Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 62
Found at i:4096731 original size:17 final size:18
Alignment explanation
Indices: 4096705--4096744 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4096695 ATTATATAGA
4096705 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
4096721 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
4096739 TATTAT
1 TATTAT
4096745 ACGTGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:4096819 original size:2 final size:2
Alignment explanation
Indices: 4096814--4096846 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4096804 TATATTTTAT
4096814 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4096847 CTTTAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4096966 original size:19 final size:19
Alignment explanation
Indices: 4096942--4096978 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4096932 ATAGTTTATT
4096942 TATATACATATTATTAATA
1 TATATACATATTATTAATA
* *
4096961 TATATATATATTCTTAAT
1 TATATACATATTATTAAT
4096979 TATTTTTATT
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:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATACATATTATTAATA
Found at i:4097032 original size:2 final size:2
Alignment explanation
Indices: 4097027--4097055 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4097017 CTTATAACTT
4097027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4097056 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4097417 original size:9 final size:8
Alignment explanation
Indices: 4097405--4097473 Score: 50
Period size: 9 Copynumber: 7.8 Consensus size: 8
4097395 TTTTTTTTCC
4097405 TTATCTTAT
1 TTAT-TTAT
4097414 TTATTTATT
1 TTATTTA-T
4097423 TTATTTATT
1 TTATTTA-T
4097432 TTATTT-T
1 TTATTTAT
*
4097439 TTCCTTTTATT
1 TT--ATTTA-T
4097450 TTATTCTAT
1 TTATT-TAT
4097459 TTATCTTAT
1 TTAT-TTAT
4097468 TTATTT
1 TTATTT
4097474 TCTTTACCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
7 3 0.06
8 5 0.10
9 37 0.73
10 3 0.06
11 3 0.06
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTAT
Found at i:4097426 original size:13 final size:13
Alignment explanation
Indices: 4097405--4097473 Score: 70
Period size: 13 Copynumber: 5.2 Consensus size: 13
4097395 TTTTTTTTCC
*
4097405 TTATCTTATTTAT
1 TTATTTTATTTAT
4097418 TTATTTTATTTATT
1 TTATTTTATTTA-T
4097432 TTATTTT-TTCCT-T
1 TTATTTTATT--TAT
4097445 TTATTTTATTCTAT
1 TTATTTTATT-TAT
*
4097459 TTATCTTATTTAT
1 TTATTTTATTTAT
4097472 TT
1 TT
4097474 TCTTTACCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
13 28 0.57
14 20 0.41
15 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:4097479 original size:9 final size:9
Alignment explanation
Indices: 4097413--4097473 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
4097403 CCTTATCTTA
4097413 TTTATTTAT
1 TTTATTTAT
4097422 TTTATTTAT
1 TTTATTTAT
4097431 TTTATTT-T
1 TTTATTTAT
4097439 TTCCT-TTTAT
1 TT--TATTTAT
4097449 TTTATTCTA-
1 TTTATT-TAT
4097458 TTTATCTTA-
1 TTTAT-TTAT
4097467 TTTATTT
1 TTTATTT
4097474 TCTTTACCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
8 6 0.13
9 33 0.72
10 7 0.15
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTAT
Found at i:4097479 original size:18 final size:17
Alignment explanation
Indices: 4097405--4097489 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
4097395 TTTTTTTTCC
4097405 TTATCTTATTTATTTATT
1 TTATCTTATTTATTT-TT
4097423 TTAT-TTATTTTATTTTT
1 TTATCTTA-TTTATTTTT
** * *
4097440 TCCTTTTATTTTATTCTAT
1 TTATCTTA-TTTATT-TTT
4097459 TTATCTTATTTATTTTCT
1 TTATCTTATTTATTTT-T
* *
4097477 TTACCTTGTTTAT
1 TTATCTTATTTAT
4097490 CTAACACATT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
17 8 0.15
18 39 0.72
19 7 0.13
ACGTcount: A:0.18, C:0.09, G:0.01, T:0.72
Consensus pattern (17 bp):
TTATCTTATTTATTTTT
Found at i:4101957 original size:102 final size:102
Alignment explanation
Indices: 4101837--4102031 Score: 259
Period size: 102 Copynumber: 1.9 Consensus size: 102
4101827 TCAATACTAC
* * *
4101837 AAAAAAATGTAGCACTTAAC-CTATACTTACACCGATGTAAGTGAATAGAATAAACAAGTGCAAC
1 AAAAAAATGTAGCACTTAACAC-ATACTTACACCGATGTAAGTAAATAAAATAAAAAAGTGCAAC
4101901 ACTTAACACATA-CTACACTAGTGTAAGTGAATAAAAT
65 ACTTAACACATATCTACACTAGTGTAAGTGAATAAAAT
* * * *
4101938 AAAAACAATGTATCACTTAACACATACTTATACCGGTGTAAGTAAATAAAATAAAAAAGTGTAAC
1 AAAAA-AATGTAGCACTTAACACATACTTACACCGATGTAAGTAAATAAAATAAAAAAGTGCAAC
* * * *
4102003 ATTTAATACATATTTGCACTAGTGTAAGT
65 ACTTAACACATATCTACACTAGTGTAAGT
4102032 ATGTACATCT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
101 5 0.06
102 60 0.75
103 15 0.19
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (102 bp):
AAAAAAATGTAGCACTTAACACATACTTACACCGATGTAAGTAAATAAAATAAAAAAGTGCAACA
CTTAACACATATCTACACTAGTGTAAGTGAATAAAAT
Found at i:4101986 original size:52 final size:52
Alignment explanation
Indices: 4101837--4102014 Score: 188
Period size: 51 Copynumber: 3.5 Consensus size: 52
4101827 TCAATACTAC
* * *
4101837 AAAAA-AATGTAGCACTTAAC-CTATACTTACACCGATGTAAGTGAATAGAAT
1 AAAAACAATGTAACACTTAACAC-ATACTTACACCGGTGTAAGTGAATAAAAT
* **
4101888 --AAACAAGTGCAACACTTAACACATAC-TACACTAGTGTAAGTGAATAAAAT
1 AAAAACAA-TGTAACACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * *
4101938 AAAAACAATGTATCACTTAACACATACTTATACCGGTGTAAGTAAATAAAAT
1 AAAAACAATGTAACACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * *
4101990 AAAAA-AGTGTAACATTTAATACATA
1 AAAAACAATGTAACACTTAACACATA
4102015 TTTGCACTAG
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
49 3 0.03
50 22 0.21
51 48 0.46
52 32 0.30
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.25
Consensus pattern (52 bp):
AAAAACAATGTAACACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
Found at i:4102170 original size:2 final size:2
Alignment explanation
Indices: 4102163--4102192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4102153 CAAATTTTAT
4102163 TA 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 TA
4102193 CATAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4102526 original size:117 final size:118
Alignment explanation
Indices: 4102383--4102601 Score: 275
Period size: 117 Copynumber: 1.9 Consensus size: 118
4102373 GTTTTTATAC
*
4102383 AAACGCCGCTACAGACTCGACTTTTAATGGCG-TTTTATA-AAAGCGTCACTACAGACTAATACT
1 AAACACCGCTACAGACTCGACTTTTAATGG-GTTTTTATACAAA-CGTCACTACAGACTAATACT
* *
4102446 TTAGTGG-CTTTTTTATACAAATGTCGATATAGACTCGACCTTTAGTGGCGATAA
64 TTAGTGGACTTTTTTATACAAACGTCGATAAAGACTCGACCTTTAGTGGCGATAA
* * * * **
4102500 AAACACCGCTATAGACTCATAC-TTTAATGGGTTTTTATACAAACGTCGCTATAGACTCGTACTT
1 AAACACCGCTACAGACTC-GACTTTTAATGGGTTTTTATACAAACGTCACTACAGACTAATACTT
* *
4102564 TAGTGGTATTTTTTTATACAAACGTCGCTAAAGACTCG
65 TAGTGG-ACTTTTTTATACAAACGTCGATAAAGACTCG
4102602 TACTTTATTG
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
116 1 0.01
117 54 0.63
118 5 0.06
119 26 0.30
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (118 bp):
AAACACCGCTACAGACTCGACTTTTAATGGGTTTTTATACAAACGTCACTACAGACTAATACTTT
AGTGGACTTTTTTATACAAACGTCGATAAAGACTCGACCTTTAGTGGCGATAA
Found at i:4102553 original size:40 final size:41
Alignment explanation
Indices: 4102364--4102608 Score: 195
Period size: 40 Copynumber: 6.1 Consensus size: 41
4102354 TTACTTGTAT
* * *
4102364 TTTAGTGGCGTTTTTATACAAACGCCGCTACAGACTC-GAC
1 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCATAC
* * * *
4102404 TTTTAATGGCG-TTTTATA-AAAGCGTCACTACAGACTAATAC
1 -TTTAGTGGCGTTTTTATACAAA-CGTCGCTATAGACTCATAC
* * * *
4102445 TTTAGTGGCTTTTTTATACAAATGTCGATATAGACTCGA-CC
1 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTC-ATAC
* **
4102486 TTTAGTGGCG-----ATAAAAACACCGCTATAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCATAC
* *
4102522 TTTAATGG-GTTTTTATACAAACGTCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCATAC
** * *
4102562 TTTAGTGGTATTTTTTTATACAAACGTCGCTAAAGACTCGTAC
1 TTTAGTGG--CGTTTTTATACAAACGTCGCTATAGACTCATAC
4102605 TTTA
1 TTTA
4102609 TTGTTTACAA
Statistics
Matches: 162, Mismatches: 28, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
35 2 0.01
36 25 0.15
39 3 0.02
40 56 0.35
41 38 0.23
42 4 0.02
43 34 0.21
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCATAC
Found at i:4102565 original size:76 final size:77
Alignment explanation
Indices: 4102364--4102569 Score: 227
Period size: 81 Copynumber: 2.6 Consensus size: 77
4102354 TTACTTGTAT
* * * * **
4102364 TTTAGTGGCGTTTTTATACAAACGCCGCTACAGACTCGACTTTTAATGGCGTTTTATAAAAGCGT
1 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCGAC-TTTAGTGGCG---TATAAAAACAC
4102429 CACTACAGACTAATAC
62 CACTACAGACTAATAC
* * * *
4102445 TTTAGTGGCTTTTTTATACAAATGTCGATATAGACTCGACCTTTAGTGGCG-ATAAAAACACCGC
1 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCGA-CTTTAGTGGCGTATAAAAACACCAC
* *
4102509 TATAGACTCATAC
65 TACAGACTAATAC
*
4102522 TTTAATGG-GTTTTTATACAAACGTCGCTATAGACTCGTACTTTAGTGG
1 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCG-ACTTTAGTGG
4102570 TATTTTTTTA
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
76 35 0.33
77 28 0.26
81 43 0.40
82 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (77 bp):
TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCGACTTTAGTGGCGTATAAAAACACCACT
ACAGACTAATAC
Found at i:4106107 original size:16 final size:16
Alignment explanation
Indices: 4106088--4106121 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4106078 TTTAACTTGA
4106088 ATGTTTGTAAACTTTG
1 ATGTTTGTAAACTTTG
