Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 26 of 126
Found at i:5667582 original size:53 final size:53
Alignment explanation
Indices: 5667508--5667637 Score: 142
Period size: 53 Copynumber: 2.5 Consensus size: 53
5667498 AGAAAAGTAA
* * *
5667508 AAAAGAAAGTCT-TCAAAAAAAATA-AAA-AAAATAAAGAAGAAAATAAAAAGAG
1 AAAAGAAATTCTATCAAAAAAAA-AGAAACAAAAGAAA-AAGAAAACAAAAAGAG
*
5667560 AAAAGAAATTCTAT-AACAAAAAAAGAAACAAAGGAAAAAGAAAACAAAAAGAG
1 AAAAGAAATTCTATCAA-AAAAAAAGAAACAAAAGAAAAAGAAAACAAAAAGAG
* **
5667613 AAAAGGAATTCTATCATGAAAAAAG
1 AAAAGAAATTCTATCAAAAAAAAAG
5667638 GAAAGAAAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
52 14 0.21
53 45 0.68
54 7 0.11
ACGTcount: A:0.69, C:0.06, G:0.13, T:0.12
Consensus pattern (53 bp):
AAAAGAAATTCTATCAAAAAAAAAGAAACAAAAGAAAAAGAAAACAAAAAGAG
Found at i:5667662 original size:53 final size:52
Alignment explanation
Indices: 5667544--5667662 Score: 125
Period size: 53 Copynumber: 2.3 Consensus size: 52
5667534 AAAAATAAAG
*
5667544 AAGA-AAATAAAAAGAGAAAAGAAATTCTATAACAAAAAAAGAAACAAAGGA
1 AAGAGAAACAAAAAGAGAAAAGAAATTCTATAACAAAAAAAGAAACAAAGGA
* * ** * *
5667595 AAAAGAAAACAAAAAGAGAAAAGGAATTCTATCATGAAAAAAGGAAAGAAA-GA
1 AAGAG-AAACAAAAAGAGAAAAGAAATTCTAT-AACAAAAAAAGAAACAAAGGA
*
5667648 TAAGAGAAAGAAAAA
1 -AAGAGAAACAAAAA
5667663 ATAGTTCGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
51 3 0.05
53 34 0.62
54 18 0.33
ACGTcount: A:0.69, C:0.05, G:0.17, T:0.09
Consensus pattern (52 bp):
AAGAGAAACAAAAAGAGAAAAGAAATTCTATAACAAAAAAAGAAACAAAGGA
Found at i:5668051 original size:93 final size:94
Alignment explanation
Indices: 5667941--5668127 Score: 243
Period size: 93 Copynumber: 2.0 Consensus size: 94
5667931 TTAAGCCTAG
* * * * *
5667941 TTAGCTAACACTAATAAGATTTAAGCCTAGTTTATA-TGGCACCAATGAGAATTAAGCCCAATTT
1 TTAGCTAACACCAATAAGATTTAAGCCTAGTTTA-AGTAGCACCAATAAAAATTAAACCCAATTT
* * *
5668005 ATCTAGCATCAATGAGAT-TTAAGCTCAAT
65 AGCTAGCATCAATAAGATATTAAGCCCAAT
* * * *
5668034 TTAGCTGACACCAATAAGATTTAAGCCTAGTTTAAGTAGCATCAATAAAAATTAAACCTAGTTTA
1 TTAGCTAACACCAATAAGATTTAAGCCTAGTTTAAGTAGCACCAATAAAAATTAAACCCAATTTA
5668099 GCTAGCATCAATAAGATATTAAGCCCAAT
66 GCTAGCATCAATAAGATATTAAGCCCAAT
5668128 GAGATTTTCA
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
92 1 0.01
93 69 0.86
94 10 0.12
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (94 bp):
TTAGCTAACACCAATAAGATTTAAGCCTAGTTTAAGTAGCACCAATAAAAATTAAACCCAATTTA
GCTAGCATCAATAAGATATTAAGCCCAAT
Found at i:5668080 original size:31 final size:31
Alignment explanation
Indices: 5667953--5668123 Score: 127
Period size: 31 Copynumber: 5.5 Consensus size: 31
5667943 AGCTAACACT
* *
5667953 AATAAGATTTAAGCCTAGTTTATA-TGGCACC
1 AATAAGATTTAAGCCTAGTTTA-AGTAGCATC
* * * * **
5667984 AATGAGAATTAAGCCCAATTTATCTAGCATC
1 AATAAGATTTAAGCCTAGTTTAAGTAGCATC
* * *
5668015 AATGAGATTTAAG-CTCAATTT-AGCT-GACACC
1 AATAAGATTTAAGCCT-AGTTTAAG-TAG-CATC
5668046 AATAAGATTTAAGCCTAGTTTAAGTAGCATC
1 AATAAGATTTAAGCCTAGTTTAAGTAGCATC
* * *
5668077 AATAAAAATTAAACCTAGTTT-AGCTAGCATC
1 AATAAGATTTAAGCCTAGTTTAAG-TAGCATC
5668108 AATAAGATATTAAGCC
1 AATAAGAT-TTAAGCC
5668124 CAATGAGATT
Statistics
Matches: 110, Mismatches: 21, Indels: 17
0.74 0.14 0.11
Matches are distributed among these distances:
30 4 0.04
31 95 0.86
32 11 0.10
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (31 bp):
AATAAGATTTAAGCCTAGTTTAAGTAGCATC
Found at i:5668237 original size:50 final size:51
Alignment explanation
Indices: 5668178--5668344 Score: 135
Period size: 50 Copynumber: 3.4 Consensus size: 51
5668168 TTGTCATAGA
**
5668178 TGAGATTTTTAAAGTTTTAAAATCTTTGA-TCAAGATTAGCCTTTAAAAGT
1 TGAGATTTTTAAAGTTTTAAAATCTTTGATTCAAGAGGAGCCTTTAAAAGT
* * ** * * *
5668228 TGAGATTTTTAAA-TTTTCAAAGCCATCATTCATGAGGAGCCTTTGAAAGT
1 TGAGATTTTTAAAGTTTTAAAATCTTTGATTCAAGAGGAGCCTTTAAAAGT
* * * * * ** *
5668278 TGAGATTATTAAAGTTTCAAAATTTTTG-TTTATGAGGAG-CTTCCAAAGA
1 TGAGATTTTTAAAGTTTTAAAATCTTTGATTCAAGAGGAGCCTTTAAAAGT
* *
5668327 GGAAATTTTTAAAGTTTT
1 TGAGATTTTTAAAGTTTT
5668345 CAACATATAT
Statistics
Matches: 90, Mismatches: 25, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
49 31 0.34
50 52 0.58
51 7 0.08
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (51 bp):
TGAGATTTTTAAAGTTTTAAAATCTTTGATTCAAGAGGAGCCTTTAAAAGT
Found at i:5669026 original size:143 final size:144
Alignment explanation
Indices: 5668762--5669031 Score: 368
Period size: 143 Copynumber: 1.9 Consensus size: 144
5668752 TGCACCTTAG
* **
5668762 AAAGGTTAAAAATTACCAAAATACCCTTTAGGGATATTTTCGTAATTTGACCTTCTCGAGTTTGG
1 AAAGGTTAAAAATTACCAAAATACCCTTTAGGGATATTTTCGTAATTTGACCTTCTCGAGTGTCA
* * * *
5668827 TTTTTTGTGAAATGCTCTAGATCATGTTTTAATATTATTTCATGAATTTTGATGTATTGAAAACC
66 ATTTTTATGAAAGGCTCTAGATCATATTTTAATATTATTTCATGAATTTTGATGTATT-AAAACC
5668892 TTAATTGCACCTCGA
130 TTAATTGCACCTCGA
* * *
5668907 AAAGGTT-GAAATTACCAAAATACCTTTTGAGGG-TATTTTCGTAATTTGACTTTCTCGAG-GTC
1 AAAGGTTAAAAATTACCAAAATACCCTTT-AGGGATATTTTCGTAATTTGACCTTCTCGAGTGTC
* * *
5668969 AATTTTTATGAAAGGCT-TCAGATCATATTTTGATATTATTTTATGAATTTTGGTGTATTAAAA
65 AATTTTTATGAAAGGCTCT-AGATCATATTTTAATATTATTTCATGAATTTTGATGTATTAAAA
5669032 TCATGAGAAT
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
142 5 0.05
143 50 0.45
144 44 0.40
145 11 0.10
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (144 bp):
AAAGGTTAAAAATTACCAAAATACCCTTTAGGGATATTTTCGTAATTTGACCTTCTCGAGTGTCA
ATTTTTATGAAAGGCTCTAGATCATATTTTAATATTATTTCATGAATTTTGATGTATTAAAACCT
TAATTGCACCTCGA
Found at i:5669087 original size:21 final size:21
Alignment explanation
Indices: 5669062--5669101 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5669052 CATAAGATTT
5669062 TTGAAAAATCATGAAAAAGGG
1 TTGAAAAATCATGAAAAAGGG
5669083 TTGAAAAATCATGAAAAAG
1 TTGAAAAATCATGAAAAAG
5669102 TGCTAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (21 bp):
TTGAAAAATCATGAAAAAGGG
Found at i:5669110 original size:21 final size:21
Alignment explanation
Indices: 5669065--5669110 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5669055 AAGATTTTTG
* *
5669065 AAAAATCATGAAAAAGGGTTG
1 AAAAATCATGAAAAAGGGCTA
*
5669086 AAAAATCATGAAAAAGTGCTA
1 AAAAATCATGAAAAAGGGCTA
5669107 AAAA
1 AAAA
5669111 CACTAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.07, G:0.17, T:0.17
Consensus pattern (21 bp):
AAAAATCATGAAAAAGGGCTA
Found at i:5669774 original size:17 final size:16
Alignment explanation
Indices: 5669739--5669772 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5669729 TTTGAGATTG
5669739 TTACTTTTTTGTTAGT
1 TTACTTTTTTGTTAGT
5669755 TTACTATTTTTGTT-GT
1 TTACT-TTTTTGTTAGT
5669771 TT
1 TT
5669773 TAGATTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.71
Consensus pattern (16 bp):
TTACTTTTTTGTTAGT
Found at i:5671973 original size:21 final size:20
Alignment explanation
Indices: 5671947--5671999 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
5671937 TTCTTGCAAT
**
5671947 TTCTCTTTAGTTTTTTTTATC
1 TTCTCTTTAGTTTTTGGTA-C
*
5671968 TTCTCTTTAATTTTTGGTAC
1 TTCTCTTTAGTTTTTGGTAC
*
5671988 TTTTCTTTAGTT
1 TTCTCTTTAGTT
5672000 GATCTTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.11, C:0.13, G:0.08, T:0.68
Consensus pattern (20 bp):
TTCTCTTTAGTTTTTGGTAC
Found at i:5673289 original size:19 final size:19
Alignment explanation
Indices: 5673267--5673303 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5673257 ACCTAAATTT
*
5673267 CAAATCCTAAACCAAACCC
1 CAAATCCAAAACCAAACCC
*
5673286 CAAATCCAAAACCCAACC
1 CAAATCCAAAACCAAACC
5673304 TTAAACATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.43, G:0.00, T:0.08
Consensus pattern (19 bp):
CAAATCCAAAACCAAACCC
Found at i:5673390 original size:14 final size:15
Alignment explanation
Indices: 5673371--5673406 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5673361 CAAATAGAAT
5673371 CCAAACCC-CAAATC
1 CCAAACCCTCAAATC
5673385 CCAAACCCTCAAATC
1 CCAAACCCTCAAATC
*
5673400 CTAAACC
1 CCAAACC
5673407 AAATAAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.42, C:0.47, G:0.00, T:0.11
Consensus pattern (15 bp):
CCAAACCCTCAAATC
Found at i:5673755 original size:21 final size:22
Alignment explanation
Indices: 5673729--5673769 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5673719 GTGTTTTAAG
5673729 AAAAAAAATTT-AAATAAAATA
1 AAAAAAAATTTCAAATAAAATA
* *
5673750 AAAAAATATTTCAAGTAAAA
1 AAAAAAAATTTCAAATAAAA
5673770 ATAATCTCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAAAAATTTCAAATAAAATA
Found at i:5674478 original size:28 final size:29
Alignment explanation
Indices: 5674433--5674510 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 29
5674423 TTCAAAATAT
* * *
5674433 TAAAATAATTTAAAAAATTTTATAACATA
1 TAAATTAATTTAAGAAATTTTACAACATA
*
5674462 TAAATTAA-TTAAGAAATTTT-CAATATA
1 TAAATTAATTTAAGAAATTTTACAACATA
* *
5674489 CAAATTAATTTAAGATATTTTA
1 TAAATTAATTTAAGAAATTTTA
5674511 ATTAAGGCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 12 0.29
28 22 0.54
29 7 0.17
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (29 bp):
TAAATTAATTTAAGAAATTTTACAACATA
Found at i:5674830 original size:54 final size:52
Alignment explanation
Indices: 5674720--5674830 Score: 136
Period size: 52 Copynumber: 2.1 Consensus size: 52
5674710 TAAATATTTT
* *
5674720 TAATATTTTAATAATAAATATTACTATTTTCATATTATTATATTAATAAAAA
1 TAATATTTTAAGAATAAATAATACTATTTTCATATTATTATATTAATAAAAA
* *
5674772 TAATATTTTAAGAAT-AGTAATACTATTTTCAATATT-TTAAAGTATTAATATAAA
1 TAATATTTTAAGAATAAATAATACTATTTTC-ATATTATT--A-TATTAATAAAAA
5674826 TAATA
1 TAATA
5674831 AATAATTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
51 15 0.29
52 19 0.37
53 1 0.02
54 16 0.31
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (52 bp):
TAATATTTTAAGAATAAATAATACTATTTTCATATTATTATATTAATAAAAA
Found at i:5674956 original size:26 final size:25
Alignment explanation
Indices: 5674917--5674975 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
5674907 AATATTAATT
*
5674917 TTTTATAATAAATAGTTTTAATATA
1 TTTTATAATAAATAATTTTAATATA
*
5674942 TTTTATTAATTAATAATTTTAATAT-
1 TTTTA-TAATAAATAATTTTAATATA
*
5674967 TTTAATAAT
1 TTTTATAAT
5674976 TATATCAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 17 0.57
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTATAATAAATAATTTTAATATA
Found at i:5674965 original size:9 final size:9
Alignment explanation
Indices: 5674927--5674976 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
5674917 TTTTATAATA
*
5674927 AATAGTTTT
1 AATAATTTT
5674936 AATATATTTT
1 AATA-ATTTT
*
5674946 ATTAA--TT
1 AATAATTTT
5674953 AATAATTTT
1 AATAATTTT
5674962 AAT-ATTTT
1 AATAATTTT
5674970 AATAATT
1 AATAATT
5674977 ATATCAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
7 6 0.18
8 8 0.24
9 13 0.38
10 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
AATAATTTT
Found at i:5674971 original size:17 final size:17
Alignment explanation
Indices: 5674927--5674976 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
5674917 TTTTATAATA
5674927 AATAGTTTTAATATATTTT
1 AATA-TTTTAATA-ATTTT
* *
5674946 ATTA-ATTAATAATTTT
1 AATATTTTAATAATTTT
5674962 AATATTTTAATAATT
1 AATATTTTAATAATT
5674977 ATATCAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 8 0.31
17 15 0.58
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
AATATTTTAATAATTTT
Found at i:5674975 original size:20 final size:21
Alignment explanation
Indices: 5674947--5674989 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
5674937 ATATATTTTA
* *
5674947 TTAATTAATAATTTTAATATT
1 TTAATTAATAATATCAATATT
*
5674968 TTAA-TAATTATATCAATATT
1 TTAATTAATAATATCAATATT
5674988 TT
1 TT
5674990 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATTAATAATATCAATATT
Found at i:5675270 original size:11 final size:11
Alignment explanation
Indices: 5675254--5675278 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5675244 GTGTAATTTA
5675254 TATATTTATAT
1 TATATTTATAT
5675265 TATATTTATAT
1 TATATTTATAT
5675276 TAT
1 TAT
5675279 GAATAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:5679280 original size:23 final size:23
Alignment explanation
Indices: 5679254--5679301 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5679244 AAATCCTATG
5679254 ATTTATATCCCTTTCTATCTCGC
1 ATTTATATCCCTTTCTATCTCGC
5679277 ATTTATATCCCTTTCTATCTCGC
1 ATTTATATCCCTTTCTATCTCGC
5679300 AT
