATAAGTTTAAAAAAGGGGTTGGAGTATCCCTTCGGAA-GAATAGG
66 AGATTTAAATTTTGATAAGTTTAAAAAAGGGGTTGGAGTATCCCCTC-GAACGAAT-GG
*
4393677 GTTGGAGTATCCCCTCGGAAGAAT-AGGGTTGGAGTG-TCCTCGATGATAACAATTTAACCGAAA
1 GTTGGAGTATCCCCTCAGAAGAATGA-GGTTGGAGTGTTCC-CGATGATAACAATTTAACCG-AA
*
4393740 ATAAGATTTAAATTTTGATAAGTTTAAAAACGGGGTTGGAGTATCCCCTCGAACGAATGG
63 ATAAGATTTAAATTTTGATAAGTTTAAAAAAGGGGTTGGAGTATCCCCTCGAACGAATGG
4393800 GATTGGAGT
1 G-TTGGAGT
4393809 GTCTCCGATG
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
122 4 0.03
123 52 0.45
124 59 0.51
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.31
Consensus pattern (122 bp):
GTTGGAGTATCCCCTCAGAAGAATGAGGTTGGAGTGTTCCCGATGATAACAATTTAACCGAAATA
AGATTTAAATTTTGATAAGTTTAAAAAAGGGGTTGGAGTATCCCCTCGAACGAATGG
Found at i:4393841 original size:97 final size:95
Alignment explanation
Indices: 4393675--4393902 Score: 341
Period size: 97 Copynumber: 2.3 Consensus size: 95
4393665 CGGAAGAATA
4393675 GGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGGAGTGTCCTCGATGATAACAATTTAACCGAAA
1 GGGTTGGAGTATCCCCTC-GAAGAAT-GGGTTGGAGTGTCCTCGATGATAACAATTTAACCGAAA
4393740 ATAAGATTTAAATTTTGATAAGTTTAAAAACG
64 ATAAGATTTAAATTTTGATAAGTTTAAAAACG
*
4393772 GGGTTGGAGTATCCCCTCGAACGAATGGGATTGGAGTGT-CTCCGATGATTACAATTTAACCGAA
1 GGGTTGGAGTATCCCCTCGAA-GAATGGG-TTGGAGTGTCCT-CGATGATAACAATTTAACCGAA
*
4393836 AATAAGATTTAAATTTTGATAAGTTTAAAAGCG
63 AATAAGATTTAAATTTTGATAAGTTTAAAAACG
* * *
4393869 AGGTTAGAGTATCCCCTCGGATGAATGGGGTTGG
1 GGGTTGGAGTATCCCCTC-GAAGAAT-GGGTTGG
4393903 TGTATCCCGA
Statistics
Matches: 121, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
96 8 0.07
97 108 0.89
98 5 0.04
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (95 bp):
GGGTTGGAGTATCCCCTCGAAGAATGGGTTGGAGTGTCCTCGATGATAACAATTTAACCGAAAAT
AAGATTTAAATTTTGATAAGTTTAAAAACG
Found at i:4395406 original size:28 final size:28
Alignment explanation
Indices: 4395362--4395415 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4395352 CCTTATCATT
*
4395362 TTGCTACATGCTTTTTGTTGTTTTTCAA
1 TTGCTACATGCTGTTTGTTGTTTTTCAA
* *
4395390 TTGCTGCATGCTGTTTGTTTTTTTTC
1 TTGCTACATGCTGTTTGTTGTTTTTC
4395416 CTTTTTCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.09, C:0.15, G:0.17, T:0.59
Consensus pattern (28 bp):
TTGCTACATGCTGTTTGTTGTTTTTCAA
Found at i:4396111 original size:20 final size:20
Alignment explanation
Indices: 4396086--4396137 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4396076 CCTACCACTC
4396086 ATTGTATCGATACATGAGAA
1 ATTGTATCGATACATGAGAA
4396106 ATTGTATCGATACATGAGAA
1 ATTGTATCGATACATGAGAA
*
4396126 ATTATATCGATA
1 ATTGTATCGATA
4396138 TATTGTCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
ATTGTATCGATACATGAGAA
Found at i:4397596 original size:8 final size:8
Alignment explanation
Indices: 4397583--4397617 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
4397573 TTAGAATTTG
4397583 AAAAAGAT
1 AAAAAGAT
4397591 AAAAAGAT
1 AAAAAGAT
*
4397599 AAAAAGTT
1 AAAAAGAT
4397607 AAAAA-AT
1 AAAAAGAT
4397614 AAAA
1 AAAA
4397618 TCATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (8 bp):
AAAAAGAT
Found at i:4399674 original size:22 final size:23
Alignment explanation
Indices: 4399634--4399688 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
4399624 AAATTTATAT
*
4399634 TAATATATTTTATATTTAAAATTAA
1 TAATA-ATTTTATATTT-AAATAAA
*
4399659 -AATAATTTTTTA-TTAAATAAA
1 TAATAATTTTATATTTAAATAAA
4399680 TAATAATTT
1 TAATAATTT
4399689 AAATTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.22
22 10 0.37
23 7 0.26
24 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATAATTTTATATTTAAATAAA
Found at i:4400140 original size:10 final size:10
Alignment explanation
Indices: 4400120--4400158 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
4400110 TAAACGCTGG
*
4400120 ATATATAATT
1 ATATTTAATT
*
4400130 ATATTTTATT
1 ATATTTAATT
4400140 ATATTATAATT
1 ATATT-TAATT
4400151 ATATTTAA
1 ATATTTAA
4400159 AATATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATTTAATT
Found at i:4400168 original size:16 final size:17
Alignment explanation
Indices: 4400149--4400199 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
4400139 TATATTATAA
4400149 TTATATTTA-AAATATT
1 TTATATTTATAAATATT
4400165 TTATATTTATATAA-ATT
1 TTATATTTATA-AATATT
*
4400182 TTA-ATTTATTAATATT
1 TTATATTTATAAATATT
4400198 TT
1 TT
4400200 TAATATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 2 0.06
16 20 0.65
17 7 0.23
18 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTATAAATATT
Found at i:4400234 original size:29 final size:29
Alignment explanation
Indices: 4400160--4400234 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 29
4400150 TATATTTAAA
* **
4400160 ATAT-TTTATATTTATATAAATTTTAATTT
1 ATATATTTATA-TAATATAAATTTTAAAAT
4400189 ATTAATATTT-T-TAATATAAATTTTAAAAT
1 A-T-ATATTTATATAATATAAATTTTAAAAT
*
4400218 ATATATTTATATCATAT
1 ATATATTTATATAATAT
4400235 TATATTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
27 6 0.16
28 2 0.05
29 22 0.59
30 1 0.03
31 3 0.08
32 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATATTTATATAATATAAATTTTAAAAT
Found at i:4400240 original size:43 final size:42
Alignment explanation
Indices: 4400188--4400270 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
4400178 AATTTTAATT
4400188 TATTAATATTTTTAATATAAATTTTAA-AATA-TATATTTATATCA
1 TATTAATATTTTTAAT-T--A-TTTAATAATATTATATTTATATCA
4400232 TATT-ATATTTTTAATTATTTAATAATATTATATTTATAT
1 TATTAATATTTTTAATTATTTAATAATATTATATTTATAT
4400271 AATTAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
39 5 0.14
40 5 0.14
41 11 0.30
42 1 0.03
43 11 0.30
44 4 0.11
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (42 bp):
TATTAATATTTTTAATTATTTAATAATATTATATTTATATCA
Found at i:4401752 original size:22 final size:21
Alignment explanation
Indices: 4401723--4401763 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
4401713 TCATTATCTT
4401723 TTATTTAATATCT-AATATTAG
1 TTATTTAATAT-TAAATATTAG
4401744 TTATATTAATATTAAATATT
1 TTAT-TTAATATTAAATATT
4401764 CAAGTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTATTTAATATTAAATATTAG
Found at i:4403232 original size:21 final size:19
Alignment explanation
Indices: 4403203--4403242 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
4403193 TTAAATACAT
4403203 ATTTAAAAATAAATATAAAAA
1 ATTTAAAAA-AAAT-TAAAAA
*
4403224 ATTTTAAAAAAATTAAAAA
1 ATTTAAAAAAAATTAAAAA
4403243 TACTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTTAAAAAAAATTAAAAA
Found at i:4404542 original size:13 final size:13