4106104 ATGTTTGTAAACTTTG
1 ATGTTTGTAAACTTTG
4106120 AT
1 AT
4106122 TTATTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (16 bp):
ATGTTTGTAAACTTTG
Found at i:4106492 original size:117 final size:117
Alignment explanation
Indices: 4106337--4106589 Score: 382
Period size: 117 Copynumber: 2.2 Consensus size: 117
4106327 AATGACCAAC
* * * * *
4106337 CTATTGCAGCATTTGTGCCCGAAGCGCCGCTAAATATCAAATTTGTTGCAATATTTGTGACTAAA
1 CTATTGCGGCATTTGTGCCCGAAACACCGCTAAATATCAAATCTGTTGCAACATTTGTGACTAAA
*
4106402 AACGTCGCTAAATAGCGAACAAGTTGCGGGAAAACGCCTATAAATATCAAA-
66 AACGTCGCTAAATAGCGAACAAGTTGCGAGAAAACGCCTATAAATATCAAAT
* *
4106453 CTTATTGCGGCGTTTGTGCCCGAAACACCGCTAAATATCAAATCTGTTGCAACGTTTGTGACTAA
1 C-TATTGCGGCATTTGTGCCCGAAACACCGCTAAATATCAAATCTGTTGCAACATTTGTGACTAA
* ** *
4106518 AAACGTCGCTAAATGGCGAACCTGTTGCGAGAAAAGGCCTATAAATATCAAAT
65 AAACGTCGCTAAATAGCGAACAAGTTGCGAGAAAACGCCTATAAATATCAAAT
4106571 CTATTGCGGCATTTGTGCC
1 CTATTGCGGCATTTGTGCC
4106590 AAAAAAATGT
Statistics
Matches: 122, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
116 1 0.01
117 120 0.98
118 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (117 bp):
CTATTGCGGCATTTGTGCCCGAAACACCGCTAAATATCAAATCTGTTGCAACATTTGTGACTAAA
AACGTCGCTAAATAGCGAACAAGTTGCGAGAAAACGCCTATAAATATCAAAT
Found at i:4106618 original size:76 final size:75
Alignment explanation
Indices: 4106484--4106623 Score: 199
Period size: 76 Copynumber: 1.9 Consensus size: 75
4106474 GAAACACCGC
* * *
4106484 TAAATATCAAATCTGTTGCAACGTTTGTGACTAAAAACGTCGCTAAATGGCGAACCTGTTGCGAG
1 TAAATATCAAATCTATTGCAACATTTGTGACAAAAAACGTCGCTAAATGGCGAACCTGTTGCGAG
4106549 AAAAGGCCTA
66 AAAAGGCCTA
** * * *
4106559 TAAATATCAAATCTATTGCGGCATTTGTGCCAAAAAAATGTCGCTATATGGCGAACCTGTTGCGA
1 TAAATATCAAATCTATTGCAACATTTGTGAC-AAAAAACGTCGCTAAATGGCGAACCTGTTGCGA
4106624 TGTTTGTATA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
75 26 0.46
76 30 0.54
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (75 bp):
TAAATATCAAATCTATTGCAACATTTGTGACAAAAAACGTCGCTAAATGGCGAACCTGTTGCGAG
AAAAGGCCTA
Found at i:4111602 original size:22 final size:23
Alignment explanation
Indices: 4111574--4111617 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4111564 GTTTTTATAA
4111574 AAGTTTTCTC-TTTTTACTTTTC
1 AAGTTTTCTCATTTTTACTTTTC
* *
4111596 AAGTTTTTTCATTTTTTCTTTT
1 AAGTTTTCTCATTTTTACTTTT
4111618 ATTTTTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.68
Consensus pattern (23 bp):
AAGTTTTCTCATTTTTACTTTTC
Found at i:4117483 original size:2 final size:2
Alignment explanation
Indices: 4117476--4117506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4117466 AACTTAATGT
4117476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4117507 GGTCATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4118149 original size:22 final size:23
Alignment explanation
Indices: 4118121--4118170 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
4118111 TTCAAAAAGG
4118121 TTTTATATT-TAATTT-AATTTAA
1 TTTTATATTAT-ATTTGAATTTAA
*
4118143 TTTTATATTATATTTGATTTTAA
1 TTTTATATTATATTTGAATTTAA
4118166 TTTTA
1 TTTTA
4118171 ATATCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTATATTATATTTGAATTTAA
Found at i:4118213 original size:14 final size:14
Alignment explanation
Indices: 4118194--4118263 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
4118184 AAATAAATTA
*
4118194 AATATTAATTTTTT
1 AATATTAATTTTAT
*
4118208 AATATT-ATATTAT
1 AATATTAATTTTAT
4118221 AGATATTAA-TTT-T
1 A-ATATTAATTTTAT
*
4118234 AATATT-ATATTAT
1 AATATTAATTTTAT
4118247 AGATATTTAATTTTAT
1 A-ATA-TTAATTTTAT
4118263 A
1 A
4118264 TCATATAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
11 1 0.02
12 7 0.16
13 10 0.23
14 16 0.36
15 3 0.07
16 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
AATATTAATTTTAT
Found at i:4118230 original size:28 final size:28
Alignment explanation
Indices: 4118195--4118260 Score: 109
Period size: 26 Copynumber: 2.4 Consensus size: 28
4118185 AATAAATTAA
4118195 ATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
4118223 ATATTAA--TTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
4118249 ATATTTAATTTT
1 ATA-TTAATTTT
4118261 ATATCATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 22 0.63
27 4 0.11
28 7 0.20
29 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
ATATTAATTTTTTAATATTATATTATAG
Found at i:4118264 original size:26 final size:26
Alignment explanation
Indices: 4118195--4118269 Score: 107
Period size: 26 Copynumber: 2.8 Consensus size: 26
4118185 AATAAATTAA
4118195 ATATTAATTTTTTAATATTATATTATAG
1 ATATTAA--TTTTAATATTATATTATAG
4118223 ATATTAATTTTAATATTATATTATAG
1 ATATTAATTTTAATATTATATTATAG
*
4118249 ATATTTAATTTT-ATATCATAT
1 ATA-TTAATTTTAATATTATAT
4118270 AAATTATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 30 0.67
27 8 0.18
28 7 0.16
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (26 bp):
ATATTAATTTTAATATTATATTATAG
Found at i:4118288 original size:26 final size:24
Alignment explanation
Indices: 4118195--4118288 Score: 81
Period size: 26 Copynumber: 3.9 Consensus size: 24
4118185 AATAAATTAA
*
4118195 ATATTAATT-TTTTAATATTATAT
1 ATATAAATTATTTTAATATTATAT
4118218 -TATAGATATTAATTTTAATATTATAT
1 ATATA-A-ATT-ATTTTAATATTATAT
* *
4118244 -TATAGA-TA-TTTAATTTTATAT
1 ATATAAATTATTTTAATATTATAT
4118265 CATATAAATTATTTTATATATTAT
1 -ATATAAATTATTTTA-ATATTAT
4118289 TAAAATTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
21 12 0.21
22 4 0.07
23 7 0.12
24 6 0.11
25 4 0.07
26 24 0.42
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATAAATTATTTTAATATTATAT
Found at i:4118316 original size:20 final size:19
Alignment explanation
Indices: 4118256--4118317 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
4118246 TAGATATTTA
*
4118256 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
4118275 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
4118293 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
4118313 ATTTT
1 ATTTT
4118318 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:4119220 original size:20 final size:20
Alignment explanation
Indices: 4119195--4119246 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4119185 CAGTTTTACT
4119195 GGTTTTCAGCCGGTTCTACC
1 GGTTTTCAGCCGGTTCTACC
*
4119215 GGTTTTCAGCCGGTTCTATC
1 GGTTTTCAGCCGGTTCTACC
4119235 GGTTTTCAGCCG
1 GGTTTTCAGCCG
4119247 ATTCATTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.27, G:0.27, T:0.37
Consensus pattern (20 bp):
GGTTTTCAGCCGGTTCTACC
Found at i:4119792 original size:31 final size:31
Alignment explanation
Indices: 4119734--4119793 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
4119724 TAGTTGTATG
* * **
4119734 AATTATTTAAATTTCATTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTACAAAACTAA
4119765 AATTATTTAAATCTCAGTATTACAAAACT
1 AATTATTTAAATCTCAGTATTACAAAACT
4119794 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTACAAAACTAA
Found at i:4121220 original size:31 final size:32
Alignment explanation
Indices: 4121185--4121266 Score: 87
Period size: 37 Copynumber: 2.4 Consensus size: 32
4121175 AAATTTTTTT
4121185 ATATTTTTAA-TTTTATAAAAAAAT-TATATAA
1 ATATTTTTAATTTTTA-AAAAAAATATATATAA
4121216 ATATTATGAATTTAATTTTTAAAAAAAATATATATAA
1 ATA-T-T---TTTAATTTTTAAAAAAAATATATATAA
4121253 ATATTTTATAATTT
1 ATATTTT-TAATTT
4121267 GTAATATTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
31 3 0.07
32 3 0.07
33 7 0.16
35 1 0.02
36 14 0.33
37 15 0.35
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
ATATTTTTAATTTTTAAAAAAAATATATATAA
Found at i:4126918 original size:16 final size:16
Alignment explanation
Indices: 4126897--4126932 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
4126887 GATGATTGAC
4126897 GATGAACATTAATAAT
1 GATGAACATTAATAAT
4126913 GATGAACATTAATAAT
1 GATGAACATTAATAAT
4126929 GATG
1 GATG
4126933 TTTATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.31
Consensus pattern (16 bp):
GATGAACATTAATAAT
Found at i:4127397 original size:14 final size:14
Alignment explanation
Indices: 4127378--4127410 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4127368 TGGAAGGGAG
4127378 AGAGCTTGACCACC
1 AGAGCTTGACCACC
4127392 AGAGCTTGACCACC
1 AGAGCTTGACCACC
4127406 A-AGCT
1 AGAGCT
4127411 AATTGTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (14 bp):
AGAGCTTGACCACC
Found at i:4128414 original size:21 final size:20
Alignment explanation
Indices: 4128390--4128443 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 20
4128380 TGACACTAGG
*
4128390 TACCTAGCTAGCTACCTCACT
1 TACCTAGCTAGCTACCT-ACC
4128411 TACCTAGCTA-C-A-CTACC
1 TACCTAGCTAGCTACCTACC
*
4128428 TACCTAGTTAGCTACC
1 TACCTAGCTAGCTACC
4128444 AAGTCAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 11 0.39
18 3 0.11
19 2 0.07
20 2 0.07
21 10 0.36
ACGTcount: A:0.26, C:0.37, G:0.09, T:0.28
Consensus pattern (20 bp):
TACCTAGCTAGCTACCTACC
Found at i:4129991 original size:12 final size:13
Alignment explanation
Indices: 4129965--4129993 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4129955 TGACCTGTTT
4129965 TTCTCTTCTTCGC
1 TTCTCTTCTTCGC
4129978 TTCTCTTC-TCGC
1 TTCTCTTCTTCGC
4129990 TTCT
1 TTCT
4129994 GTAACCTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.00, C:0.38, G:0.07, T:0.55
Consensus pattern (13 bp):
TTCTCTTCTTCGC
Found at i:4130495 original size:23 final size:23
Alignment explanation
Indices: 4130484--4130533 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
