Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008158.1 Hibiscus syriacus cultivar Beakdansim tig00110725_pilon, 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: 344415
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:9764 original size:1 final size:1
Alignment explanation
Indices: 9758--9783 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
9748 TCCTAAGTTG
9758 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
9784 CGTTTAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10765 original size:105 final size:103
Alignment explanation
Indices: 10583--11251 Score: 944
Period size: 105 Copynumber: 6.5 Consensus size: 103
10573 AGGTTTTACC
* *
10583 CAGAGCCAATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
10648 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-ATTTC-CAATTT
10688 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
10753 ACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-ATTTC-CAATTT
10793 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
10858 ACGAAGGGACCGCTGGTTGTCAA-TAAA----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAATTTCCAATTT
* *
10891 CAGGGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
10956 ACGAAGGGACCGCTGGTTGTCAA-TAAA----CAATTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAATTTCCAATTT
*
10989 CAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
11054 ACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAA-CAA-AA-TTTCCAATTT
* * * * *
11095 CAGAGCCAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
11160 ACGAAGGGACCGCTGGTTGTCAACAAGTAATTTCCCGGTTT
66 ACGAAGGGACCGCTGGTTGTCAACAA--AATTT-CCAATTT
* * * * * *
11201 TAGAGCCAATTTCAACTTCACATCAAAGGATATTGGCCTCGAAACAACGCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
11252 TCTTGCATTG
Statistics
Matches: 517, Mismatches: 37, Indels: 19
0.90 0.06 0.03
Matches are distributed among these distances:
98 185 0.36
100 1 0.00
101 2 0.00
103 1 0.00
104 2 0.00
105 191 0.37
106 135 0.26
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (103 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAAATTTCCAATTT
Found at i:12402 original size:20 final size:20
Alignment explanation
Indices: 12377--12418 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
12367 CAAGGTTCGC
* *
12377 CGCCGATGAGCGGTGGCCGG
1 CGCCGATCAGCGGCGGCCGG
12397 CGCCGATCAGCGGCGGCCGG
1 CGCCGATCAGCGGCGGCCGG
12417 CG
1 CG
12419 TGGTGGCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.36, G:0.48, T:0.07
Consensus pattern (20 bp):
CGCCGATCAGCGGCGGCCGG
Found at i:13790 original size:30 final size:31
Alignment explanation
Indices: 13720--13793 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
13710 AACGTCAAAG
* ** *
13720 TGACCAAAACTTAATAAAACAATAATGTAAG
1 TGACTAAAACTTAATAAAACAATAACATAAA
*
13751 TGA-TCAAAACTTAAT-AAATAATAACATAAA
1 TGACT-AAAACTTAATAAAACAATAACATAAA
13781 TGACTAAAACTTA
1 TGACTAAAACTTA
13794 TGTTTTTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 22 0.61
31 14 0.39
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (31 bp):
TGACTAAAACTTAATAAAACAATAACATAAA
Found at i:41331 original size:3 final size:3
Alignment explanation
Indices: 41317--41412 Score: 72
Period size: 3 Copynumber: 32.0 Consensus size: 3
41307 TTTTCCCCAT
* * *
41317 TTA TTT TTA TTA TTA TTT TTA TTA CTT- TTA TTA CTT- TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA
* * * * *
41362 TTA TTA TAA TAA TTA TTA TTA TAA TAA TTA TTC TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
41408 -TA TTA
1 TTA TTA
41413 ATAAATAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.08
3 62 0.83
4 7 0.09
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:41362 original size:15 final size:15
Alignment explanation
Indices: 41355--41408 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
41345 TATTACTTTT
41355 ATAATTATTATTATA
1 ATAATTATTATTATA
41370 ATAATTATTATTATA
1 ATAATTATTATTATA
*
41385 ATAATTATTCTTAT-
1 ATAATTATTATTATA
41399 AT-ATTATTAT
1 ATAATTATTAT
41409 ATTAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.19
14 2 0.05
15 28 0.76
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATAATTATTATTATA
Found at i:44468 original size:36 final size:36
Alignment explanation
Indices: 44421--44492 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
44411 GAGCTATGCA
*
44421 CACAAAGATCCTGTTAGATTAATACCAAAAGTATTC
1 CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
*
44457 CACAAAGATCCTGTTAGATTGATACCAAAAGCATTC
1 CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
44493 TACAGTAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (36 bp):
CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
Found at i:50046 original size:42 final size:43
Alignment explanation
Indices: 49941--50046 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 43
49931 CAATTCAGAC
* * * *
49941 AGATCCATGTGGGACATCTTGAAAGCCCATTTCAACCAGAAAT
1 AGATCCATGTGGGGCATTTTGAAAGCCCAATTCAAACAGAAAT
* * *
49984 AGA---ATGTTAGGGCATTTTGAATGCCTAATTCAAACAGAAAT
1 AGATCCATG-TGGGGCATTTTGAAAGCCCAATTCAAACAGAAAT
50025 -GATCCATGTGGGGCATTTTGAA
1 AGATCCATGTGGGGCATTTTGAA
50047 GGCTCATAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
40 5 0.10
41 27 0.53
42 13 0.25
43 6 0.12
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (43 bp):
AGATCCATGTGGGGCATTTTGAAAGCCCAATTCAAACAGAAAT
Found at i:52391 original size:36 final size:36
Alignment explanation
Indices: 52346--52466 Score: 134
Period size: 36 Copynumber: 3.3 Consensus size: 36
52336 TAGTAATGTA
52346 TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTG
* ** ** ** *
52382 TCTCGCTTGAGACAGTTTCACTCGAAACAACAATTTA
1 TCTCACTTGAGATTGTTTTTCTTAAAACAA-AATTTG
* *
52419 TCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTG
*
52455 TCTCGCTTGAGA
1 TCTCACTTGAGA
52467 CAGTTTCACT
Statistics
Matches: 65, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
36 37 0.57
37 28 0.43
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (36 bp):
TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTG
Found at i:52483 original size:36 final size:36
Alignment explanation
Indices: 52370--52490 Score: 127
Period size: 37 Copynumber: 3.3 Consensus size: 36
52360 GTTTTTCTTA
*
52370 AAACAAAATTTGTCTCGCTTGAGACAGTTTCACTCG
1 AAACAAAATTTGTCTCGCTTGAGACAGTTTCACTAG
* * ** **
52406 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA-
1 AAACAA-AATTTGTCTCGCTTGAGACAGTTTCAC-TAG
* *
52443 AAACAAGATTCGTCTCGCTTGAGACAGTTTCACTAG
1 AAACAAAATTTGTCTCGCTTGAGACAGTTTCACTAG
52479 AAACATAAATTT
1 AAACA-AAATTT
52491 CCATCGCTCG
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
35 2 0.03
36 30 0.47
37 31 0.48
38 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (36 bp):
AAACAAAATTTGTCTCGCTTGAGACAGTTTCACTAG
Found at i:52490 original size:73 final size:73
Alignment explanation
Indices: 52344--52483 Score: 253
Period size: 73 Copynumber: 1.9 Consensus size: 73
52334 AATAGTAATG
* *
52344 TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTCGAAA
1 TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACTAGAAA
52409 CAACAATT
66 CAACAATT
*
52417 TATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCGTCTCGCTTGAGACAGTTTCACTAGAAA
1 TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACTAGAAA
52482 CA
66 CA
52484 TAAATTTCCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (73 bp):
TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACTAGAAA
CAACAATT
Found at i:52838 original size:123 final size:123
Alignment explanation
Indices: 52505--52958 Score: 747
Period size: 123 Copynumber: 3.7 Consensus size: 123
52495 CGCTCGATGG
*
52505 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTATA
1 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
52570 ATGAGAAGAACTTGTTCAACCTTTTGCTCAATTCTATCCCAGAAGGAGATAGATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* *
52628 ACCAACATTTCCAGAGGAAGTTCATAAT---AAGAACTCATCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
52690 ACGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* *
52748 ATCAACGTTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGGA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
*
52812 AATGAGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* *
52871 ATCAACATTTCCAGA-TAGAGTTCATAATGAGAAGAACTCATCTGAAGGGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGGA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
52935 AATGAGAAGAACTTGTTCAACCTT
65 AATGAGAAGAACTTGTTCAACCTT
52959 AGCTTGATTC
Statistics
Matches: 310, Mismatches: 16, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
119 2 0.01
120 108 0.35
123 200 0.65
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (123 bp):
ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:53198 original size:137 final size:138
Alignment explanation
Indices: 52871--53201 Score: 431
Period size: 139 Copynumber: 2.4 Consensus size: 138
52861 ATAGATCAGC
* *
52871 ATCAACATTTCCAGATA-GAGTTCATAATGAGAAGAACTCATCTGAAGGGGAAGAAGAAGTTCAT
1 ATCAACATTTCTAGA-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * * *
52935 AATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACCTATGGAGTTGAATGAAATAAGAACC
65 AATGAAAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTAAATGAAAT-AGAACC
53000 TCACTTGAGG
129 TCACTTGAGG
*
53010 ATCAACATTT-TCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAATTTCA
1 ATCAACATTTCT-AGAAGG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
*
53073 TAATGAAAAGAACTTGTTCAACCTT-GCCTTAATTCATCACATATGAAGTTAAAT-CAAT-GACA
64 TAATGAAAAGAACTTGTTCAACCTTAG-CTTAATTCATCACATATGAAGTTAAATGAAATAGA-A
**
53135 CCTCTTTTGAGG
127 CCTCACTTGAGG
* * * *
53147 ATCAGCATTTCTAGAAGGAGTTTATAATGAGAAGAACTTATCTGAACAGGAAGAA
1 ATCAACATTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAA
53202 CTTGTTTCAC
Statistics
Matches: 170, Mismatches: 15, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
136 2 0.01
137 57 0.34
138 9 0.05
139 102 0.60
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (138 bp):
ATCAACATTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAAAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTAAATGAAATAGAACCTC
ACTTGAGG
Found at i:53425 original size:11 final size:11
Alignment explanation
Indices: 53409--53442 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
53399 TTCCCATTTA
53409 TTTTTATTATT
1 TTTTTATTATT
53420 TTTTTATTACTT
1 TTTTTATTA-TT
*
53432 TTATTATTATT
1 TTTTTATTATT
53443 ATAATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:53438 original size:3 final size:3
Alignment explanation
Indices: 53406--53500 Score: 88
Period size: 3 Copynumber: 32.0 Consensus size: 3
53396 TTTTTCCCAT
* * *
53406 TTA TTT TTA TTA TT- TTT TTA TTA CTT- TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * * *
53450 TTA TTA TAA TAA TTA TTA TTA TTA TAA TTA TTC TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
53496 -TA TTA
1 TTA TTA
53501 ATAAATAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
2 6 0.08
3 65 0.86
4 5 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:53461 original size:15 final size:15
Alignment explanation
Indices: 53432--53500 Score: 99
Period size: 15 Copynumber: 4.8 Consensus size: 15
53422 TTTATTACTT
53432 TTATTATTATTATAA
1 TTATTATTATTATAA
*
53447 TTATTATTATAATAA
1 TTATTATTATTATAA
53462 TTATTATTATTATAA
1 TTATTATTATTATAA
*
53477 TTATTCTTA-TAT-A
1 TTATTATTATTATAA
53490 TTATTA-TATTA
1 TTATTATTATTA
53501 ATAAATAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
12 2 0.04
13 8 0.16
14 3 0.06
15 36 0.73
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTATTATAA
Found at i:55047 original size:18 final size:21
Alignment explanation
Indices: 55012--55051 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
55002 TTAAGAAAAA
55012 TTATTATATTCTTCTTAATAT
1 TTATTATATTCTTCTTAATAT
55033 TTATT-TATT-TT-TTAATAT
1 TTATTATATTCTTCTTAATAT
55051 T
1 T
55052 AAAGAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 4 0.21
21 5 0.26
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTATATTCTTCTTAATAT
Found at i:59413 original size:21 final size:21
Alignment explanation
Indices: 59389--59435 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
59379 ATTCTGACTA
59389 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
59410 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
59431 TCGCA
1 TCGCA
59436 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:59460 original size:20 final size:20
Alignment explanation
Indices: 59431--59503 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
59421 TTTTCCTAAT
59431 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
59451 TCGAAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
59471 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
*
59491 TCGCAATGCGAAT
1 TCGCAACGCGAAT
59504 CTGACTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:59722 original size:22 final size:22
Alignment explanation
Indices: 59697--59758 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
59687 GGCGACATCC
59697 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
59719 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
59737 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
59759 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:60115 original size:20 final size:20
Alignment explanation
Indices: 60090--60138 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
60080 CAATGAGTGA
60090 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
60110 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
60130 ATCGCAACG
1 ATCGCAACG
60139 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:60209 original size:20 final size:20
Alignment explanation
Indices: 60180--60229 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
60170 TACGATTTTT
*
60180 GCGTTCCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
60200 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
60220 GTGTTGCGAT
1 GCGTTGCGAT
60230 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:60235 original size:20 final size:20
Alignment explanation
Indices: 60197--60251 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
60187 GATAGTCAAA
* **
60197 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
60217 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
60237 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
60252 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:60259 original size:20 final size:20
Alignment explanation
Indices: 60216--60259 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
60206 CGATAGTCAT
** *
60216 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
60236 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
60256 TTTC
1 TTTC
60260 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:62145 original size:20 final size:20
Alignment explanation
Indices: 62109--62232 Score: 125
Period size: 20 Copynumber: 6.5 Consensus size: 20
62099 AGAATAGTTT
* *
62109 ACTATCACAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
62129 ACTATTGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
62149 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
62165 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
62183 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* * **
62203 ACTATTGCAATGTGAATTTG
1 ACTATCGCAATGCGAAAATG
62223 ACTATCGCAA
1 ACTATCGCAA
62233 CGAGAGAATC
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.08
16 4 0.05
17 4 0.05
18 4 0.05
20 67 0.78
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:62183 original size:34 final size:34
Alignment explanation
Indices: 62135--62253 Score: 121
Period size: 34 Copynumber: 3.3 Consensus size: 34
62125 AATGACTATT
*
62135 GCAACGCGAAAATGACTATCGCAACGAGAGAATC
1 GCAATGCGAAAATGACTATCGCAACGAGAGAATC
* *
62169 GCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATT
1 GCAATGCGAAAATGACTATCGCAA--CG-AGA-GA--ATC
* **
62209 GCAATGTGAATTTGACTATCGCAACGAGAGAATC
1 GCAATGCGAAAATGACTATCGCAACGAGAGAATC
*
62243 GTAATGCGAAA
1 GCAATGCGAAA
62254 TGAAAATTAC
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
34 33 0.49
36 4 0.06
37 4 0.06
38 4 0.06
40 23 0.34
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (34 bp):
GCAATGCGAAAATGACTATCGCAACGAGAGAATC
Found at i:62230 original size:74 final size:74
Alignment explanation
Indices: 62109--62253 Score: 227
Period size: 74 Copynumber: 2.0 Consensus size: 74
62099 AGAATAGTTT
*
62109 ACTATCACAATGTGAAAATGACTATTGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
1 ACTATCACAATGCGAAAATGACTATTGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
62174 GCGAAAATG
66 GCGAAAATG
* * * ** *
62183 ACTATCGCAATGCGAAAATGACTATTGCAATGTGAATTTGACTATCGCAACGAGAGAATCGTAAT
1 ACTATCACAATGCGAAAATGACTATTGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
62248 GCGAAA
66 GCGAAA
62254 TGAAAATTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (74 bp):
ACTATCACAATGCGAAAATGACTATTGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
GCGAAAATG
Found at i:62316 original size:20 final size:20
Alignment explanation
Indices: 62279--62432 Score: 111
Period size: 20 Copynumber: 8.3 Consensus size: 20
62269 GATTCTCTCG
**
62279 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
62299 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
62319 TTGC-A-A-T--TTTGTTG--
1 TTGCGATAGTCATTT-TCGCA