Alignment explanation
Indices: 4404524--4404548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4404514 CAATTAATCA
4404524 TGTATCGATACAT
1 TGTATCGATACAT
4404537 TGTATCGATACA
1 TGTATCGATACA
4404549 ATGTGTCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4404546 original size:33 final size:33
Alignment explanation
Indices: 4404504--4404568 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
4404494 TTTGAAGCAA
4404504 TGTATCGATACAAT-TAATCATGTATCGATACAT
1 TGTATCGATACAATGT-ATCATGTATCGATACAT
*
4404537 TGTATCGATACAATGTGTCATGTATCGATACA
1 TGTATCGATACAATGTATCATGTATCGATACA
4404569 AACAGTAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTATCATGTATCGATACAT
Found at i:4404624 original size:20 final size:20
Alignment explanation
Indices: 4404599--4404655 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
4404589 TGCCAGTTTT
*
4404599 ATGTATCGATACAATTGTGC
1 ATGTATCGATACAATTGTAC
*
4404619 ATGTATCGATACAA-TGAAC
1 ATGTATCGATACAATTGTAC
4404638 ATGTATCGATAC-ATTGTA
1 ATGTATCGATACAATTGTA
4404656 TCATTACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.55
20 14 0.42
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTGTAC
Found at i:4405263 original size:42 final size:41
Alignment explanation
Indices: 4405204--4405310 Score: 144
Period size: 42 Copynumber: 2.6 Consensus size: 41
4405194 AAGTTTCATT
* *
4405204 TTTCTCCCCTTTTATAAAATAATTAAGGCTATTGTTTAAAAA
1 TTTCTCCCC-CTTATAAAATAATTAAGGCTATCGTTTAAAAA
* *
4405246 TTTCTCTCCCTCTATAAAATAATTAAGGCTCTCGTTTAAAAA
1 TTTCTCCCCCT-TATAAAATAATTAAGGCTATCGTTTAAAAA
4405288 TTTCTCCCCCTTGATAAAA-AATT
1 TTTCTCCCCCTT-ATAAAATAATT
4405311 TTTTCCCCCT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
41 6 0.10
42 52 0.90
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.40
Consensus pattern (41 bp):
TTTCTCCCCCTTATAAAATAATTAAGGCTATCGTTTAAAAA
Found at i:4405309 original size:21 final size:22
Alignment explanation
Indices: 4405283--4405326 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4405273 GCTCTCGTTT
4405283 AAAAA-TTTCTCCCCCTTGATA
1 AAAAATTTTCTCCCCCTTGATA
*
4405304 AAAAATTTTTTCCCCCTTGATA
1 AAAAATTTTCTCCCCCTTGATA
4405326 A
1 A
4405327 TCGTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (22 bp):
AAAAATTTTCTCCCCCTTGATA
Found at i:4406758 original size:21 final size:20
Alignment explanation
Indices: 4406684--4406758 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
4406674 TTTGTTGATG
* *
4406684 ATTTTGATGAAAAATGAAGT
1 ATTTTGATGAAAATTGAAGA
4406704 ATTTTGAAGTGAAAA-TGAAGA
1 ATTTTG-A-TGAAAATTGAAGA
* ** *
4406725 AATTTGAAAAAAATTTGATGA
1 ATTTTGATGAAAA-TTGAAGA
4406746 ATTTTGATGAAAA
1 ATTTTGATGAAAA
4406759 GATATTCGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.09
20 7 0.16
21 26 0.60
22 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (20 bp):
ATTTTGATGAAAATTGAAGA
Found at i:4411398 original size:3 final size:3
Alignment explanation
Indices: 4411392--4411421 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4411382 GAGTCAACAA
*
4411392 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
4411422 TGTCTTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (3 bp):
CAT
Found at i:4413042 original size:13 final size:13
Alignment explanation
Indices: 4413024--4413048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4413014 CAATTAATCA
4413024 TGTATCGATACAT
1 TGTATCGATACAT
4413037 TGTATCGATACA
1 TGTATCGATACA
4413049 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4413068 original size:33 final size:33
Alignment explanation
Indices: 4413004--4413068 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
4412994 TTTGAAGCAA
* *
4413004 TGTATCGATACAATTAATCATGTATCGATACAT
1 TGTATCGATACAATTAACCATGTATCAATACAT
* *
4413037 TGTATCGATACAATGT-GCCATGTATTAATACA
1 TGTATCGATACAAT-TAACCATGTATCAATACA
4413069 AACTGTGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATTAACCATGTATCAATACAT
Found at i:4413124 original size:20 final size:20
Alignment explanation
Indices: 4413099--4413155 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
4413089 TGCCAGTTTT
* *
4413099 ATGTATTGATACAATTGTGC
1 ATGTATCGATACAATTGTAC
*
4413119 ATGTATCGATACAA-TGAAC
1 ATGTATCGATACAATTGTAC
4413138 ATGTATCGATAC-ATTGTA
1 ATGTATCGATACAATTGTA
4413156 TGGATACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.56
20 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTGTAC
Found at i:4413162 original size:32 final size:33
Alignment explanation
Indices: 4413120--4413184 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
4413110 CAATTGTGCA
* *
4413120 TGTATCGATACAATG-AACATGTATCGATACAT
1 TGTATCGATACAAAGAAAAATGTATCGATACAT
*
4413152 TGTATGGATACAAAGAAAAATGTATCGATACAT
1 TGTATCGATACAAAGAAAAATGTATCGATACAT
4413185 CTGAGTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (33 bp):
TGTATCGATACAAAGAAAAATGTATCGATACAT
Found at i:4413339 original size:21 final size:22
Alignment explanation
Indices: 4413292--4413343 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
4413282 ATTTTTACTT
*
4413292 AAAAACATTTGATTTAAGGTTC
1 AAAAACATTTGATTTAAGATTC
4413314 AAAAACATTTG-TTTATA-ATTC
1 AAAAACATTTGATTTA-AGATTC
*
4413335 TAAAACATT
1 AAAAACATT
4413344 CATTGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (22 bp):
AAAAACATTTGATTTAAGATTC
Found at i:4414766 original size:18 final size:18
Alignment explanation
Indices: 4414743--4414778 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4414733 CTCTTAACTT
4414743 TTTCCTAAAACATGAGTG
1 TTTCCTAAAACATGAGTG
4414761 TTTCCTAAAACATGAGTG
1 TTTCCTAAAACATGAGTG
4414779 CTTTTCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
TTTCCTAAAACATGAGTG
Found at i:4426885 original size:54 final size:55
Alignment explanation
Indices: 4426824--4426935 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
4426814 ATGTTTAAGT
4426824 TTTTAAGAAGCTTGCTTGAT-AAAAACCTTTGAGAAAAATAA-AGTTTCTAATTAC
1 TTTTAAGAAGCTTGCTTGATCAAAAACCTTTGAGAAAAATAAGA-TTTCTAATTAC
* *
4426878 TTTTAAGAAGCTTGCTTGATCAAAAACCTTTGAGAAGAATCAGATTTCTAATTAC
1 TTTTAAGAAGCTTGCTTGATCAAAAACCTTTGAGAAAAATAAGATTTCTAATTAC
4426933 TTT
1 TTT
4426936 GAATTGAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
54 20 0.37
55 33 0.61
56 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (55 bp):
TTTTAAGAAGCTTGCTTGATCAAAAACCTTTGAGAAAAATAAGATTTCTAATTAC
Found at i:4428152 original size:35 final size:35
Alignment explanation
Indices: 4428103--4428185 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