4130474 AAATGCACTT
4130484 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
*
4130507 AAGTGCCGCGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
4130530 AAGT
1 AAGT
4130534 TCCATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:4135361 original size:23 final size:23
Alignment explanation
Indices: 4135335--4135399 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
4135325 CTCGTATAAA
*
4135335 TGCACCTAAGTGCCATATAGAAT
1 TGCACCGAAGTGCCATATAGAAT
***
4135358 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCATATAGAAT
*
4135381 TGCACCGAAGTTCCATATA
1 TGCACCGAAGTGCCATATA
4135400 AAATGTCCCT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCATATAGAAT
Found at i:4136983 original size:24 final size:21
Alignment explanation
Indices: 4136932--4136986 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
4136922 TTCCCTTGAA
*
4136932 GTGCATCGATGCATTCTACAT
1 GTGCATCGATGCATCCTACAT
*
4136953 -TGTATCGATGCATCCCTTAACAT
1 GTGCATCGATGCAT-CC-T-ACAT
4136976 GTGCATCGATG
1 GTGCATCGATG
4136987 TACTCCTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 12 0.44
21 1 0.04
22 1 0.04
23 4 0.15
24 9 0.33
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
GTGCATCGATGCATCCTACAT
Found at i:4137001 original size:19 final size:19
Alignment explanation
Indices: 4136977--4137064 Score: 158
Period size: 19 Copynumber: 4.6 Consensus size: 19
4136967 CCTTAACATG
*
4136977 TGCATCGATGTACTCCTTA
1 TGCATCGATGCACTCCTTA
4136996 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
4137015 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
4137034 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
4137053 TGCATCTATGCA
1 TGCATCGATGCA
4137065 TTAATTGCAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:4138410 original size:22 final size:22
Alignment explanation
Indices: 4138385--4138435 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
4138375 TAGTAACTGT
* *
4138385 TACAGTATGCTACATTAACTAC
1 TACAGTAAGCTACAATAACTAC
*
4138407 TACAGTAAGCTACAATAACTGC
1 TACAGTAAGCTACAATAACTAC
4138429 TACAGTA
1 TACAGTA
4138436 CCTCCGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (22 bp):
TACAGTAAGCTACAATAACTAC
Found at i:4139000 original size:33 final size:33
Alignment explanation
Indices: 4138958--4139024 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
4138948 ACCGTAGTGT
*
4138958 TAATCTGTATGACATATAAGGTCGTGTCCACCA
1 TAATCTGTATGACACATAAGGTCGTGTCCACCA
4138991 TAATCTGTATGACACATAAGGTCGTGTCCACCA
1 TAATCTGTATGACACATAAGGTCGTGTCCACCA
4139024 T
1 T
4139025 CTGTACTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (33 bp):
TAATCTGTATGACACATAAGGTCGTGTCCACCA
Found at i:4139073 original size:15 final size:15
Alignment explanation
Indices: 4139053--4139082 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4139043 AGTATAGTCC
*
4139053 TGTATGGCACATAAG
1 TGTATGACACATAAG
4139068 TGTATGACACATAAG
1 TGTATGACACATAAG
4139083 GTCGTGTCCA
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:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (15 bp):
TGTATGACACATAAG
Found at i:4139113 original size:72 final size:72
Alignment explanation
Indices: 4138996--4139139 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
4138986 CACCATAATC
4138996 TGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCTGTATGGC
1 TGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCTGTATGGC
4139061 ACATAAG
66 ACATAAG
4139068 TGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCTGTATGGC
1 TGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCTGTATGGC
4139133 ACATAAG
66 ACATAAG
4139140 GTCGTACCCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (72 bp):
TGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCTGTATGGC
ACATAAG
Found at i:4148384 original size:12 final size:12
Alignment explanation
Indices: 4148367--4148431 Score: 84
Period size: 12 Copynumber: 5.8 Consensus size: 12
4148357 TGTTCATTCC
4148367 TACAGTAACTGT
1 TACAGTAACTGT
*
4148379 TACAGTAA--GC
1 TACAGTAACTGT
4148389 TACAGTAACTGT
1 TACAGTAACTGT
*
4148401 TACAGTAA--GC
1 TACAGTAACTGT
4148411 TACAGTAACTGT
1 TACAGTAACTGT
4148423 TACAGTAAC
1 TACAGTAAC
4148432 AGCTATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 18 0.40
12 27 0.60
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (12 bp):
TACAGTAACTGT
Found at i:4148393 original size:22 final size:22
Alignment explanation
Indices: 4148366--4148430 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
4148356 CTGTTCATTC
4148366 CTACAGTAACTGTTACAGTAAG
1 CTACAGTAACTGTTACAGTAAG
4148388 CTACAGTAACTGTTACAGTAAG
1 CTACAGTAACTGTTACAGTAAG
4148410 CTACAGTAACTGTTACAGTAA
1 CTACAGTAACTGTTACAGTAA
4148431 CAGCTATAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (22 bp):
CTACAGTAACTGTTACAGTAAG
Found at i:4148394 original size:10 final size:10
Alignment explanation
Indices: 4148379--4148418 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
4148369 CAGTAACTGT
4148379 TACAGTAAGC
1 TACAGTAAGC
*
4148389 TACAGTAACTGT
1 TACAGTAA--GC
4148401 TACAGTAAGC
1 TACAGTAAGC
4148411 TACAGTAA
1 TACAGTAA
4148419 CTGTTACAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 17 0.65
12 9 0.35
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (10 bp):
TACAGTAAGC
Found at i:4149003 original size:33 final size:33
Alignment explanation
Indices: 4148966--4149032 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
4148956 ACCGTAGTGC
*
4148966 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCATGTCCACCA
4148999 TAATCCGTATGACACATAAGGTCATGTCCACCA
1 TAATCCGTATGACACATAAGGTCATGTCCACCA
4149032 T
1 T
4149033 CTGTACTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCATGTCCACCA
Found at i:4169057 original size:31 final size:31
Alignment explanation
Indices: 4169019--4169080 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
4169009 GTTGGAGGTA
4169019 GCACATTCCATGCCTCGACATCGAATGTACC
1 GCACATTCCATGCCTCGACATCGAATGTACC
4169050 GCACATTCCATGCCTCGACATCGAATGTACC
1 GCACATTCCATGCCTCGACATCGAATGTACC
4169081 TCCAGAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (31 bp):
GCACATTCCATGCCTCGACATCGAATGTACC
Found at i:4177280 original size:2 final size:2
Alignment explanation
Indices: 4177273--4177345 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
4177263 TGTTGTACAT
4177273 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
4177315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4177346 CATGCCTTCA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4177650 original size:67 final size:68
Alignment explanation
Indices: 4177538--4177860 Score: 463
Period size: 68 Copynumber: 4.8 Consensus size: 68
4177528 TGTTTAATCG
* * * * * * *
4177538 TTCATCTAACTAGCACAATTGACA-ACTTTTTGCCAAATGCACAGTTAGGCCTCAA-GGCACTTA
1 TTCATCTAACTGGCATAAATGACACA-TTTCTGTCAAATGCACAGTTAGGCCTTAACGACACTTA
4177601 GCCT
65 GCCT
* * *
4177605 TTCTTCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCATAACGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAACGACACTTAG
*
4177670 CTT
66 CCT
* *
4177673 TTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAATGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAACGACACTTAG
4177738 CCT
66 CCT
*
4177741 TTC-TCTAACTGTCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAACGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAACGACACTTAG
*
4177805 CAT
66 CCT
* *
4177808 TTCATATAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTT
4177861 TAATCTTTTA
Statistics
Matches: 231, Mismatches: 22, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
67 108 0.47
68 123 0.53
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAACGACACTTAG
CCT
Found at i:4177780 original size:135 final size:135
Alignment explanation
Indices: 4177538--4177860 Score: 497
Period size: 135 Copynumber: 2.4 Consensus size: 135
4177528 TGTTTAATCG
* * * * * *
4177538 TTCATCTAACTAGCACAATTGACA-ACTTTTTGCCAAATGCACAGTTAGGCCTCAAGGCACTTAG
1 TTCATCTAACTAGCATAAATGACACA-TTTCTGTCAAATGCACAGTTAGGCCTTAAGACACTTAG
*
4177602 CCTTTCTTCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCATAACGGCACT
65 CCTTTCTTCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCATAACGACACT
*
4177667 TAGCTT
130 TAGCAT
4177673 TTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAATGACACTTAG
1 TTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAA-GACACTTAG
* *
4177738 CCTTTC-TCTAACTGTCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAACGACACT
65 CCTTTCTTCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCATAACGACACT
4177802 TAGCAT
130 TAGCAT
* * *
4177808 TTCATATAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTT
1 TTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTT
4177861 TAATCTTTTA
Statistics
Matches: 173, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
135 158 0.91
136 15 0.09
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (135 bp):
TTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTTAAGACACTTAGC
CTTTCTTCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCATAACGACACTT
AGCAT
Found at i:4180593 original size:15 final size:16
Alignment explanation
Indices: 4180564--4180593 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4180554 TTTATTTAAT
4180564 AAATACATAATATACG
1 AAATACATAATATACG
4180580 AAATACAT-ATATAC
1 AAATACATAATATAC
4180594 ATAAAGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (16 bp):