1 AT
5679302 CGGTTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.29, G:0.04, T:0.48
Consensus pattern (23 bp):
ATTTATATCCCTTTCTATCTCGC
Found at i:5683839 original size:30 final size:30
Alignment explanation
Indices: 5683805--5683889 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
5683795 TTTGTATTAT
5683805 ATTCAAATAAATCTAT-AATTTATAACTTGC
1 ATTCAAATAAATCTATAAATTT-TAACTTGC
* * *
5683835 ATTCAAATAAA-CTTTAAATTTTAATTTGT
1 ATTCAAATAAATCTATAAATTTTAACTTGC
* * *
5683864 ATCCAAATAAATTTTTAAAATTTTAA
1 ATTCAAATAAATCTAT-AAATTTTAA
5683890 TTTATACCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 19 0.40
30 19 0.40
31 9 0.19
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (30 bp):
ATTCAAATAAATCTATAAATTTTAACTTGC
Found at i:5683888 original size:31 final size:28
Alignment explanation
Indices: 5683838--5683906 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 28
5683828 AACTTGCATT
*
5683838 CAAATAAACTTTAAATTTTAATTTGTATC
1 CAAATAAACTTTAAATTTTAATTTATA-C
*
5683867 CAAATAAATTTTTAAAATTTTAATTTATAC
1 CAAATAAA-CTTT-AAATTTTAATTTATAC
5683897 CTAAATAAAC
1 C-AAATAAAC
5683907 ACATACTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.24
30 5 0.15
31 21 0.62
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.42
Consensus pattern (28 bp):
CAAATAAACTTTAAATTTTAATTTATAC
Found at i:5686179 original size:23 final size:25
Alignment explanation
Indices: 5686133--5686190 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
5686123 TGGTCTTGTT
5686133 TTCTTCTTCTATTCTTCTGGTCTTAC
1 TTCTTCTTCTATTCTTCT-GTCTTAC
*
5686159 TTCTTCTTCTA-TCTTCT-TCTTCC
1 TTCTTCTTCTATTCTTCTGTCTTAC
5686182 TTCTT-TTCT
1 TTCTTCTTCT
5686191 CTAGTTTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 4 0.13
23 10 0.32
25 6 0.19
26 11 0.35
ACGTcount: A:0.05, C:0.29, G:0.03, T:0.62
Consensus pattern (25 bp):
TTCTTCTTCTATTCTTCTGTCTTAC
Found at i:5695209 original size:13 final size:12
Alignment explanation
Indices: 5695177--5695210 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5695167 ATAAAACCTG
*
5695177 AAAAAAAAAAAC
1 AAAAAACAAAAC
5695189 AAAAAACAAAAC
1 AAAAAACAAAAC
5695201 AAAAGAACAA
1 AAAA-AACAA
5695211 TTAAACCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:5696815 original size:18 final size:18
Alignment explanation
Indices: 5696788--5696831 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5696778 TATTTAATTT
* *
5696788 TTTAATTTTATAATATCAA
1 TTTAA-TTTACAAAATCAA
*
5696807 TTTAATTTACAAAATTAA
1 TTTAATTTACAAAATCAA
5696825 TTTAATT
1 TTTAATT
5696832 AATTATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTAATTTACAAAATCAA
Found at i:5697928 original size:20 final size:20
Alignment explanation
Indices: 5697870--5697929 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 20
5697860 TATTTTCACC
*
5697870 TTTTATTT-TAACACTTAATT
1 TTTTATTTATAATAC-TAATT
*
5697890 TTTTATTTAGAAT--T-A-T
1 TTTTATTTATAATACTAATT
5697906 TTTTATTTATAATACTAATT
1 TTTTATTTATAATACTAATT
5697926 TTTT
1 TTTT
5697930 TATGTTACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
16 13 0.41
17 1 0.03
18 2 0.06
19 1 0.03
20 13 0.41
21 2 0.06
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATTTATAATACTAATT
Found at i:5698106 original size:212 final size:211
Alignment explanation
Indices: 5697839--5698579 Score: 750
Period size: 212 Copynumber: 3.5 Consensus size: 211
5697829 ATTTAACGTT
* * * * * *
5697839 AAATTATACCAATTTTATTATTATTTTCACC-TTTTATTTTAACACTTAATTTTTTATTTAGAAT
1 AAATAATATCAATTTTATGATTATTCTCACCTTTTTATATTAACAATT-ATTTTTTATTTAGAAT
*
5697903 TATTTTTATTTATAATACTAATTTTTTTATGTTACAAATTTATTACATTTCAATAATATCCTTTT
65 TATTTTTATTTATAATACTAATTTTTTTATGTTACAAATTTATTACATTTCAATAATATCTTTTT
* * * *
5697968 ACATTTGTTATTATTTTTCATTATATTTAAATTTATTATAATTTTTTGTTAAAGTATAATGATAC
130 ACATTTGTTGTTATTTTTCATTATGTTTAAAATTATTATAATTTTTTGTTAAAGTATAACGATAC
5698033 TTCTAACCATTTTATATA
195 TTCTAACCATTTTAT-TA
*
5698051 AAATAATATTAATTTTATGATTATTCTCACCTTTTTACT-TTAACAATTATTTTTTA-TTAGAAT
1 AAATAATATCAATTTTATGATTATTCTCACCTTTTTA-TATTAACAATTATTTTTTATTTAGAAT
*
5698114 TATTTTTATTTATAATACTAATTTTTTTACGTTACAAATTTATTACATTTCAATAATATCTTTTT
65 TATTTTTATTTATAATACTAATTTTTTTATGTTACAAATTTATTACATTTCAATAATATCTTTTT
* * * * *
5698179 ACATTTGTTGTTACTTTTCATTACGTTTAAAATTGTTATAATATTTTTGTTAAGGTGTAACGATA
130 ACATTTGTTGTTATTTTTCATTATGTTTAAAATTATTATAAT-TTTTTGTTAAAGTATAACGATA
*
5698244 CTTCTAACAATTTTACTTA
194 CTTCTAACCATTTTA-TTA
* * * *** *
5698263 AAATAATACCAATTTCACT-ATTATTCTCA-CTATTTTATGTTAATTCTTATTTTTTGTTTA-AA
1 AAATAATATCAATTTTA-TGATTATTCTCACCT-TTTTATATTAACAATTATTTTTTATTTAGAA
* * * * * *
5698325 TTATTTTTTATTTGA-AATAAT-ATTTTCTTACATTGCCTACTTAA-TTATTTACGTTAT-AGTA
64 TTA-TTTTTATTT-ATAATACTAATTTT-TT-TA-TG-TTAC-AAATTTA-TTACATT-TCAATA
*** * * * * *
5698386 ATATCTTTTTATGCTTGTTGTTATCTTTCATTATGCTTAAAATTATCATAATTTTTTTCTTAGTA
120 ATATCTTTTTACATTTGTTGTTATTTTTCATTATGTTTAAAATTATTATAA-TTTTTTGTTA-AA
* * **
5698451 GTGAT-ACGATACTTTTAATCATTTTATGCC
183 GT-ATAACGATACTTCTAACCATTTTAT-TA
* * *
5698481 AAATGATATCAATTTTATGATTATTCTCACCTTTTTATATTAACAATTATTTTTTGGTTTAAAAT
1 AAATAATATCAATTTTATGATTATTCTCACCTTTTTATATTAACAATTATTTTTT-ATTTAGAAT
* *
5698546 TATTGCTTATTTATAATGA-TAATTATTTTATGTT
65 TATT-TTTATTTATAAT-ACTAATTTTTTTATGTT
5698580 GCCAAAAATA
Statistics
Matches: 439, Mismatches: 61, Indels: 53
0.79 0.11 0.10
Matches are distributed among these distances:
211 109 0.25
212 121 0.28
213 34 0.08
214 3 0.01
215 1 0.00
216 6 0.01
217 64 0.15
218 67 0.15
219 12 0.03
220 17 0.04
221 5 0.01
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.53
Consensus pattern (211 bp):
AAATAATATCAATTTTATGATTATTCTCACCTTTTTATATTAACAATTATTTTTTATTTAGAATT
ATTTTTATTTATAATACTAATTTTTTTATGTTACAAATTTATTACATTTCAATAATATCTTTTTA
CATTTGTTGTTATTTTTCATTATGTTTAAAATTATTATAATTTTTTGTTAAAGTATAACGATACT
TCTAACCATTTTATTA
Found at i:5698342 original size:17 final size:16
Alignment explanation
Indices: 5698309--5698342 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5698299 ATGTTAATTC
*
5698309 TTATTTTTTGTTTAAA
1 TTATTTTTTATTTAAA
5698325 TTATTTTTTATTTGAAA
1 TTATTTTTTATTT-AAA
5698342 T
1 T
5698343 AATATTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTATTTTTTATTTAAA
Found at i:5699123 original size:931 final size:929
Alignment explanation
Indices: 5697877--5700208 Score: 2096
Period size: 932 Copynumber: 2.5 Consensus size: 929
5697867 ACCTTTTATT
* * *
5697877 TTAACACTTAATTTTTTATTTAGAATTATTTTTATTTATAATACTAATTTTTTTATGTTA-CAAA
1 TTAACAATT-ATTTTTTATTTAGAATTATTTTTATTTATAATAATAATTTTTTTATGTTATCAAC
* * * *
5697941 TT-TATTACATTTCAATAATATCCTTTTACATTTGTTATTATTTTTCATTATATTTAAATTTATT
65 TTATATTACATTACAATAAAATCCTTTTACATTTGTTATTACTTTTCATTATATTTAAATTTATC
* * * * * * * *
5698005 ATAATTTTTTGTTAAAGTATAATGATACTTCTAACCATTTTATATAAAATAATATTAATTTTATG
130 ACAAGTTTTTCTTAAAGTATAATGACACTTATAAACATTTTACATAAAATAATATTAATTTTACG
* * *
5698070 ATTATTCTCACCTTTTTACTTTAACAATTATTTTTTATTAGAATTATTTTTATTTATAATACTAA
195 ATTATTCTCACATTTTTACGTTAACAACTATTTTTTATTAGAATTATTTTTATTTATAATACTAA
* * * *
5698135 TTTTTTTACGTTACAAATTTATTACATTTCAATAATATCTTTTTACATTTGTTGTTACTTTTCAT
260 CTTTTTTACGTTACAAATTTATTACATTCCAAAAATATCTTTTTACATTTATTGTTACTTTTCAT
* * * * *
5698200 TACGTTTAAAATTGTTATAATATTTTTGTTAAGGTGTAACGATACTTCTAACAATTTTAC-TTAA
325 TACG-TTAAAATTATTACAATATTTTTCTTAAAGTATAACGATACTTCTAACAATTTTACGTT-A
* * ** * *
5698264 AATAATACCAATTTCACTATTATTCTCACTATTTTATGTTAA-TTCTT-ATTTTTTGTTTAAATT
388 AATAATACCAATTTCACGATTATTCTCACCATTTTACATTAACTT-TTAACTTTTTATTT-AA-T
* * * *
5698327 ATTTTTTATTTGAAATAATA-TT-TTCTTACATTGCCT-ACTTAATTA-TTTA-CGTTATAGTA-
450 -TTTTTTATTTGAAATAATAGTTAAT-TTACATTG-CTAACTTAATTATTTTATCATAATAATAT
* * * * * * * * * *
5698386 ATATCTTTTTATGCTTGTTGTTATCTTTCATTATGCT-TAAAATTATCATAATTTTTTTCTTAGT
512 ATATATTTTTACGCTTGTTATTACCTTTCATTAT-ATATAAAAGTATCACAACTTTTTTCATA-A
* * * * *
5698450 A-GTGATA-CGATACTT-TTAATCATTTTATGCCAAATGATATCAATTTTATGATTATTCTCA-C
575 AGGTGATACCG-CACTTCTT-ACCATTTT-TGCCAAATAATACCAATTTTATGATTACTCTCATC
** ** * *
5698511 CTTTTTATATTAACAATTATTTTTTGG-TTTAAAATTATTGCTTATTTATAATGATAATTATTTT
637 CTTTTTATACAAACAATTATTTTTTGGTTTTAAAATTATTAATTATTTATAATAATAATTATTTC
** * * ** * *
5698575 ATGTTGCCAAAAATATTATTTTTGTTATAATAATATTTTTTTTTACTTATTCCTACTTTTTATTA
702 ACATTGCCAAAAATATTATTTATGTTACAAT-A-ATTTTTTCATAATTATTCATACTTTTTATTA
* * * * * *
5698640 CATTTAAAATTATCATAATTTTTTGTTA-AGGTGTTACGACACTTAC-AATCCAATTTATGCCAA
765 CATTTAAAATTATCACAACTCTTAGTTAGA-GTATTACGACAATT-CTAATCCAATTTATGCCAA
* ** * * * *
5698703 TTAACACCAATTTTACAACTATT-TT-TATCCTTTTATGTTACAATA-TTGTAACATATTTTACT
828 ATAACACCAATTTTACAACTATTCTTCTAT--TTTTACATTACAACACTTCTAACACATTTTACG
* * *
5698765 CTAAATAATTCCAATTTTTCAATTTTTCTCA-TCTTTTTACA
891 CCAAATAATTCCAATTTTACAA--TTACTCACT-TTTTTACA
*
5698806 TTAACAAGTTATTTTTTATTTAGAATTATTTTTATTTGTAATAATAATTTTTTTATGTTATCAAC
1 TTAACAA-TTATTTTTTATTTAGAATTATTTTTATTTATAATAATAATTTTTTTATGTTATCAAC
* * *
5698871 TTATATTTATATTACAATAAAAT-CTTTTACATTTGTTCTTACCTTTT-ATTATGTTTAGAA-TT
65 TTATA-TTACATTACAATAAAATCCTTTTACATTTGTTATTA-CTTTTCATTATATTTA-AATTT
* * * * *
5698933 ATCACAAGTTTTTCTT-AAGATATTATGACACTTATAATATATTTTACGTCAAATGATACTT-AT
127 ATCACAAGTTTTTCTTAAAG-TATAATGACACTTATAA-ACATTTTACATAAAATAATA-TTAAT
5698996 TTTACGATTATTCTCACATTTTTACGTTAA-AACT-TTTTTTA-TATGAATTATTTTTTATTTAT
189 TTTACGATTATTCTCACATTTTTACGTTAACAACTATTTTTTATTA-GAATTA-TTTTTATTTAT
* * * **
5699058 AATACTAACTTTTTTATGTTATC-GATTTATTGCATTCCAAAAATATCTTTTTATGTTTATTGTT
252 AATACTAACTTTTTTACGTTA-CAAATTTATTACATTCCAAAAATATCTTTTTACATTTATTGTT
* * * *
5699122 ACTTTTTATTACGTTAAAATTATTACAATTTTTTTCTTAAAGTATAACGATATTTCTAACTATTT
316 ACTTTTCATTACGTTAAAATTATTACAATATTTTTCTTAAAGTATAACGATACTTCTAACAATTT
* *
5699187 TACGTTAAATAATATCAATTTTACGATTATTCTCACCATTTTACATTAACTTTTAACTTTTTATT
381 TACGTTAAATAATACCAATTTCACGATTATTCTCACCATTTTACATTAACTTTTAACTTTTTATT
* * *
5699252 TAATTTTTTTGTTTGTAATAATAGTTAATTTATATTGCTAACTTAATTATTTTTATCATAATAAT
446 TAATTTTTTTATTTGAAATAATAGTTAATTTACATTGCTAACTTAATTA-TTTTATCATAATAAT
* * * * *
5699317 ATATATATTTTTACGTTTGTTATTACCTTTTATTGTATATAGAAGTATTACAACTTTTTTCATAA
510 ATATATATTTTTACGCTTGTTATTACCTTTCATTATATATAAAAGTATCACAACTTTTTTCATAA
* *
5699382 AGGTGTTACCGCACTTCTTACCATTTTTGCCAAATAATACCAATTTTATGATTACTCTCATCTTT
575 AGGTGATACCGCACTTCTTACCATTTTTGCCAAATAATACCAATTTTATGATTACTCTCATCCTT
* * *
5699447 TTTATACAAACACTTATTTTTTGGTTTTAAAATTATTAATTATTTGTAATAATAATTCTTTCACA
640 TTTATACAAACAATTATTTTTTGGTTTTAAAATTATTAATTATTTATAATAATAATTATTTCACA
* * *
5699512 TTGCCAAAAATATTATTTATGTTGCAATAATTTTTTCATAATTGTTCATACTTTTTATTACGTTT
705 TTGCCAAAAATATTATTTATGTTACAATAATTTTTTCATAATTATTCATACTTTTTATTACATTT
* * * * * * *
5699577 ATATTTATCACAACTCTTAGTTAGAGTATTATGATAATTCTAATCCAATTTATGCTAAATGATAC
770 AAAATTATCACAACTCTTAGTTAGAGTATTACGACAATTCTAATCCAATTTATGCCAAATAACAC
* * *
5699642 CAATTTTACAATTATTCTTCTATTTTTACATTACGACACTTCTAACACATTTTACGCCAAATGAT
835 CAATTTTACAACTATTCTTCTATTTTTACATTACAACACTTCTAACACATTTTACGCCAAATAAT
* *
5699707 TCTAATTTTACAATTACTCACTTTTTTACT
900 TCCAATTTTACAATTACTCACTTTTTTACA
* * * *
5699737 TTAATAATT-TTTTTAATTTAGAATTATTTTTTATTTATAATAACAAATTTTTTTATGTTGTCAA
1 TTAACAATTATTTTTTATTTAGAATTA-TTTTTATTTATAATAA-TAATTTTTTTATGTTATCAA
* * * *** * * * *
5699801 CTTA-ATTATTATGATATAATAATAT-CTTTTATGCTTGTTCTTATCTTTT-AATACATTTAAAA
64 CTTATATTA-CAT--TACAATAAAATCCTTTTACATTTGTTATTA-CTTTTCATTATATTTAAAT
* * * * * * * * ** ** **
5699863 TTATTATAA-TTTTTTTTTAGGTATTATAATATCTCTA-ACTCATTTTATGTTAAAAT-ATACCA
125 TTATCACAAGTTTTTCTTAAAGTATAATGACA-CT-TATAAACATTTTA-CATAAAATAATATTA
* * ** * * * * * *
5699925 ATTTAATGATTATTCT--TTTTTTTTC-TTAACATCTTTTTTTTGTGTAGGATCATTTTTTATTT
187 ATTTTACGATTATTCTCACATTTTTACGTTAACAACTATTTTTTAT-TAGAATTA-TTTTTATTT
* * * ** *
5699987 ATAATACTAA-TTTTTT-TGTTACCAATTTAATTATTTATGTTTTAATAATAT-TTTTTACATTT
250 ATAATACTAACTTTTTTACGTTACAAATTT-ATTA--CA--TTCCAAAAATATCTTTTTACATTT
* * * * * * * *
5700049 -TTATTACTTTTTATTACATTTAAAATTATCACAATA-TTTTATTAAAGTGTAACGATATTTATA
310 ATTGTTACTTTTCATTAC-GTTAAAATTATTACAATATTTTTCTTAAAGTATAACGATACTTCTA
* * * * ** * * *
5700112 ACCATTTTACGTTAAATAATACTAATTTTACAATTATTCTCACTTTTTTTCATTAACCTTT-ATT
374 ACAATTTTACGTTAAATAATACCAATTTCACGATTATTCTCACCATTTTACATTAACTTTTAACT
* * *
5700176 TTTTAAAACTTATTTTTTTTATTTGCAATAATA
439 TTTT---ATTTAATTTTTTTATTTGAAATAATA
5700209 TTTCTTTTAC