4428093 TGTGCTACAT
4428103 CTTA-TTTTATAGGGAATAACAGTCACATGTTATTC
1 CTTATTTTTA-AGGGAATAACAGTCACATGTTATTC
* ** *
4428138 CTTATTTTTAAGGGACTAATGGTCGCATGTTATTC
1 CTTATTTTTAAGGGAATAACAGTCACATGTTATTC
*
4428173 TTTACTTTTTAAG
1 CTTA-TTTTTAAG
4428186 CAGTAGCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 28 0.68
36 13 0.32
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.45
Consensus pattern (35 bp):
CTTATTTTTAAGGGAATAACAGTCACATGTTATTC
Found at i:4429483 original size:58 final size:58
Alignment explanation
Indices: 4429420--4429618 Score: 220
Period size: 58 Copynumber: 3.4 Consensus size: 58
4429410 GATCATGAAC
*
4429420 AATGACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCTTAGATCATGGTA
1 AATGACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCCTAGATCATGGTA
* * ** * * ** * **
4429478 AATGACCTAAAAGACATCAAAATGT-ATGAAATTACGTAGAAGTCCCTAGATCGTGAAA
1 AATGACCTAAATGGCATCAAAAT-TCAAAAAATTGCATCCAAGTCCCTAGATCATGGTA
* * *
4429536 AATAACCTAAATGGTATCAAAATTCACAAAAGTTGCAGTCCAAGTCCCTAGATCATGGTA
1 AATGACCTAAATGGCATCAAAATTCA-AAAAATTGCA-TCCAAGTCCCTAGATCATGGTA
*
4429596 AATGACCTAAATGGCATTAAAAT
1 AATGACCTAAATGGCATCAAAAT
4429619 GTCTAAAATT
Statistics
Matches: 108, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
57 1 0.01
58 64 0.59
59 6 0.06
60 37 0.34
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (58 bp):
AATGACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCCTAGATCATGGTA
Found at i:4429596 original size:118 final size:116
Alignment explanation
Indices: 4429408--4429620 Score: 327
Period size: 118 Copynumber: 1.8 Consensus size: 116
4429398 ATAAAGTTTG
* * *
4429408 TAGATCATGAACAATGACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCTTAGATCA
1 TAGATCATGAAAAATAACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCCTAGATCA
4429473 TGGTAAATGACCTAAAAGACATCAAAATGTATGAAATTACGTAGAAGTCCC
66 TGGTAAATGACCTAAAAGACATCAAAATGTATGAAATTACGTAGAAGTCCC
* * *
4429524 TAGATCGTGAAAAATAACCTAAATGGTATCAAAATTCACAAAAGTTGCAGTCCAAGTCCCTAGAT
1 TAGATCATGAAAAATAACCTAAATGGCATCAAAATTCA-AAAAATTGCA-TCCAAGTCCCTAGAT
* * *
4429589 CATGGTAAATGACCTAAATGGCATTAAAATGT
64 CATGGTAAATGACCTAAAAGACATCAAAATGT
4429621 CTAAAATTTC
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
116 34 0.40
117 9 0.10
118 43 0.50
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (116 bp):
TAGATCATGAAAAATAACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCCTAGATCA
TGGTAAATGACCTAAAAGACATCAAAATGTATGAAATTACGTAGAAGTCCC
Found at i:4429644 original size:118 final size:116
Alignment explanation
Indices: 4429408--4429664 Score: 318
Period size: 118 Copynumber: 2.2 Consensus size: 116
4429398 ATAAAGTTTG
* * *
4429408 TAGATCATGAACAATGACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCTTAGATCA
1 TAGATCATGAAAAATAACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCCTAGATCA
* * * *
4429473 TGGTAAATGACCTAAAAGACATCAAAATGTATGAAATTACGTAGAAGTCCC
66 TGGTAAATGACCTAAAAGACATCAAAATGTATAAAATTACATAAAAATCCC
* * *
4429524 TAGATCGTGAAAAATAACCTAAATGGTATCAAAATTCACAAAAGTTGCAGTCCAAGTCCCTAGAT
1 TAGATCATGAAAAATAACCTAAATGGCATCAAAATTCA-AAAAATTGCA-TCCAAGTCCCTAGAT
* * * * * *
4429589 CATGGTAAATGACCTAAATGGCATTAAAATGTCTAAAATTTCATAAAAATTCC
64 CATGGTAAATGACCTAAAAGACATCAAAATGTATAAAATTACATAAAAATCCC
* *
4429642 TAGATTATAGAAAAA-GACCTAAA
1 TAGATCAT-GAAAAATAACCTAAA
4429665 AGACATCATG
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
116 34 0.29
117 9 0.08
118 70 0.59
119 6 0.05
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (116 bp):
TAGATCATGAAAAATAACCTAAATGGCATCAAAATTCAAAAAATTGCATCCAAGTCCCTAGATCA
TGGTAAATGACCTAAAAGACATCAAAATGTATAAAATTACATAAAAATCCC
Found at i:4429854 original size:58 final size:59
Alignment explanation
Indices: 4429792--4429904 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 59
4429782 ATGTTTAAAG
*
4429792 TTACATAATAA-CCCTTAAATTATGAAAAATGACAAAAATGGAGCTAAAAT-GCATGATA
1 TTACATAATAATCCC-TAAATCATGAAAAATGACAAAAATGGAGCTAAAATAGCATGATA
* ** *
4429850 TTACATAATAATCCCTAAATCATGAAAGATGATTAAAATGGTGCTAAAATAGCAT
1 TTACATAATAATCCCTAAATCATGAAAAATGACAAAAATGGAGCTAAAATAGCAT
4429905 AAAAGGTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 41 0.85
59 7 0.15
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (59 bp):
TTACATAATAATCCCTAAATCATGAAAAATGACAAAAATGGAGCTAAAATAGCATGATA
Found at i:4429975 original size:58 final size:57
Alignment explanation
Indices: 4429913--4430131 Score: 201
Period size: 58 Copynumber: 3.8 Consensus size: 57
4429903 ATAAAAGGTT
* ****
4429913 TTAAATCATGGTAAAATACTAAAATGATCTTAAAATACATGAAATTACATAATTGGTC
1 TTAAATCAT-GAAAAATACTAAAATGATCTTAAAATACATGAAATTACATAATAACCC
* ** * ** *
4429971 TTAAAACATGGCAACTACTAAAATGAT-GAAAAAGCACATGAAATTACATAATAACCC
1 TTAAATCATGAAAAATACTAAAATGATCTTAAAA-TACATGAAATTACATAATAACCC
* * * * *
4430028 CTAAATCATGAAAAATGACTAAAATGGTAC-TAAAATGCATGAAGTTGCATAATAACCC
1 TTAAATCATGAAAAAT-ACTAAAATGAT-CTTAAAATACATGAAATTACATAATAACCC
*
4430086 TTAAATCATGAAAAATTACTAAAATGA-CTTTAAAATGCATGAAATT
1 TTAAATCATGAAAAA-TACTAAAATGATC-TTAAAATACATGAAATT
4430132 GCGTAAATGG
Statistics
Matches: 129, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
56 5 0.04
57 44 0.34
58 75 0.58
59 5 0.04
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.27
Consensus pattern (57 bp):
TTAAATCATGAAAAATACTAAAATGATCTTAAAATACATGAAATTACATAATAACCC
Found at i:4431460 original size:21 final size:21
Alignment explanation
Indices: 4431387--4431461 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
4431377 AAACATGATA
* *
4431387 TTGTATCGATAAAATATGGCT
1 TTGTATCGATACAATATAGCT
* * *
4431408 TTGTATCGATATAAT-GAGCA
1 TTGTATCGATACAATATAGCT
* * *
4431428 TCGTATCAATACAATATAACT
1 TTGTATCGATACAATATAGCT
4431449 TTGTATCGATACA
1 TTGTATCGATACA
4431462 TTGCATATTC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (21 bp):
TTGTATCGATACAATATAGCT
Found at i:4432108 original size:15 final size:16
Alignment explanation
Indices: 4432060--4432109 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
4432050 ATAGCTTTTG
*
4432060 TTAAGAACAACTTTTAT
1 TTAA-AACAACTCTTAT
*
4432077 TCAAAACAACTCTTAT
1 TTAAAACAACTCTTAT
4432093 TTAAAACAAC-CTTAT
1 TTAAAACAACTCTTAT
4432108 TT
1 TT
4432110 GGAATAGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 7 0.23
16 20 0.67
17 3 0.10
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (16 bp):
TTAAAACAACTCTTAT
Found at i:4432241 original size:16 final size:16
Alignment explanation
Indices: 4432222--4432270 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