AAATACATAATATACG
Found at i:4182247 original size:184 final size:185
Alignment explanation
Indices: 4181930--4182301 Score: 615
Period size: 184 Copynumber: 2.0 Consensus size: 185
4181920 ATTAAATTTT
* *
4181930 AAATATTAAATAAATTATATATAACATATGGGCTCAGCCTAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATAAATTATATAAAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
* *
4181995 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTTTATATAATTTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAATATTT
* *
4182060 TTATTTTATAATTATATATTATTTAAATTAATTGTAAA-TTGTTTTTTAATTA-AA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTT-TTTTTGAATTACAA
* *
4182114 AAATATTAAATATATTATATAAAACATATGGGTTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATAAATTATATAAAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
* *
4182179 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTGAA-ATT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATAT-AATATT
4182243 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTACAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTACAA
4182299 AAA
1 AAA
4182302 AATTTCATTT
Statistics
Matches: 175, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
184 166 0.95
185 9 0.05
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (185 bp):
AAATATTAAATAAATTATATAAAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAATATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTACAA
Found at i:4203768 original size:2 final size:2
Alignment explanation
Indices: 4203761--4203785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4203751 AGGGATTCAG
4203761 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4203786 CACACACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4208630 original size:29 final size:28
Alignment explanation
Indices: 4208605--4208658 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
4208595 AGGTAAATTT
*
4208605 TAAAATT-TAAAATTTTAGGTAATAAATA
1 TAAAATTATAAAATTTTAAG-AATAAATA
*
4208633 TAAATTTATAAAATTTTAAGAATAAA
1 TAAAATTATAAAATTTTAAGAATAAA
4208659 AAATATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (28 bp):
TAAAATTATAAAATTTTAAGAATAAATA
Found at i:4211385 original size:18 final size:18
Alignment explanation
Indices: 4211334--4211385 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
4211324 TTGGGCAGTT
**
4211334 CATACTTGAAAAATAATC
1 CATACTTGAAAAATAAAA
* *
4211352 CATAATT-AAAGTATAAAA
1 CATACTTGAAA-AATAAAA
4211370 CATACTTGAAAAATAA
1 CATACTTGAAAAATAA
4211386 TATGTGGTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.27
Consensus pattern (18 bp):
CATACTTGAAAAATAAAA
Found at i:4227809 original size:22 final size:21
Alignment explanation
Indices: 4227782--4227864 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 21
4227772 TATAGGGCAG
*
4227782 AGGGAATCGATACCCCCTTGA
1 AGGGAACCGATACCCCCTTGA
*
4227803 AGGGGAACCGATTCCCCCTTTGA
1 A-GGGAACCGATACCCCC-TTGA
*
4227826 ATGGGAACCGATTCCCTCCTTG-
1 A-GGGAACCGATACCC-CCTTGA
* *
4227848 AGGAAATCGATACCCCC
1 AGGGAACCGATACCCCC
4227865 CACGGGTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.04
21 12 0.23
22 15 0.28
23 22 0.42
24 2 0.04
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.20
Consensus pattern (21 bp):
AGGGAACCGATACCCCCTTGA
Found at i:4227848 original size:23 final size:22
Alignment explanation
Indices: 4227783--4227848 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 22
4227773 ATAGGGCAGA
* *
4227783 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
*
4227805 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCC-TTGAAG
4227828 GGGAACCGATTCCCTCCTTGA
1 GGGAACCGATTCCC-CCTTGA
4227849 GGAAATCGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 14 0.36
23 23 0.59
24 2 0.05
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.23
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:4234485 original size:26 final size:26
Alignment explanation
Indices: 4234455--4234508 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
4234445 TCTTGTGGTC
4234455 TCTCCATCTCTTCCCTAATGCTTGCT
1 TCTCCATCTCTTCCCTAATGCTTGCT
4234481 TCTCCATCTCTTCCCTAATGCTTGCT
1 TCTCCATCTCTTCCCTAATGCTTGCT
4234507 TC
1 TC
4234509 ACATAATCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.11, C:0.39, G:0.07, T:0.43
Consensus pattern (26 bp):
TCTCCATCTCTTCCCTAATGCTTGCT
Found at i:4234928 original size:30 final size:31
Alignment explanation
Indices: 4234874--4234936 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
4234864 TTCAACTATA
* *
4234874 TAAGAAATTATTAAATGTAAGTTTTGAAAAT
1 TAAGAAACTATTAAATGAAAGTTTTGAAAAT
*
4234905 TAAGAAACTATTAAAT-AAAGTTTTGAAGAT
1 TAAGAAACTATTAAATGAAAGTTTTGAAAAT
4234935 TA
1 TA
4234937 CCTTGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.37
Consensus pattern (31 bp):
TAAGAAACTATTAAATGAAAGTTTTGAAAAT
Found at i:4242278 original size:14 final size:14
Alignment explanation
Indices: 4242259--4242288 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4242249 TCTACTTTAT
4242259 TTTTTCACTTCACC
1 TTTTTCACTTCACC
*
4242273 TTTTTCACTTTACC
1 TTTTTCACTTCACC
4242287 TT
1 TT
4242289 CCTTCATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.30, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTCACTTCACC
Found at i:4244531 original size:30 final size:30
Alignment explanation
Indices: 4244497--4244588 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
4244487 CCCGAAGGAC
4244497 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
4244527 CTATCCAAATGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
4244557 CTATTCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
4244587 CT
1 CT
4244589 GCCCATAGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:4244606 original size:60 final size:60
Alignment explanation
Indices: 4244497--4244616 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
4244487 CCCGAAGGAC
* * * * *
4244497 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAAATGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTACCCAAAGGTCACAAAGAACCTAGGTAA
* * * *
4244557 CTATTCAGAGGTCATAAAGATCCTCGGTAACTGCCCATAGGTCCCAAAGAACCTAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTACCCAAAGGTCACAAAGAACCTAGGTAA
4244617 ATTGTCCATA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTACCCAAAGGTCACAAAGAACCTAGGTAA
Found at i:4247240 original size:2 final size:2
Alignment explanation
Indices: 4247233--4247302 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
4247223 CTGATCACAG
4247233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4247275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4247303 GTATTCCCCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4250099 original size:30 final size:30
Alignment explanation
Indices: 4250008--4250110 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
4249998 CCTGAAGGAC
*
4250008 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * *
4250038 CCATCCAAATGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
4250068 CTATTCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
4250098 CTGTCCATAGGTC
1 CTATCCAGAGGTC
4250111 CCAAATAACC
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:4250127 original size:60 final size:60
Alignment explanation
Indices: 4250014--4250127 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
4250004 GGACCTATCT
* * * *
4250014 AGAGGTCATAAAGATCCTCGGTAACCATCCAAATGTCATAAAGATCATCGGTAACTATTC
1 AGAGGTCATAAAGATCCTCGGTAACCATCCAAAGGTCACAAAGAACATAGGTAACTATTC
** * * * *
4250074 AGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCAAATAACCTAGGTAA
1 AGAGGTCATAAAGATCCTCGGTAACCATCCAAAGGTCACAAAGAACATAGGTAA
4250128 ATTGTCCATA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (60 bp):
AGAGGTCATAAAGATCCTCGGTAACCATCCAAAGGTCACAAAGAACATAGGTAACTATTC
Found at i:4257969 original size:14 final size:15
Alignment explanation
Indices: 4257949--4257982 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4257939 TAGCTAATAC
4257949 TAATAGAATAGAAAA
1 TAATAGAATAGAAAA
*
4257964 -AATAGAATATAAAA
1 TAATAGAATAGAAAA
4257978 TAATA
1 TAATA
4257983 ATATAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (15 bp):
TAATAGAATAGAAAA
Found at i:4258003 original size:17 final size:17
Alignment explanation
Indices: 4257981--4258013 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4257971 TATAAAATAA
4257981 TAATATAATAGAAAGAC
1 TAATATAATAGAAAGAC
*
4257998 TAATATAATATAAAGA
1 TAATATAATAGAAAGA
4258014 AGAGAACTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (17 bp):
TAATATAATAGAAAGAC
Found at i:4258542 original size:47 final size:48
Alignment explanation
Indices: 4258471--4258572 Score: 197
Period size: 47 Copynumber: 2.1 Consensus size: 48
4258461 TCTAACCACC
4258471 ACTCTATATCTATTTTTTTACTTCTTAATGGCAACAACTGATAGATAT
1 ACTCTATATCTATTTTTTTACTTCTTAATGGCAACAACTGATAGATAT
4258519 A-TCTATATCTATTTTTTTACTTCTTAATGGCAACAACTGATAGATAT
1 ACTCTATATCTATTTTTTTACTTCTTAATGGCAACAACTGATAGATAT
4258566 ACTCTAT
1 ACTCTAT
4258573 TTGGGGGGCC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 47 0.89
48 6 0.11
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (48 bp):
ACTCTATATCTATTTTTTTACTTCTTAATGGCAACAACTGATAGATAT
Found at i:4258899 original size:43 final size:43
Alignment explanation
Indices: 4258851--4259449 Score: 454
Period size: 43 Copynumber: 14.0 Consensus size: 43
4258841 TATGGGCATA
* * *