Statistics
Matches: 1149, Mismatches: 195, Indels: 113
0.79 0.13 0.08
Matches are distributed among these distances:
928 24 0.02
929 112 0.10
930 148 0.13
931 264 0.23
932 356 0.31
933 150 0.13
934 95 0.08
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (929 bp):
TTAACAATTATTTTTTATTTAGAATTATTTTTATTTATAATAATAATTTTTTTATGTTATCAACT
TATATTACATTACAATAAAATCCTTTTACATTTGTTATTACTTTTCATTATATTTAAATTTATCA
CAAGTTTTTCTTAAAGTATAATGACACTTATAAACATTTTACATAAAATAATATTAATTTTACGA
TTATTCTCACATTTTTACGTTAACAACTATTTTTTATTAGAATTATTTTTATTTATAATACTAAC
TTTTTTACGTTACAAATTTATTACATTCCAAAAATATCTTTTTACATTTATTGTTACTTTTCATT
ACGTTAAAATTATTACAATATTTTTCTTAAAGTATAACGATACTTCTAACAATTTTACGTTAAAT
AATACCAATTTCACGATTATTCTCACCATTTTACATTAACTTTTAACTTTTTATTTAATTTTTTT
ATTTGAAATAATAGTTAATTTACATTGCTAACTTAATTATTTTATCATAATAATATATATATTTT
TACGCTTGTTATTACCTTTCATTATATATAAAAGTATCACAACTTTTTTCATAAAGGTGATACCG
CACTTCTTACCATTTTTGCCAAATAATACCAATTTTATGATTACTCTCATCCTTTTTATACAAAC
AATTATTTTTTGGTTTTAAAATTATTAATTATTTATAATAATAATTATTTCACATTGCCAAAAAT
ATTATTTATGTTACAATAATTTTTTCATAATTATTCATACTTTTTATTACATTTAAAATTATCAC
AACTCTTAGTTAGAGTATTACGACAATTCTAATCCAATTTATGCCAAATAACACCAATTTTACAA
CTATTCTTCTATTTTTACATTACAACACTTCTAACACATTTTACGCCAAATAATTCCAATTTTAC
AATTACTCACTTTTTTACA
Found at i:5700059 original size:10 final size:11
Alignment explanation
Indices: 5700037--5700069 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
5700027 TTTAATAATA
5700037 TTTT-TTACAT
1 TTTTATTACAT
5700047 TTTTATTAC-T
1 TTTTATTACAT
5700057 TTTTATTACAT
1 TTTTATTACAT
5700068 TT
1 TT
5700070 AAAATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTATTACAT
Found at i:5700150 original size:211 final size:214
Alignment explanation
Indices: 5699762--5700151 Score: 445
Period size: 211 Copynumber: 1.8 Consensus size: 214
5699752 ATTTAGAATT
**
5699762 ATTTTTTATTTATAATAACAAATTTTTTTATGTTGTCAACTTAATTATTATGATATAATAATATC
1 ATTTTTTATTTATAATAACAAATTTTTTTATGTTACCAACTTAATTATTATGATATAATAATATC
* * * * * * * * *
5699827 TTTTATGCTTGTTCTTATCTTTTAATACATTTAAAATTATTATAATTTTTTTTTAGGTATTATAA
66 TTTTATACTTGTTATTATCTTTTAATACATTTAAAATTATCACAATTTTTATTAAAGTATAACAA
* * **
5699892 TATCTCTAACTCATTTTATGTTAAAATATACCAATTTAATGATTATTCTTTTTTTTTCTTAACAT
131 TATCTATAACTCATTTTACGTTAAAATATACCAATTTAACAATTATTCTTTTTTTTTCTTAACAT
5699957 CTTTTTTTTGTGTAGGATC
196 CTTTTTTTTGTGTAGGATC
* * * *
5699976 ATTTTTTATTTATAAT-ACTAA-TTTTTT-TGTTACCAATTTAATTATTTATGTTTTAATAATAT
1 ATTTTTTATTTATAATAACAAATTTTTTTATGTTACCAACTTAATTA-TTATGATATAATAATAT
* * *
5700038 -TTTT-TACATTTTTATTA-CTTTTTATTACATTTAAAATTATCACAATATTTTATTAAAGTGTA
65 CTTTTATAC-TTGTTATTATC-TTTTAATACATTTAAAATTATCACAAT-TTTTATTAAAGTATA
* * * *
5700100 ACGATATTTATAAC-CATTTTACGTT-AAATAATACTAATTTTACAATTATTCT
127 ACAATATCTATAACTCATTTTACGTTAAAAT-ATACCAATTTAACAATTATTCT
5700152 CACTTTTTTT
Statistics
Matches: 145, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
210 7 0.05
211 77 0.53
212 41 0.28
213 4 0.03
214 16 0.11
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (214 bp):
ATTTTTTATTTATAATAACAAATTTTTTTATGTTACCAACTTAATTATTATGATATAATAATATC
TTTTATACTTGTTATTATCTTTTAATACATTTAAAATTATCACAATTTTTATTAAAGTATAACAA
TATCTATAACTCATTTTACGTTAAAATATACCAATTTAACAATTATTCTTTTTTTTTCTTAACAT
CTTTTTTTTGTGTAGGATC
Found at i:5701129 original size:2 final size:2
Alignment explanation
Indices: 5701122--5701149 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5701112 CTATTTTCTT
5701122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5701150 CACACACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5701666 original size:18 final size:19
Alignment explanation
Indices: 5701640--5701677 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5701630 CTTTAACTTT
*
5701640 AAGATTTTC-AAGAAAATC
1 AAGAATTTCTAAGAAAATC
*
5701658 AAGAATTTCTAAGAACATC
1 AAGAATTTCTAAGAAAATC
5701677 A
1 A
5701678 TAAGATTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (19 bp):
AAGAATTTCTAAGAAAATC
Found at i:5703584 original size:13 final size:13
Alignment explanation
Indices: 5703566--5703598 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5703556 GCAAATATGT
5703566 AATAAATCATACA
1 AATAAATCATACA
*
5703579 AATAAATCATGCA
1 AATAAATCATACA
5703592 AATAAAT
1 AATAAAT
5703599 AATAAATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.61, C:0.12, G:0.03, T:0.24
Consensus pattern (13 bp):
AATAAATCATACA
Found at i:5703589 original size:33 final size:33
Alignment explanation
Indices: 5703551--5703618 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
5703541 AATAAAAAAT
** *
5703551 ATCATGCAAATATGTAATAAATCATACAAATAA
1 ATCATGCAAATAAATAATAAATCACACAAATAA
*
5703584 ATCATGCAAATAAATAATAAATCACACAATTAA
1 ATCATGCAAATAAATAATAAATCACACAAATAA
5703617 AT
1 AT
5703619 ATATAATCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.26
Consensus pattern (33 bp):
ATCATGCAAATAAATAATAAATCACACAAATAA
Found at i:5703604 original size:20 final size:20
Alignment explanation
Indices: 5703579--5703755 Score: 152
Period size: 20 Copynumber: 8.9 Consensus size: 20
5703569 AAATCATACA
5703579 AATAAATCATGCAAATAAAT
1 AATAAATCATGCAAATAAAT
** *
5703599 AATAAATCACACAATTAAAT
1 AATAAATCATGCAAATAAAT
* *
5703619 -ATATAATCATGCGAATAAAA
1 AATA-AATCATGCAAATAAAT
*
5703639 AATAAATCATGCAATTAAAT
1 AATAAATCATGCAAATAAAT
5703659 -ATATAATCATGCAAAT-AAT
1 AATA-AATCATGCAAATAAAT
** *
5703678 AAATAAATCATATAATTAAAT
1 -AATAAATCATGCAAATAAAT
5703699 -ATACAATCATGCAAAT-AAT
1 AATA-AATCATGCAAATAAAT
*
5703718 AAATAAATCATGC-AATTAA-
1 -AATAAATCATGCAAATAAAT
*
5703737 ACTAAATCCATGCAAATAA
1 AATAAAT-CATGCAAATAA
5703756 TAAATAAAAT
Statistics
Matches: 125, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
18 6 0.05
19 23 0.18
20 84 0.67
21 12 0.10
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (20 bp):
AATAAATCATGCAAATAAAT
Found at i:5703636 original size:40 final size:40
Alignment explanation
Indices: 5703583--5703763 Score: 251
Period size: 40 Copynumber: 4.5 Consensus size: 40
5703573 CATACAAATA
*
5703583 AATCATGCAAATAA-ATAATAAATCACACAATTAAATATAT
1 AATCATGCAAATAATA-AATAAATCATACAATTAAATATAT
* * *
5703623 AATCATGCGAATAAAAAATAAATCATGCAATTAAATATAT
1 AATCATGCAAATAATAAATAAATCATACAATTAAATATAT
* *
5703663 AATCATGCAAATAATAAATAAATCATATAATTAAATATAC
1 AATCATGCAAATAATAAATAAATCATACAATTAAATATAT
* *
5703703 AATCATGCAAATAATAAATAAATCATGCAATTAAA-CTA-
1 AATCATGCAAATAATAAATAAATCATACAATTAAATATAT
5703741 AATCCATGCAAATAATAAATAAA
1 AAT-CATGCAAATAATAAATAAA
5703764 ATGCAAAAAA
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
38 3 0.02
39 21 0.16
40 103 0.80
41 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (40 bp):
AATCATGCAAATAATAAATAAATCATACAATTAAATATAT
Found at i:5703775 original size:36 final size:36
Alignment explanation
Indices: 5703706--5703812 Score: 119
Period size: 35 Copynumber: 2.9 Consensus size: 36
5703696 AATATACAAT
*
5703706 CATGCAAATAATAAATAAATCATGCAATTAAACTAAATC
1 CATGCAAATAATAAATAAA--ATGCAA-AAAACTAAATC
* *
5703745 CATGCAAATAATAAATAAAATGCAAAAAACTAACTT
1 CATGCAAATAATAAATAAAATGCAAAAAACTAAATC
* *
5703781 CATG-AAAAAATGAAAT-ACATGCAAAAAACTAA
1 CATGCAAATAAT-AAATAAAATGCAAAAAACTAA
5703813 TTTCATAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
35 21 0.34
36 16 0.26
37 6 0.10
39 19 0.31
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.21
Consensus pattern (36 bp):
CATGCAAATAATAAATAAAATGCAAAAAACTAAATC
Found at i:5703790 original size:17 final size:17
Alignment explanation
Indices: 5703768--5703823 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
5703758 AATAAAATGC
*
5703768 AAAAAACTAACTTCATG
1 AAAAAACTAAATTCATG
*
5703785 AAAAAA-TGAAATACATG
1 AAAAAACT-AAATTCATG
*
5703802 CAAAAAACTAATTTCAT-
1 -AAAAAACTAAATTCATG
5703819 AAAAA
1 AAAAA
5703824 TATCATGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 6 0.19
17 13 0.41
18 12 0.38
19 1 0.03
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAAACTAAATTCATG
Found at i:5703806 original size:18 final size:17
Alignment explanation
Indices: 5703718--5703808 Score: 69
Period size: 18 Copynumber: 5.2 Consensus size: 17
5703708 TGCAAATAAT
5703718 AAATAAAT-CATGCAATTA
1 AAATAAATACATGCAA--A
* *
5703736 AACTAAATCCATGCAAA
1 AAATAAATACATGCAAA
* *
5703753 TAATAAATAAAATGCAAA
1 AAATAAAT-ACATGCAAA
* *
5703771 AAACTAACTTCATG-AAA
1 AAA-TAAATACATGCAAA
5703788 AAATGAAATACATGCAAA
1 AAAT-AAATACATGCAAA
5703806 AAA
1 AAA
5703809 CTAATTTCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 1 0.02
17 20 0.35
18 25 0.44
19 11 0.19
ACGTcount: A:0.59, C:0.13, G:0.07, T:0.21
Consensus pattern (17 bp):
AAATAAATACATGCAAA
Found at i:5705037 original size:17 final size:16
Alignment explanation
Indices: 5704997--5705040 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5704987 AACCAAAAAG
5704997 AAAATTAAAAAAAATT
1 AAAATTAAAAAAAATT
* *
5705013 AAATATTAAAAATTAGTT
1 AAA-ATTAAAAA-AAATT
5705031 AAAATTAAAA
1 AAAATTAAAA
5705041 TCAACTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AAAATTAAAAAAAATT
Found at i:5710475 original size:166 final size:166
Alignment explanation
Indices: 5710154--5710475 Score: 468
Period size: 166 Copynumber: 1.9 Consensus size: 166
5710144 AACACTAAAA
* * *
5710154 AAGGTAATATACTAAGGTAACCTGTGATTGCAAGGATAAGGCTGTGATTGATTACAAGCTTGATT
1 AAGGCAATATACTAAGGTAACCTGTGATTACAAGGATAAGGCTGTGATTGATTACAAGCTTGAGT
* * * *
5710219 GGGCACTTAGCAACCTAGGCAGCAAGGTTGTATGTTGTGATTGAGTACAAGCTTGAGAGTCATTG
66 GGGCACTGAGCAACCTAGGCAGCAAGGTTGTATGCTGTGATTGAGTACAAGCTTGAGAGGCATTA
5710284 AGACAACCTAAACCCACAAAGAGGCAATATTGAATT
131 AGACAACCTAAACCCACAAAGAGGCAATATTGAATT
* * * *
5710320 AAGGCAATATACTGAGGTAACCTAG-GATTACAAGGTTAAGGTTGTGATTGATTGCAAGCTTGAG
1 AAGGCAATATACTAAGGTAACCT-GTGATTACAAGGATAAGGCTGTGATTGATTACAAGCTTGAG
* * *
5710384 TGGGCACTGAGACAACCTAGGTAGTAAGGTTGTATGCTGTGATTGAGTACAAGCTTGAGGGGCAT
65 TGGGCACTGAG-CAACCTAGGCAGCAAGGTTGTATGCTGTGATTGAGTACAAGCTTGAGAGGCAT
* *
5710449 TAAGACTACCTAAACCCA-AGAGAGGCA
129 TAAGACAACCTAAACCCACAAAGAGGCA
5710476 TGGTTGAATG
Statistics
Matches: 138, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
166 73 0.53
167 65 0.47
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (166 bp):
AAGGCAATATACTAAGGTAACCTGTGATTACAAGGATAAGGCTGTGATTGATTACAAGCTTGAGT
GGGCACTGAGCAACCTAGGCAGCAAGGTTGTATGCTGTGATTGAGTACAAGCTTGAGAGGCATTA
AGACAACCTAAACCCACAAAGAGGCAATATTGAATT
Found at i:5711321 original size:234 final size:235
Alignment explanation
Indices: 5710902--5711330 Score: 653
Period size: 234 Copynumber: 1.8 Consensus size: 235
5710892 TTAGAGGCAA
* * * * * *
5710902 CGAGTATGATAATATGCTTATGCAAAAGTAGAACATCGAAGAAGGTAATGTACTAAGGCAACCTA
1 CGAGTATGATAATAGGCTTATACAAAAGAAGAACACCGAAGAAGGCAATATACTAAGGCAACCTA
** * *
5710967 TGATGAAGTACAAGGACTTGTGATGAAGTGCAAGGTTAAAGTTATGATTGATTGCAAGCTTAAGT
66 TGATGAAGTACAAAAACTTATGATAAAGTGCAAGGTTAAAGTTATGATTGATTGCAAGCTTAAGT
* * * *
5711032 AGGCACTGAGACAACCTAGGCATTAAGATTGTATGCTATAATTAAGTATAAGTTTGAGGGGTATT
131 AGACACTAAGACAACCTAGGCATTAAGATTGTATGCTATAATTAAGTACAAGTTTGAAGGGTATT
5711097 GAAACAACCTAGACTGACAGAAAAGCAAGGTTGAATGCAG
196 GAAACAACCTAGACTGACAGAAAAGCAAGGTTGAATGCAG
*
5711137 CGAGTATGATAATAGGCTTATACGAAAGAAGAACACCGAAGAAGGCAATATACTAAGGCAACCTA
1 CGAGTATGATAATAGGCTTATACAAAAGAAGAACACCGAAGAAGGCAATATACTAAGGCAACCTA
* * *
5711202 TGATG-AGTGCAAAAACTTATGATAAAGTGCAAGGTTAAGGTTATGATTGATTGCAAGCTTGAGT
66 TGATGAAGTACAAAAACTTATGATAAAGTGCAAGGTTAAAGTTATGATTGATTGCAAGCTTAAGT
* * * *
5711266 AGACACTAAGATAACCTAGGCGTTAAGATTGTGTGCTATAATTGAGTACAAGTTTGAAGGGTATT
131 AGACACTAAGACAACCTAGGCATTAAGATTGTATGCTATAATTAAGTACAAGTTTGAAGGGTATT
5711331 AAGACAATCT
Statistics
Matches: 172, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
234 109 0.63
235 63 0.37
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (235 bp):
CGAGTATGATAATAGGCTTATACAAAAGAAGAACACCGAAGAAGGCAATATACTAAGGCAACCTA
TGATGAAGTACAAAAACTTATGATAAAGTGCAAGGTTAAAGTTATGATTGATTGCAAGCTTAAGT
AGACACTAAGACAACCTAGGCATTAAGATTGTATGCTATAATTAAGTACAAGTTTGAAGGGTATT
GAAACAACCTAGACTGACAGAAAAGCAAGGTTGAATGCAG
Found at i:5711436 original size:58 final size:58
Alignment explanation
Indices: 5711341--5711457 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
5711331 AAGACAATCT
*
5711341 AAACCGATAGAGAGGCAATGTTGAATGCTAGGCCAAAAGTGCACTAAATCCATCAAAG
1 AAACCGATAGAGAGGCAACGTTGAATGCTAGGCCAAAAGTGCACTAAATCCATCAAAG
*