4432212 TCTTGTTTGA
4432222 AATAGCTTGCATTTAG
1 AATAGCTTGCATTTAG
* *
4432238 AATAGC-TACTATTTAC
1 AATAGCTTGC-ATTTAG
*
4432254 AATAGCTAGCATTTAG
1 AATAGCTTGCATTTAG
4432270 A
1 A
4432271 CTAACCAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 2 0.08
16 23 0.88
17 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (16 bp):
AATAGCTTGCATTTAG
Found at i:4433736 original size:19 final size:21
Alignment explanation
Indices: 4433712--4433775 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 21
4433702 CAAGGAAGGG
4433712 AGAAAAAAGGAAA-AA-AAGA
1 AGAAAAAAGGAAAGAAGAAGA
4433731 AGAAAAAAGGAAAGAAGAAGA
1 AGAAAAAAGGAAAGAAGAAGA
*
4433752 AGAAAAGAAGAAAAGGAA-AAGA
1 AGAAAA-AAGGAAA-GAAGAAGA
4433774 AG
1 AG
4433776 TGGCTTGGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 10 0.25
22 12 0.30
23 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
AGAAAAAAGGAAAGAAGAAGA
Found at i:4433760 original size:14 final size:13
Alignment explanation
Indices: 4433712--4433775 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 13
4433702 CAAGGAAGGG
*
4433712 AGAAAA-AAGGAA
1 AGAAAAGAAGAAA
4433724 A-AAAAGAAGAAAAA
1 AGAAAAGAAG--AAA
*
4433738 AGGAAAGAAGAAGA
1 AGAAAAGAAGAA-A
4433752 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
4433765 AGGAAAAGAAG
1 A-GAAAAGAAG
4433776 TGGCTTGGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
11 4 0.09
12 4 0.09
13 4 0.09
14 24 0.56
15 7 0.16
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:4436414 original size:49 final size:51
Alignment explanation
Indices: 4436331--4436457 Score: 179
Period size: 49 Copynumber: 2.5 Consensus size: 51
4436321 AAATATATTA
* * *
4436331 ATACATTTTTCATTGTATCGATACGTTCTTAGTTTTTGA-CC-ATGTATCG
1 ATACATTTTTCATTGTATCAATACATTCTGAGTTTTTGACCCAATGTATCG
4436380 ATACATTTTTCATTGTATCAATACATTCTGAGTTTTTGACCCAAATGTATCG
1 ATACATTTTTCATTGTATCAATACATTCTGAGTTTTTGACCC-AATGTATCG
*
4436432 ATACATTCTTT-AATGTATCAATACAT
1 ATACATT-TTTCATTGTATCAATACAT
4436458 GCTAGCAATT
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
49 36 0.51
50 2 0.03
52 29 0.41
53 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (51 bp):
ATACATTTTTCATTGTATCAATACATTCTGAGTTTTTGACCCAATGTATCG
Found at i:4441281 original size:35 final size:35
Alignment explanation
Indices: 4441199--4441319 Score: 178
Period size: 35 Copynumber: 3.6 Consensus size: 35
4441189 CTATCTTTTG
*
4441199 AAGGCTAAGATAGAACCTC--CC-TATC-TTGTCA
1 AAGGCTAAGATAGAACCTCTTCCTTATCTTTTTCA
*
4441230 TAGGCTAAGATAGAACCTCTTCCTTATCTTTTTCA
1 AAGGCTAAGATAGAACCTCTTCCTTATCTTTTTCA
*
4441265 AAGGCTAAGATGGAACCTCTTCCTTATCTTTTTCA
1 AAGGCTAAGATAGAACCTCTTCCTTATCTTTTTCA
*
4441300 AAGGCTAAGATGGAACCTCT
1 AAGGCTAAGATAGAACCTCT
4441320 CAATTACTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
31 18 0.22
33 2 0.02
34 4 0.05
35 58 0.71
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (35 bp):
AAGGCTAAGATAGAACCTCTTCCTTATCTTTTTCA
Found at i:4441809 original size:13 final size:13
Alignment explanation
Indices: 4441793--4441818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4441783 ACAATTCATC
4441793 ATGTATCGATACA
1 ATGTATCGATACA
4441806 ATGTATCGATACA
1 ATGTATCGATACA
4441819 GTTGAAGGGT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4442164 original size:250 final size:250
Alignment explanation
Indices: 4441715--4442169 Score: 847
Period size: 250 Copynumber: 1.8 Consensus size: 250
4441705 CTCCAATGTA
*
4441715 TTGATATATTTATAAATGTATTGATACAATGCATTTGAAATTCTAGCTGTTGGGTCACATGTATC
1 TTGATACATTTATAAATGTATTGATACAATGCATTTGAAATTCTAGCTGTTGGGTCACATGTATC
* * *
4441780 AATACAATTCATCATGTATCGATACAATGTATCGATACAGTTGAAGGGTAGCTACTGCTAGATTT
66 AATACAATTCATCATGTATCGATACAATGTATCGACACAGTCGAAGGGTAGCTACTGCCAGATTT
*
4441845 ATGTATCAATATAATTCATAGTGTATCATACAAAGCAATTTGTATCGATATAATGTATCGATCCT
131 ATGTATCAATATAATTCATAGTGTATCATACAAAGCAATTTGTATCGATATAATGTATCGATACT
4441910 TAGCAATTTGATACAATGCATCGATACAATTTGATACTTAGCAATTTGATACAAT
196 TAGCAATTTGATACAATGCATCGATACAATTTGATACTTAGCAATTTGATACAAT
*
4441965 TTGATACATTTATAAATGTATTGATATAATGCATTTGAAATTCTAGCTGTTGGGTCACATGTATC
1 TTGATACATTTATAAATGTATTGATACAATGCATTTGAAATTCTAGCTGTTGGGTCACATGTATC
*
4442030 AATACAATTCATCATGTATCGATACAATGTATCGACACAGTCGAAGGGTAGCTACTGCCAGTTTT
66 AATACAATTCATCATGTATCGATACAATGTATCGACACAGTCGAAGGGTAGCTACTGCCAGATTT
4442095 ATGTATCAATATAATTCATAGTGTATCATACAAAGCAATTTGTATCGATATAATGTATCGATACT
131 ATGTATCAATATAATTCATAGTGTATCATACAAAGCAATTTGTATCGATATAATGTATCGATACT
4442160 TAGCAATTTG
196 TAGCAATTTG
4442170 TATCGATACA
Statistics
Matches: 198, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
250 198 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (250 bp):
TTGATACATTTATAAATGTATTGATACAATGCATTTGAAATTCTAGCTGTTGGGTCACATGTATC
AATACAATTCATCATGTATCGATACAATGTATCGACACAGTCGAAGGGTAGCTACTGCCAGATTT
ATGTATCAATATAATTCATAGTGTATCATACAAAGCAATTTGTATCGATATAATGTATCGATACT
TAGCAATTTGATACAATGCATCGATACAATTTGATACTTAGCAATTTGATACAAT
Found at i:4447603 original size:30 final size:31
Alignment explanation
Indices: 4447567--4447626 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
4447557 CCTTACAACA
* * *
4447567 CTATCTTTTGA-AGGCTAGGATAGAACCTTC
1 CTATCTTTTCACAAGCTAAGATAGAACCTTC
4447597 CTATCTTTTCACAAGCTAAGATAGAACCTT
1 CTATCTTTTCACAAGCTAAGATAGAACCTT
4447627 TCAATCATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (31 bp):
CTATCTTTTCACAAGCTAAGATAGAACCTTC
Found at i:4448111 original size:21 final size:21
Alignment explanation
Indices: 4448067--4448123 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
4448057 TGTTAGGCCA
*
4448067 CATGTATCGATACAA-TTCAT
1 CATGTATCGATACAATTTAAT
4448087 CATGTATCGATACAATTTAAT
1 CATGTATCGATACAATTTAAT
4448108 CATGTATCGATACAAT
1 CATGTATCGATACAAT
4448124 CGAAGGGTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (21 bp):
CATGTATCGATACAATTTAAT
Found at i:4448210 original size:33 final size:33
Alignment explanation
Indices: 4448168--4448232 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
4448158 TAATTCATAG
4448168 TGTATCGATACAAAGCAATTTGAATCGATACAA
1 TGTATCGATACAAAGCAATTTGAATCGATACAA
** *
4448201 TGTATCGATACTTAGCAATTTGTATCGATACA
1 TGTATCGATACAAAGCAATTTGAATCGATACA
4448233 TTTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAGCAATTTGAATCGATACAA
Found at i:4452362 original size:15 final size:15
Alignment explanation
Indices: 4452339--4452370 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4452329 TCACCATATG
*
4452339 TCATCATCACGCCAA
1 TCATAATCACGCCAA
4452354 TCATAATCACGCCAA