4258851 AATTATAAAAATAAAAAGTTAGATTGAAAATATTAGGAGCCTT
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTT
* *
4258894 AATTATAAAGGTAGAAGAACGTGAGATTGAAAAAATTA-GAGACCTA
1 AATTATAAAAGTA-AA-AA-GTGAGATTGAAAAAATTAGGAG-CCTT
* *
4258940 AATTATAAAAGAAAAAAATGAGATTGAAAAAATTAGG-GACCTT
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAG-CCTT
* *
4258983 AATTA-AAAATGTAAAATGTGAGATT-AAAAAA--AGG-GCTTT
1 AATTATAAAA-GTAAAAAGTGAGATTGAAAAAATTAGGAGCCTT
** * * * *
4259022 AATTATAAAAACAAAAAGTGGGATCGAAAAAATTAGAAG-ATT
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTT
* * * * *
4259064 CAATTATAGAGGTAGAAAGTGAGATTGAAAAAATTAGGGGACTT
1 -AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTT
**
4259108 AATTATAAAAGT-AAAAGTTG-GATTGAAAGAAATTA-GAGGTTT
1 AATTATAAAAGTAAAAAG-TGAGATTGAAA-AAATTAGGAGCCTT
* * * * *
4259150 CAATTATAAATGTAAAAAGGGTGATTGAAAACATTAGGAGCCTC
1 -AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTT
* * *
4259194 AATTATAAAGGTAAAAAGT-AGGATT-AAAAAATTA-GAGGTCTC
1 AATTATAAAAGTAAAAAGTGA-GATTGAAAAAATTAGGA-GCCTT
* *
4259236 AATTATAAAGGTAAAAAGTGA-ACTT-AAAAATATTAGG-GGCTT
1 AATTATAAAAGTAAAAAGTGAGA-TTGAAAAA-ATTAGGAGCCTT
* *
4259278 CAATTATAAAAGTAGAAAGCGAGATTGAAAAAATTAGG-GCCTT
1 -AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTT
* * * *
4259321 AATTATAAAGGTAAAAAGTGAGATTG-AAAAATTATG-GTCTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTT
* * *
4259362 AATTAT-AAA-TATAAAGTATGGGATTGAAAAAAATTAAGAG-CTT
1 AATTATAAAAGTAAAAAG--TGAGATTG-AAAAAATTAGGAGCCTT
*
4259405 AAGTTATAAAGGTAAAAAAGTGAGATT-ACAAAAATTATGGAGCCT
1 AA-TTATAAAAGT-AAAAAGTGAGATTGA-AAAAATTA-GGAGCCT
4259450 ATAAAAATGT
Statistics
Matches: 448, Mismatches: 68, Indels: 77
0.76 0.11 0.13
Matches are distributed among these distances:
39 24 0.05
40 16 0.04
41 28 0.06
42 94 0.21
43 186 0.42
44 44 0.10
45 18 0.04
46 33 0.07
47 5 0.01
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (43 bp):
AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTT
Found at i:4259253 original size:85 final size:85
Alignment explanation
Indices: 4258837--4259441 Score: 463
Period size: 85 Copynumber: 7.1 Consensus size: 85
4258827 AAAAATGATT
* * * * * * *
4258837 AAATTATGGGCATAAATTATAAAAATAAAAAGTTA-GATTGAAAATATTAG-GAGCCTTAATTAT
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAG-TAGGATTGAAAAAATTAGAG-GTCTCAATTAT
4258900 AAAGGTAGAAGAACGTGAGATTGAAA
64 AAAGGTA-AA-AA-GTGAGATTG-AA
* * * * * * * *
4258926 AAATTAGAGACCTAAATTATAAAAGAAAAAAAT-GAGATTGAAAAAATTAG-GGACCTTAATTAA
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTAG-GATTGAAAAAATTAGAGG-TCTCAATTAT
* *
4258989 AAATGTAAAATGTGAGATT-AA
64 AAAGGTAAAAAGTGAGATTGAA
* * * ** * * *
4259010 AAA--AAGGGCTTTAATTATAAAAACAAAAAGTGGGATCGAAAAAATTAGAAGAT-TCAATTATA
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTAGGATTGAAAAAATTAG-AGGTCTCAATTATA
* *
4259072 GAGGTAGAAAGTGAGATTGAAA
65 AAGGTAAAAAGTGAGATTG-AA
* * * *
4259094 AAATTAGGGGACTTAATTATAAAAGT-AAAAGTTGGATTGAAAGAAATTAGAGGTTTCAATTATA
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTAGGATTGAAA-AAATTAGAGGTCTCAATTATA
* * *
4259158 AATGTAAAAAGGGTGATTGAA
65 AAGGTAAAAAGTGAGATTGAA
* *
4259179 AACATTAGGAGCCTCAATTATAAAGGTAAAAAGTAGGATT-AAAAAATTAGAGGTCTCAATTATA
1 AA-ATTAGGGGCCTCAATTATAAAAGTAAAAAGTAGGATTGAAAAAATTAGAGGTCTCAATTATA
*
4259243 AAGGTAAAAAGTGA-ACTTAAA
65 AAGGTAAAAAGTGAGA-TTGAA
* * * * *
4259264 AATATTAGGGGCTTCAATTATAAAAGTAGAAAG-CGAGATTGAAAAAATTAG-GGCCTTAATTAT
1 AA-ATTAGGGGCCTCAATTATAAAAGTAAAAAGTAG-GATTGAAAAAATTAGAGGTCTCAATTAT
4259327 AAAGGTAAAAAGTGAGATTGAA
64 AAAGGTAAAAAGTGAGATTGAA
* * * *
4259349 AAATTA-TGGTCTCAATTAT-AAA-TATAAAGTATGGGATTGAAAAAAATTA-AGAG-CTTAAGT
1 AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTA--GGATTG-AAAAAATTAGAG-GTCTCAA-T
*
4259409 TATAAAGGTAAAAAAGTGAGATTACAA
61 TATAAAGGT-AAAAAGTGAGATT-GAA
4259436 AAATTA
1 AAATTA
4259442 TGGAGCCTAT
Statistics
Matches: 423, Mismatches: 66, Indels: 56
0.78 0.12 0.10
Matches are distributed among these distances:
81 6 0.01
82 58 0.14
83 16 0.04
84 33 0.08
85 130 0.31
86 101 0.24
87 20 0.05
88 4 0.01
89 55 0.13
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (85 bp):
AAATTAGGGGCCTCAATTATAAAAGTAAAAAGTAGGATTGAAAAAATTAGAGGTCTCAATTATAA
AGGTAAAAAGTGAGATTGAA
Found at i:4259787 original size:27 final size:28
Alignment explanation
Indices: 4259710--4259813 Score: 120
Period size: 31 Copynumber: 3.6 Consensus size: 28
4259700 TTTTTCCATT
* *
4259710 TAAGTACCTAAACTATTTTTGACCAAAA
1 TAAGTACCTAAAGTATTTTTGATCAAAA
*
4259738 TAAATACCTAAAGTTATATTTTTGATCAAAA
1 TAAGTACCTAAAG---TATTTTTGATCAAAA
4259769 TAAGTACCTAAAGTATTTTTG-TCAAAA
1 TAAGTACCTAAAGTATTTTTGATCAAAA
* **
4259796 TAGGTATATAAAGTATTT
1 TAAGTACCTAAAGTATTT
4259814 AATCTTGTTC
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
27 21 0.32
28 19 0.29
31 26 0.39
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.38
Consensus pattern (28 bp):
TAAGTACCTAAAGTATTTTTGATCAAAA
Found at i:4263953 original size:17 final size:18
Alignment explanation
Indices: 4263920--4263954 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4263910 TAGTTATCTT
*
4263920 AAAAAATTATTTCATTTA
1 AAAAAATTATTTAATTTA
4263938 AAAAAATTA-TTAATTTA
1 AAAAAATTATTTAATTTA
4263955 CTAATAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAAATTATTTAATTTA
Found at i:4270683 original size:15 final size:15
Alignment explanation
Indices: 4270663--4270695 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4270653 TGAGACATTA
4270663 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
4270678 CCCGCCCCGCATCTG
1 CCCGCCCCGCATCCG
4270693 CCC
1 CCC
4270696 ACCCAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.67, G:0.18, T:0.09
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:4278230 original size:18 final size:18
Alignment explanation
Indices: 4278207--4278257 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
4278197 AGCCGCCACA
4278207 AATGCCTTTTTCTTTGAT
1 AATGCCTTTTTCTTTGAT
4278225 AATGCCTTTTTCTTTGAT
1 AATGCCTTTTTCTTTGAT
* *
4278243 AATCCCTTCTTCTTT
1 AATGCCTTTTTCTTT
4278258 AGGAGAGGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.16, C:0.22, G:0.08, T:0.55
Consensus pattern (18 bp):
AATGCCTTTTTCTTTGAT
Found at i:4280412 original size:32 final size:31
Alignment explanation
Indices: 4280326--4280419 Score: 93
Period size: 32 Copynumber: 3.0 Consensus size: 31
4280316 ATAAAGTAAA
*
4280326 CTATTATAAAATCATCATTAAATTTTACTAAG
1 CTATTATAAAAT-ATCATTAAATTTTATTAAG
* *
4280358 CTATTATAAGATAGTCACTAAATTTTATTATAG
1 CTATTATAAAATA-TCATTAAATTTTATTA-AG
* *
4280391 -TGTTGTTAAAATATCATTAAA-TTTATTAA
1 CTATT-ATAAAATATCATTAAATTTTATTAA
4280420 AGTTCTACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
30 1 0.02
31 8 0.15
32 35 0.67
33 8 0.15
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (31 bp):
CTATTATAAAATATCATTAAATTTTATTAAG
Found at i:4280828 original size:15 final size:15
Alignment explanation
Indices: 4280810--4280865 Score: 76
Period size: 15 Copynumber: 3.6 Consensus size: 15
4280800 TAACCGGTTT
4280810 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
4280825 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
4280842 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
4280857 CGATTTTAA
1 CGGTTTTAA
4280866 TATTCCAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 22 0.61
17 14 0.39
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:4280838 original size:17 final size:17
Alignment explanation
Indices: 4280813--4280863 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
4280803 CCGGTTTCGG
4280813 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
4280830 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
*
4280845 TTTTAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
4280862 TT
1 TT
4280864 AATATTCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 13 0.45
17 16 0.55
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:4281059 original size:21 final size:21
Alignment explanation
Indices: 4281035--4281108 Score: 130
Period size: 21 Copynumber: 3.5 Consensus size: 21
4281025 ACACTTAGAG
4281035 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
4281056 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
4281077 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
4281098 TACCGATTCCC
1 AACCGATTCCC
4281109 CCACGCTCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:4281325 original size:13 final size:13
Alignment explanation
Indices: 4281304--4281358 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4281294 AAGTTCGATA
*
4281304 AATTCAAATACTT
1 AATTGAAATACTT
4281317 AATTGAAATACTT
1 AATTGAAATACTT
* *
4281330 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
4281344 AATTGAAATACTT
1 AATTGAAATACTT
4281357 AA
1 AA
4281359 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:4281440 original size:32 final size:33
Alignment explanation
Indices: 4281344--4281442 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
4281334 AACTCAACAT
* * *
4281344 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
4281377 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
4281410 AATTCAAATACTTAAAAAATT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
4281442 A
1 A
4281443 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 12 0.19
33 50 0.81
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:4281462 original size:21 final size:21