**
62333 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
62352 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
**
62366 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
62386 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
62406 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
62426 TTGCGAT
1 TTGCGAT
62433 TTTAAGTTTC
Statistics
Matches: 108, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
14 11 0.10
15 4 0.04
16 8 0.07
17 6 0.06
18 6 0.06
19 8 0.07
20 65 0.60
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:63007 original size:21 final size:21
Alignment explanation
Indices: 62916--63023 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
62906 GACTCACCTG
62916 TCATCGTTCAAGAGGCCTCCTC
1 TCATCGTTCAAGAGGCC-CCTC
* *
62938 T-ATCGTTTAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
* ** *
62958 TAATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
62979 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
63000 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
63021 TCA
1 TCA
63024 ACATTCTAGA
Statistics
Matches: 64, Mismatches: 21, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
20 4 0.06
21 59 0.92
22 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:64396 original size:14 final size:14
Alignment explanation
Indices: 64377--64412 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
64367 ATTGTTTAAT
64377 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
64391 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
64405 TGATTTGT
1 TGATTTGT
64413 TTAATTAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:64572 original size:33 final size:33
Alignment explanation
Indices: 64519--64593 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
64509 CAGACTATCG
**
64519 CAATGCGTAAATGACTATCGCAACGAGAGAATCA
1 CAATGCG-AAATGAAAATCGCAACGAGAGAATCA
* *
64553 CAATGCGAAATGAAAATCGCAACGAGTGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
64586 CAATGCGA
1 CAATGCGA
64594 TTTTCATTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 30 0.81
34 7 0.19
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:64644 original size:20 final size:20
Alignment explanation
Indices: 64619--64712 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
64609 GCGATTCTCT
*
64619 CGTTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
64639 CGTTGTGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
64659 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
64679 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
64699 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
64713 AATGAATGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 64 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:67150 original size:24 final size:24
Alignment explanation
Indices: 67116--67165 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
67106 CTGAAAAATC
67116 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
67140 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
67164 AT
1 AT
67166 AACATTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:68054 original size:20 final size:20
Alignment explanation
Indices: 68029--68159 Score: 201
Period size: 20 Copynumber: 6.5 Consensus size: 20
68019 GTCAGAATCT
*
68029 CGTTGCGATTTACAAATTCG
1 CGTTGCGATTTACGAATTCG
*
68049 CGTTGCGATTTACAAATTCG
1 CGTTGCGATTTACGAATTCG
*
68069 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGAATTCG
*
68089 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGAATTCG
68109 CGTTGCGATTTACGTAA-TCG
1 CGTTGCGATTTACG-AATTCG
*
68129 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGAATTCG
68149 CGTTGCGATTT
1 CGTTGCGATTT
68160 CGCATTGCGA
Statistics
Matches: 105, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
19 1 0.01
20 103 0.98
21 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGAATTCG
Found at i:68248 original size:20 final size:20
Alignment explanation
Indices: 68225--68290 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
68215 CAGAATCGCG
68225 TTGCGAATCTGGAAACTGAT
1 TTGCGAATCTGGAAACTGAT
* * **
68245 TTGCG-ATACCGGAGA-TCGCG
1 TTGCGAAT-CTGGAAACT-GAT
68265 TTGCGAATCTGGAAACTGAT
1 TTGCGAATCTGGAAACTGAT
68285 TTGCGA
1 TTGCGA
68291 TACCGGAGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGCGAATCTGGAAACTGAT
Found at i:68250 original size:40 final size:40
Alignment explanation
Indices: 68219--68312 Score: 188
Period size: 40 Copynumber: 2.4 Consensus size: 40
68209 GATAGTCAGA
68219 ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAG
1 ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAG
68259 ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAG
1 ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAG
68299 ATCGCGTTGCGAAT
1 ATCGCGTTGCGAAT
68313 TATCGATCGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (40 bp):
ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAG
Found at i:68308 original size:20 final size:20
Alignment explanation
Indices: 68245--68310 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
68235 GGAAACTGAT
68245 TTGCGATACCGGAGATCGCG
1 TTGCGATACCGGAGATCGCG
* * **
68265 TTGCGA-ATCTGGA-AACTGAT
1 TTGCGATA-CCGGAGATC-GCG
68285 TTGCGATACCGGAGATCGCG
1 TTGCGATACCGGAGATCGCG
68305 TTGCGA
1 TTGCGA
68311 ATTATCGATC
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (20 bp):
TTGCGATACCGGAGATCGCG
Found at i:71558 original size:41 final size:42
Alignment explanation
Indices: 71453--71573 Score: 131
Period size: 41 Copynumber: 3.0 Consensus size: 42
71443 AAAGTAGAAT
* * * * *
71453 ATCGCACTTTCGATTCTTGTATAAAGTAAAACGG-AAGGAAG
1 ATCGCACTTTCGATTCTAGTCTAAAGTAGAACGGAAAGAAAC
* * *
71494 ATCACACTTTCGATTCTATTCT-AAGCAGAACGGAAAGAAAC
1 ATCGCACTTTCGATTCTAGTCTAAAGTAGAACGGAAAGAAAC
* *
71535 ATCGCACTTTCGATACTCGTCTAAAGTAGAAC-GAAAGAA
1 ATCGCACTTTCGATTCTAGTCTAAAGTAGAACGGAAAGAA
71574 GCATTACATT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
40 9 0.14
41 48 0.74
42 8 0.12
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (42 bp):
ATCGCACTTTCGATTCTAGTCTAAAGTAGAACGGAAAGAAAC
Found at i:73337 original size:18 final size:18
Alignment explanation
Indices: 73314--73349 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
73304 GACTATTATG
73314 TTAGATTCCATGTCAGCA
1 TTAGATTCCATGTCAGCA
73332 TTAGATTCCATGTCAGCA
1 TTAGATTCCATGTCAGCA
73350 ACTTTCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (18 bp):
TTAGATTCCATGTCAGCA
Found at i:78332 original size:32 final size:32
Alignment explanation
Indices: 78306--78395 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
78296 TGACCTAAAC
*
78306 CGAAAATTAATTGATCTGATATTGACCTGATT
1 CGAAAATCAATTGATCTGATATTGACCTGATT
* *
78338 CAAAAATCAATTGATCTGATATTGACCCGATT
1 CGAAAATCAATTGATCTGATATTGACCTGATT
*
78370 CGAAAATCAATTAATCTGATATTGAC
1 CGAAAATCAATTGATCTGATATTGAC
78396 TTGACCCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
CGAAAATCAATTGATCTGATATTGACCTGATT
Found at i:79389 original size:21 final size:21
Alignment explanation
Indices: 79354--79408 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
79344 AAATAATAAT
*
79354 AAAATAT-TATTTTTATTCAATA
1 AAAATATATA-TTTAATTCAA-A
*
79376 AAAATATATATTTAATTGAAA
1 AAAATATATATTTAATTCAAA
79397 AAAATAATATAT
1 AAAAT-ATATAT
79409 AGAGGGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 21 0.72
23 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAATATATATTTAATTCAAA
Found at i:81874 original size:104 final size:105
Alignment explanation
Indices: 81723--81980 Score: 346
Period size: 104 Copynumber: 2.5 Consensus size: 105
81713 GCCAATTTTT
* * * * * *
81723 GTATCGGTACTCAAGGGAGTGTCAATA--CTGAGAGT-AGAGTATCGATACTCTTAGTATGAGTA
1 GTATCGATACTCAAGGGAGTATTAATACCCTAAGA-TAAGAGTATTGATACTCTCAGTATGAGTA
* *
81785 TCAATACTTTGTTAATTTTCAGAACATCAAAACAAAATTTA
65 TCAATACTTTGATAATTTTCAAAACATCAAAACAAAATTTA
*
81826 GTATCGATACTC-AGGGTAGTATTAATACCC-CAGATAAGAGTATTGATACTCTCAGTATGAGTA
1 GTATCGATACTCAAGGG-AGTATTAATACCCTAAGATAAGAGTATTGATACTCTCAGTATGAGTA
* *
81889 TCAATACTTTGATAATTTTGAAAACATCAAAGCAAAATTTA
65 TCAATACTTTGATAATTTTCAAAACATCAAAACAAAATTTA
* *
81930 GTATCGATACTCAAGGGAGTATTGATACCCTAATATAAGAGTATTGATACT
1 GTATCGATACTCAAGGGAGTATTAATACCCTAAGATAAGAGTATTGATACT
81981 ATAGCTAGGA
Statistics
Matches: 136, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
102 4 0.03
103 20 0.15
104 89 0.65
105 23 0.17
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (105 bp):
GTATCGATACTCAAGGGAGTATTAATACCCTAAGATAAGAGTATTGATACTCTCAGTATGAGTAT
CAATACTTTGATAATTTTCAAAACATCAAAACAAAATTTA
Found at i:82085 original size:20 final size:21
Alignment explanation
Indices: 82062--82101 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