1 TCATAATCACGCCAA
4452369 TC
1 TC
4452371 CCTAAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.38, G:0.06, T:0.22
Consensus pattern (15 bp):
TCATAATCACGCCAA
Found at i:4452750 original size:90 final size:91
Alignment explanation
Indices: 4452641--4452999 Score: 379
Period size: 91 Copynumber: 4.0 Consensus size: 91
4452631 CACTCTTTTT
* * *
4452641 AAGTTCACAACTCCGTGGCA-CCC-TTTC-AAAGTCCATAACTCTATAGCACCATTTTTCTAAAG
1 AAGTCCACAACTCCGTGGCACCCCTTTTCTAAAGTCCACAACTCTGTAGCACCA-TTTTCTAAAG
* *** *
4452703 TCTATAACTCCATGGCATCTCTTTTCTA
65 TCCATAACTTTGTGGCA-CCCTTTTCTA
* * * * * *
4452731 AAGTCCACAACTCTGTGGCACCCCTTTTCTAAAGTGCACAACTCCGTGGCACCCTTCTC-AAAGT
1 AAGTCCACAACTCCGTGGCACCCCTTTTCTAAAGTCCACAACTCTGTAGCACCATTTTCTAAAGT
*
4452795 CCACAACTTTGTGGCACCCTTTTCTA
66 CCATAACTTTGTGGCACCCTTTTCTA
* * *
4452821 AAGTCCACAACTCCATGGCACCCCTTTTCTAAAGTCCACAACTTTGTTGCACCATTTTCTAAAGT
1 AAGTCCACAACTCCGTGGCACCCCTTTTCTAAAGTCCACAACTCTGTAGCACCATTTTCTAAAGT
**
4452886 CCATAACTTTGTGGCACCCTCATCTA
66 CCATAACTTTGTGGCACCCTTTTCTA
* * * * **
4452912 AAGTCCATAACTCTGTGGTACCCTTTTTCTAAAGTCCACAACTGC-GT-GACATCTTTTTTCTAA
1 AAGTCCACAACTCCGTGGCACCCCTTTTCTAAAGTCCACAACT-CTGTAG-CA-CCATTTTCTAA
* *
4452975 AGTCCACAACTTCGTGGCACCCTTT
63 AGTCCATAACTTTGTGGCACCCTTT
4453000 CAAAGCCCAC
Statistics
Matches: 224, Mismatches: 38, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
90 79 0.35
91 89 0.40
92 38 0.17
93 18 0.08
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.31
Consensus pattern (91 bp):
AAGTCCACAACTCCGTGGCACCCCTTTTCTAAAGTCCACAACTCTGTAGCACCATTTTCTAAAGT
CCATAACTTTGTGGCACCCTTTTCTA
Found at i:4452818 original size:121 final size:120
Alignment explanation
Indices: 4452559--4452999 Score: 461
Period size: 121 Copynumber: 3.7 Consensus size: 120
4452549 TTTCTTAAGA
* * * *
4452559 CCACAACT-TCATGGCAACCCTTTT-TAAAGTCCATAACTCCATGCCA-C-CCTTT-TAAAGTCA
1 CCACAACTCT-ATGGC-ACCCTTTTCTAAAGTCCACAACTCCATGGCATCTCTTTTCTAAAGTCC
* * * *
4452619 ACAACTCTGCGACACTCTTTT-T-AAGTTCACAACTCCGTGGCACCCTT-TCAAAGT
64 ACAACTCTGTGGCACCCTTTTCTAAAGTCCACAACTCCGTGGCACCCTTCTCAAAGT
* * * * *
4452673 CCATAACTCTATAGCACCATTTTTCTAAAGTCTATAACTCCATGGCATCTCTTTTCTAAAGTCCA
1 CCACAACTCTATGGCACC-CTTTTCTAAAGTCCACAACTCCATGGCATCTCTTTTCTAAAGTCCA
*
4452738 CAACTCTGTGGCACCCCTTTTCTAAAGTGCACAACTCCGTGGCACCCTTCTCAAAGT
65 CAACTCTGTGGCA-CCCTTTTCTAAAGTCCACAACTCCGTGGCACCCTTCTCAAAGT
* * * *
4452795 CCACAACTTTGTGGCACCCTTTTCTAAAGTCCACAACTCCATGGCACCCCTTTTCTAAAGTCCAC
1 CCACAACTCTATGGCACCCTTTTCTAAAGTCCACAACTCCATGGCATCTCTTTTCTAAAGTCCAC
* * * * **
4452860 AACTTTGTTGCACCATTTTCTAAAGTCCATAACTTTGTGGCACCC-TCATCTAAAGT
66 AACTCTGTGGCACCCTTTTCTAAAGTCCACAACTCCGTGGCACCCTTC-TC-AAAGT
* * * * * * *
4452916 CCATAACTCTGTGGTACCCTTTTTCTAAAGTCCACAACTGCGTGACATCTTTTTTCTAAAGTCCA
1 CCACAACTCTATGGCACCC-TTTTCTAAAGTCCACAACTCCATGGCATCTCTTTTCTAAAGTCCA
4452981 CAACT-TCGTGGCACCCTTT
65 CAACTCT-GTGGCACCCTTT
4453000 CAAAGCCCAC
Statistics
Matches: 275, Mismatches: 38, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
113 3 0.01
114 15 0.05
115 21 0.08
116 1 0.00
117 4 0.01
118 19 0.07
119 8 0.03
120 31 0.11
121 98 0.36
122 75 0.27
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (120 bp):
CCACAACTCTATGGCACCCTTTTCTAAAGTCCACAACTCCATGGCATCTCTTTTCTAAAGTCCAC
AACTCTGTGGCACCCTTTTCTAAAGTCCACAACTCCGTGGCACCCTTCTCAAAGT
Found at i:4452826 original size:30 final size:30
Alignment explanation
Indices: 4452549--4452999 Score: 378
Period size: 31 Copynumber: 15.1 Consensus size: 30
4452539 GAAAAGTAAC
* * * *
4452549 TTTCTTAAGACCACAACTTCATGGCAACCCT
1 TTTCTAAAGTCCACAACTCCGTGGC-ACCCT
* * *
4452580 TTT-TAAAGTCCATAACTCCATGCCACCC-
1 TTTCTAAAGTCCACAACTCCGTGGCACCCT
* * * * *
4452608 TTT-TAAAGTCAACAACTCTGCGACACTCT
1 TTTCTAAAGTCCACAACTCCGTGGCACCCT
*
4452637 TTT-T-AAGTTCACAACTCCGTGGCACCC-
1 TTTCTAAAGTCCACAACTCCGTGGCACCCT
* ** * *
4452664 TTTC-AAAGTCCATAACTCTATAGCACCATT
1 TTTCTAAAGTCCACAACTCCGTGGCACC-CT
* * * *
4452694 TTTCTAAAGTCTATAACTCCATGGCATCTCT
1 TTTCTAAAGTCCACAACTCCGTGGCA-CCCT
*
4452725 TTTCTAAAGTCCACAACTCTGTGGCACCCCT
1 TTTCTAAAGTCCACAACTCCGTGGCA-CCCT
*
4452756 TTTCTAAAGTGCACAACTCCGTGGCACCCT
1 TTTCTAAAGTCCACAACTCCGTGGCACCCT
* **
4452786 TCTC-AAAGTCCACAACTTTGTGGCACCCT
1 TTTCTAAAGTCCACAACTCCGTGGCACCCT
*
4452815 TTTCTAAAGTCCACAACTCCATGGCACCCCT
1 TTTCTAAAGTCCACAACTCCGTGGCA-CCCT
** * *
4452846 TTTCTAAAGTCCACAACTTTGTTGCACCAT
1 TTTCTAAAGTCCACAACTCCGTGGCACCCT
* **
4452876 TTTCTAAAGTCCATAACTTTGTGGCACCCT
1 TTTCTAAAGTCCACAACTCCGTGGCACCCT
** * * *
4452906 CATCTAAAGTCCATAACTCTGTGGTACCCTT
1 TTTCTAAAGTCCACAACTCCGTGGCACCC-T
* * **
4452937 TTTCTAAAGTCCACAACTGCGTGACATCTTT
1 TTTCTAAAGTCCACAACTCCGTGGCA-CCCT
*
4452968 TTTCTAAAGTCCACAACTTCGTGGCACCCT
1 TTTCTAAAGTCCACAACTCCGTGGCACCCT
4452998 TT
1 TT
4453000 CAAAGCCCAC
Statistics
Matches: 339, Mismatches: 70, Indels: 23
0.78 0.16 0.05
Matches are distributed among these distances:
27 3 0.01
28 55 0.16
29 33 0.10
30 104 0.31
31 142 0.42
32 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.32
Consensus pattern (30 bp):
TTTCTAAAGTCCACAACTCCGTGGCACCCT
Found at i:4453038 original size:32 final size:32
Alignment explanation
Indices: 4452979--4453283 Score: 289
Period size: 32 Copynumber: 9.6 Consensus size: 32
4452969 TTCTAAAGTC
* *
4452979 CACAACTTCGTGGC-ACCC-TTTCAAAGCCCA
1 CACAAGTTAGTGGCAACCCTTTTCAAAGCCCA
* * * *
4453009 CACAAGTTGGTGGCATCCTTTTTCAAAGCCCG
1 CACAAGTTAGTGGCAACCCTTTTCAAAGCCCA
* * * * *
4453041 CACAAGTCAATGCCAACCCCTTTAAAAGCCCA
1 CACAAGTTAGTGGCAACCCTTTTCAAAGCCCA
**
4453073 TGCAAGTTAGTGGCAACCCTTTTCAAAAGCCCA
1 CACAAGTTAGTGGCAACCCTTTTC-AAAGCCCA
* ** * *
4453106 CATAAGTCGGTGGTAA-CCTCTTTCAAAGCCTA
1 CACAAGTTAGTGGCAACCCT-TTTCAAAGCCCA
* * * * *
4453138 TATAAGTCAGAGGCAACCCTTTTCAAAAGCCTA
1 CACAAGTTAGTGGCAACCCTTTTC-AAAGCCCA
4453171 CACAAGTTAGTGGCAACCC-TTTCAAAGCCCA
1 CACAAGTTAGTGGCAACCCTTTTCAAAGCCCA
* *
4453202 CA-AAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTTAGTGGCAACCCTTTTCAAAGCCCA
* *
4453233 CACAAGTCAGTGGCAACCCTTTCCAAAGCCCA
1 CACAAGTTAGTGGCAACCCTTTTCAAAGCCCA
*
4453265 CACAAG-TGGTGGCAACCCT
1 CACAAGTTAGTGGCAACCCT
4453284 CTCAAAAGCC
Statistics
Matches: 223, Mismatches: 44, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
30 27 0.12
31 36 0.16
32 112 0.50
33 48 0.22
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (32 bp):
CACAAGTTAGTGGCAACCCTTTTCAAAGCCCA
Found at i:4453134 original size:65 final size:64
Alignment explanation
Indices: 4452988--4453298 Score: 346
Period size: 65 Copynumber: 4.9 Consensus size: 64