Alignment explanation
Indices: 4281437--4281476 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4281427 AATTCAAGTT
4281437 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
4281458 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
4281477 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:4284629 original size:46 final size:46
Alignment explanation
Indices: 4284562--4284660 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
4284552 GCGAGAATTC
4284562 AACAATAAAAATAAAAGATCATTTACAAAAGTATGGATTTTCCTTA
1 AACAATAAAAATAAAAGATCATTTACAAAAGTATGGATTTTCCTTA
*
4284608 AACAATAAAAATAAAAGATCATTTACAAAGGTATGGATTTTCCTTA
1 AACAATAAAAATAAAAGATCATTTACAAAAGTATGGATTTTCCTTA
*
4284654 AATAATA
1 AACAATA
4284661 CCATGCAACC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.30
Consensus pattern (46 bp):
AACAATAAAAATAAAAGATCATTTACAAAAGTATGGATTTTCCTTA
Found at i:4284818 original size:21 final size:21
Alignment explanation
Indices: 4284792--4284838 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
4284782 TCAAGAGGCT
4284792 GGCGTGAGTTAAAGCCCTTAA
1 GGCGTGAGTTAAAGCCCTTAA
*
4284813 GGCGTGAGTTGAAGCCCTTAA
1 GGCGTGAGTTAAAGCCCTTAA
4284834 GGCGT
1 GGCGT
4284839 TCGATCGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (21 bp):
GGCGTGAGTTAAAGCCCTTAA
Found at i:4288930 original size:3 final size:3
Alignment explanation
Indices: 4288922--4288951 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4288912 AATGTCTCGT
4288922 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4288952 CTTGAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4289512 original size:6 final size:6
Alignment explanation
Indices: 4289501--4289527 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4289491 TTAATTGCGA
4289501 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
4289528 ATATTCGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:4289728 original size:5 final size:5
Alignment explanation
Indices: 4289718--4289753 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
4289708 TAAACCGATG
*
4289718 AAATA AAATA AAATA AAATA AAAT- AAATA AGATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
4289754 TGAATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:4291910 original size:2 final size:2
Alignment explanation
Indices: 4291898--4291935 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
4291888 AACCAAAATT
* *
4291898 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TG T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4291936 TAAACATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4292017 original size:2 final size:2
Alignment explanation
Indices: 4292001--4292049 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
4291991 AGACTAAGTA
*
4292001 AT AT AT AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4292042 AT AT AT AT
1 AT AT AT AT
4292050 TAATATTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4302266 original size:5 final size:5
Alignment explanation
Indices: 4302256--4302280 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4302246 GGGTTGTAAA
4302256 CGAGT CGAGT CGAGT CGAGT CGAGT
1 CGAGT CGAGT CGAGT CGAGT CGAGT
4302281 TTGAGTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (5 bp):
CGAGT
Found at i:4302463 original size:6 final size:6
Alignment explanation
Indices: 4302443--4302480 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
4302433 AAAATTTCAG
*
4302443 GAGCTC GA-TTC GAGCTC GAGCTC GAGACTC GAGCTC GA
1 GAGCTC GAGCTC GAGCTC GAGCTC GAG-CTC GAGCTC GA
4302481 TTTTGAGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.14
6 18 0.64
7 6 0.21
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (6 bp):
GAGCTC
Found at i:4302475 original size:13 final size:12
Alignment explanation
Indices: 4302443--4302480 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
4302433 AAAATTTCAG
*
4302443 GAGCTCGA-TTC
1 GAGCTCGAGCTC
4302454 GAGCTCGAGCTC
1 GAGCTCGAGCTC
4302466 GAGACTCGAGCTC
1 GAG-CTCGAGCTC
4302479 GA
1 GA
4302481 TTTTGAGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.33
12 5 0.21
13 11 0.46
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (12 bp):
GAGCTCGAGCTC
Found at i:4302490 original size:12 final size:12
Alignment explanation
Indices: 4302473--4302518 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
4302463 CTCGAGACTC
4302473 GAGCTCGATTTT
1 GAGCTCGATTTT
* *
4302485 GAGCTCTA-TTC
1 GAGCTCGATTTT
*
4302496 AAGCTCGATTTT
1 GAGCTCGATTTT
4302508 GAGCTCGATTT
1 GAGCTCGATTT
4302519 AAGCTCGGAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (12 bp):
GAGCTCGATTTT
Found at i:4302504 original size:23 final size:23
Alignment explanation
Indices: 4302474--4302525 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
4302464 TCGAGACTCG
*
4302474 AGCTCGATTTTGAGCTCTATTCA
1 AGCTCGATTTTGAGCTCGATTCA
*
4302497 AGCTCGATTTTGAGCTCGATTTA
1 AGCTCGATTTTGAGCTCGATTCA
4302520 AGCTCG
1 AGCTCG
4302526 GACTCAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (23 bp):
AGCTCGATTTTGAGCTCGATTCA
Found at i:4302525 original size:11 final size:12
Alignment explanation
Indices: 4302474--4302525 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 12
4302464 TCGAGACTCG
*
4302474 AGCTCGATTTTG
1 AGCTCGATTTTA
* *
4302486 AGCTCTA-TTCA
1 AGCTCGATTTTA
*
4302497 AGCTCGATTTTG
1 AGCTCGATTTTA
4302509 AGCTCGA-TTTA
1 AGCTCGATTTTA
4302520 AGCTCG
1 AGCTCG
4302526 GACTCAAACT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (12 bp):
AGCTCGATTTTA
Found at i:4305362 original size:20 final size:20
Alignment explanation
Indices: 4305337--4305374 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4305327 TTGTGAGGTG
4305337 ATGCGAATTTGACTATCGTA
1 ATGCGAATTTGACTATCGTA
4305357 ATGCGAATTTGACTATCG
1 ATGCGAATTTGACTATCG
4305375 CAACGAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (20 bp):
ATGCGAATTTGACTATCGTA
Found at i:4305449 original size:20 final size:20
Alignment explanation
Indices: 4305424--4305600 Score: 130
Period size: 20 Copynumber: 9.5 Consensus size: 20
4305414 GATTCTTTCG
**
4305424 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
4305444 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
*
4305464 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
4305484 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
* **
4305498 TTGCAATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
4305517 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
4305531 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
* **
4305551 TTGCGATAGTTATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
4305571 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
4305591 ATGCGATAGT
1 TTGCGATAGT
4305601 AAACTATTCT
Statistics
Matches: 128, Mismatches: 15, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
14 13 0.10
16 12 0.09
17 6 0.05
18 5 0.04
19 6 0.05
20 86 0.67
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:4305482 original size:40 final size:38
Alignment explanation
Indices: 4305403--4305600 Score: 145
Period size: 40 Copynumber: 5.4 Consensus size: 38
4305393 GCGATTTTCA
*
4305403 TTTCGCATTGCGAT--TC-TTT-CGTTGCGATAGTCAA
1 TTTCGCATTGCGATAGTCTTTTCCGTTGCGATAGTCAT
* *
4305437 ATTCGCATTGCGATAGTCATTTTCACATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTC-TTTTC-CGTTGCGATAGTCAT
* * **
4305477 TTTCGCGTTGCGAT--T-TTGTT--GTTGCAATTTTCA-
1 TTTCGCATTGCGATAGTCTT-TTCCGTTGCGATAGTCAT
*
4305510 TTTCGCATTGCGAT--TC-TCT-CGTTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCTTTTCCGTTGCGATAGTCAT
* * *
4305544 TTTCGCGTTGCGATAGTTATTTTCGTGTTGCGATAGTCAT
1 TTTCGCATTGCGATAG-TCTTTTC-CGTTGCGATAGTCAT
*
4305584 TTTCGCAATGCGATAGT
1 TTTCGCATTGCGATAGT
4305601 AAACTATTCT
Statistics
Matches: 128, Mismatches: 20, Indels: 27
0.73 0.11 0.15
Matches are distributed among these distances:
32 1 0.01
33 25 0.20
34 35 0.27
36 4 0.03
37 3 0.02
38 6 0.05
39 1 0.01
40 53 0.41
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (38 bp):
TTTCGCATTGCGATAGTCTTTTCCGTTGCGATAGTCAT
Found at i:4305532 original size:107 final size:107
Alignment explanation
Indices: 4305396--4305589 Score: 316
Period size: 107 Copynumber: 1.8 Consensus size: 107
4305386 TTGCAATGCG
*
4305396 ATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTC
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTC
4305461 ACATTGCGATAGTCATTTTCGCGTTGCGATTTTGTTGTTGCA
66 ACATTGCGATAGTCATTTTCGCGTTGCGATTTTGTTGTTGCA
** * *
4305503 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTTATTTTC
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTC
***
4305568 GTGTTGCGATAGTCATTTTCGC
66 ACATTGCGATAGTCATTTTCGC
4305590 AATGCGATAG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 79 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (107 bp):
ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTC
ACATTGCGATAGTCATTTTCGCGTTGCGATTTTGTTGTTGCA
Found at i:4307544 original size:20 final size:20
Alignment explanation
Indices: 4307486--4307555 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
4307476 GAAACTTTAA
* **
4307486 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
4307506 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
4307526 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
4307546 ATCGCAACGC
1 ATCGCAACGC
4307556 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:4307594 original size:33 final size:34