82052 TGTGTATTGG
*
82062 TACTCAAGGG-TCAGTATCGA
1 TACTCAAGGGATCAATATCGA
*
82082 TACTGAAGGGATCAATATCG
1 TACTCAAGGGATCAATATCG
82102 GTACCGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (21 bp):
TACTCAAGGGATCAATATCGA
Found at i:86703 original size:13 final size:13
Alignment explanation
Indices: 86683--86727 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
86673 ACAATACAAA
86683 ACTTTCATATCTC
1 ACTTTCATATCTC
* * *
86696 ATTTTCATCTTTC
1 ACTTTCATATCTC
86709 ACTTTCATA-CTC
1 ACTTTCATATCTC
86721 ACTTTCA
1 ACTTTCA
86728 CATTTCATGT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (13 bp):
ACTTTCATATCTC
Found at i:89032 original size:21 final size:21
Alignment explanation
Indices: 89006--89047 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
88996 CGATGTTTTT
*
89006 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTATAGCA
89027 GTGCATCGGTACACTATAGCA
1 GTGCATCGGTACACTATAGCA
89048 TTGTTCATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
GTGCATCGGTACACTATAGCA
Found at i:89144 original size:17 final size:17
Alignment explanation
Indices: 89122--89157 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
89112 CGTGTCCCGA
89122 CCGGATGTTACGGGTAC
1 CCGGATGTTACGGGTAC
* *
89139 CCGGATTTTGCGGGTAC
1 CCGGATGTTACGGGTAC
89156 CC
1 CC
89158 AGTTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (17 bp):
CCGGATGTTACGGGTAC
Found at i:89796 original size:19 final size:19
Alignment explanation
Indices: 89769--89827 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
89759 CCGGACTCAA
89769 AACTT-ATTTCATATTCAT
1 AACTTAATTTCATATTCAT
89787 AACTTAATTTCATATTCAT
1 AACTTAATTTCATATTCAT
* *
89806 AGCTTATTTTCA-AGTTCAT
1 AACTTAATTTCATA-TTCAT
89825 AAC
1 AAC
89828 CCAATGCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.17
19 30 0.83
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (19 bp):
AACTTAATTTCATATTCAT
Found at i:97972 original size:18 final size:18
Alignment explanation
Indices: 97949--98013 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
97939 ATGATACACA
97949 ATATCATACATAATAGTC
1 ATATCATACATAATAGTC
* * **
97967 ATATCAAAGTCATGATAAAC
1 ATATCATA--CATAATAGTC
97987 AATATCATACATAATAGTC
1 -ATATCATACATAATAGTC
98006 ATATCATA
1 ATATCATA
98014 TTCTTTTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 15 0.42
19 7 0.19
20 7 0.19
21 7 0.19
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (18 bp):
ATATCATACATAATAGTC
Found at i:97973 original size:39 final size:39
Alignment explanation
Indices: 97929--98011 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
97919 CTTATGATTT
*
97929 TATCAAAACCATGATACACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
**
97968 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
98007 TATCA
1 TATCA
98012 TATTCTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.28
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATCATACATAATAGTCA
Found at i:98061 original size:13 final size:13
Alignment explanation
Indices: 98041--98100 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
98031 ACAATACAAA
*
98041 ACTTTCATATCTC
1 ACTTTCATATTTC
* *
98054 ATTTTCATCTTTC
1 ACTTTCATATTTC
98067 ACTTTCATA-TTC
1 ACTTTCATATTTC
*
98079 ACTTTCACATTTC
1 ACTTTCATATTTC
*
98092 ATTTTCATA
1 ACTTTCATA
98101 ATCCGTACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (13 bp):
ACTTTCATATTTC
Found at i:98189 original size:19 final size:19
Alignment explanation
Indices: 98160--98218 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
98150 TCGGACTCAA
98160 AACTT-ATTTCAAATTCAT
1 AACTTAATTTCAAATTCAT
* *
98178 AACTTAATTTCAGATTTAT
1 AACTTAATTTCAAATTCAT
* * *
98197 AGCTTATTTTCAAGTTCAT
1 AACTTAATTTCAAATTCAT
98216 AAC
1 AAC
98219 CCAATGCATA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
18 5 0.16
19 27 0.84
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (19 bp):
AACTTAATTTCAAATTCAT
Found at i:105155 original size:37 final size:37
Alignment explanation
Indices: 105113--105187 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
105103 TTCATATTCC
* * *
105113 TTGTCCTTTTTGTTTTATTTTTATATAGCTTCATTTT
1 TTGTCCCTTTTGTTTTATTTTGACATAGCTTCATTTT
* *
105150 TTGTCCCTTTTGTTTTGTTTTGACCTAGCTTCATTTT
1 TTGTCCCTTTTGTTTTATTTTGACATAGCTTCATTTT
105187 T
1 T
105188 ATCGTGAGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.11, C:0.15, G:0.11, T:0.64
Consensus pattern (37 bp):
TTGTCCCTTTTGTTTTATTTTGACATAGCTTCATTTT
Found at i:111847 original size:21 final size:21
Alignment explanation
Indices: 111823--111862 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
111813 AAAATTAGAG
111823 CTAAGA-ATTTAAAACTTAAGA
1 CTAAGATA-TTAAAACTTAAGA
*
111844 CTAAGATATTAAAATTTAA
1 CTAAGATATTAAAACTTAA
111863 AGTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
CTAAGATATTAAAACTTAAGA
Found at i:116406 original size:13 final size:14
Alignment explanation
Indices: 116381--116436 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 14
116371 ATAATAAATA
116381 ATTATAAATATATT
1 ATTATAAATATATT
116395 ATTATAAA-ATATT
1 ATTATAAATATATT
*
116408 ATT-TTAAT-TATT
1 ATTATAAATATATT
*
116420 -TTAAAAATATATAT
1 ATTATAAATATAT-T
116434 ATT
1 ATT
116437 CATGTAGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
11 2 0.06
12 10 0.29
13 11 0.32
14 9 0.26
15 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:117360 original size:22 final size:24
Alignment explanation
Indices: 117335--117380 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
117325 ATAATAACAC
117335 CAAAAA-TAAAAAT-TAAATTATT
1 CAAAAATTAAAAATATAAATTATT
*
117357 CAAAAATTAAAAATATATATTATT
1 CAAAAATTAAAAATATAAATTATT
117381 ACTTTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 7 0.33
24 8 0.38
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
CAAAAATTAAAAATATAAATTATT
Found at i:117724 original size:23 final size:23
Alignment explanation
Indices: 117666--117722 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
117656 TTGTGACATG
*
117666 TTCTCTGCCTTTATGGCATGTTT
1 TTCTCTGCCTTTGTGGCATGTTT
* *
117689 ATCTCTGTCTTTGTGGCAT-TTT
1 TTCTCTGCCTTTGTGGCATGTTT
117711 TTCTCTGCCTTT
1 TTCTCTGCCTTT
117723 TGGTAGCTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.07, C:0.23, G:0.16, T:0.54
Consensus pattern (23 bp):
TTCTCTGCCTTTGTGGCATGTTT
Found at i:121737 original size:14 final size:15
Alignment explanation
Indices: 121707--121739 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
121697 TTCTTTAATT
121707 AATTTAAGATAAAAA
1 AATTTAAGATAAAAA
*
121722 AATTTAA-ATCAAAA
1 AATTTAAGATAAAAA
121736 AATT
1 AATT
121740 ATATTCTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (15 bp):
AATTTAAGATAAAAA
Found at i:123259 original size:5 final size:4
Alignment explanation
Indices: 123230--123283 Score: 51
Period size: 4 Copynumber: 13.5 Consensus size: 4
123220 AACATAATGA
*
123230 AAAT AAAT -ATT AAAT -AA- AAAT AAGAT AAGAT AAAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AA-AT -AAAT AAAT AAAT AAAT
123278 AAAT AA
1 AAAT AA
123284 CAACATACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
3 6 0.14
4 26 0.60
5 9 0.21
6 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:124925 original size:3 final size:3
Alignment explanation
Indices: 124911--124956 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
124901 AGTTGTAATT
*
124911 TAA TAT TAA TAA TAAA TAA -ACA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
124957 ATTATAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 1 0.03
3 33 0.87
4 4 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:125452 original size:91 final size:91
Alignment explanation
Indices: 125292--125489 Score: 249
Period size: 91 Copynumber: 2.2 Consensus size: 91
125282 GTGACATGGC
* * * * * * * *
125292 TCCTACATGATGAGGAGGTCTGGTCGGGGGATGATACGGTTCCTACGAAATGAGGATGGCTGGCC
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTCATACGAAATGAAGATGGATGGCA
125357 ATCTTTAGG-AGTGGCGATAACACGGT
66 ATCTTTAGGAAG-GGCGATAACACGGT
* *
125383 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTCATAC-ATGATGAAGA-GTTATGG
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTCATACGA-AATGAAGATG-GATGG
*
125446 CAATCTTTAGGAAGGGCGATAACATGGT
64 CAATCTTTAGGAAGGGCGATAACACGGT
125474 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
125490 CGACTGGTTA
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 2 0.02
91 89 0.96
92 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (91 bp):
TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTCATACGAAATGAAGATGGATGGCA
ATCTTTAGGAAGGGCGATAACACGGT
Found at i:125614 original size:133 final size:134
Alignment explanation
Indices: 125376--125701 Score: 433
Period size: 133 Copynumber: 2.4 Consensus size: 134