5711399 AAACTGATAGAGAGGCAACGTTGAATGCTAGGCCAAAAGTGCACTAAATCCATCAAAG
1 AAACCGATAGAGAGGCAACGTTGAATGCTAGGCCAAAAGTGCACTAAATCCATCAAAG
5711457 A
1 A
5711458 CATGAGGTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (58 bp):
AAACCGATAGAGAGGCAACGTTGAATGCTAGGCCAAAAGTGCACTAAATCCATCAAAG
Found at i:5719064 original size:14 final size:14
Alignment explanation
Indices: 5719045--5719071 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5719035 TTTAAAAATA
5719045 AAATAAATAATAAC
1 AAATAAATAATAAC
5719059 AAATAAATAATAA
1 AAATAAATAATAA
5719072 TAAAAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAATAATAAC
Found at i:5725808 original size:144 final size:142
Alignment explanation
Indices: 5725587--5725869 Score: 372
Period size: 144 Copynumber: 2.0 Consensus size: 142
5725577 CATACTTTTG
*
5725587 AAGGTGTGAAATTACAAAATACCCATAAGAGTATTTTCATAATTTAACCTTCTCAAGGTCAAAAT
1 AAGGTGTGAAATTACAAAATACCCATAAGAGTATTTTCATAATTTAACATTCTCAAGGTCAAAAT
* * *
5725652 TTCACAAAACACTCTAG-TTCATAGTTTAATATTATTTGATGATTTTTAAAATTTTAAAAACTTT
66 TTCACAAAACACTCCAGATT-ATAGTTTAATATTATTTGATAATTTTTAAAATTTTAAAAACCTT
5725716 GATTATACCTTAA
130 GATTATACCTTAA
* * * * * * * *
5725729 AAGGTGTGAAATTACAAAAATACCCTTTAAGGGTAATTTT-GTAATTTGACATTTTTAAGTTCGA
1 AAGGTGTGAAATTAC-AAAATACCC-ATAAGAGT-ATTTTCATAATTTAACATTCTCAAGGTCAA
** *
5725793 AATTTCGTAAAACACTCCAGATTATGGTTTAATATTATTTGATAATTTTTAAAATTTTAAAAACC
63 AATTTCACAAAACACTCCAGATTATAGTTTAATATTATTTGATAATTTTTAAAATTTTAAAAACC
*
5725858 TTGATTGTACCT
128 TTGATTATACCT
5725870 GTAGACACCT
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
142 15 0.12
143 9 0.07
144 90 0.74
145 7 0.06
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (142 bp):
AAGGTGTGAAATTACAAAATACCCATAAGAGTATTTTCATAATTTAACATTCTCAAGGTCAAAAT
TTCACAAAACACTCCAGATTATAGTTTAATATTATTTGATAATTTTTAAAATTTTAAAAACCTTG
ATTATACCTTAA
Found at i:5726025 original size:6 final size:6
Alignment explanation
Indices: 5726005--5726043 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
5725995 TGGGCTTTAC
*
5726005 TTTA-T TTTA-T TTTATT TTTATT TTTATT TTTATG TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
5726044 CTATGGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:5726472 original size:31 final size:31
Alignment explanation
Indices: 5726426--5726492 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
5726416 AAATTTTTAG
* *
5726426 TTTTCGATGAATTTTTTGACA-CTAGTTGAAT
1 TTTTCAATGAATTTTTAGACATC-AGTTGAAT
* *
5726457 TTTTCAATGACTTTTTAGACATCGGTTGAAT
1 TTTTCAATGAATTTTTAGACATCAGTTGAAT
5726488 TTTTC
1 TTTTC
5726493 GATAGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (31 bp):
TTTTCAATGAATTTTTAGACATCAGTTGAAT
Found at i:5727095 original size:25 final size:26
Alignment explanation
Indices: 5727051--5727114 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
5727041 TTAATTATCT
5727051 AATGATAGAA-TTTATGAAAATT-TCA
1 AATGATA-AATTTTATGAAAATTCTCA
*
5727076 AATGATAAATTTCTAT-AAAATTCTTA
1 AATGATAAATTT-TATGAAAATTCTCA
*
5727102 AATGAGAAATTTT
1 AATGATAAATTTT
5727115 GTCTAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.06
25 16 0.47
26 16 0.47
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (26 bp):
AATGATAAATTTTATGAAAATTCTCA
Found at i:5727520 original size:162 final size:164
Alignment explanation
Indices: 5727227--5727520 Score: 423
Period size: 162 Copynumber: 1.8 Consensus size: 164
5727217 ATTAAATACA
* *
5727227 AATTACCCAATGATGAGATTCTTGAAAATTTCAAATGGTAAATTGCTAAAAAAATCTCTAGGTGA
1 AATTACCCAACGATGAGATTCTTGAAAATTTCAAATGGTAAATTGCTAAAAAAATCTCAAGGTGA
* * * *
5727292 GAAATTTTCTCTAAATTTATCCTAAATGGTGGAATAATTTAAATGAAATTTCAATAAAAGTAATT
66 GAAATTTTCTCTAAATTTATCCTAAATGGTGAAAGAATTTAAATGAAATTTCAAGAAAAATAATT
5727357 GTATTCTTTTCCAAATTTGGTTGAAATATTTGAT
131 GTATTCTTTTCCAAATTTGGTTGAAATATTTGAT
* * * * * *
5727391 AATTATCCAACGATGAGATT-TTTAGAAATTTTAAATGGTAAATT-TTTAAGAAATCTCAAGGTG
1 AATTACCCAACGATGAGATTCTTGA-AAATTTCAAATGGTAAATTGCTAAAAAAATCTCAAGGTG
* * *
5727454 AGAAA-TTTCTTTAAATTTATCTTAAATGGTGAAAGAATTTAAATGAAATTTTAAGAAAAATAAT
65 AGAAATTTTCTCTAAATTTATCCTAAATGGTGAAAGAATTTAAATGAAATTTCAAGAAAAATAAT
5727518 TGT
130 TGT
5727521 CATATTATTT
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
162 55 0.48
163 23 0.20
164 36 0.32
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (164 bp):
AATTACCCAACGATGAGATTCTTGAAAATTTCAAATGGTAAATTGCTAAAAAAATCTCAAGGTGA
GAAATTTTCTCTAAATTTATCCTAAATGGTGAAAGAATTTAAATGAAATTTCAAGAAAAATAATT
GTATTCTTTTCCAAATTTGGTTGAAATATTTGAT
Found at i:5732855 original size:21 final size:21
Alignment explanation
Indices: 5732830--5732937 Score: 135
Period size: 21 Copynumber: 5.0 Consensus size: 21
5732820 TCCTGAATCC
5732830 TCAAATGAGAATCTTTGAATT
1 TCAAATGAGAATCTTTGAATT
* *
5732851 TCAAATGAAAATCTTTAAATT
1 TCAAATGAGAATCTTTGAATT
*
5732872 TCAAATGAGAATCTTTGAGTTT
1 TCAAATGAGAATCTTTGA-ATT
*
5732894 TCAAATGAGAATCTTTGATTTT
1 TCAAATGAGAATCTTTGA-ATT
* * *
5732916 TCTAGTTAGAATCTTTGAATT
1 TCAAATGAGAATCTTTGAATT
5732937 T
1 T
5732938 TTAAGTTTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
21 38 0.50
22 38 0.50
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (21 bp):
TCAAATGAGAATCTTTGAATT
Found at i:5732877 original size:42 final size:43
Alignment explanation
Indices: 5732830--5732937 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
5732820 TCCTGAATCC
5732830 TCAAATGAGAATCTTTGAATTTCAAATGAAAATCTTT-AAATT
1 TCAAATGAGAATCTTTGAATTTCAAATGAAAATCTTTGAAATT
* * **
5732872 TCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTTGATTTT
1 TCAAATGAGAATCTTTGA-ATTTCAAATGAAAATCTTTGAAATT
* * *
5732916 TCTAGTTAGAATCTTTGAATTT
1 TCAAATGAGAATCTTTGAATTT
5732938 TTAAGTTTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 18 0.32
43 20 0.36
44 18 0.32
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (43 bp):
TCAAATGAGAATCTTTGAATTTCAAATGAAAATCTTTGAAATT
Found at i:5732938 original size:22 final size:22
Alignment explanation
Indices: 5732830--5732938 Score: 141
Period size: 22 Copynumber: 5.0 Consensus size: 22
5732820 TCCTGAATCC
5732830 TCAAATGAGAATCTTTGAA-TT
1 TCAAATGAGAATCTTTGAATTT
* *
5732851 TCAAATGAAAATCTTT-AAATT
1 TCAAATGAGAATCTTTGAATTT
*
5732872 TCAAATGAGAATCTTTGAGTTT
1 TCAAATGAGAATCTTTGAATTT
*
5732894 TCAAATGAGAATCTTTGATTTT
1 TCAAATGAGAATCTTTGAATTT
* * *
5732916 TCTAGTTAGAATCTTTGAATTT
1 TCAAATGAGAATCTTTGAATTT
5732938 T
1 T
5732939 TAAGTTTTCA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
20 2 0.03
21 32 0.42
22 43 0.56
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (22 bp):
TCAAATGAGAATCTTTGAATTT
Found at i:5733659 original size:41 final size:41
Alignment explanation
Indices: 5733504--5733919 Score: 245
Period size: 42 Copynumber: 10.0 Consensus size: 41
5733494 GATGGTCGAT
* ** * *
5733504 GAGCCTTTTACTTTTTTAAAATTGTTGAGCCTCTACTTT-GAG
1 GAGCCTTTTA-TTTTTCAAAATCATTGAGCCTCT-GTTTAGAA
*
5733546 GAG-C-TTTA-TTTTCAAAGGTCATTGAGCCTCTGTTT-GAA
1 GAGCCTTTTATTTTTCAAA-ATCATTGAGCCTCTGTTTAGAA
** *
5733584 GGAGATTTTTATTTTTCAAAAATCGTTGAGCCTCTGTTTAGAA
1 -GAGCCTTTTATTTTTC-AAAATCATTGAGCCTCTGTTTAGAA
* *
5733627 GAGCCTTTTATTTTTCAAAATCATTGAGCCTCTATTTAGAT
1 GAGCCTTTTATTTTTCAAAATCATTGAGCCTCTGTTTAGAA
* *
5733668 GAGCCTTTTATTTTTAAAAAGTCATTGAGCCTCTATTTAGATA
1 GAGCCTTTTATTTTTCAAAA-TCATTGAGCCTCTGTTTAGA-A
* * * *
5733711 -AGCCTTTTATTTTTTGAAGA-CGTTGAGCCTCTGCTTA-AA
1 GAGCCTTTTA-TTTTTCAAAATCATTGAGCCTCTGTTTAGAA
** * ** * * * * *
5733750 TGAGCCTTTTATTTTTTGAAGTTGTTGTGTCTCTATTTGGAG
1 -GAGCCTTTTATTTTTCAAAATCATTGAGCCTCTGTTTAGAA
* * ** *
5733792 GAGCATTTTATTTTTCTCAAAGTCATTGAATCTCTGTTTAGAG
1 GAGCCTTTTA-TTTT-TCAAAATCATTGAGCCTCTGTTTAGAA
* * * ** * *
5733835 GAGCATTTATTTTTTTCAAAGTTGTTGAGTCTCTATTTAGAA
1 GAGCCTTT-TATTTTTCAAAATCATTGAGCCTCTGTTTAGAA
* * * * *
5733877 GAGCTTTGTTTACTTTTTTAAAGTCATGGAGGCTCTGTTTAGA
1 GAGC-CT-TTTA-TTTTTCAAAATCATTGAGCCTCTGTTTAGA
5733920 GGAGTTTTTA
Statistics
Matches: 299, Mismatches: 55, Indels: 38
0.76 0.14 0.10
Matches are distributed among these distances:
38 12 0.04
39 15 0.05
40 11 0.04
41 89 0.30
42 98 0.33
43 47 0.16
44 27 0.09
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (41 bp):
GAGCCTTTTATTTTTCAAAATCATTGAGCCTCTGTTTAGAA
Found at i:5733659 original size:83 final size:83
Alignment explanation
Indices: 5733509--5733930 Score: 328
Period size: 83 Copynumber: 5.1 Consensus size: 83
5733499 TCGATGAGCC
* *
5733509 TTTTACTTTTTTAAAATTGTTGAGCCTCTACTTT-GAGGAG-C-TTTA--TTTTCAAAGGTCATT
1 TTTTA-TTTTTAAAAATTGTTGAGCCTCTA-TTTAGAAGAGCCTTTTATTTTTTCAAA-GTCATT
5733569 GAGCCTCTGTTT-GAAGGAGAT
63 GAGCCTCTGTTTAG-AGGAGAT
* * *
5733590 TTTTATTTTTCAAAAATCGTTGAGCCTCTGTTTAGAAGAGCCTTTTA-TTTTTCAAAATCATTGA
1 TTTTATTTTT-AAAAATTGTTGAGCCTCTATTTAGAAGAGCCTTTTATTTTTTCAAAGTCATTGA
* * **
5733654 GCCTCTATTTAGATGAGCC
65 GCCTCTGTTTAGAGGAGAT
** * * *
5733673 TTTTATTTTTAAAAAGTCATTGAGCCTCTATTTAGATA-AGCCTTTTATTTTTT-GAAGACGTTG
1 TTTTATTTTTAAAAA-TTGTTGAGCCTCTATTTAGA-AGAGCCTTTTATTTTTTCAAAGTCATTG
* * * **
5733736 AGCCTCTGCTTAAATGAGCC
64 AGCCTCTGTTTAGAGGAGAT
** * * * * * *
5733756 TTTTATTTTTTGAAGTTGTTGTGTCTCTATTTGGAGGAGCATTTTATTTTTCTCAAAGTCATTGA
1 TTTTATTTTTAAAAATTGTTGAGCCTCTATTTAGAAGAGCCTTTTATTTTT-TCAAAGTCATTGA
**
5733821 ATCTCTGTTTAGAGGAGCAT
65 GCCTCTGTTTAGAGGAG-AT
* * * *
5733841 TTATT-TTTTTCAAAGTTGTTGAGTCTCTATTTAGAAGAGCTTTGTTTACTTTTTT-AAAGTCAT
1 TT-TTATTTTTAAAAATTGTTGAGCCTCTATTTAGAAGAGC-CT-TTTA-TTTTTTCAAAGTCAT
* *
5733904 GGAGGCTCTGTTTAGAGGAG-T
62 TGAGCCTCTGTTTAGAGGAGAT
5733925 TTTTAT
1 TTTTAT
5733931 GTTATTCGAG
Statistics
Matches: 276, Mismatches: 47, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
80 8 0.03
81 26 0.09
82 34 0.12
83 99 0.36
84 39 0.14
85 32 0.12
86 28 0.10
87 5 0.02
88 5 0.02
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (83 bp):
TTTTATTTTTAAAAATTGTTGAGCCTCTATTTAGAAGAGCCTTTTATTTTTTCAAAGTCATTGAG
CCTCTGTTTAGAGGAGAT
Found at i:5733868 original size:42 final size:43
Alignment explanation
Indices: 5733590--5733880 Score: 168
Period size: 41 Copynumber: 7.0 Consensus size: 43
5733580 TGAAGGAGAT
* * * * * * *
5733590 TTTTATTTTTC-AAAAATCGTTGAGCCTCTGTTTAGAAGAGCC
1 TTTTATTTTTCTCAAAGTTGTTGAGTCTCTATTTAGAGGAGCA
* ** * * *
5733632 TTTTA-TTTT-TCAAAATCATTGAGCCTCTATTTAGATGAGCC
1 TTTTATTTTTCTCAAAGTTGTTGAGTCTCTATTTAGAGGAGCA
** ** * ** *
5733673 TTTTATTTTT-AAAAAGTCATTGAGCCTCTATTTAGATAAGCC
1 TTTTATTTTTCTCAAAGTTGTTGAGTCTCTATTTAGAGGAGCA
* ** * ** * * *
5733715 TTTTATTTTT-T-GAAGACGTTGAGCCTCTGCTTAAATGAGCC
1 TTTTATTTTTCTCAAAGTTGTTGAGTCTCTATTTAGAGGAGCA
* * *
5733756 TTTTATTTTT-T-GAAGTTGTTGTGTCTCTATTTGGAGGAGCA
1 TTTTATTTTTCTCAAAGTTGTTGAGTCTCTATTTAGAGGAGCA
** * *
5733797 TTTTATTTTTCTCAAAGTCATTGAATCTCTGTTTAGAGGAGCA
1 TTTTATTTTTCTCAAAGTTGTTGAGTCTCTATTTAGAGGAGCA
* *
5733840 -TTTATTTTTTTCAAAGTTGTTGAGTCTCTATTTAGAAGAGC
1 TTTTATTTTTCTCAAAGTTGTTGAGTCTCTATTTAGAGGAGC
5733881 TTTGTTTACT
Statistics
Matches: 206, Mismatches: 39, Indels: 8
0.81 0.15 0.03
Matches are distributed among these distances:
41 100 0.49
42 83 0.40
43 23 0.11
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (43 bp):
TTTTATTTTTCTCAAAGTTGTTGAGTCTCTATTTAGAGGAGCA
Found at i:5743975 original size:222 final size:228
Alignment explanation
Indices: 5743582--5744800 Score: 1025
Period size: 238 Copynumber: 5.2 Consensus size: 228
5743572 TCTAAGAGCA
* * * * *
5743582 AATTATTGAAGGCATTTTTTTGA-AAAAAATACCTTCAATAAATT-TCTTTT-AAAATT-TTTTT
1 AATTATTAAAGGCA-TTTCTTGAGAAAAAACACCTTGAATAAATTCT-TTTTAAAAATTGTTATT
* ** * * * **
5743643 AAAGGCGTCTTCTAGTAGAAAACCCCTTTAATA-TTCTGCTACTAAATTGCAAGAAAGTTAGTGA
64 AAAGGCAT-TTCTAG-A-AAAATGCCTTTAATATTTC-ACTACAAAATTGTAAGATGGTTAGTGA
* * * * *
5743707 AAGCGTTTATTCCAGAAAATTACCTTCACTAATTCATTCCAATTTTTGAAGGAATTTATTGAAGG
125 AGGCATTTATTCCAGAAAAATACCTTCACTAATTCATTCTAATTTTTGAAAGAATTTATTGAAGG
*
5743772 TGTTTTTTAC-TAAATACGCCTTCAATAATTTTTGTATAG
190 TGTTTTTTACAT-AATACGCCTTCAATAATTTTTGTACAG
** *
5743811 AATTATTAAAGGTGTTTCTTGAGAAAAAACACCTTGAATAAATTCTTTTTAAAAATTG-T-TT-G
1 AATTATTAAAGGCATTTCTTGAGAAAAAACACCTTGAATAAATTCTTTTTAAAAATTGTTATTAA
* * * * * *
5743873 A-G-ATTACTAG-AAAATGCCTTCAATATTTCACTAGAAAATTGTAAGACGGTTAATGAAGGCGT
66 AGGCATTTCTAGAAAAATGCCTTTAATATTTCACTACAAAATTGTAAGATGGTTAGTGAAGGCAT
* * *
5743935 TTATTCTAGAAAAATACCTTCATTAATTCATTTTAATTTTTGAAAGAATTTATTGAAGGTGTTTT
131 TTATTCCAGAAAAATACCTTCACTAATTCATTCTAATTTTTGAAAGAATTTATTGAAGGTGTTTT