Alignment explanation
Indices: 4307485--4307598 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 34
4307475 TGAAACTTTA
* * *
4307485 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCGAATATGAAAATCGC-A-ACG-CAA-G
* **
4307523 ACTATCGCAACGCGAATTTGACTATCGCAACGCAAG
1 A--ATCGCAACGCGAATATGAAAATCGCAACGCAAG
*
4307559 AATCGCAACGCGAA-ATGAAAATCGCAGCG-ACAG
1 AATCGCAACGCGAATATGAAAATCGCAACGCA-AG
4307592 AATCGCA
1 AATCGCA
4307599 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
32 1 0.02
33 20 0.32
34 13 0.21
36 2 0.03
37 2 0.03
38 4 0.06
39 1 0.02
40 20 0.32
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.13
Consensus pattern (34 bp):
AATCGCAACGCGAATATGAAAATCGCAACGCAAG
Found at i:4307985 original size:22 final size:22
Alignment explanation
Indices: 4307923--4307988 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
4307913 TGACCGTGAA
* *
4307923 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
4307945 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
4307967 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
4307989 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:4308208 original size:20 final size:20
Alignment explanation
Indices: 4308196--4308502 Score: 206
Period size: 20 Copynumber: 15.3 Consensus size: 20
4308186 TTCGCGTTAT
*
4308196 GATTTACATATTCGCATTGC
1 GATTTACGTATTCGCATTGC
4308216 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
4308236 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
4308256 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
* *
4308276 GATTTATGTATTTGCATTGC
1 GATTTACGTATTCGCATTGC
* * * * **
4308296 GAATTAGGAAAATCGCAACGC
1 GATTTACG-TATTCGCATTGC
* *
4308317 GAATTTGGA-G-AATCGCAATGC
1 G-ATTT--ACGTATTCGCATTGC
* * *
4308338 GATAGT-CAG-AATCGCGTTGC
1 GAT-TTAC-GTATTCGCATTGC
* * **
4308358 GA-AT-CTGGAAACTG-ATTTGC
1 GATTTAC-GTATTC-GCA-TTGC
* * *
4308378 GA--TACCGGAGATCGCGTTGC
1 GATTTA-CGTA-TTCGCATTGC
*
4308398 GAATTATCG-A-TCGCATTGC
1 GATTTA-CGTATTCGCATTGC
4308417 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
4308437 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
*
4308457 GATTTACGTATTCACATTGC
1 GATTTACGTATTCGCATTGC
4308477 GATTTTA-GTATTCGCATTGC
1 GA-TTTACGTATTCGCATTGC
4308497 GATTTA
1 GATTTA
4308503 GGAAAATCGC
Statistics
Matches: 242, Mismatches: 26, Indels: 39
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.02
19 22 0.09
20 178 0.74
21 28 0.12
22 7 0.03
23 1 0.00
24 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
GATTTACGTATTCGCATTGC
Found at i:4308320 original size:21 final size:21
Alignment explanation
Indices: 4308294--4308339 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
4308284 TATTTGCATT
4308294 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
4308315 GCGAATTTGGAGAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
4308336 GCGA
1 GCGA
4308340 TAGTCAGAAT
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:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:4308552 original size:201 final size:201
Alignment explanation
Indices: 4308207--4308623 Score: 773
Period size: 201 Copynumber: 2.1 Consensus size: 201
4308197 ATTTACATAT
*
4308207 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCACA
*
4308272 TTGCGATTTATGTATTTGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGAGAATCGCAATG
66 TTGCGATTTATGTATTCGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGAGAATCGCAATG
*
4308337 CGATAGTCAGAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAAT
131 CGATAGTAAGAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAAT
4308402 TATCGA
196 TATCGA
4308408 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCACA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCACA
*
4308473 TTGCGATTT-TAGTATTCGCATTGCGATTTAGGAAAATCGCAACGCGAATTTGGAGAATCGCAAT
66 TTGCGATTTAT-GTATTCGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGAGAATCGCAAT
4308537 GCGATAGTAAGAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAA
130 GCGATAGTAAGAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAA
4308602 TTATCGA
195 TTATCGA
*
4308609 TCGCATTACGATTTA
1 TCGCATTGCGATTTA
4308624 GTTGGTCATT
Statistics
Matches: 210, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
200 1 0.00
201 209 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (201 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCACA
TTGCGATTTATGTATTCGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGAGAATCGCAATG
CGATAGTAAGAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAAT
TATCGA
Found at i:4313994 original size:13 final size:13
Alignment explanation
Indices: 4313976--4314014 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
4313966 GTTATAAATC
4313976 TATGACGCGCATT
1 TATGACGCGCATT
*
4313989 TATGACACGCATT
1 TATGACGCGCATT
*
4314002 TATGACGCACATT
1 TATGACGCGCATT
4314015 ACGCTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:4314269 original size:26 final size:27
Alignment explanation
Indices: 4314214--4314275 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
4314204 ATATTGTATG
4314214 CAAAATATTGTAATCATCAATGTCGATA
1 CAAAATATTGTAATCAT-AATGTCGATA
4314242 CAAAATATTGTAATCAT-ATGTCGATA
1 CAAAATATTGTAATCATAATGTCGATA
4314268 CAAAATAT
1 CAAAATAT
4314276 CACGGCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 17 0.50
28 17 0.50
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (27 bp):
CAAAATATTGTAATCATAATGTCGATA
Found at i:4315473 original size:2 final size:2
Alignment explanation
Indices: 4315466--4315492 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4315456 GAACAATGAA
4315466 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4315493 AAAGAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4333264 original size:16 final size:15
Alignment explanation
Indices: 4333229--4333261 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4333219 TAAAATTGTC
4333229 TTTAAAAAAAATCAT
1 TTTAAAAAAAATCAT
*
4333244 TTTAATAAAAATCAT
1 TTTAAAAAAAATCAT
4333259 TTT
1 TTT
4333262 TAAGACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAAAAAATCAT
Found at i:4333992 original size:31 final size:30
Alignment explanation
Indices: 4333915--4334001 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 30
4333905 GCACAAGCAG
*
4333915 AAACTTAAGGGACT-AAATAGAAAAAACAT
1 AAACTTAAGGGACTAAAATAGAAAAAAAAT
* * *
4333944 ACATTTAAAGGACTAAAATAGAAAAAAAAAT
1 AAACTTAAGGGACTAAAATAG-AAAAAAAAT
* *
4333975 AAACTTAAGGGATTAAAATAGCAAAAA
1 AAACTTAAGGGACTAAAATAGAAAAAA
4334002 TAGAAATTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 11 0.23
30 11 0.23
31 25 0.53
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.18
Consensus pattern (30 bp):
AAACTTAAGGGACTAAAATAGAAAAAAAAT
Found at i:4337961 original size:22 final size:23
Alignment explanation
Indices: 4337895--4337955 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
4337885 ATTATTATAG
4337895 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
4337918 GGCACTACGGTGCAATTCTACG-
1 GGCACTACGGTGCAATTCTACGC
* *
4337940 TGCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
4337956 GATACGAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:4338171 original size:21 final size:21
Alignment explanation
Indices: 4338147--4338207 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
4338137 ATAAATAATT
*
4338147 TGATGATAATGATAGA-GATAA
1 TGATAATAAT-ATAGATGATAA
*
4338168 TGATAATAATATATATGATAA
1 TGATAATAATATAGATGATAA
* *
4338189 TGCTAAGAA-AGTAGATGAT
1 TGATAATAATA-TAGATGAT
4338208 GATATATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.31
Consensus pattern (21 bp):
TGATAATAATATAGATGATAA
Found at i:4343101 original size:149 final size:145
Alignment explanation
Indices: 4342815--4343112 Score: 445
Period size: 149 Copynumber: 2.0 Consensus size: 145
4342805 GTCGAGGGTT
* * * * * * *
4342815 TACGCGGTCTTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATACT
1 TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATACT
* *
4342880 TGGTCCTTAGTATATGTATATGATTCTTAGGAATGATGTGGTCCTTATGGACATTATTATATGGC
66 TGATCCTTAGTATATGTATATGATTCTTAGGAATGATGTGGTCCTTATGGACATTATTATAGGGC
4342945 ACTACGGTGCAATTC
131 ACTACGGTGCAATTC
* *
4342960 TACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
1 TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACATAC
4343025 TTGAT-CTCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
65 TTGATCCT-TAGTATATGTATATGATTCTT-AGGAATG--ATGTGGTCCTTATGGACATTATTAT
4343089 AGGGCACTACGGTGCAATTC
126 AGGGCACTACGGTGCAATTC
4343109 TACG
1 TACG
4343113 TGGCACTACG
Statistics
Matches: 137, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
145 47 0.34
146 35 0.26
147 7 0.05
149 48 0.35
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (145 bp):
TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATACT
TGATCCTTAGTATATGTATATGATTCTTAGGAATGATGTGGTCCTTATGGACATTATTATAGGGC
ACTACGGTGCAATTC
Found at i:4343157 original size:22 final size:23
Alignment explanation
Indices: 4343091--4343151 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
4343081 ATTATTATAG
4343091 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGT
4343114 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGT
*
4343137 -GCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
4343152 GATACGAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGT
Found at i:4344215 original size:37 final size:40