4452978 CCACAACTTC
* * *
4452988 GTGGC-ACCCTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTTTC-AAAGCCCGCACAAGTCA
1 GTGGCAACCCTTTCAAAGCCCACACAAGTTGGTGGCAACCCTTTTCAAAAGCCCACACAAGTCA
* * * ** * * *
4453050 ATGCCAACCCCTTTAAAAGCCCATGCAAGTTAGTGGCAACCCTTTTCAAAAGCCCACATAAGTCG
1 GTGGCAA-CCCTTTCAAAGCCCACACAAGTTGGTGGCAACCCTTTTCAAAAGCCCACACAAGTCA
* * * * ** * * *
4453115 GTGGTAACCTCTTTCAAAGCCTATATAAGTCAGAGGCAACCCTTTTCAAAAGCCTACACAAGTTA
1 GTGGCAACC-CTTTCAAAGCCCACACAAGTTGGTGGCAACCCTTTTCAAAAGCCCACACAAGTCA
*
4453180 GTGGCAACCCTTTCAAAGCCCACA-AAGTTGGTGGCAACCCATTTC-AAAGCCCACACAAGTCA
1 GTGGCAACCCTTTCAAAGCCCACACAAGTTGGTGGCAACCCTTTTCAAAAGCCCACACAAGTCA
* *
4453242 GTGGCAACCCTTTCCAAAGCCCACACAAG-TGGTGGCAACCC-TCTCAAAAGCCTACAC
1 GTGGCAACCCTTT-CAAAGCCCACACAAGTTGGTGGCAACCCTTTTCAAAAGCCCACAC
4453299 GTCGATGGCA
Statistics
Matches: 207, Mismatches: 35, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
62 34 0.16
63 51 0.25
64 51 0.25
65 71 0.34
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (64 bp):
GTGGCAACCCTTTCAAAGCCCACACAAGTTGGTGGCAACCCTTTTCAAAAGCCCACACAAGTCA
Found at i:4453634 original size:52 final size:51
Alignment explanation
Indices: 4453397--4453666 Score: 202
Period size: 52 Copynumber: 5.2 Consensus size: 51
4453387 AATGGCCTCA
* * * * * *
4453397 AATCAACACATTAGCACCTTTATCATTTTTAAGTCCGATATCGTTGGCCTTG
1 AATCAGCACATTGGCGCC-TTATCATTTTTAAGTCCAATGTCGCTGGCCTTG
* * * * * * * *
4453449 -TTCAGCATATTGGTGCCTTGACCATCTTTAAATCCAATGTTGTTGGCCTTG
1 AATCAGCACATTGGCGCCTT-ATCATTTTTAAGTCCAATGTCGCTGGCCTTG
* * * * * *
4453500 AATCAACACATTGGCACTCTCATC-TTTTTAAGTCTAATGTCACTAGCCTTG
1 AATCAGCACATTGGCGC-CTTATCATTTTTAAGTCCAATGTCGCTGGCCTTG
* * * * * *
4453551 AATCAACACATTGGCACTTATATTATTTTTAAGTCCGATGTCGCTAGCCTTG
1 AATCAGCACATTGGCGCCT-TATCATTTTTAAGTCCAATGTCGCTGGCCTTG
* * * *
4453603 AATCAGCATATTGGCGCCATTATCATCTTTAACTCCAATGTTGCTGGCCTTG
1 AATCAGCACATTGGCGCC-TTATCATTTTTAAGTCCAATGTCGCTGGCCTTG
*
4453655 AATTAGCACATT
1 AATCAGCACATT
4453667 AGCACTCGTC
Statistics
Matches: 168, Mismatches: 44, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
50 3 0.02
51 75 0.45
52 87 0.52
53 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (51 bp):
AATCAGCACATTGGCGCCTTATCATTTTTAAGTCCAATGTCGCTGGCCTTG
Found at i:4453740 original size:84 final size:84
Alignment explanation
Indices: 4453594--4453755 Score: 216
Period size: 84 Copynumber: 1.9 Consensus size: 84
4453584 TCCGATGTCG
* * *
4453594 CTAGCCTTGAATCAGCATATTGGCGCCATTATCATCTTTAACTCCAATGTTGCTGGCCTTGAATT
1 CTAGCCTTGAATCAGCATATTGGCACCATTATCATCTTTAACTCCAATGTCGCTAGCCTTGAATT
*
4453659 AGCACATTAGCACTCGTCA
66 AACACATTAGCACTCGTCA
* * * ****
4453678 CTAGTCTTGAATCAGCATATTGGCACCCTTATCATCTTTAAGTTTGGTGTCGCTAGCCTTGAATT
1 CTAGCCTTGAATCAGCATATTGGCACCATTATCATCTTTAACTCCAATGTCGCTAGCCTTGAATT
*
4453743 AACACATTGGCAC
66 AACACATTAGCAC
4453756 CCTCATCATC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (84 bp):
CTAGCCTTGAATCAGCATATTGGCACCATTATCATCTTTAACTCCAATGTCGCTAGCCTTGAATT
AACACATTAGCACTCGTCA
Found at i:4453789 original size:136 final size:136
Alignment explanation
Indices: 4453538--4453792 Score: 323
Period size: 136 Copynumber: 1.9 Consensus size: 136
4453528 TAAGTCTAAT
* * *
4453538 GTCACTAGCCTTGAATCAACACATTGGCACTTATATTATTTTTAAGTCCGATGTCGCTAGCCTTG
1 GTCACTAGCCTTGAATCAACACATTGGCACCTATATCATCTTTAAGTCCGATGTCGCTAGCCTTG
* * * * * *
4453603 AATCAGCATATTGGCGCCATTATCATCTTTAACTCCAATGTTGCTGGCCTTGAATTAGCACATTA
66 AATCAACACATTGGCACCATCATCATCTTTAACTCCAATGTCGCTAGCCTTGAATTAGCACATTA
4453668 GCACTC
131 GCACTC
* * * ** *
4453674 GTCACTAGTCTTGAATCAGCATATTGGCACCCT-TATCATCTTTAAGTTTGGTGTCGCTAGCCTT
1 GTCACTAGCCTTGAATCAACACATTGGCA-CCTATATCATCTTTAAGTCCGATGTCGCTAGCCTT
* * * *
4453738 GAATTAACACATTGGCACCCTCATCATCTTTAAGTCCTATGTCGCTAGCCTTGAA
65 GAATCAACACATTGGCACCATCATCATCTTTAACTCCAATGTCGCTAGCCTTGAA
4453793 CCAGTACATT
Statistics
Matches: 99, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
136 97 0.98
137 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (136 bp):
GTCACTAGCCTTGAATCAACACATTGGCACCTATATCATCTTTAAGTCCGATGTCGCTAGCCTTG
AATCAACACATTGGCACCATCATCATCTTTAACTCCAATGTCGCTAGCCTTGAATTAGCACATTA
GCACTC
Found at i:4453843 original size:188 final size:187
Alignment explanation
Indices: 4453496--4453845 Score: 441
Period size: 188 Copynumber: 1.9 Consensus size: 187
4453486 TGTTGTTGGC
* *
4453496 CTTGAATCAACACATTGGCACTCTCATCTTTTTAAGTCTAATGTCACTAGCCTTGAATCAACACA
1 CTTGAATCAACACATTGGCACCCTCATCTCTTTAAGTCTAATGTCACTAGCCTTGAATCAACACA
* * * * * * *
4453561 TTGGCACTTATATTATTTTTAAGTCCGATGTCGCTAGCCTTGAATCAGCATATTGGCGCCATTAT
66 TTGGCACCTACATCATCTTTAAGTCCGATGTCGCTAGCCTTGAACCAGCACATTGGCACCATTAT
* * * *
4453626 CATCTTTAACTCCAATGTTGCTGGCCTTGAATTAGCACATTAGCACTCGTCACTAGT
131 CACCTTTAACTCCAATATCGCTAGCCTTGAATTAGCACATTAGCACTCGTCACTAGT
* * * * ** * *
4453683 CTTGAATCAGCATATTGGCACCCTTATCATCTTTAAGTTTGGTGTCGCTAGCCTTGAATTAACAC
1 CTTGAATCAACACATTGGCACCCTCATC-TCTTTAAGTCTAATGTCACTAGCCTTGAATCAACAC
* * *
4453748 ATTGGCACCCT-CATCATCTTTAAGTCCTATGTCGCTAGCCTTGAACCAGTACATTGGCACCTTT
65 ATTGGCA-CCTACATCATCTTTAAGTCCGATGTCGCTAGCCTTGAACCAGCACATTGGCACCATT
* *
4453812 ATCACCTTTAAGTCCGATATCGCTAGCCTTGAAT
129 ATCACCTTTAACTCCAATATCGCTAGCCTTGAAT
4453846 CAACATTTTG
Statistics
Matches: 135, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
187 24 0.18
188 109 0.81
189 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (187 bp):
CTTGAATCAACACATTGGCACCCTCATCTCTTTAAGTCTAATGTCACTAGCCTTGAATCAACACA
TTGGCACCTACATCATCTTTAAGTCCGATGTCGCTAGCCTTGAACCAGCACATTGGCACCATTAT
CACCTTTAACTCCAATATCGCTAGCCTTGAATTAGCACATTAGCACTCGTCACTAGT
Found at i:4453857 original size:52 final size:52
Alignment explanation
Indices: 4453678--4453858 Score: 209
Period size: 52 Copynumber: 3.5 Consensus size: 52
4453668 GCACTCGTCA
* * ** *
4453678 CTAGTCTTGAATCAGCATATTGGCACCCTTATCATCTTTAAGTTTGGTGTCG
1 CTAGCCTTGAATCAACATATTGGCACCCTTATCATCTTTAAGTCCGATGTCG
* * * *
4453730 CTAGCCTTGAATTAACACATTGGCACCCTCATCATCTTTAAGTCCTATGTCG
1 CTAGCCTTGAATCAACATATTGGCACCCTTATCATCTTTAAGTCCGATGTCG
* ** * * * *
4453782 CTAGCCTTGAACCAGTACATTGGCACCTTTATCACCTTTAAGTCCGATATCG
1 CTAGCCTTGAATCAACATATTGGCACCCTTATCATCTTTAAGTCCGATGTCG
*
4453834 CTAGCCTTGAATCAACATTTTGGCA
1 CTAGCCTTGAATCAACATATTGGCA
4453859 TTTTTATCAT
Statistics
Matches: 106, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 106 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (52 bp):
CTAGCCTTGAATCAACATATTGGCACCCTTATCATCTTTAAGTCCGATGTCG