* * * *
5744000 TTGCATGATACGCCTTCAAAAATTTTTGTACAA
196 TTACATAATACGCCTTCAATAATTTTTGTACAG
* * * * *
5744033 AATTATTGAAGGCATTTCTTAAGAGAAAACACCTTGAATAAATTCCTTTTAAAATTTGTTTATAT
1 AATTATTAAAGGCATTTCTTGAGAAAAAACACCTTGAATAAATTCTTTTTAAAAATTG------T
* *
5744098 TATTAAAGGCATCTTCTAGTAAAAAATGCCTTTAATATTTCACTACTAAATTGCAAGATGGTTAG
60 TATTAAAGGCAT-TTCTAG--AAAAATGCCTTTAATATTTCACTACAAAATTGTAAGATGGTTAG
* * * * **
5744163 TGAAGGCATTTATTCTAGAAAAACACTTTTACTAATTGGTTCTAATTTTTGAAAGAATTTATTGA
122 TGAAGGCATTTATTCCAGAAAAATACCTTCACTAATTCATTCTAATTTTTGAAAGAATTTATTGA
* * * * *
5744228 AGGCGTTTTTTGCATTATACGCCTTAAATAATTTTTTTACAG
187 AGGTGTTTTTTACATAATACGCCTTCAATAATTTTTGTACAG
* ** * * *
5744270 AATTATTAAAGGCATTTTTTGAGAAAAAATGCTTTCAATAATTTCTTTTTAAAAATTTTTTTGGT
1 AATTATTAAAGGCATTTCTTGAGAAAAAACACCTTGAATAAATTCTTTTTAAAAA-----TT-G-
5744335 TTATTAAAGGCATTTTCTAGTAAAAAATGCCTTTAATA-TTCTACTACTAAAATT-TAAGATGGT
59 TTATTAAAGGCA-TTTCTAG--AAAAATGCCTTTAATATTTC-ACTAC-AAAATTGTAAGATGGT
* * * * * * *
5744398 TATTAAAGGCATTTATTCCACAAAAATGCCTTCACTAATCCA-TATAGATTTTTGAAGGAATTTA
119 TAGTGAAGGCATTTATTCCAGAAAAATACCTTCACTAATTCATTCTA-ATTTTTGAAAGAATTTA
* ** * * *
5744462 TTGAAGGTGTTTCTTACGGAATACGCCTTCGATAATTTTTGTAGAT
183 TTGAAGGTGTTTTTTACATAATACGCCTTCAATAATTTTTGTACAG
* * *** * * *
5744508 AATTATTGAAGGTATTTCTTGAGAAAAAATGTCTTTAATAATTTTCTTTTAAAAATTATTTGGGA
1 AATTATTAAAGGCATTTCTTGAGAAAAAACACCTTGAATAA-ATTCTTTTTAAAA--A-TT--G-
* * * * *
5744573 TTAATAAAGGCATCTTATAGTAGAAAATACCTTCAATATTCCACTAACAAAATTGTAAGATGGTT
59 TTATTAAAGGCAT-TTCTAG-A-AAAATGCCTTTAATATTTCACT-ACAAAATTGTAAGATGGTT
* ** * * *
5744638 AGTCAAGGCATTTATTCCAGAAAAATGGCTTTACTAATTCGTTCTAATTTTTGAAGGAATTTATT
120 AGTGAAGGCATTTATTCCAGAAAAATACCTTCACTAATTCATTCTAATTTTTGAAAGAATTTATT
* * * * *
5744703 GAATGTATTTTTTGC-TGAATATGCCTTCAATTATTTTTGTACAG
185 GAAGGTGTTTTTTACAT-AATACGCCTTCAATAATTTTTGTACAG
* * * * *
5744747 AATTATTGAAGGCATTTTTTGA-AAACAAATACCTTTAAT-AATTTTTTTTAAAAA
1 AATTATTAAAGGCATTTCTTGAGAAA-AAACACCTTGAATAAATTCTTTTTAAAAA
5744801 ATTATTTTGG
Statistics
Matches: 810, Mismatches: 137, Indels: 80
0.79 0.13 0.08
Matches are distributed among these distances:
222 173 0.21
223 4 0.00
225 5 0.01
226 1 0.00
227 1 0.00
228 8 0.01
229 37 0.05
230 10 0.01
231 1 0.00
232 1 0.00
233 2 0.00
234 5 0.01
235 1 0.00
237 195 0.24
238 210 0.26
239 149 0.18
240 3 0.00
241 1 0.00
242 2 0.00
243 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (228 bp):
AATTATTAAAGGCATTTCTTGAGAAAAAACACCTTGAATAAATTCTTTTTAAAAATTGTTATTAA
AGGCATTTCTAGAAAAATGCCTTTAATATTTCACTACAAAATTGTAAGATGGTTAGTGAAGGCAT
TTATTCCAGAAAAATACCTTCACTAATTCATTCTAATTTTTGAAAGAATTTATTGAAGGTGTTTT
TTACATAATACGCCTTCAATAATTTTTGTACAG
Found at i:5744164 original size:459 final size:469
Alignment explanation
Indices: 5743641--5744800 Score: 1294
Period size: 459 Copynumber: 2.5 Consensus size: 469
5743631 TAAAATTTTT
* ** * **
5743641 TTAAAGGCGTCTTCTAGTAGAAAACCCCTTTAATA-TTCTGCTACTAAATTGCAAGAAAGTTAGT
1 TTAAAGGCATCTTCTAGTAGAAAATACCTTTAATATTTC-ACTACTAAATTGCAAGATGGTTAGT
* * * * * *
5743705 GAAAGCGTTTATTCCAGAAAATTACCTTCACTAATTCATTCCAATTTTTGAAGGAATTTATTGAA
65 GAAGGCATTTATTCCAGAAAAATACCTTTACTAATTCGTTCTAATTTTTGAAGGAATTTATTGAA
* * ** *
5743770 GGTGTTTTTTACTAAATACGCCTTCAATAATTTTTGTATAGAATTATTAAAGGTGTTTCTTGAGA
130 GGTGTTTTTTGCTAAATACGCCTTCAATAATTTTTGTACAGAATTATTAAAGGCATTTTTTGAGA
* * *
5743835 AAAAACACCTTGAATAAATTCTTTTTAAAAA-TT-G-T-TT-GA-G-A-TTACTAG-AAAATGCC
195 AAAAATACCTTCAATAAATTCTTTTTAAAAATTTGGTTATTAAAGGCATTTACTAGAAAAATGCC
* * * *
5743891 TTCAATATT-TCACTA-GAAAATTGTAAGACGGTTAATGAAGGCGTTTATTCTAGAAAAATACCT
260 TTCAATATTCT-ACTACGAAAATT-TAAGACGGTTAATAAAGGCATTTATTCCACAAAAATACCT
* * * * * *
5743954 TCATTAATTCATTTTA-ATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATG-ATACGCCTTC
323 TCACTAATCCA-TATAGATTTTTGAAAGAATTTATTGAAGGTGTTTCTTAC-GGAATACGCCTTC
*
5744017 AAAAATTTTTGTACAAAATTATTGAAGGCATTTCTTAAGAGAAAACACCTTGAATAAATTCCTTT
386 AAAAATTTTTGTACAAAATTATTGAAGGCATTTCTTAAGAAAAAACACCTTGAATAAATTCCTTT
* * *
5744082 TAAAATTTGTTT-ATATTA
451 TAAAAATTATTTGAGATTA
* *
5744100 TTAAAGGCATCTTCTAGTAAAAAATGCCTTTAATATTTCACTACTAAATTGCAAGATGGTTAGTG
1 TTAAAGGCATCTTCTAGTAGAAAATACCTTTAATATTTCACTACTAAATTGCAAGATGGTTAGTG
* * * * *
5744165 AAGGCATTTATTCTAGAAAAACACTTTTACTAATTGGTTCTAATTTTTGAAAGAATTTATTGAAG
66 AAGGCATTTATTCCAGAAAAATACCTTTACTAATTCGTTCTAATTTTTGAAGGAATTTATTGAAG
* * * *
5744230 GCGTTTTTTGC-ATTATACGCCTTAAATAATTTTTTTACAGAATTATTAAAGGCATTTTTTGAGA
131 GTGTTTTTTGCTA-AATACGCCTTCAATAATTTTTGTACAGAATTATTAAAGGCATTTTTTGAGA
* * * *
5744294 AAAAATGCTTTCAATAATTTCTTTTTAAAAATTTTTTTGGTTTATTAAAGGCATTTTCTAGTAAA
195 AAAAATACCTTCAATAAATTCTTTTTAAAAA----TTTGG-TTATTAAAGGCATTTACTAG--AA
* * * *
5744359 AAATGCCTTTAATATTCTACTACTAAAATTTAAGATGGTTATTAAAGGCATTTATTCCACAAAAA
253 AAATGCCTTCAATATTCTACTACGAAAATTTAAGACGGTTAATAAAGGCATTTATTCCACAAAAA
* *
5744424 TGCCTTCACTAATCCATATAGATTTTTGAAGGAATTTATTGAAGGTGTTTCTTACGGAATACGCC
318 TACCTTCACTAATCCATATAGATTTTTGAAAGAATTTATTGAAGGTGTTTCTTACGGAATACGCC
* * * * * * *** * * *
5744489 TTCGATAATTTTTGTAGATAATTATTGAAGGTATTTCTTGAGAAAAAATGTCTTTAATAATTTTC
383 TTCAAAAATTTTTGTACAAAATTATTGAAGGCATTTCTTAAGAAAAAACACCTTGAATAAATTCC
*
5744554 TTTTAAAAATTATTTGGGATTA
448 TTTTAAAAATTATTTGAGATTA
* * * * * *
5744576 ATAAAGGCATCTTATAGTAGAAAATACCTTCAATATTCCACTAACAAAATTGTAAGATGGTTAGT
1 TTAAAGGCATCTTCTAGTAGAAAATACCTTTAATATTTCACT-ACTAAATTGCAAGATGGTTAGT
* **
5744641 CAAGGCATTTATTCCAGAAAAATGGCTTTACTAATTCGTTCTAATTTTTGAAGGAATTTATTGAA
65 GAAGGCATTTATTCCAGAAAAATACCTTTACTAATTCGTTCTAATTTTTGAAGGAATTTATTGAA
* * * * * *
5744706 TGTATTTTTTGCTGAATATGCCTTCAATTATTTTTGTACAGAATTATTGAAGGCATTTTTTGA-A
130 GGTGTTTTTTGCTAAATACGCCTTCAATAATTTTTGTACAGAATTATTAAAGGCATTTTTTGAGA
* *
5744770 AACAAATACCTTTAAT-AATTTTTTTTAAAAA
195 AA-AAATACCTTCAATAAATTCTTTTTAAAAA
5744801 ATTATTTTGG
Statistics
Matches: 577, Mismatches: 98, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
458 1 0.00
459 187 0.32
460 3 0.01
464 2 0.00
465 1 0.00
467 1 0.00
468 2 0.00
469 1 0.00
470 1 0.00
471 1 0.00
472 6 0.01
474 4 0.01
475 165 0.29
476 63 0.11
477 139 0.24
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (469 bp):
TTAAAGGCATCTTCTAGTAGAAAATACCTTTAATATTTCACTACTAAATTGCAAGATGGTTAGTG
AAGGCATTTATTCCAGAAAAATACCTTTACTAATTCGTTCTAATTTTTGAAGGAATTTATTGAAG
GTGTTTTTTGCTAAATACGCCTTCAATAATTTTTGTACAGAATTATTAAAGGCATTTTTTGAGAA
AAAATACCTTCAATAAATTCTTTTTAAAAATTTGGTTATTAAAGGCATTTACTAGAAAAATGCCT
TCAATATTCTACTACGAAAATTTAAGACGGTTAATAAAGGCATTTATTCCACAAAAATACCTTCA
CTAATCCATATAGATTTTTGAAAGAATTTATTGAAGGTGTTTCTTACGGAATACGCCTTCAAAAA
TTTTTGTACAAAATTATTGAAGGCATTTCTTAAGAAAAAACACCTTGAATAAATTCCTTTTAAAA
ATTATTTGAGATTA
Found at i:5744386 original size:63 final size:62
Alignment explanation
Indices: 5744272--5744411 Score: 137
Period size: 63 Copynumber: 2.2 Consensus size: 62
5744262 TTTTACAGAA
* ** ***
5744272 TTATTAAAGGCATTTTTTGAGAAAAAATGCTTTCAATAATTTCTTTTTAAAAATTT-TTTTGG
1 TTATTAAAGGCATTTTCTGAGAAAAAATGCTTTCAATAATTTCTTACT-AAAATTTAAGATGG
5744334 TTTATTAAAGGCATTTTCT-AGTAAAAAATGCCTTT-AAT-A-TTCTACTACTAAAATTTAAGAT
1 -TTATTAAAGGCATTTTCTGAG-AAAAAATG-CTTTCAATAATTTCT--TACTAAAATTTAAGAT
5744395 GG
61 GG
5744397 TTATTAAAGGCATTT
1 TTATTAAAGGCATTT
5744412 ATTCCACAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
61 4 0.06
62 25 0.38
63 33 0.50
64 4 0.06
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (62 bp):
TTATTAAAGGCATTTTCTGAGAAAAAATGCTTTCAATAATTTCTTACTAAAATTTAAGATGG
Found at i:5744741 original size:239 final size:239
Alignment explanation
Indices: 5743883--5744852 Score: 1082
Period size: 238 Copynumber: 4.1 Consensus size: 239
5743873 AGATTACTAG
* * * * * *
5743883 AAAATGCCTTCAATATTTCACTAGAAAATTGTAAGACGGTTAATGAAGGCGTTTATTCTAGAAAA
1 AAAATGCCTTCAATATTCCACTACAAAATTGTAAGATGGTTAGTGAAGGCATTTATTCCAGAAAA
* * * *
5743948 ATACCTTCATTAATTCATTTTAATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATG-ATACG
66 ATGCCTTCACTAATTCGTTCTAATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATGAATACG
* * * * * * *
5744012 CCTTCAAAAATTTTTGTACAAAATTATTGAAGGCATTTCTTAAGAGAAAACACCTTGAATAAATT
131 CCTTCAATAATTTTTGTACAGAATTATTGAAGGCATTTCTTGAGAAAAAATACCTTTAATAATTT
* **
5744077 CCTTTT-AAAATT-TGTTTATATTATTAAAGGCATCTTCTAGTAA
196 TCTTTTAAAAATTAT-TTTGGATTATTAAAGGCATCTTCTAGTAA
* * * * *
5744120 AAAATGCCTTTAATATTTCACTACTAAATTGCAAGATGGTTAGTGAAGGCATTTATTCTAGAAAA
1 AAAATGCCTTCAATATTCCACTACAAAATTGTAAGATGGTTAGTGAAGGCATTTATTCCAGAAAA
** * * * * *
5744185 ACACTTTTACTAATTGGTTCTAATTTTTGAAAGAATTTATTGAAGGCGTTTTTTGCAT-TATACG
66 ATGCCTTCACTAATTCGTTCTAATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATGAATACG
* * * * *
5744249 CCTTAAATAATTTTTTTACAGAATTATTAAAGGCATTTTTTGAGAAAAAAT-GCTTTCAATAA-T
131 CCTTCAATAATTTTTGTACAGAATTATTGAAGGCATTTCTTGAGAAAAAATACCTTT-AATAATT
* * *
5744312 TTCTTTTTAAAAATTTTTTTGGTTTATTAAAGGCATTTTCTAGTAA
195 TTC-TTTTAAAAATTATTTTGGATTATTAAAGGCATCTTCTAGTAA
* * * * *
5744358 AAAATGCCTTTAATATTCTACTACTAAAATT-TAAGATGGTTATTAAAGGCATTTATTCCACAAA
1 AAAATGCCTTCAATATTCCACTAC-AAAATTGTAAGATGGTTAGTGAAGGCATTTATTCCAGAAA
** * * * * *
5744422 AATGCCTTCACTAA-TCCATATAGATTTTTGAAGGAATTTATTGAAGGTGTTTCTTAC-GGAATA
65 AATGCCTTCACTAATTCGTTCTA-ATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATGAATA
* * * * **
5744485 CGCCTTCGATAATTTTTGTAGATAATTATTGAAGGTATTTCTTGAGAAAAAATGTCTTTAATAAT
129 CGCCTTCAATAATTTTTGTACAGAATTATTGAAGGCATTTCTTGAGAAAAAATACCTTTAATAAT
* * * *
5744550 TTTCTTTTAAAAATTATTTGGGATTAATAAAGGCATCTTATAGTAG
194 TTTCTTTTAAAAATTATTTTGGATTATTAAAGGCATCTTCTAGTAA
* *
5744596 AAAATACCTTCAATATTCCACTAACAAAATTGTAAGATGGTTAGTCAAGGCATTTATTCCAGAAA
1 AAAATGCCTTCAATATTCCACT-ACAAAATTGTAAGATGGTTAGTGAAGGCATTTATTCCAGAAA
* * * * * *
5744661 AATGGCTTTACTAATTCGTTCTAATTTTTGAAGGAATTTATTGAATGTATTTTTTGC-TGAATAT
65 AATGCCTTCACTAATTCGTTCTAATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATGAATAC
* *
5744725 GCCTTCAATTATTTTTGTACAGAATTATTGAAGGCATTTTTTGA-AAACAAATACCTTTAATAAT
130 GCCTTCAATAATTTTTGTACAGAATTATTGAAGGCATTTCTTGAGAAA-AAATACCTTTAATAAT
** * * *
5744789 TTT-TTTTAAAAAATTATTTTGGATTATTAAAGGTGTCTTCCAATGA
194 TTTCTTTT-AAAAATTATTTTGGATTATTAAAGGCATCTTCTAGTAA
*
5744835 AAAATGCCTTTAATATTC
1 AAAATGCCTTCAATATTC
5744853 ATTTTAATTT
Statistics
Matches: 613, Mismatches: 105, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
236 6 0.01
237 168 0.27
238 241 0.39
239 193 0.31
240 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (239 bp):
AAAATGCCTTCAATATTCCACTACAAAATTGTAAGATGGTTAGTGAAGGCATTTATTCCAGAAAA
ATGCCTTCACTAATTCGTTCTAATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATGAATACG
CCTTCAATAATTTTTGTACAGAATTATTGAAGGCATTTCTTGAGAAAAAATACCTTTAATAATTT
TCTTTTAAAAATTATTTTGGATTATTAAAGGCATCTTCTAGTAA
Found at i:5745565 original size:28 final size:28
Alignment explanation
Indices: 5745533--5745861 Score: 477
Period size: 28 Copynumber: 11.9 Consensus size: 28
5745523 ATTATGGTTA
5745533 GCTGAATGGTATTGTGTGATATTGTTTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
5745561 GCTGAATGGTATTGTGTGATATTGTTTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
5745589 GCTGAATGGTATTGTGTGATATTGTTTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
* *
5745617 ACTGAATAGTATTGTGTGATATTG-TTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
5745644 GCTGAATGGTATTGTGTGATATTGTTTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
* *
5745672 GTTGAATAGTATTGTGTGATATTGTTTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
* *
5745700 ACTGAATGGTATTGTGTGATAGTG-TTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
*
5745727 GCTGAATGGTATTATGTGATATTGTTTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
* *
5745755 GCTAAATAGTATTGTGTGATATTGTTTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
* *
5745783 GCTAAATAGTATTGTGTGATATTGTTTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
* * *
5745811 GTTGAATAGTATTGTGTGATATT-ATTT
1 GCTGAATGGTATTGTGTGATATTGTTTT
* *
5745838 G-TCAAATGGTATTGTATGATATTG
1 GCT-GAATGGTATTGTGTGATATTG
5745862 GTATGTTAAA
Statistics
Matches: 275, Mismatches: 22, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
26 1 0.00
27 70 0.25
28 204 0.74
ACGTcount: A:0.22, C:0.03, G:0.26, T:0.49
Consensus pattern (28 bp):
GCTGAATGGTATTGTGTGATATTGTTTT
Found at i:5745671 original size:111 final size:111