Alignment explanation
Indices: 4344066--4344268 Score: 180
Period size: 44 Copynumber: 4.9 Consensus size: 40
4344056 AAATCTGGTC
* *
4344066 GGGGATGACACTGCTCATACTATGATGAGTCTTGGCCTTCTAA
1 GGGGATGACACTGCTCATACTATGATGAATCTTGG--TTC-CA
*
4344109 GGGTGATAACACTGCTCATACTATGATGAATCTTGGTTATCCA
1 GGG-GATGACACTGCTCATACTATGATGAATCTTGG-T-TCCA
* ** *
4344152 GGGGTTGACACTGCTCATA-TGCGATGAGTCTTGG-T-CA
1 GGGGATGACACTGCTCATACTATGATGAATCTTGGTTCCA
* *
4344189 -GGGATGACACTGCTCATACTATGATGAATCTTGGCCATCTAA
1 GGGGATGACACTGCTCATACTATGATGAATCTTGG--TTC-CA
* * *
4344231 GGGTGATAACATTACTCATACTATGATGAATCTTGGTT
1 GGG-GATGACACTGCTCATACTATGATGAATCTTGGTT
4344269 ATCCAGGGTT
Statistics
Matches: 132, Mismatches: 18, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
36 17 0.13
37 14 0.11
38 1 0.01
40 1 0.01
41 12 0.09
42 16 0.12
43 10 0.08
44 61 0.46
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (40 bp):
GGGGATGACACTGCTCATACTATGATGAATCTTGGTTCCA
Found at i:4344393 original size:47 final size:47
Alignment explanation
Indices: 4344315--4344672 Score: 372
Period size: 47 Copynumber: 7.9 Consensus size: 47
4344305 TATGGTCGGT
* **
4344315 TGATGACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGG
1 TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTAGGAATGG
*
4344362 TGATAACACTGCTCATACTATGATGAA-TCTTGGTTATCCA-G---GG
1 TGATAACACTGCTCATACTATGAT-AAGTCTTGGTTATCTAGGAATGG
* * * * * *
4344405 T--TAACACAGCTCCTACGGGATGAGAAAAT-ATGG---TC--GG--T--
1 TGATAACACTGCTCATAC--TATGA-TAAGTCTTGGTTATCTAGGAATGG
* **
4344443 TGATGACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGG
1 TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTAGGAATGG
* * *
4344490 TGATAACACTGTTCATACTATGATAAGCCTTGGTTATCTAGGAAGGG
1 TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTAGGAATGG
**
4344537 TGATAACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGG
1 TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTAGGAATGG
* * *
4344584 TGATAACACTGTTCATACTATGATAAGCCTTGGTTATCTAGGAAGGG
1 TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTAGGAATGG
4344631 TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTAGG
1 TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTAGG
4344673 GTTGACACGG
Statistics
Matches: 258, Mismatches: 34, Indels: 38
0.78 0.10 0.12
Matches are distributed among these distances:
37 3 0.01
38 8 0.03
39 1 0.00
40 14 0.05
41 15 0.06
43 14 0.05
44 1 0.00
45 1 0.00
46 1 0.00
47 198 0.77
48 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (47 bp):
TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTAGGAATGG
Found at i:4344609 original size:94 final size:94
Alignment explanation
Indices: 4344443--4344800 Score: 440
Period size: 94 Copynumber: 3.9 Consensus size: 94
4344433 TATGGTCGGT
* *
4344443 TGATGACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGGTGATAACACTGTTCATAC
1 TGATAACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGGTGATAACACTGCTCATAC
4344508 TATGATAAGCCTTGGTTATCTAGGAAGGG
66 TATGATAAGCCTTGGTTATCTAGGAAGGG
*
4344537 TGATAACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGGTGATAACACTGTTCATAC
1 TGATAACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGGTGATAACACTGCTCATAC
4344602 TATGATAAGCCTTGGTTATCTAGGAAGGG
66 TATGATAAGCCTTGGTTATCTAGGAAGGG
** * * *
4344631 TGATAACACTGCTCATACTATGATAAGTCTTGGTTATCTA-G---GGT--TGACACGGCTCCTAC
1 TGATAACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGGTGATAACACTGCTCATAC
* * * *
4344690 -GTGATGAG----GAG--ATC-CGGTCAGGG
66 TATGATAAGCCTTG-GTTATCTAGG-AAGGG
* * *
4344713 -GATGACACTGCTCATACTATGATGAGTCTTGGCCATCTAGGAAGGGTGATAACACTGCTCATAC
1 TGATAACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGGTGATAACACTGCTCATAC
**
4344777 TATGATAAATCTTGGTTATCTAGG
66 TATGATAAGCCTTGGTTATCTAGG
4344801 GTTGACACTG
Statistics
Matches: 226, Mismatches: 22, Indels: 32
0.81 0.08 0.11
Matches are distributed among these distances:
81 37 0.16
82 8 0.04
83 1 0.00
84 1 0.00
85 3 0.01
87 18 0.08
88 16 0.07
90 3 0.01
91 1 0.00
92 1 0.00
93 4 0.02
94 133 0.59
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (94 bp):
TGATAACACTGCTCATACTATGATAAGTCTTGGCCATCTAGGAATGGTGATAACACTGCTCATAC
TATGATAAGCCTTGGTTATCTAGGAAGGG
Found at i:4344824 original size:128 final size:127
Alignment explanation
Indices: 4344034--4344825 Score: 829
Period size: 128 Copynumber: 6.2 Consensus size: 127
4344024 TATGAGGGTA
* * * * *
4344034 ACACGGCTCCTATGTGATGAGGAAATCTGGTCGGGGATGACACTGCTCATACTATGATGAGTCTT
1 ACACTGCTCCTACGCGATGAGAAAATCTGGTCGGGGATGACACTGCTCATACTATGATAAGTCTT
* *
4344099 GGCCTTCT---AAGGGTGATAACACTGCTCATACTATGATGAATCTTGGTTATCCAGGGGTTG
66 GGCCATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAATCTTGGTTATCCA-GGGTTG
* * *
4344159 ACACTGCTCATATGCGATGAG----TCTTGGTCAGGGATGACACTGCTCATACTATGATGAA-TC
1 ACACTGCTCCTACGCGATGAGAAAATC-TGGTCGGGGATGACACTGCTCATACTATGAT-AAGTC
* * *
4344219 TTGGCCATCT---AAGGGTGATAACATTACTCATACTATGATGAATCTTGGTTATCCAGGGTTG
64 TTGGCCATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAATCTTGGTTATCCAGGGTTG
* * * *
4344280 ACACAGCTCCTACGGGATGAGAAAATATGGTCGGTTGATGACACTGCTCATACTATGATAAGTCT
1 ACACTGCTCCTACGCGATGAGAAAATCTGGTCGG-GGATGACACTGCTCATACTATGATAAGTCT
* * *
4344345 TGGCCATCTAGGAATGGTGATAACACTGCTCATACTATGATGAATCTTGGTTATCCAGGGTTA
65 TGGCCATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAATCTTGGTTATCCAGGGTTG
* * * *
4344408 ACACAGCTCCTACGGGATGAGAAAATATGGTCGGTTGATGACACTGCTCATACTATGATAAGTCT
1 ACACTGCTCCTACGCGATGAGAAAATCTGGTCGG-GGATGACACTGCTCATACTATGATAAGTCT
* * ** *
4344473 TGGCCATCTAGGAATGGTGATAACACTGTTCATACTATGATAAGCCTTGGTTATCTAGGAAGGGT
65 TGGCCATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAATCTTGGTTATC----CAGGGT
*
4344538 GATA
126 --TG
* * * * * *
4344542 ACACTGCTCATA--CTATGA-TAAGTCTTGGCCATCTAGGAATGGTGATAACACTGTTCATACTA
1 ACACTGCTCCTACGCGATGAGAAAATC-TGG---TC---G---GG-GATGACACTGCTCATACTA
* ** *
4344604 TGATAAGCCTTGGTTATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAGTCTTGGTTATC
55 TGATAAGTCTTGGCCATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAATCTTGGTTATC
*
4344669 TAGGGTTG
120 CAGGGTTG
* * * * * *
4344677 ACACGGCTCCTACGTGATGAGGAGATCCGGTCAGGGGATGACACTGCTCATACTATGATGAGTCT
1 ACACTGCTCCTACGCGATGAGAAAATCTGGTC-GGGGATGACACTGCTCATACTATGATAAGTCT
*
4344742 TGGCCATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAATCTTGGTTATCTAGGGTTG
65 TGGCCATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAATCTTGGTTATCCAGGGTTG
* *
4344805 ACACTGCTCATATGCGATGAG
1 ACACTGCTCCTACGCGATGAG
4344826 TCTTGGCCAT
Statistics
Matches: 574, Mismatches: 62, Indels: 59
0.83 0.09 0.08
Matches are distributed among these distances:
121 25 0.04
122 84 0.15
123 1 0.00
124 8 0.01
125 54 0.09
128 265 0.46
129 2 0.00
131 3 0.01
132 13 0.02
134 14 0.02
135 13 0.02
137 11 0.02
138 4 0.01
141 77 0.13
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (127 bp):
ACACTGCTCCTACGCGATGAGAAAATCTGGTCGGGGATGACACTGCTCATACTATGATAAGTCTT
GGCCATCTAGGAAGGGTGATAACACTGCTCATACTATGATAAATCTTGGTTATCCAGGGTTG
Found at i:4345234 original size:33 final size:33
Alignment explanation
Indices: 4345194--4345295 Score: 168
Period size: 33 Copynumber: 3.1 Consensus size: 33
4345184 GTTGAATCCC
* *
4345194 CAAAGATGCCCCAATATTCGATGTTGATTGCCT
1 CAAAGATGCTCCAATATTCAATGTTGATTGCCT
*
4345227 CAAAGATGCTCAAATATTCAATGTTGATTGCCT
1 CAAAGATGCTCCAATATTCAATGTTGATTGCCT
*
4345260 CAAAGATTCTCCAATATTCAATGTTGATTGCCT
1 CAAAGATGCTCCAATATTCAATGTTGATTGCCT
4345293 CAA
1 CAA
4345296 CACTGATTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (33 bp):
CAAAGATGCTCCAATATTCAATGTTGATTGCCT
Found at i:4346309 original size:14 final size:14
Alignment explanation
Indices: 4346285--4346319 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4346275 TCTTGTCCCC
4346285 TTTTC-TTTATTTA
1 TTTTCTTTTATTTA
4346298 TTTTCTTTTATTTA
1 TTTTCTTTTATTTA
4346312 TTTTCTTT
1 TTTTCTTT
4346320 GTTTTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTATTTA
Found at i:4351425 original size:21 final size:22
Alignment explanation
Indices: 4351368--4351422 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
4351358 TTTTTTTAGG
*
4351368 AAACAATTATTTATTGTTTTAA
1 AAACGATTATTTATTGTTTTAA
4351390 AAACGATTATTTATTGTTTTAA
1 AAACGATTATTTATTGTTTTAA
4351412 AAACGATTATT
1 AAACGATTATT
4351423 ATTTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (22 bp):
AAACGATTATTTATTGTTTTAA
Found at i:4351427 original size:18 final size:18
Alignment explanation
Indices: 4351378--4351429 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 18
4351368 AAACAATTAT
*
4351378 TTATTGTTTTAAAAACGA
1 TTATTATTTTAAAAACGA
4351396 TTATTTATTGTTTTAAAAACGA
1 TTA-TTA---TTTTAAAAACGA
4351418 TTATTATTTTAA
1 TTATTATTTTAA
4351430 TTTTGGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 9 0.31
19 2 0.07
21 3 0.10
22 15 0.52
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (18 bp):
TTATTATTTTAAAAACGA
Found at i:4351534 original size:15 final size:16
Alignment explanation
Indices: 4351516--4351559 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
4351506 TAAAAACATC
4351516 TTTTTAA-AAAAA-CA
1 TTTTTAAGAAAAATCA
*
4351530 ATTTTAAGAAAAATCA
1 TTTTTAAGAAAAATCA
4351546 TTTTTAAGACAAAA
1 TTTTTAAGA-AAAA
4351560 ATCTAGTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 10 0.40
17 4 0.16
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.34
Consensus pattern (16 bp):
TTTTTAAGAAAAATCA
Done.