Found at i:4453868 original size:104 final size:104
Alignment explanation
Indices: 4453678--4453878 Score: 233
Period size: 104 Copynumber: 1.9 Consensus size: 104
4453668 GCACTCGTCA
* * * * ** * * *
4453678 CTAGTCTTGAATCAGCATATTGGCACCCTTATCATCTTTAAGTTTGGTGTCGCTAGCCTTGAATT
1 CTAGCCTTGAACCAGCACATTGGCACCCTTATCACCTTTAAGTCCGATATCGCTAGCCTTGAATC
4453743 AACACATTGGCACCCTCATCATCT-TTAAGTCCTATGTCG
66 AACACATTGGCACCCTCATCAT-TATTAAGTCCTATGTCG
* *
4453782 CTAGCCTTGAACCAGTACATTGGCACCTTTATCACCTTTAAGTCCGATATCGCTAGCCTTGAATC
1 CTAGCCTTGAACCAGCACATTGGCACCCTTATCACCTTTAAGTCCGATATCGCTAGCCTTGAATC
** *** *
4453847 AACATTTTGGCATTTTTATCATTATTAAGTCC
66 AACACATTGGCACCCTCATCATTATTAAGTCC
4453879 AACTTCACAG
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
103 1 0.01
104 78 0.99
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (104 bp):
CTAGCCTTGAACCAGCACATTGGCACCCTTATCACCTTTAAGTCCGATATCGCTAGCCTTGAATC
AACACATTGGCACCCTCATCATTATTAAGTCCTATGTCG
Found at i:4458328 original size:21 final size:21
Alignment explanation
Indices: 4458302--4458355 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
4458292 TATTCACTTA
*
4458302 TGTATCGATACATTTACTATT
1 TGTATCAATACATTTACTATT
4458323 TGTATCAATACATTTACTATT
1 TGTATCAATACATTTACTATT
4458344 TGTATCAATACA
1 TGTATCAATACA
4458356 AATTGTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (21 bp):
TGTATCAATACATTTACTATT
Found at i:4459158 original size:52 final size:52
Alignment explanation
Indices: 4459059--4459225 Score: 158
Period size: 52 Copynumber: 3.2 Consensus size: 52
4459049 CAATTTGTTG
* *
4459059 ATTCAAGGCCAATAACATTGGACTTAAAGATGAGAAGAATGTCAATGTACTA
1 ATTCAAGGCCAATGACATTGGACTTAAAAATGAGAAGAATGTCAATGTACTA
* * * * *
4459111 ATTTAGGGCCAATGACATTGGACTTAAAAATTAGAAGAATG-CTAATGTGCTG
1 ATTCAAGGCCAATGACATTGGACTTAAAAATGAGAAGAATGTC-AATGTACTA
* ** * * * * * *
4459163 ATTCAAGGCCAACGACATTAGG-CTTAGGAATGATAAAAATGCCAATATGCTG
1 ATTCAAGGCCAATGACATT-GGACTTAAAAATGAGAAGAATGTCAATGTACTA
4459215 ATTCAAGGCCA
1 ATTCAAGGCCA
4459226 GTGATATCGA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
51 1 0.01
52 92 0.96
53 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (52 bp):
ATTCAAGGCCAATGACATTGGACTTAAAAATGAGAAGAATGTCAATGTACTA
Found at i:4459240 original size:52 final size:50
Alignment explanation
Indices: 4459148--4459347 Score: 197
Period size: 52 Copynumber: 3.9 Consensus size: 50
4459138 AAATTAGAAG
* * * *
4459148 AATGCTAATGTGCTGATTCAAGGCCAACGACATTAGGCTTAGGAATGATAAA
1 AATGCCAATATGCTGATTCAAGGCCAGCGATATTA-GCTTA-GAATGATAAA
* * *
4459200 AATGCCAATATGCTGATTCAAGGCCAGTGATATCGAGCTTAAATATGATAAA
1 AATGCCAATATGCTGATTCAAGGCCAGCGATAT-TAGCTTAGA-ATGATAAA
** * *
4459252 GGTGCCAATATGCTGATTCAAGACCAGCGATATTAGACTTAAGAAAGA-AAA
1 AATGCCAATATGCTGATTCAAGGCCAGCGATATTAG-CTT-AGAATGATAAA
*
4459303 AGGTGCCAATATG-TCGATTCAAGGCCAGCGATATTAGACTTAGAA
1 A-ATGCCAATATGCT-GATTCAAGGCCAGCGATATTAG-CTTAGAA
4459348 AGAGATGGTT
Statistics
Matches: 126, Mismatches: 16, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
51 11 0.09
52 112 0.89
53 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (50 bp):
AATGCCAATATGCTGATTCAAGGCCAGCGATATTAGCTTAGAATGATAAA
Found at i:4459459 original size:33 final size:32
Alignment explanation
Indices: 4459420--4459514 Score: 129
Period size: 32 Copynumber: 2.9 Consensus size: 32
4459410 GATGCCACTG
*
4459420 ACTTGTGTGGGCTTTTGAAAGAGATTGCCACCA
1 ACTTGTGTGGGCTTTAGAAAG-GATTGCCACCA
* *
4459453 ATTTGTGTGGGCTTTAGAAAGGGTTGCCACCA
1 ACTTGTGTGGGCTTTAGAAAGGATTGCCACCA
*
4459485 ACTTGTGTGGGCTTTAAAGAAGGA-TGCCAC
1 ACTTGTGTGGGCTTTAGA-AAGGATTGCCAC
4459515 AGAGTTGTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (32 bp):
ACTTGTGTGGGCTTTAGAAAGGATTGCCACCA
Found at i:4459485 original size:32 final size:33
Alignment explanation
Indices: 4459396--4459500 Score: 135
Period size: 32 Copynumber: 3.3 Consensus size: 33
4459386 CCAACGACAT
* **
4459396 TGGGC-TTAGAAGGAGA-TGCCACTGACTTGTG
1 TGGGCTTTAGAAAGAGATTGCCACCAACTTGTG
* *
4459427 TGGGCTTTTGAAAGAGATTGCCACCAATTTGTG
1 TGGGCTTTAGAAAGAGATTGCCACCAACTTGTG
*
4459460 TGGGCTTTAGAAAG-GGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAAGAGATTGCCACCAACTTGTG
4459492 TGGGCTTTA
1 TGGGCTTTA
4459501 AAGAAGGATG
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
31 5 0.08
32 34 0.53
33 25 0.39
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.30
Consensus pattern (33 bp):
TGGGCTTTAGAAAGAGATTGCCACCAACTTGTG
Found at i:4459540 original size:27 final size:27
Alignment explanation
Indices: 4459498--4459862 Score: 122
Period size: 27 Copynumber: 12.2 Consensus size: 27
4459488 TGTGTGGGCT
* *
4459498 TTAAAGAAGGATGCCACAGAGTTGTAGAC
1 TTAAA-AAGG-TGCCACAGAGTTATGGAC
* *
4459527 TTAAAAAGGTGCCACAAAATTATGGAC
1 TTAAAAAGGTGCCACAGAGTTATGGAC
*
4459554 GT-AAAAGGATGCCAC-GAAGTTATGGAC
1 TTAAAAAGG-TGCCACAG-AGTTATGGAC
** *
4459581 TTAAAAGATAAAGGTGCCATGGAGTTGTGGAC
1 TT---A-A-AAAGGTGCCACAGAGTTATGGAC
* *
4459613 TTAAAAGGGTGCCACAGAGTTATGAAC
1 TTAAAAAGGTGCCACAGAGTTATGGAC
* ** *
4459640 TTAAAAGAAAAAAGGGTACCATGGAGTTATAGAC
1 TT------AAAAA-GGTGCCACAGAGTTATGGAC
* * * *
4459674 TTAAAAGGAAAAATGTGCCATAGAGTTGTGTAC
1 TT------AAAAAGGTGCCACAGAGTTATGGAC
* *
4459707 TTAAAAAGAAAAAAGTGCTACAGAGTTGTGGAC
1 TTAAAAAG------GTGCCACAGAGTTATGGAC
*
4459740 TTAAAAAGGTGCCACAGAGTTGTGGAC
1 TTAAAAAGGTGCCACAGAGTTATGGAC
* * * **
4459767 TTAAAAAAAAAGTTGCTACGGAGTTGGGGAC
1 TT----AAAAAGGTGCCACAGAGTTATGGAC
* *
4459798 CTAAAAAGAGTGCCACAGAGTTGTGGAC
1 TTAAAAAG-GTGCCACAGAGTTATGGAC
*
4459826 TTAAAAAAAATGGTGCCACAGAGTTATGGAT
1 TT---AAAAA-GGTGCCACAGAGTTATGGAC
4459857 TTAAAA
1 TTAAAA
4459863 GGGAAAGGTG
Statistics
Matches: 260, Mismatches: 45, Indels: 63
0.71 0.12 0.17
Matches are distributed among these distances:
26 6 0.02
27 82 0.32
28 25 0.10
29 6 0.02
31 46 0.18
32 18 0.07
33 50 0.19
34 27 0.10
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (27 bp):
TTAAAAAGGTGCCACAGAGTTATGGAC
Found at i:4459599 original size:32 final size:32
Alignment explanation
Indices: 4459556--4460412 Score: 446
Period size: 33 Copynumber: 27.4 Consensus size: 32
4459546 TTATGGACGT
*
4459556 AAAAGGATGCCACGAAGTTATGGACTTAAAAGA
1 AAAAGG-TGCCACGAAGTTGTGGACTTAAAAGA
* * *
4459589 TAAAGGTGCCATGGAGTTGTGGACTTAAAAG-
1 AAAAGGTGCCACGAAGTTGTGGACTTAAAAGA
* *
4459620 ----GGTGCCAC-AGAGTTATGAACTTAAAAGAA
1 AAAAGGTGCCACGA-AGTTGTGGACTTAAAAG-A
* * * * *
4459649 AAAAGGGTACCATGGAGTTATAGACTTAAAAGGA
1 AAAA-GGTGCCACGAAGTTGTGGACTTAAAA-GA
* * *
4459683 AAAATGTGCCA-TAGAGTTGTGTACTTAAAAAGA
1 AAAAGGTGCCACGA-AGTTGTGGACTT-AAAAGA