125366 AGTGGCGATA
*
125376 ACACGGTTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTCATACATGATGAAGAGT
1 ACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTCATACATGATGAAGAGT
* *** *
125441 TATGGCAATCTTTAGGAAGGGCGATAACATGGTTCCTACGTGATGAGGACGACTGGTTATCTA-G
66 TATGACAATCTTTAGGAAGGGCGATAACACAATTCCTACGTGATAAGGACGACTGGTTATCTATG
125505 GGTG
131 GGTG
* *
125509 ACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGATAC-GCTTCATACGTGATGAAGAG
1 ACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGC-TCATACATGATGAAGAG
* * * **
125573 TTCTGACCATCTTTAGGAAGGGCGATAACACAATTCCTACGTGATAAGGATGGTTGGTTATCTAT
65 TTATGACAATCTTTAGGAAGGGCGATAACACAATTCCTACGTGATAAGGACGACTGGTTATCTAT
*
125638 GGTTG
130 GGGTG
** ** * * *
125643 ACACGGCTCCTACACGATGA-GAGGTCTGGTTAGGGGATGACACTGTTCCTACATGATGA
1 ACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTCATACATGATGA
125702 GGATAACTTG
Statistics
Matches: 168, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
132 2 0.01
133 143 0.85
134 23 0.14
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
ACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTCATACATGATGAAGAGT
TATGACAATCTTTAGGAAGGGCGATAACACAATTCCTACGTGATAAGGACGACTGGTTATCTATG
GGTG
Found at i:125989 original size:66 final size:65
Alignment explanation
Indices: 125776--125982 Score: 168
Period size: 66 Copynumber: 3.2 Consensus size: 65
125766 GAAAAACAAA
* * * * * *
125776 CTCAAAGATGATGTGTTTCAAAAGCAACTATCTCGAAA-GAGACCAAATTCGTTTCAAGGTAAAC
1 CTCAAAGATGA-CTGTTT-AAAGGAAACTGTCTC-AAACGAGACAAAATTCGTTTCAAGGGAAAC
125840 GA-
63 GAT
* * * * * *
125842 CTCAAAAATGACT-TTTAAAGGAAACTGTCTCCAGCGAGACAAAATTTGTTTTTAAGGGAAACGT
1 CTCAAAGATGACTGTTTAAAGGAAACTGTCTCAAACGAGACAAAATTCG-TTTCAAGGGAAACGA
125906 T
65 T
* * * ** * * *
125907 CTCAAAGCTCAGTGTTTCATGGGAAGCTGTCTCAAATGAGATAAAATTCGTTTCAAGGGAAACGA
1 CTCAAAGATGACTGTTT-AAAGGAAACTGTCTCAAACGAGACAAAATTCGTTTCAAGGGAAACGA
125972 T
65 T
125973 CTCAAAGATG
1 CTCAAAGATG
125983 TTTGTTTTGT
Statistics
Matches: 108, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
62 1 0.01
63 23 0.21
64 15 0.14
65 10 0.09
66 35 0.32
67 24 0.22
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (65 bp):
CTCAAAGATGACTGTTTAAAGGAAACTGTCTCAAACGAGACAAAATTCGTTTCAAGGGAAACGAT
Found at i:126027 original size:35 final size:34
Alignment explanation
Indices: 125948--126051 Score: 102
Period size: 35 Copynumber: 3.0 Consensus size: 34
125938 TCAAATGAGA
*
125948 TAAAATTCGTTTCAAGGGAA-ACGATCTCAAAGATG
1 TAAAATTTGTTTCAAGGGAACA-GA-CTCAAAGATG
****
125983 TTTGTTTTGTTTCAAGGGAACAGACTCAAAGATGG
1 TAAAATTTGTTTCAAGGGAACAGACTCAAAGAT-G
* *
126018 TAAAATTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TAAAATTTGTTT-CAAGGGAACAGACTCAAAGAT
126052 TTTTCTCAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
34 9 0.16
35 26 0.47
36 20 0.36
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (34 bp):
TAAAATTTGTTTCAAGGGAACAGACTCAAAGATG
Found at i:126266 original size:27 final size:28
Alignment explanation
Indices: 126236--126309 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
126226 ACTCAAAGTT
*
126236 GATTTTGTT-AATAGAAACAAACTCAAA
1 GATTTTGTTCAAAAGAAACAAACTCAAA
* * *
126263 GATTTTTTTCAAAAGGAACAGACTCAAA
1 GATTTTGTTCAAAAGAAACAAACTCAAA
*
126291 GA-TTTGTTTCAAGAGAAAC
1 GATTTTG-TTCAAAAGAAAC
126310 TGTCTCAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 11 0.29
28 27 0.71
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (28 bp):
GATTTTGTTCAAAAGAAACAAACTCAAA
Found at i:126317 original size:28 final size:28
Alignment explanation
Indices: 126248--126309 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
126238 TTTTGTTAAT
* *
126248 AGAAACAAACTCAAAGATTTTTTTCAAA
1 AGAAACAGACTCAAAGATTTGTTTCAAA
* *
126276 AGGAACAGACTCAAAGATTTGTTTCAAG
1 AGAAACAGACTCAAAGATTTGTTTCAAA
126304 AGAAAC
1 AGAAAC
126310 TGTCTCAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (28 bp):
AGAAACAGACTCAAAGATTTGTTTCAAA
Found at i:128095 original size:41 final size:41
Alignment explanation
Indices: 128035--128117 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
128025 GTGTTTGTTG
* *
128035 AAGGTCAGAAAATCTCATCGTTAGAGTTCAATTTCCAAGCA
1 AAGGTAAGAAAATCGCATCGTTAGAGTTCAATTTCCAAGCA
128076 AAGGTAAGAAAATCGCATCGTTAGAGTTCAATTTCCAAGCA
1 AAGGTAAGAAAATCGCATCGTTAGAGTTCAATTTCCAAGCA
128117 A
1 A
128118 CTGACCTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (41 bp):
AAGGTAAGAAAATCGCATCGTTAGAGTTCAATTTCCAAGCA
Found at i:132415 original size:5 final size:5
Alignment explanation
Indices: 132339--132424 Score: 61
Period size: 5 Copynumber: 16.6 Consensus size: 5
132329 AACATAATGG
* * *
132339 AAATA AATATT AAATAA AAATA AGATA ACATA AAATA AAAT- AAAT- AAAT-
1 AAATA AA-ATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA
*
132388 AAATAA CAACATA CAAATG AAATA AAATA AAATA AAA
1 AAAT-A -AA-ATA -AAATA AAATA AAATA AAATA AAA
132425 AACACAACAT
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
4 12 0.18
5 38 0.56
6 10 0.15
7 6 0.09
8 2 0.03
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:135675 original size:21 final size:21
Alignment explanation
Indices: 135624--135676 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
135614 ATTATTACTA
135624 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
135645 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
135666 TCGCAATGCGA
1 TCGCAATGCGA
135677 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:135691 original size:20 final size:21
Alignment explanation
Indices: 135666--135717 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
135656 TTTTCCCAAT
*
135666 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
135686 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
135707 TCGCAATGCGA
1 TCGCAATGCGA
135718 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:135696 original size:41 final size:41
Alignment explanation
Indices: 135651--135814 Score: 127
Period size: 41 Copynumber: 4.0 Consensus size: 41
135641 AATTTCGCGT
*
135651 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
135692 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
135733 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
135774 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
135815 CGCAATTAAG
Statistics
Matches: 89, Mismatches: 28, Indels: 12
0.69 0.22 0.09
Matches are distributed among these distances:
39 2 0.02
40 8 0.09
41 77 0.87
43 1 0.01
44 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:135761 original size:21 final size:21
Alignment explanation
Indices: 135727--135799 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
135717 ATACTGACTA
* *
135727 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
135748 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
135768 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
135789 TCGCAATGCGA
1 TCGCAATGCGA
135800 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:135814 original size:20 final size:19
Alignment explanation
Indices: 135789--135874 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
135779 TTTTCATAAT
135789 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAAT-CGTAAA
* *
135809 TCGCAACGC-AATTAAGTAAA
1 TCGCAATGCGAA-T-CGTAAA
135829 TCGCAATGCGAAT--T-AA
1 TCGCAATGCGAATCGTAAA
*
135845 TCGCAATGCGAATCG-ACTA
1 TCGCAATGCGAATCGTA-AA
135864 TCGCAATGCGA
1 TCGCAATGCGA
135875 CTAAACGCGT
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
16 15 0.27
17 1 0.02
19 14 0.25
20 24 0.43
21 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (19 bp):
TCGCAATGCGAATCGTAAA
Found at i:135848 original size:16 final size:16
Alignment explanation
Indices: 135827--135857 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
135817 CAATTAAGTA
135827 AATCGCAATGCGAATT
1 AATCGCAATGCGAATT
135843 AATCGCAATGCGAAT
1 AATCGCAATGCGAAT
135858 CGACTATCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (16 bp):
AATCGCAATGCGAATT
Found at i:135868 original size:19 final size:16
Alignment explanation
Indices: 135827--135874 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 16
135817 CAATTAAGTA
*
135827 AATCGCAATGCGAATT
1 AATCGCAATGCGAATG
135843 AATCGCAATGCGAATCG
1 AATCGCAATGCGAAT-G
135860 ACTATCGCAATGCGA
1 A--ATCGCAATGCGA
135875 CTAAACGCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 15 0.54
17 1 0.04
19 12 0.43
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (16 bp):
AATCGCAATGCGAATG
Found at i:136430 original size:33 final size:33
Alignment explanation
Indices: 136393--136497 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
136383 GGAAATGACT
* **
136393 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
1 ATCGCAACGAGATAATCGCAACGCGAAACCAAA