Alignment explanation
Indices: 5745533--5745833 Score: 478
Period size: 111 Copynumber: 2.7 Consensus size: 111
5745523 ATTATGGTTA
*
5745533 GCTGAATGGTATTGTGTGATATTGTTTTGCTGAATGGTATTGTGTGATATTGTTTTGCTGAATGG
1 GCTGAATGGTATTGTGTGATATTGTTTTGCTGAATAGTATTGTGTGATATTGTTTTGCTGAATGG
*
5745598 TATTGTGTGATATTGTTTTACTGAATAGTATTGTGTGATATTG-TTT
66 TATTGTGTGATATTG-TTTACTGAATAGTATTATGTGATATTGTTTT
* *
5745644 GCTGAATGGTATTGTGTGATATTGTTTTGTTGAATAGTATTGTGTGATATTGTTTTACTGAATGG
1 GCTGAATGGTATTGTGTGATATTGTTTTGCTGAATAGTATTGTGTGATATTGTTTTGCTGAATGG
* * *
5745709 TATTGTGTGATAGTGTTTGCTGAATGGTATTATGTGATATTGTTTT
66 TATTGTGTGATATTGTTTACTGAATAGTATTATGTGATATTGTTTT
* * * * *
5745755 GCTAAATAGTATTGTGTGATATTGTTTTGCTAAATAGTATTGTGTGATATTGTTTTGTTGAATAG
1 GCTGAATGGTATTGTGTGATATTGTTTTGCTGAATAGTATTGTGTGATATTGTTTTGCTGAATGG
5745820 TATTGTGTGATATT
66 TATTGTGTGATATT
5745834 ATTTGTCAAA
Statistics
Matches: 174, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
110 24 0.14
111 150 0.86
ACGTcount: A:0.22, C:0.03, G:0.26, T:0.50
Consensus pattern (111 bp):
GCTGAATGGTATTGTGTGATATTGTTTTGCTGAATAGTATTGTGTGATATTGTTTTGCTGAATGG
TATTGTGTGATATTGTTTACTGAATAGTATTATGTGATATTGTTTT
Found at i:5745678 original size:83 final size:84
Alignment explanation
Indices: 5745534--5745861 Score: 484
Period size: 83 Copynumber: 3.9 Consensus size: 84
5745524 TTATGGTTAG
* * *
5745534 CTGAATGGTATTGTGTGATATTGTTTTGCTGAATGGTATTGTGTGATATTGTTTTGCTGAATGGT
1 CTGAATAGTATTGTGTGATATTGTTTTGCTGAATGGTATTGTGTGATATTGTTTTGCTAAATAGT
5745599 ATTGTGTGATATTGTTTTA
66 ATTGTGTGATATTGTTTTA
* *
5745618 CTGAATAGTATTGTGTGATATTG-TTTGCTGAATGGTATTGTGTGATATTGTTTTGTTGAATAGT
1 CTGAATAGTATTGTGTGATATTGTTTTGCTGAATGGTATTGTGTGATATTGTTTTGCTAAATAGT
5745682 ATTGTGTGATATTGTTTTA
66 ATTGTGTGATATTGTTTTA
* * *
5745701 CTGAATGGTATTGTGTGATAGTG-TTTGCTGAATGGTATTATGTGATATTGTTTTGCTAAATAGT
1 CTGAATAGTATTGTGTGATATTGTTTTGCTGAATGGTATTGTGTGATATTGTTTTGCTAAATAGT
*
5745765 ATTGTGTGATATTGTTTTG
66 ATTGTGTGATATTGTTTTA
* * * * *
5745784 CTAAATAGTATTGTGTGATATTGTTTTGTTGAATAGTATTGTGTGATATT-ATTTG-TCAAATGG
1 CTGAATAGTATTGTGTGATATTGTTTTGCTGAATGGTATTGTGTGATATTGTTTTGCT-AAATAG
*
5745847 TATTGTATGATATTG
65 TATTGTGTGATATTG
5745862 GTATGTTAAA
Statistics
Matches: 224, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
82 1 0.00
83 178 0.79
84 45 0.20
ACGTcount: A:0.22, C:0.03, G:0.25, T:0.49
Consensus pattern (84 bp):
CTGAATAGTATTGTGTGATATTGTTTTGCTGAATGGTATTGTGTGATATTGTTTTGCTAAATAGT
ATTGTGTGATATTGTTTTA
Found at i:5748594 original size:19 final size:19
Alignment explanation
Indices: 5748572--5748608 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5748562 CGGGAGATAG
5748572 TTTTATATGATTTTATTAT
1 TTTTATATGATTTTATTAT
5748591 TTTTATATGATTTTATTA
1 TTTTATATGATTTTATTA
5748609 CCACACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTATATGATTTTATTAT
Found at i:5753088 original size:17 final size:16
Alignment explanation
Indices: 5753065--5753112 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
5753055 TACACGATAA
5753065 ATTATTTATATATTTT
1 ATTATTTATATATTTT
* *
5753081 ACTTATTTATTTATTAT
1 A-TTATTTATATATTTT
*
5753098 ATTA-TTATCTATTTT
1 ATTATTTATATATTTT
5753113 TATTTGTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 9 0.33
16 4 0.15
17 14 0.52
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTATTTATATATTTT
Found at i:5755538 original size:31 final size:32
Alignment explanation
Indices: 5755503--5755562 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
5755493 ACTTTGTTGC
5755503 TGGAAGTAAATAGTT-AAAAAAAATTTTTATT
1 TGGAAGTAAATAGTTGAAAAAAAATTTTTATT
*
5755534 TGGAAGTAAATAGTTGAAAAGAAATTTTT
1 TGGAAGTAAATAGTTGAAAAAAAATTTTT
5755563 GTTTAAGTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.37
Consensus pattern (32 bp):
TGGAAGTAAATAGTTGAAAAAAAATTTTTATT
Found at i:5761129 original size:7 final size:7
Alignment explanation
Indices: 5761107--5761183 Score: 52
Period size: 7 Copynumber: 11.3 Consensus size: 7
5761097 AGGATCTAGG
*
5761107 TTAGGAT
1 TTAGGGT
*
5761114 TTGGGGT
1 TTAGGGT
5761121 TTAGGGT
1 TTAGGGT
**
5761128 TTACAGT
1 TTAGGGT
5761135 TTAGGG-
1 TTAGGGT
5761141 TTAGGAGT
1 TTAGG-GT
5761149 TT--GGT
1 TTAGGGT
* *
5761154 TTAAGAT
1 TTAGGGT
5761161 TTAGGGT
1 TTAGGGT
**
5761168 CCAGGGT
1 TTAGGGT
5761175 TTAGGGT
1 TTAGGGT
5761182 TT
1 TT
5761184 CAAATTTGAG
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
5 4 0.08
6 6 0.12
7 40 0.77
8 2 0.04
ACGTcount: A:0.18, C:0.04, G:0.36, T:0.42
Consensus pattern (7 bp):
TTAGGGT
Found at i:5761176 original size:26 final size:26
Alignment explanation
Indices: 5761125--5761176 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
5761115 TGGGGTTTAG
*
5761125 GGTTTACAGTTTAGGGTTAGGAGTTT
1 GGTTTACAGTTTAGGGTCAGGAGTTT
5761151 GGTTTA-AGATTTAGGGTCCAGG-GTTT
1 GGTTTACAG-TTTAGGGT-CAGGAGTTT
5761177 AGGGTTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 2 0.09
26 18 0.78
27 3 0.13
ACGTcount: A:0.19, C:0.06, G:0.35, T:0.40
Consensus pattern (26 bp):
GGTTTACAGTTTAGGGTCAGGAGTTT
Found at i:5764458 original size:31 final size:31
Alignment explanation
Indices: 5764405--5764469 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
5764395 AACCTACCAG
* *
5764405 AAAATTCAATCGACATCGAAAAAGTCATCAA
1 AAAATTCAATCAACATCAAAAAAGTCATCAA
* *
5764436 AAAATTCAATCAACGAT-AAAAAATTCATCGA
1 AAAATTCAATCAAC-ATCAAAAAAGTCATCAA
5764467 AAA
1 AAA
5764470 CTGAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.55, C:0.17, G:0.08, T:0.20
Consensus pattern (31 bp):
AAAATTCAATCAACATCAAAAAAGTCATCAA
Found at i:5765273 original size:42 final size:42
Alignment explanation
Indices: 5765173--5765586 Score: 349
Period size: 42 Copynumber: 9.9 Consensus size: 42
5765163 AAAACTCTTT
* * * * *
5765173 TAAACAAAGGCTCCATGACATT-GAAAAAATAAACAAAGCTCCTT
1 TAAACAGAGGCTCAATGACTTTAG-AAAAAT-AA-AAGGCTCCTC
* * *
5765217 TAAACAAAGGCTCAATGACTTTGAGAAAAAT-AAATGCTTCTC
1 TAAACAGAGGCTCAATGACTTT-AGAAAAATAAAAGGCTCCTC
* *
5765259 TAAACAGAGACTCAATAACTTTGAGAAAAATAAAAGGCTCCTC
1 TAAACAGAGGCTCAATGACTTT-AGAAAAATAAAAGGCTCCTC
* * * * ** * *
5765302 CAAATAGAGACACAACAACTTCA-AAAAATAAAAGACTCCTC
1 TAAACAGAGGCTCAATGACTTTAGAAAAATAAAAGGCTCCTC
* * * *
5765343 TAAGCAGATGCTCAATGAC-TTCGAAAAATAAAAGGCTTCTC
1 TAAACAGAGGCTCAATGACTTTAGAAAAATAAAAGGCTCCTC
* * *
5765384 TAAACAGAGGTTCAATGACTTTTGAAAAATAAAAGGCTCATC
1 TAAACAGAGGCTCAATGACTTTAGAAAAATAAAAGGCTCCTC
*
5765426 TAAACAGAGGCTCAATGACTTT-GAAAAATAAAAAGCTCCTC
1 TAAACAGAGGCTCAATGACTTTAGAAAAATAAAAGGCTCCTC
* * * * * *
5765467 TAAACAAAGGCTCAACGACTTTTGAAAAATAAAAGTCTCTTT
1 TAAACAGAGGCTCAATGACTTTAGAAAAATAAAAGGCTCCTC
* *
5765509 TAAACAGAGGCTCAACGGCATTT-GAAAAAT-AAA-GCTCCTC
1 TAAACAGAGGCTCAATGAC-TTTAGAAAAATAAAAGGCTCCTC
** * * ** *
5765549 TAAGTAAAGGCTTAACAACTTTAGAAAAGTAAAAGGCT
1 TAAACAGAGGCTCAATGACTTTAGAAAAATAAAAGGCT
5765587 TATCGACCAT
Statistics
Matches: 305, Mismatches: 55, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.01
40 24 0.08
41 103 0.34
42 118 0.39
43 30 0.10
44 20 0.07
45 6 0.02
46 1 0.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (42 bp):
TAAACAGAGGCTCAATGACTTTAGAAAAATAAAAGGCTCCTC
Found at i:5765415 original size:83 final size:83
Alignment explanation
Indices: 5765160--5765583 Score: 340
Period size: 83 Copynumber: 5.1 Consensus size: 83
5765150 TTTAAATAAC
* * * * *
5765160 ATAAAA-ACTCTTTTAAACAAAGGCTCCATGACATT-GAAAAAATAAACAAAGCTCCTTTAAACA
1 ATAAAAGACTCATCTAAACAGAGGCTCAATGAC-TTCG-AAAAAT-AA-AAAGCTCCTCTAAACA
* *
5765223 AAGGCTCAATGACTTTGAGAAAA
62 AAGGCTCAACGACTTT-TGAAAA
* * * * * * * *
5765246 ATAAATG-CTTC-TCTAAACAGAGACTCAATAACTTTGAGAAAAATAAAAGGCTCCTCCAAATAG
1 ATAAAAGAC-TCATCTAAACAGAGGCTCAATGAC-TT-CGAAAAATAAAAAGCTCCTCTAAACAA
* * * **
5765309 AGACACAACAAC-TTCAAAAA
63 AGGCTCAACGACTTTTGAAAA
* * * * * *
5765329 ATAAAAGACTCCTCTAAGCAGATGCTCAATGACTTCGAAAAATAAAAGGCTTCTCTAAACAGAGG
1 ATAAAAGACTCATCTAAACAGAGGCTCAATGACTTCGAAAAATAAAAAGCTCCTCTAAACAAAGG
* *
5765394 TTCAATGACTTTTGAAAA
66 CTCAACGACTTTTGAAAA
* *
5765412 ATAAAAGGCTCATCTAAACAGAGGCTCAATGACTTTGAAAAATAAAAAGCTCCTCTAAACAAAGG
1 ATAAAAGACTCATCTAAACAGAGGCTCAATGACTTCGAAAAATAAAAAGCTCCTCTAAACAAAGG
5765477 CTCAACGACTTTTGAAAA
66 CTCAACGACTTTTGAAAA
* * * * * * **
5765495 ATAAAAGTCTCTTTTAAACAGAGGCTCAACGGCATTTGAAAAAT--AAAGCTCCTCTAAGTAAAG
1 ATAAAAGACTCATCTAAACAGAGGCTCAATGAC-TTCGAAAAATAAAAAGCTCCTCTAAACAAAG
* * *
5765558 GCTTAACAACTTTAGAAAA
65 GCTCAACGACTTTTGAAAA
*
5765577 GTAAAAG
1 ATAAAAG
5765584 GCTTATCGAC
Statistics
Matches: 275, Mismatches: 55, Indels: 20
0.79 0.16 0.06
Matches are distributed among these distances:
82 69 0.25
83 121 0.44
84 30 0.11
85 20 0.07
86 26 0.09
87 8 0.03
88 1 0.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (83 bp):
ATAAAAGACTCATCTAAACAGAGGCTCAATGACTTCGAAAAATAAAAAGCTCCTCTAAACAAAGG
CTCAACGACTTTTGAAAA
Found at i:5766200 original size:22 final size:21
Alignment explanation
Indices: 5766161--5766210 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5766151 TCAAAAATTC
*
5766161 AAAGATTCTCACTGGAAAACTT
1 AAAGATTCTCACTCG-AAACTT
* * *
5766183 AAAGATTCTTATTCGAAATTT
1 AAAGATTCTCACTCGAAACTT
5766204 AAAGATT
1 AAAGATT
5766211 TTCATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (21 bp):
AAAGATTCTCACTCGAAACTT
Found at i:5766222 original size:21 final size:21
Alignment explanation
Indices: 5766176--5766231 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
5766166 TTCTCACTGG
*
5766176 AAAACTTAAAGATTCTTATTC
1 AAAATTTAAAGATTCTTATTC
* *
5766197 GAAATTTAAAGATT-TTCATTT
1 AAAATTTAAAGATTCTT-ATTC
*
5766218 AAAATTCAAAGATT
1 AAAATTTAAAGATT
5766232 ATCGTTTGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAATTTAAAGATTCTTATTC
Found at i:5766574 original size:93 final size:93
Alignment explanation
Indices: 5766465--5766651 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
5766455 AGTTTTAAAT
*
5766465 ATTCTCCAAACAACAATTCAAATGTAATGCATGTAATGTGGATGTCCATGTCGTGAAATTATGGT
1 ATTCTCCAAACAACAATGCAAATGTAATGCATGTAATGTGGATGTCCATGTCGTGAAATTATGGT
5766530 AACATGGTTTTCAAAACCCCACCATCTC
66 AACATGGTTTTCAAAACCCCACCATCTC
*
5766558 ATTCTCTAAACAACAATGCAAATGTAATGCATGTAATGTGGATGTCCATGTCGTGAAATTATGGT
1 ATTCTCCAAACAACAATGCAAATGTAATGCATGTAATGTGGATGTCCATGTCGTGAAATTATGGT
5766623 AACATGGTTTTCAAAACCCCACCATCTC
66 AACATGGTTTTCAAAACCCCACCATCTC
5766651 A
1 A
5766652 CATTTTTCCT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (93 bp):
ATTCTCCAAACAACAATGCAAATGTAATGCATGTAATGTGGATGTCCATGTCGTGAAATTATGGT
AACATGGTTTTCAAAACCCCACCATCTC
Found at i:5767581 original size:21 final size:21
Alignment explanation
Indices: 5767557--5767606 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5767547 TTTTTTTCAT
5767557 TTTTTTCTCTTTTTC-TGTCCC
1 TTTTTTC-CTTTTTCATGTCCC
* * *
5767578 TTTTCTCCTTTTTCATTTTCC
1 TTTTTTCCTTTTTCATGTCCC
5767599 TTTTTTCC
1 TTTTTTCC
5767607 CATATATTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTTCCTTTTTCATGTCCC
Found at i:5767994 original size:19 final size:18
Alignment explanation
Indices: 5767966--5768021 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 18
5767956 GTGGTATTCA
5767966 TTTTTCTTTTCTTTCTTTT-
1 TTTTT-TTTTCTTT-TTTTG
5767985 TTTTTGTTTTCTTTATTTTG
1 TTTTT-TTTTCTTT-TTTTG
5768005 TTTTTTTTTCTTTTTTT
1 TTTTTTTTTCTTTTTTT
5768022 CTACTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 4 0.12
19 25 0.74
20 5 0.15
ACGTcount: A:0.02, C:0.09, G:0.04, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTCTTTTTTTG
Found at i:5768008 original size:24 final size:24
Alignment explanation
Indices: 5767967--5768018 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5767957 TGGTATTCAT
*
5767967 TTTTCTTTTCTTTCTTTTTTTTTG
1 TTTTCTTTTCTTTCTTTTTTTTTC
*
5767991 TTTTCTTTAT-TTTGTTTTTTTTTC
1 TTTTCTTT-TCTTTCTTTTTTTTTC
5768015 TTTT
1 TTTT
5768019 TTTCTACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.85
Consensus pattern (24 bp):
TTTTCTTTTCTTTCTTTTTTTTTC
Found at i:5772158 original size:174 final size:176
Alignment explanation
Indices: 5771877--5772208 Score: 415
Period size: 175 Copynumber: 1.9 Consensus size: 176
5771867 AAAAGAATAC
*
5771877 AATTACTTTTATTAAAATTTCATCTAAATTATTCCACCACTTGAGACAAATTTAGAGAAAATTTC
1 AATTACTTTTATTAAAATTTCATCTAAATTATTCCACCACTTGAGACAAATTTAGAGAAAATTCC
* * * * *
5771942 TCACATAGAGATTTTCTTAGCAATTTACCGTTTGAAATTTTCA-AGAATCTCATCCTTGGGTAAT