* *
4459716 AAAAAGTGCTAC-AGAGTTGTGGACTT-----A
1 AAAAGGTGCCACGA-AGTTGTGGACTTAAAAGA
4459743 AAAAGGTGCCAC-AGAGTTGTGGACTTAAAA-A
1 AAAAGGTGCCACGA-AGTTGTGGACTTAAAAGA
* * * * *
4459774 AAAAGTTGCTACGGAGTTGGGGACCT--AA-A
1 AAAAGGTGCCACGAAGTTGTGGACTTAAAAGA
*
4459803 AAGA-GTGCCAC-AGAGTTGTGGACTTAAAA-A
1 AAAAGGTGCCACGA-AGTTGTGGACTTAAAAGA
* * * *
4459833 AAATGGTGCCAC-AGAGTTATGGATTTAAAAGG
1 AAAAGGTGCCACGA-AGTTGTGGACTTAAAAGA
* **
4459865 GAAAGGTGCCATAAAGTTGTGGACTTAAAAG-
1 AAAAGGTGCCACGAAGTTGTGGACTTAAAAGA
* * *
4459896 ----GATGCCACGGAGTCGTGGACTTTAAAAGA
1 AAAAGGTGCCACGAAGTTGTGGAC-TTAAAAGA
* *
4459925 AAAAAGTGCCACAAAGTTGTGGACTTAAAAG-
1 AAAAGGTGCCACGAAGTTGTGGACTTAAAAGA
*** * *
4459956 ----GGTATGATCG-AGTTATGGACATAAAAAGA
1 AAAAGGTGCCA-CGAAGTTGTGGAC-TTAAAAGA
* * **
4459985 AAAAGGTGCCAC-AGAGTTAT-GAATT--TTG-
1 AAAAGGTGCCACGA-AGTTGTGGACTTAAAAGA
* * *
4460013 AAAGGGTGCCAC-AGAGTTGTGAACTTTAAAGA
1 AAAAGGTGCCACGA-AGTTGTGGACTTAAAAGA
* *
4460045 AAAAGGTGTCACAAAGTTGTGGACTTAAAAAGA
1 AAAAGGTGCCACGAAGTTGTGGACTT-AAAAGA
* * *
4460078 AAAAGGGTGCCACGGAGTTGTAGACTTCAAAAAA
1 AAAA-GGTGCCACGAAGTTGTGGACTT-AAAAGA
*
4460112 AAAAGTTGCCACGGAA-TTGTGGACTTAAAAGGA
1 AAAAGGTGCCAC-GAAGTTGTGGACTTAAAA-GA
* *
4460145 AAAAGGTGCCACGGAGTTGTGGACTT---TG-
1 AAAAGGTGCCACGAAGTTGTGGACTTAAAAGA
* * * * *
4460173 AAAATGTGCCATGGAGTTATGGACTTTAAAGA
1 AAAAGGTGCCACGAAGTTGTGGACTTAAAAGA
* * *
4460205 AAAAGGTGCCACGGAGTTGTGAACTTTGAAA-A
1 AAAAGGTGCCACGAAGTTGTGGAC-TTAAAAGA
** *
4460237 AAAAGGCACCAC-AGAGTTGTGGACTTAAAAAA
1 AAAAGGTGCCACGA-AGTTGTGGACTTAAAAGA
* *
4460269 TAAAATGGTGCCACGGAGTTGTGAACTTCAAAAGA
1 -AAAA-GGTGCCACGAAGTTGTGGACTT-AAAAGA
* *
4460304 AAAAGGGTGCCAC-AGAGTTATGGATTTAAAAAGA
1 AAAA-GGTGCCACGA-AGTTGTGGACTT-AAAAGA
* *
4460338 AAAAAGTGCCACAAAGTTGTGGACTT--AA-A
1 AAAAGGTGCCACGAAGTTGTGGACTTAAAAGA
*
4460367 AAAAGGTGCCACGAAGTTGTGGACTTAAAAAAA
1 AAAAGGTGCCACGAAGTTGTGGACTT-AAAAGA
4460400 AAAAGGTGCCACG
1 AAAAGGTGCCACG
4460413 GAGTCGTGAA
Statistics
Matches: 635, Mismatches: 123, Indels: 132
0.71 0.14 0.15
Matches are distributed among these distances:
27 74 0.12
28 70 0.11
29 36 0.06
30 7 0.01
31 52 0.08
32 126 0.20
33 157 0.25
34 107 0.17
35 6 0.01
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (32 bp):
AAAAGGTGCCACGAAGTTGTGGACTTAAAAGA
Found at i:4459618 original size:59 final size:59
Alignment explanation
Indices: 4459504--4460425 Score: 361
Period size: 60 Copynumber: 15.0 Consensus size: 59
4459494 GGCTTTAAAG
* ** * * *
4459504 AAGGATGCCACAGAGTTGTAGACTT-----AAAAAGGTGCCACAAAATTATGGACGTAA
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* * *
4459558 AAGGATGCCAC-GAAGTTATGGACTTAAAAGATAAAGGTGCCATGGAGTTGTGGACTTAA
1 AAGGATGCCACAG-AGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* * * * * * *
4459617 AAGGGTGCCACAGAGTTATGAACTTAAAAGAAAAAAGGGTACCATGGAGTTATAGACTTAA
1 AAGGATGCCACAGAGTTGTGGACTTAAAAG-AAAAA-GGTGCCACGGAGTTGTGGACTTAA
* * * * *
4459678 AAGGAAAAATGTGCCATAGAGTTGTGTACTTAAAAAGAAAAAAGTGCTACAGAGTTGTGGACTTA
1 AAGG----A--TGCCACAGAGTTGTGGACTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGACTT-
4459743 AA
58 AA
* * * *
4459745 AAGG-TGCCACAGAGTTGTGGACTTAAAA-AAAAAGTTGCTACGGAGTTGGGGACCTAA
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* * * * *
4459802 AAAGAGTGCCACAGAGTTGTGGACTTAAAA-AAAATGGTGCCACAGAGTTATGGATTTAA
1 AAGGA-TGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* * * *
4459861 AAGGGAAAGGTGCCATAAAGTTGTGGACTTAAAAG-----GATGCCACGGAGTCGTGGACTTTAA
1 AA-GG--A--TGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTAA
* * *** * *
4459921 AAGAAAAAAGTGCCACAAAGTTGTGGACTTAAAAG-----GGTATGATC-GAGTTATGGACATAA
1 AAG----GA-TGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCA-CGGAGTTGTGGAC-TTA
4459980 A
59 A
* * * ** * * *
4459981 AAGAAAAAGGTGCCACAGAGTTAT-GAATT--TTG-AAAGGGTGCCACAGAGTTGTGAACTTTAA
1 AAG-----GATGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT--
4460042 AGAAA
58 ---AA
* * *
4460047 AAGG-TGTCACAAAGTTGTGGACTTAAAAAGAAAAAGGGTGCCACGGAGTTGTAGACTTCAAAAA
1 AAGGATGCCACAGAGTTGTGGACTT-AAAAGAAAAA-GGTGCCACGGAGTTGTGGACTT------
4460111 AA
58 AA
* * * *
4460113 AAAGTTGCCACGGAATTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTGAA
1 AAGGATGCCACAGAGTTGTGGACTTAAAA-GAAAAAGGTGCCACGGAGTTGTGGAC-TT-AA
* ** * * *
4460175 AATG-TGCCATGGAGTTATGGACTTTAAAGAAAAAGGTGCCACGGAGTTGTGAACTTTGAAA
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT--AA
** * * *
4460236 AAAAAGGCACCACAGAGTTGTGGACTTAAAAAATAAAATGGTGCCACGGAGTTGTGAACTTCAAA
1 AAGGATG--CCACAGAGTTGTGGACTTAAAAGA-AAAA-GGTGCCACGGAGTTGTGGACTT----
4460301 AGAAA
58 ---AA
* * * * **
4460306 AAGGGTGCCACAGAGTTATGGATTTAAAAAGAAAAAAGTGCCACAAAGTTGTGGACTTAAAAA
1 AAGGATGCCACAGAGTTGTGGACTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGACTT---AA
* * *
4460369 AAGG-TGCCAC-GAAGTTGTGGACTTAAAAAAAAAAAGGTGCCACGGAGTCGTGAACTT
1 AAGGATGCCACAG-AGTTGTGGACTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
4460426 TGAGAAGAGA
Statistics
Matches: 677, Mismatches: 127, Indels: 120
0.73 0.14 0.13
Matches are distributed among these distances:
53 1 0.00
54 21 0.03
57 6 0.01
58 22 0.03
59 119 0.18
60 125 0.18
61 75 0.11
62 50 0.07
63 31 0.05
64 20 0.03
65 11 0.02
66 89 0.13
67 70 0.10
68 25 0.04
69 5 0.01
70 7 0.01
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.22
Consensus pattern (59 bp):
AAGGATGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAA
Found at i:4459667 original size:34 final size:34
Alignment explanation
Indices: 4459615--4459721 Score: 119
Period size: 34 Copynumber: 3.1 Consensus size: 34
4459605 TTGTGGACTT
*
4459615 AAAAGGGTGCCACAGAGTTATGAACTTAAAAGAA
1 AAAAGGGTGCCATAGAGTTATGAACTTAAAAGAA
* * *
4459649 AAAAGGGTACCATGGAGTTAT-AGACTTAAAAGGA
1 AAAAGGGTGCCATAGAGTTATGA-ACTTAAAAGAA
* * *
4459683 AAAA-TGTGCCATAGAGTTGTGTACTTAAAAAGAA
1 AAAAGGGTGCCATAGAGTTATGAACTT-AAAAGAA
4459717 AAAAG
1 AAAAG
4459722 TGCTACAGAG
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
33 17 0.29
34 42 0.71
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (34 bp):
AAAAGGGTGCCATAGAGTTATGAACTTAAAAGAA
Found at i:4460043 original size:27 final size:28
Alignment explanation
Indices: 4459989--4460043 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4459979 AAAAGAAAAA
*
4459989 GGTGCCACAGAGTTATGAATTTTGAAAG
1 GGTGCCACAGAGTTATGAACTTTGAAAG
*
4460017 GGTGCCACAGAGTTGTGAACTTT-AAAG
1 GGTGCCACAGAGTTATGAACTTTGAAAG
4460044 AAAAAGGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (28 bp):
GGTGCCACAGAGTTATGAACTTTGAAAG
Done.