*
136426 ATCGCAACGAGATAATCGCAATGCGAAACCAAA
1 ATCGCAACGAGATAATCGCAACGCGAAACCAAA
*
136459 ATCGCAATGAGATAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGATAATCGCAACGCGAAACCAAA
136492 ATCGCA
1 ATCGCA
136498 TTGCGATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGATAATCGCAACGCGAAACCAAA
Found at i:136463 original size:19 final size:19
Alignment explanation
Indices: 136439--136503 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
136429 GCAACGAGAT
136439 AATCGCAATGCGAAACCAA
1 AATCGCAATGCGAAACCAA
* *
136458 AATCGCAAT--G--A-GAT
1 AATCGCAATGCGAAACCAA
*
136472 AATCGCAACGCGAAACCAA
1 AATCGCAATGCGAAACCAA
*
136491 AATCGCATTGCGA
1 AATCGCAATGCGA
136504 TTTTCATTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 21 0.62
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAACCAA
Found at i:136534 original size:14 final size:14
Alignment explanation
Indices: 136515--136603 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
136505 TTTCATTTCG
136515 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
136529 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
136546 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
*
136562 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
136581 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
136595 CGTTGCGAT
1 CGTTGCGAT
136604 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 25 0.41
16 10 0.16
17 10 0.16
19 16 0.26
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:136540 original size:33 final size:33
Alignment explanation
Indices: 136498--136624 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
136488 CAAAATCGCA
136498 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
136531 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
136564 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
136597 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATTTTCATTT-CGCGTTGCGATT
136625 TTCATTTCAA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 77 0.87
34 12 0.13
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:137906 original size:12 final size:12
Alignment explanation
Indices: 137889--137914 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
137879 TCCACTTCGA
137889 GAGCCATCACCT
1 GAGCCATCACCT
137901 GAGCCATCACCT
1 GAGCCATCACCT
137913 GA
1 GA
137915 TCCCGACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.38, G:0.19, T:0.15
Consensus pattern (12 bp):
GAGCCATCACCT
Found at i:138507 original size:94 final size:94
Alignment explanation
Indices: 138315--138619 Score: 469
Period size: 94 Copynumber: 3.3 Consensus size: 94
138305 TAGATTTCTT
* * *
138315 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
138376 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
138405 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
138470 ATTTGTCTTTGTTTTGTATTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* **
138499 AGTAAATTTGTTCGGTTATTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
138564 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
138593 AGTAAATTTGTT-GGTTTGCTGCCAATT
1 AGTAAATTTATTCGG-TTGCTGCCAATT
138620 GAAACTATTC
Statistics
Matches: 198, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
90 35 0.18
92 3 0.02
93 23 0.12
94 137 0.69
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:139088 original size:21 final size:21
Alignment explanation
Indices: 139064--139130 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
139054 TCATTCCTCG
139064 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
139085 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
139106 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
139127 AGAG
1 AGAG
139131 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:139088 original size:42 final size:42
Alignment explanation
Indices: 139042--139130 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
139032 CCTATTGTTG
* *
139042 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
139084 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
139126 AAGAG
1 AAGAG
139131 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:140510 original size:14 final size:14
Alignment explanation
Indices: 140476--140512 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
140466 GATTGTTTAA
140476 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
140490 ATAATTTGTAAAAG
1 TTGATTTGTAAAAG
140504 TTGATTTGT
1 TTGATTTGT
140513 TTAATTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:140656 original size:33 final size:33
Alignment explanation
Indices: 140619--140731 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
140609 AAAAATGACT
*
140619 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
*
140652 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
* * *
140685 ATCGCAACGCGAAATGAAAATTGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
140718 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
140732 CTAAATTCGC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
Found at i:140675 original size:19 final size:18
Alignment explanation
Indices: 140619--140710 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
140609 AAAAATGACT
140619 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
140638 ATCGCAA-TG--A-GAGA
1 ATCGCAAGCGAAATGAAA
140652 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
140671 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
140685 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
140704 ATTGCAA
1 ATCGCAA
140711 TGACAAAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
14 20 0.36
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 26 0.46
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:140689 original size:14 final size:14
Alignment explanation
Indices: 140637--140693 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
140627 GCGAAATGAA
*
140637 AATCGCAATGAGAG
1 AATCGCAACGAGAG
*
140651 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
140670 AATCGCAACGAGAG
1 AATCGCAACGAGAG
140684 AATCGCAACG
1 AATCGCAACG
140694 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:140759 original size:19 final size:19
Alignment explanation
Indices: 140737--140887 Score: 125
Period size: 19 Copynumber: 8.7 Consensus size: 19
140727 CGAAACTAAA
140737 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
140756 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
140772 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
140789 TTCGCATTGCGATTTTC--
1 TTCGCATTGCGATTTTCAT
*
140806 -TCG--TTGCAATTTTCAT
1 TTCGCATTGCGATTTTCAT
140822 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
140837 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
140855 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
140874 TTCCGCATTGCGAT
1 TT-CGCATTGCGAT
140888 AGACATTAAG
Statistics
Matches: 105, Mismatches: 11, Indels: 31
0.71 0.07 0.21
Matches are distributed among these distances:
14 26 0.25
16 12 0.11
17 12 0.11
19 44 0.42
20 11 0.10
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:140785 original size:33 final size:33
Alignment explanation
Indices: 140743--140867 Score: 205
Period size: 33 Copynumber: 3.8 Consensus size: 33
140733 TAAATTCGCA
* *
140743 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
140776 TTGCGATTTTCATTTCGCATTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
140809 TTGCAATTTTCATTTCGCATTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
140842 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
140868 AGTCATTTCC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:140882 original size:20 final size:19
Alignment explanation
Indices: 140840--140894 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
140830 GCGATTCTCT
**
140840 CATTGCGATTTTCATTTCG
1 CATTGCGATAGTCATTTCG
140859 CATTGCGATAGTCATTTCCG
1 CATTGCGATAGTCATTT-CG
*
140879 CATTGCGATAGACATT
1 CATTGCGATAGTCATT
140895 AAGATGACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (19 bp):
CATTGCGATAGTCATTTCG
Found at i:143422 original size:24 final size:24
Alignment explanation
Indices: 143388--143441 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
143378 CTGAAACATC
*
143388 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
143412 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
143436 ATCAAA
1 ATCAAA
143442 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:144204 original size:20 final size:20
Alignment explanation
Indices: 144183--144270 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
144173 TGTATTATCT
* *
144183 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
144203 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