66 TCACATAGAGATTTTCATAGAAATTTACCATTTGAAATTTTCATA-AATCTCATCATTGGATAAT
** *
5772006 TTGTATTTAAT-TCCAAAAAAAATATTTTTGTTTGAAAATAGATATT
130 TAATACTTAATCTCCAAAAAAAATATTTTTGTTTGAAAATAGATATT
* *** * * *
5772052 AATTA-TTGTTATTGAAACTTT-ATCTAAATTATTTTGCCATTTGAGATAAATTTAGATAAAATT
1 AATTACTT-TTATT-AAAATTTCATCTAAATTATTCCACCACTTGAGACAAATTTAGAGAAAATT
* *
5772115 CCTCACCTA-AGAATTTT-ATAGAAATTTACCATTTGAAATTTTCATAAATTTCATCATTGGATA
64 CCTCACATAGAG-ATTTTCATAGAAATTTACCATTTGAAATTTTCATAAATCTCATCATTGGATA
*
5772178 ATTAATACTTATTCTCCAAAAAAAATATTTT
128 ATTAATACTTAATCTCCAAAAAAAATATTTT
5772209 ATTTTTTTCT
Statistics
Matches: 133, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
174 51 0.38
175 76 0.57
176 6 0.05
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (176 bp):
AATTACTTTTATTAAAATTTCATCTAAATTATTCCACCACTTGAGACAAATTTAGAGAAAATTCC
TCACATAGAGATTTTCATAGAAATTTACCATTTGAAATTTTCATAAATCTCATCATTGGATAATT
AATACTTAATCTCCAAAAAAAATATTTTTGTTTGAAAATAGATATT
Found at i:5772229 original size:16 final size:15
Alignment explanation
Indices: 5772203--5772232 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5772193 CCAAAAAAAA
5772203 TATTTTATTTTTTTC
1 TATTTTATTTTTTTC
5772218 TATTTATATTTTTTT
1 TATTT-TATTTTTTT
5772233 TCTAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TATTTTATTTTTTTC
Found at i:5772761 original size:31 final size:31
Alignment explanation
Indices: 5772720--5772789 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
5772710 TATAAAACCT
*
5772720 ATAGAAAAATTCAA-TAGACATCGAAAAAGTC
1 ATAGAAAAATTCAACCAG-CATCGAAAAAGTC
* *
5772751 ATCGAAAAATTCAACCAGCATCGAAAAATTC
1 ATAGAAAAATTCAACCAGCATCGAAAAAGTC
5772782 ATAGAAAA
1 ATAGAAAA
5772790 CTAGAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (31 bp):
ATAGAAAAATTCAACCAGCATCGAAAAAGTC
Found at i:5773161 original size:4 final size:4
Alignment explanation
Indices: 5773134--5773243 Score: 56
Period size: 4 Copynumber: 28.2 Consensus size: 4
5773124 AAAACTAAAG
* * * *
5773134 ATAA ATCA AGAA A-AA ATAAA ATAA ATAA AT-A ATAG ATAA AT-C ATAA
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
***
5773180 ATAAA CATAA A-AA AT-A A-AA ATAA A-AA ATAA AGTAA AGCCC ATAA
1 AT-AA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA A-TAA A-TAA ATAA
5773224 ATAA ATAA ATAA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA A
5773244 AAGTTGGGCC
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
3 21 0.26
4 44 0.54
5 14 0.17
6 2 0.02
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:5773165 original size:13 final size:12
Alignment explanation
Indices: 5773144--5773215 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 12
5773134 ATAAATCAAG
5773144 AAAAAATAAAAT
1 AAAAAATAAAAT
5773156 AAATAAATAATAGAT
1 AAA-AAATAA-A-AT
5773171 AAATCATAAATAAACAT
1 -AA--A-AAATAAA-AT
5773188 AAAAAATAAAAAT
1 AAAAAAT-AAAAT
*
5773201 AAAAAATAAAGT
1 AAAAAATAAAAT
5773213 AAA
1 AAA
5773216 GCCCATAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
12 10 0.20
13 19 0.37
14 5 0.10
15 2 0.04
16 4 0.08
17 3 0.06
18 8 0.16
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:5773195 original size:35 final size:34
Alignment explanation
Indices: 5773132--5773201 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 34
5773122 AAAAAACTAA
5773132 AGATAAATCAAGAAAAAATAAAATAAATAAATAAT
1 AGATAAATCAAGAAAAAATAAAATAAATAAA-AAT
5773167 AGATAAATCATA-AATAAACAT-AAA-AAATAAAAAT
1 AGATAAATCA-AGAA-AAA-ATAAAATAAATAAAAAT
5773201 A
1 A
5773202 AAAAATAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
34 4 0.12
35 19 0.59
36 7 0.22
37 2 0.06
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (34 bp):
AGATAAATCAAGAAAAAATAAAATAAATAAAAAT
Found at i:5773223 original size:44 final size:44
Alignment explanation
Indices: 5773144--5773228 Score: 113
Period size: 44 Copynumber: 1.9 Consensus size: 44
5773134 ATAAATCAAG
*
5773144 AAAAAATAAAATAAATAAATAATAGATAAATCATAAATAAACAT
1 AAAAAATAAAATAAATAAATAATAGATAAACCATAAATAAACAT
5773188 AAAAAATAAAAATAAA-AAATAA-AG-TAAAGCCCATAAATAAA
1 AAAAAAT-AAAATAAATAAATAATAGATAAA--CCATAAATAAA
5773229 TAAATAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 4 0.11
43 2 0.05
44 23 0.62
45 8 0.22
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.19
Consensus pattern (44 bp):
AAAAAATAAAATAAATAAATAATAGATAAACCATAAATAAACAT
Found at i:5774399 original size:75 final size:75
Alignment explanation
Indices: 5774320--5774464 Score: 186
Period size: 75 Copynumber: 1.9 Consensus size: 75
5774310 GCCCAAAAAG
* ** *
5774320 GTAACTATC-TTTCATTAACCTCTAATTCCTCATCAACTTTCTCATCATCCTCCACT-ATCCCAT
1 GTAACT-TCATTTAATTAACCTCTAATTCCTCATCAACAATCTCATCATCCACCACTCA-CCCAT
5774383 TAGCCTAAGAAA
64 TAGCCTAAGAAA
* * * *
5774395 GTAACTTCATTTAATTAACCTCTAATTCTTCTTTAGCAATCTCATCATCCACCACTCACCCATTA
1 GTAACTTCATTTAATTAACCTCTAATTCCTCATCAACAATCTCATCATCCACCACTCACCCATTA
5774460 GCCTA
66 GCCTA
5774465 TGGAGGCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
74 2 0.03
75 57 0.95
76 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.04, T:0.35
Consensus pattern (75 bp):
GTAACTTCATTTAATTAACCTCTAATTCCTCATCAACAATCTCATCATCCACCACTCACCCATTA
GCCTAAGAAA
Found at i:5780169 original size:12 final size:11
Alignment explanation
Indices: 5780152--5780203 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
5780142 TCATTTCCTA
5780152 TATTTTTATTAT
1 TATTTTTATT-T
5780164 TA-TTTTA-TT
1 TATTTTTATTT
5780173 TA-TTTTATTGT
1 TATTTTTATT-T
5780184 TATTTTTTATTT
1 TA-TTTTTATTT
5780196 TATTTTTA
1 TATTTTTA
5780204 AAGAAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 8 0.22
10 2 0.06
11 14 0.39
12 5 0.14
13 7 0.19
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:5780180 original size:20 final size:18
Alignment explanation
Indices: 5780155--5780199 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5780145 TTTCCTATAT
5780155 TTTTATTATTATTTTATTTA
1 TTTTATTATTA-TTT-TTTA
*
5780175 TTTTATTGTTATTTTTTA
1 TTTTATTATTATTTTTTA
5780193 TTTTATT
1 TTTTATT
5780200 TTTAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.46
19 3 0.12
20 10 0.42
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTATTATTATTTTTTA
Found at i:5780193 original size:13 final size:12
Alignment explanation
Indices: 5780163--5780202 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
5780153 ATTTTTATTA
5780163 TTATTTTATTTATT
1 TTATTTTA-TT-TT
5780177 TTATTGTTATTTT
1 TTATT-TTATTTT
5780190 TTATTTTATTTT
1 TTATTTTATTTT
5780202 T
1 T
5780203 AAAGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.32
13 7 0.28
14 7 0.28
15 3 0.12
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:5780220 original size:5 final size:5
Alignment explanation
Indices: 5780155--5780201 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
5780145 TTTCCTATAT
5780155 TTTTA TTATTA TTTTA -TTTA TTTTA TTGTTA TTTTTTA TTTTA TTTT
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TT-TTA --TTTTA TTTTA TTTT
5780202 TAAAGAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.11
5 20 0.54
6 8 0.22
7 3 0.08
8 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5784939 original size:15 final size:15
Alignment explanation
Indices: 5784919--5784948 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5784909 TTTAATTTTA
5784919 AAATATATTTATTAT
1 AAATATATTTATTAT
*
5784934 AAATATATTTTTTAT
1 AAATATATTTATTAT
5784949 TTTTTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATATATTTATTAT
Found at i:5791975 original size:5 final size:6
Alignment explanation
Indices: 5791958--5791982 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5791948 AAGATTTGTC
5791958 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
5791983 TGAGGGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:5792760 original size:12 final size:12
Alignment explanation
Indices: 5792745--5792778 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5792735 TTTTTTGTAT
5792745 TTTATTTATTTG
1 TTTATTTATTTG
*
5792757 TTTATTTATGTG
1 TTTATTTATTTG
5792769 -TTATTTATTT
1 TTTATTTATTT
5792779 TTAGAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:5802324 original size:7 final size:7
Alignment explanation
Indices: 5802312--5802337 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5802302 ATCGTTGAAT
5802312 ATGTGGC
1 ATGTGGC
5802319 ATGTGGC
1 ATGTGGC
5802326 ATGTGGC
1 ATGTGGC
5802333 ATGTG
1 ATGTG
5802338 TGATGAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.42, T:0.31
Consensus pattern (7 bp):
ATGTGGC
Found at i:5802493 original size:14 final size:14
Alignment explanation
Indices: 5802470--5802501 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5802460 AATCGCAAGT
5802470 ATAT-CCAATGAAC
1 ATATGCCAATGAAC
5802483 ATATGCCAATGAAC
1 ATATGCCAATGAAC
5802497 ATATG
1 ATATG
5802502 ATGGCAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (14 bp):
ATATGCCAATGAAC
Found at i:5803520 original size:13 final size:11
Alignment explanation
Indices: 5803502--5803545 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
5803492 TTGAAAAAAG
5803502 AAAAAAAGCAAGA
1 AAAAAAAG-AA-A
5803515 AAAAAAAGAAA
1 AAAAAAAGAAA
5803526 AAAAAAA-AAA
1 AAAAAAAGAAA
5803536 AAAAGAAAGA
1 AAAA-AAAGA
5803546 CTCAAGACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 7 0.24
11 11 0.38
12 3 0.10
13 8 0.28
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:5803523 original size:9 final size:9
Alignment explanation
Indices: 5803495--5803543 Score: 62
Period size: 9 Copynumber: 5.1 Consensus size: 9
5803485 ACTAAGCTTG
5803495 AAAAAAGAAA
1 AAAAAAG-AA
5803505 AAAAGCAAGAA
1 AAAA--AAGAA
5803516 AAAAAAGAA
1 AAAAAAGAA
*
5803525 AAAAAAAAA
1 AAAAAAGAA
5803534 AAAAAAGAA
1 AAAAAAGAA
5803543 A
1 A
5803544 GACTCAAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 22 0.63
10 4 0.11
11 6 0.17
12 3 0.09
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:5805279 original size:26 final size:25
Alignment explanation
Indices: 5805229--5805278 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5805219 TTTTTTGAAA
5805229 ATTTTTATTTGAAAAAATATTTTTT
1 ATTTTTATTTGAAAAAATATTTTTT
* * *
5805254 ATTTTTGTTTGAAAAGATCTTTTTT
1 ATTTTTATTTGAAAAAATATTTTTT
5805279 TTGCTAAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (25 bp):
ATTTTTATTTGAAAAAATATTTTTT
Found at i:5805378 original size:40 final size:40
Alignment explanation
Indices: 5805336--5805412 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
5805326 TTTCTTTTTT
5805336 AAAA-AAAATAAAACCAGAAAAAAAATAAAAAAAATGGGTTA
1 AAAATAAAATAAAACCA-AAAAAAAA-AAAAAAAATGGGTTA
* * *
5805377 AAAATAAAATAAAATCAAAAAATAAAAATAAAATGG
1 AAAATAAAATAAAACCAAAAAAAAAAAAAAAAATGG
5805413 AAAAGGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 10 0.31
41 11 0.34
42 11 0.34
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.14
Consensus pattern (40 bp):
AAAATAAAATAAAACCAAAAAAAAAAAAAAAAATGGGTTA
Found at i:5805783 original size:19 final size:20
Alignment explanation
Indices: 5805759--5805798 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5805749 TGATCACCAG
*
5805759 AAACTTT-ATCAAAAAATTC
1 AAACTTTCACCAAAAAATTC
*
5805778 AAACTTTCACCGAAAAATTC
1 AAACTTTCACCAAAAAATTC
5805798 A
1 A
5805799 TCCAAACCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.28
Consensus pattern (20 bp):
AAACTTTCACCAAAAAATTC
Found at i:5806284 original size:9 final size:8
Alignment explanation
Indices: 5806265--5806297 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5806255 AAGAGAAAAG
5806265 AAAATAAA
1 AAAATAAA
5806273 AAAATGAAA
1 AAAAT-AAA
5806282 AAAATAAA
1 AAAATAAA
5806290 AAAA-AAA
1 AAAATAAA
5806297 A
1 A
5806298 CAAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.17
8 12 0.50
9 8 0.33
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (8 bp):
AAAATAAA
Found at i:5806302 original size:20 final size:22
Alignment explanation
Indices: 5806260--5806313 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
5806250 AGGAAAAGAG
* *
5806260 AAAAGAAAATAAAAAAATGAAA
1 AAAATAAAATAAAAAAATCAAA
5806282 AAAATAAAA-AAAAAAA-CAAA
1 AAAATAAAATAAAAAAATCAAA
* *
5806302 AATATAATATAA
1 AAAATAAAATAA
5806314 TATAATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.37
21 9 0.33
22 8 0.30
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAATAAAATAAAAAAATCAAA
Found at i:5806468 original size:26 final size:25
Alignment explanation
Indices: 5806439--5806524 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 25
5806429 AATAATAAAA
5806439 ACACAAATGGGCCTAATTAGGTCTGG
1 ACACAAATGGGCCTAATT-GGTCTGG
* **
5806465 ACACAAATAGGCCTAATTGGGTCCAG
1 ACACAAATGGGCCTAATT-GGTCTGG
* *
5806491 ATACAAATGGGCCTAATTGGGCTTGG
1 ACACAAATGGGCCTAATTGGTC-TGG
5806517 ACACAAAT
1 ACACAAAT
5806525 AAATGTCTAC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
25 3 0.06
26 46 0.94
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (25 bp):
ACACAAATGGGCCTAATTGGTCTGG
Found at i:5806864 original size:120 final size:120
Alignment explanation
Indices: 5806671--5806966 Score: 310
Period size: 120 Copynumber: 2.5 Consensus size: 120
5806661 AGACCGGGAC
* * * * * *
5806671 AAAATCACAAGTCAAGATGAAGTGACTAGGACCAAGTCGAGGTCAAAAATAAGTGACTGGAATGA
1 AAAATCACAAGTCAAAATAAAGTGACCAGGACCAAGTCGAGGTCAAAAATAAATGACAGGAATAA
* * * *
5806736 AACTATGAATCACAAAAAAATGATATGGAT-TGAGCCCAGATCAAATGACTGGGATG
66 AACCATGAATCA-AAAAAAATGATAT-GATCTAAGCCAAGATCAAATGACTGAGATG
* * * ** *
5806792 -AAATCACGAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTTGAAAATAAATTATCAGG-ATA
1 AAAATCACAAGTCAAAATAAAGTGACCAGGACCAAGTCGAGGTCAAAAATAAATGA-CAGGAATA
* * * *
5806855 AAACCATGAATCATAAGAAATGATCTGATCTAAGCCAAGATCAAGTGACTGAGATG
65 AAACCATGAATCAAAAAAAATGATATGATCTAAGCCAAGATCAAATGACTGAGATG
* * ** * *
5806911 AAAACCACAAGTCAAAATAAAGCGAGTAGGATCAAGTCGAGGTAAAAAATAAATGA
1 AAAATCACAAGTCAAAATAAAGTGACCAGGACCAAGTCGAGGTCAAAAATAAATGA
5806967 TCGGGATGAA
Statistics
Matches: 141, Mismatches: 31, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
118 3 0.02
119 32 0.23
120 103 0.73
121 3 0.02
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.19
Consensus pattern (120 bp):
AAAATCACAAGTCAAAATAAAGTGACCAGGACCAAGTCGAGGTCAAAAATAAATGACAGGAATAA
AACCATGAATCAAAAAAAATGATATGATCTAAGCCAAGATCAAATGACTGAGATG
Found at i:5806991 original size:120 final size:119
Alignment explanation
Indices: 5806676--5807022 Score: 284
Period size: 120 Copynumber: 2.9 Consensus size: 119
5806666 GGGACAAAAT
* * * * * * * * *
5806676 CACAAGTCAAGATGAAGTGACTAGGACCAAGTCGAGGTCAAAAATAAGTGA-CTGGAATGAAACT
1 CACAAGTCAAAATAAAGCGACCAGGACCAAGTCGAGGTAAAAAATAAATGATCAGG-ATAAAACC
** * * * * * * * *
5806740 ATGAATCACAAAAAAATGATATGGATTGAGCCCAGATCAAATGACTGGGATGAAAT
65 ACAAATCA-TAAGAAATAATCTGGATTAAGCCAAGATCAAATGACTGAGATGAAAC
* * * * ** *
5806796 CACGAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTTGAAAATAAATTATCAGGATAAAACCA
1 CACAAGTCAAAATAAAGCGACCAGGACCAAGTCGAGGTAAAAAATAAATGATCAGGATAAAACCA
** * *
5806861 TGAATCATAAGAAATGATCT-GATCTAAGCCAAGATCAAGTGACTGAGATGAAAAC
66 CAAATCATAAGAAATAATCTGGAT-TAAGCCAAGATCAAATGACTGAGATG-AAAC
** * * * *
5806916 CACAAGTCAAAATAAAGCGAGTAGGATCAAGTCGAGGTAAAAAATAAATGATCGGGATGAAATCA
1 CACAAGTCAAAATAAAGCGACCAGGACCAAGTCGAGGTAAAAAATAAATGATCAGGATAAAACCA
* * * *
5806981 CAAATTATAAGAAATAATTTGGATTGAGCCAAGATCAGATGA
66 CAAATCATAAGAAATAATCTGGATTAAGCCAAGATCAAATGA
5807023 GTGGATAATG
Statistics
Matches: 181, Mismatches: 42, Indels: 8
0.78 0.18 0.03
Matches are distributed among these distances:
118 3 0.02
119 32 0.18
120 140 0.77
121 6 0.03
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.20
Consensus pattern (119 bp):
CACAAGTCAAAATAAAGCGACCAGGACCAAGTCGAGGTAAAAAATAAATGATCAGGATAAAACCA
CAAATCATAAGAAATAATCTGGATTAAGCCAAGATCAAATGACTGAGATGAAAC
Found at i:5808595 original size:172 final size:172
Alignment explanation
Indices: 5808309--5808642 Score: 623
Period size: 172 Copynumber: 1.9 Consensus size: 172
5808299 GTTTCCACTG
*
5808309 CCCTATTCATATTTGGACGATATGAAGCTGAATTGTGATGTTTGATCTTGAACTAAATACATACC
1 CCCTATTCATATTTGGACGATATGAAGCTGAATTGTGATGTTTGATCTTGAACTAAATACATAAC
*
5808374 TCTTGCATCATCTTACTATTTAAATTTTTTGCATTGTCTAAAATGATTTTTTTGAGAGCCCATAC
66 TCTTGCATCATCTTACTATTTAAATTATTTGCATTGTCTAAAATGATTTTTTTGAGAGCCCATAC
5808439 ATGTAAATTCTTTCTCTTTTAATGAATTTGCATATCCCATTA
131 ATGTAAATTCTTTCTCTTTTAATGAATTTGCATATCCCATTA
*
5808481 CCCTATTCATCTTTGGACGATATGAAGCTGAATTGTGATGTTTGATCTTGAACTAAATACATAAC
1 CCCTATTCATATTTGGACGATATGAAGCTGAATTGTGATGTTTGATCTTGAACTAAATACATAAC
* *
5808546 TCTTGCATCATCTTACTATTTAAATTATTTGCATTGTCTAAAATGATTTTTTTGGGAGCCCATAT
66 TCTTGCATCATCTTACTATTTAAATTATTTGCATTGTCTAAAATGATTTTTTTGAGAGCCCATAC
5808611 ATGTAAATTCTTTCTCTTTTAATGAATTTGCA
131 ATGTAAATTCTTTCTCTTTTAATGAATTTGCA
5808643 AACCACTGAT
Statistics
Matches: 157, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
172 157 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (172 bp):
CCCTATTCATATTTGGACGATATGAAGCTGAATTGTGATGTTTGATCTTGAACTAAATACATAAC
TCTTGCATCATCTTACTATTTAAATTATTTGCATTGTCTAAAATGATTTTTTTGAGAGCCCATAC
ATGTAAATTCTTTCTCTTTTAATGAATTTGCATATCCCATTA
Found at i:5818439 original size:27 final size:27
Alignment explanation
Indices: 5818378--5818439 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
5818368 GATTTTTTTT
5818378 TATTTTTTTAATTTCTTATTTGAAAAA
1 TATTTTTTTAATTTCTTATTTGAAAAA
*
5818405 TATATTTTTT-ATTT-TTGTTTGAAAAGA
1 TAT-TTTTTTAATTTCTTATTTGAAAA-A
*
5818432 TCTTTTTT
1 TATTTTTT
5818440 ACTAAACCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 15 0.48
27 10 0.32
28 6 0.19
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.63
Consensus pattern (27 bp):
TATTTTTTTAATTTCTTATTTGAAAAA
Found at i:5818965 original size:19 final size:20
Alignment explanation
Indices: 5818941--5818978 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5818931 CAATCACTAG
5818941 AAAC-TTCACCGAAAAATTT
1 AAACTTTCACCGAAAAATTT
*
5818960 AAACTTTCATCGAAAAATT
1 AAACTTTCACCGAAAAATT
5818979 CATCCAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (20 bp):
AAACTTTCACCGAAAAATTT
Found at i:5819724 original size:26 final size:26
Alignment explanation
Indices: 5819660--5819724 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
5819650 ATTAGGTCTA
* * *
5819660 AACACAAATGGACCTAATTGAGTCTG
1 AACACAAATGGATCTAATTGAATCCG
*
5819686 AACATAAATGGATCTAATTGAATCCG
1 AACACAAATGGATCTAATTGAATCCG
5819712 AACACAAATGGAT
1 AACACAAATGGAT
5819725 ATCTACAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (26 bp):
AACACAAATGGATCTAATTGAATCCG
Found at i:5821470 original size:20 final size:19
Alignment explanation
Indices: 5821447--5821539 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 19
5821437 AATATTAAAA
5821447 AAAATTTCTAAAATAATTAT
1 AAAATTT-TAAAATAATTAT
*
5821467 AAAAAATTTTGAAAA-AA-CAT
1 --AAAATTTT-AAAATAATTAT
* *
5821487 TAAATATTTAAAAAAATTAT
1 AAAAT-TTTAAAATAATTAT
*
5821507 AAAATATTATAAAAT-ATTTT
1 AAAAT-TT-TAAAATAATTAT
5821527 AAAATTTTAAAAT
1 AAAATTTTAAAAT
5821540 TTTTAAACAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
18 14 0.23
19 7 0.12
20 20 0.33
21 8 0.13
22 11 0.18
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAATTTTAAAATAATTAT
Found at i:5821474 original size:10 final size:10
Alignment explanation
Indices: 5821440--5821530 Score: 51
Period size: 10 Copynumber: 8.9 Consensus size: 10
5821430 GACAGTAAAT
*
5821440 ATTAAAAAAA
1 ATTATAAAAA
*
5821450 ATTTCTAAAATA
1 A-TTATAAAA-A
5821462 ATTATAAAAA
1 ATTATAAAAA
*
5821472 ATTTTGAAAAA
1 ATTAT-AAAAA
* * *
5821483 A-CATTAAAT
1 ATTATAAAAA
5821492 ATT-TAAAAAA
1 ATTAT-AAAAA
*
5821502 ATTATAAAAT
1 ATTATAAAAA
*
5821512 ATTATAAAAT
1 ATTATAAAAA
*
5821522 ATTTTAAAA
1 ATTATAAAA
5821531 TTTTAAAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
9 5 0.08
10 35 0.56
11 20 0.32
12 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:5821545 original size:9 final size:10
Alignment explanation
Indices: 5821488--5821546 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 10
5821478 AAAAAACATT
*
5821488 AAATATTTAA
1 AAATATTTTA
* *
5821498 AAAAATTATA
1 AAATATTTTA
*
5821508 AAATATTATA
1 AAATATTTTA
5821518 AAATATTTT-
1 AAATATTTTA
5821527 AAA-ATTTTA
1 AAATATTTTA
5821536 AAAT-TTTTA
1 AAATATTTTA
5821545 AA
1 AA
5821547 CAATTGGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
8 5 0.12
9 13 0.31
10 24 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAATATTTTA
Found at i:5821710 original size:27 final size:27
Alignment explanation
Indices: 5821677--5821739 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
5821667 TTGAAAATTA
*
5821677 AAAATTTTGAAAATTT-TGAAAAAGTCT
1 AAAATTTT-AAAATTTCTAAAAAAGTCT
*
5821704 AAAATTTCTAAAATTTCTAAAAAATTCT
1 AAAATTT-TAAAATTTCTAAAAAAGTCT
*
5821732 AAATTTTT
1 AAAATTTT
5821740 TTTTTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (27 bp):
AAAATTTTAAAATTTCTAAAAAAGTCT
Found at i:5821748 original size:20 final size:22
Alignment explanation
Indices: 5821725--5821767 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5821715 AATTTCTAAA
5821725 AAATTCT-AAATTTTTT-TTTT
1 AAATTCTAAAATTTTTTATTTT
5821745 AAATTCTGAAAATTTTTTATTTT
1 AAATTCT-AAAATTTTTTATTTT
5821768 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
22 9 0.45
23 4 0.20
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (22 bp):
AAATTCTAAAATTTTTTATTTT
Found at i:5821793 original size:25 final size:23
Alignment explanation
Indices: 5821755--5821821 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 23
5821745 AAATTCTGAA
* *
5821755 AATTTTTT-ATTTTTATTTTTTAT
1 AATTTTTTGAATTTTATTTTTT-G
5821778 ATATTTTTTGAATTTTCATGTTTTTG
1 A-ATTTTTTGAATTTT-AT-TTTTTG
*
5821804 AATTTTTTGGATTTTATT
1 AATTTTTTGAATTTTATT
5821822 AATTTTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.05
24 9 0.24
25 18 0.49
26 3 0.08
27 5 0.14
ACGTcount: A:0.21, C:0.01, G:0.07, T:0.70
Consensus pattern (23 bp):
AATTTTTTGAATTTTATTTTTTG
Found at i:5821889 original size:21 final size:21
Alignment explanation
Indices: 5821843--5821903 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
5821833 TTTTAGAAAA
*
5821843 TTTTATAATCTTTTATAATTT
1 TTTTATAATCTTTCATAATTT
* *
5821864 CTTTATAATGTTTCA-AAGTTT
1 TTTTATAATCTTTCATAA-TTT
5821885 TTTTA-AAT-TTT--TAATTT
1 TTTTATAATCTTTCATAATTT
5821902 TT
1 TT
5821904 CAAAGATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 5 0.15
18 2 0.06
19 3 0.09
20 5 0.15
21 19 0.56
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTTATAATCTTTCATAATTT
Found at i:5822044 original size:39 final size:38
Alignment explanation
Indices: 5821993--5822071 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
5821983 AATTCTTATG
** *
5821993 TTTATTAAAATTTTTATTTTTTTGAATTTTTTTAGATTT
1 TTTATTAAAATTTTTAGATTTTTGAATTTTCTTA-ATTT
5822032 TTTATTAAAATTTTTAGATTTTTGAATTTTCTTAATTT
1 TTTATTAAAATTTTTAGATTTTTGAATTTTCTTAATTT
5822070 TT
1 TT
5822072 ATAATTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 6 0.16
39 31 0.84
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (38 bp):
TTTATTAAAATTTTTAGATTTTTGAATTTTCTTAATTT
Found at i:5822095 original size:28 final size:28
Alignment explanation
Indices: 5822063--5822123 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
5822053 TTGAATTTTC
5822063 TTAATTTTTATAATTTTTTAAA-AATCTT
1 TTAATTTTT-TAATTTTTTAAATAATCTT
*
5822091 TTAATTTTTTAATTTTTTAAATATTCTT
1 TTAATTTTTTAATTTTTTAAATAATCTT
5822119 TTAAT
1 TTAAT
5822124 ACTAACATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 12 0.39
28 19 0.61
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
TTAATTTTTTAATTTTTTAAATAATCTT
Found at i:5822098 original size:27 final size:28
Alignment explanation
Indices: 5822063--5822123 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
5822053 TTGAATTTTC
5822063 TTAATTTTTATAATTTTTTAAA-AATCTT
1 TTAA-TTTTATAATTTTTTAAATAATCTT
* *
5822091 TTAATTTTTTAATTTTTTAAATATTCTT
1 TTAATTTTATAATTTTTTAAATAATCTT
5822119 TTAAT
1 TTAAT
5822124 ACTAACATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
TTAATTTTATAATTTTTTAAATAATCTT
Found at i:5822106 original size:7 final size:8
Alignment explanation
Indices: 5822042--5822110 Score: 66
Period size: 8 Copynumber: 7.9 Consensus size: 8
5822032 TTTATTAAAA
5822042 TTTTTAGAT
1 TTTTTA-AT
*
5822051 TTTTGAAT
1 TTTTTAAT
5822059 TTTCTTAAT
1 TTT-TTAAT
5822068 TTTTATAAT
1 TTTT-TAAT
5822077 TTTTTAAAAAT
1 TTTTT---AAT
*
5822088 CTTTTAAT
1 TTTTTAAT
5822096 TTTTTAAT
1 TTTTTAAT
5822104 TTTTTAA
1 TTTTTAA
5822111 ATATTCTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
8 24 0.47
9 20 0.39
11 7 0.14
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (8 bp):
TTTTTAAT
Done.