144223 CGTTGCAAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
144243 CGTTACGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
144263 CGTTGCGA
1 CGTTGCGA
144271 TTTTGTATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:144304 original size:20 final size:20
Alignment explanation
Indices: 144178--144312 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
144168 GATTCTGTAT
*
144178 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
144198 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
144218 AATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
144238 AATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
144258 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
144279 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
144299 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
144313 TTTCCAAATT
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 79 0.81
21 14 0.14
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:144331 original size:41 final size:41
Alignment explanation
Indices: 144252--144333 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
144242 GCGTTACGAA
* ** * *
144252 AGTCAGTATCGCGTTGCGATTTTGTATTATCGCGTTGCGAT
1 AGTCAGTATCGCATTGCGATTTTCAAATATCGCATTGCGAT
144293 AGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCATTGCGAT
1 AGTCAGTATCGCATTGCGATTTT-CAAATATCGCATTGCGAT
144334 TTTCCAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (41 bp):
AGTCAGTATCGCATTGCGATTTTCAAATATCGCATTGCGAT
Found at i:144366 original size:20 final size:21
Alignment explanation
Indices: 144301--144373 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
144291 ATAGTCAGTA
144301 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
144322 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
144343 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
144363 TCGCATTGCGA
1 TCGCATTGCGA
144374 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 17 0.35
21 32 0.65
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:144388 original size:41 final size:42
Alignment explanation
Indices: 144300--144388 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
144290 GATAGTCAGT
* * *
144300 ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
* ** **
144342 TTCGCATTGCGA-TTTACTTATTCGCATTGCGAATTGGGAAA
1 ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
144383 ATCGCA
1 ATCGCA
144389 ACGCGAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 27 0.71
42 11 0.29
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (42 bp):
ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
Found at i:144415 original size:21 final size:22
Alignment explanation
Indices: 144363--144415 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
144353 ATTTACTTAT
144363 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
144384 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
144405 TCGCATTGCGA
1 TCGCATTGCGA
144416 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:145643 original size:17 final size:18
Alignment explanation
Indices: 145611--145644 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
145601 AAAATTTGTA
145611 ATTTATTTATAATTATAT
1 ATTTATTTATAATTATAT
*
145629 ATTTTTTTA-AATTATA
1 ATTTATTTATAATTATA
145645 ATTATGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTATTTATAATTATAT
Found at i:146199 original size:15 final size:15
Alignment explanation
Indices: 146179--146207 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
146169 TTCTGTTGTA
146179 AGAAGAAAGAAAGGG
1 AGAAGAAAGAAAGGG
146194 AGAAGAAAGAAAGG
1 AGAAGAAAGAAAGG
146208 AAAGGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
AGAAGAAAGAAAGGG
Found at i:146212 original size:20 final size:19
Alignment explanation
Indices: 146178--146225 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
146168 GTTCTGTTGT
*
146178 AAGAAGAAA-GAAAGGGAG
1 AAGAAGAAAGGAAAGGAAG
146196 AAGAAAGAAAGGAAAGGAAG
1 AAG-AAGAAAGGAAAGGAAG
146216 AAGAAGAAAG
1 AAGAAGAAAG
146226 CCCATAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.11
19 13 0.48
20 11 0.41
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAGGAAAGGAAG
Found at i:148961 original size:17 final size:15
Alignment explanation
Indices: 148939--148978 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
148929 ATATGTTATG
148939 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
148955 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
148971 TTAAATAT
1 TTAAATAT
148979 GTATGTCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:149032 original size:22 final size:22
Alignment explanation
Indices: 149007--149050 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
148997 TGTAAAAAGA
*
149007 ATAAATTTGACTATTTATAAAT
1 ATAAATTTGACTAGTTATAAAT
149029 ATAAATTTGACTAGTTATAAAT
1 ATAAATTTGACTAGTTATAAAT
149051 TCAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (22 bp):
ATAAATTTGACTAGTTATAAAT
Found at i:149139 original size:13 final size:13
Alignment explanation
Indices: 149121--149170 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
149111 TAAATAATTT
149121 TTAGTAATCATTA
1 TTAGTAATCATTA
*
149134 TTAGTAATTATTA
1 TTAGTAATCATTA
149147 -TAGCT--TCATTA
1 TTAG-TAATCATTA
*
149158 TTATTAATCATTA
1 TTAGTAATCATTA
149171 CTAAATCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
11 6 0.20
12 5 0.17
13 19 0.63
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (13 bp):
TTAGTAATCATTA
Found at i:149179 original size:24 final size:24
Alignment explanation
Indices: 149126--149180 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
149116 AATTTTTAGT
*
149126 AATCATTATTAGTAATTATTATAG
1 AATCATTATTAGTAATCATTATAG
** *
149150 CTTCATTATTATTAATCATTACTA-
1 AATCATTATTAGTAATCATTA-TAG
149174 AATCATT
1 AATCATT
149181 TGTATCAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (24 bp):
AATCATTATTAGTAATCATTATAG
Found at i:149225 original size:59 final size:59
Alignment explanation
Indices: 149152--149297 Score: 274
Period size: 59 Copynumber: 2.5 Consensus size: 59
149142 TATTATAGCT
*
149152 TCATTATTATTAATCATTACTAAATCATTTGTATCAAATCATTAAATATTAATAATAAA
1 TCATTATTAGTAATCATTACTAAATCATTTGTATCAAATCATTAAATATTAATAATAAA
*
149211 TCATTATTAGTAATCATTACTAAATCATTTGTATCAAATTATTAAATATTAATAATAAA
1 TCATTATTAGTAATCATTACTAAATCATTTGTATCAAATCATTAAATATTAATAATAAA
149270 TCATTATTAGTAATCATTACTAAATCAT
1 TCATTATTAGTAATCATTACTAAATCAT
149298 ATAGTACTAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 85 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (59 bp):
TCATTATTAGTAATCATTACTAAATCATTTGTATCAAATCATTAAATATTAATAATAAA
Found at i:149946 original size:11 final size:11
Alignment explanation
Indices: 149932--149957 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
149922 TAATAATGAG
149932 ATAAAATATAA
1 ATAAAATATAA
149943 ATAAAATATAA
1 ATAAAATATAA
149954 ATAA
1 ATAA
149958 TTCAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAATATAA
Found at i:153198 original size:16 final size:19
Alignment explanation
Indices: 153179--153220 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
153169 CTAATATAAA
153179 TTAAACAA-AAT-AT-TTT
1 TTAAACAACAATAATATTT
153195 TTAAACAACAATAATATTT
1 TTAAACAACAATAATATTT
153214 TTAAACA
1 TTAAACA
153221 TTTTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.35
17 3 0.13
18 2 0.09
19 10 0.43
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAACAACAATAATATTT
Found at i:153681 original size:52 final size:57
Alignment explanation
Indices: 153612--153731 Score: 160
Period size: 58 Copynumber: 2.2 Consensus size: 57
153602 TATACGTTTA
153612 AACAAACTAACAAACTAATTAAATAA-TTTT-TAC-ATAT-A-ATATAACTTAAACT
1 AACAAACTAACAAACTAATTAAATAATTTTTATACAATATAATATATAACTTAAACT
* * * *
153664 AAGAAACTAAGAGACTAATTAACTAATTTTTTATACAATATAATATATAACTTAAACT
1 AACAAACTAACAAACTAATTAAATAA-TTTTTATACAATATAATATATAACTTAAACT
153722 AACAAACTAA
1 AACAAACTAA
153732 TAATTTAAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
52 22 0.39
54 4 0.07
55 3 0.05
56 4 0.07
57 1 0.02
58 23 0.40
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (57 bp):
AACAAACTAACAAACTAATTAAATAATTTTTATACAATATAATATATAACTTAAACT
Found at i:153739 original size:21 final size:21
Alignment explanation
Indices: 153710--153758 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
153700 AATATAATAT
153710 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
*
153731 ATAATTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
153752 ATTAACT
1 A-TAACT
153759 AAATTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:153832 original size:17 final size:18
Alignment explanation
Indices: 153799--153832 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
153789 AACAAACTAA
153799 TAATTTATAATAATAAAC
1 TAATTTATAATAATAAAC
*
153817 TAATTTA-AATAGTAAA
1 TAATTTATAATAATAAA
153833 AATTACCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAATTTATAATAATAAAC
Found at i:153916 original size:19 final size:20
Alignment explanation
Indices: 153867--153918 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
153857 AACTTATCTC
153867 CCTTTC-TTCTTCTTCCTTT
1 CCTTTCTTTCTTCTTCCTTT
* *
153886 CCTTTATCTCTT-TTCCCTTT
1 CCTTTCTTTCTTCTT-CCTTT
153906 -CTTTCTTTCTTCT
1 CCTTTCTTTCTTCT
153919 GCTCCATGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (20 bp):
CCTTTCTTTCTTCTTCCTTT
Found at i:154080 original size:29 final size:28
Alignment explanation
Indices: 154047--154130 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
154037 GGCGTTGCTT
*
154047 GGTCGTCGGGCGTGCATGGCAACCTAGCA
1 GGTCG-CGGGCGTGCATGGCGACCTAGCA
* * **
154076 GGTCGCGCGACGTGTATGGCGACCTAGGT
1 GGTCGCG-GGCGTGCATGGCGACCTAGCA
154105 GGTCGCGGGGCGTGCATGGCGACCTA
1 GGTCGC-GGGCGTGCATGGCGACCTA
154131 CAGCTACGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 43 0.93
30 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.42, T:0.18
Consensus pattern (28 bp):
GGTCGCGGGCGTGCATGGCGACCTAGCA
Found at i:154809 original size:16 final size:17
Alignment explanation
Indices: 154790--154863 Score: 71
Period size: 16 Copynumber: 4.3 Consensus size: 17
154780 GGTTCTTGTT
154790 TTTTATT-TTATTAATA
1 TTTTATTATTATTAATA
*
154806 TTTT-TTATTATTAACA
1 TTTTATTATTATTAATA
* *
154822 TTTATATTAGTATTATTA
1 TTT-TATTATTATTAATA
*
154840 TTAATTATTATTATTATTA
1 TT--TTATTATTATTAATA
154859 TTTTA
1 TTTTA
154864 CATGTTTGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.04
16 15 0.31
17 4 0.08
18 11 0.23
19 15 0.31
20 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (17 bp):
TTTTATTATTATTAATA
Found at i:154818 original size:3 final size:3
Alignment explanation
Indices: 154792--154860 Score: 56
Period size: 3 Copynumber: 23.7 Consensus size: 3
154782 TTCTTGTTTT
* ** *
154792 TTA TT- TTA TTA ATA TT- TT- TTA TTA TTA ACA TT- TATA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
154834 TTA TTA TTAA TTA TTA TTA TTA TTA TT
1 TTA TTA TT-A TTA TTA TTA TTA TTA TT
154861 TTACATGTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 7 0.13
3 42 0.79
4 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:161678 original size:36 final size:36
Alignment explanation
Indices: 161633--161763 Score: 154
Period size: 36 Copynumber: 3.6 Consensus size: 36
161623 GTTTTCTTTG
* * * * *
161633 AAACCAATTTTGTTTCGCTTGAGGTAATTTCTCTCA
1 AAACAAATTTTGTCTCACTTAAGATAATTTCTCTCA
* *
161669 AAACAAATTTTGTCTCACTTAAGAAAACTTTCTCTAAAA
1 AAACAAATTTTGTCTCACTTAAGATAA-TTTCTCT--CA
* *
161708 AAATAAATTTTGTCTCGCTTAAGATAATTTCTCTCA
1 AAACAAATTTTGTCTCACTTAAGATAATTTCTCTCA
161744 AAACAAATTTTGTCTCACTT
1 AAACAAATTTTGTCTCACTT
161764 GAGACATTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
36 40 0.51
37 7 0.09
38 7 0.09
39 25 0.32
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCACTTAAGATAATTTCTCTCA
Found at i:161718 original size:39 final size:36
Alignment explanation
Indices: 161658--161763 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 36
161648 CGCTTGAGGT
*
161658 AATTTCTCTCAAAACAAATTTTGTCTCACTTAAGAA
1 AATTTCTCTAAAAACAAATTTTGTCTCACTTAAGAA
* * *
161694 AACTTTCTCTAAAAAAATAAATTTTGTCTCGCTTAAGAT
1 AA-TTTCTCT--AAAAACAAATTTTGTCTCACTTAAGAA
*
161733 AATTTCTCTCAAAACAAATTTTGTCTCACTT
1 AATTTCTCTAAAAACAAATTTTGTCTCACTT
161764 GAGACATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
36 21 0.35
37 7 0.12
38 7 0.12
39 25 0.42
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.39
Consensus pattern (36 bp):
AATTTCTCTAAAAACAAATTTTGTCTCACTTAAGAA
Found at i:161944 original size:66 final size:66
Alignment explanation
Indices: 161826--162014 Score: 175
Period size: 67 Copynumber: 2.8 Consensus size: 66
161816 AAAATCGACA
* * * * * * *
161826 ATCTTTGAG-TCTTTTTCTCTTAAAACAAAATTTAGTCTCTTTTAAGATAGTTT-CTATTTAAAC
1 ATCTTTGAGATC-ATTTCCCTTAAAAC-AAATTTTGTCTCATTTAAGACAGTTTCCCA-TGAAAC
* *
161889 ATAT
63 ACAG
* * *
161893 ATCTTTGAGATCATTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAGTTTCCCATGAAACACC
1 ATCTTTGAGATCATTTCCCTTAAAACAAATTTTGTCTCATTTAAGACAGTTTCCCATGAAACACA
161958 G
66 G
* * ** *
161959 ATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTAAGACAATTTCCC
1 ATCTTTGAGATCATTTCCCTT-AAAACAAATTTTGTCTCATTTAAGACAGTTTCCC
162015 TTTAAATGTC
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
66 47 0.47
67 51 0.51
68 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.40
Consensus pattern (66 bp):
ATCTTTGAGATCATTTCCCTTAAAACAAATTTTGTCTCATTTAAGACAGTTTCCCATGAAACACA
G
Found at i:162350 original size:129 final size:129
Alignment explanation
Indices: 162118--162490 Score: 373
Period size: 129 Copynumber: 2.9 Consensus size: 129
162108 AGATGCATGT
* * * *
162118 CATCCTCATCACGTAAGAGCCA-CGTCACTCCTAGATAACCAGTTGTCCTCATCATGTAGGAACG
1 CATCCTCATCACGTAAGAGCCAGTGTCAC-CCTAGATAACCA-TCGT-CTCATCACGTAGGAACC
* * * ** * *
162182 GTGTTATCATTCCTAAAGATGGCCTGATGTCCTCATCACGTAGGAACCATGTCATATACCGACAA
63 GTGTTATAATCCCTAAAGATGGCATGCCGTCCTCATCACGTAGGAACCATGTCATACACAGACAA
*
162247 TA
128 GA
*
162249 CATCCTCATCACGTAAGAG-CAGTGTCA-CCTAGATAATCATCCGTTCTCATCACGTAGGAACCG
1 CATCCTCATCACGTAAGAGCCAGTGTCACCCTAGATAACCAT-CG-TCTCATCACGTAGGAACCG
* * * *
162312 TGTTATAATCCCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTCATCCACAGACCAG
64 TGTTATAATCCCTAAAGATGGCATGCCGTCCTCATCACGTAGGAACCATGTCATACACAGACAAG
162377 A
129 A
* * * * *
162378 CCTCCTCATCACGT-AGAAGTC-GTGTCACCTCTAGATAACCAATC--ATCATCGCTTAGGAACC
1 CATCCTCATCACGTAAG-AGCCAGTGTCACC-CTAGATAACC-ATCGTCTCATCACGTAGGAACC
* *
162439 GTGTTATCACCATTCCCTAAAGATGGTATGCCGTCCTGATCACGTAGGAACC
63 GTGTTAT-A--A-TCCCTAAAGATGGCATGCCGTCCTCATCACGTAGGAACC
162491 GTGTTATCTA
Statistics
Matches: 205, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
128 24 0.12
129 104 0.51
130 5 0.02
131 34 0.17
132 38 0.19
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (129 bp):
CATCCTCATCACGTAAGAGCCAGTGTCACCCTAGATAACCATCGTCTCATCACGTAGGAACCGTG
TTATAATCCCTAAAGATGGCATGCCGTCCTCATCACGTAGGAACCATGTCATACACAGACAAGA
Found at i:162487 original size:132 final size:128
Alignment explanation
Indices: 162303--162538 Score: 337
Period size: 132 Copynumber: 1.8 Consensus size: 128
162293 TCTCATCACG
162303 TAGGAACCGTGTTATAATCCCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTCATCC
1 TAGGAACCGTGTTATAATCCCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTCATCC
* *
162368 ACAGACCAGACCTCCTCATCACGTAGAAGTCGTGTCACCTCTAGATAACCAATCATCATCGCT
66 ACAGACCAGACCTCATCATCACATAGAAGTCGTGTCACCTCTAGATAACCAATCATCATCGCT
* * * *
162431 TAGGAACCGTGTTATCACCATTCCCTAAAGATGGTATGCCGTCCTGATCACGTAGGAACCGTGTT
1 TAGGAACCGTGTTAT-A--A-TCCCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTC
* ** * *
162496 ATCTACTTACCAGGCCTCATCATCACATAGGAGTCGTGTCACC
62 ATCCACAGACCAGACCTCATCATCACATAGAAGTCGTGTCACC
162539 CTTATACGAC
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
128 15 0.16
129 1 0.01
131 1 0.01
132 76 0.82
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (128 bp):
TAGGAACCGTGTTATAATCCCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTCATCC
ACAGACCAGACCTCATCATCACATAGAAGTCGTGTCACCTCTAGATAACCAATCATCATCGCT
Found at i:166224 original size:23 final size:25
Alignment explanation
Indices: 166183--166233 Score: 79
Period size: 23 Copynumber: 2.1 Consensus size: 25
166173 TCTTAATTTA
166183 TTATGAGAAAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
*
166208 TTATGAG-AAAAAA-AATCTTTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
166231 TTA
1 TTA
166234 GAAAAACACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 12 0.48
24 6 0.24
25 7 0.28
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (25 bp):
TTATGAGAAAAAAATAATCTCTAAC
Found at i:166502 original size:26 final size:26
Alignment explanation
Indices: 166473--166564 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 26
166463 AAAAATTGAA
166473 AAAATGAACAATTATAATAAATTTCC
1 AAAATGAACAATTATAATAAATTTCC
166499 -AAA--AA-AATTATAATCAAATCGAATTCTGC
1 AAAATGAACAATTATAAT-AAAT----TTC--C
166528 AAAGAAATGAACAATTATAATAAATTTCC
1 -AA--AATGAACAATTATAATAAATTTCC
166557 AAAATGAA
1 AAAATGAA
166565 ATGAACGGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 28
0.65 0.00 0.35
Matches are distributed among these distances:
22 9 0.17
23 6 0.12
25 3 0.06
26 6 0.12
27 3 0.06
28 2 0.04
29 2 0.04
31 4 0.08
33 2 0.04
35 6 0.12
36 9 0.17
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.27
Consensus pattern (26 bp):
AAAATGAACAATTATAATAAATTTCC
Done.